Miracle-dz/UniFAR-FTUs huggingface dataset:
Strathprints Institutional Repository towards Better Measures: Evaluation of Estimated Resource Description Quality for Distributed Ir

Strathprints is designed to allow users to access the research output of the University of Strathclyde. Copyright c and Moral Rights for the papers on this site are retained by the individual authors and/or other copyright owners. You may not engage in further distribution of the material for any profitmaking activities or any commercial gain. You may freely distribute both the url (http:// strathprints.strath.ac.uk/) and the content of this paper for research or study, educational, or not-for-profit purposes without prior permission or charge. (2006) Towards better measures: evaluation of estimated resource description quality for distributed IR. In: Strathprints is designed to allow users to access the research output of the University of Strathclyde. Copyright © and Moral Rights for the papers on this site are retained by the individual authors and/or other copyright owners. Users may download and/or print one copy of any article(s) in Strathprints to facilitate their private study or for non-commercial research. You may not engage in further distribution of the material or use it for any profitmaking activities or any commercial gain. You may freely distribute the url Abstract An open problem for Distributed Information Retrieval systems (DIR) is how to represent large document repositories , also known as resources, both accurately and efficiently. Obtaining resource description estimates is an important phase in DIR, especially in non-cooperative environments. Measuring the quality of an estimated resource description is a contentious issue as current measures do not provide an adequate indication of quality. In this paper , we provide an overview of these currently applied measures of resource description quality, before proposing the Kullback-Leibler (KL) divergence as an alternative. Through experimentation we illustrate the shortcomings of these past measures, whilst providing evidence that KL is a more appropriate measure of quality. When applying KL to compare different QBS algorithms, our experiments provide strong evidence in favour of a previously unsupported hypothesis originally posited in the initial Query-Based Sampling work.
Detection of Novel Actionable Genetic Changes in Salivary Duct Carcinoma Helps Direct Patient Treatment

Purpose: Salivary duct carcinomas (SDC) are a rare and aggressive subtype of salivary gland cancers for which cytotoxic chemotherapy has limited efficacy. We investigated whether genotyping analysis could detect novel tumor-specific mutations that would help direct SDC patient treatment using targeted agents. Experimental Design: We genotyped 27 SDC archival specimens from patients followed at Massachusetts General Hospital and Massachusetts Eye and Ear Infirmary (Boston, MA) between 2000 and 2011. These included the tumors of 8 patients who were tested prospectively. Targeted mutational analysis of 13 clinically relevant cancer genes was conducted using SNaPshot multiplexed genotyping. FISH was conducted to detect HER2 gene amplification. Patient medical records and tumor histopathologic features were retrospectively reviewed. Results: Mutually exclusive genetic aberrations were detected in 15 of 27 (56%) tumors, including 2 (7%) mutations in BRAF, 5 (19%) mutations in PIK3CA, and 8 (30%) cases of HER2 gene amplification. To our knowledge, this is the first time that BRAF and PIK3CA mutations have been reported in this tumor type. Prospective clinical testing of 8 patients with SDC identified actionable genetic alterations in 6 tumors and influenced therapeutic decisions for all 6 patients. Conclusion: SNaPshot molecular profiling identified novel genetic changes in SDCs, expanded the therapeutic options for patients with this rare tumor, and is changing SDC management at our institution. These findings highlight the importance of using broad-based genetic profiling to expedite the identification of effective-targeted therapies for patients with rare malignancies. Clin Cancer Res; 19(2); 480–90. ©2012 AACR.
QSGD: Communication-Optimal Stochastic Gradient Descent, with Applications to Training Neural Networks

