Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance of Illumina® BovineHD BeadChip in genotyping Indian riverine buffalo breeds

The current study tested the suitability of Illumina® BovineHD BeadChip in genotyping three riverine breeds of buffalo viz. Jaffarabadi, Murrah and Mehsana. Of the 777962 SNPs, 670955 SNPs were called in all animals and only 13150 SNPs were found to be polymorphic at a call rate of 90%, and had Minor Allele Frequency (MAF) greater than 0.05. The average Minor Allele Frequency (MAF) of polymorphic SNPs was 0.23 and average expected heterozygosity (HE) of 0.321. Principal Component Analysis (PCA) revealed 2 different clusters where Murrah and Mehsana breeds clustered together, while Jaffarabadi breed formed a distinct cluster. Result obtained in this study indicated that the SNPs available in Illumina BovineHD BeadChip may not be good enough for studying population structure and genetic analyses in Indian buffalo breeds. Hence it might be necessary to develop a custom SNP marker panel for Indian riverine buffaloes.
Short-Term Mild Hypoxia Modulates Na,K-ATPase to Maintain Membrane Electrogenesis in Rat Skeletal Muscle

The Na,K-ATPase plays an important role in adaptation to hypoxia. Prolonged hypoxia results in loss of skeletal muscle mass, structure, and performance. However, hypoxic preconditioning is known to protect against a variety of functional impairments. In this study, we tested the possibility of mild hypoxia to modulate the Na,K-ATPase and to improve skeletal muscle electrogenesis. The rats were subjected to simulated high-altitude (3000 m above sea level) hypobaric hypoxia (HH) for 3 h using a hypobaric chamber. Isolated diaphragm and soleus muscles were tested. In the diaphragm muscle, HH increased the α2 Na,K-ATPase isozyme electrogenic activity and stably hyperpolarized the extrajunctional membrane for 24 h. These changes were accompanied by a steady increase in the production of thiobarbituric acid reactive substances as well as a decrease in the serum level of endogenous ouabain, a specific ligand of the Na,K-ATPase. HH also increased the α2 Na,K-ATPase membrane abundance without changing its total protein content; the plasma membrane lipid-ordered phase did not change. In the soleus muscle, HH protected against disuse (hindlimb suspension) induced sarcolemmal depolarization. Considering that the Na,K-ATPase is critical for maintaining skeletal muscle electrogenesis and performance, these findings may have implications for countermeasures in disuse-induced pathology and hypoxic therapy.
Health Promotion Actions and School Violence—A Cluster Analysis from Finnish Comprehensive Schools

(1) Schools have a significant role in violence prevention activities. This study aimed to first identify profiles of Finnish comprehensive schools based on school violence. The second aim was to examine the associations between profiles concerning health promotion actions, reactive or punitive actions, and school characteristics. (2) The study used the large-scale, nationally representative Benchmarking System of Health Promotion Capacity-Building (BSHPCB) data (n = 2057 schools) completed by the school’s principal together with a student welfare team. The data was analyzed by cluster analysis and Chi-squared and Kruskal–Wallis tests. For post hoc testing, Fisher’s exact test with odds ratios and Mann–Whitney U-test were used. (3) The cluster analysis yielded five profiles of school violence: “No violence”, “Adolescent violence” (violence both among pupils and from pupils towards staff, but not inappropriate behavior from school staff towards pupils), “Not known” (principals either did not respond to these questions or they did not know whether there had been any school violence incidents), “Peer violence” (school violence occurred among pupils but not from pupils towards staff, nor inappropriate behavior from school staff towards pupils), and “All violence” (all types of school violence and inappropriate behavior from school staff towards pupils). These clusters differed according to type of school and municipality. Additionally, both management and monitoring as health promotion actions were related to higher incidence of school violence whereas other actions, such as commitment, resources, common practices, and participation were not related to school violence. (4) The findings of this study indicate that schools have different profiles in terms of school violence and providing evidence and guidance for school violence prevention work.
DNA methylation at hepatitis B virus integrants and flanking host mitochondrially encoded cytochrome C oxidase III

