bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flap Closure of Spinal Defects in High-Risk Patients
Authors: Kenny Elizabeth M. , James Isaac B. , Bengür Fuat Barış , Zammerilla Lauren L. , Manders Ernest K. , Russavage James M. , Acartürk Tahsin Oğuz 
Published: April 2021

Background
Complication rates after spinal surgery are high, in part because of surgical advancements that have made procedures available to a broader range of medically complicated patients. The high rates of infection, hematoma, and dehiscence resulting in open wounds after spinal surgery often warrant plastic surgery involvement. In this study, we aim to examine the effects of preoperative and operative risk factors on complication rates, reoperation rates, and hospital length of stay after flap reconstruction of spinal defects.

Methods
A retrospective review was performed of 373 patients who required flap reconstruction for spinal wound closure at our institution between 2003 and 2013. Data regarding demographics, comorbidities, operative variables, and postreconstructive course were collected.

Results
Of the 373 patients, 97.3% had at least 1 comorbid condition associated with poor wound healing, 91.2% had a significant wound condition at the time of reconstruction, and 81.8% had a history of 2 or more spinal surgeries. After reconstruction, average hospital stay was 14 days, with 35% of patients developing complications and 30% requiring reoperation. Risk factors including elevated body mass index, diabetes, tobacco use, steroid use, low prealbumin level, therapeutic anticoagulation, infection, history of spine surgery, multilevel spinal reconstruction, and spinal hardware were associated with complications, reoperations, and prolonged length of stay.

Conclusions
Local muscle flap coverage is an effective strategy for the reconstruction of spinal defects in medically complex patients. To reduce the inherently high risks associated with paraspinous reconstruction in this challenging population, special consideration should be given to preoperative and operative variables associated with poor outcomes. Early coordination between spine and plastic surgeons should be considered in patients at high-risk of wound complications.
Structured illumination microscopy artefacts caused by illumination scattering
Authors: Mo Yanquan , Feng Fan , Mao Heng , Fan Junchao , Chen Liangyi 
Published: April 2021

Despite its wide application in live-cell super-resolution (SR) imaging, structured illumination microscopy (SIM) suffers from aberrations caused by various sources. Although artefacts generated from inaccurate reconstruction parameter estimation and noise amplification can be minimized, aberrations due to the scattering of excitation light on samples have rarely been investigated. In this paper, by simulating multiple subcellular structure with the distinct refractive index from water, we study how different thicknesses of this subcellular structure scatter incident light on its optical path of SIM excitation. Because aberrant interference light aggravates with the increase in sample thickness, the reconstruction of the 2D-SIM SR image degraded with the change of focus along the axial axis. Therefore, this work may guide the future development of algorithms to suppress SIM artefacts caused by scattering in thick samples.
This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 1)'.
mmSIM: an open toolbox for accessible structured illumination microscopy
Authors: Russell Craig T. , Shaw Michael 
Published: April 2021

Since the first practical super-resolution structured illumination fluorescence microscopes (SIM) were demonstrated more than two decades ago, the method has become increasingly popular for a wide range of bioimaging applications. The high cost and relative inflexibility of commercial systems, coupled with the conceptual simplicity of the approach and the desire to exploit and customize existing hardware, have led to the development of a large number of home-built systems. Several detailed hardware designs are available in the scientific literature, complemented by open-source software tools for SIM image validation and reconstruction. However, there remains a lack of simple open-source software to control these systems and manage the synchronization between hardware components, which is critical for effective SIM imaging. This article describes a new suite of software tools based on the popular Micro-Manager package, which enable the keen microscopist to develop and run a SIM system. We use the software to control two custom-built, high-speed, spatial light modulator-based SIM systems, evaluating their performance by imaging a range of fluorescent samples. By simplifying the process of SIM hardware development, we aim to support wider adoption of the technique.
This article is part of the Theo Murphy meeting issue ‘Super-resolution structured
illumination microscopy (part 1)’.
Genetic determinants of interventricular septal anatomy and the risk of ventricular septal defects and hypertrophic cardiomyopathy
Authors: Yu Mengyao , Harper Andrew R. , Aguirre Matthew , Pittman Maureen , Tcheandjieu Catherine , Amgalan Dulguun , Grace Christopher , Goel Anuj , Farrall Martin , Xiao Ke , Engreitz Jesse , Pollard Katherine , Watkins Hugh , Priest James R. 
Published: April 2021

