Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of male age on sperm traits and sperm competition success in the guppy (Poecilia reticulata)

Deleterious mutations can accumulate in the germline with age, decreasing the genetic quality of sperm and imposing a cost on female fitness. If these mutations also affect sperm competition ability or sperm production, then females will benefit from polyandry as it incites sperm competition and, consequently, minimizes the mutational load in the offspring. We tested this hypothesis in the guppy (Poecilia reticulata), a species characterized by polyandry and intense sperm competition, by investigating whether age affects post‐copulatory male traits and sperm competition success. Females did not discriminate between old and young males in a mate choice experiment. While old males produced longer and slower sperm with larger reserves of strippable sperm, compared to young males, artificial insemination did not reveal any effect of age on sperm competition success. Altogether, these results do not support the hypothesis that polyandry evolved in response to costs associated with mating with old males in the guppy.
Two Distinct Categories of Focal Deletions in Cancer Genomes

One of the key questions about genomic alterations in cancer is whether they are functional in the sense of contributing to the selective advantage of tumor cells. The frequency with which an alteration occurs might reflect its ability to increase cancer cell growth, or alternatively, enhanced instability of a locus may increase the frequency with which it is found to be aberrant in tumors, regardless of oncogenic impact. Here we’ve addressed this on a genome-wide scale for cancer-associated focal deletions, which are known to pinpoint both tumor suppressor genes (tumor suppressors) and unstable loci. Based on DNA copy number analysis of over one-thousand human cancers representing ten different tumor types, we observed five loci with focal deletion frequencies above 5%, including the A2BP1 gene at 16p13.3 and the MACROD2 gene at 20p12.1. However, neither RNA expression nor functional studies support a tumor suppressor role for either gene. Further analyses suggest instead that these are sites of increased genomic instability and that they resemble common fragile sites (CFS). Genome-wide analysis revealed properties of CFS-like recurrent deletions that distinguish them from deletions affecting tumor suppressor genes, including their isolation at specific loci away from other genomic deletion sites, a considerably smaller deletion size, and dispersal throughout the affected locus rather than assembly at a common site of overlap. Additionally, CFS-like deletions have less impact on gene expression and are enriched in cell lines compared to primary tumors. We show that loci affected by CFS-like deletions are often distinct from known common fragile sites. Indeed, we find that each tumor tissue type has its own spectrum of CFS-like deletions, and that colon cancers have many more CFS-like deletions than other tumor types. We present simple rules that can pinpoint focal deletions that are not CFS-like and more likely to affect functional tumor suppressors.
Informed secure watermarking using optimal transport

This paper presents several watermarking methods preventing the estimation of the secret key by an adversary. The constraints for secure embedding using distribution matching, where the decoding regions rely implicitly on the distribution of the host signal, are first formulated. In order to perform informed coding, different decoding regions are associated with the same message using an appropriate partitioning function. The minimization of the embedding distortion is afterwards casted into an optimal transport problem. Three new secure embeddings are presented and the performances of the proposed embedding functions regarding the AWGN channel for different WCRs are evaluated. Depending on the embedding and noise distortions, informed secure coding can outperform classical secure coding or classical insecure coding such as ISS or SCS.
Stability of several biochemical markers of bone metabolism.

The determination of bone metabolism markers is useful in monitoring pharmacological therapy for osteoporosis (1)(2)(3). During the course of multicenter clinical studies designed to evaluate the therapeutic efficacy of several drugs, it often is useful to carry out analysis in batches after storing the samples for differing periods, thus reducing analytical variation and cost. This requires knowledge of the behavior of the analyte in the biological matrix in terms of the length and conditions of storage. Unfortunately, these data frequently are lacking, and the information provided by a kit’s manufacturer more often than not is contradictory. Data published relative to long-term storage in biological matrices of bone turnover markers, including the seric NH2-terminal propeptide of type I procollagen (P1NP), the urinary cross-linked N-telopeptides of type I collagen (NTx), and the urinary pyridinium cross-links pyridinoline (PYD) and deoxypyridinoline (DPD), are extremely scarce (4). Therefore, our aim was to systematically study the molecular stability of these analytes in the storage mode most frequently used. In particular, the stability of storage lengths …
Coastal oceanography sets the pace of rocky intertidal community dynamics

The structure of ecological communities reflects a tension among forces that alter populations. Marine ecologists previously emphasized control by locally operating forces (predation, competition, and disturbance), but newer studies suggest that inputs from large-scale oceanographically modulated subsidies (nutrients, particulates, and propagules) can strongly influence community structure and dynamics. On New Zealand rocky shores, the magnitude of such subsidies differs profoundly between contrasting oceanographic regimes. Community structure, and particularly the pace of community dynamics, differ dramatically between intermittent upwelling regimes compared with relatively persistent down-welling regimes. We suggest that subsidy rates are a key determinant of the intensity of species interactions, and thus of structure in marine systems, and perhaps also nonmarine communities.
A survey on Data Mining: Tools, Techniques, Applications, Trends and Issues.

