Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative Analysis of Phosphotyrosine Signaling Networks Triggered by CD3 and CD28 Costimulation in Jurkat Cells1

The mechanism by which stimulation of coreceptors such as CD28 contributes to full activation of TCR signaling pathways has been intensively studied, yet quantitative measurement of costimulation effects on functional TCR signaling networks has been lacking. In this study, phosphotyrosine networks triggered by CD3, CD28, or CD3 and CD28 costimulation were analyzed by site-specific quantitative phosphoproteomics, resulting in identification of 101 tyrosine and 3 threonine phosphorylation sites and quantification of 87 sites across four cell states. As expected, CD3 stimulation induced phosphorylation of CD3 chains and upstream components of TCR pathways such as Zap70, while CD28 stimulation induced phosphorylation of CD28, Vav-1, and other adaptor proteins including downstream of tyrosine kinase 1, Grb2-associated protein 2 (Grap2), and Wiskott-Aldrich syndrome protein. CD3 and CD28 costimulation induced a complex response including decreased threonine phosphorylation in the ERK1 and ERK2 activation loops and increased phosphorylation of selected tyrosine sites on ERK1/2, p38, phospholipase C-γ, Src homology 2 domain-containing transforming protein 1, Grap2, and Vav-1, potentiating T cell activation. Hierarchical clustering and self-organizing maps were used to identify modules of coregulated phosphorylation sites within the network. Quantitative information in our study suggests quantitative and qualitative contribution by costimulation of CD28 on CD3-stimulated TCR signaling networks via enhanced phosphorylation of phospholipase C-γ/Src homology 2 domain-containing transforming protein 1/Grap2/Vav-1 and their effects on downstream components including MAPKs.
Bond‐Based 2D Quadratic Fingerprints in QSAR Studies: Virtual and In vitro Tyrosinase Inhibitory Activity Elucidation

In this report, we show the results of quantitative structure–activity relationship (QSAR) studies of tyrosinase inhibitory activity, by using the bond‐based quadratic indices as molecular descriptors (MDs) and linear discriminant analysis (LDA), to generate discriminant functions to predict the anti‐tyrosinase activity. The best two models [Eqs (6) and (12)] out of the total 12 QSAR models developed here show accuracies of 93.51% and 91.21%, as well as high Matthews correlation coefficients (C) of 0.86 and 0.82, respectively, in the training set. The validation external series depicts values of 90.00% and 89.44% for these best two equations (6) and (12), respectively. Afterwards, a second external prediction data are used to perform a virtual screening of compounds reported in the literature as active (tyrosinase inhibitors). In a final step, a series of lignans is analysed using the in silico‐developed models, and in vitro corroboration of the activity is carried out. An issue of great importance to remark here is that all compounds present greater inhibition values than Kojic Acid (standard tyrosinase inhibitor: IC50 = 16.67 μm). The current obtained results could be used as a framework to increase the speed, in the biosilico discovery of leads for the treatment of skin disorders.
Binocular Perceptual Model for Symmetric and Asymmetric 3D Stereoscopic Image Compression

The objective approaches of 3D image quality assessment play a key role in the development of compression standards and various 3D multimedia applications. The quality assessment of 3D images faces many new challenges, e.g. asymmetric stereo compression, depth perception, and virtual view synthesis, as compared with its 2D counterparts. Moreover, the widely used 2D image quality metric (e.g. PSNR) cannot be directly applied to deal with these newly introduced challenges. This statement can be verified by the low correlation between the computed objective measures and the subjectively measured mean opinion scores (MOS), when 3D images are the tested targets. In order to meet these challenges, in this work, besides traditional 2D image metrics, two binocular behaviors - the binocular combination and the Binocular Frequency Integration (BFI), are utilized as the bases for measuring the quality of stereoscopic 3D images. The effectiveness of BFI-based metrics is verified by conducting subjective evaluations on a publicly available stereo image dataset. Experimental results show that significant consistency could be reached between the measured MOS and the BFI-based metrics, in which the correlation coefficient between them can go up to 0.89 even if the stereo images have been asymmetrically HEVC compressed. Based on the proposed quality metric, we find that asymmetric-stereo compression schemes outperform the corresponding symmetric ones in high bit rate scenarios, which opens up a new research direction for 3D stereo image/video compression studies.
Three‐dimensional reconstruction of the human skeletal muscle mitochondrial network as a tool to assess mitochondrial content and structural organization

