Miracle-dz/UniFAR-FTUs huggingface dataset:
A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury

The multifactorial nature of traumatic brain injury (TBI), especially the complex secondary tissue injury involving intertwined networks of molecular pathways that mediate cellular behavior, has confounded attempts to elucidate the pathology underlying the progression of TBI. Here, systems biology strategies are exploited to identify novel molecular mechanisms and protein indicators of brain injury. To this end, we performed a meta‐analysis of four distinct high‐throughput gene expression studies involving different animal models of TBI. By using canonical pathways and a large human protein‐interaction network as a scaffold, we separately overlaid the gene expression data from each study to identify molecular signatures that were conserved across the different studies. At 24 hr after injury, the significantly activated molecular signatures were nonspecific to TBI, whereas the significantly suppressed molecular signatures were specific to the nervous system. In particular, we identified a suppressed subnetwork consisting of 58 highly interacting, coregulated proteins associated with synaptic function. We selected three proteins from this subnetwork, postsynaptic density protein 95, nitric oxide synthase 1, and disrupted in schizophrenia 1, and hypothesized that their abundance would be significantly reduced after TBI. In a penetrating ballistic‐like brain injury rat model of severe TBI, Western blot analysis confirmed our hypothesis. In addition, our analysis recovered 12 previously identified protein biomarkers of TBI. The results suggest that systems biology may provide an efficient, high‐yield approach to generate testable hypotheses that can be experimentally validated to identify novel mechanisms of action and molecular indicators of TBI. © 2014 Wiley Periodicals, Inc.
Control of Aflatoxin Production of Aspergillus flavus and Aspergillus parasiticus Using RNA Silencing Technology by Targeting aflD (nor-1) Gene

Aspergillus ﬂavus and Aspergillus parasiticus are important pathogens of cotton, corn, peanuts and other oil-seed crops, producing toxins both in the field and during storage. We have designed three siRNA sequences (Nor-Ia, Nor-Ib, Nor-Ic) to target the mRNA sequence of the aflD gene to examine the potential for using RNA silencing technology to control aflatoxin production. Thus, the effect of siRNAs targeting of two key genes in the aflatoxin biosynthetic pathway, aflD (structural) and aflR (regulatory gene) and on aflatoxin B1 (AFB1), and aflatoxin G1 (AFG1) production was examined. The study showed that Nor-Ib gave a significant decrease in aflD mRNA, aflR mRNA abundance, and AFB1 production (98, 97 and 97% when compared to the controls) in A. flavus NRRL3357, respectively. Reduction in aflD and aflR mRNA abundance and AFB1 production increased with concentration of siRNA tested. There was a significant inhibition in aflD and AFB1 production by A. flavus EGP9 and AFG1 production by A. parasiticus NRRL 13005. However, there was no significant decrease in AFG1 production by A. parasiticus SSWT 2999. Changes in AFB1 production in relation to mRNA levels of aflD showed a good correlation (R = 0.88; P = 0.00001); changes in aflR mRNA level in relation to mRNA level of aflD also showed good correlation (R = 0.82; P = 0.0001). The correlations between changes in aflR and aflD gene expression suggests a strong relationship between these structural and regulatory genes, and that aflD could be used as a target gene to develop efficient means for aflatoxin control using RNA silencing technology.
GridCast: Improving peer sharing for P2P VoD

Video-on-Demand (VoD) is a compelling application, but costly. VoD is costly due to the load it places on video source servers. Many have proposed using peer-to-peer (P2P) techniques to shift load from servers to peers. Yet, nobody has implemented and deployed a system to openly and systematically evaluate how these techniques work. This article describes the design, implementation and evaluation of GridCast, a real deployed P2P VoD system. GridCast has been live on CERNET since May of 2006. It provides seek, pause, and play operations, and employs peer sharing to improve system scalability. In peak months, GridCast has served videos to 23,000 unique users. From the first deployment, we have gathered information to understand the system and evaluate how to further improve peer sharing through caching and replication. We first show that GridCast with single video caching (SVC) can decrease load on source servers by an average of 22% from a client-server architecture. We analyze the net effect on system resources and determine that peer upload is largely idle. This leads us to changing the caching algorithm to cache multiple videos (MVC). MVC decreases source load by an average of 51% over the client-server. The improvement is greater as user load increases. This bodes well for peer-assistance at larger scales. A detailed analysis of MVC shows that departure misses become a major issue in a P2P VoD system with caching optimization. Motivated by this observation, we examine how to use replication to eliminate departure misses and further reduce server load. A framework for lazy replication is presented and evaluated in this article. In this framework, two predictors are plugged in to create the working replication algorithm. With these two simple predictors, lazy replication can decrease server load by 15% from MVC with only a minor increase in network traffic.
Combined Effect of Levels in Personal Self-Regulation and Regulatory Teaching on Meta-Cognitive, on Meta-Motivational, and on Academic Achievement Variables in Undergraduate Students

