bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fijiyama: a registration tool for 3D multimodal time-lapse imaging
Authors: Fernandez Romain , Moisy Cédric 
Published: September 2020

Abstract

Summary
The increasing interest of animal and plant research communities for biomedical 3D imaging devices results in the emergence of new topics. The anatomy, structure and function of tissues can be observed non-destructively in time-lapse multimodal imaging experiments by combining the outputs of imaging devices such as X-ray CT and MRI scans. However, living samples cannot remain in these devices for a long period. Manual positioning and natural growth of the living samples induce variations in the shape, position and orientation in the acquired images that require a preprocessing step of 3D registration prior to analyses. This registration step becomes more complex when combining observations from devices that highlight various tissue structures. Identifying image invariants over modalities is challenging and can result in intractable problems. Fijiyama, a Fiji plugin built upon biomedical registration algorithms, is aimed at non-specialists to facilitate automatic alignment of 3D images acquired either at successive times and/or with different imaging systems. Its versatility was assessed on four case studies combining multimodal and time series data, spanning from micro to macro scales.

Availability and implementation
Fijiyama is an open source software (GPL license) implemented in Java. The plugin is available through the official Fiji release. An extensive documentation is available at the official page: https://imagej.github.io/Fijiyama

Supplementary information
Supplementary data are available at Bioinformatics online.
Does it feel right?—Emotional and embodied processes as a ‘shadowy epistemology’ in difficult child protection cases
Authors: Bjerre Line Søberg , Nissen Maria Appel 
Published: September 2020

Abstract
Social workers in child protection services must make difficult decisions often based on fragmented knowledge and the inevitable risk of not knowing what is important to know about a child and the family. Cases of severe neglect have been subject to public attention of politicians and media in several European countries often followed by reforms with a strong focus on standardising risk assessment and documentation. This article argues and shows that emotional and embodied processes are an important source of knowledge in child protection. Such processes appear in social workers’ narratives about worries for the well-being and security of children underpinned by moments of silence and symbolic bodily utterances. These ways of communicating emotions help social workers navigate and make sense in child protection cases, where knowledge is limited. The question ‘Does it feel right?’ becomes crucial in terms of identifying and expressing potential risks. However, as a legitimate professional question that can lead to valuable knowledge it remains latent. Therefore, emotional and embodied processes constitute a ‘shadowy epistemology’ (Bruner, J. (1991) ‘The narrative construction of reality’, Critical Inquiry, 18(1), pp. 1–21). Instead of denouncing these processes, we need to develop a professional language of understanding and naming them, and the aim of this article is to contribute to this.
A novel RFC1 repeat motif (ACAGG) in two Asia-Pacific CANVAS families
Authors: Scriba Carolin K , Beecroft Sarah J , Clayton Joshua S , Cortese Andrea , Sullivan Roisin , Yau Wai Yan , Dominik Natalia , Rodrigues Miriam , Walker Elizabeth , Dyer Zoe , Wu Teddy Y , Davis Mark R , Chandler David C , Weisburd Ben , Houlden Henry , Reilly Mary M , Laing Nigel G , Lamont Phillipa J , Roxburgh Richard H , Ravenscroft Gianina 
Published: September 2020

Abstract
Cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) is a progressive late-onset, neurological disease. Recently, a pentanucleotide expansion in intron 2 of RFC1 was identified as the genetic cause of CANVAS. We screened an Asian-Pacific cohort for CANVAS and identified a novel RFC1 repeat expansion motif, (ACAGG)exp, in three affected individuals. This motif was associated with additional clinical features including fasciculations and elevated serum creatine kinase. These features have not previously been described in individuals with genetically-confirmed CANVAS. Haplotype analysis showed our patients shared the same core haplotype as previously published, supporting the possibility of a single origin of the RFC1 disease allele. We analysed data from &gt;26 000 genetically diverse individuals in gnomAD to show enrichment of (ACAGG) in non-European populations.
Local sleep-like cortical reactivity in the awake brain after focal injury
Authors: Sarasso Simone , D’Ambrosio Sasha , Fecchio Matteo , Casarotto Silvia , Viganò Alessandro , Landi Cristina , Mattavelli Giulia , Gosseries Olivia , Quarenghi Matteo , Laureys Steven , Devalle Guya , Rosanova Mario , Massimini Marcello 
Published: September 2020

