bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bovine Herpes Virus Type 1 (BoHV-1) seroprevalence, risk factor and Bovine Viral Diarrhoea (BVD) co-infection analysis from Ireland
Authors: Barrett D. , Lane E. , Lozano J. M. , O’Keeffe K. , Byrne A. W. 
Published: January 2024

AbstractSurveillance of endemic pathogens is essential for disease control, providing an evidence base for policy and advice. Bovine Herpes Virus Type 1 (BoHV-1), the causative agent of Infectious Bovine Rhinotracheitis (IBR), has been found to have high seroprevalence within the Irish cattle population. The aim of the present study was to establish seroprevalence levels for culled cattle in Ireland aged < 30 months and to establish whether BVD exposure and other factors was associated with BoHV-1 exposure. We employed random effects logit models coupled with repeated bootstrap sampling to provide robust estimates. The final dataset contained results for 5273 animals tested over two study years, 2018 and 2020. The animal-level seroprevalence of BoHV-1 was 21.43% (1130/5273; 95%CI: 20.32–22.53%). Univariable analysis suggested that BoHV-1 seropositivity risk was associated with BVDV serodiagnosis status, age, sex, year sampled, herd type, herd-size, and metrics of movement into the herd. Final random-effects multivariable models suggested increased risk associated with increasing herd size of the last herd, movements made by animals during the previous year, and the year the animal was sampled. Despite BVDV status and sex being retained in the final model, repeated bootstrap sampling of the regression model to estimate biased-corrected 95%CI suggested that these associations were not robust. The overall apparent prevalence of BoHV-1 exposure for culled cattle in Ireland declined in 2020 relative to 2018 (from 23.32 to 17.61%). Herd-size and the movement of animals were found to be important factors associated with animal-level risk, but there was less statistical support for sex-based or BVDV status associations.
A method for phenotypic evaluation of grapevine resistance in relation to phenological development
Authors: Schumacher Stefan , Mertes Caroline , Kaltenbach Thomas , Bleyer Gottfried , Fuchs René 
Published: January 2024

AbstractFungus-resistant grapevine cultivars, so called PIWIs, are characterized by increased resistance to powdery mildew and downy mildew. However, in order to maintain the durability of resistance in these new grape cultivars, targeted fungicide treatments are recommended. For ideal schedule of these treatments, it is necessary to recognize the most sensitive organs of the grape. This study introduces a method for phenotypic evaluation of Plasmopara viticola resistance in grape clusters under controlled and standardized conditions during phenological development over the entire season. The approach was validated with the traditional cultivar Pinot Noir and the PIWIs Cabernet Cortis (Rpv3.3, Rpv10), Solaris (Rpv3.3, Rpv10) and Souvignier Gris (Rpv3.2). All cultivars were susceptible during the early stages of development up to flowering, and resistance levels increased as phenological development progressed. Cabernet Cortis and Solaris clusters were susceptible until fruit development (BBCH 71–73) when they became almost completely resistant. No differences between Souvignier Gris and Pinot Noir were detected until berries were pea-sized (BBCH 75) when P. viticola resistance of Souvignier Gris clusters increased significantly. Ontogenetic resistance in Pinot Noir was detected at berry touch (BBCH 77–79) and clusters of this cultivar were almost completely resistant at the beginning of ripening (BBCH 81–83). These results indicate that the approach presented is suitable for determining the resistance of grape cultivars at different stages of development. Consequently, in the future, fungicide applications can be adjusted more precisely to the resistance level of a grape cultivar during the growing season.
Enhanced matrix inference with Seq2seq models via diagonal sorting
Authors: Peng Wei , Wang Yisong , Wu Maonian 
Published: January 2024

