Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of a fosA3 Carrying IncC–IncN Plasmid From a Multidrug-Resistant ST17 Salmonella Indiana Isolate

The aim of this study was to investigate the characteristics of a fosA3 carrying IncC–IncN plasmid from a multidrug-resistant Salmonella isolate HNK130. HNK130 was isolated from a chicken and identified as ST17 Salmonella enterica serovar Indiana and exhibited resistance to 13 antibiotics including the cephalosporins and fosfomycin. S1 nuclease pulsed-field gel electrophoresis and Southern blot assays revealed that HNK130 harbored only one ∼180-kb plasmid carrying fosA3 and blaCTX–M–14, which was not transferable via conjugation. We further examined 107 Escherichia coli electro-transformants and identified 3 different plasmid variants, pT-HNK130-1 (69), pT-HNK130-2 (15), and pT-HNK130-3 (23), in which pT-HNK130-1 seemed to be the same as the plasmid harbored in HNK130. We completely sequenced an example of each of these variants, and all three variants were IncC–IncN multi-incompatible plasmid and showed a mosaic structure. The fosA3 gene was present in all three and bounded by IS26 elements in the same orientation (IS26-322bp-fosA3-1758bp-IS26) that could form a minicircle containing fosA3. The blaCTX–M–14 gene was located within an IS15DI-ΔIS15DI-iroN-IS903B-blaCTX–M–14-ΔISEcp1-IS26 structure separated from the fosA3 gene in pT-HNK130-1, but was adjacent to fosA3 in pT-HNK130-3 in an inverted orientation. Linear comparison of the three variants showed that pT-HNK130-2 and pT-HNK130-3 resulted from the sequence deletion and inversion of pT-HNK130-1. Stability tests demonstrated that pT-HNK130-1 and pT-HNK130-3 could be stably maintained in the transformants without antibiotic selection but pT-HNK130-2 was unstable. This is the first description of an IncC–IncN hybrid plasmid from an ST17 S. Indiana strain and indicates that this plasmid may further facilitate dissemination of fosfomycin and cephalosporin resistance in Salmonella.
Interaction between hydroxyethyl starch and propofol: computational and laboratorial study

Background: Hydroxyethyl starch (HES) is one of the most used colloids for intravascular volume replacement during anesthesia. Aim: To investigate the existence of a chemical interaction between HES and the anesthetic propofol by in vitro propofol dosing, computational docking, and examination of a complex between propofol and HES by infrared (IR), ultraviolet (UV), and 1H and 13C nuclear magnetic resonance (NMR) spectroscopy. Methods: Ten samples with human plasma mixed with HES or lactated Ringers (n = 5 for each fluid) were prepared, and the propofol free fraction was quantified until 50 min, using gas chromatography-mass spectrometry. The docking study was performed between HES and propofol and compared with controls. The binding affinities between HES and the small molecules were evaluated by binding free energy approximation (ΔGb, kJ mol−1). The IR, UV, and NMR spectra were measured for propofol, HES, and a mixture of both obtained by the kneading method. Results: Propofol concentrations were significantly lower in the HES samples than in the LR samples (p = .021). The spectroscopic characterization of propofol combined with HES revealed differences in spectra and docking studies reinforced a potential interaction between propofol and HES. Conclusions: Propofol and HES form a complex with different physical-bio-chemical behavior than the single drugs, which may be an important drug interaction. Further studies should evaluate its clinical effects.
Quantization Step Parity-based Steganography for MP3 Audio

Petitcolas has proposed a steganographic technique called MP3Stego which can hide secret messages in a MP3 audio. This technique is well-known be cause of its high capacity. However, in rare cases, the normal audio encoding process will be term inated due to the endless loop problem caused by embedding operation. In addition, the statistica l undetectability of MP3Stego can be further improved. Inspired by MP3Stego, a new steganographic m ethod for MP3 audio is proposed in this paper. The parity bit of quantization step rather than t he parity bit of block size in MP3Stego is employed to embed secret messages. Compared with MP3Steg o, th proposed method can avoid the endless loop problem and achieve better imperceptibili ty and higher security.
What Drives Task Performance During Animal Fluency in People With Alzheimer’s Disease?

