Miracle-dz/UniFAR-FTUs huggingface dataset:
Thrombin Mutant W215A/E217A Acts as a Platelet GPIb Antagonist

Objective—Thrombin containing the mutations Trp215Ala and Glu217Ala (WE) selectively activates protein C and has potent antithrombotic effects in primates. The aim of this study was to delineate the molecular mechanism of direct WE-platelet interactions under static and shear conditions. Methods and Results—Purified platelets under static conditions bound and spread on immobilized wild-type but not WE thrombin. In PPACK-anticoagulated blood under shear flow conditions, platelets tethered and rolled on both wild-type and WE thrombin, and these interactions were abrogated by the presence of a glycoprotein Ib (GPIb)-blocking antibody. Platelet deposition on collagen was blocked in the presence of WE, but not wild-type thrombin or prothrombin. WE also abrogated platelet tethering and rolling on immobilized von Willebrand factor in whole blood under shear flow. Conclusions—These observations demonstrate that the thrombin mutant WE, while not activating platelets, retains the ability to interact with platelets through GPIb, and inhibits GPIb-dependent binding to von Willebrand factor-collagen under shear.
Health Services OutPatient Experience questionnaire: factorial validity and reliability of a patient-centered outcome measure for outpatient settings in Italy

Purpose The patient-centered approach to health care does not seem to be sufficiently developed in the Italian context, and is still characterized by the biomedical model. In addition, there is a lack of validated outcome measures to assess outpatient experience as an aspect common to a variety of settings. The current study aimed to evaluate the factorial validity, reliability, and invariance across sex of the Health Services OutPatient Experience (HSOPE) questionnaire, a short ten-item measure of patient-centeredness for Italian adult outpatients. The rationale for unidimensionality of the measure was that it could cover global patient experience as a process common to patients with a variety of diseases and irrespective of the phase of treatment course. Patients and methods The HSOPE was compiled by 1,532 adult outpatients (51% females, mean age 59.22 years, standard deviation 16.26) receiving care in ten facilities at the Santa Maria alle Scotte University Hospital of Siena, Italy. The sample represented all the age cohorts. Twelve percent were young adults, 57% were adults, and 32% were older adults. Exploratory and confirmatory factor analyses were conducted to evaluate factor structure. Reliability was evaluated as internal consistency using Cronbach’s α. Factor invariance was assessed through multigroup analyses. Results Both exploratory and confirmatory analyses suggested a clearly defined unidimensional structure of the measure, with all the ten items having salient loadings on a single factor. Internal consistency was excellent (α=0.95). Indices of model fit supported a single-factor structure for both male and female outpatient groups. Young adult outpatients had significantly lower scores on perceived patient-centeredness relative to older adults. No significant difference emerged on patient-centeredness between male and female outpatients. Conclusion The HSOPE questionnaire seemed to be a tool with high acceptability and excellent psychometric properties to measure patient-centeredness as a unidimensional construct. Limitations and implications for future research are discussed.
Population-based study evaluating and predicting the probability of death resulting from thyroid cancer and other causes among patients with thyroid cancer.

PURPOSE The purpose of this study was to evaluate the probability of death for patients with thyroid cancer and construct a comprehensive nomogram based on a competing risks model to predict cumulative incidence of death resulting from thyroid cancer, other cancers, and non-cancer-related causes. PATIENTS AND METHODS Patients diagnosed with thyroid cancer between 1988 and 2003 were selected for the study from the Surveillance, Epidemiology, and End Results program. We estimated probabilities of death resulting from thyroid cancer, other cancers, and noncancer causes and analyzed associations of patient and tumor characteristics with probability of death. A nomogram for predicting probability of death was built using a proportional subdistribution hazard competing risks model. RESULTS The entire cohort comprised 29,225 patients with malignant thyroid cancer. Median duration of follow-up until censoring or death was 85 months (range, 0 to 239 months). Five-year probabilities of death resulting from thyroid cancer, other cancer, and noncancer causes were 1.9%, 0.8%, and 1.7%, respectively. Increasing age and tumor size, male sex, poorly differentiated carcinoma, lymph node involvement, and regional and metastatic disease were associated with increased cumulative incidence of death resulting from thyroid cancer. CONCLUSION A nomogram based on a competing risks model was developed for predicting the probability of death for patients with thyroid cancer. Performance of the model was excellent. This nomogram may be useful for patients and clinicians when predictions are needed.
Serializable snapshot isolation for replicated databases in high-update scenarios

