gebhart/patrepeval huggingface dataset:
Improved neighborhood-based algorithms for large-scale recommender systems (2008)

Neighborhood-based algorithms are frequently used modules of recommender systems. Usually, the choice of the similarity measure used for evaluation of neighborhood relationships is crucial for the success of such approaches. In this article we propose a way to calculate similarities by formulating a regression problem which enables us to extract the similarities from the data in a problem-specific way. Another popular approach for recommender systems is regularized matrix factorization (RMF). We present an algorithm -- neighborhood-aware matrix factorization -- which efficiently includes neighborhood information in a RMF model. This leads to increased prediction accuracy. The proposed methods are tested on the Netflix dataset.
Horseradish Peroxidase-catalyzed Oligomerization of Ferulic Acid on a Template of a Tyrosine-containing Tripeptide (2002)

Ferulic acid (FA) is an abundantly present phenolic constituent of plant cell walls. Kinetically controlled incubation of FA and the tripeptide Gly-Tyr-Gly (GYG) with horseradish peroxidase and H2O2 yielded a range of new cross-linked products. Two predominant series of hetero-oligomers of FA linked by dehydrogenation to the peptidyl tyrosine were characterized by electrospray ionization (tandem) mass spectrometry. One series comprises GYG coupled with 4-7 FA moieties linked by dehydrogenation, of which one is decarboxylated. In the second series 4-9 FA moieties linked by dehydrogenation, of which two are decarboxylated, are coupled to the tripeptide. A third series comprises three hetero-oligomers in which the peptidyl tyrosine is linked to 1-3 FA moieties of which none is decarboxylated. Two mechanisms for the formation of the FA-Tyr oligomers that result from the dualistic, concentration-dependent chemistry of FA and their possible role in the regulation of plant cell wall tissue growth are presented.
Identification of a Dihydropyridine as a Potent α<sub>1a</sub> Adrenoceptor-Selective Antagonist That Inhibits Phenylephrine-Induced Contraction of the Human Prostate (1998)

A number of novel dihydropyridine derivatives based upon 1, 4-dihydro-3-(methoxycarbonyl)-2, 6-dimethyl-4-(4-nitrophenyl)-5-((3-(4, 4-diphenylpiperidin-1-yl)propyl)aminocarbonyl)pyridine (4) have been synthesized and tested at cloned human alpha adrenoceptors as well as the rat L-type calcium channel. Within this compound series, 5-(aminocarbonyl)-1,4-dihydro-2, 6-dimethyl-4-(4-nitrophenyl)-3-((3-(4, 4-diphenylpiperidin-1-yl)propyl)aminocarbonyl)pyridine (19) displayed good binding affinity and selectivity for the alpha1a adrenoceptor (pKi = 8.73) and potently inhibited (pA2 = 9.23) phenylephrine-induced contraction of the human prostate.
Shallow semantics for relation extraction (2005)

This paper presents a new method for extracting meaningful relations from unstructured natural language sources. The method is based on information made available by shallow semantic parsers. Semantic information was used (1) to enhance a dependency tree kernel; and (2) to build semantic dependency structures used for enhanced relation extraction for several semantic classifiers. In our experiments the quality of the extracted relations surpassed the results of kernel-based models employing only semantic class information.
Negotiating for software services (2002)

We are investigating how the routine use of engineering meta-applications can be made financially viable by using a software and hardware on-demand business model supported by an agent based electronic marketplace. The authors explains how their work has combined Web, agent and security technologies to create a robust and secure Internet based marketplace in which a trusted third party provides negotiation services between software application users and third party hardware and software service providers.
Leukopoor platelet concentrates: a direct comparison of three blood filters. (1985)

