gebhart/patrepeval huggingface dataset:
Interaction of Designed Sulfated Flavanoids with Antithrombin:  Lessons on the Design of Organic Activators (2002)

Recently, we designed (-)-epicatechin sulfate (ECS), the first small nonsaccharide molecule, as an activator of antithrombin for the accelerated inhibition of factor Xa, a key proteinase of the coagulation cascade (Gunnarsson, G. T.; Desai, U. R. J. Med. Chem. 2002, 45, 1233-1243). Although sulfated flavanoid ECS was found to bind antithrombin with an affinity ( approximately 10.7 microM) comparable to the reference trisaccharide DEF ( approximately 4.5 microM), it accelerated the inhibition of factor Xa only 10-fold as compared to the approximately 300-fold observed with DEF. To determine whether this conformational activation of the inhibitor is dependent on the structure of the organic activator and to probe the basis for the deficiency in activation, we studied the interaction of similar sulfated flavanoids with antithrombin. (+)-Catechin sulfate (CS), a chiral stereoisomer of ECS, bound plasma antithrombin with a 3-fold higher affinity (K(D) = 3.5 microM) and a 2-fold higher second-order rate constant for factor Xa inhibition (k(ACT) = 6750 M(-1) s(-1)). On the contrary, the K(D) and k(ACT) were found to be lower approximately 7.4- and approximately 2.4-fold, respectively, for its racemic counterpart, (+/-)-catechin sulfate. Dependence of the equilibrium dissociation constant on the ionic strength of the medium at pH 6.0 and 7.4 suggests that nonionic interactions contribute a major proportion ( approximately 55-73%) of the total binding energy, and only 1-2 ion pairs, in comparison to the expected approximately 4 ion pairs for the reference trisaccharide, are formed in the interaction. Competitive binding experiments indicate that activator CS does not compete with a saccharide ligand that binds antithrombin in the pentasaccharide binding site, while it competes with full-length low-affinity heparin. A molecular docking study suggests plausible binding of CS in the extended heparin binding site, which is adjacent to the binding domain for the reference trisaccharide DEF. In combination, the results demonstrate that although conformational activation of antithrombin with small sulfated flavanoids is dependent on the structure of the activator, the designed activators do not bind in the pentasaccharide binding site in antithrombin resulting in weak activation. The mechanistic investigation highlights plausible directions to take in the rational design of specific high-affinity organic antithrombin activators.
A Phase 3, Randomized, Double-Blind Comparative Study of the Efficacy and Safety of Topical Recombinant Human Thrombin and Bovine Thrombin in Surgical Hemostasis (2007)

Results of this trial suggest that rhThrombin has comparable efficacy, a similar safety profile, and is considerably less immunogenic than bovine thrombin when used for surgical hemostasis.
Theoretical analysis of effects of blood substitute affinity and cooperativity on organ oxygen transport (2002)

Hemoglobin-based O(2) carriers (HBOCs), which are developed as an alternative to blood transfusion, provide O(2) delivery. At present, there is no model to predict the O(2) transport for a red blood cell-HBOC mixture on a whole organ basis. On the basis of the first principles of mass balance, a model of O(2) transport for an organ was derived to calculate venous Po(2) (Pv(O(2))) for a given inlet arterial Po(2) (Pa(O(2))), blood flow, and oxygen consumption. The model was validated by using several in vivo animal studies on HBOC administration for a wide range of HBOC oxygen-binding parameters and predicted Pv(O(2)) for various Pa(O(2)) in the same species. The model was also used to predict the effect of HBOC affinity and cooperativity on Pv(O(2)) for humans. The results indicate that Pv(O(2)) can be increased at a constant blood flow-to-oxygen consumption ratio by reducing the affinity of HBOC for normoxia and mild hypoxia; however, a high-affinity HBOC would be more efficient in maintaining higher Pv(O(2)) for severe hypoxia (Pa(O(2)) < 40 Torr).
Removal of α-Gal Epitopes in Aortic Valve and Pericardium of Pig Using Green Coffee Bean α-Galactosidase (2008)

