jimnoneill/paper-to-field-training huggingface dataset:
Succinoglycan Production by <i>Rhizobium meliloti</i> Is Regulated through the ExoS-ChvI Two-Component Regulatory System

ABSTRACT The Rhizobium meliloti exoS gene is involved in regulating the production of succinoglycan, which plays a crucial role in the establishment of the symbiosis between R. meliloti Rm1021 and its host plant, alfalfa. The exoS96 ::Tn 5 mutation causes the upregulation of the succinoglycan biosynthetic genes, thereby resulting in the overproduction of succinoglycan. Through cloning and sequencing, we found that the exoS gene is a close homolog of the Agrobacterium tumefaciens chvG gene, which has been proposed to encode the sensor protein of the ChvG-ChvI two-component regulatory system, a member of the EnvZ-OmpR family. Further analyses revealed the existence of a newly discovered A. tumefaciens chvI homolog located just upstream of the R. meliloti exoS gene. R. meliloti ChvI may serve as the response regulator of ExoS in a two-component regulatory system. By using ExoS-specific antibodies, it was found that the ExoS protein cofractionated with membrane proteins, suggesting that it is located in the cytoplasmic membrane. By using the same antibodies, it was shown that the exoS96 ::Tn 5 allele encodes an N-terminal truncated derivative of ExoS. The cytoplasmic histidine kinase domain of ExoS was expressed in Escherichia coli and purified, as was the R. meliloti ChvI protein. The ChvI protein autophosphorylated in the presence of acetylphosphate, and the ExoS cytoplasmic domain fragment autophosphorylated at a histidine residue in the presence of ATP. The ChvI protein was phosphorylated in the presence of ATP only when the histidine kinase domain of ExoS was also present. We propose a model for regulation of succinoglycan production by R. meliloti through the ExoS-ChvI two-component regulatory system.

Topic: Legume Nitrogen Fixing Symbiosis
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
ANALYSIS OF DIFFERENCES IN PULSE RATE BEFORE AND AFTER SMOKING USING THE WILCOXON SIGNED RANK TEST WITH THE R-STUDIO PROGRAM

Smoking can cause many diseases, one of which is heart disease. The pulse rate is related to the heart rate, so the pulse rate will also experience changes if smoking is the initial assumption. The aim of this study was to see the difference in pulse rate before and after smoking. The results of this study are that there is difference in pulse rate before and after smoking with a p-value &amp;lt; 0.05. This was carried out for 20 samples with student status. It is likely to change if the sample used is a long-time smoker and with a different status or gender such as working, teenager and so on.

Topic: Public Health and Nutrition
Subfield: Pediatrics, Perinatology and Child Health
Field: Medicine
Domain: Health Sciences
Universality and herd immunity threshold: Revisiting the SIR model for COVID-19

COVID-19 pandemic has been raging all around the world for almost a year now, as of November 1, 2020. In this paper, we try to analyze the variation of the COVID-19 pandemic in different countries in the light of some modifications to the susceptible-infected-recovered (SIR) model. The SIR model was modified by taking time-dependent rate parameters. From this modified SIR model, the basic reproduction number, effective reproduction number, herd immunity, and herd immunity threshold are redefined. The re-outbreak of the COVID-19 is a real threat to various countries. We have used the above-mentioned quantities to find the reasons behind the re-outbreak of this disease. Also, the effectiveness of herd immunity to prevent an epidemic has been analyzed with respect to this model. We have also tried to show that there are certain universal aspects in the spread and containment of the disease in various countries for a short period of time. Finally, we have also analyzed the current pandemic situation in India and have attempted to discuss the possibilities in order to predict its future behavior using our model.

Topic: COVID-19 epidemiological studies
Subfield: Modeling and Simulation
Field: Mathematics
Domain: Physical Sciences
Radio Frequency Nonionizing Radiation in a Community Exposed to Radio and Television Broadcasting

Exposure to radio frequency (RF) nonionizing radiation from telecommunications is pervasive in modern society. Elevated disease risks have been observed in some populations exposed to radio and television transmissions, although findings are inconsistent. This study quantified RF exposures among 280 residents living near the broadcasting transmitters for Denver, Colorado. RF power densities outside and inside each residence were obtained, and a global positioning system (GPS) identified geographic coordinates and elevations. A view-shed model within a geographic information system (GIS) characterized the average distance and percentage of transmitters visible from each residence. Data were collected at the beginning and end of a 2.5-day period, and some measurements were repeated 8-29 months later. RF levels logged at 1-min intervals for 2.5 days varied considerably among some homes and were quite similar among others. The greatest differences appeared among homes within 1 km of the transmitters. Overall, there were no differences in mean residential RF levels compared over 2.5 days. However, after a 1- to 2-year follow-up, only 25% of exterior and 38% of interior RF measurements were unchanged. Increasing proximity, elevation, and line-of-sight visibility were each associated with elevated RF exposures. At average distances from > 1-3 km, exterior RF measurements were 13-30 times greater among homes that had > 50% of the transmitters visible compared with homes with < or = 50% visibility at those distances. This study demonstrated that both spatial and temporal factors contribute to residential RF exposure and that GPS/GIS technologies can improve RF exposure assessment and reduce exposure misclassification.

