Miracle-dz/UniFAR-FTUs huggingface dataset:
Equine abortion and stillbirth in California: a review of 1,774 cases received at a diagnostic laboratory, 1990–2022

Reproductive failure represents an important cause of economic loss for the equine industry. We reviewed the cases of equine abortion and stillbirth submitted to the California Animal Health and Food Safety Laboratory System, University of California–Davis from 1990 to 2022. A total of 1,774 cases were reviewed. A confirmed cause of abortion was determined in 29.2% of the cases. Abortion or stillbirth was attributed to infectious agents in 18.7% of the cases, with Streptococcus spp. , equine herpesvirus 1, and Leptospira spp. being the most prevalent. Noninfectious causes of abortion were established in 10.5% of the cases, with umbilical cord torsion being the most common. In 70.8% of the cases, a definitive cause of abortion could not be established. Our study demonstrated the difficulties in establishing an etiologic diagnosis, even when following a standard diagnostic work-up. New diagnostic approaches are needed to improve the likelihood of reaching a final diagnosis in cases of equine abortion and stillbirth.
Energy landscape, two-level systems, and entropy barriers in Lennard-Jones clusters

In order to study the tunneling dynamics of glasses, we develop an efficient numerical algorithm for the identification of a large number of saddle points of the potential energy function of Lennard-Jones clusters. Knowledge of the saddle points allows us to find many thousands of adjacent minima of clusters containing up to 160 argon atoms and to locate many pairs of minima with the right characteristics to form two-level systems. The true two-level systems are singled out by calculating the quantum-mechanical ground-state tunneling splitting by means of the one dimensional WKB approximation. The many-dimensions correction to the splitting is evaluated by studying a simple model potential; we find that it consists of a splitting enhancement in all isolated tunneling centers observed. @S0163-1829~99! 06529-7#
Sea Breezes Shallow and Deep on the California Coast

Abstract Analyses of Doppler lidar data reveal sea breezes occurring on two different depth and time scales at Monterey Bay, California, on a day with offshore gradient flow indicated before sunrise and after sunset. The lidar data used in this study consist of vertical cross sections and profiles of the westerly, onshore wind component u. In the morning after 0900 PST a shallow sea breeze formed, which reached a depth of 300 m by noon. Starting in early afternoon a deeper sea-breeze layer formed in the lowest kilometer, and by late afternoon the shallow sea breeze blended into the deeper sea breeze and was no longer evident. Maximum speeds of 6 m s−1 in the shallow sea breeze occurred at the surface, whereas those in the deep sea breeze (also 6 m s−1) were about 300 m above the surface. It is hypothesized that the shallow sea breeze is a local phenomenon responding to a more local temperature contrast between the sea and the region between the ocean and the mountain ranges. The deeper sea breeze, on the .
Classical Subspaces of Symplectic Grassmannians

The collinearity graph of Γ is the graph (P, ∆) where ∆ consists of all pairs of points belonging to a common line. For a point x ∈ P we will denote by ∆(x) the collection of all points collinear with x. For points x, y ∈ P and a positive integer t a path of length t from x to y is a sequence x0 = x, x1, . , xt = y such that {xi, xi+1} ∈ ∆ for each i = 0, 1, . , t− 1. The distance from x to y, denoted by d(x, y) is defined to be the length of a shortest path from x to y if some path exists and otherwise is +∞.
Do Simple Analytical Models Capture Complex Fractured Bedrock Hydraulics? Oscillatory Flow Tests Suggest Not