Mitochondria undergo continuous changes in shape as result of complex fusion and fission processes. The physiological relevance of mitochondrial dynamics is still unclear. In the field of mitochondria bioenergetics, there is a need of tools to assess cell mitochondrial content. To develop a method to visualize mitochondrial networks in high resolution and assess mitochondrial volume.
Conditional survival of patients with the four major histologic subgroups of lung cancer in Denmark.

PURPOSE The survival probability of patients with lung cancer is usually based on the extent of disease as assessed at the time of diagnosis. The discouraging 5-year survival is often reported (< 10%) without taking into account changes in the survival probability as time advances from diagnosis. PATIENTS AND METHODS Conditional survival estimates by sex, age, extent of disease, and histology were estimated for patients diagnosed with lung cancer in Denmark from 1943 to 1997. Survival probabilities were calculated by the Kaplan-Meier method, and cumulative survival estimates were used to derive conditional survival estimates. RESULTS For every additional year survived, the probability of surviving the next 5 years increases from 33% (men) and 36% (women) after the first year, to 60% (men) and 67% (women) who have survived 5 years. The 5-year survival probability of patients younger than 49 years who had survived the first year was 33%, and increased to 81% after the fifth year. Corresponding estimates for 60- to 69-year-old patients were 23% and 52%. The conditional survival differed greatly among patients with localized and regional disease (29% and 10%, respectively) in the first year, but converged with time (52% and 47%, respectively) after 5 years. The conditional survival is similar in patients with squamous cell carcinoma, adenocarcinoma, and large-cell carcinoma, but is markedly lower in patients with small-cell carcinoma. CONCLUSION For patients who have survived more than 1 year, the conditional survival probability provides a more accurate estimate of survival as compared with the conventional observed survival rates.
Gaussian Selection with Non-Overlapping Clusters for ASR in Embedded Devices

In this paper we propose a memory efficient version of the Gaussian selection (GS) scheme, which is used for speeding up the likelihood calculations of an ASR system. The memory savings are achieved by using non-overlapping (disjoint) clusters instead of the overlapping clusters normally used in GS. As we will show, the new scheme achieves 66% computational savings with a relative increase in word error rate (WER) of 4%. We will also show, that combining the new GS scheme with frame rate reduction and feature masking provides further savings in computation. 75% (4% increase in WER) and 68% (3.5% increase in WER) savings were obtained by adding frame rate reduction and feature masking, respectively
A scoping review protocol on the roles and tasks of peer reviewers in the manuscript review process in biomedical journals

Introduction The primary functions of peer reviewers are poorly defined. Thus far no body of literature has systematically identified the roles and tasks of peer reviewers of biomedical journals. A clear establishment of these can lead to improvements in the peer review process. The purpose of this scoping review is to determine what is known on the roles and tasks of peer reviewers. Methods We will use the methodological framework first proposed by Arksey and O’Malley and subsequently adapted by Levac et al and the Joanna Briggs Institute. The scoping review will include all study designs, as well as editorials, commentaries and grey literature. The following eight electronic databases will be searched (from inception to May 2017): Cochrane Library, Cumulative Index to Nursing and Allied Health Literature, Educational Resources Information Center, EMBASE, MEDLINE, PsycINFO, Scopus and Web of Science. Two reviewers will use inclusion and exclusion criteria based on the ‘Population–Concept–Context’ framework to independently screen titles and abstracts of articles considered for inclusion. Full-text screening of relevant eligible articles will also be carried out by two reviewers. The search strategy for grey literature will include searching in websites of existing networks, biomedical journal publishers and organisations that offer resources for peer reviewers. In addition we will review journal guidelines to peer reviewers on how to perform the manuscript review. Journals will be selected using the 2016 journal impact factor. We will identify and assess the top five, middle five and lowest-ranking five journals across all medical specialties. Ethics and dissemination This scoping review will undertake a secondary analysis of data already collected and does not require ethical approval. The results will be disseminated through journals and conferences targeting stakeholders involved in peer review in biomedical research.
Worldwide AI

