bluuebunny/crossref_metadata_2025_split huggingface dataset:
THE PATHOGENIC ROLE OF MICROBIAL TRIMETHYLAMINE IN IBD ASSOCIATED INTESTINAL FIBROSIS
Authors: Massey William , Mukherjee Pranab , Nguyen Quang Tam , Mrdjen Marko , Wang Zeneng , Brown J Mark , Rieder Florian 
Published: January 2024

Abstract

INTRODUCTION
Intestinal fibrosis significantly contributes to the burden of inflammatory bowel diseases (IBD). No specific anti-fibrotic therapy is available. Two modifiable risk factors that may be exploited to limit fibrosis in IBD are the diet and gut microbiome. In the metaorganismal metabolism model, microbes metabolize dietary components to primary metabolites that may themselves signal through host receptor systems or be further metabolized to secondary metabolites by other microbes or host enzymes to exert a physiological or pathophysiological effect. We hypothesize that gut microbes profoundly influence intestinal fibrosis through small molecule metabolites and may provide novel targets to address the fibrotic burden in IBD.

METHODS
To understand how the trimethylamine-N-oxide (TMAO) pathway is affected by inflammation in the intestine, LC-MS was used to quantitate a dietary precursor, choline, primary microbial metabolite, trimethylamine (TMA), and secondary metabolite, TMAO, in mice subjected to acute DSS colitis. The cellular effects of choline, TMA, and TMAO on the deposition of fibronectin and collagen I were quantitated in primary human intestinal myofibroblasts (HIMFs). Single cell RNA-sequencing (scRNA-seq) data were interrogated to determine whether expression of the TMA-to-TMAO converting enzyme, FMO3, was downregulated in human intestinal cells of Crohn’s disease patients.

RESULTS
Acute DSS colitis showed increased TMA and reduced levels of TMAO, in colon tissue, which is consistent with reduced TMA-to-TMAO conversion by FMO3. Additionally, TMA was increased in intestinal contents, which suggests that microbial production of TMA from choline may also be upregulated during intestinal inflammation. In HIMFs, TMA, but not its dietary precursor, choline, nor the secondary metabolite, TMAO, increased the deposition of the extracellular matrix proteins fibronectin and collagen I. scRNA-seq analysis of the mesenchymal compartment of human intestine revealed expression of FMO3 specifically in the fibroblast cluster and downregulation of this expression in Crohn’s disease (CD) strictures compared to controls, an observation that could contribute to TMA accumulation in vivo.

CONCLUSION
TMA is increased in experimental colitis and activates fibroblasts towards a pro-fibrogenic phenotype. This may be mediated by reduced levels of FMO3. We next aim to measure TMAO pathway metabolites in human tissues, functionally block the TMAO pathway in vivo, and explore TMA signaling through its putative receptor, trace amine-associated receptor 5 (TAAR5).
Diet-microbe-host interaction pathways represent an untapped opportunity for therapeutic intervention in multiple human disease states, such as inflammatory bowel diseases (IBD).
Calibrating ecosystem models to support ecosystem-based management of marine systems
Authors: Bentley Jacob W , Chagaris David , Coll Marta , Heymans Johanna J , Serpetti Natalia , Walters Carl J , Christensen Villy 
Published: January 2024

Abstract
Ecosystem models, such as Ecopath with Ecosim (EwE), provide a platform to simulate intricate policy scenarios where multiple species, pressures, and ecosystem services interact. Complex questions often return complex answers, necessitating evidence and advice to be communicated in terms of trade-offs, risks, and uncertainty. Calibration procedures for EwE, which can act as a source of uncertainty and bias in model results, have yet to be explored in a comprehensive way that communicates how sensitive model outputs are to different calibration approaches. As the EwE community has grown, multiple divergent approaches have been applied to calibrate models through the estimation of vulnerability multipliers: parameters that augment the consumption rate limits of predators. Here we explore the underlying principles of vulnerability multipliers as well as existing calibration approaches and their justification. Two case studies are presented: the first explores how vulnerability multipliers emerge based on the chosen calibration approach using simulated data, while the second takes two operational EwE models (Irish Sea and Northwest Atlantic Continental Shelf) and compares their outputs when calibrated following alternate calibration approaches. We show how calibration approaches can impact model-derived advice and provide a list of best practice recommendations for EwE calibration.
Social network analysis as a tool to inform anguillid eel conservation and management
Authors: Williamson Michael J , Jacoby David M P , Bašić Tea , Walker Alan , Piper Adam T 
Published: January 2024

