gebhart/patrepeval huggingface dataset:
Cell-specific cytotoxicity expressed by a conjugate of ricin and murine monoclonal antibody directed against thy 1.1 antigen. (1981)

The isolation and characterization are described of a conjugate between ricin, and a thy 1.1-specific monoclonal IgG2a murine antibody synthesized using N-succinimidyl-3-(2-pyridyldithio)propionate. The conjugate selectively inhibited protein synthesis in Thy 1.1-positive (AKR SL3) mouse leukemia cells compared to Thy 1.2-positive (AKR/Cu SL1) cells.
Algorithmic aspects in speech recognition (1997)

Speech recognition is an area with a considerable literature, but there is little discussion of the topic within the computer science algorithms literature. Many computer scientists, however, are interested in the computational problems of speech recognition. This paper presents the field of speech recognition and describes some of its major open problems from an algorithmic viewpoint. Our goal is to stimulate the interest of algorithm designers and experimenters to investigate the algorithmic problems of effective automatic speech recognition.
Rapid Detection of Aneuploidy (Trisomy 21) by Allele Quantification Combined with Melting Curves Analysis of Single-Nucleotide Polymorphism Loci (2003)

The use of melting curve analysis of multiple SNPs is an alternative to the use of small tandem repeats for the detection of trisomies. Because of the high density of SNPs, the approach may be specifically useful for very fine mapping of the regions of chromosome 21 that are critical for Down syndrome; it is also applicable to aneuploidies other than trisomy 21 and to specimens that are not amenable to cytogenetic analysis.
Discrimination of Prostate Cancer from Normal Peripheral Zone and Central Gland Tissue by Using Dynamic Contrast-enhanced MR Imaging (2003)

PURPOSE: To evaluate which parameters of dynamic magnetic resonance (MR) imaging and T2 relaxation rate would result in optimal discrimination of prostatic carcinoma from normal peripheral zone (PZ) and central gland (CG) tissues and to correlate these parameters with tumor stage, Gleason score, patient age, and tumor markers. MATERIALS AND METHODS: Of 58 patients with prostatic carcinoma, 36 were included for analysis. Patients underwent MR imaging at 1.5 T with an endorectal-pelvic phased-array coil and subsequently underwent prostatectomy. A T2-weighted turbo spin-echo sequence, an intermediate-weighted sequence, and a fast T1-weighted gradient-echo sequence (seven sections in 2.03 seconds) during bolus injection of 0.1 mmol gadopentetate dimeglumine per kilogram of body weight were performed. Contrast agent concentration-time curves were obtained for prostatic carcinoma and normal PZ and CG tissue by using whole-mount sections to guide placement of regions of interest. Onset time, time to peak, peak enhancement, relative peak enhancement, washout, and T2 relaxation rates were calculated. Multivariate receiver operating characteristic analysis was performed with and without relative peak enhancement. RESULTS: Results of multivariate receiver operating characteristic analysis showed that relative peak enhancement demonstrated the highest area under the receiver operating characteristic curve (AUC) in the PZ and the CG (AUC = 0.93, 0.82). Results of multivariate analysis without relative peak enhancement showed that relative peak enhancement in the PZ and washout in the CG demonstrated the highest AUC (AUC = 0.9, 0.81). Pearson correlation coefficients between the dynamic parameters or T2 relaxation rates in carcinoma and the tumor stage, Gleason score, patient age, and tumor markers ranged between 0.02 and 0.44. CONCLUSION: The optimal parameter for discrimination of prostatic carcinoma in the PZ and CG was relative peak enhancement. If relative peak enhancement was not used, then peak enhancement was optimal in the PZ, and washout was optimal in the CG. Poor-to-moderate correlation was present between the dynamic parameters or T2 relaxation rate in carcinoma and the tumor stage, Gleason score, patient age, tumor volume, and prostate-specific antigen
Sequences at the C-terminus of the herpes simplex virus type 1 UL30 protein are dispensable for DNA polymerase activity but not for viral origin-dependent DNA replication (1993)

