gebhart/patrepeval huggingface dataset:
Antibodies Immobilized as Arrays to Profile Protein Post-translational Modifications in Mammalian Cells (2004)

Previously, we demonstrated that antibodies printed on a solid support were able to detect protein-protein interaction in mammalian cells. Here we further developed the antibody array system for detecting proteins with various post-translational modifications in mammalian cells. In this novel approach, immunoprecipitated proteins were labeled with fluorescent dye followed by incubation over antibody arrays. Targeted proteins, captured by the antibodies immobilized on PVDF membrane or glass slide, were detected by means of near infrared fluorescent scanner or fluorescent microscopy. To demonstrate the application of the antibody arrays in protein post-translational modifications, we profiled protein tyrosine phosphorylation, ubiquitination, and acetylation in mammalian cells under different conditions. Our results indicate that antibody array technology can provide a powerful means of profiling a large number of proteins with different post-translational modifications in cells.
Investigating the Effect of Carbon Shape on Virus Adsorption (2000)

Batch adsorption isotherm and column breakthrough studies were conducted to compare two types of activated carbon with very different structural characteristics; granular Calgon F-400 and an activated carbon fiber composite (ACFC). Carbons were evaluated for virus adsorption capacity using a bacteriophage, MS2. Two mesh fractions of each carbon type were used in batch adsorption studies to determine empirical isotherm coefficients from linear regression analysis. Freundlich isotherm models adequately described MS2 bacteriophage adsorption to both carbon types. Adsorption capacity was found to vary with carbon size for both types of carbon but for different reasons. Although adsorption isotherm capacities would have predicted the GAC carbon to provide better removals than the ACFC, carbon breakthrough column performance for equal weights of material showed virus removal to be markedly more efficient on a gram-to-gram basis for ACFC than for GAC.
Effect of speaking rate and contrastive stress on formant dynamics and vowel perception (2000)

Vowel formants play an important role in speech theories and applications; however, the same formant values measured for the steady-state part of a vowel can correspond to different vowel categories. Experimental evidence indicates that dynamic information can also contribute to vowel characterization. Hence, dynamically modeling formant transitions may lead to quantitatively testable predictions in vowel categorization. Because the articulatory strategy used to manage different speaking rates and contrastive stress may depend on speaker and situation, the parameter values of a dynamic formant model may vary with speaking rate and stress. In most experiments speaking rate is rarely controlled, only two or three rates are tested, and most corpora contain just a few repetitions of each item. As a consequence, the dependence of dynamic models on those factors is difficult to gauge. This article presents a study of 2300 [iai] or [i epsilon i] stimuli produced by two speakers at nine or ten speaking rates in a carrier sentence for two contrastive stress patterns. The corpus was perceptually evaluated by naive listeners. Formant frequencies were measured during the steady-state parts of the stimuli, and the formant transitions were dynamically and kinematically modeled. The results indicate that (1) the corpus was characterized by a contextual assimilation instead of a centralization effect; (2) dynamic or kinematic modeling was equivalent as far as the analysis of the model parameters was concerned; (3) the dependence of the model parameter estimates on speaking rate and stress suggests that the formant transitions were sharper for high speaking rate, but no consistent trend was found for contrastive stress; (4) the formant frequencies measured in the steady-state parts of the vowels were sufficient to explain the perceptual results while the dynamic parameters of the models were not.
Aerosolized iloprost induces a mild but sustained inhibition of platelet aggregation (2002)

