bluuebunny/crossref_metadata_2025 huggingface dataset:
Autophagy Associated Genes (ARGs) ‐Based Predictive Model AIDPS for Prostate Cancer
Authors: Zhao Zhiyi , Yang Yongjin , Sun Zhou , Fan LianMing , Liu Lingyun
Published: January 2025

Prostate cancer (PCa) is one of the most common cancers in men worldwide. Autophagy‐related genes (ARGs) may play an important role in various biological processes of PCa. The aim of this study was to identify and evaluate autophagy‐related features to predict clinical outcomes in patients with PCa. Single‐cell sequencing data and RNA sequencing data was included from public GEO and TCGA databases. Cells were clustered and annotated by dimension reduction cluster analysis. Epithelial cells, T cells and fibroblasts were isolated to explore their heterogeneity. Autophagy‐related genes were obtained from the HADb database. Survival analysis was conducted by K–M curve, and prognostic risk model was established using 101 machine learning algorithms. In addition, we performed gene colocalisation analysis and Mendelian randomisation analysis. Univariate Cox analysis was used to screen out prognostic genes from DEGs and ARGs in each dataset. Risk model was generated by artificial intelligence‐derived prognostic signature (AIDPS), which showed better prognostic performance in every dataset than other published models for PCa. The disease‐free period (DFS) of patients in the high‐risk group was significantly worse than that in the low‐risk group (all p < 0.05). The best model is the Ridge (C‐index 0.726). We found significant differences in IC50 values of the Dactinomycin_1811, Dactolisib_1057, Luminespib_1559 and Paclitaxel_1080 between groups. In SNP sites rs2743987 and rs7768988, there was a significant correlation between prostate hyperplasia and prostate cancer. Our ARG‐based predictive model AIDPS is a reliable and effective tool for prognosis and treatment of prostate cancer.
Genetic Commonalities Between Metabolic Syndrome and Rheumatic Diseases Through Disease Interactome Modules
Authors: Shi Yinli , Guan Shuang , Liu Xi , Zhai Hongjun , Zhang Yingying , Liu Jun , Yang Weibin , Wang Zhong
Published: January 2025

This study aims to elucidate the potential genetic commonalities between metabolic syndrome (MetS) and rheumatic diseases through a disease interactome network, according to publicly available large‐scale genome‐wide association studies (GWAS). The analysis included linkage disequilibrium score regression analysis, cross trait meta‐analysis and colocalisation analysis to identify common genetic overlap. Using modular partitioning, the network‐based association between the two disease proteins in the protein–protein interaction set was divided and quantified. Clinical samples from public databases were used to confirm the mapped genes. Mendelian randomisation analyses were conducted using genetic instrumental variables for causal inference. MetS and rheumatoid arthritis (RA), ankylosing spondylitis (AS), systemic lupus erythematosus (SLE), Sjogren's syndrome (SS) and their primary module networks shared topological overlap and genetic correlation. Functional analysis highlighted the significance of these shared targets in processes such as a diverse array of metabolic pathways involving glucose, lipids, energy, protein transport, inflammatory response, autophagy and cytokine regulation, elucidating the pathways through which MetS intersects with rheumatic diseases. Causal associations were determined between MetS phenotypes and rheumatic diseases. The persistence of MetS effects on rheumatic diseases remained evident even after adjusting for alcohol consumption and smoking. We have highlighted specific genetic associations between MetS and rheumatic diseases. Several genes (e.g., PRRC2A, PSMB8, BAG6, GPSM3, PBX2, etc.) have been identified with molecular commonalities in MetS and RA, AS, SLE and SS, which may serve as potential targets for shared treatments.
Variation in the diet composition and weight–length relationship of small characids in urbanized and forested streams
Authors: de Souza Emanuelly Costa Ventura , Gouveia E. J. , Nascimento T. J. S. , Mendes S. G. F. , Ferreira A. , Araújo R. P. , Oliveira K. M. P. , Dagosta F. C. P. , Russo M. R.
Published: January 2025

The diet of indicator fish species plays a crucial role in assessing ecosystem health. This study evaluated streams with and without urban influences, focusing on abiotic parameters and the trophic ecology of Psalidodon fasciatus and Piabina argentea. Forested streams exhibited higher redox potential, dissolved oxygen, transparency, and depth, whereas urban streams had higher temperatures, greater widths, and increased levels of total dissolved solids, conductivity, total coliforms, and thermotolerant coliforms. The P. fasciatus population exhibited isometric growth in forested streams and negative allometric growth in urban streams. Conversely, P. argentea exhibited negative allometric growth in both types of environment. The diets of both species included items of autochthonous and allochthonous origin. P. fasciatus had a similar diet in both stream types, whereas P. argentea's diet varied significantly between forested and urban streams. These findings highlight the importance of understanding the interplay between environmental characteristics and species diets, offering crucial insights into the health status of streams, especially those impacted by urbanization.
Analyzing mental health among Black immigrant families through intersectionality
Authors: Hinson Jacinta D. , Weiser Dana
Published: January 2025

