bluuebunny/crossref_metadata_2025 huggingface dataset:
Hybrid Integrated Approach: Beginner’s Guide to the Balancing in Knee Arthroplasty
Authors: Deshpande Shantanu S.
Published: July 2023

Gap balancing and measured resection techniques form the basic guidance on soft tissue balancing in total knee arthroplasty teachings. The concepts around knee arthroplasty constantly evolving keeping the basics right. Surgeons across the globe are blending established known techniques with newer modifications. The anatomic, functional, and kinematic alignments of the prosthetic knee are frequently debated at conferences. Irrespective of the alignment principle one is following the aim is to achieve a balanced knee for better function. While balancing the knee arthroplasty the basic theme accepted worldwide is the combination of gap balancing and measured resection philosophy. The additional procedures that aid in are these soft tissue releases, lateralization of the prosthesis, reduction osteotomy, and downsizing of the implant which results into a modern current way of approaching the idea of balancing. The surgical workflow I have discussed here is actually the amalgamation of standard teachings and newer trends resulting into the Hybrid integrated technique (H) of balancing a prosthetic a total knee arthroplasty. From the orthopedic trainee point of view it is confusing to see the operating room execution is different than conventional books information. Hence, there is a need to create a beginner’s guide of the current workflow. The modern algorithm helps in balancing the soft tissue releases and bony releases to complement each other. The below-mentioned surgical workflow is not a novel approach but scientifically documenting the current practice implemented by many surgeons at various arthroplasty centers. Hence, it is not a presentation of a personal clinical case study series but an adaptation of various surgical steps to form a workflow.
Impact of early antiretroviral therapy, early life immunity and immune sex differences on HIV disease and posttreatment control in children
Authors: Herbert Nicholas G. , Goulder Philip J.R.
Published: July 2023

Purpose of review

To review recent insights into the factors affecting HIV disease progression in children living with HIV, contrasting outcomes: following early ART initiation with those in natural, antiretroviral therapy (ART)-naive infection; in children versus adults; and in female individuals versus male individuals.

Recent findings

Early life immune polarization and several factors associated with mother-to-child transmission of HIV result in an ineffective HIV-specific CD8+ T-cell response and rapid disease progression in most children living with HIV. However, the same factors result in low immune activation and antiviral efficacy mediated mainly through natural killer cell responses in children and are central features of posttreatment control. By contrast, rapid activation of the immune system and generation of a broad HIV-specific CD8+ T-cell response in adults, especially in the context of ‘protective’ HLA class I molecules, are associated with superior disease outcomes in ART-naive infection but not with posttreatment control. The higher levels of immune activation in female individuals versus male individuals from intrauterine life onwards increase HIV infection susceptibility in females in utero and may favour ART-naive disease outcomes rather than posttreatment control.

Early-life immunity and factors associated with mother-to-child transmission typically result in rapid HIV disease progression in ART-naive infection but favour posttreatment control in children following early ART initiation.
Decrypting biological hallmarks of aging in people with HIV
Authors: Premeaux Thomas A. , Ndhlovu Lishomwa C.
Published: July 2023

Purpose of review

HIV infection adds further complexity to the heterogenous process of aging. In this focused review, we examine and discuss recent advances to better elucidate mechanisms of biological aging perturbed and accelerated in the context of HIV, particularly among those with viral suppression through the benefits of antiretroviral therapy (ART). New hypotheses from these studies are poised to provide an improved understanding of multifaceted pathways that converge and likely form the basis for effective interventions toward successful aging.

Recent findings

Evidence to date suggests multiple mechanisms of biological aging impact people living with HIV (PLWH). Recent literature delves and expands on how epigenetic alterations, telomere attrition, mitochondrial perturbations, and intercellular communications may underpin accelerated or accentuated aging phenotypes and the disproportionate prevalence of age-related complications among PLWH. Although most hallmarks of aging are likely exacerbated in the setting of HIV, ongoing research efforts are providing new insight on the collective impact these conserved pathways may have in the aging disease processes.

New knowledge on underlying molecular disease mechanisms impacting people aging with HIV are reviewed. Also examined are studies that may facilitate the development and implementation of effective therapeutics and guidance on improving geriatric HIV clinical care.
Factors affecting association between pain severity and physical activity among people with low back pain
Authors: Saltychev Mikhail , Hellgren Henri , Juhola Juhani
Published: July 2023

The aim was to identify factors, which may affect the relationship between physical activity and pain severity among patients with low back pain (LBP). It was a cross-sectional survey-based study among 1332 consecutive patients with LBP. Linear regression models were employed. Patients were 47.6 years old and 64% were women. For the entire sample, pain severity and the intensity of physical activity were negatively associated. Higher physical activity was associated with younger age, higher educational level, normal weight and optimal perceived general health. Sex, smoking, marital status and occupation did not demonstrate significant interactions on the association. The severity of disability showed paradoxical effect on the relationship between pain and physical activity – severe disability was associated with increase in physical activity.
Ultrasonography-Guided Intra-Arterial Hyaluronidase Treatment of Vascular Occlusions
Authors: Oxton Alison , Doran Michelle Dyment
Published: July 2023

