bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptation and Validation of Version B of the Edinburgh Cognitive and Behavioural ALS Screen for the Portuguese Population
Authors: Simão Sara , Naumann Lucas L , de Carvalho Mamede , Santos Miguel Oliveira , Martins Isabel Pavão 
Published: December 2024

Abstract

Objective
This study aims to adapt and provide psychometric support for the validation of version B of the Edinburgh Cognitive and Behavioural ALS Screen (ECAS) for the Portuguese population, addressing the need for consistent cognitive evaluations in amyotrophic lateral sclerosis (ALS). A second culturally adapted ECAS screen facilitates the accurate characterization of ALS progression, mitigates learning effects, and supports tailored care management.

Methods
The adaptation process included forward-backward translation, cultural adaptation, and cognitive debriefing on a prospective sample of 193 ALS patients and 106 controls. A multiple regression analysis identified predictors relevant for establishing ECAS cut-off scores. Psychometric evaluations, including reliability assessments and tests of convergent, construct, and criterion validity, were conducted. Additionally, version A's psychometric properties were reevaluated with complementary analyses and a larger sample.

Results
Version B demonstrated good internal consistency with Cronbach's alpha of 0.802, comparable to the previously established version A. Moderate inter-item correlations further supported reliability, reflecting internal coherence. Equivalence testing between the Portuguese versions supported convergent validity, confirming version B's alignment with version A's theoretical framework. Exploratory factor analysis provided preliminary support for construct validity, and receiver operating characteristic analyses established cut-off values for both versions, revealing moderate sensitivity with a tendency toward false negatives, and higher specificity.

Conclusions
This study provided evidence for the cultural suitability, reliability, and validity of the Portuguese ECAS B. As evidence supports the equivalence of the Portuguese ECAS versions, they can be used for flexible screenings and applied with the calculated cut-off values to enhance diagnostic accuracy.
Defining normal enthesis stiffness range in a healthy adult population
Authors: Mahazer Mohammad Khairi Jahidi , Leong Sook Sam , Wong Jeannie Hsiu Ding , Rozalli Faizatul Izza , Yahya Fariz , Tee Ying Chew , Mohd Razalli Mazuin , Vijayananthan Anushya , Baharuddin Hazlyna 
Published: December 2024

Abstract

Objectives
This study explores the correlation between volunteer demographics with enthesis stiffness and intra- and interobserver agreements using shear wave elastography (SWE).

Methods
Ninety-eight healthy volunteers were recruited. SWE was performed on quadriceps, suprapatellar, infrapatellar, and Achilles entheses. The stiffness measurements were measured in shear wave velocity (SWV).

Results
Mann-Whitney test revealed insignificant difference in SWV among gender. Wilcoxon signed-rank test showed significant difference in SWV between left and right Achilles entheses. Spearman correlation test revealed moderate negative correlation between SWV and age group in quadriceps (ρ, −0.45, P &lt; .01), and weak negative correlation in suprapatellar (ρ, −0.31, P &lt; .01), and left Achilles (ρ, −0.29, P &lt; .01). Multiple linear regression analysis showed subjects’ demographic significantly predicted quadriceps, suprapatellar, and left Achilles entheses stiffness with only age statistically significantly to the prediction (P &lt; .05). Kruskal-Wallis showed significant differences in SWV for quadriceps (P = .01), suprapatellar (P = .03), and left Achilles (P = .01) among different age groups. Good interobserver [0.79-0.86 (95% CI, 0.32-0.94)] and interobserver agreement [0.78-0.89 (95% CI, 0.62-0.95)] were found in all the entheses.

Conclusion
SWE emerges as a reproducible method for entheses stiffness quantification, with the study highlighting age as a significant factor impacting SWV in quadriceps, suprapatellar, and left Achilles entheses. Among the studied entheses, SWV for Achilles enthesis is the highest in all age groups.

