Miracle-dz/UniFAR-FTUs huggingface dataset:
Some factors affecting the estimation of genetic parameters for cattle dystocia under a threshold model

Genetic parameters for dystocia in the Main-Anjou breed were estimated. Data consisted of 28 178 birth records collected between 1978 and 1989 in 995 herds, with 161, 71 and 12 415 sires, maternal grandsires and dams, respectively, represented. Original scores (1 through 5) were collapsed in order to set two dystocia definitions: dystocia 1 (scores 1+2 v. 3+4+5) and dystocia 2 (scores 1 v. 2+3+4+5). Four models were proposed for genetic parameter estimation: (1) fixed effects plus sire effects; (2) model 1 plus maternal grandsire effect; (3) model 2 plus dam within maternal grandsire effects; (4) same as model 3 but a random effect ‘herds’ replaced a fixed effect ‘regions’. Two methods of fitting models were applied: marginal maximum likelihood and the ‘tilde-hat’ approach. Estimates of genetic parameters by the two methods were similar. Models ignoring maternal effects overestimated the heritability of direct effects especially in the case of dystocia 2. Dystocia definition was responsible for the greatest difference among estimated genetic parameters. Possible reasons for this are discussed. When analysing large data sets, it is recommended judiciously to collapse dystocia categories and to apply approximate statistical procedures to complete models including maternal effects.
The impact of signal variability on epidemic growth rate estimation from wastewater surveillance data

Background: Testing samples of waste water for markers of infectious disease became a widespread method of surveillance during the COVID-19 pandemic. While these data generally correlate well with other indicators of national prevalence, samples that cover localised regions tend to be highly variable over short time scales. Methods: We introduce a procedure for estimating the real-time growth rate of pathogen prevalence using time series data from wastewater sampling. The number of copies of a target gene found in a sample is modelled as time-dependent random variable whose distribution is estimated using maximum likelihood. The output depends on a hyperparameter that controls the sensitivity to variability in the underlying data. We apply this procedure to data reporting the number of copies of the N1 gene of SARS-CoV-2 collected at water treatment works across Scotland between February 2021 and February 2023. Results: The real-time growth rate of the SARS-CoV-2 prevalence is estimated at 121 wastewater sampling sites covering a diverse range of locations and population sizes. We find that the sensitivity of the fitting procedure to natural variability determines its reliability in detecting the early stages of an epidemic wave. Applying the procedure to hospital admissions data, we find that changes in the growth rate are detected an average of 2 days earlier in wastewater than in hospital admissions data. Conclusion: We provide a robust method to generate reliable estimates of epidemic growth from highly variable data. Applying this method to samples collected at wastewater treatment works provides highly responsive situational awareness to inform public health.
Mpox vaccine and infection-driven human immune signatures

Background Mpox (formerly known as monkeypox) outbreaks outside endemic areas peaked in July 2022, infecting > 85,000 people and raising concerns about our preparedness against this emerging viral pathogen. Licensed and approved for mpox, the JYNNEOS vaccine has fewer side effects than previous smallpox vaccines and demonstrated efficacy against mpox infection in humans. Comparing JYNNEOS vaccine- and mpox-induced immunity is imperative to evaluate its immunogenicity and inform vaccine administration and design. Methods We examined the polyclonal serum (ELISA) and single B cell (heavy chain gene and transcriptome data) antibody repertoires and T cells (AIM and ICS assays) induced by the JYNNEOS vaccine as well as mpox infection. Findings Gene-level plasmablast and antibody responses were negligible and JYNNEOS vaccinee sera displayed minimal binding to recombinant mpox proteins and native proteins from the 2022 outbreak strain. In contrast, recent mpox infection (within 20-102 days) induced robust serum antibody responses to A29L, A35R, A33R, B18R, and A30L, and 4/6 convalescent sera were reactive to native mpox proteins. JYNNEOS vaccine recipients presented comparable CD4 and CD8 T cell responses against orthopox peptides to those observed after mpox infection. Interpretation: JYNNEOS immunization does not elicit a robust B cell response, and its immunogenicity may be mediated by T cells.
Influences on policy-formulation, decision-making, organisation and management for maternal, newborn and child health in Bangladesh, Ethiopia, Malawi and Uganda: The roles and legitimacy of a multi-country network

