gebhart/patrepeval huggingface dataset:
Genome Analysis of Phage JS98 Defines a Fourth Major Subgroup of T4-Like Phages in <i>Escherichia coli</i> (2007)

ABSTRACT Numerous T4-like Escherichia coli phages were isolated from human stool and environmental wastewater samples in Bangladesh and Switzerland. The sequences of the major head gene ( g23 ) revealed that these coliphages could be placed into four subgroups, represented by the phages T4, RB69, RB49, and JS98. Thus, JS98 defines a new major subgroup of E. coli T4-like phages. We conducted an analysis of the 169-kb JS98 genome sequence. Overall, 198 of the 266 JS98 open reading frames (ORFs) shared amino acid sequence identity with the reference T4 phage, 41 shared identity with other T4-like phages, and 27 ORFs lacked any database matches. Genes on the plus strand encoded virion proteins, which showed moderate to high sequence identity with T4 proteins. The right genome half of JS98 showed a higher degree of sequence conservation with T4 and RB69, even for the nonstructural genes, than did the left genome half, containing exclusively nonstructural genes. Most of the JS98-specific genes were found in the left genome half. Two came as a hypervariability cluster, but most represented isolated genes, suggesting that they were acquired separately in multiple acquisition events. No evidence for DNA exchange between JS98 phage and the E. coli host genome or coliphages other than T4 was observed. No undesired genes which could compromise its medical use were detected in the JS98 genome sequence.
Fishing Rod Guide Placement (2015)

Fishing rods are constructed of carbon fiber materials to precise dimensions. Mechanically it is equivalent to a tapered beam with a major and minor stiffness orientation. Guides are placed along the rod to transfer the line tension to the rod. The placement of the guides influences the deflected shape and stresses in the rod when landing a fish. The challenge is to develop a criteria for optimum placement of the guides to minimize the stress in the rod for a given magnitude of tension and orientation of the rod handle relative to the direction of the line to the fish. The analysis requires the use of large deflection theory and calculations are to be confirmed experimentally using strain gages attached to the rod.
Israel Rejects Its Own Offspring: The International Criminal Court (1999)

I. INTRODUcTIONIn an attempt to protect civilians from the dangers of armed conflict, various international bodies have attempted to codify harmful actions against innocent civilians into violations of international law. 1 While people in one state often commit crimes against people in another state, nation-states have had numerous difficulties in prosecuting those responsible for trans-border crimes before national criminal courts.On July 17, 1998, one hundred and twenty countries voted to adopt a multilateral treaty establishing the world's first permanent international criminal court to try individuals accused of genocide, war crimes, and crimes against humanity. 2 The International Criminal Court (ICC) adheres to the notion that individual government officials, and not just the states they govern, could be responsible, under 1.See, e.g.
Screen Partitioning Load Balancing for Parallel Rendering on a Multi-GPU Multi-Display Workstation (2019)

Commodity workstations with multiple GPUs have been built by engineers and scientists for real-time rendering applications. As a result, a high display resolution can be achieved by connecting each GPU to a display monitor (resulting in a tiled large display). Using a multi-GPU workstation may not always produce a highly interactive rendering rate due to imbalanced rendering workloads among GPUs. In this work, we propose a parallel load balancing algorithm based on a screen partitioning strategy to dynamically balance the amount of vertices and triangles rendered by each GPU. Each GPU renders a screen region whose size may be different from the screen regions of other GPUs, but the amounts of vertices and triangles in those screen regions are balanced. It is possible that a screen region rendered by a GPU has to be displayed by another GPU. We propose a frame exchanging algorithm that allows GPUs to exchange screen regions efficiently. The inter-GPU communication overhead is very small since the data transferred between GPUs are a small amount of image pixels.
Multicast tree construction and flooding in wireless ad hoc networks (2000)

