bluuebunny/crossref_metadata_2025_split huggingface dataset:
MOSBY enables multi-omic inference and spatial biomarker discovery from whole slide images
Authors: Senbabaoglu Yasin , Prabhakar Vignesh , Khormali Aminollah , Eastham Jeff , Warner Elisa , Liu Evan , Nabet Barzin , Srivast Minu , Ballinger Marcus , Liu Kai 
Published: March 2024

Abstract

The utility of deep neural nets has been demonstrated for mapping hematoxylin-and-eosin (H&E) stained image features to expression of individual genes. However, these models have not been employed to discover clinically relevant spatial biomarkers. Here we develop MOSBY (Multi-Omic translation of whole slide images for Spatial Biomarker discoverY) that leverages contrastive self-supervised pretraining to extract improved H&E whole slide images features, learns a mapping between image and bulk omic profiles (RNA, DNA, and protein), and utilizes tile-level information to discover spatial biomarkers. We validate MOSBY gene and gene set predictions with spatial transcriptomic and serially-sectioned CD8 IHC image data. We demonstrate that MOSBY-inferred colocalization features have survival-predictive power orthogonal to gene expression, and enable concordance indices highly competitive with survival-trained multimodal networks. We identify and validate 1) an ER stress-associated colocalization feature as a chemotherapy-specific risk factor in lung adenocarcinoma, and 2) the colocalization of T effector cell vs cysteine signatures as a negative prognostic factor in multiple cancer indications. The discovery of clinically relevant biologically interpretable spatial biomarkers showcases the utility of the model in unraveling novel insights in cancer biology as well as informing clinical decision-making.
Beyond Quantities: Machine Learning-based Characterization of Inequality in Infrastructure Quality Provision in Cities
Authors: Li Bo , Mostafavi Ali 
Published: March 2024

Abstract
The objective of this study is to characterize inequality in infrastructure quality across urban areas. While a growing of body of literature has recognized the importance of characterizing infrastructure inequality in cities and provided quantified metrics to inform urban development plans, the majority of the existing approaches focus primarily on measuring the quantity of infrastructure, assuming that more infrastructure is better. Also, the existing research focuses primarily on index-based approaches in which the status of infrastructure provision in urban areas is determined based on assumed subjective weights. The focus on infrastructure quantity and use of indices obtained from subjective weights has hindered the ability to properly examine infrastructure inequality as it pertains to urban inequality and environmental justice considerations. Recognizing this gap, this study examines inequality in infrastructure quality in which infrastructure quality is defined based on the extent to which infrastructure features shape environmental hazard exposure (i.e., air pollution and urban heat) of urban areas. We propose a machine learning-based approach in which infrastructure features that shape environmental hazard exposure are identified and we use the weights obtained by the model to calculate an infrastructure quality provision for spatial areas of cities and accordingly, quantify the extent of inequality in infrastructure quality. The implementation of the model in five metropolitan areas in the U.S. demonstrates the capability of the proposed approach in characterizing inequality in infrastructure quality and capturing city-specific differences in the weights of infrastructure features. The results also show that areas in which low-income populations reside have lower infrastructure quality provision, suggesting the lower infrastructure quality provision as a determinant of urban disparities. Accordingly, the proposed approach can be effectively used to inform integrated urban design strategies to promote infrastructure equity and environmental justice based on data-driven and machine intelligence-based insights.
Low-dose Oxytocin Protocol Makes No Difference in Quantitative Blood Loss in Elective Cesarean Sections; a Single-Center, Retrospective Cohort Study
Authors: Hood Courtney , Baxter Brian , Zuehl Alyssa , Patzkowski Michael 
Published: March 2024