The purpose of this article is to introduce a recommendation for an adjunct approach to the current treatment protocol for vascular occlusion (VO). Current guidelines for treatment of VO do not incorporate the use of ultrasonographic technology. Using bedside ultrasonography has gained recognition as an effective way to map out the vessels of the face to prevent VO. Ultrasonography has also been found to be helpful for treating VO as well as other hyaluronic acid filler–related complications.
An Easy and Effective Method for Avoiding Intraoperative Pedicle Vessels Kinking
Authors: Alvedro-Ruiz Pedro , Vicente-Pardo Andrea , Heredia-Alcalde Iván , Pérez-García Alberto , Thione Alessandro
Published: July 2023

Vascular pedicle twisting during a microsurgical anastomosis procedure can jeopardize the viability of the flap. Although the literature describes many maneuvers to prevent vascular pedicle twisting, we present an easy and effective method that can be used when performing microsurgical anastomosis in the operating room.
Algorithmic Fairness of Machine Learning Models for Alzheimer’s Disease Progression Prediction
Authors: Yuan Chenxi , Linn Kristin A. , Hubbard Rebecca A. ,   Alzheimer’s Disease Neuroimaging Initiative
Published: July 2023

Introduction

Alzheimer’s disease (AD) disproportionately affects older adults from marginalized communities. Predictive models using machine learning (ML) techniques have potential to improve early detection and management of AD. However, ML models potentially suffer from biases and may perpetuate or exacerbate existing disparities.

Methods

We investigated algorithmic fairness of logistic regression, support vector machines and recurrent neural networks for predicting progression to mild cognitive impairment and AD. Fairness was quantified across gender, ethnicity, and race subgroups using three measures: equal opportunity, equalized odds and demographic parity.

Results

All three ML models performed well in aggregate but demonstrated disparate performance across race and ethnicity subgroups. Compared to Non-Hispanic participants, sensitivity for predicting progression to mild cognitive impairment and to AD was 5%-9.6% and 16.8%-24.9% lower, respectively, for Hispanic participants. Sensitivity was similarly lower for Black and Asian participants compared to Non-Hispanic White participants. Models generally satisfied metrics of fairness with respect to gender.

Discussion

Although accurate in aggregate, models failed to satisfy fairness metrics. Fairness should be considered in the development and deployment of ML models for AD progression.
Cardiovascular Complications with Delivery Hospitalizations in Patients with Pulmonary Hypertension: A Nationwide Study from 2011-2020
Authors: Agrawal Ankit , Bajaj Suryansh , Bhagat Umesh , Chandna Sanya , Arockiam Aro Daniela , Jamil Yasser , Iskandarani Mahmoud El , Gupta Rahul , Nayar Divya , Michos Erin D.
Published: July 2023

Background

Pregnancy in patients with pulmonary hypertension (PH) is associated with heightened risk of various medical complications. Our study aims to understand the patient characteristics and investigate the association between PH and these complications in pregnant patients during delivery.

Methods

The National Inpatient Sample (NIS) was used to identify delivery hospitalizations from 2011 to 2020. The primary outcomes were in-hospital medical and obstetric complications. Multivariate logistic regression was performed to study the association of PH with these complications.

Results

A total of 37,482,207 delivery hospitalizations in women ≥18 years were identified from the NIS database out of which 9,593 patients had PH. Pregnant patients with PH had a higher incidence of complications during delivery including preeclampsia/eclampsia, cardiac arrhythmias, pulmonary edema amongst others, compared to pregnant patients without PH. Pregnant patients with PH had a higher incidence of in-hospital mortality compared to those without PH (0.51% vs 0.007%). In adjusted analyses, PH was independently associated with a higher risk of pulmonary edema (OR: 18.65 [95% CI: 13.71-25.38]), peripartum cardiomyopathy (14.06 [9.15-21.60]), venous thromboembolism (12.25 [7.80-19.24]), cardiac arrhythmias (11.75 [10.11-13.67]), acute kidney injury (7.53 [5.36-10.58]), preeclampsia/eclampsia (4.61 [4.04-5.25]), and acute coronary syndrome (2.83 [1.17-6.85]), compared with pregnant patients without PH. In-hospital mortality in patients with PH was associated with stroke (127.33 [78.49-206.57]), acute kidney injury (51.25 [34.40-76.36]), cardiac arrhythmias (24.80 [19.43-31.65]), peripartum cardiomyopathy (6.47 [3.23-12.97]), pulmonary edema (4.27 [2.18-8.37]), venous thromboembolism (2.75 [1.07-7.10]), and preeclampsia/eclampsia (1.87 [1.35-2.60]) compared to pregnant patients without PH.

Conclusion

Delivery hospitalizations in patients with PH are associated with high risk of various complications. Prenatal counseling and multidisciplinary care are essential to help mitigate unfavorable outcomes in these patients.
Association of Chronotype and Shiftwork with COVID-19 Infection
Authors: Quan Stuart F. , Weaver Matthew D. , Czeisler Mark É. , Barger Laura K. , Booker Lauren A. , Howard Mark E. , Jackson Melinda L. , Lane Rashon I. , McDonald Christine F. , Ridgers Anna , Robbins Rebecca , Varma Prerna , Rajaratnam Shantha M.W. , Czeisler Charles A.
Published: July 2023

Objective

This study assesses whether chronotype is related to COVID-19 infection and whether there is an interaction with shift work.

