Miracle-dz/UniFAR-FTUs huggingface dataset:
Equivalence of prospective and retrospective models in the Bayesian analysis of case-control studies

The natural likelihood to use for a case-control study is a 'retrospective' likelihood, i.e. a likelihood based on the probability of exposure given disease status. Prentice & Pyke (1979) showed that, when a logistic regression form is assumed for the probability of disease given exposure, the maximum likelihood estimators and asymptotic covariance matrix of the log odds ratios obtained from the retrospective likelihood are the same as those obtained from the 'prospective' likelihood, i.e. that based on probability of disease given exposure. We prove a similar result for the posterior distribution of the log odds ratios in a Bayesian analysis. This means that the Bayesian analysis of case-control studies may be done using a relatively simple model, the logistic regression model, which treats data as though generated prospectively and which does not involve nuisance parameters for the exposure distribution. Copyright Biometrika Trust 2004, Oxford University Press.
A Simplified Risk Score to Predict In-Hospital Newly-Diagnosed Atrial Fibrillation in Acute Ischemic Stroke Patients

Purpose Atrial fibrillation (AF) is a significant cause of stroke, and newly diagnosed AF (NDAF) is typically detected in the early period of stroke onset. We aimed to identify the factors associated with in-hospital NDAF in acute ischemic stroke patients and developed a simplified clinical prediction model. Methods Patients with cryptogenic stroke aged 18 years or older who were admitted between January 2017 and December 2021 were recruited. NDAF was determined by inpatient cardiac telemetry. Univariable and multivariable regression analyses were used to evaluate the factors associated with in-hospital NDAF. The predictive model was developed using regression coefficients. Results The study enrolled 244 eligible participants, of which 52 NDAFs were documented (21.31%), and the median time to detection was two days (1–3.5). After multivariable regression analysis, parameters significantly associated with in-hospital NDAF were elderly (>75 years) (adjusted Odds ratio, 2.99; 95% confident interval, 1.51–5.91; P = 0.002), female sex (2.08; 1.04–4.14; P = 0.04), higher admission national institute of health stroke scale (1.04; 1.00–1.09; P = 0.05), and presence of hyperdense middle cerebral artery sign (2.33; 1.13–4.79; P = 0.02). The area under the receiver operating characteristic curve resulted in 0.74 (95% CI 0.65–0.80), and the cut-point of 2 showed 87% sensitivity and 42% specificity. Conclusion The validated and simplified risk scores for predicting in-hospital NDAF primarily rely on simplified parameters and high sensitivity. It might be used as a screening tool for in-hospital NDAF in stroke patients who initially presumed cryptogenic stroke.
Dynamical Tropical Cyclone Track Forecast Errors. Part I: Tropical Region Error Sources

Abstract All highly erroneous (>300 n mi or 555 km at 72 h) Navy Operational Global Atmospheric Prediction System (NOGAPS) and U.S. Navy version of the Geophysical Fluid Dynamics Laboratory model (GFDN) tropical cyclone track forecasts in the western North Pacific during 1997 are examined. Responsible error mechanisms are described by conceptual models that are all related to known tropical cyclone motion processes that are being misrepresented in the dynamical models. Error mechanisms that predominantly occur while the tropical cyclone is still in the Tropics are described in this paper, and those errors that are more related to midlatitude circulations are addressed in a companion paper. Of the 69 NOGAPS large-error cases, 39 were attributed to excessive direct cyclone interaction (E-DCI), 12 cases of excessive ridge modification by the tropical cyclone (E-RMT), and 10 cases of excessive reverse trough formation (E-RTF). Of the 50 GFDN large-error cases, 31 were E-DCI, and only two E-RMT and two E-RTF c.
Dihydrotestosterone, and Not Testosterone, Enhances the LPS-Induced Inflammatory Cytokine Gene Expression in Human Adipocytes

