gebhart/patrepeval huggingface dataset:
Map-Reduce for Machine Learning on Multicore (2007)

We are at the beginning of the multicore era. Computers will have increasingly many cores (processors), but there is still no good programming framework for these architectures, and thus no simple and unified way for machine learning to take advantage of the potential speed up. In this paper, we develop a broadly applicable parallel programming method, one that is easily applied to many different learning algorithms. Our work is in distinct contrast to the tradition in machine learning of designing (often ingenious) ways to speed up a single algorithm at a time. Specifically, we show that algorithms that fit the Statistical Query model [15] can be written in a certain summation form, which allows them to be easily parallelized on multicore computers. We adapt Google's map-reduce [7] paradigm to demonstrate this parallel speed up technique on a variety of learning algorithms including locally weighted linear regression (LWLR), k-means, logistic regression (LR), naive Bayes (NB), SVM, ICA, PCA, gaussian discriminant analysis (GDA), EM, and backpropagation (NN). Our experimental results show basically linear speedup with an increasing number of processors.
Anastrozole for prevention of breast cancer in high-risk postmenopausal women (IBIS-II): an international, double-blind, randomised placebo-controlled trial (2013)

Cancer Research UK, the National Health and Medical Research Council Australia, Sanofi-Aventis, and AstraZeneca.
The Science of Virtual Reality and Virtual Environments (1993)

This book goals hits basic idea: giving a review on Virtual Reality and on the theory at its basis. Starting from history, going trought science as medicine, arriving at technical stuff this is in syntesis this book. For everyone interested in “How it work?”. Only one problem: sometimes is too difficoult to understand at no graduate persons dues to hi level techincal explanations in particoular in display chapter
Single-molecule DNA digestion by lambda-exonuclease (1999)

We used a bead displacement sensor to determine the enzymatic shortening of individual molecules of unstained λ-DNA attached to optically trapped beads. The setup has been described previously (Dapprich and Nicklaus: Bioimaging 6:25–32, 1998) and works by observing the change in position of a trapped bead depending on its viscous drag force during motion. The drag force of a naked bead increases with each attached DNA molecule to a characteristic level that depends on the length and the number of DNAs per bead. A single undigested DNA molecule on a bead will remain stable for extended periods and exhibit a constant drag force in flow. If λ-exonuclease is added, the drag force decreases from the level for one strand of DNA on a bead to that of a naked bead in about 45 min. This result indicates that the digestion of native λ-DNA by λ-exonuclease occurs at an average rate of approximately 15–20 Hz. Cytometry 36:163–168, 1999. © 1999 Wiley-Liss, Inc.
Mutations in active-site residues of the uracil-DNA glycosylase encoded by vaccinia virus are incompatible with virus viability (1996)

The D4R gene of vaccinia virus encodes a functional uracil-DNA glycosylase that is essential for viral viability (D. T. Stuart, C. Upton, M. A. Higman, E. G. Niles, and G. McFadden, J. Virol. 67:2503-2513, 1993), and a D4R mutant, ts4149, confers a conditional lethal defect in viral DNA replication (A. K. Millns, M. S. Carpenter, and A. M. DeLange, Virology 198:504-513, 1994). The mutant ts4149 protein was expressed in vitro and assayed for uracil-DNA glycosylase activity. Less than 6% of wild-type activity was observed at permissive temperatures, but the ts4149 protein was completely inactive at the nonpermissive temperature. Mutagenesis of the ts4149 gene back to wild type (Arg-179-->Gly) restored full activity. The ts4149 protein was considerably reduced in lysates of cells infected at the permissive temperature, and its activity was undetectable, even in the presence of the uracil glycosylase inhibitor protein, which inhibits the host uracil-DNA glycosylases but not that of vaccinia virus. Thus the ts4149 protein is thermolabile, correlating uracil removal with vaccinia virus DNA replication. Three active-site amino acids of the vaccinia virus uracil-DNA glycosylase were mutated (Asp-68-->Asn, Asn-120-->Val, and His-181-->Leu), producing proteins that were completely defective in uracil excision but still retained the ability to bind DNA. Each mutated D4R gene was transfected into vaccinia virus ts4149-infected cells in order to assess the recombination events that allowed virus survival at 40 degrees C. Genetic analysis and sequencing studies revealed that the only viruses to survive were those in which recombination eliminated the mutant locus. We conclude that the uracil cleavage activity of the D4R protein is essential for its function in vaccinia virus DNA replication, suggesting that the removal of uracil residues plays an obligatory role.
Heterologous gene expression in Lactococcus lactis subsp. lactis: synthesis, secretion, and processing of the Bacillus subtilis neutral protease (1990)

