Miracle-dz/UniFAR-FTUs huggingface dataset:
Semiparallel deep neural network hybrid architecture: first application on depth from monocular camera

Abstract. Deep neural networks have been applied to a wide range of problems in recent years. Convolutional neural network is applied to the problem of determining the depth from a single camera image (monocular depth). Eight different networks are designed to perform depth estimation, each of them suitable for a feature level. Networks with different pooling sizes determine different feature levels. After designing a set of networks, these models may be combined into a single network topology using graph optimization techniques. This “semiparallel deep neural network (SPDNN)” eliminates duplicated common network layers and can be further optimized by retraining to achieve an improved model compared to the individual topologies. Four SPDNN models are trained and have been evaluated at two stages on the KITTI dataset. The ground truth images in the first part of the experiment are provided by the benchmark, and for the second part, the ground truth images are the depth map results from applying a state-of-the-art stereo matching method. The results of this evaluation demonstrate that using postprocessing techniques to refine the target of the network increases the accuracy of depth estimation on individual mono images. The second evaluation shows that using segmentation data alongside the original data as the input can improve the depth estimation results to a point where performance is comparable with stereo depth estimation. The computational time is also discussed in this study.
An Evidence-Based Approach to the Management of Chronic Constipation in North America

Systematic Review on the Management of Chronic Constipation in North America Lawrence J. Brandt, M.D., M.A.C.G. , F.A. C.P., F.A. A.P.P.,1 Charlene M. Prather, M.D.,2 Eamonn M.M. Quigley, M.D., F.R. C.P., F.A. C.P., F.A. C.G. , F.R. C.P.I. ,3 Lawrence R. Schiller, M.D., F.A. C.P., F.A. C.G. ,4 Philip Schoenfeld, M.D., M.S.Ed., M.Sc. (Epi),5 and Nicholas J. Talley, M.D., Ph.D.6 1Division of Gastroenterology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY; 2Division of Gastroenterology, Saint Louis University School of Medicine, St. Louis, MO; 3Department of Medicine and Alimentary Pharmabiotic Center, National University of Ireland, Cork, Ireland; 4Division of Gastroenterology, Baylor University Medical Center, Dallas, TX; 5Division of Gastroenterology, University of Michigan School of Medicine, and Center for Excellence in Health Services Research, Veterans Affairs Medical Center, Ann Arbor, MI; 6Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN
Multi‐component apparent diffusion coefficients in human brain: Relationship to spin‐lattice relaxation

In vivo measurements of the human brain tissue water signal decay with b‐factor over an extended b‐factor range up to 6,000 s/mm 2 reveal a nonmonoexponential decay behavior for both gray and white matter. Biexponential parametrization of the decay curves from cortical gray (CG) and white matter voxels from the internal capsule (IC) of healthy adult volunteers describes the decay process and serves to differentiate between these two tissues. Inversion recovery experiments performed in conjunction with the extended b‐factor signal decay measurements are used to make separate measurements of the spin‐lattice relaxation times of the fast and slow apparent diffusion coefficient (ADC) components. Differences between the spin‐lattice relaxation times of the fast and slow ADC components were not statistically significant in either the CG or IC voxels. It is possible that the two ADC components observed from the extended b‐factor measurements arise from two distinct water compartments with different intrinsic diffusion coefficients. If so, then the relaxation results are consistent with two possibilities. Either the spin‐lattice relaxation times within the compartments are similar or the rate of water exchange between compartments is “fast” enough to ensure volume averaged T1 relaxation yet “slow” enough to allow for the observation of biexponential ADC decay curves over an extended b‐factor range. Magn Reson Med 44:292–300, 2000. © 2000 Wiley‐Liss, Inc.
A Method of Error Compensation in Image Based Visual Servo

This paper introduces a practical method which based on edge detecting by Canny operator and line detecting by Hough transform to compensate the error between the center of the special label and the typical target object when use the technology of special label to identify the object in the process of visual servo. The coordinates of the label center can be accurately measured by the program that can find and identify the special label. Two lines which reflect the edge of the object can be obtained by dealing with the edge points obtained using Hough transform by Canny operator. The actual coordinates of the object can be estimated according to the two lines and the coordinates of the special label. The algorithm is described in details and experimented with experiments.
A role for clonal inactivation in T cell tolerance to Mls-1a.

