bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tides in clouds: control of star formation by long-range gravitational force
Authors: Li Guang-Xing 
Published: October 2023

ABSTRACT
Gravity drives the collapse of molecular clouds through which stars form, yet the exact role of gravity in cloud collapse remains a complex issue. Studies point to a picture where star formation occurs in clusters. In a typical, pc-sized cluster-forming region, the collapse is hierarchical, and the stars should be born from regions of even smaller sizes (${\approx} 0.1\,\rm pc$). The origin of this spatial arrangement remains under investigation. Based on a high-quality surface density map towards the Perseus region, we construct a 3D density structure, compute the gravitational potential, and derive eigenvalues of the tidal tensor (λmin, λmid, λmax, λmin &lt; λmid &lt; λmax), analyse the behaviour of gravity at every location, and reveal its multiple roles in cloud evolution. We find that fragmentation is limited to several isolated, high-density ‘islands’. Surrounding them, is a vast amount of the gas ($75~{{ \rm per\ cent}}$ of the mass, $95~{{ \rm per\ cent}}$ of the volume) that stays under the influence of extensive tides where fragmentation is suppressed. This gas will be transported towards these regions to fuel star formation. The spatial arrangement of regions under different tides explains the hierarchical and localized pattern of star formation inferred from the observations. Tides were first recognized by Newton, yet this is the first time its dominance in cloud evolution has been revealed. We expect this link between cloud density structure and role gravity to be strengthened by future studies, resulting in a clear view of the star formation process.
Insights into RAG Evolution from the Identification of “Missing Link” Family A RAGL Transposons
Authors: Martin Eliza C , Le Targa Lorlane , Tsakou-Ngouafo Louis , Fan Tzu-Pei , Lin Che-Yi , Xiao Jianxiong , Huang Ziwen , Yuan Shaochun , Xu Anlong , Su Yi-Hsien , Petrescu Andrei-Jose , Pontarotti Pierre , Schatz David G 
Published: October 2023

Abstract
A series of “molecular domestication” events are thought to have converted an invertebrate RAG-like (RAGL) transposase into the RAG1–RAG2 (RAG) recombinase, a critical enzyme for adaptive immunity in jawed vertebrates. The timing and order of these events are not well understood, in part because of a dearth of information regarding the invertebrate RAGL-A transposon family. In contrast to the abundant and divergent RAGL-B transposon family, RAGL-A most closely resembles RAG and is represented by a single orphan RAG1-like (RAG1L) gene in the genome of the hemichordate Ptychodera flava (PflRAG1L-A). Here, we provide evidence for the existence of complete RAGL-A transposons in the genomes of P. flava and several echinoderms. The predicted RAG1L-A and RAG2L-A proteins encoded by these transposons intermingle sequence features of jawed vertebrate RAG and RAGL-B transposases, leading to a prediction of DNA binding, catalytic, and transposition activities that are a hybrid of RAG and RAGL-B. Similarly, the terminal inverted repeats (TIRs) of the RAGL-A transposons combine features of both RAGL-B transposon TIRs and RAG recombination signal sequences. Unlike all previously described RAG2L proteins, RAG2L-A proteins contain an acidic hinge region, which we demonstrate is capable of efficiently inhibiting RAG-mediated transposition. Our findings provide evidence for a critical intermediate in RAG evolution and argue that certain adaptations thought to be specific to jawed vertebrates (e.g. the RAG2 acidic hinge) actually arose in invertebrates, thereby focusing attention on other adaptations as the pivotal steps in the completion of RAG domestication in jawed vertebrates.
MethMotif.Org 2024: a database integrating context-specific transcription factor-binding motifs with DNA methylation patterns
Authors: Dyer Matthew , Lin Quy Xiao Xuan , Shapoval Sofiia , Thieffry Denis , Benoukraf Touati 
Published: October 2023

