Miracle-dz/UniFAR-FTUs huggingface dataset:
Current approaches using genetic distances produce poor estimates of landscape resistance to interindividual dispersal

Landscape resistance reflects how difficult it is for genes to move across an area with particular attributes (e.g. land cover, slope). An increasingly popular approach to estimate resistance uses Mantel and partial Mantel tests or causal modelling to relate observed genetic distances to effective distances under alternative sets of resistance parameters. Relatively few alternative sets of resistance parameters are tested, leading to relatively poor coverage of the parameter space. Although this approach does not explicitly model key stochastic processes of gene flow, including mating, dispersal, drift and inheritance, bias and precision of the resulting resistance parameters have not been assessed. We formally describe the most commonly used model as a set of equations and provide a formal approach for estimating resistance parameters. Our optimization finds the maximum Mantel r when an optimum exists and identifies the same resistance values as current approaches when the alternatives evaluated are near the optimum. Unfortunately, even where an optimum existed, estimates from the most commonly used model were imprecise and were typically much smaller than the simulated true resistance to dispersal. Causal modelling using Mantel significance tests also typically failed to support the true resistance to dispersal values. For a large range of scenarios, current approaches using a simple correlational model between genetic and effective distances do not yield accurate estimates of resistance to dispersal. We suggest that analysts consider the processes important to gene flow for their study species, model those processes explicitly and evaluate the quality of estimates resulting from their model.
Blind Image Deblurring by Spectral Properties of Convolution Operators

In this paper, we study the problem of recovering a sharp version of a given blurry image when the blur kernel is unknown. Previous methods often introduce an image-independent regularizer (such as Gaussian or sparse priors) on the desired blur kernel. We shall show that the blurry image itself encodes rich information about the blur kernel. Such information can be found through analyzing and comparing how the spectrum of an image as a convolution operator changes before and after blurring. Our analysis leads to an effective convex regularizer on the blur kernel which depends only on the given blurry image. We show that the minimizer of this regularizer guarantees to give good approximation to the blur kernel if the original image is sharp enough. By combining this powerful regularizer with conventional image deblurring techniques, we show how we could significantly improve the deblurring results through simulations and experiments on real images. In addition, our analysis and experiments help explaining a widely accepted doctrine; that is, the edges are good features for deblurring.
Urinary Concentrations of Steroids in Bulls under Anabolic Treatment by Revalor-XS® Implant

Despite the European ban of using anabolics in food-producing animals, growth promoters might still be illegally used in the European Union. To control the food chain and guarantee consumers' health, there is a need of highly sensitive analytical methods for the identification of marker residues of such treatments. In the present study, a group of bulls (n = 16) received trenbolone acetate (200 mg) and estradiol (40 mg) by a commercial ear implant during a time range of 71 days, and a second group (n = 16) was kept for control. The aim of the research was to measure the residual urinary concentrations of the administered drugs (β-trenbolone and β-estradiol), their main metabolites (α-trenbolone and α-estradiol), and possible alterations of the urinary profile of other endogenous hormones metabolically related. The analytical method was based on liquid chromatography-tandem mass spectrometry. Results showed average urinary concentrations of α-trenbolone and α-estradiol during treatment in the range of (0.81 ÷ 2.1) ng mL−1 and (0.96 ÷ 4.4) ng mL−1, respectively, whereas β-trenbolone and β-estradiol exhibit urinary concentrations lower than 0.22 ng mL−1 in both cases. Data obtained from the urinary profiles of endogenous steroids indicate that they could be useful to indirectly detect the ongoing treatment.
Screening for urine abnormalities among preschool children in Western Saudi Arabia

