Miracle-dz/UniFAR-FTUs huggingface dataset:
Extensive Genetic Diversity Identified Among Sporadic Methicillin-2 Resistant Staphylococcus aureus Isolates Recovered in Irish 3 Hospitals Between 2000-2012 4 5 6

6 Peter M. Kinnevey, Anna C. Shore, Grainne I. Brennan, Derek J. Sullivan, Ralf 7 Ehricht, Stefan Monecke, David C. Coleman 8 Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity 9 College Dublin, Ireland. Department of Clinical Microbiology, School of Medicine, University 10 of Dublin, Trinity College, St. James’s Hospital, Dublin 8, Ireland, National MRSA Reference 11 Laboratory, St. James's Hospital, James's St., Dublin 8, Ireland, Alere Technologies GmbH, 12 Jena, Germany. Institute for Medical Microbiology and Hygiene, Faculty of Medicine "Carl 13 Gustav Carus", Technical University of Dresden, Germany. 14 15
Type of vegetable oils used in cooking and risk of metabolic syndrome among Asian Indians

There is little data on the type of vegetable oil used and the prevalence of metabolic syndrome (MS) in Asian Indians. Food frequency questionnaire was used to document the type of cooking oil in 1875 adults in Chennai city. MS was assessed by new harmonizing criteria. The prevalence of MS was higher among sunflower oil users (30.7%) than palmolein (23.2%) and traditional oil (17.1%, p < 0.001) users. The higher prevalence of MS in sunflower oil group persisted even when stratified according to body mass index, except in obese groups. The risk of MS was further compounded by quantity of refined cereals consumed. Higher LA%E and linoleic acid/alpha-linolenic acid ratio in sunflower oil probably contributes to increased risk of MS.
Self-optimizing autonomic control of geographically distributed collaboration applications

In the past few years, cloud computing has become an integral technology both for the day to day running of corporations, as well as in everyday life as more services are offered which use a backend cloud. At the same time online collaboration tools are becoming more important as both businesses and individuals need to share information and collaborate with other entities. Previous work has presented an architecture for a collaboration online application which allows users in different locations to share videos, images and documents while at the same time video chatting. The application's servers are deployed in a cloud environment which can scale up and down based on demand. Furthermore, the design allows the application to be deployed on multiple clouds which are deployed in different geographic locations. Previous work however did not introduce how the application's up and down scaling is to be achieved. In this paper the autonomic system which manages the self-optimizing function of the cloud is presented. The autonomic system itself is a self-organizing system with a control model based on the leaky-bucket theory often used in network congestion control. A testbed for the collaboration application is used in order to gather performance metrics for the model.
Comparative Analysis of Viterbi Training and Maximum Likelihood Estimation for HMMs

We present an asymptotic analysis of Viterbi Training (VT) and contrast it with a more conventional Maximum Likelihood (ML) approach to parameter estimation in Hidden Markov Models. While ML estimator works by (locally) maximizing the likelihood of the observed data, VT seeks to maximize the probability of the most likely hidden state sequence. We develop an analytical framework based on a generating function formalism and illustrate it on an exactly solvable model of HMM with one unambiguous symbol. For this particular model the ML objective function is continuously degenerate. VT objective, in contrast, is shown to have only finite degeneracy. Furthermore, VT converges faster and results in sparser (simpler) models, thus realizing an automatic Occam's razor for HMM learning. For more general scenario VT can be worse compared to ML but still capable of correctly recovering most of the parameters.
Reverse Cholesterol Transport Revisited: Contribution of Biliary Versus Intestinal Cholesterol Excretion

Reverse cholesterol transport (RCT) is usually defined as high-density lipoprotein-mediated transport of excess cholesterol from peripheral tissues, including cholesterol-laden macrophages in vessel walls, to the liver. From the liver, cholesterol can then be removed from the body via secretion into the bile for eventual disposal via the feces. According to this paradigm, high plasma high-density lipoprotein levels accelerate RCT and hence are atheroprotective. New insights in individual steps of the RCT pathway, in part derived from innovative mouse models, indicate that the classical concept of RCT may require modification.
Organization of the pallium in the fire‐bellied toad Bombina orientalis. I: Morphology and axonal projection pattern of neurons revealed by intracellular biocytin labeling