Abstract
MethMotif (https://methmotif.org) is a publicly available database that provides a comprehensive repository of transcription factor (TF)-binding profiles, enriched with DNA methylation patterns. In this release, we have enhanced the platform, expanding our initial collection to over 700 position weight matrices (PWM), all of which include DNA methylation profiles. One of the key advancements in this release is the segregation of TF-binding motifs based on their cofactors and DNA methylation status. We have previously demonstrated that gene ontology (GO) enriched terms associated with TF target genes may differ based on their association with alternative cofactors and DNA methylation status. MethMotif provides precomputed GO annotations for each human TF of interest, as well as for TF-co-TF complexes, enabling a comprehensive analysis of TF functions in the context of their co-factors. Additionally, MethMotif has been updated to encompass data for two new species, Mus musculus and Arabidopsis thaliana, widening its applicability to a broader community. MethMotif stands out as the first and only TF-binding motifs database to incorporate context-specific PWM coupled with epigenetic information, thereby enlightening context-specific TF functions. This enhancement allows the community to explore and gain deeper insights into the regulatory mechanisms governing transcriptional processes.
Supplemental organic trace minerals and a yeast culture product in newly weaned steers: effects of use and delivery method on growth performance and hepatic trace mineral content
Authors: Ribeiro Thiago Lauro Maia , Francis Forest L , Gubbels Erin R , Griffin Jason E , Rusche Warren C , Smith Zachary K 
Published: October 2023

Abstract
The objective of this study was to determine if supplementation and delivery method of a “stress pack” composed of organic trace minerals and Saccharomyces cerevisiae yeast culture product influenced growth performance, feed efficiency, and hepatic trace mineral concentration in newly weaned steers. Crossbred steers (n = 192; 256 ± 14.0 kg) were used in a 49-day receiving phase experiment. Within 36 hours of weaning, steers were weighed, allotted to 24 pens (n = 8 steers/pen; 8 pens/treatment), and randomly assigned to treatments: 1) a traditional receiving diet (CON), 2) a traditional receiving diet plus the “stress-pack” directly in the diet (FORCE), and 3) a traditional receiving diet plus a low-moisture, cooked molasses block fortified with the “stress-pack” (TUB). The “stress-pack” was offered the first 28 day of the 49-day receiving period. Due to adverse weather conditions forecasted on day 1, biopsy samples were collected from a subsample of steers (n = 14 steers) on day 1 to establish hepatic trace mineral concentration baseline. Steers were selected based on the mean body weight (BW) from allotment (day −1) of the pen for collection of subsequent samples (n = 1 steer/pen) on days 14, 28, and 49 for hepatic trace mineral concentration determination. Cumulative dry matter intake (DMI) (P = 0.01) was greater for FORCE compared to CON and TUB. Final BW and average daily gain (ADG) tended (P ≤ 0.10) to be greater for FORCE compared to TUB and CON by 5.4% and 9.4%, respectively. Feed efficiency did not differ between treatments (P = 0.28). A treatment × day interaction (P ≤ 0.01) for hepatic Cu concentration was noted. The FORCE treatment had greater hepatic Cu compared to TUB and CON for the entire period. The steers that received TUB had greater hepatic Cu compared to CON on days 14 and 28, but similar to CON on day 49. The addition of a “stress-pack” to diets offered to newly weaned cattle enhanced hepatic trace mineral concentration, and delivery method influences DMI and daily gain.
The spectrum of central nervous system manifestations in leprosy: a systematic review of published case reports and case series
Authors: Garg Ravindra Kumar , Uniyal Ravi , Pandey Shweta , Tejan Nidhi , Rizvi Imran , Sharma Praveen Kumar , Kumar Neeraj , Malhotra Hardeep Singh 
Published: October 2023

ABSTRACTBackgroundThis systematic review aimed to investigate central nervous system (CNS) involvement in leprosy by analysing multiple cohort studies, individual cases and case series.MethodsThe Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were followed. PubMed, Scopus and Embase databases were searched up to 8 July 2023, using a predefined search strategy. Inclusion criteria included patients diagnosed with leprosy with evidence of CNS involvement. The quality of the included cases was evaluated using the Joanna Briggs Institute checklist.ResultsA total of 34 records were identified, including 18 cohort studies and 16 reports describing 27 isolated cases. Autopsies revealed macroscopic changes in the spinal cord, neurofibrillary tangles and senile plaques. Mycobacterium leprae was detected in neurons of the medulla oblongata and spinal cord using PCR and phenolic glycolipid 1 staining. Cerebrospinal fluid (CSF) analysis showed inflammatory changes, increased gamma globulins and detection of Mycobacterium leprae antigens and antibodies. In 21 patients (78%), spinal cord/brachial plexus abnormities were detected. In the majority, MRI revealed T2/fluid-attenuated inversion recovery (FLAIR) hyperintensity in the cervical cord. In patients with brainstem involvement, T2/FLAIR hyperintensity was noted in the cerebellar peduncles, facial nerve nuclei and/or other cranial nerve nuclei. Brain parenchymal involvement was noted in three patients.ConclusionsThis systematic review provides evidence of CNS involvement in leprosy, based on autopsy findings, neuroimaging, CSF analysis and neurophysiological studies.
Precipitated Opioid Withdrawal Treated With Ketamine in a Hospitalized Patient: A Case Report
Authors: Christian Nicholaus J. , Butner Jenna L. , Evarts Mariah S. , Weimer Melissa B. 
Published: October 2023