The Bacillus subtilis nprE gene lacking its own promoter sequence was inserted in the lactococcal expression vector pMG36e. Upon introduction of the recombinant plasmid into Lactococcus lactis subsp. lactis strain MG1363, neutral protease activity could be visualized by the appearance of large clearing zones around colonies grown on milk agar plates. By measuring the activities of the neutral protease and the intracellular enzyme lactate dehydrogenase in culture supernatants and cell fractions, it was demonstrated that the neutral protease was actively secreted into the growth medium. This was corroborated by using the Western blot (immunoblot) technique, which showed the presence of the mature form of the neutral protease in the culture supernatant. On the basis of these results, it is concluded that the B. subtilis neutral protease gene was expressed in L. lactis and that the gene product was secreted into the growth medium and was apparently correctly processed to produced a biologically active protein. The secretion of this particular enzyme may be helpful in achieving accelerated cheese ripening.
Dissociation of Heparan Sulfate and Receptor Binding Domains of Hepatocyte Growth Factor Reveals That Heparan Sulfate-c-Met Interaction Facilitates Signaling (2001)

Hepatocyte growth factor (HGF) is a secreted, heparan sulfate (HS) glycosaminoglycan-binding protein that stimulates mitogenesis, motogenesis, and morphogenesis in a wide array of cellular targets, including hepatocytes and other epithelial cells, melanocytes, endothelial cells, and hematopoietic cells. NK1 is an alternative HGF isoform that consists of the N-terminal (N) and first kringle (K1) domains of full-length HGF and stimulates all major HGF biological activities. Within NK1, the N domain retains the HS binding properties of full-length HGF and mediates HS-stimulated ligand oligomerization but lacks significant mitogenic or motogenic activity. In contrast, K1 does not bind HS, but it stimulates receptor and mitogen-activated protein kinase activation, mitogenesis, and motogenesis, demonstrating that structurally distinct and dissociable domains of HGF are the primary mediators of HS binding and receptor activation. Despite the absence of HS-K1 binding, K1 mitogenic activity in HS-negative cells is strictly dependent on added soluble heparin, whereas K1-stimulated motility is not. We also found that, like the receptors for fibroblast growth factors, the HGF receptor c-Met binds tightly to HS. These data suggest that HS can facilitate HGF signaling through interaction with c-Met that is independent of HGF-HS interaction and that the recruitment of specific intracellular effectors that mediate distinct HGF responses such as mitogenesis and motility is regulated by HS-c-Met interaction at the cell surface.
Direct Sparse Odometry (2017)

Direct Sparse Odometry (DSO) is a visual odometry method based on a novel, highly accurate sparse and direct structure and motion formulation. It combines a fully direct probabilistic model (minimizing a photometric error) with consistent, joint optimization of all model parameters, including geometry-represented as inverse depth in a reference frame-and camera motion. This is achieved in real time by omitting the smoothness prior used in other direct methods and instead sampling pixels evenly throughout the images. Since our method does not depend on keypoint detectors or descriptors, it can naturally sample pixels from across all image regions that have intensity gradient, including edges or smooth intensity variations on essentially featureless walls. The proposed model integrates a full photometric calibration, accounting for exposure time, lens vignetting, and non-linear response functions. We thoroughly evaluate our method on three different datasets comprising several hours of video. The experiments show that the presented approach significantly outperforms state-of-the-art direct and indirect methods in a variety of real-world settings, both in terms of tracking accuracy and robustness.
Structural Analysis of Histo-Blood Group Antigen Binding Specificity in a Norovirus GII.4 Epidemic Variant: Implications for Epochal Evolution (2011)

