bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interventions to reduce waste and improve billing compliance with medications in single-dose vials
Authors: Trovato Anthony , Tyler Linda S , Nickman Nancy A , Findlay Russell 
Published: November 2022

AbstractPurposeThe purpose of this process improvement project was to implement features in the electronic health record to help reduce inappropriate drug waste and Medicare billing noncompliance for injectable drugs in single-dose vials in outpatient settings.MethodsThe pharmacy department mapped processes from order entry to dose administration and claims processing. They used the process map to identify gaps that could lead to inappropriate drug waste. The organization then chose 3 drugs they believed to be at high risk of excess waste and possible billing noncompliance after cross-referencing drug cost, volume of use, and previous Medicare audits in outpatient settings. They tested a grouper and dose rounding on these drugs and compared 3 months of claims before and after implementation to assess the impact on waste and billing compliance.ResultsThis study evaluated 826 claims before implementation and 1,075 claims after implementation. A total of 455 of 826 (55.1%) preimplementation claims included drug waste compared to 224 of 1,075 (20.8%) postimplementation claims. Twenty-three claims before implementation included an amount of waste exceeding the smallest vial size, putting the institution at risk of billing noncompliance. No claims had excess waste in the postimplementation period. The approximate cost of total drug waste before implementation was $1,397,437, with approximately $23,730 from inappropriate carfilzomib claims. The approximate cost of waste after implementation was $569,041. This equated to a reduction in drug waste of approximately $828,396 for bevacizumab-bvzr, carfilzomib, and ipilimumab.ConclusionUsing a grouper and implementing dose rounding, the institution reduced drug waste, saved money, and reduced the incidence of claims noncompliant with Medicare Part B billing requirements.
Gender Moderates the Association Between Cognitive Reappraisal and Alcohol-Related Problems Among Adolescents
Authors: Teeters Jenni B , Laves Eliza H , King Shelby A , Brausch Amy M 
Published: November 2022

AbstractBackground/ObjectiveAlcohol use typically begins in adolescence, and the risk of later alcohol use disorders increases with earlier age of onset. Emotion dysregulation in adolescence has been linked to alcohol use. The present study seeks to extend previous findings by examining whether gender moderates the association between emotion regulation strategies (suppression and cognitive reappraisal) and alcohol-related problems in a longitudinal sample of adolescents.MethodData were collected as part of an ongoing study of high school students from the south-central region of the USA. The sample included 693 adolescents who participated in a study on suicidal ideation and risk behaviors. The majority of participants were girls (54.8%), white (85%) and heterosexual (87.7%). Baseline (T1) and 6-month follow-up (T2) data were analyzed for the present study.ResultsNegative binomial moderation analyses revealed that gender moderated the association between cognitive reappraisal and alcohol-related problems, such that the association between reappraisal and alcohol-related problems was significantly stronger for boys than for girls. Gender did not moderate the association between suppression and alcohol-related problems.ConclusionsThe results suggest that emotion regulation strategies may be a particularly useful target for prevention and intervention efforts. Future research should consider tailoring adolescent alcohol prevention and intervention efforts focused on emotion regulation strategies by gender to bolster cognitive reappraisal skills and decrease suppression.
An in silico genome-wide screen for circadian clock strength in human samples
Authors: Wu Gang , Ruben Marc D , Francey Lauren J , Lee Yin Yeng , Anafi Ron C , Hogenesch John B 
Published: November 2022

Abstract

Motivation
Years of time-series gene expression studies have built a strong understanding of clock-controlled pathways across species. However, comparatively little is known about how ‘non-clock’ pathways influence clock function. We need a strong understanding of clock-coupled pathways in human tissues to better appreciate the links between disease and clock function.

Results
We developed a new computational approach to explore candidate pathways coupled to the clock in human tissues. This method, termed LTM, is an in silico screen to infer genetic influences on circadian clock function. LTM uses natural variation in gene expression in human data and directly links gene expression variation to clock strength independent of longitudinal data. We applied LTM to three human skin and one melanoma datasets and found that the cell cycle is the top candidate clock-coupled pathway in healthy skin. In addition, we applied LTM to thousands of tumor samples from 11 cancer types in the TCGA database and found that extracellular matrix organization-related pathways are tightly associated with the clock strength in humans. Further analysis shows that clock strength in tumor samples is correlated with the proportion of cancer-associated fibroblasts and endothelial cells. Therefore, we show both the power of LTM in predicting clock-coupled pathways and classify factors associated with clock strength in human tissues.