Topic: Electromagnetic Fields and Biological Effects
Subfield: Biophysics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
A Case of Perazine-induced Enteritis - Allergy or Pseudoallergy?

Almost all adverse reactions to neuroleptic drugs in the gastro-intestinal system can be explained by their peripheral cholinergic blocking action with subsequent inhibition of intestinal tone and peristalsis. As a rare condition, severe diarrhoea due to enteritis may occur. A case with this complication is presented, the etiology and pathogenetic factors are discussed.

Topic: Contact Dermatitis and Allergies
Subfield: Dermatology
Field: Medicine
Domain: Health Sciences
LABORATORY SUSCEPTIBILITY OF <i>PLUTELLA XYLOSTELLA</i> TO <i>METARHIZIUM ANISOPLIAE</i> AND <i>NOMURAEA RILEYI</i>*

Abstract Five isolates of Metarhizium anisopliae and one isolate of Nomuraea rileyi were bioassayed against larvae of Plutella xylostella . Larvae were treated by exposing cabbage leaf discs previously immersed in conidial suspension, and were then incubated at 25 o C and observed daily. One of M. anisopliae isolates, F11248, originally from Mastotermes darwiniensis was found being most virulent against P. xylostella . The LC 50 was estimated as 2.03 times 10 4 conidia/ml with 9 d mortality data, and the LT 50 was 4.97 d at concentration of 10 7 conidia/ml. Isolate F163 ( N. rileyi ) showed virulence to P. xylostella in both tests, but no cadavers sporulated.

Topic: Entomopathogenic Microorganisms in Pest Control
Subfield: Insect Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Molecular Soybean-Pathogen Interactions

Soybean hosts a wide variety of pathogens that cause significant yield losses. The importance of soybean as a major oilseed crop has led to research focused on its interactions with pathogens, such as Soybean mosaic virus, Pseudomonas syringae, Phytophthora sojae, Phakopsora pachyrhizi, and Heterodera glycines. Pioneering work on soybean's interactions with these organisms, which represent the five major pathogen groups (viruses, bacteria, oomycetes, fungi, and nematodes), has contributed to our understanding of the molecular mechanisms underlying virulence and immunity. These mechanisms involve conserved and unique features that validate the need for research in both soybean and homologous model systems. In this review, we discuss identification of effectors and their functions as well as resistance gene–mediated recognition and signaling. We also point out areas in which model systems and recent advances in resources and tools have provided opportunities to gain deeper insights into soybean-pathogen interactions.

Topic: Legume Nitrogen Fixing Symbiosis
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Supplementary Data from The Effects of Varying Dietary Carbohydrate and Fat Content on Survival in a Murine LNCaP Prostate Cancer Xenograft Model

Supplementary Data from The Effects of Varying Dietary Carbohydrate and Fat Content on Survival in a Murine LNCaP Prostate Cancer Xenograft Model

Topic: Cancer, Lipids, and Metabolism
Subfield: Cancer Research
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Determination of Cyanide Ion by Derivatization-Gas Chromatography

Abstract A new gas chromatographic method is described for the determination of cyanide ion in water. Cyanide is converted to benzonitrile by reaction with aniline, sodium nitrite, and copper(II) sulfate. The resulting benzonitrile is extracted into chloroform and determined by gas chromatography with a flame ionization detector. The influences of several ions which may coexist with cyanide on this gas chromatographic method were investigated briefly.

Topic: Molecular Sensors and Ion Detection
Subfield: Spectroscopy
Field: Chemistry
Domain: Physical Sciences
Associations of white matter hyperintensities with cognitive decline: A longitudinal study

