Miracle-dz/UniFAR-FTUs huggingface dataset:
Epidemiological Characteristics and Spatio-Temporal Distribution of Hepatitis A in Spain in the Context of the 2016/2017 European Outbreak

The aim of our study was to describe the results of the epidemiological surveillance of hepatitis A infections in Spain in the context of the 2016/2017 European outbreak, particularly of hepatitis A outbreaks reported in the MSM population, incorporating the results of a spatio-temporal analysis of cases. Hepatitis A cases and outbreaks reported in 2016–2017 to the National Epidemiological Surveillance Network were reviewed: outbreaks in which some of the cases belonged to the MSM group were described, and clusters of hepatitis A cases in men and women were analysed using a space–time scan statistic. Twenty-six outbreaks were identified, with a median size of two cases per outbreak, with most of the outbreak-related cases belonging to the 15–44 years-old group. Nearly 85% occurred in a household setting, and in all outbreaks, the mode of transmission was direct person-to-person contact. Regarding space–time analysis, twenty statistically significant clusters were identified in the male population and eight in the female population; clusters in men presented a higher number of observed cases and affected municipalities, as well as a higher percentage of municipalities classified as large urban areas. The elevated number of cases detected in clusters of men indicates that the number of MSM-related outbreaks may be higher than reported, showing that spatio-temporal analysis is a complementary, useful tool which may improve the detection of outbreaks in settings where epidemiological investigation may be more challenging.
Effects of modafinil and caffeine on night-time vigilance of air force crewmembers: A randomized controlled trial

Background: Fatigue remains an important factor in major aviation accidents. Stimulants may counteract fatigue’s adverse effects, with modafinil as a promising alternative to caffeine. However, the effect of a single dose of modafinil after a limited period of sleep deprivation remains unknown. Aims: This study aims to determine the effect of 200 mg modafinil on vigilance during a limited period of sleep deprivation compared to 300 mg caffeine and placebo. Methods: Thirty-two volunteers of the Royal Netherlands Air Force (RNLAF) were double-blindly administered modafinil, caffeine, and placebo on three non-consecutive trial days after being awake for median 17 h. Afterwards, subjects completed six series of the Vigilance and Tracking test (VigTrack), psychomotor vigilance task (PVT), and Stanford Sleepiness Scale (SSS), yielding six primary endpoints. Results: This study revealed statistically significant effects of caffeine and modafinil compared with placebo on all endpoints, except for VigTrack mean tracking error. PVT results were less impaired 2 h after administration, followed by VigTrack parameters and SSS scores 2 h thereafter. Compared with caffeine, modafinil significantly improved PVT and SSS scores at 8 h after administration. Conclusions: The present study demonstrates that 200 mg modafinil and 300 mg caffeine significantly decrease the effects of a limited period of sleep deprivation on vigilance compared with placebo. Although PVT parameters already improved 2 h after administration, the most notable effects occurred 2–4 h later. Modafinil seems to be effective longer than caffeine, which is consistent with its longer half-life.
Part-of-Speech and Morphological Tagging of Algerian Judeo-Arabic

Most linguistic studies of Judeo-Arabic, the ensemble of dialects spoken and written by Jews in Arab lands, are qualitative in nature and rely on laborious manual annotation work, and are therefore limited in scale. In this work, we develop automatic methods for morpho-syntactic tagging of Algerian Judeo-Arabic texts published by Algerian Jews in the 19th–20th centuries, based on a linguistically tagged corpus. First, we describe our semi-automatic approach for preprocessing these texts. Then, we experiment with both an off-the-shelf morphological tagger and several specially designed neural network taggers. Finally, we perform a real-world evaluation of new texts that were never tagged before in comparison with human expert annotators. Our experimental results demonstrate that these methods can dramatically speed up and improve the linguistic research pipeline, enabling linguists to study these dialects on a much greater scale.
Effect of Zn and Ni substitution on the local electronic structure of the YBa 2 Cu 3 O 7 superconductor