Background
Although initiating buprenorphine in the presence of full opioid agonists has always been a clinical dilemma, the transition to primarily fentanyl in the drug supply has increased the urgency to find appropriate treatments for precipitated opioid withdrawal (POW). Although rare, lack of evidence on how to best treat POW threatens clinician and patient comfort in initiating life-saving medication for opioid use disorder. Ketamine has been used in emergency department settings to treat POW; this is the first case report of ketamine use in a hospitalized patient.

Case Summary
A 38-year-old male patient with severe opioid use disorder presented to the emergency department with suicidality and opioid withdrawal 24 hours after last fentanyl use. In the first 24 hours of admission, he received sublingual buprenorphine-naloxone (BNX) 16–4 mg, resulting in Clinical Opiate Withdrawal Scale score increasing from 13 to over 36. The patient was admitted, and addiction medicine was consulted. The patient was diagnosed with POW, started on ketamine infusion, and given additional BNX 8–2 mg. Twelve hours after the ketamine infusion, the patient’s Clinical Opiate Withdrawal Scale score improved to 18 but remained elevated. He received a second ketamine infusion plus additional BNX with complete resolution of symptoms within 8 hours, and he was stabilized and discharged on BNX 24–6 mg daily.

Clinical Significance
Ketamine is a promising treatment for POW due to its potentiation of μ-opioid receptor–mediated signaling. This is the first case to describe POW in the inpatient hospital setting. More research is needed to establish the effectiveness and feasibility of ketamine as treatment for POW.
Characteristics Associated With Survival in Surgically Nonresected Pancreatic Adenocarcinoma in the Military Health System
Authors: Eaglehouse Yvonne L. , Darmon Sarah , Gage Michele M. , Shriver Craig D. , Zhu Kangmin 
Published: October 2023

Objectives:
Pancreatic cancer is often diagnosed at advanced stages with high-case fatality. Many tumors are not surgically resectable. We aimed to identify features associated with survival in patients with surgically nonresected pancreatic cancer in the Military Health System.

Methods:
We used the Military Cancer Epidemiology database to identify the Department of Defense beneficiaries aged 18 and older diagnosed with a primary pancreatic adenocarcinoma between January 1998 and December 2014 who did not receive oncologic surgery as treatment. We used Cox Proportional Hazard regression with stepwise procedures to select the sociodemographic and clinical characteristics related to 2-year overall survival, expressed as adjusted hazard ratios (aHR) and 95% CIs.

Results:
Among 1148 patients with surgically nonresected pancreatic cancer, sex, race-ethnicity, marital status, and socioeconomic indicators were not selected in association with survival. A higher comorbidity count (aHR 1.30, 95% CI: 1.06-1.59 for 5 vs. 0), jaundice at diagnosis (aHR 1.57, 95% CI: 1.33-1.85 vs. no), tumor grade G3 or G4 (aHR 1.32, 95% CI: 1.05-1.67 vs. G1/G2), tumor location in pancreas tail (aHR 1.49, 95% CI: 1.22-1.83 vs. head) or body (aHR 1.30, 95% CI: 1.04-1.62 vs. head), and metastases were associated with survival. Patients receiving chemotherapy (aHR 0.66, 95% CI: 0.57-0.76) had better survival compared with no treatment.