Methods

Cross-sectional survey of 19,821 U.S. adults

Results

COVID-19 infection occurred in 40% of participants, 32.6% morning and 17.2% evening chronotypes. After adjusting for demographic and socioeconomic factors, shift work, sleep duration and comorbidities, morning chronotype was associated with a higher (aOR: 1.15, 95% CI 1.10-1.21) and evening chronotype with a lower (aOR: 0.82, 95% CI: 0.78-0.87) prevalence of COVID-19 infection in comparison to an intermediate chronotype. Working exclusively night shifts was not associated with higher prevalence of COVID-19. Morning chronotype and working some evening shifts was associated with the highest prevalence of previous COVID-19 infection (aOR: 1.87, 95% CI: 1.28-2.74).

Conclusion

Morning chronotype and working a mixture of shifts increase risk of COVID-19 infection.

Learning Outcomes

Describe the association between chronotype and prevalence of COVID-19 infection

Summarize the combined effect of chronotype and shift work on the prevalence of COVID-19 infection
Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states
Authors: Reffsin Sam , Miller Jesse , Ayyanathan Kasirajan , Dunagin Margaret C. , Jain Naveen , Schultz David C. , Cherry Sara , Raj Arjun
Published: July 2023

The ability of a virus to infect a cell type is at least in part determined by the presence of host factors required for the viral life cycle. However, even within cell types that express known factors needed for infection, not every cell is equally susceptible, suggesting that our knowledge of the full spectrum of factors that promote infection is incomplete. Profiling the most susceptible subsets of cells within a population may reveal additional factors that promote infection. However, because viral infection dramatically alters the state of the cell, new approaches are needed to reveal the state of these cells prior to infection with virus. Here, we used single-cell clone tracing to retrospectively identify and characterize lung epithelial cells that are highly susceptible to infection with SARS-CoV-2. The transcriptional state of these highly susceptible cells includes markers of retinoic acid signaling and epithelial differentiation. Loss of candidate factors identified by our approach revealed that many of these factors play roles in viral entry. Moreover, a subset of these factors exert control over the infectable cell state itself, regulating the expression of key factors associated with viral infection and entry. Analysis of patient samples revealed the heterogeneous expression of these factors across both cells and patientsin vivo. Further, the expression of these factors is upregulated in particular inflammatory pathologies. Altogether, our results show that the variable expression of intrinsic cell states is a major determinant of whether a cell can be infected by SARS-CoV-2.
Bottom-up and top-down contributions to impaired motion processing in schizophrenia
Authors: Martínez Antígona , Gaspar Pablo A. , Bermudez Dalton H. , Aburto-Ponce M. Belen , Javitt Daniel C.
Published: July 2023

Background and Hypothesis

Motion processing deficits in schizophrenia have been linked to impairments in higher-order social-cognitive processes. The neural underpinnings are not fully understood but it has been hypothesized that middle temporal area (MT+) may serve as a bridge between purely sensory and more cognitive proceseses. We investigated the interrelationship between MT+ sensory processing deficits and impairments in higher-order processing using naturalistic videos with explicit motion and static images with implied-motion cues.

Study Design

Functional magnetic resonance imaging was used to evaluate cortical and subcortical brain regions associated with real- and implied-motion processing in 28 individuals with schizophrenia and 20 neurotypical controls. These measures were related to face emotion recognition and motion-perception deficits, as measured behaviorally.

Study Results

Activation of MT+ was abnormal in schizophrenia during both real- and implied-motion processing. Dysfunction of early visual cortex and pulvinar were also associated with impaired real-motion processing. During implied-motion-perception, MT+ participated in a wider network involving sensorimotor and prefrontal nodes of the human mirror neuron system, known to play a role in social-cognitive processes. Perception of both real- and implied-motion engaged the posterior superior temporal sulcus, a key node of the social brain network.

Conclusions

The findings support concepts of MT+ as a bridge between visual sensory areas and higher-order brain regions especially in relationship to face emotion recognition and social cognition. Our data argue for greater focus on MT+ contributions to social-cognitive processing, in addition to its well-documented role in visual motion processing.
Perioperative mortality in low-, middle-, and high-income countries: Protocol for a multi-level meta-regression analysis
Authors: McIntyre Kevin J. , Choi Yun-Hee , John-Baptiste Ava , Lizotte Daniel J. , Chan Eunice Y.S. , Moodie Jessica , Stranges Saverio , Martin Janet
Published: July 2023

Background

Surgery is an indispensable component of a functional healthcare system. To date there is limited information regarding how many people die during the perioperative period globally. This study describes a protocol for a systematic review and multilevel meta-regression to evaluate time trends regarding the odds of perioperative mortality among adults undergoing a bellwether surgical procedure while accounting for higher order clustering at the national level.

Methods

Published studies reporting the number of perioperative deaths from bellwether surgical procedures among adults will be identified from MEDLINE, Embase, Cochrane CENTRAL, LILACS and Global Index Medicus. The primary outcome will be the rate of perioperative mortality across time and the secondary outcome will be investigating cause of death over time as a proportion of overall perioperative mortality. Two reviewers will independently conduct full text screening and extract the data. Disagreements will first be resolved via consensus. If consensus cannot be reached a third reviewer will be included to arbitrate. Due to human resource limitations, a risk of bias appraisal will not be conducted. From the included studies a multilevel meta-regression will be constructed to synthesize the results. This model will conceptualize patients as nested in studies which are in turn nested within countries while taking into account potential confounding variables at all levels.