Background: It is currently thought that tissue valve degeneration is related to an animal's immune response, which is mainly due to cell surface α-Gal epitopes. Cell surface α-Gal epitopes are known to be degraded by the enzyme called green coffee bean α-galactosidase. It is also well known that α-Gal epitopes are immunologically stained by Griffonia Simplicifolia isolectin type B4. We know that many commercially available tissue valves are made of aortic valves and pericardial tissue of pig. So, we investigated whether α-Gal epitopes of the aortic valve and pericardial tissue of a pig can be removed by green coffee bean α-galactosidase, and we did so by comparing immunologic staining of the tissues before and after the enzyme treatment. Material and method: After treating fresh porcine aortic valve and pericardial tissue with green coffee bean α-galactosidase at concentrations of 0.5 unit/mL, 1.0 unit/mL, 2.0 unit/mL, respectively, under the condition of pH 6.5, temperature 4 o C and 24 hours of incubation, each sample was stained with Griffonia Simplicifolia isolectin type B4 immunofluorescent labeling. We then examined whether the α-Gal epitopes were reduced or abolished in each consecutive concentration of green coffee bean α-galactosidase by comparing the degree of the Griffonia Simplicifolia isolectin B4 staining in each sample. Result: In the pig aortic valve tissue, a 1.0 unit/mL concentration of green coffee bean α-galactosidase at pH 6.5, 4 o C and reaction for 24 hours was enough for complete removal of α-Gal epitopes from the cell surface on the immunostaining with Griffonia Simplicifolia isolectin B4. On the other hand, more α-Gal epitopes were present in the pig pericardial tissue on Griffonia Simplicifolia isolectin B4 staining before the enzyme treatment, and 1.0 unit/mL of galactosidase was not sufficient for complete removal of α-Gal from the tissue. 2.0 units/mL of green coffee bean α-galactosidase was needed to completely remove the α-Gal epitopes from the pericardial tissue on immunostaining. Conclusion: The α-Gal epitopes of the pig's aortic valve and pericardial tissue were successfully stained with Griffonia Simplicifolia isolectin B4. We could remove nearly all the α-Gal epitopes using green coffee bean α-galactosidase at the concentration of 1.0 unit/mL in the aortic valve of pig, and 2.0 unit/mL was need to nearly completely remove all the α-Gal epitopes in the pericardial tissue of pig under the condition of pH 6.5, 4 o C and 24 hours of reaction time. In the near future, removal of α-Gal epitopes in the pig's aortic valve and pericardial tissue will become a powerful tool for the improvement of the tissue valve durability. It needs
IRF4 and its regulators: evolving insights into the pathogenesis of inflammatory arthritis? (2009)

Accumulating evidence from murine and human studies supports a key role for interleukin-17 (IL-17) and IL-21 in the pathogenesis of inflammatory arthritis. The pathways and molecular mechanisms that underlie the production of IL-17 and IL-21 are being rapidly elucidated. This review focuses on interferon regulatory factor 4 (IRF4), a member of the IRF family of transcription factors, which has emerged as a crucial controller of both IL-17 and IL-21 production. We first outline the complex role of IRF4 in the function of CD4(+) T cells and then discuss recent studies from our laboratory that have revealed a surprising role for components of Rho GTPase-mediated pathways in controlling the activity of IRF4. A better understanding of these novel pathways will hopefully provide new insights into mechanisms responsible for the development of inflammatory arthritis and potentially guide the design of novel therapeutic approaches.
Regulators of the Proteasome Pathway, Uch37 and Rpn13, Play Distinct Roles in Mouse Development (2010)

Rpn13 is a novel mammalian proteasomal receptor that has recently been identified as an amplification target in ovarian cancer. It can interact with ubiquitin and activate the deubiquitinating enzyme Uch37 at the 26S proteasome. Since neither Rpn13 nor Uch37 is an integral proteasomal subunit, we explored whether either protein is essential for mammalian development and survival. Deletion of Uch37 resulted in prenatal lethality in mice associated with severe defect in embryonic brain development. In contrast, the majority of Rpn13-deficient mice survived to adulthood, although they were smaller at birth and fewer in number than wild-type littermates. Absence of Rpn13 produced tissue-specific effects on proteasomal function: increased proteasome activity in adrenal gland and lymphoid organs, and decreased activity in testes and brain. Adult Rpn13(-/-) mice reached normal body weight but had increased body fat content and were infertile due to defective gametogenesis. Additionally, Rpn13(-/-) mice showed increased T-cell numbers, resembling growth hormone-mediated effects. Indeed, serum growth hormone and follicular stimulating hormone levels were significantly increased in Rpn13(-/-) mice, while growth hormone receptor expression was reduced in the testes. In conclusion, this is the first report characterizing the physiological roles of Uch37 and Rpn13 in murine development and implicating a non-ATPase proteasomal protein, Rpn13, in the process of gametogenesis.
Two New S-Phase-Specific Genes fromSaccharomyces cerevisiae (1997)