Conclusions:
In a comprehensive health system, sociodemographic characteristics were not related to survival in surgically nonresected pancreatic cancer. This implicates access to care in reducing survival disparities in advanced pancreatic cancer and emphasizes the importance of treating patients based on clinical features.
Vascularized Fibular Epiphyseal Transfer for Pediatric Limb Salvage: Review of Applications and Outcomes
Authors: Lee Christine J. , Tiourin Ekaterina , Khoshab Nima , Leis Amber R. , Nassif Nader A. , Misaghi Amir , Vyas Raj M. 
Published: October 2023

Summary:
Vascularized fibular epiphyseal transfer (VFET) offers a functional advantage in pediatric limb salvage due to the preservation of growth potential and an articular surface for remodeling. This review summarizes the available evidence on the clinical characteristics and outcomes of pediatric reconstruction applying VFET at different recipient sites and with varying techniques. VFET was used to reconstruct the proximal humerus, distal radius or ulna, proximal femur, distal fibula, calcaneus, and mandible. Although most often harvested on the anterior tibial artery, VFET has also been performed using the peroneal artery, the inferior lateral genicular artery, and a dual pedicle. Recipient site flap inset most often involved fixation with plates and/or screws as well as soft tissue reconstruction using a retained slip of biceps femoris tendon. Outcomes included limb growth, range of motion, and strength. The most common reported complications were bone flap fracture and peroneal nerve palsy. The anterior tibial artery was the most applied pedicle with reliable limb growth, but with the added risk of postoperative peroneal palsy. Bone flap fracture most often occurred at the proximal humerus and femur recipient sites. Plate fixation and the combined use of allograft had lower instances of bone flap fracture. This review highlights how the anticipated dynamic growth and remodeling this free flap offers in the long term must be weighed against its complexity and potential complications.
The Influencing Factors of Neutrophil-to-Lymphocyte Ratio as a Prognostic Marker for Sepsis: Analysis from a Large Database
Authors: Zhao Qing , Ma Yubao , Xiao Jianguo , Liu Hui 
Published: October 2023

Abstract
The neutrophil-to-lymphocyte ratio (NLR) is an important predictive prognostic tool. However, its accuracy for predicting sepsis remains debatable. This study aimed to evaluate the factors influencing the ability of NLR to predict sepsis. Adult patients with sepsis or septic shock from the eICU database were enrolled in this study. Results showed that there was a significant difference in NLR between the survival and nonsurvival groups (median [lower quartile–upper quartile], 15.27 [7.92–26.28] vs. 17.97 [8.94–31.85], P = 0.008). Area under the curve (AUC) of NLR on the sixth day was the highest. AUC of NLR was significantly higher in the Simplified Acute Physiological Score (SAPS) 3 ≤52 group than that in the SAPS3 > 52 group (0.78 ± 0.05 vs. 0.69 ± 0.03, P = 0.007). AUC of NLR in the nonshock group was significantly higher than that in the shock group (0.72 ± 0.04 vs. 0.65 ± 0.05, P < 0.01). The ability of NLR as a prognosis predictor of sepsis was influenced by admission time, SAPS3, and shock.
Difference of Clinical Characteristics in Patients with Omicron and Delta Variants of SARS-CoV-2 in Beijing, China
Authors: Tian Di , Pan Yang , Ge Ziruo , Kong Xiangjing , Zhang Yao , Zhang Qing , Wang Aibin , Yang Peng , Chen Zhihai 
Published: October 2023

Abstract

Background
Delta and Omicron are two main variants that have been prevalent since 2021. However, the Omicron variant of severe acute respiratory syndrome coronavirus 2 shows a less severe clinical presentation and high transmissibility. Therefore, we carried out this retrospective study to evaluate Omicron severity compared with the Delta variant and further comprehend the differences in clinical characteristics in patients with the Omicron variant.

Methods
We extracted clinical data and compared clinical severity, symptoms, vaccination status, laboratory parameters, viral shedding time, and computed tomography (CT) imaging between the two groups of patients, which included 109 COVID-19 cases with the Delta variant and 183 cases with the Omicron variant, from January 19 to April 1, 2022, in Beijing Ditan Hospital. In addition, the Beijing Center for Disease Prevention and Control conducted whole-genome sequencing.

