Evidential deep learning for trustworthy prediction of enzyme commission number

The rapid growth of uncharacterized enzymes and their functional diversity urge accurate and trustworthy computational functional annotation tools. However, current state-of-the-art models lack trustworthiness on the prediction of the multilabel classification problem with thousands of classes. Here, we demonstrate that a novel evidential deep learning model (named ECPICK) makes trustworthy predictions of enzyme commission (EC) numbers with data-driven domain-relevant evidence, which results in significantly enhanced predictive power and the capability to discover potential new motif sites. ECPICK learns complex sequential patterns of amino acids and their hierarchical structures from 20 million enzyme data. ECPICK identifies significant amino acids that contribute to the prediction without multiple sequence alignment. Our intensive assessment showed not only outstanding enhancement of predictive performance on the largest databases of Uniprot, Protein Data Bank (PDB) and Kyoto Encyclopedia of Genes and Genomes (KEGG), but also a capability to discover new motif sites in microorganisms. ECPICK is a reliable EC number prediction tool to identify protein functions of an increasing number of uncharacterized enzymes.

Epidemic Vulnerability Index for Effective Vaccine Distribution Against Pandemic

COVID-19 vaccine distribution route directly impacts the community's mortality and infection rate. Therefore, optimal vaccination dissemination would appreciably lower the death and infection rates. This paper proposes the Epidemic Vulnerability Index (EVI) that quantitatively evaluates the subject's potential risk. Our primary aim for the suggested index is to diminish both infection rate and death rate efficiently. EVI was accordingly designed with clinical factors determining the mortality and social factors incorporating the infection rate. Through statistical COVID-19 patient dataset analysis and social network analysis with an agent-based model that is analogous to a real-world system, we define and experimentally validate the capability of EVI. Our experiments consist of nine vaccination distribution scenarios, including existing indexes which estimate the risk and stochastically proliferate the contagion and vaccine in a 300,000 agent-based graph network. We compared the outcome and variation of the three metrics in the experiments: infection case, death case, and death rate. Through this assessment, vaccination by the descending order of EVI has shown to have a significant outcome with an average of 5.0% lower infection cases, 9.4% lower death cases, and 3.5% lower death rate than other vaccine distribution routes.

Proton Single-Energy Bragg-Peak FLASH Using Clinical Systems Can Achieve IMPT-Equivalent Plan Quality for Breast and Prostate Cancers

PURPOSE/OBJECTIVE(S)

Most current proton FLASH-RT studies focus on transmission proton techniques. In this study, we propose a novel method for achieving FLASH dose rate in hypofractionated proton radiotherapy using the Bragg peak of a single-energy proton beam. The dosimetric characteristics using this novel technique for proton pencil beam scanning (PBS) stereotactic body radiation therapy (SBRT) of prostate and breast cancers were first investigated based on the clinically available cyclotron beam parameters.

MATERIALS/METHODS

This novel approach uses the distal tracking technique that enables PBS Bragg-peak of the highest proton energy to adapt to the target distally. Positioning of the Bragg peak at different depths is achieved using a universal range shifter and range compensator. To investigate the feasibility of this approach, we developed an in-house treatment planning platform for intensity-modulated proton therapy (IMPT) delivery and performed dosimetric studies on prostate and breast SBRT cases previously treated with conventional proton PBS technique. FLASH plans were generated using a similar clinical beam arrangement to deliver 40 Gy (RBE) in 5 fractions. Dose metrics were compared between the clinical and FLASH plans. Dose-rate volume histograms (DRVH) were also calculated to investigate the 40 Gy/s coverage (V40 Gy/s) of organs-at-risk (OARs) for FLASH plans.

RESULTS

The distal tracking can precisely stop the Bragg peak at the target distal edge, and Bragg peak plans achieved tumor coverage and dose conformality equivalent to IMPT plans. The clinical IMPT plans yielded slightly superior target dose uniformity -CTV Dmax of FLASH plans was 10% higher for prostate and 2% higher for breast. There was no significant difference between the clinical and FLASH plans in dose metrics for major OARs, including rectum, large bowel, heart, and lung. Higher maximal doses to femoral heads (∼2 Gy) and urethra (∼6 Gy) were observed in prostate FLASH plans than in the clinical plans but were still within clinically accepted dose limits. The V40 Gy/s for OARs were >90% for prostate FLASH plans and >76.5% for breast FLASH plans.

CONCLUSION

The proposed single-energy Bragg-peak FLASH technique eliminates exit dose associated with transmission proton FLASH and can still yield comparable plan quality and OAR sparing while preserve sufficient FLASH dose rate coverage for prostate and breast proton SBRT. This study demonstrates the potential application of Bragg peaks for highly conformal FLASH-RT using clinical cyclotron systems to treat prostate and breast cancer patients, which moves towards clinical application.

Exploring the Clinical Characteristics and Survival of Early-Onset and Late-Onset Nasopharyngeal Carcinoma

PURPOSE/OBJECTIVE(S)

Presently, early-onset and late-onset nasopharyngeal cancer (EONPC and LONPC, defined as age ≤ 50 years and > 50 years old, respectively) are seldom studied. The purpose of this study is to determine the clinical and survival characteristics between the NPC patients of these two age groups.

MATERIALS/METHODS

Patients diagnosed with NPC in The Surveillance, Epidemiology, and End Results (SEER) database from 2000 to 2018 years, and in our institution from 2014 to 2017 years were reviewed in this study. Clinicopathological characteristics, treatment modalities, and survival outcomes of EONPC and LONPC patients were analyzed and compared.

RESULTS

A total of 2943 patients (including 935 patients with EONPC and 2008 patients with LONPC) in the SEER database and 833 domestic patients (including 518 patients with EONPC and 315 patients with LONPC) in our center were finally enrolled. In the SEER database, both EONPC and LONPC patients displayed a greater prevalence in men. EONPC patients presented with a worse staging of regional lymph node metastasis (p < 0.001), but had a better prognosis than that in the LONPC patients (p < 0.001). More EONPC patients received chemotherapy and radiation (p < 0.001). Similar results were validated in our center, and in addition, it was found that EONPC patients had an advanced clinical stage (stage III, IVA, 92.1% vs. 85.1%, p = 0.016) and larger primary tumor volume (41.7% vs. 35.7%, p = 0.049). Meanwhile, EONPC patients had a superior overall survival (OS) (p = 0.017) and cancer-specific survival (CSS) (p = 0.004) compared to that in the LONPC patients. In univariate and multivariate Cox regression analysis, early-onset was independently associated with a higher 5-year OS (82.4% vs. 73.3%, p = 0.006).

CONCLUSION

EONPC patients present with more advanced lymph node metastasis stage and clinical stage, but have a better survival compared to LONPC patients. Age ≤ 50 years was an independent prognostic factor for survival outcome in NPC patients. To achieved the better individualization of the therapeutic regimen, there is the need for further studies on EONPC.

Potential Predictive Value of Intravoxel Incoherent Motion Magnetic Resonance for Xerostomia of Nasopharyngeal Carcinoma

PURPOSE/OBJECTIVE(S)

Xerostomia, caused by radiation-induced parotid damage, is the most commonly reported complications of radiotherapy (RT) to nasopharyngeal carcinoma (NPC). This study aimed to evaluate the value of IVIM MR in monitoring radiation parotid gland damage and predicting the risk of xerostomia.

MATERIALS/METHODS

A total of 54 patients were enrolled and underwent IVIM MR scans at before RT, after the fifth fraction, halfway through the course of RT, and at the end of radiotherapy. The parameters of IVIM MR include pseudo-diffusion coefficient (D*), perfusion fraction (f), and pure diffusion coefficient (D). The degree of xerostomia in NPC patients was assessed before each MR examination using the acute radiation morbidity scoring criteria proposed by the Radiation Therapy Oncology Group (RTOG). Concurrently, the time when the patient first reported suffering from xerostomia was recorded. The IVIM parameters trend throughout the RT, and the relationships between IVIM parameters and xerostomia, were analyzed.