Abstract

Background
The prophylactic use of oxytocin after fetal delivery has been shown to reduce maternal blood loss by 40–50%, yet there remains significant clinical deviation in how the medication is dosed. In January, 2021, the Defense Health Agency (DHA) issued Procedural Instruction 6025.35 entitled Guidance for Implementation of the Postpartum Hemorrhage Bundle. This directive established a set of processes and procedures for the risk assessment and treatment of postpartum hemorrhage (PPH), including a new standardized oxytocin protocol for vaginal and cesarean deliveries.
Methods
This single-center, retrospective cohort study compared quantitative blood loss in healthy parturients undergoing elective cesarean sections that received either unmeasured, high-dose oxytocin (40 IU) or a low-dose oxytocin protocol (3 IU bolus followed by 18 IU per hour) using a multivariate linear regression model.
Results
After controlling for patient age, gestational age at time of delivery, cesarean section indication, and hemorrhagic medications given, the multivariate linear regression model found the regimen of oxytocin a patient received was not predictive of their blood loss (R2 = 0.08, adjusted R2 of -0.003, p = 0.48). Additionally, the low-dose group had less blood loss by estimated marginal means (944mL, 95% CI 724–1164, versus 769mL, 95% CI 526–1011).
Conclusions
This study suggests the low-dose oxytocin protocol released in the Defense Health Agency hemorrhage bundle is safe and effective with regards to preventing blood loss from uterine atony, and should be adopted by all military treatment facilities.
Considering Hounsfield Units in native CT- scans for diagnosing spondylodiscitis
Authors: Prost Max , Taday Roman , Matar Christian Bernard , Latz David , Beyersdorf Carl Christoph Paul , Röckner Melanie Elisabeth , Windolf Joachim , Scheyerer Max Joseph 
Published: March 2024

Abstract
Background
MRI being the method of choice for radiological diagnosis of spondylodiscitis is still often delayed. The significance of native CT Scans as an alternative diagnostic tool for spondylodiscitis is poor according to the current data. Therefore, the aim of this study was to investigate, weather spondylodiscitis leads to a significant pattern of the density distribution from the affected vertebral bodies and discs measured by Hounsfield Units (HU) in native CT Scans.
Methods
In a retrospective study we analyzed data from 136 patients, who were treated for spondylodiscitis. Patients who provided MRI- and CT- scans of the spine were included. In axial CT planes HU from the affected intervertebral disc as well as from the affected vertebral bodies and from the unaffected adjacent intervertebral discs and vertebral bodies from the level above and below as reference were measured.
Results
The average measured HU of the affected disc were 26.0% less than in the not affected adjacent discs (p < 0.001). The average measured HU of the affected vertebral bodies were 33.77% higher than in the not affected adjacent vertebral body’s (p < 0.001)). The localization of the spondylodiscitis and the degree of bony destruction according to Eysel-Peters classification had no influence on these findings.
Conclusion
Decreased HU of the affected vertebral disc of approximate 25% and / or increased HU of the affected vertebral bodies of approximate 30% compared with adjacent vertebral discs and vertebral are indicative for spondylodiscitis even in early phase without destruction and independent of the localization.
Early versus Late Onset Colorectal Cancer: Pathological Distinctions and Optimal Screening Age Determination in a Decade-Long Study
Authors: Song Jiawei , Han Tenghui , Qian Lei , Zhu Jun , Qiao Yihuan , Liu Shuai , Yu Pengfei , Chen Xiaoping , Li Jipeng 
Published: March 2024

Abstract

Background and Aim: The incidence of Early-Onset Colorectal Cancer (EOCRC) is increasing. However, the prognosis of EOCRC compared to Late-Onset Colorectal Cancer (LOCRC), and the ideal age for initial colorectal cancer (CRC) screening are not clear. In this study, we identified the pathological differences between the groups and determined the optimal screening age for CRC patients.
Methods: We included 10,172 patients diagnosed with CRC from January 2011 to December 2021 in this study. Survival differences were compared by plotting Kaplan-Meier survival curves and conducting landmark analysis. Additionally, the diagnostic age of CRC patients was analyzed using age cumulative curves.
Results: Compared to LOCRC patients, EOCRC patients had a higher proportion of defective mismatch repair (dMMR) and more advanced TNM staging (P < 0.05). The five-year survival of EOCRC patients was significantly better than that of LOCRC patients (P < 0.05). Laparoscopic surgery improved the long-term survival of EOCRC patients. Proficient mismatch repair (pMMR) favored the long-term survival of EOCRC patients. The survival rate of EOCRC patients at TNM stages I and II was higher than that of LOCRC patients at the same stages (P < 0.05). The age cumulative curve showed a substantial increase in the number of CRC patients at 40 years.
Conclusion: The long-term prognosis of EOCRC patients is better than that of LOCRC patients, especially among those with pMMR, stages I-II, and who undergo laparoscopic surgery. For high-risk groups, the starting age for CRC screening should be 40 years.
A lethal disease of the European bison - posthitis is conditionally determined by its genomics.
Authors: Kunvar Sazia , Czarnomska Sylwia , Pertoldi Cino , Stronen Astrid , Ruczyńska Iwona , Tokarska Małgorzata 
Published: March 2024

