Miracle-dz/UniFAR-FTUs huggingface dataset:
The Efficacy of an Empowerment Program for End-Stage Renal Disease Patients Treated with Hemodialysis

End-stage renal disease (ESRD) is a progressive, debilitating condition characterized by irreversible kidney dysfunction and severe health consequences Zelmer 2007 [1]. ESRD can adversely affect quality of life (QOL), and influence patients’ physical and psychological health, general well-being, and social interactions (Kazemi et al. 2011 [2]). Hemodialysis, despite being one of the most important and effective treatment modalities for ESRD, poses major challenges to patients’ QOL. As described by Cukor and Kimmel (2010) [3], a life dependent on a hemodialysis machine, nurses, technicians, and continuous treatment for up to 15 hours per week presents is overwhelming. It implies having to cope with major stressors including the symptoms of ESRD and their associated social and societal consequences [4].
THEORY AND NUMERICAL APPROXIMATIONS

We consider a nonlinear Dirac system in one space dimension with periodic boundary conditions. First, we discuss questions on the existence and uniqueness of the solution. Then, we propose an implicit-explicit finite difference method for its approximation, proving optimal order a priori error estimates in various discrete norms and showing results from numerical experiments.
SEDIGISM: Structure, excitation, and dynamics of the inner Galactic interstellar medium

Context. The origin and life-cycle of molecular clouds are still poorly constrained, despite their importance for understanding the evolution of the interstellar medium. Many large-scale surveys of the Galactic plane have been conducted recently, allowing for rapid progress in this field. Nevertheless, a sub-arcminute resolution global view of the large-scale distribution of molecular gas, from the diffuse medium to dense clouds and clumps, and of their relationshipto the spiral structure, is still missing. Aims: We have carried out a systematic, homogeneous, spectroscopic survey of the inner Galactic plane, in order to complement the many continuum Galactic surveys available with crucial distance and gas-kinematic information. Our aim is to combine this data set with recent infrared to sub-millimetre surveys at similar angular resolutions. Methods: The SEDIGISM survey covers 78 deg2 of the inner Galaxy (-60°≤l≤ 18°, |b|≤ 0.5°) in the J = 2-1 rotational transition of 13CO. This isotopologue of CO is less abundant than 12CO by factors up to 100. Therefore, its emission has low to moderate optical depths, and higher critical density, making it an ideal tracer of the cold, dense interstellar medium. The data have been observed with the SHFI single-pixel instrument at APEX. The observational setup covers the 13CO(2-1) and C18O(2-1) lines, plus several transitions from other molecules. Results: The observations have been completed. Data reduction is in progress, and the final data products will be made available in the near future. Here we give a detailed description of the survey and the dedicated data reduction pipeline. To illustrate the scientific potential of this survey, preliminary results based on a science demonstration field covering -20°≤l ≤ -18.5° are presented. Analysis of the 13CO(2-1) data in this field reveals compact clumps, diffuse clouds, and filamentary structures at a range of heliocentric distances. By combining our data with data in the (1-0) transition of CO isotopologues from the ThrUMMS survey, we are able to compute a 3D realization of the excitation temperature and optical depth in the interstellar medium. Ultimately, this survey will provide a detailed, global view of the inner Galactic interstellar medium at an unprecedented angular resolution of 30''. This publication is based on data acquired with the Atacama Pathfinder EXperiment (APEX) under programmes 092.F-9315(A) and 193.C-0584(A). APEX is a collaboration between the Max-Planck-Institut fur Radioastronomie, the European Southern Observatory, and the Onsala Space Observatory.Full Table 5 and Table A.1 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat? J/A+A/601/A124
Prospective Study of Cancer Genetic Variants: Variation in Rate of Reclassification by Ancestry