Advances in knowledge
The study significantly contributes to the understanding of enthesis stiffness by exploring the influence of gender, BMI, and age.
Comparative chloroplast genome analysis reveals powerful barcodes for combatting illegal logging of CITES-listed threatened Asian rosewoods (Dalbergia, Leguminosae, Papilionoideae)
Authors: Rather Shabir A , Wang Kaikai , Wang Ting , Liu Hongmei , Schneider Harald 
Published: December 2024

Abstract
Rosewoods (Dalbergia) are among the most heavily trafficked natural resources in the illegal global multibillion-dollar wildlife trade. Consequently, many rosewood species experience high extinction threats. To enforce the conservation of rosewood species threatened by illegal logging, reliable identification is required to distinguish between legally and illegally traded rosewood timber. DNA barcoding is considered the most promising approach to achieve rapid and reliable species identification, compared to morphological and biochemical compound analyses. This study was designed to establish a DNA barcoding approach for rosewoods by utilizing whole-chloroplast genome sequences, either as super-barcodes or as sources to identify short but highly informative DNA barcoding regions. To achieve these objectives, 81 rosewood plastomes that cover 28 species were generated de novo. The phylogenomic dataset was further expanded to include a total of 110 accessions representing 31 species of Dalbergia. The chloroplast genome structure and composition were found to be highly conserved across all the species studied. The phylogenetic hypothesis obtained using the coding sequences data were fully resolved and robust, even for closely related species. Five loci were identified as powerful DNA barcodes that corresponded to sequence variation hotspots. In summary, the whole chloroplast genomes were found to be highly powerful super-barcodes, while up to five plastome loci were identified as small barcode regions that can be amplified even for degraded DNA. This study successfully establishes the resources necessary to carry out DNA barcoding for rosewoods, serving as a main tool to provide reliable identification of threatened species traded in the illegal timber market.
The role of neutrophils in allergic disease
Authors: Trayer James , Isaza-Correa Johana , Kelly Lynne , Kelleher Maeve , Hourihane Jonathan , Byrne Aideen , Molloy Eleanor 
Published: December 2024

Abstract
Neutrophils are short-lived cells of the innate immune system and represent 50–70% of the circulating leucocytes. Their primary role is antimicrobial defence which they accomplish through rapid migration to sites of inflammation followed by phagocytosis, degranulation, and the release of neutrophil extracellular traps (NETosis). While previously considered terminally differentiated cells, they have been shown to have great adaptability and to play a role in conditions ranging from cancer to autoimmunity. This review focuses on their role in allergic disease. In particular: their role as potential amplifiers of type 1 hypersensitivity reactions leading to anaphylaxis; their involvement in alternative pathways of food and drug allergy; their role in allergic rhinitis and asthma and neutrophil dysfunction in atopic dermatitis. The use of potential biomarkers and therapeutic targets is also discussed with a view to guiding future research.
One-pot preparation of micrometer-sized monodispersed silicone hollow particles
Authors: Nishi Hyota , Ishidate Shintaro , Nakamoto Reina , Katsube Shinya , Suzuki Nozomu , Suzuki Toyoko , Minami Hideto 
Published: December 2024

Abstract
Micrometer-sized, monodispersed silicone hollow particles are functional materials with properties attributed to both their hollow structure and the silicone composition. However, there are few reports on their preparation. We have successfully prepared these particles by combining an original suspension polymerization technique, the self-assembling phase-separated polymer method, with a molecular diffusion method. The resulting particles exhibit heat resistance owing to the silicone matrix and maintain their hollow structure even after heating to 900 °C.
Functionally important components of the transcription elongation complex involved in Rho-dependent termination
Authors: Khatri Ajay , Sen Ranjan 
Published: December 2024

Abstract
Bacterial transcription terminator, Rho is an RNA (Ribonucleic Acid)-dependent ATPase that terminates transcription. Several structures of pretermination complexes of the Rho-transcription elongation complex (EC) revealed a static picture of components of the EC that come close to the nascent RNA-bound Rho, where many of the residues of EC reside ≤10 Å from the Rho residues. However, the in vitro-formed Rho-EC complexes do not reveal the in vivo Rho-EC dynamic interaction patterns during the termination process. Here we report synthetic defect analyses of various combinations of the mutations in RNAP β, β’ and ω-subunits, NusA, NusG, and Rho proteins to delineate the functional network of this process. Several mutations in the β-flap and β’-Zn-finger and -Clamp helices domains of RNAP are synthetically defective in the presence of Rho mutants indicating functional involvement of these domains. Mutations in the NusA RNA-binding domains were synthetically defective with the Rho mutants suggesting its involvement. Our genetic analyses also revealed functional antagonisms between the ω-subunit of RNAP and the NusG-CTD (c-terminal domain) during termination. We concluded that the regions surrounding the RNA exit channel, the RNA-binding domains of NusA, the RNAP ω-subunit, and NusG-CTD constitute a functional network with Rho just before the onset of in vivo Rho-dependent termination.
Is there any role for an atrial septal defect in off-loading a borderline left ventricle?
Authors: Hosseinpour Amir-Reza , González-Calle Antonio , Stümper Oliver , Barron David J 
Published: December 2024

