Miracle-dz/UniFAR-FTUs huggingface dataset:
New direct-product testers and 2-query PCPs

The "direct product code" of a function f gives its values on all k-tuples (f(x1),. ,f(xk)). This basic construct underlies "hardness amplification" in cryptography, circuit complexity and PCPs. Goldreich and Safra [12] pioneered its local testing and its PCP application. A recent result by Dinur and Goldenberg [5] enabled for the first time testing proximity to this important code in the "list-decoding" regime. In particular, they give a 2-query test which works for polynomially small success probability 1/kα, and show that no such test works below success probability 1/k. Our main result is a 3-query test which works for exponentially small success probability exp(-kα). Our techniques (based on recent simplified decoding algorithms for the same code [15]) also allow us to considerably simplify the analysis of the 2-query test of [5]. We then show how to derandomize their test, achieving a code of polynomial rate, independent of k, and success probability 1/kα. Finally we show the applicability of the new tests to PCPs. Starting with a 2-query PCP over an alphabet Σ and with soundness error 1-δ, Rao [19] (building on Raz's (k-fold) parallel repetition theorem [20] and Holenstein's proof [13]) obtains a new 2-query PCP over the alphabet Σk with soundness error exp(-δ2 k). Our techniques yield a 2-query PCP with soundness error exp(-δ √k). Our PCP construction turns out to be essentially the same as the miss-match proof system defined and analyzed by Feige and Kilian [8], but with simpler analysis and exponentially better soundness error.
The Genome Clinic: A Multidisciplinary Approach to Assessing the Opportunities and Challenges of Integrating Genomic Analysis into Clinical Care

Our increasing knowledge of how genomic variants affect human health and the falling costs of whole‐genome sequencing are driving the development of individualized genetic medicine. This new clinical paradigm uses knowledge of an individual's genomic variants to guide health care decisions throughout life, to anticipate, diagnose, and manage disease. While individualized genetic medicine offers the promise of transformative change in health care, it forces us to reconsider existing ethical, scientific, and clinical paradigms. The potential benefits of presymptomatic identification of at risk individuals, improved diagnostics, individualized therapy, accurate prognosis, and avoidance of adverse drug reactions coexist with the potential risks of uninterpretable results, psychological harm, outmoded counseling models, and increased health care costs. Here, we review the challenges of integrating genomic analysis into clinical practice and describe a prototype for implementing genetic medicine. Our multidisciplinary team of bioinformaticians, health economists, ethicists, geneticists, genetic counselors, and clinicians has designed a “Genome Clinic” research project that addresses multiple challenges in genomic medicine—ranging from the development of bioinformatics tools for the clinical assessment of genomic variants and the discovery of disease genes to health policy inquiries, assessment of clinical care models, patient preference, and the ethics of consent.
Will Sympatric Speciation Fail due to Stochastic Competitive Exclusion?

Sympatric speciation requires coexistence of the newly formed species. If divergence proceeds by small mutational steps, the new species utilize almost the same resources initially, and full speciation may be impeded by competitive exclusion in stochastic environments. We investigate this primarily ecological problem of sympatric speciation by studying the population dynamics of a diverging asexual population in a fluctuating environment. Correlation between species responses to environmental fluctuation is assumed to decrease with distance in trait space. Rapidly declining correlation in combination with high environmental variability may delay full speciation or even render it impossible. Stochastic extinctions impeding speciation are most likely when correlation decays faster than competition, for example, when demographic stochasticity is strong or when divergence is not accompanied by niche separation, such as in speciation driven entirely by sexual selection. Our general theoretical results show an interesting connection between short‐term ecological dynamics and long‐term, large‐scale evolution.
Extended fully-nonlinear and strongly-dispersive internal wave equations in a three-layer system

