bluuebunny/crossref_metadata_2025_split huggingface dataset:
Training of postgraduate year 2 critical care pharmacists in care of the obstetric patient
Authors: Mohamed Adham A , Holmes Ashley K , Ploetz Jeannette , Day Kimberly N 
Published: February 2025

Abstract

Disclaimer
In an effort to expedite the publication of articles, AJHP is posting manuscripts online as soon as possible after acceptance. Accepted manuscripts have been peer-reviewed and copyedited, but are posted online before technical formatting and author proofing. These manuscripts are not the final version of record and will be replaced with the final article (formatted per AJHP style and proofed by the authors) at a later time.

Purpose
The purpose of this study was to characterize the current state of training in the care of critically ill obstetric patients for postgraduate year 2 (PGY2) critical care pharmacy residents across the US. Additionally, we sought to compare the level of comfort in caring for these patients between those who received training during their residency and those who did not.

Methods
This was a descriptive analysis of the training provided to PGY2 critical care pharmacy residents. Two surveys were sent to residency program directors (RPDs) and to current residents and recent graduates of PGY2 critical care pharmacy training programs.

Results
A total of 44 RPDs responded to the survey. Of the respondents, 9% indicated that their program has an obstetrics rotation while 66% of programs include case reviews or topic discussions. Forty-two current residents and recent graduates of PGY2 critical care pharmacy training programs responded to the survey. Of those who responded, 24% indicated that they had a formal rotation experience. The median comfort level in care of critically ill obstetric patients was significantly higher for pharmacists who had received training vs those who had not (P &lt; 0.001).

Conclusion
These survey results highlight an opportunity for more thorough training in care of critically ill obstetric patients for PGY2 critical care pharmacy residents. This training is associated with increased comfort level in caring for these complex patients.
Normative Data for the Modified Location Learning Test (m-LLT) in the French–Quebec Population Aged Between 50 and 89 Years
Authors: St-Hilaire Alexandre , Fuduche Camille , Belzile Florence , Macoir Joël , Hudon Carol 
Published: February 2025

Abstract

Objective
This study aims to establish normative data for the modified Location Learning Test (m-LLT), considering sociodemographic characteristics such as age, sex, and educational level.

Materials and Methods
One hundred eighty-nine middle-aged and elderly people aged 50 years and older were recruited from the French-speaking population in Quebec (Canada). The m-LLT procedure described by Kessels et al. (2006) was used. Percentiles were derived for performance scores (Trial 1, Total Displacement Score, Learning Index, Delayed Recall Displacements), stratified by sociodemographic characteristics where appropriate.

Results
Regarding the sex variable, the number of displacements in Trial 1 and for the Total Displacement Score were higher in men than in women. Age was positively associated with the Total Displacement Score and Delayed Recall Displacements and negatively associated with the Learning Index. Education was positively associated with the Learning Index and Delayed Recall Displacements. Two-thirds of the normative sample achieved a perfect score on the fifth and final learning trial.

Conclusions
Learning was better in women than in men, which may be explained by the use of verbal and nonverbal strategies and environmental awareness favoring women. The decline in learning and retrieval with age can be explained, among other reasons, by a less strategic approach during the encoding phase, a decline in other cognitive domains, or poorer imagery-based representations of the stimuli. The associations between education, strategic retrieval, and cognitive reserve are discussed. Overall, these normative data will enhance the detection of cognitive decline in geriatric clinical or research settings.
Effect of D-β-hydroxybutyrate on sleep quality in healthy participants: a randomized, double-blind, placebo-controlled study
Authors: Katsuya Shohei , Kawata Yoshikazu , Kawamura Yosuke , Kawamura Jun , Tsubota Jun 
Published: February 2025

