The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered

UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms.

How did UK social distancing restrictions affect the lives of women experiencing intimate partner violence during the COVID-19 pandemic? A qualitative exploration of survivor views

BACKGROUND

Increased numbers of domestic abuse cases were reported at the start of the COVID-19 pandemic. Many people experiencing abuse faced barriers to seeking support with service closures affecting the sector. Available evidence suggests women are overrepresented in the reported cases of intimate partner violence (IPV) and we aimed to learn more about how their lives were impacted by social distancing restrictions.

METHODS

We conducted an online qualitative interview study, using reflexive thematic analysis. Interviews were conducted between April 2021 and March 2022. 18 women in the UK with past experiences of IPV provided informed consent and participated in this study.

RESULTS

During the analysis, we identified five themes relating to the impact of lockdown restrictions on participants' lives, including: (1) Lockdown meant being confined to a place where abuse was escalating, (2) Barriers to accessing support, including "cancelled" services and missed opportunities to intervene during interactions in lockdown with frontline workers. (3) Increased feelings of fear, isolation, and loss of control, particularly during the early stages of the pandemic from the combination of abuse and pandemic-related changes to daily life. (4) Some forms of support were more accessible during the pandemic, such as provision of online psychological support and social groups. Participants also accessed new forms of support for the first time during the pandemic, in some cases sparked by posts and content on social media about abuse awareness. (5) For some, psychosocial wellbeing transformed during the pandemic, with several participants using the word "freedom" when reflecting on their experience of simultaneously escaping abuse and living through the COVID-19 pandemic.

CONCLUSIONS

In this study, we explored the views of female survivors of IPV in the UK during the COVID-19 pandemic. Our results highlight the importance of combined public awareness campaigns and community intervention points for victims to safely seek help during social distancing restrictions. Having the time and space to reflect on healing after escaping abuse was described by women in our study as a benefit from their lives in lockdown, which is a factor that could be incorporated into future initiatives developed to support people subjected to violence and abuse.

Effects of classroom-based active breaks on cognition, sitting and on-task behaviour in children with intellectual disability: a pilot study

BACKGROUND

Classroom-based active breaks can help typically developing children reduce sitting, increase physical activity and improve cognitive functions and on-task behaviour. Yet, this strategy has not been tested in children with intellectual disability (ID) - a population who are insufficiently active. This study aimed to investigate the effects of a 5-week active breaks intervention on cognitive functions and on-task behaviour in schoolchildren with ID.

METHODS

Twenty-four children, aged between 8 and 12 years (37.5% girls), were recruited. Children's cognitive functions (response inhibition, lapses of attention, interference and working memory) were measured at baseline and end of trial using computer-based tests. Sitting, standing and movement patterns were assessed with inclinometers, and on-task behaviour was directly observed in the classroom before and after active breaks, at baseline, mid-trial and end of trial. Linear mixed models were used to investigate the intervention effects on cognitive functions and sedentary patterns; generalised linear mixed models were used to analyse on-task behaviour data.

RESULTS

A significant time × group interaction was found for working memory favouring the intervention (B = 11.56, 95% confidence interval [1.92, 21.21]). No significant effects were found in relation to the other measures of children's cognition or on-task behaviour. Stepping time and bouts of sitting were positively affected.

CONCLUSIONS

Classroom-based active breaks can increase physical activity and reduce sedentary behaviour in children with ID and might also benefit their working memory. Further research is required to clarify the effects on cognition and to investigate whether this strategy has other benefits in this population.

Microelimination or Not? The Changing Epidemiology of Human Immunodeficiency Virus-Hepatitis C Virus Coinfection in France 2012–2018

Background

The arrival of highly effective, well-tolerated, direct-acting antiviral agents (DAA) led to a dramatic decrease in hepatitis C virus (HCV) prevalence. Human immunodeficiency virus (HIV)-HCV–coinfected patients are deemed a priority population for HCV elimination, while a rise in recently acquired HCV infections in men who have sex with men (MSM) has been described. We describe the variations in HIV-HCV epidemiology in the French Dat’AIDS cohort.