Embedded cluster calculations at the MP2 electron correlation level of pure and Zn- and Ni-doped YBa 2 Cu 3 O 7 (Y123) ceramics reveal great changes of the local charge distribution and crystal bonding in the vicinity of impurities. In the Zn-doped ceramics the obtained changes are stronger and more extended than in the Ni-doped ceramics. This can be one of explanations of the stronger depression of T c due to Zn. The calculated increase of positive charge for both impurities, comparing with substituted Cu, indicates that the impurity atoms lose more negative charge than Cu. As a result, all nearest CuO 2 units around impurity lose their holes: completely in the Zn case and partly in the Ni case. This leads to the breaking of the hole pairs in the vicinity of impurity and correlated with an increase of the coherence length in Zn- and Ni-doped Y123 crystals measured by Timomoto et al. [Phys. Rev. B 60, 114 (1999)]. Both Zn and Ni impurities, the latter to a less extent, act as effective pair breakers due to the elimination of holes on adjacent CuO 2 groups.
Confocal Microscopes with Slit Apertures

Abstract Using slit apertures, rather than pinholes, to construct a confocal imaging system has some advantages. The signal level is increased and, if a detector array is used, a line image can be generated in real time. Slit apertures can also be used in a direct-view confocal (tandem scanning) microscope.
Bayesian Time Series Models: Expectation maximisation methods for solving (PO)MDPs and optimal control problems

As this book demonstrates, the development of efficient probabilistic inference techniques has made considerable progress in recent years, in particular with respect to exploiting the structure (e.g., factored, hierarchical or relational) of discrete and continuous problem domains. In this chapter we show that these techniques can be used also for solving Markov Decision Processes (MDPs) or partial observable MDPs (POMDPs) when formulated in terms of a structured dynamic Bayesian network (DBN). The problems of planning in stochastic environments and inference in state space models are closely related, in particular in view of the challenges both of them face: scaling to large state spaces spanned by multiple state variables, or realizing planning (or inference) in continuous or mixed continuous-discrete state spaces. Both fields developed techniques to address these problems. For instance, in the field of planning, they include work on Factored Markov Decision Processes (Boutilier et al., 1995; Koller and Parr, 1999; Guestrin et al., 2003; Kveton and Hauskrecht, 2005), abstractions (Hauskrecht et al., 1998), and relational models of the environment (Zettlemoyer et al., 2005). On the other hand, recent advances in inference techniques show how structure can be exploited both for exact inference as well as making efficient approximations. Examples are message passing algorithms (loopy Belief Propagation, Expectation Propagation), variational approaches, approximate belief representations (particles, Assumed Density Filtering, Boyen-Koller) and arithmetic compilation (see, e.g., Minka, 2001; Murphy, 2002; Chavira et al., 2006). In view of these similarities one may ask whether existing techniques for probabilistic inference can directly be translated to solving stochastic planning problems. From a complexity theoretic point of view, the equivalence between inference and planning is well-known (see, e.g., Littman et al., 2001). Inference methods have been applied before to optimal decision making in Influence Diagrams (Cooper, 1988; Pearl, 1988; Shachter, 1988). However, contrary to MDPs, these methods focus on a finite number of decisions and a non-stationary policy, where optimal decisions are found by recursing backward starting from the last decision (see (Boutilier et al., 1999) and (Toussaint, 2009) for a discussion of MDPs versus Influence Diagrams). More recently, Bui et al. (2002) have used inference on Abstract Hidden Markov Models for policy recognition, i.e., for reasoning about executed behaviors, but do not address the problem of computing optimal policies from such inference. Attias
Targeting Lymphoma-associated Macrophage Expansion via CSF1R/JAK Inhibition is a Therapeutic Vulnerability in Peripheral T-cell Lymphomas