Pathological studies have revealed that one of the main features encountered in the pulmonary vasculature of patients with pulmonary hypertension is the presence of thrombotic lesions. Open pilot studies have indicated that aerosolized iloprost may have beneficial effects in patients with pulmonary hypertension. The effects of aerosolized iloprost on platelet function and plasma cyclic adenosine monophosphate (cAMP) were studied. Platelet aggregation and plasma cAMP were measured at baseline, 30 min, 4 and 6 h after inhalation of 15 microg iloprost in 10 healthy volunteers. Maximal platelet aggregation in response to adenosine diphosphate (ADP) (2 and 6 micromol x L(-1)), collagen (2.5 and 5 microg x mL(-1)), epinephrine (1.25 and 5 micromol x L(-1)) and arachidonic acid (0.5 mg x mL(-1)) was measured. Platelet aggregation was significantly inhibited at 30 min in response to ADP (2 and 6 micromol x L(-1), epinephrine (1.25 and 5 micromol x L(-1)) and collagen (2.5 microg x mL(-1)). It was still inhibited at 4 h in response to the same agents, but normalized at 6 h. cAMP increased at 30 min, from 27.3+/-1.2 to 31.8+/-1.2 nmol x L(-1), remained increased at 4 h (29.2+/-1.3 nmol x L(-1)) and normalized at 6 h (27.4+/-1.1 nmol x L(-1)). Aerosolized iloprost induced a mild but sustained inhibition of platelet aggregation. Platelet aggregation inhibition may be one of the mechanisms which explains the beneficial effect of repeated inhalation of iloprost in pulmonary hypertension.
The Major Progesterone-modulated Proteins Secreted into the Sheep Uterus Are Members of the Serpin Superfamily of sErine Protease Inhibitors (1989)

The uterine milk proteins (UTMP) are a pair of structurally related basic glycoproteins that when newly synthesized carry phosphorylated mannosyl residues on their carbohydrate chains. They are the major proteins secreted by ovine endometrium under the influence of progesterone. RNA from a late pregnant ewe endometrium was isolated for use in in vitro translation assays and for constructing cDNA libraries. Translation experiments, initially with total cellular RNA and subsequently with RNA selected by hybridization with a specific cDNA, demonstrated the production of two polypeptides (Mr = 47,000 and 55,000) that were precipitated with antiserum to the UTMP. With microsomal membranes in the translation assay, there was increased production of an Mr = 57,000 form that was protected from protease digestion. Antibody screening of a cDNA library in lambda gt11 identified a short clone representing the 3' terminus of the mRNA that was shown by epitope selection experiments to be UTMP specific. This clone was then used to screen a lambda gt10 library. A longer clone (1.3 kilobases) was isolated and sequenced but lacked the 5' terminus to the mRNA. The latter sequence was obtained directly from the mRNA. Interesting features of the UTMP mRNA sequence, which was 1,352 bases long and contained a 1,287-base open reading frame, were two strong start codons, two potential sites for N-glycosylation and a repeat of 21 bases, six bases apart, that resulted in a repeat of seven amino acids. The inferred amino acid sequence agreed closely with the NH2-terminal amino acid sequence obtained directly from the UTMP and clearly placed the UTMP in the serpin superfamily of protease inhibitors. However, we have been unable to demonstrate inhibitory activity toward any serine protease so far tested.
Genetic defect in N-acetylglucosaminyltransferase I gene of a ricin-resistant baby hamster kidney mutant (1998)

The analysis of mutations associated with glycosylation-defective cell lines has the potential for identifying critical residues associated with the activities of enzymes involved in the biosynthesis of glycoconjugates. A ricin-resistant (RicR) baby hamster kidney (BHK) cell mutant, clone RicR14, has a deficiency in N-acetylglucosaminyltransferase I (GlcNAc-TI) activity and as a consequence is unable to synthesize complex and hybrid N-glycans. Here we show that RicR14 cells transfected with wild-type GlcNAc-TI regained the ability to synthesize complex N-glycans, demonstrating that the glycosylation defect of RicR14 cells is due solely to the lack of GlcNAc-TI activity. With the use of specific antibodies to GlcNAc-TI, RicR14 cells were shown to synthesize an inactive GlcNAc-TI protein that is correctly localized to the Golgi apparatus. We have cloned and sequenced the open reading frame of GlcNAc-TI from parental BHK and RicR14 cells. A comparison of several RicR14 cDNA clones with the parental BHK GlcNAc-TI sequence indicated the presence of two different RicR14 cDNA species. One contained a premature stop codon at position +81, whereas the second contained a point mutation in the catalytic domain of GlcNAc-TI resulting in the amino acid substitution Gly320-->Asp. The introduction of a Gly320-->Asp mutation into wild-type rabbit GlcNAc-TI resulted in a complete loss of activity; the GlcNAc-TI mutant was correctly localized to the Golgi, indicating that the inactive GlcNAc-TI protein was transport-competent. Gly320 is conserved in GlcNAc-TI from all species so far examined. Overall these results demonstrate that Gly320 is a critical residue for GlcNAc-TI activity.
Transapical approach for sutureless stent-fixed aortic valve implantation: experimental results☆ (2006)

