gebhart/patrepeval huggingface dataset:
Regulation of factor Xa in vitro in human and mouse plasma and in vivo in mouse. Role of the endothelium and plasma proteinase inhibitors. (1983)

The regulation of human Factor Xa was studied in vitro in human and mouse plasma, and in vivo in mouse. In human plasma, 125I-Factor Xa bound to alpha 1-proteinase inhibitor, antithrombin III, and alpha 2-macroglobulin in a ratio of 4.9:1.9:1 as determined by gel electrophoresis and by adsorption to IgG-(antiproteinase inhibitor)-Sepharose beads. The distribution of Factor Xa in mouse plasma was similar. The clearance of Factor Xa in mice was rapid (50% clearance in 3 min) and biphasic. alpha 1-Proteinase inhibitor-trypsin, even at a 2,000-fold molar excess, failed to inhibit the clearance of Factor Xa, while alpha 2-macroglobulin-trypsin inhibited only the later phase of clearance. The plasma clearance of diisopropylphosphoryl-Factor Xa was more rapid than native Factor Xa (50% clearance in 2.5 min), and the clearance was blocked by diisopropylphosphoryl-thrombin. Electrophoresis experiments confirmed that by 2 min after injection into the murine circulation, 90% of the bound Factor Xa was on alpha 2-macroglobulin, in marked contrast to the in vitro results. Organ distribution studies at 3 and 15 min with 125I-Factor Xa demonstrated that the majority of radioactivity was in the liver, with significant radioactivity also present in lung and kidney. Autopsies performed 30 s after injection of 125I-Factor Xa also demonstrated significant binding to the aorta and vena cava. These studies indicate that Factor Xa binds to specific thrombin-binding sites on endothelial cells, and that this binding alters its proteinase inhibitor specificity. Factor Xa binds to alpha 2-macroglobulin in vivo, whereas the predominant in vitro inhibitor of Factor Xa is alpha 1-proteinase inhibitor.
Electric field-mediated DNA transfer: transient and stable gene expression in human and mouse lymphoid cells. (1986)

The technique of DNA transfer by electroporation was investigated in an effort to evaluate its utility for the identification of developmentally controlled regulatory sequences. Transient and stable gene expression was detected in a variety of lymphoid cell lines subjected to electroporation. No correlation existed between the levels of chloramphenicol acetyltransferase (acetyl-CoA; chloramphenicol 3-O-acetyltransferase, EC 2.3.1.28) expression and stable transfection frequency. In all lymphoid cell lines tested, the simian virus 40 early region was a better promoter than was the Rous sarcoma virus long terminal repeat.
Serotype 1-Specific Monoclonal Antibody-Based Antigen Capture Immunoassay for Detection of Circulating Nonstructural Protein NS1: Implications for Early Diagnosis and Serotyping of Dengue Virus Infections (2006)

Rapid diagnosis and serotyping of dengue virus (DV) infections are important for timely clinical management and epidemiological control in areas where multiple flaviviruses are endemic. However, the speed and accuracy of diagnosis must be balanced against test cost and availability, especially in developing countries. We developed a specific antigen capture enzyme-linked immunosorbent assay (ELISA) for early detection and serotyping of DV serotype 1 (DV1) by using well-characterized monoclonal antibodies (MAbs) specific to nonstructural protein 1 (NS1) of DV1. With this assay, a total of 462 serum specimens from clinically probable DV1-infected patients during the DV1 epidemic in Guangdong, China, in 2002 and 2003 were analyzed. DV1 NS1 was detectable in blood circulation from the first day up to day 18 after onset of symptoms, with a peak at days 6 to 10. The sensitivity of DV1 NS1 detection in serum specimens with reference to results from reverse transcriptase PCR was 82%, and the specificity was 98.9% with reference to 469 healthy blood donors. No cross-reactions with any of the other three DV serotypes or other closely related members of the genus Flavivirus (Japanese encephalitis virus and Yellow fever virus) were observed when tested with the clinical specimens or virus cultures. These findings suggest that the serotype-specific MAb-based NS1 antigen capture ELISA may be a valuable tool for early diagnosis and serotyping of DV infections, while also providing a standardized assay for the analysis of a great number of clinical samples with convenience and cost-effectiveness.
Role of Cryoprotectants on the Viability and Functional Properties of Probiotic Lactic Acid Bacteria during Freeze Drying (2009)

