bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advanced multi-modal mass spectrometry imaging reveals functional differences of placental villous compartments at microscale resolution
Authors: Veličković Marija , Kadam Leena , Kim Joonhoon , Zemaitis Kevin J. , Veličković Dušan , Gao Yuqian , Wu Ruonan , Fillmore Thomas L. , Orton Daniel , Williams Sarah M. , Monroe Matthew E. , Moore Ronald J. , Piehowski Paul D. , Bramer Lisa M. , Myatt Leslie , Burnum-Johnson Kristin E. 
Published: February 2025

Abstract
The placenta is a complex and heterogeneous organ that links the mother and fetus, playing a crucial role in nourishing and protecting the fetus throughout pregnancy. Integrative spatial multi-omics approaches can provide a systems-level understanding of molecular changes underlying the mechanisms leading to the histological variations of the placenta during healthy pregnancy and pregnancy complications. Herein, we advance our metabolome-informed proteome imaging (MIPI) workflow to include lipidomic imaging, while also expanding the molecular coverage of metabolomic imaging by incorporating on-tissue chemical derivatization (OTCD). The improved MIPI workflow advances biomedical investigations by leveraging state-of-the-art molecular imaging technologies. Lipidome imaging identifies molecular differences between two morphologically distinct compartments of a placental villous functional unit, syncytiotrophoblast (STB) and villous core. Next, our advanced metabolome imaging maps villous functional units with enriched metabolomic activities related to steroid and lipid metabolism, outlining distinct molecular distributions across morphologically different villous compartments. Complementary proteome imaging on these villous functional units reveals a plethora of fatty acid- and steroid-related enzymes uniquely distributed in STB and villous core compartments. Integration across our advanced MIPI imaging modalities enables the reconstruction of active biological pathways of molecular synthesis and maternal-fetal signaling across morphologically distinct placental villous compartments with micrometer-scale resolution.
Transcriptional diversification in a human-adapting zoonotic pathogen drives niche-specific evolution
Authors: Ghosh Soma , Wu Chao-Jung , Moller Abraham G. , Launay Adrien , Hall Laina N. , Hansen Bryan T. , Fischer Elizabeth R. , Youn Jung-Ho , Khil Pavel P. , Dekker John P. 
Published: February 2025

Abstract
Bacterial pathogens can undergo striking adaptive evolutionary change in the context of infection, driven by selection forces associated with host defenses and antibiotic treatment. In this work, we analyze the transcriptional landscape associated with adaptation in an emerging zoonotic pathogen, Bordetella hinzii, as it evolved during a 45-month infection in an IL12Rβ1-deficient immunocompromised host. We find evidence of multiple niche-specific modifications in the intravascular and gastrointestinal compartments, involving the superoxide dismutase system, glutamate and ectoine metabolism, chaperone-mediated protein folding, pilus organization, and peptide transport. Individual blood lineages displayed modifications in glutathione, phenylacetate, and 3-phenylpropionate metabolism, iron cluster assembly, and electron transport, whereas individual gastrointestinal lineages demonstrated changes relating to gluconeogenesis, de novo pyrimidine synthesis, and transport of peptides and phosphate ions. Down regulation of the flagellar operon with corresponding loss of flagellar structures occurred in multiple lineages, suggesting an evolutionary tradeoff between motility and host immune evasion. Finally, methylome analysis demonstrates alteration of global genome methylation associated with loss of a Type III methyltransferase. Our findings reveal striking plasticity in how pathogen transcriptomes explore functional space as they evolve in the context of host infection, and demonstrate that such analysis may uncover phenotypic adaptations not apparent from genomic analysis alone.
Insights from the largest diverse ancestry sex-specific disease map for genetically predicted height
Authors: Papadopoulou A. , Litkowski E. M. , Graff M. , Wang Z. , Smit R. A. J. , Chittoor G. , Dinsmore I. , Josyula N. S. , Lin M. , Shortt J. , Zhu W. , Vedantam S. L. , Yengo L. , Wood A. R. , Berndt S. I. , Holm I. A. , Mentch F. D. , Hakonarson H. , Kiryluk K. , Weng C. , Jarvik G. P. , Crosslin D. , Carrell D. , Kullo I. J. , Dikilitas O. , Hayes M. G. , Wei W. -Q. , Edwards D. R. V. , Assimes T. L. , Hirschhorn J. N. , Below J. E. , Gignoux C. R. , Justice A. E. , Loos R. J. F. , Sun Y. V. , Raghavan S. , Deloukas P. , North K. E. , Marouli E. 
Published: February 2025

