Miracle-dz/UniFAR-FTUs huggingface dataset:
Arrangement of myosin heads on Limulus thick filaments

The two myosin heads with a single surface subunit on thick filaments from chelicerate arthropod muscle may originate from the same, or from axially sequential molecules, as suggested by three-dimensional reconstructions. The resolution attained in the reconstructions, however, does not permit one to distinguish unequivocally between these two possible arrangements. We examined the effect of 0.6 M KCl on relaxed thick filaments separated from Limulus muscle and filaments in which nearest myosin heads were cross-linked by the bifunctional agent, 3,3'-dithio-bis[3'(2')-O-[6-propionylamino)hexanoyl]adenosine 5'- triphosphate (bis22ATP), in the presence of vanadate (Vi). In high salt, surface myosin dissolved from both native, relaxed filaments and those exposed to 1-2 mM dithiothreitol after cross-linking, but was retained on filaments with cross-linked heads. Since bis22ATP must form intermolecular bonds between myosin heads within each subunit to prevent myosin solubilization in high salt, we conclude that each of these heads originates from a different myosin molecule, as was previously predicted by the reconstructions.
Skull Fractures Detection by Finite Element Method

In this paper an algorithm is developed that allows by means of the method of finite element to detect skull fractures. We intend the theoretical foundation that sustains when segmenting cranial images, these methods based on the method of finite element (FEM), for their initials in English, that allows us to detect fractures in the images. With the development of this paper the efficiency of the method of finite element is shown in the segmentation of images. Likewise, it is made notice the importance that up to now have acquired in the areas of segmentation of images due to their capacity to solve numeric methods. In turn, continuity is given to that the investigation groups that develop projects related with the analysis of images prescribe, continue to the so much of the area of finite element and they follow them incorporating in their algorithms, mainly in concerning tasks to the theory analysis of images and their applications.
Angluin style finite state machine inference with non-optimal counterexamples

Angluin's algorithm is a well known approach for learning black boxes as minimal deterministic finite automata in polynomial time. In order to infer finite state machines instead of automata, different variants of this algorithm have been proposed. These algorithms rely on two types of queries which can be asked to an oracle: output and equivalence queries. If the black box is not equivalent to the learnt model, the oracle replies with a counterexample. The complexity of these algorithms depends on the length of the counterexamples provided by the oracle. The aim of this paper is to compare the average practical complexity of three of these algorithms in the case of poor oracles, in particular when the counterexamples are constructed with random walks.
Front loading the curriculum: early placement experiences enhance career awareness and motivation for students with diverse career options

Deciding which career path is right for undergraduate students can be challenging and positive outcomes are linked to early work placements. The aim of the current study was to explore the student experience following the introduction of early career-based awareness-raising and reflective learning opportunities in first-year sport and exercise science-based students. Students met with the first-year coordinator to discuss career progression and career aspirations. From this meeting, students were allocated a placement. Following the placement visit, students submitted a reflection piece addressing their experiences at the placement site with six themes identified including: 1) positive experience; 2) degree selection; 3) exposure and reinforcement of practices; 4) career awareness; 5) supervisor impact; and 6) negative experience. The provision of early placement for students in an observational capacity appears to be beneficial to first year experience to assist in consolidating their choice of degree.
An interactive exploratory search system for on-line apparel shopping

Many people (especially women) tend to take relatively longer time for shopping. This paper presents a system for product retrieval inspired by psychology of women's shopping activity, and an implementation of the system for apparel products. Our study supposes products which pre-defined keywords are assigned, and prepares icons representing the combination of the keywords. The system intuitively displays various icons in a display space to demonstrate the diversity of the products. When a user selects an interested icon, the system switches the display to a set of images corresponding to the selected icon, so that the user can visually compare the similar products. The system also features user interfaces to input the preference of users, and reflects the input to the evolutionary computation which adjusts the selection of icons to their preferences. It acts real shopping behavior because we often firstly look over the shops to understand the diversity of products, and then close up the particular groups of the products. This paper introduces an experiment which demonstrates the preferable assistance of the shopping behavior of women who are interested in various products.
Field Effectiveness of Pandemic and 2009-2010 Seasonal Vaccines against 2009-2010 A(H1N1) Influenza: Estimations from Surveillance Data in France