Effect of different cryoprotectants on acid/bile tolerance, β-galactosidase activity, and cholesterol assimilation properties of freeze dried Pediococcus acidilactici, Lactobacillus plantarum, and Lactobacillus salivarius were evaluated. The retention of probiotic properties and viability of the above three cultures freeze dried with lactose, skimmed milk, and maltodextrin were found to be significant (P ≤ 0.05). In another approach, lactic acid bacteria (LAB) were subjected to cold shock first and then freeze dried. Effect of cold shock treatment on retention of probiotic properties of freeze dried LAB cultures was also investigated. The cold shock treatment resulted in an increase of 6–8%, both in viability and probiotic properties, compared with LAB freeze dried without cold shock treatment. The survival of freeze dried L. plantarum, L. salivarius, and P. acidilactici was investigated over a period of 60 d storage at 4°C. The above three cultures freeze dried with maltodextrin exhibited 83%, 68%, and 60% retention in survival percentage, respectively, in comparison with initial values.
Connection control in ATM networks (2002)

This paper describes a new connection management algorithm called parallel connection control (PCC) that allows for fast connection setup in scaleable reliable asynchronous transfer mode (ATM) networks. The two main concepts of PCC are execution of connection setup actions at multiple switches on the route of a connection in parallel, and the separation of the route computation function into servers distinct from switch processors. The associated benefits of these concepts are fast connection setup and increased per-switch call handling capacity relative to the conventional approach of setting up connections sequentially switch-by-switch with switches performing route computation. The PCC solution is designed to work in conjunction with the current ATM Forum signaling and routing standards solutions, offering a means to achieve improved call handling performance. This paper also introduces the concept of application-dependent routing for setting up logical connections, which consist of multiple network-layer connections routed through application-layer resources, such as bridges and converters. In this paper, we propose two models for handling complex communication configurations: an end-host-driven model and a network-value-added model using application-dependent route (ADR) servers.
Domain assignment for protein structures using a consensus approach: Characterization and analysis (1998)

A consensus approach for the assignment of structural domains in proteins is presented. The approach combines a number of previously published algorithms, and takes advantage of the elevated accuracy obtained when assignments from the individual algorithms are in agreement. The consensus approach is tested on a data set of 55 protein chains, for which domain assignments from four automated methods were known, and for which crystallographers assignments had been reported in the literature. Accuracy was found to increase in this test from 72% using individual algorithms to 100% when all four methods were in agreement. However a consensus prediction using all four methods was only possible for 52% of the dataset. The consensus approach [using three publicly available domain assignment algorithms (PUU, DETECTIVE, DOMAK)] was then used to make domain assignments for a data set of 787 protein chains from the Protein Data Bank. Analysis of the assignments showed 55.7% of assignments could be made automatically, and of these, 13.5% were multi-domain proteins. Of the remaining 44.3% that could not be assigned by the consensus procedure 90.4% had their domain boundaries assigned correctly by at least one of the algorithms. Once identified, these domains were analyzed for trends in their size and secondary structure class. In addition, the discontinuity of each domain along the protein chain was considered.
Block oligopeptides (L‐lysyl)m‐(L‐alanyl)n‐L‐Tyrosyl‐(L‐Alanyl)n‐(L‐Lysyl)m. II. Circular dichroism and pulsefluorimetry conformational studies (1978)

Abstract The conformation of chromatographically pure block oligopeptides ( L ‐lysyl) m ‐( L ‐alanyl) n ‐ L ‐tyrosyl‐( L ‐alanyl) n ‐( L ‐lysyl) m with n = 3 and m = 6 or 3 is investigated. By circular dichroism it is shown that these peptides may exhibit a partially α‐helical structure depending upon pH, ionic strength, solvent, and temprerature. An attempt is made to describe the helical content of these small peptides by utilizing the data obtained on high‐molecular‐weight poly( L ‐lysine). By measurement of the quantum yield and the decays of the peptides fluorescence, it is shown that, in aqueous solution, at neutral pH, the fluorescence of the peptides is quenched by interactions with the peptide carbonyl groups. The decays are multiexponential, which shows the presence of several conformations of the phenolic chromophore relative to the peptide chain. The addition of methanol, which induced the helix formation, decreases the quenching of the fluorescence and the multiexponential character of the decays. In presence of sodium hydroxide, which further increases the helical content of the peptides, a dynamic quenching occured that can be attributed to interactions between the phenol hydroxyl group of tyrosine ( i th residue) and the ε‐amino groups of the ( i +4)th and ( i ‐4)th lysyl residues.
The Prevalence and Nature of Glycan Alterations on Specific Proteins in Pancreatic Cancer Patients Revealed Using Antibody-Lectin Sandwich Arrays (2009)