Background In germline genetic testing, variants from understudied ancestries have been disproportionately classified as being of uncertain significance. We hypothesized that the rate of variant reclassification likewise differs by ancestry. Methods Nonbenign variants in actionable genes were collected from consenting subjects undergoing genetic testing at two Southern California sites from September 1996 through December 2016. Variant reclassifications were recorded as they were received, until February 2017 or reclassification to benign. Excluding duplicate variants (same ancestry, laboratory, classification), generalized linear models for the hereditary breast cancer genes (BRCA1/2) and other variants investigated whether rate of reclassification differed for seven categories of ancestry compared with non-Hispanic European. Models took into account laboratory, year, gene, sex, and current classification (handled as a time-dependent covariate) and were adjusted for multiple hypothesis testing. Results Among 1483 nonbenign variants, 693 (46.7%) involved BRCA1/2. Overall, 268 (18.1%) variants were reclassified at least once. Few (9.7%) reclassified variants underwent a net upgrade in pathogenicity. For BRCA1/2 variants, reclassification rates varied by ancestry and increased over time, more steeply for ancestries with lower initial rates (African, Ashkenazi, Chinese) than for ancestries whose initial rates were high (Middle Eastern) or similar to non-Hispanic European (non-Chinese Asian, Native American, Hispanic). In contrast, reclassification rates of non-BRCA1/2 variants did not vary over time but were elevated for most minority ancestries except non-Chinese Asian and Native American. Conclusions For nonbenign variants in cancer-related genes, the rates at which reclassifications are issued vary by ancestry in ways that differ between BRCA1/2 and other genes.
Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella

Significance Invasive nontyphoidal Salmonella disease is a major and previously neglected tropical disease responsible for an estimated ∼390,000 deaths per year in Africa, largely caused by a variant of Salmonella Typhimurium called ST313. Despite the availability of >100,000 Salmonella genomes, it has proven challenging to associate individual SNPs with pathogenic traits of this dangerous bacterium. Here, we used a transcriptomic strategy to identify a single-nucleotide change in a promoter region responsible for crucial phenotypic differences of African S. Typhimurium. Our findings show that a noncoding nucleotide of the bacterial genome can have a profound effect upon the pathogenesis of infectious disease. Salmonella enterica serovar Typhimurium ST313 is a relatively newly emerged sequence type that is causing a devastating epidemic of bloodstream infections across sub-Saharan Africa. Analysis of hundreds of Salmonella genomes has revealed that ST313 is closely related to the ST19 group of S. Typhimurium that cause gastroenteritis across the world. The core genomes of ST313 and ST19 vary by only ∼1,000 SNPs. We hypothesized that the phenotypic differences that distinguish African Salmonella from ST19 are caused by certain SNPs that directly modulate the transcription of virulence genes. Here we identified 3,597 transcriptional start sites of the ST313 strain D23580, and searched for a gene-expression signature linked to pathogenesis of Salmonella. We identified a SNP in the promoter of the pgtE gene that caused high expression of the PgtE virulence factor in African S. Typhimurium, increased the degradation of the factor B component of human complement, contributed to serum resistance, and modulated virulence in the chicken infection model. We propose that high levels of PgtE expression by African S. Typhimurium ST313 promote bacterial survival and dissemination during human infection. Our finding of a functional role for an extragenic SNP shows that approaches used to deduce the evolution of virulence in bacterial pathogens should include a focus on noncoding regions of the genome.
A PTAS for subset TSP in minor-free graphs

We give the first PTAS for the subset Traveling Salesperson Problem (TSP) in $H$-minor-free graphs. This resolves a long standing open problem in a long line of work on designing PTASes for TSP in minor-closed families initiated by Grigni, Koutsoupias and Papadimitriou in FOCS'95. The main technical ingredient in our PTAS is a construction of a nearly light subset $(1+\epsilon)$-spanner for any given edge-weighted $H$-minor-free graph. This construction is based on a necessary and sufficient condition given by \emph{sparse spanner oracles}: light subset spanners exist if and only if sparse spanner oracles exist. This relationship allows us to obtain two new results: _ An $(1+\epsilon)$-spanner with lightness $O(\epsilon^{-d+2})$ for any doubling metric of constant dimension $d$. This improves the earlier lightness bound $\epsilon^{-O(d)}$ obtained by Borradaile, Le and Wulff-Nilsen. _ An $(1+\epsilon)$-spanner with sublinear lightness for any metric of constant correlation dimension. Previously, no spanner with non-trivial lightness was known.
Hot corrosion behaviour of new candidates for thermal barrier coatings application in turbine simulated environments

