Miracle-dz/UniFAR-FTUs huggingface dataset:
Campylobacter – A Foodborne Pathogen

Campylobacter is well recognized as the leading cause of bacterial food borne diarrheal disease worldwide. Symptoms can range from mild to serious infections of the children and the elderly. The organism is a cytochrome oxidase positive, microaerophilic, curved Gram-negative rod exhibiting cork screw motility and is carried in the intestine of many wild and domestic animals, particularly avian species including poultry. Intestinal colonization results in healthy animals as carriers. In contrast with the most recent published reviews that cover specific aspects of Campylobacter/campylobacteriosis, this broad review aims at elucidating and discussing (i) genus Campylobacter, growth and survival characteristics (ii) detection, isolation and confirmation of Campylobacte (iii) campylobacteriosis and presence of virulence factors (iv)Clinical features in special set-up, antimicrobial susceptibility pattern.
Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

With read lengths of currently up to 2 × 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. However, Illumina error profiles are still poorly understood and programs are therefore not designed for the idiosyncrasies of Illumina data. A better knowledge of the error patterns is essential for sequence analysis and vital if we are to draw valid conclusions. Studying true genetic variation in a population sample is fundamental for understanding diseases, evolution and origin. We conducted a large study on the error patterns for the MiSeq based on 16S rRNA amplicon sequencing data. We tested state-of-the-art library preparation methods for amplicon sequencing and showed that the library preparation method and the choice of primers are the most significant sources of bias and cause distinct error patterns. Furthermore we tested the efficiency of various error correction strategies and identified quality trimming (Sickle) combined with error correction (BayesHammer) followed by read overlapping (PANDAseq) as the most successful approach, reducing substitution error rates on average by 93%.
Rapamycin-resistant and torin-sensitive mTOR signaling promotes the survival and proliferation of leukemic cells

The serine/threonine kinase mTOR is essential for the phosphoinositide 3-kinases (PI3K) signaling pathway, and regulates the development and function of immune cells. Aberrant activation of mTOR signaling pathway is associated with many cancers including leukemia. Here, we report the contributions of mTOR signaling to growth of human leukemic cell lines and mouse T-cell acute leukemia (T-ALL) cells. Torin, an ATP-competitive mTOR inhibitor, was found to have both cytotoxic and cytostatic effects on U-937, THP-1, and RPMI-8226 cells, but not on Jurkat or K-562 cells. All cells were relatively resistant to rapamycin even with suppressed activity of mTOR complex 1. Growth of T-ALL cells induced by Notch1 was profoundly affected by torin partially due to increased expression of Bcl2l11 and Bbc3. Of note, activation of Akt or knockdown of FoxO1 mitigated the effect of mTOR inhibition on T-ALL cells. Our data provide insight on the effect of mTOR inhibitors on the survival and proliferation of leukemic cells, thus further improving our understanding on cell-context-dependent impacts of mTOR signaling. [BMB Reports 2016; 49(1): 63-68]
The Utility of Hospital Antibiograms as Tools for Guiding Empiric Therapy and Tracking Resistance: Insights from the Society of Infectious Diseases Pharmacists

Hospital antibiograms are commonly used to help guide empiric antimicrobial treatment and are an important component of detecting and monitoring trends in antimicrobial resistance. To serve these purposes, antibiograms must be constructed using standardized methods that allow inter‐ and intrahospital comparisons. Antibiograms that include surveillance cultures and duplicate bacterial isolates can overestimate rates of resistance. In 2002, the National Committee for Clinical Laboratory Standards (now known as the Clinical and Laboratory Standards Institute [CLSI]) published standards for constructing antibiograms. According to national surveys, many of the recommended elements of the CLSI document have not been fully adopted. In lieu of full compliance with CLSI standards, it is necessary that the methods used to construct antibiograms are clearly delineated. Antibiograms have several limitations, such as their inability to track emergence of resistance during therapy. The antibiogram can serve as a valuable tool in guiding antimicrobial therapy, but other patient factors, such as previous infection history and antibiotic use, also need to be considered. Additional data are needed for specialized applications of resistance analyses.
Rumor Routing Algorithm For Sensor Networks

in micro-sensor and radio technology will enable small but smart sensors to be deployed for a wide range of environmental monitoring applications. In order to constrain communication overhead, dense sensor networks call for new and highly efficient methods for distributing queries to nodes that have observed interesting events in the network. A highly efficient data-centric routing mechanism will offer significant power cost reductions (17), and improve network longevity. Moreover, because of the large amount of system and data redundancy possible, data becomes disassociated from specific node and resides in regions of the network (10)(7)(8). This paper describes and evaluates through simulation a scheme we call Rumor Routing, which allows for queries to be delivered to events in the network. Rumor Routing is tunable, and allows for tradeoffs between setup overhead and delivery reliability. It's intended for contexts in which geographic routing criteria are not applicable because a coordinate system is not available or the phenomenon of interest is not geographically correlated.
Physiological Differences in Cryptococcus neoformans Strains In Vitro versus In Vivo and Their Effects on Antifungal Susceptibility

