bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phasing nanopore genome assembly by integrating heterozygous variations and Hi-C data
Authors: Zhang Jun , Nie Fan , Luo Feng , Wang Jianxin 
Published: November 2024

Abstract

Motivation
Haplotype-resolved genome assemblies serve as vital resources in various research domains, including genomics, medicine, and pangenomics. Algorithms employing Hi-C data to generate haplotype-resolved assemblies are particularly advantageous due to its ready availability. Existing methods primarily depend on mapping quality to filter out uninformative Hi-C alignments which may be susceptible to sequencing errors. Setting a high mapping quality threshold filters out numerous informative Hi-C alignments, whereas a low mapping quality threshold compromises the accuracy of Hi-C alignments. Maintaining high accuracy while retaining a maximum number of Hi-C alignments can be challenging.

Results
In our experiments, heterozygous variations play an important role in filtering uninformative Hi-C alignments. Here, we introduce Diphase, a novel phasing tool that harnesses heterozygous variations to accurately identify the informative Hi-C alignments for phasing and to extend primary/alternate assemblies. Diphase leverages mapping quality and heterozygous variations to filter uninformative Hi-C alignments, thereby enhancing the accuracy of phasing and the detection of switches. To validate its performance, we conducted a comparative analysis of Diphase, FALCON-Phase, and GFAse on various human datasets. The results demonstrate that Diphase achieves a longer phased block N50 and exhibits higher phasing accuracy while maintaining a lower hamming error rate.

Availability and implementation
The source code of Diphase is available at https://github.com/zhangjuncsu/Diphase
Continuous preperitoneal versus thoracic epidural analgesia in open pancreatoduodenectomy: randomized clinical trial
Authors: Lee Mirang , Jung Ji-Yoon , Han Youngmin , Chae Yoon Soo , Yun Won-Gun , Jung Hye-Sol , Cho Young Jae , Choi Yoo Jin , Lee Ho-Jin , Kwon Wooil , Kim Won Ho , Jang Jin-Young 
Published: November 2024

Abstract

Background
Thoracic epidural analgesia (TEA), once the standard for pain management in major abdominal operations, is associated with postoperative complications, making preperitoneal continuous wound infiltration (CWI) a promising alternative. This study aimed to compare the effectiveness of CWI and TEA in managing postoperative pain after open pancreatoduodenectomy.

Methods
In a single-centre, randomized, open-label non-inferiority trial, adult patients undergoing elective open pancreatoduodenectomy were assigned to either CWI or TEA for pain management. The primary outcomes were mean pain scores at rest on the first 3 postoperative days (PODs), using an 11-point numeric rating scale, with a non-inferiority margin of 1 point or less. Secondary outcomes included pain scores at rest and during coughing on PODs 1, 2, and 3; total opioid consumption; incidence of postoperative complications; quality of postoperative recovery; and duration of hospital stay.

Results
Among the 134 patients analysed (CWI 70, TEA 64), CWI was non-inferior to TEA in terms of mean pain scores at rest (mean difference −0.13, 95% c.i. −0.72 to 0.47). Additionally, CWI demonstrated superior pain relief at rest and higher-quality recovery scores on POD 3. Compared with CWI, TEA was associated with significantly decreased total opioid consumption and shortened time to the first passage of flatus, but a higher incidence of postoperative hypotension. No other outcome measures showed significant differences between the two groups.

Conclusion
CWI was non-inferior to TEA during the early postoperative period, and has emerged as a favourable alternative to TEA, offering better pain relief and enhanced recovery on POD 3. Registration number: NCT04375826 (http://www.clinicaltrials.gov).
Guidance for delivering surgical procedures outside operating theatres: scoping review
Authors: Osborne-Grinter Maia , Cousins Sian , Ramirez Jozel , Price James R , Lancerotto Luca , Gardiner Matthew , Mouton Ronelle , Hinchliffe Robert 
Published: November 2024

Abstract

Background
This review aimed to examine in-depth the extent and content of guidance related to the delivery of surgical procedures outside of the operating theatre.

