bluuebunny/crossref_metadata_2025 huggingface dataset:
Psychometric properties of outcome measures for lower-limb absence: A protocol for a systematic review
Authors: Tan Jade M. , Halford Gregory R. J. , McBain Brodwen K. , Lukin Martina , Kohler Friedbert
Published: February 2023

Background:

Outcome measures are an important part of clinical practice to assist with the care of individuals with lower-limb absence (LLA). They aid with the devising and evaluation of rehabilitation plans, and guide decisions regarding the provision and funding of prosthetic services worldwide. To date, no outcome measure has been identified as a gold standard for use in individuals with LLA. Furthermore, the large number of outcome measures available has created uncertainty regarding outcome measures that are most appropriate for individuals with LLA.

Objective:

To critically appraise the existing literature related to the psychometric properties of outcome measures for use in individuals with LLA and provide evidence as to which outcome measures may be most appropriate for this clinical population.

Study design:

This is a systematic review protocol.

Methods:

CINAHL, Embase, MEDLINE (PubMed), and PsycINFO databases will be searched using a combination of Medical Subject Headings terms and keywords. Search terms that define the population (people with LLA or amputation), intervention (outcome measures), and outcome (psychometric properties) will be used to identify studies. The reference lists of included studies will be hand-search to identify other pertinent articles, with a further search conducted through Google Scholar to ensure that all studies not yet indexed through MEDLINE are captured. Full-text peer-reviewed journal studies published in English will be included, with no date limit set. Included studies will be appraised using the 2018 and 2020 COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) checklists. Data extraction and study appraisal will be completed by two authors, with a third author serving as an adjudicator. Quantitative synthesis will be used to summarize characteristics of the included studies, with kappa statistics used to determine agreement between authors for study inclusion and the application of COSMIN. Qualitative synthesis will be conducted to report on both quality of the included studies and psychometric properties of the included outcome measures.

Conclusion:

This protocol was designed to identify, appraise, and summarize patient-reported and performance-based outcome measures that have been psychometrically tested in people with LLA. Results from this review will be used to guide a consensus process on outcome measure use for people with LLA.

Systematic review registration: PROSPERO registry number: CRD42020217820.
The Cooperative Re-Engagement Controlled Trial (CoRECT): Durable Viral Suppression Assessment
Authors: O'Shea Jesse , Fanfair Robyn Neblett , Williams Tiffany , Khalil George , Brady Kathleen A. , DeMaria Alfred , Villanueva Merceditas , Randall Liisa M. , Jenkins Heidi , Altice Frederick L. , Camp Nasima , Lucas Crystal , Buchelli Marianne , Samandari Taraz , Weidle Paul J.
Published: February 2023

Background:

A collaborative, data-to-care strategy to identify persons with HIV (PWH) newly out-of-care, combined with an active public health intervention, significantly increases the proportion of PWH re-engaged in HIV care. We assessed this strategy's impact on durable viral suppression (DVS).

Methods:

A multisite, prospective randomized controlled trial for out-of-care individuals using a data-to-care strategy and comparing public health field services to locate, contact, and facilitate access to care versus the standard of care. DVS was defined as the last viral load, the viral load at least 3 months before, and any viral load between the 2 were all <200 copies/mL during the 18-month postrandomization. Alternative definitions of DVS were also analyzed.

Results:

Between August 1, 2016–July 31, 2018, 1893 participants were randomized from Connecticut (n = 654), Massachusetts (n = 630), and Philadelphia (n = 609). Rates of achieving DVS were similar in the intervention and standard-of-care arms in all jurisdictions (all sites: 43.4% vs 42.4%, P = 0.67; Connecticut: 46.7% vs 45.0%, P = 0.67; Massachusetts: 40.7 vs 44.4%, P = 0.35; Philadelphia: 42.4% vs 37.3%, P = 0.20). There was no association between DVS and the intervention (RR: 1.01, CI: 0.91–1.12; P = 0.85) adjusting for site, age categories, race/ethnicity, birth sex, CD4 categories, and exposure categories.

Conclusion:

A collaborative, data-to-care strategy, and active public health intervention did not increase the proportion of PWH achieving DVS, suggesting additional support to promote retention in care and antiretroviral adherence may be needed. Initial linkage and engagement services, through data-to-care or other means, are likely necessary but insufficient for achieving DVS for all PWH.
A Systematic Review of the Impact of Patient Factors on BREAST-Q Outcomes After Reduction Mammoplasty
Authors: Liao Christopher D. , Xia Joyce , Wang Katherine , Zhao Kelley , Glickman Laurence T. , Agrawal Nikhil A.
Published: February 2023

Background

As reduction mammoplasty rises in popularity, it will become increasingly important to understand the patient-reported outcome measurements associated with a successful operation. There has been a growing body of literature on BREAST-Q outcomes for patients undergoing reduction mammoplasty, but meta-analyses of patient factors and BREAST-Q Reduction Module scores are lacking. This study sought to ascertain which patient factors were associated with improvements in BREAST-Q scores compared with preoperative levels.

Methods

A literature review through August 6, 2021, was conducted using the PubMed database to select publications using the BREAST-Q questionnaire to evaluate outcomes after reduction mammoplasty. Studies examining breast reconstruction, breast augmentation, oncoplastic reduction, or breast cancer patients were excluded. BREAST-Q data were stratified by comorbidities, age, body mass index (BMI), complication rate, and resection weight.

