bluuebunny/crossref_metadata_2025_split huggingface dataset:
The obstetric patient in the Covid pandemic: anaesthesia and perioperative care
Authors: Khan Ayub , Patrick Adam , Patil Vinod , Nnochiri Akobundu , Wijayatilake Sanjay 
Published: August 2021

Purpose of review
: The Coronavirus Disease 2019 (COVID-19) pandemic has had an unprecedented impact on pregnant women, maternity services and healthcare workers. We review recent literature on the course of COVID-19 infection in pregnancy, and recommendations for treatment and service provision.

Recent findings
It has been increasingly recognised that pregnant women are at higher risk of severe disease associated with COVID-19 infection. Early critical care input is crucial to guide respiratory support and techniques such as prone positioning, with a low threshold for intubation in critical illness. Timing of delivery remains a highly individualised decision. Following the RECOVERY trial, the use of a course of steroids in cases of severe COVID-19 infection has been widely adopted, and emerging guidance recommends vaccination in pregnant women.

Summary
Rapidly emerging evidence has helped guide clinicians to identify those patients most at risk of severe disease in COVID-19 and implement early interventions to reduce morbidity and mortality.
Obstetric venous thromboembolism prophylaxis, risk factors and outcomes
Authors: Friedman Alexander M. 
Published: August 2021

Purpose of review
Risk factors for obstetric venous thromboembolism (VTE), a leading cause of maternal mortality in the United States, are increasing on a population basis. This review provides the obstetrician with an update of current issues related to obstetric VTE risk, prophylaxis, outcomes, anaesthesia considerations and future research opportunities.

Recent findings
Obstetric VTE affects approximately 1 per 1000 pregnancies and accounts consistently for 9–10% of maternal deaths in the United States. In industrialized countries, risk factors for VTE, including overweight/obesity, caesarean delivery and obstetrical complications such postpartum haemorrhage and infection continue to increase. VTE prophylaxis is central to reducing maternal mortality. However, recommendations for prophylaxis from leadership societies vary widely. In the UK, maternal mortality risk from VTE has decreased significantly in the setting of broader heparin prophylaxis. In the United States where mechanical VTE prophylaxis is used more commonly, mortality risk has remained constant.

Summary
Obstetric VTE is a leading cause of maternal mortality in the United States. The incidence of risk factors for obstetric VTE continues to increase. Currently, recommendations for obstetric VTE prophylaxis vary substantially. Opportunities for research in this area exist to optimize prophylaxis and improve maternal outcomes.
Overview of the Pediatric Endoscopy Quality Improvement Network Quality Standards and Indicators for Pediatric Endoscopy
Authors: Walsh Catharine M. , Lightdale Jenifer R. , Mack David R. , Amil‐Dias Jorge , Bontems Patrick , Brill Herbert , Croft Nicholas M. , Fishman Douglas S. , Furlano Raoul I. , Gillett Peter M. , Hojsak Iva , Homan Matjaž , Huynh Hien Q. , Jacobson Kevan , Leibowitz Ian H. , Lerner Diana G. , Liu Quin Y. , Mamula Petar , Narula Priya , Oliva Salvatore , Riley Matthew R. , Rosh Joel R. , Tavares Marta , Utterson Elizabeth C. , Ambartsumyan Lusine , Otley Anthony R. , Kramer Robert E. , Connan Veronik , McCreath Graham A. , Thomson Mike A. ,   PEnQuIN Working Group
Published: August 2021