Clonal deletion plays a major part in the maintenance of natural self-tolerance in both normal and transgenic mice. Self antigens that are expressed in the thymus result in the physical elimination of autoreactive thymocytes at a particular stage in their development. For example, the majority V beta 6- and V beta 8.1-bearing T cells that recognize the minor lymphocyte-stimulating antigen, Mls-1a (ref. 10) , are clonally deleted in the thymuses of normal mice and transgenic mice expressing Mls-1a (refs 2, 3, 9). In contrast, a very different mechanism of tolerance involving the functional inactivation, but not elimination, of autoreactive cells, termed clonal inactivation or clonal anergy, has been implicated in some experimentally manipulated systems of tolerance. To test further the mechanisms involved in self-tolerance, we have generated transgenic mice expressing a V beta 8.1 beta chain on greater than 95% of peripheral T cells and have tested tolerance to Mls-1a in these mice. Surprisingly, a significant fraction of the CD4+ peripheral cells that survived deletion were non-responsive in vitro to any stimulus tested. Naturally occurring tolerance to a self antigen expressed in the thymus can thus be mediated by clonal anergy, as well as by clonal deletion.
An Efficient System for Content-Based Hand Language Video Searching under Complex Background

In this paper, we solve the searching problem by high level features used by sign language recognition. Firstly, we find the face in video frames that has complex background, and then we find the left sign and right sign in specific areas. By computing the signs’ length, position, velocity, acceleration, Fourier figure descriptor and etc, we generate the signs’ dynamic features. Consequently, we segment the video frames by motion features. As for each segment, we generate a HMM. When a clip of sign language inputs, we also get the feature serials, and then we compare the possibility of the input serials in each HMM. Experiment results on a large of sign language videos show that our searching system performs much better than existing methods on sign language video searching systems. Compared with the traditional methods, our system reduces the average searching time by half and the retrieval precision has doubled.
Statistical channel model for 60 GHz WLAN systems in conference room environment

In this work, a methodology of statistical channel modeling for 60 GHz WLAN systems is proposed and a channel model for the office conference room environment is developed. The proposed methodology takes into account the most important properties of the indoor 60 GHz propagation channel such as large propagation loss and necessity to use steerable directional antennas by the WLAN stations, quasi-optical propagation nature, clustering of the channel, and significant impact of the polarization characteristics. A general mathematical structure of the channel model that supports all the above 60 GHz propagation channel properties is presented. The application of the proposed methodology is demonstrated by development of a channel model for the conference room environment. Inter cluster, intra cluster, and polarization modeling characteristics are defined in accordance with the proposed methodology and using results of experiments and ray-tracing simulations.
Speed spinal anesthesia revisited: new drugs and their clinical effects

Purpose of review Spinal anesthesia (SPA) has not been popular for day-case surgery because of prolonged neurologic blockade with long-acting local anesthetics such as bupivacaine, thereby delaying discharge. Although the intermediate duration of action of lidocaine and mepivacaine appears to be more suitable for day-case surgery, their use is not deemed appropriate by many because of a high incidence of transient neurologic symptoms (TNSs). The present review summarizes recent clinical data on the intrathecal use of alternative local anesthetics and adjuvants that may offer valuable alternatives to general anesthesia in day-case surgery. Recent findings Prilocaine has a similar intrathecal pharmacokinetic profile as lidocaine but with a significantly lower risk of TNSs. Onset of spinal after 2-chloroprocaine is comparable with lidocaine or prilocaine, but with a considerably shorter duration of action. Also, TNS is clearly less frequent compared with lidocaine. Although its intrathecal use has recently been approved in Europe, this is still considered to be off-label in the USA. Articaine provides an extraordinary fast onset and a short duration of spinal block, the latter being approximately intermediate between chloroprocaine and prilocaine. However, articaine is associated with a high risk for intraoperative hypotension and a small risk for TNS, albeit but less frequent than after lidocaine. Concerns regarding possible neurotoxicity of articaine remain to be resolved. Summary SPA for day cases might become a most valuable method for ambulatory surgery when using short acting local anesthetics. This, however, not only depends on drugs being used but also on infrastructure (post anaesthesia care unit) and organizational issues.
Blind separation of multiple sequences from a single linear mixture using finite alphabet