Background: The development of obesity-related complications lies in the low-grade inflammatory state consequent to adipocyte dysfunction. The direct involvement of sex hormones in adipose tissue inflammation has been previously suggested, but the evidence is scarce. In this study, we evaluated the effects of sex steroids on the in-vitroexpression of inflammatory mediators in human-derived adipocytes before and after lipopolysaccharide (LPS) exposure. Methods: Human adipocytes were differentiated from the vascular stromal fraction of adipose tissue samples of subjects undergoing abdominoplasty. We evaluated MCP-1, IL-1β, IL-6, and TNF-α gene expression in the presence of the main sex steroids, testosterone (T), and 17β-estradiol (E). Furthermore, we analyzed the effects of adipocytes exposure to the non-aromatizable androgen dihydrotestosterone (DHT), together with the effects of adipocytes pre-incubation with the aromatase inhibitor anastrozole alone (A), and in combination with T (A/T) before incubation with LPS. Results: DHT, but not T, significantly enhanced the LPSinduction of MCP-1, IL-1β, IL-6, and TNF-α. Intriguingly, the exposure of adipocytes with A/T dramatically increased the LPS-induced expression of all considered inflammatory cytokines, even more than a hundred-fold. Conclusions: DHT and A/T dramatically enhance LPS-induced inflammatory cytokine expression in human-derived adipocytes. These results confirm the involvement of sex hormones in adipose tissue inflammation, suggesting a specific role for non-aromatizable androgens as the amplificatory sex hormones of the inflammatory response.
Functional Analysis of a Novel, Non-Canonical RPGR Splice Variant Causing X-Linked Retinitis Pigmentosa

X-linked retinitis pigmentosa (XLRP) caused by mutations in the RPGR gene is one of the most severe forms of RP due to its early onset and intractable progression. Most cases have been associated with genetic variants within the purine-rich exon ORF15 region of this gene. RPGR retinal gene therapy is currently being investigated in several clinical trials. Therefore, it is crucial to report and functionally characterize (all novel) potentially pathogenic DNA sequence variants. Whole-exome sequencing (WES) was performed for the index patient. The splicing effects of a non-canonical splice variant were tested on cDNA from whole blood and a minigene assay. WES revealed a rare, non-canonical splice site variant predicted to disrupt the wildtype splice acceptor and create a novel acceptor site 8 nucleotides upstream of RPGR exon 12. Reverse-transcription PCR analyses confirmed the disruption of the correct splicing pattern, leading to the insertion of eight additional nucleotides in the variant transcript. Transcript analyses with minigene assays and cDNA from peripheral blood are useful tools for the characterization of splicing defects due to variants in the RPGR and may increase the diagnostic yield in RP. The functional analysis of non-canonical splice variants is required to classify those variants as pathogenic according to the ACMG’s criteria.
Moral foundations and perceptions of rape in Colombia (Fundamentos morales y percepciones del abuso sexual en Colombia)

ABSTRACT Two studies addressed links between moral foundations, political attitudes, religiosity and perceptions of rape in Colombian respondents. In Study 1, the authors developed a Colombian version of the Moral Foundations Questionnaire (MFQ). In Study 2, the MFQ was further validated in relation to the acceptance of modern myths about sexual aggression (AMMSA), victim vs. perpetrator blaming regarding a rape vignette, political orientation and attitudes towards religion. Results showed that the Colombian MFQ was more reliable than an existing Spanish version. Endorsement of conservative foundations (ingroup loyalty, obedience to authority and purity) predicted right-wing political attitudes, higher religiosity, higher AMMSA and more rape victim blaming. Conversely, endorsement of liberal foundations (care and justice) predicted lower SDO and less rape victim blaming. These results replicate and extend previous work, including the critique that conservative foundations may reflect amoral attitudes rather than universal moral intuitions. Implications and requirements for further research are discussed.
Determination of Hypoglycemic, Hypolipidemic and Nephroprotective Effects of Berberis Calliobotrys in Alloxan-Induced Diabetic Rats

