Miracle-dz/UniFAR-FTUs huggingface dataset:
A Clustering Methodology of Web Log Data for Learning Management Systems

Learning Management Systems (LMS) collect large amounts of data. Data mining techniques can be applied to analyse their web data log files. The instructors may use this data for assessing and measuring their courses. In this respect, we have proposed a methodology for analysing LMS courses and students’ activity. This methodology uses a Markov CLustering (MCL) algorithm for clustering the students’ activity and a SimpleKMeans algorithm for clustering the courses. Additionally we provide a visualisation of the results using scatter plots and 3D graphs. We propose specific metrics for the assessment of the courses based on the course usage. These metrics applied to data originated from the LMS log files of the Information Management Department of the TEI of Kavala. The results show that these metrics, if combined properly, can quantify quality characteristics of the courses. Furthermore, the application of the MCL algorithm to students’ activities provides useful insights to their usage of the LMS platform.
Improved protein-ligand binding affinity prediction by using a curvature-dependent surface-area model

MOTIVATION Hydrophobic effect plays a pivotal role in most protein-ligand binding. State-of-the-art protein-ligand scoring methods usually treat hydrophobic free energy as surface tension, which is proportional to interfacial surface area for simplicity and efficiency. However, this treatment ignores the role of molecular shape, which has been found very important by either experimental or theoretical studies. RESULTS We propose a new empirical scoring function, named Cyscore. Cyscore improves the prediction accuracy by using a novel curvature-dependent surface-area model, which is able to distinguish convex, planar and concave surface in hydrophobic free energy calculation. Benchmark tests show that this model significantly improves the protein-ligand scoring and Cyscore outperforms a variety of well established scoring functions using PDBbind benchmark sets for binding affinity correlation and ranking tests. We expect the curvature-dependent surface-area model and Cyscore would contribute to the study of protein-ligand interactions. AVAILABILITY Cyscore is available to non-commercial users at http://clab.labshare. cn/software/cyscore.html.
A Method For Modeling Variation of In Situ Stress Related to Lithology

Assuring ground control safety in many mining and tunneling projects depends, at least in part, on an understanding of in situ stress conditions that will be encountered. Yet it is rarely practical to conduct more than a very limited number of stress measurements. Stresses along the route of a proposed excavation are typically interpolated from available measurements, often assuming a linear variation of stress with depth (or elevation). However, projects where multiple stress measurements are conducted often report more complex variations of in situ stress, usually in apparent relationship to geologic structures. These structures often include lithologies of contrasting elastic properties. A method is proposed for estimating stresses in these cases by first back-calculating regional loads from available stress measurements and then modeling the distribution of stress throughout the rock mass. The method has been successfully applied to a set of in situ stress measurements from the Coeur d’Alene Mining District of northern Idaho, USA. Results provided new insights into district stress conditions and the distribution of rockburst hazards along mine drifts and between various mines. This success should transfer readily to suitable deep tunneling projects.
Curvature and Rho activation differentially control the alignment of cells and stress fibers

Stress fibers, single cells, and densely packed cells align on gently curved surfaces and restructure upon Rho activation. In vivo, cells respond to a host of physical cues ranging from substrate stiffness to the organization of micro- and nanoscale fibrous networks. We show that macroscale substrates with radii of curvature from tens to hundreds of micrometers influence cell alignment. In a model system of fibroblasts, isolated cells aligned strongly in the axial direction on cylinders with radii similar to the cell length and more weakly on cylinders of much larger radius. Isolated vascular smooth muscle cells did not align as effectively as fibroblasts. However, both cell types aligned robustly in weak curvature fields when in confluent monolayers. We identified two distinct populations of stress fibers in both cell types: long, apical stress fibers that aligned axially and short, basal stress fibers that aligned circumferentially. Circumferential alignment of the basal stress fibers is in apparent disagreement with a long-standing hypothesis that energetic penalties for bending enforce axial alignment on cylinders. To explore this phenomenon, we manipulated stress fibers by activating Rho, a small guanosine triphosphatase that regulates stress fiber assembly. In response, apical stress fibers disassembled, whereas basal stress fibers thickened and aligned more strongly in the circumferential direction. By activating Rho in confluent monolayers of vascular smooth muscle cells, we recapitulated the circumferential alignment pattern of F-actin within these cells that is observed in cylindrical vessels in vivo. In agreement with recent theory, these results suggest that stress fiber bending penalties are overcome when stress fiber contractility is enhanced and motivate deeper study of the mechanics of these distinct stress fiber populations.
The role of physical and biological processes in biofilms in drinking water

