bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of Gut Microbiota After Fecal Microbiota Transplantation in Ulcerative Colitis: Success Linked to Control of Prevotellaceae
Authors: Pinto Susanne , Šajbenová Dominika , Benincà Elisa , Nooij Sam , Terveer Elisabeth M , Keller Josbert J , van der Meulen–de Jong Andrea E , Bogaards Johannes A , Steyerberg Ewout W 
Published: September 2024

Abstract

Background
Fecal microbiota transplantation (FMT) is an experimental treatment for ulcerative colitis (UC). We aimed to study microbial families associated with FMT treatment success.

Methods
We analyzed stools from 24 UC patients treated with 4 FMTs weekly after randomization for pretreatment during 3 weeks with budesonide (n = 12) or placebo (n = 12). Stool samples were collected 9 times pre-, during, and post-FMT. Clinical and endoscopic response was assessed 14 weeks after initiation of the study using the full Mayo score. Early withdrawal due to worsening of UC symptoms was classified as non-response.

Results
Nine patients (38%) reached remission at week 14, and 15 patients had a partial response or non-response at or before week 14. With a Dirichlet multinomial mixture model, we identified 5 distinct clusters based on the microbiota composition of 180 longitudinally collected patient samples and 27 donor samples. A Prevotellaceae-dominant cluster was associated with poor response to FMT treatment. Conversely, the families Ruminococcaceae and Lachnospiraceae were associated with a successful clinical response. These associations were already visible at the start of the treatment for a subgroup of patients and were retained in repeated measures analyses of family-specific abundance over time. Responders were also characterized by a significantly lower Simpson dominance compared to non-responders.

Conclusions
The success of FMT treatment of UC patients appears to be associated with specific gut microbiota families, such as control of Prevotellaceae. Monitoring the dynamics of these microbial families could potentially be used to inform treatment success early during FMT.

Clinical trial registration number
The study was registered in the Netherlands Trial Register, with reference number NL9858.
Perspectives of ELF-informed teachers in Taiwan
Authors: Huang Yi-Ping , Lin Lu-Chun , Tsou Wenli 
Published: September 2024

Abstract
English as a lingua franca (ELF) represents a substantial paradigm shift in ELT because it challenges the traditional norm of standard English. Despite this changing trend, there is a gap in research on incorporating ELF into in-service teachers’ professional development (PD). Given the backdrop that (trans)disciplinary courses are expected to be taught in English in compulsory K-12 education due to the Bilingual 2030 Policy in Taiwan, this paper proposes an ELF-informed PD model and specifically examines English teachers’ perspectives before, during, and after their participation in the first nationwide bilingual in-service teachers’ PD programme. We observe a growing recognition of ELF concepts among teachers, which is evident in their understanding of the pedagogic challenges and implicit tensions in ELF practice, their validating senses of being ELF teachers, and their critical reflection on ELF-informed pedagogy. The enhanced understanding highlights an alternative approach to transforming the ‘E’ in EFL.
Dystroglycan-HSPG interactions provide synaptic plasticity and specificity
Authors: Melrose James 
Published: September 2024

Abstract
Aim: This study examined the roles of the laminin and proteoglycan receptor dystroglycan (DG) in extracellular matrix stabilization and cellular mechanosensory processes conveyed through communication between the extracellular matrix (ECM) and cytoskeleton facilitated by DG. Specific functional attributes of HS-proteoglycans (HSPGs) are conveyed through interactions with DG and provide synaptic specificity through diverse interactions with an extensive range of cell attachment and adaptor proteins which convey synaptic plasticity. HSPG-DG interactions are important in phototransduction and neurotransduction and facilitate retinal bipolar-photoreceptor neuronal signaling in vision. Besides synaptic stabilization, HSPG-DG interactions also stabilize basement membranes and the ECM and have specific roles in the assembly and function of the neuromuscular junction. This provides neuromuscular control of muscle systems that control conscious body movement as well as essential autonomic control of diaphragm, intercostal and abdominal muscles and muscle systems in the face, mouth and pharynx which assist in breathing processes. DG is thus a multifunctional cell regulatory glycoprotein receptor and regulates a diverse range of biological and physiological processes throughout the human body. The unique glycosylation of the αDG domain is responsible for its diverse interactions with ECM components in cell-ECM signaling. Cytoskeletal cell regulatory switches assembled by the βDG domain in its role as a nuclear scaffolding protein respond to such ECM cues to regulate cellular behavior and tissue homeostasis thus DG has fascinating and diverse roles in health and disease.
Child drowning in Indonesia: insights from parental and community perspectives and practices
Authors: Cenderadewi Muthia , Franklin Richard C , Fathana Prima B , Devine Susan G 
Published: September 2024

