bluuebunny/crossref_metadata_2025_split huggingface dataset:
DCI: learning causal differences between gene regulatory networks
Authors: Belyaeva Anastasiya , Squires Chandler , Uhler Caroline 
Published: March 2021

Abstract

Summary
Designing interventions to control gene regulation necessitates modeling a gene regulatory network by a causal graph. Currently, large-scale gene expression datasets from different conditions, cell types, disease states, and developmental time points are being collected. However, application of classical causal inference algorithms to infer gene regulatory networks based on such data is still challenging, requiring high sample sizes and computational resources. Here, we describe an algorithm that efficiently learns the differences in gene regulatory mechanisms between different conditions. Our difference causal inference (DCI) algorithm infers changes (i.e. edges that appeared, disappeared, or changed weight) between two causal graphs given gene expression data from the two conditions. This algorithm is efficient in its use of samples and computation since it infers the differences between causal graphs directly without estimating each possibly large causal graph separately. We provide a user-friendly Python implementation of DCI and also enable the user to learn the most robust difference causal graph across different tuning parameters via stability selection. Finally, we show how to apply DCI to single-cell RNA-seq data from different conditions and cell states, and we also validate our algorithm by predicting the effects of interventions.

Availability and implementation
Python package freely available at http://uhlerlab.github.io/causaldag/dci.

Supplementary information
Supplementary data are available at Bioinformatics online.
LSTrAP-Kingdom: an automated pipeline to generate annotated gene expression atlases for kingdoms of life
Authors: Goh William , Mutwil Marek 
Published: March 2021

Abstract

Motivation
There are now more than two million RNA sequencing experiments for plants, animals, bacteria and fungi publicly available, allowing us to study gene expression within and across species and kingdoms. However, the tools allowing the download, quality control and annotation of this data for more than one species at a time are currently missing.

Results
To remedy this, we present the Large-Scale Transcriptomic Analysis Pipeline in Kingdom of Life (LSTrAP-Kingdom) pipeline, which we used to process 134 521 RNA-seq samples, achieving ∼12 000 processed samples per day. Our pipeline generated quality-controlled, annotated gene expression matrices that rival the manually curated gene expression data in identifying functionally related genes.

Availability and implementation
LSTrAP-Kingdom is available from: https://github.com/wirriamm/plants-pipeline and is fully implemented in Python and Bash.

Supplementary information
Supplementary data are available at Bioinformatics online.
Zbed3 Is Indispensable for Wnt Signaling Regulation of Cortical Layers Formation in Developing Brain
Authors: Ruan Xiangbin , Liu Gaoao , Zhou Jiafeng , Chen Pan , Sun Changjie , Liu Wei , Wu Chao , Hou Lin , Yin Bin , Qiang Boqin , Shu Pengcheng , Peng Xiaozhong 
Published: March 2021

Abstract
Wnt/β-catenin signaling plays multiple important roles during mammalian brain development, and it regulates the proliferation and differentiation of neural progenitors in a context-dependent manner and affects neocortex layer formation. However, the specific role of Wnt/β-catenin in neuronal layer fate determination in the neocortex is still unclear. Here, we report that Zbed3, which is a positive regulator of Wnt/β-catenin signaling, colocalizes with β-catenin at the endfeet of radial glia in the ventricular zone of embryo mouse neocortex. Overexpression and knockdown of Zbed3 increased and decreased the activity of Wnt/β-catenin signaling in the neocortex, respectively. Interestingly, knockdown of Zbed3 in vivo could significantly shift neuronal fates from deep layers to upper layers but is not required for the proliferation and differentiation of neural progenitors. Overexpression of Zbed3 led to increased generation of deep-layer neurons without impairing cell cycle exit of neural progenitors. More importantly, knockdown of Zbed3 could effectively block the effects of the ectopic expression of stabilized β-catenin on neocortex layer formation. Hence, our results demonstrate that Zbed3 is indispensable for Wnt/β-catenin signaling regulating neuronal layer fates in the developing brain.
Brain Basis of Psychopathy in Criminal Offenders and General Population
Authors: Nummenmaa Lauri , Lukkarinen Lasse , Sun Lihua , Putkinen Vesa , Seppälä Kerttu , Karjalainen Tomi , Karlsson Henry K , Hudson Matthew , Venetjoki Niina , Salomaa Marja , Rautio Päivi , Hirvonen Jussi , Lauerma Hannu , Tiihonen Jari 
Published: March 2021

