Miracle-dz/UniFAR-FTUs huggingface dataset:
The global decline of cheetah Acinonyx jubatus and what it means for conservation

Significance Here, we compile and present the most comprehensive data available on cheetah distribution and status. Our analysis shows dramatic declines of cheetah across its distributional range. Most cheetah occur outside protected areas, where they are exposed to multiple threats, but there is little information on population status. Simulation modeling shows that, where cheetah population growth rates are suppressed outside protected areas, extinction risk increases markedly. This result can be generalized to other “protection-reliant” species, and a decision tree is provided to improve their extinction risk estimation. Ultimately, the persistence of protection-reliant species depends on their survival outside and inside protected areas and requires a holistic approach to conservation that engages rather than alienates local communities. Establishing and maintaining protected areas (PAs) are key tools for biodiversity conservation. However, this approach is insufficient for many species, particularly those that are wide-ranging and sparse. The cheetah Acinonyx jubatus exemplifies such a species and faces extreme challenges to its survival. Here, we show that the global population is estimated at ∼7,100 individuals and confined to 9% of its historical distributional range. However, the majority of current range (77%) occurs outside of PAs, where the species faces multiple threats. Scenario modeling shows that, where growth rates are suppressed outside PAs, extinction rates increase rapidly as the proportion of population protected declines. Sensitivity analysis shows that growth rates within PAs have to be high if they are to compensate for declines outside. Susceptibility of cheetah to rapid decline is evidenced by recent rapid contraction in range, supporting an uplisting of the International Union for the Conservation of Nature (IUCN) Red List threat assessment to endangered. Our results are applicable to other protection-reliant species, which may be subject to systematic underestimation of threat when there is insufficient information outside PAs. Ultimately, conserving many of these species necessitates a paradigm shift in conservation toward a holistic approach that incentivizes protection and promotes sustainable human–wildlife coexistence across large multiple-use landscapes.
Colistin Versus Ceftazidime-Avibactam in the Treatment of Infections Due to Carbapenem-Resistant Enterobacteriaceae

Background The efficacy of ceftazidime-avibactam-a cephalosporin-β-lactamase inhibitor combination with in vitro activity against Klebsiella pneumoniae carbapenemase-producing carbapenem-resistant Enterobacteriaceae (CRE)-compared with colistin remains unknown. Methods Patients initially treated with either ceftazidime-avibactam or colistin for CRE infections were selected from the Consortium on Resistance Against Carbapenems in Klebsiella and other Enterobacteriaceae (CRACKLE), a prospective, multicenter, observational study. Efficacy, safety, and benefit-risk analyses were performed using intent-to-treat analyses with partial credit and the desirability of outcome ranking approaches. The ordinal efficacy outcome was based on disposition at day 30 after starting treatment (home vs not home but not observed to die in the hospital vs hospital death). All analyses were adjusted for confounding using inverse probability of treatment weighting (IPTW). Results Thirty-eight patients were treated first with ceftazidime-avibactam and 99 with colistin. Most patients received additional anti-CRE agents as part of their treatment. Bloodstream (n = 63; 46%) and respiratory (n = 30; 22%) infections were most common. In patients treated with ceftazidime-avibactam versus colistin, IPTW-adjusted all-cause hospital mortality 30 days after starting treatment was 9% versus 32%, respectively (difference, 23%; 95% bootstrap confidence interval, 9%-35%; P = .001). In an analysis of disposition at 30 days, patients treated with ceftazidime-avibactam, compared with those treated within colistin, had an IPTW-adjusted probability of a better outcome of 64% (95% confidence interval, 57%-71%). Partial credit analyses indicated uniform superiority of ceftazidime-avibactam to colistin. Conclusions Ceftazidime-avibactam may be a reasonable alternative to colistin in the treatment of K. pneumoniae carbapenemase-producing CRE infections. These findings require confirmation in a randomized controlled trial.
A Project Management Model to a Distributed Software Engineering Environment

This article presents a project management model (PMM) to a distributed environment that will be integrated to the DiSEN (Distributed Software Engineering Environment). The model purpose is to supply to the interested ones in the software project management the pertinent information and treat the aspects of the team member’s physical distribution. It was based in PMBOK (Project Management Body of Knowledge) and CMMI (Capability Maturity Model Integration) and the issues treated by the PMM include cultural differences between the members, distribution of knowledge, a tool to facilitate the communication between members, standardization of documents and motivating people geographically dispersed.
Nonstandard Fourier Pseudospectral Time Domain (PSTD) Schemes for Partial Differential Equations