Parallel implementations of stochastic gradient descent (SGD) have received significant research attention, thanks to excellent scalability properties of this algorithm, and to its efficiency in the context of training deep neural networks. A fundamental barrier for parallelizing large-scale SGD is the fact that the cost of communicating the gradient updates between nodes can be very large. Consequently, lossy compression heuristics have been proposed, by which nodes only communicate quantized gradients. Although effective in practice, these heuristics do not always provably converge, and it is not clear whether they are optimal. In this paper, we propose Quantized SGD (QSGD), a family of compression schemes which allow the compression of gradient updates at each node, while guaranteeing convergence under standard assumptions. QSGD allows the user to trade off compression and convergence time: it can communicate a sublinear number of bits per iteration in the model dimension, and can achieve asymptotically optimal communication cost. We complement our theoretical results with empirical data, showing that QSGD can significantly reduce communication cost, while being competitive with standard uncompressed techniques on a variety of real tasks. In particular, experiments show that gradient quantization applied to training of deep neural networks for image classification and automated speech recognition can lead to significant reductions in communication cost, and end-to-end training time. For instance, on 16 GPUs, we are able to train a ResNet-152 network on ImageNet 1.8x faster to full accuracy. Of note, we show that there exist generic parameter settings under which all known network architectures preserve or slightly improve their full accuracy when using quantization.
Use of dissolved and vapor‐phase gases to investigate methanogenic degradation of petroleum hydrocarbon contamination in the subsurface

At many sites contaminated with petroleum hydrocarbons, methanogenesis is a significant degradation pathway. Techniques to estimate CH4 production, consumption, and transport processes are needed to understand the geochemical system, provide a complete carbon mass balance, and quantify the hydrocarbon degradation rate. Dissolved and vapor‐phase gas data collected at a petroleum hydrocarbon contaminated site near Bemidji, Minnesota, demonstrate that naturally occurring nonreactive or relatively inert gases such as Ar and N2 can be effectively used to better understand and quantify physical and chemical processes related to methanogenic activity in the subsurface. In the vadose zone, regions of Ar and N2 depletion and enrichment are indicative of methanogenic and methanotrophic zones, and concentration gradients between the regions suggest that reaction‐induced advection can be an important gas transport process. In the saturated zone, dissolved Ar and N2 concentrations are used to quantify degassing driven by methanogenesis and also suggest that attenuation of methane along the flow path, into the downgradient aquifer, is largely controlled by physical processes. Slight but discernable preferential depletion of N2 over Ar, in both the saturated and unsaturated zones near the free‐phase oil, suggests reactivity of N2 and is consistent with other evidence indicating that nitrogen fixation by microbial activity is taking place at this site.
Relationships Between Cull Beef Cow Characteristics, Finishing Practices and Meat Quality Traits of Longissimus thoracis and Rectus abdominis

The aim of study was to investigate the relationships between the characteristics of cull beef cows in the Rouge des Prés breed, finishing practices and physicochemical characteristics and sensory traits of Longissimus thoracis (LT) and Rectus abdominis (RA) muscles from 111 cows. On the basis of our surveys, which qualify at cow level the animal characteristics and finishing diet, clusters of cull cows and finishing practices are created and their effects tested on LT and RA meat quality. Old and heavy cows with good suckling ability (95 months, 466 kg and 7.1/10) are characterized by LT with larger fibers, and higher intramuscular fat content and fat-to-muscle ratio. Young and heavy cows with low suckling ability (54 months, 474 kg and 4.4/10) are characterized by LT and RA with lower MyHC IIx and higher MyHC IIa and MyHC I proportions. MyHC IIx and IIa proportions are lower and a* and b* color indices higher when cows are finished on pasture, probably related to grass diet and physical activity. The fat-to-muscle ratio is higher without any effect on the intramuscular fat content when cows are finished over a short period (107 days) with a high level of concentrate (9.7 kg/day). The opposite effect is observed over a long period (142 days) with a low level of concentrate (5.8 kg/day), confirming the interaction effect between finishing duration and amount of energy concentrate on the allotment of adipose tissue deposit.
Reinsertion of stimulated nucleus pulposus cells retards intervertebral disc degeneration: An in vitro and in vivo experimental study