Results

Among 14 articles and 1816 patients, the mean age ranged from 15.8 to 55 years, mean BMI ranged from 22.5 to 32.4 kg/m2, and bilateral mean resected weight ranged from 323 to 1845.96 g. Overall complication rate was 19.9%. On average, satisfaction with breasts improved by 52.1 ± 0.9 points (P < 0.0001), psychosocial well-being improved by 43.0 ± 1.0 points (P < 0.0001), sexual well-being improved by 38.2 ± 1.2 points (P < 0.0001), and physical well-being improved by 27.9 ± 0.8 points (P < 0.0001). The mean age was positively correlated with preoperative sexual well-being (Spearman rank correlation coefficient [SRCC]: 0.61, P < 0.05). Body mass index was negatively correlated with preoperative physical well-being (SRCC: −0.78, P < 0.01) and positively correlated with postoperative satisfaction with breasts (SRCC: 0.53, P < 0.05). The mean bilateral resected weight was significantly positively correlated with postoperative satisfaction with breasts (SRCC: 0.61, P < 0.05). No significant correlations were observed between complication rate and preoperative, postoperative, or mean change in BREAST-Q scores.

Conclusions

Reduction mammoplasty improves patient satisfaction and quality of life as reflected by the BREAST-Q. Although preoperative or postoperative BREAST-Q scores may be individually influenced by age and BMI, these variables demonstrated no statistically significant effect on the average change between these scores. This literature review suggests that reduction mammoplasty delivers high satisfaction across a diverse range of patient populations, and additional prospective cohort or comparative studies gathering robust data on other patient factors would benefit this area of research.
Osseointegration for Lower Limb Amputation
Authors: Black Grant G. , Vaeth Anna M. , Chen Yunchan , Truong Albert Y. , Reif Taylor J. , Rozbruch S. Robert , Otterburn David M.
Published: February 2023

Purpose

Lower-limb osseointegrated prostheses are a novel alternative to traditional socket-suspended prostheses, which are often associated with poor fit, soft tissue damage, and pain. Osseointegration eliminates the socket-skin interface and allows for weight-bearing directly on the skeletal system. However, these prostheses can also be complicated by postoperative issues that can negatively impact mobility and quality of life. Little is known about the incidence of or risk factors for these complications as few centers currently perform the procedure.

Methods

A retrospective analysis was performed on all patients who underwent single-stage lower limb osseointegration at our institution between 2017 and 2021. Patient demographics, medical history, operative data, and outcomes were collected. Fisher exact test and unpaired t tests were performed to identify risk factors for each adverse outcome, and time-to-event survival curves were generated.

Results

Sixty patients met our study criteria: 42 males and 18 females with 35 transfemoral and 25 transtibial amputations. The cohort had an average age of 48 years (range, 25–70 years) and follow-up period of 22 months (range, 6–47 months). Indications for amputation were trauma (50), prior surgical complication (5), cancer (4), and infection (1). Postoperatively, 25 patients developed soft tissue infections, 5 developed osteomyelitis, 6 had symptomatic neuromas, and 7 required soft tissue revisions. Soft tissue infections were positively correlated with obesity and female sex. Neuroma development was associated with increased age at osseointegration. Neuromas and osteomyelitis were both associated with decreased center experience. Subgroup analysis by amputation etiology and anatomic location did not show significant differences in outcomes. Notably, hypertension (15), tobacco use (27), and prior site infection (23) did not correlate with worse outcomes. Forty-seven percent of soft tissue infections occurred in the 1 month after implantation, and 76% occurred in the first 4 months.

Conclusions

These data provide preliminary insights into risk factors for postoperative complications arising from lower limb osseointegration. These factors are both modifiable (body mass index, center experience), and unmodifiable (sex, age). As this procedure continues to expand in popularity, such results are necessary to inform best practice guidelines and optimize outcomes. Further prospective studies are needed to confirm the above trends.
Return of the Flap; The Empire State Mandate
Authors: Asadourian Paul A. , Chen Yunchan , Jung Wooram , Wang Marcos Lu , Koerner Anna , Qin Nancy , de Freitas Daniella , Chinta Malini , Andy Caroline , Rohde Christine H. , Otterburn David M.
Published: February 2023

Purpose

Immediate postmastectomy breast reconstruction plays an integral role in patient care because of its psychosocial benefits. New York State (NYS) passed the 2010 Breast Cancer Provider Discussion Law with the aim of increasing patient awareness of reconstructive options through mandating plastic surgery referral at the time of cancer diagnosis. Short-term analysis of the years surrounding implementation suggests the law increased access to reconstruction, especially for certain minority groups. However, given the continued presence of disparities in access to autologous reconstruction, we aimed to investigate the longitudinal effects of the bill on access to autologous reconstruction along various sociodemographic cohorts.

Methods

Retrospective review identified demographic, socioeconomic, and clinical data for patients undergoing mastectomy with immediate reconstruction at Weill Cornell Medicine and Columbia University Irving Medical Center from 2002 to 2019. Primary outcome was receiving implant or autologous-based reconstruction. Subgroup analysis was based on sociodemographic factors. Multivariate logistic regression identified predictors of autologous reconstruction. Interrupted time series modeling analyzed differences in reconstructive trends for subgroups before and after the 2011 implementation of the NYS law.

