Exact and Asymptotic Weighted Logrank Tests for Interval Censored Data: The interval R package

Forest harvest causes rapid changes of maternal investment strategies in ground beetles

Species recovery following anthropogenic disturbances will depend on adaptations in survivorship and fecundity. Life-history theory predicts increased environmental stress will result in (1) shifts in resource allocation from fecundity to body growth/maintenance and (2) increased provisioning among offspring at the cost of reproductive output. For remnant populations that persist after forest harvesting, selection mediated through anthropogenic disturbances may affect resilience to additional stressors such as climate change. We tested how rapid changes in environmental conditions affected maternal investment strategies in two ground beetle species, Pterostichus pensylvanicus and Pterostichus coracinus, by comparing fecundity and survivorship in populations from recently clear-cut and uncut habitats. Using parents drawn from clear-cut or uncut stands, we reared progeny in both common garden and reciprocal transplant experiments. In P. pensylvanicus, we found that neither lineage nor rearing habitat affected the number of eggs laid per female or survivorship of offspring. However, eggs laid by females from clear-cuts were more likely to hatch and offspring reached maturity more quickly, suggesting increased provisioning per offspring. In P. coracinus, females from clear-cuts laid more eggs, and their eggs hatched more rapidly and had greater hatching success, suggesting increased investment in overall reproductive output and increased offspring provisioning. In the reciprocal transplant, we observed significant habitat by lineage interactions on survival in P. coracinus, with survivorship increasing when progeny were reared in novel habitats. In both species, increased maternal investment among offspring was not associated with a reduction in overall reproductive output, as anticipated. However, maternal investment among offspring declined with increasing female size, implying trade-offs between increased metabolic demand and fecundity. Taken together, our work suggests that females from more stressful, clear-cut habitats increased investment in fecundity, compared to females from uncut habitats, and may compensate for larval mortality. These changes were driven by smaller individuals, suggesting that increased environmental stress can influence the relationship between female size and maternal investment strategy. Additionally, reciprocal increases in offspring survivorship in habitats other than the parents suggest that adjacent areas between unharvested and clear-cut habitat may be useful in maintaining biodiversity under future climate stressors.

Delirium Associated with COVID-19 in Critically ill Children: An Observational Cohort Study

OBJECTIVE

Delirium is an under-recognized problem in critically ill children. Although delirium is common in adults hospitalized with COVID-19, the relationship between pediatric COVID-19 and delirium has not been described. To address this gap, we characterized delirium in critically ill children with different manifestations of COVID-19 and investigated associations among demographic, disease, and treatment factors. We hypothesized that multisystem inflammatory syndrome in children (MIS-C) would be associated with a higher incidence of delirium given its underlying pathophysiology of hyperinflammation.

DESIGN

Retrospective, single-center cohort study.

SETTING

Quaternary-care pediatric intensive care unit (PICU).

PATIENTS

Children less than 18 years of age hospitalized in the PICU between March 2020 and March 2023 with either active SARS-CoV-2 infection or serological evidence of prior infection.

MEASUREMENTS AND MAIN RESULTS

The cohort included 149 PICU hospitalizations among children with evidence of COVID-19. Patients were categorized by reason for PICU admission: 75 (50%) for COVID-19 respiratory disease, 36 (24%) MIS-C, and 38 (26%) any other primary reason with positive COVID-19 testing. Delirium was diagnosed in 43 (29%) patients. Delirium incidence was highest in patients requiring invasive mechanical ventilation (IMV) (56% vs 7.5% in patients who did not require IMV, p < .001). Patients who were exposed to opioids, dexmedetomidine, paralytics or benzodiazepines more frequently experienced delirium compared to those unexposed (p < .001, p < .001, p < .001 and p  =  .001, respectively). After multivariable adjustment, delirium was associated with IMV (HR 3 [95% CI 1.5-5.7]), female sex (HR 2.4 [1.2-4.7]), and developmental disability (HR 3.4 [95% CI 1-11.1]). There was no association between delirium and reason for PICU hospitalization.

CONCLUSIONS

Delirium was common among children hospitalized with COVID-19. The overall incidence was much less than has been reported in adults with COVID-19. Delirium reduction efforts should focus on children with developmental disability and minimizing ongoing risks during IMV.

Time to Achieve the Minimal Clinically Important Difference in Primary Total Hip Arthroplasty: Comparison of Anterior and Posterior Surgical Approaches

BACKGROUND

Controversy remains over outcomes between total hip arthroplasty approaches. This study aimed to compare the time to achieve the minimal clinically important difference (MCID) for the Hip Disability and Osteoarthritis Outcome Score-Physical Function Short Form (HOOS-PS) and the Patient-Reported Outcomes Measurement Information System (PROMIS) Global-Physical for patients who underwent anterior and posterior surgical approaches in primary total hip arthroplasty.

METHODS

Patients from 2018 to 2021 with preoperative and postoperative HOOS-PS or PROMIS Global-Physical questionnaires were grouped by approach. Demographic and MCID achievement rates were compared, and survival curves with and without interval-censoring were used to assess the time to achieve the MCID by approach. Log-rank and weighted log-rank tests were used to compare groups, and Weibull regression analyses were performed to assess potential covariates.

RESULTS

A total of 2,725 patients (1,054 anterior and 1,671 posterior) were analyzed. There were no significant differences in median MCID achievement times for either the HOOS-PS (anterior: 5.9 months, 95% confidence interval [CI]: 4.6 to 6.4; posterior: 4.4 months, 95% CI: 4.1 to 5.1, P = .65) or the PROMIS Global-Physical (anterior: 4.2 months, 95% CI: 3.5 to 5.3; posterior: 3.5 months, 95% CI: 3.4 to 3.8, P = .08) between approaches. Interval-censoring revealed earlier times of achieving the MCID for both the HOOS-PS (anterior: 1.509 to 1.511 months; posterior: 1.7 to 2.3 months, P = .87) and the PROMIS Global-Physical (anterior: 3.0 to 3.1 weeks; posterior: 2.7 to 3.3 weeks, P = .18) for both surgical approaches.

CONCLUSIONS

The time to achieve the MCID did not differ by surgical approach. Most patients will achieve clinically meaningful improvements in physical function much earlier than previously believed.

LEVEL OF EVIDENCE

Level III, Retrospective Comparative Study.

Estimate of Patients With Missed Seizures Because of Delay in Conventional EEG

PURPOSE

There is frequent delay between ordering and placement of conventional EEG. Here we estimate how many patients had seizures during this delay.

METHODS

Two hundred fifty consecutive adult patients who underwent conventional EEG monitoring at the University of Wisconsin Hospital were retrospectively chart reviewed for demographics, time of EEG order, clinical and other EEG-related information. Patients were stratified by use of anti-seizure medications before EEG and into low-risk, medium-risk, and high-risk groups based on 2HELPS2B score (0, 1, or >1). Monte Carlo simulations (500 trials) were performed to estimate seizures during delay.

RESULTS

The median delay from EEG order to performing EEG was 2.00 hours (range of 0.5-8.00 hours) in the total cohort. For EEGs ordered after-hours, it was 2.00 hours (range 0.5-8.00 hours), and during business hours, it was 2.00 hours (range 0.5-6.00 hours). The place of EEG, intensive care unit, emergency department, and general floor, did not show significant difference (P = 0.84). Anti-seizure medication did not affect time to first seizure in the low-risk (P = 0.37), medium-risk (P = 0.44), or high-risk (P = 0.12) groups. The estimated % of patients who had a seizure in the delay period for low-risk group (2HELPS2B = 0) was 0.8%, for the medium-risk group (2HELPS2B = 1) was 10.3%, and for the high-risk group (2HELPS2B > 1) was 17.6%, and overall risk was 7.2%.

CONCLUSIONS

The University of Wisconsin Hospital with 24-hour in-house EEG technologists has a median delay of 2 hours from order to start of EEG, shorter than published reports from other centers. Nonetheless, seizures were likely missed in about 7.2% of patients.

SREBP-dependent regulation of lipid homeostasis is required for progression and growth of pancreatic ductal adenocarcinoma

Metabolic reprogramming is a necessary component of oncogenesis and cancer progression that solid tumors undergo when their growth outstrips local nutrient supply. The supply of lipids such as cholesterol and fatty acids is required for continued tumor cell proliferation, and oncogenic mutations stimulate de novo lipogenesis to support tumor growth. Sterol regulatory element-binding protein (SREBP) transcription factors control cellular lipid homeostasis by activating genes required for lipid synthesis and uptake. SREBPs have been implicated in the progression of multiple cancers, including brain, breast, colon, liver, and prostate. However, the role the SREBP pathway and its central regulator SREBP cleavage activating protein (SCAP) in pancreatic ductal adenocarcinoma (PDAC) has not been studied in detail. Here, we demonstrated that pancreas-specific knockout of Scap has no effect on mouse pancreas development or function, allowing for examination of the role for Scap in the murine KPC model of PDAC. Notably, heterozygous loss of Scap prolonged survival in KPC mice, and homozygous loss of Scap impaired PDAC tumor progression. Using subcutaneous and orthotopic xenograft models, we showed that S CAP is required for human PDAC tumor growth. Mechanistically, chemical or genetic inhibition of the SREBP pathway prevented PDAC cell growth under low serum conditions due to a lack of lipid supply. Highlighting the clinical importance of this pathway, the SREBP pathway is broadly required for cancer cell growth, SREBP target genes are upregulated in human PDAC tumors, and increased expression of SREBP targets genes is associated with poor survival in PDAC patients. Collectively, these results demonstrate that SCAP and the SREBP pathway activity are essential for PDAC cell and tumor growth in vitro and in vivo , identifying SCAP as a potential therapeutic target for PDAC.

SIGNIFICANCE

Our findings demonstrate that SREBP pathway activation is a critical part of the metabolic reprogramming that occurs in PDAC development and progression. Therefore, targeting the SREBP pathway has significant therapeutic potential.

HbA1c-dependent projection of long-term renal outcomes

BACKGROUND

Diabetes mellitus is a major risk factor for the development of chronic kidney disease (CKD). There is limited data addressing the value of glycated hemoglobin (HbA1c) to predict renal outcomes independent of diabetes status.

METHODS

This single-center retrospective observational study presents data of 19,285 subjects, irrespective of initial CKD or diabetes status. The primary endpoint was defined as the time to manifestation of moderate CKD (estimated glomerular filtration rate [eGFR] <60 mL/min/1.73 m2 ) in subjects with eGFR ≥60 mL/min/1.73 m2 at baseline. The secondary endpoint was defined as time to progression of CKD (eGFR <30 mL/min/1.73 m2 ) in subjects with eGFR 30-60 mL/min/1.73 m2 . Multivariate time-to-event and logistic regression models were applied to estimate the influences of HbA1c, sex, age, eGFR, triglycerides, and cholesterol on both endpoints.

