bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics
Authors: Mirchandani Cade D , Shultz Allison J , Thomas Gregg W C , Smith Sara J , Baylis Mara , Arnold Brian , Corbett-Detig Russ , Enbody Erik , Sackton Timothy B 
Published: December 2023

Abstract
The increasing availability of genomic resequencing data sets and high-quality reference genomes across the tree of life present exciting opportunities for comparative population genomic studies. However, substantial challenges prevent the simple reuse of data across different studies and species, arising from variability in variant calling pipelines, data quality, and the need for computationally intensive reanalysis. Here, we present snpArcher, a flexible and highly efficient workflow designed for the analysis of genomic resequencing data in nonmodel organisms. snpArcher provides a standardized variant calling pipeline and includes modules for variant quality control, data visualization, variant filtering, and other downstream analyses. Implemented in Snakemake, snpArcher is user-friendly, reproducible, and designed to be compatible with high-performance computing clusters and cloud environments. To demonstrate the flexibility of this pipeline, we applied snpArcher to 26 public resequencing data sets from nonmammalian vertebrates. These variant data sets are hosted publicly to enable future comparative population genomic analyses. With its extensibility and the availability of public data sets, snpArcher will contribute to a broader understanding of genetic variation across species by facilitating the rapid use and reuse of large genomic data sets.
Heart disease and stroke statistics 2023 update from the American Heart Association—implications for nephrology
Authors: Edwards Nicola C , Ferro Charles J , Townend Jonathan N 
Published: December 2023

ABSTRACT
The annual American Heart Association (AHA) and National Institutes of Health statistical report details the most up to date statistics related to heart disease, stroke and cardiovascular risk factors, primarily within the USA. Although not a formal systematic review or meta-analysis, this 600 page report provides the most comprehensive and best summary of cardiovascular statistics for the year in question. Although data are collated from USA data registries, it serves as a critical resource for clinicians, policymakers, administrators and researchers in the northern and southern hemispheres. In this special report, we have chosen to highlight aspects of the document that are relevant to nephrologists, given the overlap of cardiovascular and renal disease. These include (i) key and emerging cardiovascular data signals in the general and chronic kidney disease (CKD) populations, (ii) ethnic and socio-economic disparity, (iii) environmental and behavioural factors that drive high levels of cardiovascular disease and which are key components of the AHA's eight components of the Life Essential cardiovascular health score, and (iv) the impact of COVID-19 both directly and indirectly on heart health. We provide some commentary and critical analysis of both the data and of the production of such data sets suggesting that similar data on CKD could also be published and linked to the AHA and other datasets.
Characterizing utilization patterns and reoperation risk factors of interspinous process devices: analysis of a national claims database
Authors: Tan Hao , Yamamoto Erin A , Smith Spencer , Yoo Jung , Kark Jonathan , Lin Clifford , Orina Josiah , Philipp Travis , Ross Donald A , Wright Christina , Wright James , Ryu Won Hyung A 
Published: December 2023

Abstract

Introduction
Interspinous process devices (IPDs) were developed as minimally invasive alternatives to open decompression surgery for spinal stenosis. However, given high treatment failure and reoperation rates, there has been minimal adoption by spine surgeons. This study leveraged a national claims database to characterize national IPD usage patterns and postoperative outcomes after IPD implantation.

Method
Using the PearlDiver database, we identified all patients who underwent 1- or 2-level IPD implantation between 2010 and 2018. Univariate and multivariable logistic regression was performed to identify predictors of the number of IPD levels implanted and reoperation up to 3 years after the index surgery. Right-censored Kaplan-Meier curves were plotted for duration of reoperation-free survival and compared with log-rank tests.