ABSTRACTBackgroundThe interventricular septum (IVS) plays a primary role in cardiovascular physiology and a large proportion of genetic risk remains unexplained for structural heart disease involving the IVS such as hypertrophic cardiomyopathy (HCM) and ventricular septal defects (VSD).ObjectivesWe sought to develop a reproducible proxy of IVS structure from standard medical imaging, discover novel genetic determinants of IVS structure, and relate these loci to two rare diseases of the IVS.MethodsWe performed machine learning to estimate the cross-sectional area of the interventricular septum (IVS.csad) obtained from the 4-chamber view of cardiac MRI in 32,219 individuals from the UK Biobank. Using these extracted measurement of IVS.csad we performed phenome-wide association to relate this proxy measure to relevant clinical phenotypes, followed by genome-wide association studies and Mendelian Randomization.ResultsAutomated measures of IVS.csad were highly accurate, and strongly correlated with anthropometric measures, blood pressure, and diagnostic codes related to cardiovascular physiology. A Single nucleotide polymorphism in the intron ofCDKN1Awas associated with IVS.csad (rs2376620, Beta 8.4 mm2, 95% confidence intervals (CI) 5.8 to 11.0, p=2.0e-10), and a common inversion incorporatingKANSL1predicted to disrupt local chromatin structure was associated with an increase in IVS.csad (Beta 8.6 mm2, 95% CI 6.3-10.9, p=1.3e-13). Mendelian Randomization suggested that inheritance of a larger IVS.csad was causal for HCM (Beta 2.45 log odds ratio (OR) HCM per increase in SD of IVS.csad, standard error (SE) 0.48, pIVW = 2.8e-7) while inheritance of a smaller IVS.csad was causal for VSD (Beta −2.06 log odds ratio (OR) VSD per decrease in SD of IVS.csad, SE 0.75, pIVW = 0.006)ConclusionAutomated derivation of the cross sectional area of the IVS from the 4-chamber view allowed discovery of loci mapping to genes related to cardiac development and Mendelian disease. Inheritance of a genetic liability for either large or small interventricular septum, appears to confer risk for HCM or VSD respectively, which suggests that a considerable proportion of risk for structural and congenital heart disease may be localized to the common genetic determinants of cardiovascular anatomy.
Stress and Depression in the Workplace of Educators in the Philippines
Authors: Orlanda-Ventayen Caren Casama , Ventayen Randy Joy Magno 
Published: April 2021

AbstractWorkplace Stress and depression should be treated properly in order to maintain productive teaching as the noblest profession. Unmanaged stress and depression could lead to a serious outcome that affects the happy environment in the classroom. Thus, managing stress and avoiding depression in the workplace is one of the important situations that a teacher should aim in order to succeed. This study aims to determine the level of workplace stress and depression of the educators in the Philippines by gathering their profile, workplace stress, and the state of depression. A correlation was investigated if there is a significant difference in the profile to the workplace stress and state of depression. Based on the result of the study, teachers sometimes experience stress in the workplace, while some experience depression at some point in time. It is recommended that teachers should understand how to practice stress management and avoiding depression.
Learning from the resilience of hospitals and their staff to the COVID-19 pandemic: a scoping review
Authors: Traverson Lola , Stennett Jack , Mathevet Isadora , Zacarias Amanda Correia Paes , de Sousa Karla Paz , Andrade Andrea , Zinszer Kate , Ridde Valéry 
Published: April 2021

AbstractBackgroundThe COVID-19 pandemic has brought huge strain on hospitals worldwide. It is crucial that we gain a deeper understanding of hospital resilience in this unprecedented moment. This paper aims to report the key strategies and recommendations in terms of hospitals and professionals’ resilience to the COVID-19 pandemic, as well as the quality and limitations of research in this field at present.MethodsWe conducted a scoping review of evidence on the resilience of hospitals and their staff during the COVID-19 crisis in the first half of 2020. The Stephen B. Thacker CDC Library website was used to identify papers meeting the eligibility criteria, from which we selected 65 publications. After having extracted data, we presented the results synthesis using an “effects-strategies-impacts” resilience framework.ResultsWe found a wealth of research rapidly produced in the first half of 2020, describing different strategies used to improve hospitals’ resilience, particularly in terms of 1) planning, management, and security, and 2) human resources. Research focuses mainly on interventions related to healthcare workers’ well-being and mental health, protection protocols, space reorganization, personal protective equipment and resources management, work organization, training, e-health and the use of technologies. Hospital financing, information and communication, and governance were less represented in the literature.ConclusionThe selected literature was dominated by quantitative descriptive case studies, sometimes lacking consideration of methodological limitations. The review revealed a lack of holistic research attempting to unite the topics within a resilience framework. Research on hospitals resilience would benefit from a greater range of analysis to draw more nuanced and contextualized lessons from the multiple specific responses to the crisis. We identified key strategies on how hospitals maintained their resilience when confronted with the COVID-19 pandemic and a range of recommendations for practice.
NeMoR: a New Method Based on Data-Driven for Neonatal Mortality Rate Forecasting
Authors: Beluzo Carlos Eduardo , Alves Luciana Correia , Arruda Natália Martins , Sepetauskas Cátia , Silva Everton , Carvalho Tiago 
Published: April 2021