Changes to the glycan structures of proteins secreted by cancer cells are known to be functionally important and to have potential diagnostic value. However, an exploration of the population variation and prevalence of glycan alterations on specific proteins has been lacking because of limitations in conventional glycobiology methods. Here we report the use of a previously developed antibody-lectin sandwich array method to characterize both the protein and glycan levels of specific mucins and carcinoembryonic antigen-related proteins captured from the sera of pancreatic cancer patients (n = 23) and control subjects (n = 23). The MUC16 protein was frequently elevated in the cancer patients (65% of the patients) but showed no glycan alterations, whereas the MUC1 and MUC5AC proteins were less frequently elevated (30 and 35%, respectively) and showed highly prevalent (up to 65%) and distinct glycan alterations. The most frequent glycan elevations involved the Thomsen-Friedenreich antigen, fucose, and Lewis antigens. An unexpected increase in the exposure of alpha-linked mannose also was observed on MUC1 and MUC5ac, indicating possible N-glycan modifications. Because glycan alterations occurred independently from the protein levels, improved identification of the cancer samples was achieved using glycan measurements on specific proteins relative to using the core protein measurements. The most significant elevation was the cancer antigen 19-9 on MUC1, occurring in 19 of 23 (87%) of the cancer patients and one of 23 (4%) of the control subjects. This work gives insight into the prevalence and protein carriers of glycan alterations in pancreatic cancer and points to the potential of using glycan measurements on specific proteins for highly effective biomarkers.
Endogenous Marinobufagenin-Like Factor In Acute Plasma Volume Expansion (1998)

The aim of the study was to further investigate the nature of endogenous digitalis-like factors stimulated by acute plasma volume expansion (VE). 10 male Fisher 344XNB rats were given intravenous (iv) saline infusion (4% of the body mass) for 30 min, which caused a fall in % hematocrit (35.9+/-0.69 vs. 41.8+/-1.05; vs. 10 controls, P<0.01). EDLF was measured in C-18 reverse-phase extracted (32%+80% acetonitrile) tissues. VE was associated with an increase in plasma marinobufagenin-like factor (MLF)(0.49+/-0.05 vs. 0.2+/-0.06 nmol/L, P<0.01) and pituitary ouabain-like compound (OLC) (30.9+/-3.12 vs. 3.2+/-2.3 pmol/g, P<0.01). Plasma OLC decreased (0.087+/-0.018 vs. 0.21+/-0.04 nmol/L, P<0.02), and pituitary MLF did not change (0.05+/-0.01 vs. 0.07+/-0.02 pmol/g) after VE. Chloroform extracted urine from 5 volume-expanded male mongrel dogs was fractionated on reverse-phase HPLC columns in a linear gradient of 0-80% acetonitrile. The material cross-reacting with marinobufagenin antibody eluted from HPLC column as a single peak, demonstrated absorbance at 300 nm, and was distinct from ouabain-like material. Digoxin antibodies interacted with both marinobufagenin-like and ouabain-like immunoreactive material. These results provide further evidence for the presence of a bufodienolide EDLF in the mammals, and demonstrate that EDLF response to VE includes stimulation of brain OLC and plasma bufodienolide.
DataGuides: Enabling Query Formulation and Optimization in Semistructured Databases (1997)

In semistructured databases there is no schema fixed in advance. To provide the benefits of a schema in such environments, we introduce DataGuides: concise and accurate structural summaries of semistructured databases. DataGuides serve as dynamic schemas, generated from the database; they are useful for browsing database structure, formulating queries, storing information such as statistics and sample values, and enabling query optimization. This paper presents the theoretical foundations of DataGuides along with algorithms for their creation and incremental maintenance. We provide performance results based on our implementation of DataGuides in the Lore DBMS for semistructured data. We also describe the use of DataGuides in Lore, both in the user interface to enable structure browsing and query formulation, and as a means of guiding the query processor and optimizing query execution. 1. Introduction Traditional relational and object-oriented database systems force all data to adhere ...
Orientation adaptive subband coding of images (1994)