Abstract
The functional consequences of focal brain injury are thought to be contingent on neuronal alterations extending beyond the area of structural damage. This phenomenon, also known as diaschisis, has clinical and metabolic correlates but lacks a clear electrophysiological counterpart, except for the long-standing evidence of a relative EEG slowing over the injured hemisphere. Here, we aim at testing whether this EEG slowing is linked to the pathological intrusion of sleep-like cortical dynamics within an awake brain. We used a combination of transcranial magnetic stimulation and electroencephalography (TMS/EEG) to study cortical reactivity in a cohort of 30 conscious awake patients with chronic focal and multifocal brain injuries of ischaemic, haemorrhagic and traumatic aetiology. We found that different patterns of cortical reactivity typically associated with different brain states (coma, sleep, wakefulness) can coexist within the same brain. Specifically, we detected the occurrence of prominent sleep-like TMS-evoked slow waves and off-periods—reflecting transient suppressions of neuronal activity—in the area surrounding focal cortical injuries. These perilesional sleep-like responses were associated with a local disruption of signal complexity whereas complex responses typical of the awake brain were present when stimulating the contralesional hemisphere. These results shed light on the electrophysiological properties of the tissue surrounding focal brain injuries in humans. Perilesional sleep-like off-periods can disrupt network activity but are potentially reversible, thus representing a principled read-out for the neurophysiological assessment of stroke patients, as well as an interesting target for rehabilitation.
Infant Outcomes Following Maternal Infection With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): First Report From the Pregnancy Coronavirus Outcomes Registry (PRIORITY) Study
Authors: Flaherman Valerie J , Afshar Yalda , Boscardin W John , Keller Roberta L , H Mardy Anne , Prahl Mary K , T Phillips Carolyn , Asiodu Ifeyinwa V , Berghella Vincenzo , Chambers Brittany D , Crear-Perry Joia , Jamieson Denise J , Jacoby Vanessa L , Gaw Stephanie L 
Published: September 2020

Abstract
Infant outcomes after maternal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are not well described. In a prospective US registry of 263 infants, maternal SARS-CoV-2 status was not associated with birth weight, difficulty breathing, apnea, or upper or lower respiratory infection through 8 weeks of age.
The Impact of Sociodemographic Factors, Comorbidities, and Physiologic Responses on 30-Day Mortality in Coronavirus Disease 2019 (COVID-19) Patients in Metropolitan Detroit
Authors: Miller Joseph , Fadel Raef A , Tang Amy , Perrotta Giuseppe , Herc Erica , Soman Sandeep , Nair Sashi , Hanna Zachary , Zervos Marcus J , Alangaden George , Brar Indira , Suleyman Geehan 
Published: September 2020

Abstract

Background
The relationship of health disparities and comorbidities in coronavirus disease 2019 (COVID-19)–related outcomes are an ongoing area of interest. This report assesses risk factors associated with mortality in patients presenting with COVID-19 infection and healthcare disparities.

Methods
We conducted a retrospective cohort study of consecutive patients presenting to emergency departments within an integrated health system who tested positive for COVID-19 between 7 March and 30 April 2020 in metropolitan Detroit. The primary outcomes were hospitalization and 30-day mortality.

Results
A total of 3633 patients with a mean age of 58 years were included. The majority were female and Black non-Hispanic. Hospitalization was required for 64% of patients, 56% of whom were Black. Hospitalized patients were older, more likely to reside in a low-income area, and had a higher burden of comorbidities. By 30 days, 433 (18.7%) hospitalized patients died. In adjusted analyses, the presence of comorbidities, an age &gt;60 years, and more severe physiological disturbance were associated with 30-day mortality. Residence in low-income areas (odds ratio [OR], 1.02; 95% confidence interval [CI], .76–1.36) and public insurance (OR, 1.24; 95% CI, .76–2.01) were not independently associated with a higher risk of mortality. Black female patients had a lower adjusted risk of mortality (OR, 0.46; 95% CI, .27–.78).