AbstractPsychopathy is characterized by persistent antisocial behavior, impaired empathy, and egotistical traits. These traits vary also in normally functioning individuals. Here, we tested whether such antisocial personalities are associated with similar structural and neural alterations as those observed in criminal psychopathy. Subjects were 100 non-convicted well-functioning individuals, 19 violent male offenders, and 19 matched controls. Subjects underwent T1-weighted magnetic resonance imaging and viewed movie clips with varying violent content during functional magnetic resonance imaging. Psychopathic traits were evaluated with Levenson Self-Report Psychopathy Scale (controls) and Psychopathy Checklist-Revised (offenders). Psychopathic offenders had lower gray matter density (GMD) in orbitofrontal cortex and anterior insula. In the community sample, affective psychopathy traits were associated with lower GMD in the same areas. Viewing violence increased brain activity in periaqueductal grey matter, thalamus, somatosensory, premotor, and temporal cortices. Psychopathic offenders had increased responses to violence in thalamus and orbitofrontal, insular, and cingulate cortices. In the community sample, impulsivity-related psychopathy traits were positively associated with violence-elicited responses in similar areas. We conclude that brain characteristics underlying psychopathic spectrum in violent psychopathy are related to those observed in well-functioning individuals with asocial personality features.
Unmet needs for CKD care: from the general population to the CKD clinics—how many patients are we missing?
Authors: Torreggiani Massimo , Chatrenet Antoine , Fois Antioco , Coindre Jean Philippe , Crochette Romain , Sigogne Mickael , Wacrenier Samuel , Seret Guillaume , Mazé Béatrice , Lecointre Léna , Breuer Conrad , Fessi Hafedh , Piccoli Giorgina Barbara 
Published: March 2021

Abstract

Introduction
Prevalence of chronic kidney disease (CKD) varies around the world. Little is known about the discrepancy between the general population's needs and nephrology care offered. We aimed to contribute to filling this gap and propose a means to infer the number of patients needing follow-up.

Methods
All patients undergoing at least one nephrology consultation in 2019 were enrolled. We used the ratio between CKD Stages 3 and 4 reported in the literature, and considered that only 25–50% of CKD Stage 3 patients have progressive CKD, to hypothesize different scenarios to estimate the number of CKD Stage 3 patients still needing nephrology follow-up.

Results
The 1992 CKD patients were followed-up in our centre (56.93% males; age 66.71 ± 18.32 years; 16.82% Stage 1; 14.66% Stage 2; 39.46% Stage 3; 19.88% Stage 4; 7.68% Stage 5). The ratio between Stages 3 and 4 in population studies ranged from 7.72 to 51.29, being 1.98 in our centre. Hypothesizing that we followed-up 100, 70 or 50% of CKD Stage 4 patients, 528–2506 CKD Stage 3 patients in our area would need nephrology follow-up [1885–8946 per million population (p.m.p.)]. Three to 17 additional nephrologists p.m.p. would be necessary to fully cover the need for care.

Conclusions
The number of patients with CKD Stage 3 who would benefit from nephrology care is high. Considering that one patient-year of delay of dialysis could cover a nephrologist’s annual salary, interventions aimed to improve the care of advanced CKD may be economically sound.
Multimodality cardiac imaging for management of a cardiac mass in the era of COVID-19: a case report
Authors: Ranjan Pragya , LaRocca Gina , Sanz Javier , Croft Lori 
Published: March 2021

Abstract

Background
Atrial myxomas are the most common benign cardiac tumours. This case highlights an unusual presentation and complex management of a patient who was incidentally found to have a left atrial tumour concerning for a myxoma.

Case summary
A 54-year-old-woman presented with symptoms of nausea and vomiting and was found to have a left atrial mass incidentally in addition to a renal infarct. She was also found to have COVID-19 and the mass was initially thought to be a thrombus. With the help of multimodality imaging, it was determined that the mass was an atrial myxoma and she was started on short-term anticoagulation to prevent recurrent embolization. After 6 weeks of anticoagulation, she successfully underwent elective resection of the mass which was confirmed to be myxoma with superimposed thrombus.

