Miracle-dz/UniFAR-FTUs huggingface dataset:
Oxido-Reduction Potential as a Method to Determine Oxidative Stress in Semen Samples

There are different estimates for the incidence of infertility. Its occurrence may vary from area to area, but on average, it affects 15% of couples and 10–12% of men worldwide. Many aspects of infertility can be linked to reactive oxygen species (ROS) and the process of oxidative stress (OS). The association between poor semen quality and OS is well known. Unfortunately, there is no accepted protocol for the diagnosis and treatment of OS in andrology. Oxido-reduction potential (ORP) measurement is a new method for determining the ratio between oxidant and antioxidant molecules. Currently, ORP measurement is one of the fastest and most user-friendly methods of andrological OS determination and our goals were to confirm published correlations between ORP values and sperm parameters, examine how sperm concentration influences these results, and investigate whether intracellular ROS formations are also manifested in the ORP values or not after artificial ROS induction. Intracellular ROS formations were induced by menadione (superoxide anion inducer), hydrogen peroxide, and tert-butyl hydroperoxide (lipid peroxidation inducer) treatments; sperm parameters like motility and viability were determined with an SCA Scope system, and ORP changes were recorded by the Mioxsys system. Significant correlations were noticed among the ORP, spermatozoa concentration, motility, progressive motility, and viability. Nevertheless, only the ORP value after normalization with the sperm count correlated with these parameters. Due to normalization, very low and very high sperm concentrations can give misleading results. The means of the non-normalized ORP values were almost the same. All of the applied treatments resulted in decreases in the viability, motility, and progressive motility, and interestingly, altered ORP levels were detected. In addition, it was determined that seminal plasma had a significant protective effect on spermatozoa. The elimination of seminal plasma caused higher sensitivity of spermatozoa against used OS inducers, and higher ORP levels and decreased viabilities and motilities were measured. The ORP level could be a good indicator of male OS; however, in cases of low and high sperm counts, its result can be misleading. Overall, the conclusion can be drawn that ORP determination is a suitable method for detecting intracellular ROS accumulation, but it has limitations that still need to be clarified.
Estimation of multivariate frailty models with varying coefficients

ABSTRACT The complicated structures can be modeled more efficiently and their flexibility can be increased through frailty models with varying coefficients.Therefore, such models are proposed in this article. The real challenge is to estimate varying coefficients by the penalized partial likelihood without closed form. The Laplace approximation is used to solve this problem. These varying coefficients are fitted using B-splines. Moreover, the variances of random effects are estimated by maximizing an approximate profile likelihood. The performance of the proposed methods are assessed with simulation studies and real data. The results show that the methods proposed are better than the counterpart in literature.
PREVALENCE AND ANTIBIOTIC RESISTANCE OF MICROORGANISMS OF THE ENTEROBACTERIACEAE FAMILY ISOLATED FROM DOGS WITH PARVOVIRUS ENTERITIS AND CLINICALLY HEALTHY CONTROLS IN THE NORTHERN REGION OF THE REPUBLIC OF KAZAKHSTAN