Conclusions
In this large cohort of COVID-19 patients, those with comorbidities, advanced age, and physiological abnormalities on presentation had higher odds of death. Disparities in income or source of health insurance were not associated with outcomes. Black women had a lower risk of dying.
Whole-genome Sequencing to Track Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission in Nosocomial Outbreaks
Authors: Lucey Mary , Macori Guerrino , Mullane Niamh , Sutton-Fitzpatrick Una , Gonzalez Gabriel , Coughlan Suzie , Purcell Aisling , Fenelon Lynda , Fanning Séamus , Schaffer Kirsten 
Published: September 2020

Abstract

Background
During the first wave of the coronavirus disease 2019 (COVID-19) pandemic, outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare institutions posed a significant problem. Due to limited evidence, guidance on appropriate infection prevention and control (IPC) measures such as the wearing of face masks varied. Here, we applied whole virus genome sequencing (WvGS) to analyze transmission routes of SARS-CoV-2 in hospital-acquired (HA) COVID-19.

Methods
An investigation was undertaken for all HA cases of COVID-19 from March to April 2020. Fifty SARS-CoV-2 samples were analysed by WvGS and their phylogenetic relationship established.

Results
WvGS identified transmission events previously undetected by epidemiological analysis and provided evidence for SARS-CoV-2 transmission between healthcare workers (HCW) and patients and among HCW themselves. The majority of HA COVID-19 cases occurred in patients highly dependent on nursing care, suggesting the likely route of transmission was by close contact or droplet, rather than aerosol, transmission. Mortality among HA COVID-19 infections was recorded as 33%.

Conclusions
This study provides evidence that SARS-CoV-2 transmission occurs from symptomatic and asymptomatic HCWs to patients. Interventions including comprehensive screening of HCWs for COVID-19 symptoms, PCR testing of asymptomatic HCWs upon identification of HA cases and implementation of universal use of surgical masks for all clinical care is indicated to prevent viral transmission. Our study highlights the importance of close collaboration between guidance bodies and frontline IPC experts for developing control measures in an emergency pandemic situation caused by a virus with undefined transmission modus.
Best Practice Guidance for Adult Infusion Centres during the COVID-19 Pandemic: Report from the COVID-19 International Organization for the Study of IBD [IOIBD] Task Force
Authors: Dotan Iris , Panaccione Remo , Kaplan Gilaad G , O’Morain Colm , Lindsay James O , Abreu Maria T 
Published: September 2020

Abstract
Infusion centres are a central part in the management of patients with inflammatory bowel disease [IBD] and could be a source of transmission of SARS-COV-2. Here we aimed to develop global guidance for best practices of infusion centres for IBD patients and to determine the impact of the COVID-19 pandemic on these centres. Under the auspices of the International Organization for the Study of Inflammatory Bowel Disease [IOIBD], a task force [TF] was formed, an online survey was developed to query infusion centre protocols during COVID-19, and recommendations were made, based on TF experience and opinion. Recommendations focus mainly on patients screening, infusion centres re-organization, personnel protection, and protocol modifications such as shortening infusion duration or replacing it with subcutaneous alternatives. Implementing these recommendations will hopefully reduce exposure of both IBD patients and care givers to SARS-COV-2 and improve the function and safety of infusion centres during the COVID-19 pandemic as well as potential future threats.
The ‘fertile island effect’ of Welwitschia plants on soil microbiota is influenced by plant gender
Authors: Doniger Tirza , Adams Jonathan M , Marais Eugene , Maggs-Kölling Gillian , Sherman Chen , Kerfahi Dorsaf , Yang Ying , Steinberger Yosef 
Published: September 2020

