bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering the fragmentation and separation characteristics of sophorolipid biosurfactants with LC-MS-ESI
Authors: Ingham Benjamin , Hollywood Katherine , Wongsirichot Phavit , Veitch Alistair , Winterburn James 
Published: September 2024

Abstract

The application of liquid chromatography and mass spectrometry (MS) is a challenging area of research for structural identification of sophorolipids, owing to the large number of possible variations in structure and limited knowledge on the separation and fragmentation characteristics of the variants. The aims of this work was to provide a comprehensive analysis of the expected characteristics and fragmentation patterns of a wide range of sophorolipid biosurfactant congeners, providing a methodology and process alongside freely available data to inform and enable future research of commercial or novel sophorolipids. Samples of acidic and lactonic sophorolipid standards were tested using reverse-phase ultra-high performance liquid chromatography and identified using electrospray ionization MS. 37 sophorolipid variants were identified and compared for their elution order and fragmentation pattern under MS/MS. The retention time of sophorolipids was increased by the presence of lactonization, unsaturation, chain length, and acetylation as hydrophobic interactions with the C18 stationary phase increased. A key finding that acidic forms can elute later than lactonic variants was obtained when the fatty acid length and unsaturation and acetylation are altered, in contradiction to previous literature statements. Fragmentation pathways were determined for lactonic and acidic variants under negative [M–H]− and positive [M+NH4]+ ionization, and unique patterns/pathways were identified to help determine the structural components present. The first publicly available database of chromatograms and MS2 spectra has been made available to aid in the identification of sophorolipid components and provide a reliable dataset to accelerate future research into novel sophorolipids and shorten the time to innovation.

One-Sentence Summary
This article describes the process and challenges in identifying different structures of eco-friendly biosurfactants, providing a novel database to compare results.
A comparison of 2 methods of diet analysis in Neotropical frugivorous bats reveals the hidden side of bat–plant interactions
Authors: Colorado Wendy B , Castro-Luna Alejandro A , Gómez-Gil Bruno , Andrade-Torres Antonio , Galindo-González Jorge , Flores-Estévez Norma , Palestina René A 
Published: September 2024

Abstract
Phyllostomid bats are a keystone group in the succession of Neotropical plant communities and knowledge of their diet is essential in the study of bat–plant interactions. The most used method to date has been taxonomic identification of the seeds found in bat feces, but this approach underestimates plant species with large seeds that cannot be ingested. With the aim of estimating how much our knowledge of the diet of frugivorous bats changes once we include those species of plants that are underrepresented, we determine the diet of 3 bat species using 18S rDNA V9 metabarcoding. Results were compared with those obtained from morphological identification of seeds found in feces. Using metabarcoding, we identified 20 plant species and with taxonomic identification of seeds, 10 species, with the latter being a subset of the first method. Metabarcoding made it possible to detect a greater number of interactions as well as a greater percentage of the samples were determined to species level. Fifty percent of the plant species (8 species) recorded in the diet of Sturnira hondurensis, 62% (8 species) for Carollia perspicillata, and 50% (4 species) for Artibeus lituratus were exclusively detected with metabarcoding. Plant species with fleshy fruits including Clusia lundellii, Annona cherimola, and Saurauia pedunculata were exclusively detected with metabarcoding and an important item in the diet. The incorporation of molecular biology to determine the diet of 3 species of frugivorous bats made it possible to demonstrate that their diet is more diverse than previously known. Hence, in the field of plant–bat interactions and knowledge of the natural history of species, it is important to consider this new form of analysis.
The role of the third sector in public health service provision: evidence from 25,338 heterogeneous procurement datasets
Authors: Rahal Charles , Mohan John 
Published: September 2024

