gebhart/patrepeval huggingface dataset:
Heparan sulphate-degrading endoglycosidase in liver plasma membranes (1988)

An endoglycosidase is described in isolated liver plasma membranes that brings about a rapid and selective degradation of membrane-associated heparan sulphate, pre-labelled biosynthetically with Na2(35)SO4. The enzyme attacked mainly the polysaccharide chains of a hydrophobic membrane proteoglycan and it had little effect on a proteoglycan that could be displaced from the membranes with 1.0 M-NaCl. The highest activity was measured in the pH range 7.5-8.0, and the enzyme was almost completely inhibited below pH 5.5. Breakdown of susceptible polysaccharide chains was fast, being complete in 20-30 min. The major oligosaccharide fraction (Mr approx. 6000) produced by the enzyme was considerably smaller than the intact heparan sulphate chains. Enzyme activity was retained in membranes solubilized in 1% (v/v) Triton X-100. The high pH optimum and plasma-membrane association distinguish this enzyme from other heparan sulphate-degrading endoglycosidases that have acid pH optima and may be of lysosomal origin. A plasma-membrane endoglycosidase could modulate cellular interactions mediated by heparan sulphate, and/or release biologically active fragments of the polysaccharide from the cell periphery.
Optochemical control of RNA interference in mammalian cells (2013)

Short interfering RNAs (siRNAs) and microRNAs (miRNAs) have been widely used in mammalian tissue culture and model organisms to selectively silence genes of interest. One limitation of this technology is the lack of precise external control over the gene-silencing event. The use of photocleavable protecting groups installed on nucleobases is a promising strategy to circumvent this limitation, providing high spatial and temporal control over siRNA or miRNA activation. Here, we have designed, synthesized and site-specifically incorporated new photocaged guanosine and uridine RNA phosphoramidites into short RNA duplexes. We demonstrated the applicability of these photocaged siRNAs in the light-regulation of the expression of an exogenous green fluorescent protein reporter gene and an endogenous target gene, the mitosis motor protein, Eg5. Two different approaches were investigated with the caged RNA molecules: the light-regulation of catalytic RNA cleavage by RISC and the light-regulation of seed region recognition. The ability to regulate both functions with light enables the application of this optochemical methodology to a wide range of small regulatory RNA molecules.
Serum cholesterol: could it be a sixth parameter of Child-Pugh scoring system in cirrhotics due to viral hepatitis? (2012)

Hypocholesterolemia is a common finding in decompensated chronic liver disease and has got significant association with Child-Pugh class. It may increase the reliability of Child-Pugh classification in assessment of severity and prognosis in chronic liver disease patients.
Protein Structure Prediction (2000)

The number of protein sequences grows each year, yet the number of structures deposited in the Protein Data Bank remains relatively small. The importance of protein structure prediction cannot be over
Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia (2006)

Chronic myelogenous leukaemia (CML) results from the Bcr-Abl oncoprotein, which has a constitutively activated Abl tyrosine kinase domain. Although most chronic phase CML patients treated with imatinib as first-line therapy maintain excellent durable responses, patients who have progressed to advanced-stage CML frequently fail to respond or lose their response to therapy owing to the emergence of drug-resistant mutants of the protein. More than 40 such point mutations have been observed in imatinib-resistant patients. The crystal structures of wild-type and mutant Abl kinase in complex with imatinib and other small-molecule Abl inhibitors were determined, with the aim of understanding the molecular basis of resistance and to aid in the design and optimization of inhibitors active against the resistance mutants. These results are presented in a way which illustrates the approaches used to generate multiple structures, the type of information that can be gained and the way that this information is used to support drug discovery.
Telomerase and Primary T Cells: Biology and Immortalization for Adoptive Immunotherapy (2011)

Telomeres are specialized repeats, present at the end of chromosomes, whose loss during cell division is followed by growth arrest, a central mechanism of replicative senescence in human cells. Telomere length in stem cells is maintained by telomerase, a specialized reverse transcriptase, whose function is to restore shortening telomeres. Unlike most somatic cell types, human T lymphocytes are capable of briefly reactivating telomerase expression at the time of stimulation. Telomerase expression in T lymphocytes is modulated by a variety of external stimuli and by viral infections. However, telomerase reactivation in stimulated, proliferating human T lymphocytes is limited and cannot prevent the ultimate onset of senescence. Ectopic telomerase expression can rescue human and macaque antigen-specific T cells from senescence. Primary T cells have been engineered with telomerase to have substantially extended replicative lifespans without the loss of primary cell functions or malignant transformation. 'Immortal' antigen-specific T-cell lines and clones overexpressing telomerase are an invaluable source of well-characterized quasi-primary T cells for research of T-cell biology and are potentially useful for immunotherapy of cancer and AIDS.
Engineering synthetic TAL effectors with orthogonal target sites (2012)

