Miracle-dz/UniFAR-FTUs huggingface dataset:
Synteny Portal: a web-based application portal for synteny block analysis

Recent advances in next-generation sequencing technologies and genome assembly algorithms have enabled the accumulation of a huge volume of genome sequences from various species. This has provided new opportunities for large-scale comparative genomics studies. Identifying and utilizing synteny blocks, which are genomic regions conserved among multiple species, is key to understanding genomic architecture and the evolutionary history of genomes. However, the construction and visualization of such synteny blocks from multiple species are very challenging, especially for biologists with a lack of computational skills. Here, we present Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database, (ii) visualize and download syntenic relationships as high-quality images, (iii) browse synteny blocks with genetic information and (iv) download the details of synteny blocks to be used as input for downstream synteny-based analyses, all in an intuitive and easy-to-use web-based interface. We believe that Synteny Portal will serve as a highly valuable tool that will enable biologists to easily perform comparative genomics studies by compensating limitations of existing tools. Synteny Portal is freely available at http://bioinfo.konkuk. ac.kr/synteny_portal.
008-0041 AN INTELLIGENT SOLUTION APPROACH TO VEHICLE ROUTING PROBLEM

In this paper, we present a three-stage solution approach to the Vehicle Routing Problem (VRP). In the first stage, the distribution area is divided into several areas based on drivers’ experiences, and the customers in each area are further segmented into groups by Fuzzy clustering. In the second stage, a depth-first search algorithm is presented to generate feasible routing schemes. In the last stage, an integer programming model is constructed to identify the optimal routing schemes. The above approach is a combination of quantitative computing process and qualitative reasoning process.
Detection and correction of conflicting source updates for view maintenance

Data integration over multiple heterogeneous data sources has become increasingly important for modern applications. The integrated data is usually stored in materialized views for high availability and better performance. Such views must be maintained after the data sources change. In a loosely-coupled and dynamic environment, such as the Data Grid, the sources may autonomously change not only their data but also their schema, query capabilities or semantics, which may consequently cause the ongoing view maintenance fail. We analyze the maintenance errors and classify them into different classes of dependencies. We then propose several dependency detection and correction algorithms to handle these new classes of concurrency. Our techniques are not tied to specific maintenance algorithms nor to a particular data model. To our knowledge, this is the first complete solution to the view maintenance concurrency problems for both data and schema changes. We have implemented the proposed solutions and experimentally evaluated the impact of anomalies on maintenance performance and trade-offs between different dependency detection algorithms.
Falls and Atrial Fibrillation in Elderly Patients.

BACKGROUND Atrial fibrillation is a common heart rhythm disorder in older adults, and its prevalence has increased rapidly in recent years. The health issues associated with atrial fibrillation are not limited to physiological problems, as it also contributes to an increased risk of falls, which may be related to cardiovascular co-morbidities and medication use. The aim of this study was to determine which cardiovascular co-morbidities and medication use are associated with falls in older adults with atrial fibrillation. METHODS Four hundred and one patients 75 years of age or older (82.2 ± 0.2 years) were enrolled in a geriatric evaluation and management unit in Taiwan. Events associated with patient falls and medication use were recorded, and comprehensive geriatric assessment was conducted during admission. RESULTS Among the study participants, 66 (16.5%) patients had atrial fibrillation and 234 (58.4%) patients had a history of fall. We found a significantly higher prevalence of falls in patients with atrial fibrillation [odds ration (OR) 1.98, 95% confidence interval (CI) 1.08-3.63, p = 0.026] compared with those without atrial fibrillation. Using multivariate logistic regression, we found that benzodiazepine use (OR 18.22, 95% CI 2.71-122.38, p = 0.003), a history of paroxysmal atrial fibrillation (OR 12.18, 95% CI 1.37-108.70, p = 0.025) and hypertension (OR 9.49, 95% CI 1.19-75.57, p = 0.034) were independent factors for falls in atrial fibrillation patients. CONCLUSIONS A diagnosis of atrial fibrillation in elderly patients is associated with falls. Benzodiazepine use, history of paroxysmal atrial fibrillation, and hypertension were associated with a high falling prevalence among patients with atrial fibrillation. KEY WORDS Atrial fibrillation; Benzodiazepine; Falls; Hypertension.
Understanding the Dimensionality and Reliability of the Cognitive Scales of the UK Clinical Aptitude test (UKCAT): Summary Version of the Report

