Thioredoxin is a metabolic rheostat controlling regulatory B cells.

Metabolic programming is important for B cell fate, but the bioenergetic requirement for regulatory B (Breg) cell differentiation and function is unknown. Here we show that Breg cell differentiation, unlike non-Breg cells, relies on mitochondrial electron transport and homeostatic levels of reactive oxygen species (ROS). Single-cell RNA sequencing analysis revealed that TXN, encoding the metabolic redox protein thioredoxin (Trx), is highly expressed by Breg cells, unlike Trx inhibitor TXNIP which was downregulated. Pharmacological inhibition or gene silencing of TXN resulted in mitochondrial membrane depolarization and increased ROS levels, selectively suppressing Breg cell differentiation and function while favoring pro-inflammatory B cell differentiation. Patients with systemic lupus erythematosus (SLE), characterized by Breg cell deficiencies, present with B cell mitochondrial membrane depolarization, elevated ROS and fewer Trx+ B cells. Exogenous Trx stimulation restored Breg cells and mitochondrial membrane polarization in SLE B cells to healthy B cell levels, indicating Trx insufficiency underlies Breg cell impairment in patients with SLE.

sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data.

Class-switch recombination (CSR) is an integral part of B cell maturation. Here we present sciCSR (pronounced 'scissor', single-cell inference of class-switch recombination), a computational pipeline that analyzes CSR events and dynamics of B cells from single-cell RNA sequencing (scRNA-seq) experiments. Validated on both simulated and real data, sciCSR re-analyzes scRNA-seq alignments to differentiate productive heavy-chain immunoglobulin transcripts from germline 'sterile' transcripts. From a snapshot of B cell scRNA-seq data, a Markov state model is built to infer the dynamics and direction of CSR. Applying sciCSR on severe acute respiratory syndrome coronavirus 2 vaccination time-course scRNA-seq data, we observe that sciCSR predicts, using data from an earlier time point in the collected time-course, the isotype distribution of B cell receptor repertoires of subsequent time points with high accuracy (cosine similarity ~0.9). Using processes specific to B cells, sciCSR identifies transitions that are often missed by conventional RNA velocity analyses and can reveal insights into the dynamics of B cell CSR during immune response.

Pathogenic missense protein variants affect different functional pathways and proteomic features than healthy population variants.

Missense variants are present amongst the healthy population, but some of them are causative of human diseases. A classification of variants associated with "healthy" or "diseased" states is therefore not always straightforward. A deeper understanding of the nature of missense variants in health and disease, the cellular processes they may affect, and the general molecular principles which underlie these differences is essential to offer mechanistic explanations of the true impact of pathogenic variants. Here, we have formalised a statistical framework which enables robust probabilistic quantification of variant enrichment across full-length proteins, their domains, and 3D structure-defined regions. Using this framework, we validate and extend previously reported trends of variant enrichment in different protein structural regions (surface/core/interface). By examining the association of variant enrichment with available functional pathways and transcriptomic and proteomic (protein half-life, thermal stability, abundance) data, we have mined a rich set of molecular features which distinguish between pathogenic and population variants: Pathogenic variants mainly affect proteins involved in cell proliferation and nucleotide processing and are enriched in more abundant proteins. Additionally, rare population variants display features closer to common than pathogenic variants. We validate the association between these molecular features and variant pathogenicity by comparing against existing in silico variant impact annotations. This study provides molecular details into how different proteins exhibit resilience and/or sensitivity towards missense variants and provides the rationale to prioritise variant-enriched proteins and protein domains for therapeutic targeting and development. The ZoomVar database, which we created for this study, is available at fraternalilab.kcl.ac.uk/ZoomVar. It allows users to programmatically annotate missense variants with protein structural information and to calculate variant enrichment in different protein structural regions.

The role of surgery in gestational trophoblastic disease: an overview.

Gestational trophoblastic disease comprises a group of rare, and potentially malignant, conditions that arise from abnormal trophoblastic proliferation. When there is invasion and evidence of metastatic disease, gestational trophoblastic neoplasia is used. While chemotherapy is the mainstay of treatment for gestational trophoblastic neoplasia, the role of surgery has come full circle in recent years. Before the introduction of highly effective systemic treatment options, surgery was the default treatment. Surgery for gestational trophoblastic neoplasia often yielded unsatisfactory results and mortality remained high. In recent years, the role of adjuvant surgery in the management of gestational trophoblastic neoplasia has been examined with great interest. We aim to provide an overview of the various surgical approaches employed in managing gestational trophoblastic neoplasia, including their indications, techniques, and outcomes. Additionally, we discuss whether there is a role to do less in surgery for gestational trophoblastic neoplasia and describe our experience with a modified surgical technique for its treatment. By summarizing the current evidence, this article highlights the significant contributions of surgery to the holistic management of patients with gestational trophoblastic neoplasia and provides a framework on which to base management and treatment programs.