National Information and Communications Technology Australia (NICTA) is the largest ICT research center in Australia, having been established 10 years ago in 2002. It has five laboratories in four Australian capital cities: Sydney, Canberra, Melbourne, and Brisbane. There are currently around 700 staff and Ph.D. students working at NICTA. In June 2009, the 100th Ph.D. student to study at NICTA graduated. At present and averaged over the year, one new Ph.D. student studying at NICTA graduates every 10 days. NICTA has close links with its university members (Australian National University, the University of New South Wales, and the University of Melbourne) as well as with its partner universities (University of Sydney, Griffith University, Queensland University of Technology, University of Queensland, and most recently Monash University). Many of the researchers at NICTA are seconded from these universities. In addition, most of the other researchers at NICTA hold adjunct positions at one of these universities, enabling them to teach courses and supervise Ph.D. students. NICTA also has close links with a number of other research organizations (including Australia’s CSIRO, France’s INRIA, Japan’s NII, and Germany’s Fraunhofer Institute) and major companies (including Microsoft, Google, SAP, and Ericsson). Worldwide AI
Prevalent combination of virulence and plasmidic-encoded resistance in ST 131 Escherichia coli strains

Escherichia coli ST131 is an important cause of multidrug-resistant infections. Thus, the aim of this study was to evaluate the concomitant presence of resistance plasmids and pathogenicity islands (PAIs) in ST131 E. coli. From 97 extraintestinal E. coli characterized for antimicrobial susceptibility and extended-spectrum β-lactamase production, 16% of isolates were identified as CTX-M-15 producers. These strains were studied by PFGE, MLST, and phylogroups, plasmid groups, PAIs, and plasmid-mediated quinolone-resistance determinants. MLST identified one ST10 strain from phylogroup A and the remaining isolates were ST131, from group B2. Despite the genetic variability, 64% of ST131 strains presented a profile composed by PAI IV536, PAI ICFT073, and PAI IICFT073, IncF plasmid, blaCTX-M-15, and aac(6’)-lb-cr genes. The prevalent virulence and resistance profile detected among the strains may constitute an optimal combination of factors, which allow E. coli ST131 to maintain both features becoming concomitantly virulent and extremely resistant.
The immune landscape of human tumors

Understanding the spontaneous immune response of cancer patients is critical for the design of efficient anticancer immunotherapies. The power of integrative tumor immunology approaches allowed for a comprehensive view of the immune system evolution in the course of tumor progression and recurrence. We have demonstrated that tumor-infiltrating immune cells are spatiotemporally regulated, a finding that has profound implications for the development of efficient anticancer immunotherapies.
Author's Personal Copy Computer-aided Design Corner Cutting with Trapezoidal Augmentation for Area-preserving Smoothing of Polygons and Polylines

In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: a b s t r a c t Recently, a new subdivision method was introduced by the author for smoothing polygons and polylines while preserving the enclosed area [Gordon D. Corner cutting and augmentation: an area-preserving method for smoothing polygons and polylines. The new technique, called ''corner cutting and augmentation'' (CCA), operates by cutting corners with line segments and adding the cut area of each corner to two augmenting structures constructed on the two incident edges; this operation can be iterated as needed. Area is preserved in a local sense, meaning that when a corner is cut, the cut area is added to the other side of the line in immediate proximity to the cut corner. Thus, CCA is also applicable to self-intersecting polygons and polylines, and it enables local control. CCA was originally developed with triangular augmentation, which was called CCA1. This work presents CCA2, in which the augmenting structures are trapezoids. A theoretical result from previous work is used to show that certain implementation restrictions guarantee the existence and the G 1-continuity of the limit curve of CCA2, and also the preservation of convexity. The main difference between CCA1 and CCA2 is that the limit curve of CCA1 does not contain straight line segments, while CCA2 can contain such segments. CCA2 allows the user to determine how closely each iteration follows its previous polygon. Potential applications include computer aided geometric design, an alternative to spline approximation, an aid to artistic design, and a possible alternative to multiresolution curves.
Parallelizing elimination orders with linear fill