Background Animal fluency is a widely used task to assess people with Alzheimer’s disease (AD) and other neurological disorders. The mechanisms that drive performance in this task are argued to rely on language and executive functions. However, there is little information regarding what specific aspects of these cognitive processes drive performance on this task. Objective To understand which aspects of language (i.e., semantics, phonological output lexicon, phonological assembly) and executive function (i.e., mental set shifting; information updating and monitoring; inhibition of possible responses) are involved in the performance of animal fluency in people with AD. Methods Animal fluency data from 58 people with probable AD from the DementiaBank Pittsburgh Corpus were analyzed. Number of clusters and switches were measured and nine word properties (e.g., frequency, familiarity) for each of the correct words (i.e., each word counting toward the total score, disregarding non-animals and repetitions) were determined. Random forests were used to understand which variables predicted the total number of correct words, and conditional inference trees were used to search for interactions between the variables. Finally, Wilcoxon tests were implemented to cross-validate the results, by comparing the performance of participants with scores below the norm in animal fluency against participants with scores within the norm based on a large normative sample. Results Switches and age of acquisition emerged as the most important variables to predict total number of correct words in animal fluency in people with AD. Cross-validating the results, people with AD whose animal fluency scores fell below the norm produced fewer switches and words with lower age of acquisition than people with AD with scores in the normal range. Conclusion The results indicate that people with AD rely on executive functioning (information updating and monitoring) and language (phonological output lexicon, not necessarily semantics) to produce words on animal fluency.
Electro-Acupuncture Promotes the Differentiation of Endogenous Neural Stem Cells via Exosomal microRNA 146b After Ischemic Stroke

Background: Evidences indicate that exosomes-mediated delivery of microRNAs (miRNAs or miRs) is involved in the neurogenesis of stroke. This study was to investigate the role of exosomal miRNAs in non-drug therapy of electro-acupuncture (EA) regulating endogenous neural stem cells for stroke recovery. Methods: The model of focal cerebral ischemia and reperfusion in rats were established by middle cerebral artery occlusion (MCAO) and treated by EA. The exosomes were extracted from peri-ischemic striatum and identified by exosomal biomarkers, and detected differentially expressed miRNAs with microarray chip. Primary stem cells were cultured, and oxygen–glucose deprivation and reperfusion (OGD/R) was used to mimic vitro ischemic injury. Results: The levels of exosomal biomarkers TSG101 and CD81 were increased in peri-ischemic striatum after EA treatment, and we revealed 25 differentially expressed miRNAs in isolated exosomes, of which miR-146b was selected for further analysis, and demonstrated that EA increased miR-146b expression and its inhibitors could block the effects. Subsequently, we confirmed that EA upregulated miR-146b expression to promote neural stem cells differentiation into neurons in peri-ischemic striatum. In vitro, it was verified that OGD/R hindered neural stem cells differentiation, and miR-146b inhibitors furtherly suppressed its differentiation, simultaneously NeuroD1 was involved in neural stem cells differentiation into neurons. Moreover, in vivo we found EA promoted NeuroD1-mediated neural stem cells differentiation via miR-146b. In addition, EA also could improve neurological deficits through miR-146b after ischemic stroke. Conclusion: EA promotes the differentiation of endogenous neural stem cells via exosomal miR-146b to improve neurological injury after ischemic stroke.
Profile of Robert J. Sampson

