Miracle-dz/UniFAR-FTUs huggingface dataset:
Cancer‐related risk factors and preventive measures in US Hispanics/Latinos

In this article, we provide prevalence data on major cancer‐related risk factors, early detection testing, and vaccination among Hispanics using nationally representative surveys. Compared with non‐Hispanic whites, Hispanic adults are less likely to be current smokers (13% vs 22%) or frequent alcohol drinkers, but they are more likely to be obese (32% vs 26%) and to have lower levels of mammography use within the past year (46% vs 51%), colorectal screening as per recommended intervals (47% vs 61%), and Papanicolaou (Pap) test use within the past 3 years (74% vs 79%). Within the Hispanic population, the prevalence of these risk factors and early detection methods substantially vary by country of origin. For example, Cuban men (20.7%) and Puerto Rican men (19%) had the highest levels of current smoking than any other Hispanic subgroups, while Mexican women had the lowest levels of mammogram use (44%) and Pap test use (71%). Hispanic migrants have a higher prevalence of hepatitis B virus and Helicobacter pylori, which cause liver and stomach cancer, respectively. Among Hispanic adolescents, tobacco use (eg, 20.8% use of any tobacco products), alcohol use (42.9%), and obesity (23.2%) remain highly prevalent risk factors. Although 56% of Hispanic adolescents initiate human papillomavirus vaccination, only 56% of them completed the 3‐dose series. Differences in risk factors and early detection testing among Hispanic groups should be considered in clinical settings and for cancer control planning. CA Cancer J Clin 2012;. © 2012 American Cancer Society.
Dependent types for JavaScript

We present Dependent JavaScript (DJS), a statically typed dialect of the imperative, object-oriented, dynamic language. DJS supports the particularly challenging features such as run-time type-tests, higher-order functions, extensible objects, prototype inheritance, and arrays through a combination of nested refinement types, strong updates to the heap, and heap unrolling to precisely track prototype hierarchies. With our implementation of DJS, we demonstrate that the type system is expressive enough to reason about a variety of tricky idioms found in small examples drawn from several sources, including the popular book JavaScript: The Good Parts and the SunSpider benchmark suite.
Methamphetamine and cannabis abuse in adolescence: a quasi-experimental study on specific and long-term neurocognitive effects

Objectives Methamphetamine abuse affects brain structure and function. Although methamphetamine and cannabis are commonly abused together, few studies have investigated the differential neurocognitive consequences of methamphetamine abuse with or without cannabis. Furthermore, the effects of drug use on the developing adolescent brain remain poorly understood. We compared neurocognitive function between adolescents with ‘pure’ methamphetamine abuse, those with comorbid methamphetamine and cannabis abuse, and healthy controls at baseline and follow-up. Methods Individuals residing in the greater Cape Town region, between the ages of 13 and 18 years, were recruited into either Methamphetamine only group (Meth-only; n=10), Methamphetamine and cannabis group (Meth-cann; n=10) or healthy control (n=20) groups using a quasi-experimental design. All participants underwent a comprehensive neurocognitive assessment. Substance-use variables and psychiatric symptom counts were also recorded. A portion of the Meth-only and control participants completed 12-month follow-up assessments. Results While the Meth-cann group demonstrated widespread neurocognitive deficits at baseline, these deficits were restricted to the self-monitoring domain in the Meth-only group at baseline and at follow-up. Conclusions Methamphetamine abuse with cannabis abuse is associated with significantly more neurocognitive impairment than methamphetamine abuse alone, and such deficits may be enduring.
Immune Checkpoint Therapy and the Search for Predictive Biomarkers