It is widely accepted that hepatitis B virus (HBV) integrants in the human genome are one of the key factors in liver carcinogenesis. Although it is difficult to observe pre/post-HBV infection genomic-level changes in the same clinical sample pairs, they can be observed using artificially infected HBV cell lines such as HepG2.2. 15. A detailed HBV integration analysis comparing HepG2.2. 15 with HepG2 cells, especially their mitochondrial (mt) DNA, was conducted using next-generation sequencing (NGS)-based integration analysis. Following target DNA enrichment for elements of the HBV genome, NGS was used to identify HBV integration sites in the mtDNA and DNA methylation was analyzed using semi-quantitative pyrosequencing at the boundaries of the integrated region. The results revealed the HBV integration site in the mtDNA of HepG2.215, most notably the insertion of the HBV preCore, X gene fragment in exon 1 of mitochondrially encoded cytochrome C oxidase III (MT-CO3; ChrM 9652), along with a ‘CACCA’ microhomology sequence. Both boundaries of the integrated region were concordant and highly methylated (HBV side, 92.3%; MT-CO3 side, 95.5%) relative to those observed in nonintegrated HepG2 (4.3%), HepG2.2. 15 (3.0%) and PLC/PRF/5 (4.0%) cells. In conclusion, HBV integration sites were successfully identified in the MT-CO3 gene along with a ‘CACCA’ microhomology sequence using NGS-based analysis and mitochondrial heteroplasmy was identified. The present study also revealed that the HBV/MT-CO3-integrated boundary DNA was hypermethylated at both the HBV and MT-CO3 sides.
Quantum criticality of a Bose gas in an optical lattice near the Mott transition

We derive the equation of state of bosons in an optical lattice in the framework of the Bose-Hubbard model. Near the density-driven Mott transition, the expression of the pressure P({\mu},T) versus chemical potential and temperature is similar to that of a dilute Bose gas but with renormalized mass m^* and scattering length a^*. m^* is the mass of the elementary excitations at the quantum critical point governing the transition from the superfluid phase to the Mott insulating phase, while a^* is related to their effective interaction at low energy. We use a nonperturbative renormalization-group approach to compute these parameters as a function of the ratio t/U between hopping amplitude and on-site repulsion.
Lifshitz-like systems and AdS null deformations

Following K. Balasubramanian and K. Narayan [J. High Energy Phys. 08 (2010) 014], we discuss certain lightlike deformations of AdS{sub 5}xX{sup 5} in type IIB string theory sourced by a lightlike dilaton {Phi}(x{sup +}) dual to the N=4 super Yang-Mills theory with a lightlike varying gauge coupling. We argue that, in the case where the x{sup +} direction is noncompact, these solutions describe anisotropic 3+1-dim Lifshitz-like systems with a potential in the x{sup +} direction generated by the lightlike dilaton. We then describe solutions of this sort with a linear dilaton. This enables a detailed calculation of two-point correlation functions of operators dual to bulk scalars and helps illustrate the spatial structure of these theories. Following this, we discuss a nongeometric string construction involving a compactification along the x{sup +} direction of this linear dilaton system. We also point out similar IIB axionic solutions. Similar bulk arguments for x{sup +}-noncompact can be carried out for deformations of AdS{sub 4}xX{sup 7} in M theory.
Measuring the cosmological background of relativistic particles with the Wilkinson Microwave Anisotropy Probe

