Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Stability of Aggregatibacter actinomycetemcomitans during Persistent Oral Infection in Human

The genome of periodontal pathogen Aggregatibacter actinomycetemcomitans exhibits substantial variations in gene content among unrelated strains primarily due to the presence or absence of genomic islands. This study examined the genomic stability of A. actinomycetemcomitans during its persistent infection in the same host. Four pairs of A. actinomycetemcomitans strains, each pair isolated from an individual over time (0–10 years), were examined for their gains/losses of genes by whole genome sequencing, comparative genomic hybridization by microarray and PCR analysis. Possible effects due to genomic changes were further assessed by comparative transcriptome analysis using microarrays. The results showed that each pair of strains was clonally identical based on phylogenetic analysis of 150 core genes. A novel 24.1-Kb plasmid found in strain S23A was apparently lost in the sibling strain I23C. A 353-bp inversion affecting two essential genes of the serotype-specific gene cluster was found in the serotype antigen-nonexpressing strain I23C, while the same gene cluster was intact in the serotype-expressing sibling strain S23A. A 2,293-bp deletion affecting a gene encoding oxaloacetate decarboxylase and its neighbor region was found in strain SCC2302 but not in the sibling strain AAS4a. However, no evidence of gains or losses of genomic islands was found in the paired strains. Transcriptome profiles showed little or no difference in the paired strains. In conclusion, the genome of A. actinomycetemcomitans appears to be relatively stable during short-term infection. Several types of genomic changes were observed in the paired strains of A. actinomycetemcomitans recovered from the same subjects, including a mutation in serotype-specific gene cluster that may allow the bacteria to evade host immune response.
REVIEW OF MECHANICAL PROPERTIES OF HSC AT ELEVATED TEMPERATURE

A compilation of experimental results on the mechanical properties of concrete when exposed to rapid heating as in a fire is presented. Emphasis is placed on concretes with high original compressive strengths, that is, high-strength concretes (HSCs). The compiled test data were categorized by the test methods and the types of aggregate used and compared for behavioral differences. The comparison revealed distinct difference in mechanical properties of HSC and normal-strength concrete (NSC) in the range between room temperature and approximately 450°C. The differences narrowed at temperature above 450°C. Also presented is a comparison of these test results with existing code provisions on the effects of elevated temperature on concrete strength. It is shown that the Eurocode provisions and the Comites Euro-International Du Beton (CEB) design curves are more applicable to NSC than to HSC. In fact, these provisions are unsafe when compared with HSC test results. The study showed a lack of experimental data for lightweight HSC and HSC heated under a constant preload to simulate the stress conditions in HSC columns.
Anti-CD19 Monoclonal Antibodies: a New Approach to Lymphoma Therapy

CD19 is expressed on B- lineage cells and follicular dendritic cells and plays a key role in B cell malignancies and autoimmune diseases. Thus, it has been considered as potential target for several monoclonal antibodies (mAbs). For decades, chemotherapy has been known as one of the major antitumor therapies eradicating high proliferative tumor cells. But, anti- CD19 mAbs developed for treating CD19- positive lymphomas and autoimmune diseases would rank among the most novel area of research and development in the pharmaceutical industry. Moreover, several anti- CD19 mAbs are currently being tested in various clinical trials and this review provides an overview of the research accomplished so far.
Multiple light‐evoked conductance changes in the photoreceptors of Hermissenda crassicornis

1. Light responses were recorded from the photoreceptors of Hermissenda crassicornis. The response to a flash is a complex potential change involving an initial depolarization, a hyperpolarization, and a depolarizing tail. None of the phases of the response are due to synaptic interactions.
Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates

Plant species is considered to be one of the most important factors in shaping rhizobacterial communities, but specific plant–microbe interactions in the rhizosphere are still not fully understood. Arabidopsis thaliana, for which a large number of naturally occurring ecotype accessions exist, lacks mycorrhizal associations and is hence an ideal model for rhizobacterial studies. Eight Arabidopsis accessions were found to exert a marked selective influence on bacteria associated with their roots, as determined by terminal-restriction fragment length polymorphism (T-RFLP) and ribosomal intergenic spacer analysis (RISA). Community differences in species composition and relative abundance were both significant (P <0.001). The eight distinct and reproducible accession-dependent community profiles also differed from control bulk soil. Root exudates of these variants were analysed by high performance liquid chromatography (HPLC) to try to establish whether the unique rhizobacterial assemblages among accessions could be attributed to plant-regulated chemical changes in the rhizosphere. Natural variation in root exudation patterns was clearly exhibited, suggesting that differences in exudation patterns among accessions could be influencing bacterial assemblages. Other factors such as root system architecture are also probably involved. Finally, to investigate the Arabidopsis rhizosphere further, the phylogenetic diversity of rhizobacteria from accession Cvi-0 is described.
Decision-Theoretic Psychiatry

Psychiatric disorders profoundly impair many aspects of decision making. Poor choices have negative consequences in the moment and make it very hard to navigate complex social environments. Computational neuroscience provides normative, neurobiologically informed descriptions of the components of decision making that serve as a platform for a principled exploration of dysfunctions. Here, we identify and discuss three classes of failure modes arising in these formalisms. They stem from abnormalities in the framing of problems or tasks, from the mechanisms of cognition used to solve the tasks, or from the historical data available from the environment.
Realizing privacy preserving genome-wide association studies

Motivation: As genomics moves into the clinic, there has been much interest in using this medical data for research. At the same time the use of such data raises many privacy concerns. These circumstances have led to the development of various methods to perform genome-wide association studies (GWAS) on patient records while ensuring privacy. In particular, there has been growing interest in applying differentially private techniques to this challenge. Unfortunately, up until now all methods for finding high scoring SNPs in a differentially private manner have had major drawbacks in terms of either accuracy or computational efficiency. Results: Here we overcome these limitations with a substantially modified version of the neighbor distance method for performing differentially private GWAS, and thus are able to produce a more viable mechanism. Specifically, we use input perturbation and an adaptive boundary method to overcome accuracy issues. We also design and implement a convex analysis based algorithm to calculate the neighbor distance for each SNP in constant time, overcoming the major computational bottleneck in the neighbor distance method. It is our hope that methods such as ours will pave the way for more widespread use of patient data in biomedical research. Availability and implementation: A python implementation is available at http://groups.csail.mit.edu/cb/DiffPriv/. Contact: bab@csail.mit.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Comparison among performance of strain sensors based on different semiconductor thin films

In recent years, the piezoresistive properties of different semiconductor thin films, with chemical and mechanical stability, have been studied in order to use them as base material in the fabrication of strain sensors for high temperature applications. In this context, this work compares the performance of strain sensors based on sputter-deposited semiconductor thin films such as titanium dioxide (TiO2), silicon carbide (SiC) and diamond-like carbon (DLC) operated at temperatures up to 250°C. The structure of each sensor consists of four thin-film resistors, configured in Wheatstone bridge, with Ti/Au electrical contacts. These strain sensors reported here differ from our previous works in the types of materials used and in the quantity/configuration of the thin-film resistors. The strain sensors were fabricated by photolithography techiques in conjunction with lift-off processes. The beam-bending experiments were performed to characterize the sensors.
Does Quantitative Left Ventricular Regional Wall Motion Change after Fibrous Tissue Resection in Endomyocardial Fibrosis?

