Miracle-dz/UniFAR-FTUs huggingface dataset:
The Accessory Genome of Shiga Toxin-Producing Escherichia coli Defines a Persistent Colonization Type in Cattle

ABSTRACT Shiga toxin-producing Escherichia coli (STEC) strains can colonize cattle for several months and may, thus, serve as gene reservoirs for the genesis of highly virulent zoonotic enterohemorrhagic E. coli (EHEC). Attempts to reduce the human risk for acquiring EHEC infections should include strategies to control such STEC strains persisting in cattle. We therefore aimed to identify genetic patterns associated with the STEC colonization type in the bovine host. We included 88 persistent colonizing STEC (STECper) (shedding for ≥4 months) and 74 sporadically colonizing STEC (STECspo) (shedding for ≤2 months) isolates from cattle and 16 bovine STEC isolates with unknown colonization types. Genoserotypes and multilocus sequence types (MLSTs) were determined, and the isolates were probed with a DNA microarray for virulence-associated genes (VAGs). All STECper isolates belonged to only four genoserotypes (O26:H11, O156:H25, O165:H25, O182:H25), which formed three genetic clusters (ST21/396/1705, ST300/688, ST119). In contrast, STECspo isolates were scattered among 28 genoserotypes and 30 MLSTs, with O157:H7 (ST11) and O6:H49 (ST1079) being the most prevalent. The microarray analysis identified 139 unique gene patterns that clustered with the genoserotypes and MLSTs of the strains. While the STECper isolates possessed heterogeneous phylogenetic backgrounds, the accessory genome clustered these isolates together, separating them from the STECspo isolates. Given the vast genetic heterogeneity of bovine STEC strains, defining the genetic patterns distinguishing STECper from STECspo isolates will facilitate the targeted design of new intervention strategies to counteract these zoonotic pathogens at the farm level. IMPORTANCE Ruminants, especially cattle, are sources of food-borne infections by Shiga toxin-producing Escherichia coli (STEC) in humans. Some STEC strains persist in cattle for longer periods of time, while others are detected only sporadically. Persisting strains can serve as gene reservoirs that supply E. coli with virulence factors, thereby generating new outbreak strains. Attempts to reduce the human risk for acquiring STEC infections should therefore include strategies to control such persisting STEC strains. By analyzing representative genes of their core and accessory genomes, we show that bovine STEC with a persistent colonization type emerged independently from sporadically colonizing isolates and evolved in parallel evolutionary branches. However, persistent colonizing strains share similar sets of accessory genes. Defining the genetic patterns that distinguish persistent from sporadically colonizing STEC isolates will facilitate the targeted design of new intervention strategies to counteract these zoonotic pathogens at the farm level.
Intestinal Stem Cells to Advance Drug Development, Precision, and Regenerative Medicine: A Paradigm Shift in Translational Research

Recent advances in our understanding of the intestinal stem cell niche and the role of key signaling pathways on cell growth and maintenance have allowed the development of fully differentiated epithelial cells in 3D organoids. Stem cell-derived organoids carry significant levels of proteins that are natively expressed in the gut and have important roles in drug transport and metabolism. They are, therefore, particularly relevant to study the gastrointestinal (GI) absorption of oral medications. In addition, organoids have the potential to serve as a robust preclinical model for demonstrating the effectiveness of new drugs more rapidly, with more certainty, and at lower costs compared with live animal studies. Importantly, because they are derived from individuals with different genotypes, environmental risk factors and drug sensitivity profiles, organoids are a highly relevant screening system for personalized therapy in both human and veterinary medicine. Lastly, and in the context of patient-specific congenital diseases, orthotopic transplantation of engineered organoids could repair and/or replace damaged epithelial tissues reported in various GI diseases, such as inflammatory bowel disease, cystic fibrosis, and tuft enteropathy. Ongoing translational research on organoids derived from dogs with naturally occurring digestive disorders has the potential to improve the predictability of preclinical models used for optimizing the therapeutic management of severe chronic enteropathies in human patients.
Novel potassium sodium niobate/polyimide functional composite films with high dielectric permittivity