In the subband coding of images, directionality of image features has thus far been exploited very little. The proposed subband coding scheme utilizes orientation of local image features to avoid the highly objectionable Gibbs-like phenomena observed at reconstructed image edges with conventional subband schemes at low bit rates, At comparable bit rates, the subjective image quality obtained by our orientation adaptive scheme is considerably enhanced over a conventional separable subband coding scheme, as well as other separable approaches such as the JPEG compression standard.
Stage-Dependent Effect of TGF-β1 on Chondrogenic Differentiation of Human Embryonic Stem Cells (2008)

Transforming growth factor-beta (TGF-beta) is known to be a potent inducer of stem cell chondrogenic differentiation. Transforming growth factor-beta/activin/nodal-signaling pathway has also been shown to be involved in maintaining the pluripotency of embryonic stem cells (ESCs). In this study, the effect of TGF-beta1 in chondrogenic differentiation of ESCs was examined both with undifferentiated ESCs that bypassed classical embryoid body (EB) formation, and on 5-day EB-derived cells. The effect of TGF-beta1 was compared to cells differentiated in serum-free chondrogenic basal medium without growth factor supplement. Analysis by real-time polymerase chain reaction (PCR), type II collagen enzyme-linked immunosorbent assay, sulfated glycoaminoglycan quantification and fluorescence immunostaining demonstrated substantial chondrogenic differentiation of ESCs regardless of EB formation in the absence of the growth factor. Addition of TGF-beta1 significantly inhibited chondrogenic gene expression and collagen deposition with a more potent effect on the cells that bypassed EB formation. Our study using a TGF-beta/activin/nodal-signaling inhibitor suggested that TGF-beta inhibited early chondrogenic induction but was required at the later stage of differentiation, which was also reflected in the enhancing effect of TGF-beta1 on chondrogenic development at later time points in EB-derived cells. Analysis of the pluripotency markers demonstrated sustained Oct4 and Nanog expression in the presence of TGF-beta1 with Oct4-positive cells detected in subpopulations of the differentiated culture. Our results suggest that TGF-beta1 suppresses ESC chondrogenic induction and the degree of suppression is dependent on the differentiation-stage of the ESC. Transforming growth factor-beta signaling, however, is required for functional chondrogenic development of ESC. Our finding that TGF-beta can sustain an undifferentiated population of human ESCs within the differentiation culture suggests that caution should be exercised when using this growth factor as an ESC chondrogenic inducer and highlights the importance of a selection protocol for chondroprogenitor cells to avoid possible teratoma formation in vivo.
Synthesis of Aromatic Bisabolene Natural Products via Palladium-Catalyzed Cross-Couplings of Organozinc Reagents (2004)

Aromatic bisabolene derivatives were prepared by two methods involving cross-coupling of organozinc reagents. The first synthesis of (+/-)-glandulone A (10), as well as syntheses of (+/-)-curcuhydroquinone (8) and (+/-)-curcuquinone (9), were accomplished via coupling of a secondary alkyl zinc reagent (1,5-dimethyl-4-hexenylzinc halide, 18) to protected bromohydroquinones using Pd(dppf)Cl(2) as catalyst. Coupling of arylzinc halides with alkenyl triflate 16 using Pd(PPh(3))(4) catalyst provided a number of bisabolene derivatives and led to syntheses of dehydro-alpha-curcumene (2), (+/-)-curcuphenol (3), and (+/-)-elvirol (13). A high-yield synthesis of the (+/-)-heliannuol D precursor 29 is also reported using this method.
A Detailed Linkage Map of Medaka, Oryzias latipes: Comparative Genomics and Genome Evolution (2000)

We mapped 633 markers (488 AFLPs, 28 RAPDs, 34 IRSs, 75 ESTs, 4 STSs, and 4 phenotypic markers) for the Medaka Oryzias latipes, a teleost fish of the order Beloniformes. Linkage was determined using a reference typing DNA panel from 39 cell lines derived from backcross progeny. This panel provided unlimited DNA for the accumulation of mapping data. The total map length of Medaka was 1354.5 cM and 24 linkage groups were detected, corresponding to the haploid chromosome number of the organism. Thirteen to 49 markers for each linkage group were obtained. Conserved synteny between Medaka and zebrafish was observed for 2 independent linkage groups. Unlike zebrafish, however, the Medaka linkage map showed obvious restriction of recombination on the linkage group containing the male-determining region (Y) locus compared to the autosomal chromosomes.
The Effect of Statins on Erectile Dysfunction: A Meta‐Analysis of Randomized Trials (2014)