Many plants of the Berberis genus have been reported pharmacologically to possess anti-diabetic potential, and Berberis calliobotrys has been found to be an inhibitor of α-glucosidase, α-amylase and tyrosinase. Thus, this study investigated the hypoglycemic effects of Berberis calliobotrys methanol extract/fractions using in vitro and In vivo methods. Bovine serum albumin (BSA), BSA–methylglyoxal and BSA–glucose methods were used to assess anti-glycation activity in vitro, while in vivo hypoglycemic effects were determined by oral glucose tolerance test (OGTT). Moreover, the hypolipidemic and nephroprotective effects were studied and phenolics were detected using high performance liquid chromatography (HPLC). In vitro anti-glycation showed a significant reduction in glycated end-products formation at 1, 0.25 and 0.5 mg/mL. In vivo hypoglycemic effects were tested at 200, 400 and 600 mg/kg by measuring blood glucose, insulin, hemoglobin (Hb) and HbA1c. The synergistic effect of extract/fractions (600 mg/kg) with insulin exhibited a pronounced glucose reduction in alloxan diabetic rats. The oral glucose tolerance test (OGTT) demonstrated a decline in glucose concentration. Moreover, extract/fractions (600 mg/kg) exhibited an improved lipid profile, increased Hb, HbA1c levels and body weight for 30 days. Furthermore, diabetic animals significantly exhibited an upsurge in total protein, albumin and globulin levels, along with a significant improvement in urea and creatinine after extract/fractions administration for 42 days. Phytochemistry revealed alkaloids, tannins, glycosides, flavonoids, phenols, terpenoids and saponins. HPLC showed the presence of phenolics in ethyl acetate fraction that could be accountable for pharmacological actions. Therefore, it can be concluded that Berberis calliobotrys possesses strong hypoglycemic, hypolipidemic and nephroprotective effects, and could be a potential therapeutic agent for diabetes treatment.
Transport into the troposphere in a tropopause fold

A tropopause fold developed to the west of the British Isles on the western flank of a trough in the 300 mb flow on 6 October 1990. Radiosonde ascents over western Europe showed very dry stable layers beneath the jet stream in the potential temperature range 310-315 K. These were evident on profiles from 12h 6 October to 00h 8 October. The European Centre for Medium-range Weather Forecasts (ECMWF) model assimilations were examined for this period to determine how well they represented the radiosonde observations. Good agreement was found, especially for the humidity distribution. The model overestimated the vertical extent of the fold by a factor of about 2, so its representation of potential vorticity was less successful. Nevertheless, agreement was sufficiently good for the model to be used to evaluate the amount of stratosphere-troposphere exchange in the event. Isentropic trajectories were calculated for the air in the fold as represented by the ECMWF assimilation at 00h on the 7th. Those on the western edge of the fold split from the jet stream and transferred to the troposphere, while those on the eastern side ended up in the cut-off low. The model fields were used to estimate a lower bound of 1.1 × 1014 kg and2 × 1032 molecules for the amount of stratospheric air and ozone, respectively, transferred into the troposphere by this fold. Owing to the model's incomplete representation of the event, the actual amount transferred may be at least twice this estimate.
MANIFOLDS WITH CONICAL ENDS, PART II

Let ⊂ RN be a compact imbedded Riemannian manifold of dimension d ≥ 1 and define the (d+1)-dimensional Riemannian manifold M := {(x, r(x)ω) : x ∈ R, ω ∈ } with r > 0 and smooth, and the natural metric ds 2 = (1+r ' (x) 2 )dx 2 +r 2 (x)ds 2 . We require that M has conical ends: r(x) = |x|+O(x −1 ) as x → ±∞. The Hamiltonian flow on such manifolds always exhibits trapping. Dispersive estimates for the Schrodinger evolution e itM and the wave evolution e it √ −�M are obtained for data of the form f(x, ω) = Yn(ω)u(x) where Yn are eigenfunctions of −� with eigenvalues � 2. In this paper we discuss all cases d + n > 1. If n 6 0 there is the following accelerated local decay estimate: with 0 0. In particular, we introduce the notion of a zero energy resonance for this class and derive an asymptotic expansion of the Wronskian between the outgoing Jost solutions as the energy tends to zero. In particular, the division into Part I and Part II can be explained by the former being resonant at zero energy, where the present paper deals with the nonresonant case. (B) estimation of oscillatory integrals by (non)stationary phase.
Convergence of Pseudo Posterior Distributions under Informative Sampling