Repeated exposure to foreign human leukocyte antigens (HLA) present on both platelets and leukocytes often results in refractoriness to transfusions of platelet concentrates. Evidence now exists which suggests that the leukocytes are more immunogenic and that their removal from blood products may delay or prevent the development of refractoriness. In this study, the ability of three blood filters to remove leukocytes from platelet concentrates was directly compared. Pooled platelet concentrates were filtered through the Fenwal 4C 2131 depth microaggregate blood filter (MABF), the Pall Ultipor SQ 40S screen MABF, and the Terumo Imugaard IG-500 blood filter. The results were then compared to a previous study (done in the same laboratory) which used differential centrifugation to render platelet concentrates leukocyte-poor. The Fenwal and Pall MABFs did not remove leukocytes or platelets from platelet concentrates. In contrast, the Terumo filter removed 90.2 percent of the leukocytes while sacrificing 7.5 percent of the platelets; results superior to differential centrifugation which removed 84.9 percent of the leukocytes but sacrificed many more platelets, 32.3 percent. The Terumo Imugaard IG-500 blood filter produces leukocyte-poor platelet concentrates as efficiently as differential centrifugation with much less platelet loss. Use of the Terumo filter may aid further studies required to evaluate the use of leukocyte-poor platelet concentrates for the prevention of platelet refractoriness.
Determination of the microscopic quality of InGaAs-InAlAs interfaces by photoluminescence—Role of interrupted molecular beam epitaxial growth (1986)

Photoluminescence (PL) studies have been carried out on 120 Å InGaAs/InAlAs single quantum well structures grown by molecular beam epitaxy. Three types of samples were grown with the growth being interrupted before interface formation. The interruption times were 0, 2, and 3 min. The corresponding linewidth of the main excitonic transition associated with the quantum well was found to be 20, 16, and 10 meV, respectively, while the PL intensity changed by the ratio 1:0.4:0.1. We believe this behavior is due to a steady improvement in the interface quality due to interruption accompanied by impurity accumulation during the interruption. Analysis of the 10 meV linewidth, which is among the smallest ever reported, suggests that the InAlAs/InGaAs interface can be described by two-dimensional InAlAs and InGaAs islands which have a height of two monolayers and a lateral extent of about 100 Å.
General Pharmacology of CKD-732, a New Anticancer Agent: Effects on Central Nervous, Cardiovascular, and Respiratory System (2005)

CKD-732 [6-O-(4-dimethylaminoethoxy) cinnamoyl fumagillol hemioxalate] is a new fumagillin anticancer drug that belongs to an angiogenesis inhibitor. Its effect on the central nervous system (CNS), general behavior, cardiovascular-respiratory system and the other organ systems were studied. CKD-732 was intravenously administered with the dosages of 10, 30, 40 or 50 mg/kg and the highest dosage of 50 mg/kg prolonged the hexobarbital-induced sleep time. CKD-732 at the dosage of 50 mg/kg, also, caused the decrease of body temperature from 15 to 120 min after the administration, which was recovered at 240 min. In the study of the effects on gastric secretion, CKD-732 induced the increase of pH and decrease of total acidity. However, CKD-732 showed no effect on general behavior, spontaneous locomotor activity, motor coordination, analgesia, convulsion, mean arterial pressure, and cardiac functions except for heart rate of isolated rat heart, respiration, isolated smooth muscle, intestinal charcoal transport and renal function. Based on the results, we suggested that CKD-732 is safe general pharmacologically at clinical supposed dose (1.75 mg/kg) and demonstrated to have much better safety than other fumagillin derivatives.
No-carrier-added N-(3-[18F]fluoropropyl)spiroperidol: biodistribution in mice and tomographic studies in a baboon. (1987)

Two potential radioligands, no-carrier-added (NCA) N-(2-[18F]fluoroethyl)spiroperidol (3) and N-(3-[18F]fluoropropyl)spiroperidol (4) have been synthesized for PET imaging of dopamine receptors in humans. Compounds 3 and 4 were synthesized by N-alkylation of spiroperidol with NCA 1-bromo-2-[18F]-fluoroethane (2b), 1-[18F]fluoro-3-iodopropane (2c) and 1-bromo-3-[18F]fluoropropane (2d) respectively. The biodistribution of 4 in mice showed that the mouse brain uptake of radioactivity was similar to that of [18F]-N-methylspiroperidol (1.1% of the administered dose), but the activity in bone (femur) increased with time. The kinetic distribution of compound 4 in baboon brain was similar to that of [18F]-N-methylspiroperiodol, and the striatal accumulation of radioactivity was also blocked stereoselectively by butaclamol. The ratio of striatum to cerebellum radioactivities at 3 hr after injection was 5.9. Analysis of the metabolic stability of 4 in mouse brains for 1 hr indicated that, like [18F]-N-methylspiroperidol, it is relatively stable to metabolic transformation in the central nervous system. These results suggest that compound 4 may be a useful radioligand for PET studies of the dopamine receptor in humans.
CHARMMing: A New, Flexible Web Portal for CHARMM (2008)