We show that the first year results of the Wilkinson Microwave Anisotropy Probe (WMAP) constrain very efficiently the energy density in relativistic particles in the Universe. We derive new bounds on additional relativistic degrees of freedom expressed in terms of an excess in the effective number of light neutrinos $\ensuremath{\Delta}{N}_{\mathrm{eff}}. $ Within the flat \ensuremath{\Lambda}CDM scenario, the allowed range is $\ensuremath{\Delta}{N}_{\mathrm{eff}}l6$ (95% confidence level) using WMAP data only, or $\ensuremath{-}2.6l\ensuremath{\Delta}{N}_{\mathrm{eff}}l4$ with the prior ${H}_{0}=72\ifmmode\pm\else\textpm\fi{}8\mathrm{km}{\mathrm{s}}^{\ensuremath{-}1}{\mathrm{Mpc}}^{\ensuremath{-}1}. $ When other cosmic microwave background and large scale structure experiments are taken into account, the window shrinks to $\ensuremath{-}1.6l\ensuremath{\Delta}{N}_{\mathrm{eff}}l3.8. $ These results are in perfect agreement with the bounds from primordial nucleosynthesis. Nonminimal cosmological models with extra relativistic degrees of freedom are now severely restricted.
Hybrid Distributed Fiber-Optic Sensing System by Using Rayleigh Backscattering Lightwave as Probe of Stimulated Brillouin Scattering

Distributed fiber-optic sensing system has been employed for temperature and strain measurement in health monitoring of various structures, and current systems are mainly designed for static-only or dynamic-only parameters. To combine these functions, we propose and experimentally demonstrate a single-end multi-parameter distributed sensing system which can simultaneously measure static parameters and dynamic parameters by integrating Brillouin optical time domain analyzer (BOTDA) for static parameters and phase-sensitive optical time domain reflectometry (<inline-formula><tex-math notation="LaTeX">$\varphi$</tex-math></inline-formula>-OTDR) for dynamic parameters. The probe pulse of <inline-formula><tex-math notation="LaTeX">$\varphi$</tex-math></inline-formula>-OTDR and the pump pulse of BOTDA are successively injected into the sensing fiber. The first pulse is used as the probe pulse of a regular <inline-formula><tex-math notation="LaTeX">$\varphi$</tex-math></inline-formula>-OTDR for vibration measurement, and its Rayleigh backscattering (RBS) lightwave is used as the probe of BOTDA. The second pulse is used to amplify the RBS lightwave for the measurement of static-parameters. The interaction of the pulse pair is analyzed in detail, and the hybrid system is experimentally demonstrated. The experimental results show that 3 kHz vibration sensing with 10 m spatial resolution at 14 km standard single mode fiber can be realized, and the temperature of the sensing fiber can be measured simultaneously with 5 m spatial resolution and 1.29 MHz measurement accuracy of Brillouin frequency shift.
Testing symmetries in effective models of higher derivative field theories

Higher derivative field theories with interactions raise serious doubts about their validity due to severe energy instabilities. In many cases the implementation of a direct perturbation treatment to excise the dangerous negative-energies from a higher derivative field theory may lead to violations of Lorentz and other symmetries. In this work we study a perturbative formulation for higher derivative field theories that allows the construction of a low-energy effective field theory being a genuine perturbations over the ordinary-derivative theory and having a positive-defined Hamiltonian. We show that some discrete symmetries are recovered in the low-energy effective theory when the perturbative method to reduce the negative-energy degrees of freedom from the higher derivative theory is applied. In particular, we focus on the higher derivative Maxwell-Chern-Simons model which is a Lorentz invariant and parity-odd theory in 2+1 dimensions. The parity violation arises in the effective action of QED{sub 3} as a quantum correction from the massive fermionic sector. We obtain the effective field theory which remains Lorentz invariant, but parity invariant to the order considered in the perturbative expansion.
On the Hamiltonian form of 3D massive gravity

We present a Chern-Simons-like action for the general massive gravity model propagating two spin-2 modes with independent masses in three spacetime dimensions (3D), and we use it to find a simple Hamiltonian form of this model. The number of local degrees of freedom, determined by the dimension of the physical phase space, agrees with a linearized analysis except in some limits, in particular that yielding topologically new massive gravity, which therefore suffers from a linearization instability.
Annular gap model for multi-wavelength pulsed emission from young and millisecond pulsars

Abstract The multi-wavelength pulsed emission from young pulsars and millisecond pulsars can be well modeled with the single-pole 3-dimension annular gap and core gap model. To distinguish our single magnetic pole model from two-pole models (e.g. outer gap model and two-pole caustic model), the convincing values of the magnetic inclination angle and the viewing angle will play a key role.
Hyperbolicity of mapping-torus groups and spaces

