bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unravelling reference bias in ancient DNA datasets
Authors: Dolenz Stephanie , van der Valk Tom , Jin Chenyu , Oppenheimer Jonas , Sharif Muhammad Bilal , Orlando Ludovic , Shapiro Beth , Dalén Love , Heintzman Peter D 
Published: July 2024

Abstract

Motivation
The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths.

Results
For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings.

Availability and implementation
AMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts).
Policy and Practice with Lesbian, Gay, Bisexual, Trans and Queer (LGBTQ+) Care-Experienced Young People—A National Survey of Local Authorities in England
Authors: Cossar Jeanette , Belderson Pippa 
Published: July 2024

Abstract
There is scant research on the experiences and needs of lesbian, gay, bisexual, trans and queer/questioning young people growing up in care in the UK. This article reports on a national survey of local authorities (LAs) in England, which aimed to explore what data LAs collect relating to sexual orientation and gender identity, as well as exploring existing LA policies and practices in relation to LGBTQ+ young people growing up in out-of-home care. The survey asked about policy, recording, support and training. Respondents were senior managers in LAs with responsibility for looked after children. The survey response rate was 78 per cent (n = 118). The survey found a lack of specific policy relating to this population and little central recording of sexual orientation and gender identity (SOGI) data, although most LAs suggested information would be recorded in individual case records. LAs described a variety of ways in which they supported LGBTQ+ young people in practice at both individual and organisational levels but highlighted a lack of staff knowledge and confidence. Training provision was more likely to be provided for social workers than for foster carers or residential staff. Implications for practice are discussed.
2024 Clinical Practice Guideline Update by the Infectious Diseases Society of America on Complicated Intra-abdominal Infections: Risk Assessment in Adults and Children
Authors: Bonomo Robert A , Chow Anthony W , Abrahamian Fredrick M , Bessesen Mary , Dellinger E Patchen , Edwards Morven S , Goldstein Ellie , Hayden Mary K , Humphries Romney , Kaye Keith S , Potoski Brian A , Rodríguez-Baño Jesús , Sawyer Robert , Skalweit Marion , Snydman David R , Tamma Pranita D , Donnelly Katelyn , Kaur Dipleen , Loveless Jennifer 
Published: July 2024

Abstract
This paper is part of a clinical practice guideline update on the risk assessment, diagnostic imaging, and microbiological evaluation of complicated intra-abdominal infections in adults, children, and pregnant people, developed by the Infectious Diseases Society of America. In this paper, the panel provides a recommendation for risk stratification according to severity of illness score. The panel's recommendation is based on evidence derived from systematic literature reviews and adheres to a standardized methodology for rating the certainty of evidence and strength of recommendation according to the GRADE (Grading of Recommendations, Assessment, Development, and Evaluation) approach.
Neurodegenerative diseases associated with the disruption of proteostasis and their therapeutic strategies using chemical chaperones
Authors: Sugiyama Takashi , Nishitoh Hideki 
Published: July 2024

Abstract
Aberrant proteostasis is thought to be involved in the pathogenesis of neurodegenerative diseases. Some proteostasis abnormalities are ameliorated by chaperones. Chaperones are divided into three groups: molecular, pharmacological and chemical. Chemical chaperones intended to alleviate stress in organelles, such as the endoplasmic reticulum (ER), are now being administered clinically. Of the chemical chaperones, 4-phenylbutyrate (4-PBA) has been used as a research reagent, and its mechanism of action includes chaperone effects and the inhibition of histone deacetylase. Moreover, it also binds to the B-site of SEC24 and regulates COPII-mediated transport from the ER. Although its therapeutic effect may not be strong, elucidating the mechanism of action of 4-PBA may contribute to the identification of novel therapeutic targets for neurodegenerative diseases.
Genomic instability in non–breast or ovarian malignancies of individuals with germline pathogenic variants in BRCA1/2
Authors: Elze Lisa , van der Post Rachel S , Vos Janet R , Mensenkamp Arjen R , Pamidimarri Naga Samhita , Hampstead Juliet E , Vermeulen Emma , Oorsprong Michiel , Hofste Tom , Simons Michiel , Nagtegaal Iris D , Hoogerbrugge Nicoline , de Voer Richarda M , Ligtenberg Marjolijn J L 
Published: July 2024

Abstract

Background
Individuals with germline pathogenic variants in BRCA1 or BRCA2 are at a high risk of breast and ovarian carcinomas with BRCA1/2 deficiency and homologous recombination deficiency that can be detected by analysis of genome-wide genomic instability features such as large-scale state transitions, telomeric allelic imbalances, and genomic loss of heterozygosity. Malignancies with homologous recombination deficiency are more sensitive to platinum-based therapies and poly(ADP-ribose) polymerase inhibitors. We investigated the fraction of non–breast or ovarian malignancies that have BRCA1/2 deficiency and genomic instability features.