RESULTS

Lowest baseline HbA1c levels were associated with the slowest decline of kidney function (median time to manifestation of moderate CKD for HbA1c <5.7%: 15.9 years [95% confidence interval (CI): 15.2-16.7]; for HbA1c 5.7%-6.5%: 14.5 years [95% CI: 14.0-15.1]; for HbA1c 6.5%-8.5%: 11.1 years [95% CI: 10.4-11.7]; for HbA1c >8.5%: 8.3 years [95% CI: 7.8-9.2]; p < 0.001). Similar results were observed for the secondary endpoint. Covariate-adjusted time-to-event analysis demonstrated an almost linear correlation between continuous baseline HbA1c levels and the probabilities of reaching both endpoints.

CONCLUSIONS

HbA1c levels are a strong predictor for eGFR decline, irrespective of diabetes status or CKD stage, demonstrating a tight concentration-dependent relationship. This association becomes apparent in the prediabetic HbA1c range and remains constant over the entire HbA1c spectrum.

Survival Analysis as a Basis for Testing Hypotheses when Using Quantitative Ordinal Scale Disease Severity Data

Disease severity in plant pathology is often measured by the amount of a plant or plant part that exhibits disease symptoms. This is typically assessed using a numerical scale, which allows a standardized, convenient, and quick method of rating. These scales, known as quantitative ordinal scales (QOS), divide the percentage scale into a predetermined number of intervals. There are various ways to analyze these ordinal data, with traditional methods involving the use of midpoint conversion to represent the interval. However, this may not be precise enough, as it is only an estimate of the true value. In this case, the data may be considered interval-censored, meaning that we have some knowledge of the value but not an exact measurement. This type of uncertainty is known as censoring, and techniques that address censoring, such as survival analysis (SA), use all available information and account for this uncertainty. To investigate the pros and cons of using SA with QOS measurements, we conducted a simulation based on three pathosystems. The results showed that SA almost always outperformed midpoint conversion with data analyzed using a t test, particularly when data were not normally distributed. Midpoint conversion is currently a standard procedure. In certain cases, the midpoint approach required a 400% increase in sample size to achieve the same power as the SA method. However, as the mean severity increases, fewer additional samples are needed (approximately an additional 100%), regardless of the assessment method used. Based on these findings, we conclude that SA is a valuable method for enhancing the power of hypothesis testing when analyzing QOS severity data. Future research should investigate the wider use of survival analysis techniques in plant pathology and their potential applications in the discipline.

Findings from the Longitudinal CINRG Becker Natural History Study

BACKGROUND

Becker muscular dystrophy is an X-linked, genetic disorder causing progressive degeneration of skeletal and cardiac muscle, with a widely variable phenotype.

OBJECTIVE

A 3-year, longitudinal, prospective dataset contributed by patients with confirmed Becker muscular dystrophy was analyzed to characterize the natural history of this disorder. A better understanding of the natural history is crucial to rigorous therapeutic trials.

METHODS

A cohort of 83 patients with Becker muscular dystrophy (5-75 years at baseline) were followed for up to 3 years with annual assessments. Muscle and pulmonary function outcomes were analyzed herein. Age-stratified statistical analysis and modeling were conducted to analyze cross-sectional data, time-to-event data, and longitudinal data to characterize these clinical outcomes.

RESULTS

Deletion mutations of dystrophin exons 45-47 or 45-48 were most common. Subgroup analysis showed greater pairwise association between motor outcomes at baseline than association between these outcomes and age. Stronger correlations between outcomes for adults than for those under 18 years were also observed. Using cross-sectional binning analysis, a ceiling effect was seen for North Star Ambulatory Assessment but not for other functional outcomes. Longitudinal analysis showed a decline in percentage predicted forced vital capacity over the life span. There was relative stability or improved median function for motor functional outcomes through childhood and adolescence and decreasing function with age thereafter.

CONCLUSIONS

There is variable progression of outcomes resulting in significant heterogeneity of the clinical phenotype of Becker muscular dystrophy. Disease progression is largely manifest in adulthood. There are implications for clinical trial design revealed by this longitudinal analysis of a Becker natural history dataset.

SARS-CoV-2 Humoral Immune Responses in Convalescent Individuals Over 12 Months Reveal Severity-Dependent Antibody Dynamics

Background

Understanding the kinetics and longevity of antibody responses to SARS-CoV-2 is critical to informing strategies toward reducing Coronavirus disease 2019 (COVID-19) reinfections, and improving vaccination and therapy approaches.

Methods

We evaluated antibody titers against SARS-CoV-2 nucleocapsid (N), spike (S), and receptor binding domain (RBD) of spike in 98 convalescent participants who experienced asymptomatic, mild, moderate or severe COVID-19 disease and in 17 non-vaccinated, non-infected controls, using four different antibody assays. Participants were sampled longitudinally at 1, 3, 6, and 12 months post-SARS-CoV-2 positive PCR test.

Findings

Increasing acute COVID-19 disease severity correlated with higher anti-N and anti-RBD antibody titers throughout 12 months post-infection. Anti-N and anti-RBD titers declined over time in all participants, with the exception of increased anti-RBD titers post-vaccination, and the decay rates were faster in hospitalized compared to non-hospitalized participants. <50% of participants retained anti-N titers above control levels at 12 months, with non-hospitalized participants falling below control levels sooner. Nearly all hospitalized and non-hospitalized participants maintained anti-RBD titers above controls for up to 12 months, suggesting longevity of protection against severe reinfections. Nonetheless, by 6 months, few participants retained >50% of their 1-month anti-N or anti-RBD titers. Vaccine-induced increases in anti-RBD titers were greater in non-hospitalized relative to hospitalized participants. Early convalescent antibody titers correlated with age, but no association was observed between Post-Acute Sequelae of SARS-CoV-2 infection (PASC) status or acute steroid treatment and convalescent antibody titers.

Interpretation

Hospitalized participants developed higher anti-SARS-CoV-2 antibody titers relative to non-hospitalized participants, a difference that persisted throughout 12 months, despite the faster decline in titers in hospitalized participants. In both groups, while anti-N titers fell below control levels for at least half of the participants, anti-RBD titers remained above control levels for almost all participants over 12 months, demonstrating generation of long-lived antibody responses known to correlate with protection from severe disease across COVID-19 severities. Overall, our findings contribute to the evolving understanding of COVID-19 antibody dynamics.

Funding

Austin Public Health, NIAAA, Babson Diagnostics, Dell Medical School Startup.

A Decade of Experience With Alemtuzumab Therapy for Severe or Glucocorticoid-Resistant Kidney Transplant Rejection

Alemtuzumab is used as lymphocyte-depleting therapy for severe or glucocorticoid-resistant kidney transplant rejection. However, the long-term efficacy and toxicity of alemtuzumab therapy are unclear. Therefore, all cases of alemtuzumab anti-rejection therapy between 2012 and 2022 in our institution were investigated. Graft survival, graft function, lymphocyte depletion, serious infections, malignancies, and patient survival were analyzed and compared with a reference cohort of transplanted patients who did not require alemtuzumab anti-rejection therapy. A total of 225 patients treated with alemtuzumab were identified and compared with a reference cohort of 1,668 patients. Over 60% of grafts was salvaged with alemtuzumab therapy, but graft survival was significantly poorer compared to the reference cohort. The median time of profound T- and B lymphocyte depletion was 272 and 344 days, respectively. Serious infection rate after alemtuzumab therapy was 54.1/100 person-years. The risk of death (hazard ratio 1.75, 95%-CI 1.28-2.39) and infection-related death (hazard ratio 2.36, 95%-CI 1.35-4.11) were higher in the alemtuzumab-treated cohort. In conclusion, alemtuzumab is an effective treatment for severe kidney transplant rejection, but causes long-lasting lymphocyte depletion and is associated with frequent infections and worse patient survival outcomes.

Identification of Covariates Modulating B-Cell Repopulation Kinetics in Subjects Receiving Rituximab Treatment

OBJECTIVE

B-cell depletion using the anti-CD20 monoclonal antibody rituximab is a cornerstone in the therapeutic concept of multiple autoimmune diseases. B-cell depletion is associated with a higher risk for severe infections, and the time span of B-cell repopulation differs greatly between individuals. Data on factors influencing B-cell repopulation kinetics are limited. This study aims to identify patient-specific and therapy-associated covariates that modulate B-cell repopulation.

METHODS

This single-center retrospective observational study presents data of 839 subjects receiving 2,017 courses of rituximab for autoimmune diseases. Assessed covariates are patient-specific factors (sex, age, kidney function, and underlying disease) and co-immunosuppression with common agents (azathioprine, cyclosporine A, cyclophosphamide, hydroxychloroquine, methotrexate, mycophenolate mofetil, tacrolimus, and corticosteroids). The primary end point is the time to B-cell repopulation (≥5/μl). The secondary end point is the time to B-cell reconstitution (≥50/μl). Multivariate time-to-event analysis and logistic regression models were applied to estimate the influence of covariates.

RESULTS

Age over 60 years (hazard ratio [HR] 0.71 for repopulation, P = 0.008), impaired kidney function (HR 0.72, P = 0.001), antineutrophil cytoplasmic antibody-associated vasculitis (HR 0.61, P < 0.001), solid organ transplantation (HR 0.4, P < 0.001), and co-immunosuppression with corticosteroids (HR 0.64, P < 0.001) or azathioprine (HR 0.49, P < 0.001) were associated with impaired B-cell repopulation and reconstitution. Effects of corticosteroids (P = 0.043) and azathioprine (P = 0.025) were dose dependent.

CONCLUSION

Prolonged rituximab dosing intervals may be effective to achieve B-cell depletion and reduce risk of infection in advanced age or patients with impaired kidney function. Co-medication with corticosteroids or azathioprine prolongs B-cell recovery, which may increase therapeutic effects but also the rate of adverse events.

Diffusion in the corpus callosum predicts persistence of clinical symptoms after mild traumatic brain injury, a multi-scanner study

Background

Mild traumatic brain injuries (mTBIs) comprise 80% of all TBI, but conventional MRI techniques are often insensitive to the subtle changes and injuries produced in a concussion. Diffusion tensor imaging (DTI) is one of the most sensitive MRI techniques for mTBI studies with outcome and symptom associations described. The corpus callosum (CC) is one of the most studied fiber tracts in TBI and mTBI, but the comprehensive post-mTBI symptom relationship has not fully been explored.