Abstract Background White matter hyperintensities (WMHs), mainly caused by cerebrovascular injury, may lead to cognitive impairment. In order to identify whether the volume of WMHs is associated with cognitive decline over years, this longitudinal study involved 818 individuals from the ADNI‐2 dataset from August 2010 to May 2017. Method Cross‐sectional and longitudinal associations of WMHs with 8 cognitive domains were explored, using Mini‐Mental State Examination (MMSE), Montreal Cognitive Assessment (MoCA), Clinical Dementia Rating Sum of Boxes (CDRSB), Alzheimer Disease Assessment Scale‐Cognitive (ADAS‐Cog13), Rey Auditory Verbal Learning Test (RAVLT), Functional Assessment Questionnaire (FAQ), executive function (ADNI‐EF), and memory function (ADNI‐Mem). The association analyses were performed using multiple linear regression models, linear mixed models, Spearman rank correlation and Kaplan‐Meier survival curves. Result The volumes of WMHs were greater in patients with AD dementia compared with controls (p&lt;0.001) and MCI (p=0.006) patients at baseline. The bigger volumes of WMHs correlated with worse performances on ADAS‐Cog13 and ADNI‐EF (p=0.029; p=0.0032) at baseline and MMSE, MoCA, CDRSB, ADAS‐Cog13, FAQ and ADNI‐Mem (overall p&lt;0.05) longitudinally, after adjusting for age, sex, educational level, apolipoprotein E ε4 genotype, hypertension, hyperlipidemia, diabetes, smoking, infarction and diagnosis. And the correlations between the change rate of WMHs and change rates of MMSE, MoCA, CDRSB, FAQ, ADNI‐EF and ADNI‐Mem were statistically significant. Furthermore, patients with high WMH volumes showed an increased likelihood of dementia. Conclusion The results of the study suggest that WMH volume is associated with cognitive decline, and it contributes to the conversion to AD.

Topic: Dementia and Cognitive Impairment Research
Subfield: Psychiatry and Mental health
Field: Medicine
Domain: Health Sciences
Competition and stability in the banking sector: theory and empirical evidence.

Since the outbreak of the financial crises in the 1980s, the relationship between competition and stability in the banking sector has been of primary interest for both academics and policymakers. Building on the seminal paper by Beck, De Jonghe and Schepens (2013), we study how competition and stability are related using a sample of around 20,000 banks from 113 countries during the period from 1996 to 2014. We reach two major findings. Firstly, country-specific features play a crucial role in explaining the large cross-country variations in the competition-stability relationship. Secondly, the way in which competition and stability interact is non-linear and this non-linearity is highly influenced by country-specific factors.

Topic: Banking stability, regulation, efficiency
Subfield: Finance
Field: Economics, Econometrics and Finance
Domain: Social Sciences
Abundance and variation of microsatellite DNA sequences in beans (<i>Phaseolus</i> and<i>Vigna)</i>

Microsatellites or simple sequence repeats (SSRs) have been demonstrated to be abundant and hypervariable in some eukaryotic genomes. Although the presence of microsatellites is very well documented in many plant species, no information on microsatellites in beans (Phaseolus andVigna) is available. To assess the abundance and usefulness of bean microsatellites as genetic markers, 326 DNA sequences from the GenBank databases were searched. Sixty-one simple repetitive DNA sequences with 23 different types of repetitive DNA motifs were identified as potential microsatellites. Among these were 49 microsatellites from common bean (Phaseolus vulgaris) entries and 12 microsatellites from the genus Vigna. The most abundant type of microsatellite found in this search was that with di-nucleotide repeats of AT/TA . Microsatellites with tri- and tetra-nucleotide motifs were also identified. PCR analysis of 12 of the microsatellite-containing loci revealed that 11 of the 12 primer pairs could produce easily-scorable fragments, or groups of fragments. Allelic variation of the 11 loci was surveyed in 12 common bean inbred lines representing a diversity of germplasms. Seven of the 11 microsatellite loci were polymorphic and yielded 2-10 alleles. Analyses of the polymorphic loci in a common bean F 6 recombinant inbred population showed that each segregated in a Mendelian fashion.Key words: microsatellite, simple sequence repeat, molecular marker, bean.

Topic: Plant pathogens and resistance mechanisms
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Isoelectric Focusing in a Drop

A novel approach to molecular separations is investigated using a technique termed droplet-based isoelectric focusing. Drops are manipulated discretely on a superhydrophobic surface, subjected to low voltages for isoelectric focusing, and split-resulting in a preparative separation. A universal indicator dye demonstrates the generation of stable, reversible pH gradients (3-10) in ampholyte buffers, and these gradients lead to protein focusing within the drop length. Focusing was visually characterized, spectroscopically verified, and assessed quantitatively by noninvasive light scattering measurements. It was found to correlate with a quantitative model based on 1D steady-state theory. This work illustrates that molecular separations can be deployed within a single open drop, and the differential fractions can be separated into new discrete liquid elements.