Abstract
Eel Management Plans demand European silver eel (Anguilla anguilla) escapement to the sea of at least 40% of that expected historically in the absence of human impacts. Landlocked lentic waterbodies, such as drinking water reservoirs, host substantial numbers of eel, which could represent a significant contribution to catchment-based conservation targets. To optimize netting strategies for eel management policies, information on their aggregation behaviour is currently needed but lacking. We performed a fine-scale acoustic tracking study to monitor the movements of 86 European eel in a UK reservoir. Social network sampling and sensitivity analyses were used to assess whether eel aggregate at scales relevant for current capture techniques. European eel were found to aggregate at spatial and temporal scales of 50 m and 2 days, respectively, which complements current capture methodologies and recommendations. Aggregations were not driven by fixed resources, indicating that other factors, such as sociality, may drive aggregation behaviour. Results also show that current netting practices could be optimized by increasing netting lengths from 50 to 80 m. In addition to aiding conservation and management protocols, these results provide an ecological foundation for exploring the role of social behaviour in this Critically Endangered species.
The Universe Inside Hall Algebras of Coherent Sheaves on Toric Resolutions
Authors: Tsvelikhovskiy Boris 
Published: January 2024

Abstract
Let $\mathfrak {g}\neq \mathfrak {s}\mathfrak {o}_{8}$ be a simple Lie algebra of type $A,D,E$ with $\widehat {\mathfrak {g}}$ the corresponding affine Kac–Moody algebra and $\mathfrak {n}_{+}\subset \widehat {\mathfrak {g}}$ is the standard positive nilpotent subalgebra. Given $\mathfrak {n}_{+}$ as above, we provide an infinite collection of cyclic finite abelian subgroups of $SL_{3}(\mathbb {C})$ with the following properties. Let $G$ be any group in the collection, $Y=G\operatorname {-}\mbox {Hilb}(\mathbb {C}^{3})$, and $\Psi : D^{b}_{G}(Coh(\mathbb {C}^{3}))\rightarrow D^{b}(Coh(Y))$ the derived equivalence of Bridgeland, King, and Reid. We present an (explicitly described) subset of objects in $Coh_{G}(\mathbb {C}^{3})$, s.t. the Hall algebra generated by their images under $\Psi $ is isomorphic to $U(\mathfrak {n}_{+})$. In case the field $\Bbbk $ (in place of $\mathbb {C}$) is finite and $\mbox {char}(\Bbbk )$ is coprime with the order of $G$, we establish isomorphisms of the corresponding “counting” Ringel–Hall algebras and the specializations of quantized universal enveloping algebras $U_{v}(\mathfrak {n}_{+})$ at $v=\sqrt {|\Bbbk |}$.
On the Hessian of Cubic Hypersurfaces
Authors: Bricalli Davide , Francesco Favale Filippo , Pietro Pirola Gian 
Published: January 2024

Abstract
In this paper, we analyze the Hessian locus associated to a general cubic hypersurface, by describing its singular locus and its desingularization for every dimension. The strategy is based on strong connections between the Hessian and the quadrics defined as partial derivatives of the cubic polynomial. In particular, we focus our attention on the singularities of the Hessian hypersurface associated to the general cubic four-fold. It turns out to be a minimal surface of general type: its analysis is developed by exploiting the nature of this surface as a degeneracy locus of a symmetric vector bundle map and by describing an unramified double cover, which is constructed in a more general setting.
Lung Function Trajectories in Mild COVID-19 With 2-year Follow-up
Authors: Iversen Katrine K , Ronit Andreas , Ahlström Magnus G , Nordestgaard Børge G , Afzal Shoaib , Benfield Thomas 
Published: January 2024

Abstract

Background
The long-term pulmonary sequelae of mild coronavirus disease 2019 (COVID-19) remains unknown. In this study, we aimed to characterize lung function trajectories in individuals with mild COVID-19 from preinfection to 2 years postinfection.

Methods
We reinvited participants 2 years after infection from our matched cohort study of the Copenhagen General Population who had initially been examined 5.4 months after infection. We repeated lung tests and questionnaires. Linear mixed models were used to estimate dynamics in lung volumes in individuals with COVID-19 patients versus uninfected controls over two intervals: from pre-infection to 6 months postinfection and 6 months postinfection to 2 years postinfection.

