Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylodynamic Characterization of an Ocular-Tropism Coxsackievirus A24 Variant

Recent phylodynamic studies have focused on using tree topology patterns to elucidate interactions among the epidemiological, evolutionary, and demographic characteristics of infectious agents. However, because studies of viral phylodynamics tend to focus on epidemic outbreaks, tree topology signatures of tissue-tropism pathogens might not be clearly identified. Therefore, this study used a novel Bayesian evolutionary approach to analyze the A24 variant of coxsackievirus (CV-A24v), an ocular-tropism agent of acute hemorrhagic conjunctivitis. Analyses of the 915-nucleotide VP1 and 690-nt 3Dpol regions of 21 strains isolated in Taiwan and worldwide during 1985–2010 revealed a clear chronological trend in both the VP1 and 3Dpol phylogenetic trees: the emergence of a single dominant cluster in each outbreak. The VP1 sequences included three genotypes: GI (prototype), GIII (isolated 1985–1999), and GIV (isolated after 2000); no VP1 sequences from GII strains have been deposited in GenBank. Another five genotypes identified in the 3Dpol region had support values >0.9. Geographic and demographic transitions among CV-A24v clusters were clearly identified by Bayes algorithm. The transmission route was mapped from India to China and then to Taiwan, and each prevalent viral population declined before new clusters emerged. Notably, the VP1 and 3Dpol genes had high nucleotide sequence similarities (94.1% and 95.2%, respectively). The lack of co-circulating lineages and narrow tissue tropism affected the CV-A24v gene pool.
The Session Rating Scale: Preliminary Psychometric Properties of a “Working” Alliance Measure

Over 1,000 research findings (Orlinsky, Rønnestad, & Willutzki, 2004) demonstrate that a positive alliance is one of the best predictors of outcome. Paradoxically, despite the robust connection between the alliance and outcome, no alliance measures have been developed specifically as clinical tools for therapists to use on a day-to-day basis with their clients. This article describes the development and validation of an ultra-brief alliance measure, the Session Rating Scale Version 3 (SRS). The instrument’s psychometric properties are examined and reported. Based on experience with the instrument at the various sites in the study, the feasibility of the scale is also considered. Results indicate that the SRS, a clinical rather than research tool, represents a balanced tradeoff between the reliability and validity of the longer research measures, and the feasibility of this brief scale. Results and implications for clinical practice and future research are discussed.
Sportpartizipation in Deutschland: ein demo-ökonomisches Modell

Demographische und okonomische Veranderungen der Gesellschaft werfen Fragen nach deren Konsequenzen fur den Sport auf. Im Rahmen dieses Beitrags wird untersucht, in welcher Weise die Sportpartizipation in Deutschland von demogra-phischen und okonomischen Parametern abhangt und wie sich die Sportpartizipation bei einer Anderung demographischer und okonomischer Rahmenbedingungen wandelt. Das zugrunde liegende Modell fust auf der okonomischen Haushaltstheorie, die zu einem demo-okonomischen Analysemodell erweitert worden ist. Auf regressionsanalytischer Basis wird gezeigt, dass negative Effekte auf die Sportpartizipation durch die demographischen Faktoren Alterung und Migration durch Wirtschaftswachstum und Bildungsinvestitionen ausgeglichen werden konnen.
LncRNA HANR Promotes Tumorigenesis and Increase of Chemoresistance in Hepatocellular Carcinoma