Methods
Documents concerning the delivery of surgical procedures in non-operating theatre settings were eligible for inclusion. Guidance documents were identified from three sources: electronic databases (MEDLINE and Embase), professional organization websites and expert knowledge. No time limits were imposed. Endoscopic, interventional radiology/cardiology, dental and obstetric procedures were excluded. Eligible documents were included if specifications on the setting and descriptions of procedures were provided. Study titles, abstracts and full texts were screened for relevance. A standardized data extraction form was developed, focusing on: document type, surgical specialty, rationale for developing the guidance, setting specifications, staffing requirements, patient information and safety; descriptive statistics summarized data where appropriate. Verbatim text extracted was summarized descriptively.

Results
Of 375 documents identified, 173 full manuscripts were reviewed and 17 were included in the scoping review, published between 1992 and 2022. Guidance provided by documents was limited. They typically included information about general procedures, setting specifications and equipment that may be required to deliver appropriate procedures in the non-operating theatre setting. There was significant heterogeneity in the terminology used to describe the non-operating theatre setting. Appropriate procedures were commonly minor procedures performed under local or topical anaesthesia. The non-theatre setting was recommended to be of adequate size for all appropriate equipment and personnel, with considerations for lighting, waste disposal, ventilation and emergency equipment. Documents also described appropriate training for staff and requirements for personal protective equipment, surgical record keeping, and occupational health and safety guidelines.

Conclusions
This scoping review has demonstrated there is significant heterogeneity in guidance documents concerning the delivery of surgical procedures in the non-theatre setting. Standardization of terminology and definitions is required to help inform stakeholders about the development of non-theatre setting practices.
Human Immunodeficiency Virus/AIDS and Coronavirus Disease 2019: Shared Lessons From 2 Pandemics
Authors: Fauci Anthony S , Folkers Gregory K 
Published: November 2024

Abstract
The global experiences with the human immunodeficiency virus (HIV)/AIDS and coronavirus disease 2019 (COVID-19) pandemics hold important lessons for preparing for, and responding to, future outbreaks of emerging or reemerging infectious diseases. Scores of infectious diseases have emerged or reemerged over the past 4 decades, and future outbreaks are inevitable. The next emerging pathogen likely will again come from unanticipated sources and pose puzzles in terms of microbiology, transmission, natural history, pathogenesis, and epidemiology, and will present challenges to developing countermeasures such as diagnostics, therapeutics, and vaccines. Although dozens of lessons could be addressed, 8 selected lessons common to HIV/AIDS and COVID-19 are addressed here. Consideration of the commonality of lessons learned from HIV/AIDS and COVID-19, the 2 most devastating pandemics over the past half century, will help us—and those who follow us—to minimize the impact of future outbreaks and prevent them from becoming global pandemics.
Type D personality as a risk factor for 3-year cardiovascular events in patients with coronary artery disease and their spouse: a prospective cohort study
Authors: Wang Yini , Huang Bingji , Sun Mengru , Yu Bo , Lin Ping 
Published: November 2024

Abstract

Aims
Type D personality has been established as an independent psychological risk factor for adverse outcomes in coronary artery disease (CAD) patients. However, research on the association between Type D personality and cardiovascular events in couples is limited. This study investigated the correlation between Type D personality and cardiovascular outcomes among CAD patients and their spouses.

Methods and results
This prospective cohort study included 4035 CAD patients for first coronary intervention therapy and their spouses, recruited from January 2017 to July 2020. Type D personality, anxiety, depression, and baseline clinical data were assessed for both partners. The major adverse cardiac event (MACE) rate of both CAD patients and their spouses was analysed after a 3-year follow-up period. A total of 871 CAD patients and 234 spouses developed MACE during the follow-up period. The Cox proportional hazards regression analysis revealed that the Type D(+) patient/Type D(+) spouse group exhibited the highest risk of 3-year MACE in both patients [hazard ratio (HR), 3.834; 95% confidence interval (CI), 2.947–4.987; P &lt; 0.001) and spouses (HR, 2.670; 95% CI, 1.603–4.448; P &lt; 0.001). When analysing Type D as continuous variables, a synergistic interaction between patient and spouse negative affectivity (NA_patient × NA_spouse) was significantly associated with MACE in both CAD patients (HR, 1.746; 95% CI, 1.517–2.010; P &lt; 0.001) and their spouses (HR, 1.992; 95% CI, 1.843–2.152; P &lt; 0.001).