AbstractThe effectiveness of sequence-to-sequence (seq2seq) models in natural language processing has been well-established over time, and recent studies have extended their utility by treating mathematical computing tasks as instances of machine translation and achieving remarkable results. However, our exploratory experiments have revealed that the seq2seq model, when employing a generic sorting strategy, is incapable of inferring on matrices of unseen rank, resulting in suboptimal performance. This paper aims to address this limitation by focusing on the matrix-to-sequence process and proposing a novel diagonal-based sorting. The method constructs a stable ordering structure of elements for the shared leading principal submatrix sections in matrices with varying ranks. We conduct experiments involving maximal independent sets and Sudoku laws, comparing seq2seq models utilizing different sorting methods. Our findings demonstrate the advantages of the proposed diagonal-based sorting in inference, particularly when dealing with matrices of unseen ranks. By introducing and advocating for this method, we enhance the suitability of seq2seq models for investigating the laws of matrix inclusion and exploring their potential in solving matrix-related tasks.
Statistical classification of treatment responses in mouse clinical trials for stratified medicine in oncology drug discovery
Authors: Savel Hélène , Meyer-Losic Florence , Proust-Lima Cécile , Richert Laura 
Published: January 2024

AbstractTranslational oncology research strives to explore a new aspect: identifying subgroups that exhibit treatment response even during pre-clinical phases. In this study, we focus on PDX models and their implementation in mouse clinical trials (MCT). Our primary objective was to identify subgroups with different treatment responses using Latent Class Mixed Model (LCMM).We used a public dataset and focused on one treatment, encorafenib, and two indications, melanoma and colorectal cancer, for which efficacy depends on a specific mutation BRAF V600E. One LCMM per indication was implemented to classify treatment responses at the PDX level, analyzing the growth kinetics of treated tumors and matched controls within the PDX models. A simulation study was carried out to explore the performance of LCMM in this context. For both applications, LCMM identified classes for which the higher the proportion of mutated BRAF V600E PDX models the greater the treatment effect, which is aligned with encorafenib use recommendations. The simulation study showed that LCMM could identify classes with large differences in treatment effects. LCMM is a suitable tool for MCT to explore treatment response subgroups of PDX. Once these subgroups are defined, characterization of their phenotypes/genotypes could be performed to explore treatment response predictors.
Three-dimensional fine crust-mantle structure imaging and structural characteristics of Bohai Sea
Authors: Ma Yong , Gao Lei , Dong Demiao 
Published: January 2024

AbstractThis study used the consistency-constrained double-difference tomography method to invert 3D fine structure models of Vp, Vs, Vp/Vs at depths above 60 km, and precise relocation parameters of earthquakes in the Bohai Sea. According to the results, the velocity structures of P-wave and S-wave in the Bohai Sea area were highly similar and demonstrated noticeable lateral non-uniformity. The crust beneath the Tanlu Fault displayed a clear stratification structure, with a continuous velocity transition in the middle of the crust. The intricate crustal structure beneath the Zhangpeng Fault displayed high-velocity bodies in the crust and low-velocity anomalous zones connected to the top of the mantle in the lower section of the crust. The structural pattern in the deep crust of the Bohai Sea controls the occurrence characteristics of the Zhangpeng Fault and the Tanlu Fault. The earthquakes in the Bohai Sea area were concentrated mainly in the southern part near the Zhangpeng Fault. There is a good correspondence between the relocated earthquakes and velocity structure. There are many significant differences in crustal structure between the north and south of the Bohai Strait, and there are obvious velocity anomalies in the middle and upper crust. The distribution shape of high Vp/Vs value indicates that mantle material migration has occurred at the bottom of the crust. This paper provided important reference for further research on the relationship between deep tectonic features and tectonic activity in the North China Craton.
Association of PFDeA exposure with hypertension (NHANES, 2013–2018)
Authors: Li Jie , Ye Suling , Zhao Zeyuan , Xue Zhao , Ren Shupeng , Guan Yue , Sun Chuang , Yao Qiying , Chen Liang 
Published: January 2024

