bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is the Glass-Ceiling Higher Than We Think? Sex Disparity Trends in Physician Executive Positions and Academic Plastic Surgery
Authors: Marquez Jocellie E. , Zaransky Sydney , Scheiner Alyssa , Rathi Sourish , Ikizoglu Melissa , Singh Gurtej , Huston Tara L. 
Published: March 2020

Introduction
Advanced levels of professorship and executive positions are considered markers of success in medical academia. Despite sex parity in medical school graduates, sex disparities within positions of power remain unequal. The purpose of this study was to analyze sex composition at different levels of leadership at multiple academic, highly ranked institutions.

Methods
Hospital executives and academic plastic surgery faculty were identified through an internet-based search of all Accreditation Council for Graduate Medical Education–accredited plastic surgery integrated and independent residency training programs. Institutions from the U.S. News 2018–19 Top 20 Best Hospitals Honor Roll and Beckers Review 2018: 100 Great Hospitals in America were also included. Information on board of directors/trustees (BOD), administrators, and plastic surgery faculty with focus on title, sex, degree, specialty, and academic rank was collected from departmental and hospital websites. Duplicate institutions were excluded.

Results
Data on chief executive officers (CEOs)/presidents (n = 275) and BOD members (n = 5347) from 153 medical institutions were analyzed. Physicians consisted of 40.7% (n = 112) of CEOs/presidents, of which 10.7% (n = 12) were surgeons, and 15.6% (n = 835) of the BOD membership. Female physicians in executive roles were disproportionally low, consisting of 5% (n = 14) of CEOs/presidents, reaching significance (P = 0.033).
Sex representation within plastic surgery departments demonstrated similar trends. Women comprised 18.3% of the overall plastic surgery faculty (n = 1441). Significant differences between mean male and female plastic surgeons (8.2 vs 1.84, P = <0.001) were observed. In addition, female plastic surgeons represented only 26.3% of all assistant professors (P = <0.001), 18.75% of total associate professors (P = <0.001), and 7.8% of full professors (P = <0.001).

Conclusions
Although women are increasingly pursuing careers in medicine and surgery, the data suggest that there remains a paucity of female physicians in top leadership roles. At the departmental level, female plastic surgeons are also underrepresented. At the executive level, men make up over 88% of physician CEOs at the highest-ranked medical institutions. This study further highlights the need for the development of educational, mentorship, and career pathways to further improve female representation in positions of power within academia.
Electroconvulsive Therapy in Italy—Current Dissemination of Treatment and Determining Factors of the Past
Authors: Wilhelmy Saskia , Grözinger Michael , Groß Dominik , Conca Andreas 
Published: March 2020

Objectives
The history of electroconvulsive therapy (ECT) spans eight decades, over which period this method of treatment has been modernized. At the same time, however, the conflict between acceptance and rejection of ECT therapy remains unresolved today. This ambivalence is particularly noticeable in Italy, where the number of uses of ECT has been declining for several years. The aim of the present study is to examine the distribution and use of ECT in Italy today in comparison to 2009 and to analyze the factors that have influenced this downward development.

Methods
A cross-sectional study using a standardized Italian-language questionnaire was conducted in 2017 to investigate the dissemination and practice of ECT in Italy. The study was addressed to all public and private hospitals providing ECT as a treatment.

Results
Of the 145 mental health facilities in Italy, only 9 offered ECT. A total of 293 patients were treated with ECT within 1 year (mainly for depression). Rates for 3-year treatments in the centers yielded an uneven picture: 4 centers showed an increase in cases and just as many a decline. A north-south divide existed in terms of geographical distribution: centers were mainly located in the north in 2017.

