Miracle-dz/UniFAR-FTUs huggingface dataset:
Convergence Results for Neural Networks via Electrodynamics

We study whether a depth two neural network can learn another depth two network using gradient descent. Assuming a linear output node, we show that the question of whether gradient descent converges to the target function is equivalent to the following question in electrodynamics: Given $k$ fixed protons in $\mathbb{R}^d,$ and $k$ electrons, each moving due to the attractive force from the protons and repulsive force from the remaining electrons, whether at equilibrium all the electrons will be matched up with the protons, up to a permutation. Under the standard electrical force, this follows from the classic Earnshaw's theorem. In our setting, the force is determined by the activation function and the input distribution. Building on this equivalence, we prove the existence of an activation function such that gradient descent learns at least one of the hidden nodes in the target network. Iterating, we show that gradient descent can be used to learn the entire network one node at a time.
Large Variations in Risk of Hepatocellular Carcinoma and Mortality in Treatment Naïve Hepatitis B Patients: Systematic Review with Meta-Analyses

Background The complications to chronic hepatitis B (HBV) include incidence of hepatocellular carcinoma (HCC) and mortality. The risk of these complications may vary in different patient groups. Aim To estimate the incidence and predictors of HCC and in untreated HBV patients. Methods Systematic review with random effects meta-analyses of randomized controlled trials and observational studies. Results are expressed as annual incidence (events per 100 person-years) with 95% confidence intervals. Subgroup and sensitivity analyses of patient and study characteristics were performed to identify common risk factors. Results We included 68 trials and studies with a total of 27,584 patients (264,919 person-years). In total, 1,285 of 26,687 (5%) patients developed HCC and 730 of 12,511 (6%) patients died. The annual incidence was 0.88 (95% CI, 0.76–0.99) for HCC and 1.26 (95% CI, 1.01–1.51) for mortality. Patients with cirrhosis had a higher risk of HCC (incidence 3.16; 95% CI, 2.58–3.74) than patients without cirrhosis (0.10; 95% CI, 0.02–0.18). The risk of dying was also higher for patients with than patients without cirrhosis (4.89; 95% CI, 3.16–6.63; and 0.11; 95% CI, 0.09–0.14). The risk of developing HCC increased with HCV coinfection, older age and inflammatory activity. The country of origin did not clearly predict HCC or mortality estimates. Conclusions Cirrhosis was the strongest predictor of HCC incidence and mortality. Patients with HBV cirrhosis have a 31-fold increased risk of HCC and a 44-fold increased mortality compared to non-cirrhotic patients. The low incidence rates should be taken into account when considering HCC screening in non-cirrhotic patients. Trial Registration Prospero CRD42013004764
Virulence Factor Targeting of the Bacterial Pathogen Staphylococcus aureus for Vaccine and Therapeutics.

BACKGROUND Staphylococcus aureus is a major bacterial pathogen capable of causing a range of infections in humans from gastrointestinal disease, skin and soft tissue infections, to severe outcomes such as sepsis. Staphylococcal infections in humans can be frequent and recurring, with treatments becoming less effective due to the growing persistence of antibiotic resistant S. aureus strains. Due to the prevalence of antibiotic resistance, and the current limitations on antibiotic development, an active and highly promising avenue of research has been to develop strategies to specifically inhibit the activity of virulence factors produced S. aureus as an alternative means to treat disease. OBJECTIVE In this review we specifically highlight several major virulence factors produced by S. aureus for which recent advances in antivirulence approaches may hold promise as an alternative means to treating diseases caused by this pathogen. Strategies to inhibit virulence factors can range from small molecule inhibitors, to antibodies, to mutant and toxoid forms of the virulence proteins. CONCLUSION The major prevalence of antibiotic resistant strains of S. aureus combined with the lack of new antibiotic discoveries highlight the need for vigorous research into alternative strategies to combat diseases caused by this highly successful pathogen. Current efforts to develop specific antivirulence strategies, vaccine approaches, and alternative therapies for treating severe disease caused by S. aureus have the potential to stem the tide against the limitations that we face in the post-antibiotic era.
H89 dihydrochloride hydrate and calphostin C lower the body temperature through TRPV1