Predicting class switch recombination in B-cells from antibody repertoire data.

Statistical and machine learning methods have proved useful in many areas of immunology. In this paper, we address for the first time the problem of predicting the occurrence of class switch recombination (CSR) in B-cells, a problem of interest in understanding antibody response under immunological challenges. We propose a framework to analyze antibody repertoire data, based on clonal (CG) group representation in a way that allows us to predict CSR events using CG level features as input. We assess and compare the performance of several predicting models (logistic regression, LASSO logistic regression, random forest, and support vector machine) in carrying out this task. The proposed approach can obtain an unweighted average recall of 71 % $71\%$ with models based on variable region descriptors and measures of CG diversity during an immune challenge and, most notably, before an immune challenge.

Outcomes of gynecologic cancer surgery during the COVID-19 pandemic: an international, multicenter, prospective CovidSurg-Gynecologic Oncology Cancer study.

BACKGROUND: The CovidSurg-Cancer Consortium aimed to explore the impact of COVID-19 in surgical patients and services for solid cancers at the start of the pandemic. The CovidSurg-Gynecologic Oncology Cancer subgroup was particularly concerned about the magnitude of adverse outcomes caused by the disrupted surgical gynecologic cancer care during the COVID-19 pandemic, which are currently unclear. OBJECTIVE: This study aimed to evaluate the changes in care and short-term outcomes of surgical patients with gynecologic cancers during the COVID-19 pandemic. We hypothesized that the COVID-19 pandemic had led to a delay in surgical cancer care, especially in patients who required more extensive surgery, and such delay had an impact on cancer outcomes. STUDY DESIGN: This was a multicenter, international, prospective cohort study. Consecutive patients with gynecologic cancers who were initially planned for nonpalliative surgery, were recruited from the date of first COVID-19-related admission in each participating center for 3 months. The follow-up period was 3 months from the time of the multidisciplinary tumor board decision to operate. The primary outcome of this analysis is the incidence of pandemic-related changes in care. The secondary outcomes included 30-day perioperative mortality and morbidity and a composite outcome of unresectable disease or disease progression, emergency surgery, and death. RESULTS: We included 3973 patients (3784 operated and 189 nonoperated) from 227 centers in 52 countries and 7 world regions who were initially planned to have cancer surgery. In 20.7% (823/3973) of the patients, the standard of care was adjusted. A significant delay (>8 weeks) was observed in 11.2% (424/3784) of patients, particularly in those with ovarian cancer (213/1355; 15.7%; P<.0001). This delay was associated with a composite of adverse outcomes, including disease progression and death (95/424; 22.4% vs 601/3360; 17.9%; P=.024) compared with those who had operations within 8 weeks of tumor board decisions. One in 13 (189/2430; 7.9%) did not receive their planned operations, in whom 1 in 20 (5/189; 2.7%) died and 1 in 5 (34/189; 18%) experienced disease progression or death within 3 months of multidisciplinary team board decision for surgery. Only 22 of the 3778 surgical patients (0.6%) acquired perioperative SARS-CoV-2 infections; they had a longer postoperative stay (median 8.5 vs 4 days; P<.0001), higher predefined surgical morbidity (14/22; 63.6% vs 717/3762; 19.1%; P<.0001) and mortality (4/22; 18.2% vs 26/3762; 0.7%; P<.0001) rates than the uninfected cohort. CONCLUSION: One in 5 surgical patients with gynecologic cancer worldwide experienced management modifications during the COVID-19 pandemic. Significant adverse outcomes were observed in those with delayed or cancelled operations, and coordinated mitigating strategies are urgently needed.

Pan-cancer transcriptomic analysis dissects immune and proliferative functions of APOBEC3 cytidine deaminases.