RESULTS

All of the IVIM parameters increased from pre-RT to post-RT significantly (all p < 0.001). The increase rate of D from pre-RT to halfway through the RT was 32.61%, which was significantly higher than 15.64% from halfway to post-RT (p<0.001), indicating that cell necrosis in the first half of treatment is significantly higher than that in the second half. Both D* and F had significantly increased from pre-RT to halfway through the radiotherapy (p<0.001), with an increase rate of 19.58% and 29.38%, respectively. However, no significant increase was observed from Halfway to post-RT (p>0.05), with an increase rate of 4.10% and 8.30%, respectively. This may be due to radiation-induced vasculitic dilation that is significant in the first half of the radiotherapy but plateaus in the second half. Pre-D (OR = 23.85; 95% CI = 2.39, 237.82; p = .007) and pre-D* (OR = 0.75; 95% CI = 0.63, 0.91; p = 0.003) are independent influencing factors for xerostomia at 3 months after the completion of RT. D and F were significantly higher after the fifth fraction compared with Pre-RT (both p<0.05), respectively increased 31.25% and 25.16%. D* increase by 15% (p = 0.081). IVIM scans can assess parotid gland damage early. And the average time of parotid damage underwent IVIM scan was 5.99 ± 0.84 (day), much earlier than 11.84 ± 2.74 (day) according to RTOG.

CONCLUSION

Our study indicates that IVIM MR can dynamically monitor radiotherapy-induced parotid gland damage, and much earlier and objectively than RTOG.

Introducing an Experimental Approach to Predict Spot Scanning Time Parameters for a Superconducting Cyclotron Proton Therapy Machine

PURPOSE/OBJECTIVE(S)

Proton pencil beam scanning (PBS) delivery sequence varies a lot among institutions due to the differences in vendors, machine types, and beamline configurations, which impacts PBS interplay effects and treatment delivery time estimation. This study aims to develop an independent experimental approach to predict the spot scanning time parameters for a clinical superconducting cyclotron proton therapy machine.

MATERIALS/METHODS

This independent experimental approach employed an open-air parallel-plate detector with a temporal resolution of 0.05ms. A series of spot, energy, and dose rate patterns were designed and delivered, including (1) Spot switching time (SSWT) under different spot spacing for IEC-X, IEC-Y directions and diagonal direction (traveling in both X and Y direction) for three energy layers (110, 170 and 230 MeV); The Wilcoxon test is used to validate the prediction of SSWT along the diagonal direction. (2) Energy layer switching time (ELST) with different descending energy gaps for a fixed initial energy and different initial energies for a fixed descending energy gap. (3) Dose rate (MU/min) are measured for different minimum-MU-per-energy-layer (MMPEL), which are compared with the previous publication.

RESULTS

A SSWT jump at 10mm (can be customized) spot spacing is observed because of triggering the machine's "raster mode" threshold. Discontinuous two variable piecewise linear functions were used to fit the SSWT in X/Y for spot spacing and energy. SSWT in X/Y is increasing as spot spacing and energy increase. SSWT in the diagonal direction is determined by the time either in the x-direction or y-direction, whichever takes longer (see Table 1 for one example of validations). ELST is linear depending on descending energy gap. The dose rate dependence on MMPEL is confirmed with previous publications of a similar type of machine.

CONCLUSION

The study provided the first independent quantitative experimental modeling of the beam delivery time parameters without any information from vendors. Such machine-specific delivery sequence models could pave the foundation of precise interplay effect evaluation for clinical decision-making.

Pencil Beam Scanning Proton Stereotactic Body Radiation Therapy (SBRT): A Robust Single Institution Experience

PURPOSE/OBJECTIVE(S)

To describe the feasibility of treating a complex and diverse group of patients using pencil beam scanning (PBS) proton stereotactic body radiation therapy (SBRT: 5 or fewer fractions, with a fraction size of at least 5 Gy).

MATERIALS/METHODS

Our center treats on average 105-120 PBS proton treatments daily, of which 9.5% of treatment courses are proton SBRT. Statistics of disease sites, treatment planning parameters (target volume, prescriptions, number of fields, SFO vs. MFO), and treatment efficiencies (scheduled time slots, actual treatment time) are presented for 305 consecutive SBRT patients receiving 1507 fractions in the past three years. Thermoplastic masks or Vacuum-lock bags are used to immobilize SBRT patients and index the patients' treatment position. Imaging guidance of orthogonal kV images and volumetric cone-beam CT is routinely used for patient setup.

RESULTS

SBRT patients are grouped based on the target locations: pelvis (31%), liver (17%), thoracic (13%), spine (8%), abdominal (8%), brain (7%), non-spine bone (7%), ocular (6%), and head and neck (2%). Only 112 patients (37%) were receiving their 1st RT course, whereas 113 (37%) had one prior in-field RT course, and 80 (26%) had multiple prior in-field RT courses. The median [IQR] target volume was 65.4 [29.3, 168] cc (range: 0.3-2475 cc). 72% of cases were planned with SFO and 28% with MFO. On average, 3.76 fields (range: 2 to 12) were planned for each treatment. 44% of the treatments were planned with three or fewer fields, and 10% received more than five fields, most of which involved repainting for moving targets. Over 97% of treatments were delivered in 5 fractions, with ∼3% delivered in 3 fractions. The median [IQR] prescription per treatment was 8 [7, 10] Gy (range: 5-18 Gy per treatment). 85% (84%) of the SBRT treatments were scheduled (delivered) in a 45-minute or shorter slot, and 6% (7%) of treatments were scheduled (delivered) in over a one-hour slot, most commonly for multiple isocenter treatments. 93% of treatments were delivered within 15 minutes of the planned treatment time or shorter. Deep-inspiration breath-hold (DIBH) was applied to 45% of liver SBRT cases, with the remaining 55% planned on 4D CT with (14%) or without (86%) abdominal compression. DIBH was applied in 13% of lung SBRT cases. The application of other motion mitigation approaches, such as volumetric repainting, was determined by the target motion amplitude and whether the patient could tolerate DIBH.

CONCLUSION

In the most diverse and largest proton SBRT experience delivered in the world over the past 3 years, over 300 patients were treated, demonstrating the feasibility and efficiency of delivering proton SBRT in a very busy center. The planning and treatment parameter statistics reported serve as a helpful reference for the proton community.

The Feasibility of Level Ib Sparing Intensity Modulated Radiation Therapy in Nasopharyngeal Carcinoma Patients with High-Risk Factors: Based on International Guideline

PURPOSE/OBJECTIVE(S)

In spite of the rarity of level Ib recurrence after intensity-modulated radiation therapy, the International Guideline (IG) provides the risk factors for prophylactic coverage. In practice, however, there are significant differences between institutions. The purpose of this study is to examine the feasibility of sparing level Ib IMRT in NPC patients with high-risk factors based on IG.

MATERIALS/METHODS

From January 2014 to October 2017, newly-diagnostic, non-metastatic NPC patients in our center were retrospectively reviewed. According to the risk factors of prophylactic level Ib coverage in patients with negative level Ib recommended by IG, the characteristics of pre-treatment MRI were analyzed. Four high-risk factors were identified: a. involvement of the structures that drain to level Ib as first echelon (FES), including anterior half of nasal cavity, oral cavity, b. involvement of submandibular gland (SMG), c. with radiologic extranodal extension (rENE) in level II LNs, or d. maximal axial diameter (MAD)≧2 cm in level II LNs. Patients with risk factors were divided into Cohort A (with risk factors a), Cohort B (with risk factor b, but without a), and Cohort C (only with risk factors c and/or d). Recurrence rates of level Ib and regional relapse-free survival (RRFS) rates were evaluated in different cohorts.

RESULTS

A total of 961 patients were finally included. Thirty-six cases (3.7%) presented with radiologically positive level Ib metastasis. For the other patients with negative Ib LNs, there were 18, 65, 421, and 444 cases classified as FES involvement, SMG involvement, level II LNs with rENE, and level II nodal with MAD ≧2 cm. Excluding overlap, a total of 571 patients with risk factors were divided into three groups: Cohort A (n = 18), Cohort B (n = 49) and Cohort C (n = 504). Nine patients (9/961, 0.94%) developed level Ib recurrence. Except for 1 patient with positive Ib LNs at diagnosis, 2 did not meet any of the risk factors, while the other six (6/9, 66.7%) met at least one risk factor. The rate of recurrence at neck level Ib was highest in Cohort A (11.1%, 2/18; Ib-sparing group: 0/10, 0.0% vs Ib-covering group: 2/8, 25.0%; P = 0.183). In Cohort B, no cases were found with level Ib recurrence (0.0%, 0/49). In Cohort C, the rates were rare (0.8%, 4/504) in both groups (0.7%, 2/276 vs 0.9%, 2/228; P > 0.999). Among the three Cohorts, there were no significant differences in 5-year RRFS between two groups, which were 90.0% vs 62.5% (p = 0.248), 90.9% vs 92.0% (p = 0.905), and 92.6% vs 90.1% (p = 0.445), respectively. Among patients with high-risk factors, the incidence of grade 3-4 late dry mouth symptom was higher in the level Ib-covering group (3.1% vs 7.5%, P = 0.033).