An informative sampling design assigns probabilities of inclusion that are correlated with the response of interest and induces a dependence among sampled observations. Unadjusted model-based inference performed on data acquired under an informative sampling design can be biased concerning parameters of the population generating distribution if the sample design is not accounted for in the model. Known marginal inclusion probabilities may be used to weight the likelihood contribution of each observed unit to form a "pseudo" posterior distribution with the intent to adjust for the design. This article extends a theoretical result on the consistency of the posterior distribution, defined on an analyst-specified model space, at the true generating distribution to the sampling-weighted pseudo posterior distribution used to account for an informative sampling design. We construct conditions on known marginal and pairwise inclusion probabilities that define a class of sampling designs where consistency of the pseudo posterior is achieved, in probability. We demonstrate the result on an application concerning the Bureau of Labor Statistics Job Openings and Labor Turnover Survey.
Evaluation of the Effect of Distant Cold Stimulation on Pain During Palatal Injection: A Randomized Split-Mouth Study

Objective Delivery of a robust local anesthetic injection aids in the successful management of all patients' fears, anxieties, and discomfort during dental treatments. The most expected or frightening stimuli in the dental operatory are local anesthetic injections. The objective of this trial was to study the analgesic efficacy of distant cold stimulation in relieving injection pain from the greater palatine nerve block. Before receiving local anesthetic injections, employing cryotherapy by using an ice bath changes the pain perceptions and also increases the pain threshold. Purpose The aim of this study is to evaluate the effect of distant cold stimulation on palatal injection pain using an ice-cold bath. Method This was a randomized, controlled trial conducted at an oral and maxillofacial surgery department. A split-mouth technique was employed for the study, in which patients requiring bilateral greater palatine nerve block for any dental procedures were included. The bilateral greater palatine nerve block was given one at a time, separated by an interval of three days. The inclusion criteria for this study were no history of drug allergy and an extraction site free of any active infection. There were 28 participants in this experimental study. Two groups were randomly created from this research sample: group A (palatal injection with distant cold stimulation) and group B (palatal injection without distant cold stimulation). In group A, the patient was asked to put his or her hand of the same side as the palatal injection in an ice-cold bath till the time patient could tolerate it; immediately after the patient removed his hand, the greater palatine nerve block was given, and the patient was assessed for the injection pain. In group B, the patient was directly given the greater palatine nerve block without any distant cold stimulation. The time interval between the two extractions/dental procedures was three days. Outcomes of interest were pain severity with and without distant cold stimulation which were assessed using a Visual Analogue Scale (VAS) pain scale, and a comparison was made between the two groups. Results As per our study, in terms of pain, there was a statistically significant difference between the two interventions at all time points. Patients in group A had a lower score on the VAS pain scale as compared to group B. The standard deviation (STD) for group A was 0.81, and the standard deviation for group B was 0.92. P value was derived to be P < 0.001, which is suggestive of a significant difference between the pain scores of both groups. Conclusion Hence, we conclude that the use of distant cryotherapy as an adjunct is an effective way to reduce pain perception and increase pain threshold. This technique is comparatively simple, painless, and easy for the surgeon and for apprehensive patients, and it offers a fair cost solution for the suffering often associated with dental procedures requiring local anesthetic injections.
Developments of Tracking Methods of Muon Pairs with SeaQuest Spectrometer