A class of nonstandard pseudospectral time domain (PSTD) schemes for solving time-dependent hyperbolic and parabolic partial differential equations (PDEs) is introduced. These schemes use the Fourier collocation spectral method to compute spatial gradients and a nonstandard finite difference scheme to integrate forwards in time. The modified denominator function that makes the finite difference time scheme exact is transformed into the spatial frequency domain or k-space using the dispersion relation for the governing PDE. This allows the correction factor to be applied in the spatial frequency domain as part of the spatial gradient calculation. The derived schemes can be formulated to be unconditionally stable, and apply to PDEs in any space dimension. Examples of the resulting nonstandard PSTD schemes for several PDEs are given, including the wave equation, diffusion equation, and convection-diffusion equation.
Star Formation at z = 2.481 in the Lensed Galaxy SDSS J1110+6459: Star Formation Down to 30 pc Scales

We present measurements of the surface density of star formation, the star-forming clump luminosity function, and the clump size distribution function, for the lensed galaxy SGAS J111020.0+645950.8 at a redshift of z = 2.481. The physical size scales that we probe, radii r = 30–50 pc, are considerably smaller scales than have yet been studied at these redshifts. The star formation surface density we find within these small clumps is consistent with surface densities measured previously for other lensed galaxies at similar redshift. Twenty-two percent of the rest-frame ultraviolet light in this lensed galaxy arises from small clumps, with pc. Within the range of overlap, the clump luminosity function measured for this lensed galaxy is remarkably similar to those of galaxies. In this galaxy, star-forming regions smaller than 100 pc—physical scales not usually resolved at these redshifts by current telescopes—are important locations of star formation in the distant universe. If this galaxy is representative, this may contradict the theoretical picture in which the critical size scale for star formation in the distant universe is of the order of 1 kpc. Instead, our results suggest that current telescopes have not yet resolved the critical size scales of star-forming activity in galaxies over most of cosmic time.
A Comparison of Sample Size and Power in Case-Only Association Studies of Gene-Environment Interaction

Assuming continuous, normally distributed environmental and categorical genotype variables, the authors compare 6 case-only designs for tests of association in gene-environment interaction. Novel tests modeling the environmental variable as either the response or the predictor and allowing a genetic variable with multiallelic variants are included. The authors show that tests imposing the same genotypic pattern of inheritance perform similarly regardless of whether genotype is the response variable or the predictor variable. The novel tests using the genetic variable as the response variable are advantageous because they are robust to non-normally distributed environmental exposures. Dominance deviance—deviation from additivity in the main or interaction effects—is key to test performance: When it is zero or modest, tests searching for a trend with increasing risk alleles are optimal; when it is large, tests for genotypic effects are optimal. However, the authors show that dominance deviance is attenuated when it is observed at a proxy locus, which is common in genome-wide association studies, so large dominance deviance is likely to be rare. The authors conclude that the trend test is the appropriate tool for large-scale association scans where the true gene-environment interaction model is unknown. The common practice of assuming a dominant pattern of inheritance can cause serious losses of power in the presence of any recessive, or modest dominant, effects.
Efficacy of Ropel® as a coyote repellent

We examined the repellency of a commercially available animal repellent to determine the efficacy of its application to objects that are attractive to coyotes (Canis latrans). Specifically, we aimed to both prevent chewing behavior by coyotes on a nylon-like strapping material, which is used to construct barrier-arresting systems on military airstrips, and determine the ability of the solution to prevent the animals from repeating the undesired behavior. We mixed Ropel® Animal and Rodent Repellent with a liquid latex sticker to form a 2% latex and 98% Ropel solution. We used a 2% latex and 98% water solution as a control. The solutions were applied to test material placed in coyote pens. We exposed 12 mated pairs of coyotes to the Ropel and control in a 2-choice test and recorded behavior toward the materials using camera traps. Photographs and the condition of the material were used to determine when, and if, individual coyotes approached, made contact with, tasted, repeatedly tasted, or destroyed the material. There was no difference between the number of treatment and control materials tasted, but significantly more control materials were repeatedly tasted than treatment materials. However, there was no difference between the number of treatment and control materials destroyed. While results suggest that there are some repellent properties in the Ropel solution after initial tasting, we do not recommend this product be relied upon as a coyote-specific repellent.
On the Semantics of Intensionality and Intensional Recursion

