bluuebunny/crossref_metadata_2025_split huggingface dataset:
metaGWASmanager: a toolbox for an automated workflow from phenotypes to meta-analysis in GWAS consortia
Authors: Rodriguez-Hernandez Zulema , Gorski Mathias , Tellez-Plaza Maria , Schlosser Pascal , Wuttke Matthias 
Published: May 2024

Abstract

Summary
This article introduces the metaGWASmanager, which streamlines genome-wide association studies within large-scale meta-analysis consortia. It is a toolbox for both the central consortium analysis group and participating studies to generate homogeneous phenotypes, minimize unwanted variability from inconsistent methodologies, ensure high-quality association results, and implement time-efficient quality control workflows. The toolbox features a plug-in-based approach for customization of association testing.

Results
The metaGWASmanager toolbox has been successfully deployed in both the CKDGen and MetalGWAS Initiative consortia across hundreds of participating studies, demonstrating its effectiveness in GWAS analysis optimization by automating routine tasks and ensuring the value and reliability of association results, thus, ultimately promoting scientific discovery. We provide a simulated data set with examples for script customization so that readers can reproduce the pipeline at their convenience.

Availability and implementation
GitHub: https://github.com/genepi-freiburg/metaGWASmanager
CT-based radiomics model using stability selection for predicting the World Health Organization/International Society of Urological Pathology grade of clear cell renal cell carcinoma
Authors: Zhang Haijie , Yin Fu , Chen Menglin , Qi Anqi , Yang Liyang , Wen Ge 
Published: May 2024

Abstract

Objectives
This study aimed to develop a model to predict World Health Organization/International Society of Urological Pathology (WHO/ISUP) low-grade or high-grade clear cell renal cell carcinoma (ccRCC) using 3D multiphase enhanced CT radiomics features (RFs).

Methods
CT data of 138 low-grade and 60 high-grade ccRCC cases were included. RFs were extracted from four CT phases: non-contrast phase (NCP), corticomedullary phase, nephrographic phase, and excretory phase (EP). Models were developed using various combinations of RFs and subjected to cross-validation.

Results
There were 107 RFs extracted from each phase of the CT images. The NCP-EP model had the best overall predictive value (AUC = 0.78), but did not significantly differ from that of the NCP model (AUC = 0.76). By considering the predictive ability of the model, the level of radiation exposure, and model simplicity, the overall best model was the Conventional image and clinical features (CICFs)-NCP model (AUC = 0.77; sensitivity 0.75, specificity 0.69, positive predictive value 0.85, negative predictive value 0.54, accuracy 0.73). The second-best model was the NCP model (AUC = 0.76).

Conclusions
Combining clinical features with unenhanced CT images of the kidneys seems to be optimal for prediction of WHO/ISUP grade of ccRCC. This noninvasive method may assist in guiding more accurate treatment decisions for ccRCC.

Advances in knowledge
This study innovatively employed stability selection for RFs, enhancing model reliability. The CICFs-NCP model's simplicity and efficacy mark a significant advancement, offering a practical tool for clinical decision-making in ccRCC management.
Dorsal root ganglion magnetic resonance imaging biomarker correlations with pain in Fabry disease
Authors: Schindehütte Magnus , Weiner Simon , Klug Katharina , Hölzli Lea , Nauroth-Kreß Christopher , Hessenauer Florian , Kampf Thomas , Homola György A , Nordbeck Peter , Wanner Christoph , Sommer Claudia , Üçeyler Nurcan , Pham Mirko 
Published: May 2024