Abstract
A small atrial septal defect with right-to-left shunt is useful for off-loading a dysfunctional right ventricle postoperatively. However, an atrial septal defect with left-to-right shunt may not be as useful for a dysfunctional left ventricle. Experimental data are limited at present. Thus, we reconsider the related physiology to guide future approach.
Peer coaching in cardiac surgery: a pilot study on rehabilitation participation and perioperative challenges
Authors: Parhar Kanwar , Holm Aaron , Hira Ravi S , Oyetunji Lara , Collins-Brandon Jeannie , Lehr Eric J , Speck Sarah 
Published: December 2024

Abstract
Following cardiac surgery, active participation in cardiac rehabilitation (CR) is associated with reduced cardiovascular events and improved survival. However, CR attendance remains persistently low, with only ∼25% of patients participating. The Peer Coaching for Cardiac Patients (PCCP) pilot programme aimed to assess whether peer coaching could enhance CR participation and reduce perioperative anxiety and depression in cardiac surgery patients. Ten patients scheduled for elective cardiac surgery were enrolled, receiving 4 60-min coaching sessions via Zoom, by a coach who had undergone coronary artery bypass grafting in the past. Outcomes were measured by CR participation rates, Patient Health Questionnaire (PHQ)-9 scores, and a post-programme survey. Seven of the 10 patients completed the PCCP programme, all of which attended CR for an average of 19.3 ± 8.70 sessions and 9.57 ± 3.0 weeks. No statistically significant difference in PHQ-9 scores was observed (P = 0.341). Participants rated the programme highly in its role in anxiety reduction (9.0 ± 1.2) and likelihood of participating in CR (9.43 ± 1.05). These results suggests that peer coaching shows potential to support CR participation and address perioperative anxiety and depression. Future studies with larger sample sizes, well-defined control groups and extended follow-up are warranted to validate these preliminary findings.
Theta Functions and Projective Structures
Authors: Biswas Indranil , Ghigi Alessandro , Vai Luca 
Published: December 2024

Abstract
Given a compact Riemann surface $X$, we consider the line, in the space of holomorphic sections of $2\Theta $ on $J^{0}(X)$, orthogonal to all the sections that vanish at the origin. This line produces a natural meromorphic bidifferential on $X\times X$ with a pole of order two on the diagonal. This bidifferential is extensively investigated. In particular we show that it produces a projective structure on $X$, which is different from the standard ones.
Penetration of linezolid into the pleural cavity in critically ill patients with proven or suspected Gram-positive bacterial infections: a retrospective pharmacokinetic study
Authors: De Antonio-Cuscó Marta , Sorlí Luisa , Muñoz-Bermúdez Rosana , López-Mula Carlos , Parrilla Francisco José , Gracia-Arnillas Maria Pilar , Prim Núria , Campillo Ambrós Núria , Horcajada Juan P , Masclans-Enviz Joan Ramon , Grau Santiago , Luque Sònia 
Published: December 2024

Abstract

Objectives
To describe the pharmacokinetics (PK) of linezolid in plasma and pleural fluid (PF) in critically ill patients with proven or suspected Gram-positive bacterial infections.

Patients and methods
Observational PK study in 14 critically ill patients treated with linezolid at standard doses. Blood and PF samples were collected and analysed by HPLC. The ratio between PF and plasma concentrations was calculated. The PK/pharmacodynamic (PD) target of linezolid in plasma was defined as 100% of the duration of the dosing interval in which concentrations were above the MIC (%100 T &gt; MIC).