Intensionality is a phenomenon that occurs in logic and computation. In the most general sense, a function is intensional if it operates at a level finer than (extensional) equality. This is a familiar setting for computer scientists, who often study different programs or processes that are interchangeable, i.e. extensionally equal, even though they are not implemented in the same way, so intensionally distinct. Concomitant with intensionality is the phenomenon of intensional recursion, which refers to the ability of a program to have access to its own code. In computability theory, intensional recursion is enabled by Kleene’s Second Recursion Theorem. This thesis is concerned with the crafting of a logical toolkit through which these phenomena can be studied. Our main contribution is a framework in which mathematical and computational constructions can be considered either extensionally, i.e. as abstract values, or intensionally, i.e. as fine-grained descriptions of their construction. Once this is achieved, it may be used to analyse intensional recursion. To begin, we turn to type theory. We construct a modal λ-calculus, called Intensional PCF, which supports non-functional operations at modal types. Moreover, by adding Lob's rule from provability logic to the calculus, we obtain a type-theoretic interpretation of intensional recursion. The combination of these two features is shown to be consistent through a confluence argument. Following that, we begin searching for a semantics for Intensional PCF. We argue that 1-category theory is not sufficient, and propose the use of P-categories instead. On top of this setting we introduce exposures, which are P-categorical structures that function as abstractions of well-behaved intensional devices. We produce three examples of these structures, based on Godel numberings on Peano arithmetic, realizability theory, and homological algebra. The language of exposures leads us to a P-categorical analysis of intensional recursion, through the notion of intensional fixed points. This, in turn, leads to abstract analogues of classic intensional results in logic and computability, such as Godel's Incompleteness Theorem, Tarski's Undefinability Theorem, and Rice's Theorem. We are thus led to the conclusion that exposures are a useful framework, which we propose as a solid basis for a theory of intensionality. In the final chapters of the thesis we employ exposures to endow Intensional PCF with an appropriate semantics. It transpires that, when interpreted in the P-category of assemblies on the PCA K1, the Lob rule can be interpreted as the type of Kleene’s Second Recursion Theorem.
Image Super-Resolution Via Double Sparsity Regularized Manifold Learning

Over the past few years, high resolutions have been desirable or essential, e.g., in online video systems, and therefore, much has been done to achieve an image of higher resolution from the corresponding low-resolution ones. This procedure of recovering/rebuilding is called single-image super-resolution (SR). Performance of image SR has been significantly improved via methods of sparse coding. That is to say, the image frame patch can be sparse linear combinations of basis elements. However, most of these existing methods fail to consider the local geometrical structure in the space of the training data. To take this crucial issue into account, this paper proposes a method named double sparsity regularized manifold learning (DSRML). DSRML can preserve the properties of the aforementioned local geometrical structure by employing manifold learning, e.g., locally linear embedding. Based on a large amount of experimental results, DSRML is demonstrated to be more robust and more effective than previous efforts in the task of single-image SR.
Untargeted metabolomics reveals links between Tiger nut (Cyperus esculentus L.) and its geographical origin by metabolome changes associated with membrane lipids

ABSTRACT Tiger nuts and tiger nut milk are well-known Valencian products, and step-by-step these tubers and the tuber-based beverage are becoming more and more relevant products in international markets. However, the increasing demand and success of Valencian tiger nuts did not allow protected designation of origin (PDO) tuber to supply the domestic and international markets. Therefore, the verification of the geographical origin is highly required. In this research, the main objective was to combine an advance analytical method and chemometrics tools in order to decipher the geographical origin of 45 tiger nut samples from (i) ‘Xufa de València’ PDO and (ii) African samples. The analytical method, based on solid-liquid extraction followed by ultra-high performance liquid chromatography coupled to high resolution tandem mass spectrometry (UHPLC-HRMS) metabolomics approach, highlighted sensitivity and wide linear dynamic range in order to simultaneously analyse polar and non-polar metabolites. After data processing, a pronounced sample clustering according to the geographical origin was clearly observed using unsupervised models, and supervised models revealed that tiger nuts lipidome was associated with the geographical origin. As a result, African samples highlighted an overexpression of phospholipids, such as phosphatidylethanolamine 34:1, and triacylgricerols crosslinked to environmental stress and alteration of membrane lipid compositions. GRAPHICAL ABSTRACT
A Systematic Relationship Between Functional Connectivity and Intracortical Myelin in the Human Cerebral Cortex