This work reports the advanced potassium sodium niobate (K0.5Na0.5NbO3, KNN)/polyimide (KNN/PI) functional hybrid films with 5 vol%, 10 vol%, 20 vol%, 30 vol%, and 40 vol% KNN loaded. The structure, morphology, and dielectric properties of hybrid films have been measured. The results show that the KNN fillers are well dispersed in the PI matrix. An internal boundary layer capacitance structure is formed in the composite films. The dielectric permittivity of the film is as high as 22 when the concentration of KNN filler reaches 40 vol% at 102 Hz, which is five times larger than that of a pure PI matrix. Meanwhile, the loss tangent is lower than 0.05. In addition, the conductivity is lower than 10−8 (S m−1) at 102 Hz, which indicates the excellent insulation and is important for the practical use of this kind of KNN/PI hybrid films. It is believed that the KNN/PI hybrid films could be applied in future electronic fields. POLYM. COMPOS. , 35:969–974, 2014. © 2013 Society of Plastics Engineers
Insights into immune system development and function from mouse T-cell repertoires

Significance The immune system defends against pathogens in part via a diverse population of T cells that display different surface receptor proteins [T-cell receptors (TCRs)] designed to recognize MHC-presented foreign peptides. Receptor diversity is produced by an initial random gene recombination process, followed by selection for proteins that fold correctly and bind weakly to self-peptides. Using data from mice of different ages, from embryo to young adult, we quantify the changes with time in the way receptors are generated and selected for function. We find a strong increase in repertoire diversity, occurring shortly after birth, due to a sharp increase in the number of random nucleotide insertions in the primitive TCR gene recombination process. Differences between thymic and blood TCR sequence distributions allow us to infer subtle details of this “turning on” of the mouse immune system. The ability of the adaptive immune system to respond to arbitrary pathogens stems from the broad diversity of immune cell surface receptors. This diversity originates in a stochastic DNA editing process (VDJ recombination) that acts on the surface receptor gene each time a new immune cell is created from a stem cell. By analyzing T-cell receptor (TCR) sequence repertoires taken from the blood and thymus of mice of different ages, we quantify the changes in the VDJ recombination process that occur from embryo to young adult. We find a rapid increase with age in the number of random insertions and a dramatic increase in diversity. Because the blood accumulates thymic output over time, blood repertoires are mixtures of different statistical recombination processes, and we unravel the mixture statistics to obtain a picture of the time evolution of the early immune system. Sequence repertoire analysis also allows us to detect the statistical impact of selection on the output of the VDJ recombination process. The effects we find are nearly identical between thymus and blood, suggesting that our analysis mainly detects selection for proper folding of the TCR receptor protein. We further find that selection is weaker in laboratory mice than in humans and it does not affect the diversity of the repertoire.
Assessment of treatment response in tuberculosis

ABSTRACT Antibiotic treatment of tuberculosis has a duration of several months. There is significant variability of the host immune response and the pharmacokinetic-pharmacodynamic properties of Mycobacterium tuberculosis sub-populations at the site of disease. A limitation of sputum-based measures of treatment response may be sub-optimal detection and monitoring of Mycobacterium tuberculosis sub-populations. Potential biomarkers and surrogate endpoints should be benchmarked against hard clinical outcomes (failure/relapse/death) and may need tailoring to specific patient populations. Here, we assess the evidence supporting currently utilized and future potential host and pathogen-based models and biomarkers for monitoring treatment response in active and latent tuberculosis. Biomarkers for monitoring treatment response in extrapulmonary, pediatric and drug resistant tuberculosis are research priorities.
Graphical vs. Tabular Notations for Risk Models: On the Role of Textual Labels and Complexity