Fractured sedimentary bedrock aquifers represent complex flow systems that may contain fast, fracture‐dominated flow paths and slower, porous media‐dominated flow paths. Thus, characterizing the dynamics of flow and transport through these aquifers remains a fundamental hydrogeologic challenge. Recent studies have demonstrated the utility of a novel hydraulic testing approach, oscillatory flow testing, in field settings to characterize single bedrock fractures embedded in low‐porosity sedimentary bedrock. These studies employed an idealized analytical model assuming Darcian flow through a nondeforming, constant‐aperture, nonleaky fracture for data interpretation, and reported period‐dependent effective fracture flow parameters. Here, we present the application of oscillatory flow testing across a range of frequencies and inter‐well spacings on a fracture embedded in poorly cemented sedimentary bedrock with considerable primary porosity at the Field Site for Research in Fractured Sedimentary Rock. Consistent with previous studies, we show an apparent period‐dependence in returned flow parameters, with hydraulic diffusivity decreasing and storativity increasing with increasing oscillation period, when assuming an idealized fracture conceptual model. We present simple analyses that examine non‐Darcian flow and borehole storage effects as potential test design artifacts and a simple analytical model that examines fluid leakage to the surrounding host rock as a potential hydraulic mechanism that might contribute to the period‐dependent flow parameters. These analyses represent a range of conceptual assumptions about fracture behavior during hydraulic testing, none of which account for the measured responses during oscillatory flow testing, leading us to argue that other hydraulic processes (e.g., aperture heterogeneity and/or fracture hydromechanics) are necessary to accurately represent pressure propagation through fractured sedimentary bedrock.
Does kisspeptin exert a local modulatory effect on bovine ovarian steroidogenesis?

Kisspeptin, a hypothalamic neuropeptide encoded by the KISS1 gene, has a pivotal role in promoting gonadotrophin-releasing hormone secretion in mammals. Kisspeptin and its receptor (KISS1R) are also expressed in certain peripheral tissues including gonads, suggesting intra-gonadal roles. Such actions at the level of the bovine ovary have not been explored previously. The current aims were to determine whether KISS1 and KISS1R are expressed in the bovine ovary and whether kisspeptin or a kisspeptin antagonist can modulate ovarian steroid production by cultured ovarian cells. Granulosa cells (GC) and theca interna cells (TC) were collected from antral follicles (3–18 mm) categorized into five class sizes. Early, mid and regressing corpora lutea (CL) were also collected for RT-qPCR analysis of KISS1 and KISS1R expression. Bovine TC and GC cultured under both non-luteinizing (serum-free) and luteinizing (serum-supplemented) conditions were treated for 4 days with kisspeptin-10 (10–10–10–6M) or kisspeptin antagonist (kp234; 10–10–10–6M), alone and in combination with either follicle-stimulating hormone (GC), luteinizing hormone (TC) or forskolin (luteinized GC/TC). Steroid secretion (GC: oestradiol, progesterone; TC: androstenedione, progesterone; luteinized GC/TC: progesterone) was measured by ELISA and viable cell number determined by neutral red uptake assay. KISS1 and KISS1R transcripts were detected in TC, GC and CL with significant differences between follicle categories and CL stages. However, neither kisspeptin-10 nor kisspeptin antagonist affected steroid secretion or viable cell number in any of the four ovarian cell culture models. As such, the hypothesis that kisspeptin has a direct intraovarian role to modulate follicular or luteal steroidogenesis, or cell proliferation/survival, is not supported. Lay summary Kisspeptin-producing nerve cells (neurones) in the hypothalamus play a crucial role in controlling the reproductive system. Kisspeptin activates receptors on gonadotrophin-releasing hormone neurones which, in turn, stimulate the pituitary gland to release gonadotrophins. Gonadotrophins act on the gonads (ovaries or testes) to regulate their function (e.g. ovarian follicle development and steroid production). Evidence has emerged in several species that kisspeptin and its receptor are also present in certain peripheral tissues, including the ovaries, suggesting ‘local’ actions. So far, few studies have investigated this. Here, we first show that both kisspeptin and its receptor are expressed by key ovarian cell types of cattle. However, we found that treating cultured bovine theca and granulosa cells with kisspeptin or kisspeptin antagonist did not modify steroid secretion. As such, the hypothesis that kisspeptin has a direct intraovarian role to modulate ovarian steroid production is not supported.
A cross‐country comparison of pregnant women's decision‐making and perspectives when opting for non‐invasive prenatal testing in the Netherlands and Belgium