Abstract Research in the macaque monkey suggests that cortical areas with similar microstructure are more likely to be connected. Here, we examine this link in the human cerebral cortex using 2 magnetic resonance imaging (MRI) measures: quantitative T1 maps, which are sensitive to intracortical myelin content and provide an in vivo proxy for cortical microstructure, and resting‐state functional connectivity. Using ultrahigh‐resolution MRI at 7 T and dedicated image processing tools, we demonstrate a systematic relationship between T1‐based intracortical myelin content and functional connectivity. This effect is independent of the proximity of areas. We employ nonlinear dimensionality reduction to characterize connectivity components and identify specific aspects of functional connectivity that are linked to myelin content. Our results reveal a consistent spatial pattern throughout different analytic approaches. While functional connectivity and myelin content are closely linked in unimodal areas, the correspondence is lower in transmodal areas, especially in posteromedial cortex and the angular gyrus. Our findings are in agreement with comprehensive reports linking histologically assessed microstructure and connectivity in different mammalian species and extend them to the human cerebral cortex in vivo.
The Relation of Obesity-Related Hormonal and Cytokine Levels With Multiple Myeloma and Non-Hodgkin Lymphoma

This article presents the first detailed overview of the mechanisms that may underlie the relation of obesity with B-cell non-Hodgkin lymphomas (NHLs) and multiple myeloma (MM). Epidemiologic studies, including meta-analyses of prospective cohorts, have reported that the risks of NHL and MM are significantly increased in obese, relative to normal weight, women and men. Accumulating experimental and clinical evidence suggests that inflammatory cytokines, hyperinsulinemia, and sex hormones could play a role in the association of obesity with B-cell NHL and MM carcinogenesis. There is, however, a paucity of data published from appropriate large prospective cohort studies, and studies concurrently measuring these correlated factors, to formally determine the likely biologic factors driving the relationship of obesity with NHL and MM. Additional strengths and weaknesses of the current literature, as well as study design issues that need to be considered in conducting these studies, such as the exclusion of type 2 diabetics or postmenopausal women using hormone therapy, are discussed.
Mortality of patients hospitalized for active tuberculosis in King Abdulaziz University Hospital, Jeddah, Saudi Arabia

Objectives: To determine the mortality rates and predictors among patients hospitalized with active tuberculosis (TB) at King Abdulaziz University Hospital (KAUH) in Jeddah. Methods: A retrospective study was performed on 291 active TB patients hospitalized in KAUH, Jeddah, Saudi Arabia from December 2011 to December 2016. Medical records were collected and evaluated using a dedicated data extraction sheet. The records included demographics, clinical, radiological, laboratory, and drug resistance data. Results: Of the 291 patients, 168 had pulmonary TB, 39 had extrapulmonary TB, and 84 had both pulmonary and extrapulmonary TB. After a mean hospital stay of 1.74 months, 85.9% were successfully treated and discharged. However, 14% died in the hospital after a mean stay of 1.87 months. Predictors of inpatient TB mortality were older age, congestive heart failure, renal failure, diabetes mellitus, chronic lung disease, hepatitis B virus infection, bilateral pulmonary TB, miliary TB, pleural effusion, and leukopenia. In particular, a logistic regression model revealed a mortality probability of 90% in patients older than 65 with congestive heart failure and bilateral lung involvement. However, drug resistance did not significantly affect the mortality rate. Conclusions: The inpatient TB mortality rate was lower than mortality rates described previously. Nevertheless, early recognition, appropriate treatments, and education for patients and caregivers concerning treatment, efficient medical management, and effective preventive measures can further reduce mortality.
Differential Expression of Hepatic Genes of the Greater Horseshoe Bat (Rhinolophus ferrumequinum) between the Summer Active and Winter Torpid States

Hibernation is one type of torpor, a hypometabolic state in heterothermic mammals, which can be used as an energy-conservation strategy in response to harsh environments, e.g. limited food resource. The liver, in particular, plays a crucial role in adaptive metabolic adjustment during hibernation. Studies on ground squirrels and bears reveal that many genes involved in metabolism are differentially expressed during hibernation. Especially, the genes involved in carbohydrate catabolism are down-regulated during hibernation, while genes responsible for lipid β-oxidation are up-regulated. However, there is little transcriptional evidence to suggest physiological changes to the liver during hibernation in the greater horseshoe bat, a representative heterothermic bat. In this study, we explored the transcriptional changes in the livers of active and torpid greater horseshoe bats using the Illumina HiSeq 2000 platform. A total of 1358 genes were identified as differentially expressed during torpor. In the functional analyses, differentially expressed genes were mainly involved in metabolic depression, shifts in the fuel utilization, immune function and response to stresses. Our findings provide a comprehensive evidence of differential gene expression in the livers of greater horseshoe bats during active and torpid states and highlight potential evidence for physiological adaptations that occur in the liver during hibernation.