Results
Patients (n = 4865) received 1-level (n = 3246) or 2-level (n = 1619) IPDs. Patients who were older (adjusted odds ratio [aOR] 1.02, 95% confidence interval [CI] 1.01–1.03, P &lt; .001), male (aOR 1.31, 95% CI 116–1.50, P &lt; .001), and obese (aOR 1.19, 95% CI 1.05–1.36, P &lt; .01) were significantly more likely to receive a 2-level IPD than to receive a 1-level IPD. The 3-year reoperation rate was 9.3% of patients when mortality was accounted for during the follow-up period. Older age decreased (aOR 0.97, 95% CI 0.97–0.99, P = .0039) likelihood of reoperation, whereas 1-level IPD (aOR 1.37, 95% CI 1.01–1.89, P = .048), Charlson Comorbidity Index (aOR 1.07, 95% CI 1.01–1.14, P = .018), and performing concomitant open decompression increased the likelihood of reoperation (aOR 1.68, 95% CI 1.35–2.09, P = .0014).

Conclusion
Compared with 1-level IPDs, 2-level IPDs were implanted more frequently in older, male, and obese patients. The 3-year reoperation rate was 9.3%. Concomitant open decompression with IPD placement was identified as a significant risk factor for subsequent reoperation and warrants future investigation.
Short Campaigns by Hedge Funds
Authors: Appel Ian , Fos Vyacheslav 
Published: December 2023

Abstract
The number of short campaigns by hedge funds has dramatically increased over the last two decades. Nearly 80% of campaigns are undertaken by activist hedge funds, particularly those that employ hostile tactics in their long campaigns. Short campaigns are associated with negative abnormal returns of –7%, with aggregate valuation effects similar in magnitude to the gains from long activism campaigns. In contrast to long campaigns, public communication is a critical component of short campaigns. We do not find evidence that such communication is manipulative. Overall, our analysis highlights the importance of short campaigns for understanding the economic impact of activist hedge funds.
Surgical Insights and Complications of Third-generation Minimally Invasive Chevron Akin Osteotomy for Hallux Valgus
Authors: McCann Julia A. , Wu Caroline M. , Neufeld Steven K. 
Published: December 2023

Minimally invasive bunion correction is an increasingly popular surgical technique to address hallux valgus deformity. Though some complications are decreased compared with open procedures, there are still notable preventable and unavoidable complications associated with these procedures. This paper serves as a review of complications and adverse events encountered with third-generation minimally invasive Chevron and Akin osteotomy procedures, as well as how to avoid and mitigate these adverse outcomes.

Level of Evidence:
Level V. See Instructions for Authors for a complete description of levels of evidence.
Bidirectional relationship between type 2 diabetes mellitus and coronary artery disease: Prospective cohort study and genetic analyses
Authors: Zhang Wenqiang , Zhang Li , Xiao Chenghan , Wu Xueyao , Cui Huijie , Yang Chao , Yan Peijing , Tang Mingshuang , Wang Yutong , Chen Lin , Liu Yunjie , Zou Yanqiu , Zhang Ling , Yang Chunxia , Yao Yuqin , Li Jiayuan , Liu Zhenmi , Jiang Xia , Zhang Ben 
Published: December 2023

Abstract

Background:
While type 2 diabetes mellitus (T2DM) is considered a putative causal risk factor for coronary artery disease (CAD), the intrinsic link underlying T2DM and CAD is not fully understood. We aimed to highlight the importance of integrated care targeting both diseases by investigating the phenotypic and genetic relationships between T2DM and CAD.

Methods:
We evaluated phenotypic associations using data from the United Kingdom Biobank (N = 472,050). We investigated genetic relationships by leveraging genomic data conducted in European ancestry for T2DM, with and without adjustment for body mass index (BMI) (T2DM: N
case/N
control = 74,124/824,006; T2DM adjusted for BMI [T2DMadjBMI]: N
case/N
control = 50,409/523,897) and for CAD (N
case/N
control = 181,522/984,168). We performed additional analyses using genomic data conducted in multiancestry individuals for T2DM (N
case/N
control = 180,834/1,159,055).

