bluuebunny/crossref_metadata_2025_split huggingface dataset:
Psychometric properties of the Swedish version of the Patient Health Questionnaire-9: an investigation using Rasch analysis and confirmatory factor analysis
Authors: Forsström David , Badinlou Farzaneh , Johansson Magnus , Ojala Olivia , Alaoui Samir El , Månsson Kristoffer N. T. , Rozental Alexander , Lundin Johan , Jangard Simon , Shahnavaz Shervin , Sörman Karolina , Jayaram-Lindström Nitya , Lundgren Tobias , Jansson-Fröjmark Markus , Hedman-Lagerlöf Maria 
Published: January 2025

Abstract
Depression is one of the most common psychiatric conditions. Given its high prevalence and disease burden, accurate diagnostic procedures and valid instruments are warranted to identify those in need of treatment. The Patient Health Questionnaire-9 (PHQ-9) is one of the most widely used self-report measures of depression, and its validity and reliability has been evaluated in several languages. However, the Swedish translation has yet not been subject to psychometric evaluation, and no previous psychometric evaluation of the instrument have used both Rasch analysis and classic test theory. The aim of this study was to investigate validity and reliability of the PHQ-9 in a Swedish sample of individuals with self-reported current or past mental health problems using Rasch analysis and confirmatory factor analysis. A sample of 4958 participants was recruited from an online survey covering different aspects of covid-19 and mental health targeted towards individuals with mental health problems. Results showed that a one-factor solution fit the data after removing one item and that some items had a different response pattern for older respondents. Furthermore, after removing item 2 and merging the two middle response categories for item 9, the Swedish translation of PHQ-9 showed adequate psychometric properties. The findings suggests that the Swedish translation of PHQ-9 may need to be adapted in order to make adequate interpretations of an individual score and to differentiate between populations. Further tests of its validity and reliability in other Swedish samples are needed to fully understand the properties of the Swedish version of PHQ-9.
%diag_test: a generic SAS macro for evaluating diagnostic accuracy measures for multiple diagnostic tests
Authors: Muthusi Jacques K. , Young Peter W. , Mboya Frankline O. , Mwalili Samuel M. 
Published: January 2025

Abstract

Background
Measures of diagnostic test accuracy provide evidence of how well a test correctly identifies or rules-out disease. Commonly used diagnostic accuracy measures (DAMs) include sensitivity and specificity, predictive values, likelihood ratios, area under the receiver operator characteristic curve (AUROC), area under precision-recall curves (AUPRC), diagnostic effectiveness (accuracy), disease prevalence, and diagnostic odds ratio (DOR) etc. Most available analysis tools perform accuracy testing for a single diagnostic test using summarized data. We developed a SAS macro for evaluating multiple diagnostic tests using individual-level data that creates a 2 × 2 summary table, AUROC and AUPRC as part of output.

Methods
The SAS macro presented here is automated to reduce analysis time and transcription errors. It is simple to use as the user only needs to specify the input dataset, “standard” and “test” variables and threshold values. It creates a publication-quality output in Microsoft Word and Excel showing more than 15 different accuracy measures together with overlaid AUROC and AUPRC graphics to help the researcher in making decisions to adopt or reject diagnostic tests. Further, it provides for additional variance estimation methods other than the normal distribution approximation.

Results
We tested the macro for quality control purposes by reproducing results from published work on evaluation of multiple types of dried blood spots (DBS) as an alternative for human immunodeficiency virus (HIV) viral load (VL) monitoring in resource-limited settings compared to plasma, the gold-standard. Plasma viral load reagents are costly, and blood must be prepared in a reference laboratory setting by a qualified technician. On the other hand, DBS are easy to prepare without these restrictions. This study evaluated the suitability of DBS from venous, microcapillary and direct spotting DBS, hence multiple diagnostic tests which were compared to plasma specimen. We also used the macro to reproduce results of published work on evaluating performance of multiple classification machine learning algorithms for predicting coronary artery disease.