The cytoarchitecture and axonal projection pattern of pallial areas was studied in the fire‐bellied toad Bombina orientalis by intracellular injection of biocytin into a total of 326 neurons forming 204 clusters. Five pallial regions were identified, differing in morphology and projection pattern of neurons. The rostral pallium receiving the bulk of dorsal thalamic afferents has reciprocal connections with all other pallial areas and projects to the septum, nucleus accumbens, and anterior dorsal striatum. The medial pallium projects bilaterally to the medial pallium, septum, nucleus accumbens, mediocentral amygdala, and hypothalamus and ipsilaterally to the rostral, dorsal, and lateral pallium. The ventral part of the medial pallium is distinguished by efferents to the eminentia thalami and the absence of contralateral projections. The dorsal pallium has only ipsilateral projections running to the rostral, medial, and lateral pallium; septum; nucleus accumbens; and eminentia thalami. The lateral pallium has ipsilateral projections to the olfactory bulbs and to the rostral, medial, dorsal, and ventral pallium. The ventral pallium including the striatopallial transition area (SPTA) has ipsilateral projections to the olfactory bulbs, rostral and lateral pallium, dorsal striatopallidum, vomeronasal amygdala, and hypothalamus. The medial pallium can be tentatively homologized with the mammalian hippocampal formation, the dorsal pallium with allocortical areas, the lateral pallium rostrally with the piriform and caudally with the entorhinal cortex, the ventral pallium with the accessory olfactory amygdala. The rostral pallium, with its projections to the dorsal and ventral striatopallidum, resembles the mammalian frontal cortex. J. Comp. Neurol. 501:443–464, 2007. © 2007 Wiley‐Liss, Inc.
Alternate Strategies for a Win-Win Seeking Agent in Agent-Human Negotiations

With the growth of e-commerce and e-markets, there is an increasing potential for the use of software agents to negotiate business tasks with human negotiators. Guided by design science methodology, this research prescribes and validates a win-win seeking negotiation agent using strategies of "simultaneous-equivalent offers" and "delayed acceptance" and compares their effects against the use of conventional sequential-single offer and immediate acceptance strategies. To evaluate the alternate strategies, a negotiation agent system was implemented and an experiment was conducted in which 110 agent-human dyads negotiated over a four-issue online purchase task. Our results indicate that the proposed agent strategies can enhance the economic performance of the negotiated outcome (counterpart agreement ratio, individual utility, joint utility, and the distance to Pareto-efficient frontier) and maintain the human counterparts' positive perceptions toward the outcome and the agent. The findings confirm the efficacy of the proposed design and showcase an innovative system to facilitate e-commerce transactions.
Modulation of Aspergillus awamori Thaumatin Secretion by Modification of bipA Gene Expression

ABSTRACT Two different strains, Aspergillus awamori TGDTh-4 and A. awamori TGP-3 overexpressing a synthetic gene encoding the plant sweet protein thaumatin, showed an unfolded protein response. To facilitate protein secretion, the chaperone BiPA gene was expressed in A. awamori under control of the strong constitutive promoter of the gpdA gene. A good correlation was observed between the level of the bipA transcript in different strains and the amount of thaumatin secreted. Thaumatin secretion was increased 2- to 2.5-fold in transformants overexpressing the bipA gene compared with the parental strain. Secretion of the homologous proteins α-amylase and glucoamylase was not affected by the bipA gene overexpression. The requirement for BiPA for secretion of thaumatin was confirmed by attenuation of the endogenous bipA gene expression with an antisense RNA cassette. The decrease in bipA expression reduced the amount of secreted thaumatin up to 80% without affecting the secretion of the homologous α-amylase and glucoamylase proteins. The BiPA protein is, therefore, very important for secretion of some heterologous proteins, such as thaumatin in A. awamori.
Parkinson's Disease DJ-1 L166P Alters rRNA Biogenesis by Exclusion of TTRAP from the Nucleolus and Sequestration into Cytoplasmic Aggregates via TRAF6