In an ad hoc network, each host assumes the role of a router and relays packets toward final destinations. This paper studies efficient routing mechanisms for multicast and broadcast in ad hoc wireless networks. Because a packet is broadcast to all neighboring nodes, the optimality criteria of wireless network routing is different from that of wired network routing. In this paper, we point out that the number of packet forwarding is the more important cost factor than the number of links in the ad hoc network. After we show constructing minimum cost multicast tree is hard, we propose two new flooding methods, self pruning and dominant pruning. Both methods utilize neighbor information to reduce redundant transmissions. Performance analysis shows that both methods perform significantly better than blind flooding. Especially, dominant pruning performs close to the practically achievable best performance limit.
DECREASED EXPRESSION OF GALECTIN-3 IS ASSOCIATED WITH PROGRESSION OF HUMAN BREAST CANCER (1996)

Galectin-3, a member of the beta-galactoside-binding lectin family, is involved in several biological events including binding to the basement membrane glycoprotein laminin. Although the exact role of galectin-3 during the interactions between cells and laminin is not yet known, it has recently been observed that its expression is down-regulated at both the protein and the mRNA level in colon cancer tissues in correlation with progression of the disease. This study investigated the possibility that breast cancer cells might also exhibit decreased galectin-3 expression in association with their aggressiveness. The expression of galectin-3 was examined by immunoperoxidase staining, using a polyclonal antibody raised against recombinant galectin-3, in a collection of 98 human breast lesions including 12 fibroadenomas, 15 fibrocystic disease lesions, 22 in situ carcinomas, and 49 infiltrating ductal carcinomas, 19 of which had positive axillary lymph nodes. Normal breast tissue adjacent to the lesions was present in 59 biopsies. Normal breast tissue expressed high levels (3+) of galectin-3. High expression (2+ to 3+) was also found in most benign lesions examined. The expression of galectin-3 was significantly decreased in in situ carcinoma and this down-regulation was more pronounced in invasive ductal carcinoma, particularly when associated with infiltration of axillary lymph nodes. These data constitute the first observation that galectin-3 is down-regulated in breast cancer and suggest the decreased expression of this galactoside-binding lectin is associated with the acquisition of the invasive and metastatic phenotype.
Enabling incremental RET to exploit hierarchical structure across multiple designs for sub-100 nm lithography (2005)

Design tools exploit design hierarchy for speed, efficiency and reuse. Conventional optical proximity correction (OPC) tools process design layouts in a sequential mode layer by layer to ensure stability of the resolution enhancement technology (RET) corrections. A typical sub-100 nm design layout is very large and OPC expands the data volume significantly. The large data volumes and long run-times associated with conventional OPC are becoming critical bottlenecks for manufacturing turn-around time. 

In a full-chip layout comprised of a library of cells, a cell may be instantiated thousands of times. Aprio's incremental OPC technology applies a design-like methodology that exploits the hierarchical structure of the layout. OPC is applied once per master cell rather than once per cell placement. The master cells are reused and can be instantiated across different designs. These pre-OPC'ed cells are reconverged or stitched together at their interacting halo areas to build up proximity-corrected, hierarchical layouts. This alleviates the need to run OPC sequentially on multiple designs where the master cell is instantiated, thus leading to significantly reduced run-time and data size. We are able to extend this to applications such as manufacturing engineering change order (ECO) handling and design re- spins without the need to rerun the entire OPC layout. Since our incremental technology can stitch together previously OPC corrected areas and cells, we are able to combine less complex areas along with critical-care areas leading to a more robust final layout that is optimally designed for manufacturing.
Heavy water detection using ultra-high-Q microcavities (2006)

Ultra-high-Q optical microcavities (Q>10(7)) provide one method for distinguishing chemically similar species. Resonators immersed in H(2)O have lower quality factors than those immersed in D(2)O due to the difference in optical absorption. This difference can be used to create a D(2)O detector. This effect is most noticeable at 1,300 nm, where the Q(H(2)O) is 106 and the Q(D(2)O) is 107. By monitoring Q, concentrations of 0.0001% [1 part in 106 per volume] of D(2)O in H(2)O have been detected. This sensitivity represents an order of magnitude improvement over previous techniques. Reversible detection was also demonstrated by cyclic introduction and flushing of D(2)O.
FEWER ACUTE REJECTION EPISODES AND IMPROVED OUTCOME IN KIDNEY-TRANSPLANTED PATIENTS WITH SELECTION CRITERIA BASED ON CROSSMATCHING (1992)