The UL30 protein of herpes simplex virus type 1 (HSV-1) is a catalytically active DNA polymerase which is present in virus infected cells in a heterodimeric complex with an accessory subunit, the UL42 polypeptide. Both proteins are essential for viral DNA synthesis but because the UL42 protein is much more abundant it has been difficult to determine whether its role is related to, or independent of, its interaction with the UL30 protein in vivo. Since the C-terminal region of UL30 has been shown to be important for interaction with the UL42 protein but dispensable for DNA polymerase activity, a recombinant baculovirus which overexpresses a UL30 protein truncated by 27 amino acids at its C-terminus was constructed and used to assess the significance of the protein-protein interaction. The mutated protein was as active as wildtype (wt) UL30 in a DNA polymerase assay in which activated calf thymus DNA was used as template. However, in contrast to the wt protein, the activity of the truncated polymerase on this template was not stimulated by addition of purified UL42. A monoclonal antibody against the UL42 protein co-precipitated the full length but not truncated polymerase from extracts of cells which had been co-infected with a UL42-expressing recombinant baculovirus. Finally, the truncated protein was not active in a transient assay for HSV-1 origin-dependent DNA replication performed in insect cells in tissue culture. These results indicate that sequences at the C-terminus of the UL30 protein which are dispensable for DNA polymerase activity play essential roles both in viral DNA replication and interaction with the UL42 protein, and strongly suggest that the interaction between the proteins is important in vivo.
Computational rock physics at the pore scale: Transport properties and diagenesis in realistic pore geometries (2001)

Transport properties, such as permeability, are important in many geophysical and petroleum applications. However, complex pore geometry often makes modeling and simulation of transport properties in porous media very difficult. Conventional methods are usually based on partial differential equations, but the implementation of these techniques becomes very complicated when the geometry is extremely complex. As a result, simplified geometry is often used; thus the implementation depends heavily on the model. Solving the same problem in a different geometry often means that many parts of the implementation have to be changed. Therefore, a more robust and simple tool, which can handle complex pore space without oversimplification or modification of the model, is needed.
Starvation response in mouse liver shows strong correlation with life-span-prolonging processes (2004)

We have monitored global changes in gene expression in mouse liver in response to fasting and sugar-fed conditions using high-density microarrays. From ∼20,000 different genes, the significantly regulated ones were grouped into specific signaling and metabolic pathways. Striking changes in lipid signaling cascade, insulin and dehydroepiandrosterone (DHEA) hormonal pathways, urea cycle and S-adenosylmethionine-based methyl transfer systems, and cell apoptosis regulators were observed. Since these pathways have been implicated to play a role in the aging process, and since we observe significant overlap of genes regulated upon starvation with those regulated upon caloric restriction, our analysis suggests that starvation may elicit a stress response that is also elicited during caloric restriction. Therefore, many of the signaling and metabolic components regulated during fasting may be the same as those which mediate caloric restriction-dependent life-span extension.
Versatile Catalysts for the Suzuki Cross-Coupling of Arylboronic Acids with Aryl and Vinyl Halides and Triflates under Mild Conditions (2000)

Through the use of Pd2(dba)3/P(t-Bu)3 as a catalyst, a wide range of aryl and vinyl halides, including chlorides, undergo Suzuki cross-coupling with arylboronic acids in very good yield, typically at room temperature; through use of Pd(OAc)2/PCy3, a diverse array of aryl and vinyl triflates react cleanly at room temperature. Together, these two catalyst systems cover a broad spectrum of commonly encountered substrates for Suzuki couplings. Furthermore, they display novel reactivity patterns, such as the selective cross-coupling by Pd2(dba)3/P(t-Bu)3 of an aryl chloride in preference to an aryl triflate, and they can be used at low loading, even for reactions of aryl chlorides. Preliminary mechanistic work indicates that a palladium monophosphine complex is the active catalyst in the cross-coupling of aryl halides.
Leveraging Demonstrations for Deep Reinforcement Learning on Robotics Problems with Sparse Rewards (2017)