The reciprocal relationship between malignant T cells and lymphoma-associated macrophages (LAM) within the tumor microenvironment (TME) is unique, as LAMs are well poised to provide ligands for antigen, costimulatory, and cytokine receptors that promote T-cell lymphoma growth. Conversely, malignant T cells promote the functional polarization and homeostatic survival of LAM. Therefore, we sought to determine the extent to which LAMs are a therapeutic vulnerability in these lymphomas, and to identify effective therapeutic strategies for their depletion. We utilized complementary genetically engineered mouse models and primary peripheral T-cell lymphoma (PTCL) specimens to quantify LAM expansion and proliferation. A high-throughput screen was performed to identify targeted agents that effectively deplete LAM within the context of PTCL. We observed that LAMs are dominant constituents of the TME in PTCL. Furthermore, their dominance was explained, at least in part, by their proliferation and expansion in response to PTCL-derived cytokines. Importantly, LAMs are a true dependency in these lymphomas, as their depletion significantly impaired PTCL progression. These findings were extrapolated to a large cohort of human PTCL specimens where LAM proliferation was observed. A high-throughput screen demonstrated that PTCL-derived cytokines led to relative resistance to CSF1R selective inhibitors, and culminated in the identification of dual CSF1R/JAK inhibition as a novel therapeutic strategy to deplete LAM in these aggressive lymphomas. Malignant T cells promote the expansion and proliferation of LAM, which are a bone fide dependency in these lymphomas, and are effectively depleted with a dual CSF1R/JAK inhibitor. Significance: LAMs are a therapeutic vulnerability, as their depletion impairs T-cell lymphoma disease progression. Pacritinib, a dual CSF1R/JAK inhibitor, effectively impaired LAM viability and expansion, prolonged survival in preclinical T-cell lymphoma models, and is currently being investigated as a novel therapeutic approach in these lymphomas.
Ultra-Processed Food Consumption and Increased Risk of Metabolic Syndrome in Adults: The ELSA-Brasil

OBJECTIVE To investigate the association between ultra-processed food (UPF) consumption and the incidence of metabolic syndrome (MetS). RESEARCH DESIGN AND METHODS From 2008 to 2010, we enrolled 15,105 adults, aged 35–74 years, who were employees from six public education and research institutions to assemble the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil). We used a food frequency questionnaire to assess UPF consumption (measured in grams per day) at baseline. We then assessed the outcomes of those returning to visits between 2012 and 2014 and between 2017 and 2019. We defined incident MetS by the presence of at least three of the following five abnormalities: high fasting glucose level, high triglyceride level, low HDL cholesterol level, high blood pressure, and abdominal obesity, after excluding those meeting such criteria at baseline. We also excluded those who had missing data or an implausible energy intake, leaving 8,065 participants in the study. RESULTS The median age was 49 years, 59% of participants were women, and the median consumption of UPFs was 366 g/day. After 8 years, there were 2,508 new cases of MetS. In robust Poisson regression, adjusting for sociodemographics, behavioral factors, and energy intake, we found a 7% (relative risk [RR] 1.07; 95% CI 1.05–1.08) higher risk of incident MetS for an increase of 150 g/day in UPF consumption. Similarly, those in the fourth quartile (compared with the first quartile) had a 33% increased risk (RR 1.33; 95% CI 1.20–1.47). Further adjustment for BMI attenuated these associations (for 150 g/day increases in UPF consumption and for the fourth quartile compared to the first one, respectively, RR = 1.04, 95% CI 1.02–1.06; RR = 1.19, 95% CI 1.07–1.32). CONCLUSIONS Greater consumption of UPFs is associated with an increased risk of MetS. These findings have important implications for diabetes and cardiovascular disease prevention and management.
Multiscale Object Contrastive Learning-Derived Few-Shot Object Detection in VHR Imagery

The feature representation capability of the object detection model is considerably reduced if the available training samples are few-shot. The challenges of arbitrary orientation and complex background of ground objects are universal in very high spatial resolution (VHR) remote sensing imageries, resulting in massive difficulty on few-shot object detection task. However, existing methods for few-shot object detection are not explored in terms of the capabilities of feature representation in remote sensing images. To solve these issues, we propose a few-shot object detection method incorporating multiscale object contrastive learning. First, our method performs contrastive learning to represent the object feature fully by adopting the Siamese network structure in the few-shot training. On the one hand, the Siamese structure’s lower branch is embedded in the contrastive learning process to cope with the challenge of the complexity of images; on the other hand, a multiscale instance feature module is designed to obtain multiscale contrastive information. Second, we leverage the proposed contrastive multiscale proposal (CMSP) to make full use of multiscale information. It can promote our method to fit the data better. The experimental results show that the proposed method has good feature representation capabilities in the few-shot object detection. Moreover, the performance of the proposed method is better than that of related methods. The source code is available at https://github.com/RS-CSU/MSOCL.
A Predictive Model for Dysphagia after Ventilator Liberation in Severe Pneumonia Patients Receiving Tracheostomy: A Single-Center, Observational Study