APOBEC3 cytidine deaminases are largely known for their innate immune protection from viral infections. Recently, members of the family have been associated with a distinct mutational activity in some cancer types. We report a pan-tissue, pan-cancer analysis of RNA-seq data specific to the APOBEC3 genes in 8,951 tumours, 786 cancer cell lines and 6,119 normal tissues. By deconvolution of levels of different cell types in tumour admixtures, we demonstrate that APOBEC3B (A3B), the primary candidate as a cancer mutagen, shows little association with immune cell types compared to its paralogues. We present a pipeline called RESPECTEx (REconstituting SPecific Cell-Type Expression) and use it to deconvolute cell-type specific expression levels in a given cohort of tumour samples. We functionally annotate APOBEC3 co-expressing genes, and create an interactive visualization tool which 'barcodes' the functional enrichment (http://fraternalilab.kcl.ac.uk/apobec-barcodes/). These analyses reveal that A3B expression correlates with cell cycle and DNA repair genes, whereas the other APOBEC3 members display specificity for immune processes and immune cell populations. We offer molecular insights into the functions of individual APOBEC3 proteins in antiviral and proliferative contexts, and demonstrate the diversification this family of enzymes displays at the transcriptomic level, despite their high similarity in protein sequences and structures.

A sustainable model for raising colposcopy expertise in low-to-middle-income countries.

OBJECTIVE: The objective of the study was to assess the effectiveness of training low-to-middle-income countries' local healthcare providers using the Train-the-trainers model in basic colposcopy for cervical cancer prevention. METHOD: This project was designed based on a philosophy known as Train-the-trainers which train proficient colposcopists and a cadre of local trainers who can continue to train and maintain their expertise in a self-sustaining system. The Train-the-trainers workshop is a 1-day program that focuses on three domains; knowledge, communication, and practical skills. Trainer candidates were given pre-course reading assignments and presentation decks. The expert trainers provided feedback on their presentations and tips on communication skills. The practical aspects of the training are supported by proficiency at the Loop Electro-excision procedure simulator and their responses to frequently asked questions. RESULTS: Sixteen physicians from Vietnam attended the Colposcopy Workshop in 2018 and are used as controls. Eleven attended a workshop conducted by trainer candidates who went through the training program outlined above in 2019. A Wilcoxon Signed-ranks test indicated that differences between pre- and post-quizzes' scores were statistically significant in both the 2018 (Z=4.21, P=0.003, r=1.26) and 2019 cohorts (Z=3.558, P<0.001, r=0.89) while Mann-Whitney U test did not detect the difference between the 2018 and 2019 cohorts, U=70.0, P=0.359, r=0.176. The subjective feedback scores from Year 2019 were similar to scores to Year 2018. CONCLUSION: Our preliminary data did not highlight any differences between lectures delivered by expert trainers and lectures delivered by trainer candidates trained in the program. Train-the- trainers might be a more sustainable model for organically raising expertise to effectively provide cervical cancer screening and prevention in low-to-middle-income countries.

Vaping induced pneumonitis: a small community hospital's case series and analysis.

BACKGROUND: Electronic cigarettes/e-cigarettes (ECs), or vaping, is currently the most popular form of smoking amongst youth in the United States. ECs are battery-powered devices that vaporize a liquid that comes in small cartridges, or pods, that contain various chemicals, nicotine, and an array of flavors that can be modified to include cannabinoids (THC). With increasing popularity, however, there is an epidemic of pulmonary and gastrointestinal illnesses associated with vaping in the continental U.S.A. METHODS: We analyzed medical charts of three patients who were active users of ECs and presented with pneumonitis to our community medical center between January and August 2019. RESULTS: We report three cases of vaping pneumonitis in young adults, ages 18 to 21, who presented with similar symptoms, profiles, imaging studies, and disease progression. The average length of stay was approximately one week, and all patients had an extensive work-up in addition to a relapsing and remitting course of their condition. CONCLUSIONS: Early recognition and diagnosis of vaping pneumonitis are essential in the treatment of the ongoing epidemic. Extensive unnecessary work up may lead to increased healthcare costs. Our case series echoes the concerns of the CDC such that ECs should be avoided, and those with any pulmonary or gastrointestinal symptoms should seek medical attention promptly.

Does external beam radiation boost to pelvic lymph nodes improve outcomes in patients with locally advanced cervical cancer?

