Miracle-dz/UniFAR-FTUs huggingface dataset:
BCNTB bioinformatics: the next evolutionary step in the bioinformatics of breast cancer tissue banking

Abstract Here, we present an update of Breast Cancer Now Tissue Bank bioinformatics, a rich platform for the sharing, mining, integration and analysis of breast cancer data. Its modalities provide researchers with access to a centralised information gateway from which they can access a network of bioinformatic resources to query findings from publicly available, in-house and experimental data generated using samples supplied from the Breast Cancer Now Tissue Bank. This in silico environment aims to help researchers use breast cancer data to their full potential, irrespective of any bioinformatics barriers. For this new release, a complete overhaul of the IT and bioinformatic infrastructure underlying the portal has been conducted and a host of novel analytical modules established. We developed and adopted an automated data selection and prioritisation system, expanded the data content and included tissue and cell line data generated from The Cancer Genome Atlas and the Cancer Cell Line Encyclopedia, designed a host of novel analytical modalities and enhanced the query building process. Furthermore, the results are presented in an interactive format, providing researchers with greater control over the information on which they want to focus. Breast Cancer Now Tissue Bank bioinformatics can be accessed at http://bioinformatics.breastcancertissuebank. org/.
Photoselective vaporization with the green light laser vs transurethral resection of the prostate for treating benign prostate hyperplasia: a systematic review and meta‐analysis

Despite high morbidities, TURP is still considered as the ‘gold standard’ for treatment of BPH. Photoselective vaporization of the prostate (PVP) is a promising technique that is emerging as a possible alternative to TURP. However, there remains some debate about the advantages of PVP over TURP and whether PVP will be able to replace TURP as the first‐line surgical treatment. We conducted a meta‐analysis of recent papers on this subject and herein provide the overall efficacy and safety of PVP for treatment of BPH.
2D to cylindrical inverse projection of the wireless capsule endoscopy images

In this paper, a two-dimensional to three-dimensional mapping of the wireless capsule endoscopy (WCE) images is proposed as well as the alignment of the consecutive images. The aim of this project is to reduce the diagnosis time of the doctor using the acquired data. This paper resolves a serious limitation of the inverse projection of the WCE images appeared previously. The novelty of this paper lies in three aspects. Firstly, as the main axis of the WCE is not always aligned with the center of the small bowel, the angle needs to be adjusted to obtain better visual effect. The inverse projected images considering the angle of the WCE are obtained from the innovative mathematical model proposed in this project. After compensating the angle, all the information in the interior wall of the small intestine will be clearly presented. Secondly, the redundancy of the images captured along a trajectory, where, they share a portion of overlapped information is exploited by motion estimation to enhance the final resolution. Therefore, doctors do not need to inspect the same region of the images without any benefit and the diagnosis time is significantly decreased. Finally, the cropped segments are merged into a single image which can fully represent the interior wall of the small intestine.
Bounds on the Volume and Height Distributions for the MIMO Radar Ambiguity Function

The multiple-input multiple-output (MIMO) radar delay-Doppler ambiguity function is introduced as the sum of all auto- and cross-ambiguity functions of the set of K spatially diverse waveforms. The integral of this function over the range-Doppler frequency region occupied by spread clutter relates to the clutter's power at the output of the matched MIMO receiver, and it serves as a measure of orthogonality of the waveforms in this region. We derive the upper bound on the attainable "clear area" for the ambiguity function, and we show that, with respect to the conventional single-waveform ambiguity function, the maximum clear area is K times smaller for the MIMO system.
An Enhanced Histogram of Oriented Gradients for Pedestrian Detection

