gebhart/patrepeval huggingface dataset:
Seventy-five percent accuracy in protein secondary structure prediction (1997)

In this study we present an accurate secondary structure prediction procedure by using an query and related sequences. The most novel aspect of our approach is its reliance on local pairwise alignment of the sequence to be predicted with each related sequence rather than utilization of a multiple alignment. The residue-by-residue accuracy of the method is 75% in three structural states after jack-knife tests. The gain in prediction accuracy compared with the existing techniques, which are at best 72%, is achieved by secondary structure propensities based on both local and long-range effects, utilization of similar sequence information in the form of carefully selected pairwise alignment fragments, and reliance on a large collection of known protein primary structures. The method is especially appropriate for large-scale sequence analysis of efforts such as genome characterization, where precise and significant multiple sequence alignments are not available or achievable.
The launching of a plane surface wave (1955)

The subject of the paper is a theoretical and experimental investigation of surface-wave propagation over a plane conductor with dielectric coating. Special reference is made to the problem of launching such a wave.Two experimental surfaces have been constructed, and a series of measurements has confirmed the properties of the waves as reported in the literature. A number of trials of various possible launching devices have been conducted, and eventually a launcher of moderate efficiency was found. A theoretical investigation of the launching efficiency of an aperture containing a surface-wave field of the correct form was conducted, and the launcher already mentioned was used to generate such a field in an aperture. Measurements were taken to find the launching efficiency of the aperture, and the results were found to be in agreement with the theory for small apertures. The deviations from the theoretical law for larger apertures are attributed to the fact that the aperture field differed slightly from the theoretical ideal in these cases.
Regulation of C. elegans Life-Span by Insulinlike Signaling in the Nervous System (2000)

An insulinlike signaling pathway controls Caenorhabditis elegans aging, metabolism, and development. Mutations in the daf-2 insulin receptor-like gene or the downstream age-1 phosphoinositide 3-kinase gene extend adult life-span by two- to threefold. To identify tissues where this pathway regulates aging and metabolism, we restored daf-2 pathway signaling to only neurons, muscle, or intestine. Insulinlike signaling in neurons alone was sufficient to specify wild-type life-span, but muscle or intestinal signaling was not. However, restoring daf-2 pathway signaling to muscle rescued metabolic defects, thus decoupling regulation of life-span and metabolism. These findings point to the nervous system as a central regulator of animal longevity.
Community‐based use of mangrove resources in St. Lucia (1993)

The sustainable use of mangrove forests can effectively contribute to their conservation. The experience with an integrated conservation‐development project in St. Lucia showed that charcoal producers using mangrove fuelwood resources in a Marine Reserve Area have successfully changed their harvesting practices, reversing a trend of mangrove destruction. The conditions under which this change occurred included strengthening the organization of local users and their resource‐use rights, and building a community‐based management system, leading to the avoidance of open‐access conditions. Surveys of the mangrove, undertaken before and after management intervention, showed that while the mean stand diameter of the fuelwood trees did not change significantly, there was an increase in the density of stems and in total basal area of timber.
Project Hoover (2012)

Real-time data processing frameworks like S4 and Flume have become scalable and reliable solutions for acquiring, moving, and processing voluminous amounts of data continuously produced by large numbers of online sources. Yet these frameworks lack the elasticity to horizontally scale-up or scale-down their based on current rates of input events and desired event processing latencies. The Project Hoover middleware provides distributed methods for measuring, aggregating, and analyzing the performance of distributed Flume components, thereby enabling online configuration changes to meet varying processing demands. Experimental evaluations with a sample Flume data processing code show Hoover's approach to be capable of dynamically and continuously monitoring Flume performance, demonstrating that such data can be used to right-size the number of Flume collectors according to different log production rates.
CELL PROLIFERATION, APOPTOSIS AND THE EXPRESSION OF RELATED GENES IN THE DEVELOPING LUNG OF MOUSE (2000)

Objective This study is to explore the dynamic trends of cell proliferation, apoptosis and the expression significance of involved genes as p53 and bcl\|2 in developing lungs of mouse. Methods Lung tissues were taken from different developmental phases of Kunming mouse. Immunohistochemistry and TUNEL techniques were adopted to observe the variation of cell proliferation and apoptosis and the expression characteristics of p53 and bcl\|2. Results 1 From the 14th to the 16th day of gestation the positive ratio of PCNA reached its peak. After that, it descended gradually. From the 4th day to the 14th day after birth, the proliferation maintained in low level; 2 Two peaks of apoptosis emerged during the development of lungs. The first one appeared from the 14th to the 16th day of gestation; the second one appeared at the 7th day after birth; 3 The expression of bcl\|2 first appeared from the 19th day of gestation to the 14th day after birth, with constant expression sites in the epithelial cells lined in the proximal bronchia and the smooth muscle cells. 4 The expression of p53 was never seen in all phases during the developmental process. Conclusion 1 During the development of mouse lungs, cell proliferation was accompanied by apoptosis. The dynamic changes of both ratios might be correlated to the different structures appearing in different developmental phases; 2 The possible function of bcl\|2 during the lung developmental process might be that it prevented the main frame structures of the bronchial tree and the capillary network from being destroyed by apoptosis; 3 Apoptosis during the development of lung might be independent of the regulation of p53.\;
Mechanism of Stabilization of Silicone Oil−Water Emulsions Using Hybrid Siloxane Polymers (2008)

Silicone polymers, due to their high lubricity and good spreading properties, are widely used in industrial applications. Being insoluble in water and most hydrocarbons, a common mode of delivering silicones is in the form of emulsions. To stabilize silicones in the emulsion form more efficiently, it is useful to understand the mechanism of emulsion stabilization. Two different mechanisms of emulsion stabilization have been proposed in the past: film formation and precipitation (known as the Pickering mechanism). These two mechanisms are different, and there is a need to further investigate this issue. The aim of the present work was to investigate the mechanism of stabilizing silicone emulsions and to propose a generalized behavior. Several experiments including the measurement of Langmuir isotherms, rheology experiments, phase diagram studies, and microscopy experiments were conducted. All of the above techniques indicated that the functional groups interact strongly with the water phase. The emulsions were found to be stable only if the emulsifiers were soluble in silicone oil or the water phase, and the stability decreased as the emulsifier precipitated. In most cases tested here, the emulsifiers were not observed to precipitate as reported earlier for the Pickering mechanism, and the emulsion stabilization followed film formation. These results should help to predict emulsion stabilization for unknown systems.
BCR-ABL independence and LYN kinase overexpression in chronic myelogenous leukemia cells selected for resistance to STI571 (2002)

Clinical studies have shown that the tyrosine kinase inhibitor STI571 effectively controls BCR-ABL-positive chronic myelogenous leukemia (CML). However, disease progression while on STI571 therapy has been reported, suggesting de novo or intrinsic resistance to BCR-ABL-targeted therapy. To investigate possible mediators of acquired STI571 resistance, K562 cells resistant to 5 microM STI571 (K562-R) were cloned and compared to the parental cell population. K562-R cells had reduced BCR-ABL expression and limited activation of BCR-ABL signaling cascades (Stat 5, CrkL, MAPK). STI571 failed to activate caspase cascades or to suppress expression of survival genes (bcl-xL) in resistant cells. Gene sequencing and tyrosine kinase activity measurements demonstrated that K562-R cells retained wild-type and active BCR-ABL tyrosine kinase that was inhibitable by in vitro incubation with STI571, suggesting that BCR-ABL was not coupled to proliferation or survival of K562-R cells. The src-related kinase LYN was highly overexpressed and activated in K562-R cells, and its inhibition reduced proliferation and survival of K562-R cells while having limited effects of K562 cells. Specimens taken from patients with advanced CML that progressed on STI571 therapy also were analyzed for LYN kinase expression, and they were found to be elevated to a level similar to that of K562-R cells. Comparison of samples from patients taken prior to and following STI571 failure suggested that expression and/or activation of LYN/HCK occurs during disease progression. Together, these results suggest that acquired STI571 resistance may be associated with BCR-ABL independence and mediated in part through overexpression of other tyrosine kinases.
Calcium and Bone Metabolic Homeostasis in Active and Denning Black Bears (Ursus americanus) (1990)

Decreased mechanical use of the skeleton results in osteoporosis in all species that have been studied, including humans. The unique metabolic adaptations of denning bears, however, suggest that these animals have evolved osteoregulatory mechanisms to protect against osteoporosis. The authors studied calcium and bone metabolism in black bears during three seasons: summer, winter, and spring. The serum calcium concentration did not change despite the fact that the bears remained metabolically active, recumbent, and anuric for four months. Furthermore, after four months of skeletal inactivity, bone mass and other parameters of osseous metabolism, including bone formation and mineral apposition rates were unchanged over summer values. A hypermetabolic state was observed after spring arousal in response to resumed skeletal loading. These findings suggest that bears may produce an osteoregulatory mechanism that prevents bone loss during prolonged periods of skeletal inactivity. Such a substance could have potential therapeutic applications for human beings.
Acinetobacter strains carry two functional oligosaccharyltransferases, one devoted exclusively to type IV pilin, and the other one dedicated to O‐glycosylation of multiple proteins (2015)