CONCLUSION

Level Ib sparing appears safe and feasible for NPC patients with negative level Ib LNs, even if combined with risk factors: SMG involvement, and/or level II with rENE, and/or level II MAD ≧2 cm. Level Ib-sparing irradiation reduces dry mouth symptoms compared with level Ib-irradiation.

Impact of Advance Care Planning on the Hospitalization-Associated Utilization and Cost of Patients with Alzheimer's Disease-Related Disorders Receiving Primary Care via Telehealth in a Provider Shortage Area: A Quantitative Pre-Study

Telehealth has been adopted as an alternative to in-person primary care visits. With multiple participants able to join remotely, telehealth can facilitate the discussion and documentation of advance care planning (ACP) for those with Alzheimer's disease-related disorders (ADRDs). We measured hospitalization-associated utilization outcomes, instances of hospitalization and 90-day re-hospitalizations from payors' administrative databases and verified the data via electronic health records. We estimated the hospitalization-associated costs using the Nevada State Inpatient Dataset and compared the estimated costs between ADRD patients with and without ACP documentation in the year 2021. Compared to the ADRD patients without ACP documentation, those with ACP documentation were less likely to be hospitalized (mean: 0.74; standard deviation: 0.31; p < 0.01) and were less likely to be readmitted within 90 days of discharge (mean: 0.16; standard deviation: 0.06; p < 0.01). The hospitalization-associated cost estimate for ADRD patients with ACP documentation (mean: USD 149,722; standard deviation: USD 80,850) was less than that of the patients without ACP documentation (mean: USD 200,148; standard deviation: USD 82,061; p < 0.01). Further geriatrics workforce training is called for to enhance ACP competencies for ADRD patients, especially in areas with provider shortages where telehealth plays a comparatively more important role.

Comprehensive genomic analysis of the potential limitations of several published PCR primers targeting prfA-virulence gene cluster in Listeria species

Polymerase chain reaction (PCR) is commonly used to detect Listeria monocytogenes, foodborne pathogen. The present study conducted in silico genomic analysis to investigate the specificity and binding efficacy of four published pairs of PCR primers targeting Listeria prfA-virulence gene cluster (pVGC) based on Listeria sequences available. We first performed comprehensive genomic analyses of the pVGC, the main pathogenicity island in Listeria spp. In total, 2961 prfA, 642 plcB, 629 mpl, and 1181 hlyA gene sequences were retrieved from the NCBI database. Multiple sequence alignments and phylogenetic trees were generated using unique (non-identical or not-shared) sequences of each represented genes, targeting four pairs of PCR primers published previously, namely 202 prfA, 82 plcB, 150 mpl and 176 hlyA unique gene sequences. Only hlyA gene showed strong (over 94%) primer mapping results, while prfA, plcB and mpl genes showed weak (less than 50%) matching results. In addition, nucleotide variations were observed at the 3' end of the primers, indicating non-binding to the targets could potentially cause false-negative results. Thus, we propose designing degenerate primers or multiple PCR primers based on as many isolates as possible, to minimize the false-negative risk and reach the aim of low tolerable limits of detection.

[Epidemiologic characteristics and influencing factors of influenza outbreaks in Guangdong Province, 2015-2022]

Objective: To grasp the epidemiological characteristics of influenza outbreaks in Guangdong Province by analyzing the outbreaks of influenza-like cases reported in Guangdong Province from January 2015 to the end of August 2022. Methods: In response to the outbreak of epidemics in Guangdong Province from 2015 to 2022, information on on-site epidemic control was collected, and epidemiological analysis was conducted to describe the characteristics of the epidemics. The factors that influence the intensity and duration of the outbreak were determined through a logistic regression model. Results: A total of 1 901 influenza outbreaks were reported in Guangdong Province, with an overall incidence of 2.05%. Most outbreak reports occurred from November to January of the following year (50.24%, 955/1 901) and from April to June (29.88%, 568/1 901). A total of 59.23% (1 126/1 901) of the outbreaks were reported in the Pearl River Delta region, and primary and secondary schools were the main places where outbreaks occurred (88.01%, 1 673/1 901). Outbreaks with 10-29 cases were the most common (66.18%, 1 258/1 901), and most outbreaks lasted less than seven days (50.93%,906/1 779). The size of the outbreak was related to the nursery school (aOR=0.38, 95%CI:0.15-0.93), the Pearl River Delta region (aOR=0.60, 95%CI:0.44-0.83), the time interval between the onset of the first case and the time of report (>7 days compared with ≤3 days: aOR=3.01, 95%CI:1.84-4.90), the influenza A(H1N1) (aOR=2.02, 95%CI:1.15-3.55) and the influenza B (Yamagata) (aOR=2.94, 95%CI: 1.50-5.76). The duration of outbreaks was related to school closures (aOR=0.65, 95%CI: 0.47-0.89), the Pearl River Delta region (aOR=0.65, 95%CI: 0.50-0.83) and the time interval between the onset of the first case and the time of report (>7 days compared with ≤3 days: aOR=13.33, 95%CI: 8.80-20.19; 4-7 days compared with ≤3 days: aOR=2.56, 95%CI: 1.81-3.61). Conclusions: An influenza outbreak in Guangdong Province exhibits two peaks, one in the winter and spring seasons and the other in the summer. Primary and secondary schools are high-risk areas, and early reporting of outbreaks is critical for controlling influenza outbreaks in schools. Furthermore, comprehensive measures should be taken to prevent the spread of the epidemic.

[Clinical features and prognosis of 118 children with histiocytic necrotizing lymphadenitis]

Objective: To explore the clinical features and prognosis of children with histiocytic necrotizing lymphadenitis (HNL). Methods: The clinical data of 118 children with HNL diagnosed and treated in the Department of Rheumatology and Immunology of Children's Hospital, Capital Institute of Pediatrics from January 2014 to December 2021 were retrospectively analyzed. The clinical symptoms, laboratory examination, imaging examination, pathological findings, treatment and follow-up were analyzed. Results: Among the 118 patients, 69 were males and 49 were females. The age of onset was 10.0 (8.0, 12.0) years, ranging from 1.5 to 16.0 years. All the children had fever lymph node enlargement, blood system involvement in 74 cases (62.7%), skin injury in 39 cases (33.1%). The main manifestations of laboratory examination were increased erythrocyte sedimentation rate in 90 cases (76.3%), decreased hemoglobin in 58 cases (49.2%), decreased white blood cells in 54 cases (45.8%) and positive antinuclear antibody in 35 cases (29.7%). Ninety-seven cases (82.2%) underwent B-mode ultrasound of lymph nodes, showing nodular lesions with low echo in the neck; 22 cases (18.6%) underwent cervical X-ray and (or) CT; 7 cases (5.9%) underwent cervical magnetic resonance imaging. Lymph node biopsy was performed in all 118 cases, and the pathological results did not support malignant diseases such as lymphoma or Epstein-Barr virus infection, suggesting HNL. Fifty-seven cases (48.3%) recovered without treatment, 61 cases (51.7%) received oral steroid therapy, and 4 cases (3.4%) received indomethacin as anal stopper. The 118 cases were followed up for 4 (2, 6) years, ranging from 1 to 7 years, 87 cases (73.7%) had one onset and did not develop into other rheumatological diseases, and 24 cases (20.3%) had different degrees of recurrence, 7 cases (5.9%) had multiple system injuries, and all of the tested autoantibodies were positive for medium and high titers. All of them developed into other rheumatic immune diseases, among which 5 cases developed into systemic lupus erythematosus and 2 cases developed into Sjogren's syndrome; 7 cases were given oral steroid therapy, including 6 cases plus immunosuppressant and 2 cases receiving methylprednisolone 20 mg/kg shock therapy. Conclusions: The first-onset HNL portion is self-healing, hormone-sensitive and has a good prognosis. For HNL with repeated disease and multiple system injury, antinuclear antibody titer should be monitored during follow-up, and attention should be paid to the possibility of developing into other rheumatological diseases, with poor prognosis.

Harnessing deep learning into hidden mutations of neurological disorders for therapeutic challenges

The relevant study of transcriptome-wide variations and neurological disorders in the evolved field of genomic data science is on the rise. Deep learning has been highlighted utilizing algorithms on massive amounts of data in a human-like manner, and is expected to predict the dependency or druggability of hidden mutations within the genome. Enormous mutational variants in coding and noncoding transcripts have been discovered along the genome by far, despite of the fine-tuned genetic proofreading machinery. These variants could be capable of inducing various pathological conditions, including neurological disorders, which require lifelong care. Several limitations and questions emerge, including the use of conventional processes via limited patient-driven sequence acquisitions and decoding-based inferences as well as how rare variants can be deduced as a population-specific etiology. These puzzles require harnessing of advanced systems for precise disease prediction, drug development and drug applications. In this review, we summarize the pathophysiological discoveries of pathogenic variants in both coding and noncoding transcripts in neurological disorders, and the current advantage of deep learning applications. In addition, we discuss the challenges encountered and how to outperform them with advancing interpretation.

