gebhart/patrepeval huggingface dataset:
Native R-loops Persist throughout the Mouse Mitochondrial DNA Genome (2008)

Mammalian mtDNA has been found here to harbor RNA-DNA hybrids at a variety of locations throughout the genome. The R-loop, previously characterized in vitro at the leading strand replication origin (OH), is isolated as a native RNA-DNA hybrid copurifying with mtDNA. Surprisingly, other mitochondrial transcripts also form stable partial R-loops. These are abundant and affect mtDNA conformation. Current models regarding the mechanism of mammalian mtDNA replication have been expanded by recent data and discordant hypotheses. The presence of stable, nonreplicative, and partially hybridized RNA on the mtDNA template is significant for the reevaluation of replication models based on two-dimensional agarose gel analyses. In addition, the close association of a subpopulation of mtRNA with the DNA template has further implications regarding the structure, maintenance, and expression of the mitochondrial genome. These results demonstrate that variously processed and targeted mtRNAs within mammalian mitochondria likely have multiple functions in addition to their conventional roles.
Identification of a mammalian gene structurally and functionally related to the CDC25 gene of Saccharomyces cerevisiae. (1992)

The yeast Saccharomyces cerevisiae CDC25 gene encodes a nucleotide-exchange-factor (NEF) that can convert the inactive GDP-bound state of RAS proteins to an active RAS-GTP complex. CDC25 can activate the yeast RAS proteins as well as the human H-ras protein. CDC25 is a member of a family of yeast genes that likely encode NEFs capable of regulating the RAS-related proteins found in yeast. By aligning the amino acid sequence of CDC25-related gene products we found a number of conserved motifs. Using degenerate oligonucleotides that encode these conserved sequences, we have used polymerase chain reactions to amplify fragments of mouse and human cDNAs related to the yeast CDC25 gene. We show that a chimeric molecule, part mouse and part yeast CDC25, can suppress the loss of CDC25 function in the yeast S. cerevisiae.
Cascaded Pyramid Network for Multi-Person Pose Estimation (2017)

The topic of multi-person pose estimation has been largely improved recently, especially with the development of convolutional neural network. However, there still exist a lot of challenging cases, such as occluded keypoints, invisible keypoints and complex background, which cannot be well addressed. In this paper, we present a novel network structure called Cascaded Pyramid Network (CPN) which targets to relieve the problem from these "hard" keypoints. More specifically, our algorithm includes two stages: GlobalNet and RefineNet. GlobalNet is a feature pyramid network which can successfully localize the "simple" keypoints like eyes and hands but may fail to precisely recognize the occluded or invisible keypoints. Our RefineNet tries explicitly handling the "hard" keypoints by integrating all levels of feature representations from the GlobalNet together with an online hard keypoint mining loss. In general, to address the multi-person pose estimation problem, a top-down pipeline is adopted to first generate a set of human bounding boxes based on a detector, followed by our CPN for keypoint localization in each human bounding box. Based on the proposed algorithm, we achieve state-of-art results on the COCO keypoint benchmark, with average precision at 73.0 on the COCO test-dev dataset and 72.1 on the COCO test-challenge dataset, which is a 19% relative improvement compared with 60.5 from the COCO 2016 keypoint challenge.Code (https://github.com/chenyilun95/tf-cpn.git) and the detection results are publicly available for further research.
Graph Wavelets for Multiscale Community Mining (2014)

We develop a signal processing approach to the multiscale detection of communities in networks, that is of groups of nodes well connected together. The method relies on carefully engineered wavelets on graphs to introduce the notion of scale and to obtain a local view of the graph from each node. Computing the correlations between wavelets centered at different nodes, one has access to a notion of similarity between nodes, thereby enabling a clustering procedure that groups nodes according to their community at the scale of analysis. By using a collection of random vectors to estimate the correlation between the nodes, we show that the method is suitable for the analysis of large graphs. Furthermore, we introduce a notion of partition stability and a statistical test allowing us to assess which scales of analysis of the network are relevant. The effectiveness of the method is discussed first on multiscale graph benchmarks, then on real data of social networks and on models for signal processing on graphs.
Theory and practice in affinity techniques (1978)

