Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimation of Experimental Data Redundancy and Related Statistics.

Redundancy of experimental data is the basic statistic from which the complexity of a natural phenomenon and the proper number of experiments needed for its exploration can be estimated. The redundancy is expressed by the entropy of information pertaining to the probability density function of experimental variables. Since the calculation of entropy is inconvenient due to integration over a range of variables, an approximate expression for redundancy is derived that includes only a sum over the set of experimental data about these variables. The approximation makes feasible an efficient estimation of the redundancy of data along with the related experimental information and information cost function. From the experimental information the complexity of the phenomenon can be simply estimated, while the proper number of experiments needed for its exploration can be determined from the minimum of the cost function. The performance of the approximate estimation of these statistics is demonstrated on two-dimensional normally distributed random data.
Proceedings of the SIGIR 2010 Workshop on the Simulation of Interaction Automated Evaluation of Interactive IR

Simulation of human users engaged in interactive information retrieval (IIR) may be a key resource to enable evaluation of IR systems in interactive settings in ways that are scalable, objective, and cheap to implement. This paper considers generation of simulated users in an operationalist framework. It identifies several challenges due to the cognitive nature of IIR and its highly conditionalized interactions with information systems and suggests a program for user simulation must rely on results from user studies and will need to overcome several difficult modeling problems.
Feasibility of Dual-Task Gait Training for Community-Dwelling Adults after Stroke: A Case Series

This case series explored the feasibility and efficacy of cognitive-motor dual-task gait training in community-dwelling adults within 12 months of stroke. A secondary aim was to assess transfer of training to different dual-task combinations. Seven male participants within 12 months of stroke participated in 12 sessions of dual-task gait training. We examined single and dual-task performance in four different dual-task combinations at baseline, after 6 and 12 sessions, and if possible, at 1-month followup. Feasibility was assessed by asking participants to rate mental and physical fatigue, perceived difficulty, anxiety, and fear of falling at the end of each session. Five of the seven participants demonstrated reduced dual-task cost in gait speed in at least one of the dual-task combinations after the intervention. Analysis of the patterns of interference in the gait and cognitive tasks suggested that the way in which the participants allocated their attention between the simultaneous tasks differed across tasks and, in many participants, changed over time. Dual-task gait training is safe and feasible within the first 12 months after stroke, and may improve dual-task walking speed. Individuals with a combination of physical and cognitive impairments may not be appropriate for dual-task gait training.
SODA A Distributed Data Management Framework for the Internet of Services

SODA (Service Oriented Database Architecture) is a proof-of-concept prototype middleware implementation for data intensive applications, where data of relevance is stored at multiple locations over the Internet. Because of its modularity the used Web Services can be plugged together very easily, almost in a LEGO alike manner. In fact these services provide the business logic for distributed query execution, specifically supporting autonomous databases in heterogeneous environments. Operations used in this framework - like selection, projection, join, product or sort - can be orchestrated (used, added and removed) dynamically. The architecture is based on the WSRF standard and thus supports stateful Web Services. For reasons of portability it is implemented in Java and uses the WSRF-compatible Apache Muse library.
Multi-view stereo and LiDAR for outdoor scene modelling

In this paper we want to start the discussion on whether image based 3-D modelling techniques and especially multi-view stereo can possibly be used to replace LIDAR systems for outdoor 3D data acquisition. Two main issues have to be addressed in this context: (i) camera self-calibration and (ii) dense multi-view depth estimation. To investigate both, we have acquired test data from outdoor scenes with LIDAR and cameras. Using the LIDAR data as reference we provide an evaluation procedure to these two major parts of the 3D model building pipeline. The test images are available for the community as benchmark data.
Predicting fold novelty based on ProtoNet hierarchical classification

MOTIVATION Structural genomics projects aim to solve a large number of protein structures with the ultimate objective of representing the entire protein space. The computational challenge is to identify and prioritize a small set of proteins with new, currently unknown, superfamilies or folds. RESULTS We develop a method that assigns each protein a likelihood of it belonging to a new, yet undetermined, structural superfamily. The method relies on a variant of ProtoNet, an automatic hierarchical classification scheme of all protein sequences from SwissProt. Our results show that proteins that are remote from solved structures in the ProtoNet hierarchy are more likely to belong to new superfamilies. The results are validated against SCOP releases from recent years that account for about half of the solved structures known to date. We show that our new method and the representation of ProtoNet are superior in detecting new targets, compared to our previous method using ProtoMap classification. Furthermore, our method outperforms PSI-BLAST search in detecting potential new superfamilies.
Live cell image segmentation