The transapical approach provides a safe, accurate, and effective route for facilitated antegrade delivery of a stent-fixed valve. Advanced stent design will lead to better stability of the implant and may minimize the risk of paravalvular leakage in future. Identifying the appropriate population for human feasibility trials remains a challenge.
Estimation of the surface free energy of polymers (1969)

Abstract A method for measuring the surface energy of solids and for resolving the surface energy into contributions from dispersion and dipole‐hydrogen bonding forces has been developed. It is based on the measurement of contact angles with water and methylene iodide. Good agreement has been obtained with the more laborious γ c method. Evidence for a finite value of liquid‐solid interfacial tension at zero contact angle is presented. The method is especially applicable to the surface characterization of polymers.
<title>Indexing multispectral images for content-based retrieval</title> (1995)

This paper discusses our view of image databases, content-based retrieval, and our experiences with an experimental system. We present a methodology in which efficient representation and indexing are the basis for retrieval of images by content as well as associated external information. In the example system images are indexed and accessed based on properties of the individual regions in the image. Regions in each image are indexed by their spectral characteristics, as well as by their shape descriptors and position information. The goal of the system is to reduce the number of images that need to be inspected by a user by quickly excluding substantial parts of the database. The system avoids exhaustive searching through the image database when a query is submitted.
Poly(ADP-Ribose) Polymerase 1 Accelerates Single-Strand Break Repair in Concert with Poly(ADP-Ribose) Glycohydrolase (2007)

Single-strand breaks are the commonest lesions arising in cells, and defects in their repair are implicated in neurodegenerative disease. One of the earliest events during single-strand break repair (SSBR) is the rapid synthesis of poly(ADP-ribose) (PAR) by poly(ADP-ribose) polymerase (PARP), followed by its rapid degradation by poly(ADP-ribose) glycohydrolase (PARG). While the synthesis of poly(ADP-ribose) is important for rapid rates of chromosomal SSBR, the relative importance of poly(ADP-ribose) polymerase 1 (PARP-1) and PARP-2 and of the subsequent degradation of PAR by PARG is unclear. Here we have quantified SSBR rates in human A549 cells depleted of PARP-1, PARP-2, and PARG, both separately and in combination. We report that whereas PARP-1 is critical for rapid global rates of SSBR in human A549 cells, depletion of PARP-2 has only a minor impact, even in the presence of depleted levels of PARP-1. Moreover, we identify PARG as a novel and critical component of SSBR that accelerates this process in concert with PARP-1.
A Novel Computational and Signalling Method for VLSI Neural Networks (1987)

A computational style is described that mimics that of a biological neural network. Circuit forms of neural and synaptic functions are presented.
New Pacidamycin Antibiotics Through Precursor‐Directed Biosynthesis (2008)

Pacidamycins, mureidomycins and napsamycins are structurally related uridyl peptide antibiotics that inhibit translocase I, an as yet clinically unexploited target. This potentially important bioactivity coupled to the biosynthetically intriguing structure of pacidamycin make this natural product a fascinating subject for study. A precursor-directed biosynthesis approach was employed in order to access new pacidamycin derivatives. Strikingly, the biosynthetic machinery exhibited highly relaxed substrate specificity with the majority of the tryptophan analogues that were administered; this resulted in the production of new pacidamycin derivatives. Remarkably, 2-methyl-, 7-methyl-, 7-chloro- and 7-bromotryptophans produced their corresponding pacidamycin analogues in larger amounts than the natural pacidamycin. Low levels or no incorporation was observed for tryptophans substituted at positions 4, 5 and 6. The ability to generate bromo- and chloropacidamycins opens up the possibility of further functionalising these compounds through chemical cross-coupling in order to access a much larger family of derivatives.
Ospemifene, a non-oestrogen selective oestrogen receptor modulator for the treatment of vaginal dryness associated with postmenopausal vulvar and vaginal atrophy: A randomised, placebo-controlled, phase III trial (2014)