This paper deals with the geometry of metric "two dimensional" spaces, equipped with semi-flows admitting transverse foliations by forests. Our main theorem relates the Gromov-hyperbolicity of such spaces, for instance mapping-telescopes of trees, with the dynamical behaviour of the semi-flow. As a corollary, we give a new proof of Bestvina-Feighn combination theorem for mapping-tori of injective free groups endomorphisms.
Bell inequalities for multipartite qubit quantum systems and their maximal violation

We present a set of Bell inequalities for multiqubit quantum systems. These Bell inequalities are shown to be able to detect multiqubit entanglement better than previous Bell inequalities such as Werner-Wolf-Zukowski-Brukner ones. Computable formulas are presented for calculating the maximal violations of these Bell inequalities for any multiqubit states.
THE ARAUCARIA PROJECT: THE DISTANCE TO THE SCULPTOR DWARF SPHEROIDAL GALAXY FROM INFRARED PHOTOMETRY OF RR LYRAE STARS

We have obtained single-phase near-infrared magnitudes in the J and K bands for a sample of 78 RR Lyrae stars in the Sculptor dSph galaxy. Applying different theoretical and empirical calibrations of the period–luminosity–metallicity relation for RR Lyrae stars in the infrared, we find consistent results and obtain a true, reddening-corrected distance modulus of 19.67 ± 0.02 (statistical) ± 0.12 (systematic) mag for Sculptor from our data. This distance value is consistent with the value of 19.68 ± 0.08 mag which we obtain from earlier V-band data of RR Lyrae stars in Sculptor, and the V magnitude metallicity calibration of Sandage. It is also in very good agreement with the results obtained by Rizzi based on the tip of the red giant branch (TRGB, 19.64 ± 0.08 mag) and horizontal branch (HB, 19.66 ± 0.15 mag).
Isovector axial vector and pseudoscalar transition form factors of Delta in QCD

We investigate the isovector axial vector and pseudoscalar form factors of $\mathrm{\ensuremath{\Delta}}$ baryon by employing light-cone QCD sum rules. Numerical calculations show that the form factors can be well fitted by the exponential form. We make a comparison with the predictions of lattice QCD, chiral perturbation theory and quark model.
A Jacobian Separable 2-D Finite-Element Method for Electromagnetic Waveguide Problems

We propose an efficient finite-element analysis of the vector wave equation in a class of relatively general curved polygons. The proposed method is suitable for an accurate and efficient calculation of the propagation constants of waveguides filled with pieces of homogeneous materials. To apply the method, we first decompose the 2-D problem domain into a set of curved polygons of a specific characteristic. Then we divide every polygon into a set of triangular elements with two straight edges. Finally, we introduce a set of hierarchical mixed-order curl-conforming vector basis functions inside every triangular element to discretize the vector wave equation. The advantages of the method are as follows. The curved boundaries of the elements are modeled exactly and hence there is no approximation in the geometrical modeling. 2-D integrals of the matrix elements are reduced to 1-D integrals. Therefore, the matrix filling can be performed very fast. Total number of elements due to the discretization of a given domain is very small, and hence the discretization of the problem domain takes up a very small percentage of the total computational time. We validate the method by comparing the results with those of Ansoft HFSS simulator and investigate the accuracy and efficiency of the method through some numerical examples.
Detecting multiple sclerosis disease activity and progression in progress notes from electronic medical records using natural language processing and machine learning