Mutations in PARK7/DJ-1 gene are associated to autosomal recessive early onset forms of Parkinson's disease (PD). Although large gene deletions have been linked to a loss-of-function phenotype, the pathogenic mechanism of missense mutations is less clear. The L166P mutation causes misfolding of DJ-1 protein and its degradation. L166P protein may also accumulate into insoluble cytoplasmic aggregates with a mechanism facilitated by the E3 ligase TNF receptor associated factor 6 (TRAF6). Upon proteasome impairment L166P activates the JNK/p38 MAPK apoptotic pathway by its interaction with TRAF and TNF Receptor Associated Protein (TTRAP). When proteasome activity is blocked in the presence of wild-type DJ-1, TTRAP forms aggregates that are localized to the cytoplasm or associated to nucleolar cavities, where it is required for a correct rRNA biogenesis. In this study we show that in post-mortem brains of sporadic PD patients TTRAP is associated to the nucleolus and to Lewy Bodies, cytoplasmic aggregates considered the hallmark of the disease. In SH-SY5Y neuroblastoma cells, misfolded mutant DJ-1 L166P alters rRNA biogenesis inhibiting TTRAP localization to the nucleolus and enhancing its recruitment into cytoplasmic aggregates with a mechanism that depends in part on TRAF6 activity. This work suggests that TTRAP plays a role in the molecular mechanisms of both sporadic and familial PD. Furthermore, it unveils the existence of an interplay between cytoplasmic and nucleolar aggregates that impacts rRNA biogenesis and involves TRAF6.
Therapeutic options in the management of acromegaly: focus on lanreotide Autogel®

Background In acromegaly, expert surgery is curative in only about 60% of patients. Postoperative radiation therapy is associated with a high incidence of hypopituitarism and its effect on growth hormone (GH) production is slow, so that adjuvant medical treatment becomes of importance in the management of many patients. Objective To delineate the role of lanreotide in the treatment of acromegaly. Methods Search of Medline, Embase, and Web of Science databases for clinical studies of lanreotide in acromegaly. Results Treatment with lanreotide slow release and lanreotide Autogel® normalized GH and insulin-like growth factor-I (IGF-I) concentrations in about 50% of patients. The efficacy of 120 mg lanreotide Autogel® on GH and IGF-I levels was comparable with that of 20 mg octreotide LAR. There were no differences in improvement of cardiac function, decrease in pancreatic β-cell function, or occurrence of side effects, including cholelithiasis, between octreotide LAR and lanreotide Autogel®. When postoperative treatment with somatostatin analogs does not result in normalization of serum IGF-I and GH levels after noncurative surgery, pegvisomant alone or in combination with somatostatin analogs can control these levels in a substantial number of patients.
De-SAG: On the De-Anonymization of Structure-Attribute Graph Data

In this paper, we study the impacts of non-Personal Identifiable Information (non-PII) on the privacy of graph data with attribute information (e.g., social networks data with users’ profiles (attributes)), namely Structure-Attribute Graph (SAG) data, both theoretically and empirically. Our main contributions are two-fold: (i) we conduct the first attribute-based anonymity analysis for SAG data under both preliminary and general models. By careful quantification, we obtain the explicit correlation between the graph anonymity and the attribute information. We also validate our analysis through numerical and real world data-based evaluations and the results indicate that the non-PII can also lead to significant anonymity loss; and (ii) according to our theoretical analysis, we propose a new de-anonymization framework for SAG data, namely De-SAG, which takes into account both the graph structure and the attribute information to the best of our knowledge. By extensive experiments, we demonstrate that De-SAG can significantly improve the performance of state-of-the-art graph de-anonymization attacks. Our attribute-based anonymity analysis and de-anonymization framework are expected to provide data owners and researchers a more complete understanding on the privacy vulnerability of graph data, and thus shed light on future graph anonymization and de-anonymization research.
Heuristic-based semantic query optimization

