bluuebunny/crossref_metadata_2025_split huggingface dataset:
escheR: unified multi-dimensional visualizations with Gestalt principles
Authors: Guo Boyi , Huuki-Myers Louise A , Grant-Peters Melissa , Collado-Torres Leonardo , Hicks Stephanie C 
Published: December 2023

Abstract

Summary
The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to spatially-resolved transcriptomics data, but also broadly to data visualized in 2D space, such as embedding visualizations. We provide an open source R package escheR, which is built off of the state-of-the-art ggplot2 visualization framework and can be seamlessly integrated into genomics toolboxes and workflows.

Availability and implementation
The open source R package escheR is freely available on Bioconductor (https://bioconductor.org/packages/escheR).
NMJ Analyser: a novel method to quantify neuromuscular junction morphology in zebrafish
Authors: Singh Jaskaran , Pan Yingzhou Edward , Patten Shunmoogum A 
Published: December 2023

Abstract

Motivation
Neuromuscular junction (NMJ) structural integrity is crucial for transducing motor neuron signals that initiate skeletal muscle contraction. Zebrafish has emerged as a simple and efficient model to study NMJ structural morphology and function in the context of developmental neurobiology and neuromuscular diseases. However, methods to quantify NMJ morphology from voluminous data of NMJ confocal images accurately, rapidly, and reproducibly are lacking.

Results
We developed an ImageJ macro called “NMJ Analyser” to automatically and unbiasedly analyse NMJ morphology in zebrafish. From the Z-stack of a zebrafish hemisomite, both presynaptic and postsynaptic fluorescently labeled termini at NMJs are extracted from background signal, with larger clusters of termini being segmented into individual termini using an unbiased algorithm. The program then determines whether each presynaptic terminus is co-localized with a postsynaptic terminus and vice versa, or whether it is orphaned, and tabulates the number of orphan and co-localized pre- and postsynaptic termini. The usefulness of this ImageJ macro plugin will be helpful to quantify NMJ parameters in zebrafish, particularly during development and in disease models of neuromuscular diseases. It can enable high-throughput NMJ phenotypic screens in the drug discovery process for neuromuscular diseases. It could also be further applied to the investigation of NMJ of other developmental systems.

Availability and implementation
NMJ Analyser is available for download at https://github.com/PattenLab/NMJ-Analyser.git.
invMap: a sensitive mapping tool for long noisy reads with inversion structural variants
Authors: Wei Ze-Gang , Bu Peng-Yu , Zhang Xiao-Dan , Liu Fei , Qian Yu , Wu Fang-Xiang 
Published: December 2023

Abstract

Motivation
Longer reads produced by PacBio or Oxford Nanopore sequencers could more frequently span the breakpoints of structural variations (SVs) than shorter reads. Therefore, existing long-read mapping methods often generate wrong alignments and variant calls. Compared to deletions and insertions, inversion events are more difficult to be detected since the anchors in inversion regions are nonlinear to those in SV-free regions. To address this issue, this study presents a novel long-read mapping algorithm (named as invMap).

Results
For each long noisy read, invMap first locates the aligned region with a specifically designed scoring method for chaining, then checks the remaining anchors in the aligned region to discover potential inversions. We benchmark invMap on simulated datasets across different genomes and sequencing coverages, experimental results demonstrate that invMap is more accurate to locate aligned regions and call SVs for inversions than the competing methods. The real human genome sequencing dataset of NA12878 illustrates that invMap can effectively find more candidate variant calls for inversions than the competing methods.

Availability and implementation
The invMap software is available at https://github.com/zhang134/invMap.git.
Establishing mRNA and microRNA interactions driving disease heterogeneity in amyotrophic lateral sclerosis patient survival
Authors: Waller Rachel , Bury Joanna J , Appleby-Mallinder Charlie , Wyles Matthew , Loxley George , Babel Aditi , Shekari Saleh , Kazoka Mbombe , Wollff Helen , Al-Chalabi Ammar , Heath Paul R , Shaw Pamela J , Kirby Janine 
Published: December 2023