BACKGROUND: Current recommendation for locally advanced cervical cancer includes pelvic external beam radiation therapy (EBRT) with concurrent chemotherapy followed by brachytherapy. Involvement of pelvic lymph nodes is an important prognostic factor in locally advanced cervical cancer and recurrence commonly occurs despite definitive treatment. To date, there is no standard guideline on whether an EBRT boost should be applied to involved pelvic lymph nodes. Our study aims to assess if pelvic EBRT boost would reduce recurrence, benefit survival, and affect associated toxicities. METHODS: We conducted a retrospective review of locally advanced cervical cancer cases treated with definitive treatment at our institution. Involvement of pelvic lymph nodes were assessed on CT, MRI (> 10 mm or suspicious features) or PET scan (SUVmax > 2.5). EBRT dose ranged from 45 to 50.4 Gy with nodal boost ranging from 3.6-19.8 Gy. RESULTS: Between 2008 to 2015, 139 patients with locally advanced cervical cancer underwent treatment. Sixty-seven patients had positive pelvic lymph nodes, of which 53.7% received a nodal boost. Five-year recurrence free survival was 48.6% with vs. 64.5% without nodal boost (P = 0.169) and 5-year overall survival in those with positive pelvic lymph nodes was 74.3% with vs. 80.6% without nodal boost (P = 0.143). There was no significant difference in toxicity with nodal boost. CONCLUSIONS: EBRT boost to pelvic lymph nodes does not reduce recurrence or improve survival in locally advanced cervical cancer with lymph node involvement at diagnosis.

The Effectiveness of Spinal Manipulation in Increasing Muscle Strength in Healthy Individuals: A Systematic Review and Meta-Analysis.

OBJECTIVE: The purpose of this study was to systematically review the effects of spinal manipulation on muscular strength in healthy individuals and conduct a meta-analysis to appraise the quality of evidence. METHODS: Articles were searched and retrieved from MEDLINE, EMBASE, CINAHL, Cochrane Library, PubMed, Academic Search Premier, SPORTDiscus, and AMED. Searches were conducted in September 2017 without a limit on the starting period. The Physiotherapy Evidence Database scale was used to appraise the quality of the included studies. Data from eligible articles were pooled, and meta-analyses were conducted. The quality of evidence was appraised by the Grading of Recommendations, Assessment, Development and Evaluations approach. The registration number for the review on PROSPERO is CRD42017075215. RESULTS: A total of 911 records were screened, and 3 randomized controlled trials were eligible to be included in this review. There was a significant pooled standardized mean difference in isometric strength (0.93, 95% confidence interval [CI], 0.17-1.68; P = .02) between the experimental and control groups, with a moderate level of heterogeneity. CONCLUSION: This review suggests that spinal manipulative therapy augments the percentage of change in isometric strength gain among healthy participants when compared to no intervention or sham manipulation. However, the heterogeneity of pooled studies in this review suggests that the results should be interpreted with caution.

A brief report on the clinical trial on neural mobilization exercise for joint pain in patients with rheumatoid arthritis.

BACKGROUND: In rheumatoid arthritis (RA) synovitis, activation of synoviocytes and infiltration of adaptive immune cells leads to synovial hyperplasia and joint swelling. Under the elevated extra-neural pressure, free nerve endings release neuropeptides, calcitonin gene-related peptide, and substance P, thus promoting neurogenic inflammation. OBJECTIVE: This study aimed to assess the effect of therapeutic neural mobilization (NM) exercises targeting the nervous system on disease impact in RA patients. METHODS: A total of 21 RA patients were randomized into NM (n = 11) and control (n = 10) groups. NM group patients performed NM exercises targeting the median, musculocutaneous, femoral, and saphenous nerve, as well as the entire nervous system twice daily for 4-8 weeks. Control RA patients performed gentle joint mobilization exercises targeting the same joints. Primary outcome was the change in pre-/post-treatment score in the validated Rheumatoid Arthritis Impact of Disease (RAID). Secondary outcome was erythrocyte sedimentation rate (ESR). RESULTS: There were no significant differences between the groups at baseline. No adverse events were observed and compliance was over 90%. Post-treatment, favorable changes were observed in the NM group RAID score: -5.1 vs. -0.8; weighted RAID score: -0.79 vs. -0.15. ESR was reduced in the NM group, albeit non-significantly. Regarding the RAID score domains, the NM group demonstrated significant improvements in pain and coping. CONCLUSION: The current data indicate a beneficial effect of NM exercises on pain and self-efficacy in our RA patients. Larger clinical studies are warranted to determine the clinical effectiveness of NM as a treatment for pain for RA patients and simultaneously address immune and neuropeptide modulation through NM.