Topic: Electrowetting and Microfluidic Technologies
Subfield: Electrical and Electronic Engineering
Field: Engineering
Domain: Physical Sciences
Exploring Fine-Grained Task-Based Execution on Multi-GPU Systems

Using multi-GPU systems, including GPU clusters, is gaining popularity in scientific computing. However, when using multiple GPUs concurrently, the conventional data parallel GPU programming paradigms, e.g., CUDA, cannot satisfactorily address certain issues, such as load balancing, GPU resource utilization, overlapping fine grained computation with communication, etc. In this paper, we present a fine-grained task-based execution framework for multi-GPU systems. By scheduling finer-grained tasks than what is supported in the conventional CUDA programming method among multiple GPUs, and allowing concurrent task execution on a single GPU, our framework provides means for solving the above issues and efficiently utilizing multi-GPU systems. Experiments with a molecular dynamics application show that, for nonuniform distributed workload, the solutions based on our framework achieve good load balance, and considerable performance improvement over other solutions based on the standard CUDA programming methodologies.

Topic: Parallel Computing and Optimization Techniques
Subfield: Hardware and Architecture
Field: Computer Science
Domain: Physical Sciences
exBERT: A Visual Analysis Tool to Explore Learned Representations in Transformers Models

Large language models can produce powerful contextual representations that lead to improvements across many NLP tasks. Since these models are typically guided by a sequence of learned self attention mechanisms and may comprise undesired inductive biases, it is paramount to be able to explore what the attention has learned. While static analyses of these models lead to targeted insights, interactive tools are more dynamic and can help humans better gain an intuition for the model-internal reasoning process. We present exBERT, an interactive tool named after the popular BERT language model, that provides insights into the meaning of the contextual representations by matching a human-specified input to similar contexts in a large annotated dataset. By aggregating the annotations of the matching similar contexts, exBERT helps intuitively explain what each attention-head has learned.

Topic: Topic Modeling
Subfield: Artificial Intelligence
Field: Computer Science
Domain: Physical Sciences
LHD ICH-ICE2 #172812.1

High-frequency Magnetic Probe to measure high-frequency waves, e.g. waves excited by ICRF antennas or waves excited by high-energy particles. Probe head is one-turn loop with Faraday shield. Two loops are paired with different turn direction. Frequency range: approximately 10 kHz - 1 GHz. Loop size: 15 cm x 15 cm.

Topic: Particle physics theoretical and experimental studies
Subfield: Nuclear and High Energy Physics
Field: Physics and Astronomy
Domain: Physical Sciences
A comparison of sampling methods for airborne fungal spores during an outbreak of aspergillosis in the forest aviary of the North Carolina Zoological Park.

An outbreak of aspergillosis with the death of six birds in the North Carolina Zoological Park R. J. Reynolds Forest Aviary in the spring of 1993 led to an investigation of the concentration of Aspergillus fumigatus spores in the air. No Aspergillus sp. was found in the facility through use of the drop plate method (gravitometric sampling) along with swab-sampling of selected surfaces within the exhibit and plating of food samples and nesting material onto petri dishes of nutrient media. A number factors that could stress the avian population were identified. These included excessive heat in the upper portion of the aviary due to the failure of an air handling system, a malfunctioning cooling tower, and large numbers of visitors to the facility (an average of 3,500/day). In addition, the outbreak occurred during a period of increased nesting behavior. Sampling of the fungal population of the air was conducted 1 year later, when no disease was noted, to compare the sensitivity of the commonly used drop plate method (open plates of nutrient media) with a volumetric impaction method (Andersen N-6 Air Sampler). The volumetric method delivered quantitative as well as qualitative data and exhibited more sensitivity for fungal spores of size similar to those of Aspergillus sp.

Topic: Indoor Air Quality and Microbial Exposure
Subfield: Health, Toxicology and Mutagenesis
Field: Environmental Science
Domain: Physical Sciences
Fluoroquinolones Hybrid Molecules as Promising Antibacterial Agents in the Fight against Antibacterial Resistance

The emergence of bacterial resistance has motivated researchers to discover new antibacterial agents. Nowadays, fluoroquinolones keep their status as one of the essential classes of antibacterial agents. The new generations of fluoroquinolones are valuable therapeutic tools with a spectrum of activity, including Gram-positive, Gram-negative, and atypical bacteria. This review article surveys the design of fluoroquinolone hybrids with other antibacterial agents or active compounds and underlines the new hybrids’ antibacterial properties. Antibiotic fluoroquinolone hybrids have several advantages over combined antibiotic therapy. Thus, some challenges related to joining two different molecules are under study. Structurally, the obtained hybrids may contain a cleavable or non-cleavable linker, an essential element for their pharmacokinetic properties and mechanism of action. The design of hybrids seems to provide promising antibacterial agents helpful in the fight against more virulent and resistant strains. These hybrid structures have proven superior antibacterial activity and less susceptibility to bacterial resistance than the component molecules. In addition, fluoroquinolone hybrids have demonstrated other biological effects such as anti-HIV, antifungal, antiplasmodic/antimalarial, and antitumor activity. Many fluoroquinolone hybrids are in various phases of clinical trials, raising hopes that new antibacterial agents will be approved shortly.

Topic: Cancer therapeutics and mechanisms
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences