bluuebunny/crossref_metadata_2025_split huggingface dataset:
Telepharmacy services in acute care: Diverse needs within a large health system
Authors: Kester Kenneth A , Finck Karen M , Reehal Praveen , Reynolds Dorraine 
Published: January 2022

Abstract

Purpose
In this paper, we describe CommonSpirit Health’s telepharmacy service, which serves 64 hospitals in 10 states. Hospitals range in size from critical access to quaternary care centers.

Summary
Telepharmacy services in acute care may be divided into 2 primary styles: hospitals requiring after-hours support utilizing telepharmacists to bridge shifts otherwise uncovered by pharmacists and hospitals with round-the-clock onsite pharmacy services utilizing telepharmacists to enhance efficiency in processing medication orders. When providing after-hours service, telepharmacists review all medication orders. The primary goal is to provide pharmacist care at all hours. In hospitals with round-the-clock onsite pharmacy services, telepharmacists focus on efficiency of medication order review. Median turnaround times in these hospitals decreased 50% to 70% after implementing a telepharmacy service. Barriers to implementation include managing different electronic health records, variability in hospital practices, and communicating with onsite clinicians. Regular interaction with onsite leaders is a key component in overcoming these barriers. This enables the telepharmacy team to respond to hospital-specific changes and maintain competence. The service adjusts to provide additional support based on the needs of the sites. Most telepharmacists work from home. While this can present challenges, we consider it an advantage in recruitment and retention.

Conclusion
CommonSpirit Health utilizes its telepharmacy service for hospitals large and small to enhance efficiency in processing medication orders and to provide round-the-clock pharmacist care.
Rethinking Masculinities Studies
Authors: Breu Christopher 
Published: January 2022

Abstract
This review essay examines three new books in masculinities studies. It also provides a mapping of the field as it has changed over the past twenty years, exploring how our understanding of masculinity has changed with recent developments in trans, intersex, and queer theory and activism. How does the field change in response to changing conceptions of gender in the present? The review provides a provisional answer to this question.
Three recent books on masculinity in US culture provide an opportunity to examine how much the field of masculinities studies has kept up with changing frameworks around gender and embodiment in the present.
ABlooper: fast accurate antibody CDR loop structure prediction with accuracy estimation
Authors: Abanades Brennan , Georges Guy , Bujotzek Alexander , Deane Charlotte M 
Published: January 2022

Abstract

Motivation
Antibodies are a key component of the immune system and have been extensively used as biotherapeutics. Accurate knowledge of their structure is central to understanding their antigen-binding function. The key area for antigen binding and the main area of structural variation in antibodies are concentrated in the six complementarity determining regions (CDRs), with the most important for binding and most variable being the CDR-H3 loop. The sequence and structural variability of CDR-H3 make it particularly challenging to model. Recently deep learning methods have offered a step change in our ability to predict protein structures.

Results
In this work, we present ABlooper, an end-to-end equivariant deep learning-based CDR loop structure prediction tool. ABlooper rapidly predicts the structure of CDR loops with high accuracy and provides a confidence estimate for each of its predictions. On the models of the Rosetta Antibody Benchmark, ABlooper makes predictions with an average CDR-H3 RMSD of 2.49 Å, which drops to 2.05 Å when considering only its 75% most confident predictions.

Availability and implementation
https://github.com/oxpig/ABlooper.

Supplementary information
Supplementary data are available at Bioinformatics online.
EDTox: an R Shiny application to predict the endocrine disruption potential of compounds
Authors: Sakhteman Amirhossein , Ghosh Arindam , Fortino Vittorio 
Published: January 2022

Abstract

Purpose
Endocrine disruptors are a rising concern due to the wide array of health issues that it can cause. Although there are tools for mode of action (MoA)-based prediction of endocrine disruption (e.g. QSAR Toolbox and iSafeRat), none of them is based on toxicogenomics data. Here, we present EDTox, an R Shiny application enabling users to explore and use a computational method that we have recently published to identify and prioritize endocrine disrupting (ED) chemicals based on toxicogenomic data. The EDTox pipeline utilizes previously trained toxicogenomic-driven classifiers to make predictions on new untested compounds by using their molecular initiating events. Furthermore, the proposed R Shiny app allows users to extend the prediction systems by training and adding new classifiers based on new available toxicogenomic data. This functionality helps users to explore the ED potential of chemicals in new, untested exposure scenarios.