Reinsertion of autogenous nucleus pulposus, an innovative method to delay further disc degeneration, has been proved with an experimental animal model. This study examined whether coculture of nucleus pulposus cells with annulus fibrosus cells (a) activates annulus fibrosus cells and (b) retards disc degeneration when reinserted into the disc in a rabbit model of disc degeneration. Coculture of the two cell types stimulated proliferation of each, as indicated by increased DNA synthesis measured by increases in DNA polymerase α expression and uptake of 5‐bromo‐2 deoxy‐uridine assessed by an enzyme‐linked immunosorbent assay. In a model of disc degeneration in rabbits, reinsertion of activated nucleus pulposus cells delayed the formation of clusters of chondrocyte‐like cells, the destruction of disc architecture, and the elaboration of type‐II collagen as measured immunohistochemically compared with no treatment. The direct reinsertion of activated nucleus pulposus cells into the disc offers a promising line of investigation for delaying intervertebral disc degeneration, although these results obtained with notochordal cells may not necessarily apply when mature central nucleus pulposus cells are used.
Dengue fever Outburst and its Relationship with Climatic Factors

This study aims to address the effects of climatic factors (temperature, relative humidity and rainfall) on Aedes aegypti mosquito density (hereinafter called mosquito density) in the Jeddah city, Saudi Arabia. Data for climatic factors, mosquito density and dengue fever cases for the years 2004 to 2011 were collected for the study period. Descriptive and bivariate statistical analyses were conducted to determine the relationship between the climatic factors and mosquito density and also between mosquito density and dengue fever cases in the city. The results show that the there is a strong correlation between mosquito density and climatic factors of temperature and relative humidity. The results also show a strong correlation between mosquito density and dengue fever cases in the city of Jeddah. The study shows a decrease in the mosquito density and thereby the dengue fever cases in Jeddah during the last couple of years. The results of the research are discussed with conclusions and recommendations.
Accurate keyword spotting using strictly lexical fillers

Our goal is to design an accurate keyword spotter that can deal with any size of keyword set, since the size actually required in a wide range of applications is large (number of airports, number of names in a directory, etc.). This justifies the choice of an architecture based on a large-vocabulary continuous-speech recognizer. In a previous paper we introduced the use of strictly-lexical subword fillers for keyword spotting based on the INRS large-vocabulary continuous-speech recognizer showing that they are, when compared to acoustic fillers, a good compromise between memory and time consumption, keyword choice freedom and task-independence training on one hand and accuracy on the other hand. We propose here two new high-performance designs of individual strictly-lexical subword fillers that perform, this time, better than their acoustic counterparts while still keeping the mentioned advantages.
Opening a can of worms: unprecedented sympatric cryptic diversity within British lumbricid earthworms

Earthworms play a major role in many aspects of soil fertility, food web ecology and ecosystem functioning, and hence are frequently the subjects of, for example, ecological and toxicological research. Our aim was to examine the genetic structure of common earthworm species, to identify cryptic lineages or species that may be distinct ecotypes or biotypes (and hence confound current research based upon morphotypes) and to try to explain the massive cryptic diversity that eventually emerged. We demonstrated that species such as Allolobophora chlorotica, Aporrectodea longa, Aporrectodea rosea and Lumbricus rubellus all comprise highly divergent lineages with species‐level divergence at the mitochondrial cytochrome oxidase I (COI) gene. In Allo. chlorotica alone, we found 55 haplotypes for COI, with 35 of these being found in pink and 20 in green morph worms. There were no cases of the two colour morphs sharing COI haplotypes. Phylogenetic analyses of mitochondrial COI and 16S genes showed the presence of five highly divergent lineages, suggesting the presence of multiple cryptic species within Allo. chlorotica. There was no clear geographical pattern to lineage distribution and many populations were polymorphic for both mitochondrial DNA lineage and colour morph. Amplified fragment length polymorphism results, based on two primer combinations, were broadly congruent with mitochondrial DNA results with one significant exception. Despite showing over 14% divergence at COI, amplified fragment length polymorphism markers showed that the two green morph lineages may be interbreeding and therefore represent a single taxon. The cryptic diversity revealed by these results has profound consequences for all areas of earthworm research.
What's Going on in Search Engine Rankings?