Availability and implementation
LTM is available on GitHub (https://github.com/gangwug/LTMR) and figshare (https://figshare.com/articles/software/LTMR/21217604) to facilitate its use.

Supplementary information
Supplementary data are available at Bioinformatics online.
Integrating transformer and imbalanced multi-label learning to identify antimicrobial peptides and their functional activities
Authors: Pang Yuxuan , Yao Lantian , Xu Jingyi , Wang Zhuo , Lee Tzong-Yi 
Published: November 2022

Abstract

Motivation
Antimicrobial peptides (AMPs) have the potential to inhibit multiple types of pathogens and to heal infections. Computational strategies can assist in characterizing novel AMPs from proteome or collections of synthetic sequences and discovering their functional abilities toward different microbial targets without intensive labor.

Results
Here, we present a deep learning-based method for computer-aided novel AMP discovery that utilizes the transformer neural network architecture with knowledge from natural language processing to extract peptide sequence information. We implemented the method for two AMP-related tasks: the first is to discriminate AMPs from other peptides, and the second task is identifying AMPs functional activities related to seven different targets (gram-negative bacteria, gram-positive bacteria, fungi, viruses, cancer cells, parasites and mammalian cell inhibition), which is a multi-label problem. In addition, asymmetric loss was adopted to resolve the intrinsic imbalance of dataset, particularly for the multi-label scenarios. The evaluation showed that our proposed scheme achieves the best performance for the first task (96.85% balanced accuracy) and has a more unbiased prediction for the second task (79.83% balanced accuracy averaged across all functional activities) when compared with that of strategies without imbalanced learning or deep learning.

Availability and implementation
The source code and data of this study are available at https://github.com/BiOmicsLab/TransImbAMP.

Supplementary information
Supplementary data are available at Bioinformatics online.
Role of progesterone on dexamethasone-induced alterations in placental vascularization and progesterone receptors in rats
Authors: Alawadhi Mariam , Kilarkaje Narayana , Mouihate Abdeslam , Al-Bader Maie D 
Published: November 2022

Abstract

Background
Intrauterine growth restriction (IUGR) is manifested by lower maternal progesterone levels, smaller placental size, and decreased placental vascularity indicated by lower expression of vascular endothelial growth factor (VEGF). Studies showed that progesterone increases angiogenesis and induces VEGF expression in different tissues. Therefore, the aim of the present study is to evaluate the effect of progesterone on placental vascular bed and VEGF expression and the modulation of nuclear and membranous progesterone receptors (PR) in dexamethasone-induced rat IUGR model.

Methods
Pregnant Sprague–Dawley rats were allocated into four groups and given intraperitoneal injections of either saline, dexamethasone, dexamethasone, and progesterone or progesterone. Injections started on gestation day (DG) 15 and lasted until the days of euthanization (19 and 21 DG). Enzyme-linked immunosorbent assay was used to evaluate plasma progesterone levels. Real-time PCR and western blotting were used to evaluate gene and protein expressions of VEGF, and PR in labyrinth and basal placental zones. Immunohistochemistry was used to locate VEGF and different PRs in placental cells. Immunofluorescence was used to monitor the expression of blood vessel marker (αSMA).

Results
Dexamethasone decreased the vascular bed fraction and the expression of VEGF in both placental zones. Progesterone co-treatment with dexamethasone prevented this reduction. Nuclear and membrane PRs showed tissue-specific expression in different placental zones and responded differently to both dexamethasone and progesterone.