Availability and implementation
This tool is available as web application (www.edtox.fi) and stand-alone software on GitHub and Zenodo (https://doi.org/10.5281/zenodo.5817093).

Supplementary information
Supplementary data are available at Bioinformatics online.
DeepUMQA: ultrafast shape recognition-based protein model quality assessment using deep learning
Authors: Guo Sai-Sai , Liu Jun , Zhou Xiao-Gen , Zhang Gui-Jun 
Published: January 2022

AbstractMotivationProtein model quality assessment is a key component of protein structure prediction. In recent research, the voxelization feature was used to characterize the local structural information of residues, but it may be insufficient for describing residue-level topological information. Design features that can further reflect residue-level topology when combined with deep learning methods are therefore crucial to improve the performance of model quality assessment.ResultsWe developed a deep-learning method, DeepUMQA, based on Ultrafast Shape Recognition (USR) for the residue-level single-model quality assessment. In the framework of the deep residual neural network, the residue-level USR feature was introduced to describe the topological relationship between the residue and overall structure by calculating the first moment of a set of residue distance sets and then combined with 1D, 2D and voxelization features to assess the quality of the model. Experimental results on the CASP13, CASP14 test datasets and CAMEO blind test show that USR could supplement the voxelization features to comprehensively characterize residue structure information and significantly improve model assessment accuracy. The performance of DeepUMQA ranks among the top during the state-of-the-art single-model quality assessment methods, including ProQ2, ProQ3, ProQ3D, Ornate, VoroMQA, ProteinGCN, ResNetQA, QDeep, GraphQA, ModFOLD6, ModFOLD7, ModFOLD8, QMEAN3, QMEANDisCo3 and DeepAccNet.Availability and implementationThe DeepUMQA server is freely available at http://zhanglab-bioinf.com/DeepUMQA/.Supplementary informationSupplementary data are available at Bioinformatics online.
fastANCOM: a fast method for analysis of compositions of microbiomes
Authors: Zhou Chao , Wang Huimin , Zhao Hongyu , Wang Tao 
Published: January 2022

Abstract

Summary
Analysis of compositions of microbiomes (ANCOM) compares the absolute abundances of microbes between two or more ecosystems using relative abundances in specimens derived from these ecosystems. Despite its impressive performance, there are two drawbacks to ANCOM. First, with K microbes it requires fitting K(K−1)/2 models for log-ratios of counts, and so can be computationally intensive. Second, it does not output P-values for microbes detected as differentially abundant. We propose a fast implementation of ANCOM, fastANCOM, that fits only K models for log-transformed counts. fastANCOM provides P-values to declare statistical significance and outputs log fold changes of abundance between groups. We demonstrate that fastANCOM compares favorably with existing differential abundance testing methods in terms of running time, false discovery rate and power.

Availability and implementation
fastANCOM is available at https://github.com/ZRChao/fastANCOM.

Supplementary information
Supplementary data are available at Bioinformatics online.
Abnormal neurite density and orientation dispersion in frontal lobe link to elevated hyperactive/impulsive behaviours in young adults with traumatic brain injury
Authors: Cao Meng , Luo Yuyang , Wu Ziyan , Wu Kai , Li Xiaobo 
Published: January 2022