Results
52 individuals (48.6%) attended the 2-year examination at median 1.9 years (interquartile range, 1.8–2.4) after COVID-19, all with mild infection. Individuals with COVID-19 had an adjusted excess decline in forced expiratory volume in 1 second (FEV1) of 13.0 mL per year (95% confidence interval [CI], −23.5 to −2.5; P = .02) from before infection to 6 months after infection compared to uninfected controls. From 6 to 24 months after infection, they had an excess decline of 7.5 mL per year (95% CI, −25.6–9.6; P = .40). A similar pattern was observed for forced vital capacity (FVC). Participants had a mean increase in diffusing capacity for carbon monoxide (DLco) of 3.33 (SD 7.97) between the 6- and 24-month examination.

Conclusions
Our results indicate that mild COVID-19 infection affects lung function at the time of infection with limited recovery 2 years after infection.
Does Youth Resentment Matter in Understanding the Surge of Extremist Violence in Burkina Faso?
Authors: Tapsoba Alexandra T , Combes Jean-Louis , Combes Motel Pascal 
Published: January 2024

Abstract
The year 2019 marked an unprecedented step in violence in Burkina Faso. Before 2018, attacks targeted central government officials and expatriates. In 2019, the victims of sexual assaults, attacks, abductions or forced disappearances and assassinations were mostly local civilians. The surge in these violent attacks against civilians generates population movements. As of 2023, internally displaced people represent about 10% of the total population in the country. Several observers point to the youth of the attackers. This study investigates the motives that could drive young people to resort to violence in the country. It aims to highlight youth resentment's effect on violence against civilians in the country as of 2019. It takes advantage of one of the latest nationwide United Nations Children’s Fund (UNICEF)-sponsored surveys conducted in Burkina Faso before some parts of the country became inaccessible because of attacks. Among other information, this survey collected data on youth resentment towards the ability of their kinship to fulfil their needs in 2018, namely before the shift in violence against civilians. We merge this survey into an original dataset that gathers data from the Armed Conflict Location and Event Data Project (ACLED), mining data from the MINEX project and distance data computed using Burkina Faso's roads information. The results of an event count model show that youth resentment matters in understanding the occurrence of conflicts. Moreover, the presence of mining companies, the remoteness of infrastructures, ethnic diversity and polarisation also significantly affect violence against civilians.
Urechistachykinin I triggers mitochondrial dysfunction leading to a ferroptosis-like response in Saccharomyces cerevisiae
Authors: Han Giyeol , Lee Dong Gun 
Published: January 2024

Abstract

Aims
The purpose of this paper was to demonstrate the antimicrobial activity of urechistachykinin I (LRQSQFVGSR-NH2) extracted from Urechis unicinctus,and its mode of action dependent on mitochondrial dysfunction.

Methods and results
The antifungal activity of urechistachykinin I generated reactive oxygen species (ROS), as demonstrated with MitoSOX Red and hydroxyphenyl fluorescein (HPF). Overaccumulation of ROS caused oxidative damage to cells by inducing mitochondrial dysfunction. Mitochondrial disruption resulted in cell death, creating several hallmarks that included lipid peroxidation, glutathione oxidation, and depolarization. Moreover, the loss of mitochondria changed the calcium ion imbalance by depolarization of the mitochondrial membrane. In particular, iron accumulation and DNA fragmentation measurement determined the type of cell death. Our results indicate that urechistachykinin I treatment induced ferroptosis-like death in Saccharomyces cerevisiae via mitochondrial dysfunction.

Conclusions
Urechistachykinin I treatment induced mitochondrial dysfunction in S. cerevisiae by generating ROS, and the subsequent oxidative damage caused the ferroptosis-like cell death.
Lactobacillus rhamnosus dampens cytokine and chemokine secretion from primary human nasal epithelial cells infected with rhinovirus
Authors: Yarlagadda Tejasri , Zhu Yanshan , Snape Natale , Carey Alison , Bryan Emily , Maresco-Pennisi Diane , Coleman Andrea , Cervin Anders , Spann Kirsten 
Published: January 2024

Abstract

Aims
To investigate the effect of Lactobacillus rhamnosus on viral replication and cellular response to human rhinovirus (HRV) infection, including the secretion of antiviral and inflammatory mediators from well-differentiated nasal epithelial cells (WD-NECs).