This book is a fair reflection of the editors’ efforts to bring together a wider variety of experts in affinity techniques. The success of this Giittingen conference was not only in its organization, but also in its value to speakers and audience alike in demonstrating the plethora of different ways in which biological interactions may be exploited. Applications of the latter go far beyond the now generally accepted technique of affinity chromatography. This book goes a long way to proving this point: thus the dissociation of chromatographic adsorption complexes using affinity elution applies to ion exchange, hydrophobic and affinity columns. A common misconception is to judge the mechanism of an affinity column by basing one’s conclusions on desorption specificity data. Von der Haar’s useful account of interfacial salting out of proteins includes a novel powerful modification, namely the use of ligand-induced solubility changes. This paper promises to alter our whole approach to ammonium sulphate fractionation of proteins and should be on the shelf of every protein chemist. The desorption of affinity matrices has always posed problems, especially for immunoadsorbents. The review on electrophoretic desorption shows how this novel process can be applied to non-prec~pitat~g antibody systems. Some mechanistic proposals are made. The method promises to be a useful addition to the battery of desorption techniques available. Haff reviews the uses of immobilised Cibacron blue and although this field has advanced very rapidly since the conference (see J. Chromatog. (1979) 165, 301), unpublished work was presented which adds to the value of this contribution. Lowe also included unpublished data in his account of mechanistic conclusions that can be drawn from studying the interactions of inosine dehydrogenase with immobilised nucleotides. Coggin’s account of the chemistry of bisimido esters and their value in studying subunit interactions includes a section on periodate cleavable crosslmking agents. Rando’s article of kQt inhibitors present a fascinating new horizon for enzymologists. These inhibitors (which are even more specific than transient state analogues) often require a little insight into an enzyme’s mechanism before a satisfactory molecule can be designed. The four articles on affinity labelling show how Ehrlich’s original proposal of the magic bullet has developed. Affinity labelling is a highly sophisticated subject in its own right. The final article is a general account of immunoassay and might seem out of place. In fact this author goes further than many in demonstrating the importance of exploiting biospecific interactions: clinical immunoassays are used by or on everyone. There are at least seven books on the subject of affinity chromatography. This text has a breadth not covered by the others and is of value to protein chemists.
Potent, Low-Molecular-Weight Non-Peptide Inhibitors of Malarial Aspartyl Protease Plasmepsin II (1999)

A number of single-digit nanomolar, low-molecular-weight plasmepsin II aspartyl protease inhibitors have been identified using combinatorial chemistry and structure-based design. By identifying multiple, small-molecule inhibitors using the parallel synthesis of several focused libraries, it was possible to select for compounds with desirable characteristics including enzyme specificity and minimal binding to serum proteins. The best inhibitors identified have Ki's of 2-10 nM, molecular weights between 594 and 650 Da, between 3- and 15-fold selectivity toward plasmepsin II over cathepsin D, the most closely related human protease, good calculated log P values (2.86-4.56), and no apparent binding to human serum albumin at 1 mg/mL in an in vitro assay. These compounds represent the most potent non-peptide plasmepsin II inhibitors reported to date.
Synthesis and secretion of alkaline phosphatase <i>in vitro</i> from first-trimester and term human placentas (1981)

The synthesis and secretion of alkaline phosphatases in vitro by human placental tissue incubated in organ culture were studied. First-trimester placenta synthesizes and secretes two different alkaline phosphatase isoenzymes (heat-labile and heat-stable), whereas in term placenta nearly all the alkaline phosphatase synthesized and secreted is heat-stable. The specific activities of alkaline phosphatases in first-trimester and term placental tissue remain constant throughout the time course of incubation. In the media, specific activities increase with time. Hence, alkaline phosphatase synthesis seems to be the driving force for its own secretion. The rates of synthesis de novo and of alkaline phosphatases were measured. The specific radioactivities of the secreted alkaline phosphatases were higher than the corresponding specific radioactivities in the tissue throughout the entire incubation period. The intracellular distribution of the alkaline phosphatase isoenzymes was compared.
<i>Lord George Germain</i> (1963)