Discussion

The systematic review and multilevel meta-regression that will be conducted based on this protocol will provide synthesized global evidence regarding the trends of perioperative mortality. This eventual study may help policymakers and other key stakeholders with benchmarking surgical safety initiatives as well as identify key gaps in our current understanding of global perioperative mortality.

Systematic review registration

PROSPERO registration number 429040.
A novel nomogram based on serum lipid for identifying the patients at risk for rapid progression of advanced hormone-sensitive prostate cancer
Authors: Wu Mingshuang , He Yi , Pan Chenxi , Zhang Yue , Yang Bo
Published: July 2023

Background

Serum lipids were reported to be significant predictive factors in various tumors. In order to develop and validate a nomogram for predicting castration-resistant prostate cancer (CRPC) free survival in advanced hormone-sensitive prostate cancer (HSPC) patients, the goal of this study was to assess the prognostic impact of the lipid profiles.

Material and Methods

The follow-up information of 146 CRPC patients who received androgen deprivation therapy as the first and only therapy before progression were retrospectively examined. To evaluate prognostic variables, univariate and multivariate Cox regression analyses were used. The concordance index (C-index), calibration curves, receiver operating characteristic (ROC) curves, and decision curve analyses (DCA) were used to design and evaluate a novel nomogram model.

Results

Total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), apolipoprotein B (apoB), N stage and Gleason sum were determined to be independent prognostic markers and were combined to create a nomogram. This nomogram performed well in the customized prediction of CRPC development at 6th, 12th, 18th and 24th month. The C-indexes in training and validation sets were 0.740 and 0.755, respectively. ROC curves, calibration plots, and DCA all suggested favorable discrimination and predictive ability. Besides, the nomogram also performed better predictive ability than N stage and Gleason sum. The Nomogram-related risk score divided the patient population into two groups with significant progression disparities.

Conclusions

The established nomogram could aid in identifying the patients at high risk for rapid progression of advanced HSPC, so as to formulate individualized therapeutic regimens and follow-up strategies in time.
Nightshift Imposes Irregular Lifestyle Behaviors in Police Academy Trainees
Authors: Erickson Melissa L. , North Rebecca , Counts Julie , Wang Will , Porter Starr Kathryn N. , Wideman Laurie , Pieper Carl , Dunn Jessilyn , Kraus William E.
Published: July 2023

Study Objective

Shiftwork increases risk for numerous chronic diseases, which is hypothesized to be linked to disruption of circadian timing of lifestyle behaviors. However, empirical data on timing of lifestyle behaviors in real-world shift workers are lacking. To address this, we characterized the regularity of timing of lifestyle behaviors in shift-working police trainees.

Methods

Using a two-group observational study design (N=18), we compared lifestyle behavior timing during 6 weeks of in-class training during dayshift, followed by 6 weeks of field-based training duringeitherdayshift or nightshift. Lifestyle behavior timing, including sleep/wake patterns, physical activity, and meals, was captured using wearable activity trackers and mobile devices. The regularity of lifestyle behavior timing was quantified as an index score, which reflects day-to-day stability on a 24h time scale: Sleep Regularity Index (SRI), Physical Activity Regularity Index (PARI) and Mealtime Regularity Index (MRI). Logistic regression was applied to these indices to develop a composite score, termed the Behavior Regularity Index (BRI).

Results

Transitioning from dayshift to nightshift significantly worsened the BRI, relative to maintaining a dayshift schedule. Specifically, nightshift led to more irregular sleep/wake timing and meal timing; physical activity timing was not impacted. In contrast, maintaining a dayshift schedule did not impact regularity indices.

Conclusion

Nightshift imposed irregular timing of lifestyle behaviors, which is consistent with the hypothesis that circadian disruption contributes to chronic disease risk in shift workers. How to mitigate the negative impact of shiftwork on human health as mediated by irregular timing of sleep/wake patterns and meals deserves exploration.
Automated segmentation of brain metastases in T1-weighted contrast-enhanced MR images pre and post Stereotactic Radiosurgery
Authors: Kanakarajan Hemalatha , De Baene Wouter , Hanssens Patrick , Sitskoorn Margriet
Published: July 2023

Background and purpose

Accurate segmentation of brain metastases on Magnetic Resonance Imaging (MRI) is a tedious and time-consuming task for radiologists that could be optimized with deep learning (DL) methods. Previous studies that evaluated the performance of several DL algorithms focused on training and testing the models on the planning MRI only. The purpose of this study is to evaluate well-known DL approaches (nnU-Net and MedNeXt) for their performance on both planning and follow-up MRI.

Materials and methods

Pre-treatment brain MRIs were collected retrospectively for 263 patients at the Gamma Knife Center of Elisabeth-TweeSteden Hospital (ETZ). The patients were split into 203 patients for training and 60 patients for testing. For these 60 patients, the follow-up MRIs were also retrospectively collected. To increase heterogeneity, we added the publicly available MRI from the Mathematical oncology laboratory for 75 patients to the training data. The performance was compared between the two models, with and without addition of the public data.