The Theory of Self- vs. Externally-Regulated Learning™ (SRL vs. ERL) proposed different types of relationships among levels of variables in Personal Self-Regulation (PSR) and Regulatory Teaching (RT) to predict the meta-cognitive, meta-motivational and -emotional variables of learning, and of Academic Achievement in Higher Education. The aim of this investigation was empirical in order to validate the model of the combined effect of low-medium-high levels in PSR and RT on the dependent variables. For the analysis of combinations, a selected sample of 544 undergraduate students from two Spanish universities was used. Data collection was obtained from validated instruments, in Spanish versions. Using an ex-post-facto design, different Univariate and Multivariate Analyses (3 × 1, 3 × 3, and 4 × 1) were conducted. Results provide evidence for a consistent effect of low-medium-high levels of PSR and of RT, thus giving significant partial confirmation of the proposed rational model. As predicted, (1) the levels of PSR and positively and significantly effected the levels of learning approaches, resilience, engagement, academic confidence, test anxiety, and procedural and attitudinal academic achievement; (2) the most favorable type of interaction was a high level of PSR with a high level RT process. The limitations and implications of these results in the design of effective teaching are analyzed, to improve university teaching-learning processes.
Project Management within Virtual Software Teams

When implementing software development in a global environment, a popular strategy is the establishment of virtual teams. The objective of this paper is to examine the effective project management of this type of team. In the virtual team environment problems arise due to the collaborative nature of software development and the impact distance introduces. Distance specifically impacts coordination, visibility, communication and cooperation within a virtual team. In these circumstances the project management of a virtual team must be carried out in a different manner to that of a team in a single-site location. Results from this research highlighted six specific project management related areas that need to be addressed to facilitate successful virtual team operation. Organizational structure, risk management, infrastructure, process, conflict management and team structure and organization. Additional related areas are the sustained support of senior management and the provision of effective infrastructure
Up-Regulation of Endothelial Delta-like 4 Expression Correlates with Vessel Maturation in Bladder Cancer

Purpose: Angiogenesis and vascular endothelial growth factor (VEGF) expression are associated with a poor outcome in bladder cancer. To understand more about the mechanisms, we studied the role of delta-like 4 (DLL4), an endothelial-specific ligand of the Notch signaling pathway, in bladder cancer angiogenesis. Experimental Design: The expression of DLL4, CD34, and VEGF were studied in a cohort of 60 bladder tumors and 10 normal samples using quantitative PCR. In situ hybridization was used to study the pattern of DLL4 expression in 22 tumor and 9 normal samples. Serial sections were also stained for CD34 and α-smooth muscle actin (α-SMA) using conventional immunohistochemistry. Results: The expression of DLL4 was significantly up-regulated in superficial (P < 0.01) and invasive (P < 0.05) bladder cancers. DLL4 expression significantly correlated with CD34 (P < 0.001) and VEGF (P < 0.001) expression. The in situ hybridization studies showed that DLL4 was highly expressed within bladder tumor vasculature. Additionally, DLL4 expression significantly correlated with vessel maturation as judged by periendothelial cell expression of α-SMA, 98.7% of DLL4-positive tumor vessels coexpressed α-SMA, compared with 64.5% of DLL4-negative tumor vessels (P < 0.001). High DLL4 expression may have prognostic value in superficial and invasive bladder. Conclusion: DLL4 expression is associated with vascular differentiation in bladder cancer; thus, targeting DLL4 may be a novel antiangiogenic therapy.
Lift: Multi-Label Learning with Label-Specific Features

Multi-label learning deals with the problem where each example is represented by a single instance (feature vector) while associated with a set of class labels. Existing approaches learn from multi-label data by manipulating with identical feature set, i.e. the very instance representation of each example is employed in the discrimination processes of all class labels. However, this popular strategy might be suboptimal as each label is supposed to possess specific characteristics of its own. In this paper, another strategy to learn from multi-label data is studied, where label-specific features are exploited to benefit the discrimination of different class labels. Accordingly, an intuitive yet effective algorithm named LIFT, i.e. multi-label learning with Label specific Features, is proposed. LIFT firstly constructs features specific to each label by conducting clustering analysis on its positive and negative instances, and then performs training and testing by querying the clustering results. Comprehensive experiments on a total of 17 benchmark data sets clearly validate the superiority of LIFT against other well-established multi-label learning algorithms as well as the effectiveness of label-specific features.
HIV and Hepatitis C Mortality in Massachusetts, 2002–2011: Spatial Cluster and Trend Analysis of HIV and HCV Using Multiple Cause of Death