Results
The median (5th and 95th percentiles) linezolid concentration values for plasma pre-dose at steady state (Cmin,ss) and at the end of the 1-h infusion at steady state (Cmax,ss) were 1.1 (0.02–28.3) and 13.8 mg/L (2.9–38.1), respectively, and the PF pre-dose concentration (PF0 h) and PF concentration at the end of the 1-h intravenous infusion (PF1 h) were 2.8 (0.1–31.6) and 4.2 mg/L (0.1–45.2), respectively. At both times (pre-dose and post-infusion), a strong positive correlation was observed between PF and plasma linezolid concentrations (Spearman’s rho coefficients = 0.8 and 0.9, with P &lt; 0.001 for both). The defined PK/PD target in plasma was achieved in 8 (57.1%), 4 (28.6%) and 3 (21.4%) patients assuming an MIC of 1, 2 and 4 mg/L, respectively.

Conclusions
Linezolid seems to penetrate well into the PF, with concentrations exceeding those in plasma. However, high inter-individual variability, both in plasma and PF concentrations, was observed. A high proportion of patients did not achieve the PK/PD target in plasma, especially in the presence of high MIC strains.
Price Variability of Eight Common Laboratory Tests across All Licensed Tennessee Hospitals
Authors: Hart Stephanie A , Khan Ayesha , Booth Garrett S , Wiencek Joesph R 
Published: December 2024

Abstract

Background
In 2021, the United States implemented a federal price transparency mandate to help combat price variability across the country. Initial studies conducted within several months of the mandate showed persistent price variability.

Methods
To assess continued price variability for laboratory tests and factors associated with prices across all licensed hospitals in Tennessee approximately 2.5 years since the mandate, hospital websites were queried for gross, cash, and Blue Cross Blue Shield (BCBS) prices for common laboratory tests (n = 8). Hospital ownership and county demographic data including income, region, and population density were also collected.

Results
All tests showed considerable price variability. Gross price was set higher than cash and BCBS prices. For the majority (n = 6) of tests, cash was higher than BCBS price. Maximum to minimum price ratios for each test ranged from 29 to 114 for gross, 57 to 243 for cash, and 25 to 115 for BCBS prices. Gross and cash prices were associated with median household income of the hospital’s county while BCBS prices were not. Overall, prices were associated with hospital county income, for-profit status, and region.

Conclusions
Our study shows continued price variability in Tennessee 2.5 years after the federal price transparency mandate.
New indices to track interoperability among US hospitals
Authors: Strawley Catherine E , Adler-Milstein Julia , Holmgren A Jay , Everson Jordan 
Published: December 2024

Abstract

Objectives
To develop indices of US hospital interoperability to capture the current state and assess progress over time.

Materials and Methods
A Technical Expert Panel (TEP) informed selection of items from the American Hospital Association Health IT Supplement survey, which were aggregated into interoperability concepts (components) and then further combined into indices. Indices were refined through psychometric analysis and additional TEP input. Final indices included a “Core Index” measuring adoption of foundational interoperability capabilities, a “Pathfinder Index” representing adoption of advanced interoperability technologies and auxiliary exchange activities, and a “Friction Index” quantifying barriers. The first 2 indices were scored from 0 (no interoperability) to 100 (full interoperability); the Friction Index was scored 0 (no friction) to 100 (maximum friction). We calculated indices annually from 2021 to 2023, stratifying by hospital characteristics.

Results
Items within components created reliable and meaningful measures, and associations between components within indices followed the TEP’s expectations. Weighted mean scores for the Core (2023), Pathfinder (2022), and Friction (2023) Indices were 61, 57, and 30, respectively. Hospitals with 500+ beds (large), not designated as critical access, in metropolitan areas, and using market leading electronic health records had statistically significant higher mean scores on all indices. Index values also improved modestly over time.

Discussion
Hospitals performed best on the Core Index. Given recent policy and programmatic initiatives, we anticipate continued improvement across all indices.

Conclusion
Ongoing index tracking can inform policy impact evaluations and highlight persistent interoperability disparities across hospitals.
pyBioPortal: a Python package for simplifying cBioPortal data access in cancer research
Authors: Valerio Matteo , Inno Alessandro , Gori Stefania 
Published: December 2024

Abstract

Objectives
In recent years, the rise of big data and artificial intelligence has led to an increasing expansion of databases and web services in biomedical research. cBioPortal is one of the most widely used platforms for accessing cancer genomic and clinical data. The primary objective of this study was to develop a tool that simplifies programmatic interaction with cBioPortal’s web service.