Opioid Utility and Hospital Outcomes Among Inpatients Admitted With Osteoarthritis and Spine Disorders

OBJECTIVE

The aim of the study is to evaluate opioid analgesic utilization and predictors for adverse events during hospitalization and discharge disposition among patients admitted with osteoarthritis or spine disorders.

DESIGN

This is a retrospective study of 12,747 adult patients admitted to six private community hospitals from 2017 to 2020. Opioid use during hospitalization and risk factors for hospital-acquired adverse events and nonhome discharge were investigated.

RESULTS

The total number of patients using opioids decreased; however, the daily morphine milligram equivalent use for patients on opioids increased from 2017 to 2020. Increased odds of nonhome discharge were associated with older age, Medicaid, Medicare insurance, and increased lengths of stay, increased body mass index, daily morphine milligram equivalent, and electrolyte replacement in the osteoarthritis group. In the spine group, older age, Black race, Medicaid, Medicare, no insurance, increased Charlson Comorbidity Index, lengths of stay, polypharmacy, and heparin use were associated with nonhome discharge. Adverse events were associated with increased age, lengths of stay, Medicare, polypharmacy, antiemetic, and benzodiazepine use in the osteoarthritis group and increased Charlson Comorbidity Index, lengths of stay, and electrolyte replacement in the spine group.

CONCLUSIONS

Despite the decreasing number of patients using opioids over the years, patients on opioids had an increased daily morphine milligram equivalent over the same period.

Analysis of SOD1 Variants in Chinese Patients with Familial Amyotrophic Lateral Sclerosis

BACKGROUND

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease, and genetic contributors exert a significant role in the complicated pathogenesis. Identification of the genetic causes in ALS families could be valuable for early diagnosis and management. The development of potential drugs for patients with genetic defects will shed new light on ALS therapy.

AIM

To identify causative variants in three Chinese families with familial ALS (FALS), reveal the pathogenic mechanism, and look for the targeted drug for ALS.

DESIGN AND METHODS

Whole-exome sequencing and bioinformatics were used to perform genetic analysis of the ALS families. Functional analysis was performed to study the variants' function and search for potential drug targets.

RESULTS

Three heterozygous missense variants of the SOD1 gene were identified in families with FALS. The clinical manifestations of these patients include spinal onset, predominant lower motor neurons presentation, and absence of cognitive involvement. Functional analysis showed that all three SOD1 variants led to increased reactive oxygen species (ROS) levels, reduced cell viability, and formation of cytoplasmic aggregates. Remarkably, the decreased cell viability induced by variants was rescued after treatment with the ROS inhibitor N-acetylcysteine.

CONCLUSIONS

This study identified three SOD1 variants in three families with FALS. The variant SOD1 toxicity was associated with oxidative damage and aggregation, and N-acetylcysteine could rescue the decreased cell viability induced by these variants. Our findings support a pathogenic role for ROS in SOD1 deficiencies, and provide a potential drug N-acetylcysteine for ALS therapy, especially in SOD1-patients with limb onset.

Racial and Ethnic Disparity in 4Ms among Older Adults Among Telehealth Users as Primary Care

Telehealth has been widely accepted as an alternative to in-person primary care. This study examines whether the quality of primary care delivered via telehealth is equitable for older adults across racial and ethnic boundaries in provider-shortage urban settings. The study analyzed documentation of the 4Ms components (What Matters, Mobility, Medication, and Mentation) in relation to self-reported racial and ethnic backgrounds of 254 Medicare Advantage enrollees who used telehealth as their primary care modality in Southern Nevada from July 2021 through June 2022. Results revealed that Asian/Hawaiian/Pacific Islanders had significantly less documentation in What Matters (OR = 0.39, 95%, p = .04) and Blacks had significantly less documentation in Mobility (OR = 0.35, p < .001) compared to their White counterparts. The Hispanic ethnic group had less documentation in What Matters (OR = 0.18, p < .001) compared to non-Hispanic ethnic groups. Our study reveals equipping the geriatrics workforce merely with the 4Ms framework may not be sufficient in mitigating unconscious biases healthcare providers exhibit in the telehealth primary care setting in a provider shortage area, and, by extrapolation, in other care settings across the spectra, whether they be in-person or virtual.

[Efficacy and safety of belimumab treatment in childhood-onset systemic lupus erythematosus]

Objective: To evaluate the efficacy and safety of belimumab in children with systemic lupus erythematosus (cSLE). Methods: The clinical data of 49 cSLE patients admitted into the Department of Rheumatology and Immunology, Children's Hospital affiliated to the Capital Institute of Pediatrics, from August 2018 to December 2021 were collected. They were divided into the belimumab treatment group (18 cases) and the traditional treatment group (31 cases) according to whether they received belimumab treatment. The cSLE patients in the traditional group had similar baseline SLEDAI scores with the belimumab group and were treated with traditional immunosuppressive drugs. The clinical symptoms and improvements before and after treatment, as well as the differences in adverse events during follow-up were compared between the two groups. Results: In belimumab group, the age was (11.9±1.8) years old, the median (Q₁, Q₃) of disease duration was 7.5 (2.0, 16.8) months, 3 patients were male, and 15 patients completed 24 weeks of treatment. In the traditional treatment group, 31 patients with cSLE were enrolled, with an average age of (11.3±2.4) years, a median (Q₁, Q₃) of disease duration of 7.0 (2.5, 10.5) months, among whom 6 patients were male, and 25 patients completed 24 weeks of treatment. At baseline, the belimumab treatment group had a significantly lower oral prednisone dose than the conventional treatment group [(29.58±12.43) mg/d vs (38.20±14.11) mg/d, P=0.037]. After 24 weeks of treatment, the dosage of prednisone in both groups was reduced, and the dosage of prednisone in the belimumab group was (14.12±5.86) mg/d, which was lower than that in the traditional treatment group [(23.51±9.79) mg/d] (P=0.002). After 24 weeks of treatment, the levels of complement C3 and C4 increased, the dsDNA levels and SLEDAI score decreased in both groups (all P>0.05). The incidence of adverse events in belimumab group (3/15, 3 cases) was lower than that in traditional treatment group (32.0%, 8/25) (P>0.05). Conclusions: Belimumab in the treatment of cSLE can reduce the initial dose of prednisone and facilitate the reduction of prednisone dose, significantly improve the clinical symptoms and organ involvement, and reduce the disease activity. The incidence of adverse events was low during belimumab treatment.

Cryptic mutations of PLC family members in brain disorders: recent discoveries and a deep learning-based approach

Phospholipase C is an essential isozyme involved in the phosphoinositide signaling pathway, which maintains cellular homeostasis. Gain-of-function and loss-of-function mutations in phospholipase C impact enzymatic activity and are therefore associated with several disorders. Alternative splicing variants of phospholipase C can interfere with complex signaling networks associated with oncogenic transformation and other diseases, including brain disorders. Cells and tissues with various mutations in phospholipase C contribute different phosphoinositide signaling pathways and disease progression; however, identifying cryptic mutations in phospholipase C remains challenging. Herein, we review both the mechanisms underlying phospholipase C regulation of the phosphoinositide signaling pathway and the genetic variation of phospholipase C in several brain disorders. In addition, we discuss the present challenges associated with the potential of deep-learning-based analysis for the identification of phospholipase C mutations in brain disorders.