[Background] Security risk assessment methods in industry mostly use a tabular notation to represent the assessment results whilst academic works advocate graphical methods. Experiments with MSc students showed that the tabular notation is better than an iconic graphical notation for the comprehension of security risks. [Aim] We investigate whether the availability of textual labels and terse UML-style notation could improve comprehensibility. [Method] We report the results of an online comprehensibility experiment involving 61 professionals with an average of 9 years of working experience, in which we compared the ability to comprehend security risk assessments represented in tabular, UML-style with textual labels, and iconic graphical modeling notations. [Results] Tabular notation are still the most comprehensible notion in both recall and precision. However, the presence of textual labels does improve the precision and recall of participants over iconic graphical models. [Conclusion] Tabular representation better supports extraction of correct information of both simple and complex comprehensibility questions about security risks than the graphical notation but textual labels help.
Drag and drop of pores during grain boundary migration

Untersucht werden die Wechselwirkungen zwischen Poren und Korngrenzen in Polykristallen, insbesondere das Ziehen einer Pore mit und die Separation einer Pore von einer wandernden Korngrenze. Zwei relevante Transportmechanismen werden betrachtet: Oberflachendiffusion an der Pore-Festphasen Grenze und Volumendiffusion durch eine fluidgefullte Pore. Die Mobilitat einer gezogenen Pore und die kritische Geschwindigkeit, bei der sich eine Pore von einer wandernden Korngrenze lost, werden berechnet, und der Einfluss von Poren auf die Korngrenzwanderung abgeschatzt. Kritische Geschwindigkeit und Porenmobilitat werden in kompakter analytischer Form angegeben und zur Abschatzung der Beitrage der beiden Transportmechanismen verwendet. Es wird gezeigt, dass fluidgefullte Poren dazu tendieren an Korngrenzen haften zu bleiben und uber schnelle Korngrenzdiffusion aus dem System entfernt zu werden, wahrend gasgefullte Poren sich leichter von Korngrenzen losen und in einem Korn eingeschlossen werden.
Microbial competition in porous environments can select against rapid biofilm growth

Significance The overwhelming majority of bacteria live in porous environments, like soil, aquifers, and sediments, where they facilitate many important processes. Despite their importance, we understand little about how these complex environments shape the composition of the microbial communities that live within them. Here, we combine two diverse bodies of theory—fluid dynamics and game theory—to shed light on how bacteria evolve in these habitats. We show that bacteria in porous environments face a fundamental dilemma: they rely on flow for nutrients and dispersal; however, as cells grow, they tend to reduce their access to flow. A fast growing strain can, therefore, choke off its own nutrient supply, diverting it instead to competitors. In contrast with classical theory, our results suggest that cells within a biofilm can obtain a competitive advantage by growing more slowly. Microbes often live in dense communities called biofilms, where competition between strains and species is fundamental to both evolution and community function. Although biofilms are commonly found in soil-like porous environments, the study of microbial interactions has largely focused on biofilms growing on flat, planar surfaces. Here, we use microfluidic experiments, mechanistic models, and game theory to study how porous media hydrodynamics can mediate competition between bacterial genotypes. Our experiments reveal a fundamental challenge faced by microbial strains that live in porous environments: cells that rapidly form biofilms tend to block their access to fluid flow and redirect resources to competitors. To understand how these dynamics influence the evolution of bacterial growth rates, we couple a model of flow–biofilm interaction with a game theory analysis. This investigation revealed that hydrodynamic interactions between competing genotypes give rise to an evolutionarily stable growth rate that stands in stark contrast with that observed in typical laboratory experiments: cells within a biofilm can outcompete other genotypes by growing more slowly. Our work reveals that hydrodynamics can profoundly affect how bacteria compete and evolve in porous environments, the habitat where most bacteria live.
The spectrum of myocardial homeostasis mechanisms in the settings of cardiac surgery procedures

Classic cardiac surgery, determined through the function of cardiopulmonary bypass machine and myocardial cardioplegic arrest, represents the most controlled scenario for cardiomyocyte homeostatic disturbances due to systemic inflammatory response and myocardial reperfusion injury. An increasing number of studies have demonstrated that myocardial cell homeostasis in cardiac surgery procedures is a sequence of molecularly interrelated and overlapping mechanisms in the form of apoptosis, autophagy and necrosis, which are activated by a plethora of induced inflammatory mediators and gene-related signaling pathways. In this study, we outline the molecular mechanisms of the cardiomyocyte adaptive homeostatic process and the associated clinical implications, in the settings of classic cardiac surgery procedures.
NetworkView: 3D display and analysis of protein·RNA interaction networks

