gebhart/patrepeval huggingface dataset:
Pyrithione biocide interactions with bacterial phospholipid head groups (1998)

Sodium pyrithione and zinc pyrithione (NaPT and ZnPT, respectively) are antimicrobial agents widely used in both the cosmetics and fuel industries. They are also utilized in the mining industry because of their metal chelating properties. They have been shown to depolarize membrane electropotential in fungi and are also known to inhibit fungal and bacterial substrate transport processes. Recent work has shown that both pyrithiones cause the leakage of intracellular material (potassium ions and O.D.260 nm absorbing material) from exposed bacterial cells. The work here reports studies on the interactions between the pyrithiones and the bacterial phospholipid head group structures, at both a practical and a theoretical level, utilizing tube dilution neutralizer studies, scanning spectrophotometry and molecular modelling. The tube dilution neutralizer studies exhibited a decrease in minimum inhibitory concentration (MIC) for both pyrithiones in the presence of extracellular phosphatidyl-ethanolamine and EDTA. Scanning spectrophotometry exhibited the chelation of the central zinc atom from the ZnPT chelate by the addition of EDTA. Molecular modelling studies exhibited the chelation of the phosphatidyl-ethanolamine head group by ZnPT. Zinc pyrithione also exhibited an interaction with the ammonium tail of the head group structures. Sodium pyrithione exhibited electrostatic interactions with the phospholipid head groups in the molecular modelling studies.
Abnormal expression of BRCA1 and BRCA1‐interactive DNA‐repair proteins in breast carcinomas (2000)

Breast cancer is one of the most common malignancies among women. The molecular mechanisms involved in breast carcinogenesis, however, remain to be elucidated. Although somatic mutation of BRCA1 is rare, BRCA1 protein expression is reduced in about 30% of sporadic breast carcinomas (Yoshikawa et al., Clin. Cancer Res., 5:1249–1261, 1999), indicating its possible involvement even in sporadic breast carcinogenesis. Among the BRCA1-interactive proteins are hRAD51 (a human homologue of Escherichia coli rec A protein), BARD1 (BRCA1-associated RING domain 1) and p53, all of which are involved in DNA repair. We have analyzed the expression patterns of the hRAD51, BARD1 and p53 proteins in five breast cancer cell lines, including a BRCA1-deficient cell line, and in 179 breast cancer tissue samples from Japanese women, including 113 sporadic, 47 hereditary (i.e., BRCA1 status unknown), and 19 BRCA1-associated cases. Of the 179 breast carcinomas, fifty-four (30%) exhibited reduced hRAD51 expression, and sixty-two (35%) exhibited p53 overexpression. On the other hand, reduced expression level of BARD1, and of hMSH2 and hMLH1, which are components of DNA mismatch-repair pathway and are involved in colorectal carcinogenesis, was observed respectively in only 10 (6%), 8 (5%) and 3 (2%) cases. The overall frequency of sporadic breast carcinomas with abnormal expression of either BRCA1 or the BRCA1-interactive proteins was 67% (76/113). These results indicate that there may be an important role for the BRCA1-associated DNA-repair pathway, not only in BRCA1-associated breast carcinomas, but also in sporadic breast carcinomas. Int. J. Cancer 88:28–36, 2000. © 2000 Wiley-Liss, Inc.
Gene therapy for achromatopsia (2017)

The present review summarizes the current status of achromatopsia (ACHM) gene therapy-related research activities and provides an outlook for their clinical application. ACHM is an inherited eye disease characterized by a congenital absence of cone photoreceptor function. As a consequence, ACHM is associated with strongly impaired daylight vision, photophobia, nystagmus and a lack of color discrimination. Currently, six genes have been linked to ACHM. Up to 80% of the patients carry mutations in the genes CNGA3 and CNGB3 encoding the two subunits of the cone cyclic nucleotide-gated channel. Various animal models of the disease have been established and their characterization has helped to increase our understanding of the pathophysiology associated with ACHM. With the advent of adeno-associated virus vectors as valuable gene delivery tools for retinal photoreceptors, a number of promising gene supplementation therapy programs have been initiated. In recent years, huge progress has been made towards bringing a curative treatment for ACHM into clinics. The first clinical trials are ongoing or will be launched soon and are expected to contribute important data on the safety and efficacy of ACHM gene supplementation therapy.
Shading bicubic patches (1987)