Abstract
We investigated the effects of D-β-hydroxybutyric acid on sleep quality in healthy Japanese adults. In this randomized, placebo-controlled, double-blind, parallel-grouped study, each group comprised 30 healthy Japanese adults. They received either 1.5 g D-β-hydroxybutyric acid (low D-BHB group), 2.9 g D-β-hydroxybutyric acid (high D-BHB group), or placebo beverage (placebo group) for 14 days, respectively. Before and after the intervention, the Oguri–Shirakawa–Azumi sleep inventory, middle-aged and aged version (OSA-MA), and sleep state test were conducted. After 14 days, compared to the placebo group, the OSA-MA scores for “Sleepiness on rising” and “frequent dreaming” were significantly higher in both the low and high D-BHB groups. Additionally, the score for “Initiation and maintenance of sleep” was significantly higher in the low D-BHB group, and the score for “Refreshing on rising” was significantly higher in the high D-BHB group. We found that D-β-hydroxybutyric acid can improve sleep quality in healthy Japanese adults.
Characterization of the nucleoside monophosphate kinase from Thermus thermophilus phage p23-45 and its application in the biosynthesis of deoxynucleoside triphosphates
Authors: Cheng Nai-Wei , Kok Li-Ching , Cheng Hui-Chun , Chang Hwan-You 
Published: February 2025

Abstract
Nucleoside monophosphate kinases (NMKs) are essential enzymes in nucleotide biosynthesis. In this study, an NMK from Thermus thermophilus phage p23-45 (ϕNMK) was overexpressed and characterized, which exhibited relatively low sequence similarity (∼20%) to cellular NMKs. The enzyme demonstrated broad specificity for all four deoxynucleoside monophosphates (dNMPs) (KM: 0.27‒0.45 mM), optimal activity at 70 °C, and retained 95% activity after 8 h at 37 °C. Structural modeling and site-directed mutagenesis identified key catalytic roles for K39 and R66. A one-pot dNTP synthesis workflow using ϕNMK and T. thermophilus pyruvate kinase (TtPYK) enhanced ATP regeneration efficiency compared to acetate kinases, achieving &gt; 85% conversion of all dNMPs to dNTPs. These findings highlight ϕNMK's thermostability and efficiency, establishing it as a promising candidate for industrial dNTP production.
FAIRification of the DMRichR Pipeline: Advancing Epigenetic Research on Environmental and Evolutionary Model Organisms
Authors: Salam Wassim , Wojewodzic Marcin W , Frisch Dagmar 
Published: February 2025

Abstract

Summary
Bioinformatics tools often prioritize humans or human-related model organisms, overlooking the requirements of environmentally relevant species, which limits their use in ecological research. This gap is particularly challenging when implementing existing software, as inadequate documentation can delay the innovative use of environmental models for modern risk assessment of chemicals that can cause aberration in methylation patterns. The establishment of fairness in ecological and evolutionary studies is already constrained by more limited resources in these fields of study, and an additional imbalance in tool availability further hinders comprehensive ecological research.
To address these gaps, we adapted the DMRichR package, a tool for epigenetic analysis, for use with custom, non-model genomes. As an example we here use the crustacean Daphnia, a keystone grazer in aquatic ecosystems. This adaptation involved the modification of specific code, computing three new species-specific packages (BSgenome, TxDb, and org.db), and computing a CpG islands track using the makeCGI package. Additional adjustments to the DMRichR package were also necessary to ensure proper functionality. The developed workflow can now be applied not only to different Daphnia species that were previously unsupported, but also to any other species for which an annotated reference genome is available.

Availability and implementation
Code and data are available at https://github.com/wassimsalam01/DMRichR-FAIRification and at https://github.com/folkehelseinstituttet/DMRichR-FAIRification as well as DOI 10.5281/zenodo.13366959. This work is open-source software available under the GNU Affero General Public License (AGPL) version 3.0.
FoldX Force Field revisited, an improved version
Authors: Delgado Javier , Reche Raul , Cianferoni Damiano , Orlando Gabriele , van der Kant Rob , Rousseau Frederic , Schymkowitz Joost , Serrano Luis 
Published: February 2025

Abstract

Motivation
The FoldX force field was originally validated with a database of 1000 mutants at a time when there were few high-resolution structures. Here we have manually curated a database of 5556 mutants affecting protein stability, resulting in 2484 highly confident mutations denominated FoldX Stability Dataset (FSD), represented in non-redundant X-ray structures with less than 2.5 Å resolution, not involving duplicates, metals or prosthetic groups. Using this database, we have created a new version of the FoldX force field by introducing Pi stacking, pH dependency for all charged residues, improving aromatic-aromatic interactions, modifying the Ncap contribution and α-helix dipole, recalibrating the side chain entropy of Methionine, adjusting the H-bond parameters, and modifying the solvation contribution of Tryptophan and others.