Methods

This is a retrospective observational study of how quantitative DTI data of the CC and its sub-regions may relate to clinical presentation of symptoms and timing of resolution of symptoms in patients diagnosed with uncomplicated mTBI. DTI and clinical data were obtained retrospectively from 446 (mean age 42 years, range 13-82) civilian patients. From patient medical charts, presentation of the following common post-concussive symptoms was noted: headache, balance issues, cognitive deficits, fatigue, anxiety, depression, and emotional lability. Also recorded was the time between injury and a visit to the physician when improvement or resolution of a particular symptom was reported. FA values from the total CC and 3 subregions of the CC (genu or anterior, mid body, and splenium or posterior) were obtained from hand tracing on the Olea Sphere v3.0 SP12 free-standing workstation. DTI data was obtained from 8 different 3T MRI scanners and harmonized via ComBat harmonization. The statistical models used to explore the association between regional Fractional Anisotropy (FA) values and symptom presentation and time to symptom resolution were logistic regression and interval-censored semi-parametric Cox proportional hazard models, respectively. Subgroups related to age and timing of first scan were also analyzed.

Results

Patients with the highest FA in the total CC (p = 0.01), anterior CC (p < 0.01), and mid-body CC (p = 0.03), but not the posterior CC (p = 0.91) recovered faster from post-concussive cognitive deficits. Patients with the highest FA in the posterior CC recovered faster from depression (p = 0.04) and emotional lability (p = 0.01). There was no evidence that FA in the CC or any of its sub-regions was associated with symptom presentation or with time to resolution of headache, balance issues, fatigue, or anxiety. Patients with mTBI under 40 had higher FA in the CC and the anterior and mid-body subregions (but not the posterior subregion: p = 1.00) compared to patients 40 or over (p ≤ 0.01). There was no evidence for differences in symptom presentation based on loss of consciousness (LOC) or sex (p ≥ 0.18).

Conclusion

This study suggests that FA of the CC has diagnostic and prognostic value for clinical assessment of mTBI in a large diverse civilian population, particularly in patients with cognitive symptoms.

Clinical covariates influencing clinical outcomes in primary membranous nephropathy

BACKGROUND

Primary membranous nephropathy (PMN) frequently causes nephrotic syndrome and declining kidney function. Disease progression is likely modulated by patient-specific and therapy-associated factors awaiting characterization. These cofactors may facilitate identification of risk groups and could result in more individualized therapy recommendations.

METHODS

In this single-center retrospective observational study, we analyze the effect of patient-specific and therapy-associated covariates on proteinuria, hypoalbuminemia, and estimated glomerular filtration rate (eGFR) in 74 patients diagnosed with antibody positive PMN and nephrotic-range proteinuria (urine-protein-creatinine-ratio [UPCR] ≥ 3.5 g/g), treated at the University of Freiburg Medical Center between January 2000 - November 2022. The primary endpoint was defined as time to proteinuria / serum-albumin response (UPCR ≤ 0.5 g/g or serum-albumin ≥ 3.5 g/dl), the secondary endpoint as time to permanent eGFR decline (≥ 40% relative to baseline).

RESULTS

The primary endpoint was reached after 167 days. The secondary endpoint was reached after 2413 days. Multivariate time-to-event analyses showed significantly faster proteinuria / serum-albumin response for higher serum-albumin levels (HR 2.7 [95% CI: 1.5 - 4.8]) and cyclophosphamide treatment (HR 3.6 [95% CI: 1.3 - 10.3]). eGFR decline was significantly faster in subjects with old age at baseline (HR 1.04 [95% CI: 1 - 1.1]).

CONCLUSION

High serum-albumin levels, and treatment with cyclophosphamide are associated with faster proteinuria reduction and/or serum-albumin normalization. Old age constitutes a risk factor for eGFR decline in subjects with PMN.

20-Month monitoring of SARS-CoV-2 in wastewater of Curitiba, in Southern Brazil

The COVID-19 pandemic resulted in the collapse of healthcare systems and led to the development and application of several approaches of wastewater-based epidemiology to monitor infected populations. The main objective of this study was to carry out a SARS-CoV-2 wastewater based surveillance in Curitiba, Southern Brazil Sewage samples were collected weekly for 20 months at the entrance of five treatment plants representing the entire city and quantified by qPCR using the N1 marker. The viral loads were correlated with epidemiological data. The correlation by sampling points showed that the relationship between the viral loads and the number of reported cases was best described by a cross-correlation function, indicating a lag between 7 and 14 days amidst the variables, whereas the data for the entire city presented a higher correlation (0.84) with the number of positive tests at lag 0 (sampling day). The results also suggest that the Omicron VOC resulted in higher titers than the Delta VOC. Overall, our results showed that the approach used was robust as an early warning system, even with the use of different epidemiological indicators or changes in the virus variants in circulation. Therefore, it can contribute to public decision-makers and health interventions, especially in vulnerable and low-income regions with limited clinical testing capacity. Looking toward the future, this approach will contribute to a new look at environmental sanitation and should even induce an increase in sewage coverage rates in emerging countries.

Alemtuzumab treatment in real clinical practice: Experience in a multicenter cohort

BACKGROUND

Alemtuzumab is a highly effective treatment for relapsing remitting multiple sclerosis (RRMS), but in recent years safety-related concerns had emerged due to description of novel serious side effects not registered in CARE-MS I and CARE-MS II phase 3 studies, nor in TOPAZ extension study. Data about alemtuzumab use in real clinical practice are limited and based mainly on retrospective studies with small sample sizes. Therefore, more information about effectiveness and safety of alemtuzumab in this context is needed.

METHODS

A multicenter observational prospective study to investigate effectivity and safety of alemtuzumab in a real-world setting was performed. Primary endpoints were the change in annualized relapse rate (ARR), and in disability measured by EDSS score. Secondary endpoints were the cumulative probability of confirmed 6-month disability improvement and worsening. Disability worsening and disability improvement were considered when the EDSS score was increased or decreased, respectively, in 1 point if baseline EDSS score was <5.0, or in 0.5 point if baseline EDSS score was ≥5.5, confirmed over 6 months. Other secondary endpoint was the proportion of patients who achieved NEDA-3 status (absence of clinical relapses, disability EDSS progression, and MRI disease activity as depicted by new/enlarging T2 lesions or Gadolinium enhancing T1 lesions). Adverse events also were recorded.

RESULTS

A total of 195 RRMS patients (70% female) who started alemtuzumab treatment were included. Mean of follow-up was 2.38 years. Alemtuzumab significantly reduced the annualized relapse rate from baseline with risk reductions of 86%, 83.5%, and 84%, at 12, 24, and 36 months of follow-up respectively (Friedman test, p-value < 0.05 for all comparisons). Alemtuzumab also significantly reduced EDSS score over one and two years after starting alemtuzumab treatment (Friedman test, p-value<0.001 for both comparisons). A high proportion of patients presented confirmed 6-month stability or disability improvement (92%, 82%, and 79%, over 1, 2 and 3 years of follow-up respectively). The proportion of patients who retained NEDA-3 status at 12, 24 and 36 months were 61%, 49%, and 42%, respectively. Baseline characteristics associated with a lower probability of achieving NEDA-3 were younger age, sex female, high ARR, elevated number of previous treatments, and switch from a second line therapy. Infusion related reactions were the most frequent adverse event observed. The most common infections were urinary tract infections (50%), and upper respiratory tract infections (19%) over the 3 years of follow- up. Secondary thyroid autoimmunity was developed in 18.5% of patients.

CONCLUSION

Alemtuzumab has demonstrated in real clinical practice high effectiveness in controlling multiple sclerosis activity, and no unexpected adverse events were observed.

Inequalities in Exposure to Firearm Violence by Race, Sex, and Birth Cohort From Childhood to Age 40 Years, 1995-2021

Importance

The past quarter-century has seen both sharp declines and increases in firearm violence in the United States. Yet, little is known about the age of first exposure to firearm violence and how it may differ by race, sex, and cohort.

Objective

To examine race, sex, and cohort differences in exposure to firearm violence in a representative longitudinal study of children who grew up in periods with varying rates of firearm violence in the United States and to examine spatial proximity to firearm violence in adulthood.

Design, Setting, and Participants

This population-based representative cohort study included multiple cohorts of children followed-up from 1995 through 2021 in the Project on Human Development in Chicago Neighborhoods (PHDCN). Participants included Black, Hispanic, and White respondents from 4 age cohorts of Chicago, Illinois, residents, with modal birth years of 1981, 1984, 1987, and 1996. Data analyses were conducted from May 2022 to March 2023.

Main Outcomes and Measures

Firearm violence exposure, including age when first shot, age when first saw someone shot, and past-year frequency of fatal and nonfatal shootings within 250 m of residence.

Results

There were 2418 participants in wave 1 (in the mid-1990s), and they were evenly split by sex, with 1209 males (50.00%) and 1209 females (50.00%). There were 890 Black respondents, 1146 Hispanic respondents, and 382 White respondents. Male respondents were much more likely than female respondents to have been shot (adjusted hazard ratio [aHR], 4.23; 95% CI, 2.28-7.84), but only moderately more likely to have seen someone shot (aHR, 1.48; 95% CI, 1.27-1.72). Compared with White individuals, Black individuals experienced higher rates of all 3 forms of exposure (been shot: aHR, 3.05; 95% CI, 1.22-7.60; seen someone shot: aHR, 4.69; 95% CI, 3.41-6.46; nearby shootings: adjusted incidence rate ratio [aIRR], 12.40; 95% CI, 6.88-22.35), and Hispanic respondents experienced higher rates of 2 forms of violence exposure (seen someone shot: aHR, 2.59; 95% CI, 1.85-3.62; nearby shootings: aIRR, 3.77; 95% CI, 2.08-6.84). Respondents born in the mid-1990s who grew up amidst large declines in homicide but reached adulthood during city and national spikes in firearm violence in 2016 were less likely to have seen someone shot than those born in the early 1980s who grew up during the peak of homicide in the early 1990s (aHR, 0.49; 95% CI, 0.35-0.69). However, the likelihood of having been shot did not significantly differ between these cohorts (aHR, 0.81; 95% CI, 0.40-1.63).

Conclusions and Relevance

In this longitudinal multicohort study of exposure to firearm violence, there were stark differences by race and sex, yet the extent of exposure to violence was not simply the product of these characteristics. These findings on cohort differences suggest changing societal conditions were key factors associated with whether and at what life stage individuals from all race and sex groups were exposed to firearm violence.

Transmission potential of vaccinated and unvaccinated persons infected with the SARS-CoV-2 Delta variant in a federal prison, July-August 2021

BACKGROUND

The extent to which vaccinated persons who become infected with SARS-CoV-2 contribute to transmission is unclear. During a SARS-CoV-2 Delta variant outbreak among incarcerated persons with high vaccination rates in a federal prison, we assessed markers of viral shedding in vaccinated and unvaccinated persons.