Discussion
It is difficult to differentiate cardiac tumours from intracardiac thrombus and multimodality cardiac imaging is crucial to make an accurate diagnosis. While the treatment of atrial myxomas involves early surgical resection, it becomes more complicated with concurrent COVID-19 infection.
The Standard Portfolio Choice Problem in Germany
Authors: Breunig Christoph , Huck Steffen , Schmidt Tobias , Weizsäcker Georg 
Published: March 2021

AbstractWe study an investment experiment with a representative sample of German households. Respondents invest in a safe asset and a risky asset whose return is tied to the German stock market. Experimental investments correlate with beliefs about stock market returns and exhibit desirable external validity at least in one respect: they predict real-life stock market participation. But many households are unresponsive to an exogenous increase in the risky asset’s return. The data analysis and a series of additional laboratory experiments suggest that task complexity decreases the responsiveness to incentives. Modifying the safe asset’s return has a larger effect on behaviour than modifying the risky asset’s return.
Heat-killed Lactobacillus acidophilus mediates Fusobacterium nucleatum induced pro-inflammatory responses in epithelial cells
Authors: Ding Qinfeng , Sun Xuecheng , Cao Shuai , Zhao Cancan , Wang Yitong , Wang Xudong 
Published: March 2021

Abstract
Probiotics is widespreadly used nowadays. However, the safety issue with the use of live probiotics is still a matter of contention. In recent years, an expanding body of evidence supports the beneficial role of heat-killed probiotics in the maintenance of systemic health, whereas the role of these heat-killed bacteria on periodontal health remains unclear. This study aimed to evaluate the effects of heat-killed probiotics on periodontal pathogen virulence and associated mechanisms. We demonstrated that heat-killed Lactobacillus acidophilus was able to coaggregate with Fusobacterium nucleatum, the bridging bacteria of oral biofilm, and inhibit the adhesion and invasion of F. nucleatum, leading to a subsequent elimination of pro-inflammatory cytokine production in oral epithelial cells. This coaggregation further caused a suppression of the virulence gene fap2 expression in F. nucleatum. Therefore, heat-killed L. acidophilus might downregulate the pro-inflammatory cytokine expression in epithelial cells via coaggregation with F. nucleatum and suppression of F. nucleatum fap2 expression, which was the first demonstration that heat-killed probiotics modulate periodontal disease pathogenesis via coaggregation. Collectively, this finding provides new evidence that heat-killed probiotics might exert beneficial effects to periodontal health by coaggregating with periodontal pathogens and modulating their virulence.
Interactions between the WEE-1.3 kinase and the PAM-1 aminopeptidase in oocyte maturation and the earlyC. elegansembryo
Authors: Benton Dorothy , Jaeger Eva C , Kilner Arielle , Kimble Ashley , Lowry Josh , Schleicher Emily M , Power Kaiden M , Uibel Danielle , Eisele Caprice , Bowerman Bruce , Lyczak Rebecca 
Published: March 2021

AbstractPuromycin-sensitive aminopeptidases are found across phyla and are known to regulate the cell-cycle and play a protective role in neurodegenerative disease. PAM-1 is a puromycin-sensitive aminopeptidase important for meiotic exit and polarity establishment in the one-cell Caenorhabditis elegans embryo. Despite conservation of this aminopeptidase, little is known about its targets during development. In order to identify novel interactors, we conducted a suppressor screen and isolated four suppressing mutations in three genes that partially rescued the maternal-effect lethality of pam-1 mutants. Suppressed strains show improved embryonic viability and polarization of the anterior–posterior axis. We identified a missense mutation in wee-1.3 in one of these suppressed strains. WEE-1.3 is an inhibitory kinase that regulates maturation promoting factor. Although the missense mutation suppressed polarity phenotypes in pam-1, it does so without restoring centrosome–cortical contact or altering the cortical actomyosin cytoskeleton. To see if PAM-1 and WEE-1.3 interact in other processes, we examined oocyte maturation. Although depletion of wee-1.3 causes sterility due to precocious oocyte maturation, this effect was lessened in pam-1 worms, suggesting that PAM-1 and WEE-1.3 interact in this process. Levels of WEE-1.3 were comparable between wild-type and pam-1 strains, suggesting that WEE-1.3 is not a direct target of the aminopeptidase. Thus, we have established an interaction between PAM-1 and WEE-1.3 in multiple developmental processes and have identified suppressors that are likely to further our understanding of the role of puromycin-sensitive aminopeptidases during development.
Solution-Focused Brief Therapy for Substance Use: A Review of the Literature
Authors: Franklin Cynthia , Hai Audrey Hang 
Published: March 2021