The main purpose of this study was to develop a model predictive of dysphagia in hospital survivors with severe pneumonia who underwent tracheostomy during their hospital stay. The present study included 175 patients (72% male; mean age, 71.3 years) over 5 years. None of these patients had a history of deglutition disorder before hospital admission. Binary logistic regression analysis was performed to identify factors predicting dysphagia at hospital discharge. Dysphagia scores were calculated from β-coefficients and by assigning points to variables. Of the enrolled patients, 105 (60%) had dysphagia at hospital discharge. Factors prognostic of dysphagia at hospital discharge included being underweight (body mass index < 18.5 kg/m2), non-participation in a dysphagia therapy program, mechanical ventilation ≥ 15 days, age ≥ 74 years, and chronic neurologic diseases. Underweight and non-participation in a dysphagia therapy program were assigned +2 points and the other factors were assigned +1 point. Dysphagia scores showed acceptable discrimination (area under the receiver operating characteristic curve for dysphagia 0.819, 95% confidence interval: 0.754–0.873, p < 0.001) and calibration (Hosmer–Lemeshow chi-square = 9.585, with df 7 and p = 0.213). The developed dysphagia score was predictive of deglutition disorder at hospital discharge in tracheostomized patients with severe pneumonia.
Type‐curve estimation of statistical heterogeneity

The analysis of pumping tests has traditionally relied on analytical solutions of groundwater flow equations in relatively simple domains, consisting of one or at most a few units having uniform hydraulic properties. Recently, attention has been shifting toward methods and solutions that would allow one to characterize subsurface heterogeneities in greater detail. On one hand, geostatistical inverse methods are being used to assess the spatial variability of parameters, such as permeability and porosity, on the basis of multiple cross‐hole pressure interference tests. On the other hand, analytical solutions are being developed to describe the mean and variance (first and second statistical moments) of flow to a well in a randomly heterogeneous medium. We explore numerically the feasibility of using a simple graphical approach (without numerical inversion) to estimate the geometric mean, integral scale, and variance of local log transmissivity on the basis of quasi steady state head data when a randomly heterogeneous confined aquifer is pumped at a constant rate. By local log transmissivity we mean a function varying randomly over horizontal distances that are small in comparison with a characteristic spacing between pumping and observation wells during a test. Experimental evidence and hydrogeologic scaling theory suggest that such a function would tend to exhibit an integral scale well below the maximum well spacing. This is in contrast to equivalent transmissivities derived from pumping tests by treating the aquifer as being locally uniform (on the scale of each test), which tend to exhibit regional‐scale spatial correlations. We show that whereas the mean and integral scale of local log transmissivity can be estimated reasonably well based on theoretical ensemble mean variations of head and drawdown with radial distance from a pumping well, estimating the log transmissivity variance is more difficult. We obtain reasonable estimates of the latter based on theoretical variation of the standard deviation of circumferentially averaged drawdown about its mean.
Automatic x‐ray diffraction measurement of the lattice curvature of substrate wafers for the determination of linear strain patterns

An x‐ray diffraction topography goniometer (Lang camera) under computer control has been used to measure localized bending of silicon wafers. The wafer, mounted free from external stresses, is set for Bragg reflection in transmission by lattice planes perpendicular to the surface (Laue case) and it traverses across the x‐ray beam in steps of 0.01 mm or multiples thereof. At each step the angular position and the intensity of the peak of the Bragg reflection is determined by least‐squares methods from the peak profile with a precision better than the minimum angular step of 0.001°. The lattice curvature obtained from the peak shift is a direct measure of the magnitude of the strains imposed on the wafer by oxide layers, thin films, implantation, and other manufacturing processes. Therefore linear strain maps, showing, for instance, strain gradients occurring at film edges, can be measured quantitatively with high resolution, fully automatically and nondestructively in several direction across a substrate w.
Sex-Specific Associations of Red Meat and Processed Meat Consumption with Serum Metabolites in the UK Biobank