Conclusions
Progesterone treatment improves the outcomes in IUGR pregnancy. Progesterone alleviated DEX-induced IUGR probably by promoting placental VEGF and angiogenesis.
Novel role for conceptus signals in mRNA expression regulation by DNA methylation in porcine endometrium during early pregnancy
Authors: Kaczynski Piotr , van der Weijden Vera , Goryszewska-Szczurek Ewelina , Baryla Monika , Ulbrich Susanne E , Waclawik Agnieszka 
Published: November 2022

Abstract
During early pregnancy, porcine conceptuses (the embryos with associated membranes) secrete estradiol-17β (E2)—their major signal for maternal recognition of pregnancy—and prostaglandin E2 (PGE2). Both hormones induce prominent changes of the endometrial transcriptome in vivo. Studies on endometrial pathologies have shown that E2 affects gene expression by epigenetic mechanisms related to DNA methylation. Herein, we determined the effects of E2 and PGE2 alone, and a combined E2 + PGE2 treatment administered into the uterine lumen in vivo on the expression and activity of DNA-methyltransferases (DNMTs) and on CpG methylation patterns of selected genes in porcine endometrium. To compare the effect of treatment with the physiological effect of pregnancy, endometria from day 12 pregnant/cyclic gilts were included. Both E2 and PGE2 significantly reduced the expression of DNMTs. Likewise, the expressions of DNMT1 and DNMT3A were decreased on day 12 of pregnancy compared to the estrous cycle. DNMT activity increased in endometrial samples following E2 treatment and in gilts on day 12 of pregnancy. Treatment with E2 alone and/or simultaneously with PGE2 altered endometrial DNA methylation of CpG sites of ADAMTS20, ADH1C, BGN, PSAT1, and WNT5A. Different CpG methylation patterns of ADAMTS20, BGN, DMBT1, RASSF1, and WNT5A were found in the endometrium on day 12 of pregnancy compared to day 12 of the estrous cycle. Significant correlations were detected between CpG methylation and gene expression for ADAMTS20, ADH1C, BGN, DMBT1, PSAT1, and WNT5A. Our results indicate that CpG methylation induced by embryonic signals may contribute to regulating endometrial gene expression during pregnancy establishment.
Beta-defensins as marker for male fertility: a comprehensive review
Authors: Solanki Subhash , Kumar Vijay , Kashyap Poonam , Kumar Rakesh , De Sachinandan , Datta Tirtha Kumar 
Published: November 2022

AbstractBovine male fertility in animals has a direct impact on the productivity of dairy herds. The epididymal sperm maturations involve extensive sperm surface modifications to gain the fertilizing ability, especially by absorptions of the plethora of biomolecules, including glycoprotein beta-defensins (BDs), enzymes, organic ions, protein, and phospholipids. Defensins are broad-range nonspecific antimicrobial peptides that exhibit strong relations with innate and adaptive immunity, but their roles in male fertility are relatively recently identified. In the course of evolution, BD genes give rise to different clusters with specific functions, especially reproductive functions, by undergoing duplications and nonsynonymous mutations. BD polymorphisms have been reported with milk compositions, disease resistance, and antimicrobial activities. However, in recent decades, the link of BD polymorphisms with fertility has emerged as an appealing improvement of reproductive performance such as sperm motility, membrane integrity, cervical mucus penetration, evading of uterus immunosurveillance, oviduct cell attachment, and egg recognition. The reproductive-specific glycosylated BD class-A BDs (CA-BDs) have shown age- and sex-specific expressions in male reproductive organs, signifying their physiological pleiotropism, especially in the sperm maturation and sperm transport in the female reproductive tract. By considering adult male reproductive organ-specific BD expressions, importance in sperm functionalities, and bioinformatic analysis, we have selected two bovine BBD126 and BBD129 genes as novel potential biomarkers of bovine male fertility. Despite the importance of BDs, however, genomic characterization of most BD genes across most livestock and nonmodel organisms remains predictive/incomplete. The current review discusses our understanding of BD pleiotropic functions, polymorphism, and genomic structural attributes concerning the fertilizability of the male gamete in dairy animals.
Hyperconnectivity and altered interactions of a nucleus accumbens network in post-stroke depression
Authors: Oestreich Lena K L , Wright Paul , O’Sullivan Michael J 
Published: November 2022