Background In this study, we assess how effective pandemic and trivalent 2009-2010 seasonal vaccines were in preventing influenza-like illness (ILI) during the 2009 A(H1N1) pandemic in France. We also compare vaccine effectiveness against ILI versus laboratory-confirmed pandemic A(H1N1) influenza, and assess the possible bias caused by using non-specific endpoints and observational data. Methodology and Principal Findings We estimated vaccine effectiveness by using the following formula: VE = (PPV-PCV)/(PPV(1-PCV)) × 100%, where PPV is the proportion vaccinated in the population and PCV the proportion of vaccinated influenza cases. People were considered vaccinated three weeks after receiving a dose of vaccine. ILI and pandemic A(H1N1) laboratory-confirmed cases were obtained from two surveillance networks of general practitioners. During the epidemic, 99.7% of influenza isolates were pandemic A(H1N1). Pandemic and seasonal vaccine uptakes in the population were obtained from the National Health Insurance database and by telephonic surveys, respectively. Effectiveness estimates were adjusted by age and week. The presence of residual biases was explored by calculating vaccine effectiveness after the influenza period. The effectiveness of pandemic vaccines in preventing ILI was 52% (95% confidence interval: 30–69) during the pandemic and 33% (4–55) after. It was 86% (56–98) against confirmed influenza. The effectiveness of seasonal vaccines against ILI was 61% (56–66) during the pandemic and 19% (−10–41) after. It was 60% (41–74) against confirmed influenza. Conclusions The effectiveness of pandemic vaccines in preventing confirmed pandemic A(H1N1) influenza on the field was high, consistently with published findings. It was significantly lower against ILI. This is unsurprising since not all ILI cases are caused by influenza. Trivalent 2009-2010 seasonal vaccines had a statistically significant effectiveness in preventing ILI and confirmed pandemic influenza, but were not better in preventing confirmed pandemic influenza than in preventing ILI. This lack of difference might be indicative of selection bias.
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis

We describe a large-scale random approach termed reduced representation bisulfite sequencing (RRBS) for analyzing and comparing genomic methylation patterns. BglII restriction fragments were size-selected to 500–600 bp, equipped with adapters, treated with bisulfite, PCR amplified, cloned and sequenced. We constructed RRBS libraries from murine ES cells and from ES cells lacking DNA methyltransferases Dnmt3a and 3b and with knocked-down (kd) levels of Dnmt1 (Dnmt[1kd,3a−/−,3b−/−]). Sequencing of 960 RRBS clones from Dnmt[1kd,3a−/−,3b−/−] cells generated 343 kb of non-redundant bisulfite sequence covering 66212 cytosines in the genome. All but 38 cytosines had been converted to uracil indicating a conversion rate of >99.9%. Of the remaining cytosines 35 were found in CpG and 3 in CpT dinucleotides. Non-CpG methylation was >250-fold reduced compared with wild-type ES cells, consistent with a role for Dnmt3a and/or Dnmt3b in CpA and CpT methylation. Closer inspection revealed neither a consensus sequence around the methylated sites nor evidence for clustering of residual methylation in the genome. Our findings indicate random loss rather than specific maintenance of methylation in Dnmt[1kd,3a−/−,3b−/−] cells. Near-complete bisulfite conversion and largely unbiased representation of RRBS libraries suggest that random shotgun bisulfite sequencing can be scaled to a genome-wide approach.
Performance of Recommendation Systems in Dynamic Streaming Environments

In this paper, we study the behavior of collaborative filtering based recommendations under evolving user profile scenarios. We propose a systematic validation methodology that allows for simulating various controlled user profile evolution scenarios and validating the studied recommendation strategies. Through the presented work, we observe the effect of the curse of dimensionality and sparsity that can wreck havoc on collaborative filtering in a streaming scenario, and conclude that a hybrid approach with both content and collaborative filtering may be the way to go in a high sparsity streaming scenario.
The Candida albicans-Specific Gene EED1 Encodes a Key Regulator of Hyphal Extension