Data mining is a process which finds useful patterns from large amount of data. It is a powerful new technology with great potential to help companies focus on the most important information in their data warehouses. It uses machine learning, statistical and visualization techniques to discovery and present knowledge in a form which is easily comprehensible to humans. This review of literature focuses on data mining techniques, trends, issues, tools, crucial concepts and applications. In this paper we have focused a variety of techniques, approaches and different areas of the research which are helpful and marked as the important field of data mining Technologies. This paper imparts more number of applications of the data mining and also focuses on trends in the data mining which will helpful in the further research.
An interactive learning environment for teaching and learning of computer programming

This paper is to investigate how new technology can be most appropriately applied in the service of teaching computer programming at a distance. Main elements include: building an online system that provides an integrated environment for students doing programming activities and coursework; how to provide students with timely and useful feedback about programming activities without the need to have instructors and students meet at the same time and the same place; how to build effective instructor-to-student interaction; and how programming assignments can be handled and managed in a much more efficient and effective manner than the existing ways.
Comprehending the Learning Process of Peer-Feedback Activities of EFL Learners with Autism in Different Settings in Indonesia

This classroom observation study attempts to comprehend, reveal and find the learning possibilities from the social learning perspective, in the process of peer-feedback activities of EFL Learners with autism learning with different peers in different settings. This study aimed at discovering the viability of the practice of EFL learners with autism peering with other autistic students, normal students, and special needs students. The research took place in inclusive (IC) classroom, mainstreaming and Special Educational Needs (SEN) classroom.8 autistic students, 7 males and 1 female, were observed during their discussion with their peers in the teaching and learning process in English Foreign Language class. Throughout the classroom observation and discourse analysis during the students’ discussion there are four pattern of interaction took place: unique collaborative, expert-novice, and passive-passive. Wherein the unique collaborative is divided into active unique collaborative and passive unique collaborative and these are new findings and may add to the theory of peer-feedback interaction in EFL context.
Reproducible Computational Workflows with Continuous Analysis

Reproducing experiments is vital to science. Being able to replicate, validate and extend previous work also speeds new research projects. Reproducing computational biology experiments, which are scripted, should be straightforward. But reproducing such work remains challenging and time consuming. In the ideal world we would be able to quickly and easily rewind to the precise computing environment where results were generated. We would then be able to reproduce the original analysis or perform new analyses. We introduce a process termed “continuous analysis” which provides inherent reproducibility to computational research at a minimal cost to the researcher. Continuous analysis combines Docker, a container service similar to virtual machines, with continuous integration, a popular software development technique, to automatically re-run computational analysis whenever relevant changes are made to the source code. This allows results to be reproduced quickly, accurately and without needing to contact the original authors. Continuous analysis also provides an audit trail for analyses that use data with sharing restrictions. This allows reviewers, editors, and readers to verify reproducibility without manually downloading and rerunning any code. Example configurations are available at our online repository (https://github.com/greenelab/continuous_analysis).
On asynchronous Newton-iterative methods

In 9] A.H. Sherman investigated Newton-iterative methods for nonlinear systems F (x) = 0 : These are methods, where instead of the next Newton step, the linear system F 0 (x(j)) y = F 0 (x(j)) x(j) ? F (x(j)) was not solved directly, but approximated by nite many steps of a linear iterative method. He showed, that the principle of many numerical methods, namely to start with rough and to end with ne approximations, which means here to increase the number of inner or linear iterations, leads to a signiicant speed up of convergence, assuming, that the evaluations of the function F and its partial derivatives are expensive. R.E. White 11] investigated the same problem by using a synchronized parallel multisplitting method for the inner iterations. We will introduce an asynchronous Newton-iterative method, which has the same properties in speed of convergence, but in addition, inner and outer iterations are totally decoupled, and moreover, the partial derivatives of F can be evaluated or approximated totally asynchronous. Interpreting the evaluation of component functions and partial derivatives as the most complex task, our method will converge superlin-early, and under suitable conditions at least quadratically.
The MHC class I peptide repertoire is molded by the transcriptome