Abstract
We performed ancestry and sex specific Phenome Wide Association Studies (PheWAS) to explore disease related outcomes associated with genetically predicted height. This is the largest PheWAS on genetically predicted height involving up to 840,000 individuals of diverse ancestry. We explored European, African, East Asian ancestries and Hispanic population groups. Increased genetically predicted height is associated with hyperpotassemia and autism in the male cross-ancestry analysis. We report male-only European ancestry associations with anxiety disorders, post-traumatic stress and substance addiction and disorders. We identify a signal with benign neoplasm of other parts of digestive system in females. We report associations with a series of disorders, several with no prior evidence of association with height, involving mental disorders and the endocrine system. Our study suggests that increased genetically predicted height is associated with higher prevalence of many clinically relevant traits which has important implications for epidemiological and clinical disease surveillance and risk stratification.
Quality characteristics and consumer perception of non-alcoholic beers in the context of responsible alcohol consumption
Authors: Gliszczyńska-Świgło Anna , Klimczak Inga , Klensporf-Pawlik Dorota , Rybicka Iga 
Published: February 2025

Abstract
Consumers are becoming more aware of the benefits of reducing alcohol consumption, which has increased the popularity of non-alcoholic beer (NAB). However, the brewing industry still faces many difficulties in producing NAB with similar physicochemical and sensory characteristics to regular beers. To mitigate these challenges, a multidisciplinary study was conducted to: (1) determine selected quality characteristics of various NABs, (2) compare them with literature data for regular beers, and (3) find out how Polish consumers, especially young people, perceive NAB and what motivates them in their purchasing decisions. Physicochemical quality characteristics of NABs, namely pH (4.3–4.7), bitterness (IBU = 12–77), colour (EBC = 6.4–19.6), total soluble solids (2.8–8.3 °Bx), and vitamin B2 content (0.11–0.30 mg/L) were similar to alcoholic beers. Total phenolics (150–321 mg/L), Ca (13–45 mg/L), Mg (40–94 mg/L), K (192–490 mg/L), Na (0.5–57 mg/L), and P (158–467 mg/L) contents in NABs were slightly lower than in alcoholic beers, but this assortment is a healthier source of these nutrients due to the lack of alcohol-related harm. According to the consumer study, taste and availability in shops were found to be crucial factors influencing NAB purchasing decisions.
SFRP2 mediates Epstein-Barr virus and bladder cancer risk: a Mendelian randomization study and colocalization analysis
Authors: Li Jian , Yang Bing , Guo Lei , Huang Wenqi , Hu Qiong , Yan Hongting , Du Changpu , Tan Rong , Tang Dongxin 
Published: February 2025