Deep learning-based framework for slide-based histopathological image analysis

Digital pathology coupled with advanced machine learning (e.g., deep learning) has been changing the paradigm of whole-slide histopathological images (WSIs) analysis. Major applications in digital pathology using machine learning include automatic cancer classification, survival analysis, and subtyping from pathological images. While most pathological image analyses are based on patch-wise processing due to the extremely large size of histopathology images, there are several applications that predict a single clinical outcome or perform pathological diagnosis per slide (e.g., cancer classification, survival analysis). However, current slide-based analyses are task-dependent, and a general framework of slide-based analysis in WSI has been seldom investigated. We propose a novel slide-based histopathology analysis framework that creates a WSI representation map, called HipoMap, that can be applied to any slide-based problems, coupled with convolutional neural networks. HipoMap converts a WSI of various shapes and sizes to structured image-type representation. Our proposed HipoMap outperformed existing methods in intensive experiments with various settings and datasets. HipoMap showed the Area Under the Curve (AUC) of 0.96±0.026 (5% improved) in the experiments for lung cancer classification, and c-index of 0.787±0.013 (3.5% improved) and coefficient of determination ([Formula: see text]) of 0.978±0.032 (24% improved) in survival analysis and survival prediction with TCGA lung cancer data respectively, as a general framework of slide-based analysis with a flexible capability. The results showed significant improvement comparing to the current state-of-the-art methods on each task. We further discussed experimental results of HipoMap as pathological viewpoints and verified the performance using publicly available TCGA datasets. A Python package is available at https://pypi.org/project/hipomap , and the package can be easily installed using Python PIP. The open-source codes in Python are available at: https://github.com/datax-lab/HipoMap .

Association of malnutrition with in-hospital and long-term outcomes among ST-elevation myocardial infarction patients receiving primary PCI

Background

The impact of malnutrition on outcomes in a contemporary ST-segment-elevation myocardial infarction (STEMI) population is unclear. We hypothesized that malnutrition severity amongst STEMI patients undergoing primary percutaneous coronary intervention (pPCI) is associated with worse long-term outcomes.

Purpose

The aim of this study was 2-fold: 1) to establish the prevalence of malnutrition among STEMI patients undergoing pPCI; 2) to determine the association of malnutrition severity on in-hospital and 1-year outcomes in STEMI patients receiving pPCI

Methods

We retrospectively identified 1,169 STEMI patients of age ≥65 years who had received pPCI (2013–2020). Patients who had presented with out-of-hospital cardiac arrest or those who received fibrinolytic therapy were excluded. The Controlling Nutritional Status (CONUT) score, based on serum albumin, total cholesterol and lymphocyte count, was used as a tool to assess the nutritional status of included patients. Malnourished patients were defined as those with a CONUT score of 5 to 12. To account for the impact of frailty, a frailty index (FI) was determined using the health deficit accumulation model (Table 1). The primary outcome was 1-year all-cause mortality. The secondary outcome was a composite of in-hospital heart failure, cardiogenic shock, re-infarction, major bleeding, stroke, and all-cause mortality. A multivariable model adjusting for baseline covariates, including frailty index score, was performed (Figure 1).

Results

Among 1,169 STEMI patients receiving pPCI, 315 (26.9%) were classified as malnourished. Malnourished patients were older (mean 77.4 vs. 76.0 years, p=0.009) and had a higher comorbidity burden. After multivariable adjustment, worsening malnutrition was associated with increased 1-year all-cause mortality (odds ratio [OR] = 1.29, p&lt;0.001). Worsening malnutrition was also associated with a higher incidence of the in-hospital composite adverse outcome (OR = 1.12, p=0.003) and increased in-hospital all-cause mortality (OR=1.41, p&lt;0.001).

Conclusion

Among STEMI patients receiving pPCI, 1 in 4 were malnourished. Malnutrition was associated with increased rate of in-hospital composite adverse outcome and worse long-term outcomes, even when accounting for frailty. Efforts to routinely identify malnourished STEMI patients and to implement best practices to reduce the risk of adverse events in this vulnerable population are warranted.

Funding Acknowledgement

Type of funding sources: None.

[An exploratory clinical study of the efficacy and safety of tumor-infiltrating lymphocytes in the treatment of metastatic osteosarcoma]

Objective: To explore the safety and efficacy of tumor-infiltrating lymphocytes (TILs) extracted from tumor tissue in patients with pulmonary metastasis of osteosarcoma, the TILs were amplified in vitro to reach clinical dosage and reinfused to the patients combined with high-dose interleukin 2 (IL-2). Methods: Twelve subjects with pathologically diagnosed osteosarcoma were enrolled from December 2019 to June 20, 2021 in Shanghai General Hospital. All subjects progressed with metastasis after standard chemotherapy and failed multiple lines of treatments. Fresh tumor tissue was obtained from the metastatic site and extracted and amplified by Good Manufacturing Practice (GMP) workshop to produce TILs to clinical treatment dosage (10⁹-10¹¹). High-dose IL-2 (100 000-200 000 U/kg) was administered immediately after autogenous TILs infusion to promote the activation, proliferation and antitumor cytolytic activity in vivo. Adverse events (AE) were graded according to Common Terminology Criteria for Adverse Events (CTCAE) standard and tumor response was assessed according to Response Evaluation Criteria in Solid Tumors (RECIST) 1.1. Results: One patient did not receive treatment due to failure in isolating TILs, total of 11 patients received a single re-infusion of autologous TILs. There were 10 males and 1 female with a median age of 19.9 years (12-33 years). Six of these patients received higher dose levels of 1.0×10¹⁰ TILs. The 11 patients were followed-up for 1 to 13 months and tolerated well. The most common adverse events reported were fever (10/11), constipation (3/11) and elevated gamma-glutamyl transferase (GGT) (3/11). The high incidence of fever was due to the IL-2 infusion. All patients experienced a transient drop in lymphocyte count and leukopenia leading to non-myeloid ablative lymphocyte clearance. The AE included grade 4 hematologic toxicity, including 8 cases of lymphocytopenia, 2 cases of neutropenia and 1 case of thrombocytopenia. No AE of neurotoxicity occurred. Of all the 11 patients, 9 patients got stable disease (SD) and 2 patients had progressive disease (PD). The disease control rate was 9/11. The median duration of SD was more than 4 months, and the maximum tumor volume decreased by close to 20%. Patient number 9 had sustained SD status for more than 6 months. Conclusions: TILs with in vitro expansion ability could be isolated from tumor tissues of advanced osteosarcoma patients. TILs amplified and reinfused in vitro have anti-osteosarcoma activity.

Opioid-like adverse effects of tianeptine in male rats and mice

RATIONALE

Tianeptine is a mu-opioid receptor (MOR) agonist with increasing reports of abuse in human populations. Preclinical data regarding the abuse potential and other opioid-like adverse effects of tianeptine at supratherapeutic doses are sparse.

OBJECTIVES

The present study evaluated tianeptine in a rat model of abuse potential assessment and in mouse models of motor, gastrointestinal, and respiratory adverse effects.

METHODS

Abuse potential was assessed in adult male Sprague-Dawley rats using an intracranial self-stimulation (ICSS) procedure to determine effects of acute and repeated tianeptine on responding for electrical brain stimulation. Male ICR mice were used to determine the effects of tianeptine in assays of locomotor behavior and gastrointestinal motility. Male Swiss-Webster mice were monitored for respiratory changes using whole-body plethysmography.

RESULTS

In rats, acute tianeptine produced weak and delayed evidence for abuse-related ICSS facilitation at an intermediate dose (10 mg/kg, IP) and pronounced, naltrexone-preventable ICSS depression at a higher dose (32 mg/kg, IP). Repeated 7-day tianeptine (10 and 32 mg/kg/day, IP) produced no increase in abuse-related ICSS facilitation, only modest tolerance to ICSS depression, and no evidence of physical dependence. In mice, tianeptine produced dose-dependent, naltrexone-preventable locomotor activation. Tianeptine (100 mg/kg, SC) also significantly inhibited gastrointestinal motility and produced naloxone-reversible respiratory depression.

CONCLUSIONS

Tianeptine presents as a MOR agonist with resistance to tolerance and dependence in our ICSS assay in rats, and it has lower abuse potential by this metric than many commonly abused opioids. Nonetheless, tianeptine produces MOR agonist-like acute adverse effects that include motor impairment, constipation, and respiratory depression.

Editorial of Special Issue "Deep Learning and Machine Learning in Bioinformatics"

In recent years, deep learning has emerged as a highly active research field, achieving great success in various machine learning areas, including image processing, speech recognition, and natural language processing, and now rapidly becoming a dominant tool in biomedicine [...].

[Progress in research of 2019-nCoV Omicron variant]

2019-nCoV Omicron (B.1.1.529) variant, which has brought new challenges to the prevention and control of COVID-19 pandemic, has the characteristics of stronger transmissibility and more rapid transmission and more significant immune evasion. It took only two months to become a predominant strain worldwide after its identification in South Africa in November 2021. Local epidemics caused by Omicron variant have been reported in several provinces in China. However, the epidemiological characteristics of highly mutated Omicron variant remain unclear. This article summarizes the progress in the research of functional mutations, transmissibility, virulence, immune evasion and cross-reactive immune responses of Omicron variant, to provide references for the effective prevention and control of COVID-19 pandemic caused by Omicron variant.

[Clinical analysis of 5 cases of systemic juvenile idiopathic arthritis with coronary artery dilatation]

Objective: To investigate the clinical characteristics of systemic juvenile idiopathic arthritis combined with coronary artery dilatation. Methods: A retrospective analysis was performed on the clinical data, including clinical manifestations, blood routine, inflammatory factors, echocardiography, vascular ultrasound and CT angiography, treatment and outcomes, etc, of 5 cases with systemic juvenile idiopathic arthritis combined with coronary artery dilation admitted to Department of Rheumatology in the affiliated Children's Hospital of Capital Institute of Pediatrics from May 2019 to June 2021. Results: There were 2 males and 3 females among 5 cases. The onset age ranged from 7 months to 4 years 7 months.The diagnostic time ranged from 1.5 months to 3.0 months.Four cases were diagnosed as atypical Kawasaki disease. Three cases showed unilateral coronary artery dilation.Two cases showed bilateral coronary artery dilation.Four cases developed multiple organ injuries.Three cases developed macrophage activation syndrome.Three cases developed lung injury.Two cases developed pericardial effusion.One case developed pulmonary hypertension.As for treatment, 3 cases treated with methylprednisolone pulse therapy and methotrexate combined with cyclosporine, improved after the final application of biological agents, and have stopped prednisone. The other 2 cases were treated with adequate oral prednisone and gradually reduced, and methotrexate was added at the same time, 1 case relapsed in the process of reduction. No other vascular involvement was found in 5 cases. Coronary artery dilation recovered completely after 1 to 3 months of treatment. Conclusions: Systemic juvenile idiopathic arthritis combined with coronary artery dilatation has the clinical characteristics of small onset age, long diagnostic time, prone to multiple organ injuries. Corticosteroids and conventional immunosuppressive agents are not sensitive, and biological agents should be used as soon as possible.The prognosis of coronary artery dilation is good after timely treatment.

Measuring school level attributable risk to support school-based HPV vaccination programs

Background

In Australia in 2017, 89% of 15-year-old females and 86% of 15-year-old males had received at least one dose of the HPV vaccine. However, considerable variation in HPV vaccination initiation (dose one) across schools remains. It is important to understand the school-level characteristics most strongly associated with low initiation and their contribution to the overall between-school variation.

Methods

A population-based ecological analysis was conducted using school-level data for 2016 on all adolescent students eligible for HPV vaccination in three Australian jurisdictions. We conducted logistic regression to determine school-level factors associated with lower HPV vaccination initiation (< 75% dose 1 uptake) and estimated the population attributable risk (PAR) and the proportion of schools with the factor (school-level prevalence).

Results

The factors most strongly associated with lower initiation, and their prevalence were; small schools (OR = 9.3, 95%CI = 6.1–14.1; 33% of schools), special education schools (OR = 5.6,95%CI = 3.7–8.5; 8% of schools), higher Indigenous enrolments (OR = 2.7,95% CI:1.9–3.7; 31% of schools), lower attendance rates (OR = 2.6,95%CI = 1.7–3.7; 35% of schools), remote location (OR = 2.6,95%CI = 1.6–4.3; 6% of schools,) and lower socioeconomic area (OR = 1.8,95% CI = 1.3–2.5; 33% of schools). The highest PARs were small schools (PAR = 79%, 95%CI:76–82), higher Indigenous enrolments (PAR = 38%, 95%CI: 31–44) and lower attendance rate (PAR = 37%, 95%CI: 29–46).

Conclusion

This analysis suggests that initiatives to support schools that are smaller, with a higher proportion of Indigenous adolescents and lower attendance rates may contribute most to reducing the variation of HPV vaccination uptake observed at a school-level in these jurisdictions. Estimating population-level coverage at the school-level is useful to guide policy and prioritise resourcing to support school-based vaccination programs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12889-022-13088-x.

[Course of disease and related epidemiological parameters of COVID-19: a prospective study based on contact tracing cohort]

Objective: To analyze the course of disease and epidemiological parameters of COVID-19 and provide evidence for making prevention and control strategies. Methods: To display the distribution of course of disease of the infectors who had close contacts with COVID-19 cases from January 1 to March 15, 2020 in Guangdong Provincial, the models of Lognormal, Weibull and gamma distribution were applied. A descriptive analysis was conducted on the basic characteristics and epidemiological parameters of course of disease. Results: In total, 515 of 11 580 close contacts were infected, with an attack rate about 4.4%, including 449 confirmed cases and 66 asymptomatic cases. Lognormal distribution was fitting best for latent period, incubation period, pre-symptomatic infection period of confirmed cases and infection period of asymptomatic cases; Gamma distribution was fitting best for infectious period and clinical symptom period of confirmed cases; Weibull distribution was fitting best for latent period of asymptomatic cases. The latent period, incubation period, pre-symptomatic infection period, infectious period and clinical symptoms period of confirmed cases were 4.50 (95%CI:3.86-5.13) days, 5.12 (95%CI:4.63-5.62) days, 0.87 (95%CI:0.67-1.07) days, 11.89 (95%CI:9.81-13.98) days and 22.00 (95%CI:21.24-22.77) days, respectively. The latent period and infectious period of asymptomatic cases were 8.88 (95%CI:6.89-10.86) days and 6.18 (95%CI:1.89-10.47) days, respectively. Conclusion: The estimated course of COVID-19 and related epidemiological parameters are similar to the existing data.

[Treatment of 11 cases of juvenile idiopathic arthritis by intra-articular injection of adalimumab]

Objective: To evaluate the efficacy and safety of intra-articular injection of adalimumab (ADA) in the treatment of refractory oligoarticular juvenile idiopathic arthritis (JIA). Methods: This was a retrospective study. Clinical data on age, gender, and symptoms of joint swelling and pain were collected from 11 children with refractory oligoarticular JIA involving only knee joints admitted to Department of Rheumatism and Immunology of Children's Hospital, Capital Institute of Pediatrics from November 2019 to October 2020. The physician and parent-child evaluation of disease activity, the number of active joints, and the level of erythrocyte sedimentation rate (ESR) at different treatment time points were analyzed at every 4-week observation point after drug administration, and the non-parametric Kruskal-Wallis test was used to compare the differences in clinical evaluation indicators and changes in laboratory tests at different treatment times. The follow-up period was 6 months. Results: Among the 11 children, 5 were boys and 6 were girls. The age was 3.0 (2.8) years. All 11 children had symptoms of joint swelling and pain as well as limitation of movement. After 3 intra-articular injections of ADA, the joint symptoms of 11 children were better than before treatment; the joint symptoms of 7 children disappeared completely, and no recurrence occurred during the 6-month follow-up period. At different treatment times, physician and parent-child evaluation of disease activity, a gradual decrease in the number of active joints in the children, ESR, and juvenile arthritis disease activity score with 27 joints were all statistically significant (χ²=53.99, 59.37, 32.87, 40.07, 54.00, all P<0.001).No significant adverse drug reactions were observed in any of the 11 children during treatment and follow-up. Conclusion: Intra-articular injection of ADA in the treatment of refractory oligoarticular JIA has a significant effect in controlling joint symptoms and is relatively safe.

A roadmap for multi-omics data integration using deep learning

High-throughput next-generation sequencing now makes it possible to generate a vast amount of multi-omics data for various applications. These data have revolutionized biomedical research by providing a more comprehensive understanding of the biological systems and molecular mechanisms of disease development. Recently, deep learning (DL) algorithms have become one of the most promising methods in multi-omics data analysis, due to their predictive performance and capability of capturing nonlinear and hierarchical features. While integrating and translating multi-omics data into useful functional insights remain the biggest bottleneck, there is a clear trend towards incorporating multi-omics analysis in biomedical research to help explain the complex relationships between molecular layers. Multi-omics data have a role to improve prevention, early detection and prediction; monitor progression; interpret patterns and endotyping; and design personalized treatments. In this review, we outline a roadmap of multi-omics integration using DL and offer a practical perspective into the advantages, challenges and barriers to the implementation of DL in multi-omics data.