The Network for Improving Quality of Care for Maternal, Newborn and Child Health (QCN) is intended to facilitate learning, action, leadership and accountability for improving quality of care in member countries. This requires legitimacy--a networks right to exert power within national contexts. This is reflected, for example, in a governments buy-in and perceived ownership of the work of the network. During 2019- 2022 we conducted iterative rounds of stakeholder interviews, observations of meetings, document review, and hospital observations in Bangladesh, Ethiopia, Malawi, Uganda and at the global level. We developed a framework drawing on three frameworks: Tallberg and Zurn which conceptualizes legitimacy of international organisations dependent on their features, the legitimation process and beliefs of audiences; Nasiritousi and Faber, which looks at legitimacy in terms of problem, purpose, procedure, and performance of institutions; Sanderink and Nasiritousi, to characterize networks in terms of political, normative and cognitive interactions. We used thematic analysis to characterize, compare and contrast institutional interactions in a cross-case synthesis to determine salient features. Political and normative interactions were favourable within and between countries and at global level since collective decisions, collaborative efforts, and commitment to QCN goals were observed at all levels. Sharing resources and common principles were not common between network countries, indicating limits of the network. Cognitive interactions--those related to information sharing and transfer of ideas-- were more challenging, with the bi-directional transfer, synthesis and harmonization of concepts and methods, being largely absent among and within countries. These may be required for increasing government ownership of QCN work, the embeddedness of the network, and its legitimacy. While we find evidence supporting the legitimacy of QCN from the perspective of country governments, further work and time are required for governments to own and embed the work of QCN in routine care.
Index cases first identified by nasal-swab rapid COVID-19 tests had more transmission to household contacts than cases identified by other test types

Importance: At-home rapid COVID-19 tests utilize nasal-swab specimens and require high viral loads to reliably give positive results. Longitudinal studies from the onset of infection have found infectious virus can present in oral specimens days before nasal. Detection and initiation of infection-control practices may therefore be delayed when nasal-swab rapid tests are used, resulting in greater exposure and transmission to contacts. Objective: We assessed whether index cases first identified by rapid nasal-swab COVID-19 tests had more transmission to household contacts than index cases who used other test types (tests with higher analytical sensitivity but longer turnaround times, and/or that utilize non-nasal specimen types). Design: In this observational cohort study, members of households with a recent COVID-19 case were screened for infection at least daily by RT-qPCR on one or more self-collected upper-respiratory specimen types. Participants reported demographic/medical information (including COVID-19 testing), symptom and exposure information, and household infection-control practices. A two-level random intercept model was used to assess the association between the infection outcome of household contacts and each covariable (household size, race/ethnicity, age, vaccination status, viral variant, infection-control practices, and whether a rapid nasal-swab test was used to initially identify the household index case). Setting: Southern California, September 2020-June 2021 and November 2021-March 2022. Participants: Cohort of 370 individuals from 85 households. Main Outcome(s) and Measure(s): Transmission was quantified by adjusted secondary attack rates (aSAR) and adjusted odds ratios (aOR). Results: An aSAR of 53.6% (95%CI 38.8-68.3%) was observed among households where the index case first tested positive by a rapid nasal-swab COVID-19 test, which was significantly higher than the aSAR for households where the index case utilized another test type (27.2% [19.5-35.0%], P=0.003 pairwise comparisons of predictive margins). We observed an aOR of 4.90 (95%CI 1.65-14.56) for transmission to household contacts when a nasal-swab rapid test was used to identify the index case, compared to other test types. Conclusions and Relevance: Use of nasal-swab rapid COVID-19 tests for initial detection of infection and initiation of infection control may not limit transmission as well as other test types.
Comparison of volumetric brain analysis in subjects with rheumatoid arthritis and ulcerative colitis

Objectives: Rheumatoid arthritis (RA) and ulcerative colitis (UC) are two autoimmune diseases where patients report high levels of fatigue, pain, and depression. The effect of systemic inflammation from these diseases is likely affecting the brain, however, it is unknown whether there are measurable neuroanatomical changes and whether these are a contributing factor to these central symptoms. Methods: We included 258 RA patients with 774 age and sex matched controls and 249 UC patients with 747 age and sex matched controls in a case control study utilising the UK Biobank dataset. We used imaging derived phenotypes (IDPs) to determine whether there were differences in (1) hippocampal volume and (2) additional subcortical brain volumes between patients compared to controls and if there were common regions affected between these two diseases. Results: Patients with UC had moderately smaller hippocampi compared to age and sex matched controls (difference: 134.15 mm3, SD {+/-} 64.76, p = 0.035). This result was not seen in RA patients. RA patients had a significantly smaller amygdala volume than age and sex matched controls (difference: 91.27 mm3, SD {+/-} 30.85, p = 0.0021, adjusted p value = 0.012). This result was not seen in UC patients. All other subcortical structures analysed were comparable between the patients and control groups. Conclusion: These results indicate there are subcortical brain differences between UC, RA and controls but different regions of the limbic system are preferentially affected by UC and RA. This study may provide evidence for different neurodegenerative mechanisms in distinct autoimmune diseases.
Prospective Bidirectional Relations Between Depression and Metabolic Health: 30 Year Follow-up from the NHLBI CARDIA Study