Methods
The full tumor history of a large, historical, clinic-based, consecutive cohort of 2965 individuals with germline pathogenic variants in BRCA1/2 was retrieved from the Dutch nationwide pathology databank (Palga). In total, 169 non–breast or ovarian malignancies were collected and analyzed using targeted next-generation sequencing and shallow whole-genome sequencing to determine somatic second-hit alterations and genomic instabilities indicative of homologous recombination deficiency, respectively.

Results
BRCA1/2 deficiency was detected in 27% (21/79) and 23% (21/90) of 20 different types of non–breast or ovarian malignancies in individuals with germline pathogenic variants in BRCA1 and BRCA2, respectively. These malignancies had a higher genomic instability score than BRCA1- or BRCA2-proficient malignancies (P &lt; .001 and P &lt; .001, respectively).

Conclusions
BRCA1/2 deficiency and genomic instability features were found in 27% and 23% of a broad spectrum of non–breast or ovarian malignancies in individuals with germline pathogenic variants in BRCA1 and BRCA2, respectively. Evaluation of the effectiveness of poly(ADP-ribose) polymerase inhibitors in these individuals should be focused on tumors with a confirmed absence of a wild-type allele.
Dramatic response to crizotinib through MET phosphorylation inhibition in rare TFG-MET fusion advanced squamous cell lung cancer
Authors: Cheng Wanwan , Xu Ting , Yang Lu , Yan Naimeng , Yang Jie , Fang Shencun 
Published: July 2024

Abstract
With the widespread use of next-generation sequencing (NGS) for solid tumors, mesenchymal-to-epithelial transition factor (MET) rearrangement/fusion has been confirmed in multiple cancer types. MET amplification and MET exon 14 skipping mutations induce protein autophosphorylation; however, the pathogenic mechanism and drug sensitivity of MET fusion remain unclear. The following report describes the clinical case of a patient diagnosed with squamous lung cancer bearing a TFG-MET gene fusion. In vitro assays demonstrated MET phosphorylation and oncogenic capacity due to the TFG-MET rearrangement, both of which were inhibited by crizotinib treatment. The patient was treated with crizotinib, which resulted in sustained partial remission for more than 17 months. Collectively, cellular analyses and our case report emphasize the potential of MET fusion as a predictive biomarker for personalized target therapy for solid tumors.
Soybean ethylene response factors GmENS1 and GmENS2 promote nodule senescence
Authors: Xiao Aifang , Wu Jiashan , Wang Weiyun , Guan Yuxin , Zhuang Mengting , Guo Xiaoli , Zhu Hui , Yu Haixiang , Cao Yangrong 
Published: July 2024

Abstract
The final phase in root nodule development is nodule senescence. The mechanism underlying the initiation of nodule senescence requires further elucidation. In this study, we investigate the intrinsic signals governing soybean (Glycine max L. Merr.) nodule senescence, uncovering ethylene as a key signal in this intricate mechanism. Two AP2/ethylene response factor (ERF) transcription factor (TF) genes, GmENS1 and GmENS2 (Ethylene-responsive transcription factors required for Nodule Senescence), exhibit heightened expression levels in both aged nodules and nodules treated with ethylene. An overexpression of either GmENS1 or GmENS2 accelerates senescence in soybean nodules, whereas the knockout or knockdown of both genes delays senescence and enhances nitrogenase activity. Furthermore, our findings indicate that GmENS1 and GmENS2 directly bind to the promoters of GmNAC039, GmNAC018, and GmNAC030, encoding 3 NAC (NAM, ATAF1/2, and CUC2) TFs essential for activating soybean nodule senescence. Notably, the nodule senescence process mediated by GmENS1 or GmENS2 overexpression is suppressed in the soybean nac039/018/030 triple mutant compared with the wild-type control. These data indicate GmENS1 and GmENS2 as pivotal TFs mediating ethylene-induced nodule senescence through the direct activation of GmNAC039/GmNAC018/GmNAC030 expression in soybean.
Selective decision-making and collective behavior of fish by the motion of visual attention
Authors: Ito Susumu , Uchida Nariya 
Published: July 2024

Abstract
Collective motion provides a spectacular example of self-organization in Nature. Visual information plays a crucial role among various types of information in determining interactions. Recently, experiments have revealed that organisms such as fish and insects selectively utilize a portion, rather than the entirety, of visual information. Here, focusing on fish, we propose an agent-based model where the direction of attention is guided by visual stimuli received from the images of nearby fish. Our model reproduces a branching phenomenon where a fish selectively follows a specific individual as the distance between two or three nearby fish increases. Furthermore, our model replicates various patterns of collective motion in a group of agents, such as vortex, polarized school, swarm, and turning. We also discuss the topological nature of the visual interaction, as well as the positional distribution of nearby fish and the map of pairwise and three-body interactions induced by them. Through a comprehensive comparison with existing experimental results, we clarify the roles of visual interactions and issues to be resolved by other forms of interactions.
Upper Limb Function in People With Upper and Lower Limb Loss 8 Years Postinjury: The Armed Services Trauma Outcome Study (ADVANCE) Cohort Study
Authors: Watson Fraje C E , Kedgley Angela E , Schofield Susie , Behan Fearghal P , Boos Christopher J , Fear Nicola T , Bennett Alexander N , Bull Anthony M J 
Published: July 2024