Conclusion
This study suggests that having Type D personality, either in the CAD patient or their spouse, is associated with an increased risk of adverse cardiovascular outcomes in both individuals. Accordingly, the assessment of Type D personality in both partners and the development of tailored, couple-centred interventions are warranted.
Albiglutide and atrial fibrillation in patients with Type 2 diabetes and established cardiovascular disease: insights from the Harmony Outcomes trial
Authors: Krychtiuk Konstantin A , Marquis-Gravel Guillaume , Murphy Shannon , Chiswell Karen , Green Jennifer B , Leiter Lawrence A , Lopes Renato D , Del Prato Stefano , McMurray John J V , Hernandez Adrian F , Granger Christopher B 
Published: November 2024

Abstract

Aims
Atrial fibrillation and flutter (AF) are common in patients with Type 2 diabetes and are associated with worse outcomes.

Methods and results
Harmony Outcomes was a multi-centre, event-driven, double-blind, placebo-controlled trial comparing the effects of albiglutide, a glucagon-like peptide-1 receptor agonist, with placebo on a composite of major adverse cardiac events (MACEs; non-fatal myocardial infarction, non-fatal stroke, and cardiovascular death) in 9463 patients aged &gt;40 years with Type 2 diabetes and established cardiovascular disease. Herein, the cardiovascular effects of albiglutide in patients with and without AF, as well as the effects on AF events during follow-up, were analysed. Patients with a history of AF (8.9%) exhibited a higher event rate for the primary composite MACE endpoint during 1.6 years of follow-up {12.7 vs. 6.3 events/100 person-years, adjusted hazard ratio [aHR] 1.41 [95% confidence interval (CI) 1.14–1.74], P = 0.001}. Treatment with albiglutide reduced the occurrence of the primary endpoint irrespective of history of AF at baseline (history of AF: aHR 0.83 [0.58–1.19], no history of AF: aHR 0.77 [0.66–0.90]; Pinteraction = 0.71). During follow-up, 239 patients (2.5%) experienced an AF event. Overall, albiglutide was associated with numerically fewer AF events [108 vs. 131; hazard ratio 0.82 (0.63–1.06), P = 0.12], irrespective of baseline history of AF (Pinteraction = 0.92).

Conclusion
In patients with Type 2 diabetes, treatment with albiglutide, compared with placebo, reduced the risk of cardiovascular events irrespective of history of AF. Further, albiglutide treatment did not increase AF adverse events but was associated with a trend to a lower rate of AF events during follow-up without reaching statistical significance
Different complex regulatory phenotypes underlie hybrid male sterility in divergent rodent crosses
Authors: Hunnicutt Kelsie E , Callahan Colin M , Keeble Sara , Moore Emily C , Good Jeffrey M , Larson Erica L 
Published: November 2024

Abstract
Hybrid incompatibilities are a critical component of species barriers and may arise due to negative interactions between divergent regulatory elements in parental species. We used a comparative approach to identify common themes in the regulatory phenotypes associated with hybrid male sterility in two divergent rodent crosses, dwarf hamsters and house mice. We investigated three potential characteristic gene expression phenotypes in hybrids including the propensity of transgressive differentially expressed genes toward over or underexpression, the influence of developmental stage on patterns of misexpression, and the role of the sex chromosomes on misexpression phenotypes. In contrast to near pervasive overexpression in hybrid house mice, we found that misexpression in hybrid dwarf hamsters was dependent on developmental stage. In both house mouse and dwarf hamster hybrids, however, misexpression increased with the progression of spermatogenesis, although to varying extents and with potentially different consequences. In both systems, we detected sex chromosome-specific overexpression in stages of spermatogenesis where inactivated X chromosome expression was expected, but the hybrid overexpression phenotypes were fundamentally different. Importantly, misexpression phenotypes support the presence of multiple developmental blocks to spermatogenesis in dwarf hamster hybrids, including a potential role of meiotic stalling or breakdown early in spermatogenesis. Collectively, we demonstrate that while there are some similarities in hybrid expression phenotypes of house mice and dwarf hamsters, there are also clear differences that point toward unique mechanisms underlying hybrid male sterility. Our results highlight the potential of comparative approaches in helping to understand the causes and consequences of disrupted gene expression in speciation.
Combating Ageism with Science: Robert Butler’s Shaping of the National Institute on Aging
Authors: Levy Becca R 
Published: November 2024