Objective: This study investigated prospective bidirectional relationships between depression and metabolic syndrome (MetS), and the moderating effects of race, sex, and health behaviors in a diverse cohort followed for 30 years. Methods: Data were analyzed from the NHLBI CARDIA study, a 30 year-prospective study of young adults (N = 5113; M age = 24.76 (SD = 3.63) at baseline; 45% male) who were tested every 5 years between 1985-2015. Measures included biological assessments of MetS components, and self-reported depressive symptoms based on the Center for Epidemiologic Studies Depression (CESD) scale. Data analyses included bi-directional general estimating equations analyses of time-lagged associations between depressive symptoms and MetS. Results: There was a consistent, bi-directional relationship between depressive symptoms and MetS over time. Individuals with more CESD depressive symptoms were more likely to develop MetS over time compared to those reporting fewer symptoms (Wald Chi-Square = 7.09 (1), p < 0.008), and MetS was similarly predictive of CESD. MetS more consistently predicted depressive symptoms at each 5-year exam than depressive symptoms predicted MetS. Race and sex moderated relationships between depression and MetS, with White females, White individuals overall, and females overall demonstrating significant relationships. Health behaviors were not related to depression-MetS associations. Conclusion: In a diverse young adult population prospectively followed into late middle age, MetS more consistently predicted depression over time than depression predicted MetS. The relation between MetS and depressive symptoms was moderated by race and sex, but not health behaviors. Keywords: metabolic syndrome, depression, race, sex, longitudinal study
Population‐level lateralization of boxing displays enhances fighting success in male Great Himalayan leaf‐nosed bats

Abstract Behavioral lateralization with left‐ and right‐hand use is common in the Animal Kingdom and can be advantageous for social species. The existence of a preferential use of the hands during agonistic interactions has been described for a number of invertebrate and vertebrate species. Bats compose the second largest order of mammals. They not only use their forelimbs for flight but also agonistic interactions. However, whether bat species show a population‐level lateralized aggressive display has largely been unexplored. Here, we examine the lateralization of boxing displays during agonistic interactions in male Great Himalayan leaf‐nosed bats, Hipposideros armiger, from three different populations. We found a population‐level lateralization of boxing displays: Males from all three populations show a preferential use of the left forearm to attack opponents. In addition, left‐handed boxers have higher fighting success over right‐handed boxers. This study expands our knowledge of the handedness of bats and highlights the role of behavioral lateralization in conflict resolution in nocturnal mammals.
Aberrant immunoexpression of p53 tumour-suppressor and Bcl-2 family proteins (Bcl-2 and Bax) in ameloblastomas and odontogenic keratocysts

Background The growth of ameloblastomas (odontogenic tumours) and odontogenic keratocyst (OKC) (developmental cyst) is associated with the expression of proteins related to cell survival and apoptosis. Bcl-2-associated protein X (Bax) and the tumour suppressor protein p53 collectively promote p53-mediated apoptosis. This study aimed to assess the immunohistochemical expression of p53, Bcl-2 and Bax in conventional ameloblastoma (CA), unicystic ameloblastoma (UA) types, and OKC sporadic (OKC-NS/S) and syndromic (OKC-NBSCC). Material and Methods Paraffinized blocks of CA (n=18), UA (n=15), OKC-NS/S (n=18) and OKC-NBSCC (n=15) fixed in 10% formalin were used. After diagnosis, tissue specimens were stained by immunohistochemistry for p53, Bcl-2 and Bax marker. Stained cells were randomly counted in five high power fields. The data analysis was performed via Shapiro-Wilk test, ANOVA with Tukey’s multiple comparisons or Kruskal-Wallis with Dunn’s multiple comparisons. Statistical significance was defined as p<0.05. Results We did not observe differences between p53 expression in CA, mural UA (MUA), intraluminal/luminal UA (I/LUA), OKC-NS/S, and OKC-NBSCC (19.69%, 18.74%, 16.76%, 12.35% and 9.04%, respectively). Similar results were recognized for Bax expression in CA, MUA, I/LUA, OKC-NS/S, and OKC-NBSCC (33.72%, 34.95%, 22.94, 21.58% and 20.76%, respectively). However, we recognized significant differences between Bcl-2 expression in OKC-NS/S vs MUA, OKC-NS/S vs I/LUA, OKC-NS/S vs CA, OKC-NBSCC vs MUA, OKC-NBSCC vs I/LUA, and I/LUA vs CA. P53, Bcl-2 and Bax levels were higher in mural morphological areas versus intraluminal and luminal morphological areas in UA. Conclusions There is a tendency for an increased expression of p53, Bcl-2, and Bax proteins in CA, and mural proliferation of UA, compared to lesions with a cystic morphology, which could be associated with a local aggressive behaviour. Key words:p53, Bcl-2, Bax protein, apoptosis, odontogenic tumour, odontogenic cyst.
Noninvasive measurement of local stress inside soft materials with programmed shear waves