The ability to engineer biological circuits that process and respond to complex cellular signals has the potential to impact many areas of biology and medicine. Transcriptional activator-like effectors (TALEs) have emerged as an attractive component for engineering these circuits, as TALEs can be designed de novo to target a given DNA sequence. Currently, however, the use of TALEs is limited by degeneracy in the site-specific manner by which they recognize DNA. Here, we propose an algorithm to computationally address this problem. We apply our algorithm to design 180 TALEs targeting 20 bp cognate binding sites that are at least 3 nt mismatches away from all 20 bp sequences in putative 2 kb human promoter regions. We generated eight of these synthetic TALE activators and showed that each is able to activate transcription from a targeted reporter. Importantly, we show that these proteins do not activate synthetic reporters containing mismatches similar to those present in the genome nor a set of endogenous genes predicted to be the most likely targets in vivo. Finally, we generated and characterized TALE repressors comprised of our orthogonal DNA binding domains and further combined them with shRNAs to accomplish near complete repression of target gene expression.
Arylation reactions with organobismuth reagents (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTArylation reactions with organobismuth reagentsJean Pierre FinetCite this: Chem. Rev. 1989, 89, 7, 1487–1501Publication Date (Print):November 1, 1989Publication History Published online1 May 2002Published inissue 1 November 1989https://pubs.acs.org/doi/10.1021/cr00097a005https://doi.org/10.1021/cr00097a005research-articleACS PublicationsRequest reuse permissionsArticle Views1954Altmetric-Citations165LEARN 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
Hydrogel Microsphere Encapsulation of a Cell-Based Gene Therapy System Increases Cell Survival of Injected Cells, Transgene Expression, and Bone Volume in a Model of Heterotopic Ossification (2010)

Bone morphogenetic proteins (BMPs) are well known for their osteoinductive activity, yet harnessing this capacity remains a high-priority research focus. We present a novel technology that delivers high BMP-2 levels at targeted locations for rapid endochondral bone formation, enhancing our preexisting cell-based gene therapy system by microencapsulating adenovirus-transduced cells in nondegradable poly(ethylene glycol) diacrylate (PEGDA) hydrogels before intramuscular delivery. This study evaluates the in vitro and in vivo viability, gene expression, and bone formation from transgenic fibroblasts encapsulated in PEGDA microspheres. Fluorescent viability and cytotoxicity assays demonstrated >95% viability in microencapsulated cells. ELISA and alkaline phosphatase assays established that BMP-2 secretion and specific activity from microencapsulated AdBMP2-transduced fibroblasts were not statistically different from monolayer. Longitudinal transgene expression studies of AdDsRed-transduced fibroblasts, followed through live animal optical fluorescent imaging, showed that microencapsulated cells expressed longer than unencapsulated cells. When comparable numbers of microencapsulated AdBMP2-transduced cells were intramuscularly injected into mice, microcomputed tomography evaluation demonstrated that the resultant heterotopic bone formation was approximately twice the volume of unencapsulated cells. The data suggest that microencapsulation protects cells and prolongs and spatially distributes transgene expression. Thus, incorporation of PEGDA hydrogels significantly advances current gene therapy bone repair approaches.
Capsule Endoscopy versus Colonoscopy for the Detection of Polyps and Cancer (2009)

The use of capsule endoscopy of the colon allows visualization of the colonic mucosa in most patients, but its sensitivity for detecting colonic lesions is low as compared with the use of optical colonoscopy. (ClinicalTrials.gov number, NCT00604162.)
Stereopopulation control. 9. Rate and equilibrium enhancement in the lactonization of (o-hydroxyphenyl)acetic acids (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereopopulation control. 9. Rate and equilibrium enhancement in the lactonization of (o-hydroxyphenyl)acetic acidsPaul S. Hillery and Louis A. CohenCite this: J. Org. Chem. 1983, 48, 20, 3465–3471Publication Date (Print):October 1, 1983Publication History Published online1 May 2002Published inissue 1 October 1983https://doi.org/10.1021/jo00168a018RIGHTS & PERMISSIONSArticle Views359Altmetric-Citations32LEARN 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 (923 KB) Get e-Alerts Get e-Alerts
Calibration of atomic-force microscope tips (1993)