Extended fully-nonlinear and strongly-dispersive internal wave equations in a three-layer system Keisuke Nakayama Kobe University nakayama@phoenix.kobe-u.ac. jp Kenji Shimizu Formerly at CSIRO Oceans and Atmosphere kenji.shimizu. rc@gmail.com Abstract The KdV, MKdV, Boussinesq-type, Benjamin-Ono, NLS, and eKdV equations have been applied to analyze nonlinear internal waves in a two-layer system. The KP and Boussinesq-type equations have also been used for the analysis of two-layer motions with two horizontal dimensions. However, there are only few equations for a three-layer system applicable to particular or special conditions, such as breather solutions in a three-layer system based on the Gardner equation. Nakayama et al. (2015) have proposed the Fully-nonlinear and strongly-Dispersive Internal wave equations in a three-Layer System (FDI-3LS equations) by extending the two dimensional counterpart (FDI-2LS equations; Nakayama and Kakinuma, 2010), which successfully reproduced a large-amplitude Mach stem due to soliton resonance. This study aims to investigate the applicability of the FDI-3LS equations to analyze internal waves in a three-layer system. Introduction Monismith (1986) demonstrated that Wedderburn Number (Thompson and Imberger, 1980) could be useful for evaluating upwelling phenomena in a three-layer stratification with constant density in the upper and bottom layers and a linear transition between the two. Imberger and Patterson (1990) revealed that the occurrence of upwelling in the VIII th Int. Symp. Stratified Flows, San Diego, USA, Aug. 29 – Sept. 1, 2016
Induction and repression of the Drosophila Sgs‐3 glue gene are mediated by distinct sequences in the proximal promoter.

The normal developmental expression of the Drosophila salivary gland secretion protein gene Sgs‐3 requires the interaction of a distal and proximal regulatory element. A deletion/replacement analysis of the proximal promoter in stably transformed lines shows that induction of an Sgs‐3/Adh fusion gene is normal if sequences from +10 to −50 are replaced by those of the hsp70 gene. Sequences between −98 and −50 are necessary for this expression but there is internal redundancy within this region as two distinct upstream sequences of 18 and 22 bp respectively are sufficient for stage‐ and tissue‐specific expression, albeit at reduced levels. A point mutation at −53 eliminates the ecdysone‐mediated repression of the Sgs‐3 promoter at pupariation. We report mosaicisms of expression within the salivary gland for a number of stably transformed lines.
Is Saki #delicious?: The Food Perception Gap on Instagram and Its Relation to Health

Food is an integral part of our life and what and how much we eat crucially affects our health. Our food choices largely depend on how we perceive certain characteristics of food, such as whether it is healthy, delicious or if it qualifies as a salad. But these perceptions differ from person to person and one person's "single lettuce leaf" might be another person's "side salad". Studying how food is perceived in relation to what it actually is typically involves a laboratory setup. Here we propose to use recent advances in image recognition to tackle this problem. Concretely, we use data for 1.9 million images from Instagram from the US to look at systematic differences in how a machine would objectively label an image compared to how a human subjectively does. We show that this difference, which we call the "perception gap", relates to a number of health outcomes observed at the county level. To the best of our knowledge, this is the first time that image recognition is being used to study the "misalignment" of how people describe food images vs. what they actually depict.
Distribution of cultivated and uncultivated cyanobacteria and Chloroflexus-like bacteria in hot spring microbial mats