Find information about UTP Journals. University of Toronto Press is Canada’s leading academic publisher and one of the largest university presses in North America, with particular strengths in the social sciences, humanities, and business. The Book Publishing Division is widely recognized in Canada for its strength in history, political science, sociology, Indigenous studies, and cultural studies. Internationally, UTP is a leading publisher of medieval, Renaissance, Italian, Iberian, Slavic, and urban studies, as well as studies in book and print culture.
Introducción (2004)

Mapa de América del Sur La biografía es una de las maneras más difíciles de escribir la Historia», afirmó un día Jacques Le Goff, recordando sin duda la larga elaboración de su magnífico San Luis. Durante mucho tiempo han sospechado de este género, y con buenas razones, los partidarios de una historiografía renovada. Lo encontraban demasiado marcado por los resortes de la literatura heroica, demasiado impregnado en muchos casos, aunque lo nieguen los autores, por la creencia implícita en lo...
Chemoattractants stimulate degradation of methylated phospholipids and release of arachidonic acid in rabbit leukocytes. (1979)

When rabbit peritoneal leukocytes were treated with chemoattractants such as fMet-Leu-Phe, an apparent decrease of [3H]methyl incorporation into the lipid fraction from L-[methyl-3H]methionine was observed. This decrease was a result of increased degradation of methylated phospholipids, not of decreased synthesis. Chemotactic peptides did not affect the metabolism of the phospholipids in which [methyl-14C]choline was incorporated. The disappearance of the [3H]methyl group was associated with the release of [1-14C]arachidonic acid from phospholipids prelabeled with these compounds. These findings suggested the activation by chemoattractants of phospholipase A2, an enzyme that removes an unsaturated fatty acid from phospholipids. The order of potency of chemoattractants for the stimulated degradation of phospholipids was in good agreement with that for chemotaxis. Mepacrine (quinacrine) and hydrocortisone inhibited and a phorbol ester enhanced both chemotaxis and phospholipase A2 activity. These results, taken together, suggest close association of the metabolism of methylated phospholipids with chemotaxis in rabbit peritoneal leukocytes.
Effect of Gelatin on Osteogenic Cell Sheet Formation Using Canine Adipose-Derived Mesenchymal Stem Cells (2016)

Osteogenically differentiated cell sheet techniques using mesenchymal stem cells (MSCs) are available to stimulate bone regeneration. The advantage of the cell sheet technique is delivering live cells effectively into the focal region. We developed a novel osteogenic cell sheet technique by adding gelatin to osteogenic cell medium. Gelatin-induced osteogenic cell sheets (GCSs) were compared to conventional osteogenic cell sheets (OCSs). Undifferentiated MSCs (UCs) were used as a control. The morphology of these cell sheets was evaluated microscopically and histologically. The time-dependent cell proliferation rate was estimated by DNA quantification. The expression of osteogenic gene markers and the number of calcium depositions were assessed by quantitative real-time polymerase chain reaction and Alizarin red S (ARS) staining, respectively. GCSs were thicker and stronger than OCSs. GCSs showed a significantly higher cell proliferation rate compared to OCSs (p < 0.05). GCSs exhibited significantly higher upregulation of BMP-7 mRNA compared to OCSs (p < 0.05). Both GCSs and OCSs showed negative ARS reactivity on day 10, but only GCSs showed positive ARS reactivity on day 21. With this technique, we observed active cell proliferation with abundant ECM and upregulation of osteogenic bone markers, and our results suggest that GCSs could be promising for therapeutic applications in bone regeneration.
Parameterized dataflow modeling for DSP systems (2001)

