bluuebunny/crossref_metadata_2025_split huggingface dataset:
ICARUS, an interactive web server for single cell RNA-seq analysis
Authors: Jiang Andrew , Lehnert Klaus , You Linya , Snell Russell G 
Published: April 2022

Abstract
Here we present ICARUS, a web server to enable users without experience in R to undertake single cell RNA-seq analysis. The focal point of ICARUS is its intuitive tutorial-style user interface, designed to guide logical navigation through the multitude of pre-processing, analysis and visualization steps. ICARUS is easily accessible through a dedicated web server (https://launch.icarus-scrnaseq.cloud.edu.au/) and avoids installation of software on the user's computer. Notable features include the facility to apply quality control thresholds and adjust dimensionality reduction and cell clustering parameters. Data is visualized through 2D/3D UMAP and t-SNE plots and may be curated to remove potential confounders such as cell cycle heterogeneity. ICARUS offers flexible differential expression analysis with user-defined cell groups and gene set enrichment analysis to identify likely affected biological pathways. Eleven organisms including human, dog, mouse, rat, zebrafish, fruit fly, nematode, yeast, cattle, chicken and pig are currently supported. Visualization of multimodal data including those generated by CITE-seq and the 10X Genomics Multiome kit is included. ICARUS incorporates a function to save the current state of analysis avoiding computationally intensive steps during repeat analysis. The complete analysis of a typical single cell RNA-seq dataset by inexperienced users may be achieved in 1–2 h.
SigCom LINCS: data and metadata search engine for a million gene expression signatures
Authors: Evangelista John Erol , Clarke Daniel J B , Xie Zhuorui , Lachmann Alexander , Jeon Minji , Chen Kerwin , Jagodnik Kathleen M , Jenkins Sherry L , Kuleshov Maxim V , Wojciechowicz Megan L , Schürer Stephan C , Medvedovic Mario , Ma’ayan Avi 
Published: April 2022

Abstract
Millions of transcriptome samples were generated by the Library of Integrated Network-based Cellular Signatures (LINCS) program. When these data are processed into searchable signatures along with signatures extracted from Genotype-Tissue Expression (GTEx) and Gene Expression Omnibus (GEO), connections between drugs, genes, pathways and diseases can be illuminated. SigCom LINCS is a webserver that serves over a million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. SigCom LINCS is built with Signature Commons, a cloud-agnostic skeleton Data Commons with a focus on serving searchable signatures. SigCom LINCS provides a rapid signature similarity search for mimickers and reversers given sets of up and down genes, a gene set, a single gene, or any search term. Additionally, users of SigCom LINCS can perform a metadata search to find and analyze subsets of signatures and find information about genes and drugs. SigCom LINCS is findable, accessible, interoperable, and reusable (FAIR) with metadata linked to standard ontologies and vocabularies. In addition, all the data and signatures within SigCom LINCS are available via a well-documented API. In summary, SigCom LINCS, available at https://maayanlab.cloud/sigcom-lincs, is a rich webserver resource for accelerating drug and target discovery in systems pharmacology.
BioSimulators: a central registry of simulation engines and services for recommending specific tools
Authors: Shaikh Bilal , Smith Lucian P , Vasilescu Dan , Marupilla Gnaneswara , Wilson Michael , Agmon Eran , Agnew Henry , Andrews Steven S , Anwar Azraf , Beber Moritz E , Bergmann Frank T , Brooks David , Brusch Lutz , Calzone Laurence , Choi Kiri , Cooper Joshua , Detloff John , Drawert Brian , Dumontier Michel , Ermentrout G Bard , Faeder James R , Freiburger Andrew P , Fröhlich Fabian , Funahashi Akira , Garny Alan , Gennari John H , Gleeson Padraig , Goelzer Anne , Haiman Zachary , Hasenauer Jan , Hellerstein Joseph L , Hermjakob Henning , Hoops Stefan , Ison Jon C , Jahn Diego , Jakubowski Henry V , Jordan Ryann , Kalaš Matúš , König Matthias , Liebermeister Wolfram , Sheriff Rahuman S Malik , Mandal Synchon , McDougal Robert , Medley J Kyle , Mendes Pedro , Müller Robert , Myers Chris J , Naldi Aurelien , Nguyen Tung V N , Nickerson David P , Olivier Brett G , Patoliya Drashti , Paulevé Loïc , Petzold Linda R , Priya Ankita , Rampadarath Anand K , Rohwer Johann M , Saglam Ali S , Singh Dilawar , Sinha Ankur , Snoep Jacky , Sorby Hugh , Spangler Ryan , Starruß Jörn , Thomas Payton J , van Niekerk David , Weindl Daniel , Zhang Fengkai , Zhukova Anna , Goldberg Arthur P , Schaff James C , Blinov Michael L , Sauro Herbert M , Moraru Ion I , Karr Jonathan R 
Published: April 2022