Abstract
Studies suggest a possible association between Epstein-Barr virus (EBV) infection and bladder cancer (BCa) risk, though this remains unclear. Secreted frizzled-related protein (sFRP) is also linked to BCa, with some DNA viruses potentially regulating its expression. This study used Mendelian randomization (MR) and colocalization analysis to explore the causal relationship between EBV infection, BCa risk, and the mediating role of sFRP. We first performed a two-sample MR study to assess the causal relationship between 5 EBV-related antibodies (AEB-IgG, EA-D, EBNA-1, VCA-p18, ZEBRA) and BCa using the Finnish Consortium’s R11 dataset, validated with R10. Reverse MR analysis followed. For significant results, multivariable MR (MVMR) was applied to adjust for confounding risk factors. A two-step MR explored the potential mediating role of 3 sFRPs (sFRP1, sFRP2, sFRP3) between positive exposures and BCa. Colocalization analysis were conducted for positive exposures, mediators, and BCa, with multiple sensitivity analyses confirming the robustness of the results. The two-sample Mendelian randomization study found that EBNA-1 (OR = 1.15, 95% CI: 1.01–1.30; p = 0.039) and VCA-p18 (OR = 1.36, 95% CI: 1.13–1.64; p = 0.001) may increase BCa risk, with only VCA-p18 (P_fdr = 0.006) showing a significant effect after False Discovery Rate (FDR) correction. The Finnish Consortium R10 replication study yielded similar results, and reverse MR analysis did not suggest reverse causality. After MVMR adjusted for relevant confounders, VCA-p18 (OR = 1.40, 95% CI: 1.13–1.74; p = 0.002) still significantly increased BCa risk. Two-step MR identified sFRP2 as a mediator, with VCA-p18 down-regulating sFRP2 expression to elevate BCa risk. Colocalization analysis suggested a shared causal variant (nearby gene HLA-DQA1) between VCA-p18 and BCa (PPH4 = 65.44%). Multiple sensitivity analyses confirmed the robustness of the results. Our study suggests that EBV infection (VCA-p18 antibody) may increase the risk of BCa by lowering sFRP2 levels. Additionally, EBNA-1 antibodies may also contribute to an elevated risk of BCa. We hope these findings will provide new insights for future research on the association between EBV and BCa.
Gestational hyperglycaemia impacts glucose control and insulin sensitivity in mouse offspring
Authors: Hribar K. , Fisher J. C. , Eichhorn D. , Smit M. , Kloosterhuis N. J. , Bakker B. M. , Oosterveer M. H. , Kruit J. K. , van der Beek E. M. 
Published: February 2025

Abstract
Gestational diabetes mellitus (GDM) predisposes offspring to the development of obesity and type 2 diabetes. While GDM is studied in the context of maternal obesity and insulin resistance, the consequences of GDM in lean, insulin sensitive women for offspring health are unclear. This preclinical study investigated whether GDM in lean dams characterized by reduced insulin secretion affects offspring metabolic health. Lean GDM was induced by short-term 60% high-fat diet and low-dose streptozotocin injections before mating in mice. The control dams received only high-fat diet (HF) or low-fat diet (LF). Glucose homeostasis was studied in chow-fed offspring. GDM resulted in decreased birth weight, that resolved at postnatal day 15 (PN15). At PN100, higher postprandial glucose responses were found in GDM offspring, while insulin secretion was lower in both GDM and HF offspring. Female GDM offspring showed lower endogenous glucose production and increased liver insulin sensitivity at PN100 compared to controls. No differences in metabolic parameters were observed at PN200 and PN300. Prenatal exposure to elevated maternal glucose levels without maternal obesity modestly affected glucose regulation in mouse offspring during early adulthood. Future studies should clarify if a less favourable postnatal diet may further challenge metabolic health in offspring of GDM dams.
Nance-Horan-syndrome-like 1b controls mesodermal cell migration by regulating protrusion and actin dynamics during zebrafish gastrulation
Authors: Escot Sophie , Hassanein Yara , Elouin Amélie , Torres-Paz Jorge , Mellottee Lucille , Ignace Amandine , David Nicolas B. 
Published: February 2025