Once-daily oral ospemifene 60 mg was effective for the treatment of VVA in postmenopausal women with vaginal dryness.
A general method for the synthesis of 3′-sulfhydryl and phosphate group containing oligonucleotides (1991)

The syntheses are described of polymer supports useful for the synthesis of 3'-partially protected sulfhydryl, free sulfhydryl or phosphate group containing oligonucleotides. The supports are compatible with established phosphoramidite chemistry of oligonucleotide synthesis giving rise to oligonucleotides with terminal 3'-partially protected sulfhydryl, free sulfhydryl or phosphate function during final deprotection. Crosslinking of the thiol group containing oligonucleotide to sulfhydryl group specific fluorescent probes was carried out with high selectivity, in high yields under mild conditions. 3-Aminopropylated Controlled Pore Glass (CPG) was succinylated with succinic anhydride followed by the reaction with S-(2-thio-5-nitropyridyl)-2-mercaptoethanol in the presence of dicyclohexylcarbodiimide (DCC). The resultant polymer support was reacted with 4,4'-dimethoxytrityloxyalkanthiol 5(a - c) to yield the derivatized polymer supports 5(a - c). The support 5a directly leads to oligonucleotide-3'-phosphate on deprotection with ammonical DTT at 55 degrees C while the supports 5b and 5c lead to oligonucleotide-3'-thiols or partially protected 3'-sulfhydryl group containing oligonucleotides during final deprotection.
Attribit (2013)

We present AttribIt, an approach for people to create visual content using relative semantic attributes expressed in linguistic terms. During an off-line processing step, AttribIt learns semantic attributes for design components that reflect the high-level intent people may have for creating content in a domain (e.g. adjectives such as "dangerous", "scary" or "strong") and ranks them according to the strength of each learned attribute. Then, during an interactive design session, a person can explore different combinations of visual components using commands based on relative attributes (e.g. "make this part more dangerous"). Novel designs are assembled in real-time as the strengths of selected attributes are varied, enabling rapid, in-situ exploration of candidate designs. We applied this approach to 3D modeling and web design. Experiments suggest this interface is an effective alternative for novices performing tasks with high-level design goals.
.alpha.-Diketone and .alpha.-keto ester derivatives of N-protected amino acids and peptides as novel inhibitors of cysteine and serine proteinases (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT.alpha.-Diketone and .alpha.-keto ester derivatives of N-protected amino acids and peptides as novel inhibitors of cysteine and serine proteinasesMichael R. Angelastro, Shujaath Mehdi, Joseph P. Burkhart, Norton P. Peet, and Philippe BeyCite this: J. Med. Chem. 1990, 33, 1, 11–13Publication Date (Print):January 1, 1990Publication History Published online1 May 2002Published inissue 1 January 1990https://pubs.acs.org/doi/10.1021/jm00163a002https://doi.org/10.1021/jm00163a002research-articleACS PublicationsRequest reuse permissionsArticle Views790Altmetric-Citations127LEARN 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
Apurinic endonucleases from Saccharomyces cerevisiae (1978)

Three endonuclease activities have been partially purified from Saccharomyces cerevisiae on the basis of their activity against x-irradiated closed-circular supercoiled bacteriophage PM2 DNA. These endonucleases also nick apurinic DNA and two out of the three activities incise DNA UV-irradiated with high doses. The endonuclease activities have also been distinguished on the basis of their magnesium requirement and sensitivity to EDTA.
Inhibition of bone resorption in culture by inhibitors of thiol proteinases (1980)