The Netherlands and Belgium have been among the first countries to offer non‐invasive prenatal testing (NIPT) as a first‐tier screening test. Despite similarities, differences exist in counseling modalities and test uptake. This study explored decision‐making and perspectives of pregnant women who opted for NIPT in both countries.
Repeated Emergence of Variant TetR Family Regulator, FarR, and Increased Resistance to Antimicrobial Unsaturated Fatty Acid among Clonal Complex 5 Methicillin-Resistant Staphylococcus aureus

Resistance-nodulation-division (RND) superfamily efflux pumps promote antibiotic resistance in Gram-negative pathogens, but their role in Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA) is undocumented. However, recent in vitro selections for resistance of S. aureus to an antimicrobial fatty acid, linoleic acid, and an antibiotic, rhodomyrtone, identified H121Y and C116R substitution variants, respectively, in a TetR family regulator, FarR, promoting increased expression of the RND pump FarE. Hypothesizing that in vivo selection pressures have also promoted the emergence of FarR variants, we searched available genome data and found that strains with FarRH121Y from human and bovine hosts have emerged sporadically in clonal complexes (CCs) CC1, CC30, CC8, CC22, and CC97, whereas multiple FarR variants have occurred within CC5 hospital-associated (HA)-MRSA. ABSTRACT Resistance-nodulation-division (RND) superfamily efflux pumps promote antibiotic resistance in Gram-negative pathogens, but their role in Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA) is undocumented. However, recent in vitro selections for resistance of S. aureus to an antimicrobial fatty acid, linoleic acid, and an antibiotic, rhodomyrtone, identified H121Y and C116R substitution variants, respectively, in a TetR family regulator, FarR, promoting increased expression of the RND pump FarE. Hypothesizing that in vivo selection pressures have also promoted the emergence of FarR variants, we searched available genome data and found that strains with FarRH121Y from human and bovine hosts have emerged sporadically in clonal complexes (CCs) CC1, CC30, CC8, CC22, and CC97, whereas multiple FarR variants have occurred within CC5 hospital-associated (HA)-MRSA. Of these, FarRE160G and FarRE93EE were exclusive to CC5, while FarRC116Y, FarRP165L, and FarRG166D also occurred in nonrelated CCs, primarily from bovine hosts. Within CC5, FarRC116Y and FarRG166D strains were polyphyletic, each exhibiting two emergence events. FarRC116Y and FarRE160G were individually sufficient to confer increased expression of FarE and enhanced resistance to linoleic acid (LA). Isolates with FarRE93EE were most closely related to S. aureus N315 MRSA and exhibited increased resistance independently of FarRE93EE. Accumulation of pseudogenes and additional polymorphisms in FarRE93EE strains contributed to a multiresistance phenotype which included fosfomycin and fusidic acid resistance in addition to increased linoleic acid resistance. These findings underscore the remarkable adaptive capacity of CC5 MRSA, which includes the polyphyletic USA100 lineage of HA-MRSA that is endemic in the Western hemisphere and known for the acquisition of multiple resistance phenotypes.
Next-Generation Numerical Weather Prediction: Bridging Parameterization, Explicit Clouds, and Large Eddies

WHat: Scientists from Korea, Japan, France, England, Finland, and the United States met to discuss recent developments in the parameterizations of physical processes in next-generation, highresolution numerical weather prediction (NWP) models (http://nml.yonsei.ac.kr/20100829/). WHen: 30 August–1 September 2010 WHere: Seoguipo, Jeju, South Korea s ix years after the second international workshop on the physical parameterizations in numerical weather prediction (NWP) models in 2004 (Lee and Hong 2005), attendees at the third workshop on next-generation NWP models met to discuss progress in high-resolution NWP modeling and share ideas about future challenges. The main theme of the meeting was “The Cloud-Resolving Modeling Approach and Beyond. ” As of 2010, convection-permitting and cloud-resolving scale modeling has become practically feasible, along with the successful usage of largeeddy simulation (LES) in developing subgrid-scale parameterizations for these models. Many national hydrometeorological centers are now running models in the 2–5-km grid-size range, and will be increasing resolution at a steady rate such that several centers may be at around 1 km in 5 yr. The main topic of the workshop focused on future problems in physics as NWP models go to finer scales where there are “gray zones” in which the explicit model dynamics are almost capable of resolving features that were parameterized at coarser scales. The following questions were posed for the workshop:
Dynamics of Anti-influenza Mucosal IgA Over a Season in a Cohort of Individuals Living or Working in a Long-term Care Facility