Abstract
Cell migrations are crucial for embryonic development, wound healing, the immune response, as well as for cancer progression. During mesenchymal cell migration, the Rac1-WAVE-Arp2/3 signalling pathway induces branched actin polymerisation, which protrudes the membrane and allows migration. Fine-tuning the activity of the Rac1-WAVE-Arp2/3 pathway modulates protrusion lifetime and migration persistence. Recently, NHSL1, a novel interactor of the Scar/WAVE complex has been identified as a negative regulator of cell migration in vitro. We here analysed its function in vivo, during zebrafish gastrulation, when nhsl1b is expressed in migrating mesodermal cells. Loss and gain of function experiments revealed that nhsl1b is required for the proper migration of the mesoderm, controlling cell speed and migration persistence. Nhsl1b localises to the tip of actin-rich protrusions where it controls protrusion dynamics, its loss of function reducing the length and lifetime of protrusions, whereas overexpression has the opposite effect. Within the protrusion, Nhsl1b knockdown increases F-actin assembly rate and retrograde flow. These results identify Nhsl1b as a cell type specific regulator of cell migration and highlight the importance of analysing the function of regulators of actin dynamics in physiological contexts.
Multimodale Interventionen in der Therapie von Adipositas im
Alter
Authors: Kiesswetter Eva , Torbahn Gabriel , Schoene Daniel 
Published: February 2025

ZusammenfassungMit der zunehmenden Prävalenz von Adipositas bei älteren Menschen gewinnen
maßgeschneiderte therapeutische Strategien an Bedeutung. Aktuelle Leitlinien
empfehlen multimodale Ansätze für das Gewichtsmanagement bei Erwachsenen,
enthalten jedoch keine spezifischen Empfehlungen für ältere Menschen.
Altersbedingte Veränderungen der Körperzusammensetzung, geriatrische Syndrome
und Multimorbidität sind bei Therapieentscheidungen zu berücksichtigen. Eine
Gewichtsreduktion kann den altersbedingten Verlust von Muskel- und Knochenmasse
verstärken und das Risiko ungünstiger Folgen erhöhen. Daher sind
Therapiekonzepte notwendig, die den Verlust von Fettmasse, den Erhalt von
Muskel- und Knochenmasse sowie die Verbesserung des funktionellen Status
anstreben.Dieser Artikel gibt einen Überblick über die multimodale Adipositastherapie im
Alter und fasst klinische Studien zusammen, die solche Interventionen bei
älteren Menschen mit spezifischen Komorbiditäten durchgeführt haben. Multimodale
Interventionen, die moderate Kalorienrestriktion, kombiniertes Kraft- und
Ausdauertraining sowie verhaltenstherapeutische Strategien umfassen, haben sich
als sicher und effektiv erwiesen. Allerdings wurden Komorbiditäten und
geriatrische Syndrome in den Studien selten berücksichtigt. Zudem gibt es wenige
Studien, die spezielle Krankheitsbilder oder Syndrome wie Herzinsuffizienz,
Arthrose oder Gebrechlichkeit als Einschlusskriterium adressieren, was die
Übertragbarkeit der Ansätze einschränkt.
Lower Extremity Vein Thrombosis And Recurrence in Patients with
Behcetʼs Syndrome: How And When?
Authors: Kaban Nedim , Harman Halil , Balcı Mehmet Ali 
Published: February 2025