Oligodeoxynucleotide hybridization probes were developed to complement specific regions of the small subunit (SSU) rRNA sequences of cultivated and uncultivated cyanobacteria and Chloroflexus-like bacteria, which inhabit hot spring microbial mats. The probes were used to investigate the natural distribution of SSU rRNAs from these species in mats of Yellowstone hot springs of different temperatures and pHs as well as changes in SSU rRNA distribution resulting from 1-week in situ shifts in temperature, pH, and light intensity. Synechococcus lividus Y-7c-s SSU rRNA was detected only in the mat of a slightly acid spring, from which it may have been initially isolated, or when samples from a more alkaline spring were incubated in the more acid spring. Chloroflexus aurantiacus Y-400-fl SSU rRNA was detected only in a high-temperature mat sample from the alkaline Octopus Spring or when lower-temperature samples from this mat were incubated at the high-temperature site. SSU rRNAs of uncultivated species were more widely distributed. Temperature distributions and responses to in situ temperature shifts suggested that some of the uncultivated cyanobacteria might be adapted to high-, moderate-, and low-temperature ranges whereas an uncultivated Chloroflexus-like bacterium appears to have broad temperature tolerance. SSU rRNAs of all uncultivated species inhabiting a 48 to 51 degrees C Octopus Spring mat site were most abundant in the upper 1 mm and were not detected below a 2.5-to 3.5-mm depth, a finding consistent with their possible phototrophic nature. However, the effects of light intensity reduction on these SSU rRNAs were variable, indicating the difficulty of demonstrating a phototrophic phenotype in light reduction experiments.
Transforaminal hypertonic saline for the treatment of lumbar lateral canal stenosis: a double-blinded, randomized, active-control trial.

BACKGROUND Degenerative lumbar spinal stenosis is one of the most common causes of chronic lower back pain and radiculopathy. Spinal stenosis is anatomically classified as central and lateral spinal canal stenosis. Many treatment modalities and techniques, including surgery and epidural injection, have been used to manage the pain. However, the effect of hypertonic saline injection via the transforaminal approach has not yet been studied. OBJECTIVES The aim of this study is to determine the effect of adding hypertonic saline to conventional transforaminal epidural steroid injections (TFEI) to provide pain relief for chronic radiculopathy patients secondary to lateral canal spinal stenosis. STUDY DESIGN A double-blind, randomized, active-control trial. SETTING An interventional pain management practice in a hospital, Republic of Korea. METHODS Two groups: the hypertonic group received hypertonic saline combined with triamcinolone and the control group received normal saline combined with triamcinolone. A total of 68 patients were randomly allocated into either 2 groups by a computer-generated randomization program. Twenty-seven patients in the hypertonic group and 26 patients in the control group were assessed. A total of 53 patients were included in this analysis. Outcome measures were taken at baseline, one, 2, 3, 4, and 6 months post-procedure. The primary outcome measures included the numerical rating scale (NRS) and the proportion of substantial responders. The secondary outcome measures included the Oswestry disability index (ODI), the proportion of substantial and moderate responders, and patient satisfaction. RESULTS Transforaminal epidural injection of steroids, with or without the addition of 10% hypertonic saline, was effective and provided significant pain relief with the improvement of functional outcome within 4 months. The addition of hypertonic saline was superior in efficacy compared with conventional TFEI at 3 months follow-up. The differences in the absolute pain scores did not demonstrate statistical significance between the 2 groups. The reduction in pain intensity from the baseline was greater in the hypertonic group and demonstrated higher rates of satisfaction. The use of hypertonic saline also extended the duration of significant pain relief to 6 months compared with baseline. LIMITATIONS The lack of placebo group and small sample size. CONCLUSION Superior short-term pain relieving efficacy, but limited long-term effects of hypertonic saline, when added to TFEIs.
Characterizing the influence of atmospheric river orientation and intensity on precipitation distributions over North Coastal California

Atmospheric rivers (ARs) are long (>2000 km) and narrow (500–1000 km) corridors of enhanced vertically integrated water vapor and enhanced integrated water vapor transport (IVT) that are responsible for a majority of global poleward moisture transport and can result in extreme orographic precipitation. Observational evidence suggests that ARs within different synoptic‐scale flow regimes may contain different water vapor source regions, orientations, and intensities and may result in different precipitation distributions. This study uses k‐means clustering to objectively identify different orientations and intensities of ARs that make landfall over the California Russian River watershed. The ARs with different orientations and intensities occur within different synoptic‐scale flow patterns in association with variability in IVT direction and quasi‐geostrophic forcing for ascent and lead to different precipitation distributions over the Russian River watershed. These differences suggest that both mesoscale upslope moisture flux and synoptic‐scale forcing for ascent are important factors in modulating precipitation distributions during landfalling ARs.
The structure of alanine racemase from Acinetobacter baumannii