A major requirement of an automated, real-time, computer vision-based cell tracking system is an efficient method for segmenting cell images. The usual segmentation algorithms proposed in the literature exhibit weak performance on live unstained cell images, which can be characterized as being of low contrast, intensity-variant, and unevenly illuminated. The authors propose a two-stage segmentation strategy which involves: 1) extracting an approximate region containing the cell and part of the background near the cell, and 2) segmenting the cell from the background within this region. The approach effectively reduces the influence of peripheral background intensities and texture on the extraction of a cell region. The experimental results show that this approach for segmenting cell images is both fast and robust. <<ETX>>
Gene Polymorphisms in African Buffalo Associated with Susceptibility to Bovine Tuberculosis Infection

Bovine tuberculosis (BTB) is a chronic, highly infectious disease that affects humans, cattle and numerous species of wildlife. In developing countries such as South Africa, the existence of extensive wildlife-human-livestock interfaces poses a significant risk of Mycobacterium bovis transmission between these groups, and has far-reaching ecological, economic and public health impacts. The African buffalo (Syncerus caffer), acts as a maintenance host for Mycobacterium bovis, and maintains and transmits the disease within the buffalo and to other species. In this study we aimed to investigate genetic susceptibility of buffalo for Mycobacterium bovis infection. Samples from 868 African buffalo of the Cape buffalo subspecies were used in this study. SNPs (n = 69), with predicted functional consequences in genes related to the immune system, were genotyped in this buffalo population by competitive allele-specific SNP genotyping. Case-control association testing and statistical analyses identified three SNPs associated with BTB status in buffalo. These SNPs, SNP41, SNP137 and SNP144, are located in the SLC7A13, DMBT1 and IL1α genes, respectively. SNP137 remained significantly associated after permutation testing. The three genetic polymorphisms identified are located in promising candidate genes for further exploration into genetic susceptibility to BTB in buffalo and other bovids, such as the domestic cow. These polymorphisms/genes may also hold potential for marker-assisted breeding programmes, with the aim of breeding more BTB-resistant animals and herds within both the national parks and the private sector.
Measuring the Effect of Subsidized Training Programs on Movements in Andout of Employment

We present a variety of alternative estimates of the effect of training on the probability of employment for adult male participants in the 1976 Comprehensive Employment and Training Act (CETA) program. Our results suggest that CETA participation increased the probability of employment in the three years after training by from 2 to 5 percentage points. Classroom training programs appear to have had significantly larger effects than on-the--job programs, although the estimated effects of both kinds of programs are consistently positive. We also find that movements in and out of employment for the trainees and a control group of nonparticipants are reasonably well described by a first-order Markov process, conditional on individual heterogeneity. In the context of this model, CETA participation appears to have increased both the probability of moving into employment, and the probability of continuing employment.
A New 13 Million Year Old Gavialoid Crocodylian from Proto-Amazonian Mega-Wetlands Reveals Parallel Evolutionary Trends in Skull Shape Linked to Longirostry

Gavialoid crocodylians are the archetypal longirostrine archosaurs and, as such, understanding their patterns of evolution is fundamental to recognizing cranial rearrangements and reconstructing adaptive pathways associated with elongation of the rostrum (longirostry). The living Indian gharial Gavialis gangeticus is the sole survivor of the group, thus providing unique evidence on the distinctive biology of its fossil kin. Yet phylogenetic relationships and evolutionary ecology spanning ~70 million-years of longirostrine crocodylian diversification remain unclear. Analysis of cranial anatomy of a new proto-Amazonian gavialoid, Gryposuchus pachakamue sp. nov., from the Miocene lakes and swamps of the Pebas Mega-Wetland System reveals that acquisition of both widely separated and protruding eyes (telescoped orbits) and riverine ecology within South American and Indian gavialoids is the result of parallel evolution. Phylogenetic and morphometric analyses show that, in association with longirostry, circumorbital bone configuration can evolve rapidly for coping with trends in environmental conditions and may reflect shifts in feeding strategy. Our results support a long-term radiation of the South American forms, with taxa occupying either extreme of the gavialoid morphospace showing preferences for coastal marine versus fluvial environments. The early biogeographic history of South American gavialoids was strongly linked to the northward drainage system connecting proto-Amazonian wetlands to the Caribbean region.
Genomic profiling of adult acute lymphoblastic leukemia by single nucleotide polymorphism oligonucleotide microarray and comparison to pediatric acute lymphoblastic leukemia