With the Black immigrant population in the United States rapidly increasing, there is a pressing need to understand their unique challenges. We examine the mental health issues of Black immigrant families in the US through the lens of intersectionality. We explore how overlapping identities, race, immigration status, and socioeconomic conditions impact mental health outcomes. Despite their growing numbers, Black immigrants remain underrepresented in mental health research, facing barriers such as language, cultural stigma, and limited access to services. Specific findings reveal how structural racism and migration stress compound to worsen mental health outcomes. This review highlights the importance of targeted, culturally sensitive interventions and comprehensive healthcare practices by analyzing these factors. We advocate for an intersectional approach to address systemic barriers and improve mental health outcomes for Black immigrant families, emphasizing the urgent need for expanded research to promote social justice and equity.
Why is traditional polygamy unjust? Implications for egalitarian nonmonogamy
Authors: Sriwannawit Perri
Published: January 2025

The notion of equality attracts both proponents and critics of nonmonogamy. Inequality is a widely discussed objection to nonmonogamy. Simultaneously, equality is highlighted as a core value in ethical nonmonogamy. The notions of equality and inequality in these debates have not been clearly conceptualized. In order to propose a conception of egalitarian nonmonogamy, it is important to first understand possible inequalities within it. This paper establishes a clearer and in‐depth understanding of inequalities in nonmonogamy by categorizing inequalities in traditional polygamy into different kinds. I argue that these inequalities are generally unjust. Although these inequalities are common in traditional polygamy, the objection that polygamy—as a type of marriage—is inherently unequal and unjust is not a convincing argument. By contrast, not all kinds of equality—such as equal love or equal number of partners—are morally significant. I conclude this paper by providing some groundwork for future research on egalitarian nonmonogamy.
Molecular and biochemical evolution of casbene‐type diterpene and sesquiterpene biosynthesis in rice
Authors: Zhou Shen , Zhan Chuansong , Zhu Jinjin , Yang Chenkun , Zhao Qiaoqiao , Sun Yangyang , Zhou Junjie , Shen Shuangqian , Luo Jie
Published: January 2025

Casbene and neocembrene are casbene‐type macrocyclic diterpenes; their derivatives play significant roles in plant defense and have pharmaceutical applications. We had previously characterized a casbene synthase, TERPENE SYNTHASE 28 (OsTPS28), in rice (Oryza sativa). However, the mechanism of neocembrene biosynthesis in rice remained unclear. In this study, we identified two genes of the TPS‐a1 subfamily, OsTPS2 and OsTPS10, encoding a neocembrene synthase and sesquiterpene synthase, respectively, as supported by enzyme activity assays and determination of subcellular localization. Metabolic profiling of rice lines overexpressing either TPS confirmed the catalytic functions of OsTPS2 and OsTPS10, and suggested that OsTPS10 enhances resistance to rice bacterial blight. An evolutionary analysis revealed that OsTPS10 is conserved in monocots and first appeared in wild rice, whereas OsTPS2 and OsTPS28 sequentially evolved through gene duplication, transit peptide recruitment, and mutation of key amino acids such as H362R. In summary, this study not only deepens our understanding of the metabolic pathways and evolutionary history governing the biosynthesis of casbene‐type diterpenoids in rice, representing parallel and divergent evolution within the gene family, and offers gene resources for the improvement of rice.
Impact of Pediatric Posterior Fossa Tumor Treatments on Working Memory Tracts Using Resting‐State fMRI and Tractography
Authors: Habibi Abir Troudi , Alaya Ines Ben , Tensaouti Fatima , Baudou Eloïse , Arribarat Germain , Pollidoro Lisa , Péran Patrice , Chaix Yves , Labidi Salam , Laprie Anne
Published: January 2025

Background and Purpose

Working memory, a primary cognitive domain, is often impaired in pediatric brain tumor survivors, affecting their attention and processing speed. This study investigated the long‐term effects of treatments, including surgery, radiotherapy (RT), and chemotherapy (CT), on working memory tracts in children with posterior fossa tumors (PFTs) using resting‐state functional MRI (rs‐fMRI) and diffusion MRI tractography.

Methods

This study included 16 medulloblastoma (MB) survivors treated with postoperative RT and CT, 14 pilocytic astrocytoma (PA) survivors treated with surgery alone, and 16 healthy controls from the Imaging Memory after Pediatric Cancer in children, adolescents, and young adults study (NCT04324450). Working memory tracts were identified by combining seed masks from rs‐fMRI maps and whole‐brain tractography from diffusion MRI. Connectivity alterations were assessed qualitatively and quantitatively, alongside neuropsychological evaluations and correlations with behavioral outcomes and mean supratentorial dose.

Results

Compared to controls, MB survivors exhibited significant impairments in the working memory network, including reductions in tract volume (TV), fiber density, fiber cross‐section (FC), mean streamline length (MLS), and fractional anisotropy (FA) (all p = 0.04). Lower working memory scores were correlated with reduced TV and FA in MB survivors. Higher mean supratentorial doses were associated with lower TV, FC, and FA values across multiple tracts, particularly in the arcuate and superior longitudinal fasciculi.

Conclusions

Tractography‐derived features highlighted white matter damage as a biomarker of treatment‐related neurotoxicity in PFTs survivors. These findings underscore the detrimental impact of RT and CT on working memory networks and emphasize the importance of preserving cognitive function during treatment planning.
Becoming as Open‐Minded and Organized as My Classmates? Peer Effects on Self‐Reported Personality Trait Development in the Classroom
Authors: Johannsen Mieke , Brandt Naemi D. , Lüdtke Oliver , Wagner Jenny
Published: January 2025

Introduction

How does a student's personality development relate to the personality of their classmates? The school class builds a pertinent comparison group during adolescence that has been identified as a critical factor in students' development of abilities and self‐perceptions. This study empirically tests the impact of classroom personality composition on changes in adolescents' Big Five personality traits. We hypothesized positive associations between class‐level openness and conscientiousness and the individual development of these traits given their role in academic performance.