The outstanding Histogram-of-Oriented-Gradients (HOG) feature proposed by Dalal and Triggs is a state-of-art technique for pedestrian detection, and it is usually applied with a linear support vector machine (SVM) in a sliding-window framework. Most other algorithms for pedestrian detection use HOG as the basic feature, and combine other features with HOG to form the feature set. Hence, the HOG feature is actually the most efficient and fundamental feature for pedestrian detection. However, the HOG feature cannot adequately handle scale variation of pedestrians. In addition, simply downsampling an image into a different scale, or decomposing via wavelet into multi-resolution subimages, calculating their HOG feature and combining them cannot enhance performance. Therefore, in this paper, based on the idea of multi-resolution feature descriptors, we propose a new robust edge feature referred to as Enhanced HOG (eHOG). It is a complementary descriptor for the histograms-of-oriented-gradients feature. Though the extraction process of the eHOG descriptor is derived only from HOG itself, similar to the process of extracting edge information from the downscaling image, it retains much more information for the edge gradient than that of the original HOG, without significantly increasing the complexity of computation. In the INRIA pedestrian dataset, many experiments have been conducted with eHOG and HOG, and the results show that the proposed new feature consistently improves the detection rate more than the original HOG feature detector. Particularly, eHOG with a Histogram Intersection Kernel SVM (HIKSVM) classifier has greatly improved performance. These results suggest that eHOG may be a better substitute for HOG for pedestrian detection in many applications.
Methodological issues limit interpretation of negative effects of satellite cell depletion on adult muscle hypertrophy

We are writing regarding the recent publication in Development entitled ‘Satellite cell depletion prevents fiber hypertrophy in skeletal muscle’ ([Egner et al., 2016][1]). Egner et al. claim to have ‘essentially repeated’ our work ([McCarthy et al., 2011][2]); however, we think that
Ieee Transactions on Visualization and Computer Graphics 1 a Parallel Coordinates Style Interface for Exploratory Volume Visualization

—We present a user interface, based on parallel coordinates, that facilitates exploration of volume data. By explicitly representing the visualization parameter space, the interface provides an overview of rendering options and enables users to easily explore different parameters. Rendered images are stored in an integrated history bar that facilitates backtracking to previous visualization options. Initial usabilty testing showed clear agreement between users and experts of various backgrounds (usability, graphic design, volume visualization, and medical physics) that the proposed user interface is a valuable data exploration tool. A parallel coordinates display consists of one axis for each parameter. 2. Parameter sets are represented as lines that connect the parameters and the resultant image together. 3. A history bar provides access to previous settings. 4. Existing parameter nodes are modified with an editor to create new nodes. 5. A row and column are chosen with checkboxes and a table view is created.
Intelligent zoning design using multi-objective evolutionary algorithms

This paper discusses the use of multi objective evolutionaryalgorithms applied to the engineering of zoning forhandwriten recognition. Usually a task fulfilled by an humanexpert, zoning design relies on specific domain knowledgeand a trial and error process to select an adequatedesign. Our proposed approach to automatically define thezone design was tested and was able to define zoning strategiesthat performed better than our former strategy definedmanually.
Objective Assessment of Surgical Restaging after Concurrent Chemoradiation for Locally Advanced Pancreatic Cancer

The role of neoadjuvant chemoradiation therapy in locally advanced pancreatic cancer (LAPC) is still controversial. The aim of this study was to evaluate surgical downstaging after concurrent chemoradiation therapy (CCRT) for LAPC by measuring the objective changes after treatment. From January 2003 through July 2011, 54 patients with LAPC underwent neoadjuvant CCRT. Computed tomography findings of the tumor size, including major vessel invasion, were analyzed before and after CCRT. Among the total recruited patients, 14 had borderline resectable malignancy and another 40 were unresectable before CCRT. After CCRT, a partial response was achieved in four patients. Stable disease and further disease progression were achieved in 36 and 14 patients, respectively. Tumor size showed no significant difference before and after CCRT (3.6 ± 1.1 vs. 3.6 ± 1.0 cm, P = 0.61). Vessel invasion showed improvement in two patients, while 13 other patients showed further tumor progression. Thirty-nine patients with unresectable malignancy and 11 patients with borderline resectable malignancy at time of initial diagnosis remained unchanged after CCRT. Four patients with borderline pancreatic malignancy progressed to an unresectable stage, whereas one unresectable pancreatic malignancy improved to a borderline resectable stage. Only one patient with borderline resectable disease underwent operation after CCRT; however, curative resection failed due to celiac artery invasion and peritoneal seeding. The adverse events associated with CCRT were tolerable. In conclusion, preoperative CCRT in LAPC rarely leads to surgical downstaging, and it could lower resectability rates. Graphical Abstract
The Karlsruhe Institute of Technology Translation Systems for the WMT 2015