Under steady-state conditions, major histocompatibility complex (MHC) I molecules are associated with self-peptides that are collectively referred to as the MHC class I peptide (MIP) repertoire. Very little is known about the genesis and molecular composition of the MIP repertoire. We developed a novel high-throughput mass spectrometry approach that yields an accurate definition of the nature and relative abundance of unlabeled peptides presented by MHC I molecules. We identified 189 and 196 MHC I–associated peptides from normal and neoplastic mouse thymocytes, respectively. By integrating our peptidomic data with global profiling of the transcriptome, we reached two conclusions. The MIP repertoire of primary mouse thymocytes is biased toward peptides derived from highly abundant transcripts and is enriched in peptides derived from cyclins/cyclin-dependent kinases and helicases. Furthermore, we found that ∼25% of MHC I–associated peptides were differentially expressed on normal versus neoplastic thymocytes. Approximately half of those peptides are derived from molecules directly implicated in neoplastic transformation (e.g., components of the PI3K–AKT–mTOR pathway). In most cases, overexpression of MHC I peptides on cancer cells entailed posttranscriptional mechanisms. Our results show that high-throughput analysis and sequencing of MHC I–associated peptides yields unique insights into the genesis of the MIP repertoire in normal and neoplastic cells.
A Copula-Based Fraud Detection (CFD) Method for Detecting Evasive Fraud Patterns in a Corporate Mobile Banking Context

This paper examines some special fraud patterns called evasive fraud patterns (which are types of evasive fraudulent behaviours) caused by a set of marginal fraud risk factors (i.e. individual fraud risk factors) which have inter-dependencies in the form of negative correlations. These inter-dependencies, if not captured properly, may prevent a bank's fraud detection system from detecting such evasive fraud patterns effectively. Using corporate m-banking (m-banking) as an application context, this paper proposes a novel fraud detection method, the CFD method, to address this open issue. The CFD method measures an aggregated fraud risk value for a given corporate m-banking transaction. Different from existing methods, which typically assume that the different marginal fraud risk factors are independent of each other, the CFD method can capture evasive fraud patterns caused by fraud risk factors that are inter-dependent or independent of each other. Evaluation results using Monte Carlo simulations showed that the CFD method is more effective in detecting evasive fraud patterns than the independence-based aggregation method.
Reputation Revision Method for Selecting Cloud Services Based on Prior Knowledge and a Market Mechanism

The trust levels of cloud services should be evaluated to ensure their reliability. The effectiveness of these evaluations has major effects on user satisfaction, which is increasingly important. However, it is difficult to provide objective evaluations in open and dynamic environments because of the possibilities of malicious evaluations, individual preferences, and intentional praise. In this study, we propose a novel unfair rating filtering method for a reputation revision system. This method uses prior knowledge as the basis of similarity when calculating the average rating, which facilitates the recognition and filtering of unfair ratings. In addition, the overall performance is increased by a market mechanism that allows users and service providers to adjust their choice of services and service configuration in a timely manner. The experimental results showed that this method filtered unfair ratings in an effective manner, which greatly improved the precision of the reputation revision system.
Software Design Guidelines for Usability

For years, the Human Computer Interaction (HCI) community has defined the expected characteristics of usable software systems. However, from a Software Engineering (SE) perspective, the process of incorporating usability into software is not always straightforward, as many usability features have strong implications in the underlying architecture. For example, successfully including a "cancel" feature in an application may involve complex interrelated data structures and functionalities. Our work is focused upon providing developers with a set of guidelines to assist them in including such usability features with high impact on software design into their developments effectively.
Consistent surface model for SPH-based fluid transport

Surface effects play an essential role in fluid simulations. A vast number of dynamics including wetting of surfaces, cleansing, and foam dynamics are based on surface-surface and surface-bulk interactions, which in turn rely on a robust surface computation. In this paper we introduce a conservative Lagrangian formulation of surface effects based upon incompressible smoothed particle hydrodynamics (SPH). The key concept of our approach is to realize an implicit definition of the fluid's (free) surface by assigning each particle a value estimating its surface area. Based on this consistent surface representation, a conservative coupling of bulk and surface is achieved. We demonstrate the applicability and robustness of our approach for several types of surface-relevant effects including adsorption, diffusion and reaction kinetics.
History-Based Arbitration for Fairness in Processor-Interconnect of NUMA Servers

NUMA (non-uniform memory access) servers are commonly used in high-performance computing and datacenters. Within each server, a processor-interconnect (e.g., Intel QPI, AMD HyperTransport) is used to communicate between the different sockets or nodes. In this work, we explore the impact of the processor-interconnect on overall performance -- in particular, the performance un- fairness caused by processor-interconnect arbitration. It is well known that locally-fair arbitration does not guarantee globally-fair bandwidth sharing as closer nodes receive more bandwidth in a multi-hop network. However, this work demonstrates that the opposite can occur in a commodity NUMA server where remote nodes receive higher bandwidth (and perform better). We analyze this problem and iden- tify that this occurs because of external concentration used in router micro-architectures for processor-interconnects without globally-aware arbitration. While accessing remote memory can occur in any NUMA system, performance un- fairness (or performance variation) is more critical in cloud computing and virtual machines with shared resources. We demonstrate how this unfairness creates significant performance variation when a workload is executed on the Xen virtualization platform. We then provide analysis using synthetic workloads to better understand the source of unfair- ness and eliminate the impact of other shared resources, including the shared last-level cache and main memory. To provide fairness, we propose a novel, history-based arbitration that tracks the history of arbitration grants made in the previous history window. A weighted arbitration is done based on the history to provide global fairness. Through simulations, we show our proposed history-based arbitration can provide global fairness and minimize the processor- interconnect performance unfairness at low cost.
The UK economy : analysis of long-term performance and strategic challenges March 2008

