Miracle-dz/UniFAR-FTUs huggingface dataset:
Cooperation between Paxillin-like Protein Pxl1 and Glucan Synthase Bgs1 Is Essential for Actomyosin Ring Stability and Septum Formation in Fission Yeast

In fungal cells cytokinesis requires coordinated closure of a contractile actomyosin ring (CAR) and synthesis of a special cell wall structure known as the division septum. Many CAR proteins have been identified and characterized, but how these molecules interact with the septum synthesis enzymes to form the septum remains unclear. Our genetic study using fission yeast shows that cooperation between the paxillin homolog Pxl1, required for ring integrity, and Bgs1, the enzyme responsible for linear β(1,3)glucan synthesis and primary septum formation, is required for stable anchorage of the CAR to the plasma membrane before septation onset, and for cleavage furrow formation. Thus, lack of Pxl1 in combination with Bgs1 depletion, causes failure of ring contraction and lateral cell wall overgrowth towards the cell lumen without septum formation. We also describe here that Pxl1 concentration at the CAR increases during cytokinesis and that this increase depends on the SH3 domain of the F-BAR protein Cdc15. In consequence, Bgs1 depletion in cells carrying a cdc15ΔSH3 allele causes ring disassembly and septation blockage, as it does in cells lacking Pxl1. On the other hand, the absence of Pxl1 is lethal when Cdc15 function is affected, generating a large sliding of the CAR with deposition of septum wall material along the cell cortex, and suggesting additional functions for both Pxl1 and Cdc15 proteins. In conclusion, our findings indicate that CAR anchorage to the plasma membrane through Cdc15 and Pxl1, and concomitant Bgs1 activity, are necessary for CAR maintenance and septum formation in fission yeast.
Limb apraxia in acute ischemic stroke: A neglected clinical challenge?

Symptoms of limb apraxia and executive dysfunctions are currently not explicitly considered by the National Institutes of Health Stroke Scale and, thus, not routinely tested by clinicians in the acute care of patients with suspected stroke. Neuropsychological testing, clinical examination, MRI, and functional magnetic resonance imaging (fMRI) were performed in a right-handed patient with acute onset of left-sided sensorimotor hemiparesis due to a right hemisphere ischemic stroke. Deficits in the execution of meaningless and meaningful gestures were not detected properly on initial clinical examination but were revealed later on through neuropsychological testing. Instead, the patient’s inability to respond to specific instructions in the acute care setting was mistaken to reflect severe deficits in auditory comprehension. fMRI revealed right-hemispheric localization of language in the right-handed patient. We suggest including a bedside test for limb apraxia symptoms in acute clinical care of stroke patients. The distinction between deficits in limb praxis and impairments of language can be complicated owing to the common hemispheric co-localization of the two functions.
The Applications of Nanotechnology in Food Industry

Nanotechnology has the potential of application in the food industry and processing as new tools for pathogen detection, disease treatment delivery systems, food packaging, and delivery of bioactive compounds to target sites. The application of nanotechnology in food systems will provide new methods to improve safety and the nutritional value of food products. This article will review the current advances of applications of nanotechnology in food science and technology. Also, it describes new current food laws for nanofood and novel articles in the field of risk assessment of using nanotechnology in the food industry.
Information flow control for standard OS abstractions

Decentralized Information Flow Control (DIFC) is an approach to security that allows application writers to control how data flows between the pieces of an application and the outside world. As applied to privacy, DIFC allows untrusted software to compute with private data while trusted security code controls the release of that data. As applied to integrity, DIFC allows trusted code to protect untrusted software from unexpected malicious inputs. In either case, only bugs in the trusted code, which tends to be small and isolated, can lead to security violations. We present Flume, a new DIFC model that applies at the granularity of operating system processes and standard OS abstractions (e.g., pipes and file descriptors). Flume was designed for simplicity of mechanism, to ease DIFC's use in existing applications, and to allow safe interaction between conventional and DIFC-aware processes. Flume runs as a user-level reference monitor onLinux. A process confined by Flume cannot perform most system calls directly; instead, an interposition layer replaces system calls with IPCto the reference monitor, which enforces data flowpolicies and performs safe operations on the process's behalf. We ported a complex web application (MoinMoin Wiki) to Flume, changingonly 2% of the original code. Performance measurements show a 43% slowdown on read workloadsand a 34% slowdown on write workloads, which aremostly due to Flume's user-level implementation.
HGF Modulates Actin Cytoskeleton Remodeling and Contraction in Testicular Myoid Cells