OBJECTIVES: We compared left ventricular regional wall motion, the global left ventricular ejection fraction, and the New York Heart Association functional class pre- and postoperatively. INTRODUCTION: Endomyocardial fibrosis is characterized by fibrous tissue deposition in the endomyocardium of the apex and/or inflow tract of one or both ventricles. Although left ventricular global systolic function is preserved, patients exhibit wall motion abnormalities in the apical and inferoapical regions. Fibrous tissue resection in New York Heart Association FC III and IV endomyocardial fibrosis patients has been shown to decrease morbidity and mortality. METHODS: We prospectively studied 30 patients (20 female, 30±10 years) before and 5±8 months after surgery. The left ventricular ejection fraction was determined using the area-length method. Regional left ventricular motion was measured by the centerline method. Five left ventricular segments were analyzed pre- and postoperatively. Abnormality was expressed in units of standard deviation from the mean motion in a normal reference population. RESULTS: Left ventricular wall motion in the five regions did not differ between pre- and postoperative measurements. Additionally, the left ventricular ejection fraction did not change after surgery (0.45±0.13% x 0.43±0.12% pre- and postoperatively, respectively). The New York Heart Association functional class improved to class I in 40% and class II in 43% of patients postoperatively (p<0.05). CONCLUSIONS: Although endomyocardial fibrosis patients have improved clinical symptoms after surgery, the global left ventricular ejection fraction and regional wall motion in these patients do not change. This finding suggests that other explanations, such as improvements in diastolic function, may be operational.
Aminopyrine breath test: development of a 13C-breath test for quantitative assessment of liver function in humans.

BACKGROUND/AIM 14C-aminopyrine breath test (ABT) has been shown to be well correlated to the severity of liver diseases, but its use is limited in countries where radioactive isotopes are severely controlled. The goal of this study was to develop a 13C-ABT based on a highly sensitive method to measure 13CO2 in breath samples. MATERIALS AND METHODS The relevant parameters were studied in 26 controls and 27 patients: the 13CO2 enrichment of expired breath between t-10 and t+60 minutes was determined as the most simple and clinically useful parameter. The 13C-ABT was then prospectively compared to clinico-biological data and the galactose elimination capacity (GEC) in 82 patients. RESULTS The 13C-ABT was well correlated to: i) the Child-Pugh classification; ii) GEC results; iii) the hepatic volume. The presence of ascites or alcoholic consumption did not alter significantly the results of the test. 13C-ABT appeared more sensitive than GEC to evaluate minor liver dysfunctions. CONCLUSIONS The 13C-ABT is a simple and sensitive test to measure liver function. The use of the stable isotope 13C ensures the harmlessness of the test and the possibility to repeat it in a given patient.
A policy framework for trading configurable goods and services in open electronic markets

In recent years, electronic markets have gained much attention as institutions to allocate goods and services efficiently between buyers and sellers. However, calculating suitable allocations between buyers and sellers in such markets can easily become very tricky, particularly if the services and goods involved are complex and described by multiple attributes. Since such trading objects typically provide various configurations with different corresponding prices, complex pricing functions and purchase preferences have to be taken into account when computing allocations. In this paper, we present a policy description framework that draws from utility theory to capture configurable products with multiple attributes. The framework thus allows the declarative description of seller pricing policies as well as buyer preferences over these configurations. As part of the framework, we present a machine-processible representation language for the policies and a method to evaluate different trading object configurations based on these policies. In addition, we show how policies can be aggregated and how the framework can be applied in a Web service selection scenario.
Detecting Horizontal Gene Transfer by Mapping Sequencing Reads Across Species Boundaries

Horizontal gene transfer (HGT) is a fundamental mechanism that enables organisms such as bacteria to directly transfer genetic material between distant species. This way, bacteria can acquire new traits such as antibiotic resistance or pathogenic toxins. Current bioinfor-matics approaches focus on the detection of past HGT events by exploring phylogenetic trees or genome composition inconsistencies. However, this normally requires the availability of finished and fully annotated genomes and of sufficiently large deviations that allow detection. Thus, these techniques are not widely applicable. Especially in an outbreak scenario where new HGT mediated pathogens emerge, there is need for fast and precise HGT detection. Next-generation sequencing (NGS) technologies can facilitate swift analysis of unknown pathogens but, to the best of our knowledge, so far no approach uses NGS data directly to detect HGTs. We present Daisy, a novel mapping-based tool for HGT detection directly from NGS data. Daisy determines HGT boundaries with split-read mapping and evaluates candidate regions relying on read pair and coverage information. Daisy can successfully detect HGT regions with base pair resolution in both simulated and real data, and outperforms alternative approaches using a genome assembly of the reads. We see our approach as a powerful complement for a comprehensive analysis of HGT in the context of NGS data. Daisy is freely available from http://github.com/ktrappe/daisy.
Basic concepts and models in continuum damage mechanics