We propose a general and model-free approach for Reinforcement Learning (RL) on real robotics with sparse rewards. We build upon the Deep Deterministic Policy Gradient (DDPG) algorithm to use demonstrations. Both demonstrations and actual interactions are used to fill a replay buffer and the sampling ratio between demonstrations and transitions is automatically tuned via a prioritized replay mechanism. Typically, carefully engineered shaping rewards are required to enable the agents to efficiently explore on high dimensional control problems such as robotics. They are also required for model-based acceleration methods relying on local solvers such as iLQG (e.g. Guided Policy Search and Normalized Advantage Function). The demonstrations replace the need for carefully engineered rewards, and reduce the exploration problem encountered by classical RL approaches in these domains. Demonstrations are collected by a robot kinesthetically force-controlled by a human demonstrator. Results on four simulated insertion tasks show that DDPG from demonstrations out-performs DDPG, and does not require engineered rewards. Finally, we demonstrate the method on a real robotics task consisting of inserting a clip (flexible object) into a rigid object.
Tn916 insertion mutagenesis in Escherichia coli and Haemophilus influenzae type b following conjugative transfer (1992)

Transposon Tn916 was shown to be capable of direct conjugative transfer in broth and membrane matings between strains of Escherichia coli K12 and between E. coli K12 and Haemophilus influenzae type b. Only Tn916 was transferred, but Tn916 donor ability was not itself inheritable by the recipients and seemed to be associated with the presence of Tn916 on a non-conjugative pBR322-derived vector in the original donor strain. Transfer of Tn916 by conjugation was found to be an efficient method for producing insertion mutations in the chromosome of recipient cells. Although such insertions were unstable when the cells were grown under non-selective conditions, it was possible to show that over 40% of the isolated Tn916 insertions in the chromosome of E. coli K12 were in gene(s) concerned with histidine biosynthesis, implying that there is a partial hot-spot for Tn916 insertion on the E. coli K12 chromosome. When a strain of H. influenzae type b was used as a recipient, out of approximately 1500 transconjugants tested, two mutants were isolated with insertions in genes controlling the expression of iron-regulated transferrin-binding proteins. These mutants constitutively produced major 76 kDa and minor 90 kDa proteins which bound transferrin, even when grown under iron-sufficient conditions. Tn916 insertion mutagenesis, following transfer by conjugation, is a convenient method for isolating mutations in genes concerned with iron acquisition by this important human pathogen.
A recombinant human Fab expressed in Escherichia coli neutralizes rabies virus (1992)

A recombinant human anti-rabies monoclonal antibody (MAb-57) Fab was prepared by cloning the heavy (Fd)- and light-chain domains into the same bacterial expression vector. To construct the recombinant Fab, mRNA was extracted from MAb-57-producing hybridoma cells, reverse transcribed, and then amplified by polymerase chain reaction (PCR) by using oligonucleotides specific for immunoglobulin heavy- and light-chain DNA sequences. PCR-amplified Fd-chain cDNA was fused, in frame, between a bacterial leader peptide (PelB) at the amino terminus and a 10-amino-acid peptide tag at the carboxy terminus. The PCR-amplified lambda-chain cDNA was also fused to the PelB leader peptide. The immunoglobulin Fab was then expressed as a dicistronic message in bacteria by using the isopropyl-beta-D-thiogalactopyranoside-inducible lactose promotor (lacZ). DNA sequencing was used to define the gamma-chain isotype (immunoglobulin G1) and VH (VHI) chain and VL (V lambda II) chain gene usage. The recombinant Fab (rFab57) specifically bound the rabies virus coat glycoprotein, while the Fd and lambda chains, when expressed individually, did not. The binding specificity of rFab57 was indistinguishable from that of the intact MAb in direct enzyme-linked immunosorbent assays; however, the dissociation constant of rFab57 for rabies virus protein G was approximately 1 log10 U lower than that of complete MAb-57 in competition enzyme-linked immunosorbent assays. A fluorescent-focus inhibition assay showed that bacterially expressed rFab was capable of neutralizing rabies virus strain CVS-11. We conclude that a human Fab expressed in bacteria maintains its specificity and biologic activity.
Vertebral Artery Occlusion in Duplex Color-Coded Ultrasonography (2004)

Duplex color-coded ultrasonography can accurately diagnose the site of VA occlusion.
A promoter SNP rs4073T>A in the common allele of the interleukin 8 gene is associated with the development of idiopathic pulmonary fibrosis via the IL-8 protein enhancing mode (2011)

The common allele of a promoter SNP, rs4073T>A, may increase susceptibility to the development of IPF via up-regulation of IL-8.
Supporting PIM-SM in All-Optical Lambda-Switched Networks (2001)