Susceptibility to norovirus (NoV), a major pathogen of epidemic gastroenteritis, is associated with histo-blood group antigens (HBGAs), which are also cell attachment factors for this virus. GII.4 NoV strains are predominantly associated with worldwide NoV epidemics with a periodic emergence of new variants. The sequence variations in the surface-exposed P domain of the capsid protein resulting in differential HBGA binding patterns and antigenicity are suggested to drive GII.4 epochal evolution. To understand how temporal sequence variations affect the P domain structure and contribute to epochal evolution, we determined the P domain structure of a 2004 variant with ABH and secretor Lewis HBGAs and compared it with the previously determined structure of a 1996 variant. We show that temporal sequence variations do not affect the binding of monofucosyl ABH HBGAs but that they can modulate the binding strength of difucosyl Lewis HBGAs and thus could contribute to epochal evolution by the potentiated targeting of new variants to Lewis-positive, secretor-positive individuals. The temporal variations also result in significant differences in the electrostatic landscapes, likely reflecting antigenic variations. The proximity of some of these changes to the HBGA binding sites suggests the possibility of a coordinated interplay between antigenicity and HBGA binding in epochal evolution. From the observation that the regions involved in the formation of the HBGA binding sites can be conformationally flexible, we suggest a plausible mechanism for how norovirus disassociates from salivary mucin-linked HBGA before reassociating with HBGAs linked to intestinal epithelial cells during its passage through the gastrointestinal tract.
Differential Expression of the Arabidopsis 2S Albumin Genes and the Effect of Increasing Gene Family Size (1990)

Philippe Guerche, Christine Tire, Fatima Grossi de Sa, Ann De Clercq, Marc Van Montagu, Enno Krebbers, Differential Expression of the Arabidopsis 2S Albumin Genes and the Effect of Increasing Gene Family Size, The Plant Cell, Vol. 2, No. 5 (May, 1990), pp. 469-478
Antimicrobial/Anti-Infective Materials (1999)

As our consciousness of microbes increases, it appears that our desire to control our interactions with germs also increases in proportion. This is clearly demonstrated by examining the incredible growth in the number and sales volume of consumer products with antimicrobial claims. In the medical field as well, there is much interest in the use of
Palladium-catalyzed formation of carbon-nitrogen bonds. Reaction intermediates and catalyst improvements in the hetero cross-coupling of aryl halides and tin amides (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPalladium-catalyzed formation of carbon-nitrogen bonds. Reaction intermediates and catalyst improvements in the hetero cross-coupling of aryl halides and tin amidesFrederic Paul, Joe Patt, and John F. HartwigCite this: J. Am. Chem. Soc. 1994, 116, 13, 5969–5970Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://pubs.acs.org/doi/10.1021/ja00092a058https://doi.org/10.1021/ja00092a058research-articleACS PublicationsRequest reuse permissionsArticle Views12173Altmetric-Citations715LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Stem cell transplantation in the treatment of gastrointestinal diseases (2008)

The stem cells with self-renewal ability are capable to form one or more cell types. They will be in the target of cell and gene therapy because of their multipotency and easy retrieval. Application of adult mesenchymal, neuronal, epidermal and haematopoietic stem cell can be favourable in the treatment of cardiac (myocardial infarction), bone (osteoarthritis), neurological (Parkinson's, Alzheimer's) and hematological (hemophilia, thrombocytopenia) disorders. Authors summarize the knowledge in connection with their application in the therapy of gastrointestinal diseases. Haematopoietic stem cell transplantation has been successful for the treatment of refractory Crohn's disease, as well as in selected group of celiac patients. Mesenchymal stem cell transplantation has been proved beneficial in the prevention of liver fibrotic process. It will gain more grounds in the treatment of autoimmune liver diseases: autoimmune hepatitis, primary biliary cirrhosis and primary sclerosing cholangitis in the future. Well-designed, multicentric, prospective studies are needed to confirm the results of case reports and clinical studies with small group of patients.
Processor-Based Strong Physical Unclonable Functions With Aging-Based Response Tuning (2013)