Methods

This was a retrospective analysis of a prospective cohort of persons living with HIV (PLWH) from 2012 to 2018. We determined HCV prevalence, HCV incidence, proportion of viremic patients, treatment uptake, and mortality rate in the full cohort and by HIV risk factors.

Results

From 2012 to 2018, 50 861 PLWH with a known HCV status were followed up. During the period, HCV prevalence decreased from 15.4% to 13.5%. HCV prevalence among new HIV cases increased from 1.9% to 3.5% in MSM but remained stable in other groups. Recently acquired HCV incidence increased from 0.36/100 person-years to 1.25/100 person-years in MSM. The proportion of viremic patients decreased from 67.0% to 8.9%. MSM became the first group of viremic patients in 2018 (37.9%). Recently acquired hepatitis represented 59.2% of viremic MSM in 2018. DAA treatment uptake increased from 11.4% to 61.5%. More treatments were initiated in MSM in 2018 (41.2%) than in intravenous drug users (35.6%). In MSM, treatment at the acute phase represented 30.0% of treatments in 2018.

Conclusions

A major shift in HCV epidemiology was observed in PLWH in France from 2012 to 2018, leading to a unique situation in which the major group of HCV transmission in 2018 was MSM.

Clinical Trials Registration. NCT02898987.

Referral, Assessment and Use of Screening Measures Related to Autism Spectrum Disorder at a Tertiary Hospital Setting

Children with developmental concerns in Australia continue to experience inequitable healthcare and service-related delays, even when diagnostic risk is identified. This study sought to explore service and demographic pathway factors leading up to autism spectrum disorder (ASD) assessment, including value of screening measures applied at triage. Following a trial of centralised intake for referred young children with suspected ASD, observational, retrospective pathway data was explored using bivariate and regression analyses. The mean age of 159 children referred with autism symptoms was 3.6 years, and 64% were diagnosed with ASD. Service allocation was associated with diagnosis, whilst screening tool results were not. Improved pathways are needed to limit wasted waiting times and direct each child to needs-based services.

Indications for hyperthermic intraperitoneal chemotherapy with cytoreductive surgery: a clinical practice guideline

Objective

The purpose of the present review was to provide evidence-based guidance about the provision of cytoreductive surgery (crs) with hyperthermic intraperitoneal chemotherapy (hipec) in the treatment of peritoneal cancers.

Methods

The guideline was developed by the Program in Evidence-Based Care together with the Surgical Oncology Program at Ontario Health (Cancer Care Ontario) through a systematic review of relevant literature, patient- and caregiver-specific consultation, and internal and external reviews.

Results

Recommendation 1a: For patients with newly diagnosed stage iii primary epithelial ovarian or fallopian tube carcinoma, or primary peritoneal carcinoma, hipec should be considered for those with at least stable disease after neoadjuvant chemotherapy at the time that interval crs (if complete) or optimal cytoreduction is achieved. Recommendation 1b: There is insufficient evidence to recommend the addition of hipec when primary crs is performed for patients with newly diagnosed advanced primary epithelial ovarian or fallopian tube carcinoma, or primary peritoneal carcinoma, outside of a clinical trial. Recommendation 2: There is insufficient evidence to recommend hipec with crs in patients with recurrent ovarian cancer outside the context of a clinical trial. Recommendation 3: There is insufficient evidence to recommend hipec with crs in patients with peritoneal colorectal carcinomatosis outside the context of a clinical trial. Recommendation 4: There is insufficient evidence to recommend hipec with crs for the prevention of peritoneal carcinomatosis in colorectal cancer outside the context of a clinical trial; however, hipec using oxaliplatin is not recommended. Recommendation 5: There is insufficient evidence to recommend hipec with crs for the treatment of gastric peritoneal carcinomatosis outside the context of a clinical trial. Recommendation 6: There is insufficient evidence to recommend hipec with crs for the prevention of gastric peritoneal carcinomatosis outside the context of a clinical trial. Recommendation 7: There is insufficient evidence to recommend hipec with crs as a standard of care in patients with malignant peritoneal mesothelioma; however, patients should be referred to hipec specialty centres for assessment for treatment as part of an ongoing research protocol. Recommendation 8: There is insufficient evidence to recommend hipec with crs as a standard of care in patients with disseminated mucinous neoplasm in the appendix; however, patients should be referred to hipec specialty centres for assessment for treatment as part of an ongoing research protocol.