Multiple sclerosis (MS) phenotypes provide useful disease descriptions but lack complete information regarding the continuing disease process. Disease activity and progression are meaningful modifiers of the MS phenotypes which can further guide prognosis, therapeutic decisions, and clinical trial designs and outcomes, which were not explicitly documented in patients electronic medical records (EMRs). We aimed to detect disease activity and progression in patients with MS from clinical notes in the EMR using Natural Language Processing and Machine Learning models. Using randomly selected progress notes from MS patients at the University of Rochester MS clinic, we integrated NLP and machine learning technologies to predict selected phenotype modifiers that represent disease activity and progression. The method was evaluated by the performance of both the NLP models and machine learning models, as well as the interpretability of the integrated method. We identified 460 progress notes from 287 MS patients. The NLP model had an average of 0.92 in precision, 0.87 in recall, and 0.89 in F-score for entity extraction. It had an average of 0.85 in precision, 0.84 in recall, and 0.85 in F-score for entity relation extraction. The sensitivities and specificities of the classification algorithms in predicting phenotype modifiers were: 67% and 93% for predicting modifier "Active", 61% and 82% for predicting modifier "Worsening", 92% and 98% for predicting modifier "Progression", 80% and 94% for predicting modifier "New MRI Lesion", respectively. We showed that the integrated method of NLP with machine learning classification is capable of detecting evidence of disease activity and clinical progression from clinical notes. The classification algorithms yielded interpretable and largely clinically relevant features (symptoms and clinical conditions) that were persistently associated with disease activity and progression. This method holds promise for facilitating the screening of MS clinical trial participants and potentially identifying early evidence of disease progression.
Utility of human judgment ensembles during times of pandemic uncertainty: A case study during the COVID-19 Omicron BA.1 wave in the USA

Responding to a rapidly evolving pandemic like COVID-19 is challenging, and involves anticipating novel variants, vaccine uptake, and behavioral adaptations. Human judgment systems can complement computational models by providing valuable real-time forecasts. We report findings from a study conducted on Metaculus, a community forecasting platform, in partnership with the Virginia Department of Health, involving six rounds of forecasting during the Omicron BA.1 wave in the United States from November 2021 to March 2022. We received 8355 probabilistic predictions from 129 unique users across 60 questions pertaining to cases, hospitalizations, vaccine uptake, and peak/trough activity. We observed that the case forecasts performed on par with national multi-model ensembles and the vaccine uptake forecasts were more robust and accurate compared to baseline models. We also identified qualitative shifts in Omicron BA.1 wave prognosis during the surge phase, demonstrating rapid adaptation of such systems. Finally, we found that community estimates of variant characteristics such as growth rate and timing of dominance were in line with the scientific consensus. The observed accuracy, timeliness, and scope of such systems demonstrates the value of incorporating them into pandemic policymaking workflows.
Vegetarianism and mental health: longitudinal evidence in the 1970 British Cohort Study.

Background. Reducing animal product consumption has benefits for population health and the environment. The relationship between vegetarianism and mental health, however, remains poorly understood. This study explores this relationship in a nationally representative birth cohort in Great Britain. Methods. We use data from the 1970 British Cohort Study, which collected information on diet at age 30 (n = 11,204) and psychological distress (PD) using the nine-item Malaise Inventory at ages 26, 30, 34, 42, and 46-48. We first developed a statistical adjustment strategy by regressing PD at age 30 on vegetarianism and 14 potential confounders measured at ages 10 and 26 (including PD at age 26). We then ran multilevel growth curve models, testing whether within-person changes in PD between ages 30 and 46-48 differed by vegetarianism, before and after statistical adjustment. Models were reproduced using red meat consumption at age 30 as a sensitivity analysis. Results. At age 30, 4.5% of participants reported being vegetarian. In the cross-sectional models at age 30, vegetarians reported more distress compared with non-vegetarians in bivariate analysis (b = 0.30, 95%CI 0.09, 0.52), but this difference disappeared in the fully-adjusted model (b = 0.02, 95%CI -0.17, 0.21). In the longitudinal models between ages 30 and 46/48, there were no differences in within-person changes in psychological distress between vegetarians and non-vegetarians (p = .723). Sensitivity analyses yielded similar findings. Conclusion. In this British cohort, vegetarianism at age 30 was not associated with changes in psychological distress during mid-adulthood. Since psychological distress in early adulthood predicted vegetarianism at age 30, more studies are needed to disentangle the progression of this relationship over the life-course.