Abstract

Posthitis is an incurable lethal disease of males in the European bison (Bison bonasus), regarded as one of the major threats of the survival of the iconic species. Multiple attempts have been undertaken in the last 30 years to identify a source of infection and a primary pathogen. A genetic background for the disease was suggested after tools developed for cattle (Bos taurus) permitted the discovery of genomic regions possibly associated with the occurrence of posthitis. In this study, we applied deep coverage targeted sequencing to 74 regions on 10 of the bison’s chromosomes (1, 9, 12, 13, 15, 23, 25, 26, 29, and X) in a search for species-specific single nucleotide polymorphism (SNP) markers that could help to explain the mechanism of the disease and be used to test for posthitis susceptibility. The association results were ranked based on p-values lower than 0.005 and odds ratios (OR) higher than 1. We obtained 30 SNP markers within these requirements, all located on chromosome 25. Major difficulties are conditional nature of posthitis and ‘false negative’ sampling. Thus we recommend complex genomic and environmental factors association assay that could eventually explain the puzzling etiology of the disease and support the species conservation.
Engineering piezoelectric efficiency in phase-separated PVDF nanocomposites using In 2 O 3 -ZnO heterostructure
Authors: Yempally Swathi , Bhapkar Abhishek R. , Prasad Rishi , Laad Meena , Bhame Shekhar , Ponnamma Deepalekshmi 
Published: March 2024

Abstract

The current research explores the piezoelectric output voltage efficiency of polyvinylidene fluoride (PVDF) nanocomposites containing In2O3-ZnO heterostructure fabricated by the phase separation methodology. Non-solvent induced phase separation using octanol creates uniform pores and spherulites within the polymer composites. Heterostructures of nanomaterials of ZnO quasi-spherical interface with In2O3 crystalline nucleus enhances the number of crystallites with reduced size, thereby contributing to the piezoelectric performance. Phase separation creates granular and rough surface morphology for the PVDF spherulites with advancement in the β-phase, which is the major reason for power generation. A specific circular sample of 2% PVDF/IZO with a diameter of 3cm and thickness of ~ 150 µm produced the highest output voltage of 1.32 V, almost 26 times higher than that obtained from the neat PVDF film of the same dimension. The study highlights the application of phase separation as a cost-effective self-polarization strategy to considerably increase the phase content and, thereby, sustainable energy harvesting.
Hydroclimate intensification aided Early Holocene Arctic glacier survival
Authors: Auer Andreea , Bilt Willem van der , Schomacker Anders 
Published: March 2024

Abstract

Accelerated Arctic warming and wetting has global impacts, as the region`s glaciers and ice caps respond to changes in temperature (melt) and precipitation (growth), driving on-going sea-level change. However, as the observations needed to calibrate models are scarce and uncertain, predictions cannot confirm if future increases in snowfall can counterbalance ice loss. To help answer this key question, we present evidence of Arctic glacier survival throughout the warmer-than-present Holocene Thermal Maximum (HTM). For this purpose, we analyzed 14 ka long sediment records from two glacial lakes – continuous recorders of past glacier change, fed by Åsgardfonna – an ice cap that survived HTM heat based on mass balance simulations, on Svalbard – a climate change hotspot characterized by the region`s highest rates of warming, sea ice loss, and precipitation change. End Member Modelling Analysis (EMMA) allows us to unmix the diluted diagnostic grain size signal of rock flour – a widely used proxy for past glacier change, and surface runoff – an indicator of hydrological intensification. These reconstructions reveal that Åsgardfonna even advanced under HTM conditions because seasonal sea-ice loss enhanced snowfall. Our findings thus suggest that the near-future retreat and sea-level contribution of Arctic glaciers and ice caps might be slower than assumed.
Sugar-sweetened beverage consumption and metabolic dysfunction associated steatotic liver disease
Authors: Jeon Hong Jae , Rou Woo Sun , Kim Seok Hyun , Lee Byung Seok , Kim Ha Neul , Choi Hei-Gwon , Seo Jaehee , Eun Hyuk Soo , Jung Sukyoung 
Published: March 2024