Dataflow has proven to be an attractive computation model for programming digital signal processing (DSP) applications. A restricted version of dataflow, termed synchronous dataflow (SDF), that offers strong compile-time predictability properties, but has limited expressive power, has been studied extensively in the DSP context. Many extensions to synchronous dataflow have been proposed to increase its expressivity while maintaining its compile-time predictability properties as much as possible. We proposed a parameterized dataflow framework that can be applied as a meta-modeling technique to significantly improve the expressive power of any dataflow model that possesses a well-defined concept of a graph iteration, Indeed, the parameterized dataflow framework is compatible with many of the existing dataflow models for DSP including SDF, cyclo-static dataflow, scalable synchronous dataflow, and Boolean dataflow. In this paper, we develop precise, formal semantics for parameterized synchronous dataflow (PSDF)-the application of our parameterized modeling framework to SDF-that allows data-dependent, dynamic DSP systems to be modeled in a natural and intuitive fashion. Through our development of PSDF, we demonstrate that desirable properties of a DSP modeling environment such as dynamic reconfigurability and design reuse emerge as inherent characteristics of our parameterized framework. An example of a speech compression application is used to illustrate the efficacy of the PSDF approach and its amenability to efficient software synthesis techniques. In addition, we illustrate the generality of our parameterized framework by discussing its application to cyclo-static dataflow, which is a popular alternative to the SDF model.
Prospective Study of Small LDLs as a Risk Factor for Non–Insulin Dependent Diabetes Mellitus in Elderly Men and Women (1995)

This study is the first to demonstrate that a predominance of small LDL particles is a risk factor for the future development of NIDDM, and it implies that small LDL contributes to risk of coronary heart disease in prediabetics.
Novel Anonymous Key Establishment Protocol for Isolated Smart Meters (2019)

In a smart grid, fine-grained usage reports of consumers are gathered using some computationally constrained smart measurement devices. One of the most challenging requirements in the data aggregation is how to securely read the consumption data, while putting the least possible overhead on smart meters. For this reason, recently, two efficient security protocols have been proposed to be used for subsequent secure consumption reports gathered from isolated smart measurement devices. Nonetheless, in both protocols, for each key establishment, the smart reader requires to connect to the electricity service provider (ESP) via the Internet. This paper proposes a novel key establishment protocol, which is free from the ESP involvement during the key agreement and benefits from notable reduction in the communication cost. Our thorough efficiency and security analyses indicate the eminence of the proposed security protocol.
The Changing Face of Prostate Cancer (2005)

Prostate cancer remains the most common noncutaneous human malignancy, and the second most lethal tumor among men. However, the natural history of the disease is often prolonged, and the survival benefits of local therapy for men with low-risk tumors may not be realized for a decade or more, as is increasingly well demonstrated in long-term observational cohorts in both the United States and Europe. A significant proportion of men with prostate cancer may be overdiagnosed, in the sense that diagnosis may not improve their lifespan or quality of life. However, the extent to which overdiagnosis represents a true problem relates to the consistency with which diagnosis leads invariably to active treatment. Prostate cancer is diagnosed at progressively earlier stages and with lower risk features; despite these trends, patients are less likely now than a decade ago to undergo a trial of active surveillance. Rates of brachytherapy and hormonal therapy use, in particular, have risen markedly. Important progress has been made in recent years in prostate cancer risk assessment. These advances, in combination with biomarkers in later stages of development, should be expected in the coming years to yield further improvements in clinicians' ability to diagnose prostate cancer early, and guide appropriately selected patients toward increasingly tailored treatment.
The <i>Drosophila disembodied</i> gene controls late embryonic morphogenesis and codes for a cytochrome P450 enzyme that regulates embryonic ecdysone levels (2000)

Ecdysteroids regulate a wide variety of cellular processes during arthropod development, yet little is known about the genes involved in the biosynthesis of these hormones. Previous studies have suggested that production of 20-hydroxyecdysone in Drosophila and other arthropods involves a series of cytochrome P450 catalyzed hydroxylations of cholesterol. In this report, we show that the disembodied (dib) locus of Drosophila codes for a P450-like sequence. In addition, we find that dib mutant embryos have very low titers of ecdysone and 20-hydroxyecdysone (20E) and fail to express IMP-E1 and L1, two 20E-inducible genes, in certain tissues of the embryo. In situ hybridization studies reveal that dib is expressed in a complex pattern in the early embryo, which eventually gives way to restricted expression in the prothoracic portion of the ring gland. In larval and adult tissues, dib expression is observed in the prothoracic gland and follicle cells of the ovaries respectively, two tissues known to synthesize ecdysteroids. Phenotypic analysis reveals that dib mutant embryos produce little or no cuticle and exhibit severe defects in many late morphogenetic processes such as head involution, dorsal closure and gut development. In addition, we examined the phenotypes of several other mutants that produce defective embryonic cuticles. Like dib, mutations in the spook (spo) locus result in low embryonic ecdysteroid titers, severe late embryonic morphological defects, and a failure to induce IMP-E1. From these data, we conclude that dib and spo likely code for essential components in the ecdysone biosynthetic pathway and that ecdysteroids regulate many late embryonic morphogenetic processes such as cell movement and cuticle deposition.
CloudView: Describe and Maintain Resource View in Cloud (2010)