Results

All models obtained a good Dice Similarity Coefficient (all DSC >= 0.928) for planning MRI. MedNeXt trained with combined data was the best performing model for follow-ups at 3, 15 and 21 months (DSC of 0.796, 0.725, and 0.720 respectively) while nnU-Net trained with combined data was the best performing model for follow-ups at 6, 9 and 12 months (DSC of 0.738, 0.740 and 0.713 respectively).

Conclusion

The models achieved a good performance score for planning MRI. Though the models performed worse for follow-ups, addition of public data enhanced their performance, providing a viable solution to improve their efficacy for the follow-ups. There was only limited difference in performance of the two algorithms. These algorithms hold promise as a valuable tool for clinicians for automated segmentation of pre- and postsurgical MRI during treatment planning and response evaluations, respectively.
Leveraging Generative AI to Prioritize Drug Repurposing Candidates: Validating Identified Candidates for Alzheimer’s Disease in Real-World Clinical Datasets
Authors: Yan Chao , Grabowska Monika E. , Dickson Alyson L. , Li Bingshan , Wen Zhexing , Roden Dan M. , Stein C. Michael , Embí Peter J. , Peterson Josh F. , Feng QiPing , Malin Bradley A. , Wei Wei-Qi
Published: July 2023

Drug repurposing represents an attractive alternative to the costly and time-consuming process of new drug development, particularly for serious, widespread conditions with limited effective treatments, such as Alzheimer’s disease (AD). Emerging generative artificial intelligence (GAI) technologies like ChatGPT offer the promise of expediting the review and summary of scientific knowledge. To examine the feasibility of using GAI for identifying drug repurposing candidates, we iteratively tasked ChatGPT with proposing the twenty most promising drugs for repurposing in AD, and tested the top ten for risk of incident AD in exposed and unexposed individuals over age 65 in two large clinical datasets: 1) Vanderbilt University Medical Center and 2) theAll of UsResearch Program. Among the candidates suggested by ChatGPT, metformin, simvastatin, and losartan were associated with lower AD risk in meta-analysis. These findings suggest GAI technologies can assimilate scientific insights from an extensive Internet-based search space, helping to prioritize drug repurposing candidates and facilitate the treatment of diseases.
CLIPB4 is a central node in the protease network that regulates humoral immunity inAnopheles gambiaemosquitoes
Authors: Zhang Xiufeng , Zhang Shasha , Kuang Junyao , Sellens Kathleen A. , Morejon Bianca , Saab Sally A. , Li Miao , Metto Eve C. , An Chunju , Culbertson Christopher T. , Osta Mike A. , Scoglio Caterina , Michel Kristin
Published: July 2023

Insect humoral immune responses are regulated in part by protease cascades, whose components circulate as zymogens in the hemolymph. In mosquitoes, these cascades consist ofclip domainserineproteases (cSPs) and/or their non-catalytichomologs (cSPHs), which form a complex network, whose molecular make-up is not fully understood. Using a systems biology approach, based on a co-expression network of gene family members that function in melanization and co-immunoprecipitation using the serine protease inhibitor (SRPN)2, a key negative regulator of the melanization response in mosquitoes, we identify the cSP CLIPB4 from the African malaria mosquitoAnopheles gambiaeas a central node in this protease network.CLIPB4is tightly co-expressed withSRPN2and forms protein complexes with SRPN2 in the hemolymph of immune-challenged female mosquitoes. Genetic and biochemical approaches validate our network analysis and show that CLIPB4 is required for melanization and antibacterial immunity, acting as a prophenoloxidase (proPO)-activating protease, which is inhibited by SRPN2. In addition, we provide novel insight into the structural organization of the cSP network inAn. gambiae, by demonstrating that CLIPB4 is able to activate proCLIPB8, a cSP upstream of the proPO-activating protease CLIPB9. These data provide the first evidence that, in mosquitoes, cSPs provide branching points in immune protease networks and deliver positive reinforcement in proPO activation cascades.
Antisense transcription and PRC2 repression function in parallel during vernalization
Authors: Nielsen Mathias , Menon Govind , Zhao Yusheng , Mateo-Bonmati Eduardo , Wolff Philip , Zhou Shaoli , Howard Martin , Dean Caroline
Published: July 2023

Non-coding transcription induces chromatin changes that can mediate environmental responsiveness, but the causes and consequences of these mechanisms are still unclear. Here, we investigate how antisense transcription interfaces with Polycomb Repressive Complex 2 silencing during winter-induced epigenetic regulation of ArabidopsisFLOWERING LOCUS C(FLC). Through genetic, chromatin, and computational analyses, we show thatFLCis silenced through pathways that function with different dynamics: an antisense transcription-mediated pathway capable of fast response; and in parallel a slow Polycomb Repressive Complex 2 (PRC2) switching mechanism that maintains each allele in an epigenetically silenced state. Components of both the antisense and PRC2 pathways are regulated by a common transcriptional regulator (NTL8), which accumulates slowly due to reduced growth at low temperatures. The parallel activities of the regulatory steps, which we encapsulate in a mathematical model, creates a flexible system for registering widely fluctuating natural temperature conditions that change year on year, and yet ensure robust epigenetic silencing ofFLC.