ABSTRACTIntroduction:Pediatric‐specific quality standards for endoscopy are needed to define best practices, while measurement of associated indicators is critical to guide quality improvement. The international Pediatric Endoscopy Quality Improvement Network (PEnQuIN) working group was assembled to develop and define quality standards and indicators for pediatric gastrointestinal endoscopic procedures through a rigorous guideline consensus process.Methods:The Appraisal of Guidelines for REsearch and Evaluation (AGREE) II instrument guided PEnQuIN members, recruited from 31 centers of various practice types representing 11 countries, in generating and refining proposed quality standards and indicators. Consensus was sought via an iterative online Delphi process, and finalized at an in‐person conference. Quality of evidence and strength of recommendations were rated according to the GRADE (Grading of Recommendation Assessment, Development, and Evaluation) approach.Results:Forty‐nine quality standards and 47 indicators reached consensus, encompassing pediatric endoscopy facilities, procedures, endoscopists, and the patient experience. The evidence base for PEnQuIN standards and indicators was largely adult‐based and observational, and downgraded for indirectness, imprecision, and study limitations to “very low” quality, resulting in “conditional” recommendations for most standards (45/49).Conclusions:The PEnQuIN guideline development process establishes international agreement on clinically meaningful metrics that can be used to promote safety and quality in endoscopic care for children. Through PEnQuIN, pediatric endoscopists and endoscopy services now have a framework for auditing, providing feedback, and ultimately, benchmarking performance. Expansion of evidence and prospective validation of PEnQuIN standards and indicators as predictors of clinically relevant outcomes and high‐quality pediatric endoscopic care is now a research priority.
Pediatric Endoscopy Quality Improvement Network Quality Standards and Indicators for Pediatric Endoscopic Procedures
Authors: Lightdale Jenifer R. , Walsh Catharine M. , Oliva Salvatore , Jacobson Kevan , Huynh Hien Q. , Homan Matjaž , Hojsak Iva , Gillett Peter M. , Furlano Raoul I. , Fishman Douglas S. , Croft Nicholas M. , Brill Herbert , Bontems Patrick , Amil‐Dias Jorge , Utterson Elizabeth C. , Tavares Marta , Rosh Joel R. , Riley Matthew R. , Narula Priya , Mamula Petar , Mack David R. , Liu Quin Y. , Lerner Diana G. , Leibowitz Ian H. , Otley Anthony R. , Kramer Robert E. , Ambartsumyan Lusine , Connan Veronik , McCreath Graham A. , Thomson Mike A. ,   PEnQuIN Working Group
Published: August 2021

ABSTRACTIntroduction:High‐quality pediatric gastrointestinal procedures are performed when clinically indicated and defined by their successful performance by skilled providers in a safe, comfortable, child‐oriented, and expeditious manner. The process of pediatric endoscopy begins when a plan to perform the procedure is first made and ends when all appropriate patient follow‐up has occurred. Procedure‐related standards and indicators developed to date for endoscopy in adults emphasize cancer screening and are thus unsuitable for pediatric medicine.Methods:With support from the North American and European Societies of Pediatric Gastroenterology Hepatology and Nutrition (NASPGHAN and ESPGHAN), an international working group of the Pediatric Endoscopy Quality Improvement Network (PEnQuIN) used the methodological strategy of the Appraisal of Guidelines for REsearch and Evaluation (AGREE) II instrument to develop standards and indicators relevant for assessing the quality of endoscopic procedures. Consensus was sought via an iterative online Delphi process and finalized at an in‐person conference. The quality of evidence and strength of recommendations were rated according to the GRADE (Grading of Recommendation Assessment, Development, and Evaluation) approach.Results:The PEnQuIN working group achieved consensus on 14 standards for pediatric endoscopic procedures, as well as 30 indicators that can be used to identify high‐quality procedures. These were subcategorized into three subdomains: Preprocedural (3 standards, 7 indicators), Intraprocedural (8 standards, 18 indicators), and Postprocedural (3 standards, 5 indicators). A minimum target for the key indicator, “rate of adequate bowel preparation,” was set at ≥80%.Discussion:It is recommended that all facilities and individual providers performing pediatric endoscopy worldwide initiate and engage with the procedure‐related standards and indicators developed by PEnQuIN to identify gaps in quality and drive improvement.
Impact of the COVID-19 Pandemic on Emergency Adult Surgical Patients and Surgical Services
Authors: Winter Beatty Jasmine , Clarke Jonathan M. , Sounderajah Viknesh , Acharya Amish , Rabinowicz Simon , Martin Guy , Warren Leigh R. , Yalamanchili Seema , Scott Alasdair J. , Burgnon Elizabeth , Purkayastha Sanjay , Markar Sheraz , Kinross James M. ,   on behalf of the PANSURG-PREDICT Collaborative∗
Published: August 2021

Objectives:
The PREDICT study aimed to determine how the COVID-19 pandemic affected surgical services and surgical patients and to identify predictors of outcomes in this cohort.

Background:
High mortality rates were reported for surgical patients with COVID-19 in the early stages of the pandemic. However, the indirect impact of the pandemic on this cohort is not understood, and risk predictors are yet to be identified.