Background/Aims: Hepatocellular carcinoma (HCC) is the fifth most common cancer in the world and the third leading cause of cancer-related death. Critical roles for long non-coding RNAs (lncRNAs) have recently been demonstrated for a variety of cancers, including hepatocellular carcinoma. However, the effect and mechanism of lncRNAs in HCC tumorigenesis and chemoresistance have not been extensively characterized. Methods: In the current study, we have identified a HCC-expressed lncRNA termed as HANR (HCC associated long non-coding RNA). We identified HANR by microarray analysis and validated its up-regulated expression by quantitative PCR. RNA pull-down and pathway analyses were conducted to evaluate physical and functional interactions with HANR. In vivo experiments were performed to assess tumorigenesis and increase of chemoresistance. In addition, the HANR expression in HCC specimens was detected by FISH. Xenograft and orthotopic mice model was constructed to observe the effect of HANR on tumorigenesis and chemoresistance in vivo. Results: HANR was demonstrated to be up-regulated in HCC patients and HCC cell lines. Increased HANR expression in HCC predicted short survival of patients. Knock-down of HANR markedly retarded cell proliferation, suppressed HCC xenograft/orthotopic tumor growth, induced apoptosis and enhanced chemosensitivity to doxorubicin, while over-expression of HANR showed the opposite effects. It was found that HANR bind to GSKIP for regulating the phosphorylation of GSK3β in HCC. Conclusion: Our results demonstrate that HANR contributes to the development of HCC and is a promising therapeutic target for chemosensitization of HCC cells to doxorubicin, which may represent a promising therapeutic target in the future.
Sub-LET Threshold SEE Cross Section Dependency With Ion Energy

This study focuses on the ion species and energy dependence of the heavy ion SEE cross section in the sub-LET threshold region through a set of experimental data. In addition, a Monte Carlo based model is introduced and applied, showing a good agreement with the data in the several hundred MeV/n range while evidencing large discrepancies with the measurements in the 10-30 MeV/n interval, notably for the Ne ion. Such discrepancies are carefully analyzed and discussed.
Time course of cisplatin-induced nephrotoxicity and hepatotoxicity

Background: One of the main therapeutic limitations of cisplatin (CP) is nephrotoxicity which is time-dependent. Objectives: The purpose of this study was to determine the optimal timing for initiation of CP toxicity. Materials and Methods: Sixty male and female Wistar rats were randomly divided into five groups. All the animals in groups 2-5 received single dose of CP (10 mg/kg; i.p.), and were evaluated 25, 50, 75, and 100 hours after CP administration. Group 1 as an untreated group did not receive any agent and was considered as time zero. Results: The data indicated time-dependent progression of kidney and hepatic toxicity due to CP administration. Histological examination showed increase in kidney tissue damage score (KTDS) at hour 25, which peaked 75-100 hours after CP administration. Significant body weight loss and reduction of alkaline phosphatase (ALP) 50 hours after CP injection were observed. Blood urea nitrogen (BUN), creatinine (Cr), and serum nitrite increased significantly 75 hours after CP injection. Also, enhancement of kidney and testis weights, and alkaline aspartate aminotransferase (AST) level; and reduction of alanine aminotransferase (ALT) level and uterus weight occurred significantly 100 hours after the injection, while kidney malondialdehyde level enhanced significantly 75 hours after CP administration. Conclusions: These findings suggest that the CP-induced nephrotoxicity started to develop almost 3 days after administration of the drug in rats. CP surprisingly reduced the serum levels ALP and ALT while AST increased 100 hours after CP injection. CP-induced nephrotoxicity and hepatotoxicity are time-dependent, and the related biomarkers may alter by different trends.
The peripheral connexions between the lingual and hypoglossal nerves.

The peripheral connexions between the lingual and hypoglossal nerves have merited special study for the following reasons. (1) The accounts of these connexions in the current textbooks of human anatomy are at variance with some of the older works. Current descriptions are similar to that of Schafer & Symington (1909), in which we find that beyond the point where the lingual nerve gives off its supply to the submandibular ganglion, 'one or two filaments descend over the fore-part of the hyoglossus muscle to join in loops with similar branches of the hypoglossal nerve'. On the other hand, Testut (1905) states that this connexion may be plexiform; and Poirier, Charpy & Cuneo (1908) illustrate a plexiform connexion on the hyoglossus muscle, and show in addition what appears to be an intramuscular lingual-hypoglossal linkage further forwards. (2) Boyd (1941), in his study of the hypoglossal nerve in the rabbit, has noted 'some plexus formation' between branches of the lingual and hypoglossal nerves. We have not been able to find any other reference to peripheral lingual-hypoglossal connexions in lower mammals. (3) The functional significance of the lingual-hypoglossal connexions does not appear to have been the subject of any previous investigation.
Genetics of Lateral Plate and Gillraker Phenotypes in a Rapidly Evolving Population of Threespine Stickleback