Results

We included 3178 patients; 2418 (76.1%) and 760 (23.9%) patients underwent implant and autologous-based reconstruction, respectively. Multivariate analysis indicated that race, Hispanic status, and income were not predictors of autologous reconstruction. Interrupted time series showed that with each year leading up to 2011 implementation, patients were 19% less likely to receive autologous-based reconstruction. Following implementation, there was a 34% increase in the odds of receiving autologous-based reconstruction with each passing year. Following implementation, Asian American and Pacific Islander patients experienced a 55% greater increase in the rate of flap reconstruction than White patients. Following implementation, the highest-income quartile experienced a 26% greater increase in the rate of autologous-based reconstruction compared with the lowest-income quartile. After implementation, Hispanic patients experienced a 30% greater decrease in the rate of autologous-based reconstruction compared with non-Hispanic patients.

Conclusions

Our data indicate the long-term efficacy of the NYS Breast Cancer Provider Discussion Law in increasing access to autologous-based reconstruction, especially for certain minority groups. These findings underscore the importance of this bill and encourage its adoption into other states.
Extensive Defect Reconstruction With Pre-expanded Anterolateral Thigh Flap
Authors: Zang Mengqing , Wang Miao , Wang Danying , Du Qingyan , Zhu Shan , Chen Bo , Li Shanshan , Chen Zixiang , Liu Yuanbo
Published: February 2023

Background

Previously reported pre-expansion techniques of the anterolateral thigh flap are mainly perforator-based. The expansion will interfere with the flap harvest if the requisite perforator is found unsuitable as a pedicle. Expansion of the peripheral territories of the flap donor site can minimize the interference from the expansion.

Methods

Forty-eight peripheral pre-expansions of the anterolateral thigh flap were retrospectively reviewed in 38 patients from 2012 to 2021. The reconstructive outcomes, including flap success, increase in flap size, donor-site closure, and complications, were assessed. In addition, subgroup analysis was performed based on the expanded territories.

Results

Rate of successful flap elevation of 100% and flap survival rate of 97.9% were achieved. One patient had total flap necrosis, which was salvaged with skin grafting. Peripheral expansion attained a mean 55.5% ± 19.6% increase in flap width. Primary donor-site closure was accomplished in 95.8% of flaps and fascial restoration in 97.9% of the donor sites. Three patients developed major expansion-related complications, which required surgical intervention. One patient had wound dehiscence in the donor site, which healed by secondary intention. Compared with other subgroups, the lateral-and-medial-side expansion provided a larger flap for reconstruction (P = 0.001).

Conclusions

If time is not of the essence, peripheral pre-expansion permits direct donor-site closure with size augment of the anterolateral thigh flap. In addition, it preserves the reliability and versatility of the anterolateral thigh flap.
Aortic balloon occlusion in distal zone 3 reduces blood loss from obstetric hemorrhage in placenta accreta spectrum
Authors: Kluck Sarah L. , Russo Rachel M. , Appel Noah B. , Frankfurt Alan I. , Weltge Craig , Shimer Tricia , Feagins Brian , Frotan Amin , Rinehart Brian , Cohen Robert A.
Published: February 2023

BACKGROUND

Peripartum hemorrhage is a significant cause of maternal death. We developed a standardized, multidisciplinary cesarean hysterectomy protocol for placenta accreta spectrum (PAS) using prophylactic resuscitative endovascular balloon occlusion of the aorta (REBOA). We initially placed the balloon in proximal zone 3, below the renal arteries. An internal review revealed more bleeding than expected, and we subsequently changed our protocol to occlude the origin of the inferior mesenteric artery (distal zone 3), to decrease blood flow through collateral circulation. We hypothesized that distal zone 3 occlusion would reduce blood loss and transfusion volume and may permit a longer duration of occlusion compared with proximal zone 3 occlusion without increasing ischemic complications.

METHODS

We conducted a single-center retrospective cohort study of patients with suspected PAS who underwent REBOA-assisted cesarean hysterectomy from December 2018 to March 2022. Medical records of all patients with PAS were reviewed. Data were extracted from hospital admission through 3 months postpartum.

RESULTS

Forty-four patients met the inclusion criteria. Nine never had the balloon inflated. Eighteen patients had placement in proximal zone 3, whereas twenty-six patients had placement in distal zone 3. Background and clinical characteristics were similar in both groups. Placental pathology was obtained in every case. After adjusting for relevant risk factors, multivariate analysis revealed that distal occlusion was associated with a 45.9% (95% confidence interval, 23.8–61.6%) decrease in estimated blood loss, 41.5% (13.7–60.4%) decrease in red blood cell transfusion volume, and 44.9% (13.5–64.9%) reduction in total transfusion volume. There were no vascular access or resuscitative endovascular balloon occlusion of the aorta–related complications in either group.

CONCLUSION

This study highlights the safety of prophylactic REBOA in planned cesarean hysterectomy for PAS and provides a rationale for distal zone 3 positioning to reduce blood loss. Resuscitative endovascular balloon occlusion of the aorta should be considered at other institutions with placenta accreta programs, especially in patients with extensive collateral flow.

