gebhart/patrepeval huggingface dataset:
Isolation and heterologous expression of a cDNA encoding bovine inositol polyphosphate 1-phosphatase. (1990)

Inositol polyphosphate 1-phosphatase, an enzyme of the phosphatidylinositol signaling pathway, catalyzes the hydrolysis of the 1-position phosphate from inositol 1,3,4-trisphosphate and inositol 1,4-bisphosphate. The protein was isolated from calf brain and digested with trypsin or CNBr, and the amino acid sequence of several peptides was determined. Degenerate oligonucleotide primers were designed from amino acid sequence and used to synthesize an 80-base-pair (bp) fragment by the polymerase chain reaction. This product was used to isolate a 1.6-kbp cDNA with an open reading frame of 400 amino acids, 185 bp of 5' untranslated region, and 171 bp of 3' untranslated region followed by a putative poly(A) tail. The coding region of the cDNA was inserted into an expression vector that was used to obtain the recombinant protein from Escherichia coli cells. The recombinant enzyme (44 kDa) had a specific activity and other properties similar to those of native bovine brain inositol polyphosphate 1-phosphatase. It hydrolyzed both inositol phosphate substrates and was inhibited by lithium ions. The enzyme shows minimal sequence similarity to inositol monophosphate phosphatase, the other enzyme inhibited by lithium ions in the signaling pathway.
The Effects of Platelet Count on Clot Retraction and Tissue Plasminogen Activator-Induced Fibrinolysis on Thrombelastography (2005)

Clot retraction and fibrinolysis may present as a decrease in amplitude on thrombelastography (TEG). The former represents normal or hyperactive platelet function, and the latter represents a fibrinolytic state. It is important to distinguish clot retraction from fibrinolysis because the treatment of each condition is different. To distinguish between these phenomena, we performed TEG with platelet-poor plasma (PPP) and platelet-rich plasma (PRP) with an increasing platelet count (range, 50-1200 x 10(9)/L) with or without abciximab. Maximum amplitude (MA) and the percentage decrease of amplitude at 30 and 60 min after MA were examined for each sample. Blood samples to which tissue plasminogen activator (tPA) was added served as positive controls for fibrinolysis. Morphological changes of clots and D-dimer levels were also examined. With higher platelet counts, the percentage decrease of amplitude after MA increased significantly at 30 and 60 min, but not in the abciximab samples. Morphological changes of clots have shown clot retraction in PRP, but not in PPP or PRP pretreated with abciximab. D-dimer levels increased only in samples to which tPA was added, but not in native PPP or PRP samples. In conclusion, we have shown that the decrease in amplitude at 30 and 60 min can be due to platelet-mediated clot retraction and can be attenuated by sample pretreatment with abciximab, which interrupts platelet-fibrin(ogen) binding.
Rec. ST6Gal-I variants to control enzymatic activity in processes of in vitro glycoengineering (2013)