We present several techniques for implementing Phong shading in hardware for bicubic patches. Patches are shaded, not by subdividing into polygons, but by drawing many curves close together leaving no pixel gaps. Each curve is drawn using an adaptive forward difference algorithm which generates the coordinates as well as the shading parameters as cubic functions incrementally evaluated along the curve. The forward difference step size is adaptively adjusted so that it generates approximately one pixel along the curve per forward difference step. The hardware implements Phong shading directly with a surprisingly simple configuration built from general purpose compute units and look-up tables. Two new methods are presented for deriving bicubic approximations to the shading parameters over a bicubic patch. One method uses two Coons patches to approximate the unnormalized N&middot;L , and N&middot;H , and a third Coons patch for N&middot;N , where N is the surface normal, L is the light direction, and H is the direction of maximum highlight. In this case the hardware performs the normalization per pixel. The second method uses two Coons patches to approximate the normalized dot products N&middot;L , and N&middot;H. The method is suitable for both hardware and software implementations.
Molecular Modification of 2,7-Diphenyl[1]benzothieno[3,2-<i>b</i>]benzothiophene (DPh-BTBT) with Diarylamino Substituents: From Crystalline Order to Amorphous State in Evaporated Thin Films (2009)

Abstract Introduction of diarylamino substituents on 2,7-diphenyl[1]benzothieno[3,2-b]benzothiophene (DPh-BTBT) caused morphological change in the evaporated thin-film state: from highly crystalline films with edge-on molecular orientation for DPh-BTBT to amorphous films for the diarylamino derivatives. The former was unsuitable as a hole-transporting layer in organic light-emitting diodes (OLEDs), whereas the latter acted as a superior hole-transporting layer in multilayered OLEDs.
Studies on dynemicin. A nonradical cycloaromatization pathway for the azabicyclo[7.3.1]enediyne core structure initiated by thiolate addition (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies on dynemicin. A nonradical cycloaromatization pathway for the azabicyclo[7.3.1]enediyne core structure initiated by thiolate additionPhilip Magnus, Shane A. Eisenbeis, William C. Rose, Nada Zein, and Wyle SolomonCite this: J. Am. Chem. Soc. 1993, 115, 26, 12627–12628Publication Date (Print):December 1, 1993Publication History Published online1 May 2002Published inissue 1 December 1993https://doi.org/10.1021/ja00079a069RIGHTS & PERMISSIONSArticle Views188Altmetric-Citations28LEARN 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 InReddit PDF (231 KB) Get e-AlertsSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Monoclonal antibodies to Staphylococcus aureus laminin-binding proteins cross-react with mammalian cells (1988)

We and others have previously shown that some microorganisms, including bacteria, express on their surfaces receptors that specifically recognize extracellular matrix proteins, such as laminin, fibronectin, or both. The ability of microorganisms to adhere and to invade might depend on the existence of receptors which could, thus, be correlated with pathogenicity. In the present paper, we report the isolation of five stable cell lines that were producers of monoclonal antibodies to Staphylococcus aureus laminin receptors. One of these antibodies, which was of the immunoglobulin M isotype, blocked the binding of laminin to bacteria before and after fixation and recognized the putative 52-kilodalton laminin-binding protein in whole bacterial extracts. Also, purified receptor was isolated by immunoaffinity chromatography and shown to bind laminin. Furthermore, the same antibodies bound the 67-kilodalton putative receptor from mouse melanoma cells and gave positive immunofluorescence reactions against mammalian tumor cells. These data strongly suggest either the evolutionary conservation of at least some sequences in both procaryotic and eucaryotic laminin-binding proteins or convergent evolution and positive selection of epitopes cross-reacting with laminin. Some of these antibodies to the procaryotic protein could therefore become useful markers for the expression of laminin receptors by cancer cells.
Dual-wavelength picosecond optical pulse generation using an actively mode-locked multichannel grating cavity laser (1994)