The transient receptor potential vanilloid (TRPV1) serves as a negative regulator of body temperature, and during fever conditions its expression can lead to a decrease in temperature. TRPV1 is regulated by a variety of enzymes; however, it is currently unclear whether the regulation of TRPV1 phosphorylation may serve a role in the increase in TRPV1 expression during fever. In the present study, using an in vivo experimental method, rat brain ventricles were injected with the protein kinase A (PKA) antagonist, H89, and the protein kinase C (PKC) antagonist, calphostin C, and fever was induced using lipopolysaccharide (LPS) in order to detect the expression of TRPV1 and phosphorylated (p-)TRPV1, the intracellular Ca2+ concentration [(Ca2+)i] of hypothalami and rat body temperature. The results demonstrated that following the generation of fever using LPS, the expressions of TRPV1 and p-TRPV1, and hypothalamic [Ca2+]i markedly increased. In addition, following an injection with the PKA or PKC antagonist, the temperature increased further due to the inhibition of p-TRPV1. Thus, it was hypothesized that PKA and PKC may be involved in TRPV1 phosphorylation, resulting in a temperature reduction during LPS-induced fever conditions.
Multi-population Genomic Relationships for Estimating Current Genetic Variances Within and Genetic Correlations Between Populations

Relationships between individuals are important to estimate genetic variances within a population and covariances between populations. Here, Wientjes. Different methods are available to calculate multi-population genomic relationship matrices. Since those matrices differ in base population, it is anticipated that the method used to calculate genomic relationships affects the estimate of genetic variances, covariances, and correlations. The aim of this article is to define the multi-population genomic relationship matrix to estimate current genetic variances within and genetic correlations between populations. The genomic relationship matrix containing two populations consists of four blocks, one block for population 1, one block for population 2, and two blocks for relationships between the populations. It is known, based on literature, that by using current allele frequencies to calculate genomic relationships within a population, current genetic variances are estimated. In this article, we theoretically derived the properties of the genomic relationship matrix to estimate genetic correlations between populations and validated it using simulations. When the scaling factor of across-population genomic relationships is equal to the product of the square roots of the scaling factors for within-population genomic relationships, the genetic correlation is estimated unbiasedly even though estimated genetic variances do not necessarily refer to the current population. When this property is not met, the correlation based on estimated variances should be multiplied by a correction factor based on the scaling factors. In this study, we present a genomic relationship matrix which directly estimates current genetic variances as well as genetic correlations between populations.
School Bag Usage, Postural and Behavioral Habits and Its Effect on Back Pain Occurrence Among School Children

Back pain is currently growing as a major health problem among school age group children, which can limit or hinder their daily life activities. The aim of the study was to determine the effect of school bag use, postural and behaviors habits on back pain occurrence among school children. Descriptive correlation design was used. This study was conducted at ten governmental preparatory schools from both rural and urban schools in Menouf district, Menoufia Governorate, Egypt. Random sample of 598 preparatory school children including 239 boys and 359 girls aged between 12-15 years of both rural and urban selected schools. Tools: Self-administered structured questionnaire, back pain assessment questionnaire, back pain & body posture evaluation instrument, behavioral habits questionnaire, school bag use questionnaire, and physiological measurements. The main results showed that 74.1% of the studied schoolchildren had suffered from back pain. Female students had significant risk of suffering from back pain by five times than male students. Among school children with back pain, 51.3% had reported moderate pain, the most affected area by pain was shoulder and about one fourth (24.4%) reported that the pain prevented them from performing daily activities. The mean weight of schoolbag carried by all school children was 7.46+ 2. 62 kg and the mean school bag weight as % of body weight was 14.36% ± 4.22. There was significant relationship between back pain and school bag weight, % of body weight, method and duration of carriage. Also, there was a significant relationship between back pain and improper sitting posture for writing, using computer, and sitting in classroom. The study was concluded that back pain among studied school children was high and the pain influences activities of daily life in about one fourth of students. Most of school children carry school bags more than the recommended weights of their body weight. It was associated with sex, parents' history of back pain, duration of sedentary activities, improper posture adopted in performing daily activities, weight of schoolbag, method & duration of carrying schoolbag. Recommendations: The need for developing and implementing of preventative programs in schools about proper postures during daily activities and guidelines for school bag usage.
Uropathogens and Host Characteristics