LEVEL OF EVIDENCE

Therapeutic/Care Management; Level IV.
Population density does not affect seasonal regulation of reproductive physiology in male water voles
Authors: Poissenot Kevin , Moussu Chantal , Brachet Morgane , Chesneau Didier , Chemineau Philippe , Lainé Anne-Lyse , Migaud Martine , Charbonnel Nathalie , Keller Matthieu
Published: February 2023

Most small rodent species display cyclic fluctuations in their population density. The mechanisms behind these cyclical variations are not yet clearly understood. Density-dependent effects on reproductive function could affect these population variations. The fossorial water vole ecotype,
Arvicola terrestris
, exhibits multi-year cyclical dynamics with outbreak peaks. Here, we monitored different water vole populations over 3 years, in spring and autumn, to evaluate whether population density is related to male reproductive physiology. Our results show an effect of season and inter-annual factors on testis mass, plasmatic testosterone level, and androgen-dependent seminal vesicle mass. By contrast, population density does not affect any of these parameters, suggesting a lack of modulation of population dynamics by population density.
Stability of multi-layer ecosystems
Authors: Wang Ye , Yang Yuguang , Li Aming , Wang Long
Published: February 2023

Community structure is reported to play a critical role in ecosystem stability, which indicates the ability of a system to return to equilibrium after perturbations. However, current studies rely on the assumption that the community consists of only a single-layer structure. In practice, multi-layer structures are common in ecosystems, e.g. the distributions of both microorganisms in strata and fish in the ocean usually stratify into multi-layer structures. Here we use multi-layer networks to model species interactions within each layer and between different layers, and study the stability of multi-layer ecosystems under different interaction types. We show that competitive interactions within each layer have a more substantial stabilizing effect in multi-layer ecosystems relative to their impact in single-layer ecosystems. Surprisingly, between different layers, we find that competition between species destabilizes the ecosystem. We further provide a theoretical analysis of the stability of multi-layer ecosystems and confirm the robustness of our findings for different connectances between layers, numbers of species in each layer, and numbers of layers. Our work provides a general framework for investigating the stability of multi-layer ecosystems and uncovers the double-sided role of competitive interactions in the stability of multi-layer ecosystems.
Ultrasensitive capacitive sensing system for smart medical devices with ability to monitor fracture healing stages
Authors: Conceição Cassandra , Completo António , Soares dos Santos Marco P.
Published: February 2023

Bone fractures are a global public health problem. A sustained increase in the number of incident cases has been observed in the last few decades, as well as the number of prevalent cases and the number of years lived with disability. Current monitoring techniques are based on imaging techniques, which are highly subjective, radioactive, expensive and unable to provide daily monitoring of fracture healing stages. The development of reliable, non-invasive and non-subjective technologies is mandatory to minimize non-union risks. Delayed healing and non-union conditions require timely medical intervention, such that preventive procedures and shortened treatment periods can be carried out. This work proposes the development of an ultrasensitive capacitive sensing system for smart implantable fixation implants with ability to effectively monitor the evolution of bone fractures. Both
in vitro
experimental tests and numerical simulations highlight that networks of co-surface capacitive systems are able: (i) to detect four different bone healing phases, capacitance decrease patterns occurring as the healing process progresses and (ii) to monitor the callus evolution in multiple target regions. These are very promising results that highlight the potential of capacitive technologies to minimize the individual and social burdens related to fracture management, mainly when delayed healing or non-union conditions occur.
Spatial transcriptomes and microbiota reveal immune mechanism that respond to pathogen infection in the posterior intestine ofSebastes schlegelii
Authors: Cao Min , Xue Ting , Huo Huijun , Zhang Xiaoyan , Wang Ning Ning , Yan Xu , Li Chao
Published: February 2023

The intestine is a site of immune cell priming at birth. Therefore, spatial transcriptomes were performed to define how the transcriptomic landscape was spatially organized in the posterior intestine ofSebastes schlegeliifollowingEdwardsiella piscicidainfection. In the healthy condition, we identified a previously unappreciated molecular regionalization of the posterior intestine. Following bacterial infection, most immune-related genes were identified in mucosa layer. Moreover, investigation of immune-related genes and genes in immune-related KEGG pathways based on spatial transcriptomes shed light on which sections of these genes are in the posterior intestine. Meanwhile, the high expression of genes related to regeneration also indicated that the posterior intestine was responding to the invasion of pathogens by constantly proliferating new cells. In addition, the increasing microbiota communities indicated that these bacteria maintained posterior intestine integrity and shaped the mucosal immune system. Taken together, spatial transcriptomes and microbiota compositions have significant implications for understanding the immune mechanism that responds toE. piscicidainfection in the posterior intestine ofS. schlegelii, which also provides a theoretical basis for the spatial distribution of immune genes and changes in bacterial flora in other teleosts in the process of resisting pathogens.
Improving in silico prediction of influenza vaccine effectiveness by genome analysis incorporating epitope information
Authors: Cao Lirong , Lou Jingzhi , Li Qi , Zheng Hong , Mok Chris Ka Pun , Chen Zigui , Chan Renee Wan Yi , Cheung Peter Pak Hang , Chong Marc Ka Chun , Yeoh Eng Kiong , Wu William Ka Kei , Yu Jun , Chan Paul Kay Sheung , Zee Benny Chung-Ying , Wang Maggie Haitian
Published: February 2023