ABSTRACTReduction in child mortality is one of the United Nations Sustainable Development Goals for 2030. In Brazil, despite recent reduction in child mortality in the last decades, the neonatal mortality is a persistent problem and it is associated with the quality of prenatal, childbirth care and social-environmental factors. In a proper health system, the effect of some of these factors could be minimized by the appropriate number of newborn intensive care units, number of health care units, number of neonatal incubators and even by the correct level of instruction of mothers, which can lead to a proper care along the prenatal period. With the intent of providing knowledge resources for planning public health policies focused on neonatal mortality reduction, we propose a new data-driven machine leaning method forNeonatalMortalityRate forecasting calledNeMoR, which predicts neonatal mortality rates for 4 months ahead, usingNeoDeathForecast, a monthly base time series dataset composed by these factors and by neonatal mortality rates history (2006-2016), having 57,816 samples, for all 438 Brazilian administrative health regions. In order to build the model, Extra-Tree, XGBoost Regressor, Gradient Boosting Regressor and Lasso machine learning regression models were evaluated and a hyperparameters search was also performed as a fine tune step. The method has been validated using São Paulo city data, mainly because of data quality. On the better configuration the method predicted the neonatal mortality rates with a Mean Square Error lower than 0.18. Besides that, the forecast results may be useful as it provides a way for policy makers to anticipate trends on neonatal mortality rates curves, an important resource for planning public health policies.Graphical AbstractHighlightsProposition of a new data-driven approach for neonatal mortality rate forecast, which provides a way for policy-makers to anticipate trends on neonatal mortality rates curves, making a better planning of health policies focused on NMR reduction possible;a method for NMR forecasting with a MSE lower than 0.18;an extensive evaluation of different Machine Learning (ML) regression models, as well as hyperparameters search, which accounts for the last stage in NeMoR;a new time series database for NMR prediction problems;a new features projection space for NMR forecasting problems, which considerably reduces errors in NRM prediction.
Role of non-aerosols activities in the transmission of SARS-Cov-2 infection among health care workers
Authors: Paris Christophe , Tadié Emilie , Heslan Christopher , Gary-Bobo Pierre , Oumary Sitty , Sitruk Anaïs , Wild Pascal , Tattevin Pierre , Thibault Vincent , Garlantezec Ronan 
Published: April 2021

AbstractBackgroundSince the emergence of SARS-CoV-2, health care workers (HCWs) have been on the front line in caring for COVID-19 patients. Better knowledge of risk factors for SARS-CoV-2 infection is crucial for the prevention of disease among this population.MethodsWe conducted a seroprevalence survey among HCWs in a French university hospital after the first wave (May-June 2020), based on a validated lateral flow immuno-assay test (LFIAT) for SARS-CoV-2. Demographic characteristics as well as data on the working characteristics of COVID-19 and non-COVID-19 wards and 23 care activities were systematically recorded. The effectiveness of protective equipment was also estimated, based on self-declaration of mask use. SARS-CoV-2 IgG status was modelled by multiple imputations approach, accounting for the performance of the test and data on serum validation ELISA immunoassay.FindingsAmong the 3,234 enrolled HCWs, the prevalence of SARS-CoV-2 IgG was 3.8%. Contact with relatives or HCWs who developed COVID-19 were risk factors for SARS-CoV-2 infection, but not contact with COVID-19 patients. In multivariate analyses, suboptimal use of protective equipment during naso-pharyngeal sampling, patient mobilisation, clinical and eye examination was associated with SARS-CoV-2 infection. In addition, patients washing and dressing and aerosol-generating procedures were risk factors for SARS-CoV-2 infection with or without self-declared appropriate use of protective equipment.InterpretationMain routes of transmission of SARS-CoV-2 IgG among HCWs were i) contact with relatives or HCWs with COVID-19, ii) close or prolonged contact with patients, iii) aerosol-generating procedures.
Selective attention is insensitive to reward and to dopamine in Parkinson’s disease
Authors: Pilgrim Matthew , Andy Ou Zhen-Yi , Sharp Madeleine 
Published: April 2021