Twenty-seven crosses were used to study the genetics of rapidly evolving traits in a recently founded population of threespine stickleback in Loberg Lake, Alaska. Lateral plate morph segregation ratios were inconsistent with all published models of lateral plate morph genetics except Avise's (1976) general two-locus model. Incompatibility of the results of our plate morph crosses with those of most previous studies suggests that the genetic architecture underlying lateral plate morphs differs among populations or is more complex than presently recognized. Segregation ratios for lateral plate morphs indicate that consistently low frequencies of partial morphs observed in the Loberg Lake population at least partly reflect genetic architecture. Gillraker number and probably low morph lateral plate number are highly heritable and correlated with each other. Lateral plate asymmetry was high but not significantly heritable. Low and complete morph lateral plate number do not appear to be genetically correlated, indicating a significant element of independent genetic control.
Ecological Genomics of Marine Roseobacters

ABSTRACT Bacterioplankton of the marine Roseobacter clade have genomes that reflect a dynamic environment and diverse interactions with marine plankton. Comparative genome sequence analysis of three cultured representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds (polyamines, allophanate, and urea), while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites. An unexpectedly large number of genes are predicted to encode proteins involved in the production, degradation, and efflux of toxins and metabolites. A mechanism likely involved in cell-to-cell DNA or protein transfer was also discovered: vir-related genes encoding a type IV secretion system typical of bacterial pathogens. These suggest a potential for interacting with neighboring cells and impacting the routing of organic matter into the microbial loop. Genes shared among the three roseobacters and also common in nine draft Roseobacter genomes include those for carbon monoxide oxidation, dimethylsulfoniopropionate demethylation, and aromatic compound degradation. Genes shared with other cultured marine bacteria include those for utilizing sodium gradients, transport and metabolism of sulfate, and osmoregulation.
Artificial Seawater Media Facilitate Cultivating Members of the Microbial Majority from the Gulf of Mexico

The difficulty in cultivating many microbial taxa vexes researchers intent on understanding the contributions of these organisms to natural systems, particularly when these organisms are numerically abundant, and many cultivation attempts recover only rare taxa. Efforts to improve this conundrum with marine bacterioplankton have been successful with natural seawater media, but that approach suffers from a number of drawbacks and there have been no comparable artificial alternatives created in the laboratory. This work demonstrates that a newly developed suite of artificial seawater media can successfully cultivate many of the most abundant taxa from seawater samples and many taxa previously only cultivated with natural seawater media. This methodology therefore significantly simplifies efforts to cultivate bacterioplankton and greatly improves our ability to perform physiological characterization of cultures postisolation. ABSTRACT High-throughput cultivation studies have been successful at bringing numerous important marine bacterioplankton lineages into culture, yet these frequently utilize natural seawater media that can hamper portability, reproducibility, and downstream characterization efforts. Here we report the results of seven experiments with a set of newly developed artificial seawater media and evaluation of cultivation success via comparison with community sequencing data from the inocula. Eighty-two new isolates represent highly important marine clades, including SAR116, OM60/NOR5, SAR92, Roseobacter, and SAR11. For many, isolation with an artificial seawater medium is unprecedented, and several organisms are also the first of their type from the Gulf of Mexico. Community analysis revealed that many isolates were among the 20 most abundant organisms in their source inoculum. This method will expand the accessibility of bacterioplankton cultivation experiments and improve repeatability by avoiding normal compositional changes in natural seawater. IMPORTANCE The difficulty in cultivating many microbial taxa vexes researchers intent on understanding the contributions of these organisms to natural systems, particularly when these organisms are numerically abundant, and many cultivation attempts recover only rare taxa. Efforts to improve this conundrum with marine bacterioplankton have been successful with natural seawater media, but that approach suffers from a number of drawbacks and there have been no comparable artificial alternatives created in the laboratory. This work demonstrates that a newly developed suite of artificial-seawater media can successfully cultivate many of the most abundant taxa from seawater samples and many taxa previously only cultivated with natural-seawater media. This methodology therefore significantly simplifies efforts to cultivate bacterioplankton and greatly improves our ability to perform physiological characterization of cultures postisolation.
The Receptor Mosaic Hypothesis of the Engram: Possible Relevance of Boolean Network Modelling