Abstract
Child drowning is a significant public health issue in Indonesia, however, there is insufficient understanding of the issue and its associated risk factors within communities. This qualitative study aimed to explore parental and community perceptions and practices related to child drowning in Indonesian communities, and the perceived causes and risk factors. Seven focus group discussions (n = 62) were conducted with parents of children aged under-5 years and village community leaders in seven villages across all districts of Lombok Island, West Nusa Tenggara Province of Indonesia. Participants were recruited using purposive and snowball sampling. The thematic analysis, guided by Braun and Clarke’s framework, used both deductive approaches, utilizing the Health Belief Model’s constructs and inductive approaches. Most participants were unaware of the susceptibility of their children and others in their community to drowning and of the potential severe outcomes of drowning such as injury, disability and death. Participants generally associated drowning with beaches or open seas. Unprotected wells, tubs and buckets were identified as notable risk factors for child drowning in and around the home, shaped by some experience of child drowning incidents in the community. Supervision was identified as protective factor, however, mothers were often unavailable to supervise children, and supervision responsibility was often delegated to other family and community members. This study highlights the urgent need to enhance public awareness regarding children’s susceptibility to drowning. Further exploration of local contexts and social determinants of drowning in Indonesian communities is crucial for ensuring effective water safety and drowning prevention strategies.
The Discursive Evolution of Human Rights Law: Empirical Insights from a Computational Analysis of 180,000 UN Recommendations
Authors: Keydar Renana , Shikhelman Vera , Broude Tomer , Elkobi Jonathan 
Published: September 2024

Abstract
Building on an independent database of 180,000 UN recommendations and a novel computational method, we present the most comprehensive study of human rights (HR) debates to date. We develop a unique empirical model that measures topical density of discourse. This innovative instrument measures the discursive activity of UN HR bodies through a machine-learning textual analysis of their outputs, offering a dynamic map of evolving trends in human rights, both over time (diachronically) and across different mechanisms (synchronically) within the UN HR ecosystem. Leveraging this comprehensive dataset and sophisticated computational methodologies, we identify which protected groups are central to different mechanisms’ attention and highlight the major human rights issues that have witnessed significant changes in attention. Our research presents significant findings on the density of UN HR discourse and its implications for two major debates in the field of HR law—HR proliferation and the structural critique of UN HR bodies.
Association Between SARS-CoV-2 Viral Load and COVID-19 Vaccination in 4 Phase 3 Trials
Authors: Janes Holly , Fisher Leigh H , Kee Jia Jin , Parameswaran Lalitha , Goepfert Paul A , Falsey Ann R , Ludwig James , Magaret Craig A , Gilbert Peter B , Kublin James G , Rouphael Nadine , Sobieszczyk Magdalena E , El Sahly Hana M , Baden Lindsey R , Grinsztejn Beatriz , Walsh Stephen R , Gray Glenda E , Kotloff Karen L , Gay Cynthia L , Greninger Alexander L , Tapia Milagritos D , Hammershaimb E Adrianne , Priddy Frances H , Green Justin A , Struyf Frank , Dunkle Lisa , Neuzil Kathleen M , Corey Lawrence , Huang Yunda 
Published: September 2024