Abstract
Traumatic brain injury is a major public health concern. A significant proportion of individuals experience post-traumatic brain injury behavioural impairments, especially in attention and inhibitory control domains. Traditional diffusion-weighted MRI techniques, such as diffusion tensor imaging, have provided tools to assess white matter structural disruptions reflecting the long-term brain tissue alterations associated with traumatic brain injury. The recently developed neurite orientation dispersion and density imaging is a more advanced diffusion MRI modality, which provides more refined characterization of brain tissue microstructures by assessing the neurite orientation dispersion and neurite density properties. In this study, neurite orientation dispersion and density imaging data from 44 young adults with chronic traumatic brain injury (who had no prior-injury diagnoses of any sub-presentation of attention deficits/hyperactivity disorder or experience of severe inattentive and/or hyperactive behaviours) and 45 group-matched normal controls were investigated, to assess the post-injury morphometrical and microstructural brain alterations and their relationships with the behavioural outcomes. Maps of fractional anisotropy, neurite orientation dispersion index and neurite density index were calculated. Vertex-wise and voxel-wise analyses were conducted for grey matter and white matter, respectively. Post hoc region-of-interest-based analyses were also performed. Compared to the controls, the group of traumatic brain injury showed significantly increased orientation dispersion index and significantly decreased neurite density index in various grey matter regions, as well as significantly decreased orientation dispersion index in several white matter regions. Brain–behavioural association analyses indicated that the reduced neurite density index of the left precentral gyrus and the reduced orientation dispersion index of the left superior longitudinal fasciculus were significantly associated with elevated hyperactive/impulsive symptoms in the patients with traumatic brain injury. These findings suggest that post-injury chronical neurite intracellular volume and angular distribution anomalies in the frontal lobe, practically the precentral area, can significantly contribute to the onset of hyperactive/impulsive behaviours in young adults with traumatic brain injury.
Mucosal-associated invariant T cells are activated in an interleukin-18-dependent manner in Epstein–Barr virus-associated T/natural killer cell lymphoproliferative diseases
Authors: Ishikawa Yuriko , Yamada Masaki , Wada Naomi , Takahashi Etsuko , Imadome Ken-Ichi 
Published: January 2022

AbstractMucosal-associated invariant T (MAIT) cells are a type of innate immune cells that protect against some infections. However, the involvement of MAIT cells in Epstein–Barr virus-associated T/natural killer cell lymphoproliferative diseases (EBV-T/NK-LPD) is unclear. In this study, we found that MAIT cells were highly activated in the blood of patients with EBV-T/NK-LPD. MAIT cell activation levels correlated with disease severity and plasma IL-18 levels. Stimulation of healthy peripheral blood mononuclear cells with EBV resulted in activation of MAIT cells, and this activation level was enhanced by exogenous IL-18. MAIT cells stimulated by IL-18 might thus be involved in the immunopathogenesis of EBV-T/NK-LPD.
Intrinsic dynamics and topography of sensory input systems
Authors: Çatal Yasir , Gomez-Pilar Javier , Northoff Georg 
Published: January 2022

Abstract
The brain is continuously bombarded by external stimuli, which are processed in different input systems. The intrinsic features of these sensory input systems remain yet unclear. Investigating topography and dynamics of input systems is the goal of our study in order to better understand the intrinsic features that shape their neural processing. Using a functional magnetic resonance imaging dataset, we measured neural topography and dynamics of the input systems during rest and task states. Neural dynamics were probed by scale-free activity, measured with the power-law exponent (PLE), as well as by order/disorder as measured with sample entropy (SampEn). Our main findings during both rest and task states are: 1) differences in neural dynamics (PLE, SampEn) between regions within each of the three sensory input systems 2) differences in topography and dynamics among the three input systems; 3) PLE and SampEn correlate and, as demonstrated in simulation, show non-linear relationship in the critical range of PLE; 4) scale-free activity during rest mediates the transition of SampEn from rest to task as probed in a mediation model. We conclude that the sensory input systems are characterized by their intrinsic topographic and dynamic organization which, through scale-free activity, modulates their input processing.
Hyperexcitable and immature-like neuronal activity in the auditory cortex of adult rats lacking the language-linked CNTNAP2 gene
Authors: Scott Kaela E , Mann Rajkamalpreet S , Schormans Ashley L , Schmid Susanne , Allman Brian L 
Published: January 2022

Abstract
The contactin-associated protein-like 2 gene, CNTNAP2, is a highly penetrant risk gene thought to play a role in the genetic etiology of language-related disorders, such as autism spectrum disorder and developmental language disorder. Despite its candidacy for influencing language development, few preclinical studies have examined the role of CNTNAP2 in auditory processing. Using in vivo and in vitro electrophysiological recordings in a rat model with translational validity, we report that a loss of the Cntnap2 gene function caused immature-like cortical evoked potentials, delayed multiunit response latencies to acoustic stimuli, impaired temporal processing, and led to a pattern of hyperexcitability in both multiunit and single cell recordings in adulthood. These collective results provide direct evidence that a constitutive loss of Cntnap2 gene function in rats can cause auditory processing impairments similar to those seen in language-related human disorders, indicating that its contribution in maintaining cortical neuron excitability may underlie the cortical activity alterations observed in Cntnap2−/− rats.
Low-intensity focused ultrasound stimulation reverses social avoidance behavior in mice experiencing social defeat stress
Authors: Wang Yimeng , Bai Yang , Xiao Xi , Wang Ling , Wei Ganjiang , Guo Mingkun , Song Xizi , Tian Yutao , Ming Dong , Yang Jiajia , Zheng Chenguang 
Published: January 2022