ABSTRACT Uropathogens other than Escherichia coli occur with greater frequency in patients with risk factors for urinary tract infection (UTI). However, little is known about associations between uropathogen species and host characteristics. Three hundred nineteen urine specimens containing a balanced distribution of uropathogen species were selected from inpatients and outpatients at a university hospital clinical microbiology laboratory. Information on host characteristics was retrospectively collected by chart review. Differences in the frequencies of host characteristics in UTI groups, as defined by the causative uropathogen, were compared by chi-square/Fisher analysis. Multivariate classification and regression tree analysis were used to identify host characteristic subsets that distinguish among uropathogen groups. In this exploratory study, several uropathogen species were found to be strongly linked to host characteristics relevant to UTI. Patients with Pseudomonas aeruginosa UTIs were more likely to have undergone urinary tract procedures (43% versus 15% overall), to have a neurogenic bladder (29% versus 12% overall), to have received recent antibiotic therapy (52% versus 24% overall), and to be male (76% versus 28% overall). Patients with Proteus mirabilis UTIs were more likely to have a foreign body in the lower urinary tract (48% versus 30% overall). The classification tree identified males over the age of 27 years who had undergone a prior urinary tract procedure as belonging to a host characteristic profile associated with P. aeruginosa UTI: 38% of patients with P. aeruginosa UTIs fit this profile. These data may be useful for planning future targeted prophylaxis studies.
A Quantitative Test of Population Genetics Using Spatiogenetic Patterns in Bacterial Colonies

It is widely accepted that population-genetics theory is the cornerstone of evolutionary analyses. Empirical tests of the theory, however, are challenging because of the complex relationships between space, dispersal, and evolution. Critically, we lack quantitative validation of the spatial models of population genetics. Here we combine analytics, on- and off-lattice simulations, and experiments with bacteria to perform quantitative tests of the theory. We study two bacterial species, the gut microbe Escherichia coli and the opportunistic pathogen Pseudomonas aeruginosa, and show that spatiogenetic patterns in colony biofilms of both species are accurately described by an extension of the one-dimensional stepping-stone model. We use one empirical measure, genetic diversity at the colony periphery, to parameterize our models and show that we can then accurately predict another key variable: the degree of short-range cell migration along an edge. Moreover, the model allows us to estimate other key parameters, including effective population size (density) at the expansion frontier. While our experimental system is a simplification of natural microbial community, we argue that it constitutes proof of principle that the spatial models of population genetics can quantitatively capture organismal evolution.
Risk‐taking in vaccination, surgery, and gambling environments: Evidence from a framed laboratory experiment

Vaccination involves a tradeoff between two risky alternatives, namely, susceptibility and immunization. By designing a controlled laboratory experiment, we investigate the association between risk preferences and immunization decisions. To contrast the role of risk preferences in vaccination decisions with other domains, we implemented four frames: vaccination, surgery, complex neutral, and simple neutral. We found direct framing effects for females but not for males. For the former, the demand for the safer alternative is significantly larger in the surgery frame than in all other frames. For male subjects, we found a significant association between stated risk preferences and choice behavior in the simple neutral frame but not in the other three frames. For female subjects, we observed the exact opposite. Although the complexity of the decision problem matters, there is no indication of differential roles of risk preferences for a given complexity. We found that the share of consistent choices is significantly larger in the surgery frame as compared to the two neutral frames, that is, context improves decision making. This does not apply to the vaccination frame, so there is something about vaccinations that prevents individuals from better understanding the decision problem at hand.
Impacts of large-scale circulation on urban ambient concentrations of gaseous elemental mercury in New York, USA