Cross-matches performed on sera from presensitized patients have so far failed to differentiate clinically "relevant" from clinically "irrelevant" antibodies due to insufficient specificity characterization. In order to find a basis for such a possibility, 72 consecutive kidney transplanted patients were selected and studied retrospectively. Our policy has been to accept weakly positive (less than 50%) cytotoxicity on donor B splenic lymphocytes in the crossmatch test. Forty-six patients who had early acute rejections and 26 who had no acute rejections were selected for the study. Antibodies in current sera were characterized according to their target cell reactivity, immunoglobulin class, and HLA/non-HLA specificities. Crossmatches were performed using both the cytotoxicity and the flow cytometric method. We found that the factor that differentiates clinically "relevant" from clinically "irrelevant" antibodies is the HLA specificity of the lymphocyte-reactive antibodies. A high proportion of patients with posttransplant complications such as acute rejections had antibodies with specificities for HLA (particularly class I) antigens, while patients without rejections had either no detectable antibodies or antibodies reactive with non-HLA antigens only. In the present study, after elimination of false-positive reactions by ultracentrifugation of current sera, we found that flow cytometric crossmatches may not necessarily be more specific than the ordinary cytotoxicity crossmatch, since a positive flow cytometric crossmatch is often, but not always, associated with a weakly positive B cell cytotoxic crossmatch (10-25% reactivity). Antibodies causing a positive flow cytometric crossmatch could constitute low-titerd complement-fixing antibodies, non-complement-fixing antibodies, or both. Thus our study shows that it is possible to identify, prior to transplantation, patients with a risk of early posttransplant immunological complications such as acute rejection and to differentiate these from those who are more likely to have an uncomplicated posttransplant clinical course. A more careful patient selection based on adequate crossmatch testing, including specificity determination, might reduce the frequency of acute rejections and improve the outcome of transplantation.
MAMMOGRAPHIC PARENCHYMAL PATTERN AND BREAST CANCER RISK: A CRITICAL APPRAISAL OF THE EVIDENCE1 (1988)

Journal Article MAMMOGRAPHIC PARENCHYMAL PATTERN AND BREAST CANCER RISK: A CRITICAL APPRAISAL OF THE EVIDENCE Get access PAMELA J. GOODWIN, PAMELA J. GOODWIN Search for other works by this author on: Oxford Academic PubMed Google Scholar NORMAN F. BOYD NORMAN F. BOYD Reprint requests to Dr. Norman F. Boyd Search for other works by this author on: Oxford Academic PubMed Google Scholar American Journal of Epidemiology, Volume 127, Issue 6, June 1988, Pages 1097–1108, https://doi.org/10.1093/oxfordjournals.aje.a114904 Published: 01 June 1988
Carbon nanotubes: Sensor properties. A review (2016)

Recent publications dealing with dealing with the fabrication of gas and electrochemical biosensors based on carbon nanotubes have been reviewed. Experimental and theoretical data on the working principles of nanotubes have been presented. The main regularities of the structure, energy parameters and sensor properties of modified semiconducting systems on the basis of cabon nanotubes have been studied by analyzing the mechanisms of nanotubule interaction with functional groups (including carboxyl and amino groups), metallic nanoparticles and polymers leading to the formation of chemically active sensors. The possibility of using boundary modified nanotubes for the identification of metals has been discussed. Simulation results have been reported for the interaction of nanotubes boundary modified by –СООН and –NH2 groups with atoms and ions of potassium, sodium and lithium. The simulation has been carried out using the molecular cluster model and the MNDO and DFT calculation methods. Sensors fabricated using this technology will find wide application for the detection of metallic atoms and their ions included in salts and alkali.
Growth and Survival Mechanisms Associated with Perineural Invasion in Prostate Cancer (2004)