Methods and results
The WD-NECs from healthy adult donors (N = 6) were cultured in vitro, exposed to different strains of L. rhamnosus (D3189, D3160, or LB21), and infected with HRV (RV-A16) after 24 h. Survival and adherence capacity of L. rhamnosus in a NEC environment were confirmed using CFSE-labelled isolates, immunofluorescent staining, and confocal microscopy. Shed virus and viral replication were quantified using TCID50 assays and RT-qPCR, respectively. Cytotoxicity was measured by lactate dehydrogenase (LDH) activity. Pro-inflammatory mediators were measured by multiplex immunoassay, and interferon (IFN)-λ1/3 was measured using a standard ELISA kit. Lactobacillus rhamnosus was able to adhere to and colonize WD-NECs prior to the RV-A16 infection. Lactobacillus rhamnosus did not affect shed RV-A16, viral replication, RV-A16-induced IFN-λ1/3 production, or LDH release. Pre-exposure to L. rhamnosus, particularly D3189, reduced the secretion of RV-A16-induced pro-inflammatory mediators by WD-NECs.

Conclusions
These findings demonstrate that L. rhamnosus differentially modulates RV-A16-induced innate inflammatory immune responses in primary NECs from healthy adults.
Bridging the digital health divide—patient experiences with mobile integrated health and facilitated telehealth by community-level indicators of health disparity
Authors: Daniels Brock , McGinnis Christina , Topaz Leah Shafran , Greenwald Peter , Turchioe Meghan Reading , Creber Ruth Marie Masterson , Sharma Rahul 
Published: January 2024

Abstract

Objective
Evaluate the impact of community tele-paramedicine (CTP) on patient experience and satisfaction relative to community-level indicators of health disparity.

Materials and Methods
This mixed-methods study evaluates patient-reported satisfaction and experience with CTP, a facilitated telehealth program combining in-home paramedic visits with video visits by emergency physicians. Anonymous post-CTP visit survey responses and themes derived from directed content analysis of in-depth interviews from participants of a randomized clinical trial of mobile integrated health and telehealth were stratified into high, moderate, and low health disparity Community Health Districts (CHD) according to the 2018 New York City (NYC) Community Health Survey.

Results
Among 232 CTP patients, 55% resided in high or moderate disparity CHDs but accounted for 66% of visits between April 2019 and October 2021. CHDs with the highest proportion of CTP visits were more adversely impacted by social determinants of health relative to the NYC average. Satisfaction surveys were completed in 37% of 2078 CTP visits between February 2021 and March 2023 demonstrating high patient satisfaction that did not vary by community-level health disparity. Qualitative interviews conducted with 19 patients identified differing perspectives on the value of CTP: patients in high-disparity CHDs expressed themes aligned with improved health literacy, self-efficacy, and a more engaged health system, whereas those from low-disparity CHDs focused on convenience and uniquely identified redundancies in at-home services.

Conclusions
This mixed-methods analysis suggests CTP bridges the digital health divide by facilitating telehealth in communities negatively impacted by health disparities.
Effects of dietary Nisin on growth performance, immune function, and gut health of broilers challenged by Clostridium perfringens
Authors: Yuan Hua , Bai Guangdong , Lin Yu , Yu Xilong , Yang Qinghui , Dou Renkai , Sun Hao , Zhao Zeyu , Li Zhongyu , Chen Zhihui , Xu Liangmei 
Published: January 2024