A strong physically unclonable function (PUF) is a circuit structure that extracts an exponential number of unique chip signatures from a bounded number of circuit components. The strong PUF unique signatures can enable a variety of low-overhead security and intellectual property protection protocols applicable to several computing platforms. This paper proposes a novel lightweight (low overhead) strong PUF based on the timings of a classic processor architecture. A small amount of circuitry is added to the processor for on-the-fly extraction of the unique timing signatures. To achieve desirable strong PUF properties, we develop an algorithm that leverages intentional post-silicon aging to tune the inter- and intra-chip signatures variation. Our evaluation results show that the new PUF meets the desirable inter- and intra-chip strong PUF characteristics, whereas its overhead is much lower than the existing strong PUFs. For the processors implemented in 45 nm technology, the average inter-chip Hamming distance for 32-bit responses is increased by 16.1% after applying our post-silicon tuning method; the aging algorithm also decreases the average intra-chip Hamming distance by 98.1% (for 32-bit responses).
Inducible nitric oxide synthase expression in periodontitis (2000)

Recently, nitric oxide (NO) has been shown to be vital in inflammatory processes. Nitric oxide synthase (NOS) exists in three different isoforms, two constitutively produced with physiological roles, and an inducible form, iNOS, which is involved in inflammation. This study examined the localisation of iNOS in biopsies from patients with periodontitis using immunohistochemistry, and compared these with healthy tissue biopsies. Biopsies were obtained from 16 periodontitis patients undergoing periodontal surgery and from clinically healthy tissues of 5 patients having crown lengthening procedures. The periodontitis diseased tissue demonstrated a greater level of iNOS expression than the healthy tissue. The source of iNOS in the periodontal tissues was determined by our monoclonal antibody to be the macrophage, with the endothelial cells also contributing. A role for NO in the inflammatory response of periodontal tissues is suggested, but the precise role requires further elucidation.
Miglustat therapy in the French cohort of paediatric patients with Niemann-Pick disease type C (2012)

Miglustat can improve or stabilize neurological manifestations in paediatric patients with the late-infantile and juvenile-onset forms of NP-C. Among early-infantile onset patients, a shorter delay between neurological disease onset and miglustat initiation was associated with an initial better therapeutic outcome in one patient, but miglustat did not seem to modify overall disease course in this subgroup. More experience is required with long-term miglustat therapy in early-infantile onset patients treated from the very beginning of neurological manifestations.
The Oral Microbiota: Living with a Permanent Guest (2009)

The oral cavity of healthy individuals contains hundreds of different bacterial, viral, and fungal species. Many of these can associate to form biofilms, which are resistant to mechanical stress or antibiotic treatment. Most are also commensal species, but they can become pathogenic in responses to changes in the environment or other triggers in the oral cavity, including the quality of an individual's personal hygiene. The complexity of the oral microbiome is being characterized through the newly developed tools of metagenomics. How the microbiome of the oral cavity contributes to health and disease is attracting the interest of a growing number of cell biologists, microbiologists, and immunologists.
Chemokines and dendritic cells: A crucial alliance (2002)

Dendritic cells (DC) are bone marrow-derived professional antigen-presenting cells that function as sentinels of the immune system. Their importance in immunity resides in their unique ability to prime or tolerize T lymphocytes, thereby initiating or inhibiting immune responses. They reside in all tissues and organs and upon appropriate activation, migrate to secondary lymphoid organs to present antigen to T lymphocytes in the T cell zones. Because of this central role in T cell activation, there is a great deal of interest in using DC therapeutically to deliver positive or negative signals to the immune system. The DC system is critically dependent on the ability of DC at different stages of maturation to respond to a range of soluble and cell-bound signals, including members of the chemokine gene superfamily. This review will describe the interactions between DC and the chemokine system.
UNCERTAINTY ANALYSIS IN PROPELLER OPEN WATER TESTS (1996)

