bluuebunny/crossref_metadata_2025_split huggingface dataset:
Broadband surface wave manipulation by periodic barriers in unsaturated soil
Authors: Wu Liangliang , Shi Zhifei 
Published: July 2024

Periodic wave barriers have been widely used to manipulate elastic waves propagating in saturated and single-phase soil due to their attenuation zone properties. However, it is difficult to promote application of periodic barriers in unsaturated soils due to their complex constitutive relationship. In this study, manipulation of surface waves by periodic in-filled trench barriers in unsaturated soil has been studied based on the periodic theory. The dispersion relations of a periodic structure for surface waves in unsaturated soil are determined. The attenuation mechanism of evanescent surface waves is revealed. Next, the effects of several key parameters of unsaturated soil on the attenuation zones of the periodic in-filled trench barriers are comprehensively discussed. It is found that in a particular range for material parameter, the surface waves are attenuated over the entire frequency range due to the viscosity of fluid. Finally, a periodic in-filled trench barrier is designed according to a field test of ground vibration induced by a train, and its performances in mitigating surface waves propagating in unsaturated and saturated soils are conducted and compared by conducting analysis in time domain. This investigation provides a new insight for manipulating surface waves by periodic barriers.
This article is part of the theme issue ‘Current developments in elastic and acoustic metamaterials science (Part 1)’.
Successive pattern in winter wheat main stem structure modeling
Authors: Yin Jingru , Zhu Chen , Li Qing , Li Pengyan , Fan Chaoyu , Gao Yangmingrui 
Published: July 2024

1.AbstractWith the rise of research on functional structural plant models (FSPMs), it is particularly important to realistically describe the structural traits of a plant. In 3D FSPMs, the true structural information of the canopy can make the model’s estimation of functional traits more accurate. Since canopy is the medium of the crop stands that sense and respond to the external environment, accurate estimation of detailed organ sizes in crop canopy is crucial, and current FSPMs still need to be improved. Here the structure of wheat (Triticum aestivum) was measured in detail at the phytomer level. Dataset was built which covers a set of ∼100 cultivars and 11 site-year under various field managements such as sowing density, inter-row, nitrogen fertilizer and sowing date. The relationships of successive phytomer sizes were quantified and the variance was analyzed for each independent experiment, only site was found as a significant impact factor. A conceptual model based on the successive pattern was proposed and validated for detailed final phytomer sizes. Then we coupled the meteorology data - the ratio of average daily gross radiation and temperature during the emergence and architecture mature with the model. The validation has taken place three times to emphasize model’s independent of cultivars, sites dependent and the ability of model parameters deriving from environmental factors, respectively. The results revealed the feasibility of the newly built wheat main stem structure model with the R2higher than 0.85. Compared with ADEL-Wheat and Sirius Quality, the model achieved better performance in blade width and blade area estimation. According to the concise and easily acquired parameters of this model, it has potential for high throughput phenotyping detail wheat canopy structure. Previous work on the relationship between blade width and circumference of apex shoot in maize illustrated that the cell number was the most likely explanation for this pattern, which means the same work holds for similar crops.
Melanocortin system activates carotid body arterial chemoreceptors in hypertension
Authors: Pauza Audrys G. , Thakkar Pratik , Shen Xin , Felippe Igor , Roßmann Kilian , Oya Manami , Nakamura Kazuhiro , Broichhagen Johannes , Hodson David J. , Pauza Dainius H. , Murphy David , Paton Julian F.R. 
Published: July 2024