Abstract
We examine the role of nonprofits within publicly funded healthcare which runs parallel to private provision in a ‘two-tier’ system through a unique Big Data pipeline. Scraping tens of thousands of heterogeneous transaction datasets across a commissioning hierarchy, the processed dataset contains over £445Bn worth of transactions in 1.9m+ rows of clean data, spanning 2012–2020. We utilize this dataset to test a range of hypotheses related to the introduction of the Health and Social Care Act of 2012. The proportion of contracts placed with nonprofit organizations is relatively low, with limited evidence as to whether the Act increased the involvement of third sector organizations in line with NHS ‘marketization’. We analyse the pattern of procurement by corporate category, the field of service delivery (International Classification of Nonprofit Organizations and Standard Industrial Classification codes), and ‘expense area’ to show the unique array of services which voluntary organizations supply. We also analyse the pattern of commissioning across entity class and size distributions of registered charities. We conclude with a consideration of high-value Community Interest Companies, and discuss potential further areas of research within a healthcare context which such government transaction data makes possible.
Conversational networks: prophets and kings in the Old Testament
Authors: Lee John S Y , Webster Carol 
Published: September 2024

Abstract
This article analyzes discourse in the Old Testament in terms of the frequency of direct speech between the main characters. We visualize the speakers, the hearers, and the amount of conversation between them in graphs known as conversational networks. We investigate whether these networks can help identify speech genres and significant relationships between biblical kings, prophets, and God. In an analysis on three books in the Minor Prophets, the networks are shown to reveal differences in book structure and speech genres including prophetic call, prayer, vision report, judgment speech, and historical narrative. In an analysis on the books of Samuel and King, the networks are shown to capture the web of relationships between kings and prophets, as well as divine communication with kings and prophets. Furthermore, we demonstrate that a comparison between these networks and their counterparts in Chronicles can visualize some major content differences identified in biblical research. These findings are expected to promote conversational networks as a visualization tool to support quantitative discourse analysis in the Bible.
Modelling the impact of host galaxy dust on type Ia supernova distance measurements
Authors: Popovic B , Wiseman P , Sullivan M , Smith M , González-Gaitán S , Scolnic D , Duarte J , Armstrong P , Asorey J , Brout D , Carollo D , Galbany L , Glazebrook K , Kelsey L , Kessler R , Lidman C , Lee J , Lewis G F , Möller A , Nichol R C , Sánchez B O , Toy M , Tucker B E , Vincenzi M , Abbott T M C , Aguena M , Andrade-Oliveira F , Bacon D , Brooks D , Burke D L , Carnero Rosell A , Carretero J , Castander F J , da Costa L N , Pereira M E S , Davis T M , Desai S , Everett S , Ferrero I , Flaugher B , García-Bellido J , Gaztanaga E , Gruendl R A , Gutierrez G , Hinton S R , Hollowood D L , Honscheid K , James D J , Kuehn K , Lahav O , Lee S , Marshall J L , Mena-Fernández J , Miquel R , Myles J , Ogando R L C , Palmese A , Pieres A , Plazas Malagón A A , Sanchez E , Sanchez Cid D , Schubnell M , Sevilla-Noarbe I , Suchyta E , Swanson M E C , Tarle G , Vikram V , Weaverdyck N ,   (DES Collaboration)
Published: September 2024

ABSTRACT
Type Ia Supernovae (SNe Ia) are a critical tool in measuring the accelerating expansion of the universe. Recent efforts to improve these standard candles have focused on incorporating the effects of dust on distance measurements with SNe Ia. In this paper, we use the state-of-the-art Dark Energy Survey 5 year sample to evaluate two different families of dust models: empirical extinction models derived from SNe Ia data and physical attenuation models from the spectra of galaxies. In this work, we use realistic simulations of SNe Ia to forward-model different models of dust and compare summary statistics in order to test different assumptions and impacts on SNe Ia data. Among the SNe Ia-derived models, we find that a logistic function of the total-to-selective extinction $R_V$ best recreates the correlations between supernova distance measurements and host galaxy properties, though an additional 0.02 mag of grey scatter is needed to fully explain the scatter in SNIa brightness in all cases. These empirically derived extinction distributions are highly incompatible with the physical attenuation models from galactic spectral measurements. From these results, we conclude that SNe Ia must either preferentially select extreme ends of galactic dust distributions, or that the characterization of dust along the SNe Ia line-of-sight is incompatible with that of galactic dust distributions.
Serum creatinine is more strongly associated with hyperuricemia than eGFR in males but not in females
Authors: Chihara Yukana , Wakabayashi Ichiro , Kataoka Yuki , Yamamoto Tetsuya 
Published: September 2024