Results:
Observational analysis suggested a bidirectional relationship between T2DM and CAD (T2DM→CAD: hazard ratio [HR] = 2.12, 95% confidence interval [CI]: 2.01–2.24; CAD→T2DM: HR = 1.72, 95% CI: 1.63–1.81). A positive overall genetic correlation between T2DM and CAD was observed (r
g = 0.39, P = 1.43 × 10–75), which was largely independent of BMI (T2DMadjBMI–CAD: r
g = 0.31, P = 1.20 × 10–36). This was corroborated by six local signals, among which 9p21.3 showed the strongest genetic correlation. Cross-trait meta-analysis replicated 101 previously reported loci and discovered six novel pleiotropic loci. Mendelian randomization analysis supported a bidirectional causal relationship (T2DM→CAD: odds ratio [OR] = 1.13, 95% CI: 1.11–1.16; CAD→T2DM: OR = 1.12, 95% CI: 1.07–1.18), which was confirmed in multiancestry individuals (T2DM→CAD: OR = 1.13, 95% CI: 1.10–1.16; CAD→T2DM: OR = 1.08, 95% CI: 1.04–1.13). This bidirectional relationship was significantly mediated by systolic blood pressure and intake of 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors, with mediation proportions of 54.1% (95% CI: 24.9–83.4%) and 90.4% (95% CI: 29.3–151.5%), respectively.

Conclusion:
Our observational and genetic analyses demonstrated an intrinsic bidirectional relationship between T2DM and CAD and clarified the biological mechanisms underlying this relationship.
Setting positive end-expiratory pressure: the use of esophageal pressure measurements
Authors: Somhorst Peter , Mousa Amne , Jonkman Annemijn H. 
Published: December 2023

Purpose of review
To summarize the key concepts, physiological rationale and clinical evidence for titrating positive end-expiratory pressure (PEEP) using transpulmonary pressure (P
L) derived from esophageal manometry, and describe considerations to facilitate bedside implementation.

Recent findings
The goal of an esophageal pressure-based PEEP setting is to have sufficient P
L at end-expiration to keep (part of) the lung open at the end of expiration. Although randomized studies (EPVent-1 and EPVent-2) have not yet proven a clinical benefit of this approach, a recent posthoc analysis of EPVent-2 revealed a potential benefit in patients with lower APACHE II score and when PEEP setting resulted in end-expiratory P
L values close to 0 ± 2 cmH2O instead of higher or more negative values. Technological advances have made esophageal pressure monitoring easier to implement at the bedside, but challenges regarding obtaining reliable measurements should be acknowledged.

Summary
Esophageal pressure monitoring has the potential to individualize the PEEP settings. Future studies are needed to evaluate the clinical benefit of such approach.
Prevalence and Correlates of Unmet Medical and Social Needs in Virginia’s Medicaid Managed Long Term Services and Supports Program
Authors: Marks Sarah J. , Saunders Heather , Shadowen Hannah , McCray Neil , Bachireddy Chethan , Dagenhart Sandra , Brown Sandra , Guerra Lauren , Cunningham Peter J. 
Published: December 2023

Background:
Medicaid Long Term Services and Support (LTSS) programs serve individuals with complex medical and social needs. Increasingly, state Medicaid programs are contracting with managed care organizations to administer LTSS programs.

Objectives:
Understand the prevalence of and risk factors for unmet medical and social needs among a sample of patients within a Medicaid managed LTSS program.

Methods:
We surveyed a cross-sectional random sample of 798 community-residing individuals over 21 in Virginia who were served by the state Medicaid managed LTSS program. Outcomes of interest include 3 distinct medical needs: medical appointments, medical transportation, and prescriptions; 4 distinct social needs: housing security, food security, utility bills, and nonmedical transportation, and composite measures of unmet social and medical needs.

Results:
We found that 12.5% of our sample had any unmet medical need, while far more (62.2%) of our sample had any unmet social needs, with food insecurity being the most common. We found that members of color had almost 2 times the odds of having both unmet social and medical needs [social: adjusted odds ratio (aOR): 2.21; 95% confidence Interval (CI): (1.59, 3.09); medical aOR: 2.25 ; 95% CI: (1.34, 3.8)].