The presence of the HGF/Met system in the testicular myoid cells was first discovered by our group. However, the physiological role of this pathway remains poorly understood. We previously reported that HGF increases uPA secretion and TGF-β activation in cultured tubular fragments and that HGF is maximally expressed at Stages VII–VIII of the seminiferous epithelium cycle, when myoid cell contraction occurs. It is well known that the HGF/Met pathway is involved in cytoskeletal remodeling; moreover, the interaction of uPA with its receptor, uPAR, as well as the activation of TGF-β have been reported to be related to the actin cytoskeleton contractility of smooth muscle cells. Herein, we report that HGF induces actin cytoskeleton remodeling in vitro in isolated myoid cells and myoid cell contraction in cultured seminiferous tubules. To better understand these phenomena, we evaluated: (1) the regulation of the uPA machinery in isolated myoid cells after HGF administration; and (2) the effect of uPA or Met inhibition on HGF-treated tubular fragments. Because uPA activates latent TGF-β, the secretion of this factor was also evaluated. We found that both uPA and TGF-β activation increase after HGF administration. In testicular tubular fragments, HGF-induced TGF-β activation and myoid cell contraction are abrogated by uPA or Met inhibitor administration.
Randomized Sorting as a Big Data Search Algorithm

A search problem may be formulated in which a goal state is sought, using comparisons of data elements against a large database to evaluate progress towards the goal. Given a big data aided algorithm for such a problem, we ask whether the algorithm converges to the desired goal, and if not, what can be said about the state at which the algorithm terminates. converges. To this end, we present a randomized sorting algorithm called consensus sorting, which makes use of queries to a large database of permutations. The algorithm refers decisions on randomly selected pairs of elements to the database, which uses a consensus of permutation scores to determine whether swapping is a good sorting decision. Depending on the scoring method used, the algorithm converges with differing degrees of sortedness. The convergence behavior is described, and an explanation of the behavior is formulated.
Automatic synthesis of control programs in polynomial time for an assembly line

The industry wants provably correct and fast formal methods for handling combinatorial dynamical systems. One example of such problems is error recovery in industrial processes. We have used a provably correct, polynomial-time planning algorithm to plan for a miniature assembly line, which assembles toy cars. Although somewhat limited, this process has many similarities with real industrial processes. By exploring the structure of this assembly line we have extended a previously presented algorithm, thus extending the class of problems that can be handled in polynomial time. The planning tool presented here contains general-purpose algorithms that generate plans in the form of GRAFCET charts that are automatically translated into PLC code using a commercial PLC compiler.
Learning humanoid motion dynamics through sensory-motor mapping in reduced dimensional spaces

Optimization of robot dynamics for a given human motion is an intuitive way to approach the problem of learning complex human behavior by imitation. In this paper, we propose a methodology based on a learning approach that performs optimization of humanoid dynamics in a low-dimensional subspace. We compactly represent the kinematic information of humanoid motion in a low dimensional subspace. Motor commands in the low dimensional subspace are mapped to the expected sensory feedback. We select optimal motor commands based on sensory-motor mapping that also satisfy our kinematic constraints. Finally, we obtain a set of novel postures that result in superior motion dynamics compared to the initial motion. We demonstrate results of the optimized motion on both a dynamics simulator and a real humanoid robot
Culturally sensitive and community-based HIV/AIDS prevention messages for African American women