I read with interest a study by Alharthi et al1 on the screening for urine abnormalities among preschool children in western Saudi Arabia. The authors stated that dipstick urine analysis (DUA) revealed abnormal findings in 25.1% of the screened children. The most common dipstick abnormalities were positive nitrite test in 18.1%, hematuria in 16.9%, and positive leukocyte esterase test in 14.3% of the cases. The most common abnormality in microscopic urine examination was crystals in 13% of the cases. Pyuria were evident in 5% of cases and hematuria in 2.5%. The most common bacteria in positive urine culture samples was Escherichia coli in 62.6%. In view of the aforementioned data, the authors recommended implementing DUA screening among preschool children. Unexpectedly, the authors did not consider limitations in their study before making that recommendation. Hence, I presume that their recommendation ought to be cautiously considered owing to the presence of the following 4 limitations: 1) The study period was relatively short (August-December); 2) The data were obtained from a single center. It is, therefore, not truly representative of the whole pediatric population in the Kingdom of Saudi Arabia (KSA); 3) Generally, the magnitude of a certain health problem in a given population ought to be sizable in order to merit screening. The reported incidence of pediatric chronic kidney diseases (CKDs) was recently reported to be <1.0-8, and end-stage renal diseases (ESRDs) in the developing countries had been 3.4-35 per million child population.2 However, the exact magnitude of pediatric CKDs in KSA is not yet known as there is no current national epidemiologic data on that issue;3 and 4) The cost-effectiveness ratio of DUA for the early detection of CKDs needs to be considered. In an interesting American study,4 decision analysis was used to model a screening DUA strategy relative to a no-screening strategy. The expected costs and effectiveness for the no-screening strategy were 0 dollars as no resources were used, and no cases of CKDs were diagnosed. However, the screening strategy involved a cost of 3.05 dollars per dipstick. Accounting for true-positive and false-positive initial screens, 14.2% of patients required a second dipstick as per typical clinical care, bringing the expected cost of the screening strategy to 3.47 dollars per patient. In the screening strategy, one case of CKD was diagnosed per 800 screened, and the incremental cost-effectiveness ratio was 2,779.50 dollars per case diagnosed.4 In brief, I presume that conducting large scale multicenter studies over an extended period of time to assess the yield of DUA in early detecting urine abnormalities together with the determination of cost-benefit ratio for Saudi pediatric population are essential prerequisites to justify the implementation of DUA screening program.
Examining the Relationship between Urogenital Schistosomiasis and HIV Infection

Background Urogenital schistosomiasis, caused by infection with Schistosoma haematobium, is widespread and causes substantial morbidity on the African continent. The infection has been suggested as an unrecognized risk factor for incident HIV infection. Current guidelines recommend preventive chemotherapy, using praziquantel as a public health tool, to avert morbidity due to schistosomiasis. In individuals of reproductive age, urogenital schistosomiasis remains highly prevalent and, likely, underdiagnosed. This comprehensive literature review was undertaken to examine the evidence for a cause-effect relationship between urogenital schistosomiasis and HIV/AIDS. The review aims to support discussions of urogenital schistosomiasis as a neglected yet urgent public health challenge. Methodology/Principal Findings We conducted a systematic search of the literature including online databases, clinical guidelines, and current medical textbooks. We describe plausible local and systemic mechanisms by which Schistosoma haematobium infection could increase the risk of HIV acquisition in both women and men. We also detail the effects of S. haematobium infection on the progression and transmissibility of HIV in co-infected individuals. We briefly summarize available evidence on the immunomodulatory effects of chronic schistosomiasis and the implications this might have for populations at high risk of both schistosomiasis and HIV. Conclusions/Significance Studies support the hypothesis that urogenital schistosomiasis in women and men constitutes a significant risk factor for HIV acquisition due both to local genital tract and global immunological effects. In those who become HIV-infected, schistosomal co-infection may accelerate HIV disease progression and facilitate viral transmission to sexual partners. Establishing effective prevention strategies using praziquantel, including better definition of treatment age, duration, and frequency of treatment for urogenital schistosomiasis, is an important public health priority. Our findings call attention to this pressing yet neglected public health issue and the potential added benefit of scaling up coverage of schistosomal treatment for populations in whom HIV infection is prevalent.
How Language Programs the Mind

Many animals can be trained to perform novel tasks. People, too, can be trained, but sometime in early childhood people transition from being trainable to something qualitatively more powerful-being programmable. We argue that such programmability constitutes a leap in the way that organisms learn, interact, and transmit knowledge, and that what facilitates or enables this programmability is the learning and use of language. We then examine how language programs the mind and argue that it does so through the manipulation of embodied, sensorimotor representations. The role language plays in controlling mental representations offers important insights for understanding its origin and evolution.
The Yin and Yang of VEGF and PEDF: Multifaceted Neurotrophic Factors and Their Potential in the Treatment of Parkinson’s Disease

Over the last few decades, vascular endothelial growth factor (VEGF) and pigment epithelium-derived factor (PEDF) have emerged as multifaceted players in not only the pathogenesis, but potential treatment, of numerous diseases. They activate diverse intracellular signaling cascades known to have extensive crosstalk, and have been best studied for their effects in cardiology and cancer biology. Recent work with the two factors indicates that the activity of one growth factor is often directly related to the action of the other. Their respective neuroprotective effects, in particular, raise important questions regarding the treatment of neurodegenerative disorders, including Parkinson’s disease.
Formation of Micro, Nano and Atomic-Level Structure of CoAIOICo-AI Cermets Prepared by Mechanical Alloying