Multiple species within the Acinetobacter genus are nosocomial opportunistic pathogens of increasing relevance worldwide. Among the virulence factors utilized by these bacteria are the type IV pili and a protein O-glycosylation system. Glycosylation is mediated by O-oligosaccharyltransferases (O-OTases), enzymes that transfer the glycan from a lipid carrier to target proteins. O-oligosaccharyltransferases are difficult to identify due to similarities with the WaaL ligases that catalyze the last step in lipopolysaccharide synthesis. A bioinformatics analysis revealed the presence of two genes encoding putative O-OTases or WaaL ligases in most of the strains within the genus Acinetobacter. Employing A. nosocomialis M2 and A. baylyi ADP1 as model systems, we show that these genes encode two O-OTases, one devoted uniquely to type IV pilin, and the other one responsible for glycosylation of multiple proteins. With the exception of ADP1, the pilin-specific OTases in Acinetobacter resemble the TfpO/PilO O-OTase from Pseudomonas aeruginosa. In ADP1 instead, the two O-OTases are closely related to PglL, the general O-OTase first discovered in Neisseria. However, one of them is exclusively dedicated to the glycosylation of the pilin-like protein ComP. Our data reveal an intricate and remarkable evolutionary pathway for bacterial O-OTases and provide novel tools for glycoengineering.
Cloning and Characterization of Multiple Human Genes and cDNAs Encoding Highly Related Type II Keratin 6 Isoforms (1995)

The human type II keratin 6 (K6; 56 kDa) is expressed in a heterogeneous array of epithelial tissues under normal conditions, but is better known for its strong induction in stratified epithelia that feature an enhanced cell proliferation rate or abnormal differentiation. Previous work has established the existence of two functional genes encoding K6 protein isoforms in the human genome, although only a partial cDNA clone is available for K6a, the dominant human K6 isoform in skin epithelial tissues (Tyner, A., and Fuchs, E. (1986) J. Cell Biol. 103, 1945-1955). We screened human genomic and skin cDNA libraries with probes derived from the K6b gene, and isolated clones containing the full-length gene and cDNA predicted to encode K6a. A thorough characterization of a large number of genomic (57) as well as cDNA (64) clones further revealed the existence of as many as six different human K6 protein isoforms that are highly related at the gene structure, nucleotide sequence, and predicted amino acid sequence levels. Based on the information accumulated to date we propose an evolutionary model in which the multiplicity of human K6 genes is explained by successive gene duplication events. We further demonstrate that K6a is clearly the dominant K6 isoform in skin tissue samples and cultured epithelial cell lines and that the various isoforms are differentially regulated within and between epithelial tissue types. Our findings have direct implications for an understanding of the regulation and function of K6 during hyperproliferation in stratified epithelia and the search for disease-causing mutations in K6 sequences in the human population.
Adaptation of RNN Transducer with Text-To-Speech Technology for Keyword Spotting (2020)

With the advent of recurrent neural network transducer (RNN-T) model, the performance of keyword spotting (KWS) systems has greatly improved. However, the KWS systems, employed for wake-word detection, still rely on the availability of keyword specific training data for achieving reasonable performance on each keyword. With a goal to improve the KWS performance for these keywords without having to collect additional natural speech data, we explore Text-To-Speech (TTS) technology to synthetically generate training data for such keywords. Employing an RNN-T based KWS model, already well trained on large keyword-independent natural speech dataset, as a seed model, we run adaptation experiments using the generated keyword-specific TTS data. Besides observing a considerable improvement in the overall performance for the low-resource keywords, we find that the performance improvement with TTS-generated training data, similar to natural speech data, depends on speaker diversity, amount of data per speaker and data simulation. We get additional improvement in performance by selectively adapting specific parts of the RNN-T model and gain key insights into different architectural constructs of RNN-T model.
Insights into the Neurobiology of Impulsive Behavior from Serotonin Receptor Knockout Mice (1997)

Although the concept of impulsivity has proved useful in human and animal studies of addiction, violent aggression, and violent suicide, and has been recognized as an important component of human behavior, little research has been done to understand the underlying psychobiological mechanisms. We explore the concept of impulsivity and its relation with the neurotransmitter serotonin in the context of aggressive behavior and behavior associated with positive reinforcement using a knockout mouse that lacks one of the serotonin receptors, the 5-HT1B receptor. This knockout mouse shows more impulsive aggression, acquires cocaine self-administration faster, and drinks more alcohol than the corresponding wild-type control. We show that the impulsive characteristics of these mice are not due to change in cognitive functions: in a cognitive task involving a choice between a small immediate one and a larger more delayed reward, knockout mice showed intact choice and timing capabilities and good discrimination of reward amounts. Thus, this mouse may prove an animal model of addiction and motor impulsivity.
T lymphocytes express B7 family molecules following interaction with dendritic cells and acquire bystander costimulatory properties (2002)