Methods:
PREDICT is an international longitudinal cohort study comprising surgical patients presenting to hospital between March and August 2020, conducted alongside a survey of staff redeployment and departmental restructuring. A subgroup analysis of 3176 adult emergency patients, recruited by 55 teams across 18 countries is presented.

Results:
Among adult emergency surgical patients, all-cause in-hospital mortality (IHM) was 3.6%, compared to 15.5% for those with COVID-19. However, only 14.1% received a COVID-19 test on admission in March, increasing to 76.5% by July.
Higher Clinical Frailty Scale scores (CFS >7 aOR 18.87), ASA grade above 2 (aOR 4.29), and COVID-19 infection (aOR 5.12) were independently associated with significantly increased IHM.
The peak months of the first wave were independently associated with significantly higher IHM (March aOR 4.34; April aOR 4.25; May aOR 3.97), compared to non-peak months.
During the study, UK operating theatre capacity decreased by a mean of 63.6% with a concomitant 27.3% reduction in surgical staffing.

Conclusion:
The first wave of the COVID-19 pandemic significantly impacted surgical patients, both directly through co-morbid infection and indirectly as shown by increasing mortality in peak months, irrespective of COVID-19 status.
Higher CFS scores and ASA grades strongly predict outcomes in surgical patients and are an important risk assessment tool during the pandemic.
Evaluation of ChIC-based data requires normalization that properly retains signal-to-noise ratios
Authors: Liu Bofeng , Chen Fengling , Xie Wei 
Published: August 2021

AbstractSeveral chromatin immunocleavage-based (ChIC) methods using Tn5 transposase have been developed to profile histone modifications and transcription factors bindings1-5. A recent preprint by Wang et al. raised potential concerns that these methods are prone to open chromatin bias6. While the authors are appreciated for alerting the community for this issue, it has been previously described and discussed by Henikoff and colleagues in the original CUT&Tag paper3,7. However, as described for CUT&Tag3, the signal-to-noise ratio is essential for Tn5-based profiling methods and all antibody-based enrichment assays. Based on this notion, we would like to point out a major analysis issue in Wang et al. that caused a complete loss or dramatic reduction of enrichment at true targets for datasets generated by Tn5-based methods, which in turn artificially enhanced the relative enrichment of potential open chromatin bias. Such analysis issue is caused by distinct background normalizations used towards ChIP-based (chromatin immunoprecipitation) data and Tn5-based data in Wang et al. Only the normalization for Tn5-based data, but not ChIP-seq based data, yielded such effects. Distortion of such signal-to-noise ratio would consequently lead to misleading results.
Differences in working memory coding of biological motion attributed to oneself and others
Authors: Woźniak Mateusz , Schmidt Timo Torsten , Wu Yuan-hao , Blankenburg Felix , Hohwy Jakob 
Published: August 2021

AbstractThe question how the brain distinguishes between information about oneself and the rest of the world is of fundamental interest to both philosophy and neuroscience. This question can be approached empirically by investigating how associating stimuli with oneself leads to differences in neurocognitive processing. However, little is known about the brain network involved in forming such self-associations for, specifically, bodily stimuli. In this fMRI study, we sought to distinguish the neural substrates of representing a full-body movement as one’s movement and as someone else’s movement. Participants performed a delayed match-to-sample working memory task where a retained full-body movement (displayed using point-light walkers) was arbitrarily labelled as one’s own movement or as performed by someone else. By using arbitrary associations we aimed to address a limitation of previous studies, namely that our own movements are more familiar to us than movements of other people. A searchlight multivariate decoding analysis was used to test where information about types of movement and about self-association was coded. Movement specific activation patterns was found in a network of regions also involved in perceptual processing of movement stimuli, however not in early sensory regions. Information about whether a memorized movement was associated with the self or with another person was found to be coded by activity in the left middle frontal gyrus (MFG), left inferior frontal gyrus (IFG), bilateral supplementary motor area, and (at reduced threshold) in the left temporoparietal junction (TPJ). These areas are frequently reported as involved in action understanding (IFG, MFG) and domain-general self/other distinction (TPJ). Finally, in univariate analysis we found that selecting a self-associated movement for retention was related to increased activity in the ventral medial prefrontal cortex.
Clonal dynamics of haematopoiesis across the human lifespan
Authors: Mitchell Emily , Chapman Michael Spencer , Williams Nicholas , Dawson Kevin , Mende Nicole , Calderbank Emily F , Jung Hyunchul , Mitchell Thomas , Coorens Tim , Spencer David , Machado Heather , Lee-Six Henry , Davies Megan , Hayler Daniel , Fabre Margarete , Mahbubani Krishnaa , Abascal Fede , Cagan Alex , Vassiliou George , Baxter Joanna , Martincorena Inigo , Stratton Michael R , Kent David , Chatterjee Krishna , Parsy Kourosh Saeb , Green Anthony R , Nangalia Jyoti , Laurenti Elisa , Campbell Peter J 
Published: August 2021