One of the main problems in the treatment of infectious diseases in pets is the spread of strains of microorganisms resistant to antimicrobial drugs. The aim of the study was to isolate conditionally pathogenic microorganisms of the Enterobacteriaceae family from dogs with parvavirus enteritis and clinically healthy animals, with the determination of phenotypic and genotypic resistance to antimicrobial drugs. In the period from March 2021 to March 2023, biological material from dogs with parvavirus enteritis (n = 152) and healthy dogs (n = 196), taken in veterinary clinics of Kostanay, was analyzed. Eighty-two isolates of conditionally pathogenic microorganisms of the Enterobacteriaceae family were isolated and studied from 348 biomaterial samples taken from dogs with enteritis. Conditionally pathogenic Enterobacteriaceae were isolated in 26.3% of cases (40 strains), among them: 65% of E.coli strains, 12% - Klebsiella, 10% - Proteus, 8% - Citrobacter, 5%- Enterobacter. Forty two microorganisms were isolated from healthy dogs: 83% are E.coli microorganisms, 5% are Klebsiella and Proteus isolates, and 2% are Citrobacter and Enterobacter microorganisms. In all isolated isolates, the resistance/sensitivity to the action of antibacterial drugs was determined by the disco-diffuse method. It was revealed that all isolated strains of microorganisms showed sensitivity to the action of streptomycin, belonging to the group of aminoglycosides, showed resistance to tetracycline, doxycycline, ofloxacin, ampicillin, amoxicillin. Resistance genes have been identified to beta-lactams, aminoglycosides, tetracyclines, and sulfonamides. The resistance gene to fluoroquinolones was isolated from 1 E. coli isolate, from a healthy animal. Resistance genes were not detected in the DNA of Citrobacter, Enterobacter and Proteus isolates isolated from clinically healthy dogs. The most common genes were genes encoding resistance to aminoglycosides - 28% of strains, to beta-lactams - 21.9%, to tetracyclines - 13.4% of animals. It was concluded that the uncontrolled and frequent use of antibacterial drugs of the beta-lactam group and tetracyclines in dogs leads to the spread of genotypic resistance among microorganisms of the Enterobacteriaceae family.
Normal Mode Wave-Vortex Decompositions of Mesoscale Simulations

The kinetic energy spectrum of the atmosphere has been well observed to exhibit a k−3 power law at synoptic scales with a transition to a shallower k−5/3 power law at the mesoscale. To better understand the mesoscale kinetic energy spectrum, the spectrum can be decomposed into the two dominant modes at this scale: quasi-horizontal vortex motion and inertia-gravity wave motion. A commonly used technique for this is a Helmholtz decomposition of the horizontal velocity into rotational and divergent components, representing the geostrophically balanced and inertia-gravity wave modes, respectively. This decomposition is a crude approximation, since geostrophically balanced flows have small but non-zero divergence and inertia-gravity waves can have non-zero rotational energy. We investigate the mesoscale spectrum generated in a moderate-resolution, doubly-periodic, non-hydrostatic simulation of a baroclinically unstable jet. A three-dimensional normal mode decomposition is used to decompose the total energy into geostrophic and ageostrophic components. We compare the results with the Helmholtz decomposition and find they are qualitatively similar, but ageostrophic modes increasingly dominate with increasing vertical wave number. Specifically, we find the geostrophic mode in the mesoscale to have a steeper spectral slope than the spectral slope of the rotational component of the Helmholtz decomposition at −3.1 and −2.7, respectively. The difference between the spectral slopes of the ageostrophic and divergent modes are much greater, with mesoscale slope values of −2.7 and −1.9, respectively. We find that the reason for these differences can be attributed to both the inclusion of the available potential energy in the normal mode decomposition, and the inclusion of rotational energy in the ageostrophic mode of the normal mode decomposition.
A re‐evaluation of fixed effect(s) meta‐analysis

Meta‐analysis is a common tool for synthesizing results of multiple studies. Among methods for performing meta‐analysis, the approach known as ‘fixed effects’ or ‘inverse variance weighting’ is popular and widely used. A common interpretation of this method is that it assumes that the underlying effects in contributing studies are identical, and for this reason it is sometimes dismissed by practitioners. However, other interpretations of fixed effects analyses do not make this assumption, yet appear to be little known in the literature. We review these alternative interpretations, describing both their strengths and their limitations. We also describe how heterogeneity of the underlying effects can be addressed, with the same minimal assumptions, through either testing or meta‐regression. Recommendations for the practice of meta‐analysis are given; it is hoped that these will foster more direct connection of the questions that meta‐analysts wish to answer with the statistical methods they choose.
Acceleration of UHECRs in AGN jets and backflows