AbstractPerfluoroalkyl and polyfluoroalkyl substances (PFASs) is a series of artificial compounds which is associated with human health. However, there are few studies on the relationship between PFASs and hypertension. In this study, we examined the association between different kinds of PFASs and hypertension. Multivariable logistic regression and subgroup analysis were adopted to assess the associations between PFASs and hypertension. Spline smoothing plots and linear regression were used to assess the relationship between PFASs and blood pressure. We found a positive association between serum PFDeA concentrations and the prevalence of hypertension after fully adjusting confounders (OR = 1.2, P = 0.01), but other types of PFASs showed no positive results. Subgroup analysis stratified by ethnicity showed there was a stronger relationship among non-Hispanics than Hispanics. Serum PFDeA concentrations were positively associated with systolic pressure (β = 0.7, P< 0.01) and diastolic blood pressure (β = 0.8, P< 0.01) among non-Hispanics who did not take antihypertensive drugs. This study showed that PFDeA exposure was associated with hypertension in Americans who identify as non-Hispanic. There was a positive association between PFDeA and blood pressure in non-Hispanic Americans who did not take antihypertensive drugs.
Microfluidically frequency-reconfigurable compact self-quadruplexing tunable antenna with high isolation based on substrate integrated waveguide
Authors: Barik Rusan Kumar , Koziel Slawomir 
Published: January 2024

AbstractThis communication presents a novel concept of microfluidically frequency-reconfigurable self-quadruplexing tunable antenna for quad-band applications. At the initial design stage, a substrate-integrated square cavity is divided into four unequal quarter-mode cavity resonators by inserting an X-shaped slot on the top surface of the cavity. Applying four 50-Ω microstrip feed-lines to these four quarter-mode cavity resonators enables quad-band operation with self-quadruplexing capabilities. The feed lines are organized orthogonally and off-center, which leads to port isolation greater than 32.3 dB. An equivalent network model is developed to validate the proposed antenna. To realize frequency reconfigurability, two microfluidic channels corresponding to each port are created by engraving the bottom surface of the cavity. To create a reconfigurable self-quadruplexing antenna, the channels are either filled with air or dielectric liquids of higher permittivity, so that the design offers independent tunability of the operating frequencies. As a proof of concept, the prototype of a self-quadruplexing tunable antenna is fabricated and validated through measurements. The antenna prototype occupies a footprint area of 0.37λg2. The design exhibits frequency tuning ranges of 350 MHz (8.3%), 500 MHz (10.3%), 610 MHz (11.2%), and 845 MHz (14.1%) for the first, second, third, and fourth operating bands, respectively. In all bands and across the entire tuning range, the realized gains of the designed antenna exceed 4.05 dBi. The electromagnetic modeling responses agree extremely well with the measured characteristics.
Range of protein induced by vitamin K absence or antagonist-II levels in neonates at birth
Authors: Sameshima Tomohiro , Ashina Mariko , Fukuda Takuya , Kido Takumi , Abe Shinya , Watanabe Yuko , Sato Itsuko , Yano Yoshihiko , Tanimura Kenji , Nagase Hiroaki , Nozu Kandai , Fujioka Kazumichi 
Published: January 2024