Fast evaluation of vaccine effectiveness (VE) is valuable for facilitating vaccine development and making vaccination strategy. In previous studies, we developed the computational model linking molecular variations and VE for the influenza and COVID-19, through which VE prediction prior to mass vaccination and infection is possible. In this study, we perform a complete survey of the predictive effect of major functional regions of the influenza virus for VE. Interestingly, we found that the genetic distance measured on the antigenic sites being also the effective mutations for epidemics is a strong predictor for influenza VE. Based on the identified optimal predictor codon set, we develop the improved VE-Genetic Distance model for influenza (VE-GD flu). The prediction accuracy of the new model is R-square 87.1% for H3N2 (p-value < 0.001) on VE data of the United States. Leave-one-out cross validation shows that the concordance correlation coefficient of the predicted and observed VE is 90.6% (95% CI: 73.8-96.9). Significant prediction improvement is also found for pH1N1. Accurate prediction of influenza VE before vaccine deployment may facilitate reverse vaccinology to optimize vaccine antigen design and government preparedness of influenza epidemics.
State switching and high-order spatiotemporal organization of dynamic Functional Connectivity are disrupted by Alzheimer’s Disease
Authors: Arbabyazd Lucas , Petkoski Spase , Breakspear Michael , Solodkin Ana , Battaglia Demian , Jirsa Viktor
Published: February 2023

Spontaneous activity during the resting state, tracked by BOLD fMRI imaging, or shortly rsfMRI, gives rise to brain-wide dynamic patterns of inter-regional correlations, whose structured flexibility relates to cognitive performance. Here we analyze resting state dynamic Functional Connectivity (dFC) in a cohort of older adults, including amnesic Mild Cognitive Impairment (aMCI,N= 34) and Alzheimer’s Disease (AD,N= 13) patients, as well as normal control (NC,N= 16) and cognitively “super-normal” (SN,N= 10) subjects. Using complementary state-based and state-free approaches, we find that resting state fluctuations of different functional links are not independent but are constrained by high-order correlations between triplets or quadruplets of functionally connected regions. When contrasting patients with healthy subjects, we find that dFC between cingulate and other limbic regions is increasingly bursty and intermittent when ranking the four groups from SNC to NC, aMCI and AD. Furthermore, regionsaffected at early stages of AD pathologyare less involved in higher-order interactions in patient than in control groups, while pairwise interactions are not significantly reduced. Our analyses thus suggest that the spatiotemporal complexity of dFC organization is precociously degraded in AD and provides a richer window into the underlying neurobiology than time-averaged FC connections.

Author Summary

Brain functions emerge from the coordinated dynamics of many brain regions. Dynamic Functional Connectivity (dFC) analyses are a key tool to describe such dynamic complexity and have been shown to be good predictors of cognitive performance. This is particularly true in the case of Alzheimer’s Disease (AD) in which an impoverished dFC could indicate compromised functional reserve due to the detrimental effects of neurodegeneration. Here we observe that in healthy ageing dFC is indeed spatiotemporally organized, as reflected by high-order correlations between multiple regions. However, in people with aMCI or AD, dFC becomes less “entangled”, more random-like, and intermittently bursty. We speculate that this degraded spatiotemporal coordination may reflect dysfunctional information processing, thus ultimately leading to worsening of cognitive deficits.
LiteRev, an Automation Tool to Support Literature Reviews: A Case Study on Acute and Early HIV Infection in Sub-Saharan Africa
Authors: Orel Erol , Ciglenecki Iza , Thiabaud Amaury , Temerev Alexander , Calmy Alexandra , Keiser Olivia , Merzouki Aziza
Published: February 2023

Background

Literature Reviews (LRs) identify, evaluate, and synthesise relevant papers to a particular research question to advance understanding and support decision making. However, LRs, especially traditional systematic reviews are slow, resource intensive, and are outdated quickly.

Objective

Using recent Natural Language Processing (NLP) and Unsupervised Machine Learning (UML) methods, this paper presents a tool named LiteRev that supports researchers in conducting LRs.

Methods

Based on the user’s query, LiteRev can perform an automated search on different open-access databases and retrieve relevant metadata on the resulting papers. Papers (abstracts or full texts) are text processed and represented as a Term Frequency-Inverse Document Frequency (TF-IDF) matrix. Using dimensionality reduction (PaCMAP) and clustering (HDBSCAN) techniques, the corpus is divided into different topics described by a list of keywords. The user can select one or several topics of interest, enter additional keywords to refine their search, or provide key papers to the research question. Based on these inputs, LiteRev performs an iterative nearest neighbours search, and suggests a list of potentially interesting papers. The user can tag the relevant ones and trigger a new search until no additional paper is suggested for screening. To assess the performance of LiteRev, we ran it in parallel to a manual LR on the burden and care for acute and early HIV infection in sub-Saharan Africa. We assessed the performance of LiteRev using True and False Predictive Values, recall and Work Saved over Sampling.

Results

We extracted, text processed and represented into a TF-IDF matrix 631 unique papers from PubMed. The topic modelling module identified 5 main topics and 16 topics (ranging from 13 to 98 papers) and extracted the 10 most important keywords for each. Then, based on 18 key papers, we were able to identify 2 topics of interest with 7 key papers in each of them. Finally, we ran the k-nearest neighbours module and LiteRev suggested first a list of 110 papers for screening, among which 45 papers were confirmed as relevant. From these 45 papers, LiteRev suggested 26 additional papers, out of which 8 were confirmed as relevant. At the end of the iterative process (4 iterations), 193 papers out of 613 papers in total (31.5% of the whole corpus) were suggested by LiteRev. After title/abstract screening, LiteRev identified 64 out of the 87 relevant papers (i.e., recall of 73.6%). After full text screening, LiteRev identified 42 out of the 48 relevant papers (i.e., recall of 87.5%, and Work Saved over Sampling of 56.0%).