Abstract
Coronavirus disease 2019 (COVID-19) vaccines reduce severe disease and mortality and may lessen transmission, measured by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load (VL). Evaluating vaccine associations in VL at COVID-19 diagnosis in 4 phase 3 randomized, placebo-controlled vaccine trials, July 2020 to July 2021, VL reductions were 2.78 log10 copies/mL (95% confidence interval [CI], 1.38–4.18; n = 60 placebo, 11 vaccine) and 2.12 log10 copies/mL (95% CI, 1.44–2.80; n = 594 placebo, 36 vaccine) for NVX-CoV2373 and mRNA-1273, respectively. Associations were not significant for AZD1222 (0.59 log10 copies/mL; 95% CI, −.19 to 1.36; n = 90 placebo, 78 vaccine) or Ad26.COV2.S (0.23 log10 copies/mL; 95% CI, −.01 to .47; n = 916 placebo, 424 vaccine). Thus, vaccines potentially decreased transmission when ancestral SARS-CoV-2 predominated.
Clinical Trials Registration. NCT04470427, NCT04505722, NCT04516746, NCT04611802.
Update on the management of ductal carcinoma in situ of the breast: current approach and future perspectives
Authors: Kanbayashi Chizuko , Iwata Hiroji 
Published: September 2024

Abstract
The standard treatment for ductal carcinoma in situ became well established through the results of several valuable clinical trials, and its therapeutic benefits have now come to be taken for granted. Ductal carcinoma in situ has an extremely good prognosis with the current treatment approach, with a 10-year breast cancer-specific survival rate of 97–98%. According to one retrospective cohort study, the breast cancer-specific survival rate of patients with low-grade ductal carcinoma in situ does not differ significantly between patients undergoing and not undergoing surgery. Some patients with ductal carcinoma in situ are not at a risk of progression to invasive cancer, but the predictors of such progression have not yet been clearly identified. Therefore, the same therapeutic strategies have been used to treat ductal carcinoma in situ and under the assumption that they have risks of invasive breast cancer, and a well-balanced risk/benefit ratio in respect of treatment has not yet been achieved. Based on the results of several recent clinical trials aimed at ensuring provision of a well-balanced treatment for patients with ductal carcinoma in situ which carries a good prognosis, de-escalation of postoperative adjuvant therapy has now begun. Currently, not only is the optimization of postoperative adjuvant therapy accelerating, but also clinical trials to de-escalate basic surgical treatments are under way. There is a possibility of achieving individualized treatment for patients with ductal carcinoma in situ of the breast with reduced treatment intervention. In this review, we present an overview of the current treatment approaches and potential future management strategies for ductal carcinoma in situ of the breast.
Relationship between a company’s adequate response to near-misses and occupational accidents: a 1-year prospective cohort study
Authors: Inagaki Mizuho , Nagata Tomohisa , Odagami Kiminori , Adi Nuri Purwito , Mori Koji ,   for the W2S-Ohpm study, Matsuyama Akiko , Yama Asumi , Yamamoto Ayaka , Ogasawara Ayana , Fujiwara Hideki , Matsuoka Juri , Tsutsumi Kakeru , Matsuyama Kazufumi , Moriya Kenta , Odagami Kiminori , Mori Koji , Sakai Kosuke , Nagata Masako , Omori Miho , Kawasumi Mika , Inagaki Mizuho , Ito Naoto , Minohara Rina , Inoue Shunusuke , Taira Suo , Mori Takahiro , Nagata Tomohisa , Sawajima Tomoko 
Published: September 2024