In this paper, the KIT systems submitted to the Shared Translation Task are presented. We participated in two translation directions: from German to English and from English to German. Both translations are generated using phrase-based translation systems. The performance of the systems was boosted by using language models built based on different tokens such as word, part-of-speech, and automacally generated word clusters. The difference in word order between German and English is addressed by part-of-speech and syntactic tree-based reordering models. In addition to a discriminative word lexicon, we used hypothesis rescoring using the ListNet algorithm after generating the translation with the phrase-based system. We evaluated the rescoring using only the baseline features as well as using additional computational complex features.
Computers’ impact on students’ writing skills

Learning new vocabulary compromises a significant factor for success within language learning since without the adequate knowledge of words and their meaning, learners are not able to use the target language efficiently. Moreover, vocabulary tends to be forgotten if it is not acquired and used through the right methods that will provide learners with language inputs in genuine target language environment. In this regard, the increasing access to different multimedia and technology resources facilitate spontaneous vocabulary acquisition for the contemporary age learners. In particular, movies with subtitles can be a great tool in bringing students closer to authentic real life communication vocabulary. As a result, previous studies have found out several benefits of using subtitled movies by confirming that subtitles indeed improve vocabulary development.
Implementing Remote procedure calls

Remote procedure calls (RPC) are a useful paradigm for providing communication across a network between programs written in a high level language. This paper describes a package, written as part of the Cedar project, providing a remote procedure call facility. The paper describes the options that face a designer of such a package, and the decisions we made. We describe the overall structure of our RPC mechanism, our facilities for binding RPC clients, the transport level communication protocol, and some performance measurements. We include descriptions of some optimisations we used to achieve high performance and to minimize the load on server machines that have many clients. Our primary aim in building an RPC package was to make the building of distributed systems easier. Previous protocols were sufficiently hard to use that only members of a select group of communication experts were willing to undertake the construction of distributed systems. We hoped to overcome this by providing a communication paradigm as close as possible to the familiar facilities of our high level languages. To achieve this aim, we concentrated on making remote calls efficient, and on making the semantics of remote calls as close as possible to those of local calls.
Symbiotic jobscheduling for a simultaneous mutlithreading processor

Simultaneous Multithreading machines fetch and execute instructions from multiple instruction streams to increase system utilization and speedup the execution of jobs. When there are more jobs in the system than there is hardware to support simultaneous execution, the operating system scheduler must choose the set of jobs to coscheduleThis paper demonstrates that performance on a hardware multithreaded processor is sensitive to the set of jobs that are coscheduled by the operating system jobscheduler. Thus, the full benefits of SMT hardware can only be achieved if the scheduler is aware of thread interactions. Here, a mechanism is presented that allows the scheduler to significantly raise the performance of SMT architectures. This is done without any advance knowledge of a workload's characteristics, using sampling to identify jobs which run well together.We demonstrate an SMT jobscheduler called SOS. SOS combines an overhead-free sample phase which collects information about various possible schedules, and a symbiosis phase which uses that information to predict which schedule will provide the best performance. We show that a small sample of the possible schedules is sufficient to identify a good schedule quickly. On a system with random job arrivals and departures, response time is improved as much as 17% over a schedule which does not incorporate symbiosis.
Increased Levels of Lipoprotein (a) Are Related to Family Risk Factors of Cardiovascular Disease in Children and Adolescents From Maracaibo, Venezuela