Method

To test these hypotheses and explore additional composition effects, we employed three approaches of multilevel structural equation modeling on two large longitudinal samples of German adolescents (N1 = 5470; N2 = 788).

Results

Our analyses yielded two principal findings: First, individual personality levels remained highly stable across different time periods. Second, contrary to our hypotheses, baseline class‐level openness and conscientiousness were not positively linked to individual personality development. Instead, there were some indications that higher class‐level openness was negatively linked to individual openness to experiences at the second measurement point.

Conclusions

We discuss the absence of systematic composition effects at the classroom level and consider methodological challenges in investigating these effects.
Persuasion in Networks With Strategic Substitutes
Authors: Li Guopeng , Sun Yang
Published: January 2025

We study Bayesian persuasion with local strategic substitutes in networks. A designer commits to a public signal to maximize total activity. Equilibria are characterized by the network's maximum ‐insulated sets for each realization. We solve the optimal information structure and characterize beneficial persuasion. While agents individually prefer higher states, the designer's payoff is non‐monotonic in the posterior mean due to substitution effects. This provides a rationale for downwardplaying mechanisms: revealing low states truthfully and mixing signals when high. Moreover, for tree, nested split, and core‐periphery networks, the designer strictly benefits if the prior mean insulated set size is less than the highest state set size.
Preliminary feasibility and efficacy of a brief behavioural treatment for insomnia after acquired brain injury: A case series
Authors: Gardani Maria , Baylan Satu , Zouhar Veronika
Published: January 2025

Insomnia after acquired brain injury (ABI) is common and can negatively impact an individual's rehabilitation, recovery, and quality of life. The present study investigated the feasibility and preliminary efficacy of a Brief Behavioural Treatment for Insomnia (BBTI) in a community sample following ABI. Ten participants were recruited. Seven participants attended four weekly sessions of BBTI and kept a daily sleep diary. Participants completed a semi‐structured sleep interview at baseline and self‐report measures of sleep, anxiety, and depression pre‐ and post‐treatment as well as a treatment acceptability questionnaire post‐treatment. Follow‐up data were collected at 1‐, 2‐, and 3‐months post‐treatment. Visual analyses of the data were performed on a case‐by‐case basis. Five of the seven participants (71%) no longer met the criteria for insomnia disorder on the Sleep Condition Indicator (SCI) post‐treatment. Treatment effects on sleep outcomes were either maintained or augmented at follow‐ups. BBTI was found to be well tolerated, as evidenced by the high overall retention rates (70%) and positive feedback on the treatment acceptability questionnaire. These results provide preliminary evidence of BBTI being both feasible to use and potentially efficacious in individuals with post‐brain‐injury insomnia. Larger‐scale randomised controlled trials are needed to establish the effectiveness of BBTI following ABI.
The Theory of Social Representation: Its Various Models and Their Imbrication
Authors: Lo Monaco Grégory , Rateau Patrick
Published: January 2025

This article begins with a summary of the four major theoretical and methodological models of social representations—the sociogenetic, structural, sociodynamic and dialogical models—and then explores new and original approaches to integrating these frameworks. The aim is to move beyond the mere accumulation or juxtaposition usually used in presenting these models and to propose methods for imbricating and interweaving them from three perspectives: conceptual innovation, methodological innovation and the temporal logic of research. We demonstrate how these imbrications—though still requiring extensive empirical research—facilitate a better understanding of how individuals and groups represent the objects in their environment.
Hybridization and Introgression in Black Hakes (Merluccius polli and M. senegalensis): Evolutionary Dynamics and Conservation Implications in the Contact Zone Exploited by Multi‐Species Fisheries
Authors: Blanco‐Fernandez Carmen , Rodriguez‐Roche Jorge , Mateo Juan L. , Erzini Karim , Garcia‐Vazquez Eva , Machado‐Schiaffino Gonzalo
Published: January 2025

Hybridization is relatively common between closely related species that share part of their distribution. Understanding its dynamics is important both for conservation purposes and to determine its role as an evolutionary mechanism. Here we have studied the case of black hakes (Merluccius polli and Merluccius senegalensis) in its contact zone. The area of study is located in the FAO fishing area 34, in Mauritania and Senegal waters, where both species are exploited jointly in multi‐species fisheries involving national and foreign fleets. Using a ddRADSeq approach and based on a set of 5820 SNPs and a total of 240 individuals, we identified one F1 hybrid and several backcrossed individuals among 90 M. polli samples and none in 90 M. senegalensis samples obtained in 2020, suggesting unidirectional introgression towards M. polli. Hybridization signals were not found in any of the 60 historical samples from 2000. Excluding the hybrids and developing two separate sets of SNPs (5093 SNPs for M. polli and 2794 SNPs for M. senegalensis), our results detected two distinct genetic clusters within M. polli that show different genetic diversity estimates, with one of the clusters showing a higher potential vulnerability to exploitation. This pattern was observed in both contemporary and historical samples, and both groups presented subtle depth segregation. Moreover, 109 outlier loci were identified between the two groups, that could be developed into molecular markers to further study differentiation between both clusters and contribute to improved stock assessment and management of these important demersal resources.
Landscape of Cyclic Vomiting Syndrome: From Bedside to Bench, Past to Present
Authors: Li B U. K.
Published: January 2025