AbstractWe aimed to investigate the risk and time to recurrence of venous thrombosis
(VT) in patients with BS, focusing on clinical features and laboratory
parameters.A total of 67 BS patients with (n=32) and without (n=35) venous thrombosis
(VT) fulfilled the diagnostic criteria of the International Criteria for
Behcet’s Disease (ICBD) and were included in the study. Clinical features
(onset of BS-related symptoms, presence of VT relapse and cutaneous ulcer,
and the results of vascular system imaging), demographical data, duration of
symptoms, time to diagnosis, delayed time to diagnosis, and patient
follow-up periods were retrospectively obtained from medical records.
Disease activity was assessed using the Behcet’s Disease Current Activity
Form (BDCAF).VT was statistically more common in the male population. In the VT group,
superficial thrombophlebitis (STF) was more frequent, while papulopustular
lesions (PPL) and arthritis were also observed more often compared to the
non-VT group. Median time to VT onset was 2 years (minimum: 0–27). The first
episode of VT occurred within the first 5 years of disease onset in 68.75%
(n=22/32) of patients. VT recurrence occurred in 21.8% of patients (n=7/32).
The time to VT recurrence was a median of 3 years (min, max, 3–5 years)
following the first VT episode. There was a statistically significant
correlation between post-thrombotic cutaneous ulcers (PTCUs) and a positive
pathergy test (p=0.048). Time to VT onset was 2.23 years in smokers and 6.38
years in non-smokers. This difference was found to be statistically
significant when evaluated by a log-rank test (p=0.05).VT develops earlier in BS patients who smoke and have a family history of BS.
One of the unique findings of our study is that pathergy test positivity
predicts the risk of developing PTCUs. Although VT is most common within the
first 5 years of the BS, VT recurrence occurs within the first 10 years.
Endoscopic ultrasound-guided tissue sampling: European Society of Gastrointestinal Endoscopy (ESGE) Technical and Technology Review
Authors: Facciorusso Antonio , Arvanitakis Marianna , Crinò Stefano Francesco , Fabbri Carlo , Fornelli Adele , Leeds John , Archibugi Livia , Carrara Silvia , Dhar Jahnvi , Gkolfakis Paraskevas , Haugk Beate , Iglesias Garcia Julio , Napoleon Bertrand , Papanikolaou Ioannis S. , Seicean Andrada , Stassen Pauline M. C. , Vilmann Peter , Tham Tony C. , Fuccio Lorenzo 
Published: February 2025

AbstractThis Technical and Technology Review from the European Society of Gastrointestinal Endoscopy (ESGE) represents an update of the previous document on the technical aspects of endoscopic ultrasound (EUS)-guided sampling in gastroenterology, including the available types of needle, technical aspects of tissue sampling, new devices, and specimen handling and processing. Among the most important new recommendations are:ESGE recommends end-cutting fine-needle biopsy (FNB) needles over reverse-bevel FNB or
fine-needle aspiration (FNA) needles for tissue sampling of solid pancreatic lesions; FNA may
still have a role when rapid on-site evaluation (ROSE) is available.ESGE recommends EUS-FNB or mucosal incision-assisted biopsy (MIAB) equally for tissue
sampling of subepithelial lesions ≥20 mm in size. MIAB could represent the first choice for
smaller lesions (<20 mm) if proper expertise is available.ESGE does not recommend the use of antibiotic prophylaxis before EUS-guided tissue
sampling of solid masses and EUS-FNA of pancreatic cystic lesions.
Detection Accuracy of [68Ga] PSMA PET/CT with Rising PSA in Prostate Cancer
Authors: Mohan Parul , Wadhwa Palak , Mahajan Harsh , Kumar Dileep , Aringhieri Giacomo , Cioni Dania 
Published: February 2025

