bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep unsupervised clustering for prostate auto-segmentation with and without hydrogel spacer
Authors: Zhao Hengrui , Wang Biling , Dohopolski Michael , Bai Ti , Jiang Steve , Nguyen Dan 
Published: January 2025

Abstract

Introduction. Clinical datasets for training deep learning (DL) models often exhibit high levels of heterogeneity due to differences such as patient characteristics, new medical techniques, and physician preferences. In recent years, hydrogel spacers have been used in some prostate cancer patients receiving radiotherapy to separate the prostate and the rectum to better spare the rectum while achieving adequate dose coverage on the prostate. However, this substantially affects the computed tomography image appearance, which downstream reduced the contouring accuracy of auto-segmentation algorithms. This leads to highly heterogeneous dataset. Methods. To address this issue, we propose to identify underlying clusters within the dataset and use the cluster labels for segmentation. We collected a clinical dataset of 909 patients, including those with two types of hydrogel spacers and those without. First, we trained a DL model to locate the prostate and limit our field of view to the local area surrounding the prostate and rectum. We then used Uniform Manifold Approximation and Projection (UMAP) for dimensionality reduction and employed k-means clustering to assign each patient to a cluster. To leverage this clustered data, we propose a text-guided segmentation model, contrastive language and image pre-training (CLIP)-UNet, which encodes the cluster information using a text encoder and combines the encoded text information with image features for segmentation. Results. The UMAP results indicated up to three clusters within the dataset. CLIP-UNet with cluster information achieved a Dice score of 86.2% compared to 84.4% from the baseline UNet. Additionally, CLIP-UNet outperforms other state-of-the-art models with or without cluster information. Conclusion. Automatic clustering assisted by DL can reveal hidden data clusters in clinical datasets, and CLIP-UNet effectively utilizes clustered labels and achieves higher performance.
Improved irradiation resistance of high entropy nanolaminates through interface engineering
Authors: Şopu Daniel 
Published: January 2025

Abstract
Bi-phase interfacial engineering is an effective method for improving irradiation resistance, as interfaces play a critical role in defect generation and annihilation. In this work, molecular dynamics (MD) simulations are performed to investigate the evolution of the high entropy crystalline/amorphous laminates under ion irradiation. The effects of the crystalline/amorphous interface (ACI) on the distribution of point defects in the high entropy alloy (HEA) as well as on the microstructure evolution in metallic glass (MG) plates are investigated. During irradiation, fewer activated point defects were found in the HEA plate of the MG/HEA laminates compared to a free-standing HEA. In addition, the interface acts as a defect sink, accelerating the annihilation of interstitials at the interface. As a result, residual vacancies accumulate in the crystalline region following the first cascade, leading to a segregated distribution and an imbalance between the vacancies and interstitials in the HEA plate. Vacancy accumulation and clustering are responsible for the formation of stacking faults and complex dislocation networks in the HEA plate in the subsequent overlapping cascades. The interface also acts as a crystallization seed, accelerating the crystallization of the MG plate during irradiation process. However, the structural damage in the MG plate is mitigated by the redistribution of the free volume generated in the collision cascade zone, resulting in structural stability of the MG plate in the overlapping cascades.
United Nations Peacekeeping and the Politics of Authoritarianism
Authors: von Billerbeck Sarah , Gippert Birte Julia , Oksamytna Kseniya , Tansey Oisín 
Published: January 2025