Abstract
The physician, scholar, and activist Robert Butler devoted much of his life to trying to end ageism in order to create a society that provides older persons with equal rights and opportunities. His passion for fighting ageism led to his becoming the founding director of the National Institute of Aging (NIA) and set the stage for many of its achievements during the past 50 years. This article explores how Butler first became committed to overcoming ageism, how he made a strong case for setting up NIA as a headquarters to combat ageism with science, and how he launched NIA as a multidisciplinary organization that could draw on research, training, and public policy as weapons against ageism. Finally, this article highlights how Butler, through his anti-ageism activities in later life, personified the possibilities he had done so much to make available to older persons through his launch of NIA.
Lower obstetrician and gynecologist (OBGYN) supply in abortion-ban states, despite minimal state-level changes in the 2 years post-Dobbs
Authors: Strasser Julia , Schenk Ellen , Luo Qian , Chen Candice 
Published: November 2024

Abstract
Since the Dobbs v Jackson Women's Health Organization Supreme Court decision in June 2022, emerging reports suggest that the obstetrician and gynecologist (OBGYN) workforce is moving into states without abortion bans. Using a large national administrative database, we identified OBGYNs enrolling in new states from July 2017 through June 2024. We used difference-in-differences (DID) analyses to estimate the effect of Dobbs on enrollments by state abortion policy (ban vs no ban). Enrollments in ban states were lower than in no-ban states in most academic years (June–July) throughout the study period. In the 2 years post-Dobbs, DID models found no significant differences in enrollments in ban states relative to no-ban states. These findings indicate minimal state-level shifts in the OBGYN workforce following Dobbs. Past research has found that a complex constellation of factors drives physician movement, including state licensure, job availability, income, spousal job opportunities, and social support. While the effect of the Dobbs decision on the workforce are likely to be significant, the full impacts on the workforce will take years to fully unfold.
Comprehensive Assessment of Initial Adaptation of Extended-Spectrum β-Lactamase–Positive ST131 Escherichia coli to Carbapenem Exposure
Authors: Shropshire William C , Song Xinhao , Bremer Jordan , Seo Seokju , Rodriguez Susana , Selvaraj Anand Selvalakshmi , Dinh An Q , Bhatti Micah M , Konovalova Anna , Arias Cesar A , Kalia Awdhesh , Shamoo Yousif , Shelburne Samuel A 
Published: November 2024

Abstract

Background
It remains unclear how high-risk Escherichia coli lineages, like sequence type (ST) 131, initially adapt to carbapenem exposure in their progression to carbapenem resistance.

Methods
Carbapenem mutation frequency was measured in multiple subclades of extended-spectrum β-lactamase (ESBL)–positive ST131 clinical isolates using a fluctuation assay followed by whole genome sequencing (WGS) characterization. Genomic, transcriptomic, and porin analyses of the ST131 C2/H30Rx isolate MB1860, under prolonged, increasing carbapenem exposure was performed using 2 experimental evolutionary platforms to measure fast versus slow adaptation.

Results
All 13 ESBL-positive ST131 strains selected from a diverse (n = 184) ST131 bacteremia cohort had detectable ertapenem (ETP) mutational frequencies, with a positive correlation between initial ESBL gene copy number and mutation frequency (r = 0.87, P &lt; 1e-5). WGS analysis of mutants showed that initial response to ETP exposure resulted in significant increases in ESBL gene copy numbers or mutations in Omp genes in the absence of ESBL gene amplification with subclade-specific associations. In both experimental evolutionary platforms, MB1860 responded to initial ETP exposure by increasing blaCTX-M-15 copy numbers via modular, IS26-mediated pseudocompound transposons (PCTns). Increased transcript level of genes present within the PCTn was a conserved expression signal in both experimental evolutionary platforms. Stable mutations in Omp encoding genes were detected only after prolonged increasing carbapenem exposure, consistent with clinical observations.