The patterns and dynamics of social life have intrigued Robert Sampson since his childhood. “One of my earliest memories as a kid is flipping through National Geographic magazines and being mesmerized by maps: maps of the world, the connections and social patterning of life, and its variability across the globe,” he recalls. “I was taken by that and puzzled by it. ” Sampson, the Henry Ford II Professor of the Social Sciences and chair of the sociology department at Harvard University (Cambridge, MA), has built his career on studying social patterns, formulating influential sociological theory, and developing methods to study the complex social networks of neighborhoods and cities. For his work on the origins of crime and violence and on the influence of neighborhoods on the life course, Sampson was elected to the National Academy of Sciences in 2006. In his Inaugural Article in this issue of PNAS, Sampson examines how growing up in severely disadvantaged neighborhoods affects verbal ability in black children (1). Growing up in the small, industrial city of Utica, NY, in the 1960s, Sampson witnessed firsthand the changing patterns within his city. Utica is “a microcosm of the changes that have gone on in some of the larger, more famous cities in the United States,” he says. Once a bustling city, his hometown was hit with hard times as industries left and almost half of the town's population went with them. “I witnessed those changes growing up and was fascinated—why are some communities declining and people leaving, and why are others thriving? ” he asks. From a young age, Sampson was a keen observer of community and city life. The self-described “upstate New York kid” did not stray far from home for college or graduate school, choosing to attend the State University of New York (SUNY). As …
Spatial and cellular localization of calcium-dependent protease (CDP II) in Allomyces arbuscula

Immunogold labeling of calcium-dependent neutral protease II (CDPII) with specific antibodies in near median longitudinal ultrathin sections of Allomyces arbuscula showed that the enzyme is predominantly localized in the growing hyphal and rhizoidal apices. The tips in both cell type had more enzyme than the distal regions and showed a gradient distribution. Labeling of the ultrathin sections and western blot analysis of purified subcellular fractions showed that CDPII is mainly cytosolic. Catalytic activity of the enzyme measured with synthetic substrate (Bz-Arg-pNA) showed that 90% of its activity is present in the soluble fraction, although a small amount is associated with the nuclei (0.2%), plasma membranes (0.7%) and microsomes (3.9%). This association is discussed in the context of the functional role of the enzyme and its possible localized activation. Western blot analysis of the crude extract and indirect immunofluorescence of the fixed permeabilized hypahe after treatment with CDPII showed that theα -tubulin is a specific target of the enzyme.
CYP11A1 stimulates the hydroxylase activity of CYP11B1 in mitochondria of recombinant yeast in vivo and in vitro.

In mammals, hydrocortisone synthesis from cholesterol is catalyzed by a set of five specialized enzymes, four of them belonging to the superfamily of cytochrome P-450 monooxygenases. A recombinant yeast expression system was recently developed for the CYP11B1 (P45011beta) enzyme, which performs the 11beta hydroxylation of steroids such as 11-deoxycortisol into hydrocortisone, one of the three mitochondrial cytochrome P-450 proteins involved in steroidogenesis in mammals. This heterologous system was used to test the potential interaction between CYP11B1 and CYP11A1 (P450scc), the mitochondrial cytochrome P-450 enzyme responsible for the side chain cleaving of cholesterol. Recombinant CYP11B1 and CYP11A1 were targeted to Saccharomyces cerevisiae mitochondria using the yeast cytochrome oxidase subunit 6 mitochondrial presequence fused to the mature form of the two proteins. In yeast, the presence of CYP11A1 appears to improve 11beta hydroxylase activity of CYP11B1 in vivo and in vitro. Fractionation experiments indicate the presence of the two proteins in the same membrane fractions, i.e. inner membrane and contact sites of mitochondria. Thus, yeast mitochondria provide interesting insights to study some molecular and cellular aspects of mammalian steroid synthesis. In particular, recombinant yeast should permit a better understanding of the mechanism permitting the synthesis of steroids (sex steroids, mineralocorticoids and glucocorticoids) with a minimal set of enzymes at physiological level, thus avoiding disease states.
On some variants of second-order unification