Abstract
Fabry disease is a rare monogenetic, X-linked lysosomal storage disorder with neuropathic pain as one characteristic symptom. Impairment of the enzyme alpha-galactosidase A leads to an accumulation of globotriaosylceramide in the dorsal root ganglia. Here, we investigate novel dorsal root ganglia MR imaging biomarkers and their association with Fabry genotype and pain phenotype. In this prospective study, 89 Fabry patients were examined using a standardized 3 T MRI protocol of the dorsal root ganglia. Fabry pain was assessed through a validated Fabry pain questionnaire. The genotype was determined by diagnostic sequencing of the alpha-galactosidase A gene. MR imaging end-points were dorsal root ganglia volume by voxel-wise morphometric analysis and dorsal root ganglia T2 signal. Reference groups included 55 healthy subjects and Fabry patients of different genotype categories without Fabry pain. In patients with Fabry pain, T2 signal of the dorsal root ganglia was increased by +39.2% compared to healthy controls (P = 0.001) and by +29.4% compared to painless Fabry disease (P = 0.017). This effect was pronounced in hemizygous males (+40.7% compared to healthy; P = 0.008 and +29.1% compared to painless; P = 0.032) and was consistently observed across the genotype spectrum of nonsense (+38.1% compared to healthy, P &lt; 0.001) and missense mutations (+39.2% compared to healthy; P = 0.009). T2 signal of dorsal root ganglia and globotriaosylsphingosine levels were the only independent predictors of Fabry pain (P = 0.047; P = 0.002). Volume of dorsal root ganglia was enlarged by +46.0% in Fabry males in the nonsense compared to missense genotype category (P = 0.005) and by +34.5% compared to healthy controls (P = 0.034). In painful Fabry disease, MRI T2 signal of dorsal root ganglia is increased across different genotypes. Dorsal root ganglion MRI T2 signal as a novel in vivo imaging biomarker may help to better understand whether Fabry pain is modulated or even caused by dorsal root ganglion pathology.
Glucosylceramides impact cellulose deposition and cellulose synthase complex motility in Arabidopsis
Authors: Villalobos Jose A , Cahoon Rebecca E , Cahoon Edgar B , Wallace Ian S 
Published: May 2024

Abstract
Cellulose is an abundant component of plant cell wall matrices, and this para-crystalline polysaccharide is synthesized at the plasma membrane by motile Cellulose Synthase Complexes (CSCs). However, the factors that control CSC activity and motility are not fully resolved. In a targeted chemical screen, we identified the alkylated nojirimycin analog N-Dodecyl Deoxynojirimycin (ND-DNJ) as a small molecule that severely impacts Arabidopsis seedling growth. Previous work suggests that ND-DNJ-related compounds inhibit the biosynthesis of glucosylceramides (GlcCers), a class of glycosphingolipid associated with plant membranes. Our work uncovered major changes in the sphingolipidome of plants treated with ND-DNJ, including reductions in GlcCer abundance and altered acyl chain length distributions. Crystalline cellulose content was also reduced in ND-DNJ-treated plants as well as plants treated with the known GlcCer biosynthesis inhibitor N-[2-hydroxy-1-(4-morpholinylmethyl)-2-phenyl ethyl]-decanamide (PDMP) or plants containing a genetic disruption in GLUCOSYLCERAMIDE SYNTHASE (GCS), the enzyme responsible for sphingolipid glucosylation that results in GlcCer synthesis. Live-cell imaging revealed that CSC speed distributions were reduced upon treatment with ND-DNJ or PDMP, further suggesting an important relationship between glycosylated sphingolipid composition and CSC motility across the plasma membrane. These results indicate that multiple interventions compromising GlcCer biosynthesis disrupt cellulose deposition and CSC motility, suggesting that GlcCers regulate cellulose biosynthesis in plants.
Pairing metagenomics and metaproteomics to characterize ecological niches and metabolic essentiality of gut microbiomes
Authors: Wang Tong , Li Leyuan , Figeys Daniel , Liu Yang-Yu 
Published: May 2024

Abstract
The genome of a microorganism encodes its potential functions that can be implemented through expressed proteins. It remains elusive how a protein’s selective expression depends on its metabolic essentiality to microbial growth or its ability to claim resources as ecological niches. To reveal a protein’s metabolic or ecological role, we developed a computational pipeline, which pairs metagenomics and metaproteomics data to quantify each protein’s gene-level and protein-level functional redundancy simultaneously. We first illustrated the idea behind the pipeline using simulated data of a consumer-resource model. We then validated it using real data from human and mouse gut microbiome samples. In particular, we analyzed ABC-type transporters and ribosomal proteins, confirming that the metabolic and ecological roles predicted by our pipeline agree well with prior knowledge. Finally, we performed in vitro cultures of a human gut microbiome sample and investigated how oversupplying various sugars involved in ecological niches influences the community structure and protein abundance. The presented results demonstrate the performance of our pipeline in identifying proteins’ metabolic and ecological roles, as well as its potential to help us design nutrient interventions to modulate the human microbiome.
Phylogenomic analysis expands the known repertoire of single-stranded DNA viruses in benthic zones of the South Indian Ocean
Authors: Bezuidt Oliver K I , Makhalanyane Thulani P 
Published: May 2024