Statins cause a clinically relevant improvement of erectile function as measured by the five-item version of the IIEF.
Oxygen Reduction on Silver Low-Index Single-Crystal Surfaces in Alkaline Solution:  Rotating Ring DiskAg(hkl) Studies (2006)

The rotating ring disk method is applied to investigate the oxygen reduction reaction on Ag single-crystal surfaces in alkaline solution over the temperature range 293-333 K. At all temperatures, the oxygen reduction reaction proceeds through the 4e- reaction pathway with a very small (approximately 0.5-2%) peroxide formation. At the same temperature and overpotentials, the kinetics of the ORR always increases in the order (100) < or = (111) < (110), indicating that the reaction is structure-sensitive. We present an interpretation of the structure sensitivity based on the supposition that it arises from (i) a potential-dependent adsorption of spectator hydroxyl ions and (ii) variations in activation energies, which are determined by the O2 adsorption on Ag single-crystal surfaces covered by adsorbed oxygenated species.
Biomolecular Ultrasound and Sonogenetics (2018)

Visualizing and modulating molecular and cellular processes occurring deep within living organisms is fundamental to our study of basic biology and disease. Currently, the most sophisticated tools available to dynamically monitor and control cellular events rely on light-responsive proteins, which are difficult to use outside of optically transparent model systems, cultured cells, or surgically accessed regions owing to strong scattering of light by biological tissue. In contrast, ultrasound is a widely used medical imaging and therapeutic modality that enables the observation and perturbation of internal anatomy and physiology but has historically had limited ability to monitor and control specific cellular processes. Recent advances are beginning to address this limitation through the development of biomolecular tools that allow ultrasound to connect directly to cellular functions such as gene expression. Driven by the discovery and engineering of new contrast agents, reporter genes, and bioswitches, the nascent field of biomolecular ultrasound carries a wave of exciting opportunities.
CPP32/Apopain Is a Key Interleukin 1β Converting Enzyme-like Protease Involved in Fas-mediated Apoptosis (1996)

Cysteine proteases of the interleukin 1 beta Converting Enzyme (ICE)/CED-3 family have been implicated in the effector process of apoptosis in several systems, including Fas-mediated apoptosis. We have recently isolated and partially characterized a protease present in extracts from anti-Fas antibody treated Jurkat T cells that promotes apoptotic changes in isolated nuclei (Schlegel, J., Peters, I., and Orrenius, S. (1995) FEBS Lett. 364, 139-142). We now show that this protease cleaves poly-(ADP-ribose) polymerase (PARP) with high efficiency and specificity. Both PARP proteolysis and the proapoptotic effects of the protease are inhibited by nanomolar concentrations of a selective inhibitor of apopain (CPP32), while an inhibitor of IL-1 beta converting enzyme is much less effective, requiring micromolar concentrations for the inhibition of the isolated protease. Kinetic analysis of the isolated protease reveals kinetic constants similar to those reported for apopain. The isolated protease is recognized by antibodies specific for CPP32/apopain but not by an anti-ICE antibody. Furthermore, a selective inhibitor of apopain prevents Fas-induced apoptosis in intact Jurkat T cells. We therefore conclude that CPP32/apopain is activated in Fas-induced apoptosis.
Two-dimensional circularly polarized pump–probe spectroscopy (2003)

A novel two-dimensional (2D) circularly polarized (CP) pump–probe (PP) spectroscopy is theoretically studied and proposed. Utilizing circularly polarized pump field, one can measure both the left- and right-CP PP spectra in the 2D frequency space spanned by the pump and probe field frequencies. Although the dominant contribution to the measured signal is all electricdipole-allowed four-wave-mixing term, it can be removed by taking the difference between the left- and right-CP PP signals. Taking the first-order terms with respect to either magnetic dipole- or quadrupole-pump field interaction, we find that two distinctively different contributions to the third-order CP-PP polarization are important. However, by controlling the crossing angle between the pump and probe field propagation directions to be the magic angle, θ=tan−1(1/√), it is shown that the magnetic dipole–field interaction contribution to the third-order polarization can be selectively measured. It is observed that the relationship between the linear polarization PP and CP-PP is similar to that between the linear absorption and circular dichroism. Numerically calculated 2D CP-PP spectra for model systems are presented and compared with the absorption, circular dichroism, and linearly polarized PP spectra.