An implementation of a heuristic-based semantic query optimizer generator that uses a set of semantic transformation heuristics to produce an executable optimizer is described. This generator can also be used to construct optimizers that perform both semantic and conventional optimization. The use of contradictions and tautologies to provide solutions to queries without accessing the database is examined. Some experimental results using a working optimizer and a sample database are given. The results demonstrate the effectiveness of semantic query optimization using actual system performance. <<ETX>>
Territoriality in collaborative tabletop workspaces

Researchers seeking alternatives to traditional desktop computers have begun exploring the potential collaborative benefits of digital tabletop displays. However, there are still many open issues related to the design of collaborative tabletop interfaces, such as whether these systems should automatically orient workspace items or enforce ownership of workspace content. Understanding the natural interaction practices that people use during tabletop collaboration with traditional media (e.g., pen and paper) can help to address these issues. Interfaces that are modeled on these practices will have the additional advantage of supporting the interaction skills people have developed over years of collaborating at traditional tables. To gain a deeper understanding of these interaction practices we conducted two observational studies of traditional tabletop collaboration in both casual and formal settings. Our results reveal that collaborators use three types of tabletop territories to help coordinate their interactions within the shared tabletop workspace: personal, group, and storage territories. Findings from a spatial analysis of collaborators' tabletop interactions reveal important properties of these tabletop territories. In order to provide a comprehensive picture of the role of tabletop territoriality in collaboration, we conclude with a synthesis of our findings and previous research findings and with several relevant design implications.
The RMS survey: radio observations of candidate massive YSOs in the southern hemisphere

Abstract The Red MSX Source (RMS) survey (Hoare et al. 2005) is a multi-wavelength programme of follow-up observations designed to distinguish between genuine massive young stellar objects (MYSOs) and other embedded or dusty objects, such as ultra compact (UC) HII regions, evolved stars and planetary nebulae (PNe). We have identified nearly 2000 MYSOs candidates by comparing the colours of MSX and 2MASS point sources to those of known MYSOs. There are several other types of embedded or dust enshrouded objects that have similar colours as MYSOs and contaminate our sample. Two sources of contamination are from UCHII regions and PNe, both of which can be identified from the radio emission emitted by their ionised nebulae. In order to identify UCHII regions and PNe that contaminate our sample we have conducted high resolution radio continuum observations at 3.6 and 6 cm of all southern MYSOs candidates (235° < l < 350°) using the Australia Telescope Compact Array (ATCA).
Coordinated sensor deployment for improving secure communications and sensing coverage

Sensor network has a great potential in applications such as habitat monitoring, wildlife tracking, building surveillance, and military combat. The design of a sensor network system involves several important issues, including the sensing coverage, node-to-node or node-to-base-station communications, and the security in information gathering and relay by the sensors. In this paper, we show that the system performance on these aspects depends closely on how the sensors are deployed in the field, and on how the sensor locations can be adjusted after the initial deployment. For static sensor deployment, we investigate the hexagon and square lattice topology and analyze their impact on secure connectivity and sensing coverage. For advanced sensing devices that allow for location adjustment after deployment, we have established a new framework for coordinated updates of sensor locations. We propose two new sensor location updating algorithms, the VFSec and the Weighted Centroid algorithm, to jointly optimize sensing coverage and secure connectivity. Simulation results show that these new algorithms provide superior tradeoff over the existing approaches that do not take security into considerations.
Ambiguity attitudes: An experimental investigation

This paper reports the results of experiments designed to test (a) whether and to what extent individuals display non-neutral ambiguity attitudes in their choice behavior and (b) if and how do ambiguity attitudes change as a result of interpersonal interactions and persuation. To address the first question we designed and conducted experiments involving individual choice between betting on ambiguous and unambiguous events of their choice. We found that a large majority of subjects display ambiguityneutral attitudes, many others display ambiguity-incoherent attitudes, and few subjects display either ambiguity-averse attitudes or ambiguity-seeking attitudes. To address the second question we introduced a new experimental design with a built-in incentive to persuade. We found that interpersonal interactions without incentive to persuade have no effect on behavior, but when incentives were introduced, the ambiguity-neutral subjects were better able to persuade ambiguity seeking and ambiguity-incoherent subjects to follow ambiguity-neutral choice behavior. No such influence was detected with respect to ambiguity-neutral subjects.
The Relationship Between Long-Range Chromatin Occupancy and Polymerization of the Drosophila ETS Family Transcriptional Repressor Yan