Images and force measurements taken by an atomic-force microscope (AFM) depend greatly on the properties of the spring and tip used to probe the sample’s surface. In this article, we describe a simple, nondestructive procedure for measuring the force constant, resonant frequency, and quality factor of an AFM cantilever spring and the effective radius of curvature of an AFM tip. Our procedure uses the AFM itself and does not require additional equipment.
Vision systems based on the 128×128 focal plane cellular visual microprocessor chips (2003)

Focal plane cellular visual microprocessor chip development reached the necessary technology level that it can be applied in industrial vision systems. These TeraOPS speed, internally analog visual chips can capture and process thousands of medium resolution images in a second. The price for this extraordinary high speed is that their hardware-software environment and programming method is far from trivial. In this paper, we discuss architecture considerations, and introduce a standalone vision system family development case study.
Synthesis of Perfluoroalkylated Carboranes by Cross-Metathesis of Allylcarboranes and Perfluoroalkylpropenes (2010)

A ruthenium complex (Hoveyda–Grubbs second-generation) catalyzed cross-metathesis of allylcarboranes with perfluoroalkylpropenes under standard reaction conditions furnished perfluoroalkylated carboranes in good isolated yields (31–53%). The reaction proceeded with various carboranes and carborane sandwich complexes bearing the bridging allylthioether moiety. This method constitutes a simple and versatile procedure for the preparation of fluorophilic carboranes.
Lipofection does not require the removal of serum (1992)

Journal Article Lipofection does not require the removal of serum Get access Elisa Brunette, Elisa Brunette Cancer Research Institute, University of California San Francisco Medical Center, San FranciscoCA 94143-0128, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Roscoe Stribling, Roscoe Stribling Cancer Research Institute, University of California San Francisco Medical Center, San FranciscoCA 94143-0128, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Robert Debs Robert Debs * Cancer Research Institute, University of California San Francisco Medical Center, San FranciscoCA 94143-0128, USA * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 20, Issue 5, 11 March 1992, Page 1151, https://doi.org/10.1093/nar/20.5.1151 Published: 11 March 1992 Article history Accepted: 26 December 1991 Published: 11 March 1992
Voltage clamp analysis of tetrodotoxin-sensitive and -insensitive sodium channels in rat muscle cells developing in vitro (1985)

Sodium currents in cultured rat muscle cells converted to myoballs by treatment with colchicine were recorded using a giga-ohm seal voltage clamp procedure in the whole cell configuration. The mean peak Na+ conductance of the myoballs was 90 pS/microns2 of surface membrane. Half-maximal activation of Na+ currents was observed for test pulses to -31 mV and half-maximal inactivation was observed for prepulses to -74 mV. Titration of the inhibition of Na+ currents by tetrodotoxin (TTX) yielded a biphasic inhibition curve consistent with the presence of two classes of Na+ channels differing in affinity for TTX. The TTX-sensitive channels carried 28% of the Na+ current and had an apparent KD for TTX of 13 nM at 20 degrees C. The TTX-insensitive Na+ channels had an apparent KD for TTX of 3.2 microns. Inhibition of TTX-insensitive Na+ channels by TTX was enhanced by repetitive stimulation of the myoballs at 2 Hz, whereas the inhibition of TTX-sensitive Na+ channels by TTX was not frequency dependent. We conclude that rat muscle cells developing in vitro synthesize physiologically functional, TTX-sensitive Na+ channels in the absence of innervation. These channels, which are characteristic of adult skeletal muscle, function in parallel with TTX-insensitive Na+ channels that are present in embryonic muscle.
Endothelial induction of the T-cell chemokine CCL21 in T-cell autoimmune diseases (2003)