ABSTRACT

Objectives
Serum creatinine and estimated glomerular filtration ratio (eGFR) are factors associated with hyperuricemia, though which is more closely associated with hyperuricemia remains unclear.

Subjects and Methods
This retrospective cross-sectional study examined the associations of serum creatinine and eGFR with hyperuricemia using health check-up findings. Enrolled were 6020 individuals (3509 males, 2511 females) who underwent health check-ups from 2017 to 2021. The subjects were divided based on serum uric acid level into the normuricemia (males 1.5–7.0 mg/dl, females 1.5–&lt; 6.0 mg/dl) and hyperuricemia (males &gt;7.0 mg/dl, female ≥ 6.0 mg/dl) groups. Matched-pair analysis was used to evaluate the association between hyperuricemia and variables related to serum uric acid.

Results
Matched-pair analysis results showed a significant association of serum creatinine with hyperuricemia in male subjects but not in females. Furthermore, propensity score obtained by binominal logistic regression demonstrated that serum creatinine had a greater association with hyperuricemia than eGFR in the males but not in females.

Conclusions
The present findings indicate an association of serum creatinine with hyperuricemia in males not only because of reduced renal function but other factors related to greater muscle mass, such as increased intake of protein-rich foods containing purines and increased uric acid production induced by accelerated creatinine metabolism.
Successful treatment of anti-melanoma differentiation-associated gene 5 antibody-positive dermatomyositis with rapidly progressive interstitial lung disease complicated by bilateral breast cancer following the additional tofacitinib: A case report
Authors: Yamane Takashi , Kitayama Midori 
Published: September 2024

ABSTRACT
Anti-melanoma differentiation-associated gene 5 (MDA-5) antibody-positive dermatomyositis (MDA5-DM) often causes rapidly progressive interstitial lung disease (RP-ILD). Although cancer complications in MDA5-DM are less frequently reported compared to other forms of DM, they do occur. For MDA5-DM patients with cancer, particularly in paraneoplastic settings, the primary treatment strategy often targets the malignancy first. However, surgery, chemotherapy, and radiotherapy carry significant risks of exacerbating ILD, especially in patients with respiratory failure. Despite improved prognosis with initial immunosuppressive combination therapy, some cases of MDA5-DM with RP-ILD remain refractory to treatment. Recent studies have shown the potential benefit of Janus kinase (JAK) inhibitors for refractory cases, though their impact on cancer progression remains a concern. We report a 48-year-old woman with MDA5-DM, RP-ILD, and bilateral breast cancer. Due to her respiratory condition, radical surgery and chemotherapy were initially not possible. Endocrine therapy and immunosuppressive therapy were administered, but the disease remained refractory. Tofacitinib, combined with plasma exchange, improved her ILD, allowing for bilateral mastectomy. One year later, MDA5 antibody titers became negative, and glucocorticoids were discontinued after two years. Three years later, neither MDA5-DM nor breast cancer has recurred. This is the first report of MDA5-DM complicated by breast cancer, and the first use of JAK inhibitors in such a case. Effective treatment requires close collaboration with oncologists to balance the risks and benefits of therapy in cases of MDA5-DM with RP-ILD and cancer.
Testis-specific H2B.W1 disrupts nucleosome integrity by reducing DNA–histone interactions
Authors: Ding Dongbo , Pang Matthew Y H , Deng Mingxi , Nguyen Thi Thuy , Liu Yue , Sun Xulun , Xu Zhichun , Zhang Yingyi , Zhai Yuanliang , Yan Yan , Ishibashi Toyotaka 
Published: September 2024