Investigations into mechanisms of cyclic(al) vomiting syndrome (CVS) began at the bedside more than a century ago. The modern era started with the formation of the Cyclic Vomiting Syndrome Association in 1993 that helped initiate robust efforts in education, advocacy, family physician conferences, scientific symposia, dedicated clinical programs, therapeutic guidelines, and research. Even today, bedside clues continue to emerge with the recent description of cannabinoid hyperemesis syndrome (CHS) and subsequent evidence of a perturbed endocannabinoid system. The clinical picture of CVS has evolved from that of a straightforward emetic disorder related to migraine requiring short‐term antiemetics or prophylactic anti‐migraine therapy, to a complicated, heterogenous one with multiple comorbid associations (anxiety, dysautonomia) and endophenotypes (migraine, Sato, CHS). This expanded view has important therapeutic implications which necessitate managing the comorbidities which can in turn impact the disease itself and proffered promising evidence that behavioral management (meditation) and vagal neuromodulation appear efficacious with few untoward effects, perhaps by reestablishing autonomic (parasympathetic) balance. The pathophysiologic picture now appears to be inscribed on an autonomic polyvagal design but multiple additional pathways interact, some confirmed (NK1, CB1, HPA axis, PPM1D gene, biological calendar, estrogen), and others, possible (TRPV‐1, CGRP, GDF‐15, mitochondrial dysfunction, impaired cation transport). CVS and its cousin CHS continue to challenge clinicians and perplex investigators and in the current era require not only a critical mass of specific pathway expertise but also syncretic biopsychosocial thinking to integrate these disparate threads. We may have reached such a tipping point at this Symposium.
Utility of Monitoring Fasting Phase During Pediatric Colonic Manometry Studies
Authors: Dorfman Lev , El‐Chammas Khalil , Khanna Sahana , Fei Lin , Kaul Ajay
Published: January 2025

Introduction

Colonic manometry (CM) is a diagnostic procedure used to evaluate pediatric patients with refractory constipation, fecal incontinence, Hirschsprung disease, and pediatric intestinal pseudo‐obstruction. Pan‐colonic high‐amplitude propagated contractions (HAPCs), measured by CM, reflect an intact neuromuscular function of the colon. Current guidelines recommend starting CM with fasting recording for 1–2 h, but no prior evaluation has determined the diagnostic yield of the fasting phase.

We aimed to determine the utility of the fasting phase during CM studies.

Methods

We evaluated CM studies conducted at a tertiary pediatric center (2018–2022). Fasting phases of normal CM studies were evaluated.

Key Results

In 433 included studies 241 (55.7%) females, median age (9.7 years), the average fasting recording lasted 126 min. A total of 193 (44.6%) studies exhibited fasting HAPCs, with 123 (28.4%) being pan‐colonic. The presence of pan‐colonic HAPCs was based solely on the fasting phase in 11 (2.5%) studies.

Patients with fasting pan‐colonic HAPCs were younger (median age of 6.9 vs. 9.8 years, p = 0.0001) and had a higher rate of postprandial HAPCs (69.1% vs. 25.2%, p < 0.0001).

Most fasting pan‐colonic HAPCs presented during the first 60 min (94/123, 76.4%). All studies demonstrated HAPCs after stimulation with bisacodyl.

In analyzing just the initial 30 min of fasting on CM, only 2 (0.5%) studies would have been misclassified as abnormal, with no bisacodyl administration in these studies.

Conclusions & Inferences

Shortening the fasting phase minimally affects next‐day CM results and could reduce patient inconvenience, hospital‐related costs, and potential side effects.
Assessing Water Content of the Human Colonic Chyme Using the MRI Parameter T1: A Key Biomarker of Colonic Function
Authors: Dellschaft Neele , Murray Kathryn , Ren Yi , Marciani Luca , Gowland Penny , Spiller Robin , Hoad Caroline
Published: January 2025

Background

The human colon receives 2 L of fluid daily. Small changes in the efficacy of absorption can lead to altered stool consistency with diarrhea or constipation. Drugs and formulations can also alter colonic water, which can be assessed using the magnetic resonance imaging (MRI) longitudinal relaxation time constant, T1. We explore the use of regional T1 assessment in evaluating disorders of colonic function.

Methods

Individual participant data analysis of data from 12 studies from a single center of patients with constipation, irritable bowel syndrome with diarrhea (IBS‐D), and healthy volunteers (HV). T1 was quantified by measuring the signal from the tissue at different times after a pulse which inverts the magnetization.

Key Results

When diarrhea was induced by a macrogol laxative T1 in the ascending colon, T1AC was negatively correlated with stool bacterial content, r2 = 0.78, p < 0.001. T1AC was increased by another laxative, rhubarb. Patients with IBS‐D had elevated fasting T1AC (0.78 ± 0.28 s, N = 67) compared to HV (0.62 ± 0.21 s, N = 92) while those with constipation lay within the normal range (HV 10–90th centiles 0.33–0.91 s). Fasting T1AC in IBS‐D was reduced by mesalazine treatment. T1 in the descending colon was consistently lower than T1AC, with a bigger reduction in patients with constipation than HV. Pre‐feeding dietary fiber (bran, nopal, and psyllium) was associated with fasting T1AC at or above the normal 90th centile.