Conclusions
ESBL gene amplification is a conserved response to initial carbapenem exposure, especially within the high-risk ST131 C2/H30Rx subclade. Targeting such amplification could assist with mitigating carbapenem resistance development.
Business intelligence systems for population health management: a scoping review
Authors: Roorda Els , Bruijnzeels Marc , Struijs Jeroen , Spruit Marco 
Published: November 2024

Abstract

Objective
Population health management (PHM) is a promising data-driven approach to address the challenges faced by health care systems worldwide. Although Business Intelligence (BI) systems are known to be relevant for a data-driven approach, the usage for PHM is limited in its elaboration. To explore available scientific publications, a systematic review guided by PRISMA was conducted of mature BI initiatives to investigate their decision contexts and BI capabilities.

Materials and Methods
PubMed, Embase, and Web of Science were searched for articles published from January 2012 through November 2023. Articles were included if they described a (potential) BI system for PHM goals. Additional relevant publications were identified through snowballing. Technological Readiness Levels were evaluated to select mature initiatives from the 29 initiatives found. From the 11 most mature systems the decision context (eg, patient identification, risk stratification) and BI capabilities (eg, data warehouse, linked biobank) were extracted.

Results
The initiatives found are highly fragmented in decision context and BI capabilities. Varied terminology is used and much information is missing. Impact on population’s health is currently limited for most initiatives. Care Link, CommunityRx, and Gesundes Kinzigtal currently stand out in aligning BI capabilities with their decision contexts.

Discussion and Conclusion
PHM is a data-driven approach that requires a coherent data strategy and understanding of decision contexts and user needs. Effective BI capabilities depend on this understanding. Designing public-private partnerships to protect intellectual property while enabling rapid knowledge development is crucial. Development of a framework is proposed for systematic knowledge building.
Case series: effects of platelet-rich plasma (PRP) on the recovery of bilateral muscle injuries after removal of semitendinosus and gracilis grafts in bilateral anterior cruciate ligament (ACL) reconstruction
Authors: De Castro Pochini Alberto , Bueno Anna Carolina , Mattos Roque Antonio Cury , Ejnisman Benno , Cohen Moises 
Published: November 2024

Abstract
To assess the healing of acute bilateral muscle injury in cases of bilateral anterior cruciate ligament reconstruction using platelet-rich plasma (PRP) after tendon graft removal. The study included 12 cases of bilateral anterior cruciate ligament reconstruction using semitendinosus and gracilis (STG) grafts. In the right knee, the STG graft was removed, and saline solution was applied; in the left knee, the graft was removed, and PRP was applied. Patients were evaluated using the visual analog scale, pre and postoperative isokinetic tests (5 months), and muscle area analysis. A slight difference in results was observed at 15 and 30 days on the PRP-treated side, but there was no variation in circumference and muscle strength. Due to the small sample size, the study will be continued to increase the number of cases, aiming for the publication of results.
Benardete Paradoxes, Causal Finitism, and the Unsatisfiable Pair Diagnosis
Authors: Schmid Joseph C , Malpass Alex 
Published: November 2024

Abstract
We examine two competing solutions to Benardete paradoxes: causal finitism, according to which nothing can have infinitely many causes, and the unsatisfiable pair diagnosis (UPD), according to which such paradoxes are logically impossible and no metaphysical thesis need be adopted to avoid them. We argue that the UPD enjoys notable theoretical advantages over causal finitism. Causal finitists, however, have levelled two main objections to the UPD. First, they urge that the UPD requires positing a ‘mysterious force’ that prevents paradoxes from arising. Since such a force is implausible, the UPD is in trouble. Second, they employ recombination or patchwork principles to argue that paradoxical situations would be possible if causal finitism were false. Since such situations are not possible, causal finitism is true, and so a substantive metaphysical thesis is needed to avoid the paradoxes. We argue that the UPD proponent can successfully respond to these objections.