Background Glycosylation is an important posttranslational modification of proteins influencing protein folding, stability and regulation of the biological activity. The sialyl mojety (sialic acid, 5-N-acetylneuramic acid) is usually exposed at the terminal position of N-glycosylation and therefore, a major contributor to biological recognition and ligand function, e.g. IgG featuring terminal sialic acids were shown to induce less inflammatory response and increased serum half-life. The biosynthesis of sialyl conjugates is controlled by a set of sugar-active enzymes including sialyltransferases which are classified as ST3, ST6 and ST8 based on the hydroxyl position of the glycosyl acceptor the Neu5Ac is transferred to [1]. The ST6 family consists of 2 subfamilies, ST6Gal and ST6GalNAc. ST6Gal catalyzes the transfer of Neu5Ac residues to the hydroxyl group in C6 of a terminal galactose residue of type 2 disaccharide (Galb1-4GlcNAc). To our knowledge, the access to recombinant ST6GalI for therapeutic applications is still limited due to low expression and/or poor activity in various hosts (Pichia pastoris, Spodoptera frugiperda and E. coli). The present study describes the high-yield expression of two variants of human beta-galactoside alpha-2,6 sialyltransferase 1 (ST6Gal-I, EC 2.4.99.1; data base entry P15907) by transient gene expression in HEK293 cells with yields >100 mg/L featuring distinct mono(G2 +1SA) as well as bi(G2+2SA) sialylation activity. Materials and methods Two N-terminally truncated fragments of human ST6Gal-I (delta89, residues 89-406, and delta108, residues 109-406) were designed for transient gene expression (TGE): Instead of the natural leader sequence and N-terminal residues, both ST6Gal-I coding regions harbor the Erythropoietin (EPO) signal sequence in order to ensure correct processing of the polypeptides by the secretion machinery. Following cloning into pM1MT, expression of the ST6Gal-I coding sequences is under control of a hCMV promoter followed by an intron A. Sialyltransferase assays: 1. Asialofetuin was used as acceptor and CMP-9F-NANA as donor substrate. Enzymatic activity was determined by measuring the transfer of 9F-NANA to asialofetuin. 2. Recombinant humanized IgG1 and IgG4 monoclonal antibodies (mabs), characterized as G2+0SA, as well as desialylated EPO were used as targets in sialylation experiments (30 μg enzyme/300 μg target protein). Both enzyme variants of ST6Gal-I (delta89 and delta108) were used under identical reaction conditions and the sialylation status was analyzed by mass spectrometry.
Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets (2015)

MicroRNAs (miRNAs) direct post-transcriptional regulation of human genes by guiding Argonaute proteins to complementary sites in messenger RNAs (mRNAs) targeted for repression. An enigmatic feature of many conserved mammalian miRNA target sites is that an adenosine (A) nucleotide opposite miRNA nucleotide-1 confers enhanced target repression independently of base pairing potential to the miRNA. In this study, we show that human Argonaute2 (Ago2) possesses a solvated surface pocket that specifically binds adenine nucleobases in the 1 position (t1) of target RNAs. t1A nucleotides are recognized indirectly through a hydrogen-bonding network of water molecules that preferentially interacts with the N6 amine on adenine. t1A nucleotides are not utilized during the initial binding of Ago2 to its target, but instead function by increasing the dwell time on target RNA. We also show that N6 adenosine methylation blocks t1A recognition, revealing a possible mechanism for modulation of miRNA target site potency.
A credit-payment scheme for packet forwarding fairness in mobile ad hoc networks (2005)

Routing protocols for mobile ad hoc networks (MANETs) have assumed that all nodes voluntarily participate in forwarding others' packets. This was a reasonable assumption because all nodes in previous MANETs belonged to a single authority. In the near future, however, a MANET may consist of nodes that belong to multiple organizations since various civilian applications are expected to appear. In this situation, mobile nodes may deliberately avoid packet forwarding to save their own energy, resulting in network partition. To make nodes volunteer in packet forwarding we suggest a payment scheme called protocol-independent fairness algorithm (PIFA). In this type of schemes, nodes need credits to transmit their own packets, and this credit can be earned by forwarding others' packets. PIFA can be utilized irrespective of the type of basic routing protocols, while previous methods are compatible only with source routing like DSR. Simulation results show that PIFA can prevent network partition and network performance degradation due to selfish nodes by inducing them to participate in forwarding packets.
The diagnostic criteria of polycythaemia rubra vera. (1996)

There is no single diagnostic marker for polycythaemia vera (PV). The Polycythemia Vera Study Group established diagnostic criteria more than twenty years ago. Since some new laboratory and clinical investigations have developed, these criteria can now be updated. It is proposed that the overall pattern of major and minor criteria should remain. A raised red cell mass (greater than 25% above the patient's mean normal predicted value based on surface area) and absence of a cause of secondary polycythaemia are essential criteria. Then either palpable splenomegaly or the presence of a marker of clonal haemopoiesis would support the diagnosis of PV. In the absence of both of these latter major criteria, at least two minor criteria must be present to secure the diagnosis. These are: platelet count > 400 x 10(9)/l; neutrophil count > 10 x 10(9)/l; splenomegaly demonstrated by a scanning technique; characteristic BFU-E growth or reduced serum erythropoietin value.
Balanced antenna structures of mobile terminals (2010)