ABSTRACT
Desert and semi-desert plants are often associated with a distinct soil biota under the plants and close to the root system. We aimed to understand if similar effects could be found in the taxonomically isolated desert gymnosperm Welwitschia mirabilis in the Namib Desert, and whether this island effect varied with climate and with gender of plants. We took soil cores adjacent to the plants in environments ranging from extreme desert to arid shrubland, and in nearby control sites between the plants. Soil chemistry was analysed, and deoxyribonucleic acid was extracted and sequenced for the bacterial 16s region. Soil under the plants was richer in organic C, N and moisture. Despite the range of climates, the soil around Welwitschia plants was consistently associated with a particular bacterial community composition that was distinct from samples further away. Compared to unvegetated control patches, bacterial diversity close to the plants was reduced. In the plant-associated soil community, there was a clear gender effect across all sites with a distinct community composition and greater diversity under male plants. It is unclear what differences in the soil environment might be producing these gender-associated differences, which provide an additional dimension to the fertile island effect.
Temporal dynamics of bacterial communities during seed development and maturation
Authors: Chesneau Guillaume , Torres-Cortes Gloria , Briand Martial , Darrasse Armelle , Preveaux Anne , Marais Coralie , Jacques Marie-Agnès , Shade Ashley , Barret Matthieu 
Published: September 2020

ABSTRACTSeed microbiota acts as a starting point for the assembly of the plant microbiota and contributes to successful plant establishment. To date, the order and timing of microbial taxa immigration during seed development and maturation remained unknown. We investigated the temporal dynamics of seed bacterial communities in bean and radish. A high phylogenetic turnover was observed for both plant species with few taxa associated with all seed developmental stages. Greater heterogeneity in communities structure within each stage was observed for radish. While, about one-third of radish seed bacterial taxa were detected in buds, flowers and fruits, very few taxa seem to be transmitted by the floral route in bean. In the latter species, bacterial populations belonging to the P. fluorescens species complex were found either in buds, flowers and fruits or in seeds. The relative phylogenetic proximity of these bacterial populations combined with their habitat specificity led us to explore the genetic determinants involved in successful seed transmission in bean. Comparative genomic analyses of representatives bacterial strains revealed dozens of coding sequences specifically associated with seed-transmitted strains. This study provided a first glimpse on processes involved in seed microbiota assembly, which could be used for designing plant-beneficial microbial consortia.
Programmed death-ligand 1 expression in the tumour stroma of colorectal liver oligometastases and its association with prognosis after liver resection
Authors: Peng Jian-Hong , Tai Yi , Zhao Yi-Xin , Luo Bao-Jia , Ou Qing-Jian , Pan Zhi-Zhong , Zhang Lin , Lu Zhen-Hai 
Published: September 2020

Abstract

Background
The clinical value of programmed death-ligand 1 (PD-L1) expression in colorectal liver oligometastases (CLOs) remains undefined. This study aimed to detect PD-L1 in the microenvironment of CLOs and determine its association with patient prognosis.

Methods
We collected 126 liver-resection specimens from CLO patients who underwent curative liver resection between June 1999 and December 2016. Immunohistochemistry (IHC) was performed to assess PD-L1 expression in paraffin-embedded specimens. Overall survival (OS) and recurrence-free survival (RFS) were analysed using the Kaplan–Meier method and log-rank test.

Results
PD-L1 was mainly expressed in the stroma of liver oligometastases. Patients with high PD-L1 expression had a higher proportion of clinical-risk scores (CRSs) of 2–4 (67.7% vs 40.4%; P = 0.004). With a median 58-month follow-up, patients with high PD-L1 expression had a significantly lower 3-year OS rate (65.5% vs 92.7%; P = 0.001) and 3-year RFS rate (34.7% vs 83.8%; P &lt; 0.001) than patients with low PD-L1 expression. Multivariate Cox analysis demonstrated that high PD-L1 expression (hazard ratio [HR] = 3.581; 95% confidence interval [CI] 2.301–9.972; P = 0.015), CRS 2–4 (HR = 6.960; 95% CI 1.135–42.689; P = 0.036) and increased preoperative CA19-9 (HR = 2.843; 95% CI 1.229–6.576; P = 0.015) were independent risk factors for OS. High PD-L1 expression (HR = 4.815; 95% CI 2.139–10.837; P &lt; 0.001) and lymph-node metastasis (HR = 2.115; 95% CI 1.041–4.297; P = 0.038) were independent risk factors for RFS.