Abstract
Why do countries hosting United Nations (UN) peacekeeping operations tend to consolidate authoritarian forms of governance, despite the UN’s own stated aim of promoting democratization? This book advances a theoretically innovative and empirically rich answer to this question: while the UN does not intentionally promote authoritarianism, it faces a number of constraints and dilemmas that give rise to what we call authoritarian enabling. Enabling can occur through two mechanisms, capacity-building and the creation of a permissive environment, which enhance the ability of host governments to engage in authoritarian behavior and signal to them that doing so is low cost. We illustrate these two mechanisms with four in-depth case studies of UN peacekeeping operations: the UN Transitional Administration in Cambodia (UNTAC), the UN Mission in the Democratic Republic of Congo / UN Stabilization Mission in the Democratic Republic of Congo (MONUC/MONUSCO), the United Nations Stabilization Mission in Haiti / Mission des Nations Unies pour la Stabilisation en Haïti (MINUSTAH), and the UN Mission in Liberia (UNMIL). While enabling stops short of the outright promotion of authoritarianism, it explains why the UN’s activities often appear to contradict its stated objectives and the outcomes it delivers fall short of its goals. In addition to its theoretical and empirical contributions, the book suggests how these dilemmas and challenges can be overcome.
Functional genotype classification groups distinguish disease severity in recessive dystrophic epidermolysis bullosa
Authors: Pathmarajah Pirunthan , Eid Edward , Nazaroff Jaron , So Jodi , Mittal Vaishali , Harris Nicki , Li Shufeng , Lucky Anne W , Gorell Emily S , Peoples Kathleen G , Pope Elena , Lara-Corrales Irene , Paller Amy S , Wiss Karen , Perman Marissa J , Eichenfield Lawrence F , Levy Moise L , Morel Kimberly D , García-Romero Maria T , McCuaig Catherine C , Saber Melissa , Marinkovich M Peter , Oro Anthony , Bruckner Anna L , Tang Jean Y 
Published: January 2025

Abstract
Recessive dystrophic epidermolysis bullosa (RDEB) is a genetic disorder due to pathogenic variants in the COL7A1 gene. In this study we determined the association between different categories of COL7A1 variants and clinical disease severity in 236 RDEB patients in North America. Published reports or in-silico predictions were used to assess the impact of pathogenic variants in COL7A1 on type VII collagen (C7) protein function. Three impact categories were postulated: genotypes that would likely cause a low impact on C7 function (splice B/missense, missense/missense), medium impact [premature termination codon (PTC)/splice B, splice A/splice B, PTC/missense, splice A/missense, splice B/splice B] and high impact (PTC/PTC, PTC/splice A, splice A/splice A). Splice A variants are predicted to cause downstream PTCs while splice B variants cause in-frame exon skipping and are therefore less deleterious. Severity of functional impact was significantly associated with history of gastrostomy tube placement, esophageal dilation, hand surgery, anemia, renal disease, chronic wounds, diffuse skin involvement and history of squamous cell carcinoma. Odds of death were 3.25 (1.24-8.50, p=0.02) higher in the high vs medium impact group. High impact group patients had worse clinical outcomes. Functional genotype categories are a feasible approach to risk stratify patients based on predicted C7 function.
Predicting acute kidney injury in trauma using extreme gradient boosting model: a temporal validation study
Authors: Yi Yongjin , Tae Minwoo , Shin Sujong , Choi Sang-Il 
Published: January 2025

Abstract

Background
Acute kidney injury (AKI) is a significant complication in patients with trauma. The early identification of AKI in these patients poses challenges. This study aimed to predict AKI in trauma patients 24 or 48 hours in advance using an extreme gradient boosting (XGBoost) model.

Methods
We analyzed 17 859 trauma patients admitted to a regional trauma center between January 2015 and July 2023. Demographic, clinical, and laboratory parameters were collected. The model was developed using data until July 2021 and validated using data from August 2021. We developed models to predict AKI stages 1 to 3 and AKI stages 2 and 3 occurring 48 and 24 h later and measured predictive performance in the validation group. The models' performance was evaluated using the area under the receiver operating characteristic curve (AUROC), and feature importance was assessed through SHapley Additive exPlanations values.