Microorganisms, such as bacteria, fungi, viruses and protozoa, colonise the inner surfaces of drinking water pipes and form biofilms. Drinking water biofilms act to protect the microorganisms that they house from the harsh conditions that we impose such as disinfection. Biofilms are generally thought of as being detrimental in drinking water distribution systems; they can harbour pathogens that intermittently emerge at the tap and they can affect the aesthetics of drinking water. The formation and dissolution of biofilms are intricately linked with the flow conditions and therefore, if we are to manage biofilms in drinking water systems, then it is imperative that we understand the crucial role that hydrodynamics play. Thus, my thesis focuses on the growth of biofilms in drinking water under three distinct flow regimes: turbulent, transition and laminar, and under stagnant conditions, and reveals the role that hydrodynamics play in shaping biofilms in drinking water distribution systems. Not all bacteria are merely passive tracers in flow whose fate is governed by the physical flow alone. This thesis presents evidence that there might be key bacteria in aggregation in drinking water, whose biology acts to enhance the formation of multi-species biofilms. I explored that by testing the role that the Methylobacterium strain DSM 18358 played in the formation of biofilms on surfaces that starts with the formation of aggregates in the bulk water. I also explored whether the ability of this Methylobacterium strain to form aggregates was influenced by the flow regime. Ultimately, this research reveals whether the formation and structure of those aggregates in drinking water is influenced by the subtle interplay between biological and physical processes. Given that they are bacteria that can degrade various dangerous chlorine disinfection by-products I explored the role of the Methylobacterium strain DSM 18358 in the concentration of trihalomethanes in drinking water as these chlorine disinfection by-products can cause serious problems to human health when they occur at high concentrations in drinking water. Overall, I identified whether the presence of this Methylobacterium strain in drinking water can actually deliver a service that contributes to better drinking water quality.
Convex Clustering: An Attractive Alternative to Hierarchical Clustering

The primary goal in cluster analysis is to discover natural groupings of objects. The field of cluster analysis is crowded with diverse methods that make special assumptions about data and address different scientific aims. Despite its shortcomings in accuracy, hierarchical clustering is the dominant clustering method in bioinformatics. Biologists find the trees constructed by hierarchical clustering visually appealing and in tune with their evolutionary perspective. Hierarchical clustering operates on multiple scales simultaneously. This is essential, for instance, in transcriptome data, where one may be interested in making qualitative inferences about how lower-order relationships like gene modules lead to higher-order relationships like pathways or biological processes. The recently developed method of convex clustering preserves the visual appeal of hierarchical clustering while ameliorating its propensity to make false inferences in the presence of outliers and noise. The solution paths generated by convex clustering reveal relationships between clusters that are hidden by static methods such as k-means clustering. The current paper derives and tests a novel proximal distance algorithm for minimizing the objective function of convex clustering. The algorithm separates parameters, accommodates missing data, and supports prior information on relationships. Our program CONVEXCLUSTER incorporating the algorithm is implemented on ATI and nVidia graphics processing units (GPUs) for maximal speed. Several biological examples illustrate the strengths of convex clustering and the ability of the proximal distance algorithm to handle high-dimensional problems. CONVEXCLUSTER can be freely downloaded from the UCLA Human Genetics web site at http://www.genetics. ucla.edu/software/
Two 21-kilodalton components of the Epstein-Barr virus capsid antigen complex and their relationship to ZEBRA-associated protein p21 (ZAP21)