Abstract. The impact of large-scale circulation on urban gaseous elemental mercury (GEM) was investigated through analysis of 2008–2015 measurement data from an urban site in New York City (NYC), New York, USA. Distinct annual cycles were observed in 2009–2010 with mixing ratios in warm seasons (i.e., spring–summer) 10–20 ppqv ( ∼ 10–25 %) higher than in cool seasons (i.e., fall–winter). This annual cycle was disrupted in 2011 by an anomalously strong influence of the US East Coast trough in that warm season and was reproduced in 2014 associated with a particularly strong Bermuda High. The US East Coast trough axis index (TAI) and intensity index (TII) were used to characterize the effect of the US East Coast trough on NYC GEM, especially in winter and summer. The intensity and position of the Bermuda High appeared to have a significant impact on GEM in warm seasons. Regional influence on NYC GEM was supported by the GEM–carbon monoxide (CO) correlation with r of 0.17–0.69 (p ∼ 0) in most seasons. Simulated regional and local anthropogenic contributions to wintertime NYC anthropogenically induced GEM concentrations were averaged at ∼ 75 % and 25 %, with interannual variation ranging over 67 %–83 % and 17 %–33 %, respectively. Results from this study suggest the possibility that the increasingly strong Bermuda High over the past decades could dominate over anthropogenic mercury emission control in affecting ambient concentrations of mercury via regional buildup and possibly enhancing natural and legacy emissions.
Do Gametes Woo? Evidence for Their Nonrandom Union at Fertilization

A fundamental tenet of inheritance in sexually reproducing organisms such as humans and laboratory mice is that gametes combine randomly at fertilization, thereby ensuring a balanced and statistically predictable representation of inherited variants in each generation. This principle is encapsulated in Mendel’s First Law. But exceptions are known. With transmission ratio distortion, particular alleles are preferentially transmitted to offspring. Preferential transmission usually occurs in one sex but not both, and is not known to require interactions between gametes at fertilization. A reanalysis of our published work in mice and of data in other published reports revealed instances where any of 12 mutant genes biases fertilization, with either too many or too few heterozygotes and homozygotes, depending on the mutant gene and on dietary conditions. Although such deviations are usually attributed to embryonic lethality of the underrepresented genotypes, the evidence is more consistent with genetically-determined preferences for specific combinations of egg and sperm at fertilization that result in genotype bias without embryo loss. This unexpected discovery of genetically-biased fertilization could yield insights about the molecular and cellular interactions between sperm and egg at fertilization, with implications for our understanding of inheritance, reproduction, population genetics, and medical genetics.
Physical properties and swelling of natural rubber compounds containing rice husk ash

Rice husk ash, used as received (RHA) or milled (MHA), was investigated in natural rubber (NR) for its potential as a new type of filler. The physical testing of the NR vulcanizates involved tensile, tear, and abrasion resistance, hardness and resilience. The interaction between rice husk ash and natural rubber was investigated by swelling in an organic solvent. The effect of the coupling agent, bis(3-triethoxy-silylpropyl)-tetrasulfane (Si-69), on the curing and physical properties of the vulcanizates was investigated. The presence of the silane coupling agent has not brought the expected increase in properties, yet MHA exhibits the best overall vulcanizates properties when compared to RHA, although still inferior to commercial fillers as precipitated silica (Zeosil-175) and carbon black (N762), especially with regard to tensile strength and abrasion resistance.
Lethal and sublethal effects of oil, chemical dispersant, and dispersed oil on the ctenophore Mnemiopsis leidyi