African American women account for almost two thirds of all women living with HIV/AIDS in the United States. These epidemiological data highlight a critical need to develop intervention campaigns that communicate risk reduction strategies to this population. Using the framework of the Information-Motivation-Behavioral skills (IMB) model, the current study recruited African American women to view one of four brochures in which two experimental treatments were crossed: African American/individual prevention; Caucasian/individual prevention; African American/community prevention and Caucasian/community prevention. Attitude toward the message, risk perception, self-efficacy and community responsibility were measured through a survey questionnaire. Results showed that participants who viewed brochures featuring African American women displayed more favorable attitudes, increased selfefficacy, increased community responsibility and increased perceived risk for other African American women. The limitations of this study and implications for future research and development of HIV/AIDS prevention strategies are discussed.
Dynamics of Influenza Seasonality at Sub-Regional Levels in India and Implications for Vaccination Timing

Background Influenza surveillance is an important tool to identify emerging/reemerging strains, and defining seasonality. We describe the distinct patterns of circulating strains of the virus in different areas in India from 2009 to 2013. Methods Patients in ten cities presenting with influenza like illness in out-patient departments of dispensaries/hospitals and hospitalized patients with severe acute respiratory infections were enrolled. Nasopharangeal swabs were tested for influenza viruses by real-time RT-PCR, and subtyping; antigenic and genetic analysis were carried out using standard assays. Results Of the 44,127 ILI/SARI cases, 6,193 (14.0%) were positive for influenza virus. Peaks of influenza were observed during July-September coinciding with monsoon in cities Delhi and Lucknow (north), Pune (west), Allaphuza (southwest), Nagpur (central), Kolkata (east) and Dibrugarh (northeast), whereas Chennai and Vellore (southeast) revealed peaks in October-November, coinciding with the monsoon months in these cities. In Srinagar (Northern most city at 34°N latitude) influenza circulation peaked in January-March in winter months. The patterns of circulating strains varied over the years: whereas A/H1N1pdm09 and type B co-circulated in 2009 and 2010, H3N2 was the predominant circulating strain in 2011, followed by circulation of A/H1N1pdm09 and influenza B in 2012 and return of A/H3N2 in 2013. Antigenic analysis revealed that most circulating viruses were close to vaccine selected viral strains. Conclusions Our data shows that India, though physically located in northern hemisphere, has distinct seasonality that might be related to latitude and environmental factors. While cities with temperate seasonality will benefit from vaccination in September-October, cities with peaks in the monsoon season in July-September will benefit from vaccination in April-May. Continued surveillance is critical to understand regional differences in influenza seasonality at regional and sub-regional level, especially in countries with large latitude span.
Isolation and partial characterization of ΦSP‐1, a Salmonella specific lytic phage from intestinal content of broiler chicken

Salmonella enterica subsp. enterica serovar Enteritidis is a major causative agent of gastroenteritis with contaminated eggs and chicken meat being the major source of infection. Phages are seriously being considered as a safe and cheaper alternative to antibiotics. The intestinal content of chicken was used as source for isolating phages. Phage designated as ΦSP‐1 was selected for the study. Transmission electron microscopy (TEM) of phage ΦSP‐1 revealed that it belonged to family Podoviridae. The optimal multiplicity of infection (MOI) was 5 phages/cell. Latent and rise period were calculated to be 30 and 55 minutes respectively, while burst size was 44 phages/bacterial cell. The genome size of ΦSP‐1 was estimated to be 86 kb from pulsed‐field gel electrophoresis analysis (PFGE). The effect of different physical and chemical parameters like temperature, pH, salinity and CaCl2 were analyzed to optimize the conditions for large scale production of phages and to check the viability of ΦSP‐1 under different physiochemical conditions. A temperature of 40 °C, pH 8 and 0.25 M NaCl were found to be optimum for phage adsorption and it was able to survive up to a temperature of 50 °C for 3 min. Capability to survive under hostile environmental conditions, absence of virulence genes in genome and genus specificity suggest suitability of ΦSP‐1 to be used as a biocontrol agent.
Role for DNA Methylation in the Regulation of miR-200c and miR-141 Expression in Normal and Cancer Cells