Significance

The role of non-coding transcription in establishing and maintaining chromatin states is controversial, mainly because of extensive feedbacks complicating analysis of the relationship between co-transcriptional processing, chromatin state and transcription. This controversy has extended to the role of antisense transcription in the Polycomb-mediated epigenetic silencing of ArabidopsisFLC, a key step in the process of vernalization. Here, we show that antisense transcription and PRC2 silenceFLCin parallel pathways that are affected by growth dynamics and temperature fluctuations. These features explain the varied importance of antisense transcription in cold-inducedFLCepigenetic silencing seen in various studies using different environmental and growth conditions. The parallel repressive inputs and extensive feedbacks make the mechanism counter-intuitive but provide great flexibility to the plant.
Exploring alternative quorum sensing model structures and quorum quenching strategies
Authors: Cimolato Chiara , Bellato Massimo , Selvaggio Gianluca , Marchetti Luca , Giordano Giulia , Schenato Luca
Published: July 2023

Bacterial quorum sensing (QS) is a cell-to-cell communication mechanism through which bacteria share information about cell density, and tune gene expression accordingly. Pathogens exploit QS to orchestrate virulence and regulate the expression of genes related to antimicrobial resistance. Despite the vast literature on QS, the properties of the underlying molecular network are not entirely clear. We compare two synthetic QS circuit architectures: in the first, a single positive feedback loop autoinduces the synthesis of the signal molecule; the second includes an additional positive feedback loop enhancing the synthesis of the signal molecule receptor. Our comprehensive analysis of the two systems and their equilibria highlights the differences in the bistable and hysteretic behaviors of the alternative QS structures. Finally, we investigate three different QS inhibition approaches; numerical analysis predicts their effect on the steady-state behavior of the two different QS models, revealing critical parameter thresholds that guarantee an effective QS suppression.
Temporal Pattern of Mutation Accumulation in SARS-CoV-2 Proteins: Insights from Whole Genome Sequences Pan-India Using Data Mining Approach
Authors: Varun Chakrakodi N
Published: July 2023

Mutation is a fundamental factor that affects host-pathogen biology and consequently viral survival and spread. Close monitoring and observation of such mutation help decipher essential changes in the SARS Cov2 genome. A plethora of mutations have been documented owing to increased whole genomic sequencing. Understanding how conserved the specific mutations are and the temporal pattern of mutation accumulation is of paramount interest. Using an in-house data mining approach, pan-India data was mined and analysed for 26 proteins expressed by SARS-CoV-2 to understand the spread of mutations over 28 months (January 2021-April 2023). It was observed that proteins such as Nsp3, Nsp4, ORF9b, among others, acquired mutations over the period. In contrast, proteins such as Nsp6-10 were highly stable, with no detectable conserved mutations. Further, it was observed that many of the mutations that were highly prevalent in the delta variants were not observed in the omicron variants, which probably influenced the host-pathogen relationship. The study attempts to catalogue and focus on well-conserved mutations across all the SARS-CoV-2 proteins, highlighting the importance of understanding non-spike mutations.
Pax3lineage-specific deletion ofGpr161is associated with spinal neural tube and craniofacial malformations during embryonic development
Authors: Kim Sung-Eun , Chothani Pooja J , Shaik Rehana , Pollard Westley , Finnell Richard H
Published: July 2023

Shh signaling is the morphogen signaling that regulates embryonic craniofacial and neural tube development. G protein-coupled receptor 161 (Gpr161) is a negative regulator of Shh signaling, and its inactivation in mice results in embryo lethality with craniofacial and neural tube defects (NTDs). However, the structural defects of later embryonic stages inGpr161null mice and cell lineages underlying abnormalities were not well characterized due to their limited lifespan. We found thePax3lineage-specific deletion ofGpr161in mice presented with tectal hypertrophy (anterior dorsal neuroepithelium), cranial vault and facial bone hypoplasia (cranial neural crest (CNC)), vertebral abnormalities (somite), and the closed form of spina bifida (posterior dorsal neuroepithelium). In particular, the closed form of spina bifida is partly due to the reducedPax3andCdx4gene expression of the posterior dorsal neural tubes ofGpr161mutant embryos involving decreased Wnt signaling whereas Shh signaling was increased. This study provides the novel role of Gpr161 in the posterior neural tube development and confirms its role on CNC- and somite-derived skeletogenesis and midbrain morphogenesis in mice.
B cell repertoire sequencing of HIV-1 pediatric elite-neutralizers identifies multiple broadly neutralizing antibody clonotypes
Authors: Kumar Sanjeev , Bajpai Prashant , Joyce Collin , Kabra Sushil Kumar , Lodha Rakesh , Burton Dennis R. , Briney Bryan , Luthra Kalpana
Published: July 2023