Background Infectious diseases, while associated with a much smaller proportion of deaths than they were 50 years ago, still play a significant role in mortality across the state of Massachusetts. Most analysis of infectious disease mortality in the state only take into account the underlying cause of death, rather than contributing causes of death, which may not capture the full extent of mortality trends for infectious diseases such as HIV and the Hepatitis C virus (HCV). Methods In this study we sought to evaluate current trends in infectious disease mortality across the state using a multiple cause of death methodology. We performed a mortality trend analysis, identified spatial clusters of disease using a 5-step geoprocessing approach and examined spatial-temporal clustering trends in infectious disease mortality in Massachusetts from 2002–2011, with a focus on HIV/AIDS and HCV. Results Significant clusters of high infectious disease mortality in space and time throughout the state were detected through both spatial and space time cluster analysis. The most significant clusters occurred in Springfield, Worcester, South Boston, the Merrimack Valley, and New Bedford with other smaller clusters detected across the state. Multiple cause of death mortality rates were much higher than underlying cause mortality alone, and significant disparities existed across race and age groups. Conclusions We found that our multi-method analyses, which focused on contributing causes of death, were more robust than analyses that focused on underlying cause of death alone. Our results may be used to inform public health resource allocation for infectious disease prevention and treatment programs, provide novel insight into the current state of infectious disease mortality throughout the state, and benefited from approaches that may more accurately document mortality trends.
Student misconceptions of osmosis and diffusion

student misconceptions about two fundamental science concepts, osmosis and diffusion, were elicited using an interview-about-events approach. ii A concept map and list of 25 propositional statements were used to define the knowledge regarded as important for a sound understanding of the concepts of osmosis and diffusion. The interview probed students• understandings of the propositions. Eighteen students from a local metropolitan high school were interviewed. ~hese students were selected from four dlfferent science classes. Nine students studied Year ~2 Biology and nine studied Year 12 Human Biology. Diffusion and osmosis are inteqral concepts required for thorough understanding of both subjects. The interview-about-events procedure elicited st~dent understanding of the sUb-microscopic processes operating within the concrete phenomena provided at various stages during the interview. Interview data were recorded on tape and later transcribed. Additional information was provided in the ! orm of brief notes compiled at the time of the interview by the researcher and diagrams constructed by
Robust optimization method based on scenario analysis for unit commitment considering wind uncertainties

With increasing wind farm integrations, unit commitment (UC) is more difficult to solve because of the intermittent and random nature of wind power outputs. A robust optimization model for UC is built to deal with the errors on wind power predictions. The robust optimization method is based on scenario analysis, while the probability of each selected scenario is derived mathematically. In the proposed UC formulation, spinning reserve requirement is specially considered to support possible wind power change between any two successive periods. Network security constraints are considered by DC power flow equations and the whole UC formulation is a mixed-integer programming problem. Case studies on the IEEE 30-bus system demonstrate the effectiveness of the proposed method. The influences of wind power on UC results and network security are also discussed.
Second international round robin for the quantification of serum non-transferrin-bound iron and labile plasma iron in patients with iron-overload disorders

Non-transferrin-bound iron and its labile (redox active) plasma iron component are thought to be potentially toxic forms of iron originally identified in the serum of patients with iron overload. We compared ten worldwide leading assays (6 for non-transferrin-bound iron and 4 for labile plasma iron) as part of an international inter-laboratory study. Serum samples from 60 patients with four different iron-overload disorders in various treatment phases were coded and sent in duplicate for analysis to five different laboratories worldwide. Some laboratories provided multiple assays. Overall, highest assay levels were observed for patients with untreated hereditary hemochromatosis and β-thalassemia intermedia, patients with transfusion-dependent myelodysplastic syndromes and patients with transfusion-dependent and chelated β-thalassemia major. Absolute levels differed considerably between assays and were lower for labile plasma iron than for non-transferrin-bound iron. Four assays also reported negative values. Assays were reproducible with high between-sample and low within-sample variation. Assays correlated and correlations were highest within the group of non-transferrin-bound iron assays and within that of labile plasma iron assays. Increased transferrin saturation, but not ferritin, was a good indicator of the presence of forms of circulating non-transferrin-bound iron. The possibility of using non-transferrin-bound iron and labile plasma iron measures as clinical indicators of overt iron overload and/or of treatment efficacy would largely depend on the rigorous validation and standardization of assays.
Varenicline in the Treatment of Alcohol Use Disorders