Thermal barrier coatings (TBCs) are used gas turbine engines. The current material of choice (YSZ) degrades when it contacts with impurities arise from low quality fuels such vanadium and sulfur. YSZ cannot be used in temperature higher than 900˚C. Higher efficiency and performance of gas turbine engines will require a new generation of thermal barrier coatings (TBCs). In current work, hot corrosion behavior of new candidates including Gd2Zr2O7, ZrO2 stabilized with Ta2O5, zirconia stabilized with both Ta2O5 and Y2O3 and zirconia stabilized with CeO2 and TiO2 is investigated. For YSZ case, the reaction between NaVO3 and Y2O3 produces YVO4 and leads to the transformation of tetragonal ZrO2 to monoclinic ZrO2. Comparing to YSZ, under a temperature of 1050 °C, Gd2Zr2O7 is found to be more stable, both thermally and chemically, than YSZ, and exhibits a better hot corrosion resistance. To examine the effect of stabilizing zirconia with tantalum oxide, different compositions of ZrO2-Ta2O5 samples in the presence of molten mixture of Na2SO4 + V2O5 at 1100˚C were tested. Hot corrosion results show that orthorhombic zirconium-tantalum oxide is more stable, both thermally and chemically in Na2SO4+V2O5 media at 1100˚C, and shows a better hot corrosion resistance than the tetragonal phase. When zirconia stabilized with yttria and tantalum oxide (TaYSZ sample), minor amounts of NaTaO3, TaVO5 and Ta9VO25 are formed as the hot corrosion products with only traceable amounts of YVO4. Due to the synergic effect of doping of zirconia with both Y2O3 and Ta2O5, the TaYSZ sample has a much better hot corrosion resistance than YSZ. In zirconia stabilized with CeO2 coating, the formation of CeVO4 crystals possibly postponed the formation of YVO4 and transformation of tetragonal zirconia to monoclinic. On surface of zirconia stabilized with TiO2 coating, TiVO4 crystals are significantly smaller (about 5µm in length) than the large plate shaped YVO4 and CeVO4 found on the YSZ and CSZ samples. TiSZ coating was found to have a better hot corrosion resistance at a temperature of 1050˚C than both YSZ and CSZ coatings.
Congruency Sequence Effects without Feature Integration or Contingency Learning Confounds

The congruency effect in distracter interference (e.g., Stroop) tasks is often reduced after incongruent trials, relative to congruent trials. It has been proposed that this congruency sequence effect (CSE) results from trial-by-trial adjustments of attention, which are triggered by changes in response conflict, expectancy, or negative affect. Hence, a large literature has developed to investigate the source(s) of attention adaptation in distracter interference tasks. Recent work, however, suggests that CSEs may stem from feature integration and/or contingency learning processes that are confounded with congruency sequence in the vast majority of distracter interference tasks. By combining an established method for measuring CSEs in the absence of these learning and memory confounds with a prime-probe task, we observed robust CSEs in two experiments. These findings provide strong evidence of CSEs independent of learning and memory confounds, which might be explainable by trial-by-trial adjustments of attention. They also reveal a highly effective approach for observing CSEs independent of the typical confounds, which will facilitate future studies of how people adapt to distraction.
Quantifying the uncertainties in uranium dose assessments

Signicant uncertainty is known to be present in the internal radiation dose assessments for intakes of uranium compounds. The aim of this thesis was to investigate the sources of the uncertainty in the dose assessment and in particular the biokinetic models used to describe the movement of uranium in the body. A variety of numerical and statistical approaches have been used to explore the uncertainty in the dose assessments. In particular Bayesian techniques have been applied to historical uranium in urine measurements to derive best estimates for important biokinetic parameters. Posterior probability distributions for the important lung solubility parameters have been calculated from six historical exposure cases. It was shown that improved estimates of these parameters can be obtained by sharing the information in each of the cases in the Bayesian calculation. Using these estimates, the uncertainty in the radiation doses from occupational intakes of uranium have been quantifed. Lastly, a novel Bayesian approach to identifying intakes of uranium from bioassay measurements has been developed and tested. This Bayesian approach provides a number of advantages as it incorporates the uncertainty in the bioassay measurements, intake parameters and the bioassay model parameters in a coherent way.
Clostridium Bacteria and Autism Spectrum Conditions: A Systematic Review and Hypothetical Contribution of Environmental Glyphosate Levels