Conclusions
The study shows that the dissemination and use of ECT have reached a historical low in Italy. It further documents the extent to which the use of ECT declined after 2009. Three factors that have accompanied this development are discussed. If this downward trend is to be reversed, it will be necessary to develop a new approach so as to engender a perception of ECT as a viable treatment option.
Potential biochemical markers to identify severe cases among COVID-19 patients
Authors: Xiang Jialin , Wen Jing , Yuan Xiaoqing , Xiong Shun , Zhou Xue , Liu Changjin , Min Xun 
Published: March 2020

AbstractThere is a high mortality and long hospitalization period for severe cases with 2019 novel coronavirus disease (COVID-19) pneumonia. Therefore, it makes sense to search for a potential biomarker that could rapidly and effectively identify severe cases early. Clinical samples from 28 cases of COVID-19 (8 severe cases, 20 mild cases) in Zunyi District from January 29, 2020 to February 21, 2020 were collected and otherwise statistically analysed for biochemical markers. Serum urea, creatinine (CREA) and cystatin C (CysC) concentrations in severe COVID-19 patients were significantly higher than those in mild COVID-19 patients (P<0.001), and there were also significant differences in serum direct bilirubin (DBIL), cholinesterase (CHE) and lactate dehydrogenase (LDH) concentrations between severe and mild COVID-19 patients (P<0.05). Serum urea, CREA, CysC, DBIL, CHE and LDH could be used to distinguish severe COVID-19 cases from mild COVID-19 cases. In particular, serum biomarkers, including urea, CREA, CysC, which reflect glomerular filtration function, may have some significance as potential indicators for the early diagnosis of severe COVID-19 and to distinguish it from mild COVID-19. Glomerular filtration function injury in severe COVID-19 patients should also be considered by clinicians.
gapseq: Informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
Authors: Zimmermann Johannes , Kaleta Christoph , Waschina Silvio 
Published: March 2020

AbstractMicrobial metabolic processes greatly impact ecosystem functioning and the physiology of multi-cellular host organisms. The inference of metabolic capabilities and phenotypes from genome sequences with the help of reference biomolecular knowledge stored in online databases remains a major challenge in systems biology. Here, we presentgapseq: a novel tool for automated pathway prediction and metabolic network reconstruction from microbial genome sequences.gapseqcombines databases of reference protein sequences (UniProt, TCDB), in tandem with pathway and reaction databases (MetaCyc, KEGG, ModelSEED). This enables the prediction of an organism’s metabolic capabilities from sequence homology and pathway topology criteria. By incorporating a novel LP-based gap-filling algorithm,gapseqfacilitates the construction of genome-scale metabolic models that are suitable for metabolic phenotype predictions by using constraint-based flux analysis. We validatedgapseqby comparing predictions to experimental data for more than 3, 000 bacterial organisms comprising 14, 895 phenotypic traits that include enzyme activity, energy sources, fermentation products, and gene essentiality. This large-scale phenotypic trait prediction test showed, thatgapseqyields an overall accuracy of 81% and thereby outperforms other commonly used reconstruction tools. Furthermore, we illustrate the application ofgapseq-reconstructed models to simulate biochemical interactions between microorganisms in multi-species communities. Altogether,gapseqis a new method that improves the predictive potential of automated metabolic network reconstructions and further increases their applicability in biotechnological, ecological, and medical research.gapseqis available athttps://github.com/jotech/gapseq.
Express saccades during a countermanding task
Authors: Errington Steven P. , Schall Jeffrey D. 
Published: March 2020

ABSTRACTExpress saccades are unusually short latency, visually guided saccadic eye movements. They are most commonly observed when the fixation spot disappears at a consistent, short interval before a target spot appears at a repeated location. The saccade countermanding task includes no fixation-target gap, variable target presentation times, and the requirement to withhold saccades on some trials. These testing conditions should discourage production of express saccades. However, two macaque monkeys performing the saccade countermanding task produced consistent, multimodal distributions of saccadic latencies. These distributions consisted of a longer mode extending from 200 ms to as much as 600 ms after target presentation and another consistently less than 100 ms after target presentation. Simulations revealed that by varying express saccade production, monkeys could earn more reward. If express saccades were not rewarded, they were rarely produced. The distinct mechanisms producing express and longer saccade latencies were revealed further by the influence of regularities in the duration of the fixation interval preceding target presentation on saccade latency. Temporal expectancy systematically affected the latencies of regular but not of express saccades. This study highlights that cognitive control can integrate information across trials and strategically elicit intermittent very short latency saccades to acquire more reward.
Impact of library preparation-induced low GC sequencing bias onSalmonellaserotype prediction using SeqSero2
Authors: Li Shaoting , Zhang Shaokang , Deng Xiangyu 
Published: March 2020