Conclusions and Inferences

T1 is an MRI parameter which could be used to monitor effectiveness of novel agents designed to alter colonic water content and stool consistency.
Complex and Bidirectional Interplay Between Marital Quality, Catastrophizing, Psychological Dysfunction, and Quality of Life in Married Malay Women With Disorder of Gut–Brain Interactions
Authors: Hamid Nurhazwani , Kueh Yee Cheng , Muhamad Rosediani , Zahari Zalina , van Tilburg Miranda A. L. , Palsson Olafur S. , Whitehead William E. , Ma Zheng Feei , Tagiling Nashrulhaq , Lee Yeong Yeh
Published: January 2025

Background

Disorders of gut–brain interactions (DGBI) affect more women, and marital quality may have been a factor that explains clinical manifestations of DGBI—however, the mechanism is unclear. This study aimed to elucidate supported relationships between DGBI with marital quality and clinical attributes in married Malay women.

Methods

This cross‐sectional study involved married Malay women with functional dyspepsia (FD), irritable bowel syndrome (IBS), and FD‐IBS overlap per Rome IV criteria. Multivariate analysis of variance (MANOVA) and Pearson correlation analysis were performed to determine the association between DGBI, marital quality, and clinical attributes of catastrophizing, psychological dysfunction, and quality of life. Path analysis models were developed, tested, and fitted to elucidate relationships that satisfied significance testing and fit indices (termed supported relationship).

Key Results

Of 1130 screened participants, 513 were analyzed. The prevalence of FD, IBS, and FD‐IBS overlap was 33.9% (n = 174), 29.5% (n = 151), and 36.6% (n = 188), respectively. Of 17 variables in MANOVA, significant differences in variables were observed for FD vs. FD‐IBS overlap (10), IBS versus FD (10), and IBS versus FD‐IBS overlap (5). Pearson correlation matrices found significant correlations for 15 of 17 variables. After testing and fitting, the third path model (Model 3) was deemed the final model. Model 3 suggested that relationships between DGBI and marital and clinical attributes were complex and bidirectional. The number of supported relationships were 50, 43, and 39 for FD‐IBS overlap, FD, and IBS, respectively.

Conclusions and Inferences

Relationships between DGBI, marital quality, and clinical attributes among married Malay women are complex and bidirectional.
Primary Peristalsis Is the Dominant Mechanism of Refluxate Clearance Following Gastroesophageal Reflux
Authors: Marchetti Lorenzo , Rogers Benjamin D. , Patel Amit , Sifrim Daniel , Gyawali C. Prakash
Published: January 2025

Background

Refluxate volume and pH drop following gastroesophageal reflux are mostly cleared by peristalsis. We evaluated the roles of primary volume clearing peristaltic wave (VCPW), secondary VCPW, post‐reflux swallow‐induced peristaltic wave (PSPW), and late primary peristaltic wave (LPPW) in refluxate clearance.

Methods

We retrospectively analyzed pH‐impedance studies performed off therapy in 40 patients with typical esophageal symptoms. Mechanism of refluxate clearance was evaluated for each reflux episode (primary VCPW vs. secondary VCPW vs. none), as well as presence of PSPW, LPPW when PSPW was absent, and pH recovery with each mechanism. Per‐episode and per‐patient analyses determined the dominant mechanism of refluxate clearance and pH recovery.

Results

Of 958 reflux episodes, 88% were acidic. A primary VCPW was the dominant mechanism for volume clearance (48.4% acid, 47.8% non‐acid reflux episodes), and ≥ 50% pH recovery (58.7%). Of reflux episodes lacking pH recovery, PSPW resulted in ≥ 50% pH recovery in 40.2%, and LPPW in 60.9%. In logistic regression models, primary peristaltic wave (primary VCPW, PSPW, or LPPW) had the highest likelihood of pH recovery in per‐episode analysis (OR 2.1, CI 1.3–3.0, p < 0.001), and in per‐patient analysis (OR 11.0, CI 1.5–20.5, p = 0.025), among which primary VCPW was the most effective (OR 3.4, CI 1.5–7.7, p = 0.003).

Conclusions

A primary peristaltic wave from a swallow, either in the form of a VCPW, PSPW, or LPPW, is the dominant mechanism of pH recovery after gastroesophageal reflux. When a primary VCPW does not correct pH drop, PSPW, and LPPW are equivalent salvage mechanisms for pH recovery.
Improving sulforaphane content in broccoli sprouts by applying Se: transcriptome profiling and coexpression network analysis provide insights into the mechanistic response
Authors: Mao Shuxiang , Wang Junwei , Guo Zhijun , Huang Huiping , Wang Shengze , Fei Dandan , Liu Juan , Wu Qi , Nie Jin , Wu Qiuyun , Huang Ke
Published: January 2025