Results
We obtained 94 strains of variants of concern/Delta and 110 strains of variants of concern/Omicron. For the 110 Omicron strains, three were assigned as BA.1.1, 53 as BA.2, and 54 as BA.2.2. Among patients with the Delta variant, 54% (59/109) were moderate, which was significantly higher than that of patients with the Omicron variant (7% (12/183), P < 0.001). The number of patients with mild symptoms in the Omicron group was significantly higher than in the Delta group (80% vs. 35%, P < 0.001). Compared with the Omicron group, patients with underlying diseases or obesity, 60 years or older, or unvaccinated in the Delta group had more severe disease, and there was a significant difference between the two groups. The viral shedding time in the Omicron group was shorter than in the Delta group ((11.9 ± 5.9) vs. (14.0 ± 5.8) days, P = 0.003). Among the 183 patients in the Omicron group, 104 (57%) had dry or sore throat symptoms, more than those in the Delta group (34% (37/109); P < 0.001). In the Delta group, patients in the moderate group had more fever and cough symptoms than those in the mild group. The remission time of CT imaging in the Omicron group was shorter than in the Delta group ((9.0 ± 5.2) vs. (13.2 ± 4.2) days, P = 0.018).

Conclusions
Patients with Delta variants are more likely to have pneumonia, mainly with fever and cough symptoms, while patients with the Omicron variant are mostly mild, with more prominent dry or sore throat symptoms. In addition, patients with the Omicron variant have a short viral shedding time and rapid absorption of pneumonia.
“I did not expect the doctor to treat a ghost”: a systematic review of published reports regarding chronic postamputation pain in British First World War veterans
Authors: Dixon Smith Sarah , Aldington Dominic , Hay George , Kumar Alexander , Le Feuvre Peter , Moore Andrew , Soliman Nadia , Wever Kimberley E. , Rice Andrew S.C. 
Published: October 2023

Abstract
Limb trauma remains the most prevalent survivable major combat injury. In the First World War, more than 700,000 British soldiers received limb wounds and more than 41,000 underwent an amputation, creating one of the largest amputee cohorts in history. Postamputation pain affects up to 85% of military amputees, suggesting that up to 33,000 British First World War veterans potentially reported postamputation pain. This qualitative systematic review explores the professional medical conversation around clinical management of chronic postamputation pain in this patient cohort, its development over the 20th century, and how this information was disseminated among medical professionals. We searched The Lancet and British Medical Journal archives (1914–1985) for reports referring to postamputation pain, its prevalence, mechanisms, descriptors, or clinical management. Participants were First World War veterans with a limb amputation, excluding civilians and veterans of all other conflicts. The search identified 9809 potentially relevant texts, of which 101 met the inclusion criteria. Reports emerged as early as 1914 and the discussion continued over the next 4 decades. Unexpected findings included early advocacy of multidisciplinary pain management, concerns over addiction, and the effect of chronic pain on mental health emerging decades earlier than previously thought. Chronic postamputation pain is still a significant issue for military rehabilitation. Similarities between injury patterns in the First World War and recent Iraq and Afghanistan conflicts mean that these historical aspects remain relevant to today's military personnel, clinicians, researchers, and policymakers.
The Utility of Methylphenidate for Fatigue in Long-Term Neurological Conditions: A Meta-analytical Review
Authors: Hagan Alexander James , Kumar Ram 
Published: October 2023

Objective
Fatigue is a chronic and debilitating symptom of many long-term neurological conditions (LTNCs). Although methylphenidate provides some promise in alleviating fatigue in other clinical groups, little work has explored its potential utility within LTNCs. The current systematic review and meta-analysis evaluates the utility of methylphenidate for symptoms of fatigue in LTNCs.

Methods
Five databases (PsycINFO, MEDLINE, Embase, Scopus, and Cochrane Library) were searched for relevant articles from their inception to February 2022. A purpose-developed evaluation tool was used to assess each study's research quality (QuEST:F).

Results
Of the 1698 articles identified, 11 articles were included within this review (n = 370). Meta-analytical findings reported an overall significant benefit of methylphenidate for symptoms of fatigue across a mixed neurological sample (g = −0.44; 95% confidence interval, −0.77 to −0.11). Subgroup analyses identified a significantly greater benefit (P < 0.001) of methylphenidate for fatigue in LTNCs with static pathogenic trajectories (eg, traumatic brain injury) (number needed to treat = 2.5) compared with progressive conditions (eg, multiple sclerosis) (number needed to treat = 40.2).

Conclusions
Methylphenidate may pose an effective intervention for the treatment of fatigue in a number of LTNCs. Nonetheless, given the quality of the current evidence base, there exists a clear need for further robust assessment of the utility of methylphenidate—with a focus on subgroup-specific variability.