Conclusion
The SAS macro presented here is a powerful analytic tool for analyzing data from multiple diagnostic tests. The SAS programmer can modify the source code to include other diagnostic measures and variance estimation methods. By automating analysis, the macro adds value by saving analysis time, reducing transcription errors, and producing publication-quality outputs.
Uterine histomorphological and immunohistochemical investigation during the follicular phase of estrous cycle in Saidi sheep
Authors: Abd-Elkareem Mahmoud , Khormi Mohsen A. , Alfattah Mohammed A. , Hassan Mervat S. 
Published: January 2025

Abstract

Background
Saidi sheep are one of the most important farm animals in Upper Egypt, particularly in the Assiut governorate. Since they can provide meat, milk, fiber, and skins from low-quality roughages, sheep are among the most economically valuable animals bred for food in Egypt. Regarding breeding, relatively little is known about the Saidi breed. In mammals, the uterus is a crucial reproductive organ. Therefore, the purpose of this work was to provide further details on the histological, histochemical, and immunohistochemical analyses of superoxide dismutase 2 (SOD2), glutathione reductase (GR), and progesterone receptor alpha (PRA) as well as terminal deoxynucleotidyl transferase (TdT) dUTP nick-end labeling assay (TUNEL) of the uterus during the follicular phase of estrous cycle in Saidi sheep. Thus, 11 healthy Saidi ewes (38.5 ± 2.03 kg weight) ranging in age from 2 to 5 years were used to examine the histological changes in the uterus.

Results
In Saidi sheep, the uterine histological and immunological picture during the follicular phase of the estrous cycle was characterized by epithelial and stromal proliferation and apoptosis. Leucocytic recruitment (lymphocytes, plasma, and mast cells) was also observed. Uterine gland adenogenesis, vascular angiogenesis, oxidative marker expression, and PRA expression in the muscles, stroma, and epithelium were the most noticeable features of the follicular phase.

Conclusion
This study provides new evidence of the role of PRA, SOD2, GR, and mast cells in controlling uterine epithelial proliferation and apoptosis in the Saidi sheep during the follicular phase of the estrus cycle. These findings have growing significance in understanding the key mechanisms that characterize successful reproduction and enhancing the fertility and reproductive efficiency in Saidi Sheep.
An assessment of burden associated with problem joints in children and adults with moderate or severe haemophilia A: analysis of the CHESS-Paediatrics and CHESS II cross-sectional studies
Authors: McLaughlin Paul , De la Corte-Rodriguez Hortensia , Burke Tom , Nissen Francis , Aizenas Martynas , Moreno Katya , O’Hara Jamie 
Published: January 2025

Abstract

Background
Clinical research has offered many definitions and fragmented perspectives of joint morbidity in haemophilia. As joint damage, pain and mobility impairment can be present without clinical record of persistent bleeding, a person-centric joint morbidity characterisation remained a priority for the haemophilia community, giving rise to the ‘problem joint’ concept.
As diagnosing and managing joint morbidity is critical, the aim of this study was to analyse the holistic burden of problem joints in people with moderate or severe haemophilia A (HA).
Data from the ‘Cost of Haemophilia in Europe: a Socioeconomic Survey’ (CHESS) cross-sectional studies were used. CHESS-Paediatrics included male paediatric patients (≤ 17 years) with congenital moderate or severe haemophilia, while CHESS II included adult males (≥ 18 years) of any severity. Both studies sought to collect detailed information on the clinical, economic and humanistic burden of haemophilia.
Demographics, clinical outcomes, treatment regimen, adherence, physical activity, healthcare resource use and number of problem joints were evaluated and described by HA severity and number of problem joints (none, 1, ≥ 2).