ABSTRACT In this paper, we present some basic elements of macroscopic modelling of damage. We then recall the general approach of continuum damage based on the thermodynamics of irreversible processes and its application to isotropic damage modelling. The study of damage-induced anisotropy is treated by considering a second order tensorial damage variable. Finally, we present an original macroscopic approach through which is addressed the question of unilateral effects due to the microcracks closure.
Experiment on box-section sandwich beams in three-point bending

The structural stiffness is explored for box-section beams in three-point bending. Four hollow tubes of various topologies are designed, manufactured and tested. The observed results show that a significant local compliance exists at the centre of the upper tube wall under the loading patch, in addition to the macroscopic bending of the hollow tube. The predicted and measured stiffnesses are in good agreement for a hollow tube with monolithic walls, and a hollow tube with foam-cored sandwich walls. However, the predicted stiffnesses are much greater than the measured values for two hollow tubes with sandwich walls comprising lattice corrugated cores. This can be ascribed to the imperfections introduced by the manufacturing route either by welding or adhesive bonding, and to the local yielding and large plastic deformations of the upper tube walls under the loading patch.
Toxic Alcohol Ingestions: Focus on Ethylene Glycol and Methanol

ABSTRACTThe ingestion of toxic alcohols, specifically ethylene glycol (EG) and methanol, provides unique therapeutic challenges for emergency personnel. If untreated, these agents can result in significant morbidity and mortality. The toxicity of EG and methanol is dependent on endogenous metabolic processes rather than the actual parent compound ingested. These metabolites lead to the characteristic metabolic acidosis and cellular dysfunction typically seen with toxic alcohol ingestions. Fortunately, several options exist for the treatment of these ingestions, which, if implemented in the appropriate time period, can significantly decrease associated morbidity and mortality. The intent of this review is to discuss relevant management issues associated with EG and methanol intoxication in the emergency department.
Effect of Helicobacter pylori Eradication on the Development of Reflux Esophagitis and Gastroesophageal Reflux Symptoms: A Nationwide Multi-Center Prospective Study

Background/Aims A two-year, prospective, nationwide multicenter study was undertaken to evaluate the effect of Helicobacter pylori eradication on the development of reflux esophagitis (RE) and gastroesophageal reflux disease (GERD) symptoms in the Korean population. Methods In total, 1,489 subjects without RE were enrolled at the outpatient clinics of 12 tertiary hospitals nationwide, and 452 subjects underwent follow-up (F/U) for 2 years to evaluate the development of RE and GERD symptoms. Results RE was found in 33 subjects (7.3% of 452 subjects) and 14 subjects (7.3% of 192 subjects) during the first and second year of F/U, respectively. H. pylori status was not associated with the development of RE. RE was found in six (9.0%) of 67 H. pylori-negative patients, in 26 (11.2%) of 233 eradicated subjects and in eight (7.0%) of 114 noneradicated subjects (p=0.532). Multivariate analysis showed that age ≥60 years (odds ratio [OR], 7.11; 95% confidence interval [CI], 1.92 to 26.41), alcohol consumption (OR, 4.43; 95% CI, 1.03 to 19.19) and F/U cholesterol levels ≥200 mg/dL (OR, 5.03; 95% CI, 1.32 to 19.17) were significant risk factors for the development of RE. There was no significant difference in the development of GERD symptoms or weight according to H. pylori status during the 2-year F/U. Conclusions Eradication of H. pylori did not affect the development of reflux esophagitis or GERD symptoms among patients in outpatient gastroenterology clinics in South Korea.
A Case of Chloroquine-Induced Cardiomyopathy That Presented as Sick Sinus Syndrome