A new web portal for the CHARMM macromolecular modeling package, CHARMMing (CHARMM interface and graphics, http://www.charmming.org), is presented. This tool provides a user-friendly interface for the preparation, submission, monitoring, and visualization of molecular simulations (i.e., energy minimization, solvation, and dynamics). The infrastructure used to implement the web application is described. Two additional programs have been developed and integrated with CHARMMing: GENRTF, which is employed to define structural features not supported by the standard CHARMM force field, and a job broker, which is used to provide a portable method for using grid and cluster computing with CHARMMing. The use of the program is described with three proteins: 1YJP , 1O1O , and 1UFY . Source code is provided allowing CHARMMing to be downloaded, installed, and used by supercomputing centers and research groups that have a CHARMM license. Although no software can replace a scientist's own judgment and experience, CHARMMing eases the introduction of newcomers to the molecular modeling discipline by providing a graphical method for running simulations.
Export Pathway Selectivity of Escherichia coli Twin Arginine Translocation Signal Peptides (2007)

The Escherichia coli genome encodes at least 29 putative signal peptides containing a twin arginine motif characteristic of proteins exported via the twin arginine translocation (Tat) pathway. Fusions of the putative Tat signal peptides plus six to eight amino acids of the mature proteins to three reporter proteins (short-lived green fluorescent protein, maltose-binding protein (MBP), and alkaline phosphatase) and also data from the cell localization of epitope-tagged full-length proteins were employed to determine the ability of the 29 signal peptides to direct export through the Tat pathway, through the general secretory pathway (Sec), or through both. 27/29 putative signal peptides could export one or more reporter proteins through Tat. Of these, 11 signal peptides displayed Tat specificity in that they could not direct the export of Sec-only reporter proteins. The rest (16/27) were promiscuous and were capable of directing export of the appropriate reporter either via Tat (green fluorescent protein, MBP) or via Sec (PhoA, MBP). Mutations that conferred a >or=+1 charge to the N terminus of the mature protein abolished or drastically reduced routing through the Sec pathway without affecting the ability to export via the Tat pathway. These experiments demonstrate that the charge of the mature protein N terminus affects export promiscuity, independent of the effect of the folding state of the mature protein.
A new technique for blind source separation using subband subspace analysis in correlated multichannel signal environments (2002)

We investigated a new framework for the problem of blind source identification in multichannel signal processing. Inspired by a neurophysiological data environment, where an array of closely spaced recording electrodes is surrounded by multiple neural cell sources, significant spatial correlation of source signals motivated the need for an efficient technique for reliable multichannel blind source identification. In a previous work Oweiss and Anderson (see Proceedings of the 34th. Asilomar Conference on Signals, Systems and Computers, Pacific Grove, 2000) adopted a new approach for noise suppression based on thresholding an array discrete wavelet transform (ADWT) representation of the multichannel data. We extend the work of Oweiss and Anderson to identify sources from the observation mixtures. The technique relies on separating sources with highest spatial energy distribution in each frequency subband spanned by the corresponding wavelet basis. Accordingly, the best basis selection criterion we propose benefits from the additional degree of freedom offered by the space domain. The amplitude and shift invariance properties revealed by this technique make it very efficient to track spatial source variations sometimes encountered in multichannel neural recordings. Results from multichannel multiunit neural data are presented and the overall performance is evaluated.
Novel lambda FRET spectral confocal microscopy imaging method (2008)