In the past 15 years, several lines of evidence have shown that receptors for chemical signals can interact in domains of the plasma membrane and possibly form molecular circuits encoding logical operators. In this frame, the receptor mosaic hypothesis of the engram was advanced. According to this proposal, aggregates of different receptor species (mosaics) may form in neuronal membranes (typically synapses) and constitute a memory trace (engram) of its activity. In the present paper, we present an attempt to model the functioning of aggregates of interacting receptors in membrane domains by means of random Boolean networks.
Chronotropic effect of cardiac glycosides in cats, dogs, and rabbits.

We have tested the widely accepted hypothesis that digitalis, in nontoxic concentration, can act directly on cells of the sinoatrial pacemaker to cause slowing. The effect of autonomic nerves on sinoatrial cells was eliminated either by chronic cardiac denervation or by use of autonomic blocking agents such as atropine, 0.5 mg/kg, and propranolol, 2 mg/kg, or MJ-1999, 3 mg/kg. When the effects of autonomic nerves were eliminated, acetylstrophanthidin, 0.120 mg/kg, failed to cause slowing of sinus rate in the anesthetized cat and the anesthetized dog. Similarly, ouabain, 5 x 10-7M, and acetylstrophanthidin, 1.5 µg/ml, after prior administration of autonomic blocking agents failed to cause slowing of the isolated rabbit right atrium perfused with Tyrode's solution. These results indicate that the sinus slowing caused by cardiac glycosides may be mediated entirely by alteration of the neural control of the heart and that the drug, in nontoxic concentration, does not have a direct negative chronotropic action.
Experience: An Open Platform for Experimentation with Commercial Mobile Broadband Networks

Open experimentation with operational Mobile Broadband (MBB) networks in the wild is currently a fundamental requirement of the research community in its endeavor to address the need of innovative solutions for mobile communications. Even more, there is a strong need for objective data about stability and performance of MBB (e.g., 3G/4G) networks, and for tools that rigorously and scientifically assess their status. In this paper, we introduce the MONROE measurement platform: an open access and flexible hardware-based platform for measurements and custom experimentation on operational MBB networks. The MONROE platform enables accurate, realistic and meaningful assessment of the performance and reliability of 11 MBB networks in Europe. We report on our experience designing, implementing and testing the solution we propose for the platform. We detail the challenges we overcame while building and testing the MONROE testbed and argue our design and implementation choices accordingly. We describe and exemplify the capabilities of the platform and the wide variety of experiments that external users already perform using the system.
Thin film flow down a porous substrate in the presence of an insoluble surfactant: Stability analysis