Results
The study population exhibited an incidence of AKI of 6.6% in the development group and 5.4% in the validation group. The models demonstrated predictive performances with AUROCs of 0.864 and 0.886 for 48-hour predictions of AKI stages 1 to 3 and stages 2 and 3, and 0.904 and 0.903 for 24-hour predictions of AKI stages 1 to 3 and stages 2 and 3, respectively. Key features influencing model predictions included baseline and in-hospital serum creatinine values, injury severity score, age, lactate dehydrogenase, D-dimer, platelets, albumin, and C-reactive protein levels.

Conclusions
The XGBoost models effectively predicted AKI in trauma patients up to 48 h in advance using clinical data.
Guiding plant conservation using physiological tools: how mechanistic research can bridge disciplinary divides
Authors: Tomlinson Sean 
Published: January 2025

Lay Summary
This editorial introduces a special issue of Conservation Physiology reporting on ‘Traits and Measurements in Plant Conservation’. This article covers previous preferences by different fields of conservation biology in reporting plant or animal research and the manner in which physiological analyses can bridge these divides. Focusing on plant physiology, it summarizes the research of a dozen papers published in the special issue and some burning questions identified by the broader authorship group who contributed to the special issue.
Recruiting Intensity, Hires, and Vacancies: Evidence from Firm-Level Data
Authors: Forsythe Eliza , Weinstein Russell 
Published: January 2025

Abstract
We investigate employer recruiting behaviour, using detailed firm-level data from a national survey of employers hiring recent college graduates. We find this behaviour is responsive to the business cycle, beliefs about labour market tightness, and the intended number of hires. Specifically, employers adjust planned recruiting effort and compensation. We then show that when firms expend greater recruiting effort they ultimately hire more individuals per vacancy. These results suggest that when firms want to increase hires they adjust both the quantity of vacancies and the recruiting intensity per vacancy. If this is true more broadly in the labour market, it may help explain the breakdown in the standard matching function during the Great Recession.
State-level LGBTQ+ policies and health: the role of political determinants in shaping health equity
Authors: Akré Ellesse-Roselee L , Rapfogel Nicole , Miller Gabe H 
Published: January 2025

Abstract
Lesbian, gay, bisexual, transgender, and queer/questioning (LGBTQ+) individuals in the United States experience higher rates of discrimination and stressors that negatively impact health compared with their straight, cisgender counterparts. Using 2022 Behavioral Risk Factor Surveillance Survey (BRFSS) data, estimating multilevel mixed-effects logistic regressions, we examined the relationship between state LGBTQ+ policies and health among LGBT people. Findings reveal a statistically significant inverse link between protective (high) state policy scores and poor self-rated health, poor mental health days, and poor physical health days. Specifically, with each 1-point increase in policy score, the odds of poor self-rated health are reduced by 0.03%, high mental health burden by 0.02%, and high physical health burden by 0.02%. Inequalities in self-rated health, high mental health burden, and high physical health burden are greater in policy environments with fewer state-level protections, with LGBT individuals reporting better health where there are more protections. These results indicate that discriminatory state policies are linked to poorer health for LGBT individuals and suggest that protective policies could improve health. Further research with comprehensive data is needed to deepen understanding.
Metagenomic analysis of microbial dynamics in water kefir grains: influence of soy protein on biomass growth and development of alternative beverage
Authors: Kaya Yiğit , Akgün Hasan Alptuğ , Taş Tuğba Kök 
Published: January 2025

Abstract
The primary aim of this article is to determine the changes in the microbial community within the current water kefir grains when developed in a protein-supplemented environment through metagenomic analysis. Supplied nutrients directly alter structures that contain complex microbial communities in nature. Considering the much more complex human intestinal microbiota, there are numerous articles indicating changes due to nutrition. This study validates this system on a micro scale. The second objective is to create alternatives for the current water kefir beverage and increase its consumption. The properties of these beverages were determined through chemical, sugar composition, microbiological, and sensory analyses. The research identified that the microbial content in water kefir grains changes, resulting in a high biomass structure due to the increased presence of bacteria producing excessive exopolysaccharides. Based on all analysis findings, the ginger and basil-flavored beverage group was determined to be the most suitable product. Further research is required to optimize other flavor components.
Validation of the Alzheimer’s disease-Commonwealth Scientific and Industrial Research Organisation food frequency questionnaire using weighed food records and biomarkers: the method of triads model
Authors: Gardener Samantha L , Doecke James D , Lyons-Wall Philippa , Martins Ralph N , Rainey-Smith Stephanie R 
Published: January 2025