AbstractThe excitatory neurons of the medial prefrontal cortex (mPFC) respond to social stimuli. However, little is known about how the neural activity is altered during social avoidance, and whether it could act as a target of low-intensity focused ultrasound stimulation (LIFUS) to rescue social deficits. The present study aimed to investigate the mechanisms of neuronal activities and inflammatory responses underlying the effect of LIFUS on social avoidance. We found that chronic LIFUS stimulation can effectively improve social avoidance in the defeated mice. Calcium imaging recordings by fiber photometry in the defeated mice showed inhibited ensemble activity during social behaviors. LIFUS instantaneously triggered the mPFC neuronal activities, and chronic LIFUS significantly enhanced their neuronal excitation related to social interactions. We further found that the excessive activation of microglial cells and the overexpression of the inflammation signaling, i.e. Toll-like receptors(TLR4)/nuclear factor-kappaB(NF-КB), in mPFC were significantly inhibited by LIFUS. These results suggest that the LIFUS may inhibit social avoidance behavior by reducing activation of the inflammatory response, increasing neuronal excitation, and protecting the integrity of the neuronal structure in the mPFC. Our findings raised the possibility of LIFUS being applied as novel neuromodulation for social avoidance treatment in neuropsychiatric diseases.
The convergence and divergence of episodic and semantic functions across lateral parietal cortex
Authors: Humphreys Gina F , Jung JeYoung , Lambon Ralph Matthew A 
Published: January 2022

Abstract
Decades of research have highlighted the importance of lateral parietal cortex (LPC) across a myriad of cognitive domains. Yet, the underlying function of LPC remains unclear. Two domains that have emphasized LPC involvement are semantic memory and episodic memory retrieval. From each domain, sophisticated functional models have been proposed, as well as the more domain-general assumption that LPC is engaged by any form of internally directed cognition (episodic/semantic retrieval being examples). Here we used a combination of functional magnetic resonance imaging, functional connectivity, and diffusion tensor imaging white-matter connectivity to show that (i) ventral LPC (angular gyrus [AG]) was positively engaged during episodic retrieval but disengaged during semantic memory retrieval and (ii) activity negatively varied with task difficulty in the semantic task whereas episodic activation was independent of difficulty. In contrast, dorsal LPC (intraparietal sulcus) showed domain general activation that was positively correlated with task difficulty. Finally, (iii) a dorsal–ventral and anterior–posterior gradient of functional and structural connectivity was found across the AG (e.g. mid-AG connected with episodic retrieval). We propose a unifying model in which LPC as a whole might share a common underlying neurocomputation (multimodal buffering) with variations in the emergent cognitive functions across subregions arising from differences in the underlying connectivity.
Modeling the Impact of Vaccination Strategies for Nursing Homes in the Context of Increased Severe Acute Respiratory Syndrome Coronavirus 2 Community Transmission and Variants
Authors: Holmdahl Inga , Kahn Rebecca , Slifka Kara Jacobs , Dooling Kathleen , Slayton Rachel B 
Published: January 2022

