A contextual information based scholary paper recommender system using big data platform

Recommender systems for research papers have been increasingly popular. In the past 14 years more than 170 research papers,patents and webpageshave been published in this field. Scientific papers recommender systemsare trying to provide some recommendations to each user which are consistent with the users' personal interests based on performance, personal tastes and users behaviors.Since the volume of papers are growing day after day and the recommender systemshave not the ability for covering these huge volumes ofprocessing papers according to the users' preferences it is necessary to use parallel processing (mapping – reducing programming) for covering and fast processing of these volumes of papers. The suggested system for this research constitutes a profile for each paper which contains context information and the scope of paper. Then, the system will advise some papers to the user according to the user work domain and the papers domain. For implementing the system it has been used hadoop bed and the parallel programming because the volume of data was a part of a big data and the time was also an important factor. The performance of the suggested system was measured by the criteria such as user satisfaction and the accuracy and the results have been satisfactory.Keywords: Recommender systems; big data; Hadoop; contextual informatio

Ultrastructure of cytoplasmic fragments in human cleavage stage embryos

Purpose: The goal of this study was to evaluate the ultrastructure of cytoplasmic fragments along with the effect of cytoplasmic fragment and perivitelline space coarse granulation removal (cosmetic microsurgery) from embryos before embryo transfer on ART outcomes. Methods: One hundred and fifty intracytoplasmic sperm injection cycles with male factor infertility were included in this prospective study. Patients were divided into three groups of case (n = 50), sham (n = 50), and control (n = 50). Embryos with 10–50 % fragmentation were included in this study. Cosmetic microsurgery and zona assisted hatching were only performed in case and sham groups respectively. Extracted fragments were evaluated ultrastructurally by transmission electron microscopy (TEM). Rates of clinical pregnancy, live birth, miscarriage, multiple pregnancies, and congenital anomaly in the three groups were also compared. Results: Micrographs from TEM showed that mitochondria were the most abundant structures found in the fragments along with mitochondria-vesicle complexes, Golgi apparatus, primary lysosomes, and vacuoles. There were no significant differences in demographic characteristics, laboratory and clinical data, or embryo morphological features between the groups. The rate of clinical pregnancy in control, sham, and case groups had no significant differences (24, 18, and 18 %, respectively). The rates of live birth, miscarriage, multiple pregnancy, and congenital anomaly were also similar between the different groups. Conclusions: Our data demonstrated that cosmetic microsurgery on preimplantation embryos had no beneficial effect on ART outcomes in unselected groups of patients. As mitochondria are the most abundant organelles found in cytoplasmic fragments, fragment removal should be performed with more caution in embryos with moderate fragmentation

Classification on imbalanced data sets, taking advantage of errors to improve performance

Classification methods usually exhibit a poor performance when they are applied on imbalanced data sets. In order to overcome this problem, some algorithms have been proposed in the last decade. Most of them generate synthetic instances in order to balance data sets, regardless the classification algorithm. These methods work reasonably well in most cases; however, they tend to cause over-fitting. In this paper, we propose a method to face the imbalance problem. Our approach, which is very simple to implement, works in two phases; the first one detects instances that are difficult to predict correctly for classification methods. These instances are then categorized into “noisy” and “secure”, where the former refers to those instances whose most of their nearest neighbors belong to the opposite class. The second phase of our method, consists in generating a number of synthetic instances for each one of those that are difficult to predict correctly. After applying our method to data sets, the AUC area of classifiers is improved dramatically. We compare our method with others of the state-of-the-art, using more than 10 data sets

Synthetic data shuffling accelerates the convergence of federated learning under data heterogeneity

In federated learning, data heterogeneity is a critical challenge. A straightforward solution is to shuffle the clients' data to homogenize the distribution. However, this may violate data access rights, and how and when shuffling can accelerate the convergence of a federated optimization algorithm is not theoretically well understood. In this paper, we establish a precise and quantifiable correspondence between data heterogeneity and parameters in the convergence rate when a fraction of data is shuffled across clients. We prove that shuffling can quadratically reduce the gradient dissimilarity with respect to the shuffling percentage, accelerating convergence. Inspired by the theory, we propose a practical approach that addresses the data access rights issue by shuffling locally generated synthetic data. The experimental results show that shuffling synthetic data improves the performance of multiple existing federated learning algorithms by a large margin