Two new yeast genes, ASF1 (Anti-Silencing Function) and ASF2, as well as a C-terminal fragment of SIR3, were identified as genes that derepressed the silent mating type loci when overexpressed. ASF2 overexpression caused a greater derepression than did ASF1. ASF1 overexpression also weakened repression of genes near telomeres, but, interestingly, ASF2 had no effect on telomeric silencing. Sequences of these two genes revealed open reading frames of 279 and 525 amino acids for ASF1 and ASF2, respectively. The ASF1 protein was evolutionarily conserved, MCB motifs, sequences commonly present upstream of genes transcribed specifically in S phase, were found in front of both genes, and, indeed, both genes were transcribed specifically in the S phase of the cell cycle. While an asf2 mutant was viable and had no obvious phenotypes, an asf1 mutant grew poorly. Neither mutant exhibited derepression of the silent mating type loci. The asf1 mutant was sensitive to methyl methane sulfonate, slightly UV-sensitive and somewhat deficient in minichromosome maintenance. It also lowered the restrictive temperature of a cdc13ts mutant. These phenotypes suggested a role for ASF1 in DNA repair and chromosome maintenance.
A Segmentation-based automatic navigation technique for virtual endoscopy (2005)

Virtual endoscopy (VE) mimics the examination consisting of introducing an endoscope into a tubular structure for diagnostic purposes. One of the main problems in VE is the computation of the navigation path that the virtual camera will travel while producing the animation that will be viewed by the specialist. We propose a technique that allows the automatic computation of navigation paths connecting a starting and one or more end points inside the structure to be visualized. The computation of the path uses the connectedness map produced by the segmentation algorithm that has been used to identify the structure to be visualized in the image. A simple smoothing operation is then applied to this path to produce the final navigation path.
A wavelength scannable XeCl oscillator—ring amplifier laser system (1982)

A holographic grating at grazing angle of incidence was used to achieve tunable, narrow bandwidth (0.005 nm) operation of a XeCl oscillator for injection locking of a ring amplifier. The amplifier’s narrow bandwidth output energy was constant and equal to the untuned, broadband output (∼15 mJ) in regions where injection locking was achieved. Scanning was provided by use of a stepping motor-driven differential micrometer on the tuning mirror. This system was used to produce a laser excitation spectrum of hydroxyl radicals (OH) in a flame.
The Strained η<sup>2</sup>‐<i>N</i><sub>Amido</sub>−<i>N</i><sub>Pyridine</sub> Coordination of Aminopyridinato Ligands (2003)

Abstract This review gives an account of the syntheses and structures of group‐3 (including lanthanides), ‐4 and ‐5 metal complexes stabilised by strained η 2 ‐coordinated aminopyridinato ligands. Reactivity studies and catalytic applications of the coordination compounds are discussed. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
The Relationships between Information Systems Implementation Performance and User Attitude, User Education and Training - Focused on Corporation D - (1998)

This study intends to identify the effects of user attitude, user education & training on the information systems implementation performance. In order to obtain data, survey questionnaires were distributed to the users of 'D' company, the major findings can be summarized as follows. First, it's suggested from the analyses that user attitude and user education & training independently have statistically significant effects on information systems implementation performance. Second, it's revealed that even though the interaction effects by both user attitude and user education & training have positive effects on the level of usage, but have no statistically significant effects on satisfaction level. Based on these results, it's recommended to convert user attitude favorably toward user environment and to increase the level of user education & training, in order to promote information systems implementation performance. Especially, differentiated user education & training are highly recommended.
Repeated Intraperitoneal -Radioimmunotherapy of Ovarian Cancer in Mice (2009)