Abstract
Post-stroke depression is a common complication of stroke. To date, no consistent locus of injury is associated with this complication. Here, we probed network dynamics and structural alterations in post-stroke depression in four functional circuits linked to major depressive disorder and a visual network, which served as a control network. Forty-four participants with recent stroke (mean age = 69.03, standard deviation age = 8.59, age range = 51–86 and gender: female = 10) and 16 healthy volunteers (mean age = 71.53, standard deviation age = 10.62, age range = 51–84 and gender: female = 11) were imaged with 3-Tesla structural, diffusion and resting-state functional MRI. The Geriatric Depression Scale was administered to measure depression severity. Associations between depression severity and functional connectivity were investigated within networks seeded from nucleus accumbens, amygdala, dorsolateral prefrontal cortex and primary visual cortex. In addition, the default mode network was identified by connectivity with medial prefrontal cortex and posterior cingulate cortex. Circuits that exhibited altered activity associated with depression severity were further investigated by extracting within-network volumetric and microstructural measures from structural images. In the stroke group, functional connectivity within the nucleus accumbens-seeded network (left hemisphere: P = 0.001; and right hemisphere: P = 0.004) and default mode network (cluster one: P &lt; 0.001; and cluster two: P &lt; 0.001) correlated positively with depressive symptoms. Normal anticorrelations between these two networks were absent in patients with post-stroke depression. Grey matter volume of the right posterior cingulate cortex (Pearson correlation coefficient = −0.286, P = 0.03), as well as microstructural measures in the posterior cingulate cortex (right: Pearson correlation coefficient = 0.4, P = 0.024; and left: Pearson correlation coefficient = 0.3, P = 0.048), right medial prefrontal cortex (Pearson correlation coefficient = 0.312, P = 0.039) and the medial forebrain bundle (Pearson correlation coefficient = 0.450, P = 0.003), a major projection pathway interconnecting the nucleus accumbens-seeded network and linking to medial prefrontal cortex, were associated with depression severity. Depression after stroke is marked by reduced mutual inhibition between functional circuits involving nucleus accumbens and default mode network as well as volumetric and microstructural changes within these networks. Aberrant network dynamics present in patients with post-stroke depression are therefore likely to be influenced by secondary, pervasive alterations in grey and white matter, remote from the site of injury.
Use of omics analysis for low-dose radiotoxicology and health risk assessment: the case of uranium
Authors: Grison Stéphane , Souidi Maâmar 
Published: November 2022

Abstract
Exposure to environmental pollution and the increase in the incidence of multifactorial diseases in the population have become health problems for industrialized countries. In this context, the question of the health impact of exposure to these pollutants is not clearly identified in the low-dose range. This article looks at this problem using the example of preclinical studies of the effects of chronic low-dose exposure to uranium in rats. These studies demonstrate the value of molecular screening analyses (omics) and multimodal integrative approaches, of which the extreme sensitivity and breadth of observation spectrum make it possible to observe all the biological processes affected and the mechanisms of action triggered at the molecular level by exposure to low doses. They also show the value of these analytical approaches for finding diagnostic biomarkers or indicators of prognosis, which can be necessary to evaluate a risk. Finally, the results of these studies raise the question of the health risk caused by epigenomic deregulations occurring during critical developmental phases and their potential contribution to the development of chronic diseases that are metabolic in origin or to the development of certain cancer liable in the long term to affect the exposed adult and possibly its progeny.
Real-world perioperative outcomes of segmentectomy versus lobectomy for early-stage lung cancer: a propensity score-matched analysis
Authors: Ichinose Junji , Yamamoto Hiroyuki , Aokage Keiju , Kondo Haruhiko , Sato Yukio , Suzuki Kenji , Chida Masayuki 
Published: November 2022

Abstract

OBJECTIVES
This study aimed to compare the real-world outcomes of segmentectomy and lobectomy for lung cancer after adjusting for background factors and the extent of lymphadenectomy.

METHODS
This retrospective cohort study used a nationwide database in Japan. The data of patients with clinical stage 0/IA lung cancer who underwent segmentectomy or lobectomy between 2017 and 2019 were retrieved. Short-term postoperative outcomes were compared between the segmentectomy and lobectomy groups using propensity score-matched analysis.