Resource view is the user defined table to provide specific view on resource status in cloud computing environment. It provides a convenient way to retrieve resource data for applications at infrastructure, platform and service layers. But the description and maintenance of these diverse resource views are inconvenient and dramatically difficult due to massive, heterogeneous and dynamic characteristics of the cloud resources involved. In this paper we present a resource view description scheme RQL and the corresponding system Cloud View to address these difficulties. RQL provides users a scheme to specify the data processing flow from resource raw data collected to resource view data objected. By constructing data processing a cyclic graph based on view definitions and using basic routines, view maintenance mechanism update user defined resource views automatically and periodically. Cloud View use a centralized scheduler to distribute maintenance jobs to a set of scalable worker nodes. It leverages distributed key-value database to store view data. Compared to related resource monitoring and discovering systems, Cloud View is flexible in application oriented view description and maintenance. Experiments show it updates typical user defined views with desired performance.
Fuzzy Sets and Fuzzy Decision-Making (1995)

The Basics of Fuzzy Set Theory Fuzzy Phenomena and Fuzzy Concepts Naive Thoughts of Fuzzy Sets Definition of Fuzzy Sets Basic Operations of Fuzzy Sets The Resolution Theorem A Representation Theorem Extension Principles References Factor Spaces What are Factors? The State Space of Factors Relations and Operations Between Factors Axiomatic Definition of Factor Spaces Describing Concepts in a Factor Space References The Basics of Fuzzy Decision-Making Feedback Extension and Its Applications Feedback Ranks and Degrees of Coincidence Equivalence Between Sufficient Factors and Coincident Factors How to Improve the Precision of a Feedback Extension Representation of the Intention of a Concept Basic Forms of Fuzzy Decision-Making Limitations of the Weighted Average Formula References Determination of Membership Functions A General Method for Determining Membership Functions The Three-Phase Method The Incremental Method The Multiphase Fuzzy Statistical Method The Method of Comparisons The Absolute Comparison Method The Set-Valued Statistical Iteration Method Ordering by Precedence Relations The Relative Comparison Method and the Mean Pair-Wise Comparison Method References Multifactorial Analysis Background of the Problem Multifactorial Functions Axiomatic Definition of Additive Standard Multifactorial Functions Properties of ASMm-funcs Generations of ASMm-funcs Applications of ASMm-funcs in Fuzzy Decision-Making A General Model of Multifactorial Decision-Making References Variable Weights Analysis Defining the Problem An Empirical Variable Weight Formula Principles of Variable Weights References Multifactorial Decision-Making with Multiple Objectives Background and Models Multifactorial Evaluation The Multifactorial Evaluation Approach to the Classification of Quality Incomplete Multifactorial Evaluation Multi-Level Multifactorial Evaluation An Application of Multifactorial Evaluation in Textile Engineering References Set-Valued Statistics and Degree Analysis Fuzzy Statistics and Random Sets The Falling Shadow of Random Sets Set-Valued Statistics Degree Analysis Random and Set-Valued Experiments A Mathematical Model for Employee Evaluation References Refinements of Fuzzy Operators The Axiomatic Structure of Zadeh's Operators Common Fuzzy Operators Generalized Fuzzy Operators The Strength of Fuzzy Operators AND and OR Fuzzy Operators Based on the Falling Shadow Theory References Multifactorial Decision Based on Theory of Evidence A Brief Introduction to Theory of Evidence Composition of Belief Measures Multifactorial Evaluation Based on the Theory of Evidence Two Special Types of Composition Functions The Maximum Principle for Multiple Object Evaluations References