The viral capsid antigen complex of Epstein-Barr virus (EBV), an important serodiagnostic marker of infection with the virus, consists of at least four components, with molecular masses of 150, 110, 40, and 21 kDa. Here we show that the 21-kDa component of the viral capsid antigen consists of products of two EBV genes, BFRF3 and BLRF2. Both products were expressed from late transcripts, were recognized by human antisera, and were present in virions. The BFRF3 product, but not that of BLRF2, fulfilled the definition of ZEBRA-associated protein p21 (ZAP21). In cells in which EBV was lytically replicating, BFRF3 protein was coimmunoprecipitated together with ZEBRA by a rabbit antiserum directed against amino acids 197 to 245 of BZLF1. In EBV-negative cells cotransfected with BZLF1 and BFRF3 expression vectors, BFRF3 was also coimmunoprecipitated with this antiserum. Although this antiserum could not detect BFRF3 on an immunoblot, it was able to immunoprecipitate BFRF3 in the absence of ZEBRA expression. The rabbit antiserum to amino acids 197 to 245 of BZLF1 was found to detect the same epitope at the carboxy end of BFRF3 as was recognized by rabbit antiserum to BFRF3 itself. Thus, coimmunoprecipitation of BFRF3 p21 with ZEBRA appeared to be due to cross-reactivity of the immunoprecipitating antiserum rather than to direct association of ZEBRA and BFRF3 p21.
Cardiac toxicity of some echinocandin antifungals

Background: Unexplained cardiovascular decompensation has been observed during central venous administration of some echinocandins. Objective: The purpose of this study was to assess cardiac toxicity associated with the echinocandins. Methods: Isolated rat hearts (Langendorff model) were perfused with anidulafungin (ANID), caspofungin (CASP), or micafungin (MICA) at exposures of 1, 4, and 10 times therapeutic concentrations. Changes in left ventricular contractility with experimental exposure were compared to control, and histologic and transmission electron microscopy (TEM) examinations of tissue were performed. Results: Mean concentrations of ANID (10 – 80 µg/ml) and CASP (6 – 48 µg/ml) were associated with significant decreases in contractility (-77.1 ± 9.4% and -40.6 ± 15.6%, respectively; p < 0.05). MICA was associated with an increase in contractility (13.6 ± 2.8%, p = NS). On TEM, samples exposed to ANID and CASP had enlarged mitochondria and disintegrating myofibrils. Samples exposed to MICA showed some enlarged mitochondria. Conclusion: Mean concentrations of ANID and CASP were associated with statistically significant decreases in left ventricular contractility at concentrations that may be achievable in humans after peripheral administration, while MICA caused no change. TEM studies suggest this may be a result of mitochondrial damage. Caution may be warranted with central administration of these agents to patients with preexisting cardiac dysfunction.
Trichoderma (Hypocrea) species with green ascospores from China

Stromata of Trichoderma species having green ascospores were collected in various regions of China. Based on morphology of the sexual and asexual morph, culture characteristics, and sequence analyses of rpb2 and tef1 genes, 17 species with green ascospores were identified. Among them, Trichoderma rosulatum, T. rufobrunneum and T. stipitatum are described as new species, and seven other species are reported for the first time from China. Trichoderma rosulatum produces small bright yellow or pale greenish stromata with dense dark green ostioles and gliocladium-like conidiophores, shows a close relationship to T. thelephoricola, and belongs to the Chlorospora clade. Trichoderma rufobrunneum, which typically forms reddish brown stromata, is recognised as a member of the Harzianum clade. Trichoderma stipitatum is characterised by turbinate, pale yellow to nearly orange stromata and verticillium-like conidiophores; it forms a distinct, independent lineage with strong bootstrap support in the phylogenetic trees. The distinctions between the new species and their close relatives are discussed, and their phylogenetic positions are explored.
Low Levels of Antibodies Against Phosphorylcholine Predict Development of Stroke in a Population-Based Study From Northern Sweden