An uncertainty analysis for a propeller open water test is described. The method used follows that of the American National Standards Institute (ANSI) and American Society of Mechanical Engineers (ASME) standard on Measurement uncertainty, adopted by these two bodies in 1985 and 1986 respectively, and the approach described by Coleman and Steele in their 1989 book Experimentation and uncertainty analysis for engineers. The uncertainty analysis was done to identify which sources of error had the most influence on the total uncertainty in the measurements as well as to ascertain the overall level of uncertainty in the measurements during these tests. The aim was to use the results to reduce future uncertainty levels in doing these tests and to provide a starting point or guide for uncertainty analysis in similar tests at other testing facilities.
Regulation of innate immune responses by autophagy-related proteins (2010)

Pattern recognition receptors detect microbial components and induce innate immune responses, the first line of host defense against infectious agents. However, aberrant activation of immune responses often causes massive inflammation, leading to the development of autoimmune diseases. Therefore, both activation and inactivation of innate immune responses must be strictly controlled. Recent studies have shown that the cellular machinery associated with protein degradation, such as autophagy, is important for the regulation of innate immunity. These studies reveal that autophagy-related proteins are involved in the innate immune response and may contribute to the development of inflammatory disorders.
Long noncoding RNA in genome regulation (2010)

Long noncoding RNAs (lncRNAs) are pervasively transcribed and critical regulators of the epigenome[1, 2]. These long, polyadenylated RNAs do not code for proteins, but function directly as RNAs, recruiting chromatin modifiers to mediate transcriptional changes in processes ranging from X-inactivation (XIST) to imprinting (H19)[3]. The recent discovery that lncRNA HOTAIR can link chromatin changes to cancer metastasis[4] furthers the relevance of lncRNAs to human disease. Here, we discuss lncRNAs as regulatory modules and explore the implications for disease pathogenesis. Although large-scale analyses of mammalian transcriptomes have revealed that more than 50% of transcripts have no protein coding potential[2, 5, 6], the functions of these putative transcripts are largely unknown. A subset of these noncoding transcripts are termed long noncoding RNAs (lncRNAs), based on an arbitrary minimum length of 200 nucleotides. LncRNAs are roughly classified based on their position relative to protein-coding genes: intergenic (between genes), intragenic/intronic (within genes), and antisense[2]. Initial efforts to characterize these molecules demonstrated that they function in cis, regulating their immediate genomic neighbors. Examples include AIR, XIST, and Kcnq1ot (reviewed in [1, 7, 8]), which recruit chromatin modifying complexes to silence adjacent sites. The scope of lncRNAs in gene regulation was advanced with the finding that lncRNA HOTAIR exhibited trans regulatory capacities. HOTAIR is transcribed at the intersection of opposing chromatin domains in the HOXC locus, but targets Polycomb Repressive Complex 2 (PRC2) to silence 40 kilobases of HOXD[9], a locus involved in developmental patterning. A subsequent study revealed that HOTAIR is overexpressed in approximately one quarter of human breast cancers, directing PRC2 to approximately 800 ectopic sites in the genome, which leads to histone H3 lysine 27 trimethylation and changes in gene expression[4]. The impacts of lncRNA-mediated chromatin changes are noteworthy: not only did HOTAIR drive metastasis in a mouse model, but HOTAIR expression in human breast cancer was found to be an independent prognostic marker for death and metastasis[4]. The fact that HOTAIR drives chromatin reprogramming genome-wide suggests that long-range regulation by lncRNAs may be a widespread mechanism. This is supported by a study showing that > 20% of tested lncRNAs are bound by PRC2 and other chromatin modifiers[10]. Furthermore, this is an underestimate of the total RNAs involved in chromatin modification, as PRC2 target genes also transcribe smaller 50-200 nt RNAs that interact with SUZ12 to mediate gene repression[11]. These findings provoke questions regarding the initial triggers for HOTAIR overexpression and whether understanding of lncRNA mechanics may have clinical relevance.