Abstract
Multiple testis-specific histone variants are involved in the dynamic chromatin transitions during spermatogenesis. H2B.W1 (previously called H2BFWT) is an H2B variant specific to primate testis with hitherto unclear functions, although its single-nucleotide polymorphisms (SNPs) are closely associated with male non-obstructive infertility. Here, we found that H2B.W1 is only expressed in the mid-late spermatogonia stages, and H2B.W1 nucleosomes are defined by a more flexible structure originating from weakened interactions between histones and DNA. Furthermore, one of its SNPs, H2B.W1-H100R, which is associated with infertility, further destabilizes the nucleosomes and increases the nucleosome unwrapping rate by interfering with the R100 and H4 K91/R92 interaction. Our results suggest that destabilizing H2B.W1 containing nucleosomes might change the chromatin structure of spermatogonia, and that H2B.W1-H100R enhances the nucleosome-destabilizing effects, leading to infertility.
TCR3d 2.0: expanding the T cell receptor structure database with new structures, tools and interactions
Authors: Lin Valerie , Cheung Melyssa , Gowthaman Ragul , Eisenberg Maya , Baker Brian M , Pierce Brian G 
Published: September 2024

Abstract
Recognition of antigens by T cell receptors (TCRs) is a key component of adaptive immunity. Understanding the structures of these TCR interactions provides major insights into immune protection and diseases, and enables design of therapeutics, vaccines and predictive modeling algorithms. Previously, we released TCR3d, a database and resource for structures of TCRs and their recognition. Due to the growth of available structures and categories of complexes, the content of TCR3d has expanded substantially in the past 5 years. This expansion includes new tables dedicated to TCR mimic antibody complex structures, TCR-CD3 complexes and annotated Class I and II peptide–MHC complexes. Additionally, tools are available for users to calculate docking geometries for input TCR and TCR mimic complex structures. The core tables of TCR–peptide–MHC complexes have grown by 50%, and include binding affinity data for experimentally determined structures. These major content and feature updates enhance TCR3d as a resource for immunology, therapeutics and structural biology research, and enable advanced approaches for predictive TCR modeling and design. TCR3d is available at: https://tcr3d.ibbr.umd.edu.
Contextualising Long Covid: Viral Sequelae, ‘Post-Encephalitis’ Lethargica and the Modern British Healthcare System, c. 1918–1945
Authors: McAllister Kate 
Published: September 2024

Summary
In the months after March 2020, people across Britain began to seek medical attention for protracted illness following an infection with coronavirus disease 2019. Through the efforts of patients, these illnesses were eventually gathered into the diagnostic category of ‘Long Covid’ and therefore viewed as viral sequelae, in turn opening up the possibility for medical care and treatment in the British health system. This article adds to such patient-made knowledge of Long Covid through a comparative historical analysis with the problem of ‘Post-Encephalitis’ Lethargica (EL). In the early twentieth century, the viral sequelae of EL were parsed in line with and thus shaped by the binary divisions that were becoming used to structure healthcare in Britain. By telling this story of the past, this article provides a framework to understand if and how such administrative divisions within the National Health Service (NHS) might continue to inform perceptions of and responses to Long Covid in the present.
Cover Cropping Attenuates Population Growth of Macrophomina phaseolina by Limiting Weed Biomass, Despite Asymptomatic Colonization of Cover Crops
Authors: Qin Clara , Goldman Polly H. , Leap Jim , Henry Peter Montgomery 
Published: September 2024