Abstract
Single-stranded (ss) DNA viruses are ubiquitous and constitute some of the most diverse entities on Earth. Most studies have focused on ssDNA viruses from terrestrial environments resulting in a significant deficit in benthic ecosystems including aphotic zones of the South Indian Ocean (SIO). Here, we assess the diversity and phylogeny of ssDNA in deep waters of the SIO using a combination of established viral taxonomy tools and a Hidden Markov Model based approach. Replication initiator protein-associated (Rep) phylogenetic reconstruction and sequence similarity networks were used to show that the SIO hosts divergent and as yet unknown circular Rep-encoding ssDNA viruses. Several sequences appear to represent entirely novel families, expanding the repertoire of known ssDNA viruses. Results suggest that a small proportion of these viruses may be circular genetic elements, which may strongly influence the diversity of both eukaryotes and prokaryotes in the SIO. Taken together, our data show that the SIO harbours a diverse assortment of previously unknown ssDNA viruses. Due to their potential to infect a variety of hosts, these viruses may be crucial for marine nutrient recycling through their influence of the biological carbon pump.
Antibiotic dose and nutrient availability differentially drive the evolution of antibiotic resistance and persistence
Authors: Windels Etthel M , Cool Lloyd , Persy Eline , Swinnen Janne , Matthay Paul , Van den Bergh Bram , Wenseleers Tom , Michiels Jan 
Published: May 2024

Abstract
Effective treatment of bacterial infections proves increasingly challenging due to the emergence of bacterial variants that endure antibiotic exposure. Antibiotic resistance and persistence have been identified as two major bacterial survival mechanisms, and several studies have shown a rapid and strong selection of resistance or persistence mutants under repeated drug treatment. Yet, little is known about the impact of the environmental conditions on resistance and persistence evolution and the potential interplay between both phenotypes. Based on the distinct growth and survival characteristics of resistance and persistence mutants, we hypothesized that the antibiotic dose and availability of nutrients during treatment might play a key role in the evolutionary adaptation to antibiotic stress. To test this hypothesis, we combined high-throughput experimental evolution with a mathematical model of bacterial evolution under intermittent antibiotic exposure. We show that high nutrient levels during antibiotic treatment promote selection of high-level resistance, but that resistance mainly emerges independently of persistence when the antibiotic concentration is sufficiently low. At higher doses, resistance evolution is facilitated by the preceding or concurrent selection of persistence mutants, which ensures survival of populations in harsh conditions. Collectively, our experimental data and mathematical model elucidate the evolutionary routes toward increased bacterial survival under different antibiotic treatment schedules, which is key to designing effective antibiotic therapies.
Expanding active living after cancer to underserved cancer survivors and their caregivers
Authors: Mama Scherezade K , Mitchell Stacy J , Tracy Patricia V , Pena Luz Y , Moreno Carolina D , Valdes Adriana , Liao Yue , Lee Che Young , Alexander Ashley , Raber Margaret R , McNeill Lorna H , Basen-Engquist Karen 
Published: May 2024

Abstract

Background
Physical activity improves physical and psychological health in cancer survivors. This study evaluated Active Living After Cancer (ALAC), a community-based program to improve physical activity, physical function, and quality of life (QOL) in minority and medically underserved cancer survivors and their caregivers.

Methods
Participants completed 12 weekly ALAC sessions and assessments of physical activity, physical functioning, and QOL at baseline and follow-up (week 12). Paired samples t tests were used to assess changes in outcomes over time.

Results
A total of 540 cancer survivors (mean age = 61.1 [SD = 11.3] years) and 87 caregivers (mean age = 62.3 [SD = 13.1] years) were enrolled. Most were women (91.4%), Hispanic (61.1%) or non-Hispanic Black (19.3%), and medically underserved (86.4%). The percent of cancer survivors meeting physical activity recommendations increased from 28.9% to 60.2% (d = 0.75), and the number of sit-to-stand repetitions in a 30-second period increased from 12.3 to 14.3 (d = 0.39) from 0-12 weeks. Cancer survivors reported statistically significant improvements in physical (t score Δ = 1.7, d = 0.06) and mental (t score Δ = 2.3, d = 0.31) health–related QOL. Caregivers also improved their physical activity, physical function, and QOL, and there were no statistically significant differences between breast and other cancer survivors and between cancer survivors and caregivers.