Picosecond pulse generation by active mode locking has been achieved simultaneously at two wavelengths using a multichannel grating cavity Laser. For a spectral channel separation of 2.2 nm, pulses of duration of 60 ps and with a spectral width of 11 GHz have been obtained. The pulse widths are limited by the spectral dispersion of the grating used.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Glucose-Dependent Insulinotropic Polypeptide Stimulates Osteopontin Expression in the Vasculature via Endothelin-1 and CREB (2015)

Glucose-dependent insulinotropic polypeptide (GIP) is an incretin hormone with extrapancreatic effects beyond glycemic control. Here we demonstrate unexpected effects of GIP signaling in the vasculature. GIP induces the expression of the proatherogenic cytokine osteopontin (OPN) in mouse arteries via local release of endothelin-1 and activation of CREB. Infusion of GIP increases plasma OPN concentrations in healthy individuals. Plasma endothelin-1 and OPN concentrations are positively correlated in patients with critical limb ischemia. Fasting GIP concentrations are higher in individuals with a history of cardiovascular disease (myocardial infarction, stroke) when compared with control subjects. GIP receptor (GIPR) and OPN mRNA levels are higher in carotid endarterectomies from patients with symptoms (stroke, transient ischemic attacks, amaurosis fugax) than in asymptomatic patients, and expression associates with parameters that are characteristic of unstable and inflammatory plaques (increased lipid accumulation, macrophage infiltration, and reduced smooth muscle cell content). While GIPR expression is predominantly endothelial in healthy arteries from humans, mice, rats, and pigs, remarkable upregulation is observed in endothelial and smooth muscle cells upon culture conditions, yielding a "vascular disease-like" phenotype. Moreover, the common variant rs10423928 in the GIPR gene is associated with increased risk of stroke in patients with type 2 diabetes.
Suppression of a deletion mutation in the gene encoding essential PBP2b reveals a new lytic transglycosylase involved in peripheral peptidoglycan synthesis in <scp><i>S</i></scp><i>treptococcus pneumoniae</i> D39 (2016)

In ellipsoid-shaped ovococcus bacteria, such as the pathogen Streptococcus pneumoniae (pneumococcus), side-wall (peripheral) peptidoglycan (PG) synthesis emanates from midcells and is catalyzed by the essential class B penicillin-binding protein PBP2b transpeptidase (TP). We report that mutations that inactivate the pneumococcal YceG-domain protein, Spd_1346 (renamed MltG), remove the requirement for PBP2b. ΔmltG mutants in unencapsulated strains accumulate inactivation mutations of class A PBP1a, which possesses TP and transglycosylase (TG) activities. The 'synthetic viable' genetic relationship between Δpbp1a and ΔmltG mutations extends to essential ΔmreCD and ΔrodZ mutations that misregulate peripheral PG synthesis. Remarkably, the single MltG(Y488D) change suppresses the requirement for PBP2b, MreCD, RodZ and RodA. Structural modeling and comparisons, catalytic-site changes and an interspecies chimera indicate that pneumococcal MltG is the functional homologue of the recently reported MltG endo-lytic transglycosylase of Escherichia coli. Depletion of pneumococcal MltG or mltG(Y488D) increases sphericity of cells, and MltG localizes with peripheral PG synthesis proteins during division. Finally, growth of Δpbp1a ΔmltG or mltG(Y488D) mutants depends on induction of expression of the WalRK TCS regulon of PG hydrolases. These results fit a model in which MltG releases anchored PG glycan strands synthesized by PBP1a for crosslinking by a PBP2b:RodA complex in peripheral PG synthesis.
Leucocyte depleted blood. (1984)