The extension of germ tubes into elongated hyphae by Candida albicans is essential for damage of host cells. The C. albicans-specific gene EED1 plays a crucial role in this extension and maintenance of filamentous growth. eed1Δ cells failed to extend germ tubes into long filaments and switched back to yeast growth after 3 h of incubation during growth on plastic surfaces. Expression of EED1 is regulated by the transcription factor Efg1 and ectopic overexpression of EED1 restored filamentation in efg1Δ. Transcriptional profiling of eed1Δ during infection of oral tissue revealed down-regulation of hyphal associated genes including UME6, encoding another key transcriptional factor. Ectopic overexpression of EED1 or UME6 rescued filamentation and damage potential in eed1Δ. Transcriptional profiling during overexpression of UME6 identified subsets of genes regulated by Eed1 or Ume6. These data suggest that Eed1 and Ume6 act in a pathway regulating maintenance of hyphal growth thereby repressing hyphal-to-yeast transition and permitting dissemination of C. albicans within epithelial tissues.
A Hereditary Enteropathy Caused by Mutations in the SLCO2A1 Gene, Encoding a Prostaglandin Transporter

Previously, we proposed a rare autosomal recessive inherited enteropathy characterized by persistent blood and protein loss from the small intestine as chronic nonspecific multiple ulcers of the small intestine (CNSU). By whole-exome sequencing in five Japanese patients with CNSU and one unaffected individual, we found four candidate mutations in the SLCO2A1 gene, encoding a prostaglandin transporter. The pathogenicity of the mutations was supported by segregation analysis and genotyping data in controls. By Sanger sequencing of the coding regions, 11 of 12 other CNSU patients and 2 of 603 patients with a diagnosis of Crohn’s disease were found to have homozygous or compound heterozygous SLCO2A1 mutations. In total, we identified recessive SLCO2A1 mutations located at seven sites. Using RT-PCR, we demonstrated that the identified splice-site mutations altered the RNA splicing, and introduced a premature stop codon. Tracer prostaglandin E2 uptake analysis showed that the mutant SLCO2A1 protein for each mutation exhibited impaired prostaglandin transport. Immunohistochemistry and immunofluorescence analyses revealed that SLCO2A1 protein was expressed on the cellular membrane of vascular endothelial cells in the small intestinal mucosa in control subjects, but was not detected in affected individuals. These findings indicate that loss-of-function mutations in the SLCO2A1 gene encoding a prostaglandin transporter cause the hereditary enteropathy CNSU. We suggest a more appropriate nomenclature of “chronic enteropathy associated with SLCO2A1 gene” (CEAS).
Arthritis-Associated HLA-DR Molecules Sclerosis- and Rheumatoid Binding Motifs of Copolymer 1 to Multiple

Copolymer 1 (Cop 1, poly (Y, E, A, K)) is a random synthetic amino acid copolymer effective in the treatment of relapsing forms of multiple sclerosis (MS). Cop 1 binds promiscuously, with high afﬁnity and in a peptide-speciﬁc manner to puriﬁed MS-associated HLA-DR2 (DRB1*1501) and rheumatoid arthritis-associated HLA-DR1 (DRB1*0101) or HLA-DR4 (DRB1*0401) molecules. In the present work at least 95% of added Cop 1 could be bound to recombinant “empty” HLA-DR1 and -DR4, and 80% could be bound to HLA-DR2 proteins. Amino acid composition, HPLC proﬁles, and sequencing patterns of Cop 1 eluted by acid extraction from HLA-DR molecules were similar to those of the unseparated Cop 1. Protruding N-terminal ends of Cop 1 bound to HLA-DR1, -DR2, or -DR4 molecules were then treated with aminopeptidase I, followed by elution, HPLC, and pool sequencing. In contrast to untreated or unbound Cop 1, this material exhibited distinct motifs at some positions with increases in levels of E at the ﬁrst and second cycles, of K at the second and third cycles, and of Y (presumably at P1 of the bound peptide) at the third to ﬁfth cycles, regardless of the HLA-DR molecule employed. No preference was seen at the following cycles that were mainly A. These ﬁrst pooled HLA-DR binding epitopes provide clues to the components of Cop 1 that are biologically active in suppressing MS and possibly rheumatoid arthritis. The Journal of Immunology, 1999, 162:
Accumulation of Flavonoids in an Ntra Ntrb Mutant Leads to Tolerance to Uv-c