In this paper, we propose an approach exploiting the relationship between the position of the clustering centers of the observed data and the mixing parameters to realize blind separation of multiple sequences, drawn from finite alphabet set, from a single linear mixture. In theory, we prove that the system estimation by the algorithm is optimum in the sense of least square (LS) by mathematical induction method. In the noise case, the simulation results show that the system estimation deteriorates smoothly with the increasing of noise variance.
Methods to Quantify Soft Tissue–Based Cranial Growth and Treatment Outcomes in Children: A Systematic Review

Context Longitudinal assessment of cranial dimensions of growing children provides healthcare professionals with information about normal and deviating growth as well as treatment outcome. Objective To give an overview of soft tissue–based methods for quantitative longitudinal assessment of cranial dimensions in children until age 6 years and to assess the reliability of these methods in studies with good methodological quality. Data source PubMed, EMBASE, Cochrane Library, Web of Science, Scopus, and CINAHL were searched. A manual search was performed to check for additional relevant studies. Study selection Primary publications on facial growth and treatment outcomes in children younger than age 6 years were included. Data extraction Independent data extraction was performed by two observers. A quality assessment instrument was used to determine methodological quality. Methods used in studies with good methodological quality were assessed for reliability expressed as the magnitude of the measurement error and the correlation coefficient between repeated measurements. Results In total, 165 studies were included, forming three groups of methods: head circumference anthropometry, direct anthropometry, and 2D photography and 3D imaging techniques (surface laser scanning and stereophotogrammetry). In general, the measurement error was below 2 mm, and correlation coefficients were very good. Conclusion Various methods for measuring cranial dimensions have shown to be reliable. Stereophotogrammetry is the most versatile method for quantitative longitudinal assessment of cranial dimensions and shapes in children. However, direct anthropometry continues to be the best method for routine clinical assessments of linear cranial dimensions in growing children until age 6 years.
Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks1[C][W]

Analysis of gene expression data generated by high-throughput microarray transcript profiling experiments has demonstrated that genes with an overall similar expression pattern are often enriched for similar functions. This guilt-by-association principle can be applied to define modular gene programs, identify cis-regulatory elements, or predict gene functions for unknown genes based on their coexpression neighborhood. We evaluated the potential to use Gene Ontology (GO) enrichment of a gene's coexpression neighborhood as a tool to predict its function but found overall low sensitivity scores (13%–34%). This indicates that for many functional categories, coexpression alone performs poorly to infer known biological gene functions. However, integration of cis-regulatory elements shows that 46% of the gene coexpression neighborhoods are enriched for one or more motifs, providing a valuable complementary source to functionally annotate genes. Through the integration of coexpression data, GO annotations, and a set of known cis-regulatory elements combined with a novel set of evolutionarily conserved plant motifs, we could link many genes and motifs to specific biological functions. Application of our coexpression framework extended with cis-regulatory element analysis on transcriptome data from the cell cycle-related transcription factor OBP1 yielded several coexpressed modules associated with specific cis-regulatory elements. Moreover, our analysis strongly suggests a feed-forward regulatory interaction between OBP1 and the E2F pathway. The ATCOECIS resource (http://bioinformatics.psb.ugent.be/ATCOECIS/) makes it possible to query coexpression data and GO and cis-regulatory element annotations and to submit user-defined gene sets for motif analysis, providing an access point to unravel the regulatory code underlying transcriptional control in Arabidopsis (Arabidopsis thaliana).
Joint Workshop on Interfaces and Human Decision Making for Recommender Systems (#IntRS)

As an interactive intelligent system, recommender systems are developed to give recommendations that match users' preferences. Since the emergence of recommender systems, a large majority of research focuses on objective accuracy criteria and less attention has been paid to how users interact with the system and the efficacy of interface designs from users' perspectives. The field has reached a point where it is ready to look beyond algorithms, into users' interactions, decision making processes, and overall experience. Following from the success of the joint IntRS 2014 workshop and previous workshops on Interfaces and Decisions in Recommender Systems, this workshop will focus on the aspect of integrating different theories of human decision making into the construction of recommender systems. It will focus particularly on the impact of interfaces on decision support and overall satisfaction, and on ways to compare and evaluate novel techniques and applications in this area.
The Sequence of the Human Genome

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies—a whole-genome assembly and a regional chromosome assembly—were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional ∼12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.
Predictors of malignancies and overall mortality in Japanese patients with biopsy‐proven non‐alcoholic fatty liver disease