Abstract: We describe a protocol to construct optical multicast trees in lambdaswitched networks running PIM-SM. Based on the MPLS architecture, the protocol maps a multicast tree constructed by PIM-SM onto point-to-multipoint LSPs that are connected to form an equivalent WDM multicast tree. LSP set-up request is receiver-initiated in the protocol. A mechanism to collect information about the capability of each WDM node along a path is used to provide receivers with sufficient information to form appropriate LSP set-up requests. This facilitates the set-up of LSPs, in particular in heterogeneous networks.
Mechanisms of Toxicity of Amorphous Silica Nanoparticles on Human Lung Submucosal Cells in Vitro: Protective Effects of Fisetin (2012)

There is growing evidence that amorphous silica nanoparticles (SiO₂-NP) can cause an inflammatory response in the lung. We studied in vitro the effects of exposing human lung submucosal cells to SiO₂-NP of various sizes (10, 150, and 500 nm) for 2-24 h. Cell survival, reactive oxygen species (ROS), malondialdehyde (MDA) levels, cytokine production, inflammatory gene expression, and genotoxicity were measured after exposure of Calu-3 cells to 10SiO₂-NP in the presence or absence of the flavanoid fisetin and an antioxidant enzyme catalase. The exposure of Calu-3 cells to 10SiO₂-NP resulted in (1) increased cytotoxicity and cell death in a time- and concentration-dependent manner, with a lethal concentration (LC₅₀) of 9.7 μg/mL after 24 h; (2) enhanced gene expression of interleukin (IL)-6, IL-8, and matrix metalloproteinase-9; (3) a significant correlation between increases in MDA and cytotoxicity at 18 h; (4) ROS production; (5) IL-6 and IL-8 release; and (6) up-regulation of the pro-apoptotic genes, p53 and caspase-3. Cell death and inflammatory reactions were attenuated by fisetin and catalase. We observed that 150- and 500SiO₂-NP exerted no toxic effects on Calu-3 cells. In conclusion, the nanotoxicity of amorphous 10SiO₂-NP on submucosal cells is associated with inflammation, the release of ROS leading to apoptosis, and decreased cell survival. The nanotoxic effects of 10SiO₂-NP can be decreased by fisetin and catalase treatment, implicating oxidative stress in this injury.
Nonlinear fluorescence quenching and the origin of positive curvature in Stern-Volmer plots (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNonlinear fluorescence quenching and the origin of positive curvature in Stern-Volmer plotsJoel KeizerCite this: J. Am. Chem. Soc. 1983, 105, 6, 1494–1498Publication Date (Print):March 1, 1983Publication History Published online1 May 2002Published inissue 1 March 1983https://pubs.acs.org/doi/10.1021/ja00344a013https://doi.org/10.1021/ja00344a013research-articleACS PublicationsRequest reuse permissionsArticle Views5247Altmetric-Citations277LEARN 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
Management and monitoring of anticoagulation for children undergoing cardiopulmonary bypass in cardiac surgery. (2010)

Cardiopulmonary bypass (CPB) creates a pro-coagulant state by causing platelet activation and inflammation leading to thrombin generation and platelet dysfunction. It is associated with severe derangements in normal homeostasis resulting in both thrombotic and hemorrhagic complications. This derangement is greater in children with congenital heart disease than in adults because of the immaturity of the coagulation system, hemodilution of coagulation factors, hyperreactive platelets, and in some patients, physiologic changes associated with cyanosis. During CPB, an appropriate amount of heparin is given with the goal of minimizing the risk of thrombosis and platelet activation and at the same time reducing the risk of bleeding from over anticoagulation. In young children, this balance is more difficult to achieve because of inherent characteristics of the hemostatic system in these patients. Historically, protocols for heparin dosing and monitoring in children have been adapted from adult protocols without re-validation for children. Extreme hemodilution of coagulation factors and platelets in young children affects the accuracy of anticoagulation monitoring in children. The activated clotting time does not correlate with plasma levels of heparin. In addition, recent studies suggest that children need larger doses of heparin than adults, because they have lower antithrombin levels, and they metabolize heparin more rapidly. Preliminary studies demonstrated that the use of individualized heparin and protamine monitoring and management in children is associated with reduced platelet activation and dysfunction and improved clinical outcomes. However, this review article clearly establishes that further studies are necessary to obtain evidence-based protocols for the proper management of anticoagulation of children undergoing cardiopulmonary bypass.
Detection of linkage disequilibrium between the myotonic dystrophy locus and a new polymorphic DNA marker. (1991)