AbstractComputational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations.
rRNA operon multiplicity as a bacterial genome stability insurance policy
Authors: Fleurier Sebastien , Dapa Tanja , Tenaillon Olivier , Condon Ciarán , Matic Ivan 
Published: April 2022

Abstract
Quick growth restart after upon encountering favourable environmental conditions is a major fitness contributor in natural environment. It is widely assumed that the time required to restart growth after nutritional upshift is determined by how long it takes for cells to synthesize enough ribosomes to produce the proteins required to reinitiate growth. Here we show that a reduction in the capacity to synthesize ribosomes by reducing number of ribosomal RNA (rRNA) operons (rrn) causes a longer transition from stationary phase to growth of Escherichia coli primarily due to high mortality rates. Cell death results from DNA replication blockage and massive DNA breakage at the sites of the remaining rrn operons that become overloaded with RNA polymerases (RNAPs). Mortality rates and growth restart duration can be reduced by preventing R-loop formation and improving DNA repair capacity. The same molecular mechanisms determine the duration of the recovery phase after ribosome-damaging stresses, such as antibiotics, exposure to bile salts or high temperature. Our study therefore suggests that a major function of rrn operon multiplicity is to ensure that individual rrn operons are not saturated by RNAPs, which can result in catastrophic chromosome replication failure and cell death during adaptation to environmental fluctuations.
A widespread family of WYL-domain transcriptional regulators co-localizes with diverse phage defence systems and islands
Authors: Picton David M , Harling-Lee Joshua D , Duffner Samuel J , Went Sam C , Morgan Richard D , Hinton Jay C D , Blower Tim R 
Published: April 2022

Abstract
Bacteria are under constant assault by bacteriophages and other mobile genetic elements. As a result, bacteria have evolved a multitude of systems that protect from attack. Genes encoding bacterial defence mechanisms can be clustered into ‘defence islands’, providing a potentially synergistic level of protection against a wider range of assailants. However, there is a comparative paucity of information on how expression of these defence systems is controlled. Here, we functionally characterize a transcriptional regulator, BrxR, encoded within a recently described phage defence island from a multidrug resistant plasmid of the emerging pathogen Escherichia fergusonii. Using a combination of reporters and electrophoretic mobility shift assays, we discovered that BrxR acts as a repressor. We present the structure of BrxR to 2.15 Å, the first structure of this family of transcription factors, and pinpoint a likely binding site for ligands within the WYL-domain. Bioinformatic analyses demonstrated that BrxR-family homologues are widespread amongst bacteria. About half (48%) of identified BrxR homologues were co-localized with a diverse array of known phage defence systems, either alone or clustered into defence islands. BrxR is a novel regulator that reveals a common mechanism for controlling the expression of the bacterial phage defence arsenal.
MtEFD and MtEFD2: Two transcription factors with distinct neofunctionalization in symbiotic nodule development
Authors: Jardinaud Marie-Françoise , Fromentin Justine , Auriac Marie-Christine , Moreau Sandra , Pecrix Yann , Taconnat Ludivine , Cottret Ludovic , Aubert Grégoire , Balzergue Sandrine , Burstin Judith , Carrere Sébastien , Gamas Pascal 
Published: April 2022