Abstract

Objective
Upper limb (UL) disability in people with UL loss is well reported in the literature, less so for people with lower limb loss. This study aimed to compare UL disability in injured (major trauma) and uninjured UK military personnel, with particular focus on people with upper and lower limb loss.

Methods
A volunteer sample of injured (n = 579) and uninjured (n = 566) UK military personnel who served in a combat role in the Afghanistan war were frequency matched on age, sex, service, rank, regiment, role, and deployment period and recruited to the Armed Services Trauma Rehabilitation Outcome (ADVANCE) longitudinal cohort study. Participants completed the Disability of the Arm, Shoulder, and Hand (DASH) questionnaire, scored from 0 (no disability) to 100 (maximum disability) 8 years postinjury. Mann–Whitney U and Kruskal–Wallis tests were used to compared DASH scores between groups. An ordinal model was used to assess the effect of injury and amputation on DASH scores.

Results
DASH scores were higher in the Injured group compared to the Uninjured group (3.33 vs 0.00) and higher in people with lower limb loss compared to the Uninjured group (0.83 vs 0.00), although this was not statistically significant. In the adjusted ordinal model, the odds of having a higher DASH score was 1.70 (95% CI = 1.18–2.47) times higher for people with lower limb loss compared to the Uninjured group. DASH score was not significantly different between people with major and partial UL loss (15.42 vs 12.92). The odds of having a higher DASH score was 8.30 (95% CI = 5.07–13.60) times higher for people with UL loss compared to the Uninjured group.

Conclusion
People with lower limb loss have increased odds of having more UL disability than the Uninjured population 8 years postinjury. People with major and partial UL loss have similar UL disability. The ADVANCE study will continue to follow this population for the next 20 years.

Impact
For the first time, potential for greater long-term UL disability has been shown in people with lower limb loss, likely resulting from daily biomechanical compensations such as weight-bearing, balance, and power generation. This population may benefit from prophylactic upper limb rehabilitation, strength, and technique.
Clinical Outcomes Associated With a Remote Postpartum Hypertension Monitoring Program
Authors: Lemon Lara S. , Quinn Beth , Binstock Anna , Larkin Jacob C. , Simhan Hyagriv N. , Hauspurg Alisse 
Published: July 2024

OBJECTIVE:
To evaluate differences in health care utilization and guideline adherence for postpartum individuals with hypertensive disorders of pregnancy (HDP) who are engaged in a remote monitoring program, compared with usual care.

METHODS:
This was a retrospective cohort study of postpartum individuals with HDP who delivered between March 2019 and June 2023 at a single institution. The primary exposure was enrollment in a remote hypertension management program that relies on patient home blood pressure (BP) measurement and centralized nursing team management. Patients enrolled in the program were compared with those receiving usual care. Outcomes included postpartum readmission, office visit within 6 weeks postpartum, BP measurement within 10 days, and initiation of antihypertensive medication. We performed multivariable logistic and conditional regression in a propensity score matched cohort. Propensity scores, generated by modeling likelihood of program participation, were assessed for even distribution by group, ensuring standardized bias of less than 10% after matching.

RESULTS:
Overall, 12,038 eligible individuals (6,556 participants, 5,482 in the control group) were included. Program participants were more likely to be White, commercially insured, be diagnosed with preeclampsia, and have higher prenatal and inpatient postpartum BPs. Differences in baseline factors were well-balanced after implementation of propensity score. Program enrollment was associated with lower 6-week postpartum readmission rates, demonstrating 1 fewer readmission for every 100 individuals in the program (propensity score–matched adjusted risk difference [aRD] −1.5, 95% CI, −2.6 to −0.46; adjusted risk ratio [aRR] 0.78, 95% CI, 0.65–0.93). For every 100 individuals enrolled in the program, 85 more had a BP recorded within 10 days (propensity score–matched aRD 85.4, 95% CI, 84.3–86.6), and six more had a 6-week postpartum office visit (propensity score–matched aRD 5.7, 95% CI, 3.9–7.6). Program enrollment was also associated with increased initiation of an antihypertensive medication postpartum (propensity score–matched aRR 4.44, 95% CI, 3.88–5.07).