A limited subset of HIV-1 infected adult individuals typically after at least 2-3 years of chronic infection, develop broadly neutralizing antibodies (bnAbs), suggesting that highly conserved neutralizing epitopes on the HIV-1 envelope glycoprotein are difficult for B cell receptors to effectively target, during natural infection. Recent studies have shown the evolution of bnAbs in HIV-1 infected infants. We used bulk BCR sequencing (BCR-seq) to profile the B cell receptors from longitudinal samples (3 time points) collected from a rare pair of antiretroviral-naïve, HIV-1 infected pediatric monozygotic twins (AIIMS_329 and AIIMS_330) who displayed elite plasma neutralizing activity against HIV-1. BCR-seq of both twins revealed convergent antibody characteristics including V-gene use, CDRH3 lengths and somatic hypermutation (SHM). Further, antibody clonotypes with genetic features similar to highly potent bnAbs isolated from adults showed ongoing development in donor AIIMS_330 but not in AIIMS_329, corroborating our earlier findings based on plasma bnAbs responses. An increase in SHM was observed in sequences of the IgA isotype from AIIMS_330. This study suggests that children living with chronic HIV-1 can develop clonotypes of HIV-1 bnAbs against multiple envelope epitopes similar to those isolated from adults, highlighting that such B cells could be steered to elicit bnAbs responses through vaccines aimed to induce bnAbs against HIV-1 in a broad range of people including children.
Multiple TonB Homologs are Important for Carbohydrate Utilization byBacteroides thetaiotaomicron
Authors: Pollet Rebecca M , Foley Matthew H , Kumar Supriya Suresh , Elmore Amanda , Jabara Nisrine T , Venkatesh Sameeksha , Pereira Gabriel Vasconcelos , Martens Eric C , Koropatkin Nicole M
Published: July 2023

The human gut microbiota is able to degrade otherwise undigestible polysaccharides, largely through the activity of theBacteroides. Uptake of polysaccharides intoBacteroidesis controlled by TonB-dependent transporters (TBDT) whose transport is energized by an inner membrane complex composed of the proteins TonB, ExbB, and ExbD.Bacteroides thetaiotaomicron(B. theta) encodes 11 TonB homologs which are predicted to be able to contact TBDTs to facilitate transport. However, it is not clear which TonBs are important for polysaccharide uptake. Using strains in which each of the 11 predictedtonBgenes are deleted, we show that TonB4 (BT2059) is important but not essential for proper growth on starch. In the absence of TonB4, we observed an increase in abundance of TonB6 (BT2762) in the membrane ofB. theta, suggesting functional redundancy of these TonB proteins. Growth of the single deletion strains on pectin galactan, chondroitin sulfate, arabinan, and levan suggests a similar functional redundancy of the TonB proteins. A search for highly homologous proteins across otherBacteroidesspecies and recent work inB. fragilissuggests that TonB4 is widely conserved and may play a common role in polysaccharide uptake. However, proteins similar to TonB6 are found only inB. thetaand closely related species suggesting that the functional redundancy of TonB4 and TonB6 may be limited across theBacteroides. This study extends our understanding of the protein network required for polysaccharide utilization inB. thetaand highlights differences in TonB complexes acrossBacteroidesspecies.

Importance

The human gut microbiota, including the Bacteroides, is required for the degradation of otherwise undigestible polysaccharides. The gut microbiota uses polysaccharides as an energy source and the fermentation products such as short chain fatty acids are beneficial to the human host. This use of polysaccharides is dependent on the proper pairing of a TonB protein with polysaccharide-specific TonB-dependent transporters; however, formation of these protein complexes is poorly understood. In this study, we examine the role of 11 predicted TonB homologs in polysaccharide uptake. We show that two proteins, TonB4 and TonB6, may be functionally redundant. This may allow for development of drugs targetingBacteroidesspecies containing only a TonB4 homolog with limited impact on species encoding the redundant TonB6.
A conserved antigen induces respiratory Th17-mediated serotype-independent protection against pneumococcal superinfection
Authors: Liu Xue , Van Maele Laurye , Matarazzo Laura , Soulard Daphnée , Alves Duarte da Silva Vinicius , de Bakker Vincent , Dénéréaz Julien , Bock Florian P. , Taschner Michael , Gruber Stephan , Nizet Victor , Sirard Jean-Claude , Veening Jan-Willem
Published: July 2023

Several vaccines targeting bacterial pathogens show reduced efficacy in the context of intercurrent viral infection indicating a new vaccinology approach is required to protect against such superinfections. To find antigens for the human pathogenStreptococcus pneumoniaethat are effective following influenza infection, we performed CRISPRi-seq in a murine model of superinfection and identified the highly conservedlafBgene as virulence factor. We show that LafB is a membrane-associated, intracellular protein that catalyzes the formation of galactosyl-glucosyl-diacylglycerol, a glycolipid we show is important for cell wall homeostasis. Respiratory vaccination with recombinant LafB, in contrast to subcutaneous vaccination, was highly protective against all serotypes in a murine model. In contrast to standard pneumococcal capsule-based conjugate vaccines, protection did not require LafB-specific antibodies but was dependent on airway CD4+T helper 17 cells. Healthy human individuals can elicit LafB-specific immune responses, suggesting its merit as a universal pneumococcal vaccine antigen that remains effective following influenza infection.