SUMMARY NetworkView is an application for the display and analysis of protein·RNA interaction networks derived from structure and/or dynamics. These networks typically model individual protein residues and nucleic acid monomers as nodes and their pairwise contacts as edges with associated weights. NetworkView projects the network onto the underlying 3D molecular structure so that visualization and analysis of the network can be coupled to physical and biological properties. NetworkView is implemented as a plugin to the molecular visualization software VMD. AVAILABILITY AND IMPLEMENTATION NetworkView is included with VMD, which is available at http://www.ks. uiuc.edu/Research/vmd/. Documentation, tutorials and supporting programs are available at http://www.scs.illinois.edu/schulten/software/. CONTACT networkview@scs.illinois.edu
Graphene-Based Polymer Nanocomposites

Abstract : The reinforcement mechanisms in graphene-based nanocomposites have been studied in this project, which primarily consists of three parts: the size and orientation effects of the graphene-based nano-fillers and their interfacial adhesion with the matrix. Overall Raman spectroscopy has been demonstrated to be a powerful technique to study the graphene-based nanocomposites. The deformation of small size graphene has been followed and a new model has been established. Additionally, the deformation of monolayer graphene oxide (GO) has been followed for the first time. It appears that continuum mechanics is still valid, and the approximately constant strain distribution along the GO flake suggests a better stress transfer efficiency of GO than that of graphene. The spatial orientation of graphene has been studied based on the Raman scattering obtained from transverse sections of graphene, where the Raman bands intensities show a strong polarization dependence. Based on this, a new model has been established to quantify the spatial orientation of graphene in terms of an orientation distribution function, and the spatial orientation of monolayer graphene has been further confirmed by its surface roughness. It is also shown how the spatial orientation of graphene-based fillers affects the mechanical properties of the nanocomposites, through the first determination of the Krenchel orientation factor for nanoplatelets. The findings on both the size and orientation effects have been employed to study the deformation mechanics of bulk GO reinforced nanocomposite films. It has been demonstrated for the first time that the effective modulus of GO can be estimated using the Raman D band shift rate, and this is in agreement with the value measured using conventional mechanical testing. The effective modulus of GO is found to be lower than its Young s modulus, probably due to the mis-orientation, waviness, wrinkling and agglomeration of the GO fillers.
InTeReC: In-text Reference Corpus for Applying Natural Language Processing to Bibliometrics

Bibliometrics is more and more interested in the full text processing and the study of the structure of scientific papers. The contexts of in-text references present in articles are particularly relevant for such studies. This work describes the construction of the InTeReC dataset, which is an in-text reference corpus that aims to promote experimental reproducibility and to provide a standard dataset for further research. The InTeReC dataset is a set of sentences containing in-text references together with all the data necessary for their recontextualization in papers using standard CSV format. This should encourage the implementation of natural language processing tools for Bibliometric studies and related research in information retrieval and visualization.
Analysis of the genome sequence and prediction of B cell epitopes of the envelope protein of MERS

ABSTARCT-The outbreak of Middle East respiratory syndrome-coronavirus (MERS-CoV) in South Korea in April 2015 led to 186 infections and 37 deaths by the end of October 2015. MERS-CoV was isolated from the imported patient in China. The envelope (E) protein, a small structural protein of MERS-CoV, plays an important role in host recognition and infection. To identify the conserved epitopes of the E protein, sequence analysis was performed by comparing the E proteins from 42 MERS-CoV strains that triggered severe pandemics and infected humans in the past. To predict the potential B cell epitopes of E protein, three most effective online epitope prediction programs, the ABCpred, Bepipred and Protean programs from the LaserGene software were used. All the nucleotides and amino acids sequences were obtained from the NCBI Database. One potential epitope with a suitable length (amino acids 58–82) was confirmed and predicted to be highly antigenic. This ep itope had scores of >0.80 in ABCpred and level 0.35 in Bepipred programs. Due to the lack of X-ray crystal structure of the E protein in the PDB database, the simulated 3D structure of the E protein were also predicted using PHYRE 2 and Pymol programs. In conclusion, using bioinformatics methods, we analyzed the genome sequence of MERS-CoV and identified a potential B-cell epitope of the E protein, which might significantly improve our current MERS vaccine development strategies.
Reference gene selection for qRT-PCR assays in Stellera chamaejasme subjected to abiotic stresses and hormone treatments based on transcriptome datasets