AbstractImmune checkpoint therapy has started a revolution in the field of oncology. The concept that the immune system plays a critical role in antitumor responses, which has been around for decades, has finally been proven and firmly established with elegant preclinical studies and dramatic clinical responses in patients as a result of antibodies that block inhibitory T-cell pathways. However, the clinical responses being achieved are only in a subset of patients, and more work is needed to provide a better understanding of the mechanisms that elicit tumor rejection, which will enable identification of appropriate biomarkers, reveal new targets, provide data to guide combination studies, and eventually dictate a platform that allows more patients to derive clinical benefit, including cures, with immune checkpoint therapy.
Generating more realistic images using gated MRF's

Probabilistic models of natural images are usually evaluated by measuring performance on rather indirect tasks, such as denoising and inpainting. A more direct way to evaluate a generative model is to draw samples from it and to check whether statistical properties of the samples match the statistics of natural images. This method is seldom used with high-resolution images, because current models produce samples that are very different from natural images, as assessed by even simple visual inspection. We investigate the reasons for this failure and we show that by augmenting existing models so that there are two sets of latent variables, one set modelling pixel intensities and the other set modelling image-specific pixel covariances, we are able to generate high-resolution images that look much more realistic than before. The overall model can be interpreted as a gated MRF where both pair-wise dependencies and mean intensities of pixels are modulated by the states of latent variables. Finally, we confirm that if we disallow weight-sharing between receptive fields that overlap each other, the gated MRF learns more efficient internal representations, as demonstrated in several recognition tasks.
Neural Question Answering at BioASQ 5B

This paper describes our submission to the 2017 BioASQ challenge. We participated in Task B, Phase B which is concerned with biomedical question answering (QA). We focus on factoid and list question, using an extractive QA model, that is, we restrict our system to output substrings of the provided text snippets. At the core of our system, we use FastQA, a state-of-the-art neural QA system. We extended it with biomedical word embeddings and changed its answer layer to be able to answer list questions in addition to factoid questions. We pre-trained the model on a large-scale open-domain QA dataset, SQuAD, and then fine-tuned the parameters on the BioASQ training set. With our approach, we achieve state-of-the-art results on factoid questions and competitive results on list questions.
A model for the induction of autism in the ecosystem of the human body: the anatomy of a modern pandemic?

Background The field of autism research is currently divided based on a fundamental question regarding the nature of autism: Some are convinced that autism is a pandemic of modern culture, with environmental factors at the roots. Others are convinced that the disease is not pandemic in nature, but rather that it has been with humanity for millennia, with its biological and neurological underpinnings just now being understood. Objective In this review, two lines of reasoning are examined which suggest that autism is indeed a pandemic of modern culture. First, given the widely appreciated derailment of immune function by modern culture, evidence that autism is strongly associated with aberrant immune function is examined. Second, evidence is reviewed indicating that autism is associated with ‘triggers’ that are, for the most part, a construct of modern culture. In light of this reasoning, current epidemiological evidence regarding the incidence of autism, including the role of changing awareness and diagnostic criteria, is examined. Finally, the potential role of the microbial flora (the microbiome) in the pathogenesis of autism is discussed, with the view that the microbial flora is a subset of the life associated with the human body, and that the entire human biome, including both the microbial flora and the fauna, has been radically destabilized by modern culture. Conclusions It is suggested that the unequivocal way to resolve the debate regarding the pandemic nature of autism is to perform an experiment: monitor the prevalence of autism after normalizing immune function in a Western population using readily available approaches that address the well-known factors underlying the immune dysfunction in that population.
Analog macromodeling using kernel methods

In this paper we explore the potential of using a general class of functional representation techniques, kernel-based regression, in the nonlinear model reduction problem. The kernel-based viewpoint provides a convenient computational framework for regression, unifying and extending the previously proposed polynomial and piecewise-linear reduction methods. Furthermore, as many familiar methods for linear system manipulation can be leveraged in a nonlinear context, kernels provide insight into how new, more powerful, nonlinear modeling strategies can be constructed. We present an SVD-like technique for automatic compression of nonlinear models that allows systematic identification of model redundancies and rigorous control of approximation error.
Patterns of Reproductive Isolation in Toads