Abstract
Rhizobium–legume nitrogen-fixing symbiosis involves the formation of a specific organ, the root nodule, which provides bacteria with the proper cellular environment for atmospheric nitrogen fixation. Coordinated differentiation of plant and bacterial cells is an essential step of nodule development, for which few transcriptional regulators have been characterized. Medicago truncatula ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULE DIFFERENTIATION (MtEFD) encodes an APETALA2/ETHYLENE RESPONSIVE FACTOR (ERF) transcription factor, the mutation of which leads to both hypernodulation and severe defects in nodule development. MtEFD positively controls a negative regulator of cytokinin signaling, the RESPONSE REGULATOR 4 (MtRR4) gene. Here we showed that that the Mtefd-1 mutation affects both plant and bacterial endoreduplication in nodules, as well as the expression of hundreds of genes in young and mature nodules, upstream of known regulators of symbiotic differentiation. MtRR4 expressed with the MtEFD promoter complemented Mtefd-1 hypernodulation but not the nodule differentiation phenotype. Unexpectedly, a nonlegume homolog of MtEFD, AtERF003 in Arabidopsis (Arabidopsis thaliana), could efficiently complement both phenotypes of Mtefd-1, in contrast to the MtEFD paralog MtEFD2 expressed in the root and nodule meristematic zone. A domain swap experiment showed that MtEFD2 differs from MtEFD by its C-terminal fraction outside the DNA binding domain. Furthermore, clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9) mutagenesis of MtEFD2 led to a reduction in the number of nodules formed in Mtefd-1, with downregulation of a set of genes, including notably NUCLEAR FACTOR-YA1 (MtNF-YA1) and MtNF-YB16, which are essential for nodule meristem establishment. We, therefore, conclude that nitrogen-fixing symbiosis recruited two proteins originally expressed in roots, MtEFD and MtEFD2, with distinct functions and neofunctionalization processes for each of them.
Developing and testing a case-management intervention to support the return to work of health care workers with common mental health disorders
Authors: Parsons V , Juszczyk D , Gilworth G , Ntani G , Henderson M , Smedley J , McCrone P , Hatch S L , Shannon R , Coggon D , Molokhia M , Griffiths A , Walker-Bone K , Madan I 
Published: April 2022

Abstract

Background
To assess the feasibility and acceptability of conducting a trial of the clinical effectiveness and cost-effectiveness of a new case-management intervention to facilitate the return to work of health care workers, on sick leave, having a common mental disorder (CMD).

Methods
A mixed methods feasibility study.

Results
Systematic review examined 40 articles and 2 guidelines. Forty-nine National Health Service Occupational Health (OH) providers completed a usual care survey. We trained six OH nurses as case managers and established six recruitment sites. Forty-two out of 1938 staff on sick leave with a CMD were screened for eligibility, and 24 participants were recruited. Out of them, 94% were female. Eleven participants received the intervention and 13 received usual care. Engagement with most intervention components was excellent. Return-to-work self-efficacy improved more in the intervention group than in the usual care group. Qualitative feedback showed the intervention was acceptable.

Conclusions
The intervention was acceptable, feasible and low cost to deliver, but it was not considered feasible to recommend a large-scale effectiveness trial unless an effective method could be devised to improve the early OH referral of staff sick with CMD. Alternatively, the intervention could be trialled as a new stand-alone OH intervention initiated at the time of usual OH referral.
Comparative Effectiveness of Antipsychotics in Preventing Readmission for First-Admission Schizophrenia Patients in National Cohorts From 2001 to 2017 in Taiwan
Authors: Lin Yi-Hsuan , Wu Chi-Shin , Liu Chen-Chung , Kuo Po-Hsiu , Chan Hung-Yu , Chen Wei J 
Published: April 2022

Abstract

Background and Hypothesis
Antipsychotics remain the main treatment for schizophrenia, but their effectiveness is challenging to compare. We aimed to assess the comparative real-world effectiveness of antipsychotics in preventing readmission among patients in Asia with early-stage schizophrenia to inform clinical decision making.

Study Design
We did a retrospective cohort study of first-admission schizophrenia patients (ICD-9-CM: 295; ICD-10-CM: F20 and F25) from January 1, 2001, to December 31, 2017. The cohort was identified from the National Health Insurance Research Database NHIRD for Psychiatric Inpatients. The exposure was any antipsychotics prescribed post-discharge. The primary outcome was the readmission risk due to psychotic disorders, which was measured by adjusted hazard ratios (aHRs). Within-individual extended Cox models were applied for analyses, where the periods of oral risperidone use served as his or her own control.