Many proposals for managing replicated data use sites running the Snapshot Isolation (SI) concurrency control mechanism, and provide 1-copy SI or something similar, as the global isolation level. This allows good scalability, since only ww-conflicts need to be managed globally. However, 1-copy SI can lead to data corruption and violation of integrity constraints [5]. 1-copy serializability is the global correctness condition that prevents data corruption. We propose a new algorithm Replicated Serializable Snapshot Isolation (RSSI) that uses SI at each site, and combines this with a certification algorithm to guarantee 1-copy serializable global execution. Management of ww-conflicts is similar to what is done in 1-copy SI. But unlike previous designs for 1-copy serializable systems, we do not need to prevent all rw-conflicts among concurrent transactions. We formalize this in a theorem that shows that many rw-conflicts are indeed false positives that do not risk non-serializable behavior. Our proposed RSSI algorithm will only abort a transaction when it detects a well-defined pattern of two consecutive rw-edges in the serialization graph. We have built a prototype that integrates our RSSI with the existing open-source Postgres-R(SI) system. Our performance evaluation shows that there is a worst-case overhead of about 15% for getting full 1-copy serializability as compared to 1-copy SI in a cluster of 8 nodes, with our proposed RSSI clearly outperforming the previous work [6] for update-intensive workloads.
Ultimate strength prediction of braided textile composites using a multi-scale approach

In this paper, the strength of braided textile composites is predicted using a multi-scale approach bridging the mesoscale and microscale regimes. Mesoscale finite element models of representative unit cells of biaxial and triaxial braided composites are developed for predicting strength. The constituent stresses of tows inside the braided unit cell are calculated using micromechanics. Correlations between mesoscale stresses and microscale constituent stresses are established by using stress amplification factors. After calculating microscale stresses, a micromechanics-based progressive damage model is employed to determine the damage statuses of braided composites. A volume-averaging homogenization method is utilized to eliminate damage localization in the matrix of tows, and a parametric study is performed to evaluate the effects of damage homogenization. Subsequently, the ultimate strength is predicted for braided composites in which the braiding angle ranges from 15° to 75°. The prediction results are compared with the experimental values, and good agreement is observed.
SHEAR STRENGTH OF REINFORCED CONCRETE BEAMS WITHOUT TRANSVERSE REINFORCEMENT

This paper presents a simplified analytical model to compute the shear strength of reinforced concrete members without stirrups. The approach uses basic principles of mechanics and a parametric study of experimental data. The main variables considered are: the compressive strength of concrete; longitudinal reinforcement ratio; and shear span-to-effective depth ratio. Using the simplified analytical model, an evaluation procedure, a parametrically derived equation, and a simplified design equation are proposed to calculate shear strength. The evaluation procedure and equations were compared with test data and found to be in good agreement. In addition, the approach is shown to be accurate, yet simpler than a number of commonly used empirical and analytical expressions. Changes to shear strength expressions in the ACI Code are proposed.
Electronic display system for computational holography

We present an electro-optical apparatus capable of displaying a computer generated hologram (CGH) in real time. The CGH is calculated by a supercomputer, read from a fast frame buffer, and transmitted to a high-bandwidth acousto-optic modulator (AOM). Coherent light is modulated by the AOM and optically processed to produce a three-dimensional image with horizontal parallax.
Replication Study Confirms Link between TSPAN18 Mutation and Schizophrenia in Han Chinese