In this thesis we present several results about Second-Order Unification. It is well known that the Second-Order Unification Problem is in general undecidable; the frontier between its decidable and undecidable subclasses is thin and it still has not been completely defined. Our purpose is to shed some light on the Second-Order Unification problem and study some of its variants. We have mainly focused our attention on Context Unification and Linear Second-Order Unification. Roughly speaking, these problems are variants of Second-Order Unification where second-order variables are required to be linear. Context Unification was defined more than ten years ago and its decidability has been an open question since then. Here we make relevant contributions to the study of this question. The first result that we present is a simplification on these problems thanks to "curryfication". We show that the Context Unification problem can be NP-reduced to the Context Unification problem where, apart from variables, just a single binary function symbol, and first-order constants, are used. We also show that a similar result also holds for Second-Order Unification. The main result of this thesis is the definition of a non-trivial sufficient and necessary condition on the unifiers, for the decidability of Context Unification. The condition is called rank-bound conjecture in order to enforce our belief about its truthness. It lies on a non-trivial measure of terms, the rank, and claims that, whenever an instance of the Context Unification problem is satisfiable, there exists a unifier with a rank not exceeding a certain bound depending on the size of the problem. Under the assumption of this conjecture, we give a reduction of the satisfiability problem for Context Unification to the (decidable) satisfiability problem of Word Unification with regular constraints. Finally, in the same spirit of the extension of Word Unification with reg
Isolation and characterization of a new bacteriophage, Cp-1, infecting Streptococcus pneumoniae

Several pneumococcal phages showing a morphology completely different from those of all other previously found pneumococcal bacteriophages have been isolated. Bacteriophage Cp-1, one of the phages isolated, showed an irregular hexagonal structure and a short tail of 20 nm. The virion density was 1.46 g/cm3. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed the presence of nine polypeptides. The polypeptide showing a molecular weight of 39,000 accounted for more than the 90% of the total protein. The nucleic acid of Cp-1 was linear, double-stranded DNA with a mean length of 6.3 microns and a guanine-plus-cytosine content of 41%; its buoyant density was 1.699 and 1.422 g/cm3 in CsCl and CS2SO4, respectively. Its sedimentation coefficient (S20,w) was 19S. Cp-1 DNA showed a remarkable resistance to a large number of restriction endonucleases. A total of 12 fragments, ranging in molecular weight from 1.3 X 10(6) to 0.09 X 10(6), were produced by AluI, two fragments (molecular weight, 5.5 X 10(6) and 0.9 X 10(6)) were generated by HindIII, and two fragments (molecular weight, 6.0 X 10(6) and 5.7 X 10(6)) were produced by HaeIII. The easy visualization of th plaques produced by Cp-1, the small size of Cp-1 DNA (12 X 10(6) daltons), and other biological and physiochemical properties make this phage potentially useful for genetic studies.
Rapid and Sensitive Quantification of Vibrio cholerae and Vibrio mimicus Cells in Water Samples by Use of Catalyzed Reporter Deposition Fluorescence In Situ Hybridization Combined with Solid-Phase Cytometry

ABSTRACT A new protocol for rapid, specific, and sensitive cell-based quantification of Vibrio cholerae/Vibrio mimicus in water samples was developed. The protocol is based on catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) in combination with solid-phase cytometry. For pure cultures, we were able to quantify down to 6 V. cholerae cells on one membrane with a relative precision of 39% and down to 12 cells with a relative precision of 17% after hybridization with the horseradish peroxidase (HRP)-labeled probe Vchomim1276 (specific for V. cholerae and V. mimicus) and signal amplification. The corresponding position of the probe on the 16S rRNA is highly accessible even when labeled with HRP. For the first time, we were also able to successfully quantify V. cholerae/V. mimicus via solid-phase cytometry in extremely turbid environmental water samples collected in Austria. Cell numbers ranged from 4.5 × 101 cells ml−1 in the large saline lake Neusiedler See to 5.6 × 104 cells ml−1 in an extremely turbid shallow soda lake situated nearby. We therefore suggest CARD-FISH in combination with solid-phase cytometry as a powerful tool to quantify V. cholerae/V. mimicus in ecological studies as well as for risk assessment and monitoring programs.
A Novel Approach for the Colour Deconvolution of Multiple Histological Stains