The crystal structure of A. baumannii alanine racemase (AlrAba) from the highly antibiotic resistant NCTC13302 strain has been solved to 1.9 Å resolution. Comparison of (AlrAba) with alanine racemases from closely related bacteria demonstrates a conserved overall fold.
A Strong Immune Response in Young Adult Honeybees Masks Their Increased Susceptibility to Infection Compared to Older Bees

Honeybees, Apis mellifera, show age-related division of labor in which young adults perform maintenance (“housekeeping”) tasks inside the colony before switching to outside foraging at approximately 23 days old. Disease resistance is an important feature of honeybee biology, but little is known about the interaction of pathogens and age-related division of labor. We tested a hypothesis that older forager bees and younger “house” bees differ in susceptibility to infection. We coupled an infection bioassay with a functional analysis of gene expression in individual bees using a whole genome microarray. Forager bees treated with the entomopathogenic fungus Metarhizium anisopliae s.l. survived for significantly longer than house bees. This was concomitant with substantial differences in gene expression including genes associated with immune function. In house bees, infection was associated with differential expression of 35 candidate immune genes contrasted with differential expression of only two candidate immune genes in forager bees. For control bees (i.e. not treated with M. anisopliae) the development from the house to the forager stage was associated with differential expression of 49 candidate immune genes, including up-regulation of the antimicrobial peptide gene abaecin, plus major components of the Toll pathway, serine proteases, and serpins. We infer that reduced pathogen susceptibility in forager bees was associated with age-related activation of specific immune system pathways. Our findings contrast with the view that the immunocompetence in social insects declines with the onset of foraging as a result of a trade-off in the allocation of resources for foraging. The up-regulation of immune-related genes in young adult bees in response to M. anisopliae infection was an indicator of disease susceptibility; this also challenges previous research in social insects, in which an elevated immune status has been used as a marker of increased disease resistance and fitness without considering the effects of age-related development.
Efectos del cambio climático en los recursos hídricos de México

El Instituto Mexicano de Tecnología del Agua publicó en fecha reciente el libro Efectos del cambio climático en los recursos hídricos de México, cuyo autor es el Dr. Polioptro Martínez Austria, Director General del propio Instituto. Este texto, documentado en una sólida información técnica, nos va presentando en forma sencilla y clara la realidad de las condiciones climatológicas que prevalecen hoy día en el planeta y particularmente en México, y su relación con el valioso recurso agua y la manera en que impactará nuestro entorno, de acuerdo con los diferentes escenarios de cambio climático a futuro, desarrollados por el Panel Intergubernamental sobre Cambio Climático (IPCC, por sus siglas en inglés) y que son, también, materia de esta publicación.
The Role of miR-34a in the Hepatoprotective Effect of Hydrogen Sulfide on Ischemia/Reperfusion Injury in Young and Old Rats

Hydrogen sulfide (H2S) can protect the liver against ischemia-reperfusion (I/R) injury. However, it is unknown whether H2S plays a role in the protection of hepatic I/R injury in both young and old patients. This study compared the protective effects of H2S in a rat model (young and old animals) of I/R injury and the mechanism underlying its effects. Young and old rats were assessed following an injection of NaHS. NaHS alone reduced hepatic I/R injury in the young rats by activating the nuclear erythroid-related factor 2 (Nrf2) signaling pathway, but it had little effect on the old rats. NaHS pretreatment decreased miR-34a expression in the hepatocytes of the young rats with hepatic I/R. Overexpresion of miR-34a decreased Nrf-2 and its downstream target expression, impairing the hepatoprotective effect of H2S on the young rats. More importantly, downregulation of miR-34a expression increased Nrf-2 and the expression of its downstream targets, enhancing the effect of H2S on hepatic I/R injury in the old rats. This study reveals the different effects of H2S on hepatic I/R injury in young and old rats and sheds light on the involvement of H2S in miR-34a modulation of the Nrf-2 pathway.
Residential Proximity to Major Roadway and 10-Year All-Cause Mortality After Myocardial Infarction