Study Results
We selected 75 986 patients (men, 53.4%; mean [SD] age, 37.6 [12.0] years; mean [SD] duration of follow-up, 8.9 [5.0]) who were first admitted to psychiatric wards with schizophrenia in Taiwan. Among them, 47 150 patients (62.05%) had at least one readmission within 4 years. Compared to the period under treatment with oral risperidone, that under monotherapy with long-acting injectable antipsychotics (LAIs) had the lowest risk for psychotic readmission, with a risk reduction of 15–20%. However, the prevalence of person-prescription prevalence of LAIs remained low (&lt; 10%) during the follow-up period.

Conclusions
The use of LAIs after the first admission for schizophrenia has notable advantages in preventing readmission. Such formulations should be offered earlier in the course of illness.
Banging while Believing: The Intersection of Religiosity, Gang Membership, and Violence
Authors: Lauger Timothy R , Rivera Craig J 
Published: April 2022

Abstract
Religious groups and street gangs typically exhibit contrasting cultural systems that produce different behavioral consequences, especially relating to crime and violence. This study introduces and develops the isolated and integrated affiliation models to explain the potential intersection of gang membership and religious affiliation. The isolated affiliation model predicts that gang membership and personal religiosity are incompatible affiliations and will not overlap. The integrated affiliation model predicts that individuals can simultaneously embrace and negotiate gang and religious affiliations even when they seem opposed to each other. Using Add Health data, this study examines the intersection between religiosity, youth gang membership, and violence. Findings indicate that gang members do report being religious, although they are significantly less religious than non-gang peers on three of the four individual measures of religiosity, with a marginally significant difference on the overall religiosity scale. Among the full sample, religiosity is inversely associated with violence while gang membership is positively associated with violence. Among a gang-only subsample, personal religiosity is inversely related to the prevalence but not the extent of violence. These findings provide insight into potential role and identity conflicts experienced by religious youth gang members. Seemingly oppositional affiliations can overlap with religious life, influencing some forms of behavior.
Stem Cells from Human Exfoliated Deciduous Teeth Ameliorate Autistic-Like Behaviors of SHANK3 Mutant Beagle Dogs
Authors: Zhao Lu , Li Yuan , Kou Xiaoxing , Chen Benchi , Cao Jing , Li Jun , Zhang Jianqi , Wang Heng , Zhao Jianping , Shi Songtao 
Published: April 2022

Abstract
Mesenchymal stem cell-based therapy has emerged as a great potential approach to treat individuals with autism spectrum disorders (ASD), a group of developmental disabilities characterized by impairments in social interaction and communication. Stem cells from human exfoliated deciduous teeth (SHED), holding earlier developing characteristics, have immune-modulatory and anti-inflammatory properties. To investigate whether SHED transplantation can rescue autistic-like symptoms in SHANK3 mutant beagle dogs, 12 SHANK3 mutant beagle dogs were randomly assigned into 2 groups according to their behavior evaluated by social interaction tests. Six mutant dogs received 6 intravenous infusions of SHED and were followed up for 3 months by testing social interaction and inflammatory cytokine levels. We found that infusion of SHED significantly improved impaired social novel preference of SHANK3 mutant beagle dogs at 1- and 3-month follow-ups. Social intimacies (following, sniffing, and licking) between mutant beagle dogs and human experimenters were partly improved. Stressed tail posture, indicating social stress, was also significantly alleviated. In addition, we showed that the levels of serum interferon-γ and interleukin-10 were notably increased and decreased, respectively, in SHANK3 mutant beagle dogs. Infusion of SHED was able to rescue altered interferon-γ and interleukin-10 levels. We failed to observe any serious adverse events after infusion of SHED. In summary, SHED transplantation may be a safe and effective therapy for ASD. The correction in the levels of serum interferon-γ and interleukin-10 may serve as an index to predict autistic severity and therapeutic outcomes.
New Drug for Atopic Dermatitis
Authors: Aschenbrenner Diane S. 
Published: April 2022