Abstract
Background: Near-misses in the workplace indicate potential safety hazards, and their adequate management is considered extremely important in preventing occupational accidents. However, the impact of a company’s response to near-misses on the occurrence of subsequent accidents remains unclear. This study examined the relationship between the adequacy of a company’s responses to near-misses and the occurrence of occupational accidents.
Methods: We conducted a 1-year prospective cohort study using an online self-administered questionnaire, targeting workers in Japan. The study included 2755 participants who had experienced and reported near-misses. We categorized company responses to these near-misses as adequate, inadequate, or no response. The outcome was the incidence of occupational accidents over the past year. We calculated odds ratios (ORs) and 95% CIs using multilevel logistic regression adjusting for covariates.
Results: Among all participants, 59.0% were in the adequate response group, 30.1% were in the inadequate response group, and 10.8% were in the no response group. In the multivariate-adjusted model, the ORs of the inadequate response and the no response groups were 1.53 (95% CI, 1.25-1.88; P &lt; .001) and 1.75 (95% CI, 1.32-2.33; P &lt; .001), respectively.
Conclusions: Our results suggest that the adequacy of a company’s response to near-misses reported by workers can be significantly related to the occurrence of subsequent occupational accidents. Companies need to thoroughly respond to near-misses reported by workers and adequately inform workers about the company’s safety activities. This may lead to a reduction in the number of subsequent occupational accidents.
Sink strength, nutrient allocation, cannabinoid yield, and associated transcript profiles vary in two drug-type Cannabis chemovars
Authors: Jost Ricarda , Berkowitz Oliver , Pegg Amelia , Hurgobin Bhavna , Tamiru-Oli Muluneh , Welling Matthew T , Deseo Myrna A , Noorda Hannah , Brugliera Filippa , Lewsey Mathew G , Doblin Monika S , Bacic Antony , Whelan James 
Published: September 2024

Abstract
Cannabis sativa L. is one of the oldest domesticated crops. Hemp-type cultivars, which predominantly produce non-intoxicating cannabidiol (CBD), have been selected for their fast growth, seed, and fibre production, while drug-type chemovars were bred for high accumulation of tetrahydrocannabinol (THC). We investigated how the generation of CBD-dominant chemovars by introgression of hemp- into drug-type Cannabis impacted plant performance. The THC-dominant chemovar showed superior sink strength, higher flower biomass, and demand-driven control of nutrient uptake. By contrast, the CBD-dominant chemovar hyperaccumulated phosphate in sink organs leading to reduced carbon and nitrogen assimilation in leaves, which limited flower biomass and cannabinoid yield. RNA-seq analyses determined organ- and chemovar-specific differences in expression of genes associated with nitrate and phosphate homeostasis as well as growth-regulating transcription factors that were correlated with measured traits. Among these were genes positively selected for during Cannabis domestication encoding an inhibitor of the phosphate starvation response, SPX DOMAIN GENE3, nitrate reductase, and two nitrate transporters. Altered nutrient sensing, acquisition, or distribution are likely a consequence of adaption to growth on marginal, low-nutrient-input lands in hemp. Our data provide evidence that such ancestral traits may become detrimental for female flower development and consequently overall CBD yield in protected cropping environments.
PROTAC-DB 3.0: an updated database of PROTACs with extended pharmacokinetic parameters
Authors: Ge Jingxuan , Li Shimeng , Weng Gaoqi , Wang Huating , Fang Meijing , Sun Huiyong , Deng Yafeng , Hsieh Chang- Yu , Li Dan , Hou Tingjun 
Published: September 2024

Abstract
Proteolysis-targeting chimera (PROTAC) is an emerging therapeutic technology that leverages the ubiquitin-proteasome system to target protein degradation. Due to its event-driven mechanistic characteristics, PROTAC has the potential to regulate traditionally non-druggable targets. Recently, AI-aided drug design has accelerated the development of PROTAC drugs. However, the rational design of PROTACs remains a considerable challenge. Here, we present an updated online database, PROTAC-DB 3.0. In this third version, we have expanded the database to include 6111 PROTACs (87% increase compared to the 2.0 version). Additionally, the database now contains 569 warheads (small molecules targeting the protein), 2753 linkers, and 107 E3 ligands (small molecules recruiting E3 ligases). The number of target-PROTAC-E3 ternary complex structures has also increased to 959. Recognizing the importance of druggability in PROTAC design, we have incorporated pharmacokinetic data to PROTAC-DB 3.0. To enhance user experience, we have added features for sorting based on molecular similarity and literature publication date. PROTAC-DB 3.0 is accessible at http://cadd.zju.edu.cn/protacdb/.
Identifying Network Ties from Panel Data: Theory and an Application to Tax Competition
Authors: de Paula Áureo , Rasul Imran , Souza Pedro C L 
Published: September 2024