AbstractAge-related change in human haematopoiesis causes reduced regenerative capacity1, cytopenias2, immune dysfunction3 and increased risk of blood cancer. The cellular alterations that underpin the abruptness of this functional decline after the age of 70 years remain elusive. We sequenced 3579 genomes from single-cell-derived colonies of haematopoietic stem cell/multipotent progenitors (HSC/MPPs) across 10 haematologically normal subjects aged 0-81 years. HSC/MPPs accumulated 17 mutations/year after birth and lost 30bp/year of telomere length. Haematopoiesis in adults aged <65 was massively polyclonal, with high indices of clonal diversity and a stable population of 20,000–200,000 HSC/MPPs contributing evenly to blood production. In contrast, haematopoiesis in individuals aged >75 showed profoundly decreased clonal diversity. In each elderly subject, 30-60% of haematopoiesis was accounted for by 12-18 independent clones, each contributing 1-34% of blood production. Most clones had begun their expansion before age 40, but only 22% had known driver mutations. Genome-wide selection analysis estimated that 1/34 to 1/12 non-synonymous mutations were drivers, occurring at a constant rate throughout life, affecting a wider pool of genes than identified in blood cancers. Loss of Y chromosome conferred selective benefits on HSC/MPPs in males. Simulations from a simple model of haematopoiesis, with constant HSC population size and constant acquisition of driver mutations conferring moderate fitness benefits, entirely explained the abrupt change in clonal structure in the elderly. Rapidly decreasing clonal diversity is a universal feature of haematopoiesis in aged humans, underpinned by pervasive positive selection acting on many more genes than currently identified.
AMPing up the search: An in silico approach to identifying Antimicrobial Peptides (AMPs) with potential anti-biofilm activity
Authors: Mhade Shreeya , Panse Stutee , Tendulkar Gandhar , Awate Rohit , Kadam Snehal , Kaushik Karishma S 
Published: August 2021

AbstractAntibiotic resistance is a public health threat, and the rise of multidrug-resistant bacteria, including those that form protective biofilms, further compounds this challenge. Antimicrobial peptides (AMPs) have been recognized for their anti-infective properties, including their ability to target processes important for biofilm formation. However, given the vast array of natural and synthetic AMPs, determining potential candidates for anti-biofilm testing is a significant challenge. In this study, we present an in silico approach, based on open-source tools, to identify AMPs with potential anti-biofilm activity. This approach is developed using the sortase-pilin machinery, important for adhesion and biofilm formation, of the multidrug-resistant, biofilm-forming pathogen C. striatum as the target. Using homology modeling, we modeled the structure of the C. striatum sortase C protein, resembling the semi-open lid conformation adopted during pilus biogenesis. Next, we developed a structural library of 5544 natural and synthetic AMPs from sequences in the DRAMP database. From this library, AMPs with known anti-Gram positive activity were filtered, and 100 select AMPs were evaluated for their ability to interact with the sortase C protein using in-silico molecular docking. Based on interacting residues and docking scores, we built a preference scale to categorize candidate AMPs in order of priority for future in vitro and in vivo biofilm studies. The considerations and challenges of our approach, and the resources developed, which includes a search-enabled repository of predicted AMP structures and protein-peptide interaction models relevant to biofilm studies (B-AMP), can be leveraged for similar investigations across other biofilm targets and biofilm-forming pathogens.
Hierarchical Bayesian models of transcriptional and translational regulation processes with delays
Authors: Cortez Mark Jayson , Hong Hyukpyo , Choi Boseung , Kim Jae Kyoung , Josić Krešimir 
Published: August 2021