Results
In total, 1171 people with non-inhibitor moderate or severe HA from CHESS-Paediatrics (n = 703) and CHESS II (n = 468) were included in this analysis.
Presence of problem joints was more prevalent among CHESS II participants (44%) than in CHESS-Paediatrics (14%). Around two-thirds (67%) of CHESS-Paediatrics and 39% of CHESS II participants received prophylactic factor VIII replacement therapy. The presence of chronic pain was greater in severe HA with ‘ ≥ 2’ problem joints in both cohorts. Clinical symptoms and bleed-related hospitalizations were more prevalent in the presence of problem joints regardless of HA severity in both cohorts.

Conclusions
This analysis of the CHESS population studies has expanded on previous work by examining the relevance of the problem joint measure of haemophilic morbidity and its associated burden. Adverse clinical symptoms and increased bleed-related hospitalizations were observed in the presence of problem joints in both children/adolescents and adults across HA severities. Use of person-centric characterizations of joint morbidity may improve analysis of long-term outcomes and lead to improvements in future haemophilia care.
Upregulated astrocyte HDAC7 induces Alzheimer-like tau pathologies via deacetylating transcription factor-EB and inhibiting lysosome biogenesis
Authors: Ye Jinwang , Zhong Suyue , Wan Huali , Guo Xing , Yao Xuanbao , Liu Qiong , Chen Liming , Wang Jian-Zhi , Xiao Shifeng 
Published: January 2025

Abstract

Background
Astrocytes, the most abundant glial cell type in the brain, will convert into the reactive state in response to proteotoxic stress such as tau accumulation, a characteristic feature of Alzheimer's disease (AD) and other tauopathies. The formation of reactive astrocytes is partially attributed to the disruption of autophagy lysosomal signaling, and inhibiting of some histone deacetylases (HDACs) has been demonstrated to reduce the molecular and functional characteristics of reactive astrocytes. However, the precise role of autophagy lysosomal signaling in astrocytes that regulates tau pathology remains unclear.

Methods
We investigated the expression of class IIa HDAC7 in astrocytes from AD patients and PS19 mice. PS19 mice were treated with AAVs expressing shRNA for HDAC7 with astrocyte-specific promoter and with a selective class IIa HDAC inhibitor, TMP195, and the effects on tau pathology, gliosis, synaptic plasticity and cognition-related behavioral performance were measured. Tau uptake and degradation assays in cultured astrocytes were utilized to investigate the role of HDAC7 on astrocyte-mediated tau clearance. Immunoprecipitation, immunofluorescence, western blotting, RT-qPCR, mass spectrometric, and luciferase reporter assay were used to identify HDAC7 substrates, modification site and related signaling pathways in astrocyte-tau clearance. We generated a new antibody to clarify the role of HDAC7-mediated signaling in AD patients and PS19 mice.

Results
Here, we found that the level of histone deacetylase 7 (HDAC7) was remarkably increased in the astrocytes of AD patients and P301S tau transgenic (PS19) mice. Genetic or pharmacological inhibition of HDAC7 effectively enhanced astrocytic clearance of tau with improved cognitive functions in PS19 mice. HDAC7 could modulate astrocytic uptake and lysosomal degradation of tau proteins through a transcriptional factor EB (TFEB) acetylation-dependent manner. Specifically, deacetylation of TFEB at K310 site by HDAC7 prevented TFEB nuclear translocation with reduced lysosomal biogenesis and tau clearance in astrocytes, whereas inhibiting HDAC7 restored astrocytic TFEB acetylation level at K310 with improved tau pathology and cognitive functions in PS19 mice.

Conclusions
Our findings suggest that upregulation of HDAC7 induces AD-like tau pathologies via deacetylating TFEB and inhibiting lysosomal biogenesis in astrocytes, and downregulating HDAC7-TFEB signaling is promising for arresting AD and other tauopathies.
Comparative analysis of regression algorithms for drug response prediction using GDSC dataset
Authors: Ha Soojung , Park Juho , Jo Kyuri 
Published: January 2025

Abstract

Background
Drug response prediction can infer the relationship between an individual’s genetic profile and a drug, which can be used to determine the choice of treatment for an individual patient. Prediction of drug response is recently being performed using machine learning technology. However, high-throughput sequencing data produces thousands of features per patient. In addition, it is difficult for researchers to know which algorithm is appropriate for prediction as various regression and feature selection algorithms exist.