[Analysis on characteristics and influencing factors of COVID-19 confirmed cases with viral nucleic acid re-positive after discharge in Guangdong Province]

Objective: To analyze the epidemiological characteristics and influencing factors of COVID-19 confirmed cases with viral nucleic acid re-positive in anal and/or throat swabs after discharge during the domestic imported epidemic stage in Guangdong Province in early 2020. Methods: The COVID-19 confirmed cases with the onset time before March 1, 2020 in Guangdong Province were collected to analyze the demographic data, epidemiological characteristics, and specimen collection and testing data after discharge. Logistic regression model was used for influencing factors analysis of re-positive cases. Results: A total of 1 286 COVID-19 confirmed cases were included, the M(Q₁,Q₃) of age was 44(32,58)years, 617 cases were male, 224 cases were re-positive in anal and/or throat swabs with the re-positive rate 17.42%. The M(Q₁,Q₃) of age of re-positive cases was 35(23, 50) years, which was younger than that of re-negative cases age was those 46(33, 59) years (P<0.001). With the increase of age, re-positive rate decreased (χ²_trend=52.73, P<0.001). 85.27% (191/224) of re-positive cases were found in 14 d after discharge, the duration time of re-positive status was 13(7, 24) d, and 81.69% (183/224) of re-positive cases were re-tested negative in 28 d after re-positive date. No fever and other symptoms had been observed among re-positive cases during the whole follow-up. No secondary infectious cases had been found among close contacts after 14 d of centralized isolation and sampling screening. Univariate logistic regression model analysis revealed that the influencing factors of the re-positive cases included age, occupation, clusters, clinical types, and admission time. Multivariate logistic regression model analysis revealed that age was an independent risk factor. Conclusions: SARS-CoV-2 viral nucleic acid re-positive is found in COVID-19 confirmed cases after discharge in Guangdong Province. Most re-positive cases are confirmed among 14 d after discharge and re-test to negative among 28 d after re-positive date. Age is an risk factor for re-positive cases after discharge.

Development of a high-resolution typing method for SLA-3, swine MHC class I antigen 3

We developed a high-resolution and comprehensive typing method for swine leukocyte antigen 3 (SLA-3), an MHC class I gene, employing locus-specific genomic PCR followed by subsequent direct sequencing. A total of 292 individuals from nine pure, one cross-breed and six cell lines were successfully typed. A total of 21 SLA-3 alleles were identified, of which four were found to be novel alleles. However, the allelic diversity of SLA-3 was lower than that of previously reported class I genes, SLA-1 and -2. More SLA-3 alleles were observed in the Landrace and Yorkshire breeds than the other breeds. SLA-3*04:01 was identified in seven out of nine breeds and was the most widely distributed allele across all breeds. Therefore, the typing method reported in this study completes our efforts to develop high-resolution typing methods for major SLA molecules, facilitating the combined analysis of major SLA genes from field samples, which is important to understand the relationship between the adaptive immune responses against pathogens and the immunogenetic makeup of an individual.

1312 Characteristics of Those Who Present with Self-Inflicted Burns: A Burns Unit Service Evaluation Which Challenges Stereotypes

Introduction

Self-harm rates in the UK are increasing. Healthcare professionals’ beliefs regarding repeat attendance; attention-seeking; and poor treatment compliance may contribute to patients’ stigma. Self-inflicted burns (SIB) constitute a minority of burns cases, but require disproportionate healthcare input, yet little is known about these patients. Our aim was to evaluate presentations, compliance and outcomes in this patient group.

Method

A retrospective audit of outpatients with SIBs attending a UK Burns Unit over four years (Jan 2016-Dec 2019).

Results

Over the study period, 58 patients presented with 94 burn wounds. Incidence doubled over one year (2018-2019). Most patients were female (85%) with a median age of 29 years (range 19-62). The most commonly associated psychiatric diagnosis was personality disorder. On presentation 22% (n = 21) were admitted under the Mental Health Act. For 83% (n = 48) it was their first presentation with a SIB, although 74% had previously presented with non-burn self-harm. Median burn size was 0.5% TBSA, the most common mechanism was contact (48%) and 77% were deep (n = 77). 92% were compliant with treatment and did not tamper with their wounds or dressings.

Conclusions

The majority, 70% (n = 41), of patients only presented once to the Burns Department during the study period. This challenges the commonly held stereotype that those who self-harm will also seek attention through repeat presentation. Ongoing education among health professionals may dispel some myths regarding these individuals. Further, larger investigations, may permit rigorous comparison of treatment outcomes with non-SIB patients.

[Analysis of 13 cases with pediatric rheumatic disease combined with endocrine disorder]

Objective: To summarize the clinical characteristics of children with rheumatic disease combined with endocrine disorder. Methods: A retrospective analysis was performed on the clinical data, including sex, age, clinical presentation, laboratory tests, treatment and outcome, of 13 patients with rheumatic diseases combined with endocrine disorder, who were admitted to our department in Children's Hospital, Capital Institute of Pediatrics from January 2014 to December 2020. Results: Among the 13 cases, 3 were males and 10 were females, without family history. Their age was (10±4) years. And the average course of disease was 4.1 months. Eight of them were diagnosed with systemic lupus erythematosus (JSLE), 2 with juvenile idiopathic arthritis (JIA), 1 with childhood vasculitis, 1 with juvenile-onset systemic sclerosis (JSSc) and 1 had juvenile dermatomyositis (JDM). Regarding the initial presentation, 10 cases had symptoms of rheumatic disease, 2 had polydipsia and polyuria, and 1 had goiter. All the 13 patients had multiple system involvement. Regarding endocrine disorder, 10 had thyroiditis or subclinical thyroiditis, 4 had diabetes mellitus and one had both thyroid and pancreas involvement. Thyroid stimulating hormone in 10 patient with thyroid involvment was 19.6 (5.2-34.0) mU/L, and their total thyroxine was 75.3 (45.2-105.4) nmol/L. Besides, thyroid peroxidase antibody or thyroglobulin antibody was positive in 7 cases. The blood glucose of 4 children with pancreatic injury was 25.0 (17.0-33.0) mmol/L, and C-peptide was 0.4 (0.3-0.5) mg/L. Glutamate dehydrogenase antibody, protein tyrosine phosphatase antibody and zinc transporter 8 antibody were positive in two cases. After treatement with immunosuppressant or immunoglobulin combined with glucocorticoid or nonsteroidal antiinflammatory drugs for rheumatic symptoms, and levothyroxine or insulin for endocrine diseases, they were all followed up for more than 6 months and maintained clinical stability. Conclusions: Rheumatic diseases in children can be complicated with endocrine disorders, and the involved organs are usually thyroid and pancreas. In children with rheumatic disease, thyroid injury usually has subtle onset, whereas pancreas injury develops rapidly, even life-threatening. Insulin should be used persistently under the instruction of endocrinologist.

Differences in school factors associated with adolescent HPV vaccination initiation and completion coverage in three Australian states

BACKGROUND

Schools are the primary setting for the delivery of adolescent HPV vaccination in Australia. Although this strategy has achieved generally high vaccination coverage, gaps persist for reasons that are mostly unknown. This study sought to identify school-level correlates of low vaccination course initiation and completion in New South Wales, Tasmania, and Western Australia to inform initiatives to increase uptake.

METHODS

Initiation was defined as the number of first doses given in a school in 2016 divided by vaccine-eligible student enrolments. Completion was the number of third doses given in a school in 2015-2016 divided by the number of first doses. Low initiation and completion were defined as coverage ≤ 25thpercentile of all reporting schools. We investigated correlations between covariates using Spearman's rank correlation coefficients. Due to multicollinearity, we used univariable logistic regression to investigate associations between school characteristics and low coverage.

RESULTS

Median initiation was 84.7% (IQR: 75.0%-90.4%) across 1,286 schools and median completion was 93.8% (IQR: 86.0%-97.3%) across 1,295 schools. There were strong correlations between a number of school characteristics, particularly higher Indigenous student enrolments and lower attendance, increasing remoteness, higher postcode socioeconomic disadvantage, and smaller school size. Characteristics most strongly associated with low initiation in univariate analyses were small school size, location in Tasmania, and schools catering for special educational needs. Low completion was most strongly associated with schools in Tasmania and Western Australia, remote location, small size, high proportion of Indigenous student enrolments, and low attendance rates.

CONCLUSION

This study provides indicative evidence that characteristics of schools and school populations are associated with the likelihood of low initiation and completion of the HPV vaccination course. The findings will guide further research and help target initiatives to improve vaccination uptake in schools with profiles associated with lower coverage.