This paper presents an algorithm for finding parallel elimination orders for Gaussian elimination. Viewing a system of equations as a graph, the algorithm can be applied directly to interval graphs and chordal graphs. For general graphs, the algorithm can be used to parallelize the order produced by some other heuristic such as minimum degree. In this case, the algorithm is applied to the chordal completion that the heuristic generates from the input graph. In general, the input to the algorithm is a chordal graph G with n nodes and m edges. The algorithm produces an order with height at most O(log/sup 3/ n) times optimal, fill at most O(m), and work at most O(W*(G)), where W*(G) is the minimum possible work over all elimination orders for G. Experimental results show that when applied after some other heuristic, the increase in work and fill is usually small. In some instances the algorithm obtains an order that is actually better, in terms of work and fill, than the original one. We also present an algorithm that produces an order with a factor of log n less height, but with a factor of O(/spl radic/log n) more fill.
Change detection and analysis with radarsat-1 SAR image

In the present paper, according to data analysis, the problem of change detection has been addressed with unsupervised change detection with multi-temporal single- channel single-polarization RADARSAT-1 SAR images. Method proposed in this paper is based on four main steps: (1) Data preprocessing. SAR images are rectified and calibrated to Gauss-Kruger projection firstly. Moreover they are co-registered to ensure the condition of good accuracy of change detection. (2) Change detection. The window log-ratio approach is adopted to compare multi-temporal SAR data, because of the multiplicative speckle in the images. Then a proper window is selected to average pixels from the two SAR data in log-ratio process instead of pixel by pixel. (3) Selection of optimal threshold value. Minimum error threshold is applied to find the optimal threshold. (4) Change detection map can be obtained by segmentation of window log-ratio image. Experiments show the approach deal well with change detection in water area.
An improved LMMSE algorithm for SC-FDMA

The channel estimation algorithm which has excellent performance is necessary for Single Carrier Frequency Division Multiple Access (SC-FDMA) system. The traditional Least Square (LS) algorithm and Linear Minimum Mean-Square (LMMSE) algorithm exist many problems. The problem of the LMMSE algorithm which is too complex is found to be applied effectively by researching LMMSE algorithm. The traditional LMMSE algorithm can be improved with the help of Jacobi iterative algorithm for solving linear equations. Meantime, theoretical analysis and simulation results indicate that: The improved LMMSE algorithm has more superior performance at low SNR, it not only can reduce the computational complexity, but also has more precise estimation result.
Defining the role adjustment profile of learners and instructors online

The purpose of this research was to analyze the experience of post-secondary first time online students combining time spent in the classroom-workshop with an online course access, and their interactions with instructors. In the following discussion, and following Cleveland et al (1) model, a comparison between the categories ‘student’s role adjustment’ and ‘instructors’ role’ is presented.
The Development, Maturation, and Turnover Rate of Mouse Spleen Dendritic Cell Populations