METHODS

Consenting incarcerated persons with confirmed SARS-CoV-2 infection provided mid-turbinate nasal specimens daily for 10 consecutive days and reported symptom data via questionnaire. Real-time reverse transcription-polymerase chain reaction (RT-PCR), viral whole genome sequencing, and viral culture was performed on these nasal specimens. Duration of RT-PCR positivity and viral culture positivity was assessed using survival analysis.

RESULTS

A total of 957 specimens were provided by 93 participants, of whom 78 (84 %) were vaccinated and 17 (16 %) were unvaccinated. No significant differences were detected in duration of RT-PCR positivity among vaccinated participants (median: 13 days) versus those unvaccinated (median: 13 days; p = 0.50), or in duration of culture positivity (medians: 5 days and 5 days; p = 0.29). Among vaccinated participants, overall duration of culture positivity was shorter among Moderna vaccine recipients versus Pfizer (p = 0.048) or Janssen (p = 0.003) vaccine recipients. In post-hoc analyses, Moderna vaccine recipients demonstrated significantly shorter duration of culture positivity compared to unvaccinated participants (p = 0.02). When restricted to participants without reported prior infection, the difference between Moderna vaccine recipients and unvaccinated participants was more pronounced (medians: 3 days and 6 days, p = 0.002).

CONCLUSIONS

Infectious periods for vaccinated and unvaccinated persons who become infected with SARS-CoV-2 are similar and can be highly variable, though some vaccinated persons are likely infectious for shorter durations. These findings are critically important, especially in congregate settings where viral transmission can lead to large outbreaks. In such settings, clinicians and public health practitioners should consider vaccinated, infected persons to be no less infectious than unvaccinated, infected persons.

Proteomic aptamer analysis reveals serum markers that characterize preclinical systemic sclerosis (SSc) patients at risk for progression toward definite SSc

BACKGROUND

The study of molecular mechanisms characterizing disease progression may be relevant to get insights into systemic sclerosis (SSc) pathogenesis and to intercept patients at very early stage. We aimed at investigating the proteomic profile of preclinical systemic sclerosis (PreSSc) via a discovery/validation two-step approach.

METHODS

SOMAcan aptamer-based analysis was performed on a serum sample of 13 PreSSc (discovery cohort) according to 2001 LeRoy and Medsger criteria (characterized solely by Raynaud phenomenon plus a positive nailfold capillaroscopy and SSc-specific antibodies without any other sign of definite disease) and 8 healthy controls (HCs) age, gender, and ethnicity matched. Prospective data were available up to 4±0.6 years to determine the progression to definite SSc according to the EULAR/ACR 2013 classification criteria. In proteins with relative fluorescence units (RFU) > |1.5|-fold vs HCs values, univariate analysis was conducted via bootstrap aggregating models to determine the predicting accuracy (progression vs non-progression) of categorized baseline protein values. Gene Ontologies (GO terms) and Reactome terms of significant proteins at the adjusted 0.05 threshold were explored. Significant proteins from the discovery cohort were finally validated via ELISAs in an independent validation cohort of 50 PreSSc with clinical prospective data up to 5 years. Time-to-event analysis for interval-censored data was used to evaluate disease progression.

RESULTS

In the discovery cohort, 286 out of 1306 proteins analyzed via SomaScan, were differentially expressed versus HCs. Ten proteins were significantly associated with disease progression; analysis through GO and Reactome showed differentially enriched pathways involving angiogenesis, endothelial cell chemotaxis, and endothelial cell chemotaxis to fibroblast growth factor (FGF). In the validation cohort, endostatin (HR=10.23, CI95=2.2-47.59, p=0.003) was strongly associated with disease progression, as well as bFGF (HR=0.84, CI95=0.709-0.996, p=0.045) and PAF-AHβ (HR=0.372, CI95=0.171-0.809, p=0.013) CONCLUSIONS: A distinct protein profile characterized PreSSc from HCs and proteins associated with hypoxia, vasculopathy, and fibrosis regulation are linked with the progression from preclinical to definite SSc. These proteins, in particular endostatin, can be regarded both as markers of severity and molecules with pathogenetic significance as well as therapeutic targets.

Human leukocyte antigen alleles associate with COVID-19 vaccine immunogenicity and risk of breakthrough infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine immunogenicity varies between individuals, and immune responses correlate with vaccine efficacy. Using data from 1,076 participants enrolled in ChAdOx1 nCov-19 vaccine efficacy trials in the United Kingdom, we found that inter-individual variation in normalized antibody responses against SARS-CoV-2 spike and its receptor-binding domain (RBD) at 28 days after first vaccination shows genome-wide significant association with major histocompatibility complex (MHC) class II alleles. The most statistically significant association with higher levels of anti-RBD antibody was HLA-DQB1*06 (P = 3.2 × 10-9), which we replicated in 1,677 additional vaccinees. Individuals carrying HLA-DQB1*06 alleles were less likely to experience PCR-confirmed breakthrough infection during the ancestral SARS-CoV-2 virus and subsequent Alpha variant waves compared to non-carriers (hazard ratio = 0.63, 0.42-0.93, P = 0.02). We identified a distinct spike-derived peptide that is predicted to bind differentially to HLA-DQB1*06 compared to other similar alleles, and we found evidence of increased spike-specific memory B cell responses in HLA-DQB1*06 carriers at 84 days after first vaccination. Our results demonstrate association of HLA type with Coronavirus Disease 2019 (COVID-19) vaccine antibody response and risk of breakthrough infection, with implications for future vaccine design and implementation.

Early visual deprivation disrupts the mental representation of numbers in visually impaired children

Several shreds of evidence indicate that visual deprivation does not alter numerical competence neither in adults nor in children. However, studies reporting non-impaired numerical abilities in the visually impaired population present some limitations: (a) they mainly assessed the ability to process numbers (e.g. mathematical competence) rather than represent numbers (e.g. mental number line); (b) they principally focused on positive rather than negative number estimates; (c) they investigated numerical abilities in adult individuals except one focusing on children (Crollen et al. in Cognition 210:104586, 2021). Overall, this could limit a comprehensive explanation of the role exerted by vision on numerical processing when vision is compromised. Here we investigated how congenital visual deprivation affects the ability to represent positive and negative numbers in horizontal and sagittal planes in visually impaired children (thirteen children with low vision, eight children with complete blindness, age range 6-15 years old). We adapted the number-to-position paradigm adopted by Crollen et al. (Cognition 210:104586, 2021), asking children to indicate the spatial position of positive and negative numbers on a graduated rule positioned horizontally or sagittally in the frontal plane. Results suggest that long-term visual deprivation alters the ability to identify the spatial position of numbers independently of the spatial plane and the number polarity. Moreover, results indicate that relying on poor visual acuity is detrimental for low vision children when asked to localize both positive and negative numbers in space, suggesting that visual experience might have a differential role in numerical processing depending on number polarity. Such findings add knowledge related to the impact of visual experience on numerical processing. Since both positive and negative numbers are fundamental aspects of learning mathematical principles, the outcomes of the present study inform about the need to implement early rehabilitation strategies to prevent the risk of numerical difficulties in visually impaired children.

Separating the effects of air and soil temperature on silver birch. Part I. Does soil temperature or resource competition determine the timing of root growth?

The aboveground parts of boreal forest trees mostly grow earlier, and the roots later, in the growing season. We aimed to experimentally test whether the extrinsic driver of soil temperature or the intrinsic driver (resource competition between plant parts) is a more important control for the root and shoot growth of silver birch (Betula pendula Roth) seedlings. Sixteen two-year-old seedlings were grown in controlled environment rooms for two simulated growing seasons (GS1, GS2). In GS1, all the seedlings were acclimatized under the same conditions, but in GS2, the soil temperature treatments were: (i) constant 10 °C (Cool); (ii) constant 18 °C (Warm); (iii) early growing season at 10 °C, switched to 18 °C later (Early Cool Late Warm, ECLW) and (iv) early growing season 18 °C, switched to 10 °C later (Early Warm Late Cool, EWLC). The treatments did not affect growth allocation between shoots and roots. Warm soil benefitted shoot elongation as it slowed down in EWLC and accelerated in ECLW after the soil temperature switch. However, whole-tree biomasses were similar to Cool and the seedlings grew largest in Warm. Phenology was not strongly affected by soil temperature, and root and shoot growth did not usually peak simultaneously. Short root mortality increased strongly in ECLW and decreased in EWLC after the soil temperature switch. Long root longevity was not significantly affected but long root growth ceased earliest in ECLW. Soil warming increased foliar nutrient contents. Growth dynamics were not solely driven by soil temperature, but resource competition also played a significant role. The study showed the importance of soil temperature for fine root dynamics not only through root growth but also via root mortality, as soil warming increased mortality even more than growth. Soil temperature has complex effects on tree and soil functioning, which further affects carbon dynamics in forest ecosystems that have a climate feedback.

The case against censoring of progression-free survival in cancer clinical trials - A pandemic shutdown as an illustration

Background

Missing data may lead to loss of statistical power and introduce bias in clinical trials. The Covid-19 pandemic has had a profound impact on patient health care and on the conduct of cancer clinical trials. Although several endpoints may be affected, progression-free survival (PFS) is of major concern, given its frequent use as primary endpoint in advanced cancer and the fact that missed radiographic assessments are to be expected. The recent introduction of the estimand framework creates an opportunity to define more precisely the target of estimation and ensure alignment between the scientific question and the statistical analysis.

Methods

We used simulations to investigate the impact of two basic approaches for handling missing tumor scans due to the pandemic: a “treatment policy” strategy, which consisted in ascribing events to the time they are observed, and a “hypothetical” approach of censoring patients with events during the shutdown period at the last assessment prior to that period. We computed the power of the logrank test, estimated hazard ratios (HR) using Cox models, and estimated median PFS times without and with a hypothetical 6-month shutdown period with no patient enrollment or tumor scans being performed, varying the shutdown starting times.

Results

Compared with the results in the absence of shutdown, the “treatment policy” strategy slightly overestimated median PFS proportionally to the timing of the shutdown period, but power was not affected. Except for one specific scenario, there was no impact on the estimated HR. In general, the pandemic had a greater impact on the analyses using the “hypothetical” strategy, which led to decreased power and overestimated median PFS times to a greater extent than the “treatment policy” strategy.

Conclusion

As a rule, we suggest that the treatment policy approach, which conforms with the intent-to-treat principle, should be the primary analysis to avoid unnecessary loss of power and minimize bias in median PFS estimates.