Background Stellera chamaejasme Linn, an important poisonous plant of the China grassland, is toxic to humans and livestock. The rapid expansion of S. chamaejasme has greatly damaged the grassland ecology and, consequently, seriously endangered the development of animal husbandry. To draft efficient prevention and control measures, it has become more urgent to carry out research on its adaptive and expansion mechanisms in different unfavorable habitats at the genetic level. Quantitative real-time polymerase chain reaction (qRT-PCR) is a widely used technique for studying gene expression at the transcript level; however, qRT-PCR requires reference genes (RGs) as endogenous controls for data normalization and only through appropriate RG selection and qRT-PCR can we guarantee the reliability and robustness of expression studies and RNA-seq data analysis. Unfortunately, little research on the selection of RGs for gene expression data normalization in S. chamaejasme has been reported. Method In this study, 10 candidate RGs namely, 18S, 60S, CYP, GAPCP1, GAPDH2, EF1B, MDH, SAND, TUA1, and TUA6, were singled out from the transcriptome database of S. chamaejasme, and their expression stability under three abiotic stresses (drought, cold, and salt) and three hormone treatments (abscisic acid, ABA; gibberellin, GA; ethephon, ETH) were estimated with the programs geNorm, NormFinder, and BestKeeper. Result Our results showed that GAPCP1 and EF1B were the best combination for the three abiotic stresses, whereas TUA6 and SAND, TUA1 and CYP, GAPDH2 and 60S were the best choices for ABA, GA, and ETH treatment, respectively. Moreover, GAPCP1 and 60S were assessed to be the best combination for all samples, and 18S was the least stable RG for use as an internal control in all of the experimental subsets. The expression patterns of two target genes (P5CS2 and GI) further verified that the RGs that we selected were suitable for gene expression normalization. Discussion This work is the first attempt to comprehensively estimate the stability of RGs in S. chamaejasme. Our results provide suitable RGs for high-precision normalization in qRT-PCR analysis, thereby making it more convenient to analyze gene expression under these experimental conditions.
Optineurin Functions for Optimal Immunity

Optineurin (OPTN) was identified 20 years ago in a yeast-two-hybrid screen with a viral protein known to inhibit the cytolytic effects of tumor necrosis factor. Since then, OPTN has been identified as a ubiquitin-binding protein involved in many signaling pathways and cellular processes, and mutations in the OPTN gene have been associated with glaucoma, Paget’s disease of bone and neurodegenerative pathologies. Its role in autophagy, however, has attracted most attention in recent years and may explain (some of) the mechanisms behind the disease-associated mutations of OPTN. In this brief review, we focus on the role of OPTN in inflammation and immunity and describe how this may translate to its involvement in human disease.
Mini-screw supported molar distalization: A new method

The aim of this report was to present the results of most effective intraoral upper molar distalization system supported with mini-screw. The mini-screws with a 2.0 mm diameter and 8 mm length were used for intra-osseous anchorage. The screws were placed right and left buccal side of the maxilla. Nickel-titanium (NiTi) coil springs were set bilaterally on a 0.016 inch diameter NiTi archwire between the first molar tubes and the first premolar braces. The first premolars were ligated to the mini-screw to provide anchorage. Other mini-screws with a 2.0 mm diameter and 10 mm length were placed right and left palatal side. A spring consisted of a 0.017 × 0.025 inch beta-titanium-alloy wire situated palatally. The activated wire was inserted among the first molar palatal sheath and the mini-screw. Distalization of the upper molars was achieved in average 5 months. According to the results, the maxillary first molars showed mean 4 mm distal movement and 4° distal tipping.