Conclusions

We presented LiteRev, an automation tool that uses NLP and UML methods to streamline and accelerate LRs and to support researchers in getting quick and in-depth overviews on any topic of interest.
Splenic T follicular helper cells compromiseMycobacterium tuberculosisclearance in aged C57BL/6 mice
Authors: Pahwa Falak , Chaudhary Shweta , Chaturvedi Shivam , Nanda Ranjan Kumar
Published: February 2023

Ageing increases susceptibility to infectious diseases like tuberculosis (TB), however limited reports are available on the cellular and molecular details in aged (>60 years) patients. In this study, we asked how low aerosol dose ofMycobacterium tuberculosisH37Rv (Mtb) affects aged (17/19 months; M) C57BL/6 mice in their bacterial clearance, liver micronutrient levels, circulatory cytokines and T cell distribution compared to younger (2/4M) controls. Till 6 weeks post infection, aged mice showed similar tissue (lung, spleen, and liver) Mtb load as young mice. Interestingly, aged mice showed a delayed lung Mtb clearance at 2 weeks post rifampicin (RIF) - isoniazid (INH) treatment compared to younger mice. Aged mice showed unregulated liver Fe levels upon Mtb infection while young mice had lower Fe levels. Aged Mtb infected mice revealed a lower proportion of splenic T-follicular helper (TFH) like CD4+T cells, which provides B cell help in generating high affinity antibodies and immune memory. Aged mice had higher basal circulatory IL-6 levels. Circulatory IFN-γ levels in aged (19M) C57BL/6 mice failed to resolve upon RIF-INH treatment. Splenic CD4+CD44+T cells of aged mice showed deregulated levels of mitochondrial proteins (4-hydroxy-2-oxoglutarate aldolase and aspartate aminotransferase). Overall, while filling in knowledge gaps on the host age-related responses to Mtb infection and during treatment, this study provides new perspectives for T cell distribution and function, which opens avenue for adjunct therapeutic development for geriatric TB patients.
Advanced marker-assisted selection versus genomic selection in breeding programs
Authors: Degen Bernd , Müller Niels
Published: February 2023

Advances in DNA sequencing technologies allow the sequencing of whole genomes of thousands of individuals and provide several million single nucleotide polymorphisms (SNPs) per individual. These data combined with precise and high-throughput phenotyping enable genome-wide association studies (GWAS) and the identification of SNPs underlying traits with complex genetic architectures. The identified causal SNPs and estimated allelic effects could then be used for advanced marker-assisted selection (MAS) in breeding programs. But could such MAS compete with the broadly used genomic selection? This question is of particular interest for the lengthy tree breeding strategies. Here, with our new software SNPscan we simulated a simple tree breeding program and compared the impact of different selection criteria on genetic gain and inbreeding. Further, we assessed different genetic architectures and different levels of kinship among individuals of the breeding population. Interestingly, apart from progeny-testing, genomic selection (GS) using gBLUP performed best under almost all simulated scenarios. MAS based on GWAS results outperformed GS only if the allelic effects were estimated in large populations (ca. 10,000 individuals) of unrelated individuals. Notably, GWAS using 3,000 extreme phenotypes performed as good as the use of 10,000 phenotypes. Genomic selection increased inbreeding and thus reduced genetic diversity more strongly compared to progeny testing and GWAS-based selection. In conclusion, our analyses further support the potential of genomic selection for forest tree breeding and improvement although MAS may gain relevance with decreasing sequencing costs in the future.
Low-threshold, high-resolution, chronically stable intracortical microstimulation by ultraflexible electrodes
Authors: Lycke Roy , Kim Robin , Zolotavin Pavlo , Montes Jon , Sun Yingchu , Koszeghy Aron , Altun Esra , Noble Brian , Yin Rongkang , He Fei , Totah Nelson , Xie Chong , Luan Lan
Published: February 2023

Intracortical microstimulation (ICMS) enables applications ranging from neuroprosthetics to causal circuit manipulations. However, the resolution, efficacy, and chronic stability of neuromodulation is often compromised by the adverse tissue responses to the indwelling electrodes. Here we engineer ultraflexible stim-Nanoelectronic Threads (StimNETs) and demonstrate low activation threshold, high resolution, and chronically stable ICMS in awake, behaving mouse models.In vivotwo-photon imaging reveals that StimNETs remain seamlessly integrated with the nervous tissue throughout chronic stimulation periods and elicit stable, focal neuronal activation at low currents of 2 μA. Importantly, StimNETs evoke longitudinally stable behavioral responses for over eight months at markedly low charge injection of 0.25 nC/phase. Quantified histological analysis show that chronic ICMS by StimNETs induce no neuronal degeneration or glial scarring. These results suggest that tissue-integrated electrodes provide a path for robust, long-lasting, spatially-selective neuromodulation at low currents which lessen risks of tissue damage or exacerbation of off-target side-effects.
New insights on the genetics of hair whorls from twins and the Southern hemisphere
Authors: Willems Marjolaine , Hennocq Quentin , Cortés Santander Juan José , Khonsari Roman Hossein
Published: February 2023