Abstract
Objectives The objective of this study was to evaluate the clinical utility of gallium-68 [68Ga] prostate-specific membrane antigen (PSMA) positron emission tomography/computed tomography (PET/CT) with rising prostate-specific antigen (PSA) levels in prostate cancer diagnosis.
Methods This is a retrospective, single-center, observational cross-sectional study, which is provided after ethics committee clearance, from May 2, 2022 to June 25, 2022. Study includes sample size of 50 patients with prostate adenocarcinoma with varying PSA levels and Gleason score of 6 to 9 who underwent [68Ga] PSMA PET/CT scan. The patients included in this study underwent PET/CT scan on uMI550 (United Imaging Healthcare, Shanghai, China).
Results All patients were divided into three groups based on PSA levels in ng/mL as: PSA ≤ 0.2 (8%), 0.2 < PSA ≤ 1 (10%), 1 < PSA ≤ 3 (8%), 3 < PSA ≤ 10 (18%), and PSA > 10 (56%). Among 50 scans, at least one PSMA avid lesion was visualized in 41 scans (78.9%). These scans were considered positive and included in this study, rest of the scans had insignificant PSMA uptake and were considered negative. [68Ga] PSMA PET/CT detection rates were 75.0, 20.0, 50.0, 88.90, and 89.3% in patients with PSA ≤ 0.2, 0.2 < PSA ≤ 1, 1 < PSA ≤ 3, 3 < PSA ≤ 10, and PSA > 10, respectively. In addition to prostate bed, lesions were also visualized in lymph nodes (32%), liver (2%), skeleton (28%), and thorax (6%). Considering lesions in the prostate bed a significant direct correlation was detected between maximal standardized uptake value (SUVmax) and PSA value (p = 0.03).
Discussion PSMA PET/CT has been demonstrated to be an effective method for identifying both low-grade Gleason score tumors and low PSA levels. The study provides support for the use of [68Ga] PSMA PET/CT in conjunction with PSA levels for the evaluation of prostate cancer, including local recurrence and distant metastases.
Conclusion The findings of this study indicate that PSMA PET/CT is an effective method for diagnosing prostate cancer, as it allows for the detection of high SUVmax values in pathological tissues. Furthermore, high sensitivity and detection rates are noted with PSMA PET/CT scan even in cases where PSA levels were low. Therefore, this study demonstrates that [68Ga] PSMA PET/CT is beneficial for the early detection of prostate cancer and the prediction of treatment outcomes.
Machine-assisted quantitizing designs: augmenting humanities and social sciences with artificial intelligence
Authors: Karjus Andres 
Published: February 2025

Abstract
The increasing capacities of large language models (LLMs) have been shown to present an unprecedented opportunity to scale up data analytics in the humanities and social sciences, by automating complex qualitative tasks otherwise typically carried out by human researchers. While numerous benchmarking studies have assessed the analytic prowess of LLMs, there is less focus on operationalizing this capacity for inference and hypothesis testing. Addressing this challenge, a systematic framework is argued for here, building on mixed methods quantitizing and converting design principles, and feature analysis from linguistics, to transparently integrate human expertise and machine scalability. Replicability and statistical robustness are discussed, including how to incorporate machine annotator error rates in subsequent inference. The approach is discussed and demonstrated in over a dozen LLM-assisted case studies, covering nine diverse languages, multiple disciplines and tasks, including analysis of themes, stances, ideas, and genre compositions; linguistic and semantic annotation, interviews, text mining and event cause inference in noisy historical data, literary social network construction, metadata imputation, and multimodal visual cultural analytics. Using hypothesis-driven topic classification instead of “distant reading” is discussed. The replications among the experiments also illustrate how tasks previously requiring protracted team effort or complex computational pipelines can now be accomplished by an LLM-assisted scholar in a fraction of the time. Importantly, the approach is not intended to replace, but to augment and scale researcher expertise and analytic practices. With these opportunities in sight, qualitative skills and the ability to pose insightful questions have arguably never been more critical.
X-ray analysis of nanowires and nanowire devices: structure, function and synthesis
Authors: Chayanun Lert , Benter Sandra , Mikkelsen Anders , Timm Rainer , Wallentin Jesper 
Published: February 2025

Abstract
X-ray methods can offer unique insights into the structural and electronic properties of nanomaterials. Recent years have seen a dramatic improvement in both x-ray sources and x-ray optics, providing unprecedented resolution and sensitivity. These developments are particularly useful for nanowires, which are inherently small and give weak signals. This review gives an overview of how different x-ray methods have been used to analyze nanowires, showing the different types of insight that can be gained. The methods that are discussed include x-ray diffraction, x-ray fluorescence, x-ray photoelectron spectroscopy and x-ray photoelectron emission microscopy, as well as several others. The review is especially focused on high spatial resolution methods used at the single nanowire level, but it also covers ensemble experiments.