The origin of the ultra high energy cosmic rays is still under debate. Although observational data indicate that the arrival direction of UHECRs is coincident with starburst galaxies and Active Galactic Nuclei (AGN), the former do not have enough power to accelerate particles up to ultra high energies. On the other hand, recent theoretical advances indicate that backflows in the termination region of AGN jets can accelerate particles up to the Hillas limit. In addition, the interaction of stars with the AGN jet can serve as an effective mechanism for the jet mass loading; needed to explain the heavy composition of UHECRs as indicated by Pierre Auger data. In the present contribution we review these results and present our future perspectives
Analysis of Topological Chaos in Ghost Rod Mixing at Finite Reynolds Numbers Using Spectral Methods

Analysis of Topological Chaos in Ghost Rod Mixing at Finite Reynolds Numbers Using Spectral Methods. (December 2009) Pradeep Chandrakant Rao, B.E. , University of Mumbai Chair of Advisory Committee: Dr. Andrew Duggleby The effect of finite Reynolds numbers on chaotic advection is investigated for two dimensional lid-driven cavity flows that exhibit topological chaos in the creeping flow regime. The emphasis in this endeavor is to study how the inertial effects present due to small, but non-zero, Reynolds number influence the efficacy of mixing. A spectral method code based on the Fourier-Chebyshev method for two-dimensional flows is developed to solve the Navier-Stokes and species transport equations. The high sensitivity to initial conditions and the exponentional growth of errors in chaotic flows necessitate an accurate solution of the flow variables, which is provided by the exponentially convergent spectral methods. Using the spectral coefficients of the basis functions as solved through the conservation equations, exponentially accurate values of velocity everywhere in the flow domain are obtained as required for the Lagrangian particle tracking. Techniques such as Poincaré maps, the stirring index based on the box counting method, and the tracking of passive scalars in the flow are used to analyse the topological chaos and quantify the mixing efficiency.
HAWC observations of microquasars as powerful particle accelerators

Microquasars are one of the classes of powerful Galactic particle accelerators that emit gamma rays beyond multi-TeV energies. Recently, gamma-ray emission above tens of TeV has been detected from some of these objects. The High Altitude Water Cherenkov (HAWC) observatory has previously reported gamma-ray emission with a median energy of 25 TeV from the microquasar SS 433, suggesting that gamma-ray binaries can accelerate particles to above 100 TeV inside the jets. With 2,321 days of data and better reconstruction algorithms, the HAWC observatory detected emissions above 20 TeV from two other binaries, V4641 Sagittarii and LS 5039. The V4641 Sgr is detected with a significance great than 9 sigma. It’s a low-mass X-ray binary(LMXB) that has been observed with a small-scale jet-like structure in the radio wavelength. In this talk, I will present the preliminary results from V4641 Sgr and discuss possible scenarios for gamma-ray production. We will also present future plans to search for additional X-ray binaries with HAWC.
From Diagnosis to Melioration of Sustainable Development in SMEs: The SME-Sustainability Compass

The paper presents the Sustainability compass, which aims at supporting small and medium-sized enterprises (SMEs) to improve the performance of their sustainable development; hereafter called the SME Sustainable compass (SME-SC). Firstly, the paper introduces the result of the first step of the project that proposes the Sustainability compass as an online diagnostic tool. Thus, the paper continues with the second step of the project, which uses the data captured in the previous step to develop a recommender system to suggest the models to follow, and specific recommendations of those role models. Accordingly, a general architecture for the SME-SC is presented. Finally, the paper ends with a discussion, conclusion, and further research directions.
Geometry-Incorporated Posing of a Full-Body Avatar From Sparse Trackers