The mechanisms determining the rotation direction and position of hair whorls are unknown. Here we report observations on twins suggesting that the morphological parameters of whorls have genetic bases, and provide comparative data on whorls from children born in the Northern and Southern hemispheres, indicating that whorl formation also depends on environmental factors. Our results underline the importance of unusual morphological phenomena for providing general information on normal developmental processes, and plead for large-scale epidemiological assessments to support our surprizing initial findings.
Comparison between Canine and Porcine Models of Chronic Deep Venous Thrombosis
Authors: Wang Chuang , Tang Tao , Ye Sheng-Lin , Jiang Xu-Dong , Xiang Guang-Yuan , Xiao Lun , Wang Lu-Lu , Xu Tian-Ze , Song Bin , Hu Nan , Du Xiao-Long , Li Xiao-Qiang
Published: February 2023

Venous thromboembolism(VTE) refers to deep venous thrombosis(DVT) and pulmonary embolism(PE), which is a worldwide problem and has very high morbidity and mortality. The research of venous thrombosis involves pathogenesis, pathophysiology, and therapeutic attempt. Alternative experimental animal models have changed dramatically over the past 20 years, from small murine models to large ones. Larger animal models offer more options and are more consistent with human physiology. This article aims to induce chronic deep venous thrombosis in the left iliac vein in canine and porcine models and compare these two models. We think that feasible large animal models can better translate the results of therapeutic research into clinical application.
Utilizing Pre-trained Network Medicine Models for Generating Biomarkers, Targets, Re-purposing Drugs, and Personalized Therapeutic Regimes: COVID-19 Applications
Authors: Xiong Jianghui
Published: February 2023

In this paper, we present a novel pre-trained network medicine model called Selective Remodeling of Protein Networks by Chemicals (SEMO). We divide the global human protein-protein interaction (PPI) network into smaller sub-networks, and quantify the potential effects of chemicals by statistically comparing their target and non-target gene sets. By combining 9607 PPI gene sets with 2658 chemicals, we created a pre-trained pool of SEMOs, which we then used to identify SEMOs related to Covid-19 severity using DNA methylation profiling data from two clinical cohorts. The nutraceutical-derived SEMO features provided an effective model for predicting Covid-19 severity, with an AUC score of 81% in the training data and 80% in the independent validation data. Our findings suggest that Vitamin D3, Lipoic Acid, Citrulline, and Niacin, along with their associated protein networks, particularly STAT1, MMP2, CD8A, and CXCL8 as hub nodes,could be used to effectively predict Covid-19 severity. Furthermore, the severity-associated SEMOs were found to be significantly correlated with CD4+ and monocyte cell proportions. These insights can be used to generate personalized nutraceutical regimes by ranking the relative severity risk associated with each SEMO. Thus, our pre-trained SEMO model can serve as a fundamental knowledge map when coupled with DNA methylation measurements, allowing us to simultaneously generate biomarkers, targets, re-purposing drugs, and nutraceutical interventions.
Mechanisms of Nuclear Pore Complex disassembly by the mitotic Polo-Like Kinase 1 (PLK-1) inC. elegansembryos
Authors: Nkoula Sylvia Nkombo , Velez-Aguilera Griselda , Ossareh-Nazari Batool , Hove Lucie Van , Ayuso Cristina , Legros Véronique , Chevreux Guillaume , Thomas Laura , Seydoux Géraldine , Askjaer Peter , Pintard Lionel
Published: February 2023

The nuclear envelope, which protects and organizes the interphase genome, is dismantled during mitosis. In theC. eleganszygote, nuclear envelope breakdown (NEBD) of the parental pronuclei is spatially and temporally regulated during mitosis to promote the unification of the parental genomes. During NEBD, Nuclear Pore Complex (NPC) disassembly is critical for rupturing the nuclear permeability barrier and removing the NPCs from the membranes near the centrosomes and between the juxtaposed pronuclei. By combining live imaging, biochemistry, and phosphoproteomics, we characterized NPC disassembly and unveiled the exact role of the mitotic kinase PLK-1 in this process. We show that PLK-1 disassembles the NPC by targeting multiple NPC sub-complexes, including the cytoplasmic filaments, the central channel, and the inner ring. Notably, PLK-1 is recruited to and phosphorylates intrinsically disordered regions of several multivalent linker nucleoporins, a mechanism that appears to be an evolutionarily conserved driver of NPC disassembly during mitosis. (149/150 words)

One-Sentence Summary

PLK-1 targets intrinsically disordered regions of multiple multivalent nucleoporins to dismantle the nuclear pore complexes in theC. eleganszygote.
Visual experience shapes functional connectivity between occipital and non-visual networks
Authors: Tian Mengyu , Xiao Xiang , Hu Huiqing , Cusack Rhodri , Bedny Marina
Published: February 2023