Background and Purpose— Natural immunoglobulin M antibodies specific for phosphorylcholine (anti-PC) have been implicated in atherosclerosis. We have shown previously that high levels of anti-PC predict a slower progression of atherosclerosis in humans and that low levels of anti-PC are associated with higher risk for cardiovascular disease. Here we determine the association between anti-PC and the incidence of stroke. Methods— Using a nested case control study design, we examined 227 incident cases (125 men and 102 women) of first-time stroke and 455 age- and sex-matched controls identified during a 13-year time period (1985 to 1999) within the population-based cohorts of the Västerbotten Intervention Project (VIP) and the World Health Organization Monitoring Trends and Determinants in Cardiovascular Disease (WHO MONICA) project in Northern Sweden. Odds ratios of stroke with 95% CIs with adjustments for age, gender, smoking, serum cholesterol, diabetes, body mass index, and blood pressure were determined. Anti-PC levels were measured using ELISA. Results— A significant association between low levels of anti-PC at baseline and incident stroke was seen for the whole group of anti-PC levels below the 30th percentile (multivariately adjusted odds ratio, 1.62; CI, 1.11 to 2.35). Analyses of gender-specific associations indicated fairly strong associations for females, especially at the lowest 30th percentile (multivariately adjusted odds ratio, 2.65; CI, 1.41 to 4.95). No associations were noted for men. Conclusion— Low anti-PC is a novel independent risk marker for development of stroke. Measurements of anti-PC could be used to identify immunodeficient subjects at an increased risk for stroke. The possibility that such subjects might be targets for novel modes of treatment such as immunotherapies deserves further investigation.
Biomarker analysis of the phase 3 TORCH trial for first line erlotinib versus chemotherapy in advanced non-small cell lung cancer patients

Background The TORCH phase III trial compared the efficacy of first-line erlotinib followed by chemotherapy at progression (experimental arm) with the reverse sequence (standard arm) in unselected advanced non-small cell lung cancer (NSCLC) patients. Here we report biomarker analyses. Methods EGFR and KRAS mutation, expression of EGFR family members and of cMET and PTEN and EGFR and ABCG2 germline polymorphisms were tested on tumor tissue or blood samples to either confirm previously proposed predictive role or describe it in an explorative setting. Progression-free survival (PFS) was the primary end-point, overall survival, response rate and side effects (diarrhoea and skin toxicity) were secondary end-points. Interactions between biomarkers and treatment were studied with multivariable models (either Cox model or logistic regression). Statistical analyses accounted for multiple comparisons. Results At least one biomarker was assessed in 324 out of 760 patients in the TORCH study. EGFR mutation was more common in female (P = 0.0001), East Asians (P < 0.0001) and never smoker (P < 0.0001) patients; low MET protein expression by IHC (H-score <200) was more frequent in squamous (P < 0.00009) and ABCG2 C/A or A/A polymorphism was more frequent among East-Asian patients (P = 0.0003). A significant interaction was found for EGFR mutation in PFS and response rate analyses while no predictive effect on OS was found for any biomarker. No biomarker tested was prognostic for PFS and OS. No polymorphism was significantly associated with skin toxicity or diarrhea. Conclusion In the present study, beyond the known role of EGFR mutation, no other biomarker has predictive or prognostic role.
Fungi in the future: interannual variation and effects of atmospheric change on arbuscular mycorrhizal fungal communities

Understanding the natural dynamics of arbuscular mycorrhizal (AM) fungi and their response to global environmental change is essential for the prediction of future plant growth and ecosystem functions. We investigated the long-term temporal dynamics and effect of elevated atmospheric carbon dioxide (CO2) and ozone (O3) concentrations on AM fungal communities. Molecular methods were used to characterize the AM fungal communities of soybean (Glycine max) grown under elevated and ambient atmospheric concentrations of both CO2 and O3 within a free air concentration enrichment experiment in three growing seasons over 5 yr. Elevated CO2 altered the community composition of AM fungi, increasing the ratio of Glomeraceae to Gigasporaceae. By contrast, no effect of elevated O3 on AM fungal communities was detected. However, the greatest compositional differences detected were between years, suggesting that, at least in the short term, large-scale interannual temporal dynamics are stronger mediators than atmospheric CO2 concentrations of AM fungal communities. We conclude that, although atmospheric change may significantly alter AM fungal communities, this effect may be masked by the influences of natural changes and successional patterns through time. We suggest that changes in carbon availability are important determinants of the community dynamics of AM fungi.
Molecular Contactin Associates with Sodium Channel Nav 1 . 3 in Native Tissues and Increases Channel Density at the Cell Surface