Abstract
Substance use is a prevalent public health issue. Most social workers may encounter substance use in their work with clients and need effective therapeutic strategies for this issue. Since the 1980s, solution-focused brief therapy (SFBT) has been practiced with clients who have substance use problems, and clinical training materials have been developed to help practitioners learn and use SFBT in substance use treatment. Despite the longevity of the use of SFBT in practice, there are no published reviews of outcome studies to guide practitioners using SFBT. This article fills a gap in current literature on SFBT and substance use treatment by reviewing the published studies on SFBT where the focus was on substance use treatment. Five databases were searched to identify eligible studies. Experts and reference lists of relevant studies were also consulted. Nine studies were identified and included in the review. All studies reviewed found promising evidence on SFBT’s effectiveness in improving substance use behaviors and related psychosocial problems. Five of the nine studies reviewed showed that SFBT can change substance use and comorbid mental health and psychosocial problems such as depression, trauma, and school- and work-related behavior problems. The article concludes with a discussion of the study results’ implications for clinical practice and future research.
Mental Health Service Utilization among Adults with Head Injury with Loss of Consciousness: Implications for Social Work
Authors: Coxe Kathryn A , Lee Guijin , Kagotho Njeri , Eads Ray 
Published: March 2021

Abstract
The purpose of this study was to identify factors associated with mental health service utilization among adults with head injury with loss of consciousness (LOC) using Andersen’s model of health. This secondary data analysis used the 2011–2014 National Health and Nutrition Examination Survey with data collected from 7,399 adults. Binary logistic regression was conducted to determine odds associated with predisposing, enabling, and needs factors on head injury with LOC and mental health service utilization. A total of  948 (12.8 percent) adults 40 years and older self-reported head injury with LOC. Head injury with LOC was higher among men and people with lower income, illicit drug use history, and moderate to severe depression. Mental health service utilization for people with head injury with LOC was lower among older-age adults and those with no health insurance. However, utilization was higher among adults with military service, history of drug use, and moderate to severe depression. Social workers in health care settings play critical roles serving adults with traumatic brain injury (TBI) through mental health and substance use disorder treatment and bridging gaps in service access. Social workers should recognize the complex needs of clients with TBI and factors affecting mental health service use.
Use of a Contained Mycobacterium tuberculosis Mouse Infection Model to Predict Active Disease and Containment in Humans
Authors: Duffy Fergal J , Olson Gregory S , Gold Elizabeth S , Jahn Ana , Aderem Alan , Aitchison John D , Rothchild Alissa C , Diercks Alan H , Nemeth Johannes 
Published: March 2021

Abstract
Previous studies have identified whole-blood transcriptional risk and disease signatures for tuberculosis; however, several lines of evidence suggest that these signatures primarily reflect bacterial burden, which increases before symptomatic disease. We found that the peripheral blood transcriptome of mice with contained Mycobacterium tuberculosis infection (CMTI) has striking similarities to that of humans with active tuberculosis and that a signature derived from these mice predicts human disease with accuracy comparable to that of signatures derived directly from humans. A set of genes associated with immune defense are up-regulated in mice with CMTI but not in humans with active tuberculosis, suggesting that their up-regulation is associated with bacterial containment. A signature comprising these genes predicts both protection from tuberculosis disease and successful treatment at early time points where current signatures are not predictive. These results suggest that detailed study of the CMTI model may enable identification of biomarkers for human tuberculosis.
Implicit-based computer-aided design for additively manufactured functionally graded cellular structures
Authors: Nguyen Cong Hong Phong , Kim Youngdoo , Do Quang Thang , Choi Young 
Published: March 2021