AbstractProtein induced by vitamin K absence or antagonist-II (PIVKA-II) is avitamin K (VK) deficiency indicator in neonates. However, PIVKA-II detection frequency in neonatal blood at birth and the correlation between PIVKA-II and gestational age are unclear. We retrospectively analyzed infants admitted to our institution between June 1, 2018, and March 31, 2022, whose clinical and PIVKA-II data were available, and classified them into preterm and term infant groups. Overall incidence of PIVKA-II-positive cases (≥ 50 mAU/mL) was 42.8%, including 0.6% apparent VK deficiency (≥ 5000 mAU/mL), 3.1% experimental VK deficiency (1000–4999 mAU/mL), and 10.7% latent VK deficiency (200–999 mAU/mL) cases. Incidence of PIVKA-II-positive cases was significantly higher in the term group than in the preterm group (49.4% vs. 29.7%, p < 0.001). Gestational age correlated with PIVKA-II levels (r2 = 0.117, p < 0.0001). Median serum PIVKA-II levels and incidence of PIVKA-II-positive cases (≥ 50 mAU/mL, 16.4%) were lower at 5 days after birth than at birth, possibly reflecting the postnatal VK prophylaxis impact. Only one infant was diagnosed with VK deficiency bleeding (PIVKA-II levels, at birth: 10,567 mAU/mL; at day 5: 2418 mAU/mL). Thus, serum PIVKA-II levels after birth weakly correlated with gestational age. VK deficiency was more common in term infants than in preterm infants.
A Pregnancy and Childhood Epigenetics Consortium (PACE) meta-analysis highlights potential relationships between birth order and neonatal blood DNA methylation
Authors: Li Shaobo , Spitz Natalia , Ghantous Akram , Abrishamcar Sarina , Reimann Brigitte , Marques Irene , Silver Matt J. , Aguilar-Lacasaña Sofía , Kitaba Negusse , Rezwan Faisal I. , Röder Stefan , Sirignano Lea , Tuhkanen Johanna , Mancano Giulia , Sharp Gemma C. , Metayer Catherine , Morimoto Libby , Stein Dan J. , Zar Heather J. , Alfano Rossella , Nawrot Tim , Wang Congrong , Kajantie Eero , Keikkala Elina , Mustaniemi Sanna , Ronkainen Justiina , Sebert Sylvain , Silva Wnurinham , Vääräsmäki Marja , Jaddoe Vincent W. V. , Bernstein Robin M. , Prentice Andrew M. , Cosin-Tomas Marta , Dwyer Terence , Håberg Siri Eldevik , Herceg Zdenko , Magnus Maria C. , Munthe-Kaas Monica Cheng , Page Christian M. , Völker Maja , Gilles Maria , Send Tabea , Witt Stephanie , Zillich Lea , Gagliardi Luigi , Richiardi Lorenzo , Czamara Darina , Räikkönen Katri , Chatzi Lida , Vafeiadi Marina , Arshad S. Hasan , Ewart Susan , Plusquin Michelle , Felix Janine F. , Moore Sophie E. , Vrijheid Martine , Holloway John W. , Karmaus Wilfried , Herberth Gunda , Zenclussen Ana , Streit Fabian , Lahti Jari , Hüls Anke , Hoang Thanh T. , London Stephanie J. , Wiemels Joseph L. 
Published: January 2024

AbstractHigher birth order is associated with altered risk of many disease states. Changes in placentation and exposures to in utero growth factors with successive pregnancies may impact later life disease risk via persistent DNA methylation alterations. We investigated birth order with Illumina DNA methylation array data in each of 16 birth cohorts (8164 newborns) with European, African, and Latino ancestries from the Pregnancy and Childhood Epigenetics Consortium. Meta-analyzed data demonstrated systematic DNA methylation variation in 341 CpGs (FDR adjusted P < 0.05) and 1107 regions. Forty CpGs were located within known quantitative trait loci for gene expression traits in blood, and trait enrichment analysis suggested a strong association with immune-related, transcriptional control, and blood pressure regulation phenotypes. Decreasing fertility rates worldwide with the concomitant increased proportion of first-born children highlights a potential reflection of birth order-related epigenomic states on changing disease incidence trends.
Automatically discovering ordinary differential equations from data with sparse regression
Authors: Egan Kevin , Li Weizhen , Carvalho Rui 
Published: January 2024

AbstractDiscovering nonlinear differential equations that describe system dynamics from empirical data is a fundamental challenge in contemporary science. While current methods can identify such equations, they often require extensive manual hyperparameter tuning, limiting their applicability. Here, we propose a methodology to identify dynamical laws by integrating denoising techniques to smooth the signal, sparse regression to identify the relevant parameters, and bootstrap confidence intervals to quantify the uncertainty of the estimates. We evaluate our method on well-known ordinary differential equations with an ensemble of random initial conditions, time series of increasing length, and varying signal-to-noise ratios. Our algorithm consistently identifies three-dimensional systems, given moderately-sized time series and high levels of signal quality relative to background noise. By accurately discovering dynamical systems automatically, our methodology has the potential to impact the understanding of complex systems, especially in fields where data are abundant, but developing mathematical models demands considerable effort.
Autotaxin–lysolipid signaling suppresses a CCL11–eosinophil axis to promote pancreatic cancer progression
Authors: Bhattacharyya Sohinee , Oon Chet , Diaz Luis , Sandborg Holly , Stempinski Erin S. , Saoi Michelle , Morgan Terry K. , López Claudia S. , Cross Justin R. , Sherman Mara H. 
Published: January 2024