Results
These changes have led to significant improvements for the prediction of specific mutants involving the above residues/interactions and a statistically significant increase of FoldX predictions, as well as for the majority of the 20 aa. Removing all training sets data from FSD (VFSD dataset), resulted in improved predictions from R = 0.693 (RMSE = 1.277 kcal/mol) to R = 0.706 (RMSE = 1.252 kcal/mol) when compared with the previously released version. FoldX achieves 95% accuracy considering an error of ± 0.85 kcal/mol in prediction, and an AUC = 0.78, for the VFSD, predicting the sign of the energy change upon mutation.

Availability
FoldX versions 4.1 & 5.1 are freely available for academics at https://foldxsuite.crg.eu/.

Supplementary information
Supplementary data are available at Bioinformatics online.
OoCount: A Machine-Learning Based Approach to Mouse Ovarian Follicle Counting and Classification
Authors: Folts Lillian , Martinez Anthony S , Williams Jaelyn A , Bunce Corey , Capel Blanche , McKey Jennifer 
Published: February 2025

Abstract
The number and distribution of follicles in each growth stage provides a reliable readout of ovarian health and function. Leveraging techniques for three-dimensional imaging of ovaries in toto has the potential to uncover total, accurate ovarian follicle counts. Due to the size and holistic nature of these images, counting oocytes is time consuming and difficult. The advent of machine-learning algorithms has allowed for the development of ultra-fast, automated methods to analyze microscopy images. In recent years, these pipelines have become more accessible to non-specialists. We used these tools to create OoCount, a high-throughput, open-source method for automatic oocyte segmentation and classification from fluorescent 3D microscopy images of whole mouse ovaries using a deep-learning convolutional neural network (CNN) based approach. We developed a fast tissue-clearing and imaging protocol to obtain 3D images of whole mount mouse ovaries. Fluorescently labeled oocytes from 3D images were manually annotated in Napari to develop a training dataset. This dataset was used to retrain StarDist using a CNN within DL4MicEverywhere to automatically label all oocytes in the ovary. In a second phase, we utilize Accelerated Pixel and Object Classification, a Napari plugin, to sort oocytes into growth stages. Here, we provide an end-to-end pipeline for producing high-quality 3D images of mouse ovaries and obtaining follicle counts and staging. We demonstrate how to customize OoCount to fit images produced in any lab. Using OoCount, we obtain accurate oocyte counts from each growth stage in the perinatal and adult ovary, improving our ability to study ovarian function and fertility.
Relational In/Justice Journeys: Revising Procedural Justice Theory Through An Analysis of Rape and Sexual Assault Victims’ Experiences of Police Investigations
Authors: Hohl Katrin , Jackson Jonathan , Bradford Ben 
Published: February 2025

Abstract
Procedural justice theory has much to say about police-citizen interactions, but the high-stakes, long-duration and quite specific nature of police investigations involving rape and sexual assault victims compel us to re-examine and re-conceptualize some of its core propositions. We draw on data from the largest national survey of rape and sexual assault victims’ experiences of the police in the United Kingdom. We find that negative officer behaviour can signal to sexual violence victims that they are not deserving of agency, connectedness, competence and care. For rape and sexual assault victims, police investigations are relational journeys of (mis)recognition and (mis)affirmation with profound impacts on victim’s personal well-being and subjective access to police safeguarding and criminal justice.
Metastatic malignant cylindroma arising on a background of digenic inheritance of BRCA2 and CYLD pathogenic variants targeted with PARP inhibition
Authors: Fostier William , Husain Akhtar , Namini Shirin , Mathew Bipin , Holt Georgie , Memari Yasin , Davies Helen , Koh Gene Ching Chiek , Nik-Zainal Serena , Rajan Neil 
Published: February 2025

Abstract

Background
CYLD cutaneous syndrome (CCS) is caused by germline heterozygous pathogenic variants in CYLD and results in progressive formation of cylindromas, spiradenomas, or trichoepitheliomas. Malignant cylindroma is a rare skin adnexal tumour occurring in CCS that can metastasize with lethal outcomes and has limited genomic characterization. BRCA2 loss in CCS is not described and may modulate the cutaneous cancer risk of CCS.