Materials and Methods
We developed the pyBioPortal Python package, which leverages the cBioPortal REST API to access genomic and clinical data. The retrieved data is returned as a Pandas DataFrame, a format widely used for data analysis in Python.

Results
pyBioPortal offers an efficient interface between the user and the cBioPortal database. The data is provided in formats conducive to further analysis and visualization, promoting workflows and improving reproducibility.

Discussion
The development of pyBioPortal addresses the challenge of accessing and processing large volumes of biomedical data. By simplifying the interaction with the cBioPortal API and providing data in Pandas DataFrame format, pyBioPortal allows users to focus more on the analytical aspects rather than data extraction.

Conclusion
This tool facilitates the retrieval of heterogeneous biological and clinical data in a standardized format, making it more accessible for analysis and enhancing the reproducibility of results in cancer informatics. Distributed as an open-source project, pyBioPortal is available to the broader bioinformatics community, promoting collaboration and advancing research in cancer genomics.
GPLD1+ cancer stem cells contribute to chemotherapy resistance and tumour relapse in intestinal cancer
Authors: Mizoo Taisuke , Oka Takeru , Sugahara Osamu , Minato Takafumi , Higa Tsunaki , Nakayama Keiichi I 
Published: December 2024

Abstract
Cancer stem cells (CSCs) play a central role in cancer progression, therapy resistance, and disease recurrence. With the use of a quadruple-mutant mouse intestinal cancer organoid model and single-cell RNA-sequencing analysis, we have now identified glycosylphosphatidylinositol-specific phospholipase D1 (GPLD1), an enzyme that catalyzes the cleavage of glycosylphosphatidylinositol (GPI) anchors of membrane proteins, as a marker of slowly cycling CSCs. Ablation of Gpld1+ cells in combination with 5-fluorouracil treatment greatly attenuated cell viability in and regrowth of the intestinal cancer organoids. In addition, we identified serine protease 8 (PRSS8) as a key substrate of GPLD1 in human colorectal cancer cells. GPLD1 cleaves the GPI anchor of PRSS8 and thereby mediates release of the protease from the plasma membrane, resulting in the activation of Wnt signalling and promotion of the epithelial-mesenchymal transition (EMT) in the cancer cells. Pharmacological inhibition of GPLD1 suppressed Wnt signalling activity and EMT in association with upregulation of the amount of functional PRSS8 at the plasma membrane. Our findings suggest that targeting of GPLD1 in colorectal cancer might contribute to a new therapeutic strategy that is based on suppression of Wnt signalling and EMT-related cancer progression driven by CSCs.
An application on intuitionistic fuzzy weakly 2-absorbing ideals of lattices
Authors: Yazar Salih , Onar Serkan , Özkan E Mehmet 
Published: December 2024

Abstract
In this study, we investigate the notion of an intuitionistic fuzzy prime ideal and intuitionistic fuzzy weakly 2-absorbing ideal of a lattice as an expansion of a notion of a weakly prime ideal. Then, we characterize the concept of intuitionistic fuzzy weakly 2-absorbing ideals and intuitionistic fuzzy weakly primary ideals and give some results. Finally, we suggest the concept of an intuitionistic fuzzy weakly 2-absorbing ideals in a product of lattices.
Patenting measurements
Authors: Müller Martin 
Published: December 2024

Abstract
At the European Patent Office (EPO), an invention can only be patented if it has technical character and solves a technical problem. According to established case law, in line with probably universal agreement, measurement methods have the required technical character. In its decision G1/19, the Enlarged Board of Appeal has confirmed this principle and stated it extends to what are called indirect measurements. This question is gaining increasing attention, following G1/19, as a potential argument to acknowledge a technical contribution made by an otherwise entirely computer-implemented (‘numerical’) invention, and it may be relevant for any method of analysis, testing or diagnosis of technical devices or patients, for instance in the context of digital twins. Against this backdrop, the article investigates what may or may not be considered an (indirect) measurement for the purpose of patentability.