One-Sentence Summary

Discovery of a universal pneumococcal vaccine protective during superinfection.
Reduced binding associated with resistance to Vip3Aa in the corn earworm (Helicoverpa zea)
Authors: Kerns Dawson D. , Yang Fei , Kerns David L. , Stewart Scott D. , Jurat-Fuentes Juan Luis
Published: July 2023

Transgenic corn and cotton expressing Cry and Vip insecticidal proteins from the bacterium,Bacillus thuringiensis(Bt), have been a valuable tool for the management of lepidopteran pests. In 2019, a Vip3Aa-resistant strain ofHelicoverpa zea(CEW-Vip-RR) was isolated from F2screens of field populations in Texas. Characterizing the resistance mechanism in this strain is important for predicting the sustained efficacy of current commercial Bt traits and guiding the development of future transgenic traits. Resistance to insecticidal proteins in Bt traits is commonly associated with reduced toxin binding, with the exception of Vip3Aa resistance being associated to altered proteolytic processing in the insect host gut. Therefore, Vip3Aa protoxin processing was tested by incubation with midgut fluids from CEW-Vip-RR relative to a susceptible strain (CEW-SS). Finding no significant processing differences, alterations in Vip3Aa binding were tested by comparing binding of radiolabeled and biotinylated Vip3Aa toxin to midgut brush border membrane vesicles (BBMV) from CEW-Vip-RR and CEW-SS larvae. Specific Vip3Aa binding to CEW-Vip-RR BBMV in these experiments was consistently reduced when compared with CEW-SS BBMV. These results support that an altered Vip3Aa- receptor is associated with resistance in CEW-Vip-RR. Understanding this resistance mechanism could have important implications for resistance management decisions considering widespread Cry1 and Cry2 resistance inH. zeapopulations.

IMPORTANCE

Helicoverpa zeais a major crop pest in the United States that is managed with transgenic corn and cotton producing insecticidal proteins from the bacterium,Bacillus thuringiensis(Bt). However,H. zeahas evolved widespread resistance to the Cry proteins produced in Bt corn and cotton, leaving Vip3Aa as the only plant incorporated protectant in Bt crops consistently providing excellent control ofH. zea. The benefits provided by Bt crops will be substantially reduced if widespread Vip3Aa resistance develops inH. zeafield populations. Therefore, it is important to identify resistance alleles and mechanisms that contribute to Vip3Aa resistance to ensure that informed resistance management strategies are implemented. This study is the first report of reduced binding of Vip3Aa to midgut receptors associated with resistance.
Fixation times ofde novoand standing beneficial variants in subdivided populations
Authors: Sudbrack Vitor , Mullon Charles
Published: July 2023

The rate at which beneficial alleles fix in a population depends on the probability of and time to fixation of such alleles. Both of these quantities can be significantly impacted by population subdivision and limited gene flow. Here, we investigate how limited dispersal influences the rate of fixation of beneficialde novomutations, as well as fixation time from standing genetic variation. We investigate this for a population structured according to the island model of dispersal allowing us to use the diffusion approximation, which we complement with simulations. We find that fixation may take on average fewer generations under limited dispersal than under panmixia when selection is moderate. This is especially the case if adaptation occurs fromde novorecessive mutations, and dispersal is not too limited (such that approximatelyFST< 0.2). The reason is that mildly limited dispersal leads to only a moderate increase in effective population size (which slows down fixation), but is sufficient to cause a relative excess of homozygosity due to inbreeding, thereby exposing rare recessive alleles to selection (which accelerates fixation). We also explore the effect of meta-population dynamics through local extinction followed by recolonization, finding that such dynamics always accelerate fixation from standing genetic variation, whilede novomutations show faster fixation interspersed with longer waiting times. Finally, we discuss the implications of our results for the detection of sweeps, suggesting that limited dispersal mitigates the expected differences between the genetic signatures of sweeps involving recessive and dominant alleles.
Distinct structural motifs are necessary for targeting and import of Tim17 inTrypanosoma bruceimitochondrion
Authors: Darden Chauncey , Donkor Joseph , Korolkova Olga , Khan Barozai Muhammad Younas , Chaudhuri Minu
Published: July 2023

Nuclear-encoded mitochondrial proteins are correctly translocated to their proper sub-mitochondrial destination using location specific mitochondrial targeting signals (MTSs) and via multi-protein import machineries (translocases) in the outer and inner mitochondrial membranes (TOM and TIMs, respectively). However, MTSs of multi-pass Tims are less defined. Here we report the characterization of the MTSs ofTrypanosoma bruceiTim17 (TbTim17), an essential component of the most divergent TIM complex. TbTim17 possesses a characteristic secondary structure including four predicted transmembrane (TM) domains in the center with hydrophilic N- and C-termini. After examining mitochondrial localization of various deletion and site-directed mutants of TbTim17 inT. bruceiusing subcellular fractionation and confocal microscopy we located at least two internal signals, 1) within TM1 (31-50 AAs) and 2) TM4 + Loop 3 (120-136 AAs). Both signals are required for proper targeting and integration of TbTim17 in the membrane. Furthermore, a positively charged residue (K122) is critical for mitochondrial localization of TbTim17. This is the first report of characterizing the internal mitochondrial targeting signals (ITS) for a multipass inner membrane protein in a divergent eukaryote, likeT. brucei.

Internal targeting signals within the TM1, TM4 with Loop 3, and residue K122 are required collectively for import and integration of TbTim17 in theT. bruceimitochondrion. This information could be utilized to block parasite growth.