AbstractBackgroundThe body’s internal milieu is controlled by a system of interoceptors coupled to motor outflows that drive compensatory adaptive responses. These include the arterial chemoreceptors, best known for sensing arterial oxygen. In cardiometabolic diseases, such as essential hypertension, the carotid bodies (CB) exhibit heightened reflex sensitivity and tonic activity without an apparent stimulus. The mechanisms behind CB sensitization in these conditions are not well understood.MethodsGuided by functional genomics, a range of functional assays is used to interrogate downstream intracellular and interorgan signalling pathways involved in arterial chemosensory function.ResultsHere, we report the presence of the Melanocortin 4 receptor (MC4R) in the mammalian CB and show its elevated expression in experimental hypertension. We demonstrate that melanocortin agonists activate arterial chemosensory cells, modulating CB chemosensory afferent drive to influence both resting and chemoreflex-evoked sympathetic and ventilatory activity. Transcriptional analysis of hypertensive CB implicates the activation of the Mash1 (Ascl1) regulatory network in driving elevatedMc4rexpression.ConclusionsCollectively, our data indicate a primarily pathophysiological role of melanocortin signalling in arterial chemosensation, contributing to excess sympathetic activity in cardiometabolic disease.
EFFECT OF TOBACCO CHEWING ON METABOLIC RISK FACTORS IN NORTH INDIAN ADULT MALES
Authors: Gupta Abhishek , Singh Arun Kumar , Gupta Vani 
Published: July 2024

AbstractTobacco consumption remains one of the leading preventable causes of morbidity and mortality worldwide. Tobacco use is a major public health concern despite widespread public health efforts and strict regulations. Within the framework of the NCEP ATP-III criteria, the goal of the study was to investigate the effects of tobacco consumption on metabolic risk factors in young adult males. This case-control study comprised of 50 male participants aged 18 to 30 years; 25 male tobacco chewers were assigned to the study group, and 25 males who did not chew tobacco (non-tobacco chewers) were assigned to the control group. Anthropometric and metabolic risk factors that were compared between the study and control groups included waist circumference (WC), blood glucose, serum level of triglycerides (TG) and total cholesterol (TC), Insulin resistance (IR) and the homeostatic model assessment (HOMA) index, which is a measure of IR. The results of the study demonstrated that compared to non-tobacco chewers, tobacco chewers had significantly higher glucose (p=0.026), TC (p=0.0013), insulin (p=0.015), and IR (p=0.027). However, there were no discernible variations in HDL, VLDL, and TG levels, or WC. Nine male tobacco chewers and eight male non-tobacco chewers from the respective groups exhibited metabolic risk based on the NCEP ATP-III criterion of three out of five risk factors. Thus, we draw the conclusion that while tobacco chewers’ lipid profiles stayed similar, their TC, hyperglycaemia, hyperinsulinemia, and HOMA Index increased, making them more susceptible to the onset of metabolic syndrome.
Limitations in mitochondrial programming restrain the differentiation and maturation of human stem cell-derived β cells
Authors: Lietzke Anne C. , Bealer Elizabeth , Crumley Kelly , King Jessica , Stendahl Ava M. , Zhu Jie , Pearson Gemma L. , Levi-D’Ancona Elena , Henry-Kanarek Belle , Reck Emma C. , Arnipalli Manikanta , Sidarala Vaibhav , Walker Emily M. , Pennathur Subramaniam , Madsen Jesper G.S. , Shea Lonnie D. , Soleimanpour Scott A. 
Published: July 2024

ABSTRACTPluripotent stem cell (SC)-derived islets offer hope as a renewable source for β cell replacement for type 1 diabetes (T1D), yet functional and metabolic immaturity may limit their long-term therapeutic potential. Here, we show that limitations in mitochondrial transcriptional programming impede the formation and maturation of SC-derived β (SC-β) cells. Utilizing transcriptomic profiling, assessments of chromatin accessibility, mitochondrial phenotyping, and lipidomics analyses, we observed that SC-β cells exhibit reduced oxidative and mitochondrial fatty acid metabolism compared to primary human islets that are related to limitations in key mitochondrial transcriptional networks. Surprisingly, we found that reductions in glucose- stimulated mitochondrial respiration in SC-islets were not associated with alterations in mitochondrial mass, structure, or genome integrity. In contrast, SC-islets show limited expression of targets of PPARIZ and PPARγ, which regulate mitochondrial programming, yet whose functions in β cell differentiation are unknown. Importantly, treatment with WY14643, a potent PPARIZ agonist, induced expression of mitochondrial targets, improved insulin secretion, and increased the formation and maturation of SC-β cells bothin vitroand following transplantation. Thus, mitochondrial programming promotes the differentiation and maturation of SC-β cells and may be a promising target to improve β cell replacement efforts for T1D.
Whole genome sequencing of 76 Mexican Indigenous reveals recent selection signatures linked to pathogens and diet adaptation
Authors: Miron-Toruno F. , Morett E. , Aguilar-Ordonez I. , Reynolds A.W. 
Published: July 2024