RESULTS
In the total cohort of 59 663 patients, 11 975 and 47 688 patients were in the segmentectomy and lobectomy groups, respectively. After propensity score matching, 8426 matched patients from each group were retrieved. All confounders including age, sex, comorbidities, smoking history, respiratory function, tumour size, clinical stage, affected lobe and extent of lymphadenectomy were appropriately adjusted. The overall complication rate and the cardiopulmonary complication rate were lower in the segmentectomy group than in the lobectomy group (8.5% vs 11.2%, P &lt; 0.001 and 7.5% vs 10.3%, P &lt; 0.001, respectively). The incidence of prolonged air leak was also lower after segmentectomy than after lobectomy (3.6% vs 5.3%). Surgical mortality, operative time and blood loss volume were comparable between the 2 groups.

CONCLUSIONS
The postoperative complication rate was lower with segmentectomy than with lobectomy for early-stage lung cancer.
Security force assistance to Cameroon: how building enclave units deepens autocracy
Authors: Harkness Kristen A 
Published: November 2022

Abstract
Western countries have increasingly turned to security force assistance (SFA) to build partner capacity and counter terrorist threats in weakly governed states. This trend sits uncomfortably alongside widespread pessimism that coup-proofed and patronage ridden armies can be meaningfully reformed and made combat effective. Searching for new solutions, both scholars and practitioners have converged on the idea of creating ‘enclave units’—elite forces isolated from the broader military that can be proficiently trained and then deployed on counterterrorism missions. But can enclave units resolve the fundamental interest misalignments that have undermined SFA more broadly? This article leverages the case of the Bataillons d'Intervention Rapide in Cameroon to build theoretical insights into the promises and perils of enclave units. I find that achieving combat proficiency perversely deepens autocracy by strengthening the repressive capacity of dictators. When harshening policies and further marginalization then lead to uprisings, often among ethnic minority groups, embattled autocrats redeploy western trained enclave units against civilians. Extending these insights to the shadow cases of the Iraqi Golden Division and Somali Danab suggests that an indefinite western commitment to remain in-country and directly command enclave units may be necessary to prevent their political misuse.
Unravelling early sinus node dysfunction after pediatric cardiac surgery: a pre-existing arrhythmogenic substrate
Authors: Ramdat Misier Nawin L , Taverne Yannick J H J , van Schie Mathijs S , Kharbanda Rohit K , van Leeuwen Wouter J , Kammeraad Janneke A E , Bogers Ad J J C , de Groot Natasja M S 
Published: November 2022

Abstract
Early post-operative sinus node dysfunction (SND) is common in paediatric patients undergoing surgical correction of congenital heart defects (CHD). At present, the pathophysiology of these arrhythmias is incompletely understood. In this case series, we present three paediatric patients in whom we performed intraoperative epicardial mapping and who developed early post-operative SND. All patients had either an inferior or multiple sinoatrial node (SAN) exit sites, in addition to extensive conduction disorders at superior and inferior right atrium. Our findings contribute to the hypothesis that pre-existing alterations in SAN exit sites in combination with atrial conduction disorders may predispose paediatric patients with CHD for early post-operative SND. Such insights in the development of arrhythmias are crucial as it may be the first step in identifying high-risk patients.
Relative Stable Pairs and a Non-Calabi–Yau Wall Crossing
Authors: Pădurariu Tudor 
Published: November 2022

Abstract
Let $Y$ be a smooth projective threefold, and let $f:Y\to X$ be a birational map with $Rf_*\mathcal {O}_Y=\mathcal {O}_X$. When $Y$ is Calabi–Yau, Bryan–Steinberg (BS) defined enumerative invariants associated to such maps called $f$-relative stable (or BS) invariants. When $X$ has Gorenstein singularities and $f$ has relative dimension one, they compared these invariants to the Donaldson–Thomas, or equivalently Pandharipande–Thomas invariants (PT) of $Y$. We define BS invariants for maps $f$ as above without assuming that $Y$ is Calabi–Yau. For $X$ with Gorenstein and rational singularities, $f$ of relative dimension one, and for insertions from $X$ and arbitrary descendant levels, we conjecture a relation between the generating functions of BS and PT of $Y$. We check the conjecture for the contraction $f: Y\to X$ of a rational curve $C$ with normal bundle $N_{C/Y}\cong \mathcal {O}_C(-1)^{\oplus 2}$ using degeneration and localization techniques to reduce to a Calabi–Yau situation, which we then treat using Joyce’s motivic Hall algebra.