Objective: To summarize the efficacy and safety data for the use of varenicline in the treatment of alcohol use disorders. Data Sources: A literature search was conducted in PubMed, International Pharmaceutical Abstracts, and Cochrane Library (through May 2014). Key search terms included varenicline, alcohol, alcohol dependence, alcoholism, ethanol, and nicotinic acetylcholine receptor. Additional references were identified from literature citations. Study Selection and Data Extraction: Results were limited to clinical trials and case reports that discussed either the use of varenicline in alcohol drinking patients or adverse effects experienced with its use. Only English language studies in humans were reviewed. Data Synthesis: In all, 7 randomized, placebo-controlled clinical trials and 1 open-label study were identified that evaluated the impact of varenicline on various drinking-related end points. The studies were conducted in patients dependent on alcohol (n = 4), non-alcohol-dependent patients (n = 3), and patients with a history of alcohol dependence but who had been abstinent for at least 6 months (n = 1). The majority of the studies classified their participants as heavy drinkers; however, this definition varied across studies. Most studies included smokers, but 2 trials included both smokers and nonsmokers. Conclusions: Evidence supports the use of varenicline for the reduction of alcohol craving as well as for the reduction of overall alcohol consumption in patients with alcohol use disorders. However, it is not likely to improve abstinence rates. Although most of the data were derived from patients with concurrent nicotine dependence, the effects of varenicline appear to occur independent of baseline smoking status.
A field-consistency approach to plate elements

The design of robust plate and shell elements has been a very challenging area for several decades. The main difficulty has been the shear locking phenomenon in plate elements and the combined shear and membrane locking phenomena in the shell elements. Among the various artifices or devices which are used to develop elements free of these problems is the field-consistency approach. In this paper this approach is reviewed. It turns out that not only Mindlin-type elements but also elements based on higher-order theories could be developed using the technique.
TCP performance improvement in wireless networks with cooperative communications and network coding

Cooperative communications and network coding are considered as effective technologies to provide robust and efficient communications. Most existing studies focus on lower layer performance, such as bandwidth efficiency, and little attention has been paid to the performance in the upper layers, such as transmission control protocol (TCP) throughput. In this paper, we investigate TCP throughput in wireless networks with cooperative communications and network coding, and take a cross-layer design approach to improve TCP throughput. Wireless channels are modeled as finite sate Markov channels to characterize the structure of the fading process, and the TCP performance improvement problem is formulated as a stochastic decision process, which can be solved using linear programming and primal-dual index heuristic algorithm. Simulation results show that cooperative communications and network coding have significant impact on TCP throughput, and the TCP throughput can be improved substantially by the proposed scheme.
Web news ranking for elementary school children based on degree of SNS users' attention and popular search queries among children

Recently, NIE (Newspaper In Education) is attracting attention at many elementary schools around the world. The use of newspapers for education has been specified in the Japanese government course guidelines since school year 2011. However, newspaper articles are written in kanji characters or terms which elementary school children cannot read and understand. The purpose of our research is to construct a Web news recommendation system for elementary school children, in order to enhance the effectiveness of NIE. This paper proposes Web news ranking for elementary school children based on the degree of SNS users' attention and popular search queries of children. The effectiveness of the proposed method is examined by two experiments.
Intravesical OnabotulinumtoxinA Injection for Overactive Orthotopic Ileal Neobladder: Feasibility and Efficacy

The efficacy of intravesical onabotulinumtoxinA (BTXA) in the treatment of overactive bladder (OAB) has been well documented. The use of BTXA injection in orthotopic neobladders is yet to be studied. We present 4 cases of patients injected with intravesical BTXA for overactive orthotopic ileal neobladder. We recorded patient demographics, presenting and follow-up symptoms, urodynamic profiles, and Patient Global Impression of Improvement (PGI-I) scores. The 4 patients reported varying degrees of subjective improvements in the symptoms, including urgency, urge incontinence, and pad usage. Mean follow-up duration was 8.3 months (range, 5–14 months). Average PGI-I score was 3 (“a little better”) (range, 2–4). To our knowledge, the current study is the first case series examining BTXA injection for orthotopic neobladder overactivity. BTXA injection yielded varying degrees of objective and subjective improvements, without significant complications. Intravesical BTXA injection is feasible and may be considered as a potential treatment alternative for OAB in orthotopic neobladders, although further study is warranted.
Freely Annotating C#

Reflective programming is becoming popular due to the increasing set of dynamic services provided by execution environments like JVM and CLR. With custom attributes Microsoft introduced an extensible model of reflection for CLR: they can be used as additional decorations on element declarations. The same notion has been introduced in Java 1.5. The annotation model, both in Java and in C#, limits annotations to classes and class members. In this paper we describe [a]C# a , an extension of the C# programming language, that allows programmers to annotate statements and code blocks and retrieve these annotations at run-time. We show how this extension can be reduced to the existing model. A set of operations on annotated code blocks to retrieve annotations and manipulate bytecode is introduced. We also discuss how to use [a]C# to annotate programs giving hints on how to parallelize a sequential method and how it can be implemented by means of the abstractions provided by the run-time of the language. Finally, we show how our model for custom attributes has been realized.