Red meat consumption has been found to closely related to cardiometabolic health, with sex disparity. However, the specific metabolic factors corresponding to red meat consumption in men and women have not been examined previously. We analyzed the sex-specific associations of meat consumption, with 167 metabolites using multivariable regression, controlling for age, ethnicity, Townsend deprivation index, education, physical activity, smoking, and drinking status among ~79,644 UK Biobank participants. We also compared the sex differences using an established formula. After accounting for multiple testing with false discovery rate < 5% and controlling for confounders, the positive associations of unprocessed red meat consumption with branched-chain amino acids and several lipoproteins, and the inverse association with glycine were stronger in women, while the positive associations with apolipoprotein A1, creatinine, and monounsaturated fatty acids were more obvious in men. For processed meat, the positive associations with branched-chain amino acids, several lipoproteins, tyrosine, lactate, glycoprotein acetyls and inverse associations with glutamine, and glycine were stronger in women than in men. The study suggests that meat consumption has sex-specific associations with several metabolites. This has important implication to provide dietary suggestions for individuals with or at high risk of cardiometabolic disease, with consideration of sex difference.
On Recessive and Dominant Solutions for Half-linear Difference Equations

Recessive and dominant solutions for the half-linear difference equation where with {a n } and {b n } are positive real sequences for are studied. By the unique solvability of certain boundary value problems, recessive solutions are defined as “smallest solutions in a neighbourhood of infinity”. The equivalency with other properties, namely with the Riccati property and the convergence or divergence of a suitable series, is also proved.
Some Properties of Harmonic Functions Defined by Convolution

In this paper, we introduce and study a comprehensive family of harmonic univalent functions which contains various well-known classes of harmonic univalent functions as well as many new ones. Also, we improve some results obtained by Frasin [3] and obtain coefficient bounds, distortion bounds and extreme points, convolution conditions and convex combination are also determined for functions in this family. It is worth mentioning that many of our results are either extensions or new approaches to those corresponding previously known results.
Temperature dependent phase transition of EuO on MgO(100)

We investigated the changes of magnetic properties and phase transition in EuO films grown on a MgO(100) substrate as a function of temperature. As the temperature was varied, we observed a clear phase transition and polarization change at 69K using spin resolved photoemission spectroscopy and low energy electron diffraction. We will elucidate the temperature driven changes in the electronic and magnetic properties of EuO films on a MgO(100) substrate.
In vitro quantitation of human femoral artery atherosclerosis using near-infrared Raman spectroscopy

Near-infrared Raman spectroscopy has been used in vitro to identify calcified atherosclerotic plaques in human femoral arteries. Raman techniques allow for the identification of these plaques in a nondestructive manner, which may allow for the diagnosis of coronary artery disease in cardiac patients in the future. As Raman spectroscopy also reveals chemical information about the composition of the arteries, it can also be used as a prognostic tool. The in vivo detection of atherosclerotic plaques at risk for rupture in cardiac patients will enhance treatment methods while improving clinical outcomes for these procedures. Raman spectra were excited by an Invictus 785-nm NIR laser and measured with a fiber-coupled micro-Raman RXN system (Kaiser Optical Systems, Inc., Ann Arbor, MI) equipped with a 785 nm CW laser and CCD detector. Chemical mapping of arteries obtained post mortem allowed for the discrete location of atherosclerotic plaques. Raman peaks at 961 and 1073 cm-1 reveal the presence of calcium hydroxyapatite and carbonate apatite, which are known to be present in calcified plaques. By mapping the locations of these peaks the boundaries of the plaques can be precisely determined. Areas of varying degrees of calcification were also identified. Because this can be useful in determining the degree of plaque calcification and vessel stenosis, this may have a significant impact on the clinical treatment of atherosclerotic plaques in the future.