Sulforaphane (SF) is a sulfur (S)‐containing isothiocyanate found in cruciferous vegetables and is known for its potent anticancer properties. Broccoli sprouts, in particular, are considered safe and healthy dietary choices due to their high SF content and other beneficial biological activities, such as enhanced metabolite ingestion. The application of selenium (Se) is an excellent approach to enhance the abundance of SF. Previous studies have often focused on gene expression and changes in the synthetic substrates of glucoraphanin (RAA) to explain SF variation in response to Se application. However, the regulatory network and other physiological and biochemical reactions involved in the regulation of SF biosynthesis are poorly understood. In this study, Se‐treated broccoli sprouts had higher SF and RAA contents; they increased with increasing Se application. Using RNA‐seq in combination with KEGG, GO, phenotypic, and WGCNA analyses, it was observed that not only gene expression was induced but also that glutathione serves as an S donor for SF biosynthesis and acts as an oxidative stress reliever as a result of Se treatment. Additionally, a module related to glucosinolate biosynthesis was identified. Yeast one‐hybrid system and dual luciferase reporter assay were utilized. These assays demonstrated the hub transcription factors GATA22, ERF12‐like, and MYB108 would directly bind to SUR1 promoter and positively regulate its expression. Our study presents the first global overview of the role of GSH metabolism in response to Se for SF biosynthesis, and provides a novel and valuable gene resource for the molecular breeding of high‐SF broccoli.
Gene tree conflict in chloroplast‐based phylogenies in Pyropia species
Authors: San Myat Htoo , Kawamura Yoshio , Kimura Kei , Witharana Eranga Pawani , Shimogiri Takeshi , Fujiyoshi Eiji , Nagano Yukio
Published: January 2025

Chloroplast genomes are widely used in studying evolutionary relationships and conducting phylogenetic analyses. However, few studies have specifically addressed gene tree conflicts. Using the taxonomically complex seaweed genus Pyropia, comprising a group of red algae in the family Bangiaceae commonly found in intertidal zones worldwide, we analyzed gene tree conflicts within Pyropia species. Traditionally, the classification of Pyropia species has relied on morphological traits and short genetic markers such as the chloroplast RuBisCO large subunit (rbcL) and small subunit (SSU) genes. In the present study, we performed phylogenetic analyses using the chloroplast genomes of 15 Pyropia species, including five newly sequenced genomes: Pyropia tanegashimensis, Pyropia acanthophora, Pyropia pseudolinearis, Pyropia kanakaensis and Pyropia kinositae. Notably, P. tanegashimensis and P. acanthophora exhibited structural changes similar to those previously reported in P. vietnamensis. Our analysis revealed that, although previous studies reported conflicting topologies for the phylogenetic relationships among the four major clades of Pyropia, we have resolved these conflicts, at least in terms of the evolution of the chloroplast genome. By contrast to the traditional view of chloroplast genomes as single evolutionary units, our findings suggest that this assumption does not always hold true, leading to different topological patterns across chloroplast genes. Furthermore, we identified several incongruences between individual gene trees and the species tree within clades of Pyropia. These findings highlight the complexities and challenges in resolving phylogenetic relationships within Pyropia, providing valuable insights for future evolutionary studies.
Promoting performance in multilevel governance and delivery of homelessness services
Authors: Coutin Jordy , Musso Juliet , Stanley J. Woody
Published: January 2025

The current study contributes to practice in interagency performance management through a study of the system of federal grants awarded by the Department of Housing and Urban Development to local Continuum of Care (CoC). The mixed methods design synthesizes a multivariate analysis of the relationship between grantee performance and funding levels, a national survey of CoCs and follow‐up interviews with CoC administrators. Findings reveal little association between reported improvements in system‐level performance and annual funding amounts awarded to CoCs. Nevertheless, interviews reveal that the system has fostered commitment to use of data and performance management practices. The study suggests that intergovernmental performance systems should address issues of capacity and be more attuned to the context in which grant recipients work to attain measurable goals. In particular, the value of the performance system is less a carrot/stick relationship between principals and agents, and more a communicative opportunity for federal entities and localities regarding local achievements and constraints.
Fish Sludge as Feed in Circular Bioproduction: Overview of Biological and Chemical Hazards in Fish Sludge and Their Potential Fate via Ingestion by Invertebrates
Authors: Pettersen Kristin S. , Sele Veronika , Araujo Pedro , Belghit Ikram , Benestad Sylvie L. , Bernhoft Aksel , Booth Andy M. , Eriksen Gunnar S. , Farkas Julia , Handå Aleksander H. , Hansen Bjørn Henrik , Helgesen Kari O. , Holst‐Jensen Arne , Johannessen Gro S. , Liland Nina S. , Lundebye Anne‐Katrine , Malzahn Arne M. , Nilsen Hanne , Nordtvedt Tom S. , Norström Madelaine , Owczarek‐Kościelniak Magdalena M. , Øines Øivind , Patel Sonal J. , Sindre Hilde , Standal Inger B. , Hagemann Andreas
Published: January 2025