Abstract
Amyotrophic lateral sclerosis is a fatal neurodegenerative disease, associated with the degeneration of both upper and lower motor neurons of the motor cortex, brainstem and spinal cord. Death in most patients results from respiratory failure within 3–4 years from symptom onset. However, due to disease heterogeneity some individuals survive only months from symptom onset while others live for several years. Identifying specific biomarkers that aid in establishing disease prognosis, particularly in terms of predicting disease progression, will help our understanding of amyotrophic lateral sclerosis pathophysiology and could be used to monitor a patient’s response to drugs and therapeutic agents. Transcriptomic profiling technologies are continually evolving, enabling us to identify key gene changes in biological processes associated with disease. MicroRNAs are small non-coding RNAs typically associated with regulating gene expression, by degrading mRNA or reducing levels of gene expression. Being able to associate gene expression changes with corresponding microRNA changes would help to distinguish a more complex biomarker signature enabling us to address key challenges associated with complex diseases such as amyotrophic lateral sclerosis. The present study aimed to investigate the transcriptomic profile (mRNA and microRNA) of lymphoblastoid cell lines from amyotrophic lateral sclerosis patients to identify key signatures that are distinguishable in those patients who suffered a short disease duration (&lt;12 months) (n = 22) compared with those that had a longer disease duration (&gt;6 years) (n = 20). Transcriptional profiling of microRNA–mRNA interactions from lymphoblastoid cell lines in amyotrophic lateral sclerosis patients revealed differential expression of genes involved in cell cycle, DNA damage and RNA processing in patients with longer survival from disease onset compared with those with short survival. Understanding these particular microRNA–mRNA interactions and the pathways in which they are involved may help to distinguish potential therapeutic targets that could exert neuroprotective effects to prolong the life expectancy of amyotrophic lateral sclerosis patients.
A systematic review and meta-analysis of transthoracic echocardiogram vs. cardiac magnetic resonance imaging for the detection of left ventricular thrombus
Authors: Phuah YuZhi , Tan Ying Xin , Zaghloul Sheref , Sim Sharmaine , Wong Joshua , Usmani Saba , Snell Lily , Thavabalan Karish , García-Pérez Carmen Lucia , Kumar Niraj S , Glatzel Hannah , Ahmad Reubeen Rashid , Candilio Luciano , Bray Jonathan J H , Ahmed Mahmood , Providencia Rui 
Published: December 2023

Abstract
Transthoracic echocardiography (TTE) is the most commonly used imaging modality to diagnose left ventricular thrombus (LVT), however, cardiac magnetic resonance (CMR) remains the gold standard investigation. A comparison of the diagnostic performance between two modalities is needed to inform guidelines on a diagnostic approach towards LVT. We performed a systematic review and meta-analysis to investigate the diagnostic performance of three methods of TTE (non-contrast, contrast, and apical wall motion scoring) for the detection of LVT compared to CMR as a reference test. Studies comprising 2113 patients investigated for LVT using both TTE and CMR were included in the meta-analysis. For non-contrast TTE, pooled sensitivity and specificity were 47% [95% confidence interval (CI): 32–62%], and 98% (95% CI: 96–99%), respectively. In contrast, TTE pooled sensitivity and specificity values were 58% (95% CI: 46–69%), and 98% (95% CI: 96–99%), respectively. Apical wall motion scoring on non-contrast TTE yielded a sensitivity of 100% [95% CI: 93–100%] and a specificity of 54% (95% CI: 42–65%). The area under the curve (AUC) values from our summary receiver operating characteristic curve (SROC) for non-contrast and contrast TTE were 0.87 and 0.86 respectively, with apical wall motion studies having the highest AUC of 0.93. Despite high specificity, routine contrast and non-contrast TTE are likely to miss a significant number of LVT, making it a suboptimal screening tool. The addition of apical wall motion scoring provides a promising method to reliably identify patients requiring further investigations for LVT, whilst excluding others from unnecessary testing.
Cerebral blood flow and neurocognition in patients undergoing transcatheter aortic valve replacement for severe aortic stenosis
Authors: Lazar Ronald M , Myers Terina , Gropen Toby I , Leesar Massoud A , Davies James , Gerstenecker Adam , Norling Amani , Pavol Marykay A , Marshall Randolph S , Kodali Susheel 
Published: December 2023

Abstract

Aims
Aortic valve stenosis (AS) results in higher systolic pressure to overcome resistance from the stenotic valve, leading to heart failure and decline in cardiac output. There has been no assessment of cerebral blood flow (CBF) association with neurocognition in AS or the effects of valve replacement. The goal was to determine if AS is associated with altered cerebral haemodynamics and impaired neurocognition, and whether transcatheter aortic valve replacement (TAVR) improves haemodynamics and cognition.