Schizophrenia (SCZ) is a severe psychiatric disorder associated with many different risk factors, both genetic and environmental. A recent genome-wide association study (GWAS) of Han Chinese identified three single-nucleotide polymorphisms (SNPs rs11038167, rs11038172, and rs835784) in the tetraspanins gene TSPAN18 as possible susceptibility loci for schizophrenia. Hoping to validate these findings, we conducted a case-control study of Han Chinese with 1093 schizophrenia cases and 1022 healthy controls. Using the LDR-PCR method to genotype polymorphisms in TSPAN18, we found no significant differences (P>0.05) between patients and controls in either the allele or genotype frequency of the SNPs rs11038167 and rs11038172. We did find, however, that the frequency of the ‘A’ allele of SNP rs835784 is significantly higher in patients than in controls. We further observed a significant association (OR = 1.197, 95%CI = 1.047–1.369) between risk for SCZ and this ‘A’ allele. These results confirm the significant association, in Han Chinese populations, of increased SCZ risk and the variant of the TSPAN18 gene containing the ‘A’ allele of SNP rs835784.
RAPD and ISSR fingerprints as useful genetic markers for analysis of genetic diversity, varietal identification, and phylogenetic relationships in peanut (Arachis hypogaea) cultivars and wild species.

Abstract: Twenty-one random and 29 SSR primers were used to assess genetic variation and interrelationships among subspecies and botanical varieties of cultivated peanut, Arachis hypogaea (2n = 4x = 40), and phylogenetic relationships among cultivated peanut and wild species of the genus Arachis. In contrast with the previous generalization that peanut accessions lack genetic variation, both random and SSR primers revealed 42.7 and 54.4% polymorphism, respectively, among 220 and 124 genetic loci amplified from 13 accessions. Moreover, the dendrograms based on RAPD, ISSR, and RAPD + ISSR data precisely organized the five botanical varieties of the two subspecies into five clusters. One SSR primer was identified that could distinguish all the accessions analysed within a variety. Although the polymorphic index content varied from 0.1 to 0.5 for both ISSR and RAPD markers, primer index values were substantially higher for RAPD primers (0.35-4.65) than for SSR primers (0.35-1.73). It was possible to identify accessions, particularly those of divergent origins, by RAPD and (or) ISSR fingerprints. Based on these results, marker-based genetic improvement in A. hypogaea appears possible. None of the 486 RAPD and 330 ISSR amplification products were found to be commonly shared among 13 species of section Arachis and one species each of sections Heteranthae, Rhizomatosae, and Procumbentes. Dendrograms constructed from RAPD, ISSR, and RAPD + ISSR data showed overall similar topologies. They could be resolved into four groups corresponding to the species grouped in four taxonomic sections. The present results strongly support the view that Arachis monticola (2n = 4x = 40) and A. hypogaea are very closely related, and indicate that A. villosa and A. ipaensis are the diploid wild progenitors of these tetraploid species.
Microglia from Creutzfeldt-Jakob Disease-Infected Brains Are Infectious and Show Specific mRNA Activation Profiles

ABSTRACT Neurons are often assumed to be the principal sites for replication of the infectious agents causing Creutzfeldt-Jakob disease (CJD), scrapie, and bovine spongiform encephalopathy because they express high levels of normal and pathological prion protein (PrP). However, isolated brain cell types have not been evaluated for either infection or gene expression. Microglia purified from CJD-infected mice showed infectivity comparable to that of starting brain homogenate but expressed ∼50-fold less PrP. CJD-infected microglia also displayed morphological changes indicative of cellular activation. To determine the molecular pathways of activation, we evaluated pertinent transcripts, including those linked to inflammation. Semiquantitative reverse transcription-PCR showed a >4-fold increase in cathepsin S, an enzyme important in antigen presentation, the cytokine interleukin-1β, and the chemokine B-lymphocyte chemoattractant. The profile of microglial changes induced by the CJD agent differed substantially from activation induced by bacterial lipopolysaccharide or by β-amyloid, a structure comparable to pathological PrP. These microglial studies emphasize migratory hematopoietic cells in the dispersion, and possibly replication, of the CJD agent. The low PrP levels in these highly infectious and activated cells further support the concept that pathological PrP is the result of infection rather than the infectious agent itself. Because microglia develop a specific pattern of responses to the CJD agent, microglial markers may be exploited in the diagnosis of these spongiform encephalopathies.
P‐69: PDP Fabricated with Low‐Temperature Processes Below 300°C Using Sol‐Gel Hybrid Polymers (Hybrimer PDP)