Statistical methodologies for evaluation of the rate of persistence of Ebola virus in semen of male survivors in Sierra Leone

The 2013-2016 Ebola virus (EBOV) outbreak in West Africa was the largest and most complex outbreak ever, with a total number of cases and deaths higher than in all previous EBOV outbreaks combined. The outbreak was characterized by rapid spread of the infection in nations that were weakly prepared to handle it. EBOV ribonucleic acid (RNA) is known to persist in body fluids following disease recovery, and studying this persistence is crucial for controlling such epidemics. Observational cohort studies investigating EBOV persistence in semen require following up recently recovered survivors of Ebola virus disease (EVD), from recruitment to the time when their semen tests negative for EBOV, the endpoint being time-to-event. Because recruitment of EVD survivors takes place weeks or months following disease recovery, the event of interest may have already occurred. Survival analysis methods are the best suited for the estimation of the virus persistence in body fluids but must account for left- and interval-censoring present in the data, which is a more complex problem than that of presence of right censoring alone. Using the Sierra Leone Ebola Virus Persistence Study, we discuss study design issues, endpoint of interest and statistical methodologies for interval- and right-censored non-parametric and parametric survival modelling. Using the data from 203 EVD recruited survivors, we illustrate the performance of five different survival models for estimation of persistence of EBOV in semen. The interval censored survival analytic methods produced more precise estimates of EBOV persistence in semen and were more representative of the source population than the right censored ones. The potential to apply these methods is enhanced by increased availability of statistical software to handle interval censored survival data. These methods may be applicable to diseases of a similar nature where persistence estimation of pathogens is of interest.

Health-related quality of life after restrictive versus liberal RBC transfusion for cardiac surgery: Sub-study from a randomized clinical trial

BACKGROUND

Transfusion Requirements in Cardiac Surgery III (TRICS III), a multi-center randomized controlled trial, demonstrated clinical non-inferiority for restrictive versus liberal RBC transfusion for patients undergoing cardiac surgery. However, it is uncertain if transfusion strategy affects long-term health-related quality of life (HRQOL).

STUDY DESIGN AND METHODS

In this planned sub-study of Australian patients in TRICS III, we sought to determine the non-inferiority of restrictive versus liberal transfusion strategy on long-term HRQOL and to describe clinical outcomes 24 months postoperatively. The restrictive strategy involved transfusing RBCs when hemoglobin was <7.5 g/dl; the transfusion triggers in the liberal group were: <9.5 g/L intraoperatively, <9.5 g/L in intensive care, or <8.5 g/dl on the ward. HRQOL assessments were performed using the 36-item short form survey version 2 (SF-36v2). Primary outcome was non-inferiority of summary measures of SF-36v2 at 12 months, (non-inferiority margin: -0.25 effect size; restrictive minus liberal scores). Secondary outcomes included non-inferiority of HRQOL at 18 and 24 months.

RESULTS

Six hundred seventeen Australian patients received allocated randomization; HRQOL data were available for 208/311 in restrictive and 217/306 in liberal group. After multiple imputation, non-inferiority of restrictive transfusion at 12 months was not demonstrated for HRQOL, and the estimates were directionally in favor of liberal transfusion. Non-inferiority also could not be concluded at 18 and 24 months. Sensitivity analyses supported these results. There were no differences in quality-adjusted life years or composite clinical outcomes up to 24 months after surgery.

DISCUSSION

The non-inferiority of a restrictive compared to a liberal transfusion strategy was not established for long-term HRQOL in this dataset.

Somewhere to go: assessing the impact of public restroom interventions on reports of open defecation in San Francisco, California from 2014 to 2020

BACKGROUND

Open defecation due to a lack of access to sanitation facilities remains a public health issue in the United States. People experiencing homelessness face barriers to accessing sanitation facilities, and are often forced to practice open defecation on streets and sidewalks. Exposed feces may contain harmful pathogens posing a significant threat to public health, especially among unhoused persons living near open defecation sites. The City of San Francisco's Department of Public Works implemented the Pit Stop Program to provide the unhoused and the general public with improved access to sanitation with the goal of reducing fecal contamination on streets and sidewalks. The objective of this study was to assess the impact of these public restroom interventions on reports of exposed feces in San Francisco, California.

METHODS

We evaluated the impact of various public restroom interventions implemented from January 1, 2014 to January 1, 2020 on reports of exposed feces, captured through a 311 municipal service. Publicly available 311 reports of exposed feces were spatially and temporally matched to 31 Pit Stop restroom interventions at 27 locations across 10 San Francisco neighborhoods. We conducted an interrupted time-series analysis to compare pre- versus post-intervention rates of feces reports near the restrooms.

RESULTS

Feces reports declined by 12.47 reports per week after the installation of 13 Pit Stop restrooms (p-value = 0.0002). In the same restrooms, the rate of reports per week declined from the six-month pre-intervention period to the post-intervention period (slope change = -0.024 [95% CI = -0.033, -0.014]). In a subset of restrooms, where new installations were made (Mission and Golden Gate Park), and in another subset of restrooms where restroom attendants were provided (Mission, Castro/Upper Market, and Financial District/South Beach), feces reports also declined.

CONCLUSIONS

Increased access to public toilets reduced feces reports in San Francisco, especially in neighborhoods with people experiencing homelessness. The addition of restroom attendants also appeared to have reduced feces reports in some neighborhoods with PEH. These interventions should be audited for implementation quality, observed utilization data, and user experience at the neighborhood level in order to tailor sanitation interventions to neighborhood-specific needs.

Developmental Variability in Autism Across 17 000 Autistic Individuals and 4000 Siblings Without an Autism Diagnosis: Comparisons by Cohort, Intellectual Disability, Genetic Etiology, and Age at Diagnosis

Importance

Presence of developmental delays in autism is well established, yet few studies have characterized variability in developmental milestone attainment in this population.

Objective

To characterize variability in the age at which autistic individuals attain key developmental milestones based on co-occurring intellectual disability (ID), presence of a rare disruptive genetic variant associated with neurodevelopmental disorders (NDD), age at autism diagnosis, and research cohort membership.

Design

The study team harmonized data from 4 cross-sectional autism cohorts: the Autism Genetics Research Exchange (n = 3284; 1997-2015), The Autism Simplex Collection (n = 694; 2008-2011), the Simons Simplex Collection (n = 2753; 2008-2011), and the Simons Foundation Powering Autism Research for Knowledge (n = 10 367; 2016-present). The last sample further included 4145 siblings without an autism diagnosis or ID.

Participants

Convenience sample of 21 243 autistic individuals or their siblings without an autism diagnosis aged 4 to 17 years.

Main Outcomes and Measures

Parents reported ages at which participants attained key milestones including smiling, sitting upright, crawling, walking, spoon-feeding self, speaking words, speaking phrases, and acquiring bladder and bowel control. A total of 5295 autistic individuals, and their biological parents, were genetically characterized to identify de novo variants in NDD-associated genes. The study team conducted time-to-event analyses to estimate and compare percentiles in time with milestone attainment across autistic individuals, subgroups of autistic individuals, and the sibling sample.

Results

Seventeen thousand ninety-eight autistic individuals (mean age, 9.15 years; 80.8% male) compared with 4145 siblings without autism or ID (mean age, 10.2 years; 50.2% female) showed delays in milestone attainment, with median (IQR) delays ranging from 0.7 (0.3-1.6) to 19.7 (11.4-32.2) months. More severe and more variable delays in autism were associated with the presence of co-occurring ID, carrying an NDD-associated rare genetic variant, and being diagnosed with autism by age 5 years. More severe and more variable delays were also associated with membership in earlier study cohorts, consistent with autism's diagnostic and ascertainment expansion over the last 30 years.

Conclusions and Relevance

As the largest summary to date of developmental milestone attainment in autism, to our knowledge, this study demonstrates substantial developmental variability across different conditions and provides important context for understanding the phenotypic and etiological heterogeneity of autism.

Development and validation of predictive risk models for sight threatening diabetic retinopathy in patients with type 2 diabetes to be applied as triage tools in resource limited settings

Background

Delayed diagnosis and treatment of sight threatening diabetic retinopathy (STDR) is a common cause of visual impairment in people with Type 2 diabetes. Therefore, systematic regular retinal screening is recommended, but global coverage of such services is challenging. We aimed to develop and validate predictive models for STDR to identify 'at-risk' population for retinal screening.

Methods

Models were developed using datasets obtained from general practices in inner London, United Kingdom (UK) on adults with type 2 Diabetes during the period 2007-2017. Three models were developed using Cox regression and model performance was assessed using C statistic, calibration slope and observed to expected ratio measures. Models were externally validated in cohorts from Wales, UK and India.

Findings

A total of 40,334 people were included in the model development phase of which 1427 (3·54%) people developed STDR. Age, gender, diabetes duration, antidiabetic medication history, glycated haemoglobin (HbA1c), and history of retinopathy were included as predictors in the Model 1, Model 2 excluded retinopathy status, and Model 3 further excluded HbA1c. All three models attained strong discrimination performance in the model development dataset with C statistics ranging from 0·778 to 0·832, and in the external validation datasets (C statistic 0·685 - 0·823) with calibration slopes closer to 1 following re-calibration of the baseline survival.

Interpretation

We have developed new risk prediction equations to identify those at risk of STDR in people with type 2 diabetes in any resource-setting so that they can be screened and treated early. Future testing, and piloting is required before implementation.

Funding

This study was funded by the GCRF UKRI (MR/P207881/1) and supported by the NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology.

Oocyst Shedding Dynamics in Children with Cryptosporidiosis: a Prospective Clinical Case Series in Ethiopia

Knowledge on the duration of Cryptosporidium oocyst shedding, and how shedding may be affected by subtypes and clinical parameters, is limited. Reduced transmission may be a secondary benefit of cryptosporidiosis treatment in high-prevalence areas. We conducted a prospective clinical case series in children of <5 years presenting with diarrhea to a health center and a hospital in Ethiopia over an 18-month period. Stool samples were collected repeatedly from children diagnosed with cryptosporidiosis for up to 60 days. Samples were examined, and Cryptosporidium shedding was quantified, using auramine phenol, immunofluorescent antibody staining, and quantitative PCR (qPCR). In addition, species determination and subtyping were used to attempt to distinguish between new infections and ongoing shedding. Duration and quantity of shedding over time were estimated by time-to-event and quantitative models (sex- and age-adjusted). We also explored how diarrheal severity, acute malnutrition, and Cryptosporidium subtypes correlated with temporal shedding patterns. From 53 confirmed cryptosporidiosis cases, a median of 4 (range 1 to 5) follow-up stool samples were collected and tested for Cryptosporidium. The median duration of oocyst shedding was 31 days (95% confidence interval [CI], 26 to 36 days) after onset of diarrhea, with similar estimates from the quantitative models (31 days, 95% CI 27 to 37 days). Genotype shift occurred in 5 cases (9%). A 10-fold drop in quantity occurred per week for the first 4 weeks. Prolonged oocyst shedding is common in a pediatric clinical population with cryptosporidiosis. We suggest that future intervention trials should evaluate both clinical efficacy and total parasite shedding duration as trial endpoints. IMPORTANCE Cryptosporidiosis is an important cause of diarrhea, malnutrition, and deaths in young children in low-income countries. The infection spreads from person to person. After infection, prolonged release of the Cryptosporidium parasite in stool (shedding) may contribute to further spread of the disease. If diagnosis and treatment are made available, diarrhea will be treated and deaths will be reduced. An added benefit may be to reduce transmission to others. However, shedding duration and its characteristics in children is not well known. We therefore investigated the duration of shedding in a group of young children who sought health care for diarrhea in a hospital and health center in Ethiopia. The study followed 53 children with cryptosporidiosis for 2 months. We found that, on average, children released the parasite for 31 days after the diarrhea episode started. Point-of-care treatment of cryptosporidiosis may therefore reduce onward spread of the Cryptosporidium parasite within communities and households.