Many people use search engines every day to retrieve documents from the Web. Although the social influence of search engine rankings has become significant, ranking algorithms are not disclosed. In this paper, we have investigated three major search engine rankings by analyzing two kinds of data. One is the weekly ranking snapshots of top 250 Web pages we collected for almost one year by submitting 1,000 preselected queries; the other comprises back-linked Web pages gathered by our own Web crawling. As a result, we have confirmed that (1) several top 10 rankings are mutually similar, however, the following ranked Web pages are almost different, (2) ranking transitions have their own characteristics, and (3) each search engine's ranking has its own correlation with the number of back-linked Web pages.
Pathoproteomic profiling of the skeletal muscle matrisome in dystrophinopathy associated myofibrosis

The gradual accumulation of collagen and associated proteins of the extracellular matrix is a crucial myopathological parameter of many neuromuscular disorders. Progressive tissue damage and fibrosis play a key pathobiochemical role in the dysregulation of contractile functions and often correlates with poor motor outcome in muscular dystrophies. Following a brief introduction into the role of the extracellular matrix in skeletal muscles, we review here the proteomic profiling of myofibrosis and its intrinsic role in X‐linked muscular dystrophy. Although Duchenne muscular dystrophy is primarily a disease of the membrane cytoskeleton, one of its most striking histopathological features is a hyperactive connective tissue and tissue scarring. We outline the identification of novel factors involved in the modulation of the extracellular matrix in muscular dystrophy, such as matricellular proteins. The establishment of novel proteomic markers will be helpful in improving the diagnosis, prognosis, and therapy monitoring in relation to fibrotic substitution of contractile tissue. In the future, the prevention of fibrosis will be crucial for providing optimum conditions to apply novel pharmacological treatments, as well as establish cell‐based approaches or gene therapeutic interventions. The elimination of secondary abnormalities in the matrisome promises to reduce tissue scarring and the loss of skeletal muscle elasticity.
Regulation of mouse steroidogenesis by WHISTLE and JMJD1C through histone methylation balance

The dynamic exchange of histone lysine methylation status by histone methyltransferases and demethylases has been previously implicated as an important factor in chromatin structure and transcriptional regulation. Using immunoaffinity TAP analysis, we purified the WHISTLE-interacting protein complexes, which include the heat shock protein HSP90α and the jumonji C-domain harboring the histone demethylase JMJD1C. In this study, we demonstrate that JMJD1C specifically demethylates histone H3K9 mono- and di-methylation, and mediates transcriptional activation. We also provide evidence suggesting that both WHISTLE and JMJD1C performs functions in the development of mouse testes by regulating the expression of the steroidogenesis marker, p450c17, via SF-1-mediated transcription. Furthermore, we demonstrate that WHISTLE is recruited to the p450c17 promoter via SF-1 and represses the transcription of prepubertal stages of steroidogenesis, after which JMJD1C replaces WHISTLE and activates the expression of target genes via SF-1-mediated interactions. Our results demonstrate that the histone methylation balance mediated by HMTase WHISTLE and demethylase JMJD1C perform a transcriptional regulatory function in mouse testis development.
Association of cancer history with Alzheimer's disease onset and structural brain changes