We have examined the linkage of two new polymorphic DNA markers (D19S62 and D19S63) and a previously unreported polymorphism with an existing DNA marker (ERCC1) to the myotonic dystrophy (DM) locus. In addition, we have used pulsed-field gel electrophoresis to obtain a fine-structure map of this region. The detection of linkage disequilibrium between DM and one of these markers (D19S63) is the first demonstration of this phenomenon in a heterogeneous DM population. The results suggest that at least 58% of DM patients in the British population, as well as those in a French-Canadian subpopulation, are descended from the same ancestral DM mutation. We discuss the implications of this finding in terms of strategies for cloning the DM gene, for a possible role in modification of risk for prenatal and presymptomatic testing, and we speculate on the origin and number of existing mutations which may result in a DM phenotype.
DOTA Conjugate with an Albumin-Binding Entity Enables the First Folic Acid–Targeted 177Lu-Radionuclide Tumor Therapy in Mice (2012)

The modification of a folate radioconjugate with an albumin-binding entity resulted in a significant increase of the tumor-to-kidney ratio of radioactivity, enabling for the first time, to our knowledge, the preclinical application of folic acid-targeted radionuclide therapy in mice.
Enhanced repair of a cisplatin‐damaged reporter chloramphenicol‐O‐acetyltransferase gene and altered activities of DNA polymerases α and β, and DNA ligase in cells of a human malignant glioma following in vivo cisplatin therapy (1994)

Current evidence suggest an important role for increased repair of drug-induced DNA damage as one of the major mechanisms involved in tumor cell resistance to cis-DDP. In this study, we examined the DNA repair capacity and the activities of three DNA repair related proteins, namely, DNA polymerases alpha and beta, and total DNA ligase in cells of a malignant oligodendroglioma obtained from a patient before therapy and compared it with those of a specimen of the tumor acquired after the patient had failed cis-DDP therapy. DNA repair capacity was quantitated as the extent of reactivation of the chloramphenicol-O-acetyltransferase (CAT) gene in a eukaryotic expression vector that had been damaged and inactivated by prior treatment with cis-DDP and then transfected into the tumor cells. The extent of DNA-platinum adduct formation in the expression vector was determined by flameless atomic absorption spectrometry. The level of cis-DDP resistance of cells of the two tumors was determined with the capillary tumor stem cell assay. We observed a 2.8-fold increased capacity to repair Pt-DNA adducts and reactivate the CAT gene in cells of the tumor obtained after cis-DDP therapy, compared to cells of the untreated tumor. This was associated with increases of 9.4-fold and a 2.3-fold, respectively, in DNA polymerase beta and total DNA ligase activities in cells of the treated tumor. At 5 microM cis-DDP, there was a 5.9-fold increase in the in vitro cis-DDP resistance of post-therapy tumor cells relative to cells of the untreated tumor.(ABSTRACT TRUNCATED AT 250 WORDS)
Essential Role of CCR2 in Neutrophil Tissue Infiltration and Multiple Organ Dysfunction in Sepsis (2010)

Collectively, these data identify CCR2 as a key receptor that drives the inappropriate infiltration of neutrophils into remote organs during sepsis. Therefore, CCR2 blockade is a novel potential therapeutic target for treatment of sepsis-induced MODS.
Adjunctive Selectin Blockade Successfully Reduces Infarct Size Beyond Thrombolysis in the Electrolytic Canine Coronary Artery Model (1995)

Selectin blockade as an adjunct to rTPA-mediated thrombolysis significantly reduces infarct size and myocardial neutrophil infiltration well beyond thrombolysis alone in the electrolytic canine model. These data suggest that selectin blockade is extremely effective at reducing ischemia-reperfusion injury and myocardial infarct size in this model and that the neutrophil is a potent mediator of ischemia-reperfusion injury.