We established the lethal levels for water-accommodated fractions of Corexit ® 9500A chemical dispersant, crude oil (WAF), and dispersed crude oil (CEWAF) for the ctenophore Mne- miopsis leidyi at both 15 and 23°C. This gelatinous zooplankter was sensitive to dispersant at both temperatures, as well as to oil solutions, with some increase in toxicity of CEWAF as compared to WAF. Subsequent sublethal assays for routine respiration rate, bioluminescence, and glutathione- s-transferase (GST) activity were conducted on individuals surviving 24 h exposures to test solu- tions at both 15 and 23°C. GST activity increased significantly in 2.5 and 5 mg l �1 dispersant solu- tions at 15°C, suggesting a metabolic detoxification response to the dispersant-containing solutions, but no effect of any solution type on routine respiration rate was observed. Light emis- sion through mechanically stimulated bioluminescence and photocyte lysis decreased with exposure to crude oil WAF and CEWAF at both temperatures and to dispersant exposure at 23°C. Collectively, these results demonstrate that M. leidyi exhibits both lethal and sublethal effects from acute crude oil exposure, with an elevation of some sublethal responses upon addition of chemical dispersant. Sublethal effects of oil and dispersants in pelagic species, most notably impairment of luminescence, should be considered when evaluating oil spill response strategies.
REVISITING THE “FLIP-FLOP” INSTABILITY OF HOYLE–LYTTLETON ACCRETION

We revisit the flip-flop instability of two-dimensional planar accretion using high-fidelity numerical simulations. By starting from an initially steady-state axisymmetric solution, we are able to follow the growth of this overstability from small amplitudes. In the small-amplitude limit, before any transient accretion disk is formed, the oscillation period of the accretion shock is comparable to the Keplerian period at the Hoyle–Lyttleton accretion radius (Ra), independent of the size of the accreting object. The growth rate of the overstability increases dramatically with decreasing size of the accretor, but is relatively insensitive to the upstream Mach number of the flow. We confirm that the flip-flop does not require any gradient in the upstream flow. Indeed, a small density gradient as used in the discovery simulations has virtually no influence on the growth rate of the overstability. The ratio of specific heats does influence the overstability, with smaller γ leading to faster growth of the instability. For a relatively large accretor (a radius of 0.037 Ra) planar accretion is unstable for γ = 4/3, but stable for γ ⩾ 1.6. Planar accretion is unstable even for γ = 5/3 provided the accretor has a radius of < 0.0025 Ra. We also confirm that when the accretor is sufficiently small, the secular evolution is described by sudden jumps between states with counter-rotating quasi-Keplerian accretion disks.
Snow Disaster Early Warning in Pastoral Areas of Qinghai Province, China

It is important to predict snow disasters to prevent and reduce hazards in pastoral areas. In this study, we build a potential risk assessment model based on a logistic regression of 33 snow disaster events that occurred in Qinghai Province. A simulation model of the snow disaster early warning is established using a back propagation artificial neural network (BP-ANN) method and is then validated. The results show: (1) the potential risk of a snow disaster in the Qinghai Province is mainly determined by five factors. Three factors are positively associated, the maximum snow depth, snow-covered days (SCDs), and slope, and two are negative factors, annual mean temperature and per capita gross domestic product (GDP); (2) the key factors that contribute to the prediction of a snow disaster are (from the largest to smallest contribution): the mean temperature, probability of a spring snow disaster, potential risk of a snow disaster, continual days of a mean daily temperature below −5 °C, and fractional snow-covered area; and (3) the BP-ANN model for an early warning of snow disaster is a practicable predictive method with an overall accuracy of 80%. This model has quite a few advantages over previously published models, such as it is raster-based, has a high resolution, and has an ideal capacity of generalization and prediction. The model output not only tells which county has a disaster (published models can) but also tells where and the degree of damage at a 500 m pixel scale resolution (published models cannot).