AbstractWhole genome scans for natural selection signatures across Mexican Indigenous (MI) Populations remain underrepresented in the literature. Here, we conducted the first comparative analysis of genetic adaptation in MI populations using whole genome sequencing (WGS) data from 76 individuals representing 27 different ethnic groups in Mexico. We divided the cohort into Northern, Central, and Southern populations and identified signals of natural selection within and across populations. We find evidence of adaptation to pathogenic environments in all our populations, including significant signatures in the Duffy blood group gene in Central MI populations. Despite each region exhibiting unique local adaptation profiles, selection signatures onARHGAP15, VGLL4, LINGO2, SYNDIG1, andTFAP2Bwere common to all populations. Our results also suggest that selection signatures falling within enhancers or promoters are usually connected to non-coding features, with notable exceptions likeARHGAP15andGTDC1. This paper provides new evidence on the selection landscape of Mexican Indigenous Populations and lays the foundation for additional work on Mexican phenotypic characterization.Significance statementPrevious research has identified distinct patterns of genomic adaptation across the different regions of Mexico, highlighting evidence of natural selection within metabolic and immune-related genes. However, the characterization of the Mexican selection landscape from a whole-genome perspective remains unexplored. Here, we conducted the first whole-genome scan for natural selection in 76 Mexican Indigenous individuals from 27 different ethnic groups divided into Northern, Central, and Southern populations. Our findings revealed distinct local adaptation profiles for each Mexican region, with different evidence of adaptation to pathogenic environments across these groups. In contrast, all populations had common selection signatures onARHGAP15, VGLL4, LINGO2, SYNDIG1, andTFAP2B. This paper provides new evidence on the genetic basis of adaptation of Indigenous groups in Mexico. Moreover, it provides a foundation for additional work on Mexican phenotypic characterization.
Proliferative arrest induces neuronal differentiation and innate immune responses in normal and Creutzfeldt-Jakob Disease agent (CJ) infected rat septal neurons
Authors: Pagano Nathan , Perez Gerard Aguilar , Garcia-Milian Rolando , Manuelidis Laura 
Published: July 2024

ABSTRACTRat post-mitotic septal neurons, engineered to proliferate and arrest under physiological conditions can be maintained for weeks without cytotoxic effects. Nine independent cDNA libraries were made to follow arrest-induced neural differentiation and innate immune responses in normal uninfected and CJ agent infected septal neurons for weeks. CJ infection created a non-productive latent (CJ-) and a productive (CJ+) high infectivity model (10 logs/gm). Arrest of normal uninfected cells upregulated a plethora of anti-proliferative transcripts and known neuronal differentiation transcripts (e.g., Agtr2, Neuregulin-1, GDF6, SFRP4 and Prnp). Notably, many activated IFN innate immune genes were simultaneously upregulated (e.g., OAS1, RTP4, ISG20, GTB4, CD80, cytokines, chemokines and complement) along with clusterin (CLU) that binds misfolded proteins. Arrest of latently infected CJ-cells induced even more profound global transcript differences. CJ+ cells markedly downregulated the anti-proliferative controls seen in arrested normal cells. CJ+ infection also suppressed neuronal differentiation transcripts, including Prnp which is essential for CJ agent infection. Additionally, IFN and cytokine/chemokine pathways were also strongly enhanced. Analysis of the 342 CJ+ unique transcripts revealed additional innate immune and anti-viral-linked transcripts, e.g., Il17, ISG15, and RSAD2 (viperin). These data show: 1) innate immune transcripts are produced by normal neurons during differentiation; 2) CJ infection enhances and expands anti-viral responses; 3) non-productive latent infection can epigenetically imprint many proliferative pathways to thwart complete arrest. Consequently, human blood and intestinal myeloid peripheral cells that are latently infected (silent) for many years may be stimulated in vitro to produce CJ+ linked diagnostic transcripts.
Protein Set Transformer: A protein-based genome language model to power high diversity viromics
Authors: Martin Cody , Gitter Anthony , Anantharaman Karthik 
Published: July 2024

AbstractExponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperformed other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrated protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.
Investigation of Intestinal Bacteria-binding Monoclonal Antibodies Derived from Rabbit Single B Cells
Authors: Anwar Khairil , Kaneko Shota , Kawakita Itsuki , Adinegoro Daffa Sean , Kihara Monami , Ojima-Kato Teruyo , Nakano Hideo 
Published: July 2024

AbstractImmunoglobulins in the intestine have been reported to play a pivotal role in regulating the composition and function of intestinal microbiota. However, the relationship between monoclonal antibodies (mAbs) and intestinal bacteria remains elusive due to the lack of analytical methods. Here we report the utilization of Ecobody technology, a single B cell technique developed by our group, for obtaining and investigating intestinal bacteria-binding mAbs derived from single B cells of a non-immunized rabbit.Bacteroides cellulosilyticusisolated from the rabbit stool was used as the antigen for selecting B cells, followed by antibody gene amplification, mAb expression in cell-free protein synthesis (CFPS), and activity evaluation. For large-scale and cost-effective production of the selected mAb, we employed the secretion expression system for antigen-binding fragment (Fab) usingBrevibacillus choshinensis, and successfully yielded ∼2.0 mg/L-culture of purified antibody with high affinity to the target bacterium. Purified Fab showed binding activity towards various intestinal bacteria, suggesting the broad specificity toward intestinal bacteria-associated antigens.
Alzheimer’s disease clinical decision points for two plasma p-tau217 laboratory developed tests in neuropathology confirmed samples
Authors: Mammel Anna E. , Hsiung Ging-Yuek Robin , Mousavi Ali , Hallett Kelsey , Mackenzie Ian R. , Hirsch-Reinshagen Veronica , Biehl Don , Gill Pradip , Encarnacion Mary , Frykman Hans 
Published: July 2024

ABSTRACTINTRODUCTIONWe evaluated the diagnostic performance of two commercial plasma p-tau217 immunoassays compared to CSF testing and neuropathology.METHODS170 plasma samples from University of British Columbia Hospital Clinic for Alzheimer’s (AD) and Related Disorders were analyzed for p-tau217 using Fujirebio and ALZpath assays. Decision points were determined using CSF testing and autopsy findings as the standard.RESULTSFujirebio and ALZpath p-tau217 had similar overall analytical and clinical performance, with distinct decision points for each assay. Based on autopsy finding, both p-tau217 assays identified individuals with AD from other neurodegenerative diseases (ALZpath AUC = 0.94, Fujirebio AUC= 0.90). The ALZpath assay detected AD pathology at milder disease stages compared to the Fujirebio assay.DISCUSSIONOur study reinforces the clinical utility of plasma p-tau217 as an AD biomarker. Differences in test performance and clinical decision points suggest an assay specific diagnostic approach is required for plasma p-tau217 in clinical practice.
BPF-GILD study: an observational cohort study of UK pigeon fanciers
Authors: Allen Richard J , Wellens-Mensah Jude , Leavy Olivia C , Bourke Stephen , Henderson Will , Smith Howard , Johnson Emma , Marks Daniella , Myat Ye , Rafique Cecillia , Parcesepe Gina , Hernandez-Beeftink Tamara , Guillen-Guio Beatriz , Cheng Eric , Chan Carmen , Clark Gabrielle , Dickson Stuart , Pearson Andrew , Embley Mathew , Lynch Phillip , Boyd Gavin , Gooptu Bibek , Ji Yuan , McSharry Charles , Wain Louise V , Spears Mark 
Published: July 2024