Extended Human Papillomavirus Genotyping to Predict Progression to High-Grade Cervical Precancer: A Prospective Cohort Study in the Southeastern United States

BACKGROUND

High-risk human papillomavirus (hrHPV) testing is utilized in primary cervical cancer screening, generally along with cytology, to triage abnormalities to colposcopy. Most screening-based hrHPV testing involves pooled detection of any hrHPV or of HPV16/18. Cervical neoplasia progression risks based on extended hrHPV genotyping-particularly non-16/18 hrHPV types-are not well characterized. HPV genotype-specific incidence of high-grade cervical intraepithelial neoplasia or more severe (CIN2+) following an abnormal screening result was examined.

METHODS

We assessed a US-based prospective, multiracial, clinical cohort of 343 colposcopy patients with normal histology (n = 226) or CIN1 (n = 117). Baseline cervical samples underwent HPV DNA genotyping, and participants were followed up to 5 years. Genotype-specific CIN2+ incidence rates (IR) were estimated with accelerated failure time models. Five-year CIN2+ risks were estimated nonparametrically for hierarchical hrHPV risk groups (HPV16; else HPV18/45; else HPV31/33/35/52/58; else HPV39/51/56/59/68).

RESULTS

At enrollment, median participant age was 30.1 years; most (63%) were hrHPV-positive. Over follow-up, 24 participants progressed to CIN2+ (7.0%). CIN2+ IR among hrHPV-positive participants was 3.4/1,000 person-months. CIN2+ IRs were highest for HPV16 (8.3), HPV33 (7.8), and HPV58 (4.9). Five-year CIN2+ risk was higher for HPV16 (0.34) compared with HPV18/45 (0.12), HPV31/33/35/52/58 (0.12), and HPV39/51/56/59/68 (0.16) (P = 0.05).

CONCLUSIONS

Non-16/18 hrHPV types are associated with differential CIN2+ progression rates. HPV16, 33, and 58 exhibited the highest rates over 5 years. HPV risk groups warrant further investigation in diverse US populations.

IMPACT

These novel data assessing extended HPV genotyping in a diverse clinical cohort can inform future directions to improve screening practices in the general population.

R package DCchoice for dichotomous choice contingent valuation: a contribution to open scientific software and its impact

The R package DCchoice is designed to mitigate programing-related barriers to the application of dichotomous choice contingent valuation (DCCV) methods in empirical studies. Since its release in 2014, DCchoice has been updated. This paper introduces the current version of DCchoice which supports single-, one-and-one-half-, and double-bounded DCCVs, with and without a spike. Additionally, the willingness-to-pay and its confidence intervals can be calculated for a representative respondent as well as for a user-defined specific respondent using the current version. The associated web tutorial and R Commander plug-in for basic usage of DCchoice are also available. DCchoice has advanced DCCV applications in various fields.

Improved nonparametric penalized maximum likelihood estimation for arbitrarily censored survival data

Nonparametric maximum likelihood estimation encompasses a group of classic methods to estimate distribution-associated functions from potentially censored and truncated data, with extensive applications in survival analysis. These methods, including the Kaplan-Meier estimator and Turnbull's method, often result in overfitting, especially when the sample size is small. We propose an improvement to these methods by applying kernel smoothing to their raw estimates, based on a BIC-type loss function that balances the trade-off between optimizing model fit and controlling model complexity. In the context of a longitudinal study with repeated observations, we detail our proposed smoothing procedure and optimization algorithm. With extensive simulation studies over multiple realistic scenarios, we demonstrate that our smoothing-based procedure provides better overall accuracy in both survival function estimation and individual-level time-to-event prediction (imputation) by reducing overfitting. Our smoothing procedure decreases the bias (discrepancy between the estimated and true simulated survival function) using interval-censored data by up to 48% compared to the raw un-smoothed estimate, with similar improvements of up to 34% and 23% in within-sample and out-of-sample prediction, respectively. Our smoothing algorithm also demonstrates significant overall improvement across all three metrics when compared to a popular semiparametric B-splines estimation method. Finally, we apply our method to real data on censored breast cancer diagnosis, which similarly shows improvement when compared to empirical survival estimates from uncensored data. We provide an R package, SISE, for implementing our penalized likelihood method.

TADfit is a multivariate linear regression model for profiling hierarchical chromatin domains on replicate Hi-C data

Topologically associating domains (TADs) are fundamental building blocks of three dimensional genome, and organized into complex hierarchies. Identifying hierarchical TADs on Hi-C data helps to understand the relationship between genome architectures and gene regulation. Herein we propose TADfit, a multivariate linear regression model for profiling hierarchical chromatin domains, which tries to fit the interaction frequencies in Hi-C contact matrix with and without replicates using all-possible hierarchical TADs, and the significant ones can be determined by the regression coefficients obtained with the help of an online learning solver called Follow-The-Regularized-Leader (FTRL). Beyond the existing methods, TADfit has an ability to handle multiple contact matrix replicates and find partially overlapping TADs on them, which helps to find the comprehensive underlying TADs across replicates from different experiments. The comparative results tell that TADfit has better accuracy and reproducibility, and the hierarchical TADs called by it exhibit a reasonable biological relevance.

TADfit is a computational method that can identify hierarchical or partially overlapping TADs from Hi-C data, in part by using information from multiple replicates to improve detection power.

Analyzing cohort studies with interval-censored data: A new model-based linear rank-type test

To compare two or more survival distributions with interval-censored data, various nonparametric tests have been proposed. Some are based on the G ρ $$ {G}^{\rho } $$ -family introduced by Harrington and Fleming (1991) that allows flexibility for situations in which the hazard ratio decreases monotonically to unity. However, it is unclear how to choose the appropriate value of the parameter ρ $$ \rho $$ . In this work, we propose a novel linear rank-type test for analyzing interval-censored data that derived from a proportional reversed hazard model. We show its relationship with decreasing hazard ratio. This test statistic provides an alternative to the G ρ $$ {G}^{\rho } $$ -based test statistics by bypassing the choice of the ρ $$ \rho $$ parameter. Simulation results show its good behavior. Two studies on breast cancer and drug users illustrate its practical uses and highlight findings that would have been overlooked if other tests had been used. The test is easy to implement with standard software and can be used for a wide range of situations with interval-censored data to test the equality of survival distributions between two or more independent groups.

The Replica Set Method is a Robust, Accurate, and High-Throughput Approach for Assessing and Comparing Lifespan in C. elegans Experiments

The advent of feeding based RNAi in Caenorhabditis elegans led to an era of gene discovery in aging research. Hundreds of gerogenes were discovered, and many are evolutionarily conserved, raising the exciting possibility that the underlying genetic basis for healthy aging in higher vertebrates could be quickly deciphered. Yet, the majority of putative gerogenes have still only been cursorily characterized, highlighting the need for high-throughput, quantitative assessments of changes in aging. A widely used surrogate measure of aging is lifespan. The traditional way to measure mortality in C. elegans tracks the deaths of individual animals over time within a relatively small population. This traditional method provides straightforward, direct measurements of median and maximum lifespan for the sampled population. However, this method is time consuming, often underpowered, and involves repeated handling of a set of animals over time, which in turn can introduce contamination or possibly damage increasingly fragile, aged animals. We have previously developed an alternative “Replica Set” methodology, which minimizes handling and increases throughput by at least an order of magnitude. The Replica Set method allows changes in lifespan to be measured for over one hundred feeding-based RNAi clones by one investigator in a single experiment- facilitating the generation of large quantitative phenotypic datasets, a prerequisite for development of biological models at a systems level. Here, we demonstrate through analysis of lifespan experiments simulated in silico that the Replica Set method is at least as precise and accurate as the traditional method in evaluating and estimating lifespan, and requires many fewer total animal observations across the course of an experiment. Furthermore, we show that the traditional approach to lifespan experiments is more vulnerable than the Replica Set method to experimental and measurement error. We find no compromise in statistical power for Replica Set experiments, even for moderate effect sizes, or when simulated experimental errors are introduced. We compare and contrast the statistical analysis of data generated by the two approaches, and highlight pitfalls common with the traditional methodology. Collectively, our analysis provides a standard of measure for each method across comparable parameters, which will be invaluable in both experimental design and evaluation of published data for lifespan studies.

Deposition rates and residence time of litter varies among beaches in the Lofoten archipelago, Norway

A considerable portion of marine litter pollutes the world's coastlines. Its accumulation on beaches represents the product of deposition and retention, processes which are not well understood. A mark-recapture study was performed with a two-week sampling interval at three sites in Lofoten, Norway. Deposition and retention vary over relatively small spatial scales (approx. 13 km radius). No correlation was found among sites in the timing of high and low deposition events, suggesting these are governed by local factors. Contrastingly, the correlation in the timing of high and low retention events was generally stronger among sites, suggesting these may be affected by regional factors. The results underline the importance of customising cleanup frequency for different beaches as spatiotemporal variation in the relative importance of deposition and retention dictate the optimal frequency for maximal removal of litter from circulation in the local marine environment, which cannot be discerned from accumulation (i.e., standing stock) alone.

Adaptive Vertical Positioning as Anti-Predator Behavior: The Case of a Prey Fish Cohabiting with Multiple Predatory Fish within Temperate Marine Algal Forests

Simple Summary

Fish cohabiting within structurally complex habitats (e.g., coral reefs, seagrass meadows, algal forests) include abundant small-bodied prey fish and specialized piscivorous fish. Habitat structural complexity mediating fish predator–prey interactions has been shown to be an important mechanism sustaining this coexistence. However, the effect of the vertical stratification of habitat structure on predator–prey interactions remains poorly known, especially within a forest-like marine habitat, i.e., a habitat containing three vertical strata (understory, canopy and open-water). We set up tank experiments to test how such habitat vertical stratification affects predator–prey lethal and behavioral interactions, using one prey and two predator model species cohabiting in Mediterranean algal forest. We found that prey anti-predator behavior was predator-specific. When exposed to a sit-and-wait predator, the prey increased its vertical distance from the predator, regardless of the habitat structure. Conversely, when exposed to a stalk-and-attack predator, the prey sought refuge within forest structures. Prey hide motionless within the canopy, the most complex strata, while they avoid and escape from predators within the understory, which is a less complex stratum allowing for fast prey movements but still protected from predators by the canopy above. Our results suggest the crucial role of habitat vertical stratification in influencing predator–prey interactions, which should be studied in three dimensions.