Understanding the general features of speciation is an important goal in evolutionary biology, and despite significant progress, several unresolved questions remain. We analyzed an extensive comparative dataset consisting of more than 1900 crosses between 92 species of toads to infer patterns of reproductive isolation. This unique dataset provides an opportunity to examine the strength of reproductive isolation, the development and sex ratios of hybrid offspring, patterns of fertility and infertility, and polyploidization in hybrids all in the context of genetic divergence between parental species. We found that the strength of intrinsic postzygotic isolation increases with genetic divergence, but relatively high levels of divergence are necessary before reproductive isolation is complete in toads. Fertilization rates were not correlated to genetic divergence, but hatching success, the number of larvae produced, and the percentage of tadpoles reaching metamorphosis were all inversely related with genetic divergence. Hybrids between species with lower levels of divergence developed to metamorphosis, while hybrids with higher levels of divergence stopped developing in gastrula and larval stages. Sex ratios of hybrid offspring were biased towards males in 70% of crosses and biased towards females in 30% of crosses. Hybrid females from crosses between closely related species were completely fertile, while approximately half (53%) of hybrid males were sterile, with sterility predicted by genetic divergence. The degree of abnormal ploidy in hybrids was positively related to genetic divergence between parental species, but surprisingly, polyploidization had no effect on patterns of asymmetrical inviability. We discuss explanations for these patterns, including the role of Haldane's rule in toads and anurans in general, and suggest mechanisms generating patterns of reproductive isolation in anurans.
Biology of Francisella tularensis Subspecies holarctica Live Vaccine Strain in the Tick Vector Dermacentor variabilis

Background The γ-proteobacterium Francisella tularensis is the etiologic agent of seasonal tick-transmitted tularemia epizootics in rodents and rabbits and of incidental infections in humans. The biology of F. tularensis in its tick vectors has not been fully described, particularly with respect to its quanta and duration of colonization, tissue dissemination, and transovarial transmission. A systematic study of the colonization of Dermacentor variabilis by the F. tularensis subsp. holarctica live vaccine strain (LVS) was undertaken to better understand whether D. variabilis may serve as an inter-epizootic reservoir for F. tularensis. Methodology/Principal Findings Colony-reared larva, nymph, and adult D. variabilis were artificially fed LVS via glass capillary tubes fitted over the tick mouthparts, and the level of colonization determined by microbial culture. Larvae and nymphs were initially colonized with 8.8±0.8×101 and 1.1±0.03×103 CFU/tick, respectively. Post-molting, a significant increase in colonization of both molted nymphs and adults occurred, and LVS persisted in 42% of molted adult ticks at 126 days post-capillary tube feeding. In adult ticks, LVS initially colonized the gut, disseminated to hemolymph and salivary glands by 21 days, and persisted up to 165 days. LVS was detected in the salivary secretions of adult ticks after four days post intra-hemocoelic inoculation, and LVS recovered from salivary gland was infectious to mice with an infectious dose 50% of 3 CFU. LVS in gravid female ticks colonized via the intra-hemocoelic route disseminated to the ovaries and then to the oocytes, but the pathogen was not recovered from the subsequently-hatched larvae. Conclusions/Significance This study demonstrates that D. variabilis can be efficiently colonized with F. tularensis using artificial methods. The persistence of F. tularensis in D. variabilis suggests that this tick species may be involved in the maintenance of enzootic foci of tularemia in the central United States.
The cool side of Lyman alpha emitters