NADPH-dependent thioredoxin reductases (NTRs) are key regulatory enzymes determining the redox state of thioredoxins. There are two genes encoding NTRs (NTRA and NTRB) in the Arabidopsis genome, each encoding a cytosolic and a mitochondrial isoform. A double ntra ntrb mutant has recently been characterized and shows slower plant growth, slightly wrinkled seeds and a remarkable hypersensitivity to buthionine sulfoximine (BSO), a specific inhibitor of gluta-thione biosynthesis. In this paper, we demonstrate that this mutant also accumulates higher level of flavonoids. Analysis of transcriptome data showed that several genes of the flavonoid pathway are overexpressed in the ntra ntrb mutant. Accumulation of flavonoids is generally considered a hallmark of plant stress. Nevertheless, no elevation of the expression of genes encoding ROS-detoxification enzymes was observed, suggesting that the ntra ntrb plants do not suffer from oxidative disease. Another hypothesis suggests that flavonoids are specifically synthesized in the ntra ntrb mutant in order to rescue the inactivation of NTR. To test this, the ntra ntrb mutant was crossed with transparent testa 4 (tt4) plants with a mutation in the gene encoding the first enzyme in flavonoid biosynthesis. As ntra ntrb plants are more resistant to UV-C treatment than wild-type plants, this higher resistance was abolished in the ntra ntrb tt4 mutant, suggesting that accumulation of flavonoids in the ntra ntrb mutant protects plants against UV-light.
Biocontrol and plant growth-promoting activity of rhizobacteria from Chinese fields with contaminated soils

The aim of this study was to inventory the types of plant growth‐promoting rhizobacteria (PGPR) present in the rhizosphere of plants grown in soils contaminated with heavy metals, recalcitrant organics, petroleum sewage or salinity in China. We screened 1223 isolates for antifungal activity and about 24% inhibited Rhizoctonia solani or Sclerotinia sclerotiorum. Twenty‐four strains inhibitory to R. solani, Gaeumannomyces graminis var. tritici and/or S. sclerotiorum and representing the dominant morphotypes were assayed for PGPR activity. Seven strains contained phlD, prnD, pltC or phzF genes and produced the antibiotics 2,4‐diacetylphloroglucinol, pyrrolnitrin, pyoluteorin and phenazines respectively. Six strains contained acdS, which encodes 1‐aminocyclopropane‐1‐carboxylic acid deaminase. Phylogenetic analysis of 16S rDNA and phlD, phzF and acdS genes demonstrated that some strains identified as Pseudomonas were similar to model PGPR strains Pseudomonas protegens Pf‐5, Pseudomonas chlororaphis subsp. aureofaciens 30–84 and P. brassicacearum Q8r1‐96. Pseudomonas protegens‐ and P. chlororaphis‐like strains had the greatest biocontrol activity against Rhizoctonia root rot and take‐all of wheat. Pseudomonas protegens and P. brassicacearum‐like strains showed the greatest promotion of canola growth. Our results indicate that strains from contaminated soils are similar to well‐described PGPR found in agricultural soils worldwide.
An integrated framework for devising optimum generation schedules

An integrated framework for generating optimum unit commitment and dispatch schedules is presented in this paper. The work reported here employs a hybrid technique by which a genetic population can be confined to a set of feasible solutions. Heuristics are used to ensure that all the constraints, both linear and nonlinear, are fuQilled for each member of the population. The use of this technique, which combines the advantages of knowkdgebased methods with the strengths of evolutionary algorithms, results in consideruble reduction in computing time, making its application viable in daily operation scheduling.
Automatic artifacts removal from epileptic EEG using a hybrid algorithm

Electroencephalogram (EEG) examination plays a very important role in the diagnosis of disorders related to epilepsy in clinic. However, epileptic EEG is often contaminated with lots of artifacts such as electrocardiogram (ECG), electromyogram (EMG) and electrooculogram (EOG). These artifacts confuse EEG interpretation, while rejecting EEG segments containing artifacts probably results in a substantial data loss and it is very time-consuming. The purpose of this study is to develop a novel algorithm for removing artifacts from epileptic EEG automatically. The collected multi-channel EEG data are decomposed into statistically independent components with Independent Component Analysis (ICA). Then temporal and spectral features of each independent component, including Hurst exponent, skewness, kurtosis, largest Lyapunov exponent and frequency-band energy extracted with wavelet packet decomposition, are calculated to quantify the characteristics of different artifact components. These features are imported into trained support vector machine to determine whether the independent components represent EEG activity or artifactual signals. Finally artifact-free EEGs are obtained by reconstructing the signal with artifact-free components. The method is evaluated with EEG recordings acquired from 15 epilepsy patients. Compared with previous work, the proposed method can remove artifacts such as baseline drift, ECG, EMG, EOG, and power frequency interference automatically and efficiently, while retaining important features for epilepsy diagnosis such as interictal spikes and ictal segments.
Deferred Incremental Refresh of XML Materialized Views : Algorithms and Performance Evaluation