Nowadays, there seems to be a consensus about the multifactorial nature of autism spectrum disorders (ASD). The literature provides hypotheses dealing with numerous environmental factors and genes accounting for the apparently higher prevalence of this condition. Researchers have shown evidence regarding the impact of gut bacteria on neurological outcomes, altering behavior and potentially affecting the onset and/or severity of psychiatric disorders. Pesticides and agrotoxics are also included among this long list of ASD-related environmental stressors. Of note, ingestion of glyphosate (GLY), a broad-spectrum systemic herbicide, can reduce beneficial bacteria in the gastrointestinal tract microbiota without exerting any effects on the Clostridium population, which is highly resistant to this herbicide. In the present study, (i) we performed a systematic review to evaluate the relationship between Clostridium bacteria and the probability of developing and/or aggravating autism among children. For that purpose, electronic searches were performed on Medline/PubMed and Scielo databases for identification of relevant studies published in English up to December 2017. Two independent researches selected the studies and analyzed the data. The results of the present systematic review demonstrate an interrelation between Clostridium bacteria colonization of the intestinal tract and autism. Finally, (ii) we also hypothesize about how environmental GLY levels may deleteriously influence the gut–brain axis by boosting the growth of Clostridium bacteria in autistic toddlers.
Crying a river: how much salt-laden jelly can a leatherback turtle really eat?

ABSTRACT Leatherback turtles (Dermochelys coriacea) are capital breeders that accumulate blubber (33 kJ g−1 wet mass) by hyperphagia on a gelatinous diet at high latitudes; they breed in the tropics. A jellyfish diet is energy poor (0.1–0.2 kJ g−1 wet mass) so leatherbacks must ingest large quantities. Two published estimates of feeding rate [50% body mass day−1 (on Rhizostoma pulmo) and 73% body mass day−1 (on Cyanea capillata)] have been criticised as too high. Jellyfish have high salt and water contents that must be removed to access organic material and energy. Most salt is removed (as NaCl) by paired lachrymal salt glands. Divalent ions are lost via the gut. In this study, the size of adult salt glands (0.622 kg for a 450 kg turtle; relatively three times the size of salt glands in cheloniid turtles) was measured for the first time by computed tomography scanning. Various published values for leatherback field metabolic rate, body fluid composition and likely blubber accumulation rates are combined with known jellyfish salt, water and organic compositions to calculate feasible salt gland secretion rates and feeding rates. The results indicate that leatherbacks can produce about 10–15 ml secretion g−1 salt gland mass h−1 (tear osmolality 1800 mOsm kg−1). This will permit consumption of 80% body mass day−1 of C. capillata. Calculations suggest that leatherbacks will find it difficult/impossible to accumulate sufficient blubber for reproduction in a single feeding season. Rapid jellyfish digestion and short gut transit times are essential. Summary: Leatherback turtles feed on salty jellyfish to accumulate blubber that fuels reproduction. They eat 80% of their body mass per day and secrete 6–9 l of tears per hour to remove salt.
Basic principles of mixed Virtual Element Methods

The aim of this paper is to give a simple, introductory presentation of the extension of the Virtual Element Method to the discretization of H (div)-conforming vector fields (or, more generally, of ( n − 1) − Cochains ). As we shall see, the methods presented here can be seen as extensions of the so-called BDM family to deal with more general element geometries (such as polygons with an almost arbitrary geometry). For the sake of simplicity, we limit ourselves to the 2-dimensional case, with the aim of making the basic philosophy clear. However, we consider an arbitrary degree of accuracy k (the Virtual Element analogue of dealing with polynomials of arbitrary order in the Finite Element Framework).
Experiments on Rayleigh–Bénard convection, magnetoconvection and rotating magnetoconvection in liquid gallium