Conclusions
The ALAC program demonstrated increased physical activity, physical function, and QOL in medically underserved cancer survivors and their caregivers. Furthermore, ALAC was successfully implemented by community partners and serves as a good model for reaching medically underserved cancer survivors and improving survivorship. Additional efforts are warranted to further extend reach, improve cancer survivorship, and reduce cancer health disparities among underserved cancer survivors.
Exotic plant species with longer seed bank longevity and lower seed dry mass are more likely to be invasive in China
Authors: Pan Yueyan , Xie Lumeng , Shang Ruiyan , Engel Bernard A , Chen Jingqiu , Zhou Shijun , Li Yi , Zhang Mingxiang , Zhang Zhenming , Liu Jiakai 
Published: May 2024

Abstract
Globalization of social and economic activities has led to the large-scale redistribution of plant species. It is still unclear how the traits aid the successful invasion of alien species. Here, we downloaded global plant trait data from the TRY-Plant Trait Database and classified alien species in China into four groups: high, medium, need attention and harmless according to their distribution and degree of harm to local plant communities based on existed studies. The relationship between plant functional traits and invasion level was clarified, and we established a prediction model based on plant functional traits and taxonomy. The results showed that species with smaller seeds, smaller individuals, lower special leaf area and longer seed bank longevity (SL) are more likely to be an invasive species after introduction to foreign ecosystems. In summary, exotic species with longer SL and lower seed dry mass are more likely to be invasive in China. We also trained two predictive models to check if we can predict a species’ invasion. Combining the two models together, statistically, we could predict if a species is invasive from its traits and taxonomy with a 91.84% accuracy. This model could help local governments, managers and stakeholders to evaluate shall we introduce some plant species in China.
Unusual acute right abdominal pain. Distal ileum mesenteric cystic lymphangioma in adult, a rare case and literature review
Authors: Ahmed Muhsin Mohammed , Shareef Farman Uthman , Abdul Aziz Jeza Muhamad , Mohammed San Khasraw , Karim Hawnaz Atta , Maulud Mihraban Abdulrahman , Fareeq Daro Hadi , Aziz Dlivan Fattah , Rashid Muhammad Jabar 
Published: May 2024

Abstract
Lymphangiomas in the peritoneal cavity are rare in adults, with most cases occurring in children. We present the case of a 49-year-old woman who was admitted with severe lower abdominal pain. The diagnostic assessment revealed a multiloculated cystic structure in the mesentery of the distal ileum, suggesting a lymphangioma. The patient underwent laparotomy and resection, with successful removal of the mass. Histopathological examination confirmed the diagnosis of intestinal lymphangioma, a rare benign vascular neoplasm of the small bowel. Postoperatively, the patient experienced resolution of postoperative ileus and mild back and abdominal pain, with no complaints during follow-up. Awareness of this uncommon condition is crucial for accurate diagnosis and appropriate treatment. Surgical resection, supported by radiological and histopathological investigations, is the primary treatment modality for symptomatic lymphangioma. Regular follow-up with imaging may be necessary to monitor recurrence.
Seegene Anyplex II assays detect HPV consistently using DNA extracts from different extraction methods
Authors: Balgovind Prisha , Murray Gerald , Machalek Dorothy A , Garland Suzanne M , Azzato Francesco , Hinaut Jee A , Danielewski Jennifer , Molano Monica , Haqshenas Gholamreza 
Published: May 2024

Abstract
The efficiency of PCR-based diagnostic assays can be impacted by the quality of DNA template, and anal samples can be particularly problematic due to the presence of faecal contaminants. Here, we compared the Quick-DNA Viral Kit (Zymo, Zymo Research, CA) and MagNA Pure 96 DNA and Viral NA Small Volume Kit (MP96, Roche) for use of the Seegene Anyplex II HPV28 assay (Anyplex28, Seegene) with anal samples. A total of 94 anal samples extracted using the MP96 and Zymo kits were tested via the Anyplex28, which detects high-risk human papillomavirus (HR-HPV, Panel A) and low-risk (LR-HPV, Panel B) HPV types. Testing the HR-HPV types (Panel A), 86 (91.5%) MP96 and 84 (89.4%) Zymo samples were deemed assessable. Overall agreement between the two methods was 87/94 (92.6%, 95% CI: 85.3–97.0) with the Kappa value of 0.678 (0.5–0.9). Of the 87 assessable samples, 50 (57.5%) were concordant, 34 (39.1%) partially concordant, and 10 (11.5%)discordant. In conclusion, the Anyplex28 produces comparable HPV genotyping results when using DNA extracts from either of these two methods.
Albuminuria predicts kidney events in IgA nephropathy
Authors: Faucon Anne-Laure , Lundberg Sigrid , Lando Stefania , Wijkström Julia , Segelmark Mårten , Evans Marie , Carrero Juan-Jesús 
Published: May 2024

ABSTRACT

Background and hypothesis
KDIGO recommends proteinuria &lt;1 g/d as a treatment target in patients with immunoglobulin A nephropathy (IgAN) because of high risk of progression to kidney failure. However, long-term kidney outcomes in patients with low-grade proteinuria remain insufficiently studied.