Methods
We compared and evaluated the performance of 13 representative regression algorithms using Genomics of Drug Sensitivity in Cancer (GDSC) dataset. Three analyses was conducted to show the effect of feature selection methods, multiomics information, and drug categories on drug response prediction.

Results
In the experiments, Support Vector Regression algorithm and gene features selected with LINC L1000 dataset showed the best performance in terms of accuracy and execution time. However, integration of mutation and copy number variation information did not contribute to the prediction. Among the drug groups, responses of drugs related with hormone-related pathway were predicted with relatively high accuracy.

Conclusion
This study can help bioinformatics researchers design data processing steps and select algorithms for drug response prediction, and develop a new drug response prediction model based on the GDSC or other high-throughput sequencing datasets.
CRISPR/Cas9-editing of PRNP in Alpine goats
Authors: Allais-Bonnet Aurélie , Richard Christophe , André Marjolaine , Gelin Valérie , Deloche Marie-Christine , Lamadon Aurore , Morin Gwendoline , Mandon-Pépin Béatrice , Canon Eugénie , Thépot Dominique , Laubier Johann , Moazami-Goudarzi Katayoun , Laffont Ludivine , Dubois Olivier , Fassier Thierry , Congar Patrice , Lasserre Olivier , Aguirre-Lavin Tiphaine , Vilotte Jean-Luc , Pailhoux Eric 
Published: January 2025

Abstract
Misfolding of the cellular PrP (PrPc) protein causes prion disease, leading to neurodegenerative disorders in numerous mammalian species, including goats. A lack of PrPc induces complete resistance to prion disease. The aim of this work was to engineer Alpine goats carrying knockout (KO) alleles of PRNP, the PrPc-encoding gene, using CRISPR/Cas9-ribonucleoproteins and single-stranded donor oligonucleotides. The targeted region preceded the PRNP

Ter
mutation previously described in Norwegian goats. Genome editors were injected under the zona pellucida prior to the electroporation of 565 Alpine goat embryos/oocytes. A total of 122 two-cell-stage embryos were transferred to 46 hormonally synchronized recipient goats. Six of the goats remained pregnant and naturally gave birth to 10 offspring. Among the 10 newborns, eight founder animals carrying PRNP genome-edited alleles were obtained. Eight different mutated alleles were observed, including five inducing KO mutations. Three founders carried only genome-edited alleles and were phenotypically indistinguishable from their wild-type counterparts. Among them, one male carrying a one base pair insertion leading to a KO allele is currently used to rapidly extend a PRNP-KO line of Alpine goats for future characterization. In addition to KO alleles, a PRNP

del6
genetic variant has been identified in one-third of founder animals. This new variant will be tested for its potential properties with respect to prion disease. Future studies will also evaluate the effects of genetic background on other characters associated with PRNP KO, as previously described in the Norwegian breed or other species.
North American avian species that migrate in flocks show greater long-term non-breeding range shift rates
Authors: Vickers Stephen H. , Meehan Timothy D. , Michel Nicole L. , Franco Aldina M. A. , Gilroy James J. 
Published: January 2025

Abstract

Background
Many species are exhibiting range shifts associated with anthropogenic change. For migratory species, colonisation of new areas can require novel migratory programmes that facilitate navigation between independently-shifting seasonal ranges. Therefore, in some cases range-shifts may be limited by the capacity for novel migratory programmes to be transferred between generations, which can be genetically and socially mediated.

Methods
Here we used 50 years of North American Breeding Bird Survey and Audubon Christmas Bird Count data to test the prediction that breeding and/or non-breeding range-shifts are more prevalent among flocking migrants, which possess a capacity for rapid social transmission of novel migration routes.