AbstractIntroductionHypersensitivity pneumonitis (HP), a common interstitial lung disease (ILD), comprises two distinct but related forms, acute and fibrotic (fHP). HP is classically described as a disease triggered by antigen exposure. However, a wide range of triggers are described and in ∼50% of cases no cause is identified, rendering observational studies challenging. The British Pigeon Fanciers Genetics of ILD (BPF-GILD) study aims to address this by studying a population with a clear history of exposure to a common trigger.MethodsParticipants were recruited from 2019 to 2023 at large UK Pigeon Fancier meetings. Each participant performed spirometry, completed a standardised questionnaire with a doctor, and provided blood samples. We present our baseline data in this manuscript.Results417 subjects were recruited from four shows. The median age of the cohort was 63 years, 95% were male and 94% self-reported white ethnicity. The median number of pigeons kept was 80 [range 4-800], with fanciers spending 14 hours per week [1-100] in their lofts. 52% of participants had occupational dust exposures.49% of the cohort reported at least one respiratory symptom related to loft exposure. 14% had a history of ILD and these individuals had more loft-related respiratory symptoms, poorer lung function, and appeared more likely to wear a mask with their pigeons than those without (74% vs 57%). 41% of participants had positive responses to questions employed to detect occult connective tissue disease in ILD clinics.DiscussionOur well characterised cohort of pigeon fanciers commonly experience acute HP symptoms and are likely to be at increased risk of fHP. Subsequent work using stored samples will enable us to determine genetic risk factors and pathways relevant to the development of fHP.
Two Billion Infected: An Inexpensive Method to Measure Latent Toxoplasmosis and its Economic Consequences*
Authors: Achtziger Anja , Alós-Ferrer Carlos , Garagnani Michele 
Published: July 2024

AbstractOver two billion people worldwide are infected with the protozoan Toxoplasma gondii, which influences human behavior and cognition. Standard diagnosis methods involve costly medical tests, which prevents widespread testing and hinders the study of the infection’s effects. We propose and validate an inexpensive and easy-to-deploy diagnostic method for latent Toxoplasmosis infections using response times and finite-mixture models. A clinical study showed that the method is sensitive and accurate. A large, representative UK study showed that the infection’s consequences are relevant and pervasive, both economically (decrease in yearly income and employment) and behaviorally (increase in risky behaviors, stress, and depression).
Estimating Species-specific U.S. Waterfowl Harvest
Authors: Augustine Ben C. , Royle J. Andrew 
Published: July 2024

AbstractThe U.S. Fish and Wildlife Service monitors species-specific waterfowl (ducks, seaducks, geese, and brant) harvest through two hunter surveys, one that estimates the total harvest for each waterfowl group, and a second that estimates the species composition of each waterfowl group. Point estimates for species-specific harvest can be computed by multiplying the estimated total harvest by the estimated proportion of the total harvest of each species. However, to date, no uncertainty estimates have been available. Here, we combine these two data sources to provide species-specific harvest estimates at the state and flyway level while characterizing the uncertainty via Bayesian estimation. We take a similar approach to Smithet al. (2022), providing both estimates that treat yearly data as independent and estimates that share information across years via a random walk process. We then discuss the advantages and disadvantages of each approach.
Caught in the act of triplication: TNF superfamily
Authors: Menon Namita , K Kaushiki , Goswami Moushmi , Singh Anmol , Srinivasan Subhashini 
Published: July 2024

ABSTRACTThe first sighting of a homolog of tumor necrosis factor in invertebrates,DmEiger, was in 2002 fromDrosophila melanogasterwith a potential role in apoptosis. More recently, the presence of a Eiger homolog along with homologs of all the genes from TNF-TNFR signaling pathway in a malaria vector, suggests the existence of this modality of signaling since 700 mya. Furthermore, a comparison of the crystal structure configuration of DmEiger bound to its receptor DmGrnd and that of HuTNF-HuTNFR complex predates the ligand-receptor configuration to 700 mya. In human, there are 29 paralogs of TNF superfamily with 19 receptor genes suggesting active evolution of TNF-TNFR system within species. The recent explosion in proteomes of thousands of organisms from species covering every branch of Metazoa provides a rich source to study the mode of expansion of this system within species. Here, we have studied 148 near-complete proteomes under each major phylum and report presence/absence of TNF-TNFR homologs across the animal kingdom. The system is lost in Nematoda, Tardigrada, Chelicerates, and parasitic species under Platyhelminthes. By interrogating the topologies of genes containing multiple homologs of TNF and TNFR domains in species under Cnidaria, Mollusca, Crustacea, and Annelida, we hypothesize that heterotrimeric ligand oligomerization for signaling may have predated function expansion by homotrimerization followed by receptor evolution in a yin-yang manner.