Abstract

Prey fish cohabit with specialized predator fish within structurally complex habitats. How the vertical stratification of the habitat affects lethal and behavioral predator–prey interactions and contributes to explaining these patterns has never been investigated within a forest-like marine habitat, i.e., a habitat containing three vertical strata (understory, canopy, open-water above). We studied this in tank experiments, with a model prey (the wrasse Symphodus ocellatus) and two model predators (the stalk-and-attack comber Serranus cabrilla and the sit-and-wait scorpionfish Scorpaena porcus), which are among the most abundant prey and predators cohabiting in Mediterranean Cystoseira forests. Wrasse anti-predator behavior was predator-specific. When exposed to the scorpionfish, the wrasse increased its vertical distance from the predator, regardless of the habitat structure. Conversely, when exposed to the comber, the wrasse sought refuge within forest structures: (1) the canopy provides more hiding opportunities due to its high complexity, and (2) the understory provides more escape/avoidance opportunities due to (a) its low complexity that allows for fast prey movements, and (b) the presence of the canopy above that limits the comber’s access to the understory. Our results suggest that habitat vertical stratification mediates predator–prey interactions and potentially promotes the co-existence of prey and multiple predators within marine forests.

Social Behavior Deficiencies in Captive American Alligators (Alligator mississippiensis)

Understanding how the behavior of captive American alligator (Alligator mississippiensis) congregations compares to wild congregations is essential to assessing the welfare of alligators in captivity. Wild alligator congregations perform complex social behaviors, but it is unknown if such behaviors occur in captive congregations as frequently. We observed the behaviors of a captive and wild congregation of American alligators in Florida, USA in January 2021. Social behaviors were, on average, 827% more frequent in the wild congregation than the captive, and the wild congregation had a richer repertoire of social behaviors, with growling and HOTA (head oblique tail arched) behaviors being particularly common. High walking, a nonsocial behavior, dominated the behavioral repertoire of the captive congregation (94% of behaviors, excluding feeding) and may be a stereotypy that can be used as an indicator of welfare. Both congregations experienced human disturbance and displayed flushing as a species-specific defense reaction. Captive environments differ from the wild with respect to size, structure, stocking density, resource availability, and human presence. These differences translate into behavioral differences between wild and captive congregations. We identified important behavioral differences between wild and captive alligator congregations that can serve as a platform for more detailed investigations of alligator welfare in captivity.

Randomized two-stage optimal design for interval-censored data

Interval-censored data occur in a study where the exact event time of each participant is not observed but it is known to be within a certain time interval. Multiple tests were proposed for such data, including the logrank test by Sun, the proportional hazard test by Finkelstein, and the Wilcoxon-type test by Peto and Peto. We propose sample size calculations based on these tests for a parallel one-stage or two-stage design. When the proportional hazard assumption is met, the proportional hazard test and the logrank test need smaller sample sizes than the Wilcoxon-type test, and the sample size savings are substantial. But this trend is reversed when the proportional hazard assumption does not hold, and the sample size savings using the Wilcoxon-type test are sizable. An example from a lung cancer clinical trial is used to illustrate the application of the proposed sample size calculations.

Cooperation Between Systemic and Mucosal Antibodies Induced by Virosomal Vaccines Targeting HIV-1 Env: Protection of Indian Rhesus Macaques Against Low-Dose Intravaginal SHIV Challenges

A virosomal vaccine inducing systemic/mucosal anti-HIV-1 gp41 IgG/IgA had previously protected Chinese-origin rhesus macaques (RMs) against vaginal SHIV_SF162P3 challenges. Here, we assessed its efficacy in Indian-origin RMs by intramuscular priming/intranasal boosting (n=12/group). Group K received virosome-P1-peptide alone (harboring the Membrane Proximal External Region), Group L combined virosome-rgp41 plus virosome-P1, and Group M placebo virosomes. Vaccination induced plasma binding but no neutralizing antibodies. Five weeks after boosting, all RMs were challenged intravaginally with low-dose SHIV_SF162P3 until persistent systemic infection developed. After SHIV challenge #7, six controls were persistently infected versus only one Group L animal (vaccine efficacy 87%; P=0.0319); Group K was not protected. After a 50% SHIV dose increase starting with challenge #8, protection in Group L was lost. Plasmas/sera were analyzed for IgG phenotypes and effector functions; the former revealed that protection in Group L was significantly associated with increased binding to FcγR2/3(A/B) across several time-points, as were some IgG measurements. Vaginal washes contained low-level anti-gp41 IgGs and IgAs, representing a 1-to-5-fold excess over the SHIV inoculum's gp41 content, possibly explaining loss of protection after the increase in challenge-virus dose. Virosomal gp41-vaccine efficacy was confirmed during the initial seven SHIV challenges in Indian-origin RMs when the SHIV inoculum had at least 100-fold more HIV RNA than acutely infected men's semen. Vaccine protection by virosome-induced IgG and IgA parallels the cooperation between systemically administered IgG1 and mucosally applied dimeric IgA2 monoclonal antibodies that as single-agents provided no/low protection - but when combined, prevented mucosal SHIV transmission in all passively immunized RMs.

Efficacy and Safety of Vamorolone in Duchenne Muscular Dystrophy: A 30-Month Nonrandomized Controlled Open-Label Extension Trial

IMPORTANCE

Vamorolone is a synthetic steroidal drug with potent anti-inflammatory properties. Initial open-label, multiple ascending dose-finding studies of vamorolone among boys with Duchenne muscular dystrophy (DMD) found significant motor function improvement after 6 months treatment in higher-dose (ie, ≥2.0 mg/kg/d) groups.

OBJECTIVE

To investigate outcomes after 30 months of open-label vamorolone treatment.

DESIGN, SETTING, AND PARTICIPANTS

This nonrandomized controlled trial was conducted by the Cooperative International Neuromuscular Research Group at 11 US and non-US study sites. Participants were 46 boys ages 4.5 to 7.5 years with DMD who completed the 6-month dose-finding study. Data were analyzed from July 2020 through November 2021.

INTERVENTIONS

Participants were enrolled in a 24-month, long-term extension (LTE) study with vamorolone dose escalated to 2.0 or 6.0 mg/kg/d.

MAIN OUTCOMES AND MEASURES

Change in time-to-stand (TTSTAND) velocity from dose-finding baseline to end of LTE study was the primary outcome. Efficacy assessments included timed function tests, 6-minute walk test, and NorthStar Ambulatory Assessment (NSAA). Participants with DMD treated with glucocorticoids from the Duchenne Natural History Study (DNHS) and NorthStar United Kingdom (NSUK) Network were matched and compared with participants in the LTE study receiving higher doses of vamorolone.

RESULTS

Among 46 boys with DMD who completed the dose-finding study, 41 boys (mean [SD] age, 5.33 [0.96] years) completed the LTE study. Among 21 participants treated with higher-dose (ie, ≥2.0 mg/kg/d) vamorolone consistently throughout the 6-month dose-finding and 24-month LTE studies with data available at 30 months, there was a decrease in mean (SD) TTSTAND velocity from baseline to 30 months (0.206 [0.070] rises/s vs 0.189 (0.124) rises/s), which was not a statistically significant change (-0.011 rises/s; CI, -0.068 to 0.046 rises/s). There were no statistically significant differences between participants receiving higher-dose vamorolone and matched participants in the historical control groups receiving glucocorticoid treatment (75 patients in DNHS and 110 patients in NSUK) over a 2-year period in NSAA total score change (0.22 units vs NSUK; 95% CI, -4.48 to 4.04]; P = .92), body mass index z score change (0.002 vs DNHS SD/mo; 95% CI, -0.006 to 0.010; P = .58), or timed function test change. Vamorolone at doses up to 6.0 mg/kg/d was well tolerated, with 5 of 46 participants discontinuing prematurely and for reasons not associated with study drug. Participants in the DNHS treated with glucocorticoids had significant growth delay in comparison with participants treated with vamorolone who had stable height percentiles (0.37 percentile/mo; 95% CI, 0.23 to 0.52 percentile/mo) over time.

CONCLUSIONS AND RELEVANCE

This study found that vamorolone treatment was not associated with a change in TTSTAND velocity from baseline to 30 months among boys with DMD aged 4 to 7 years at enrollment. Vamorolone was associated with maintenance of muscle strength and function up to 30 months, similar to standard of care glucocorticoid therapy, and improved height velocity compared with growth deceleration associated with glucocorticoid treatment, suggesting that vamorolone may be an attractive candidate for treatment of DMD.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier: NCT03038399.

High β ‐ carotene concentration in plasma enhances cyclic progesterone production in nonpregnant Japanese Black cows

β-Carotene is an essential nutrient in cattle reproduction. The objective of this study was to evaluate the effect of β-carotene supplementation on ovarian activities throughout the estrous cycle in nonpregnant Japanese Black cows. The estrous cycles of eight nonpregnant Japanese Black cows were synchronized using a double synch protocol, and the cows were divided into two groups. The cows in the β-carotene (BC) group received supplementation with 1000 mg/day β-carotene for 46 days including the synchronization period. The cows in the control (C) group did not receive β-carotene supplementation. The results showed that β-carotene supplementation at 1000 mg/day was sufficient to maintain a high plasma β-carotene concentration and increase the plasma retinol concentration and that β-carotene supplementation had no significant effects on the dominant follicle diameter, total number of estrus behaviors, or length of the estrous cycle. In contrast, the areas under the P₄ concentration curves in the BC group were higher than those obtained for the C group. In conclusion, a high plasma β-carotene concentration in Japanese Black cows promotes P₄ production in the luteal phase of the estrous cycle and total P₄ production throughout the estrous cycle without changing the length of the estrous cycle.

Clinical utility of diagnostic biomarkers in malignant pleural mesothelioma: a systematic review and meta-analysis

Malignant pleural mesothelioma (MPM) is characterised by late-stage diagnosis and poor prognosis. Currently, no screening tool is advocated and diagnosis is based on invasive techniques, which are not well tolerated. Non-invasive diagnostic biomarkers have shown potential and could have a huge clinical benefit. However, despite extensive research, there is no consensus yet on their clinical use, with many articles reporting contradicting results, limiting their clinical implementation. The aim of this systematic review is therefore to explore the different semi- and non-invasive diagnostic markers in several human matrices and identify those that might clinically be relevant. A total of 100 articles were selected through Web of Science and PubMed, with 56 articles included in the quantitative analysis. Although many studies have reported on the diagnostic accuracy of MPM biomarkers such as serum mesothelin and high-mobility group box protein 1 and plasma fibulin-3, none have resulted in a validated test for early detection. Future research should focus on external validation, combinations into biomarker panels, the inclusion of early stage MPM patients and a combination of different biomarker matrices, as well as new markers.