A 52-year-old woman with rheumatoid arthritis who had been treated with prednisone and hydroxychloroquine for >12 years presented with chest discomfort and a seizure. She was diagnosed with restrictive cardiomyopathy combined with sick sinus syndrome. A myocardial muscle biopsy was performed to identify the underlying cardiomyopathy, which showed marked muscle fiber hypertrophy, fiber dropout, slightly increased interstitial fibrous connective tissue, and extensive cytoplasmic vacuolization of the myocytes under light microscopy. Electron microscopy of the myocytes demonstrated dense, myeloid, and curvilinear bodies. The diagnosis of hydroxychloroquine-induced cardiomyopathy was made based on the clinical, hemodynamic, and pathologic findings. This is the first case report describing chloroquine-induced cardiomyopathy involving the heart conduction system.
Feature Vector Extraction for Carpus for Human Identification

Now a day's human identification through Image processing is one of the emerging requirements in the world. The use of X-rays is generally used in detection of cracks and fractures in bones. This paper presents a novel & more efficient kind of approach for human identification using feature vector extraction of carpus bones. We will be focusing on the adult age group (18-35 yrs.) of that person because by this time the growths of the bones are stable. The aim of this paper is to identify an unknown person from the database registry using carpus bones distance calculation pattern.
Synchronous fire activity in the tropical high Andes: an indication of regional climate forcing

Global climate models suggest enhanced warming of the tropical mid and upper troposphere, with larger temperature rise rates at higher elevations. Changes in fire activity are amongst the most significant ecological consequences of rising temperatures and changing hydrological properties in mountainous ecosystems, and there is a global evidence of increased fire activity with elevation. Whilst fire research has become popular in the tropical lowlands, much less is known of the tropical high Andean region (>2000masl, from Colombia to Bolivia). This study examines fire trends in the high Andes for three ecosystems, the Puna, the Paramo and the Yungas, for the period 1982–2006. We pose three questions: (i) is there an increased fire response with elevation? (ii) does the El Niño‐ Southern Oscillation control fire activity in this region? (iii) are the observed fire trends human driven (e.g., human practices and their effects on fuel build‐up) or climate driven? We did not find evidence of increased fire activity with elevation but, instead, a quasicyclic and synchronous fire response in Ecuador, Peru and Bolivia, suggesting the influence of high‐frequency climate forcing on fire responses on a subcontinental scale, in the high Andes. ENSO variability did not show a significant relation to fire activity for these three countries, partly because ENSO variability did not significantly relate to precipitation extremes, although it strongly did to temperature extremes. Whilst ENSO did not individually lead the observed regional fire trends, our results suggest a climate influence on fire activity, mainly through a sawtooth pattern of precipitation (increased rainfall before fire‐peak seasons (t‐1) followed by drought spells and unusual low temperatures (t0), which is particularly common where fire is carried by low fuel loads (e.g., grasslands and fine fuel). This climatic sawtooth appeared as the main driver of fire trends, above local human influences and fuel build‐up cyclicity.
Quantitative Phase Field Study on the Precipitation Dynamics of γ′ Phase in Ni-Based Superalloys with Different Concentration

A quantitative phase field simulation was performed on the dynamics evolution of γ′ (L12-Ni3X) phase in Ni-based superalloys, the microstructure, the volume fraction and the particle size distribution (PSD) of γ′ phase for Ni-Al alloys aged at 1173K with the Al concentration c=0.178, 0.180 and 0.182 were investigated, and the results were compared with Lifshitz-Slyozov-Wagner (LSW) theory and Brailsford-Wynblatt (BW) theory. As the Al concentration increases the γ′ phase morphology changed from the separated cuboidal shape to the connected rectangle shape, the nucleation and growth of γ′ phase became faster and the volume fraction of the γ′ phase increased. The average particle radius of γ′ phase and the aging time t has a exponent relationship ~ tn at the coarsening stage with the exponents n=0.313, 0.235 and 0.204 for c=0.178, 0.180 and 0.182, respectively. The peaks of the fitted PSDs are less than the predicted value from the LSW theory and the fitted PSDs are wider than that of LSW predicted, while they are similar to that of the BW theory as the Al concentration increases. The peaks appear at a smaller r/ than the predictions of the LSW and BW theories.