Methods and results
In 42 patients with planned TAVR, transcranial Doppler (TCD) assessed bilateral middle cerebral artery (MCA) mean flow velocities (MFVs); abnormality was &lt;34.45 cm/s. The neurocognitive battery assessed memory, language, attention, visual–spatial skills, and executive function, yielding a composite Z-score. Impairment was &lt;1.5 SDs below the normative mean. The mean age was 78 years, 59% Male, and the mean valve gradient was 46.87 mm/Hg. Mean follow-up was 36 days post-TAVR (range 27–55). Pre-TAVR, the mean MFV was 42.36 cm/s (SD = 10.17), and the mean cognitive Z-score was −0.22 SDs (range −1.99 to 1.08) below the normative mean. Among the 34 patients who returned after TAVR, the MFV was 41.59 cm/s (SD = 10.42), not different from baseline (P = 0.66, 2.28–3.67). Post-TAVR, average Z-scores were 0.17 SDs above the normative mean, not meeting the pre-specified threshold for a clinically significant 0.5 SD change.

Conclusion
Among patients with severe AS, there was little impairment of MFV on TCD and no correlation with cognition. Transcatheter aortic valve replacement did not affect MFV or cognition. Assumptions about diminished CBF and improvement after TAVR were not supported.
Gender and Leadership in Organisations: the Threat of Backlash
Authors: Chakraborty Priyanka , Serra Danila 
Published: December 2023

Abstract
Decisions made by leaders please some people and upset others. We examine whether the possibility of backlash has a differential impact on men’s and women’s self-selection into leadership roles, and their decisions as leaders. In a laboratory experiment that simulates corporate decision-making, we find that women are significantly less likely to self-select into a leadership position when they can receive backlash. Once in a leadership role, women get more backlash. There are some gender differences in leaders’ decision-making and communication styles under the threat of backlash, but little difference in final outcomes. An online experiment sheds light on possible mechanisms.
The additive effects of anaemia and transfusion on long-term survival after coronary artery bypass surgery
Authors: Abreu Armando , Máximo José , Almeida Cláudia , Lourenço André , Leite-Moreira Adelino 
Published: December 2023

Abstract

OBJECTIVES
To compare the independent and combined effects of anaemia and red blood cell transfusion on late survival after isolated coronary artery bypass grafting.

METHODS
Retrospective analysis of 5243 consecutive patients undergoing primary isolated coronary artery bypass grafting, performed from 2000 to 2015, in a Portuguese Academic Hospital. We identified 1649 patients with preoperative anaemia (A+) and 1422 patients who received a perioperative transfusion (T+)—the 4 possible combinations allowed for the creation of 4 subgroups (A−/T−, A−/T+, A+/T− and A+/T+). The primary endpoint was all-cause mortality at 10 years. We employed inverse probability weighting to control for confounding variables.

RESULTS
Thirty-one percent of the patients had preoperative anaemia, and 27.0% had at least one packed red blood cell transfusion. Inverse probability weighting was effective in eliminating differences in all significant baseline characteristics. The primary endpoint of all-cause mortality at 10 years occurred in 568 patients (20.5%) in the A−/T− group, as compared with 204 (24.4%) in the A−/T+ group (hazard ratio, 1.14; 95% confidence interval, 1.00 to 1.31; P = 0.053), 358 (33.8%) in the A+/T− group (hazard ratio, 1.53; 95% confidence interval, 1.38 to 1.71; P &lt; 0.001), 254 (43.6%) in the A+/T+ group (hazard ratio, 2.25; 95% confidence interval, 1.97 to 2.56; P &lt; 0.001).

CONCLUSIONS
This longitudinal, population-level study emphasizes the adverse long-term outcomes of preoperative anaemia and perioperative red blood cell transfusion. It stresses the importance of an evidence-based, multimodal and multidisciplinary approach to conserving blood resources and optimizing outcomes in patients at high risk for transfusion.
Cost of illness of the vaccine-preventable diseases influenza, herpes zoster and pneumococcal disease in France
Authors: Brown Lauren , Sutton Kelly J , Browne Chantelle , Bartelt-Hofer José , Greiner Wolfgang , Petitjean Audrey , Roiz Julie 
Published: December 2023

Abstract

Background
The incidence of certain vaccine-preventative diseases, such as influenza, herpes zoster and pneumococcal infection, continues to be high despite the availability of vaccines, resulting in a substantial health and economic burden on society, particularly among older adults aged ≥65 years.