We report a highly specific, sensitive, and robust method for analyzing fluorescence resonance energy transfer (FRET) based on spectral laser scanning confocal microscopy imaging. The lambda FRET (lambdaFRET) algorithm comprises imaging of a FRET sample at multiple emission wavelengths rendering a FRET spectrum, which is separated into its donor and acceptor components to obtain a pixel-based calculation of FRET efficiency. The method uses a novel off-line precalibration procedure for spectral bleed-through correction based on the acquisition of reference reflection images, which simplifies the method and reduces variability. LambdaFRET method was validated using structurally characterized FRET standards with variable linker lengths and stoichiometries designed for this purpose. LambdaFRET performed better than other well-established methods, such as acceptor photobleaching and sensitized emission-based methods, in terms of specificity, reproducibility, and sensitivity to distance variations. Moreover, lambdaFRET analysis was unaffected by high fluorochrome spectral overlap and cellular autofluorescence. The lambdaFRET method demonstrated outstanding performance in intra- and intermolecular FRET analysis in both fixed and live cell imaging studies.
Synthesis, electron paramagnetic resonance, and magnetic studies of binuclear bis(.eta.5-cyclopentadienyl)titanium(III) compounds with bridging pyrazolate, biimidazolate, and bibenzimidazolate anions (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis, electron paramagnetic resonance, and magnetic studies of binuclear bis(.eta.5-cyclopentadienyl)titanium(III) compounds with bridging pyrazolate, biimidazolate, and bibenzimidazolate anionsBenjamin F. Fieselmann, David N. Hendrickson, and Galen D. StuckyCite this: Inorg. Chem. 1978, 17, 8, 2078–2084Publication Date (Print):August 1, 1978Publication History Published online1 May 2002Published inissue 1 August 1978https://pubs.acs.org/doi/10.1021/ic50186a009https://doi.org/10.1021/ic50186a009research-articleACS PublicationsRequest reuse permissionsArticle Views1115Altmetric-Citations103LEARN 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 Get e-Alerts
A prospective study of plasma total cysteine and risk of breast cancer. (2003)

Cysteine is the precursor of glutathione, a powerful intracellular antioxidant and an important detoxifying agent of carcinogens. However, data relating plasma total cysteine to breast cancer risk are sparse. We conducted a prospective nested case-control study among 32826 women in the Nurses' Health Study who provided blood specimens during 1989-1990. Through 1996, a total of 712 incident breast cancer cases were identified and individually matched to 712 controls by year of birth, time of day that blood was drawn, fasting status, month of blood sampling, recent use of postmenopausal hormones at the time of blood collection, and menopausal status. Conditional logistic regression with adjustment for other risk factors for breast cancer was used to estimate the relative risks and 95% confidence intervals of breast cancer by levels of plasma total cysteine. Higher plasma total cysteine concentrations were significantly associated with a lower risk of breast cancer. For women in the highest quintile of plasma total cysteine, compared with those in the lowest quintile, the multivariate relative risk was 0.44 (95% confidence interval, 0.26-0.74). This association was dose dependent (P for trend = 0.002) and independent of plasma measures of folate, vitamin B(6), vitamin B(12), and total homocysteine. The inverse association between plasma total cysteine concentrations and risk of breast cancer was not significantly modified by other risk factors for breast cancer, except that a stronger association was observed among women who were leaner. The findings from this prospective study suggest that higher plasma concentrations of total cysteine predict a reduced risk of breast cancer. Cysteine or its precursors might have the potential to be chemopreventive against breast cancer.
Effect of Metabolic Control on Serum Protein Concentrations in Diabetes (1991)

Serum albumin, transferrin, transthyretin (prealbumin), and retinol binding protein concentrations were determined in 74 children with insulin-dependent diabetes mellitus before and after a 10-day camp session during which blood glucose concentrations were controlled. Initial concentrations of albumin and transferrin in the subjects were not different from those in 21 children and adults without diabetes, and did not change during the study period. Transthyretin and retinol binding protein concentrations were lower in subjects with diabetes than in the control population, and increased from 182 +/- 49 mg/l and 42.5 +/- 13.4 mg/l to 232 +/- 71 mg/l and 47.2 +/- 13.5 mg/l, respectively. We observed correlations between the changes in transferrin, transthyretin, and retinol binding protein. Although reductions in glycated albumin and transferrin indicated improvement in blood glucose control, there was no correlation between changes in the glycated markers and the concentrations of serum transport proteins. Thus, serum protein concentrations were influenced by the metabolic control of diabetes, but did not directly reflect blood glucose.
Characterization of Hepatitis B Virus (HBV)-Specific T-Cell Dysfunction in Chronic HBV Infection (2007)