The UK economy: analysis of long-term performance and strategic challenges The text in this document (excluding the Royal Coat of Arms and departmental logos) may be reproduced free of charge in any format or medium providing that it is reproduced accurately and not used in a misleading context. The material must be acknowledged as Crown copyright and the title of the document specified. If you require this information in another language, format or have general enquiries about HM Treasury and its work, contact: Printed on at least 75% recycled paper. When you have finished with it please recycle it again. The UK economy: analysis of long-term performance and strategic challenges
Amplification for Infants and Children with Hearing Loss*

In October 1994, Vanderbilt University, Bill Wilkerson Center, and the Academy of Dispensing Audiologists cosponsored a conference designed to address various contemporary issues associated with hearing aids for children. The proceedings of this conference, ''Amplification for Children With Auditory Deficits" (Bess, Gravel, & Tharpe, 1996), is available through the Bill Wilkerson Center Press, Nashville, Tenn. Following the conference, a small working group was assembled from the conference faculty to develop a Position Statement on amplification for infants and children with hearing loss. The members of the committee who prepared the following statement include: Fred H. Bess, Chair, Vanderbilt University School of Medicine / Bill Wilkerson Center, Nashville, Tennessee; Patricia A. Chase, Vanderbilt University School of Medicine, Nashville, Tennessee; Judith S. Gravel, Albert Einstein College of Medicine, Bronx, New York; Richard C. Seewald, The University of Western Ontario, London-Ontario, Canada; Patricia G. Stelmachowicz, Boys Town National Research Hospital, Omaha, Nebraska, Anne Marie Tharpe, Louisiana State University Medical Center, New Orleans, Louisiana;
Effect of different growth hormone (GH) mutants on the regulation of GH-receptor gene transcription in a human hepatoma cell line.

OBJECTIVE G to A transition at position 6664 of the growth hormone (GH-1) gene results in the substitution of Arg183 by His (R183H) in the GH protein and causes a new form of autosomal dominant isolated GH deficiency (IGHD type II). The aim of this study was to assess the bioactivity of this R183H mutant GH in comparison with both other GH variants and the 22-kDa GH in terms of GH-receptor gene regulation. DESIGN AND METHODS The regulation of the GH-receptor gene (GH-receptor/GH binding protein, GHR/GHBP) transcription following the addition of variable concentrations (0, 12.5, 25, 50 and 500 ng/ml) of R183H mutant GH was studied in a human hepatoma cell line (HuH7) cultured in a serum-free hormonally defined medium. In addition, identical experiments were performed using either recombinant human GH (22-kDa GH) as a positive control or two GH-receptor antagonists (R77C mutant GH and pegvisomant (B-2036-PEG)) as negative controls. GHR/GHBP mRNA expression was quantitatively assessed by RT-PCR amplification after 0, 1, 3 and 6 h incubation. RESULTS Following the addition of R183H mutant GH, GHR/GHBP mRNA changed at a similar rate to that seen in experiments where 22-kDa GH was added, indicating equal bioactivity. At all times and concentrations studied, the addition of R77C mutant GH, however, resulted in a significantly lower increase (P<0.001) of GHR/GHBP mRNA concentration compared with that caused by the addition of either 22-kDa GH or R183H mutant GH. Furthermore, in additional experiments, pegvisomant resulted in an absolute block of GHR/GHBP mRNA expression identical to that seen in control experiments where no 22-kDa GH was added at all. CONCLUSIONS These data indicate that the R183H mutant GH, although causing an autosomal dominant form of IGHD has an identical effect on GHR/GHBP transcription as its wild-type, the 22-kDa GH. This implies that the IGHD caused by the R183H heterozygous mutation of the GH-1 gene is mainly due to a block of its regulated GH secretion. In addition, the R77C-GH variant and pegvisomant have an antagonistic effect at the level of GHR/GHBP transcription. All these data were confirmed by run-on experiments. In addition, these data highlight, as far as the GH variants are concerned, that a mutational alteration within the GH-1 gene might cause short stature also on the basis of an altered secretory pathway. This fact has to be taken into consideration when growth retardation is clinically diagnosed and studied at the molecular level. Secretory pathways and, therefore, cell-biological mechanisms are of importance and have to be considered in future not only at the scientific but also at the clinical level.