In this paper the feasibility of balanced antenna structures in the mobile terminal environment has been investigated concerning bandwidth and radiation properties. It has also been studied if the effect of the user's hand on frequency de-tuning and decrease in radiation efficiency could be reduced with the balanced antenna structures compared to the traditional antenna structures. In addition, emphasis has been put on the specific absorption rate (SAR) and hearing-aid compatibility (HAC) performance of balanced antenna structures.
Insertion of a Synthetic Peptide into a Recombinant Protein Framework:  A Protein Biosensor (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTInsertion of a Synthetic Peptide into a Recombinant Protein Framework: A Protein BiosensorGraham J. Cotton, Brenda Ayers, Rong Xu, and Tom W. MuirView Author Information Laboratories of Synthetic Protein Chemistry and Physical Biochemistry Rockefeller University 1230 York Avenue, New York, New York 10021 Cite this: J. Am. Chem. Soc. 1999, 121, 5, 1100–1101Publication Date (Web):January 22, 1999Publication History Received2 November 1998Published online22 January 1999Published inissue 1 February 1999https://pubs.acs.org/doi/10.1021/ja983804bhttps://doi.org/10.1021/ja983804brapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views822Altmetric-Citations91LEARN 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 (1)»Supporting Information Supporting Information SUBJECTS:Fluorescence,Genetics,Ligands,Ligation,Peptides and proteins Get e-Alerts
Effects of Long-Term Pioglitazone Treatment on Peripheral and Central Markers of Aging (2010)

While current research efforts continue to identify the underlying processes responsible for the progressive decline in cognitive function seen during normal aging, available medical treatments are still very limited. Because TZDs have been shown to have benefits in age-related conditions such as T2DM and AD, our study was aimed at elucidating PIO's potentially beneficial actions in normal aging. Using a clinically-relevant dose and delivery method, long-term PIO treatment was able to blunt several indices of aging but apparently affected neither age-related cognitive decline nor peripheral/central age-related increases in inflammatory signaling.
Identification of 1,3-butadiene, benzene, and other volatile organics from wok oil emissions. (1995)

As part of a program to determine the underlying factors responsible for genotoxicity and perhaps lung cancer risk in Chinese women, we qualitatively identified the volatile components emitted during the heating of cooking oils to 265 degrees C. 1,3-Butadiene, benzene, and a series of aldehydes, olefins, and saturated hydrocarbons were elucidated in vapors from Chinese rapeseed oil. On a relative basis, the intensity of 1,3-butadiene vapors from this were 15.7-, 6.3-, and 1.4-fold greater than in the vapors from peanut, soybean, and Canola oils, respectively. Thus, the Chinese rapeseed oil yielded a higher emission rate of 1,3-butadiene than the other three oils investigated. The benzene formation rate followed a similar trend, i.e., its intensity in Chinese rapeseed oil was 14-, 6.6-, and 1.7-fold greater than in vapors from peanut, soybean, and Canola oils, respectively.
Lung carcinoma (1999)

A favorable Th1- and Tc1-dominant pathway is induced in the tumor tissues of operable patients, but their pathway can be expected to shift from Th1 or Tc1 to Th2 or Tc2 with the progression of cancer.
The effects of alterations within the 3' untranslated region of the pyruvate kinase messenger RNA upon its stability and translation inSaccharomyces cerevisiae (1987)