Tralokinumab-ldrm (Adbry) is now approved for the treatment of moderate to severe atopic dermatitis in adults whose disease has not been controlled by topical therapies.Nurses and NPs should teach patients how to administer the drug subcutaneously and that more than one injection is needed to fulfill the prescribed dose.
Tezspire Approved for Severe Asthma
Authors: Aschenbrenner Diane S. 
Published: April 2022

Tezepelumab-ekko (Tezspire) has been approved by the Food and Drug Administration as an add-on maintenance therapy for people ages 12 years and older with severe asthma symptoms not controlled by current medication.The drug must be given subcutaneously by a health care provider.
Age-Related Changes in Facial Soft Tissue of Han Chinese: A Computed Tomographic Study
Authors: Wang Dawei , Zhang Qi , Zeng Ning , Wu Yiping 
Published: April 2022

BACKGROUND
Facial lifting and volume restoration are the major strategies of facial rejuvenation, but the aging of facial soft tissues has not been sufficiently explored.

OBJECTIVE
This study aimed to reveal the age-related changes in full facial soft tissue of Han Chinese by using computed tomography.

MATERIALS AND METHODS
The measurements were performed on head computed tomographic images of 200 Han Chinese subjects (100 men and 100 women). The thickness of facial soft tissue was measured at 20 anthropological landmarks of the skull.

RESULTS
The thickness at rhinion was increased, whereas the thickness at midphiltrum, supradentale, and infradentale was decreased, indicating the significant differences in both sexes. Besides, the thickness at glabella, nasion, supramentale, and menton was decreased significantly in women. The thickness at supraorbital and lateral orbit was increased with aging in either sex. The thickness at frontal eminence, infraorbital, supraglenoid, and gonion showed significant age-related increases in women, and the thickness at zygomatic arch, supra M2, and infra M2 was significantly decreased in men.

CONCLUSION
These results suggest that soft tissues in different areas of the face are selectively thickened or thinned with aging, thus providing a reference for rejuvenation procedures.
DEXAMETHASONE INTRAVITREAL IMPLANT COMPLICATIONS INCLUDING VITREOUS HEMORRHAGE AND HYPOTONY
Authors: Yu Jeffrey J. , Adrean Sean D. 
Published: April 2022

Purpose:
To describe cases of visually significant vitreous hemorrhage (VH) following dexamethasone intravitreal implant in our practice and present two cases that required surgical intervention and a case of VH and hypotony following dexamethasone implant. An injection technique that may minimize the incidence of these complications is described and illustrated.

Methods:
Retrospective case series.

Results:
The overall incidence of VH was 1.7% (8 of 467 injections) and those that required surgical intervention was 0.4% (2/467) over a 10-year period, from June 2010 to June 2020 (Table 1). Overall, 75% (6 of 8) VH resolved spontaneously over time, without surgical intervention.

Conclusion:
Nonclearing VH and hypotony are rare but serious complications of dexamethasone implant.
NONARTERITIC ANTERIOR ISCHEMIC OPTIC NEUROPATHY ASSOCIATED WITH IPSILATERAL HYPOPLASTIC INTERNAL CAROTID ARTERY
Authors: Abri Aghdam Kaveh , Aghajani Ali , Ghamari Kiandokht , Soltan Sanjari Mostafa 
Published: April 2022

Background:
Vascular insufficiency of the optic nerve head is the cause of nonarteritic ischemic optic neuropathy (NAION). Carotid artery abnormalities are now considered as a predisposing factor for developing NAION. In this report, we present a case of NAION associated with ipsilateral internal carotid artery hypoplasia.

Methods:
A 69-year-old female with decreased vision in her right eye due to NAION was evaluated. the magnetic resonance imaging showed a considerably smaller left internal carotid artery than the right side. The magnetic resonance angiography confirmed the disparity and perfusion abnormalities of intracranial carotid arteries.

Results:
The diagnosis of left internal carotid artery hypoplasia was made and verified by depicting a left side small carotid canal on the computed tomography scan.

Conclusion:
This report suggests that internal carotid artery hypoplasia could be associated with NAION.