Background Differences in survival have been reported between pediatric and adult acute lymphoblastic leukemia. The inferior prognosis in adult acute lymphoblastic leukemia is not fully understood but could be attributed, in part, to differences in genomic alterations found in adult as compared to in pediatric acute lymphoblastic leukemia. Design and Methods We compared two different sets of high-density single nucleotide polymorphism array genotyping data from 75 new diagnostic adult and 399 previously published diagnostic pediatric acute lymphoblastic leukemia samples. The patients’ samples were randomly acquired from among Caucasian and Asian populations and hybridized to either Affymetrix 50K or 250K single nucleotide polymorphism arrays. The array data were investigated with Copy Number Analysis for GeneChips (CNAG) software for allele-specific copy number analysis. Results The high density single nucleotide polymorphism array analysis of 75 samples of adult acute lymphoblastic leukemia led to the identification of numerous cryptic and submicroscopic genomic lesions with a mean of 7.6 genomic alterations per sample. The patterns and frequencies of lesions detected in the adult samples largely reproduced known genomic hallmarks detected in previous single nucleotide polymorphism-array studies of pediatric acute lymphoblastic leukemia, such as common deletions of 3p14.2 (FHIT), 5q33.3 (EBF), 6q, 9p21.3 (CDKN2A/B), 9p13.2 (PAX5), 13q14.2 (RB1) and 17q11.2 (NF1). Some differences between adult and pediatric acute lymphoblastic leukemia were identified when the pediatric data set was partitioned into hyperdiploid and non-hyperdiploid cases and then compared to the nearly exclusively non-hyperdiploid adult samples. In this analysis, adult samples had a higher rate of deletions of chromosome 17p (TP53) and duplication of 17q. Conclusions Our analysis of adult acute lymphoblastic leukemia cases led to the identification of new potential target lesions relevant for the pathogenesis of acute lymphoblastic leukemia. However, no unequivocal pattern of submicroscopic genomic alterations was found to separate adult acute lymphoblastic leukemia from pediatric acute lymphoblastic leukemia. Therefore, apart from different therapy regimen, differences of prognosis between adult and pediatric acute lymphoblastic leukemia are probably based on genetic subgroups according to cytogenetically detectable lesions but not focal genomic copy number microlesions.
Single-feed Microstrip Antenna with Two-layer Substrate for Circular Polarization

The low cost, high efficiency, single-feed microstrip antenna with a two-layer substrate for circular polarization (CP) is presented. A new CP design of a singlefeed nearly square patch with two truncated square corners is also described here. The two-layer substrate consists of an FR4 dielectric layer and a foam layer. The effects of the foam substrate on the impedance bandwidth, axial ratio, antenna gain (efficiency), and radiation pattern of the circularly polarized microstrip antenna are analyzed and discussed. Results show that the inserted foam substrate can effectively improve the CP performances of a microstrip antenna printed on an FR4 circuit board substrate.
A unification of behavior models

In a software design process, behavior models can be used to support specification, transformation, and verification of behavior designs. In state-of-the-art software design processes, a number of behavior models are utilized to specify behavior designs. Usually, these models are selected and utilized in combination in the design process in an informal way. The unification and integration of behavior models are not addressed thoroughly in existing work and hence results in significant design effort in the design process. In this research, we focus on devising a unification scheme of these behavior models. Designers can specify each part of behavior designs in its suitable behavior model correspondingly. Designs specified in different behavior models can then be unified and integrated on the basis of this work in a formal way. This can reduce integration effort and facilitates further tasks of design transformation and design verification.
Telomeric repeat-containing RNA TERRA: a noncoding RNA connecting telomere biology to genome integrity

Telomeres are dynamic nucleoprotein structures that protect the ends of chromosomes from degradation and activation of DNA damage response. For this reason, telomeres are essential to genome integrity. Chromosome ends are enriched in heterochromatic marks and proper organization of telomeric chromatin is important to telomere stability. Despite their heterochromatic state, telomeres are transcribed giving rise to long noncoding RNAs (lncRNA) called TERRA (telomeric repeat-containing RNA). TERRA molecules play critical roles in telomere biology, including regulation of telomerase activity and heterochromatin formation at chromosome ends. Emerging evidence indicate that TERRA transcripts form DNA-RNA hybrids at chromosome ends which can promote homologous recombination among telomeres, delaying cellular senescence and sustaining genome instability. Intriguingly, TERRA RNA-telomeric DNA hybrids are involved in telomere length homeostasis of telomerase-negative cancer cells. Furthermore, TERRA transcripts play a role in the DNA damage response (DDR) triggered by dysfunctional telomeres. We discuss here recent developments on TERRA's role in telomere biology and genome integrity, and its implication in cancer.
The impact of simulation-based teaching on home hemodialysis patient training