PDP was fabricated using low‐temperature processable sol‐gel hybrid polymers (hybrimers) as the dielectric and barrier rib materials replacing the glass frits. All the processes including dielectric coating, barrier rib molding fabrication, phosphor printing and sealing were performed at low temperature below 300°C. This new process is easy, simple and cheap to be capable of producing a large PDP with high yield without applying high temperature processes.
Design of Smart Home System Based on WiFi Smart Plug

This paper presents a low-cost and flexible solution to control and monitor home appliances using Smart Plug devices. The Smart Plug is a power switch which can be accessed via WiFi connection. It integrates two temp sensors, a current sensor and an IRemitter. Users can plug devices into the Smart Plug to remotely switch power on/off, get information of device’s power consumption and ambient temperature, and eventually control the nearby devices using the integrated IR-emitter. There are two ways to access Smart Plug, that is, either connecting it directly in WiFi Ad-Hoc mode or connecting it with a router in WiFi infrastructure mode and accessing online with IP-connectivity. The paper utilizes RESTful based Web services in which the overall system architecture is client/server model and the Web client uses JavaScript and Ajax to transfer data. An Android-based Smartphone application employs standard operations such as Get and Post requests that return responses to communicate between the remote user and the Web server. Depending on the use cases, users can use Smart Plug as lighting switch, timing switch, infrared controller and temp regulator.
An improved fast-response vacuum-UV resonance fluorescence CO instrument

The fast-response resonance fluorescence instrument for the airborne measurement of carbon monoxide described by Gerbig et al. [1996] was modified by implementing an improved optical filter with more efficient optics and an optimized resonance lamp. Besides reductions in size and weight, the new instrument achieves a sensitivity 10 times higher, a lower background (65 ppb compared with 250 ppb), and a faster time response (<0.1 s) than the original instrument. The precision is ±1.5 ppb at an atmospheric mixing ratio of 100 ppb CO, and the detection limit is 3 ppb (2σ) for an integration time of 1 s. First results from the North Atlantic Regional Aerosol Characterization Experiment (ACE-2) campaign during July 1997, when the new instrument was deployed aboard the U.K. Meteorological Office C-130 aircraft, are used to demonstrate the performance of the new instrument.
A Readability Checker with Supervised Learning Using Deep Indicators

Tim vor der Bruck, Sven Hartrumpf, Hermann HelbigIntelligent Information and Communication Systems (IICS)FernUniversitat in Hagen, 58084 Hagen, GermanyE-mail: rstname.lastname@fernuni-hagen.deKeywords: readability, syntactic and semantic analysis, nearest neighborReceived: May 11, 2008Checking for readability or simplicity of texts is important for many institutional and individual users.Formulas for approximately measuring text readability have a long tradition. Usually, they exploit surface-oriented indicators like sentence length, word length, word frequency, etc. However, in many cases, thisinformation is not adequate to realistically approximate the cognitive difculties a person can have tounderstand a text. Therefore we use deep syntactic and semantic indicators in addition. The syntacticinformation is represented by a dependency tree, the semantic information by a semantic network. Bothrepresentations are automatically generated by a deep syntactico-semantic analysis. A global readabilityscore is determined by applying a nearest neighbor algorithm on 3,000 ratings of 300 test persons. Theevaluation showed that the deep syntactic and semantic indicators lead to promising results comparable tothebestsurface-basedindicators. Thecombinationofdeepandshallowindicatorsleadstoanimprovementover shallow indicators alone. Finally, a graphical user interface was developed which highlights difcultpassages, depending on the individual indicator values, and displays a global readability score.Povzetek: Strojno u cenje z odvisnostnimi drevesi je uporabljeno za ugotavljanje berljivosti besedil.
Understanding the visual speech signal