Dysfunctional CD8+ T cells present in chronic virus infections can express programmed death 1 (PD-1) molecules, and the inhibition of the engagement of PD-1 with its ligand (PD-L1) has been reported to enhance the antiviral function of these T cells. We took advantage of the wide fluctuations in levels of viremia which are typical of chronic hepatitis B virus (HBV) infection to comprehensively analyze the impact of prolonged exposure to different virus quantities on virus-specific T-cell dysfunction and on its reversibility through the blocking of the PD-1/PD-L1 pathway. We confirm that chronic HBV infection has a profound effect on the HBV-specific T-cell repertoire. Despite the use of a comprehensive panel of peptides covering all HBV proteins, HBV-specific T cells were rarely observed directly ex vivo in samples from patients with chronic infection, in contrast to those from patients with acute HBV infection. In chronic HBV infection, virus-specific T cells were detected mainly in patients with lower levels of viremia. These HBV-specific CD8+ T cells expressed PD-1, and their function was improved by the blocking of PD-1/PD-L1 engagement. Thus, a broad spectrum of anti-HBV immunity is expressed by patients with chronic HBV infection and this spectrum is proportional to HBV replication levels and can be improved by blocking the PD-1/PD-L1 pathway. This information may be useful for the design of immunotherapeutic strategies to complement and optimize available antiviral therapies.
Successful Treatment of Painful Irreparable Partial Meniscal Defects With a Polyurethane Scaffold (2012)

Background: A novel, biodegradable, polyurethane scaffold was designed to fulfill an unmet clinical need in the treatment of patients with painful irreparable partial meniscal defects. Hypothesis: The use of an acellular polyurethane scaffold for new tissue generation in irreparable partial meniscal defects provides both pain relief and improved functionality. Study Design: Case series; Level of evidence, 4. Methods: Fifty-two patients with irreparable partial meniscal defects (34 medial and 18 lateral, 88% with 1-3 previous surgeries on the index meniscus) were implanted with a polyurethane scaffold in a prospective, single-arm, multicenter, proof-of-principle study. Safety was assessed by the rate of scaffold-related serious adverse events (SAEs) and the International Cartilage Repair Society articular cartilage scoring system comparing magnetic resonance imaging (MRI) at 24 months to MRI at baseline (1 week). Kaplan-Meier time to treatment failure distributions were performed. Clinical outcomes were measured comparing visual analog scale, International Knee Documentation Committee, Knee Injury and Osteoarthritis Outcome Score (KOOS), and Lysholm scores at 24 months from baseline (entry into study). Results: Clinically and statistically significant improvements ( P &lt; .0001) compared with baseline were reported in all clinical outcome scores (baseline/24 months): visual analog scale (45.7/20.3), International Knee Documentation Committee (45.4/70.1), KOOS symptoms (64.6/78.3), KOOS pain (57.5/78.6), KOOS activities of daily living (68.8/84.2), KOOS sports (30.5/59.0), KOOS quality of life (33.9/56.6), and Lysholm (60.1/80.7), demonstrating improvements in both pain and function. The incidence of treatment failure was 9 (17.3%) patients, of which 3 patients (8.8%) had medial meniscal defects and 6 patients (33.3%) had lateral meniscal defects. There were 9 SAEs requiring reoperation. Stable or improved International Cartilage Repair Society cartilage grades were observed in 92.5% of patients between baseline and 24 months. Conclusion: At 2 years after implantation, safety and clinical outcome data from this study support the use of the polyurethane scaffold for the treatment of irreparable, painful, partial meniscal defects.