CONCLUSION:
Participation in a postpartum remote BP monitoring program was associated with fewer postpartum hospital readmissions, higher attendance at postpartum visits, improved guideline adherence, and higher rates of antihypertensive use.
From Bed to Bench: Pre-analytical Stability of 29 Anti-infective Agents in Plasma and Whole Blood to Improve Accuracy of Therapeutic Drug Monitoring
Authors: Magreault Sophie , Pierredon Dorine , Akinotcho-Relouzat Judith , Méchaï Frédéric , Lamy Brigitte , Jaureguy Françoise , Jullien Vincent 
Published: July 2024

Background:
Therapeutic drug monitoring requires a validated assay and appropriate conditions for sample shipment and storage based on the stability of the compound to be analyzed. This study evaluated the stability of 29 antimicrobial compounds in whole blood (WB) and plasma samples under various storage conditions.

Methods:
The pre-analytical stability of 22 antibiotics (amoxicillin, aztreonam, cefazolin, cefepime, cefotaxime, cefoxitin, ceftazidime, ceftobiprole, ceftolozane, ceftriaxone, ciprofloxacin, clindamycin, cloxacillin, daptomycin, levofloxacin, linezolid, meropenem, metronidazole, moxifloxacin, piperacillin, sulfamethoxazole, and trimethoprim), 2 beta-lactamase inhibitors (avibactam, tazobactam), and 5 antituberculosis drugs (ethambutol, isoniazid, pyrazinamide, rifabutin, and rifampicin) was assessed by WB for up to 24 hours at room temperature (RT) and 72 hours at +4°C. The stability in plasma was evaluated for up to 6 hours at RT, 24 hours at +4°C, 1 month at −20°C, and 6 months at −80°C.

Results:
Concerning WB stability, all investigated compounds were stable for 24 hours at RT, except meropenem and isoniazid, which were stable for 6 hours; however, for 24 hours at +4°C, all the compounds were stable. For storage durations of 48 and 72 hours at +4°C, all compounds were stable, except for ciprofloxacin, cotrimoxazole, and isoniazid. Concerning stability in plasma, all compounds were stable for 6 hours at RT, and all except isoniazid were stable for 24 hours at +4°C. All the tested compounds were stable for 7 days at −20°C, except isoniazid, for which a degradation of approximately 20% was observed. An important degradation was observed for beta-lactam antibiotics after 1 month at −20°C. All compounds were stable at −80°C for 6 months.

Conclusions:
The pre-analytical stabilities of several anti-infective compounds was described. The present results can be used to determine the appropriate conditions for shipping and storing samples dedicated to therapeutic drug monitoring of the investigated compounds.
Quantification of the Plasma Concentration of Vadadustat by High-Performance Liquid Chromatography with Ultraviolet Detection and Ultra-Performance Liquid Chromatography-Tandem Mass Spectrometry
Authors: Yokoyama Satoshi , Nakagawa Junichi , Shimada Michiko , Ueno Kayo , Ishiyama Masahiro , Nakamura Norio , Tomita Hirofumi , Niioka Takenori 
Published: July 2024

Background:
An inexpensive, simple, and accurate plasma concentration measurement system is needed to actively conduct pharmacokinetic and pharmacodynamic analyses of vadadustat, hypoxia-inducible factor-prolyl hydroxylase inhibitor, in clinical settings. In this study, the authors aimed to develop a method for measuring vadadustat in human plasma that could be applied for therapeutic drug monitoring using high-performance liquid chromatography with ultraviolet detection (HPLC-UV) in a clinical setting.

Methods:
Plasma samples (100 μL) were pretreated with acetonitrile using butyl paraoxybenzoate as an internal standard. Chromatographic separation was performed on a SunShell PFP C18 column (2.6 μm, 4.6 mm × 150 mm). The mobile phase consisted of (A) 20 mM of phosphate buffer (pH 2.4) and (B) acetonitrile (60:40, v/v), delivered isocratically at a flow rate of 1 mL/min. The analytes were detected by UV absorbance at a wavelength of 220 nm, and the column temperature was 40°C. To evaluate the applicability of HPLC-UV in a clinical setting, blood samples were collected at 19 time points from 7 patients who had been taking vadadustat.

Results:
The calibration curve was linear over the concentration range of 0.2–150 mcg/mL (R

2
> 0.99). Intra-assay and interassay accuracy, precision, and stability met the Food and Drug Administration recommendations. The vadadustat plasma concentrations of patients analyzed using the current HPLC-UV method were almost equal to those measured using ultra-performance liquid chromatography-tandem mass spectrometry (mean difference: 0.13 mcg/mL). Large variability in the dose-adjusted plasma concentrations of vadadustat at 12 hours after administration was observed between patients (coefficient of variation = 57.6%).

Conclusions:
This HPLC-UV method is a simple, accurate quantification method for evaluating plasma concentrations in patients taking vadadustat in a clinical setting.