Background The microRNA-200 family participates in the maintenance of an epithelial phenotype and loss of its expression can result in epithelial to mesenchymal transition (EMT). Furthermore, the loss of expression of miR-200 family members is linked to an aggressive cancer phenotype. Regulation of the miR-200 family expression in normal and cancer cells is not fully understood. Methodology/Principal Findings Epigenetic mechanisms participate in the control of miR-200c and miR-141 expression in both normal and cancer cells. A CpG island near the predicted mir-200c/mir-141 transcription start site shows a striking correlation between miR-200c and miR-141 expression and DNA methylation in both normal and cancer cells, as determined by MassARRAY technology. The CpG island is unmethylated in human miR-200/miR-141 expressing epithelial cells and in miR-200c/miR-141 positive tumor cells. The CpG island is heavily methylated in human miR-200c/miR-141 negative fibroblasts and miR-200c/miR-141 negative tumor cells. Mouse cells show a similar inverse correlation between DNA methylation and miR-200c expression. Enrichment of permissive histone modifications, H3 acetylation and H3K4 trimethylation, is seen in normal miR-200c/miR-141-positive epithelial cells, as determined by chromatin immunoprecipitation coupled to real-time PCR. In contrast, repressive H3K9 dimethylation marks are present in normal miR-200c/miR-141-negative fibroblasts and miR-200c/miR-141 negative cancer cells and the permissive histone modifications are absent. The epigenetic modifier drug, 5-aza-2′-deoxycytidine, reactivates miR-200c/miR-141 expression showing that epigenetic mechanisms play a functional role in their transcriptional control. Conclusions/Significance We report that DNA methylation plays a role in the normal cell type-specific expression of miR-200c and miR-141 and this role appears evolutionarily conserved, since similar results were obtained in mouse. Aberrant DNA methylation of the miR-200c/141 CpG island is closely linked to their inappropriate silencing in cancer cells. Since the miR-200c cluster plays a significant role in EMT, our results suggest an important role for DNA methylation in the control of phenotypic conversions in normal cells.
Digital Scholarship and Disciplinary Culture: An Investigation of Sultan Qaboos University, Oman

The emergence of networked information and communication has transformed the accessibility and delivery of scholarly information and fundamentally impacted on the processes of research and scholarly communication. The purpose of this study is to investigate disciplinary differences in the use of networked information for research and scholarly communication at Sultan Qaboos University, Oman. This study has produced quantitative data about how and why academics within different disciplines utilize networked information that is made available either internally through the university library, or externally through networked services accessed by the Internet. The results indicate some significant differences between the attitudes and practice of academics in the science disciplines when compared to those from the social sciences and humanities. While respondents from science disciplines show overall longer and more frequent use of networked information, respondents from humanities and social sciences indicated more positive attitudes and a greater degree of satisfaction toward library networked services. Keywords—Academics, Arab World, Disciplinary Culture, Networked Information, Scholarly Communication, Sultan Qaboos University, Oman.
Enhancing co-design reliability by inter-organizational learning and loose coupling concepts

The aim of this article is to enable actors of different organizations to self-adapt, to self-organize and, in fine, to make functional and structural improvements together. We examine formal cooperative processes and informal cooperative practices which are expressions of tight and loose couplings within a complex socio-technical system. We use a systemic approach to understand close relations between loose couplings and their potential outcomes (in terms of organizational learning, cooperative effect and consequences). We propose a co-design reliability model which enables us to better understand intra- and inter-organizational learning during cooperative actions. Our findings confirm that loose couplings are crucial in complex organizations. Loose couplings enhance the reliability of co-design operations by enabling informal cooperative practices which often underlie the success of formal cooperative processes. Our future work will be to test the impact of enhancements to co-design operations through the application of newly developed material and process artefacts informed by the holistic understanding of cooperative actions.
Does the Impact of the Type of Anesthesia on Outcomes Differ by Patient Age and Comorbidity Burden?