Nevirapine Use Is Associated with Higher Bone Mineral Density in HIV-1 Positive Subjects on Long-Term Antiretroviral Therapy

We assessed bone mineral density (BMD) in a cohort of human immunodeficiency virus (HIV)-positive patients after a median of 11 years of combination antiretroviral therapy (cART) and evaluated the respective role of HIV infection and antiretroviral drugs (ARVs). A cross-sectional study of 162 participants (131 male) from the ANRS-C08 cohort was performed with bone dual-energy X-ray absorptiometry (DXA) scans and renal assessment. The window of exposure to ARVs was defined as an exposure of more than six cumulative months during the last 3 years before the DXA evaluation to account for a cumulative exposure that could affect bone remodeling. The association with low BMD (Z-score < -2) was assessed by a multiple logistic regression model. The study population was 50 years (median), hepatitis C virus (HCV) (18%), and hepatitis B virus (HBV) (8%) coinfection with HIV-RNA <50 c/mL in 89%, median CD4 of 619/mm³. Prevalence of low BMD was 18% in males and 6% in females. The factors associated with a Z-score < -2 in males were uric acid renal loss [adjusted odds ratio (aOR): 6.1; 95% confidence interval (CI): 1.2-31.5; p = .03], HCV coinfection (aOR: 4.0; 95% CI: 1.3-12.2; p = .02), and less frequent window of exposure to nevirapine (NVP) (aOR: 0.1; 95% CI: 0.02-0.6; p = .01). For the full study sample, there was a strong positive association between duration of exposure to NVP and lumbar spine Z-score (p = .004). HIV-positive patients exposed to long-term cART have a high incidence of low BMD. Tenofovir disoproxil fumarate and ritonavir-boosted protease inhibitors did not seem to be associated with increased risk of low BMD, whereas NVP exposure appeared to have an independent positive association.

Young Children with ASD Participate in the Same Level of Physical Activity as Children Without ASD: Implications for Early Intervention to Maintain Good Health

Primary-school-aged children and adolescents with autism spectrum disorder (ASD) are reported to engage in lower levels of moderate-to-vigorous physical activity (MVPA) compared to typically developing (TD) children (Jones et al. in PLoS ONE, 12(2):1-23, 2017). Levels of MVPA in young children with ASD remain unclear. This study aimed to investigate MVPA in 4-to-7-year-old children with (n = 37) and without (n = 40) ASD, to determine if MVPA is related to ASD diagnosis; and examine correlates to better inform interventions. Results indicated children with ASD engage in the same levels of MVPA as TD children. Future studies need to further explore MVPA in children with ASD over time to uncover when the divergence in MVPA levels occur and what factors may be associated.

Impact of body mass index on 30-day postoperative morbidity in pediatric and adolescent patients undergoing continent urinary tract reconstruction

INTRODUCTION

Obesity has been thought to increase the risk of complications and need for additional resources with surgery, but only a limited amount of evidence is available in the pediatric population.

OBJECTIVE

The objectives were to describe the weight status of pediatric and adolescent patients undergoing a continent urinary tract reconstruction and to determine the association between obesity and 30-day postoperative morbidity.

STUDY DESIGN

A retrospective cohort study was performed for pediatric and adolescent patients aged up to 20 years who underwent a continent urinary tract reconstruction between January 2010 and November 2016. Weight status was stratified by the body mass index (BMI) for age z-scores as follows: underweight (<5th percentile), normal (5th to <85th percentiles), overweight (85th to <95th percentiles), and obese (≥95th percentile). Primary outcomes included the duration of intensive care and hospitalization as well as re-admissions and complications within 30 days.

RESULTS

A total of 182 continent reconstructions were identified during the study period. Demographic and peri-operative data are provided in the Table. Weight status was not associated with any primary outcomes on univariate or multivariate analysis. There was also no association in an analysis between the non-overweight or non-obese group (BMI for age z-score <85th) and overweight or obese group (BMI for age z-score ≥85th percentiles); a subgroup analysis between patients with and without myelomeningocele; or a subgroup analysis for wound, infectious, or high-grade (Clavien-Dindo grades III or higher) complications.