Abstract
Nisin (Ni) is a polypeptide bacteriocin produced by lactic streptococci (probiotics) that can inhibit the majority of gram-positive bacteria, and improve the growth performance of broilers, and exert antioxidative and anti-inflammatory properties. The present study investigated the potential preventive effect of Nisin on necrotic enteritis induced by Clostridium perfringens (Cp) challenge. A total of 288 Arbor Acres broiler chickens of 1-d-olds were allocated using 2 × 2 factorial arrangement into four groups with six replicates (12 chickens per replicate), including: (1) control group (Con, basal diet), (2) Cp challenge group (Cp, basal diet + 1.0 × 108 CFU/mL Cp), (3) Ni group (Ni, basal diet + 100 mg/kg Ni), and (4) Ni + Cp group (Ni + Cp, basal diet + 100 mg/kg Ni + 1.0 × 108 CFU/mL Cp). The results showed that Cp challenge decreased the average daily gain (ADG) of days 15 to 21 (P&lt;0.05) and increased interleukin-6 (IL-6) content in the serum (P &lt; 0.05), as well as a significant reduction in villus height (VH) and the ratio of VH to crypt depth (VCR) (P&lt;0.05) and a significant increase in crypt depth (CD) of jejunum (P&lt;0.05). Furthermore, the mRNA expressions of Occludin and Claudin-1 were downregulated (P&lt;0.05), while the mRNA expressions of Caspase3, Caspase9, Bax, and Bax/Bcl-2 were upregulated (P&lt;0.05) in the jejunum. However, the inclusion of dietary Ni supplementation significantly improved body weight (BW) on days 21 and 28, ADG of days 15 to 21 (P&lt;0.05), decreased CD in the jejunum, and reduced tumor necrosis factor-α (TNF-α) content in the serum (P&lt;0.05). Ni addition upregulated the mRNA levels of Claudin-1 expression and downregulated the mRNA expression levels of Caspase9 in the jejunum (P&lt;0.05). Moreover, Cp challenge and Ni altered the cecal microbiota composition, which manifested that Cp challenge decreased the relative abundance of phylum Fusobacteriota and increased Shannon index (P&lt;0.05) and the trend of phylum Proteobacteria (0.05&lt;P&lt;0.10), while Ni addition increased the relative abundance of phylum Cyanobacteria (P&lt;0.05). In conclusion, the results demonstrated that the addition of Ni effectively mitigated the negative impact of Cp challenge-induced the damage of growth performance and intestine in broilers via reducing inflammatory responses and intestinal apoptosis and modulating cecal microbial composition.
Stress indicators in dairy cows adapting to virtual fencing
Authors: Fuchs Patricia , Stachowicz Joanna , Schneider Manuel K , Probo Massimiliano , Bruckmaier Rupert M , Umstätter Christina 
Published: January 2024

Abstract
Virtual fencing (VF) enables livestock grazing without physical fences by conditioning animals to a virtual boundary delimited with an audio tone (AT) and an electric pulse (EP). The present study followed the adaptation process of lactating dairy cows to a VF system with changing virtual boundaries and investigated its impact on animal welfare. Twenty cows were divided into stratified groups (2× VF; 2× electric fencing, EF) of five individuals. Each group grazed half-days in a separate EF paddock of comparable size during 3 d of acclimation (P0), followed by 21, 14, 14, and 7 d of experimental treatment (P1 to P4). At the start of the trial, all cows were equipped with an IceQube pedometer (Peacock Technology Ltd, Stirling, UK) and a VF collar (Nofence AS, Batnfjordsøra, Norway). During P0, cows were accustomed to their first paddock with a deactivated virtual boundary and wearing the sensors. In P1 to P4, an active virtual boundary for the VF groups, and a second EF for the EF groups was set up parallel to an outer EF within their paddock. Throughout the trial, the sensors continuously tracked cow positions and activity behavior at 15-min intervals. From P1 onwards, the VF collars additionally recorded each AT and EP per cow with a georeferenced time stamp. During P0 to P4, daily feed intake, body weight, and milk yield were recorded in the barn. A total of 26 milk samples were collected per cow to determine milk cortisol levels. Behavioral observations were conducted for 2 h on day 23 to record agonistic behaviors, vocalizations, and excretions. The total number of stimuli per cow ranged from 37 to 225 ATs (mean ± SD: 1.9 ± 3.3 per day) and 3 to 11 EPs (mean ± SD: 0.1 ± 0.7 per day) throughout the trial. The maximum number of EPs per day was 8 for an individual cow and occurred once on D1. Mean EP/AT decreased by 55% during the first three half-days of grazing and with each paddock change from 0.2 EP/AT in week 1 to 0.03, 0.02, and 0 EP/AT in weeks 4, 6, and 8, respectively. Linear and generalized mixed effects models revealed that milk yield and cortisol, feed intake, body weight, and activity and lying behavior did not significantly differ between VF and EF groups. A higher number of agonistic behaviors were observed in the VF groups when the VF system was activated. However, due to the short observation periods only few contacts were observed in total. Overall, all cows adapted to the VF system without evidence of lasting adverse effects on animal welfare.