Dendritic cells (DC) play a pivotal role in the initiation, maintenance and regulation of the immune response. Here we obtained the first evidence that DC, in the absence of any foreign antigens, induce the expression of B7 family costimulatory molecules, such as CD80, CD86, B7-H1, PD-L2, B7-H3, and B7RP-1, on autologous T lymphocytes. Cell-to-cell contact between DC and T cells was needed in order to obtain this expression on T cells. De novo expressed B7 molecules on T cells were functional since B7+ T cells were able to costimulate the proliferation of highly purified T cells. While both autologous and allogeneic DC were able to induce similar levels of costimulatory molecule expression, the chemokine receptor repertoire on B7+ T cells after interaction with DC varied depending on the presence of allo-antigens during the interaction (CCR7-, CCR5+) or the absence of antigens (CCR7+, CCR5-). In accordance with this different pattern of chemokine receptors in the two conditions, we propose that, after the encounter with DC in lymphoid organs, this peculiar T cell population should reside in the T cell areas of the lymph nodes or migrate to peripheral sites of inflammation, providing a second signal for activating or switching off, respectively, naive or peripheral effector T cells.
Taskmaster: recasting email as task management (2002)

Email has come to play a central role in task management, yet email tool features have remained relatively static in recent years, lagging behind users ’ evolving practices. The Taskmaster system narrows this gap by recasting email as task management and embedding task-centric resources directly in the client. During this workshop, we will describe the field research that inspired Taskmaster and the principles behind its design. We will also show how user studies conducted with “live ” email data over a two-week period revealed the value of a task-centric approach to email system design and its potential benefits for overloaded users.
Fabrication of Red‐Blood‐Cell‐Like Polyelectrolyte Microcapsules and Their Deformation and Recovery Behavior Through a Microcapillary (2013)

Multilayer microcapsules with a biconcave discoidal shape mimicking red blood cells (RBCs) are fabricated. The structure of the RBC-like microcapsules is verified by scanning electron and confocal laser scanning microscopies. The capsules show elastic deformation after being forced through a microcapillary with a smaller diameter, exhibiting a high recovery ratio of ≈90%. When the capsules are coated with hemoglobin (Hb),they are able to reversibly bind and release oxygen.
Lyme Borreliosis in the Soviet Union: A Cooperative US-USSR Report (1988)

We identified 90 patients with tick-borne erythema migrans in the Union of Soviet Socialist Republics (USSR) in areas from the western Baltic Republics to the Maritime Territory on the Pacific Ocean. Symptoms associated with the erythema included fever, malaise and fatigue, headache, myalgias, arthralgias, or regional lymphadenopathy. Within two weeks to four months, 58 (64%) of the patients developed neurological abnormalities, particularly radicular pain, cranial neuritis, or lymphocytic meningitis, and four (4%) patients developed monoarticular or oligoarticular arthritis. We tested the sera from 35 Soviet patients by using an isolate from the United States. The serological data showed elevated IgM and/or IgG antibody titers to Borrelia burgdorferi in 2 of 10 patients with erythema migrans, 15 of 21 with neurological abnormalities, and 2 of 4 with arthritis. Our observations suggest that Lyme borreliosis occurs in diverse areas of the USSR.
ChemInform Abstract: Reaction of Acetals and Orthoesters with Triisobutylaluminum. (1987)

Abstract The reactions between the cyclic acetals (I) or (III) and iBu3Al according to method A) occur at 100 °C to yield the acyclic ethers (II) and (IV), which result from hydrogenation of the acetals (I) and (III) by iBu3Al and concomitant evolution of isobutene.
Controlled Free-Radical Polymerization of Phenol Derivatives by Enzyme-Catalyzed Reactions in Organic Solvents (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTControlled Free-Radical Polymerization of Phenol Derivatives by Enzyme-Catalyzed Reactions in Organic SolventsMadhu S. Ayyagari, Kenneth A. Marx, Sukant K. Tripathy, Joseph A. Akkara, and David L. KaplanCite this: Macromolecules 1995, 28, 15, 5192–5197Publication Date (Print):July 1, 1995Publication History Published online1 May 2002Published inissue 1 July 1995https://pubs.acs.org/doi/10.1021/ma00119a005https://doi.org/10.1021/ma00119a005research-articleACS PublicationsRequest reuse permissionsArticle Views1027Altmetric-Citations111LEARN 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-Alertsclose Get e-Alerts