Background— The relationship between residential proximity to roadway and long-term survival after acute myocardial infarction (AMI) is unknown. We investigated the association between distance from residence and major roadway and 10-year all-cause mortality after AMI in the Determinants of Myocardial Infarction Onset Study (Onset Study), hypothesizing that living closer to a major roadway at the time of AMI would be associated with increased risk of mortality. Methods and Results— The Onset Study enrolled 3886 individuals hospitalized for AMI in 64 centers across the United States from 1989 to 1996. Institutionalized patients, those providing only post office boxes, and those whose addresses could not be geocoded were excluded, leaving 3547 patients eligible for analysis. Addresses were geocoded, and distance to the nearest major roadway was assigned. Cox regression was used to calculate hazard ratios, with adjustment for personal characteristics (age, sex, race, education, marital status, distance to nearest acute care hospital), clinical characteristics (smoking, body mass index, comorbidities, medications), and neighborhood-level characteristics derived from US Census block group data (household income, education, urbanicity). There were 1071 deaths after 10 years of follow-up. In the fully adjusted model, compared with living >1000 m, hazard ratios (95% confidence interval) for living ⩽100 m were 1.27 (1.01–1.60), for 100 to ⩽200 m were 1.19 (0.93–1.60), and for 200 to ⩽1000 m were 1.13 (0.99–1.30) (Ptrend=0.016). Conclusions— In this multicenter study, living close to a major roadway at the time of AMI was associated with increased risk of all-cause 10-year mortality; this relationship persisted after adjustment for individual and neighborhood-level covariates.
A Comprehensive Evaluation of Colonic Mucosal Isolates of Sutterella wadsworthensis from Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) arises in genetically susceptible individuals as a result of an unidentified environmental trigger, possibly a hitherto unknown bacterial pathogen. Twenty-six clinical isolates of Sutterella wadsworthensis were obtained from 134 adults and 61 pediatric patients undergoing colonoscopy, of whom 69 and 29 respectively had IBD. S. wadsworthensis was initially more frequently isolated from IBD subjects, hence this comprehensive study was undertaken to elucidate its role in IBD. Utilizing these samples, a newly designed PCR was developed, to study the prevalence of this bacterium in adult patients with ulcerative colitis (UC). Sutterella wadsworthensis was detected in 83.8% of adult patients with UC as opposed to 86.1% of control subjects (p = 0.64). Selected strains from IBD cases and controls were studied to elicit morphological, proteomic, genotypic and pathogenic differences. This study reports Scanning Electron Microscopy (SEM) appearances and characteristic MALDI-TOF MS protein profiles of S. wadsworthensis for the very first time. SEM showed that the bacterium is pleomorphic, existing in predominantly two morphological forms, long rods and coccobacilli. No differences were noted in the MALDI-TOF mass spectrometry proteomic analysis. There was no distinct clustering of strains identified from cases and controls on sequence analysis. Cytokine response after monocyte challenge with strains from patients with IBD and controls did not yield any significant differences. Our studies indicate that S. wadsworthensis is unlikely to play a role in the pathogenesis of IBD. Strains from cases of IBD could not be distinguished from those identified from controls.
Safe parallel programming using dynamic dependence hints

Speculative parallelization divides a sequential program into possibly parallel tasks and permits these tasks to run in parallel if and only if they show no dependences with each other. The parallelization is safe in that a speculative execution always produces the same output as the sequential execution. In this paper, we present the dependence hint, an interface for a user to specify possible dependences between possibly parallel tasks. Dependence hints may be incorrect or incomplete but they do not change the program output. The interface extends Cytron's do-across and recent OpenMP ordering primitives and makes them safe and safely composable. We use it to express conditional and partial parallelism and to parallelize large-size legacy code. The prototype system is implemented as a software library. It is used to improve performance by nearly 10 times on average on current multicore machines for 8 programs including 5 SPEC benchmarks.