We extend a previous study of Lyman alpha emitters (LAEs) based on hydrodynamical cosmological simulations, by including two physical processes important for LAEs: (i) Lyα and continuum luminosities produced by cooling of collisionally excited HI in the galaxy and (ii) dust formation and evolution; we follow these processes on a galaxy-by-galaxy basis. H i cooling on average contributes 16-18 per cent of the Lyα radiation produced by stars, but this value can be much higher in low-mass LAEs and further increased if the HI is clumpy. The continuum luminosity is instead almost completely dominated by stellar sources. The dust content of galaxies scales with their stellar mass, M dust α M 0.7 * , and stellar metallicity, Z * , such that M dust ∝ Z 1.7 * . As a result, the massive galaxies have Lyα escape fraction as low as f α = 0.1, with a LAE-averaged value decreasing with redshift: 〈f α 〉 = (0.33, 0.23) at z = (5.7, 6.6). The ultraviolet (UV) continuum escape fraction shows the opposite trend with z, possibly resulting from clumpiness evolution. The model successfully reproduces the observed Lyα and UV luminosity functions at different redshifts and the Lyα equivalent width scatter to a large degree, although the observed distribution appears to be more more extended than the predicted one. We discuss possible reasons for such tension.
Biochemical structure of mitochondria. II. Radioactive labeling of intra-mitochondrial nucleotides during oxidative phosphorylation.

In a recent paper (2) we postulated that during oxidative phosphorylation by isolated mitochondria the turnover rates of the adenine nucleotides within the mitochondria are much more rapid than their passage in and out of the mitochondria. This paper presents evidence to confirm that hypothesis by using radioactivity measurements as a more direct method of determining turnover and diffusion. The data also suggest that the mitochondrial enzyme, adenylate kinase (3-5), exists in two sites in the mitochondrion. Based on these results, a scheme is presented for certain aspects of the biochemical structure of the mitochondrion, and the possible rale of such a structure in regulating oxidation is discussed.
Recovering Distributions from Gaussian RKHS Embeddings

Recent advances of kernel methods have yielded a framework for nonparametric statistical inference called RKHS embeddings, in which all probability distributions are represented as elements in a reproducing kernel Hilbert space, namely kernel means. In this paper, we consider the recovery of the information of a distribution from an estimate of the kernel mean, when a Gaussian kernel is used. To this end, we theoretically analyze the properties of a consistent estimator of a kernel mean, which is represented as a weighted sum of feature vectors. First, we prove that the weighted average of a function in a Besov space, whose weights and samples are given by the kernel mean estimator, converges to the expectation of the function. As corollaries, we show that the moments and the probability measures on intervals can be recovered from an estimate of the kernel mean. We also prove that a consistent estimator of the density of a distribution can be defined using a kernel mean estimator. This result confirms that we can in fact completely recover the information of distributions from RKHS embeddings.
Leveraging pre-commit hooks for context-sensitive checklists: a case study

The need to increase the efficiency of software development creates a demand for unobtrusive in-process means of software quality assurance that align well with agile processes. Many version control system clients provide facilities for running scripts or other executables before a change is committed to the repository. These ”pre-commit hooks” can be client-side or server-side, both having distinct advantages. Client-side pre-commit hooks are well suited to implement context-sensitive checklists and automatic quality checks, but their potential has not been fully realized in practice and corresponding research is missing. To narrow this gap, we did an industrial case study on this use of client-side pre-commit hooks. The case study used the tool ”TortoiseChecklist” and was focused on increasing continuous integration build stability. The results were positive, with a notable increase in stability and no significant disadvantages noticed.
Longevity and Composition of Cellular Immune Responses Following Experimental Plasmodium falciparum Malaria Infection in Humans