AbstractA recent study by Uezle et al. reported a lack of O antigen prediction by SeqSero2. We found that Nextera XT-prepared genomes in the study were abnormally challenging for O antigen prediction because of unusually high sequencing bias against low GC regions that was not seen in similarly prepared genomes from other laboratories. We recommend that SeqSero2 users be mindful of the GC-related sequencing bias when analyzing Nextera XT-prepared genomes. Although it is unusual for such biases to compromise serotype prediction by SeqSero2 per our knowledge and analysis, it is unknown whether they could affect subtyping and characterization of other low-GC regions, such asSalmonellapathogenicity islands, when genome assembly is affected by such biases.
In SilicoAnalysis ofB3GALTLGene Reveling 13 Novel Mutations Associated with Peters’-plus syndrome
Authors: Abdelmoneim Abdelrahman H. , Satti Arwa A. , Abdelmageed Miysaa I. , Murshed Naseem S. , Elfadol Nafisa M. , Mustafa Mujahed I. , Makhawi Abdelrafie M. 
Published: March 2020

AbstractBackgroundPeters’-plus syndrome is a rare autosomal recessive disorder, which is characterized by a specific malformation of the eye that includes corneal opaqueness and iridocorneal adhesions (Peters’ anomaly) along with other systemic manifestations. Furthermore, various researches report the association between B3GALTL gene and Peters’-plus syndrome. In the current work we aim to analyze the deleterious SNPs in B3GALTL gene that predispose to Peters’-plus syndrome.Methodthe associated SNPs of the coding region of the B3GALTL gene was acquired from National Center for Biotechnology Information and then analyzed by eight softwares (SIFT, Polyphen2, Proven, SNAP2, SNP@GO, PMut, Imutant and Mupro). The physiochemical properties of the resulted SNPs were then analyzed by Hope project website and visualized by chimera software.ResultThirteen novel mutations (Y172C, A222V, C260R, C260Y, D349G, I354K, R377C, G379C, G393R, G393E, G395E, G425E, R445W) are discovered in B3GALTL gene to cause deleterious effects leading to the development of Peters’-plus syndrome.ConclusionThirteen novel mutations in B3GALTL gene are predicted to cause Peters’-plus syndrome.
Identification of a plant kinase that phosphorylates the bacterial effector AvrPtoB
Authors: Lei Lei , Stevens Danielle M. , Coaker Gitta 
Published: March 2020

AbstractA critical component controlling bacterial virulence is the delivery of pathogen effectors into plant cells during infection. Effectors alter host metabolism and immunity for pathogen benefit. Multiple effectors are phosphorylated by host kinases, and this posttranslational modification is important for their activity. We sought to identify host kinases involved in effector phosphorylation. Multiple phosphorylated effector residues matched the proposed consensus motif for the plant calcium-dependent protein kinase (CDPK) and Snf1-related kinase (SnRK) superfamily. The conservedPseudomonaseffector AvrPtoB acts as an E3 ubiquitin ligase and promotes bacterial virulence. We identified a member of the Arabidopsis SnRK family, SnRK2.8, which associated with AvrPtoB in yeast andin planta.SnRK2.8was required for AvrPtoB virulence functions, including facilitating bacterial colonization, suppression of callose deposition, and targeting the plant defense regulator NPR1 and flagellin receptor FLS2. Mass spectrometry revealed AvrPtoB phosphorylation at multiple serine residuesin planta, with S258 phosphorylation significantly reduced in thesnrk2.8knockout. AvrPtoB phospho-null mutants exhibited compromised virulence functions and were unable to suppress NPR1 accumulation, FLS2 accumulation, or inhibit FLS2-BAK1 complex formation upon flagellin perception. These data identify a conserved plant kinase utilized by a pathogen effector to promote disease.
A New, Simple Projection Model for COVID-19 Pandemic
Authors: Lu Jian 
Published: March 2020