The aim of this study was to investigate the therapeutic efficacy of alpha-radioimmunotherapy of ovarian cancer in mice using different fractionated treatment regimens. The study was performed using the monoclonal antibody MX35 F(ab')(2) labeled with the alpha-particle emitter (211)At. Methods. Nude mice were intraperitoneally inoculated with ~1 x 10(7) cells of the cell line NIH:OVCAR-3. Four weeks later 6 groups of animals were given 400 kBq (211)At-MX35 F(ab')(2) as a single or as a repeated treatment of up to 6 times (n = 18 in each group). The fractionated treatments were given every seventh day. Control animals were treated with unlabeled MX35 F(ab')(2) (n = 12). Eight weeks posttreatment the animals were sacrificed and the presence of macro- and microscopic tumors and ascites was determined. Results. The tumor-free fractions (TFFs) of the animals, defined as the fraction of animals with no macro- and microtumors and no ascites, were 0.17, 0.11, 0.39, 0.44, 0.44, and 0.67 when treated with 400 kBq (211)At-MX35 F(ab')(2) once or 2, 3, 4, 5, or 6 times, respectively. Repeated treatment 3 times or more resulted in a significantly higher (P < .05) TFF than compared to treatment once or twice. The presence of ascites decreased from 15 out of 18 animals in the group given only one treatment to zero for the 2 groups given 5 or 6 fractions. Treatment with unlabeled MX35 F(ab')(2) resulted in a TFF of zero. Conclusion. Weekly repeated intraperitoneal injections of tolerable amounts of activity of (211)At-MX35 F(ab')(2) of up to 6 times produced increased therapeutic efficacy without observed toxicity, indicating a potential increase of the therapeutic index.
The comparative effectiveness of tumor necrosis factor–blocking agents in patients with rheumatoid arthritis and patients with ankylosing spondylitis: A six‐month, longitudinal, observational, multicenter study (2005)

In this real-life setting, patients with AS experienced improvement in HRQOL that was comparable to, and sometimes greater than, that observed in RA patients. These results support the idea that patients with AS should have the same access to TNF-blocking agents as patients with RA.
DNA Mismatch Repair Gene Polymorphisms Affect Survival in Pancreatic Cancer (2011)

MMR gene variants may have potential value as prognostic markers for OS in pancreatic cancer patients.
Vinylene Carbonate and Li Salicylatoborate as Additives in LiPF[sub 3](CF[sub 2]CF[sub 3])[sub 3] Solutions for Rechargeable Li-Ion Batteries (2003)

Merck KGaA developed (LiFAP) as a new electrolyte that can replace the commonly used in Li-ion batteries. Vinylene carbonate and Li salicylato borate (Merck's AD25) were studied as additives for LiFAP solutions in mixtures of ethylene, dimethyl, and diethyl carbonates with composite graphite and electrodes. The tools for this study included voltammetry (fast and slow scan rates), chronopotentiometry, impedance spectroscopy, electron microscopy, Fourier transform infrared spectroscopy, and X-ray photoelectron spectroscopy. It was found that LiFAP solutions containing VC were superior for both graphite and (spinel) electrodes. The effect of additives on the electrodes' performance can be clearly attributed to their impact on the surface chemistry of these electrodes. © 2003 The Electrochemical Society. All rights reserved.
Efficient malic acid production from glycerol with Ustilago trichophora TZ1 (2016)

This titer is the highest reported for microbial malate production, making U. trichophora TZ1 a promising microbial production host for malate from crude glycerol, especially since it is not genetically engineered. Since this production process starts from an industrial waste stream as substrate and yields an interesting platform chemical, which can be used to replace petro-chemicals, it greatly contributes to a sustainable bio-economy.
[Activity of small intestine alkaline phosphatase in the feces in chronic intestinal diseases]. (1980)

In comparison to normal controls (n = 71) the activity of intestinal alkaline phosphatase in feces is reduced in chronic bowel disease using an immunoprecipitation method: patients with Crohns disease (n = 40) or inactive ulcerative colitis (n = 29) demonstrate small changes of fecal intestinal alkaline phosphate activity in comparison to normal controls. Intestinal alkaline phosphatase is reduced in patients with active ulcerative colitis (n = 11) to 50%, in patients with uraemic enteropathy (n = 18) to 30% and in patients with coeliac disease (n = 14) to 20% of the activity observed in normal controls. During cytostatic treatment of malignant tumors, fecal intestinal alkaline phosphatase activity increases as a sign of toxic damage of the intestinal mucosa.
Advanced sounding: 1. The FMCW alternative (1985)