Perineural invasion (PNI) is the major mechanism of prostate cancer spread outside the prostate. Apoptotic and proliferation indices were determined in PNI cells using the PNI in vitro model and human PNI in tissue microarrays. RNA was extracted from the PNI model and controls and evaluated by cDNA microarray analysis. Differential expression of candidate genes was confirmed by real-time quantitative PCR, fluorescence, and immunohistochemistry using tissue microarrays. Genistein and BAY 11-7085 were added to the supernatant of cocultures and controls in microchamber cultures. The significance of nuclear factor kappaB (NFkappaB) nuclear translocation in human PNI was analyzed using Kaplan-Meier analysis. An increase in proliferation and a decrease in apoptosis were observed in human PNI cells and the PNI model as compared with controls. Three of 15 genes up-regulated in the cDNA microarray were involved in the apoptosis signaling pathway (NFkappaB), and its downstream targets defender against cell death 1 and PIM-2. The increase was corroborated by real-time quantitative PCR and immunofluorescence. NFkappaB nuclear translocation was seen in the in vitro model and human tissues, where strong nuclear expression was associated with a decrease in recurrence-free survival. Addition of genistein and BAY 11-7085 resulted in a decrease in NFkappaB, PIM-2 and defender against cell death 1 as well as a reversal of the inhibition of apoptosis. This is the first description of a biological mechanism and functional significance of PNI. Cancer cells in a perineural location acquire a survival and growth advantage using a NFkappaB survival pathway. Targeting PNI might help detain local spread of the tumor and influence survival.
Insecticide Activity and Structure, Insecticidal Properties of Some Diethyl Nitronaphthyl Phosphates (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInsecticide Activity and Structure, Insecticidal Properties of Some Diethyl Nitronaphthyl PhosphatesT. R. Fukuto, R. L. Metcalf, Mary Frederickson, and M. Y. WintonCite this: J. Agric. Food Chem. 1964, 12, 3, 228–231Publication Date (Print):May 1, 1964Publication History Published online1 May 2002Published inissue 1 May 1964https://pubs.acs.org/doi/10.1021/jf60133a010https://doi.org/10.1021/jf60133a010research-articleACS PublicationsRequest reuse permissionsArticle Views50Altmetric-Citations4LEARN 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
Artificial MicroRNAs as Novel Secreted Reporters for Cell Monitoring in Living Subjects (2016)

Reporter genes are powerful technologies that can be used to directly inform on the fate of transplanted cells in living subjects. Imaging reporter genes are often employed to quantify cell number, location(s), and viability with various imaging modalities. To complement this, reporters that are secreted from cells can provide a low-cost, in vitro diagnostic test to monitor overall cell viability at relatively high frequency without knowing the locations of all cells. Whereas protein-based secretable reporters have been developed, an RNA-based reporter detectable with amplification inherent PCR-based assays has not been previously described. MicroRNAs (miRNAs) are short non-coding RNAs (18-22 nt) that regulate mRNA translation and are being explored as relatively stable blood-based disease biomarkers. We developed an artificial miRNA-based secreted reporter, called Sec-miR, utilizing a coding sequence that is not expressed endogenously and does not have any known vertebrate target. Sec-miR was detectable in both the cells and culture media of transiently transfected cells. Cells stably expressing Sec-miR also reliably secreted it into the culture media. Mice implanted with parental HeLa cells or HeLa cells expressing both Sec-miR and the bioluminescence imaging (BLI) reporter gene Firefly luciferase (FLuc) were monitored over time for tumor volume, FLuc signal via BLI, and blood levels of Sec-miR. Significantly (p<0.05) higher Sec-miR was found in the blood of mice bearing Sec-miR-expressing tumors compared to parental cell tumors at 21 and 28 days after implantation. Importantly, blood Sec-miR reporter levels after day 21 showed a trend towards correlation with tumor volume (R2 = 0.6090; p = 0.0671) and significantly correlated with FLuc signal (R2 = 0.7067; p<0.05). Finally, we could significantly (p<0.01) amplify Sec-miR secretion into the cell media by chaining together multiple Sec-miR copies (4 instead of 1 or 2) within an expression cassette. Overall, we show that a novel complement of BLI together with a unique Sec-miR reporter adds an in vitro RNA-based diagnostic to enhance the monitoring of transplanted cells. While Sec-miR was not as sensitive as BLI for monitoring cell number, it may be more sensitive than clinically-relevant positron emission tomography (PET) reporter assays. Future work will focus on improving cell detectability via improved secretion of Sec-miR reporters from cells and more sensitive detection platforms, as well as, exploring other miRNA sequences to allow multiplexed monitoring of more than one cell population at a time. Continued development may lead to more refined and precise monitoring of cell-based therapies.
RECENT ADVANCES IN SODIUM INTERCALATION POSITIVE ELECTRODE MATERIALS FOR SODIUM ION BATTERIES (2013)