Abstract Background Serological surveys are used to ascertain influenza infection and immunity, but evidence for the utility of mucosal immunoglobulin A (IgA) as a correlate of infection or protection is limited. Methods We performed influenza-like illness (ILI) surveillance on 220 individuals living or working in a retirement community in Gainesville, Florida from January to May 2018, and took pre- and postseason nasal samples of 11 individuals with polymerase chain reaction (PCR)-confirmed influenza infection and 60 randomly selected controls. Mucosal IgA against 10 strains of influenza was measured from nasal samples. Results Overall, 28.2% and 11.3% of individuals experienced a 2-fold and 4-fold rise, respectively, in mucosal IgA to at least 1 influenza strain. Individuals with PCR-confirmed influenza A had significantly lower levels of preseason IgA to influenza A. Influenza-associated respiratory illness was associated with a higher rise in mucosal IgA to influenza strains of the same subtype, and H3N2-associated respiratory illness was associated with a higher rise in mucosal IgA to other influenza A strains. Conclusions By comparing individuals with and without influenza illness, we demonstrated that mucosal IgA is a correlate of influenza infection. There was evidence for cross-reactivity in mucosal IgA across influenza A subtypes.
Types and correlates of school absenteeism among students with intellectual disability.

BACKGROUND It appears that students with intellectual disability (ID) are more frequently absent from school compared with students without ID. The objective of the current study was to estimate the frequency of absence among students with ID and the reasons for absence. Potential reasons included the attendance problems referred to as school refusal, where absence is related to emotional distress; truancy, where absence is concealed from parents; school exclusion, where absence is instigated by the school; and school withdrawal, where absence is initiated by parents. METHODS Study participants were 629 parents (84.6% mothers) of Australian school students (Mage = 11.18 years; 1.8% Aboriginal and/or Torres Strait Islander) with an ID. Participants completed a questionnaire battery that included the School Non-Attendance ChecKlist via which parents indicated the reason their child was absent for each day or half-day absence their child had over the past 20 school days. The absence data presented to parents had been retrieved from school records. RESULTS Across all students, absence occurred on 7.9% of the past 20 school days. In terms of school attendance problems as defined in existing literature, school withdrawal accounted for 11.1% of absences and school refusal for 5.3% of absences. Students were also absent for other reasons, most commonly illness (32.0%) and appointments (24.2%). Of students with more than one absence (n = 217; 34.5%), about half were absent for more than one reason. Students attending mainstream schools had lower attendance than those attending special schools. CONCLUSIONS Students with ID were absent for a range of reasons and often for multiple reasons. There were elevated rates of school withdrawal and school refusal. Understanding the reasons for absenteeism can inform targeted prevention and intervention supports.
A Virus-Packageable CRISPR System Identifies Host Dependency Factors Co-Opted by Multiple HIV-1 Strains

With a small genome of ~9.2 kb that encodes 14 major proteins, HIV must hijack host cellular machinery to successfully establish infection. These host proteins necessary for HIV replication are called “dependency factors. ” Whole-genome, and then targeted screens were done to try to comprehensively identify all dependency factors acting throughout the HIV replication cycle. ABSTRACT At each stage of the HIV life cycle, host cellular proteins are hijacked by the virus to establish and enhance infection. We adapted the virus packageable HIV-CRISPR screening technology at a genome-wide scale to comprehensively identify host factors that affect HIV replication in a human T cell line. Using a smaller, targeted HIV Dependency Factor (HIVDEP) sublibrary, we then performed screens across HIV strains representing different clades and with different biological properties to define which T cell host factors are important across multiple HIV strains. Nearly 90% of the genes selected across various host pathways validated in subsequent assays as bona fide host dependency factors, including numerous proteins not previously reported to play roles in HIV biology, such as UBE2M, MBNL1, FBXW7, PELP1, SLC39A7, and others. Our ranked list of screen hits across diverse HIV-1 strains form a resource of HIV dependency factors for future investigation of host proteins involved in HIV biology. IMPORTANCE With a small genome of ~9.2 kb that encodes 14 major proteins, HIV must hijack host cellular machinery to successfully establish infection. These host proteins necessary for HIV replication are called “dependency factors. ” Whole-genome, and then targeted screens were done to try to comprehensively identify all dependency factors acting throughout the HIV replication cycle. Many host processes were identified and validated as critical for HIV replication across multiple HIV strains.
The impact of COVID-19 on firm risk and performance in MENA countries: Does national governance quality matter?