Bhaval S. Shah,1,2,3* Anthony M. Rush,1,2,3* Shujun Liu,1,2,3 Lynda Tyrrell,1,2,3 Joel A. Black,1,2,3 Sulayman D. Dib-Hajj,1,2,3 and Stephen G. Waxman1,2,3 1Department of Neurology and 2The Center for Neuroscience and Regeneration Research, Yale University School of Medicine, New Haven, Connecticut 06510, and 3Rehabilitation Research Center, Veterans Affairs Connecticut Healthcare Center, West Haven, Connecticut 06516
Individual and Household Level Population Data for 2001 Census Output Areas in the UK

Acknowledgements The UK ESRC funded this work under contract code RES-149-25-0034. MPJ Express was used to parallelise the Java programs to take advantage of multi-processor computer architectures. This allowed results to be generated within a more reasonable time frame. The University of Leeds and the UK National Grid Service supported this work by: providing computational resources on which results were generated; and, expertise to support the development and execution of programs and the management of data on the computational resources. Thanks to NCeSS collaborators, especially those working on MoSeS and to the University of Leeds for your help and support over the years. Abstract Generation of individual and household level population data for 2001 census output areas in the United Kingdom (UK) was work undertaken by the modelling and simulation for e-Social Science (MoSeS) node of the UK National Centre for e-Social Science. There are at least three ways to approach this. One is to synthetically create individual records and households in a way such that their aggregate characteristics match those in census area based aggregate statistics (CAS). Another approach is the focus of this paper, and a third approach could be a mixture of the other ways. This paper details an implementation of a data integration approach which essentially involves selecting sets of records from samples of individual anonymised records to represent the populations of CAS output areas. Comparable area based aggregate statistics generated from the sets of anonymised records are compared with CAS data values. The paper details Genetic Algorithm (GA) optimisation that seek a well fitting set of anonymised records based on goodness of fit measures. Results are presented for 222626 output areas in the UK. Two results are presented with graph based visualisations revealing the goodness of fit of optimisation constraints. These results have both been submitted to the UK data archive and are being made available via the Economic and Social Data Service (ESDS) for others to use as Study Number 6763 (ESDS, 2011). One result uses the Individual Licensed SAR (ISAR) records to represent both the household population and the communal establishment population. The other result uses the Special Licensed Household SAR (HSAR) to represent the household population. Control constraints were imposed to ensure the results matched some criteria. Optimisation constraints were selected to produce results for applications focussed mainly on the health and social care needs of the dependent population (children, elderly, infirm …
Retinotopic organization of early visual spatial attention effects as revealed by PET and ERPs

Cerebral blood flow PET scans and high‐density event‐related potentials (ERPs) were recorded (separate sessions) while subjects viewed rapidly‐presented, lower‐visual‐field, bilateral stimuli. Active attention to a designated side of the stimuli (relative to passive‐viewing conditions) resulted in an enhanced ERP positivity (P1 effect) from 80–150 msec over occipital scalp areas contralateral to the direction of attention. In PET scans, active attention vs. passive showed strong activation in the contralateral dorsal occipital cortex, thus following the retinotopic organization of the early extrastriate visual sensory areas, with some weaker activation in the contralateral fusiform. Dipole modeling seeded by the dorsal occipital PET foci yielded an excellent fit for the P1 attention effect. In contrast, dipoles constrained to the fusiform foci fit the P1 effect poorly, and, when the location constraints were released, moved upward to the dorsal occipital locations during iterative dipole fitting. These results argue that the early ERP P1 attention effects for lower‐visual‐field stimuli arise mainly from these dorsal occipital areas and thus also follow the retinotopic organization of the visual sensory input pathways. These combined PET/ERP data therefore provide strong evidence that sustained visual spatial attention results in a preset, top‐down biasing of the early sensory input channels in a retinotopically organized way. Hum. Brain Mapping 5:280–286, 1997. © 1997 Wiley‐Liss, Inc.