Abstract
The objective was to apply the triangular approach, the Method of Triads, to determine validity of the Alzheimer’s disease-Commonwealth Scientific and Industrial Research Organisation FFQ (AD-CSIROFFQ) in 98 cognitively unimpaired Australian older adults using blood biomarkers and 4-day weighed food records (WFRs).
Spearman’s correlation coefficients were calculated between each dietary method and the validity coefficient was calculated using the Method of Triads. 95% confidence intervals for the validity coefficients were estimated using bootstrap sampling.
Spearman’s correlation coefficients between FFQ and WFR intake for docosahexaenoic acid (DHA) and vitamin E (r = 1.00 and r = 0.95, respectively), and the FFQ intake and beta carotene biomarker level were positively associated (r = 0.35; all p &lt; 0.001). The validity coefficient of the FFQ was highest for DHA (0.94), with a moderate coefficient observed for beta carotene (0.47). The Method of Triads could not be applied to vitamin E and eicosapentaenoic acid (EPA) as one of the individual correlation coefficients was negative.
Validity coefficients were comparable to those of the few other published studies utilising this same approach. The study provides evidence towards validity of the AD-CSIROFFQ in the measurement of DHA and beta carotene, however, was unable to determine validity of vitamin E and EPA intake using this method.
Characterization of lactic acid bacteria and yeast strains isolated from traditional yoghurts to obtain new starter culture combinations and the properties of products during the storage period
Authors: Çetin Zahide , Karahan Aynur Gül 
Published: January 2025

Summary
This study aimed to create new starter culture combinations by isolating lactic acid bacteria (LAB) and yeast strains from traditional yoghurts. Accordingly, 80 strains were isolated from 23 samples. The strains developed acidity within 16 hours, with pH 4.13-5.98. Subsequently, 26 of these strains produced exopolysaccharide (EPS, 0.0-3.3 mg/L), and 5 showed proteolytic activity. The 10 superior strains were identified as Lactiplantibacillus (L.) plantarum, Lactobacillus (L.) rhamnosus, Enterococcus (E.) faecium, Enterococcus sp., and Candida (C.) kefyr. Four groups of yoghurts were produced with three starter culture combinations and a control. During the 21-day storage all groups exhibited similarities in physicochemical properties and protein profiles by SDS-PAGE. However, the volatile component content varied depending on the starter culture combination and storage period. Sensory analysis showed that the experimental yoghurts were preferred over the control group. These findings suggest that the starter culture combinations could be effectively used in industrial yoghurt production.
Improved ability of liposomes to encapsulate ascorbic acid via coating with xanthan gum
Authors: Li Zemin , Zhou Xianghuai , Pan Min-hsiung , Chiou Yi-shiou , Ding Baomiao 
Published: January 2025

Summary
The ability of liposomes (LP) to entrap ascorbic acid (AA) was improved via coating with xanthan gum (XG). The encapsulation efficiency of AA liposomes (AA-LP) increased from 29.7% to 76.2%, and their retention ratio in simulated gastric and intestinal fluids reduced from 43.0% to 29.4% and 78.56% to 49.2%, respectively, after coating with XG, indicating that AA-LP stability was effectively increased. XG-AA-LP zeta potential and particle size increased from −29.4 mV to −51.6 mV and 240.9 nm to 291.4 nm, respectively. The increase in XG-AA-LP P values indicated that XG inhibited the movement of phospholipids, leading to a decrease in phospholipid bilayer mobility. Furthermore, FTIR results implied that noncovalent bonding forces such as hydrogen bonding, electrostatic forces, etc. played crucial roles in the binding of XG to AA-Lip, and DSC results indicated that the thermal stability of LP increased after coating with XG. TEM results signified that some irregular substances bound to the surface of AA-LP and the liposome particles became larger compared to those of AA-LP, and the surface of AA-LP was coated with XG. These findings suggest that XG coating can be an effective strategy to develop LP ability to deliver AA and to increase AA-LP stability.
Dough rheology properties as affected by the inclusion of oat-drink residue flour: a multivariate analysis approach
Authors: Rashed Mahmoud Said , Gallagher Eimear , Frias Jesus M , Pojić Milica , Pathania Shivani 
Published: January 2025