Mechanical stresses across different length scales play a fundamental role in understanding biological systems’ functions and engineering soft machines and devices. However, it is challenging to noninvasively probe local mechanical stresses in situ, particularly when the mechanical properties are unknown. We propose an acoustoelastic imaging–based method to infer the local stresses in soft materials by measuring the speeds of shear waves induced by custom-programmed acoustic radiation force. Using an ultrasound transducer to excite and track the shear waves remotely, we demonstrate the application of the method by imaging uniaxial and bending stresses in an isotropic hydrogel and the passive uniaxial stress in a skeletal muscle. These measurements were all done without the knowledge of the constitutive parameters of the materials. The experiments indicate that our method will find broad applications, ranging from health monitoring of soft structures and machines to diagnosing diseases that alter stresses in soft tissues.
Efficient sampling of rare event pathways: from simple models to nucleation

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The impact of COVID-19 pandemic on the health services provided by the Cardiothoracic Minia University Hospital in Egypt: A single-center retrospective observational study

Background The emergence of the new coronavirus (severe acute respiratory syndrome coronavirus 2, or SARS-CoV-2) in late 2019 resulted in a worldwide pandemic, which had severe consequences on the global health systems. There were drastic strains on the public health services. This, in turn, markedly affected patients with non-coronavirus disease (COVID-19) problems. Aim This study aimed to evaluate the impact of COVID-19 infection on the health services provided to patients at the cardiothoracic university hospital, Minia University. Methods A retrospective analysis of data about services provided to patients at Minia Cardiothoracic University hospital was obtained from pre-pandemic era (2018–2019) and during the pandemic time (2020–2021). The two sets of data were compared together. Data were collected about the number of patients who underwent different procedures such as Pulmonary Function Tests (PFTs), sleep studies or interventional chest procedures (bronchoscopy and thoracoscopy). Also, data were collected about the number of patients admitted in the chest ward, respiratory intensive care unit (ICU) or Coronary care unit and the number of patients who visited cardiothoracic, cardiology or chest outpatient clinics. Results There is 81.4% reduction in the number of Pulmonary Function Testsperformed during the period 2020–2021 compared with the period 2018–2019, where the number of patients admitted to chest inward decreased by 66.4%. The number of sleep studies performed reduced by 61.5%, while the number of different outpatient clinical visits reduced to similar values (45.8% for cardiothoracic clinic, 45.4% for cardiology clinic and 40.5% for chest clinic). Regarding respiratory ICU admissions, the study reported a reduction of 35.7% and also Coronary care unit admissions decreased by 30.6%. Interventional pulmonary procedures had the lowest reduction rate (0.7%). Conclusion Different health services were negatively affected by the emergence of COVID-19 era in both pulmonary and non-pulmonary fields.
Semiparametric Comparison of Regression Curves

The comparison of nonparametric regression curves is considered. It is assumed that there are parametric (possibly nonlinear) transformations of the axes which map one curve into the other. Estimation and testing of the parameters in the transformations are studied. The rate of convergence is n −1/2 although the nonparametric components of the model typically have a rate slower than that. A statistic is provided for testing the validity of a given completely parametric model
Linking plant diversity–productivity relationships to plant functional traits of dominant species and changes in soil properties in 15‐year‐old experimental grasslands

Abstract Positive plant diversity–productivity relationships are known to be driven by complementary resource use via differences in plant functional traits. Moreover, soil properties related to nutrient availability were shown to change with plant diversity over time; however, it is not well‐understood whether and how such plant diversity‐dependent soil changes and associated changes in functional traits contribute to positive diversity–productivity relationships in the long run. To test this, we investigated plant communities of different species richness (1, 2, 6, and 9 species) in a 15‐year‐old grassland biodiversity experiment. We determined community biomass production and biodiversity effects (net biodiversity [NEs], complementarity [CEs], and selection effects [SEs]), as well as community means of plant functional traits and soil properties. First, we tested how these variables changed along the plant diversity gradient and were related to each other. Then, we tested for direct and indirect effects of plant and soil variables influencing community biomass production and biodiversity effects. Community biomass production, NEs, CEs, SEs, plant height, root length density (RLD), and all soil property variables changed with plant diversity and the presence of the dominant grass species Arrhenatherum elatius (increase except for soil pH, which decreased). Plant height and RLD for plant functional traits, and soil pH and organic carbon concentration for soil properties, were the variables with the strongest influence on biomass production and biodiversity effects. Our results suggest that plant species richness and the presence of the dominant species, A. elatius, cause soil organic carbon to increase and soil pH to decrease over time, which increases nutrient availability favoring species with tall growth and dense root systems, resulting in higher biomass production in species‐rich communities. Here, we present an additional process that contributes to the strengthening positive diversity–productivity relationship, which may play a role alongside the widespread plant functional trait‐based explanation.