Objectives
To establish if BRCA deficiency drives metastatic malignant cylindroma and report the phenotype of three siblings with digenic inheritance of CYLD and BRCA2 pathogenic variants, one of whom developed metastatic cylindroma aged 28.

Methods
A kindred study reporting seven members of a CCS family was conducted in a tertiary hospital setting within the United Kingdom from April 2021 - February 2023. Clinical phenotype, pathological, radiological and genetic findings, and treatment data were collected. Whole genome sequencing of the primary malignant cylindroma occurring in one patient was performed to identify targetable driver mutations and signatures.

Results
Malignant cylindroma arose in one (proband) of the two male siblings with digenic inheritance of BRCA2 (c.5158insT) and CYLD (c.2689-2A&gt;G) pathogenic variants. A further female sibling with digenic inheritance of the same BRCA2 and CYLD PVs developed early breast cancer. Whole genome sequencing of the primary malignant cylindroma in the affected patient showed loss of heterozygosity of both BRCA2 and CYLD. Bioinformatic analysis revealed confirmed homologous repair deficiency (HRD). These data supported the use of the poly ADP ribose (PARP) inhibitor, Rucaparib, to target HRD in a non-canonical BRCA deficient skin cancer.

Conclusions
Digenic inheritance of pathogenic variants in cancer predisposing genes should prompt clinicians to be vigilant for atypical malignant presentations. We demonstrate that rapid whole genome sequencing can inform the treatment of metastatic malignant cylindroma and identify novel systemic therapies.
The hidden interplay between sex and adverse outcomes in incident dialysis patients: the role of aortic calcification
Authors: Zhao Xue , Lei Zitong , Wang Meng , Liu Hua , Yan Mengyao , Huo Linhui , Gao Zhumei , Jiang Hongli , Wei Limin 
Published: February 2025

Abstract

Background
Research on the sex disparity in the prognosis of chronic kidney disease (CKD), particularly among those who are newly initiating dialysis, is limited and inconclusive. This study aimed to investigate the associations between sex and all-cause mortality and major cardiovascular adverse events (MACE), with a particular focus on the presence of aortic calcification (AC).

Methods
We conducted a post hoc analysis of 1459 incident dialysis patients included in this prospective cohort study. The primary outcome of interest was all-cause mortality, and the secondary endpoint was a composite of MACE.

Results
During a median follow-up period of 3.55 years, 362 (269 male and 93 female) patients died and 477 (342 male and 135 female) patients developed MACE. The risks for all-cause mortality (HR 0.61, 95% CI 0.47-0.79) and MACE (HR 0.74, 95% CI 0.60-0.93) were lower in females than in males. This finding was robust across multiple sensitivity analyses and most subgroups. Moreover, the associations between sex and adverse outcomes were significantly modified by AC status at dialysis initiation (p for interaction &lt; 0.05). Specifically, among patients without AC, females exhibited lower risks for all-cause mortality (HR 0.45, 95% CI 0.29-0.69; p &lt; 0.001) and MACE (HR 0.67, 95% CI 0.49-0.93; p=0.015),whereas no differences were observed for all-cause mortality (HR 0.82; 95% CI 0.59-1.15; p=0.256) or MACE (HR 0.80, 95% CI 0.59-1.10; p=0.174) among patients with AC.

Conclusions
In patients with renal failure receiving dialysis, AC abolished the survival and cardiovascular protection observed in female versus male patients. This finding supports the need for greater awareness of the AC burden in female dialysis patients.
Ability of Upper Airway Metrics to Predict Obstructive Sleep Apnea Severity: A Systematic Review
Authors: Taha Yara M , Abu el Sadat Shaimaa M , Gaber Ramy M , Farid Mary M 
Published: February 2025

Abstract:

Objectives
The lack of consensus regarding the association between airway narrowing and the severity of obstructive sleep apnea (OSA) presents a significant challenge in understanding and diagnosing this sleep disorder. The study aimed to systematically review the literature to investigate the relationship between upper airway measurements and the severity of OSA defined by the apnea-hypopnea index (AHI).