Abstract
Using an agent-based model, we examined the impact of community prevalence, the Delta variant, staff vaccination coverage, and booster vaccines for residents on outbreak dynamics in nursing homes. Increased staff coverage and high booster vaccine effectiveness leads to fewer infections, but cumulative incidence is highly dependent on community transmission.
Epidemiology of native kidney disease in Flanders: results from the FCGG kidney biopsy registry
Authors: Laurens Wim , Deleersnijder Dries , Dendooven Amélie , Lerut Evelyne , De Vriese An S , Dejagere Tom , Helbert Mark , Hellemans Rachel , Koshy Priyanka , Maes Bart , Pipeleers Lissa , Van Craenenbroeck Amaryllis H , Van Laecke Steven , Vande Walle Johan , Coutteneye Marie M , De Meester Johan , Sprangers Ben ,   The FCGG collaborative group, De Vriese An , De Rycke Anja , Bogaert Anne-Marie , Woestenburg Annemie , Denys Bart , Maes Bart , Peeters Domien , Vanbelleghem Hilde , Donck Jan , Scharpé Johan , De Clippeleir Nele , Vanparys Joris , Meyvis Karen , Vandepitte Kurt , Reyns Liza-Maria , Verresen Luc , Decupere Marc , Helbert Mark , Zeegers Miranda , Neirynck Nathalie , Bernaert Pascale , Dejagere Tom , Lemahieu Wim , Sprangers Ben , Pipeleers Lissa , Hellemans Rachel , Van Laecke Steven , Levtchenko Elena , Karamaria Sevasti , Van Hoeck Koen , Trouet Dominique , Mauel Reiner , Dendooven Amélie , Hoorens Anne , Van Dorpe Jo , Praet Marleen , Geers Caroline , Lerut Evelyne , Koshy Priyanka , Roskams Tania , Aydin Selda , Siozopoulou Vasiliki , Schelfhout Anne-Marie , De Raeve Hendrik , Steenkiste Edwin , Dedeurwaerdere Francesca , Dalle Ignace , Cokelaere Kristof , Deloose Stijn , De Paepe Pascale , Van Eyken Peter 
Published: January 2022

ABSTRACT

Background
The Flemish Collaborative Glomerulonephritis Group (FCGG) registry is the first population-based native kidney biopsy registry in Flanders, Belgium. In this first analysis, we report on patient demographics, frequency distribution and incidence rate of biopsied kidney disease in adults in Flanders.

Methods
From January 2017 to December 2019, a total of 2054 adult first native kidney biopsies were included. A ‘double diagnostic coding’ strategy was used, in which every biopsy sample received a histopathological and final clinical diagnosis. Frequency distribution and incidence rate of both diagnoses were reported and compared with other European registries.

Results
The median age at biopsy was 61.1 years (interquartile range, 46.1–71.7); male patients were more prevalent (62.1%) and biopsy incidence rate was 129.3 per million persons per year. Immunoglobulin A nephropathy was the most frequently diagnosed kidney disease (355 biopsies, 17.3% of total) with a similar frequency as in previously published European registries. The frequency of tubulointerstitial nephritis (220 biopsies, 10.7%) and diabetic kidney disease (154 biopsies, 7.5%) was remarkably higher, which may be attributed to changes in disease incidence as well as biopsy practices. Discordances between histopathological and final clinical diagnoses were noted and indicate areas for improvement in diagnostic coding systems.

Conclusions
The FCGG registry, with its ‘double diagnostic coding’ strategy, provides useful population-based epidemiological data on a large Western European population and allows subgroup selection for future research.
The Role of Wind and Semiochemicals in Mediating Switching Behavior in the Southern Pine Beetle (Coleoptera: Curculionidae: Scolytinae)
Authors: Sullivan Brian T , Brownie Cavell 
Published: January 2022

Abstract
Aggressive bark beetles colonize and kill healthy conifers through pheromone-mediated mass aggregation. In several species, the focal point of aggregation moves progressively from mass-attacked ‘focus trees’ to adjacent, unattacked ‘recipient trees’, resulting in infestation growth. This process, termed ‘switching’, is hypothesized to be mediated in whole or in part by antiaggregation pheromones released by beetles as colonization intensifies on a focus tree. We tested this hypothesis with the southern pine beetle, Dendroctonus frontalis Zimmermann (Coleoptera: Curculionidae: Scolytinae), by using a windvane apparatus that maintained an unbaited, black, cylindrical trap (surrogate for a recipient tree) continuously 4 m downwind from an identical trap baited with synthetic aggregation attractant (surrogate for a focus tree). In two of three replicated trials, addition of pheromone components with antiaggregation activity, endo-brevicomin or verbenone, to the upwind trap caused a significant but small (&lt;15%) increase in the proportion of beetles caught in the downwind trap. In one of two trials with endo-brevicomin, this shift was associated with a significant reduction in catches in the downwind trap and an overall reduction in catches of beetles by the trap pair. This suggests that an inhibitor-induced increase in landings on the recipient relative to the focus tree may be countered by the radial effects of the inhibitor, which at sufficiently high release may reduce responses to both the focus and recipient tree. We discuss spatial factors that might govern the role of antiaggregation pheromones in stimulating infestation growth as well as additional factors that likely govern switching behavior.