AbstractPatients with Parkinson’s disease exhibit reduced reward sensitivity in addition to early cognitive deficits, among which attention impairments are common. Attention allocation is controlled at multiple levels and recent work has shown that reward, in addition to its role in the top-down goal-directed control of attention, also guides the automatic allocation of attention resources, a process thought to rely on striatal dopamine. Whether Parkinson’s patients, due to their striatal dopamine loss, suffer from an inability to use reward information to guide the allocation of their attention is unknown. To address this question, we tested Parkinson’s patients (n=43) ON and OFF their dopaminergic medication, and compared them to a group of older controls (n=31). We used a standard two-phase attention capture task in which subjects were first implicitly trained to make colour-reward associations. In the second phase, the previously reward-associated colours were used as distractors in a visual search task. We found that patients did not use reward information to modulate their attention; they were similarly distracted by the presence of low and high-reward distractors. However, contrary to our predictions, we did not find evidence that dopamine modulated this inability to use reward to guide attention allocation. Additionally, we found slightly increased overall distractibility in Parkinson’s patients compared to older controls, but interestingly, the degree of distractibility was not influenced by dopamine replacement. Our results suggest that loss of reward-guided attention allocation may contribute to early attention deficits and raise the possibility that this inability to prioritize cognitive resource allocation could contribute to executive deficits more broadly in Parkinson’s disease.
Effects of high dosage methamphetamine on glutamatergic neurotransmission in the nucleus accumbens and prefrontal cortex
Authors: Mishra Devesh , Pena-Bravo Jose I , Ghee Shannon M , Berini Carole , Reichel Carmela M , Lavin Antonieta 
Published: April 2021

AbstractRationaleMethamphetamine (METH) induces changes in the glutamatergic system and elicits cellular alterations in the cortico-accumbens circuit.ObjectiveWhile there is a body of literature on the effects of METH on dopaminergic transmission, there is a gap in knowledge regarding the effects of a high dose of METH on synaptic glutamatergic neurotransmission, specifically in brain regions involved in goal directed behavior (nucleus accumbens core; NAc core) and executive functions (prefrontal cortex;PFC).MethodsIn order to fill that gap we assessed synaptic glutamatergic transmission using a well established METH administration regime (4 × 4 mg/kg ip at 2 hr intervals) followed by 7 days of abstinence. Rats were then sacrificed and whole cell and field recordings were performed in the NAc core and medial PFC.ResultsMETH treatment elicited a significant decrease in paired pulse ratio in NAc core and a significant increase in AMPA/NMDA ratio driven by increases in AMPA currents. On the other hand, there were no significant changes in measures of synaptic glutamate in the PFC.ConclusionThese results suggest that a high dose of METH treatment followed by a period of abstinence elicits significant increases in indices of glutamatergic transmission in the NAc core with no detectable changes in mPFC, denoting that neurons and glutamate terminals in this limbic region have a higher susceptibility to a neurotoxic METH regime.
Predicting functional effect of missense variants using graph attention neural networks
Authors: Zhang Haicang , Xu Michelle S. , Chung Wendy K. , Shen Yufeng 
Published: April 2021

AbstractAccurate prediction of damaging missense variants is critically important for interpreting genome sequence. While many methods have been developed, their performance has been limited. Recent progress in machine learning and availability of large-scale population genomic sequencing data provide new opportunities to significantly improve computational predictions. Here we describe gMVP, a new method based on graph attention neural networks. Its main component is a graph with nodes capturing predictive features of amino acids and edges weighted by coevolution strength, which enables effective pooling of information from local protein context and functionally correlated distal positions. Evaluated by deep mutational scan data, gMVP outperforms published methods in identifying damaging variants inTP53, PTEN, BRCA1, andMSH2. Additionally, it achieves the best separation ofde novomissense variants in neurodevelopmental disorder cases from the ones in controls. Finally, the model supports transfer learning to optimize gain- and loss-of-function predictions in sodium and calcium channels. In summary, we demonstrate that gMVP can improve interpretation of missense variants in clinical testing and genetic studies.
Prefusion conformation of SARS-CoV-2 receptor-binding domain favours interactions with human receptor ACE2
Authors: Kumawat Nitesh , Tucs Andrejs , Bera Soumen , Chuev Gennady N. , Fedotova Marina V. , Tsuda Koji , Kruchinin Sergey E. , Sljoka Adnan , Chakraborty Amit 
Published: April 2021

ABSTRACTA new coronavirus pandemic COVID-19, caused by Severe Acute Respiratory Syndrome coronavirus (SARS-CoV-2), poses a serious threat across continents, leading the World Health Organization to declare a Public Health Emergency of International Concern. In order to block the entry of the virus into human host cells, major therapeutic and vaccine design efforts are now targeting the interactions between the SARS-CoV-2 spike (S) glycoprotein and the human cellular membrane receptor angiotensin-converting enzyme, hACE2. By analyzing cryo-EM structures of SARS-CoV-2 and SARS-CoV-1, we report here that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) that binds with hACE2 has expanded in size, undergoing a large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits higher intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction has caused a significant structural rigidification, favoring proteolytic processing of S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification in the RBD dynamics and their likely impact on infectivity.