Thermal convection experiments in a liquid gallium layer subject to a uniform rotation and a uniform vertical magnetic field are carried out as a function of rotation rate and magnetic field strength. Our purpose is to measure heat transfer in a low-Prandtl-number (Pr = 0.023), electrically conducting fluid as a function of the applied temperature difference, rotation rate, applied magnetic field strength and fluid-layer aspect ratio. For Rayleigh–Bénard (non-rotating, non-magnetic) convection we obtain a Nusselt number–Rayleigh number law Nu = 0.129Ra0. 272±0.006 over the range 3.0 × 103 < Ra < 1.6 × 104. For non-rotating magnetoconvection, we find that the critical Rayleigh number RaC increases linearly with magnetic energy density, and a heat transfer law of the form Nu ∼ Ra1/2. Coherent thermal oscillations are detected in magnetoconvection at ∼ 1.4RaC. For rotating magnetoconvection, we find that the convective heat transfer is inhibited by rotation, in general agreement with theoretical predictions. At low rotation rates, the critical Rayleigh number increases linearly with magnetic field intensity. At moderate rotation rates, coherent thermal oscillations are detected near the onset of convection. The oscillation frequencies are close to the frequency of rotation, indicating inertially driven, oscillatory convection. In nearly all of our experiments, no well-defined, steady convective regime is found. Instead, we detect unsteady or turbulent convection just after onset.
Simple dynamic algorithms for Maximal Independent Set and other problems

Most graphs in real life keep changing with time. These changes can be in the form of insertion or deletion of edges or vertices. Such rapidly changing graphs motivate us to study dynamic graph algorithms. However, three important graph problems that are perhaps not sufficiently addressed in the literature include independent sets, maximum matching (exact) and maximum flows. Maximal Independent Set (MIS) is one of the most prominently studied problems in the distributed setting. Recently, the first dynamic MIS algorithm for distributed networks was given by Censor-Hillel et al. [PODC16], requiring expected $O(1)$ amortized rounds with $O(\Delta)$ messages per update, where $\Delta$ is the maximum degree of a vertex in the graph. They suggested an open problem to maintain MIS in fully dynamic centralized setting more efficiently. Assadi et al. [STOC18] presented a deterministic centralized fully dynamic MIS algorithm requiring $O(\min\{\Delta,m^{3/4}\})$ amortized time per update. This result is quite complex involving an exhaustive case analysis. We report a surprisingly simple deterministic centralized algorithm which improves the amortized update time to $O(\min\{\Delta,m^{2/3}\})$. Additionally, we present some other minor results related to dynamic MIS, Maximum Flow, and Maximum Matching. A common trait of all our results is that despite improving state of the art upper bounds or matching state of the art lower bounds, they are surprisingly simple and are analysed using simple amortization arguments. Further, they use no complicated data structures or black box algorithms for their implementation.
Prevalence and predictors of late presentation for HIV care in South Africa

Background Many people living with HIV in South Africa (SA) are not aware of their seropositive status and are diagnosed late during the course of HIV infection. These individuals do not obtain the full benefit from available HIV care and treatment services. Objectives To describe the prevalence of late presentation for HIV care among newly diagnosed HIV-positive individuals and evaluate sociodemographic variables associated with late presentation for HIV care in three high-burden districts of SA. Methods We used data abstracted from records of 8 138 newly diagnosed HIV-positive individuals in 35 clinics between 1 June 2014 and 31 March 2015 to determine the prevalence of late presentation among newly diagnosed HIV-positive individuals in selected high-prevalence health districts. Individuals were categorised as ‘moderately late’, ‘very late’ or ‘extremely late’ presenters based on specified criteria. Descriptive analysis was performed to measure the prevalence of late presentation, and multivariate regression analysis was conducted to identify variables independently associated with extremely late presentation. Results Overall, 79% of the newly diagnosed cases presented for HIV care late in the course of HIV infection (CD4+ count ≤500 cells/ μL and/or AIDS-defining illness in World Health Organization (WHO) stage III/IV), 19% presented moderately late (CD4+ count 351 – 500 cells/μL and WHO clinical stage I or II), 27% presented very late (CD4+ count 201 – 350 cells/μL or WHO clinical stage III), and 33% presented extremely late (CD4+ count ≤200 cells/μL and/or WHO clinical stage IV) for HIV care. Multivariate regression analysis indicated that males, non-pregnant women, individuals aged >30 years, and those accessing care in facilities located in townships and inner cities were more likely to present late for HIV care. Conclusions The majority of newly diagnosed HIV-positive individuals in the three high-burden districts (Gert Sibande, uThukela and City of Johannesburg) presented for HIV care late in the course of HIV infection. Interventions that encourage early presentation for HIV care should be prioritised in SA and should target males, non-pregnant women, individuals aged >30 years and those accessing care in facilities located in inner cities and urban townships.