Epidemiological studies show a reciprocal inverse association between cancer and Alzheimer's disease (AD). The common mechanistic theory for this effect posits that cells have an innate tendency toward apoptotic or survival pathways, translating to increased risk for either neurodegeneration or cancer. However, it has been shown that cancer patients experience cognitive dysfunction pre- and post-treatment as well as alterations in cerebral gray matter density (GMD) on MRI. To further investigate these issues, we analyzed the association between cancer history (CA±) and age of AD onset, and the relationship between GMD and CA± status across diagnostic groups in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort study. Data was analyzed from 1609 participants with information on baseline cancer history and AD diagnosis, age of AD onset, and baseline MRI scans. Participants were CA+ (N = 503) and CA− (N = 1106) diagnosed with AD, mild cognitive impairment (MCI), significant memory concerns (SMC), and cognitively normal older adults. As in previous studies, CA+ was inversely associated with AD at baseline (P = 0.025); interestingly, this effect appears to be driven by non-melanoma skin cancer (NMSC), the largest cancer category in this study (P = 0.001). CA+ was also associated with later age of AD onset (P < 0.001), independent of apolipoprotein E (APOE) ε4 allele status, and individuals with two prior cancers had later mean age of AD onset than those with one or no prior cancer (P < 0.001), suggesting an additive effect. Voxel-based morphometric analysis of GMD showed CA+ had lower GMD in the right superior frontal gyrus compared to CA− across diagnostic groups (Pcrit < 0.001, uncorrected); this cluster of lower GMD appeared to be driven by history of invasive cancer types, rather than skin cancer. Thus, while cancer history is associated with a measurable delay in AD onset independent of APOE ε4, the underlying mechanism does not appear to be cancer-related preservation of GMD.
Modeling Splitting and Spalling of Columnar Ice Compressed Biaxially: The Role of Crack Nucleation

Columnar ice exhibits three failure modes under increasing lateral confinement across the columns: splitting, Coulombic shear faulting, and spalling. Modeling of the splitting‐to‐spalling transition under increasing confined compression is considered here. Shear faulting is not considered. A three‐dimensional crack nucleation model, based on a grain boundary sliding approach, is formulated to model brittle failure mechanisms under biaxial compression along and across the columns. The growth of the nucleated crack is based on the wing crack approach. The numerical results were in good agreement with experimental data for both across‐column and along‐column biaxial compression. The model shows that in columnar ice, crack nucleation preceded by sliding along tapered grain boundaries induces splitting‐to‐spalling transition under increasing confinement.
Roles of the Nand C-termini of GLUT 4 in endocytosis

The GLUT4 glucose transporter isoform is found in adipose and muscle cells, and is responsible for the glucose uptake regulated by insulin (Rea and James, 1997). In adipose cells, GLUT4 are constantly recycling between intracellular compartments and the plasma membrane (Slot et al., 1991; Satoh et al., 1993). In the basal state, the majority (>90%) of the GLUT4 is located in an intracellular tubulo-vesicular compartment, referred to as the GLUT4 storage compartment (GSC). Insulin induces an increase in the rate of exocytosis of GLUT4-containing vesicles, resulting in a rapid shift in the steady-state distribution of GLUT4 to the plasma membrane. On the cell surface, GLUT4 are internalized by a dynamin-and clathrin-dependent mechanism (Al-Hasani et al., 1998; Kao et al., 1998) and transported into the endosomal system. Eventually, they are recycled back into the GSC by an unknown mechanism. Several studies have pointed out possible signal sequences within GLUT4 that may be responsible and sufficient for the subcellular targeting of GLUT4 in cultured insulin responsive-Two particular amino acid motifs have been connected to the subcellular trafficking of GLUT4 by the majority of the studies: the phenylalanine in position 5 (F5) in the N-terminus and the dileucine motif at position 489/490 (LL489/90) in the C-terminus. However, attempts to clarify the specific roles of the N-terminal F5-motif and the C-terminal LL489/90-motif, respectively, by measuring the kinetics of GLUT4 trafficking were carried out by expression of mutant GLUT4 (Araki et al.,
Recent Developments in the Evolution of Morphologies and Controllers for Physically Simulated Creatures

Karl Sims' work [25, 26] on evolving body shapes and controllers for three-dimensional, physically simulated creatures generated wide interest on its publication in 1994. The purpose of this article is threefold: (a) to highlight a spate of recent work by a number of researchers in replicating, and in some cases extending, Sims' results using standard PCs (Sims' original work was done on a Connection Machine CM-5 parallel computer). In particular, a re-implementation of Sims' work by the authors will be described and discussed; (b) to illustrate how off-the-shelf physics engines can be used in this sort of work, and also to highlight some deficiencies of these engines and pitfalls when using them; and (c) to indicate how these recent studies stand in respect to Sims' original work.