bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electroconvulsive Therapy in Germany
Authors: Jolivet Alix , Grözinger Michael 
Published: July 2020

Objectives
The use of electroconvulsive therapy (ECT) in Europe varies broadly between the extremes of Sweden on one side and Italy on the other. Here, we document the frequency, practice and standards of ECT in Germany in 2016, compare it with a survey of 2008, and describe the historical background.

Methods
A questionnaire was sent electronically to the 396 psychiatric institutions in Germany. Repeated follow-up calls yielded a complete list of hospitals performing ECT and a high rate of detailed responses.

Results
Forty-five percent (178/396) of the psychiatric hospitals performed ECT. Of those, 73.6% (131/178) completed the questionnaire. Based on 2 procedures, we estimated an incidence of 60,000 single treatments and 5700 patients treated, with a rate of 6.9 patients per 105 inhabitants. As in 2008, regional differences proved to be significant. The rate at which patients are referred to ECT hospitals from other clinics for the special purpose of ECT has increased since 2008. Maintenance treatments and the use of ketamine for anesthesia have gone up considerably while fewer hospitals offered outpatient treatments.

Conclusions
The application of ECT has increased markedly in the last 8 years, showing an exponential growth over the last 4 decades in Germany. The accessibility to the treatment seems to have improved and some global trends have been well received. Electroconvulsive therapy has become a modern, increasingly used medical intervention.
Treating Posttraumatic Stress Disorder Symptoms With Low Amplitude Seizure Therapy (LAP-ST) Compared With Standard Right Unilateral Electroconvulsive Therapy
Authors: Youssef Nagy A. , Dhanani Sadiya , Rosenquist Peter B. , McCloud Laryssa , McCall William V. 
Published: July 2020

Objectives
An important barrier to further studying electroconvulsive therapy (ECT) in posttraumatic stress disorder (PTSD) is the cognitive adverse effects. However, recent data suggest that low amplitude seizure therapy (LAP-ST) has no or minimal cognitive adverse effects. The aims of this report were to examine the efficacy of LAP-ST in PTSD and to compare LAP-ST with standard right unilateral (RUL) ECT using a pilot randomized clinical trial.

Methods
Patients were randomized to LAP-ST or RUL ECT. Posttraumatic stress disorder was assessed using clinical interview based on the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, and symptom severity with PTSD Checklist (PCL). The scores pertaining to PCL were analyzed using descriptive analysis for this pilot study.

Results
Eleven patients consented to be enrolled. Seven were randomly allocated to LAP-ST or RUL ECT. Five completed the study and had completed PCL before and after the course. In both groups, PTSD symptoms showed fast improvement. The effect size of improvement seems promising. The mean baseline PCL score for patients in the LAP-ST group was 42.5 (SD = 16.26) and the mean end point PCL score after treatment was 31 (SD = 15.56). The mean baseline PCL score for patients in the standard RUL ECT group was 64.7 (SD = 1.15) and the mean end point was 41 (SD = 15.62).

Conclusions
Both LAP-ST and standard RUL ECT showed reduction in PTSD symptoms with fast improvement. This first PTSD LAP-ST study adds support to the prior LAP-ST proof-of-concept clinical trial that LAP-ST can produce effective therapeutic outcomes. Replication of this trial is warranted in larger clinical trials (ClinicalTrials.gov ID: NCT02583490).
Need for Standardization of Measurement of Time to Reorientation as a Predictor of Cognitive Adverse Effects of Electroconvulsive Therapy
Authors: Tripathi Chidrup , Khan Bilal , Youssef Nagy A. 
Published: July 2020