Background Simulation has been associated with positive educational benefits in the training of healthcare professionals. It is unknown whether the use of simulation to supplement patient training for home hemodialysis (HHD) will assist in improving a patient's transition to home. We aim to assess the impact of simulation training on home visits, retraining and technique failure. Methods Since February 2013, patients training for HHD are required to dialyze independently in a dedicated training room (innovation room) which simulates a patient's home prior to graduation from the program. We performed a single-center retrospective, observational, cohort study comparing patients who completed training using the innovation room (n = 28) versus historical control (n = 21). The outcome measures were number of home visits, retraining visits and technique failure. Results Groups were matched for age, gender, race, body mass index and comorbidities. Compared with controls, significantly more cases had a permanent vascular access at the commencement of training (57.1 versus 28.6%, χ2 P = 0.04). Cases spent a median of 2 days [IQR (1.75)] in the innovation room. Training duration was not statistically different between groups {cases: median 10.0 weeks [IQR (6.0)] versus controls: 11.0 [IQR (4.0)]}. Compared with controls, cases showed a trend towards needing less home visits with no difference in the number of re-training session or technique failure. Conclusions Simulation-based teaching in NHHD training is associated with a trend to a reduction in the number of home visits but had no effect on the number of re-training sessions or proportion of patients with technique failure.
Impact of Contact Force Technology on Atrial Fibrillation Ablation: A Meta-Analysis

Background Catheter–tissue contact is essential for effective lesion formation, thus there is growing usage of contact force (CF) technology in atrial fibrillation ablation. We conducted a meta-analysis to assess the impact of CF on clinical outcomes and procedural parameters in comparison to conventional catheter for atrial fibrillation ablation. Methods and Results An electronic search was performed using major databases. Outcomes of interest were recurrence rate, major complications, total procedure, and fluoroscopic times. Continuous variables were reported as standardized mean difference; odds ratios were reported for dichotomous variables. Eleven studies (2 randomized controlled studies and 9 cohorts) involving 1428 adult patients were identified. CF was deployed in 552 patients. The range of CF used was between 2 to 60 gram-force. The follow-up period ranged between 10 and 53 weeks. In comparing CF and conventional catheter groups, the recurrence rate was lower with CF (35.1% versus 45.5%, odds ratio 0.62 [95% CI 0.45–0.86], P=0.004). Shorter procedure and fluoroscopic times were achieved with CF (procedure time: 156 versus 173 minutes, standardized mean difference −0.85 [95% CI −1.48 to −0.21], P=0.009; fluoroscopic time: 28 versus 36 minutes, standardized mean difference −0.94 [95% CI −1.66; −0.21], P=0.01). Major complication rate was lower numerically in the CF group but not statistically significant (1.3% versus 1.9%, odds ratio 0.71 [95% CI 0.29–1.73], P=0.45). Conclusions The use of CF technology results in significant reduction of the atrial fibrillation recurrence rate after atrial fibrillation ablation in comparison to the conventional catheter group. CF technology is able to significantly reduce procedure and fluoroscopic times without compromising complication rate.
Feature Extraction and Identification of Handwritten Characters

Handwritten character recognition techniques are quickly developed during past years. In this paper, we summarize both feature extraction and classification recognition methods of off-line handwritten characters recognition. The feature extraction methods mainly include two classes: statistic features and structure features, and the classification methods usually covers pattern matching, statistical classifier, neural network classifier, etc. These techniques are analyzed and comprised, and the technology trends of handwritten character recognition are also discussed.
Factors Governing the Form of the Relation Between Muscle Force and the Electromyogram ( EMG ) : A Simulation Study

The dependence of the form of the electromyogram (EMG)-force relation on key motoneuron and muscle properties was explored using a simulation approach. Surface EMG signals and isometric forces were simulated using existing motoneuron pool, muscle force, and surface EMG models, based primarily on reported properties of the first dorsal interosseous (FDI) muscle in man. Our simulation results indicate that the relation between electrical and mechanical properties of the individual motor unit level plays the dominant role in determining the overall EMG amplitude-force relation of the muscle, while the underlying motor unit firing rate strategy appears to be a less important factor. However, different motor unit firing rate strategies result in substantially different relations between counts of the numbers of motoneuron discharges and the isometric force. Our simulation results also show that EMG amplitude (estimated as the average rectified value) increases as a result of synchronous discharges of different motor units within the pool, but the magnitude of this increase is determined primarily by the action potential duration of the synchronized motor units. Furthermore, when the EMG effects are normalized to their maximum levels, motor unit synchrony does not exert significant effects on the form of the EMG-force relation, provided that the synchrony level is held similar at different excitation levels.