Accurately rendering a user’s full body in a virtual environment is crucial for embodied mixed reality (MR) experiences. Conventional MR systems provide sparse trackers such as a headset and two hand-held controllers. Recent studies have intensively investigated learning methods to regress untracked joints from sparse trackers and have produced plausible poses in real time for MR applications. However, most studies have assumed that they either know the position of the root joint or constrain it, yielding stiff pelvis motions. This paper presents the first geometry-incorporated learning method to generate the position and rotation of all joints, including the root joint, from the head and hands information for a wide range of motions. We split the problem into identifying a reference frame and a pose inference with respect to the new reference frame. Our method defines an avatar frame by setting a non-joint as the origin and transforms joint data in a world coordinate system into the avatar coordinate system. Our learning builds on a propagating long short-term memory (LSTM) network exploiting prior knowledge of the kinematic chains and the previous time domain. The learned joints are transformed back to obtain the positions with respect to the world frame. In our experiments, our method achieves competitive accuracy and robustness with the state-of-the-art speed of approximately 130 fps on motion capture datasets and the wild tracking data obtained from commercial MR devices. Our experiments confirm that the proposed method is practically applicable to MR systems.
Fully Quantized Distributed Gradient Descent

n major distributed optimization system, the main bottleneck is often the communication between the different machines. To reduce the time dedicated to communications, some heuristics have been developed to reduce the precision of the messages sent and have been shown to produce good results in practice, and [Alistarh et al, 2017] introduced the quantization framework to analyze theoretically the effects of lossy compression on the convergence rate of gradient descent algorithms. This works identifies an issue in one of the proofs in [Alistarh et al, 2017] and provides a new approach to reduce the error introduced by low-precision updates.
Association between the antiadhesion membrane and small bowel obstruction after open gastrectomy: A supplemental analysis of the randomized controlled JCOG1001 trial

Abstract Aim Postoperative small bowel obstruction (SBO) is one of the major complications that is mainly caused by postoperative adhesion. Recently, the antiadhesion membrane has become popular for postoperative SBO prevention. However, its efficacy is yet to be confirmed in the gastric cancer surgery field. Here, we conducted the supplemental analysis of the randomized controlled trial JCOG1001 to investigate the efficacy of the antiadhesion membrane on SBO prevention in patients with open gastrectomy for gastric cancer. Methods Of the 1204 patients enrolled in JCOG1001, 1200 patients were included. The development of SBO of Grade ≥ IIIa according to the Clavien–Dindo classification was recorded. Univariable and multivariable analyses were performed using the Fine and Gray model to determine the risk factors for SBO. Results Fifty‐one patients developed SBO (median follow‐up duration: 5.6 years). Total gastrectomy, combined resection, and blood loss significantly increased the risk for SBO development in the univariable analysis. Large amount of blood loss was independently associated with SBO development in the multivariable analysis (hazard ratio [HR], 3.089; 95% confidence interval [CI], 1.562–6.109, p = 0.0012). Antiadhesion membrane did not reduce the risk for SBO (HR, 1.299; 95% CI 0.683–2.470; p = 0.4246). In the patients belonging to subgroup analyses who received distal and total gastrectomy, the antiadhesion membrane was not associated with the incidence of SBO. Conclusions Antiadhesion membrane did not decrease SBO occurrence rate after open gastrectomy. Therefore, the use of antiadhesion membrane would not be effective for preventing SBO in gastric cancer surgery.
Modeling Expected TIGERISS Observations

The Trans-Iron Galactic Element Recorder for the International Space Station (TIGERISS) is designed to measure the abundances of the rare ultra-heavy Galactic cosmic rays (UHGCRs) 30 Zn and heavier, and is planned to launch to the ISS in 2026. TIGERISS uses planes of crossed silicon strip detectors at the top and bottom for charge (Ohmic side) and trajectory (strip side) determination and acrylic and silica aerogel Cherenkov detectors for velocity and charge determination. Following selection in the second NASA Astrophysics Pioneers Program call, instrument configurations are being studied for available ISS external payload accommodation locations on the Japanese Experiment Module (JEM) “Kibo” Exposed Facility (EF) and the European Space Agency Columbus Laboratory (SOX). Expected UHGCR observations are modelled using differential geometry factors determined for detector orientations within the geomagnetic field over the ISS 51.6 ◦ inclination orbit to determine geomagnetic screening. Energy spectra are integrated using the higher of the energy needed to trigger the instrument as a function of incidence angle determined by Geant4 simulations or the energy needed to penetrate the geomagnetic field for time-weighted bins of geomagnetic latitude, instrument orientation, and incidence angle. The expected abundance measurements are reduced by the fraction of events calculated to fragment in the instrument as a function of incidence angle.
Multimessenger Potential of the Radio Neutrino Observatory in Greenland