Three distinct subtypes of dendritic cells (DC) are present in mouse spleen, separable as CD4−8α−, CD4+8α−, and CD4−8α+ DC. We have tested whether these represent stages of development or activation within one DC lineage, or whether they represent separate DC lineages. All three DC subtypes appear relatively mature by many criteria, but all retain a capacity to phagocytose particulate material in vivo. Although further maturation or activation could be induced by bacterially derived stimuli, phagocytic capacity was retained, and no DC subtype was converted to the other. Continuous elimination of CD4+8− DC by Ab depletion had no effect on the levels of the other DC subtypes. Bromodeoxyuridine labeling experiments indicated that all three DC subtypes have a rapid turnover (half-life, 1.5–2.9 days) in the spleen, with none being the precursor of another. The three DC subtypes showed different kinetics of development from bone marrow precursors. The CD8α+ spleen DC, apparently the most mature, displayed an extremely rapid turnover based on bromodeoxyuridine uptake and the fastest generation from bone marrow precursors. In conclusion, the three splenic DC subtypes behave as rapidly turning over products of three independent developmental streams.
Recommender system for contextual advertising in IPTV scenarios

This paper presents a recommender system for contextual targeted advertisement in Video-on-demand scenarios. The proposal arises from a real case of a Japanese company planning to add advertisement to its On-Demand IPTV services. The advertisements consist of icon or text-based links that may be shown before, during or after the playing of the film the customer has selected to watch. The goal of the company is to maximize the number of times customers follow the links to advertised sites because its revenues depends on this. Since only a small portion of the advertising links can be included in a movie, these must be selected carefully. This work proposes a recommender system for selecting the most appropriate advertisement for a certain customer based on the success the advertisement has had in the past among other customers having similar preferences. The paper describes the proposed method, shows the implementation work done so far and describes the remaining work in order to test it in the real scenario.
Multiview Canonical Correlation Analysis Networks for Remote Sensing Image Recognition

In the past decade, deep learning (DL) algorithms have been widely used for remote sensing (RS) image recognition tasks. As the most typical DL model, convolutional neural networks (CNNs) achieves outstand performance for big RS data classification. Recently, a variant of CNN, dubbed canonical correlation analysis network (CCANet), was proposed to abstract the two-view image features. Extensive experiments conducted on several benchmark databases validate the effectiveness of CCANet. However, the CCANet structure is powerless when the observations arrive from more than two sources. To serve the multiview purpose, in this letter, we propose multiview CCANets (MCCANets). Particularly, the MCCANet model learns the stacked multiperspective filter banks by the MCCA method and builds a deep convolutional structure. In the output stage, the binarization and the blockwise histogram are employed as nonlinear processing and feature pooling, respectively. To access the effectiveness of the MCCANet, we conduct a host of experiments on the RSSCN7 RS database. Extensive experimental results demonstrate that the MCCANet outperforms the two-view CCANet.
Straight Line Scoring by Clinical Competency Committees Using Emergency Medicine Milestones.

Background In 2013, milestone ratings became a reporting requirement for emergency medicine (EM) residency programs. Programs rate each resident in the fall and spring on 23 milestone subcompetencies. Objective This study examined the incidence of straight line scoring (SLS) for EM Milestone ratings, defined as a resident being assessed the same score across the milestone subcompetencies. Methods This descriptive analysis measured the frequencies of SLS for all Accreditation Council for Graduate Medical Education (ACGME)-accredited EM programs during the 2015-2016 academic year. Outcomes were the frequency of SLS in the fall and spring milestone assessments, changes in the number of SLS reports, and reporting trends. Chi-square analysis compared nominal variables. Results There were 6257 residents in the fall and 6588 in the spring. Milestone scores were reported for 6173 EM residents in the fall (99% of 6257) and spring (94% of 6588). In the fall, 93% (5753 residents) did not receive SLS ratings and 420 (7%) did, with no significant difference compared with the spring (5776 [94%] versus 397 [6%]). Subgroup analysis showed higher SLS results for residents' first ratings (183 of 2136 versus 237 of 4220, P < .0001) and for their final ratings (200 of 2019 versus 197 of 4354, P < .0001). Twenty percent of programs submitted 10% or more SLS ratings, and a small percentage submitted more than 50% of ratings as SLS. Conclusions Most programs did not submit SLS ratings. Because of the statistical improbability of SLS, any SLS ratings reduce the validity assertions of the milestone assessments.