Abstract
The global shift towards plant-based food consumption presents significant environmental benefits, yet the consequential rise in related by-products sill imposes a challenge to be addressed. The present work was carried out to evaluate the rheological properties of bread dough as affected by the incorporation of dry fractionated oat-drink residue flours as a functional ingredient to identify the optimum condition for incorporating fibre-rich ingredients in bakery products. Mechanically dry fractionated dried oat-drink residue flour of particle size F1: &gt; 150, F2: 150–224, F3: 224-300 μm were blended with strong wheat flour at 10 and 20% substitution levels of the wheat flour. The resulting doughs were assessed for their rheological characteristics. Results from Mixolab®, Rapid Visco Analyser, and gel texture properties revealed that 10F3 showed the highest peak viscosity; 20F2 exhibited the highest water absorption value (66.7%), whereas 20F2 showed the lowest gel hardness level compared to control (100% wheat flour). Principal component analysis showed that the specific surface area of the flour composite is a key feature determining dough rheological properties. Additionally, cluster analysis results revealed that, within measured parameters, flour-pasting properties are the most representative of the flour composite characteristics. Moreover, the analysis was able to discriminate between different flour composites based on their rheological properties. The TOPSIS- Shannon entropy approach was used to increase the inclusion level of non-wheat components in the bread formulations while maintaining the structural quality of the bread. The comparison between different flour composites via TOPSIS analysis revealed that 10F2 was the best formulation in terms of instrumental quality properties of resultant bread among other flour composites. It was observed that the effect of inclusion level outweighs the effect of particle size distribution on incorporated fibre-rich ingredients in terms of affecting the texture quality characteristics of resultant bread. Results highlight the potential application of fractionated oat-drink residue flour for blending with wheat flour properties for to produce fibre-rich bakery products.
Carvacrol encapsulated in chia mucilage nanocapsules reduces salmonella population in chicken meat
Authors: Cacciatore Fabíola Ayres , Scherer Alina , Brandelli Adriano , da Silva Malheiros Patrícia 
Published: January 2025

Abstract
Salmonella contamination in poultry products remains a significant concern worldwide, affecting food safety and public health. In this study, carvacrol encapsulated in chia mucilage nanocapsules (CMNP) was tested against a cocktail of Salmonella enterica artificially inoculated into chicken meat. The Bactericidal Inactivation Concentration (BIC) of CMNP and carvacrol emulsion (CE) was 0.92 mg/mL and 1.77 mg/mL, respectively, while no inhibitory effect was observed for unloaded nanocapsules (UCMN). A reduction of approximately 2 log CFU/g in the viable Salmonella count was observed in 0.25 h when CMNP was applied and remained constant for 72 h. For CE, the maximum reduction (1.7 log CFU/g) occurred at 6 h and, for UCMN, the peak reduction in the viable Salmonella count occurred after 2 h (0.7 log CFU/g). The colour of all the samples after the experiments was whitish, like that of cooked chicken. The texture of the samples exposed to 48 h and 72 h of contact showed significant variations. Despite this, CMNP has the potential to be used as an antimicrobial in processed chicken foods, such as nuggets or burgers, considering that changes in colour and texture may not be visually noticeable after heat treatment.