The aims of this study were to determine Lipoprotein (a) [Lp(a)] concentrations in a sample of subjects from Maracaibo, Venezuela, and to determine the relationship of family risk factors for cardiovascular disease and their Lp(a) levels. Two hundred twenty-seven healthy individuals between 5 and 19 years of age of both genders and multiethnic origins were selected. A complete background clinical chart and laboratory test was conducted for each patient to discard cardiovascular diseases and confirm their healthy state. The Lp(a) concentration was determined using the double antibody enzyme-linked immunosorbent assay method. For inferential statistical analysis, one-factor analysis of variance tests and Student t test for independent observations were used according to each case, considered significant when P value was <0.05. No significant differences were observed when evaluating Lp(a) levels according to gender in all ages. Males showed no significant difference in Lp(a) levels between groups, but, in females, a significantly lower level (P < 0.03) in the group 5 to 9 years of age was found. When considering only age, significantly lower levels were observed (P < 0.03) in the 5- to 9-year-old group. When studying family risk factors of cardiovascular diseases, it was found that the group with family risk factors had a significantly higher Lp(a) concentration (P < 0.01) than those without family risk factors, observing that those who had four or more factors exhibited a significantly higher concentration than those with two to three risk factors (30.6 ± 4.5 mg/dL versus 18.5 ± 12.2 mg/dL, P < 0.009) and than those with one risk factor (30.6 ± 4.5 mg/dL versus 21.6 ± 1.4 mg/dL, P < 0.03). These results emphasize the clusters of family risk factors of cardiovascular disease with higher Lp(a) levels and also indicate that the evaluation of its concentration should be taken as an independent risk factor of atherosclerosis for the population in developmental ages.
Multilocus sequence analysis of genus Kurthia, and a description of the novel species, Kurthia populi sp. nov.

Four novel bacteria strains, belonging to the genus Kurthia, were isolated from the surface of Curculionidae (Kurthia strain 10y-14T), and from hybrid poplar, Populus × euramericana (Kurthia strains 6-3, 2-5, and 06C10-3-14), different bark samples in Puyang, Henan Province, China. Phylogenetic analyses of the 16S rRNA gene and MLSA data showed that the four strains form a distinct cluster in the genus Kurthia, indicating that they all belong to a single taxon within the genus. DNA-DNA hybridization levels between the 10y-4T and Kurthia huakuii LAM0618T and Kurthia massiliensis DSM 24639T were 58.31% and 53.92%, respectively. This indicates that the four novel strains represent a species distinct from these closely two species. DNA G+C content of the type strain is 42.1-42.6%. The major fatty acids are iso-C15:0 and anteiso-C15:0. The major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unknown phospholipid and unidentified aminophospholipids. The predominant menaquinones were MK-7 (90%) and MK-6 (10%). The major cell wall amino acids were lysine, alanine, glutamic acid, glycine. On the basis of the MLSA and 16S rRNA gene phylogenetic analyses, percentage of DNA-DNA reassociation, DNA base composition, and biochemical and phenotypic characteristics, the four strains represent a new species within the genus Kurthia, for which the name Kurthia populi sp. nov. is proposed. The type strain is 10y-14T (=CFCC 11600T=KCTC 33522T).
Peningkatan Pemahaman Materi Kuantisasi Besaran Fisis pada Calon Guru Fisika menggunakan Metode Diskusi Kelas dan Scaffolding