DISCUSSION

Obesity has been consistently associated with an increased risk of surgical site infections and wound complications after a wide variety of surgeries in adults. The results from the present study conflict with those of the few available studies in the pediatric population. The high-risk nature of the present cohort may have mitigated any effect of obesity on 30-day postoperative morbidity. The limitations of the present study include its retrospective design at a single center and the potential misclassification of weight status with the BMI.

CONCLUSIONS

Almost 30% of pediatric and adolescent patients undergoing a continent urinary tract reconstruction were overweight or obese. Obesity as determined by the BMI was not associated with 30-day postoperative morbidity.

Intercomparison of far-infrared transmittance measurements

We present the results of the first systematic "round-robin" comparison of far-infrared transmittance spectra measurements, which was performed by five laboratories and piloted by Physikalisch-Technische (PTB). The transmittance spectra of four different samples were measured by the participating laboratories in the 600 cm^-1 to 10 cm^-1 range (16.67 µm to 1000 µm) in a blind comparison. Different types of instruments, Fourier transform infrared (FT-IR) spectrometers of Michelson type and a laser radiation-based system were used for the transmittance measurements. FT-IR spectrometers are the most popular and commonly used instruments for the spectral characterization of materials in the infrared spectral range, and are well established for quantitative measurements in the mid- and near-infrared spectral ranges. However, obtaining quantitative transmittance measurements in the far-infrared spectral range by means of these instruments is challenging, because it involves weaker radiation sources, stronger diffraction effects, significant radiation originating from the sample itself and temperature gradients inside the spectrometer that may not be given proper consideration. Therefore, this comparison was initiated to test the actual capability of and identify problems with FT-IR transmittance measurements in this spectral region. We discuss the results and the possible reasons for the observed discrepancies.

Comparison of biological and alloplastic meshes in ventral incisional hernia repair

PURPOSE

The aim of our retrospective analysis was to compare the results of incisional hernia repair by porcine small intestinal submucosa-derived (SIS) meshes with those obtained by alloplastic polypropylene-based (PP) meshes in comparable surgical indications by matched-pair design. We hypothesized that in incisional hernia, SIS mesh repair is associated with fewer recurrences and SSO than PP mesh repair in incisional hernias.

METHODS

Twenty-four matched pairs (SIS vs. PP mesh repair between 1 January 2005 and 31 December 2013) were identified by matching criteria: gender, age, comorbidities, body mass index, EHS hernia classification, mesh implantation technique, CDC wound classification, and source of contamination/primary surgery leading to incisional hernia. Minimal follow-up time was 24 months. Means and standard deviations were compared by paired t test; categorial data were compared by McNemar's test. Poisson's distribution and negative binominal distribution were employed to detect significant correlation.

RESULTS

There were no statistically significant differences between both groups in the pre- and perioperative factors and the follow-up times. There were significantly more wound complications (19 vs. 12, p = 0.041), longer hospital stay (22.0 ± 6.3 vs. 12.0 ± 3.1 days, p = 0.010), and significantly more recurrent hernias (25 vs. 12.5%, p = 0.004) after SIS mesh repair. Both the Poisson's distribution and the negative binominal distribution unveiled significantly more complication points (3-6 vs. 1-2) per month after SIS mesh repair.

CONCLUSION

There is no advantage of SIS meshes compared to PP meshes in incisional hernia repair with different degrees of wound contamination in this matched-pair analysis. Further prospective and randomized trials or at least registry studies such as the EHS register with standardized and defined conditions are warranted.

Exploring factors related to the anger superiority effect in children with Autism Spectrum Disorder

Despite face and emotion recognition deficits, individuals with Autism Spectrum Disorder (ASD) appear to experience the anger superiority effect, where an angry face in a crowd is detected faster than a neutral face. This study extended past research to examine the impacts of ecologically valid photographic stimuli, gender and anxiety symptoms on the anger superiority effect in children with and without ASD. Participants were 81, 7-12year old children, 42 with ASD matched on age, gender and perceptual IQ to 39 typically developing (TYP) children. The photographic stimuli did not impact on task performance in ASD with both groups exhibiting the anger superiority effect. There were no gender differences and no associations with anxiety. Age was associated with the effect in the TYP but not ASD group. These findings confirm a robust effect of speeded detection of threat in ASD which does not appear to be confounded by gender or anxiety, but may have different underlying age-associated mechanisms.