Macrophomina phaseolina is a fungus that causes charcoal rot in strawberry and a wide variety of crop species. Little is known about its potential to asymptomatically colonize crop plants or grow saprophytically on their tissues, both of which would create a potential for alternate, asymptomatic hosts to lead to increases in inoculum. To test the impact of cover cropping on M. phaseolina abundance, we conducted randomized-block field experiments in soils infested by M. phaseolina. None of the 15 cover crop varieties showed symptoms of charcoal rot. All Fabaceae and Brassicaceae varieties were asymptomatically colonized at varying rates, but among Poaceae M. phaseolina was recovered from only one individual oat plant. Soil samples collected at the time of planting, tillage, and 8 weeks after tillage showed that cover cropping attenuated the growth of M. phaseolina relative to fallow plots harboring the weedy legume Medicago polymorpha. This weed species was abundantly colonized by this pathogen in both living root samples and plant residue collected 8 weeks after tillage. Cover cropping also influenced the diversity and composition of bulk soil bacterial and fungal communities, but these effects were not associated with M. phaseolina population density. Although M. phaseolina was not detected in living wheat tissues, it was recovered from wheat residue, suggesting that it may be facultatively saprophytic. These results suggest that cover cropping does not pose a risk for increasing disease caused by M. phaseolina and could be beneficial as conducive weed species, such as M. polymorpha, are suppressed. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Allergen-specific immunotherapy at the extremes of age: below 5 years and elderly: evidence beyond indications?
Authors: Özdemiral Cansu , Gurel Deniz Ilgun , Sahiner Umit 
Published: September 2024

Purpose of review
Allergen-specific immunotherapy (AIT) has been used in clinical practice to treat allergic diseases for over 100 years. The effectiveness and safety of AIT have been substantiated in numerous studies; however, children before 5 years of age and elderly are not encompassed generally. This review aims to present the current understanding of AIT in the extremes of age.

Recent findings
Early allergen immunotherapy during infancy or early childhood may prevent the development of allergic sensitization to common allergens, thereby reducing the risk of developing allergic diseases later in life. In the elderly, improved symptoms and quality of life and reduced dependence on medication are indicated the importance on the implementation of AIT. Both clinical and immunological parameters demonstrated that the treatment was effective at the time of cessation and trend to sustained tolerance.

Summary
There is no specific lower or upper age limit for initiating immunotherapy; however, it is important to thoroughly evaluate the severity of disease and the risks and benefits in each case.
Urban–rural disparities in mortality due to stroke subtypes in China and its provinces, 2015–2020
Authors: Ren Yi , Yang Jia , Yin Peng , Liu Wei , Long Zheng , Zhang Chen , Wang Zixin , Liu Haijie , Zhou Maigeng , Ma Qingfeng , Hao Junwei 
Published: September 2024

Abstract

Background:
Death burden of stroke is severe in China with over one-third rural residents, but there is still a lack of specific national and high-quality reports on the urban–rural differences in stroke burden, especially for subtypes. We aimed to update the understanding of urban–rural differences in stroke deaths.

Methods:
This is a descriptive observational study. Data from the national mortality surveillance system, which covers 323.8 million with 605 disease surveillance points (DSPs) across all 31 provinces, municipalities, and autonomous regions in China. All deaths from stroke as the underlying cause from 2015 to 2020 according to DSPs. Crude mortality rate and age-standardized mortality rate (ASMR) were estimated through DSPs. Average annual percentage change was used to explain the change in mortality rate.

Results:
From 2015 to 2020, the majority of deaths from all stroke subtypes occurred in rural areas. There were significant differences between the changes of urban and rural ASMRs. On the whole, the changes in urban areas were evidently better, and the ASMR differences were basically expanding. Stroke ASMR in urban China decreased by 15.5%. The rural ASMR of ischemic stroke (IS) increased by 12.9%. The rural and urban ASMRs of intracerebral hemorrhage decreased by 24.9% and 27.4%, and those of subarachnoid hemorrhage decreased by 29.5% and 40.4%, respectively. The highest ASMRs of all stroke subtypes and the increasing trend of IS ASMR make rural males the focus of stroke management.

Conclusions:
The death burden of stroke varies greatly between urban and rural China. Rural residents face unique challenges.