Abstract
Testing for time to reorientation (TRO) after electroconvulsive therapy (ECT) has been one of the most predictive measures for cognitive adverse effects of ECT. However, measuring TRO varies between clinical trials, and there is no standardized approach on its measurement between studies. The objective of this report is to systematically review the literature on the different ways of measuring TRO. This would be a first step to establish a consensus on a standard method for TRO. We performed a systematic literature review from 1968 to October 2019 for clinical trials with a sample size of more than 50 and published in English that describe measures of TRO. We searched both PubMed and Web of Science databases. The literature search generated 12 clinical trials, which met the inclusion criteria. Studies measured TRO using 3-, 5-, or 10-item questionnaires. Most studies measured full orientation as answering 4/5 questions. Other studies smaller than 50 required 14/14 items to be answered correctly. There was wide variation between studies on how often and when orientation questions were initiated. These factors have obvious implications to the results and interpretation of the ECT literature.There was no clear consensus on measuring TRO in a uniform fashion. Research and clinical care would benefit from a standardized approach to measuring TRO. Measuring TRO using a 4/5 method seems the most common and quickest way, whereas using a 14/14 method seems to be the most rigorous and sensitive to change in trials.
Statements issued by academic medical institutions after George Floyd’s killing by police and subsequent unrest in the United States: cross-sectional study
Authors: Kiang Mathew V. , Tsai Alexander C. 
Published: July 2020

AbstractBackgroundThe horrific nature of George Floyd’s killing by a Minneapolis Police Department officer on May 25, 2020 has sparked more than a month of nationwide protests against police brutality and in support of the Black Lives Matter movement. At critical junctures of the nation’s public health such as these, academic medical institutions may exert leadership by issuing public statements to communicate institutional values.MethodsWe obtained statements issued by 56 leading U.S. medical schools relevant to George Floyd’s killing and subsequent protests. We tokenized statements into words, n-grams of sizes 2 and 3, and sentences; removed non-informative stop words and words that would compromise de-identification; and stemmed the remaining words using the Porter algorithm. We followed a predefined set of rules for identifying important elements of these statements related to leadership in antiracism and public health.ResultsNearly all named George Floyd (50 [89%]), a majority noted the role of racism (43 [77%]) and acknowledged the Black community specifically (41 [73%]). Fewer ╌ slightly more than half ╌ referenced the act resulting in Floyd’s death (31 [55%]) or made explicit reference to the police (29 [52%]). Only 7 (13%) explicitly used terms denoting active support, like “antiracism” or “Black Lives Matter.” Most (45 [80%]) included references to negative sequelae resulting from racism like “disparities” or “inequality”. All included hopeful language.ConclusionOnly a minority of institutions made reference to the killing of George Floyd by the police, and most failed to address this country’s targeted, historically engrained, and sustained oppression of Black people through white supremacy. Thus, our study identifies significant opportunities for U.S. medical schools to exert meaningful leadership in health.
SUV39 SET domains mediate crosstalk of heterochromatic histone marks
Authors: Stirpe Alessandro , Guidotti Nora , Northall Sarah J. , Kilic Sinan , Hainard Alexandre , Vadas Oscar , Fierz Beat , Schalch Thomas 
Published: July 2020

AbstractThe SUV39 class of methyltransferase enzymes deposits histone H3 lysine 9 di- and trimethylation (H3K9me2/3), the hallmark of constitutive heterochromatin. How these enzymes are regulated to mark specific genomic regions as heterochromatic is poorly understood. Clr4 is the sole H3K9me2/3 methyltransferase in the fission yeastS. pombeand recent evidence suggests that ubiquitination of lysine 14 on histone H3 (H3K14ub) plays a key role in H3K9 methylation. However, the molecular mechanism of this regulation and its role in heterochromatin formation remains to be determined. Our structure-function approach shows that the H3K14ub substrate binds specifically and tightly to the catalytic domain of Clr4, and thereby stimulates the enzyme by over 250-fold. Mutations that disrupt this mechanism lead to a loss of H3K9me2/3 and abolish heterochromatin silencing similar toclr4deletion. Comparison with mammalian SET domain proteins suggests that the Clr4 SET domain harbours a conserved sensor for H3K14ub, which mediates licensing of heterochromatin formation.
Organization of Areal Connectivity in the Monkey Frontoparietal Network
Authors: Conklin Bryan D. 
Published: July 2020