Conclusion
This study found that PD-L1 was commonly expressed in the tumour stroma of CLOs and high PD-L1 expression was associated with poor prognosis.
Crustal attenuation from USArray ML amplitude tomography
Authors: Hearn Thomas M 
Published: September 2020

SUMMARYSeismic attenuation across the US is estimated using station ML magnitude data from the USArray. Station magnitudes are recalibrated back to amplitude and back projected in a 2-D tomography. Data represent the amplitudes of the horizontal components of the Lg phase. The western US shows regions of very high attenuation and contrasts with the lesser attenuation of the eastern US. Individual attenuation anomalies can be clearly tied to regional geology. Station gains show broad regional variations that match geographic regions. Most of the high-attenuation areas are regions of high geothermal activity suggesting that intrinsic attenuation dominates over scattering attenuation. An exception is the central San Andreas Fault zone because it lacks any localized heat-flow anomaly. The US east of the Rocky Mountains is bland and contains none of the high-attenuation regions of the western US. Instead, the central US has low-attenuation patches that do not obviously correspond to geologic province. Sediments of the Gulf Coast Plain, Willison Basin and Michigan Basin do show up as intermediate attenuation while the Illinois Basin, Appalachian Basin and other basins are not apparent. In Alaska, attenuation is generally less than the western US, but still much greater than the eastern US. In southeast Alaska, the Wrangell Volcanic Field causes a sizeable high-attenuation zone. The volcanic Aleutian Mountains also have high attenuation. However, moderate to high attenuation also correlates with the tertiary sedimentary basins in Alaska. The North Slope Basin does not seem to attenuate. Thicker crust and mountain roots tend to show less attenuation, if anything, but this correspondence is most likely due to differences in temperature and seismic velocity. Heat, scattering and young sedimentary basins create seismic attenuation in the continental crust.
The effectiveness of (Rabbinic) prenuptial agreements in preventing marital captivity
Authors: Broyde Michael J 
Published: September 2020

Abstract
Jewish law (also known as Halakha) requires that a man give and a woman receive a get, a Jewish bill of divorce, in order to end their Jewish marriage, which has a legal existence independent of their civil marriage and is not ended by a civil divorce. Since around 1960, there have been many attempts to solve this problem of marital captivity in North America. American prenuptial agreements (PNAs) best address this problem of Orthodox Jewish husbands withholding a get. This article explains why Jewish law prefers contract-based solutions over legislative or judicial solutions and presents empirical research on which type of PNA best solves this problem in America.
Cortical Transcriptomic Alterations in Association With Appetitive Neuropeptides and Body Mass Index in Posttraumatic Stress Disorder
Authors: Stone Lauren A , Girgenti Matthew J , Wang Jiawei , Ji Dingjue , Zhao Hongyu , Krystal John H , Duman Ronald S 
Published: September 2020

Abstract

Background
The molecular pathology underlying posttraumatic stress disorder (PTSD) remains unclear mainly due to a lack of human PTSD postmortem brain tissue. The orexigenic neuropeptides ghrelin, neuropeptide Y, and hypocretin were recently implicated in modulating negative affect. Drawing from the largest functional genomics study of human PTSD postmortem tissue, we investigated whether there were molecular changes of these and other appetitive molecules. Further, we explored the interaction between PTSD and body mass index (BMI) on gene expression.

Methods
We analyzed previously reported transcriptomic data from 4 prefrontal cortex regions from 52 individuals with PTSD and 46 matched neurotypical controls. We employed gene co-expression network analysis across the transcriptomes of these regions to uncover PTSD-specific networks containing orexigenic genes. We utilized Ingenuity Pathway Analysis software for pathway annotation. We identified differentially expressed genes (DEGs) among individuals with and without PTSD, stratified by sex and BMI.

Results
Three PTSD-associated networks (P &lt; .01) contained genes in signaling families of appetitive molecules: 2 in females and 1 in all subjects. We uncovered DEGs (P &lt; .05) between PTSD and control subjects stratified by sex and BMI with especially robust changes in males with PTSD with elevated vs normal BMI. Further, we identified putative upstream regulators (P &lt; .05) driving these changes, many of which were enriched for involvement in inflammation.

Conclusions
PTSD-associated cortical transcriptomic modules contain transcripts of appetitive genes, and BMI further interacts with PTSD to impact expression. DEGs and inferred upstream regulators of these modules could represent targets for future pharmacotherapies for obesity in PTSD.