Abstract

Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most common liver disease. Accumulating evidence suggests a relationship between sugar-sweetened beverage (SSB) consumption and MASLD development; however, this relationship has not been investigated. We aimed to determine whether SSB consumption was associated with an increased risk of MASLD in Korean adults. This study used data from the Korea National Health and Nutrition Examination Survey 2012–2016 (n = 8,310, age 40–64 years). In the present study, soft drink consumption (> 200 mL/week) was associated with increased odds of MASLD (OR 1.40, 95%CI 1.08–1.81, P-trend = 0.01), and Korean traditional drink consumption (> 200 mL/week) was associated with decreased odds of MASLD (OR 0.65, 95%CI 0.47–0.90, P-trend = 0.01). When stratified by sex, a positive association between soft drinks and MASLD was observed in females (OR 1.60, 95%CI 1.13–2.26, P-trend = 0.001) but not in males; a suggestive inverse association between Korean traditional drinks and MASLD was observed in males (OR 0.74, 95%CI 0.51–1.08, P-trend = 0.13) but not in females. In conclusion, soft drink consumption of at least one serving (200 mL) per week was positively associated with MASLD, whereas consumption of the same amount of Korean traditional drinks was inversely associated with MASLD.
Early warning values of the kappa/lambda ratio based on serum detection for M-proteinemia diagnosis
Authors: Lu Jie , Zhu Ying , Huang Huifang , Yang Qian , Qi Songnan 
Published: March 2024

Abstract
Objective
To introduce the kappa/lambda ratio (K/L) to humoral immunity testing reports to improve the detection rate of M-proteinemia disease.
Method
Patient samples were accumulated from January 2021 to December 2023 in the First Affiliated People’s Hospital of Soochow University. The positive control group included 156 patients of M-proteinemia. These samples were classified according to light chain positivity. The negative group included samples from 4,722 patients with non-plasma-cell monoclonal disease and 742 healthy individuals. Receiver operating characteristic (ROC) curves were used to check the reliability of K/L for M-proteinemia diagnosis.
Results
For K-type M-proteinemia, the area under the curve (AUC) was 0.932 when K/L was > 2.39, with a sensitivity of 87.3% and specificity of 92.3%. False positives were mainly found in samples with sicca syndrome (16.67%), mantle cell lymphoma (20.37%), and hepatitis (16.0%). For L-type M-proteinemia, when K/L < 1.44, the AUC was 0.863, the sensitivity was 72.9%, and the specificity was 88.8%. The false positives were mainly found in samples with ANCA-associated systemic vasculitis (21.88%), angioimmunoblastic lymphadenopathy–like T-cell lymphoma (31.25%), NK-/T-cell lymphoma (17.39%), T-cell lymphoma (11.11%), systemic lupus erythematosus (16.83%), cirrhosis (15.69%), infection (12.69%), systemic sclerosis (20.93%), and dermatomyositis (13.95%). False negatives were mainly found in AL (52.0%) and ML (36.36%) .
Conclusion
K/L > 2.39 and K/L < 1.44 should be used as warning values for M-proteinemia. The content of the heavy chain in IgA- or IgM-type M-proteinemia must be considered to improve the detection rate.
Epidemiology of Bovine Fascioliasis: Assessing Prevalence and Investigating Hemato-Biochemical Alterations in Katsinaabattoir North Western Nigeria
Authors: YUSUF BUHARI SHINKAFI , AHMAD ABDULHAMID , suleman Muhammed , KANKIYA IBRAHIM HAMZA , BALA AMINU YABO , ADAMU TUKUR 
Published: March 2024

Abstract

Bovine fascioliasis, caused by liver flukes Fasciola hepatica and Fasciola gigantica, significantly impacts global cattle health and production. This study aimed to assess the prevalence of bovine fascioliasis and its associated hematobiochemical changes on cattles brought for slaughter at Katsina central abattoir. Fecal and blood samples were collected from total of 134 cattles. Fecal samples were examined using sedimentation technique, revealing an infection prevalence of 3.73%. Notably, females exhibited a higher prevalence (4.55%) compared to males (2.17%), though the difference was not statistically significant (P > 0.05). The age group 2–3 years showed the highest prevalence (25.00%), while those aged 5 and above had the lowest prevalence (1.74%). Among cattle breeds, Wadara had the highest prevalence (20.00%), while White Fulani exhibited the least (4.93%). Concerning body condition score (BCS), medium-conditioned cattle had the highest prevalence (6.67%), and good-conditioned ones showed the least (1.37%). Hematological analysis of Fasciola-infected cattle revealed significant reductions (P > 0.05) in packed cell volume (PCV), hemoglobin (Hb), and total erythrocyte count (RBC) compared to the non-infected ones. Additionally, infected cattle demonstrated a significant decrease in white blood cell (WBC) count, mean cellular volume (MCV), and mean cellular hemoglobin concentration (MCHC) compared to the uninfected. Moreover, differential leukocyte counts indicated a notable increase in neutrophils and a decrease in eosinophils, monocytes, and basophils in infected cattle compared to the uninfected, although the difference is not statistically significant (P > 0.05). Biochemical analysis unveiled significantly elevated levels of alanine transaminase (ALT) and aspartate transaminase (AST), along with increased alkaline phosphatase (ALP) and total bilirubin (TB) in infected cattle (P < 0.05). Conversely, albumin (ALB), total protein (TP), and conjugated bilirubin (CB) levels were significantly reduced among infected than uninfected cattle (P < 0.05). Our findings, further confirmed that Bovine fascioliasis has significant impact on the health and productivity of Cattle bred in Katsina state and elsewhere. Understanding its prevalence and associated heamato-biochemical changes among infected animals is essential for implementing effective control and management strategies.
The causal impact of bioavailable testosterone levels on osteoarthritis: a bidirectional Mendelian randomized study Running Title: Causality of testosterone on OA in bidirectional MR study
Authors: Jiang Zong , Yao Xiaoling , Yang Yuzheng , Tang Fang , Ma Wukai , Yao Xueming , Lan Weiya 
Published: March 2024