Aquaculture farming discharges large volumes of fish sludge, consisting of particulate organic matter from feed spill and feces. Fish sludge from land‐based salmonid aquaculture systems can potentially be used to feed low‐trophic species such as marine polychaetes and insects. Further use of these invertebrates as feed may provide a more sustainable feed chain. However, food security must not compromise feed or food safety. The use of fish sludge as feed is currently not permitted in the European Union (EU). A regulatory assessment that considers the integration of fish sludge in the circular bioeconomy requires knowledge of the potential chemical and biological risks involved. This review has compiled data from existing literature on the occurrence of chemical and biological hazards, as well as the physical properties of fish sludge. The potential risks along this feed chain, from fish sludge to novel feed ingredient production, are discussed in light of the EU regulatory framework. Within the available, but scarce, literature on biological hazards in fish sludge, there is no clear evidence that fish sludge is unsafe for use as a feed material for invertebrates if treatment criteria established in the EU regulations are followed. Scarcity implies a level of uncertainty, but not necessary of risk. For the chemical hazards, some elements are of concern and may exceed regulatory limits, and there are limited data on the occurrence of organic pollutants. This review highlights considerable knowledge gaps concerning the use of fish sludge in a circular feed and food system.
Effects of Chinese Import Competition on Self‐Employed Business Owners in the US
Authors: Unel Bulent
Published: January 2025

Exploiting variation in exposure to Chinese import growth across local markets, I investigate the effects of import competition on self‐employment in the US. The China trade shock had a sizable negative impact on incorporated self‐employed business owners (i.e., entrepreneurs) in manufacturing. The reduction in entrepreneurs also significantly contributed to the decline in total manufacturing employment. The analysis also indicates that other sectors have not absorbed entrepreneurs released from manufacturing. Finally, the effects on entrepreneurship are similar across different demographic groups characterized by gender, age, and education.
Characterisation of Eight Novel HLA‐A Alleles From Bone Marrow Volunteers
Authors: Loginova Maria , Dudina Julia , Paramonov Igor
Published: January 2025

Identification of eight novel HLA‐A alleles by next‐generation sequencing.
Infections Management in the Lung Transplant Setting in Italy: A Web‐Survey
Authors: Lombardi Andrea , Grossi Paolo , Mikulska Malgorzata , Giannella Maddalena , Pascale Renato , Marinello Serena , Montagnani Francesca , Seminari Elena , Corcione Silvia , Bandera Alessandra , Bertani Alessandro , Mularoni Alessandra ,   for the Infection Prevention and Treatment Working Group of the LUNG‐SITO study group
Published: January 2025

Introduction

Infections significantly impact morbidity and mortality in lung transplant (LuTx) recipients. This survey focused on documenting current practices regarding the prevention and management of infections in LuTx in Italy.

Methods

A 52‐question survey was administered online in the period from December 1, 2023, to January 31, 2024, assessing center characteristics, Tx team organization, microbiological investigations, infection prevention, and management. All Italian LuTx centers were invited to participate.

Results

Nine out of 10 Italian LuTx centers answered. Most centers (6/9, 67%) performed LuTx only on adults.

Chronic infection or colonization by Mycobacterium abscessus and Burkholderia cenocepacia is considered a contraindication to LuTx in five and two centers, respectively.

For cytomegalovirus D+/R‐ patients, prophylaxis is used in six centers (67%), with a variable duration from 3 to 12 months. Two centers also use IgG. Three centers (33%) use a pre‐emptive strategy. Four centers (45%) screen for Human herpesvirus 8 infection.

Regarding antibiotic prophylaxis, most centers (6/9, 67%) utilise a dual regimen of anti‐pseudomonal penicillin plus glycopeptide. The two most common durations of antibiotic prophylaxis were 72 h and 7 days, each reported by two centers (22%).

Targeted prophylaxis against fungal infections is employed by a minority of centers (4/9, 44%). Inhaled amphotericin B is the most common antifungal, used as targeted prophylaxis (2/4, 50%) and universal prophylaxis (2/5, 40%).

Almost all centers (8/9, 89%) involve the Tx infectious diseases specialist in the recipient management since the pre‐listing period.

Conclusion

There is considerable heterogeneity in infection management among Italian LuTx centers. Establishing a shared platform for data collection and outcome evaluation is essential to improve infection management.

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Development of Local Ductile Failure Assessment Method and Its Application to Four Alloys—Part II: Incorporation of the Effect of Lode Angle
Authors: Takahashi Yukio , Shigeyama Haruhisa
Published: January 2025

In order to guarantee the presence of adequate margin against ultimate fracture, it is essential to establish a reliable methodology for estimating ductile fracture behavior of structures. Following the development of equations for describing true stress–strain relation and their application to notched bar and grooved plate specimens made of four materials used in nuclear power plants without or with the effects of damage depending on stress triaxiality factor, incorporation of the effect of the Lode angle was explored for improving the consistency with the test results. Dependency of true rupture strain on the Lode angle as well as on the stress triaxiality factor was introduced in the new approach. Damage calculated by summing a ratio of equivalent plastic strain increment to the true rupture strain was used for determining failure point and reduction of preceding deformation resistance. Furthermore the effect of the Lode angle on the resistance against plastic deformation was introduced in a separate way to address some situation. After examining the behavior of these parameters in each specimen type, related material constants for each combination of material and temperature were determined by iterating calculations with different constants and comparisons of predicted load–displacement relations with experimental ones. Although constants needed to be adjusted according to materials and temperatures, reasonable agreements were achieved eventually between the experimental and predicted load–displacement curves for all the specimen types investigated. In particular, the maximum load and the displacement at failure could be predicted within an error of about 5% and 10%, respectively, providing compelling evidence for the soundness of the approach.
Multiscale Finite Element Modeling of Human Ear for Acoustic Wave Transmission Into Cochlea and Hair Cells Fatigue Failure
Authors: Jiang Yijie , Bradshaw John J. , Sharma Roshan , Gan Rong Z.
Published: January 2025