ABSTRACT Cryptococcus neoformans is an environmentally ubiquitous fungal pathogen that primarily causes disease in people with compromised immune systems, particularly those with advanced AIDS. There are estimated to be almost 1 million cases per year of cryptococcal meningitis in patients infected with human immunodeficiency virus, leading to over 600,000 annual deaths, with a particular burden in sub-Saharan Africa. Amphotericin B (AMB) and fluconazole (FLC) are key components of cryptococcal meningitis treatment: AMB is used for induction, and FLC is for consolidation, maintenance and, for occasional individuals, prophylaxis. However, the results of standard antifungal susceptibility testing (AFST) for AMB and FLC do not correlate well with therapeutic outcomes and, consequently, no clinical breakpoints have been established. While a number of explanations for this absence of correlation have been proffered, one potential reason that has not been adequately explored is the possibility that the physiological differences between the in vivo infection environment and the in vitro AFST environment lead to disparate drug susceptibilities. These susceptibility-influencing factors include melanization, which does not occur during AFST, the size of the polysaccharide capsule, which is larger in infecting cells than in those grown under normal laboratory conditions, and the presence of large polyploid “titan cells,” which rarely occur under laboratory conditions. Understanding whether and how C. neoformans differentially expresses mechanisms of resistance to AMB and FLC in the AFST environment compared to the in vivo environment could enhance our ability to interpret AFST results and possibly lead to the development of more applicable testing methods.
Exercise as a supportive therapy in incurable cancer: exploring patient preferences

Objective: Therapeutic exercise may benefit patients with incurable cancer, but there is little data on its practicality. We have explored the acceptability of six exercise programmes based on different types of exercise, the preferred delivery method, location and time relative to anticancer treatments and whether various patient characteristics influence choice of exercise.
Current‐noise‐power spectra of amorphous silicon thin‐film transistors

Current‐noise‐power spectra of thin‐film transistors (TFTs) fabricated from hydrogenated amorphous silicon were measured. TFTs with aspect ratios ranging from 1:1 to 16:1 were examined in both the conducting and nonconducting modes. In the conducting mode, the noise levels could be predicted to within an order of magnitude by theories developed for crystalline metal‐oxide field‐effect transistors. In the nonconducting mode, the noise was found to scale with the TFT leakage current in a power‐law fashion.
Visual perception changes and optical stability after intracorneal ring segment implantation: comparison between 3 months and 1 year after surgery

Purpose: To prospectively evaluate intracorneal ring segment (ICRS) implantation on quality of life (QoL) of patients with keratoconus changes and identify factors responsible. Methods: Sixty-nine eyes of 42 keratoconus patients were implanted with the Keraring (Mediphacos, Belo Horizonte, Brazil). Best corrected visual acuity (BCVA), refraction, and steep keratometry were analyzed 3 months and 1 year after surgery. All patients self-administered the National Eye Institute Refractive Error Quality of life instrument at 2 time points: after having worn best correction for at least 30 days since evaluation (mean 4 months after surgery) and 1 year after surgery. To analyze if the use of the appropriate correction at 1 year follow up had any impact on visual acuity and V-QoL, patients were divided into 2 groups: group A (appropriate correction) and B (not appropriate correction). Results: After 1 year, QoL changes related to scales ‘clarity of vision’, ‘near vision’, and ‘far vision’. Keratometric values, sphere, and spherical equivalent did not differ significantly between 3 months and 1 year postoperative. Cylinder increase was statistically but not clinically significant. Binocular BCVA did not change 1 year after surgery in group A and showed a clinically significant impairment in group B. A year after surgery, 18 patients did not use correction suggested by a physician 3 months after surgery. QoL was not statistically different 1 year after surgery between group A and group B. Conclusion: Our findings show that the way keratoconic patients see is difficult to analyze using only quantitative and 1-visit metrics. They highlight the importance of patients’ self perception and performing longitudinal analysis to consider neural compensation to optical changes from surgery.
Selection in Modular Organisms: Is Intraclonal Variation in Macroalgae Evolutionarily Important?