Although used to select medical and dental students since 2006 the structure of the UKCAT has not been published to date. The dimensionality of the UKCAT responses has implications for how the test scores are summarised and used in the selection process. Moreover, a number of independent researchers have questioned the very high (internal) reliability figures cited by the annual technical reports. Understanding the dimensionality of the UKCAT will allow for accurate reliability estimates to be derived using widely accepted methods. Consequently the UKCAT research panel commissioned an item-level analysis involving both exploratory and confirmatory factor analyses in order to elicit the structure of the test and hence establish its reliability. The analysis was conducted in December 2013. The UKCAT is delivered in a number of versions which use differing permutations of the four subtests (abstract reasoning [AR], decision analysis [DA], quantitative reasoning [QR] and verbal reasoning [VR]. For this study item responses from the 2013 version 1 were analysed from a total of 5,053 testees, randomly divided into 2,488 observations to be used as the ‘training’ dataset and 2,565 observations to be used as the ‘prediction’ or ‘confirmatory’ dataset. A parallel analysis (Horn 1965) adapted for binary response data was used to evaluate the dimensionality of the response data. In order to reduce the risk of such item dependency (which could artefactually inflate reliability coefficients) only one item from each group of questions shown to be related to the same stem was randomly selected for inclusion in the final analysis. The only subtest that this approach could not be used with was decision analysis as all the items used in a particular form of decision analysis (only two forms are used in each sitting) were related to a single stem. Once plausible structures for the response data were established using the parallel analysis and exploratory factor analyses, these were then tested using the confirmatory dataset from version 1 of the UKCAT 2013. Confirmation of the data structure was also conducted in version 6 of the UKCAT test conducted in 2013. Thus confirmation was conducted in
Improving Label Quality in Crowdsourcing Using Noise Correction

This paper proposes a novel framework that introduces noise correction techniques to further improve label quality after ground truth inference in crowdsourcing. In the framework, an adaptive voting noise correction algorithm (AVNC) is proposed to identify and correct the most likely noises with the help of estimated qualities of labelers provided by the ground truth inference. The experimental results on two real-world datasets show that (1) the framework can improve label quality regardless of inference algorithms, especially under the circumstance that each example has a few noisy labels; and (2) since the algorithm AVNC considers both the number of and the probability of potential noises, it outperforms a baseline noise correction algorithm.
International Journal of C 2009 Institute for Scientific Numerical Analysis and Modeling Computing and Information Dimension Splitting Method for 3d Rotating Compressible Navier-stokes Equations in the Turbomachinery

In this paper, we propose a dimension splitting method for Navier-Stokes equations(NSEs). The main idea is as follows. The domain of flow in 3D is decomposed into several thin layers. In each layer, The 3D NSEs can be represented as the sum of a membrane operator and a normal (bending) operator on the boundary of layer. And The Euler central difference is used to approximate the bending operator. When restricting the 3D NSEs on the boundary in each layer, we obtain a series of two dimensional-three components NSEs (called as 2D-3C NSEs). Then we construct an approximate solution of 3D NSES by solutions of those 2D-3C NSEs.
Menstrual-like breakdown and apoptosis in human endometrial explants.

BACKGROUND Apoptosis occurs in late secretory and menstrual human endometrium and is thought to play an important role in endometrial physiology. Menstrual-like breakdown has been observed in vitro in endometrial explants. The purpose of this study was to assess the role of apoptosis in menstrual-like breakdown in human endometrial explants. METHODS Human endometrial tissue was obtained during the mid-secretory phase and cultured with or without estrogen and progesterone. The occurrence of breakdown was assessed by histology. Apoptosis was determined by gel electrophoresis for the detection of DNA fragmentation and by immunohistochemistry using the M30 CytoDEATH and anti-cleaved caspase-3 (CASP3) antibodies for the detection of caspase activity. Expression of BCL2 and BAX was quantified using real-time PCR analysis. RESULTS Apoptosis occurred in human endometrial explants at all time-points studied. Cleaved CASP3 and M30 antigen expression increased in all explants, suggesting the involvement of CASP3 in the apoptosis. Low BCL2:BAX ratios were observed in all samples when compared with pre-culture controls. Estradiol and progesterone supplementation of the culture media reduced or eliminated menstrual-like breakdown but did not affect the degree of apoptosis observed. CONCLUSIONS The apoptosis observed in endometrium during the late secretory phase and menstrual phase does not appear to be mechanistically related to the tissue breakdown but rather may be involved in the impending remodelling that occurs in the endometrium in the transition from secretory to proliferative phase following the menses.
A new fuzzy control method based on PSO for Maximum Power Point Tracking of photovoltaic system