AbstractLipids and their modifying enzymes regulate diverse features of the tumor microenvironment and cancer progression. The secreted enzyme autotaxin (ATX) hydrolyzes extracellular lysophosphatidylcholine to generate the multifunctional lipid mediator lysophosphatidic acid (LPA) and supports the growth of several tumor types, including pancreatic ductal adenocarcinoma (PDAC). Here we show that ATX suppresses the accumulation of eosinophils in the PDAC microenvironment. Genetic or pharmacologic ATX inhibition increased the number of intratumor eosinophils, which promote tumor cell apoptosis locally and suppress tumor progression. Mechanistically, ATX suppresses eosinophil accumulation via an autocrine feedback loop, wherein ATX–LPA signaling negatively regulates the activity of the AP-1 transcription factor c-Jun, in turn suppressing the expression of the potent eosinophil chemoattractant CCL11 (eotaxin-1). Eosinophils were identified in human PDAC specimens, and rare individuals with high intratumor eosinophil abundance had the longest overall survival. Together with recent findings, this study reveals the context-dependent, immune-modulatory potential of ATX–LPA signaling in cancer.
Millennial-scale variations in Arctic sea ice are recorded in sedimentary ancient DNA of the microalga Polarella glacialis
Authors: Harðardóttir Sara , Haile James S. , Ray Jessica Louise , Limoges Audrey , Van Nieuwenhove Nicolas , Lalande Catherine , Grondin Pierre-Luc , Jackson Rebecca , Skaar Katrine Sandnes , Heikkilä Maija , Berge Jørgen , Lundholm Nina , Massé Guillaume , Rysgaard Søren , Seidenkrantz Marit-Solveig , De Schepper Stijn , Lorenzen Eline D. , Lovejoy Connie , Ribeiro Sofia 
Published: January 2024

AbstractSea ice is a critical component of the Earth’s Climate System and a unique habitat. Sea-ice changes prior to the satellite era are poorly documented, and proxy methods are needed to constrain its past variability. Here, we demonstrate the potential of sedimentary DNA from Polarella glacialis, a sea-ice microalga, for tracing past sea-ice conditions. We quantified P. glacialis DNA (targeting the nuclear ribosomal ITS1 region) in Arctic marine and fjord surface sediments and a sediment core from northern Baffin Bay spanning 12,000 years. Sea ice and sediment trap samples confirmed that cysts of P. glacialis are common in first-year sea ice and sinking particulate matter following sea-ice melt. Its detection is more efficient with our molecular approach than standard micropaleontological methods. Given that the species inhabits coastal and marine environments in the Arctic and Antarctic, P. glacialis DNA has the potential to become a useful tool for circum-polar sea-ice reconstructions.
Role of Large Igneous Provinces in continental break-up varying from “Shirker” to “Producer”
Authors: Koptev Alexander , Cloetingh Sierd 
Published: January 2024

AbstractTraditionally, the emplacement of the Large Igneous Provinces (LIPs) is considered to have caused continental break-up. However, this does not always seem to be the case, as illustrated by, for example, the Siberian Traps, one of the most voluminous flood basalt events in Earth history, which was not followed by lithospheric rupture. Moreover, the classical model of purely active (plume-induced) rifting and continental break-up often fails to do justice to widely varying tectonic impacts of Phanerozoic LIPs. Here, we show that the role of the LIPs in rupture of the lithosphere ranges from initial dominance (e.g., Deccan LIP) to activation (e.g., Central Atlantic Magmatic Province, CAMP) or alignment (e.g., Afar LIP). A special case is the North Atlantic Igneous Province (NAIP), formed due to the “re-awakening” of the Iceland plume by the lateral propagation of the spreading ridge and the simultaneous approach of the plume conduit to adjacent segments of the thinner overlying lithosphere. The proposed new classification of LIPs may provide useful guidance for future research, particularly with respect to some inherent limitations of the common paradigm of purely passive continental break-up and the assumption of a direct link between internal mantle dynamics and the timing of near-surface magmatism.