Methods
A cost calculator was developed to assess the cost of illness of influenza, herpes zoster and pneumococcal disease in France. Direct medical costs related to diagnosis and treatment in the older adult population in both inpatient and outpatient settings were modelled over a 1-year time horizon. Scenario analyses were conducted to determine the impact of hospitalizations on the results by considering only influenza-attributed diagnoses.

Results
In France, influenza has the highest incidence, followed by herpes zoster and pneumococcal disease. Similarly, influenza poses the greatest cost burden among all older adults, while pneumococcal disease poses the greatest cost burden among those aged 65–74 years. When considering only influenza-attributed diagnoses, the number of inpatient visits and associated costs was reduced by 63% in the overall older adult population. In the low-incidence season, the number of inpatient visits and associated costs were reduced by 69%, while in the high-incidence season, the number of inpatient visits and associated costs increased by 63%.

Conclusion
Influenza remains a leading vaccine-preventable disease among older adults in France, resulting in a substantial economic burden that could be prevented by increasing vaccine uptake.
Investigation of gut microbiota changes and allergic inflammation of mice with milk protein-induced allergic enteritis
Authors: Wang Zhongmin , Wu Qiao , Guan Minchang , Li Ze , Pan Wei , Tang Weihong 
Published: December 2023

AbstractThis study aimed to investigate the changes of gut microbiota and allergic inflammation in mice with allergic enteritis caused by milk protein. In this study, female BALB\C mice in the whey protein (WP-sensitized) group were gavaged with WP and normal saline, the sham-sensitized group was given normal saline once a week for 5 weeks. One week later, the WP-sensitized mice were administered 60 mg β-lactoglobulin (BLG). The results showed that mice's body weight decreased, feces with loose and bloody, and systemic allergic reactions and ear swelling increased in the WP-sensitized group. The levels of WP-specific Ig, mMCP-1, calprotectin of feces, and inflammation-related factors in the WP-sensitized group were increased. WP-sensitized group intestine tissues were damaged severely and the expressions of ZO-1, Claudin-1, and Occludin reduced. The results of 16S rRNA sequencing showed that there were differences in operational taxonomic units (OUT) levels of gut microbes between the two groups, o_Clostridiales, c_Clostridia, and f_Lachnospiraceae were more abundant in the WP-sensitized group. In conclusion, the WP sensitization can induce the allergic inflammation, intestinal injury and intestinal barrier dysfunction in mice, and the gut microbes were also changed, which provided a reference for the treatment of WP-sensitized mice.
The Role of Political Leaders’ Emotions in Shaping International Rivalries: The Case of Former Bolivian President Evo Morales
Authors: Thiers Consuelo 
Published: December 2023

Abstract
This study applies the appraisal theory of emotions to explore how they influence leaders’ responses in the context of long-standing rivalries between states. It argues that policymakers’ emotions toward a rival country can help elucidate periods of higher and lower tensions in their bilateral relationship. Focusing on the Bolivian–Chilean rivalry, this study examines the case of Bolivia’s former president Evo Morales to shed light on the noticeable change in foreign policy toward Chile during two of his presidential terms. The findings reveal that Morales’s emotions were distinctly different during the period of cooperation or de-escalation compared to the period of escalation of tensions. The period of cooperation is characterized by strategies that promote contact, aligning with motive-consistent appraisals of events. Conversely, the period of escalation is marked by strategies that favor distance, stemming from motive-inconsistent appraisals.
A bibliometric analysis of research trends for missing persons globally and in East Asia from 2000 to 2021
Authors: Zeng Zixuan , Dikeledi Ishmael , Lv Yehui 
Published: December 2023