AbstractAnatomical connectivity between cortical areas condition the set of observable functional activity in a neural network. The large-scale cortical monkey frontoparietal network (FPN) has been shown to facilitate complex cognitive functions. However, the organization of anatomical connectivity between areas in the FPN supporting such function is unknown. Here, a new connectivity matrix is proposed which shows the FPN utilizes a small-world architecture with an over-reliance on the M9 dynamical relay 3-node motif and degree distributions which can be characterized as single scale. The FPN uses its small-world architecture to achieve the kind of simultaneous integration and specialization of function which cognitive functions like attention and working memory require. Contrary to many real-world networks, the in and out single scale degree distributions illustrate the relatively homogeneous connectivity of each area in the FPN, suggesting an absence of hubs. Crucially, the M9 dynamical relay motif is the optimal arrangement for previously reported near-zero and non-zero phase synchrony to propagate through the network, serving as a candidate topological mechanism. These results signify the impact of the organization of anatomical connectivity in the FPN. They can serve as a benchmark to be used in the network-level treatment of neurological disorders where the types of cognition the FPN supports are impaired. Additionally, they can inform future neuromorphic circuit designs which aim to perform aspects of cognition.
Streamlining Data-Intensive Biology With Workflow Systems
Authors: Reiter Taylor , Brooks Phillip T. , Irber Luiz , Joslin Shannon E.K. , Reid Charles M. , Scott Camille , Brown C. Titus , Pierce N. Tessa 
Published: July 2020

AbstractAs the scale of biological data generation has increased, the bottleneck of research has shifted from data generation to analysis. Researchers commonly need to build computational workflows that include multiple analytic tools and require incremental development as experimental insights demand tool and parameter modifications. These workflows can produce hundreds to thousands of intermediate files and results that must be integrated for biological insight. Data-centric workflow systems that internally manage computational resources, software, and conditional execution of analysis steps are reshaping the landscape of biological data analysis, and empowering researchers to conduct reproducible analyses at scale. Adoption of these tools can facilitate and expedite robust data analysis, but knowledge of these techniques is still lacking. Here, we provide a series of practices and strategies for leveraging workflow systems with structured project, data, and resource management to streamline large-scale biological analysis. We present these strategies in the context of high-throughput sequencing data analysis, but the principles are broadly applicable to biologists working beyond this field.Author SummaryWe present a guide for workflow-enabled biological sequence data analysis, developed through our own teaching, training and analysis projects. We recognize that this is based on our own use cases and experiences, but we hope that our guide will contribute to a larger discussion within the open source and open science communities and lead to more comprehensive resources. Our main goal is to accelerate the research of scientists conducting sequence analyses by introducing them to organized workflow practices that not only benefit their own research but also facilitate open and reproducible science.
Negative screening for 12 rare LRRK2 pathogenic variants in a cohort of Nigerians with Parkinson’s disease
Authors: Rizig Mie , Ojo Oluwadamilola O. , Athanasiou-Fragkouli Alkyoni , Agabi Osigwe P. , Oshinaike Olajumoke O. , Houlden H , Okubadejo Njideka U. 
Published: July 2020

AbstractMutations in the leucine-rich repeat kinase 2 (LRRK2) gene are the most commonly identified genetic variants in familial and sporadic Parkinson’s disease (PD). Over three hundredLRRK2variants have been described in the literature, of which at least 17 have a confirmed or probable pathogenic role in PD. The distribution of these rare pathogenic variants has been shown to be different among ethnic groups including Caucasians, Latin Americans and East and South Asians. However, to date no PD-relatedLRRK2pathogenic variant has been described in persons of black African ancestry within or outside Africa. We previously reported that theLRRK2 p.gly2019sermutation was not found in 126 PD patients and 55 controls from Nigeria. Using Kompetitive Allele-Specific Polymerase chain reaction (KASP), we screened a new cohort of 92 Nigerians with PD and 210 healthy ethnically matched controls for 12 rareLRRK2variants (which have been shown to be pathogenic in other ethnic populations) including:p.gly2019ser, p.Arg1441His, p.Gly2385Arg, p.Ala419Val, p.Arg1628Pro, p.Pro755Leu, p.Ile2020ThrandTyr1699Cys. All 12 rare variants were absent in PD patients and controls from this cohort. These results endorse our previous findings and confirm that rareLRRK2pathogenic variants reported in Caucasians, Asians and persons of mixed ancestry are absent in West Africans. Applying next generation sequencing technologies in future studies is necessary to explore possible novelLRRK2variants indigenous to black Africans.
Synchronization and interaction of proline, ascorbate and oxidative stress pathways under abiotic stress combination in tomato plants
Authors: Lopez-Delacalle María , Silva Christian J , Mestre Teresa C , Martinez Vicente , Blanco-Ulate Barbara , Rivero Rosa M 
Published: July 2020