ETS family transcription factors are evolutionarily conserved downstream effectors of Ras/MAPK signaling with critical roles in development and cancer. In Drosophila, the ETS repressor Yan regulates cell proliferation and differentiation in a variety of tissues; however, the mechanisms of Yan-mediated repression are not well understood and only a few direct target genes have been identified. Yan, like its human ortholog TEL1, self-associates through an N-terminal sterile α-motif (SAM), leading to speculation that Yan/TEL1 polymers may spread along chromatin to form large repressive domains. To test this hypothesis, we created a monomeric form of Yan by recombineering a point mutation that blocks SAM-mediated self-association into the yan genomic locus and compared its genome-wide chromatin occupancy profile to that of endogenous wild-type Yan. Consistent with the spreading model predictions, wild-type Yan-bound regions span multiple kilobases. Extended occupancy patterns appear most prominent at genes encoding crucial developmental regulators and signaling molecules and are highly conserved between Drosophila melanogaster and D. virilis, suggesting functional relevance. Surprisingly, although occupancy is reduced, the Yan monomer still makes extensive multikilobase contacts with chromatin, with an overall pattern similar to that of wild-type Yan. Despite its near-normal chromatin recruitment, the repressive function of the Yan monomer is significantly impaired, as evidenced by elevated target gene expression and failure to rescue a yan null mutation. Together our data argue that SAM-mediated polymerization contributes to the functional output of the active Yan repressive complexes that assemble across extended stretches of chromatin, but does not directly mediate recruitment to DNA or chromatin spreading.
Gamma regression of interevent waiting times versus poisson regression of daily event counts: inside the epidemiologist's toolbox-selecting the best modeling tools for the job.

In this issue of EPIDEMIOLOGY, Checkley et al introduced what may be a new analytic tool for epidemiologists called gamma regression for the analysis of the determinants of the lengths of waiting times between subsequent events in a sparse time-series. This model is well known in survival analyses and in econometrics, but a recent search of the PubMed data base yielded only 4 hits for (epidemiology AND “gamma regression”). Gamma regression is typically used in survival analyses when trying to explain a distribution of waiting times (or counts) with a long tail. Gamma regression allows models to fit a distinct parameter for the variance of the counts that does not need to be related to the mean. In the present analysis, the time units are the discrete numerical count of days between discrete hospital admissions for Kawasaki disease. Although this conceptualization focuses on the times between events, the same time-series can also be assessed for the determinants of the count of daily events using Poisson regression. Such models are routinely used in air pollution epidemiology to assess the impact of pollutants and meteorological conditions on the risks of morbidity or mortality based on the number of daily adverse events in a time-series. The authors’ juxtaposition of results between a gamma regression analysis of the waiting times between sparse events, and a corresponding Poisson regression analysis of the daily event counts in the Checkley et al article provides an opportunity to consider the potential advantages of each method.
Application of metaheuristic methods to reactive power planning: a comparative study for GA, PSO and EPSO

This paper proposes the application of metaheuristic methods to Reactive Power Planning (RPP). RPP involves optimal allocation of reactive sources to satisfy voltage constraints during normal and contingency states. The main objective of the proposed RPP is to make a trade-off between economy and security by determining the optimal combination of fast and slow controls (load shedding, new slow and fast VAR devices). The overall problem is formulated as a large scale mixed integer nonlinear programming problem. The proposed RPP problem is a combinatorial optimization problem, which cannot be solved easily by conventional optimization methods. Metaheuristic methods are reported to be efficient to solve combinatorial optimization problems. Among the well-known metaheuristic methods, this paper discovers the efficiency of Genetic Algorithm (GA), Particle Swarm Optimization (PSO) and Evolutionary PSO (EPSO) in solving the proposed RPP problem. The proposed approaches have been successfully tested on IEEE 14 bus system and a comparative study is illustrated.