For machines to lipread, or understand speech from lip movement, they decode lip-motions (known as visemes) into the spoken sounds. We investigate the visual speech channel to further our understanding of visemes. This has applications beyond machine lipreading; speech therapists, animators, and psychologists can benefit from this work. We explain the influence of speaker individuality, and demonstrate how one can use visemes to boost lipreading.
Architecture-Based Planning of Software Evolution

Software architecture allows us to make many decisions about a software system and analyze it even before it has been implemented, so as to make planned development possible. Similarly, architecture-based software evolution planning makes planned evolution possible by allowing us to make many decisions about the evolution of a software system and to analyze its evolution at the level of architecture design before software evolution is realized. In this paper, we develop a framework for architecture-based software evolution planning. It is done by defining various foundational terms and concepts, providing a taxonomy of software evolution plans, and then showing how to calculate values for various types of plans. By identifying and defining constituent foundational concepts, this conceptual framework makes precise the notion of "architecture-based software planning". By developing a value-calculation framework for software evolution plans, it also provides a basis for concrete methods for designing and evaluating evolution plans.
Optimizing Multi-Feature Queries for Image Databases

In digital libraries image retrieval queries can be based on the similarity of objects, using several feature attributes like shape, texture, color or text. Such multi-feature queries return a ranked result set instead of exact matches. Besides, the user wants to see only the k top-ranked objects. We present a new algorithm called Quick-Combine (European patent pending, nr. EP 00102651.7) for combining multi-feature result lists, guaranteeing the correct retrieval of the k top-ranked results. For score aggregation virtually any combining function can be used, including weighted queries. Compared to Fagin’s algorithm we have developed an improved termination condition in tuned combination with a heuristic control flow adopting itself narrowly to the particular score distribution. Top-ranked results can be computed and output incrementally. We show that we can dramatically improve performance, in particular for non-uniform score distributions. Benchmarks on practical data indicate efficiency gains by a factor of 30. For very skewed data observed speed-up factors are even larger. These performance results scale through different database sizes and numbers of result sets to combine.
Visualizing Association Rules : Introduction to the R-extension Package arulesViz

Association rule mining is a popular data mining method available in R as the extension package arules . However, mining association rule often results in a very large number of found rules, leaving the analyst with the task to go through all the rules and discover interesting ones. Sifting manually through large sets of rules is time consuming and strenuous. Visualization has a long history of making large data sets better accessible using techniques like selecting and zooming. In this paper we present the R-extension package arulesViz which implements several known and novel visualization techniques to explore association rules. With examples we show how these visualization techniques can be used to analyze a data set
Novel Approach to Meta-Analysis of Microarray Datasets Reveals Muscle Remodeling-related Drug Targets and Biomarkers in Duchenne Muscular Dystrophy

Elucidation of new biomarkers and potential drug targets from high-throughput profiling data is a challenging task due to a limited number of available biological samples and questionable reproducibility of differential changes in cross-dataset comparisons. In this paper we propose a novel computational approach for drug and biomarkers discovery using comprehensive analysis of multiple expression profiling datasets. The new method relies on aggregation of individual profiling experiments combined with leave-one-dataset-out validation approach. Aggregated datasets were studied using Sub-Network Enrichment Analysis algorithm (SNEA) to find consistent statistically significant key regulators within the global literature-extracted expression regulation network. These regulators were linked to the consistent differentially expressed genes. We have applied our approach to several publicly available human muscle gene expression profiling datasets related to Duchenne muscular dystrophy (DMD). In order to detect both enhanced and repressed processes we considered up- and down-regulated genes separately. Applying the proposed approach to the regulators search we discovered the disturbance in the activity of several muscle-related transcription factors (e.g. MYOG and MYOD1), regulators of inflammation, regeneration, and fibrosis. Almost all SNEA-derived regulators of down-regulated genes (e.g. AMPK, TORC2, PPARGC1A) correspond to a single common pathway important for fast-to-slow twitch fiber type transition. We hypothesize that this process can affect the severity of DMD symptoms, making corresponding regulators and downstream genes valuable candidates for being potential drug targets and exploratory biomarkers.