Leupeptin, antipain, tosyl-lysylchloromethane (Tos-Lys-CH2Cl) and benzyloxy-carbonylphenylalanylalanyldiazomethane (Z-Phe-Ala-CHN2) inhibit reversibly the resorption induced by parathyroid hormone or heparin in cultured mouse bones. Leupeptin and antipain do not affect collagenase production and activity or the enhanced secretion of beta-glucuronidase induced by the bone-resorbing agents. They might thus act by a direct (extracellular?) inhibition of lysosomal thiol proteinases.
Deployment of Maintenance Decision Support Systems for Winter Operations (2006)

The art and science of road maintenance during adverse winter conditions has long been hampered by a lack of true integration of weather information into operations. Beginning in 1999, the Federal Highway Administration (FHWA) began to study this deficiency with its Surface Transportation Weather Decision Support Requirements (STWDSR) effort. The results clearly showed that road maintenance personnel desire better, more specific weather forecast information, which could improve the productivity and efficiency of winter maintenance practices and ultimately lead to improved mobility and a safer driving environment. Beginning in 2000, the FHWA convened a team of national laboratories and created a stakeholder group of interested personnel from state departments of transportation (DOTs), private-sector weather service providers and academia. With guidance from the stakeholder community, the laboratories combined state-of-the-art weather forecasting capabilities with computerized winter maintenance rules of practice. This was the genesis of the winter Maintenance Decision Support System (MDSS) prototype. This prototype underwent several development cycles and three seasons of field demonstrations and evaluations--two in Iowa and one in Colorado. By 2004, MDSS technologies were mature enough for interested private-sector companies to begin to incorporate MDSS features into their product lines and begin to provide services to state DOTs. At this point, the FHWA MDSS effort transitioned from prototype enhancement to a focus on technology transfer to both the private sector and the states. Based on the national MDSS effort, as well as related activities, a group of eight states (led by South Dakota DOT) initiated a pooled-fund study in 2002 to develop and implement an operational version of MDSS for their agencies. The study has focused upon refinement, validation, and wide-scale deployment of sustainable MDSS technology, as demonstrated in a successful operational testing period over the 2004-2005 winter. Based on these complementary efforts, it is clear that the MDSS presents a valid and viable operational strategy, but not without its development and deployment challenges. This paper details strategies for the continued evolution of MDSS technologies into the marketplace as well as advancement of the state of the practice of winter maintenance. Details of the pooled-fund MDSS project are presented as one success story of deployment.
Expression profiling identifies microRNA signature in pancreatic cancer (2006)

microRNAs are functional, 22 nt, noncoding RNAs that negatively regulate gene expression. Disturbance of microRNA expression may play a role in the initiation and progression of certain diseases. A microRNA expression signature has been identified that is associated with pancreatic cancer. This has been accomplished with the application of real-time PCR profiling of over 200 microRNA precursors on specimens of human pancreatic adenocarcinoma, paired benign tissue, normal pancreas, chronic pancreatitis and nine pancreatic cancer cell lines. Hierarchical clustering was able to distinguish tumor from normal pancreas, pancreatitis and cell lines. The PAM algorithm correctly classified 28 of 28 tumors, 6 of 6 normal pancreas and 11 of 15 adjacent benign tissues. One hundred microRNA precursors were aberrantly expressed in pancreatic cancer or desmoplasia (p < 0.01), including microRNAs previously reported as differentially expressed in other human cancers (miR-155, miR-21, miR-221 and miR-222) as well as those not previously reported in cancer (miR-376a and miR-301). Most of the top aberrantly expressed miRNAs displayed increased expression in the tumor. Expression of the active, mature microRNA was validated using a real-time PCR assay to quantify the mature microRNA and Northern blotting. Reverse transcription in situ PCR showed that three of the top differentially expressed miRNAs (miR-221, -376a and -301) were localized to tumor cells and not to stroma or normal acini or ducts. Aberrant microRNA expression may offer new clues to pancreatic tumorigenesis and may provide diagnostic biomarkers for pancreatic adenocarcinoma.