A 53 basepair deletion was constructed within the 3' untranslated region (3' UTR) of the yeast pyruvate kinase (PYK) gene borne upon a centromeric plasmid. Various modular assemblies of the pUC13 polylinker DNA (single unit = 44 bp) were used to replace the deleted region, and the effects of these modifications upon both transcript stability and translation ascertained in yeast. The use of a differential probing stratagem, based on the hybridisation of specific oligonucleotides to either pUC13 polylinker or unaltered PYK 3' UTR sequences, allowed for discrimination between mutant (plasmid borne) and wild-type (chromosomal) PYK transcripts. In no construct was there any significant alteration in mRNA stability, but translation of the PYK mRNA was severely curtailed by truncation of the 3' UTR or the presence of a strong hairpin-loop structure in the 3' UTR. A specific mutation in the N-terminal coding sequences, which created a premature termination codon in both a 3' 'tagged' PYK plasmid and a PYK/LacZ fusion gene, aborted the translation of a majority of their transcripts but left their chemical half-lives unaltered. This observation is at variance with some previously published data (Losson & Lacroute (1979) Proc Natl Acad Sci USA 76, 5134; Pelsey & Lacroute (1984) Curr Genet 8, 277), but is consistent with our own earlier observation that there is no obvious link between ribosome loading and mRNA stability in yeast (Santiago et al. (1986) Nucleic Acids Res 14, 8347). Possible reasons for this disparity are discussed.
Analysis of a human V beta gene subfamily. (1986)

We have isolated and sequenced five germline V beta gene segments that are homologous to the V region of the YT35 cDNA encoding the beta chain of the T cell antigen receptor from the tumor MOLT-3. One of these gene segments is identical to the YT35 V segment, and therefore is the corresponding germline V beta gene segment encoding the YT35 cDNA. The other four V beta members exhibit 77-98% homology to the YT35 V gene segment. Two of these V beta gene segments are pseudogenes. Analyses of the coding region sequences reveal that, although the V beta segments are very diverse, they are mutating at a rate comparable to that observed in most eukaryotic genes. Analyses of the genomic clones show that the spacing distance between germline V beta gene segments ranges from 3 kb to greater than 30 kb, and the entire V beta 8 subfamily appears to be linked by a total of no more than 110 kb of DNA.
Naturally Occurring Antibodies Reactive with Sperm Proteins: Apparent Deficiency in AIDS Sera (1985)

A set of naturally occurring immunoglobulin M (IgM) antibodies that are reactive with a defined subset of proteins in the acrosomal cap region of human sperm has been identified. These antibodies are present in a broad spectrum of human sera from males and females, 1 day to 40 years of age, and are absent or markedly deficient in a large proportion of sera from individuals with the acquired immune deficiency syndrome (AIDS) or at risk for AIDS. The subset of proteins with which the IgM antibodies are reactive includes a factor (or factors) capable of inhibiting lectin-induced T-lymphocyte proliferation. The prevalence of the sperm-reactive IgM antibodies indicates that they are not elicited by sperm. Further, immunoreactivity of the sperm proteins resulting in depletion of specific circulating IgM antibodies, or other interactions between the sperm proteins and elements of the immune system, may be a factor in the suppressed state of the immune system in AIDS.
Fields of Experts for Image-based Rendering (2006)

Image priors for novel view synthesis have traditionally been non-parametric models based on large libraries of image patch exemplars, producing highquality results but making inference very slow. Recently a parametric framework, called Fields of Experts, has been proposed for image restoration that promises to speed up inference dramatically. In this paper we apply Fields of Experts for the first time to the problem of novel view synthesis, posed as a Markov random field labelling problem with very large cliques. Additionally, we introduce to computer vision for the first time a new optimization algorithm from statistical physics which reaches better minima than the ICM and simulated annealing algorithms to which such large-clique problems have previously been restricted.
Glucose in Epidural Catheter Aspirate (1993)

Frequently fluid may be aspirated from epidural catheters during epidural anesthesia/analgesia. This fluid may be either cerebrospinal fluid or local anesthetic. Several methods for differentiation of the two fluids have been recommended. In this study, the reliability of the "glucose test" was analyzed. Epidural catheters were inserted into 43 healthy, nondiabetic parturients and then gently aspirated. Aspirate was tested for glucose using glucose oxidase paper. Positive aspirates were assessed for the presence of prealbumin, which is a protein marker for cerebrospinal fluid. Of the patients undergoing cesarean section, 17 of 27 patients yielded a glucose-positive aspirate, and of the patients undergoing labor analgesia, 6 of 16 patients were found to be positive for glucose. None of these patients developed total spinal anesthesia or postdural puncture headache. Visually, none of the aspirates were significantly blood-tinged, blood being a possible source of glucose. When the glucose-positive aspirates were subjected to immunoelectrophoresis, 6 of 7 aspirates revealed a prealbumin band. In conclusion, the glucose test for cerebrospinal fluid may be misleading. The source of this glucose may be normal cerebrospinal fluid drainage into the epidural space.
Dysregulated Autophagy Contributes to Podocyte Damage in Fabry’s Disease (2013)