ABSTRACTAdverse environmental conditions have a devastating impact on plant productivity. In nature, multiple abiotic stresses occur simultaneously, and plants have evolved unique responses to cope against this combination of stresses. Here, we coupled genome-wide transcriptional profiling and untargeted metabolomics with physiological and biochemical analyses to characterize the effect of salinity and heat applied in combination on the metabolism of tomato plants. Our results demonstrate that this combination of stresses causes a unique reprogramming of metabolic pathways, including changes in the expression of 1,388 genes and the accumulation of 568 molecular features. Pathway enrichment analysis of transcript and metabolite data indicated that the proline and ascorbate pathways act synchronously to maintain cellular redox homeostasis, which was supported by measurements of enzymatic activity and oxidative stress markers. We also identified key transcription factors from the basic Leucine Zipper Domain (bZIP), Zinc Finger Cysteine-2/Histidine-2 (C2H2) and Trihelix families that are likely regulators of the identified up-regulated genes under salinity+heat combination. Our results expand the current understanding of how plants acclimate to environmental stresses in combination and unveils the synergy between key cellular metabolic pathways for effective ROS detoxification. Our study opens the door to elucidating the different signaling mechanisms for stress tolerance.HIGHLIGHTSThe combination of salinity and heat causes a unique reprogramming of tomato metabolic pathways by changing the expression of specific genes and metabolic features.Proline and ascorbate pathways act synchronously to maintain cellular redox homeostasisKey transcription factors from the basic Leucine Zipper Domain (bZIP), Zinc Finger Cysteine-2/Histidine-2 (C2H2) and Trihelix families were identified as putative regulators of the identified up-regulated genes under salinity and heat combination.
A Parallel Implementation of the Finite State Projection Algorithm for the Solution of the Chemical Master Equation
Authors: Vo Huy , Munsky Brian 
Published: July 2020

AbstractStochastic reaction networks are a popular modeling framework for biochemical processes that treat the molecular copy numbers within a single cell as a continuous time Markov chain, whose forward Chapman-Kolmogorov equation is known in biochemistry literature as the chemical master equation (CME). The solution of the CME contains extremely useful information that can be compared to experimental data in order to improve the quantitative understanding of biochemical reaction networks within the cell. However, this solution is costly to compute as it requires integrating an enormous system of differential equations that grows exponentially with the number of chemical species. To address this issue, we introduce a novel multiple-sinks Finite State Projection algorithm that approximates the CME with an adaptive sequence of reduced-order models with an effecient parallelization based on MPI. The implementation is tested on models of sizable state spaces using a high-performance computing node on Amazon Web Services, showing favorable scalability.
Variance and limiting distribution of coalescence times in a diploid model of a consanguineous population
Authors: Severson Alissa L. , Carmi Shai , Rosenberg Noah A. 
Published: July 2020

AbstractRecent modeling studies interested in runs of homozygosity (ROH) and identity by descent (IBD) have sought to connect these properties of genomic sharing to pairwise coalescence times. Here, we examine a variety of features of pairwise coalescence times in models that consider consanguinity. In particular, we extend a recent diploid analysis of mean coalescence times for lineage pairs within and between individuals in a consanguineous population to derive the variance of coalescence times, studying its dependence on the frequency of consanguinity and the kinship coefficient of consanguineous relationships. We also introduce a separation-of-time-scales approach that treats consanguinity models analogously to mathematically similar phenomena such as partial selfing, using this approach to obtain coalescence-time distributions. This approach shows that the consanguinity model behaves similarly to a standard coalescent, scaling population size by a factor 1 − 3c, wherecrepresents the kinship coefficient of a randomly chosen mating pair. It provides the explanation for an earlier result describing mean coalescence time in the consanguinity model in terms ofc. The results extend the potential to make predictions about ROH and IBD in relation to demographic parameters of diploid populations.
EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes
Authors: Richter Daniel J. , Berney Cédric , Strassert Jürgen F. H. , Poh Yu-Ping , Herman Emily K. , Muñoz-Gómez Sergio A. , Wideman Jeremy G. , Burki Fabien , de Vargas Colomban 
Published: July 2020