Abstract
Additive manufacturing has enabled the fabrication of complex structures such as cellular structures. Although numerous design frameworks have been proposed for cellular structures, their effectiveness was limited owing to the use of B-rep-based representation. To address the limitations in previous research, this study proposes an implicit-based computer-aided design framework customized for additively manufactured functionally graded cellular structures (AM-FGCSs). The proposed design framework effectively aids in both single- and multiscale structural optimization for designing FGCSs. Moreover, implicit-based modeling afforded a reliable geometric representation that could efficiently assist computation tasks such as visualization, validation, and process planning for fabrication. In addition, two case studies were conducted to demonstrate the effectiveness of the proposed framework for designing FGCSs. The first case study on a three-point bending beam design problem proved the practicality of implicit-based representation in multiscale structural design. Meanwhile, the second case study validated the proficiency of the proposed framework in process planning for fabrication and engineering analysis, the two most vital computation tasks in designing cellular structures.
Spatial Distribution of Chesapeake Bay Riparian Hemlock Forests Threatened by Hemlock Woolly Adelgid
Authors: Fajvan Mary Ann , Morin Randall S 
Published: March 2021

Abstract
Landscape-scale maps of tree species densities are important tools for managing ecosystems threatened by forest pests. Eastern hemlock dominates riparian forests throughout its range. As a conifer in a deciduous landscape, hemlock plays an ecohydrological role, especially when other species are dormant. The nonnative, hemlock woolly adelgid has caused widespread hemlock decline and mortality. We used two existing basal area raster layers first to identify Chesapeake Bay subwatersheds with ≥6 percent hemlock basal area and second to quantify hemlock basal area densities within fixed-width riparian buffers of 50 m, 100 m, 250 m, and 500 m. Hemlock densities were higher in riparian zones compared with entire subwatersheds. In five subwatersheds, 50 m and 100 m zones had higher percentages of pixels with ≥25 percent hemlock basal area. We produced maps identifying hemlock riparian densities in the Pine Creek Watershed, which managers can use to prioritize sites for supplemental conifer planting under anticipated hemlock decline.
Delayed chylothorax in the absence of radiological evidence of rib or vertebral body fractures following blunt trauma
Authors: Mazhar Khurum , Mohamed Saifullah , Patel Akshay Jatin , Berger-Veith Sarah , Abid Qamar , Ghosh Shilajit 
Published: March 2021

Abstract
Our case report illustrates effective implementation of conservative measures without the need for more invasive procedures, which can be required in refractory cases. Our patient was a 42-year-old female who fell from a horse and presented with a 1-week history of dyspnoea. Investigations revealed her to have a large right chylothorax, which was treated conservatively with chest drainage and octreotide. The patient remained in hospital for a total of 3 days prior to being discharged home without further complications. Blunt traumatic chylothorax should be considered as part of the differential diagnosis in patients who present with ongoing dyspnoea or chest discomfort within a 2-week preceding history of blunt trauma. Radiological imaging should be mandatory and the absence of posterior thoracic fractures does not exclude the diagnosis. Conservative management with pleural drainage, medium-chain triglyceride diet and octreotide yielded excellent results in our case.
Kozak Sequence Acts as a Negative Regulator for De Novo Transcription Initiation of Newborn Coding Sequences in the Plant Genome
Authors: Hata Takayuki , Satoh Soichirou , Takada Naoto , Matsuo Mitsuhiro , Obokata Junichi 
Published: March 2021

Abstract
The manner in which newborn coding sequences and their transcriptional competency emerge during the process of gene evolution remains unclear. Here, we experimentally simulated eukaryotic gene origination processes by mimicking horizontal gene transfer events in the plant genome. We mapped the precise position of the transcription start sites (TSSs) of hundreds of newly introduced promoterless firefly luciferase (LUC) coding sequences in the genome of Arabidopsis thaliana cultured cells. The systematic characterization of the LUC-TSSs revealed that 80% of them occurred under the influence of endogenous promoters, while the remainder underwent de novo activation in the intergenic regions, starting from pyrimidine-purine dinucleotides. These de novo TSSs obeyed unexpected rules; they predominantly occurred ∼100 bp upstream of the LUC inserts and did not overlap with Kozak-containing putative open reading frames (ORFs). These features were the output of the immediate responses to the sequence insertions, rather than a bias in the screening of the LUC gene function. Regarding the wild-type genic TSSs, they appeared to have evolved to lack any ORFs in their vicinities. Therefore, the repulsion by the de novo TSSs of Kozak-containing ORFs described above might be the first selection gate for the occurrence and evolution of TSSs in the plant genome. Based on these results, we characterized the de novo type of TSS identified in the plant genome and discuss its significance in genome evolution.