The view mechanism can provide the user with an appropriate portion of database through data filtering and integration. Views are often materialized for query performance improvement, and in that case, their consistency needs to be maintained against the updates of the underlying data. They can be either recomputed or incrementally refreshed by reflecting only the relevant updates. With the emergence of XML as the standard for data exchange on the Web, active research is under way for efficient storing and querying XML documents with the DBMS. In this paper, we investigate XML views, their materialization and incremental refresh. The object-relational DBMS is employed for storing XML documents and their materialized views, and the update log is used for deferred view refresh. The algorithms for checking a update's relevance to views and for generating the operations and data necessary for view refresh are proposed. The experimental results show that the proposed scheme outperforms recomputation of XML views.
Enhanced Antitumor Effect of Oncolytic Adenovirus Expressing Interleukin-12 and B7-1 in an Immunocompetent Murine Model

Purpose: We investigated whether an armed viral platform, where lytic property of a viral infection is coupled to viral-mediated delivery of therapeutic genes, could increase the therapeutic potential of a viral-based therapy. Experimental Design: We generated interleukin (IL)-12-expressing oncolytic adenovirus (YKL-IL-12) and IL-12- and B7-1-expressing (YKL-IL12/B7) oncolytic adenovirus. Therapeutic efficacy of these newly engineered adenoviruses was then evaluated in vivo using an immunocompetent mouse bearing murine melanoma B16-F10 tumors. Overall survival was assessed with the Kaplan-Meier method. The induction of immune cell cytotoxicity was assessed by CTL assay, IFN-γ enzyme-linked immunospot assay, and immunohistochemical studies. Results: YKL-IL12/B7 oncolytic adenovirus, expressing both IL-12 and B7-1, showed a higher incidence of complete tumor regression compared with the analogous oncolytic adenovirus, YKL-1, or IL-12-expressing, YKL-IL12. Significant survival advantage was also seen in response to YKL-IL12/B7. Moreover, IL-12 and IFN-γ levels produced in tumors treated with YKL-IL12/B7 was significantly greater than those treated with YKL-IL12. The enhanced survival advantage was mediated by the induction of immune cell cytotoxicity. In agreement with these results, massive infiltration of CD4+ and CD8+ T cells into tissues surrounding the necrotic area of the tumor was observed following in situ delivery of YKL-IL12/B7. Conclusion: Combination of oncolysis and the enhancement of antitumor immune response by oncolytic adenovirus expressing both IL-12 and B7-1 elicits potent antitumor effect and survival advantage.
Refining Chandra/ACIS Subpixel Event Repositioning Using a Backside-illuminated CCD Model

Subpixel event repositioning (SER) techniques have been demonstrated to significantly improve the already unprecedented spatial resolution of Chandra X-ray imaging with the Advanced CCD Imaging Spectrometer (ACIS). Chandra CCD SER techniques are based on the premise that the impact position of events can be refined, based on the distribution of charge among affected CCD pixels. ACIS SER models proposed thus far are restricted to corner split (3 and 4 pixel) events and assume that such events take place at the split-pixel corners. To improve the event-counting statistics, we modified the ACIS SER algorithms to include 2 pixel split events and single-pixel events, using refined estimates for photon impact locations. Furthermore, simulations that make use of a high-fidelity backside-illuminated (BI) CCD model demonstrate that mean photon impact positions for split events are energy dependent, leading to further modification of subpixel event locations according to event type and energy, for BI ACIS devices. Testing on Chandra CCD X-ray observations of the Orion Nebula Cluster indicates that these modified SER algorithms further improve the spatial resolution of Chandra/ACIS, to the extent that the spreading in the spatial distribution of photons is dominated by the high-resolution mirror assembly, rather than by ACIS pixelization.