Abstract

A bibliometric analysis was performed to explore the current research status and development trends for missing persons globally and in East Asia and to identify research hotspots and frontiers relating to this topic. A search was conducted to identify relevant literature on missing persons using the Web of Science Core Collection database for the period 2000–2021. Subsequently, a knowledge map was constructed using CiteSpace software to perform a visual analysis of the distribution of authors and institutions, journals, and national/regional distribution; citation frequency; high-frequency keywords; and emerging research hotspots. The results showed firstly that discussions on missing persons and related topics in East Asia are held at the regional scale. There is a paucity of research on this topic, which has been conducted on a limited scale, lacks depth and possibly innovation, and entails limited discussion in this region. Secondly, there is a lack of social science research on missing persons and related topics worldwide. Thirdly, relevant research in East Asia should continue to preserve its own characteristics, effectively addressing current issues and enabling more people to participate in social science-oriented discussions focusing on the topic of missing persons. This approach provides a promising direction for pursuing the sustainable development of the topic of missing persons.

Key points
Chromosome-Level Genome Assembly of the Blacktail Brush Lizard,Urosaurus nigricaudus, Reveals Dosage Compensation in an Endemic Lizard
Authors: Davalos-Dehullu Elizabeth , Baty Sarah M , Fisher Robert N , Scott Peter A , Dolby Greer A , Munguia-Vega Adrian , Cortez Diego 
Published: December 2023

AbstractUrosaurus nigricaudus is a phrynosomatid lizard endemic to the Baja California Peninsula in Mexico. This work presents a chromosome-level genome assembly and annotation from a male individual. We used PacBio long reads and HiRise scaffolding to generate a high-quality genomic assembly of 1.87 Gb distributed in 327 scaffolds, with an N50 of 279 Mb and an L50 of 3. Approximately 98.4% of the genome is contained in 14 scaffolds, with 6 large scaffolds (334–127 Mb) representing macrochromosomes and 8 small scaffolds (63–22 Mb) representing microchromosomes. Using standard gene modeling and transcriptomic data, we predicted 17,902 protein-coding genes on the genome. The repeat content is characterized by a large proportion of long interspersed nuclear elements that are relatively old. Synteny analysis revealed some microchromosomes with high repeat content are more prone to rearrangements but that both macro- and microchromosomes are well conserved across reptiles. We identified scaffold 14 as the X chromosome. This microchromosome presents perfect dosage compensation where the single X of males has the same expression levels as two X chromosomes in females. Finally, we estimated the effective population size for U. nigricaudus was extremely low, which may reflect a reduction in polymorphism related to it becoming a peninsular endemic.
Barriers primary care clinic leaders face to improving value in a consumer choice health plan design
Authors: McDonald Tim , Debbarma Arindam , Whaley Christopher , Reid Rachel , Dowd Bryan 
Published: December 2023

Abstract
Primary care clinics are a frequent focus of policy initiatives to improve the value of health care; yet, it is unclear whether they have the ability or incentive to take on the additional tasks that these initiatives ask of them. This paper reports on a qualitative study assessing barriers that clinic leaders face to reducing cost within a tiered cost-sharing commercial health insurance benefit design that gives both consumers and clinics a strong incentive to reduce cost. We conducted semi-structured interviews of clinical and operational leaders at a diverse set of 12 Minnesota primary care clinics and identified 6 barriers: insufficient information on drivers of cost; clinics controlling a portion of spending; patient preference for higher cost specialists; administrative challenges; limited resources; and misalignment of incentives. We discuss approaches to reducing these barriers and opportunities to implement them.
How policymakers innovate around behavioral health: adoption of the New Mexico “No Behavioral Health Cost-Sharing” law
Authors: Harris Samantha J , Golberstein Ezra , Maclean Johanna Catherine , Stein Bradley D , Ettner Susan L , Saloner Brendan 
Published: December 2023

Abstract
State policymakers have long sought to improve access to mental health and substance use disorder (MH/SUD) treatment through insurance market reforms. Examining decisions made by innovative policymakers (“policy entrepreneurs”) can inform the potential scope and limits of legislative reform. Beginning in 2022, New Mexico became the first state to eliminate cost-sharing for MH/SUD treatment in private insurance plans subject to state regulation. Based on key informant interviews (n = 30), this study recounts the law's passage and intended impact. Key facilitators to the law's passage included receptive leadership, legislative champions with medical and insurance backgrounds, the use of local research evidence, advocate testimony, support from health industry figures, the severity of MH/SUD, and increased attention to MH/SUD during the COVID-19 pandemic. Findings have important implications for states considering similar laws to improve access to MH/SUD treatment.