Methods
PubMed, Scopus and Web of Science were systematically searched on the 21st of March 2023 for articles of OSA patients as diagnosed by polysomnography, investigating the correlation between upper airway measurements and AHI using CBCT or MDCT. Quality assessment was done using the New Castle-Ottawa Scale. The results were subsequently synthesized descriptively.

Results
The database search identified 1253 results. Fourteen studies, encompassing 720 patients, met the eligibility criteria. Upper airway length showed moderate to weak positive correlation with AHI. Minimal cross-sectional area had varying correlations with AHI, ranging from strong negative to no correlation. Nasopharyngeal volumes showed moderate negative to weak correlations with AHI. Total upper airway volume ranged from strong negative to weak correlation with AHI. Other measurements exhibited weak or very weak correlations with AHI.

Conclusions
Among the variables investigated, the minimal cross-sectional area and, to a lesser extent, the volume of the upper airway in OSA patients demonstrated the most promising correlation with the AHI. However, the preponderance of evidence suggests that upper airway length, cross-sectional area and volume as measured by CBCT or MDCT are weak predictors of OSA.
Refusing Algorithmic Recognition
Authors: Petersmann Marie 
Published: February 2025

Abstract
The Black Technical Object retraces and problematizes the entanglements between technology, data and race. Ramon Amaro’s genealogy of racial sorting argues that machine learning is preconditioned by a prototypical Whiteness that relegates Black beings as objects measured against a White norm. In raising salient questions about technological, political and legal agency – which intersect with various modes of critique of algorithmic governance – I explore three main contributions the book makes to international law. First, machine learning and algorithmic decision-making are increasingly deployed in different domains of international law. The Black Technical Object speaks to emergent strands of scholarship that map how these developments reconfigure and disrupt key legal concepts and categories. Second, both the individual ‘subject’ and the collective ‘public’ of (international) law come into formation differently through these technological systems. Amaro helps us engage with these modalities of subject-making and understand their lineages and political stakes. Finally, the book provides a distinct political perspective of refusal and resistance – a refusal of recognition to resist the reinforcement of racial constructs (re)produced in the digital space.
Physical activity and heat stress shape water needs in pregnant endurance athletes
Authors: Sadhir Srishti , McGrosky Amanda , Swanson Zane S , Tavormina Anna , Tomechko Keri , Pontzer Herman 
Published: February 2025

Abstract

Background and Objectives
Pregnancy, heat stress, and physical activity are all known to independently increase human water requirements. We hypothesize that climate conditions and behavioral strategies interact to shape water needs in highly active pregnancies.

Methodology
We recruited 20 female endurance runners who were pregnant (8-16 weeks gestational age; n=13) or planning to be pregnant (n=7) for an observational, prospective cohort study. At three timepoints in the study (preconception, 8-16 weeks, and 32-35 weeks), we measured water turnover using the deuterium dilution and elimination technique, physical activity using ActiGraph wGT3X-BT accelerometers, and heat index using historical temperature and humidity data. We also compared athletes to non-athletes from a previously published study.

Results
Athletes maintained high water turnover from preconception through the end of pregnancy. Physical activity was positively associated with water turnover among athletes for preconception and early pregnancy time periods, but not for the third trimester. Heat index weakly moderated the relationship between physical activity and water turnover in predicting a more positive slope in hotter and more humid weather conditions. Water turnover in athletes was higher than in non-athletes, but this difference attenuated during the third trimester, as non-athletes increased their water turnover.

Conclusions and Implications
Athletes experience higher water turnover with greater levels of physical activity, and this relationship is somewhat stronger in higher heat index conditions. With the threat of climate change expected to exacerbate extreme heat conditions, evidence-based, global policies are required for particularly vulnerable populations.