Non-haemolytic febrile transfusion reactions (NHFTR) are commonly associated with the production of leucocyte antibodies, especially in multitransfused patients. These reactions can be prevented or ameliorated by the transfusion of leucocyte depleted red cells. Manual centrifugation techniques are least effective and risk the loss of excessive red cells. Saline washing can be effective, but is either tedious (manual techniques) or results in slight excess red cell losses (machine techniques). Sedimentation with high molecular weight polymers such as dextran produce excellent leucocyte depletion and small red cell losses. Filtration is both relatively straightforward and relatively cheap, and results in very effective red cell depletion with acceptable red cell losses. Microaggregate filtration is an alternative low cost bedside technique whose effectiveness does not depend entirely on maximum total leucocyte depletion. Freezing and thawing of red cells is very effective but is costly. Whatever technique is chosen, leucocyte depletion of at least 80% should be aimed for. The final choice however will depend on factors such as available facilities, experience and expense, and additional clinical factors such as the requirements for platelet depletion and plasma removal.
Antigenically intact hemagglutinin in circulating avian and swine influenza viruses and potential for H3N2 pandemic (2013)

The 2009 swine-origin H1N1 influenza, though antigenically novel to the population at the time, was antigenically similar to the 1918 H1N1 pandemic influenza, and consequently was considered to be "archived" in the swine species before reemerging in humans. Given that the H3N2 is another subtype that currently circulates in the human population and is high on WHO pandemic preparedness list, we assessed the likelihood of reemergence of H3N2 from a non-human host. Using HA sequence features relevant to immune recognition, receptor binding and transmission we have identified several recent H3 strains in avian and swine that present hallmarks of a reemerging virus. IgG polyclonal raised in rabbit with recent seasonal vaccine H3 fail to recognize these swine H3 strains suggesting that existing vaccines may not be effective in protecting against these strains. Vaccine strategies can mitigate risks associated with a potential H3N2 pandemic in humans.
MicroRNA-29b suppresses tumor angiogenesis, invasion, and metastasis by regulating matrix metalloproteinase 2 expression (2011)

miR-29b deregulation contributes to angiogenesis, invasion, and metastasis of HCC. Restoration of miR-29b represents a promising new strategy in anti-HCC therapy.
Diode-HBT-logic circuits monolithically integrable with ECl/CML circuits (1992)

A novel logic approach, diode-HBT logic (DHL), that is implemented with GaAlAs/GaAs HBTs and Schottky diodes to provide high-density and low-power digital circuit operation is described. This logic family was realized with the same technology used to produce emitter-coupled-logic/current-mode-logic (ECL/CML) circuits. The logic operation was demonstrated with a 19-stage ring oscillator and a frequency divider. A gate delay of 160 ps was measured with 1.1 mW of power per gate. The divider worked properly up to 6 GHz. Layouts of a DHL flip-flop and divider showed that circuit area and transistor count can be reduced by about a factor of 3, relative to ECL/CML circuits. The new logic approach allows monolithic integration of high-speed ECL/CML circuits with high-density DHL circuits with high-density DHL circuits.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Security Perspective on Unikernels (2020)

Cloud-based infrastructures have grown in popularity over the last decade leveraging virtualisation, server, storage, compute power and network components to develop flexible applications. The requirements for instantaneous deployment and reduced costs have led the shift from virtual machine deployment to containerisation, increasing the overall flexibility of applications and increasing performances. However, containers require a fully fleshed operating system to execute, increasing the attack surface of an application. Unikernels, on the other hand, provide a lightweight memory footprint, ease of application packaging and reduced start-up times. Moreover, Unikernels reduce the attack surface due to the self-contained environment only enabling low-level features. In this work, we provide an exhaustive description of the unikernel ecosystem; we demonstrate unikernel vulnerabilities and further discuss the security implications of Unikernel-enabled environments through different use-cases.
<title>Compressing images for the Internet</title> (1998)