The Radio Neutrino Observatory in Greenland (RNO-G) is the only ultrahigh energy (UHE, ${\gtrsim}30$~PeV) neutrino monitor of the Northern sky and will soon be the world's most sensitive high-uptime detector of UHE neutrinos. Because of this, RNO-G represents an important piece of the multimessenger landscape over the next decade. In this talk, we will highlight RNO-G's multimessenger capabilities and its potential to provide key information in the search for the most extreme astrophysical accelerators. In particular, we will highlight opportunities enabled by RNO-G's unique field-of-view, its potential to constrain the sources of UHE cosmic rays, and its complementarity with IceCube at lower energies.
Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada

The deep terrestrial subsurface, hundreds of meters to kilometers below the surface, is characterized by oligotrophic conditions, dark and often anoxic settings, with fluctuating pH, salinity, and water availability. Despite this, microbial populations are detected and active, contributing to biogeochemical cycles over geological time. Because it is extremely difficult to access the deep biosphere, little is known about the identity and metabolisms of these communities, although they likely possess unknown pathways and might interfere with deep waste deposits. Therefore, we analyzed rock and groundwater microbial communities from deep, isolated brine aquifers in two regions dating back to the Ordovician and Devonian, using amplicon and whole genome sequencing. We observed significant differences in diversity and community structure between both regions, suggesting an impact of site age and composition. The deep hypersaline groundwater did not contain typical halophilic bacteria, and genomes suggested pathways involved in protein and hydrocarbon degradation, and carbon fixation. We identified mainly one strategy to cope with osmotic stress: compatible solute uptake and biosynthesis. Finally, we detected many bacteriophage families, potentially indicating that bacteria are infected. However, we also found auxiliary metabolic genes in the viral genomes, probably conferring an advantage to the infected hosts.
Diagnostic value of loop-mediated isothermal amplification in detecting lower respiratory pathogens.

INTRODUCTION To investigate the diagnostic value of loop-mediated thermostatic amplification (LAMP) in detecting pathogenic bacteria from bronchoalveolar lavage fluid (BALF) of patients with pulmonary disorders combined with lower respiratory tract infections (LRTI). METHODOLOGY This cross-sectional study included patients with pulmonary disorders combined with LRTI, including chronic obstructive pulmonary disease (COPD), bronchiectasis, or lung cancer, hospitalized in Meizhou People's Hospital between January 2020 and October 2021. BALF was collected using local bronchoalveolar lavage and electronic bronchoscopy. The presence of the pathogens was confirmed using the LAMP method and the bacterial culture method. RESULTS In total, 249 patients were included (135 with COPD, 73 with bronchiectasis, and 41 with lung cancer). The proportions of Methicillin-resistant Staphylococcus aureus (4.8% vs 0.4%, p = 0.02) and Haemophilus influenzae (6.8% vs 0.4%, p < 0.001) detected by the LAMP method was higher, while the proportion of Pseudomonas aeruginosa was lower compared with that of the culture method (6.8% vs 12.4%, p = 0.034). The bacterial species with the highest agreement coefficient was Stenotrophomonas maltophilia (Kappa = 0.798, p < 0.001). Furthermore, 9 COPD patients exhibited mixed infections as determined by the LAMP method, whereas the culture method detected only 2 of these cases (1.48%) (p < 0.05). CONCLUSIONS LAMP can detect more pathogenic bacteria, notably Haemophilus influenza, Methicillin-resistant Staphylococcus aureus, and atypical pathogens in patients with clinically common pulmonary disorders combined with LRTI. LAMP may provide etiological evidence to guide the clinical use of antibiotics in primary hospitals.