SummaryBackgroundWith the worldwide outbreak of COVID-19, an accurate model to predict how the coronavirus pandemic will evolve in individual countries becomes important and urgent. Our goal is to provide a prediction model to help policy makers in different countries address the epidemic outbreak and adjust the control policies to contain the spread of the severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) more effectively.MethodsUnlike the classic public health and virus propagation models, this new projection model takes both government intervention and public response into account to generate reliable projections of the outbreak 10 days to 2 weeks in advance. This method is an observation based projection similar than the classic Moore’s Law in miroelectronics. The Moore’s law is not based on any physics law and yet has anticipated the development of microelectronics for decades. This work is an empirical relation to decribe the evolution of epidemic to pandemic situations in different countries. The country was selected as an observation unit because the regulation and political decision is an national decision for numerous measures such as the implementation of social distancing, the quarantine of suspected cases, and the closing of borders to achieve territorial containment.FindingsThis model has been successfully applied to predict the evolution of pendemic situation in China. Then the model was also validated by the South Korean data. With a reduction of cases calculated as reduction coefficient of the increase rate of daily cases Rc = 2% per day, we observed a very efficient policy with a strict systematic control in both China and South Korea. For the moment, the Canada, USA, Australia may have difficulties to limit the fast evolution of the epidemic. With a Rc<0.5%, it’s particularly important for the USA to consider escalating the control measures because the affected cases can reach more than one million very soon.InterpertationDue to the difference of national disciplines and historical culture, the national policy may be implemented and observed with different efficiency. The starting point where the government decided to apply total containment can also play a key role for the evolution of the pendemic situation. The model will allow each national government of the nations still affected by the pandemic to project the situation for the coming 10 to 14 days. It’s very important for the deployment of national and international efforts to stop the pandemic situation.FundingNational Key R&D Program of China (Ministry of Science & Technology (MOST, China))
Tracking and forecasting milepost moments of the epidemic in the early-outbreak: framework and applications to the COVID-19
Authors: Wang Huiwen , Zhang Yanwen , Lu Shan , Wang Shanshan 
Published: March 2020

AbstractBackgroundThe outbreak of the 2019 novel coronavirus (COVID-19) has attracted global attention. In the early stage of the outbreak, the most important question concerns some meaningful milepost moments, including (1) the time when the number of daily confirmed cases decreases, (2) the time when the number of daily confirmed cases becomes smaller than that of the daily removed (recovered and death), (3) the time when the number of daily confirmed cases becomes zero, and (4) the time when the number of patients treated in hospital is zero, which indicates the end of the epidemic. Intuitively, the former two can be regarded as two important turning points which indicate the alleviation of epidemic to some extent, while the latter two as two “zero” points, respectively. Unfortunately, it is extremely difficult to make right and precise prediction due to the limited amount of available data at a early stage of the outbreak.MethodTo address it, in this paper, we propose a flexible framework incorporating the effectiveness of the government control to forecast the whole process of a new unknown infectious disease in its early-outbreak. Specially, we first establish the iconic indicators to characterize the extent of epidemic spread, yielding four periods of the whole process corresponding to the four meaningful milepost moments: two turning points and two “zero” points. Then we develop the tracking and forecasting procedure with mild and reasonable assumption. Finally we apply it to analyze and evaluate the COVID-19 using the public available data for mainland China beyond Hubei Province from the China Centers for Disease Control (CDC) during the period of Jan 29th, 2020, to Feb 29th, 2020, which shows the effectiveness of the proposed procedure.ResultsResults show that our model can clearly outline the development of the epidemic at a very early stage. The first prediction results on Jan 29th reveal that the first and second milepost moments for mainland China beyond Hubei Province would appear on Jan 31st and Feb 14th respectively, which are only one day and three days behind the real world situations. Forecasting results indicate that the number of newly confirmed cases will become zero in the mid-late March, and the number of patients treated in the hospital will become zero between mid-March and mid-April in mainland China beyond Hubei Province. The framework proposed in this paper can help people get a general understanding of the epidemic trends in counties where COVID-19 are raging as well as any other outbreaks of new and unknown infectious diseases in the future.
Cell profiling of mouse acute kidney injury reveals conserved cellular responses to injury
Authors: Kirita Yuhei , Wu Haojia , Uchimura Kohei , Wilson Parker C. , Humphreys Benjamin D. 
Published: March 2020