Maximum Power Point Tracking (MPPT) is the key technology in the solar energy photovoltaic system, which plays an important role in enhancing energy utilization effectively. Aiming at problems existing in traditional fuzzy tracking method, such as pre-confirmation of control parameters, weak self-study ability, and effective tracking cannot be organized under the circumstance that the environment condition is changed greatly, a kind of fuzzy control method based on Particle Swarm Optimization algorithm (PSO) was put forward in this paper, adjusting the membership function parameters of fuzzy control with the use of PSO's self-adaptation mechanism, so that the controller can adjust the tracking step through real-time study and that the photovoltaic system can gain the maximum power point(MPP) more rapidly and accurately when the outer environment changes. The experiment comparative analysis was carried out with the use of the emulation model of photovoltaic batteries, and results proved the validity and robustness of this method.
A Limited Feedback Joint Precoding for Amplify-and-Forward Relaying

This paper deals with the practical precoding design for a dual hop downlink with multiple-input multiple-output (MIMO) amplify-and-forward relaying. First, assuming that full channel state information (CSI) of the two hop channels is available, a suboptimal dual hop joint precoding scheme, i.e., precoding at both the base station and relay station, is investigated. Based on its structure, a scheme of limited feedback joint precoding using joint codebooks is then proposed, which uses a distributed codeword selection to concurrently choose two joint precoders such that the feedback delay is considerably decreased. Finally, the joint codebook design for the limited feedback joint precoding system is analyzed, and results reveal that independent codebook designs at the base station and relay station using the conventional Grassmannian subspace packing method is able to guarantee that the overall performance of the dual hop joint precoding scheme improves with the size of each of the two codebooks. Simulation results show that the proposed dual hop joint precoding system using distributed codeword selection scheme exhibits a rate or BER performance close to the one using the optimal centralized codeword selection scheme, while having lower computational complexity and shorter feedback delay.
Improved GSO Optimized ESN Soft-Sensor Model of Flotation Process Based on Multisource Heterogeneous Information Fusion

For predicting the key technology indicators (concentrate grade and tailings recovery rate) of flotation process, an echo state network (ESN) based fusion soft-sensor model optimized by the improved glowworm swarm optimization (GSO) algorithm is proposed. Firstly, the color feature (saturation and brightness) and texture features (angular second moment, sum entropy, inertia moment, etc.) based on grey-level co-occurrence matrix (GLCM) are adopted to describe the visual characteristics of the flotation froth image. Then the kernel principal component analysis (KPCA) method is used to reduce the dimensionality of the high-dimensional input vector composed by the flotation froth image characteristics and process datum and extracts the nonlinear principal components in order to reduce the ESN dimension and network complex. The ESN soft-sensor model of flotation process is optimized by the GSO algorithm with congestion factor. Simulation results show that the model has better generalization and prediction accuracy to meet the online soft-sensor requirements of the real-time control in the flotation process.
Association of pre-pregnancy body mass index with cardiovascular disease mortality: The Child Health and Development Studies

Overweight early in life may contribute to cardiovascular disease mortality through progression to later life obesity or through a cumulative effect of excess weight. Few studies have investigated the relationship between body mass index (BMI) before middle age and cardiovascular disease mortality in women. Using the Child Health and Development Studies cohort of 11,006 pregnant women recruited between 1959 and 1967, the hypothesis that higher self‐reported prepregnancy BMI is associated with increased stroke and coronary heart disease mortality was tested.
Trivalent M-related protein as a component of next generation group A streptococcal vaccines

Purpose There is a need to broaden protective coverage of M protein–based vaccines against group A streptococci (GAS) because coverage of the current 30-valent M protein vaccine does not extend to all emm types. An additional GAS antigen and virulence factor that could potentially extend vaccine coverage is M-related protein (Mrp). Previous work indicated that there are three structurally related families of Mrp (MrpI, MrpII, and MrpIII) and peptides of all three elicited bactericidal antibodies against multiple emm types. The purpose of this study was to determine if a recombinant form containing Mrp from the three families would evoke bactericidal antiserum and to determine if this antiserum could enhance the effectiveness of antisera to the 30-valent M protein vaccine. Materials and Methods A trivalent recombinant Mrp (trMrp) protein containing N-terminal fragments from the three families (trMrp) was constructed, purified and used to immunize rabbits. Anti-trMrp sera contained high titers of antibodies against the trMrp immunogen and recombinant forms representing MrpI, MrpII, and MrpIII. Results The antisera opsonized emm types of GAS representing each Mrp family and also opsonized emm types not covered by the 30-valent M protein–based vaccine. Importantly, a combination of trMrp and 30-valent M protein antiserum resulted in higher levels of opsonization of GAS than either antiserum alone. Conclusion These findings suggest that trMrp may be an effective addition to future constructs of GAS vaccines.
Immigrants' Adaptation and Interracial/Interethnic Interactions in Natural Environments