The SeaQuest experiment is a fixed-target experiment located at Fermi Nation Accelerator Laboratory (Fermilab). It detects Drell-Yan muon pairs from protonproton collisions induced by a 120GeV beam ( √ s= 11GeV). A new method which allows the track reconstruction of dimuons in high multiplicity data recorded during the first commissioning run at the SeaQuest experiment is presented in this thesis. The SeaQuest spectrometer is a forward spectrometer optimized by a focusing magnet to be particularly sensitive to high-pT muon pairs. A large iron block is placed inside the focusing magnet to stop hadronic background. Four tracking stations are used for track reconstruction. The first three stations consist of drift chambers, and the fourth station consists of drift tubes. Hodoscope arrays in each tracking station trigger dimuon events. A separate analyzing magnet measures the momenta of muons. The Drell-Yan process occurs in high-energetic hadron collisions when a quark of one hadron and an antiquark of another hadron annihilate, creating a virtual photon, which then decays into a pair of oppositely charged muons. The dimuon kinematics are directly related to the antiquarks in the proton. In spring 2012, the first 120GeV proton beam was successfully extracted from the Fermilab Main Injector Ring to the fixed target beamline of SeaQuest. The average intensity of the protons during the 6 weeks of commissioning run was 7× 1011 per spill. This thesis reports developments of analysis methods for the dimuon track reconstruction based on data from the commissioning run. The track reconstruction at SeaQuest consists of two steps: the ’track finding’ which combines hits in the different drift chambers to a track candidate, and the ’track fitting’ which determines the momentum of a muon track based on the known map of the magnetic field of the spectrometer. The duty factor of the delivered beam during the commissioning run was unstable and it caused large multiplicities. The average occupancies of the drift chambers were between 30% and 60% in each tracking station per event. In order to deal with these high occupancies, an innovative track finder algorithm was developed. It is capable of quickly correlating dimuon hits in the first three tracking stations and building track candidates with an efficiency above 98%. The drift chamber occupancies could be reduced to 10% by only considering drift chamber hits which can successfully be associated to muon track candidates. The algorithm significantly improved the absolute yield of reconstructed dimuons. IV
FULLY COUPLED ANALYSIS OF ORBIT RESPONSE MATRICES AT THE ALS

In order to understand the current limitations of the dynamic (momentum) aperture it is essential to have a good model representing the realistic lattice. Since some years an analysis of measured orbit response matrices is used to calibrate the lattice model at the ALS. Measurements of the response matrices are carried out weekly. Recently the orbit response matrix analysis has been expanded to a fully coupled analysis. In order to keep the computation time needed for the coupled analysis of a complete response matrix in resonable limits a new algorithm to calculate the model response matrix elements was written. The modified code was successfully used to determine localized coupling strengths. Predictions of the calibrated, coupled model are in good agreement with the results of independent measurements of several machine parameters.
Methodology for Analyzing Coupling Mechanisms in RFI Problems Based on PEEC

In this article, a method for analyzing coupling mechanisms in radio frequency interference (RFI) problems is proposed. The partial element equivalent circuit (PEEC) method is first used to derive the retarded inductances and capacitances between different mesh cells. With the introduction of a novel partitioning algorithm, the capacitive coupling and inductive coupling between arbitrary layout parts can be quantified based on the magnitude of the displacement current and induced voltage drop. The accuracy of the PEEC models is validated by comparison with different commercial tools. The proposed coupling mechanism analysis flow provides a useful prelayout tool for RFI risk analysis.
Impacts of Rock Mineral and Traditional Phosphate Fertilizers on Mycorrhizal Communities in Pasture Plants

Intensive fertilizer use can constrain contributions from soil biological processes in pastures, including those associated with arbuscular mycorrhizal (AM) fungi. We evaluated the effect of fertilizers of different P solubility on the colonization of the roots of two common pasture plants by a community of AM fungi in a pasture soil. The treatments were a rock mineral fertilizer, a chemical fertilizer and a microbial inoculant. Subterranean clover and annual ryegrass were grown in pots for 10 weeks. Both fertilizers reduced the proportion and length of roots colonized by naturally occurring AM fungi. However, by 10 weeks, there was a much greater length of mycorrhizal root for annual ryegrass than for subterranean clover. The relative abundance of mycorrhizal fungi in the families Glomeraceae and Acaulosporaceae in roots was not affected by the form of fertilizer, but diversity indices of AM fungi in roots were altered. The chemical fertilizer had a greater negative effect on AM fungal diversity indices in the annual ryegrass roots compared with the subterranean clover roots. The reduction in OTU richness of AM fungi with fertilizer application corresponded with reduced soil pH. Differential effects of P fertilizers on naturally occurring AM fungi in this agricultural soil have the potential to influence the efficacy of P fertilizer use and dominance of plant species in grasslands.