AbstractAfter acute kidney injury (AKI), patients either recover or alternatively develop fibrosis and chronic kidney disease. Interactions between injured epithelia, stroma and inflammatory cells determine whether kidneys repair or undergo fibrosis, but the molecular events that drive these processes are poorly understood. Here, we use single nucleus RNA sequencing of a mouse model of AKI to characterize cell states during repair from acute injury. We identify a distinct proinflammatory and profibrotic proximal tubule cell state that fails to repair. Deconvolution of bulk RNA-seq datasets indicates that this “failed-repair proximal tubule cell” or FR-PTC, state can be detected in other models of kidney injury, increasing in the aging rat kidney and over time in human kidney allografts. We also describe dynamic intercellular communication networks and discern transcriptional pathways driving successful vs. failed repair. Our study provides a detailed description of cellular responses after injury and suggests that the FR-PTC state may represent a therapeutic target to improve repair.Significance StatementSingle nucleus RNA sequencing revealed gene expression changes during repair after acute kidney injury. We describe a small population of proximal tubule cells that fail to repair (FR-PTC). Since this subpopulation expresses abundant pro-inflammatory and profibrotic genes, it may represent a new therapeutic target to improve repair and reduce fibrosis after AKI.
Topoisomerase 3B (TOP3B) DNA and RNA Cleavage Complexes and Pathway to Repair TOP3B-linked RNA and DNA Breaks
Authors: Saha Sourav , Sun Yilun , Huang Shar-Yin , Jo Ukhyun , Zhang Hongliang , Tse-Dinh Yuk-Ching , Pommier Yves 
Published: March 2020

SUMMARYGenetic inactivation of TOP3B is linked with schizophrenia, autism, intellectual disability and cancer. The present study demonstrates thatin vivoTOP3B forms both RNA and DNA cleavage complexes (TOP3Bccs) and reveals a pathway for repairing TOP3Bccs. For detecting cellular TOP3Bccs, we engineered a “self-trapping” mutant of TOP3B (R338W TOP3B) and to determine how human cells repair TOP3Bccs, we depleted tyrosyl-DNA phosphodiesterases (TDP1 and TDP2). TDP2-deficient cells produced elevated TOP3Bccs both in DNA and RNA. Conversely, overexpression of TDP2 lowered cellular TOP3Bccs. Using recombinant human TDP2, we demonstrate that TDP2 cannot excise the native form of TOP3Bccs. Hypothesizing that TDP2 cannot access phosphotyrosyl linkage unless TOP3B is either proteolyzed or denatured, we found that cellular TOP3Bccs are ubiquitinated by the E3 Ubiquitin Ligase TRIM41 before undergoing proteasomal degradation and excision by TDP2.HIGHLIGHTSMethod forin vivodetection of TOP3B cleavage complexes (TOP3Bccs) formed both in DNA and RNA, using a religation defective “self-trapping” R338W TOP3B mutant.First evidence that TDP2 excises TOPccs produced by a type IA topoisomerase.TDP2 processes both RNA and DNA TOP3Bccs following their ubiquitylation and proteasomal degradation inside cell.TRIM41 is the first reported E3 ubiquitin ligase for TOP3Bcc ubiquitylation and proteasomal degradation.