Hearing loss is highly related to acoustic injuries and mechanical damage of ear tissues. The mechanical responses and failures of ear tissues are difficult to measure experimentally, especially cochlear hair cells within the organ of Corti (OC) at microscale. Finite element (FE) modeling has become an important tool for simulating acoustic wave transmission and studying cochlear mechanics. This study harnessed a multiscale FE model to investigate the mechanical behaviors of ear tissues in response to acoustic wave and developed a fatigue mechanical model to describe the outer hair cells (OHCs) failure. A three-dimensional (3D) multiscale FE model consisting of a macroscale model of the ear canal, middle ear, and three-chambered cochlea and a microscale OC model on a representative basilar membrane section, including the hair cells, membranes, and supporting cells, was established. Harmonic acoustic mode was used in the FE model for simulating various acoustic pressures and frequencies. The cochlear basilar membrane and the cochlear pressure induced by acoustic pressures were derived from the macroscale model and used as inputs for microscale OC model. The OC model identified the stress and strain concentrations in the reticular lamina (RL) at the root of stereocilia hair bundles and in the Deiter’s cells at the connecting ends with OHCs, indicating the potential mechanical damage sites. OHCs were under cyclic loading and the alternating stress was quantified by the FE model. A fatigue mechanism for OHCs was established based on the modeling results and experimental data. This mechanism would be used for predicting fatigue failure and the resulting hearing loss.
Influence of Geometric Parameters on the Hemodynamic Characteristics of the Vertebral Artery
Authors: Chen Yanlu , Cheng Yuzhou , Luo Kun , Fan Jianren
Published: January 2025

The carotid arteries (CAs) and vertebral arteries (VAs) are principal conduits for cerebral blood supply and are common sites for atherosclerotic plaque formation. To date, there has been extensive clinical and hemodynamic reporting on carotid arteries; however, studies focusing on the hemodynamic characteristics of the VA are notably scarce. This article presents a systematic analysis of the impact of VA diameter and the angle of divergence from the subclavian artery (SA) on hemodynamic properties, facilitated by the construction of an idealized VA geometric model. Research indicates that the increase in the diameter of the VA is associated with a corresponding increase in the complexity of the vortex structures at the bifurcation with the SA. When the VA diameter is constant, a 30 deg VA–SA angle yields better hemodynamic capacity than 45 deg and 60 deg angles, and the patterns of blood flow and helicity values are consistent across different angles. Elevated oscillatory shear index (OSI) zones are mainly at the origin of the VA, with an elliptical low OSI region within. As the diameter increases, the high OSI region spreads downstream. Increasing the bifurcation angle decreases OSI values in and below the elliptical low OSI region. These findings are valuable for studying the physiological and pathological mechanisms of VA atherosclerosis.
A Nodal-Lie-Group Beam Element for Absolute Nodal Coordinate Formulations
Authors: Zhang Binghua , Fan Wei , Ren Hui
Published: January 2025

A new 12DOF beam element is proposed to simulate large deformation and large rotation based on the 24DOF absolute nodal coordinate formulation (ANCF) beam element proposed before. The centerline of the beam is interpolated by Hermite shape functions, and the frame of the beam is interpolated by linear shape functions. To reduce DOFs, the Lie-group method is used to normalize and orthogonalize the frame on each node of the beam. This way of using the Lie-group method keeps a linear relationship between the nodal vectors and shape functions and leads to the constant mass matrix and elastic tensors. Therefore, the generalized elastic and inertial forces do not require Gaussian integration at each time-step. To avoid singularity of the rotation, a relative rotation vector is adopted; correspondingly, the generalized-α integrator based on the Lie group is used to solve the dynamic equations. To improve the convergency speed and alleviate the shear locking and Poisson locking problems of this element, the assumed natural strain (ANS) method is adopted. To improve the calculational accuracy of axis stretching and torsion effects, the enhanced assumed strain (EAS) method is adopted. The formulas presented in this paper have been successfully tested in several static and dynamic examples of other ANCF beam elements and analytic solutions.
Modal Analysis for Localization in Multiple Nonlinear Tuned Mass Dampers Installed on a Structure
Authors: Harata Yuji , Ikeda Takashi , Matsuura Shuma
Published: January 2025

Localization may occur in systems where multiple nonlinear units are coupled with each other. Additionally, localization may occur in multiple nonlinear tuned mass dampers (TMDs) installed on a structure subjected to harmonic excitation. This paper clarifies the cause of localization via modal analysis. First, the equations of motion for a structure with multiple nonlinear TMDs, which are expressed in physical coordinates, are transformed to equations in modal coordinates. When identical TMDs are used, the lowest and highest modes are decoupled in the linear terms to the other modes; however, all these modes are nonlinearly coupled with each other. In addition, the lowest and highest modes are directly excited by an external force, but the other modes are not directly excited. Therefore, the modal equations of motion form an autoparametric system. Van der Pol's method is employed to determine the frequency response curves (FRCs) for harmonic vibrations in modal coordinates. The FRCs and time histories in modal coordinates are calculated when two or three TMDs are installed on the structure; subsequently, those in physical coordinates are determined via coordinate transformation. Numerical results indicate that localization may occur when more than two modes appear simultaneously. Furthermore, the excitation frequency range where localization occurs is theoretically clarified based on backbone curves.