Kuantisasi besaran fisis merupakan materi penting dalam Fisika kuantum. Topiknya merupakan jembatan dan titik awal revolusi pemikiran Fisis dikenalnya Fisika Kuantum. Penelitian ini bertujuan untuk mengetahui penerapan metode diskusi untuk meningkatkan hasil belajar mahasiswa pendidikan fisika pada materi kuantisasi besaran fisis. Penelitian ini dilakukan di Jurusan Fisika Universitas Negeri Surabaya pada matakuliah Fisika Kuantum khususnya materi Kuantisasi Besaran Fisis. Penelitian ini merupakan Penelitian Tindakan Kelas dengan obyek penelitian mahasiswa Pendidikan Fisika B 2012 dan/atau mahasiswa yang memprogam matakuliah Fisika Kuantum pada tahun ajaran 2014/2015. Penelitian dilakukan dengan 2 siklus. Pada siklus pertama, hasil belajar mahasiswa sebesar 63,6%. Siklus dilanjutkan hingga hasil belajar mahasiswa lebih dari 75% yakni pada siklus kedua sebesar 79,4%. Perbedaan utama dari siklus 1 dan siklus 2 adalah adanya scaffolding oleh dosen di siklus kedua. Scaffolding yang diberikan berupa pertanyaan-pertanyaan bantuan agar mahasiswa mampu menjelaskan konsep materi yang diajarkan dan proses diskusi dapat berjalan dengan lebih baik . The Improvement of Quantification of Physical Size Understanding of The Pre-Service Physics Teachers using Class Discussion Methods and Scaffolding Physical quantities quantization is an essential subject in Quantum Physics. The topic used as a bridge and a starting point of the revolution of physical thinking into the real Quantum Physics. This study aims to determine the application of discussion methods to enhance the learning outcomes of physics education students on the topic of quantization of physical quantities. This research conducted at the Physics Department, Universitas Negeri Surabaya on the subject of Quantum Physics. This research is a Classroom Action Research with research object is students of Physics Education B 2012 and students who programmed Quantum Physics course in academic year 2014/2015. The study conducted with two cycles. In the first cycle, the learning outcomes are 63.6%. The cycle is continued until the learning outcomes more than 75%, that is, in the second cycle is 79.4%. The main difference between cycle 1 and cycle 2 is the presence of scaffolding by lecturers in the second cycle. Scaffolding was given in the form of helping questions so that the students can explain the concept of the material being taught and the discussion process can run better.
Infant mortality statistics from the 2003 period linked birth/infant death data set.

OBJECTIVES This report presents 2003 period infant mortality statistics from the linked birth/infant death data file by a variety of maternal and infant characteristics. The linked file differs from the mortality file, which is based entirely on death certificate data. METHODS Descriptive tabulations of data are presented and interpreted. Excluding rates by cause of death, the infant mortality rate is now published with two decimal places. RESULTS The U.S. infant mortality rate was 6.84 infant deaths per 1,000 live births in 2003, a return to the rate in 2001, compared with 6.95 in 2002. Infant mortality rates ranged from 4.83 per 1,000 live births for Asian or Pacific Islander mothers to 13.60 for non-Hispanic black mothers. Among Hispanics, rates ranged from 4.57 for Cuban mothers to 8.18 for Puerto Rican mothers. Infant mortality rates were higher for those infants whose mothers were born in the 50 States and the District of Columbia, were unmarried, or smoked during pregnancy. Infant mortality was also higher for male infants, multiple births, and infants born preterm or at low birthweight. Infants born at the lowest birthweights and gestational ages have a large impact on overall U.S. infant mortality. Nearly one-half (49 percent) of all infant deaths in the U.S. in 2003 occurred to the 0.8 percent of infants whose birthweight was less than 1,000 grams. The three leading causes of infant death--Congenital malformations, low birthweight, and SIDS--taken together accounted for 45 percent of all infant deaths. For infants of non-Hispanic black mothers, the cause-specific infant mortality rate for low birthweight was nearly four times that for infants of non-Hispanic white mothers. For infants of non-Hispanic black and American Indian mothers, the SIDS rates were more than double the rate for non-Hispanic white mothers.
Development of New Mouse Lung Tumor Models Expressing EGFR T790M Mutants Associated with Clinical Resistance to Kinase Inhibitors

Background The EGFR T790M mutation confers acquired resistance to kinase inhibitors in human EGFR mutant lung adenocarcinoma, is occasionally detected before treatment, and may confer genetic susceptibility to lung cancer. Methodology/Principal Findings To study further its role in lung tumorigenesis, we developed mice with inducible expression in type II pneumocytes of EGFRT790M alone or together with a drug-sensitive L858R mutation. Both transgenic lines develop lung adenocarcinomas that require mutant EGFR for tumor maintenance but are resistant to an EGFR kinase inhibitor. EGFRL858R+T790M-driven tumors are transiently targeted by hsp90 inhibition. Notably, EGFRT790M-expressing animals develop tumors with longer latency than EGFRL858R+T790M-bearing mice and in the absence of additional kinase domain mutations. Conclusions/Significance These new mouse models of mutant EGFR-dependent lung adenocarcinomas provide insight into clinical observations. The models should also be useful for developing improved therapies for patients with lung cancers harboring EGFRT790M alone or in conjunction with drug-sensitive EGFR kinase domain mutations.