Results
Across 122 North American bird species, social migration was a significant positive predictor for the magnitude of non-breeding centre of abundance (COA) shift within our study region (conterminous United States and Southern Canada). Across a subset of 81 species where age-structured flocking was determined, migrating in mixed-age flocks produced the greatest shifts and solo migrants the lowest. Flocking was not a significant predictor of breeding COA shifts, which were better explained by absolute population trends and migration distance.

Conclusions
Our results suggest that social grouping may play an important role in facilitating non-breeding distributional responses to climate change in migratory species. We highlight the need to gain a better understanding of migratory programme inheritance, and how this influences spatiotemporal population dynamics under environmental change.
Understanding the private-public school performance gap in PISA: evidence from Portugal
Authors: Colaço Ricardo , Freitas Pedro , Nunes Luis Catela , Reis Ana Balcão 
Published: January 2025

Abstract
We analyse the PISA-reported convergence in the performance of private and public schools in Portugal. When PISA sampling weights are used, the number of students enrolled in those types of schools and specific grades/tracks of study differs significantly from official population figures. To account for those differences, we apply a post-stratification adjustment; however, sample sizes are small, resulting in estimates with low precision for several subgroups. We propose recommendations for improving the handling of these issues in future PISA cycles. In an additional analysis, we also account for changes in the composition of the student population. When all factors are considered, the convergence in scores is far less impressive than reported. For instance, in Science, after adjusting the sampling weights and removing population composition effects, the reported convergence of 46 points between private and public schools from 2015 to 2018 amounts to only 9 points. The decomposition and sample adjustment methods used in this paper can be easily adapted to other contexts.
Age-dependent differences in the association between blood interleukin-6 levels and mortality in patients with sepsis: a retrospective observational study
Authors: Shimazui Takashi , Oami Takehiko , Shimada Tadanaga , Tomita Keisuke , Nakada Taka-aki 
Published: January 2025

Abstract

Background
Interleukin-6 (IL-6) is a cytokine that predicts clinical outcomes in critically ill patients, including those with sepsis. Elderly patients have blunted and easily dysregulated host responses to infection, which may influence IL-6 kinetics and alter the association between IL-6 levels and clinical outcomes.

Methods
This retrospective observational study included patients aged ≥ 16 years who were admitted to the intensive care unit at Chiba University Hospital. The patients were categorized into two groups: non-elderly (< 70 years) and elderly (≥ 70 years). Associations between log-transformed blood IL-6 levels and 28-day in-hospital mortality (primary outcome) and multiple organ dysfunction (MOD) on days 3 and 7 (secondary outcomes) were examined.

Results
The non-elderly and elderly groups included 272 and 247 patients, respectively. There were no significant differences in the Sequential Organ Failure Assessment score, components of the APACHE II score (Acute physiology score and Chronic health points), MOD at baseline, or any of the outcome measures between the groups. In the non-elderly group, univariate Cox regression analysis showed a significant association between IL-6 levels and mortality (hazard ratio [HR] 1.71, 95% confidence interval [CI] 1.25–2.37, P < 0.001). This association remained significant after adjusting for sex, body mass index, steroid use prior to sepsis onset, and number of chronic organ dysfunctions (HR 1.66, 95% CI 1.20–2.32, P = 0.002). However, no significant association was observed in the elderly group in either the univariate (P = 0.69) or multivariable analyses (P = 0.77). Multivariable logistic regression analysis of MOD on days 3 and 7 revealed significant associations between MOD and IL-6 levels in both groups.

Conclusions
Blood IL-6 levels were significantly associated with mortality in non-elderly patients with sepsis, but not in elderly patients. IL-6 levels were associated with MOD in both groups. Therefore, IL-6 levels should be interpreted with caution when predicting mortality in elderly patients with sepsis.

Trial registration: Not applicable.