Theoretical and practical difficulties occur when defining the units of selection in modular organisms that grow by iteration of repeated parts (modules). Modules may become physically autonomous through fragmentation and may vary because of genetic variation arising in somatic cell lineages. Since cells destined for gamete production are not sequestered in early development, heritable variation and selection among asexual progeny are possible. We used the branching red macroalgae Delisea pulchra and Asparagopsis armata to test whether modules fulfill three fundamental criteria for units of selection: that they replicate, that they display heritable variation, and that selective agents distinguish among the variants. We detected significant phenotypic variation among modules for fitness‐related traits (growth, secondary metabolite concentrations, and rates of tissue loss to herbivory) in each species and significant heritability estimates for secondary metabolite production and tissue loss to herbivory in D. pulchra. Variation in growth rate among A. armata modules was largely phenotypic with small but important estimates of genetic variation. Our results indicate that selection may indeed act on phenotypic variation among modules within individuals and that this process may effect evolutionary change within asexual lineages given sufficient genetic variation in the traits examined.
In Vitro Transcription by the Turnip Yellow Mosaic Virus RNA Polymerase: a Comparison with the Alfalfa Mosaic Virus and Brome Mosaic Virus Replicases

ABSTRACT Recently, we showed that the main determinant in the tRNA-like structure of turnip yellow mosaic virus RNA to initiate minus-strand synthesis in vitro is the 3′ ACCA end. By mutational analysis of the 3′-terminal hairpin, we show here that only a non-base-paired ACCA end is functional and that the stability of the wild-type 3′-proximal hairpin is the most favorable, in that it has the lowest ΔG value and a high transcription efficiency. With a nested set of RNA fragments, we show that the minimum template length is 9 nucleotides and that transcription is improved with increasing the length of the template. The results also suggest that proper base stacking contributes to efficient transcription initiation. Internal initiation is shown to take place on every NPyCPu sequence of a nonstructured template. However, the position of the internal initiation site in the template is important, and competition between the different sites takes place. Internal initiation was also studied with the RNA-dependent RNA polymerase of brome mosaic virus (BMV) and alfalfa mosaic virus (AlMV). The BMV polymerase can start internally on ACCA sequences, though inefficiently. Unexpectedly, the polymerases of both AlMV and BMV can start efficiently on an internal AUGC sequence.
ECG on the Road: Robust and Unobtrusive Estimation of Heart Rate

Modern automobiles include an increasing number of assistance systems to increase the driver's safety. This feasibility study investigated unobtrusive capacitive ECG measurements in an automotive environment. Electrodes integrated into the driving seat allowed to measure a reliable ECG in 86% of the drivers; when only (light) cotton clothing was worn by the drivers, this value increased to 95%. Results show that an array of sensors is needed that can adapt to the different drivers and sitting positions. Measurements while driving show that traveling on the highway does not distort the signal any more than with the car engine turned OFF, whereas driving in city traffic results in a lowered detection rate due to the driver's heavier movements. To enable robust and reliable estimation of heart rate, an algorithm is presented (based on principal component analysis) to detect and discard time intervals with artifacts. This, then, allows a reliable estimation of heart rate of up to 61% in city traffic and up to 86% on the highway: as a percentage of the total driving period with at least four consecutive QRS complexes.
The ornithine transcarbamylase leader peptide directs mitochondrial import through both its midportion structure and net positive charge

The cytoplasmically synthesized precursor of the mitochondrial matrix enzyme, ornithine transcarbamylase (OTC), is targeted to mitochondria by its NH2-terminal leader peptide. We previously established through mutational analysis that the midportion of the OTC leader peptide is functionally required. In this article, we report that study of additional OTC precursors, altered in either a site-directed or random manner, reveals that (a) the midportion, but not the NH2-terminal half, is sufficient by itself to direct import, (b) the functional structure in the midportion is unlikely to be an amphiphilic alpha-helix, (c) the four arginines in the leader peptide contribute collectively to import function by conferring net positive charge, and (d) surprisingly, proteolytic processing of the leader peptide does not require the presence of a specific primary structure at the site of cleavage, in order to produce the mature OTC subunit.
Prevalence and Characterization of Diarrheagenic Escherichia coli Isolated from Adults and Children in Mangalore, India

Background: Diarrheal diseases are a major cause of morbidity and mortality in resource-limited countries. Among the bacterial pathogens, diarrheagenic E. coli (DEC) are most frequently implicated in cases of epidemic and endemic diarrhea worldwide. The objective of this study was to determine the prevalence of DEC in stool specimens from patients with acute diarrhea using polymerase chain reaction (PCR). Materials and Methods: Escherichia coli stool samples were collected from 115 hospitalized children and adults with acute diarrhea in Mangalore, a coastal city, in southern India. PCR amplification of eae, bfp, stx, ehx genes were used for detection of enteropathogenic (EPEC) and shigatoxigenic E. coli (STEC), lt and st genes were used for enterotoxigenic E. coli (ETEC) and astA gene for enteroaggregative E. coli (EAEC). Results: During the 24 month study period, of the 115 stool samples, DEC type was detected in 20 (17.4%) using the PCR method. The most prevalent DEC was atypical EPEC accounting for 12 (10.4%) cases followed by 4 cases of EAEC (3.4%) and 4 of STEC (3.4%). No ETEC strains were isolated from any of the examined stool samples. Conclusion: This study suggests that the atypical EPEC are the newly emerging group among DEC stains in Southern India. Further studies are needed to evaluate the epidemiology and virulence properties of atypical EPEC strains.
Prevalence of Diabetes and Cardiovascular Comorbidity in the Canadian Community Health Survey 2002–2003