Conclusion:
Medicaid members may not be fully realizing the potential of LTSS programs and would benefit from both Medicaid agency and managed care organizations' strategies aimed at addressing social drivers of health. To achieve health equity for LTSS members of color, Medicaid agencies may consider policies specifically targeting racial disparities.
Clinical Nurse Specialists Using Evidence-Based Practice to Prevent Falls
Authors: Pate Kimberly , Rutledge Sarah R. , Belin Latasia 
Published: December 2023

Abstract

Purpose/Objectives
The purpose of this quality improvement project was to reduce inpatient falls and falls with injury by implementing the Hester Davis Fall Program, a comprehensive, evidence-based prevention program, with the leadership of clinical nurse specialists.

Description of the Project/Program
The Plan-Do-Study-Act model was utilized to implement the program at 2 adult acute care facilities. Clinical nurse specialists collaborated with nurse managers to guide planning, implementation, and evaluation of patient outcomes. Routine meetings with Hester Davis sustainability coaches and access to data analytic dashboards provided visibility of audit data, allowing for the intentional selection of targeted strategies to improve risk assessment scoring and implementation of appropriate interventions.

Outcome
Although both facilities demonstrated overall favorable trends in fall rates, one facility demonstrated rates less than the National Database of Nursing Quality Indicators mean. In the 9 months following implementation, total falls for both facilities decreased from 744 to 692 for the same period in the previous year, resulting in estimated cost-savings of $202 176 to $491 400.

Conclusion
Clinical nurse specialists play a key role in the successful implementation of evidence-based programs. As organizations look to improve quality measures, it is vital that senior nurse leaders ensure the availability of appropriate resources including the identification of individuals with the appropriate skill set to lead quality improvement.
Umbilical Cord Tissue
Authors: Midthun Kari M. 
Published: December 2023

Abstract
Umbilical cord tissue (UCT) traditionally has been used as an antemortem matrix for identifying and monitoring fetal exposure to drugs suspected to have been used during pregnancy. The specimen offers several advantages as a testable tissue, including accessibility and ease of collection, ample sample volume, a long window of detection, and ability to detect for a wide range of drugs. Despite these advantages, little to no research exists on the use of UCT as a postmortem forensic toxicology specimen. This article aims to provide insights into UCT toxicological testing and infer potential applications for postmortem use, such as investigations into stillbirths and infant abandonment. Umbilical cord tissue offers several benefits as a postmortem toxicological specimen. Importantly, it can be collected with or without an autopsy being performed and may help explain factors that contribute to the underdevelopment and death of the neonate. With the limited sample volumes present in infant investigations, toxicological analysis of UCT could become a valuable tool for neonatal medicolegal death investigations.
Prescribed and Diverted Methadone Toxicity in South Australia
Authors: Stephenson Lilli , Van Den Heuvel Corinna , Humphries Melissa , Byard Roger W. 
Published: December 2023

Abstract
Methadone is one of the most common medications currently prescribed for the treatment of opioid use disorders (OUDs). While methadone maintenance programs (MMPs) have been highly successful in the management and treatment of OUDs resulting in a reduced number of fatalities, the risk of overdose/toxicity remains. The current study was undertaken to analyze trends in overdoses attributed to prescribed and diverted methadone in South Australia (SA) between 2000 and 2019. Over the 20-year period, 344 methadone-related deaths occurred in SA with a significant increase in deaths over the study period (P = 0.03). The mean age of decedents was 42.5 years with a male to female ratio of 1.8:1, with approximately 20% of decedents enrolled in a MMP at the time of death. Overall, only 5.2% of cases demonstrated methadone diversion, which was associated with methadone prescribed for chronic pain and was most likely to be diverted from a friend/housemate or a partner. However, the source of methadone in more than half of cases was unknown, so this is likely a significant underestimate of actual MMP methadone diversion and total methadone diversion.
Child Sexual Abuse
Authors: Lupariello Francesco , Lauria Barbara , Mirri Federica , Aguzzi Sonia , Castagno Emanuele , Bondone Claudia , Di Vella Giancarlo 
Published: December 2023