AbstractEukProt is a database of published and publicly available predicted protein sets selected to represent the breadth of eukaryotic diversity, currently including 993 species from all major supergroups as well as orphan taxa. The goal of the database is to provide a single, convenient resource for gene-based research across the spectrum of eukaryotic life, such as phylogenomics and gene family evolution. Each species is placed within the UniEuk taxonomic framework in order to facilitate downstream analyses, and each data set is associated with a unique, persistent identifier to facilitate comparison and replication among analyses. The database is regularly updated, and all versions will be permanently stored and made available via FigShare. The current version has a number of updates, notably ‘The Comparative Set’ (TCS), a reduced taxonomic set with high estimated completeness while maintaining a substantial phylogenetic breadth, which comprises 196 predicted proteomes. A BLAST web server and graphical displays of data set completeness are available at http://evocellbio.com/eukprot/. We invite the community to provide suggestions for new data sets and new annotation features to be included in subsequent versions, with the goal of building a collaborative resource that will promote research to understand eukaryotic diversity and diversification.
Three times NO: no relationship between frontal alpha asymmetry and depressive disorders in a multiverse analysis of three studies
Authors: Kołodziej Aleksandra , Magnuski Mikołaj , Ruban Anastasia , Brzezicka Aneta 
Published: July 2020

AbstractFor decades, the frontal alpha asymmetry (FAA) - a disproportion in EEG alpha oscillations power between right and left frontal channels - has been one of the most popular measures of depressive disorders (DD) in electrophysiology studies. Patients with DD often manifest a left-sided FAA: relatively higher alpha power in the left versus right frontal lobe. Recently, however, multiple studies failed to confirm this effect, questioning its reproducibility. Our purpose is to thoroughly test the validity of FAA in depression by conducting a multiverse analysis - running many related analyses and testing the sensitivity of the effect to changes in the analytical approach - on data from three independent studies. Only two of the 81 analyses revealed significant results. We conclude the paper by discussing theoretical assumptions underlying the FAA and suggest a list of guidelines for improving and expanding the EEG data analysis in future FAA studies.
Resting-state functional connectivity predicts recovery from visually induced motion sickness
Authors: Miyazaki Jungo , Yamamoto Hiroki , Ichimura Yoshikatsu , Yamashiro Hiroyuki , Murase Tomokazu , Yamamoto Tetsuya , Umeda Masahiro , Higuchi Toshihiro 
Published: July 2020

AbstractMovies depicting certain types of motion often provoke uncomfortable symptoms similar to motion sickness, termed visually induced motion sickness (VIMS). VIMS generally evolves slowly during the viewing of a motion stimulus and, when the stimulus is removed, the recovery proceeds over time. Recent human neuroimaging studies have provided new insights into the neural bases underlying the evolution of VIMS. In contrast, no study has investigated the neural bases underlying the recovery from VIMS. Study of the recovery process is critical for the development of a way to promote recovery and could provide further clues for understanding the mechanisms of VIMS. We thus investigated brain activity during the recovery from VIMS with functional connectivity (FC) magnetic resonance imaging. We found enhanced recovery-related FC patterns involving brain areas such as the insular, cingulate, and visual cortical regions, which have been suggested to play important roles in the emergence of VIMS. These regions also constituted large interactive networks. Furthermore, the increase in FC was correlated with the subjective awareness of recovery for the following 5 pairs of brain regions: insula–superior temporal gyrus, claustrum–left and right inferior parietal lobules, claustrum–superior temporal gyrus, and superior frontal gyrus–lentiform nucleus. Considering the previous findings on the functions of these regions and the present findings, it is suggested that the increase in FC may reflect brain processes such as enhanced interoceptive awareness to one’s own bodily state, a neuroplastic change in visual processing circuits, and/or the maintenance of visual spatial memory.