This study investigated the impact of the COVID-19 crisis on firm risk and performance in different country-level governance qualities in the MENA region. Analyzing a sample of 739 non-financial listed firms in 12 MENA countries for the period 2011–2020, we found that the COVID-19 crisis negatively impacted the performance of firms, especially low-performance firms, in most industries, and increased firm risk in general. Moreover, we found that national governance quality plays an important role in mitigating the negative impact of the COVID-19 crisis on firm operations. Specifically, national governance quality reduces the negative impact of the COVID-19 crisis on firm performance and the positive impact of the crisis on firm risk. The results are consistent with our contention that national governance quality contributes to creating a positive environment for businesses activities and reducing economic shocks.
Wake states and frequency selection of a streamwise oscillating cylinder

Abstract This paper presents the results of an in-depth study of the flow past a streamwise oscillating cylinder, examining the impact of varying the amplitude and frequency of the oscillation, and the Reynolds number of the incoming flow. These findings are presented in a framework that shows that the relationship between the frequency of vortex shedding ${f}_{s} $ and the amplitude of oscillation ${A}^{\ast } $ is governed by two primary factors: the first is a reduction of ${f}_{s} $ proportional to a series in ${A}^{\ast 2} $ over a wide range of driving frequencies and Reynolds numbers; the second is nonlinear synchronization when this adjusted ${f}_{s} $ is in the vicinity of $N= {(1- {f}_{s} / {f}_{d} )}^{- 1} $ , where $N$ is an integer. Typically, the influence of higher-order terms is small, and truncation to the first term of the series ( ${A}^{\ast 2} $ ) well represents the overall trend of vortex shedding frequency as a function of amplitude. However, discontinuous steps are overlaid on this trend due to the nonlinear synchronization. When ${f}_{s} $ is normalized by the Strouhal frequency ${f}_{St} $ (the frequency of vortex shedding from an unperturbed cylinder), the rate at which ${f}_{s} / {f}_{St} $ decreases with amplitude, at least for ${f}_{d} / {f}_{St} = 1$ , shows a linear dependence on the Reynolds number. For a fixed $\mathit{Re}= 175$ , the truncated series shows that the rate of decrease of ${f}_{s} / {f}_{St} $ with amplitude varies as ${(2- {f}_{d} / {f}_{St} )}^{- 1/ 2} $ for $1\leqslant {f}_{d} / {f}_{St} \leqslant 2$ , but is essentially independent of ${f}_{d} / {f}_{St} $ for ${f}_{d} / {f}_{St} \lt 1$ . These trends of the rate of decrease of ${f}_{s} $ with respect to amplitude are also used to predict the amplitudes of oscillation around which synchronization occurs. These predicted amplitudes are shown to fall in regions of the parameter space where synchronized modes occur. Further, for the case of varying ${f}_{d} / {f}_{St} $ , a very reasonable prediction of the amplitude of oscillation required for the onset of synchronization to the mode where ${f}_{s} = 0. 5{f}_{d} $ is given. In a similar manner, amplitudes at which ${f}_{s} = 0$ are calculated, predicting where the natural vortex shedding is completely supplanted by the forcing. These amplitudes are found to coincide approximately with those at which the onset of a symmetric vortex shedding mode is observed. This result is interpreted as meaning that the symmetric shedding mode occurs when the dynamics crosses over from being dominated by the vortex shedding to being dominated by the forcing.