The Immediate Effect of Lateral Wedge Insoles, With and Without a Subtalar Strap, on the Lateral Trunk Lean Motion in Patients With Knee Osteoarthritis

Background: Orthotic interventions for knee osteoarthritis (OA) aim to reduce mechanical loading on the medial compartment of the knee and may lessen the lateral trunk lean as the most important compensatory gait strategy. The lateral wedge insole is a known orthotic intervention for knee OA. However, the question whether the addition of a subtalar strap to the wedge improves its effect has not been addressed in the literature. Objective: To compare the effects of lateral wedge insoles, with and without a subtalar strap, on the lateral trunk lean in patients with knee OA. Methods: Twenty-three patients aged over 40 years, with grade I or II OA of the medial compartment of one knee, based on the American College of Rheumatology criteria, were included in this study. The patients were diagnosed with OA based on a clinical examination, and the diagnosis was confirmed with radiographs. A 3-dimensional motion measurement system was used to collect the gait data for 3 different conditions: (1) with no insole, (2) with a lateral wedge insole, and (3) with a lateral wedge insole and a subtalar strap. The immediate effect of the 3 test conditions on the lateral trunk lean was compared during a gait cycle a stance phase and at the point of midstance. Results: Based on the laboratory coordinate system, the 3 conditions had no significant effect on the lateral trunk lean during a gait cycle and a stance phase and at the point of midstance in patients with knee OA. Conclusion: The results of this study demonstrated that the lateral wedge insoles, with and without a subtalar strap, had no immediate effect on the lateral trunk lean in patients with knee OA. However, the long-term effect of lateral wedge insoles on the lateral trunk lean in these patients requires further investigation. © The Author(s) 2013

Targeting negative regulation of p53 by MDM2 and WIP1 as a therapeutic strategy in cutaneous melanoma

BACKGROUND: Cutaneous melanoma is the most serious skin malignancy and new therapeutic strategies are needed for advanced melanoma. TP53 mutations are rare in cutaneous melanoma and hence activation of wild-type p53 is a potential therapeutic strategy in cutaneous melanoma. Here, we investigated the WIP1 inhibitor, GSK2830371, and MDM2–p53 binding antagonists (nutlin-3, RG7388 and HDM201) alone and in combination treatment in cutaneous melanoma cell lines and explored the mechanistic basis of these responses in relation to the genotype and induced gene expression profile of the cells. // METHODS: A panel of three p53WT (A375, WM35 and C8161) and three p53MUT (WM164, WM35-R and CHL-1) melanoma cell lines were used. The effects of MDM2 and WIP1 inhibition were evaluated by growth inhibition and clonogenic assays, immunoblotting, qRT–PCR gene expression profiling and flow cytometry. // RESULTS: GSK2830371, at doses (10 μM) that alone had no growth-inhibitory or cytotoxic effects on the cells, nevertheless significantly potentiated the growth-inhibitory and clonogenic cell killing effects of MDM2 inhibitors in p53WT but not p53MUT melanoma cells, indicating the potentiation worked in a p53-dependent manner. The siRNA-mediated knockdown of p53 provided further evidence to support the p53 dependence. GSK2830371 increased p53 stabilisation through Ser15 phosphorylation and consequent Lys382 acetylation, and decreased ubiquitination and proteasome-dependent degradation when it was combined with MDM2 inhibitors. These changes were at least partly ATM mediated, shown by reversal with the ATM inhibitor (KU55933). GSK2830371 enhanced the induction of p53 transcriptional target genes, cell cycle arrest and apoptosis. // CONCLUSIONS: GSK2830371, a WIP1 inhibitor, at doses with no growth-inhibitory activity alone, potentiated the growth-inhibitory and cytotoxic activity of MDM2 inhibitors by increasing phosphorylation, acetylation and stabilisation of p53 in cutaneous melanoma cells in a functional p53-dependent manner

Bovine Tuberculosis in a Nebraska Herd of Farmed Elk and Fallow Deer: A Failure of the Tuberculin Skin Test and Opportunities for Serodiagnosis