The World Wide Web has rapidly become the hot new mass communications medium. Content creators are using similar design and layout styles as in printed magazines, i.e., with many color images and graphics. The information is transmitted over plain telephone lines, where the speed/price trade-off is much more severe than in the case of printed media. The standard design approach is to use palettized color and to limit as much as possible the number of colors used, so that the images can be encoded with a small number of bits per pixel using the Graphics Interchange Format (GIF) file format. The World Wide Web standards contemplate a second data encoding method (JPEG) that allows color fidelity but usually performs poorly on text, which is a critical element of information communicated on this medium. We analyze the spatial compression of color images and describe a methodology for using the JPEG method in a way that allows a compact representation while preserving full color fidelity.
The atlas of RNase H antisense oligonucleotide distribution and activity in the CNS of rodents and non-human primates following central administration (2020)

Antisense oligonucleotides (ASOs) have emerged as a new class of drugs to treat a wide range of diseases, including neurological indications. Spinraza, an ASO that modulates splicing of SMN2 RNA, has shown profound disease modifying effects in Spinal Muscular Atrophy (SMA) patients, energizing efforts to develop ASOs for other neurological diseases. While SMA specifically affects spinal motor neurons, other neurological diseases affect different central nervous system (CNS) regions, neuronal and non-neuronal cells. Therefore, it is important to characterize ASO distribution and activity in all major CNS structures and cell types to have a better understanding of which neurological diseases are amenable to ASO therapy. Here we present for the first time the atlas of ASO distribution and activity in the CNS of mice, rats, and non-human primates (NHP), species commonly used in preclinical therapeutic development. Following central administration of an ASO to rodents, we observe widespread distribution and target RNA reduction throughout the CNS in neurons, oligodendrocytes, astrocytes and microglia. This is also the case in NHP, despite a larger CNS volume and more complex neuroarchitecture. Our results demonstrate that ASO drugs are well suited for treating a wide range of neurological diseases for which no effective treatments are available.
Computation-scalable algorithm for scalable video coding (2011)

This paper presents a strategy that efficiently allocates the limited resource and still maintains the coding performance for the spatial scalability of H.264/SVC. An integrated computation-scalable algorithm is proposed on the basis of priority-based mode decision (PBMD) and activity-based motion estimation (ABME). The rate-distortion cost (RD-cost) of base layer is utilized as the priority to decide the mode in the enhancement layer, and the motion vector difference (MVD) in the base layer is employed to determine the search range as well. Through the proposed approach, computation complexity of the enhancement layer could be reduced efficiently and well allocated. A fast algorithm with early termination mechanism is also proposed in this paper. Experimental results demonstrate that the various rate-distortion and time-saving performances with computation scalability are realized.
Ten Simple Rules for Digital Data Storage (2016)

Data is the central currency of science, but the nature of scientific data has changed dramatically with the rapid pace of technology. This change has led to the development of a wide variety of data formats, dataset sizes, data complexity, data use cases, and data sharing practices. Improvements in high throughput DNA sequencing, sustained institutional support for large sensor networks, and sky surveys with large-format digital cameras have created massive quantities of data. At the same time, the combination of increasingly diverse research teams and data aggregation in portals (e.g. for biodiversity data, GBIF or iDigBio) necessitates increased coordination among data collectors and institutions. As a consequence, “data” can now mean anything from petabytes of information stored in professionally-maintained databases, through spreadsheets on a single computer, to hand-written tables in lab notebooks on shelves. All remain important, but data curation practices must continue to keep pace with the changes brought about by new forms and practices of data collection and storage.