Cellular responses to Plasmodium falciparum parasites, in particular interferon-gamma (IFNγ) production, play an important role in anti-malarial immunity. However, clinical immunity to malaria develops slowly amongst naturally exposed populations, the dynamics of cellular responses in relation to exposure are difficult to study and data about the persistence of such responses are controversial. Here we assess the longevity and composition of cellular immune responses following experimental malaria infection in human volunteers. We conducted a longitudinal study of cellular immunological responses to sporozoites (PfSpz) and asexual blood-stage (PfRBC) malaria parasites in naïve human volunteers undergoing single (n = 5) or multiple (n = 10) experimental P. falciparum infections under highly controlled conditions. IFNγ and interleukin-2 (IL-2) responses following in vitro re-stimulation were measured by flow-cytometry prior to, during and more than one year post infection. We show that cellular responses to both PfSpz and PfRBC are induced and remain almost undiminished up to 14 months after even a single malaria episode. Remarkably, not only ‘adaptive’ but also ‘innate’ lymphocyte subsets contribute to the increased IFNγ response, including αβT cells, γδT cells and NK cells. Furthermore, results from depletion and autologous recombination experiments of lymphocyte subsets suggest that immunological memory for PfRBC is carried within both the αβT cells and γδT compartments. Indeed, the majority of cytokine producing T lymphocytes express an CD45RO+ CD62L- effector memory (EM) phenotype both early and late post infection. Finally, we demonstrate that malaria infection induces and maintains polyfunctional (IFNγ+IL-2+) EM responses against both PfRBC and PfSpz, previously found to be associated with protection. These data demonstrate that cellular responses can be readily induced and are long-lived following infection with P. falciparum, with a persisting contribution by not only adaptive but also (semi-)innate lymphocyte subsets. The implications hereof are positive for malaria vaccine development, but focus attention on those factors potentially inhibiting such responses in the field.
A comparison of ray pointing techniques for very large displays

Ray-pointing techniques are often advocated as a way for people to interact with very large displays from several meters away. We are interested in two factors that can affect ray pointing: the particular technique's control type, and parallax. Consequently, we tested four ray pointing variants on a wall display that covers a large part of the user's field of view. Tasks included horizontal and vertical targeting, and tracing. Our results show that (a) techniques based on 'rotational control' perform better for targeting tasks, and (b) techniques with low parallax are best for tracing tasks. We also show that a Fitts's law analysis based on angles (as opposed to linear distances) better approximates people's ray pointing performance.
Assessment of User Perspectives of Cardiac Point of Care Technologies in Chest Pain Diagnosis

The assessment of the value of point of care technologies for cardiac marker testing in patients presenting with chest pain was carried out using an on-line survey tool to garner the views and opinions of healthcare professionals on point of care testing (POCT). The preliminary results of the survey are presented here. A total of 38 responses were received, from health care professionals within Northern Ireland Health Trusts. A number of concerns were raised relating to the implementation of a POCT service. These included clinical governance, quality assurance, accreditation and regulation, which should be addressed by the central laboratory. The main POCT user groups were clinical, nursing and laboratory staff, with nursing staff being the most frequent users. The general opinion amongst healthcare professionals was that POCT implementation and accreditation should be overseen and regulated by the central laboratory. Troponin I was the most important cardiac marker measured by POCT devices. POCT turnaround times were perceived by survey respondents as shorter between 15-30 minutes compared to laboratory testing, 60-90 minutes. The perception of POCT data quality was considered by the majority of respondents to be of equivalent quality and accuracy to central laboratory cardiac marker testing Laboratory and biomedical scientists indicated that the implementation of a POCT service would alter their relationships to clinical, nursing staff and patients. The survey suggested that POCT may create new roles for biomedical scientists outside the pathology laboratory involving supporting nursing staff at ward level and validation of patient test results.
A practical technique for bounding the time between events in concurrent real-time systems

Showing that concurrent systems satisfy timing constraints on their behavior is difficult, but may be essential for critical applications. Most methods are based on some form of reachability analysis and require construction of a state space of size that is, in general, exponential in the number of components in the concurrent system. In an earlier paper with L. K. Dillon and J. E. Wileden, we described a technique for finding bounds on the time between events without enumerating the state space, but the technique applies chiefly to the case of logically concurrent systems executing on a uniprocessor, in which events do not overlap in time. In this paper, we extend that technique to obtain upper bounds on the time between events in maximally parallel concurrent systems. Our method does not require construction of the state space and the results of preliminary experiments show that, for at least some systems with large state spaces, it is quite tractable. We also briefly describe the application of our method to the case in which there are multiple processors, but several processes run on each processor.