AbstractMotivationSimultaneous recordings of gene network dynamics across large populations have revealed that cell characteristics vary considerably even in clonal lines. Inferring the variability of parameters that determine gene dynamics is key to understanding cellular behavior. However, this is complicated by the fact that the outcomes and effects of many reactions are not observable directly. Unobserved reactions can be replaced with time delays to reduce model dimensionality and simplify inference. However, the resulting models are non-Markovian, and require the development of new inference techniques.ResultsWe propose a non-Markovian, hierarchical Bayesian inference framework for quantifying the variability of cellular processes within and across cells in a population. We illustrate our approach using a delayed birth-death process. In general, a distributed delay model, rather than a popular fixed delay model, is needed for inference, even if only mean reaction delays are of interest. Using in silico and experimental data we show that the proposed hierarchical framework is robust and leads to improved estimates compared to its non-hierarchical counterpart. We apply our method to data obtained using time-lapse microscopy and infer the parameters that describe the dynamics of protein production at the single cell and population level. The mean delays in protein production are larger than previously reported, have a coefficient of variation of around 0.2 across the population, and are not strongly correlated with protein production or growth rates.AvailabilityAccompanying code in Python is available at https://github.com/mvcortez/Bayesian-Inference.Contactkresimir.josic@gmail.comkresimir.josic@gmail.com, jaekkim@kaist.ac.krjaekkim@kaist.ac.kr, cbskust@korea.ac.krcbskust@korea.ac.kr
SemiBin: Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs)
Authors: Pan Shaojun , Zhu Chengkai , Zhao Xing-Ming , Coelho Luis Pedro 
Published: August 2021

ABSTRACTMetagenomic binning is the step in building metagenome-assembled genomes (MAGs) when sequences predicted to originate from the same genome are automatically grouped together. The most widely-used methods for binning are reference-independent, operating de novo and allow the recovery of genomes from previously unsampled clades. However, they do not leverage the knowledge in existing databases. Here, we propose SemiBin, an open source tool that uses neural networks to implement a semi-supervised approach, i.e. SemiBin exploits the information in reference genomes, while retaining the capability of binning genomes that are outside the reference dataset. SemiBin outperforms existing state-of-the-art binning methods in simulated and real microbiome datasets across three different environments (human gut, dog gut, and marine microbiomes). SemiBin returns more high-quality bins with larger taxonomic diversity, including more distinct genera and species. SemiBin is available as open source software at https://github.com/BigDataBiology/SemiBin/.
Bias in miRNA enrichment analysis related to gene functional annotations
Authors: Zagganas Konstantinos , Vergoulis Thanasis , Georgakilas Georgios K. , Skiadopoulos Spiros , Dalamagas Theodore 
Published: August 2021

AbstractBackgroundmiRNA functional enrichment is a type of analysis that is used to predict which biological functions may be affected by a group of miRNAs or validate whether a list of dysregulated miRNAs are linked to a diseased state. The standard method for functional enrichment analysis uses the hypergeometric distribution to produce p-values, depicting the strength of the association between a group of miRNAs and a biological function. However, in 2015, it was shown that this approach suffers from a bias related to miRNA targets produced by target prediction algorithms and a new randomization test was proposed to alleviate this issue.ResultsWe demonstrate the existence of another previously unreported underlying bias which affects gene annotation data sets; additionally, we show that the statistical measure used for the established randomization test is not sensitive enough to account for it. In this context, we show that the use of Jaccard coefficient (an alternative statistical measure) is able to alleviate the aforementioned issue.ConclusionsIn this paper, we illustrate the existence of a new bias affecting the miRNA functional enrichment analysis. This bias makes Fisher’s exact test unsuitable for miRNA functional enrichment analyses and there is also a need to adjust the established unbiased test accordingly. We propose the use of a modified version of the established test and in order to facilitate its use, we introduce a novel unbiased miRNA enrichment analysis tool that implements the proposed method. At the same time, by leveraging bit vectors, our tool guarantees fast and scalable execution.AvailabilityAll datasets used in the experiments throughout this paper are openly accessible on Zenodo (https://doi.org/10.5281/zenodo.5175819).