Abstract
Social interactions determine many economic behaviours, but information on social ties does not exist in most publicly available and widely used datasets. We present results on the identification of social networks from observational panel data that contains no information on social ties between agents. In the context of a canonical social interactions model, we provide sufficient conditions under which the social interactions matrix, endogenous and exogenous social effect parameters are globally identified if networks are constant over time. We also provide an extension of the method for time-varying networks. We then describe how high-dimensional estimation techniques can be used to estimate the interactions model based on the adaptive elastic net Generalized Method of Moments. We employ the method to study tax competition across U.S. states. The identified social interactions matrix implies that tax competition differs markedly from the common assumption of competition between geographically neighbouring states, providing further insights into the long-standing debate on the relative roles of factor mobility and yardstick competition in driving tax setting behaviour across states. Most broadly, our identification and application show that the analysis of social interactions can be extended to economic realms where no network data exist.
Bone Scintigraphy in 2 Cases of Complex Regional Pain Syndrome
Authors: van der Zant Friso M. , Wondergem Maurits , Knol Remco J.J. 
Published: September 2024

Abstract
A 59-year-old woman was presented to the outpatient clinic with persistent pain after a hyperextension/inversion trauma of the ankle. Six months after the incident, a 3-phase bone scan was performed. A second patient, a 54-year-old man, was referred for a 3-phase bone scan 2 months after his right hand was twisted while using a drill. In both patients, scintigraphy showed diffuse increased uptake in the affected limb in all 3 phases. The x-rays of the affected limbs showed osteopenia. These findings are consistent with (early phase) complex regional pain syndrome.
A Comprehensive Meta-Analysis of Breast Cancer Gene Expression
Authors: Nwosu Ifeanyichukwu O. , Piccolo Stephen R. 
Published: September 2024

AbstractBackgroundTriple-negative breast cancers (TNBC) occur more frequently in African Americans and are associated with worse outcomes when compared to other subtypes of breast cancer. These cancers lack expression of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2) and have limited treatment options. To shed light on mechanisms behind these differences and suggest novel treatments, we used a meta-analytic approach to identify gene expression differences in breast tumors for people with self-reported African or European ancestry; additionally, we compared gene expression levels based on ER, PR, HER2 and TNBC status.MethodsAfter gathering and standardizing gene expression data and metadata from 106 datasets (representing 27,000 samples), we identified genes that were expressed differently between these groups via random-effects meta-analyses. To evaluate the robustness of these gene lists, we devised a novel computational methodology that uses cross validation and classification. We also computed overlaps between the most significant genes and known signaling pathways.ResultsUsing a false discovery rate threshold of 0.05, we identified genes that are known to play a significant role in their respective breast cancer subtypes (e.g.,ESR1for ER status andERBB2for HER2 status), thus confirming the validity of our findings. We also discovered genes that have not been reported previously and may be new targets for breast cancer therapy.GATA3,CA12,TBC1D9,XBP1andFOXA1were among the most significant genes for ER, PR, and TNBC. However, none of these genes overlapped with HER2 status, supporting prior research that HER2 tumors are mechanistically different from endocrine breast cancers. The genes identified from the race meta-analysis—includingDNAJC15,HLA-DPA1,STAP2,CEP68,MOGS—have not been associated previously with race-specific breast-cancer outcomes, highlighting a potential area of further research.ConclusionsWe have carried out a large meta-analysis of breast cancer gene expression data, identifying novel genes that may serve as potential biomarkers for breast cancer in diverse populations. We have also developed a computational method that identifies gene sets small enough to be analyzed and explored in future studies. This method has the potential to be applied to other cancers.
Developmental Effects of Lithium and Zinc in Planaria
Authors: Molano Alberto 
Published: September 2024

AbstractAn investigation was carried out of the stage-specific effects of lithium and zinc on planaria embryologic development. These two reagents had dramatically different effects on the morphological development of planaria: Zinc induced the formation of bifurcations or trifurcations of the head region. In contrast, lithium induced the formation of round masses of cells. The earliest embryological stages (S1 and S2, cryptic larva formation) exhibited extreme sensitivity to lithium, since the lethal dose was at least one order of magnitude lower than for subsequent stages 3-5, suggesting that beta-catenin 1 expression is tightly regulated during the initial embryologic stages and that even slightly increased activity is lethal.