Diagnostic biomarkers for malignant pleural mesothelioma seem promising; however, further research is necessary to prove their clinical value. This review provides a thorough overview of the different markers and compares them in several matrices.https://bit.ly/35ni6UO

Why Environmental Biomarkers Work: Transcriptome-Proteome Correlations and Modeling of Multistressor Experiments in the Marine Bacterium Trichodesmium

Ocean microbial communities are important contributors to the global biogeochemical reactions that sustain life on Earth. The factors controlling these communities are being increasingly explored using metatranscriptomic and metaproteomic environmental biomarkers. Using published proteomes and transcriptomes from the abundant colony-forming cyanobacterium Trichodesmium (strain IMS101) grown under varying Fe and/or P limitation in low and high CO₂, we observed robust correlations of stress-induced proteins and RNAs (i.e., involved in transport and homeostasis) that yield useful information on the nutrient status under low and/or high CO₂. Conversely, transcriptional and translational correlations of many other central metabolism pathways exhibit broad discordance. A cellular RNA and protein production/degradation model demonstrates how biomolecules with small initial inventories, such as environmentally responsive proteins, achieve large increases in fold-change units as opposed to those with a higher basal expression and inventory such as metabolic systems. Microbial cells, due to their immersion in the environment, tend to show large adaptive responses in both RNA and protein that result in transcript-protein correlations. These observations and model results demonstrate multi-omic coherence for environmental biomarkers and provide the underlying mechanism for those observations, supporting the promise for global application in detecting responses to environmental stimuli in a changing ocean.

Initiating Pancreatic Neuroendocrine Tumor (pNET) Screening in Young MEN1 Patients: Results From the DutchMEN Study Group

CONTEXT

Nonfunctioning pancreatic neuroendocrine tumors (NF-pNETs) are highly prevalent and constitute an important cause of mortality in patients with multiple endocrine neoplasia type 1 (MEN1). Still, the optimal age to initiate screening for pNETs is under debate.

OBJECTIVE

The aim of this work is to assess the age of occurrence of clinically relevant NF-pNETs in young MEN1 patients.

METHODS

Pancreatic imaging data of MEN1 patients were retrieved from the DutchMEN Study Group database. Interval-censored survival methods were used to describe age-related penetrance, compare survival curves, and develop a parametric model for estimating the risk of having clinically relevant NF-pNET at various ages. The primary objective was to assess age at occurrence of clinically relevant NF-pNET (size ≥ 20 mm or rapid growth); secondary objectives were the age at occurrence of NF-pNET of any size and pNET-associated metastasized disease.

RESULTS

Five of 350 patients developed clinically relevant NF-pNETs before age 18 years, 2 of whom subsequently developed lymph node metastases. No differences in clinically relevant NF-pNET-free survival were found for sex, time frame, and type of MEN1 diagnosis or genotype. The estimated ages (median, 95% CI) at a 1%, 2.5%, and 5% risk of having developed a clinically relevant tumor are 9.5 (6.5-12.7), 13.5 (10.2-16.9), and 17.8 years (14.3-21.4), respectively.

CONCLUSION

Analyses from this population-based cohort indicate that start of surveillance for NF-pNETs with pancreatic imaging at age 13 to 14 years is justified. The psychological and medical burden of screening at a young age should be considered.

High rates of evolution preceded shifts to sex-biased gene expression in Leucadendron, the most sexually dimorphic angiosperms

Differences between males and females are usually more subtle in dioecious plants than animals, but strong sexual dimorphism has evolved convergently in the South African Cape plant genus Leucadendron. Such sexual dimorphism in leaf size is expected largely to be due to differential gene expression between the sexes. We compared patterns of gene expression in leaves among 10 Leucadendron species across the genus. Surprisingly, we found no positive association between sexual dimorphism in morphology and the number or the percentage of sex-biased genes (SBGs). Sex bias in most SBGs evolved recently and was species specific. We compared rates of evolutionary change in expression for genes that were sex biased in one species but unbiased in others and found that SBGs evolved faster in expression than unbiased genes. This greater rate of expression evolution of SBGs, also documented in animals, might suggest the possible role of sexual selection in the evolution of gene expression. However, our comparative analysis clearly indicates that the more rapid rate of expression evolution of SBGs predated the origin of bias, and shifts towards bias were depleted in signatures of adaptation. Our results are thus more consistent with the view that sex bias is simply freer to evolve in genes less subject to constraints in expression level.

Neonatal Feeding Trajectories in Mothers With Bipolar Disorder Taking Lithium: Pharmacokinetic Data

Purpose: Women who take lithium during pregnancy and continue after delivery may choose to breastfeed, formula feed, or mix these options. The aim of the study was to evaluate the neonatal lithium serum concentrations based on these three feeding trajectories. Methods: We followed 24 women with bipolar disorder treated with lithium monotherapy during late pregnancy and postpartum (8 per trajectory). Lithium serum concentrations were determined by an AVL 9180 electrolyte analyser with a 0.10 mEq/L detection limit and a 0.20 mEq/L limit of quantification (LoQ). Results: There was complete lithium placental passage at delivery, with a mean ratio of lithium concentration in the umbilical cord to maternal serum of 1.12 ± 0.17. The median times to LoQ were 6-8, 7-8, and 53-60 days for formula, mixed, and exclusive breastfeeding respectively. The generalized log-rank testing indicated that the median times to LoQ differ according to feeding trajectory (p = 0.037). According to the multivariate analysis-adjusted lithium serum concentrations at birth, times to LoQ are, on average, longer under exclusive breastfeeding (formula, p = 0.015; mixed, p = 0.012). No lithium accumulation was observed in infants under either exclusive or mixed breastfeeding. During the lactation follow-up, there was no acute growth or developmental delays in any neonate or infant. Indeed, lithium concentrations in the three trajectories declined in all cases. However, the time needed to reach the LoQ was much longer for those breastfeeding exclusively. Conclusions: In breastfeed infant no sustained accumulation of lithium and no adverse effects on development or growth were observed.

Carboxypeptidase E mRNA: Overexpression predicts recurrence and death in lung adenocarcinoma cancer patients

BACKGROUND

Effective biomarkers for prediction of recurrence of lung adenocarcinoma cancer (LADC) patients are needed to determine treatment strategies post-surgery to improve outcome.

OBJECTIVE

This study evaluates the efficacy of carboxypeptidase E (CPE) mRNA including its splice isoforms, CPE-ΔN, as a biomarker for predicting recurrence in adenocarcinoma patients.

METHODS

RNA was extracted from resected tumors from 86 patients with different stages of non-small cell LADC. cDNA was synthesized and qRT-PCR carried out to determine the copy numbers of CPE/CPE-ΔN mRNA. Patients were followed for 7 years post-tumor resection to determine recurrence and death.

RESULTS

ROC curve analysis showed the overall AUC for CPE/CPE-ΔN copy number was 0.563 in predicting recurrence and 0.563 in predicting death. Kaplan-Meier survival analysis showed statistical difference (p= 0.018), indicating that patients with high CPE/CPE-ΔN copy numbers had a shorter time of disease-free survival and also shorter time to death (p= 0.035). Subgroup analyses showed that association of disease-free survival time with CPE/CPE-ΔN copy number was stronger among stage I and II LADC patients (p= 0.047).

CONCLUSIONS

CPE/CPE-ΔN mRNA is a potentially useful biomarker for predicting recurrence and death in LADC patients, especially in identifying patients at high risk of recurrence at early stages I and II.

Impact of attention-deficit/hyperactivity disorder comorbidity on longitudinal course in Internet gaming disorder: a 3-year clinical cohort study

BACKGROUND

Although attention-deficit/hyperactivity disorder (ADHD) symptoms were identified as a key risk factor for Internet gaming disorder (IGD), the effect of ADHD comorbidity on longitudinal course of IGD in the clinical population remains to be further examined. This study aimed to investigate whether ADHD comorbidity in IGD patients affects the recovery, recurrence rates, and trajectories of IGD symptoms, and examine the relationship between the changes in IGD and ADHD symptoms.

METHODS

The study included 128 IGD patients without any psychiatric comorbidities (pure-IGD group) and 127 IGD patients with comorbid ADHD (ADHD-IGD group) aged 11 to 42 years. IGD and ADHD were diagnosed according to DSM-5 criteria at enrollment. Participants were offered 8-week treatment with additional care provided as needed and followed up over a 3-year period. IGD diagnosis was reassessed annually and used as a dichotomous outcome. The severity of IGD and ADHD symptoms was measured using the Young Internet Addiction Scale and the Korean ADHD rating scale, respectively, at baseline and each annual follow-up.

RESULTS

The recovery rates of IGD by Year 3 were 60% and 93% in ADHD-IGD and in pure-IGD groups, respectively. The ADHD-IGD group showed lower rates of recovery, higher odds of recurrence within 1 year, and higher severity of IGD symptoms over time than the pure-IGD group. Family environment was also associated with the trajectories of IGD symptoms. The changes in ADHD symptoms were significantly associated with the changes in IGD symptoms.

CONCLUSIONS

This study found that ADHD comorbidity in IGD patients was associated with poor clinical course of IGD and that the changes in ADHD symptoms were associated with the changes in IGD symptoms over time. Our findings suggest that evaluation and treatment of ADHD symptoms and family environment in IGD patients may be important in improving the prognosis of IGD.

No Expression Divergence despite Transcriptional Interference between Nested Protein-Coding Genes in Mammals

Nested protein-coding genes accumulated throughout metazoan evolution, with early analyses of human and Drosophila microarray data indicating that this phenomenon was simply due to the presence of large introns. However, a recent study employing RNA-seq data uncovered evidence of transcriptional interference driving rapid expression divergence between Drosophila nested genes, illustrating that accurate expression estimation of overlapping genes can enhance detection of their relationships. Hence, here I apply an analogous approach to strand-specific RNA-seq data from human and mouse to revisit the role of transcriptional interference in the evolution of mammalian nested genes. A genomic survey reveals that whereas mammalian nested genes indeed accrued over evolutionary time, they are retained at lower frequencies than in Drosophila. Though several properties of mammalian nested genes align with observations in Drosophila and with expectations under transcriptional interference, contrary to both, their expression divergence is not statistically different from that between unnested genes, and also does not increase after nesting. Together, these results support the hypothesis that lower selection efficiencies limit rates of gene expression evolution in mammals, leading to their reliance on immediate eradication of deleterious nested genes to avoid transcriptional interference.