Biomineralization of Dental Tissues Treated with Silver Diamine Fluoride

Silver diamine fluoride (SDF) is a dental biomaterial used to arrest dental caries. To better understand SDF's mechanism of action, we examined the localization of silver within the tissues of SDF-treated teeth. Carious primary teeth fixed within 2 min of SDF application (SDF-minutes, n = 3), at 3 wk after SDF application in vivo (SDF-weeks, n = 4), and at 2 y after multiple SDF applications in vivo (SDF-multiple, n = 1) were investigated in this study. Carious primary teeth without SDF application (no-SDF, n = 3) served as controls. Mineral density and structural analyses were performed via micro-X-ray computed tomography and scanning electron microscopy. Elemental analyses were performed through X-ray fluorescence microprobe and energy-dispersive X-ray spectroscopic techniques. SDF-treated teeth revealed higher X-ray-attenuated surface and subsurface regions within carious lesions, and similar regions were not present in no-SDF teeth. Regions of higher mineral density correlated with regions of silver abundance in SDF-treated teeth. The SDF penetration depth was approximated to 0.5 ± 0.02 mm and 0.6 ± 0.05 mm (mean ± SD) for SDF-minutes and SDF-weeks specimens, respectively. A higher percentage of dentin tubular occlusion by silver or calcium phosphate particles was observed in primary teeth treated with SDF-weeks as compared with SDF-minutes. Elemental analysis also revealed zinc abundance in carious lesions and around the pulp chamber. SDF-weeks teeth had significantly increased tertiary dentin than SDF-minutes and no-SDF teeth. These results suggest that SDF treatment on primary teeth affected by caries promotes pathologic biomineralization by altering their physicochemical properties, occluding dentin tubules, and increasing tertiary dentin volume. These seemingly serendipitous effects collectively contribute to the cariostatic activity of SDF.

PathCNN: interpretable convolutional neural networks for survival prediction and pathway analysis applied to glioblastoma

MOTIVATION

Convolutional neural networks (CNNs) have achieved great success in the areas of image processing and computer vision, handling grid-structured inputs and efficiently capturing local dependencies through multiple levels of abstraction. However, a lack of interpretability remains a key barrier to the adoption of deep neural networks, particularly in predictive modeling of disease outcomes. Moreover, because biological array data are generally represented in a non-grid structured format, CNNs cannot be applied directly.

RESULTS

To address these issues, we propose a novel method, called PathCNN, that constructs an interpretable CNN model on integrated multi-omics data using a newly defined pathway image. PathCNN showed promising predictive performance in differentiating between long-term survival (LTS) and non-LTS when applied to glioblastoma multiforme (GBM). The adoption of a visualization tool coupled with statistical analysis enabled the identification of plausible pathways associated with survival in GBM. In summary, PathCNN demonstrates that CNNs can be effectively applied to multi-omics data in an interpretable manner, resulting in promising predictive power while identifying key biological correlates of disease.

AVAILABILITY AND IMPLEMENTATION

The source code is freely available at: https://github.com/mskspi/PathCNN.

Functional coordination of BET family proteins underlies altered transcription associated with memory impairment in fragile X syndrome

Bromodomain and extraterminal proteins (BET) are epigenetic readers that play critical roles in gene regulation. Pharmacologic inhibition of the bromodomain present in all BET family members is a promising therapeutic strategy for various diseases, but its impact on individual family members has not been well understood. Using a transcriptional induction paradigm in neurons, we have systematically demonstrated that three major BET family proteins (BRD2/3/4) participated in transcription with different recruitment kinetics, interdependency, and sensitivity to a bromodomain inhibitor, JQ1. In a mouse model of fragile X syndrome (FXS), BRD2/3 and BRD4 showed oppositely altered expression and chromatin binding, correlating with transcriptional dysregulation. Acute inhibition of CBP/p300 histone acetyltransferase (HAT) activity restored the altered binding patterns of BRD2 and BRD4 and rescued memory impairment in FXS. Our study emphasizes the importance of understanding the BET coordination controlled by a balanced action between HATs with different substrate specificity.

FoxO1 as a Regulator of Aquaporin 5 Expression in the Salivary Gland

Forkhead box O1 (FoxO1) is a multifunctional initiator, mediator, and repressor of autoimmune diseases in an organ- or disease-specific manner. However, the role of FoxO1 in the salivary gland has not yet been elucidated. In this study, we discovered that FoxO1 and aquaporin 5 (AQP5) are both significantly downregulated in the patients with primary Sjögren syndrome, an autoimmune disease accompanying salivary gland dysfunction. Pharmacologic or genetic perturbation of FoxO1 in the rat salivary gland acinar cell line, SMG-C6, induced a significant downregulation of AQP5 expression, as observed in clinical specimens. There was a strong correlation between FoxO1 and AQP5 expression because FoxO1 is a direct regulator of AQP5 expression in salivary gland acinar cells through its interaction with the promoter region of AQP5. Serial injection of a FoxO1 inhibitor into mice induced a reduction of AQP5 expression in submandibular glands and, consequently, hyposalivation, which is one of the major clinical symptoms of primary Sjögren syndrome. However, there was no sign of inflammation or cell damage in the submandibular glands harvested from mice treated with the FoxO1 inhibitor. In conclusion, our findings indicate that FoxO1 in salivary gland tissue acts as a direct regulator of AQP5 expression. Thus, downregulation of FoxO1 observed in primary Sjögren syndrome is a putative mechanism for hyposalivation without the involvement of previously reported soluble factors in primary Sjögren syndrome patient sera.

Calcium Signaling in T Cells and Chronic Inflammatory Disorders of the Oral Cavity

Acute immune responses to microbial insults in the oral cavity often progress to chronic inflammatory diseases such as periodontitis and apical periodontitis. Chronic oral inflammation causes destruction of the periodontium, potentially leading to loss of the dentition. Previous investigations have demonstrated that the composition of oral immune cells, rather than the overall extent of cellular infiltration, determines the pathological development of chronic inflammation. The role of T lymphocyte populations, including Th1, Th2, Th17, and Treg cells, has been extensively described. Studies now propose pathogenic Th17 cells as a distinct subset, uniquely classifiable from traditional Th17 populations. In situ differentiation of pathogenic Th17 cells has been verified as a source of destructive inflammation, which critically drives pathogenesis in chronic inflammatory diseases such as diabetes, rheumatoid arthritis, and inflammatory bowel disease. Pathogenic Th17 cells resemble a Th1 penotype and produce not only interleukin 17 (IL-17) but also γ-interferon (IFN-γ) and granulocyte-macrophage colony-stimulating factor (GM-CSF). The proinflammatory cytokine-specific mechanisms known to induce IL-17 expression in Th17 cells are well characterized; however, differentiation mechanisms that lead to pathogenic Th17 cells are less understood. Recently, Ca2⁺ signaling through Ca²⁺ release-activated Ca²⁺ channels (CRAC) in T cells has been uncovered as a major signaling axis involved in the regulation of T-cell-mediated chronic inflammation. In particular, pathogenic Th17 cell-mediated immunological diseases appear to be effectively targeted via such Ca²⁺ signaling pathways. Pathogenic plasticity of Th17 cells has been extensively illustrated in autoimmune and chronic inflammatory diseases. Although their specific causal relationship to oral infection-induced chronic inflammatory diseases is not fully established, pathogenic Th17 cells may be involved in the underlining mechanism. This review highlights the current understanding of T-cell phenotype regulation, calcium signaling pathways in this event, and the potential role of pathogenic Th17 cells in chronic inflammatory disorders of the oral cavity.

Endovascular and percutaneous transabdominal embolisation of pseudoaneurysms in pancreatitis: an experience from a tertiary-care referral centre

AIM

To analyse the technical challenges, clinical success, and associated complications of endovascular and percutaneous embolisation of pancreatitis-related pseudoaneurysms.

MATERIALS AND METHODS

A retrospective study of patients referred for embolisation of pancreatitis-related pseudoaneurysms between January 2014 and March 2019 was conducted. Computed tomography angiography (CTA) was performed to assess the morphology of the aneurysms prior to any intervention. Percutaneous or endovascular embolisation was performed. Details of CTA and methods of embolisation were recorded. Technical success, clinical success, and complications were reported.

RESULTS

A total of 80 patients (mean age, 40.69 ± 13.41 years, 73 male) underwent embolisation during the study period. Pseudoaneurysms were related to chronic pancreatitis (CP) in 44 (55%) patients and acute pancreatitis (AP) in 36 (45%) patients. Pseudoaneurysms were detected in 65 (81.2%) patients on CTA. The most common site of pseudoaneurysms was gastroduodenal artery (GDA) followed by splenic artery. Seven patients were treated with percutaneous thrombin injection and five were treated with percutaneous glue injection under ultrasound/fluoroscopy guidance. The remaining patients (n=68) underwent catheter angiography with endovascular embolisation. Technical success was achieved in 4/7 (57%) percutaneous thrombin cases and in all the cases (5/5, 100%) with percutaneous glue or endovascular (68/68,100%) embolisation.

CONCLUSION

Endovascular or percutaneous embolisation of pseudoaneurysms has high technical success with an excellent safety profile.