Comparisons across adults with different sensory histories (blind vs. sighted) have uncovered effects of experience on human brain function. In people born blind visual cortices are responsive to non-visual tasks and show altered functional connectivity at rest. Since almost all research has been done with adults, little is known about the developmental origins of this plasticity. Are infant visual cortices initially functionally like those of sighted adults and blindness causes reorganization? Alternatively, do infants start like blind adults, with vision required to set up the sighted pattern? To distinguish between these possibilities, we compare resting state functional connectivity across blind (n= 30) and blindfolded sighted (n= 50) adults to a large cohort of sighted infants (Developing Human Connectome Project,n= 475). Remarkably, we find that infant secondary visual cortices functionally resemble those of blind more than sighted adults, consistent with the idea that visual experience is required to set up long-range functional connectivity. Primary visual cortices show a mixture of instructive effects of vision and reorganizing effects of blindness. Specifically, in sighted adults, visual cortices show stronger functional coupling with nonvisual sensory-motor networks (i.e., auditory, somatosensory/motor) than with higher-cognitive prefrontal cortices (PFC). In blind adults, visual cortices show stronger coupling with PFC. In infants, connectivity of secondary visual cortices is stronger with PFC, while V1 shows equal sensory-motor/PFC connectivity. In contrast, lateralization of occipital-to-frontal connectivity resembles the sighted adults at birth and is reorganized by blindness, possibly due to recruitment of occipital networks for lateralized cognitive functions, such as language.
Myomatrix arrays for high-definition muscle recording
Authors: Chung Bryce , Zia Muneeb , Thomas Kyle A. , Michaels Jonathan A. , Jacob Amanda , Pack Andrea , Williams Matthew J. , Nagapudi Kailash , Teng Lay Heng , Arrambide Eduardo , Ouellette Logan , Oey Nicole , Gibbs Rhuna , Anschutz Philip , Lu Jiaao , Wu Yu , Kashefi Mehrdad , Oya Tomomichi , Kersten Rhonda , Mosberger Alice C. , O’Connell Sean , Wang Runming , Marques Hugo , Mendes Ana Rita , Lenschow Constanze , Kondakath Gayathri , Kim Jeong Jun , Olson William , Quinn Kiara N. , Perkins Pierce , Gatto Graziana , Thanawalla Ayesha , Coltman Susan , Kim Taegyo , Smith Trevor , Binder-Markey Ben , Zaback Martin , Thompson Christopher K. , Giszter Simon , Person Abigail , Goulding Martyn , Azim Eiman , Thakor Nitish , O’Connor Daniel , Trimmer Barry , Lima Susana Q. , Carey Megan R. , Pandarinath Chethan , Costa Rui M. , Pruszynski J. Andrew , Bakir Muhannad , Sober Samuel J.
Published: February 2023

Neurons coordinate their activity to produce an astonishing variety of motor behaviors. Our present understanding of motor control has grown rapidly thanks to new methods for recording and analyzing populations of many individual neurons over time. In contrast, current methods for recording the nervous system’s actual motor output – the activation of muscle fibers by motor neurons – typically cannot detect the individual electrical events produced by muscle fibers during natural behaviors and scale poorly across species and muscle groups. Here we present a novel class of electrode devices (“Myomatrix arrays”) that record muscle activity at unprecedented resolution across muscles and behaviors. High-density, flexible electrode arrays allow for stable recordings from the muscle fibers activated by a single motor neuron, called a “motor unit”, during natural behaviors in many species, including mice, rats, primates, songbirds, frogs, and insects. This technology therefore allows the nervous system’s motor output to be monitored in unprecedented detail during complex behaviors across species and muscle morphologies. We anticipate that this technology will allow rapid advances in understanding the neural control of behavior and in identifying pathologies of the motor system.
A methyl-seq tool to capture genomic imprinted loci
Authors: Jean-Noël Hubert , Nathalie Iannuccelli , Cédric Cabau , Eva Jacomet , Yvon Billon , Rémy-Felix Serre , Céline Vandecasteele , Cécile Donnadieu , Julie Demars
Published: February 2023

Genomic imprinting represents an original model of epigenetic regulation resulting in a parent-of-origin expression. Despite the critical role of imprinted genes in mammalian growth, metabolism and neuronal function, there is no molecular tool specifically targeting them for a systematic evaluation. Here, we optimized and compared to bisulfite-based standard a novel methyl-seq system to capture 165 candidate regions for genomic imprinting and ultimately detect parent-of-origin methylation, the main hallmark of imprinting.
Drug metabolic activity as a selection factor for pluripotent stem cell-derived hepatic progenitor cells
Authors: Akiyama Saeko , Saku Noriaki , Miyata Shoko , Ite Kenta , Nonaka Hidenori , Toyoda Masashi , Kamiya Akihide , Kiyono Tohru , Kimura Tohru , Kasahara Mureo , Umezawa Akihiro
Published: February 2023

As a metabolic organ, the liver plays a variety of roles, including detoxification. It has been difficult to obtain stable supplies of hepatocytes for transplantation and for accurate hepatotoxicity determination in drug discovery research. Human pluripotent stem cells, capable of unlimited self-renewal, may be a promising source of hepatocytes. In order to develop a stable supply of embryonic stem cell (ESC)-derived hepatocytes, we have purified human ESC-derived hepatic progenitor cells with exposure to cytocidal puromycin by using their ability to metabolize drugs. Hepatic progenitor cells stably proliferated at least 2^20-fold over 120 days, maintaining hepatic progenitor cell-like properties. High drug-metabolizing hepatic progenitor cells can be matured into liver cells by suppressing hepatic proliferative signals. The method we developed enables the isolation and proliferation of functional hepatic progenitors from human ESCs, thereby providing a stable supply of high-quality cell resources at high efficiency. Cells produced by this method may facilitate cell therapy for hepatic diseases and reliable drug discovery research.