Colour Deconvolution (CD) is a commonly used tool in histological medical image analysis that separates histochemical or immunohistochemical stains into their component parts. Traditional CD uses matrix inversion to change the Red, Green and Blue (RGB) channels of an image into a new domain that is representative of reference colours but this limits the total number of stains that can be separated. This is problematic for histological staining protocols that use more than three stains, such as FAST staining. This limitation has restricted the use of multicolour staining in light microscopy. To address this issue, this paper evaluates the use of Non Negative Matrix Factorisation (NNMF) and Non Negative Least Squares (NNLS) to enable the decomposition of multistained histological sections into its source components. It will be shown that NNLS is better suited to imaging modalities such as Whole Slide Image (WSI) scanners and that the multiple staining metrics produced from a single sample are analogous to those generated by applying single reagents to contiguous tissue sections.
À propos du zénaga. Vocalisme et morphologie verbale en berbère

En berbere, l'opposition fondamentale, avant l'introduction dans le systeme verbal de base de l'aoriste intensif, etait entre l'aoriste et le preterit. Ces deux formes, conjuguees avec les memes affixes, correspondent toutes deux aux formes a prefixes du chamito-semitique. Dans beaucoup de parlers berberes, seuls quelques verbes distinguent leur aoriste de leur preterit par des changements vocaliques. Dans d'autres, ces changements sont beaucoup plus systematiques. Une etude du zenaga de Mauritanie montre que dans ce parler les bi-syllabiques presentent des changements reguliers, l'aoriste (et l'imperatif) etant caracterise par une suite a — i ou a — u (‘a' — ‘non-a') alors que le preterit l'est par les sequences inversees i — a et u — a (‘non-a'— ‘a'). A la lumiere de ces resultats, un re-examen des fait berberes est propose. Il apparait que, pour chaque dialecte considere, la generalite des alternances et des contrastes est en rapport direct avec l'organisation du systeme vocalique. A la difference des parlers septentrionaux, les parlers berberes meridionaux ont, dans leur ensemble, conserve une opposition de quantite (d'ou un systeme vocalique comprenant au moins deux voyelles breves). Ils presentent donc un plus grand nombre de changements vocaliques reguliers que les parlers du nord, mais les principes memes qui gouvernent encore alternances et apophonie semblent avoir ete communs a tout l'ensemble berbere.
Rapid Nucleic Acid Extraction and Purification Using a Miniature Ultrasonic Technique

Miniature ultrasonic lysis for biological sample preparation is a promising technique for efficient and rapid extraction of nucleic acids and proteins from a wide variety of biological sources. Acoustic methods achieve rapid, unbiased, and efficacious disruption of cellular membranes while avoiding the use of harsh chemicals and enzymes, which interfere with detection assays. In this work, a miniature acoustic nucleic acid extraction system is presented. Using a miniature bulk acoustic wave (BAW) transducer array based on 36° Y-cut lithium niobate, acoustic waves were coupled into disposable laminate-based microfluidic cartridges. To verify the lysing effectiveness, the amount of liberated ATP and the cell viability were measured and compared to untreated samples. The relationship between input power, energy dose, flow-rate, and lysing efficiency were determined. DNA was purified on-chip using three approaches implemented in the cartridges: a silica-based sol-gel silica-bead filled microchannel, nucleic acid binding magnetic beads, and Nafion-coated electrodes. Using E. coli, the lysing dose defined as ATP released per joule was 2.2× greater, releasing 6.1× more ATP for the miniature BAW array compared to a bench-top acoustic lysis system. An electric field-based nucleic acid purification approach using Nafion films yielded an extraction efficiency of 69.2% in 10 min for 50 µL samples.