ABSTRACT This study examined the role of leisure in natural environments in immigrants' adaptation, with a particular emphasis on facilitating interracial/interethnic interactions. Berry's adaptation framework was used as a theoretical framework. The project used in-depth individual interviews with 70 immigrants from China, Latin America, Morocco, Turkey, Ukraine, and Vietnam residing in the United States, the Netherlands, Germany, and Poland. The findings showed that recreation in natural environments promoted immigrants' psychological adaptation by helping to improve psychological and emotional well-being, develop feelings of attachment, strengthen social ties, and build memories and family traditions. The sociocultural adaptation was increased when immigrants learned about the culture of the host countries. The natural environments were not particularly conducive to establishing interactions with strangers but were convenient settings for interacting with families and members of the ethnic community.
Metastatic Colorectal Cancer: From Improved Survival to Potential Cure

Context: The treatment of colorectal cancer has improved considerably in recent years, but it remains the second commonest cause of cancer deaths in men and women in the United States. Better therapies have resulted in prolonged median survival for patients with metastatic disease and a select number of patients can now be cured. Evidence Acquisition: We conducted a computerized search using PubMed and Google Scholar for reports published between January 1993 and August 2009 using mesh headings and key words relating to the treatment of colorectal cancer. If reports identified by these criteria referred to other papers not in the initial search, then these were also reviewed if relevant to metastatic colorectal cancer (MCRC). Results: Seven new chemotherapy agents have been licensed for the treatment of advanced colorectal cancer, with associated improved median survival from 5 months to 2 years. Complete responses are rare with systemic chemotherapy alone, but higher overall response rates to systemic and intrahepatic chemotherapies have enabled initially unresectable patients to undergo potentially curative surgical resection of metastases. Improved surgical expertise together with the adjunctive use of radiofrequency ablation has further expanded the definition of resectability. Advances in the understanding of tumor biology have resulted in the development of clinically useful biomarkers and the emergence of active biological therapies. Conclusions: The multidisciplinary management of MCRC incorporating improved systemic and local therapies continues to improve median survival and enlarge the cohort of patients that can be approached with curative intent. Recent technological advances have facilitated a better understanding of tumor biology that promises continued advancements in patient care.
Toward A Formalism for Conversation Protocols Using Joint Intention Theory

Conversation protocols are used to achieve certain goals or to bring about certain states in the world. Therefore, one may identify the landmarks or the states that must be brought about during the goal–directed execution of a protocol. Accordingly, the landmarks, characterized by propositions that are true in the state represented by that landmark, are the most important aspect of a protocol. Families of conversation protocols can be expressed formally as partially ordered landmarks after the landmarks necessary to achieve a goal have been identified. Concrete protocols represented as joint action expressions can, then, be derived from the partially ordered landmarks and executed directly by joint intention interpreters. This approach of applying Joint Intention theory to protocols also supports flexibility in the actions used to get to landmarks, shortcutting protocol execution, automatic exception handling, and correctness criterion for protocols and protocol compositions.
Why are Arctic ground squirrels more stressed in the boreal forest than in alpine meadows?

Abstract Arctic ground squirrels (Spermophilus parryii plesius Richardson) in the southeastern Yukon live in both boreal forest and alpine tundra habitats. We live-trapped young male and female squirrels in both habitat types and subjected them to a standardized hormonal-challenge protocol to assess the responsiveness of their hypothalamic-pituitary-adrenal axis. Alpine squirrels had levels of free cortisol at the baseline (initial) bleed following their removal from traps that were 3 times higher in males and 5 times higher in females compared with boreal forest squirrels. Females, but not males, from the boreal forest were dexamethasone resistant, while neither sex from the alpine habitat was resistant. Free cortisol in alpine squirrels also responded more dramatically after the injection of adrenocorticotropic hormone. Corticosteroid-binding globulin levels were significantly lower in forest than alpine squirrels and these levels were not markedly affected by the challenge protocol. Glucose levels were significantly higher in boreal than alpine squirrels and the pattern differed between the two sites in response to the protocol. Hematocrits were significantly higher in alpine squirrels. Collectively, this evidence suggests that Arctic ground squirrels were more chronically stressed in the boreal forest than in the alpine meadows. The most likely explanation for our results is higher predation risk in the forest compared with alpine meadows, as forage availability and population density were not significantly different between the two habitats.
Thermodynamics , diffusion , and process control and simulation applications

his article presents the current status of the use of Artificial Neural Networks (ANNs) in process engineering applications where common mathematical methods do not completely represent the behavior shown by experimental observations, results, and plant operating data. Three examples of the use of ANNs in typical process engineering applications such as prediction of activity in solvent-polymer binary systems, prediction of a surfactant self-diffusion coefficient of micellar systems, and process control and simulation are shown. These examples are important for polymerization applications, enhanced-oil recovery, and automatic process control.