Some patients with non‐alcoholic fatty liver disease (NAFLD) develop hepatocellular carcinoma (HCC) and have higher mortality than others. The evidence causally linking NAFLD to extrahepatic malignancies is scarce. Our aim was to determine the incidence of and risk factors for HCC, extrahepatic cancer and mortality in Japanese patients with biopsy‐proven NAFLD.
High-Capacity Dynamic Indoor Network Employing Optical-Wireless and 60-GHz Radio Techniques

We demonstrate a hybrid radio–optical wireless communication system using a photonic integrated all-optical-cross-connect (OXC) chip to realize a highly reconfigurable and reliable bidirectional indoor wireless network that provides the ultimate capacity per user. By remote wavelength-tuning, narrow optical beams are directed to the users employing a passive two-dimensional beam steering module fixed at the ceiling in each room. Robustness regarding line-of-sight issues is achieved by implementing 60-GHz radio protection channels generated optically using a shared amplitude modulator via the OXC chip. The use of a 35-GHz reflective electroabsorption modulator (REAM) monolithically integrated with a semiconductor optical amplifier (SOA) chip is proposed for upstream wideband analog applications. The REAM-SOA provides similar performances as an REAM, but over a wide range of input optical powers and wavelengths. This mitigates the need for accurate control of the input signal, especially at remote sites where simplicity is strictly required. System experiments showed downstream optical-wireless transmission capacities of up to 35 Gb/s per user and 60-GHz protection channels with a capacity of 20 Gb/s. Upstream radio-over-fiber transmission rates of more than 35 Gb/s have also been achieved.
Lead and delinquency.

g:Profiler (http://biit.cs.ut.ee/gprofiler/) is a public web server for characterising and manipulating gene lists resulting from mining high-throughput genomic data. g:Profiler has a simple, user-friendly web interface with powerful visualisation for capturing Gene Ontology (GO), pathway, or transcription factor binding site enrichments down to individual gene levels. Besides standard multiple testing corrections, a new improved method for estimating the true effect of multiple testing over complex structures like GO has been introduced. Interpreting ranked gene lists is supported from the same interface with very efficient algorithms. Such ordered lists may arise when studying the most significantly affected genes from high-throughput data or genes co-expressed with the query gene. Other important aspects of practical data analysis are supported by modules tightly integrated with g:Profiler. These are: g:Convert for converting between different database identifiers; g:Orth for finding orthologous genes from other species; and g:Sorter for searching a large body of public gene expression data for co-expression. g:Profiler supports 31 different species, and underlying data is updated regularly from sources like the Ensembl database. Bioinformatics communities wishing to integrate with g:Profiler can use alternative simple
Indexing Strategies for Rapid Searches of Short Words in Genome Sequences

Searching for matches between large collections of short (14–30 nucleotides) words and sequence databases comprising full genomes or transcriptomes is a common task in biological sequence analysis. We investigated the performance of simple indexing strategies for handling such tasks and developed two programs, fetchGWI and tagger, that index either the database or the query set. Either strategy outperforms megablast for searches with more than 10,000 probes. FetchGWI is shown to be a versatile tool for rapidly searching multiple genomes, whose performance is limited in most cases by the speed of access to the filesystem. We have made publicly available a Web interface for searching the human, mouse, and several other genomes and transcriptomes with oligonucleotide queries.
Consensus Statement on Research Definitions for Drug-Resistant Tuberculosis in Children

Few children with drug-resistant (DR) tuberculosis (TB) are identified, diagnosed, and given an appropriate treatment. The few studies that have described this vulnerable population have used inconsistent definitions. The World Health Organization (WHO) definitions used for adults with DR-TB and for children with drug-susceptible TB are not always appropriate for children with DR-TB. The Sentinel Project on Pediatric Drug-Resistant Tuberculosis was formed in 2011 as a network of experts and stakeholders in childhood DR-TB. An early priority was to establish standardized definitions for key parameters in order to facilitate study comparisons and the development of an evidence base to guide future clinical management. This consensus statement proposes standardized definitions to be used in research. In particular, it suggests consistent terminology, as well as definitions for measures of exposure, drug resistance testing, previous episodes and treatment, certainty of diagnosis, site and severity of disease, adverse events, and treatment outcome.