Significant progress has been achieved in the research on sodium intercalation compounds as positive electrode materials for Na-ion batteries. This paper presents an overview of the breakthroughs in the past decade for developing high energy and high power cathode materials. Two major classes, layered oxides and polyanion compounds, are covered. Their electrochemical performance and the related crystal structure, solid state physics and chemistry are summarized and compared.
Rectification of single GABA-gated chloride channels in adult hippocampal neurons (1985)

The properties of single chloride channels activated by gamma-aminobutyric acid (GABA) were investigated with hippocampal slices from adult guinea pigs. After the slices were treated with proteolytic enzymes, gigaseal recordings were made from excised patches of pyramidal or granule cell membranes. This newly developed preparation permits the application of patch-clamp techniques to the adult mammalian central nervous system. Guinea pig hippocampal slices were prepared in a conventional manner. Once prepared, the slices were treated with two different enzymes for brief periods and gently agitated. Slices generally split apart along the boundaries of the cell body regions, exposing neuronal somata. Standard patch-clamp techniques were used for the gigaseal recordings from excised patches. Solutions for both sides of the patches consisted of symmetrical concentrations of chloride, with all cation channels blocked. GABA at concentrations of 0.5-1.0 microM was added to the solution for the extracellular side of the patches. At transmembrane potentials negative to the chloride reversal potential (0 mV), the conductance through the GABA-gated chloride channels was approximately 20 pS. When the transmembrane potential was changed to positive values, the chloride conductance increased dramatically. For example, at +40 mV the conductance through the GABA-gated channels was almost 40 pS. Ramp-clamp commands were used to measure the current-voltage (I-V) relationship through single open channels. The open-channel I-V curves displayed outward rectification. The relationship between open-channel conductance and voltage could be fitted reasonably well by a single energy-barrier model for the channel, with the higher energy barrier placed near the cytoplasmic side of the membrane (at a fractional distance through the membrane of 0.73).(ABSTRACT TRUNCATED AT 250 WORDS)
Designer Zinc Finger Proteins:  Tools for Creating Artificial DNA-Binding Functional Proteins (2005)

The design of artificial functional DNA-binding proteins has long been a goal for several research laboratories. The zinc finger proteins, which typically contain many fingers linked in tandem fashion, are some of the most studied DNA-binding proteins. The zinc finger protein's tandem arrangement and its the ability to recognize a wide variety of DNA sequences make it an attractive framework to design novel DNA-binding peptides/proteins. Our laboratory has utilized several design strategies to create novel zinc finger peptides by re-engineering the C(2)H(2)-type zinc finger motif of transcription factor Sp1. Some of the engineered zinc fingers have shown nuclease and catalytic functional properties. Based on these results, we present the design strategies for the creation of novel zinc fingers.
Disorders of the Sebaceous Glands (2010)

This chapter contains sections titled: Structure and distribution Acne vulgaris Aetiology of acne Clinical features Treatment Uncommon associations with acne Severe acne variants Ectopic sebaceous glands Sebaceous gland hyperplasia, adenoma and carcinoma 'Sebaceous' (epidermoid) cysts and steatocystoma multiplex References
Environmental and genetic factors affecting bone mass similarity of bone density among members of healthy families (1995)

The BMD of children in healthy families was related to the BMD of their parents as well as to environmental factors, confirming the contribution of genetic inheritance in the determination of bone density in young adults, especially in girls.