In 2009, Mycobacterium bovis infection was detected in a herd of 60 elk (Cervus elaphus) and 50 fallow deer (Dama dama) in Nebraska, USA. Upon depopulation of the herd, the prevalence of bovine tuberculosis (TB) was estimated at ∼71–75%, based upon histopathology and culture results. Particularly with elk, gross lesions were often severe and extensive. One year ago, the majority of the elk had been tested for TB by single cervical test (SCT), and all were negative. After initial detection of a tuberculous elk in this herd, 42 of the 59 elk were tested by SCT. Of the 42 SCT-tested elk, 28 were TB-infected with only 3/28 reacting upon SCT. After SCT, serum samples were collected from the infected elk and fallow deer from this herd at necropsy and tested by three antibody detection methods including multiantigen print immunoassay, cervidTB STAT-PAK, and dual path platform VetTB (DPP). Serologic test sensitivity ranged from 79 to 97% depending on the test format and host species. Together, these findings demonstrate the opportunities for use of serodiagnosis in the rapid detection of TB in elk and fallow deer

A de novo substitution in BCL11B leads to loss of interaction with transcriptional complexes and craniosynostosis

Craniosynostosis, the premature ossification of cranial sutures, is a developmental disorder of the skull vault, occurring in approximately 1 in 2250 births. The causes are heterogeneous, with a monogenic basis identified in ~25% of patients. Using whole-genome sequencing, we identified a novel, de novo variant in BCL11B, c.7C>A, encoding an R3S substitution (p.R3S), in a male patient with coronal suture synostosis. BCL11B is a transcription factor that interacts directly with the nucleosome remodelling and deacetylation complex (NuRD) and polycomb-related complex 2 (PRC2) through the invariant proteins RBBP4 and RBBP7. The p.R3S substitution occurs within a conserved amino-terminal motif (RRKQxxP) of BCL11B and reduces interaction with both transcriptional complexes. Equilibrium binding studies and molecular dynamics simulations show that the p.R3S substitution disrupts ionic coordination between BCL11B and the RBBP4-MTA1 complex, a subassembly of the NuRD complex, and increases the conformational flexibility of Arg-4, Lys-5 and Gln-6 of BCL11B. These alterations collectively reduce the affinity of BCL11B p.R3S for the RBBP4-MTA1 complex by nearly an order of magnitude. We generated a mouse model of the BCL11B p.R3S substitution using a CRISPR-Cas9-based approach, and we report herein that these mice exhibit craniosynostosis of the coronal suture, as well as other cranial sutures. This finding provides strong evidence that the BCL11B p.R3S substitution is causally associated with craniosynostosis and confirms an important role for BCL11B in the maintenance of cranial suture patency

Animal-side serologic assay for rapid detection of Mycobacterium bovis infection in multiple species of free-ranging wildlife

Numerous species of mammals are susceptible to Mycobacterium bovis, the causative agent of bovine tuberculosis (TB). Several wildlife hosts have emerged as reservoirs of M. bovis infection for domestic livestock in different countries. In the present study, blood samples were collected from Eurasian badgers (n=1532), white-tailed deer (n=463), brushtail possums (n=129), and wild boar (n=177) for evaluation of antibody responses to M. bovis infection by a lateral-flow rapid test (RT) and multiantigen print immunoassay (MAPIA). Magnitude of the antibody responses and antigen recognition patterns varied among the animals as determined by MAPIA; however, MPB83 was the most commonly recognized antigen for each host studied. Other seroreactive antigens included ESAT-6, CFP10, and MPB70. The agreement of the RT with culture results varied from 74% for possums to 81% for badgers to 90% for wild boar to 97% for white-tailed deer. Small numbers of wild boar and deer exposed to M. avium infection or paratuberculosis, respectively, did not cross-react in the RT, supporting the high specificity of the assay. In deer, whole blood samples reacted similarly to corresponding serum specimens (97% concordance), demonstrating the potential for field application. As previously demonstrated for badgers and deer, antibody responses to M. bovis infection in wild boar were positively associated with advanced disease. Together, these findings suggest that a rapid TB assay such as the RT may provide a useful screening tool for certain wildlife species that may be implicated in the maintenance and transmission of M. bovis infection to domestic livestock.The authors are grateful to Peter Andersen and Jim McNair for kindly providing certain antigens used in C this study. Badger samples were taken under projects funded by the Department for Environment, Food, and Rural Affairs (Defra), UK. The authors acknowledge the support of staff from CSL, VLA Starcross, Defra Wildlife Unit, and permission from the Independent Scientific Group for use of sera from the RBCT. Spanish wild boar samples were obtained with support from MEC Plan Nacional AGL2005-07401 and Santander - Fundacion M. Botin