Diabetes mellitus is a major risk factor for heart disease (heart attack, angina, and heart failure), stroke, and hypertension, which shorten the average life expectancy. The main objective of this study was to describe the prevalence of heart disease, hypertension, and stroke among Canadians with diabetes compared to those without diabetes in the Canadian general population aged 12 years and over. It also estimated the strength of association between diabetes, heart disease, hypertension, and other factors such as age, gender, cigarette smoking, alcohol drinking, education status, body mass index (BMI), and other socioeconomic factors. Descriptive statistics were used initially to estimate the prevalence of related comorbidities by age and gender. Logistic regression was then employed to determine the potential strength of association between various effects. Data included 127,610 individuals who participated in the 2.1 cycles of the Canadian Community Health Survey (CCHS) in 2002–2003. The prevalence of self-reported hypertension, heart disease, and stroke among individuals with diabetes were 51.9, 21.7, and 4.8%, respectively. By comparison, prevalence among those without diabetes was 12.7, 4.2, and 0.9%. Adjusted Odds Ratios (OR) were 4.15, 5.04, and 6.75 for males, and 4.10, 5.29, and 4.56 for females hypertension, heart disease, and stroke, respectively. Lower income (OR from 1.27—1.94) and lower education (OR from 1.23—1.86) were independently associated with a high prevalence of hypertension, heart disease, and stroke among diabetics. Alcohol consumption (OR from 1.06—1.38), high BMI (OR from 1.17—1.40), physical inactivity (OR from 1.21—2.45), ethnicity, and immigration status were also strongly associated with hypertension, heart disease, and stroke. The adjusted prevalence of hypertension, heart disease, and stroke in the CCHS-2003 health survey in Canada was significantly higher among those with diabetes compared to those without. Other factors such as age, gender, BMI, lifestyle, family incomes, physical activity levels, and socioeconomic status also affected the strength of association between diabetes and resulting comorbidities.
Interaction of a peptide nanotube with a water–membrane interface

Inserting peptide nanotubes into lipid bilayers modulates the permeability properties of the cell wall, thus conferring potential bacteriocidal capability. Interaction of a peptide nanotube formed by eight cyclo[RRKWLWLW] subunits with the surface of a hydrated dimyristoylphosphatidylcholine bilayer is investigated using molecular dynamics simulations. The present sequence of alternated D–L-α-amino acids has been shown to yield remarkable antibacterial in vitro activity, and the chosen topoisomer corresponds to the optimum amphipathy of the tubular structure, whereby non-polar and charged side chains are segregated by the aqueous interface. The cohesion of the nanotube is ensured by a scaffold of intermolecular hydrogen bonds between adjacent cyclic peptides, supplemented by favorable like-charged contacts of arginine side chains. It is further reinforced by interactions of charged residues with the lipid head groups and of non-polar residues with the lipid acyl chains. The simulation reveals a partial breaking of the synthetic channel accompanying its early insertion into the lipid bilayer. The latter opens new questions about how peptide nanotubes permeate the membrane, in particular whether or not (i) self-assembly precedes partitioning and (ii) translocation occurs with the complete tubular structure.
Simultaneous Localization and Map Building in Large-Scale Cyclic Environments Using the Atlas Framework

In this paper we describe Atlas, a hybrid metrical/topological approach to simultaneous localization and mapping (SLAM) that achieves efficient mapping of large-scale environments. The representation is a graph of coordinate frames, with each vertex in the graph representing a local frame and each edge representing the transformation between adjacent frames. In each frame, we build a map that captures the local environment and the current robot pose along with the uncertainties of each. Each map’s uncertainties are modeled with respect to its own frame. Probabilities of entities with respect to arbitrary frames are generated by following a path formed by the edges between adjacent frames, computed using either the Dijkstra shortest path algorithm or breath-first search. Loop closing is achieved via an efficient map-matching algorithm coupled with a cycle verification step. We demonstrate the performance of the technique for post-processing large data sets, including an indoor structured environment (2.2 km path length) with multiple nested loops using laser or ultrasonic ranging sensors.