Fabry's disease results from an inborn error of glycosphingolipid metabolism that is due to deficiency of the lysosomal hydrolase α-galactosidase A. This X-linked defect results in the accumulation of enzyme substrates with terminally α-glycosidically bound galactose, mainly the neutral glycosphingolipid Globotriaosylceramide (Gb3) in various tissues, including the kidneys. Although end-stage renal disease is one of the most common causes of death in hemizygous males with Fabry's disease, the pathophysiology leading to proteinuria, hematuria, hypertension, and kidney failure is not well understood. Histological studies suggest that the accumulation of Gb3 in podocytes plays an important role in the pathogenesis of glomerular damage. However, due to the lack of appropriate animal or cellular models, podocyte damage in Fabry's disease could not be directly studied yet. As murine models are insufficient, a human model is needed. Here, we developed a human podocyte model of Fabry's disease by combining RNA interference technology with lentiviral transduction of human podocytes. Knockdown of α-galactosidase A expression resulted in diminished enzymatic activity and slowly progressive accumulation of intracellular Gb3. Interestingly, these changes were accompanied by an increase in autophagosomes as indicated by an increased abundance of LC3-II and a loss of mTOR kinase activity, a negative regulator of the autophagic machinery. These data suggest that dysregulated autophagy in α-galactosidase A-deficient podocytes may be the result of deficient mTOR kinase activity. This finding links the lysosomal enzymatic defect in Fabry's disease to deregulated autophagy pathways and provides a promising new direction for further studies on the pathomechanism of glomerular injury in Fabry patients.
Biological Determinants of Cancer Progression in Men With Prostate Cancer (1999)

The % Gleason grade 4/5, cancer volume, positive lymph node findings, and intraprostatic vascular invasion were independently associated with prostate cancer progression, defined by an increasing PSA level. Techniques to accurately measure cancer volume and % Gleason grade 4/5 are needed to better predict which patient will experience cancer progression. The commonly accepted predictors of progression-capsular penetration and positive surgical margins-were not independently predictive of failure after radical prostatectomy.
The Case for Extensible Operating Systems (1996)

For over 3.5 years, SARS CoV-2 is continuing to evolve threatening to return all and any improvement the world has made into square one. In this clinically oriented systematic review and perspective, the author explains how the best current medical evidence is strongly supporting the use of the low cost, widely available and very safe nitazoxanide in early management of COVID-19, debates the relevant theoretical studies that negated or doubted this benefit, and suggests an African roadmap to preempt the worst-case scenario if or when a new SARS CoV-2 (sub) variant or even a new respiratory virus causes a new global surge of morbidity and mortality. Kelleni's protocol, including nitazoxanide as an integral component, is continuing to perfectly save lives of patients infected with many viruses, including SARS CoV-2 and the author stresses that respiratory RNA viruses are best managed with early pharmacological treatment. Broad-spectrum antimicrobials as nitazoxanide and azithromycin together with other therapeutics as non-steroidal anti-inflammatory drugs and the antihistaminic loratadine should be considered first to personalize the clinical management of COVID-19 and selected other alarming viral infections.
Complex polysaccharides as PCR inhibitors in feces: Helicobacter pylori model (1997)

A model was developed to study inhibitors present in feces which prevent the use of PCR for the detection of Helicobacter pylori. A DNA fragment amplified with the same primers as H. pylori was used to spike samples before extraction by a modified QIAamp tissue method. Inhibitors, separated on an Ultrogel AcA44 column, were characterized. Inhibitors in feces are complex polysaccharides possibly originating from vegetable material in the diet.