Abstract
Background: It has been shown that low testosterone levels are associated with the development of osteoarthritis (OA). In our study, we aimed to investigate a bidirectional causal relationship between bioavailable testosterone levels and OA using Mendelian randomization (MR) analysis.
Methods: In our study, the datasets from publicly available genome-wide association study (GWAS) were adopted, including the OA-related dataset (ukb-b-14486) and the bioavailable testosterone levels-related dataset (ebi-a-GCST90012104). In total, five methods were utilized, namely MR Egger, Weighted median, Inverse variance weighted (IVW), Simple mode, and Weighted mode. Among them, IVW was the main analytical method. Additionally, the sensitivity analysis was carried out through the heterogeneity test, the horizontal pleiotropy test, and the Leave-One-Out (LOO) method.
Results: The result of forward MR analysis demonstrated that bioavailable testosterone levels were considerably relevant to OA, and were a risk factor for OA (OR = 1.009, 95% CI: 1.001-1.017, P = 0.020). However, through reverse MR analysis, we did not find a causal relationship between OA and bioavailable testosterone levels. Moreover, the results of the sensitivity analysis suggested that our results were reliable.
Conclusion: The results of our study supported a causal relationship between bioavailable testosterone levels and OA.
Uncovering Seed vigor Responsive miRNA in hybrid Wheat and its parents by Deep Sequencing
Authors: Yue Jie-ru , Liu Yong-jie , Yuan Shao-hua , Sun Hui , Lou Hong-yao , Li Yan-mei , Guo Hao-yu , Liu Zi-han , Zhang Feng-ting , Zhang Sheng-quan , Bai Jian-fang , Zhang Li-ping 
Published: March 2024

Abstract

Background: Two-line hybrid wheat technology system is one way to harness wheat heterosis both domestically and internationally. Seed vigor is a crucial parameter for assessing seed quality, as enhanced seed vigor can lead to yield increments of over 20% to a certain extent. MicroRNAs (miRNAs) were known to participate in the development and vigor of seed in plants, but its impact on seed vigor in two-line hybrid wheat remains poorly elucidated.
Results: The hybrid (BS1453/11GF5135) wheat exhibited superiority in seed vigor and anti-aging capacity, compared to its male parent (11GF5135, MP) and female parent (BS1453, FP). We identified four miRNAs associated with seed vigor, all of which are novel miRNAs. The majority of targets of miRNAs were related to ubiquitin ligases, kinases, sucrose synthases and hydrolases, involving in starch and sucrose metabolism, hydrolysis, catalysis, plant hormone signal transduction, and other pathways, which played crucial roles in seed development. Additionally, we also found miR531 was differentially expressed in both male parent and hybrid, and its target interact with dihydrolipoamide acetyltransferase (E2) and dihydrolipoyl dehydrogenase (E3). Finally, We established a presumptive interaction model to speculate the relationshipof miR531 and seed vigor.
Conclusions: This study analyzed the seed vigor of two-line hybrid wheat, and screened seed vigor-related miRNAs. Meanwhile speculated the genetic relationship of hybrid and parents, in terms of miRNAs. Consequently, the present study provides new insights into the miRNA-mediated gene and protein interaction network that regulates seed vigor. These findings hold significance for enhancing the yield and quality of two-line hybrid wheat, facilitating its future applications.