Micro, nano and atomic scale structure of Co-Al cermet prepared by mechanical alloying of Co-Al powders followed by hydrothermal treatment and calcination in the air were studied by X-Ray diffraction pattern (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy-dispersive X-Ray spectroscopy (EDX) and internal field 59Co NMR techniques. The set of physicochemical methods revealed that the cermet metallic part of their particles includes regions comprised of Co and Co-Al alloy with the average Co: Al ratio~2. In turn, the oxide matrix is contained the mixture of cobalt aluminates (Co2AlO4 and CoAl2O4) and cobalt oxides (Co3O4, CoO). The interface between these two cermet parts is represented by aluminum oxide Al2O3 shell protecting the metallic core against further oxidation. The presence of metallic cores containing Co and Co-Al alloy increases CoAlO/Co-Al cermets crushing strength up to 700-800 kg/cm^2 that greatly exceeds Al2O3/Al cermet crushing resistance (10-100 kg/cm^2).
The “Good Cop, Bad Cop” Effect in the RT-Based Concealed Information Test: Exploring the Effect of Emotional Expressions Displayed by a Virtual Investigator

Concealing the possession of relevant information represents a complex cognitive process, shaped by contextual demands and individual differences in cognitive and socio-emotional functioning. The Reaction Time-based Concealed Information Test (RT-CIT) is used to detect concealed knowledge based on the difference in RTs between denying recognition of critical (probes) and newly encountered (irrelevant) information. Several research questions were addressed in this scenario implemented after a mock crime. First, we were interested whether the introduction of a social stimulus (facial identity) simulating a virtual investigator would facilitate the process of deception detection. Next, we explored whether his emotional displays (friendly, hostile or neutral) would have a differential impact on speed of responses to probe versus irrelevant items. We also compared the impact of introducing similar stimuli in a working memory (WM) updating context without requirements to conceal information. Finally, we explored the association between deceptive behavior and individual differences in WM updating proficiency or in internalizing problems (state / trait anxiety and depression). Results indicated that the mere presence of a neutral virtual investigator slowed down participants' responses, but not the appended lie-specific time (difference between probes and irrelevants). Emotional expression was shown to differentially affect speed of responses to critical items, with positive displays from the virtual examiner enhancing lie-specific time, compared to negative facial expressions, which had an opposite impact. This valence-specific effect was not visible in the WM updating context. Higher levels of trait / state anxiety were related to faster responses to probes in the negative condition (hostile facial expression) of the RT-CIT. These preliminary findings further emphasize the need to take into account motivational and emotional factors when considering the transfer of deception detection techniques from the laboratory to real-life settings.
On Dark Chemist ry What ’ s Dark Mat ter and How Mind Inf luences Brain Through Proact ive Spin

Benjamin has written an article entitled “ Dark Chemistry or Psychic Spin Pixel? ” which promotes a “ dark chemistry” model of mind and discuss the spin-mediated theory. This hypothetical chemistry is based on the hypothetical axion dark matter. Although Benjamin is commendable for boldly going where no one has gone before, he may find himself still in the “ bright” territory instead of the “ dark” side, if he is willing to use Occam’s razor to cut out “ dark” things and replace them with non-local effects. Based on our recent experimental findings, our contentions are two-fold: (1) dark matter is likely the cosmological manifestation of quantum entanglement; and (2) the hypothetical axion dark matter is, therefore, replaceable by non-local effects mediated by the primordial spin processes. We also discuss the cause of apparent dark energy. In particular, we explore the issue how mind influences the brain through said spin processes. Our thoughts are that the manifestation of free will is intrinsically associated with the nuclear and/or electron spin processes inside the varying high electric voltage environment of the neural membranes and proteins which likely enable the said spin processes to be “ proactive,” that is, being able to utilize non-local energy (potential) and quantum information to influence brain activities through spin chemistry and possibly other chemical/physical processes in defiance of the second law of thermodynamics.
Identifying Differentially Expressed Genes in Meta‐Analysis via Bayesian Model‐Based Clustering

A Bayesian model‐based clustering approach is proposed for identifying differentially expressed genes in meta‐analysis. A Bayesian hierarchical model is used as a scientific tool for combining information from different studies, and a mixture prior is used to separate differentially expressed genes from non‐differentially expressed genes. Posterior estimation of the parameters and missing observations are done by using a simple Markov chain Monte Carlo method. From the estimated mixture model, useful measure of significance of a test such as the Bayesian false discovery rate (FDR), the local FDR (Efron et al., 2001), and the integration‐driven discovery rate (IDR; Choi et al., 2003) can be easily computed. The model‐based approach is also compared with commonly used permutation methods, and it is shown that the model‐based approach is superior to the permutation methods when there are excessive under‐expressed genes compared to over‐expressed genes or vice versa. The proposed method is applied to four publicly available prostate cancer gene expression data sets and simulated data sets. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Gamma irradiation in multi-cycle ABS recycling- effects on ABS properties and the recovery of antimony