Methods
We enrolled patients with biopsy-proven primary IgAN from the Swedish Renal Registry and analyzed associations between urine albumin-to-creatinine ratio (uACR, in categories &lt;0.3, 0.3–0.5, 0.5–1.0, 1.0–1.5, 1.5–2.0, and ≥2.0 g/g) and the occurrence of major adverse kidney events [MAKE, a composite of kidney replacement therapy (KRT) and &gt;30% decline in estimated glomerular filtration rate (eGFR)]. We also explored the risk of kidney events associated with change in uACR within a year.

Results
We included 1269 IgAN patients (74% men, median 53 years, mean eGFR 33 ml/min/1.73 m², median uACR 0.7 g/g). Over a median follow-up of 5.5 [2.8; 9.2] years, 667 MAKE and 517 KRT events occurred, and 528 patients experienced &gt;30% eGFR decline. Compared with uACR &lt; 0.3 g/g, any higher uACR category was strongly and incrementally associated with the risk of MAKE [adjusted hazard ratios (HR) ranging from 1.56 (95%CI 1.14–2.14) if uACR 0.3–0.5 g/g to 4.53 (3.36–6.11) if uACR ≥ 2.0 g/g], KRT (HR ranging from 1.39 to 4.65), and eGFR decline &gt;30% (HR ranging from 1.76 to 3.47). In 785 patients who had repeated uACR measurements within a year, and compared with stable uACR, the risk of kidney events was lower if uACR decreased by 2-fold (HR ranging from 0.47 to 0.49), and higher if uACR increased by 2-fold (HR from 1.18 to 2.56), irrespective of baseline uACR.

Conclusions
There is substantial risk of adverse kidney outcomes among patients with IgAN and uACR between 0.3 and 1.0 g/g, a population currently considered at low risk of CKD progression. Reduction in uACR is associated with better kidney outcomes, irrespective of baseline uACR.
Shoulder terminal sensory articular nerve radiofrequency ablation for nonsurgical refractory shoulder pain due to rotator cuff pathology and osteoarthritis: a technical note
Authors: Burnham Taylor R , Miller Scott , Cooper Amanda N , Conger Aaron , Nagpal Ameet S , Eckmann Max , McCormick Zachary L 
Published: May 2024

Abstract

Background
Given the high prevalence of chronic shoulder pain and encouraging early results of terminal sensory articular branch radiofrequency ablation to treat shoulder pain, research is warranted to refine the procedural technique on the basis of updated neuroanatomic knowledge with the goal of further improving patient outcomes.

Objective
We describe an updated radiofrequency ablation protocol that accounts for varied locations of the terminal sensory articular branches of the suprascapular, axillary, subscapular, and lateral pectoral nerves within individual patients.

Design
Technical note.

Methods
Cadaveric studies delineating the sensory innervation of the shoulder joint were reviewed, and a more comprehensive radiofrequency ablation protocol is proposed relative to historical descriptions.

Conclusions
The proposed radiofrequency ablation protocol, which is based on neuroanatomic dissections of the shoulder joint, will provide a safe means of more complete sensory denervation and potentially improve clinical outcomes compared with historical descriptions, the efficacy of the new protocol must be confirmed in prospective studies.
Enhancing employment conditions for migrant seasonal workers—Assessing consumer preferences for ‘fair-labour’ apples
Authors: Thiermann Insa , Götze Henrike , Lohmann Uwe-Latacz 
Published: May 2024

Abstract
Criticisms over labour practices in agricultural production often target the living and working conditions of migrant seasonal workers. This article assesses consumer preferences for apples produced under social conditions exceeding current legal standards. The analysis is based on a discrete choice experiment (DCE) with a sample of 204 German consumers, who were asked to choose among domestic ‘fair-labour’ apples and standard apples. The former differed in six attributes describing the social conditions facing migrant seasonal workers on German farms. A mixed logit and latent class model were used to analyse the data. The predicted probability of choosing a ‘fair-labour’ apple was 85 per cent. Consumers valued higher minimum wages, the inclusion of migrant workers in Germany's social security system, and bonus payments for work on Sundays and public holidays. Improved accommodation and limits on the maximum permissible weekly working hours were considered less important. The low-price elasticity suggests that farmers could recoup a large share of the extra costs involved in providing enhanced living and working conditions for their workers.