On the VC-Dimension of Unique Round-Trip Shortest Path Systems.

The VC-dimension, which has wide uses in learning theory, has been used in the analysis and design of graph algorithms recently. In this paper, we study the problem of bounding the VC-dimension of unique round-trip shortest path set systems (URTSP), which are set systems induced by sets of vertices in unique round-trip shortest paths in directed graphs. We first show that different from the VC-dimensions of set systems induced by unique undirected and directed shortest paths in undirected and directed graphs respectively, the VC-dimension of URTSP can be larger than 3. We then prove that the VC-dimension of URTSP is at most 32. Furthermore, we apply the VC-dimension result to the minimum k-round-trip shortest path cover problem (k-RTSPC), which is to find for a directed graph a minimum vertex set to intersect every round-trip shortest path containing at least k vertices, and derive an upper bound on the size of the vertex set. The k-RTSPC problem can be useful in many real-world applications, including optimal placement of facilities.

Changes in Lower Limb Strength and Function Following Lumbar Spinal Mobilization.

OBJECTIVE: The purpose of this study was to investigate whether grade III passive lumbar rotational mobilization on L2-3 can improve hip flexor strength and performance in the single-leg triple-hop test in asymptomatic young adults. METHODS: Twenty-four participants (12 men, 12 women) aged from 19 to 26 years who were positive in the hip flexor "break" test were recruited in this study. They were randomly allocated to the treatment group or sham group. Isometric hip flexor torque (N·m) and single-leg triple-hop distance (cm) were measured before and after a passive lumbar rotational mobilization or a sham intervention. RESULTS: After the intervention, both the treatment and sham groups exhibited a significant increase in longest hop distance (P = .040 and .044, respectively). The treatment group had a significantly higher (3.41 ± 5.44%) positive percentage change in torque than the sham group (-2.36 ± 5.81%) (P = .02). CONCLUSION: The study results indicated a potential effect of grade III passive lumbar rotational mobilization in improving hip flexor strength. However, whether the improvement in hopping performance was the result of a treatment effect or a learning effect could not be determined.

Personal utility is inherent to direct-to-consumer genomic testing.

People for and against direct-to-consumer (DTC) genomic tests are arguing around two issues: first, on whether an autonomy-based account can justify the tests; second, on whether the tests bring any personal utility. Bunnik et al, in an article published in this journal, were doubtful on the latter, especially in clinically irrelevant and uninterpretable sequences, and how far this claim could go in the justification. Here we argue that personal utility is inherent to DTC genomic tests and their results. We discuss Bunnik et al's account of personal utility and identify problems in its motivation and application. We then explore concepts like utility and entertainment which suggest that DTC genomic tests bring personal utility to their consumers, both in the motivation and the content of the tests. This points to an alternative account of personal utility which entails that entertainment value alone is adequate to justify DTC genomic tests, given appropriate strategies to communicate tests results with the consumers. It supports the autonomy-based justification of the test by showing that DTC genomic test itself stands as a valuable option and facilitates meaningful choice of the people.

Neutron and X-ray crystal structures of a perdeuterated enzyme inhibitor complex reveal the catalytic proton network of the Toho-1 ß-lactamase for the acylation reaction.

The mechanism by which class A ß-lactamases hydrolyze ß-lactam antibiotics has been the subject of intensive investigation using many different experimental techniques. Here, we report on the novel use of both neutron and high resolution x-ray diffraction to help elucidate the identity of the catalytic base in the acylation part of the catalytic cycle, wherein the ß-lactam ring is opened and an acyl-enzyme intermediate forms. To generate protein crystals optimized for neutron diffraction, we produced a perdeuterated form of the Toho-1 ß-lactamase R274N/R276N mutant. Protein perdeuteration, which involves replacing all of the hydrogen atoms in a protein with deuterium, gives a much stronger signal in neutron diffraction and enables the positions of individual deuterium atoms to be located. We also synthesized a perdeuterated acylation transition state analog, benzothiophene-2-boronic acid, which was also isotopically enriched with (11)B, as (10)B is a known neutron absorber. Using the neutron diffraction data from the perdeuterated enzyme-inhibitor complex, we were able to determine the positions of deuterium atoms in the active site directly rather than by inference. The neutron diffraction results, along with supporting bond-length analysis from high resolution x-ray diffraction, strongly suggest that Glu-166 acts as the general base during the acylation reaction.