HF radar employing linear frequency‐modulated continuous wave or “chirp” modulation provides an alternative to the more conventional pulsed amplitude modulation technique in advanced ionosphere sounding. An analysis is presented which shows that the phases of the discrete Fourier components of the receiver output can be used in the same fashion as the phases of pulsed, fixed frequency ionospheric echoes to evaluate the standard digital parameters, including group path by the method of stationary phase. This can be used to overcome the group path/Doppler velocity ambiguity of linear frequency modulation. A description is given of a sounding structure from which unambiguous group range, angle of arrival, O / X mode, and Doppler velocity can be evaluated. A simple error analysis is also given.
The Photo-Fries Rearrangement (2003)

In 1960, Anderson and Reese [1] reported that cathecol monoacetate (1) undergoes rearrangement to 2,3-and 3,4-dihydroxyacetophenone (2 and 3, respectively) upon illumination with ultraviolet (UV) light (Scheme 1). This report was the first one of a long list of articles and reviews [2-16] dealing with the photorrerarrangement of aromatic esters, which was extended to amides, carbonates, carbamates, thioesters, sulfonates, and related compounds.
Effect of Top Electrode Material on Resistive Switching Properties of $\hbox{ZrO}_{2}$ Film Memory Devices (2007)

The influence of top electrode material on the resistive switching properties of ZrO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> -based memory film using Pt as a bottom electrode was investigated in this letter. In comparison with Pt/ZrO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /Pt and Al/ZrO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /Pt devices, the Ti/ZrO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /Pt device exhibits different resistive switching current-voltage (I- V) curve, which can be traced and reproduced by a dc voltage more than 1000 times only showing a little decrease of resistance ratio between high and low resistance states. Furthermore, the broad dispersions of resistive switching characteristics in the Pt/ZrO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /Pt and Al/ZrO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /Pt devices are generally observed during successive resistive switching, but those dispersions are suppressed by the device using Ti as a top electrode. The reliability results, such as cycling endurance and continuous readout test, are also presented. The write-read-erase-read operations can be over 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> cycles without degradation. No data loss is found upon successive readout after performing various endurance cycles
Ionization efficiency data and fragmentation mechanisms for ferrocene, nickelocene, and ruthenocene (1972)

Ionization efficiency (lE) data for the M+, MCp+, and MCp2+ ions of ferrocene (FeCp2), nickelocene (NiCp2), and ruthenocene (RuCp2) are interpreted by a deconvolution–convolution technique to yield ionic bond dissociation energies in the 6–7 eV range for D(CpM+–Cp) and in the 4–5 eV range for D(M+–Cp). Additional direct experimental evidence in support of these values was obtained from lE data for appropriate metastable ion transitions.Probable errors in the interpretation of lE data for other molecular systems are discussed with reference to the approach for metallocenes presented here.
microRNA-34 family and treatment of cancers with mutant or wild-type p53 (Review) (2011)

In the last decade, microRNAs (miRNAs; small noncoding RNA molecules) as post-transcriptional regulators have been a hotspot in research for their involvement in biological processes and tumour development. However, there have been few reviews focusing on a single miRNA family. The dysregulation of miRNAs appears to play a crucial role in cancer pathogenesis where they exert their effect as oncogenes or as tumour suppressors. This review summarises current studies on the dysregulation of the microRNA-34 (miR-34) family in different types of cancers and its role in the p53 network. The structure of the miR-34 family members includes p53-binding sites reflecting their function as tumour suppressors downstream of the p53 pathway. miR-34 dysregulation occurs in cancers, including several epithelial cancers, melanomas, neuroblastomas, leukemias and sarcomas, in the presence or absence of the p53 mutation. For these cancers, functional restoration of miR-34 is a useful novel therapy. As evidenced from preclinical and clinical studies, the miR-34 family plays an important role in the treatment of miR-34-dysregulated cancers with mutant or wild-type p53. This review will have a potential impact in the clinical treatment of p53-mutant and/or miR-34-dysregulated cancers using a miR-34 restoration approach.