The stability of a gravity-driven film flow on a porous inclined substrate is considered, when the film is contaminated by an insoluble surfactant, in the frame work of Orr-Sommerfeld analysis. The classical long-wave asymptotic expansion for small wave numbers reveals the occurrence of two modes, the Yih mode and the Marangoni mode for a clean/a contaminated film over a porous substrate and this is confirmed by the numerical solution of the Orr-Sommerfeld system using the spectral-Tau collocation method. The results show that the Marangoni mode is always stable and dominates the Yih mode for small Reynolds numbers; as the Reynolds number increases, the growth rate of the Yih mode increases, until, an exchange of stability occurs, and after that the Yih mode dominates. The role of the surfactant is to increase the critical Reynolds number, indicating its stabilizing effect. The growth rate increases with an increase in permeability, in the region where the Yih mode dominates the Marangoni mode. Also, the growth rate is more for a film (both clean and contaminated) over a thicker porous layer than over a thinner one. From the neutral stability maps, it is observed that the critical Reynolds number decreases with an increase in permeability in the case of a thicker porous layer, both for a clean and a contaminated film over it. Further, the range of unstable wave number increases with an increase in the thickness of the porous layer. The film flow system is more unstable for a film over a thicker porous layer than over a thinner one. However, for small wave numbers, it is possible to find the range of values of the parameters characterizing the porous medium for which the film flow can be stabilized for both a clean film/a contaminated film as compared to such a film over an impermeable substrate; further, it is possible to enhance the instability of such a film flow system outside of this stability window, for appropriate choices of the porous substrate characteristics.
Effects of prostaglandin E2 on p53 mRNA transcription and p53 mutagenesis during T‐cell‐independent human B‐cell clonal expansion

Within T‐cell‐dependent germinal centers, p53 gene transcription is repressed by Bcl‐6 and is thus less vulnerable to mutation. Malignant lymphomas within inflamed extranodal sites exhibit a relatively high incidence of p53 mutations. The latter might originate from normal B‐cell clones manifesting activation‐induced cytosine deaminase (AID) and up‐regulated p53 following T‐cell‐independent (TI) stimulation. We here examine p53 gene transcription in such TI clones, with a focus on modulatory effects of prostaglandin E2 (PGE2), and evaluate progeny for p53 mutations. Resting IgM+IgD+CD27‐ B cells from human tonsils were labeled with CFSE and stimulated in vitro with complement‐coated antigen surrogate, IL‐4, and BAFF ± exogenous PGE2 (50 nM) or an analog specific for the EP2 PGE2 receptor. We use flow cytometry to measure p53 and AID protein within variably divided blasts, qRT‐PCR of p53 mRNA from cultures with or without actinomycin D to monitor mRNA transcription/stability, and single‐cell p53 RT‐PCR/sequencing to assess progeny for p53 mutations. We report that EP2 signaling triggers increased p53 gene transcriptional activity in AID+ cycling blasts (P<0.01). Progeny exhibit p53 mutations at a frequency (8.5 × 10–4) greater than the baseline error rate (<0.8 × 10–4). We conclude that, devoid of the repressive influences of Bcl‐6, dividing B lymphoblasts in inflamed tissues should display heightened p53 transcription and increased risk of p53 mutagenesis. —Haque, S. , Yan, X. J., Rosen, L. , McCormick, S. , Chiorazzi, N. , Mongini, P. K. A. Effects of prostaglandin E2 on p53 mRNA transcription and p53 mutagenesis during T‐cell‐independent human B‐cell clonal expansion. FASEB J. 28, 627–643 (2014). www.fasebj. org
Timing of Peritoneal Dialysis Catheter Removal after Pediatric Renal Transplantation

Background A peritoneal dialysis (PD) catheter is in place at the time of kidney transplantation in children receiving PD. Removal of the catheter eliminates the risk of catheter-related infections. However, the patient benefits from leaving the catheter in place if dialysis is necessary posttransplantation. There is currently no consensus on the proper timing of PD catheter removal after kidney transplantation in children. Objective To identify the risks and benefits of an indwelling PD catheter after renal transplantation in children. Design Retrospective single-center study of infectious complications and posttransplantation PD catheter use in 31 renal transplantations in 26 children. Results Peritoneal dialysis catheters were used postoperatively in 13 of the 31 transplantations. In 12 instances the catheter was needed during the first month after transplantation, and 2 of the patients involved did not have a catheter in place when needed. Six catheter-related infections occurred in 5 patients posttransplantation, with only 1 infection taking place within 1 month after transplantation. Conclusion Our data suggest that the need for catheter use occurs predominantly during the first month, while infectious complications usually happen later. This strongly suggests that PD catheters should not be removed until approximately 1 month after kidney transplantation.