Electronic waste, also called waste electrical and electronic equipment (WEEE), is the fastest growing waste stream in Europe today. The fast exchange pace of mobile phones, televisions and computers creates an important need to develop recycling areas to take care of, reuse and recycle these materials. Metals and plastics are equally important to recover from the waste, especially to fulfil the European Directives on the minimum amount of reused and recycled material. In order to facilitate the recycling, this project has looked into the possibilities of leaching antimony (Sb) with various weak acids from one of the main plastic constituents in electrical and electronic equipment (EEE): acrylonitrile butadiene styrene (ABS). Sb is a synergist to brominated flame retardants and a hazardous substance. The influence of gamma-irradiation on ABS has been investigated in a series of experiments. Firstly the hypothesis that irradiation would have a beneficial effect on the recycling of the plastics by re-extrusion, the plastic was also aged by heating it in an oven (90 oC, 144 h). Secondly the effect of irradiation on the rheological properties such as viscosity was investigated. Thirdly, the influence of irradiation on the leaching of the antimony from the plastic was studied. The main results show that antimony can be leached from ABS by heated sodium hydrogen tartrate in dimethyl sulfoxide (DMSO) with an estimated efficiency of 50 %. Gamma-irradiation has an impact on the mechanical and rheological properties of ABS. The yield stress increased with irradiation doses of 0, 10, 50 and 400 kGy. The viscosity also increased in the test samples with irradiation doses of 0, 10, 100 and 200 kGy. In the multi-recycling and accelerated aging test there was a significant reduction in stiffness for the gamma-irradiated samples after the second out of four cycles which is not fully understood. There was no ductile to brittle transition noticed with respect to the strain rate. Keywords: ABS, WEEE, gamma-irradiation, recycling, antimony, plastics
Stability of scroll excitation waves in human atria during fibrillation: A computational study

We computationally evaluated the functional roles of atrial fibrillation induced electrical remodelling (AFER) on human atrial electrical excitations at cellular, tissue and whole organ levels. Our results show that AFER produced a dramatic reduction in action potential duration, slowing down of intra-atrial conduction, decrease in tissuepsilas temporal vulnerability, but remarkable increase in tissuepsilas spatial vulnerability to arrythmogenesis in response to premature stimulus. It also increased stability of re-entrant waves in 2D and 3D models. With AFER, the rate of atrial excitation was much higher and re-entry degenerated into persistent spatio-temporal chaos. In conclusion, our simulations substantiate a link between AFER and persistence of AF. This study provided a mechanistic insight into the mechanisms underlying the perpetuation and maintenance of AF.
How Grammatical is Character-level Neural Machine Translation? Assessing MT Quality with Contrastive Translation Pairs

Analysing translation quality in regards to specific linguistic phenomena has historically been difficult and time-consuming. Neural machine translation has the attractive property that it can produce scores for arbitrary translations, and we propose a novel method to assess how well NMT systems model specific linguistic phenomena such as agreement over long distances, the production of novel words, and the faithful translation of polarity. The core idea is that we measure whether a reference translation is more probable under a NMT model than a contrastive translation which introduces a specific type of error. We present LingEval97, a large-scale data set of 97000 contrastive translation pairs based on the WMT English->German translation task, with errors automatically created with simple rules. We report results for a number of systems, and find that recently introduced character-level NMT systems perform better at transliteration than models with byte-pair encoding (BPE) segmentation, but perform more poorly at morphosyntactic agreement, and translating discontiguous units of meaning.
Mannan Oligosaccharides in Nursery Pig Nutrition and Their Potential Mode of Action

Simple Summary The aim of the paper is to provide a review of mannan oligosaccharide products in relation to their growth promoting effect and mode of action. Mannan oligosaccharide products maintain intestinal integrity and the digestive and absorptive function of the gut in the post-weaning period in pigs and enhance disease resistance by promoting antigen presentation. We find that dietary supplementation has growth promoting effects in pigs kept in a poor hygienic environment, while the positive effect of MOS is not observed in healthy pig herds with high hygienic standards. Abstract Mannan oligosaccharides (MOSs) are often referred to as one of the potential alternatives for antimicrobial growth promoters. The aim of the paper is to provide a review of mannan oligosaccharide products in relation to their growth promoting effect and mode of action based on the latest publications. We discuss the dietary impact of MOSs on (1) microbial changes, (2) morphological changes of gut tissue and digestibility of nutrients, and (3) immune response of pigs after weaning. Dietary MOSs maintain the intestinal integrity and the digestive and absorptive function of the gut in the post-weaning period. Recent results suggest that MOS enhances the disease resistance in swine by promoting antigen presentation facilitating thereby the shift from an innate to an adaptive immune response. Accordingly, dietary MOS supplementation has a potential growth promoting effect in pigs kept in a poor hygienic environment, while the positive effect of MOS is not observed in healthy pig herds with high hygienic standards that are able to maintain a high growth rate after weaning.