Online monitoring of stable carbon isotopes of methane in anaerobic digestion as a new tool for early warning of process instability

Effective control of anaerobic digestion in biogas plants requires the monitoring of process sensitive and rapid response parameters in order to ensure efficient biogas production and to prevent potential process failure. In this study, stable carbon isotopes of methane (δ(13)CCH4) produced in a full-scale continuous stirred-tank reactor were investigated as a potential new monitoring tool for this purpose. Over a six-month period with variable organic loading rates, δ(13)CCH4-values were measured online by a portable high-precision laser absorption spectrometer. During a stress period of consecutive high organic loading, δ(13)CCH4-values early indicated process changes in contrast to traditionally monitored parameters where a change was observed some five to ten days later. Comparison of the stable isotope values with data from microbial analyses showed a distinct relationship between the quantity of potentially acetoclastic methanogens and δ(13)CCH4-values. This finding indicates an association between dominant methanogenic pathways and carbon isotope values.

Antifungal agents use in a French administrative region

BACKGROUND

The increased use of new costly antifungal agents has led to a considerable increase in pharmaceutical expenditure. In December 2011, the Lorraine Regional Health Agency commissioned the Antibiolor network to evaluate costly antifungal agent stewardship using as reference regional, French, and international recommendations.

METHODS

We performed a regional retrospective multicenter study. The criteria for evaluation were the appropriateness of the indication for treatment, the choice of the agent or of a combination, compliance with dose and treatment duration, and the absence of any alternative.

RESULTS

One hundred and fourteen prescriptions were analyzed, in 7 intensive care units, 4 hematology units, and 1 infectious diseases unit. The indication for costly antifungal treatment was appropriate in 110 cases (96.5%), the choice of the antifungal agent in 102 cases (93%), the dose in 98 cases (89%), treatment duration in 102 cases (93%), and an alternative antifungal treatment was possible in 10 cases (9%). Eighty-two prescriptions (74.5%) complied with the marketing authorization, 19 (17%) were related to a protocol for temporary use, and 9 (8%) were considered as inappropriate.

CONCLUSION

Our results show a high rate of appropriate prescriptions. The easily accessible and regularly updated local recommendations probably resulted in the standardization and optimization of costly antifungal agent prescriptions.

Real-life rilpivirine resistance and potential emergence of an E138A-positive HIV strain in north-eastern France

OBJECTIVES

To assess the prevalence of resistance to rilpivirine and mutations at position 138 in reverse transcriptase and to identify associated epidemiological and biological characteristics.

METHODS

This retrospective study included 238 patients with available HIV-1 nucleotide sequences analysed at the Laboratory of Virology at the University Hospital of Nancy between January 2011 and June 2013. Resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) was evaluated according to the ANRS algorithm (version 23) and correlated with clinico-epidemiological and therapeutic data. The virus strains were analysed by evaluating the distance and distribution of the phylogenetic tree (MEGAv5).

RESULTS

Among previously treated patients (111/238, 46.6%), 68/111 (61.3%) had received NNRTIs; all were rilpivirine-naive. The prevalence of rilpivirine resistance in the whole cohort was 12.6% (30/238), and was 10.2% (13/127) and 15.3% (17/111) in naive and pre-treated patients, respectively. The E138A mutation was the most frequent mutation associated with resistance to rilpivirine (P < 0.0001). The prevalence of the E138A mutation tended to increase over time, from 3.6% (2/55) during the first half of 2011 to 9.3% (4/43) during the first half of 2013 (P = 0.0614). Seven viral strains from seven naive male patients positive for the E138A mutation appeared in the same cluster.

CONCLUSIONS

In our cohort of patients, we observed significantly increased resistance to rilpivirine, mostly because of the E138A mutation, probably due to an E138A strain circulating in newly diagnosed men who have sex with men. Taken together, our results emphasize the need to investigate the prevalence of rilpivirine resistance-associated mutations in the coming years both in France and abroad.