The signals that mediate T-cell infiltration during T-cell autoimmune diseases are poorly understood. The chemokine CCL21 (originally isolated by us and others as Exodus-2/6Ckine/SLC/TCA4) is highly potent and highly specific for stimulating T-cell migration. However, it is thought to be expressed only in secondary lymphoid organs, directing naive T cells to areas of antigen presentation. It is not thought to play a role in T-cell effector function during a normal immune response. In this study we tested the expression of T-cell chemokines and their receptors during T-cell autoimmune infiltrative skin diseases. By using immunohistology it was found that the expression of CCL21 but not CCL19 or 20 was highly induced in endothelial cells of T-cell autoimmune diseases. The receptor for CCL21, CCR7, was also found to be highly expressed on the infiltrating T cells, most of which expressed the memory CD45Ro phenotype. These data imply that the usual loss of CCL21 responsiveness in the normal development of memory T-cell effector function does not hold for autoimmune skin diseases.
Enzymic Synthesis and Regeneration of 3'-Phosphoadenosine 5'-Phosphosulfate (PAPS) for Regioselective Sulfation of Oligosaccharides (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnzymic Synthesis and Regeneration of 3'-Phosphoadenosine 5'-Phosphosulfate (PAPS) for Regioselective Sulfation of OligosaccharidesChun-Hung Lin, Gwo-Jenn Shen, Eduardo Garcia-Junceda, and Chi-Huey WongCite this: J. Am. Chem. Soc. 1995, 117, 30, 8031–8032Publication Date (Print):August 1, 1995Publication History Published online1 May 2002Published inissue 1 August 1995https://pubs.acs.org/doi/10.1021/ja00135a028https://doi.org/10.1021/ja00135a028research-articleACS PublicationsRequest reuse permissionsArticle Views739Altmetric-Citations43LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Nanolocomotion—Catalytic Nanomotors and Nanorotors (2009)

Nature's nanomachines, built of dynamically integrated biochemical components, powered by energy-rich biochemical processes, and designed to perform a useful task, have evolved over millions of years. They provide the foundation of all living systems on our planet today. Yet synthetic nanomotors, driven by simple chemical reactions and which could function as building blocks for synthetic nanomachines that can perform useful tasks, have been discovered only in the last few years. Why did it take so long to power-up a myriad of synthetic nanostructures from their well-known static states to new and exciting dynamic ones of the kind that abound in nature? This article will delve into this disconnect between the world of biological and abiological nanomotors, then take a look at some recent developments involving chemically powered nanoscale motors and rotors, and finally try to imagine: what's next for nanolocomotion?
Synthesis of pinacol esters of 1‐alkyl‐1H‐pyrazol‐5‐yl‐ and 1‐alkyl‐1H‐pyrazol‐4‐ylboronic acids (2004)

Abstract Starting from 1 H ‐pyrazol, a wide number of 1‐alkyl‐1 H ‐pyrazol‐4‐yl and 1‐alkyl‐1 H ‐pyrazol‐5‐ylboronic acids and their pinacol esters were synthesized and characterized. The key step in the described methodology is the regioselective lithiation of the pyrazole ring. The synthesized pinacolates are stable under prolonged storage and can be used as convenient reagents in organic synthesis.
In-line yield prediction methodologies using patterned wafer inspection information (1998)

Due to the advances in in-line inspection technology it is now possible to obtain an early in-line prediction of yield. This paper introduces and compares two new in-line yield prediction methodologies: (1) multilayer critical area method and (2) defect-type-size kill-ratio method. These methods are more accurate than the past and other current approaches used in the semiconductor industry. The first method uses the design layout information along with the in-line defect data, whereas the second method uses the defect and yield data to empirically derive the kill-ratios. We demonstrate our methodologies using data collected in a real wafer fabrication facility at the polysilicon gate (Poly), and the first and second interconnect (Metal 1 and Metal 2) post etch inspection layers. We compare our in-line predictions with the actual yield.
The case for fine-grained traffic engineering in data centers (2010)

Data center traffic characteristics are not well understood.&#13;\nIn particular, it is not clear how the prevalent&#13;\ntraffic patterns may impact candidate mechanisms for&#13;\nmanaging traffic inside the data centers. In this paper,&#13;\nwe conduct a measurement study of network-level traffic&#13;\npatterns inside data centers. Based on our empirical&#13;\ninsights, we design a traffic generator for creating representative&#13;\nworkloads for traffic between TOR switches in&#13;\na data center. We use this generator to evaluate several&#13;\ntraffic engineering techniques and data center network&#13;\narchitectures, and analyze their short comings. Our findings&#13;\nhighlight the need for fine-grained traffic engineering&#13;\n(TE) mechanisms. We design and implement such an&#13;\napproach using OpenFlow and show how it can significantly&#13;\nimprove data center TE.
A Simple Route toN,N-Dialkyl Derivatives of 2-Amino-5-thiophenecarboxylates (2000)

Starting from acetamides 4 and using three different routes − via thioacetamides 5, 3-amino-thioacrylamides 7, or 3-chloropropeniminium salts 6 − a series of new N,N-dialkyl derivatives of 2-amino-5-thiophenecarboxylates 10 has been prepared and analytically and spectroscopically characterized.