Introduction Neuraxial anesthesia may provide perioperative outcome benefits versus general anesthesia in orthopedic surgical patients. As subgroup analyses are lacking, we evaluated the influence of the type of anesthesia on outcomes in patient groups of different age and the presence of cardiopulmonary disease. Methods Data from approximately 500 hospitals in the United States regarding total hip and total knee arthroplasties performed between 2006 and 2012 were accessed. Patients were categorized by age (ie, <65, 65–74, or ≥75 years) as well as the presence of cardiopulmonary disease. Resulting groups were compared with regard to patient, hospital, procedure, and comorbidity-related variables, as well as incidence of major perioperative complications. A multivariable logistic regression analysis was performed to assess the independent influence of the type of anesthesia on complications within each patient subgroup. Results We identified 795,135 records of patients who underwent total hip arthroplasty or total knee arthroplasty. The incidence of major complications was highest in the oldest patient group with cardiopulmonary disease (26.1%) and the lowest in the youngest group without cardiopulmonary disease (4.5%). Multivariable logistic regressions showed that neuraxial anesthesia was associated with decreased odds for combined major complications, need for intensive care services, and prolonged length of stay compared with general anesthesia in all patient subgroups. For patients without major cardiopulmonary comorbidities, the positive impact of neuraxial anesthesia increased with increasing age. Conclusions Neuraxial anesthesia is associated with decreased odds for major complications and resource utilization after joint arthroplasty for all patient groups, irrespective of age and comorbidity burden.
Linguistic representation of Finnish in a limited domain speech-to-speech translation system

This paper describes the development of Finnish linguistic resources for use in MedSLT, an Open Source medical domain speech-to-speech translation system. The paper describes the collection of the medical sub-domain corpora for Finnish, the creation of the Finnish generation grammar by adapting the original English grammar, the composition of the domain specific Finnish lexicon and the definition of interlingua to Finnish mapping rules for multilingual translation. It is shown that Finnish can be effectively introduced into the existing MedSLT framework and that despite the differences between English and Finnish, the Finnish grammar can be created by manual adaptation from the original English grammar. An initial evaluation of English to Finnish speech-to-speech translation is also presented.
Query Optimization for Parallel Execution

Parallel query processing has received a lot of attention in the database community because customer applications on databases are growing in size and complexity with an ever increasing demand for performance. The main objective of parallel query processing is to achieve speedup, scaleup and high throughput. Parallel machines are necessary for achieving the speedup, however eecient resource utilization and workload scheduling is crucial for maximizing throughput of database systems. Query optimization is identi-ed as the most important aspect in achieving this objective, and so will be the main topic of this study. Query Optimization basically deals with exploiting the inherent parallelism available in queries. We study the diierent forms of parallelism that have been addressed in literature and comment on the suitability of each. Query optimizers are used to generate query evaluation plans for parallel execution of queries by identifying the diierent forms of parallelism, i.e., inter-query, intra-query and a combination of both. The other issues related to database system performance such as degree of parallelism, query scheduling and workload scheduling are discussed in context of dynamic query optimization, wherein the query optimizer prepares query evaluation plans containing enough information to take decisions dynamically at run time.
An Algorithm for Improving Non-Local Means Operators via Low-Rank Approximation

We present a method for improving a non-local means (NLM) operator by computing its low-rank approximation. The low-rank operator is constructed by applying a filter to the spectrum of the original NLM operator. This results in an operator, which is less sensitive to noise while preserving important properties of the original operator. The method is efficiently implemented based on Chebyshev polynomials and is demonstrated on the application of natural images denoising. For this application, we provide a comparison of our method with other denoising methods.