Abstract
In the scientific literature, few authors deal with child sexual abuse (CSA) in boys. In addition, these authors debate this phenomenon in most available articles without statistically evaluating the occurrence of different or similar distributions of variables under sex. In light of the above, the authors compared multiple variables between female and male samples. The aim was to explore the characteristics of boys' CSA, identifying the main differences existing compared with the same phenomenon occurring in girls. The authors selected 2 samples for sex: group A, females; group B, males. The authors statistically compared the main variables between the 2 groups. The study yielded the following main results: the population was characterized by 607 children (476 were females—group A; 131 were males—group B); the variables' source of the referral and the type of anogenital findings were statistically significant. These data gave new insights into the CSA phenomenon. Because this study pointed out that sexual abuse does not have the same characteristics in boys and girls, researchers and safeguarding agencies should consider the abovementioned differences when planning preventive strategies against CSA.
Optimization of Muscle Selection for Needle Electromyography in Isolated C6 Root Lesion
Authors: Rayegani Seyed Mansoor , Bahrami Mohammad Hasan , Aalipour Kianmehr , Malek Mahmoudi Rashin , Maleki Kahaki Sara 
Published: December 2023

Objectives
The aim of the study is to evaluate muscles with more prominent needle electromyographic findings to optimize needle electromyography screening of isolated C6 radiculopathy in patients with C6 root lesions.

Design
This prospective clinical study was performed on 39 patients with isolated and unilateral cervical radiculopathy selected from all referrals of 1733 patients to the electrodiagnosis unit of the physical medicine and rehabilitation department of a tertiary medical center (from April 2021 to December 2021). The presence of fibrillation potentials, positive sharp waves, and/or neurogenic motor action potentials that occurred in isolation or combination with selected muscles was considered an abnormal finding.

Results
Of 1733 referrals, 39 patients (18 males [46.1%] and 21 females [53.8%]), with a mean age of 49.7 ± 9.6 yrs, were found eligible. According to needle electromyography findings, the most involved muscles in C6 root lesion were pronator teres (100%), followed by extensor carpi radialis longus (94.8%), flexor carpi radialis (89.7%), brachioradialis (82%), infraspinatus (82%), supraspinatus (79.4%), deltoid (74.3%), biceps brachii (64.1%), extensor digitorum communis (33.3%), and triceps brachii (15.3%) muscles.

Conclusions
The pronator teres is the most involved muscle of patients diagnosed with C6 radiculopathy. It might be considered the key muscle for screening and accurate diagnosis of C6 root involvement.
Surgical Treatment of Trigonocephaly, Simplified Technique for Moderate Cases
Authors: Kalantar-Hormozi Abdoljalil , Mohammadi Mofrad Rastin , Noori Mehran , Kalantar Hormozi Hadis 
Published: December 2023

Background:
The prevalence of trigonocephaly has increased worldwide over the past 2 decades. Early identification and appropriate treatment are critical. The aim of this study is to evaluate the outcomes and the effect of metopic suture excision, perisutural frontal bone shave, and bilateral pericranial flap method on the shape of the forehead after surgical correction in infants with moderate trigonocephaly.

Methods:
The present study was performed as a cross-sectional study on 40 infants of 3 to 12 months old with trigonocephalus who underwent metopic suture excision and pericardial flap surgery in Mofid Pediatric Hospital from 2016 to 2022. The definitive diagnosis of patients’ trigonocephaly was made based on clinical signs and computed tomography scan findings by a plastic surgeon.

Results:
Overall in 40 patients operated by this technique, 23 (57.5%) of cases were males, and 17 (42.5%) were females. The mean age of patients was 7.86 ± 2.22 months. Hospital stay was 2 to 4 days (mean: 3 d), intensive care unit admission was in 33 cases for 24 hours, and no intensive care unit admission for 7 cases. Blood was transfused during surgery for 25 patients, and 15 patients did not require blood transfusion use. Results were evaluated in 6 to 12 months after surgery by 3 independent plastic surgeons, with pre and postoperative photos. Satisfaction with the results of forehead shape was excellent for 60% of patients, good for 37.5%, and moderate for 2.5%. Only one female patient had a recurrence after the surgery.

Conclusion:
This study showed that the pericranial flap method after full metopic suture excision and frontal shave was very effective in the treatment of infants with moderate trigonocephaly.