gebhart/patrepeval huggingface dataset:
The structure of residues 7-16 of the A alpha-chain of human fibrinogen bound to bovine thrombin at 2.3-A resolution. (1992)

The tetradecapeptide Ac-D-F-L-A-E-G-G-G-V-R-G-P-R-V-OMe, which mimics residues 7f-20f of the A alpha-chain of human fibrinogen, has been co-crystallized with bovine thrombin from ammonium sulfate solutions in space group P2(1) with unit cell dimensions of a = 83.0 A, b = 89.4 A, c = 99.3 A, and beta = 106.6 degrees. Three crystallographically independent complexes were located in the asymmetric unit by molecular replacement using the native bovine thrombin structure as a model. The standard crystallographic R-factor is 0.167 at 2.3-A resolution. Excellent electron density could be traced for the decapeptide, beginning with Asp-7f and ending with Arg-16f in the active site of thrombin; the remaining 4 residues, which have been cleaved from the tetradecapeptide at the Arg-16f/Gly-17f bond, are not seen. Residues 7f-11f at the NH2 terminus of the peptide form a single turn of alpha-helix that is connected by Gly-12f, which has a positive phi angle, to an extended chain containing residues 13f-16f. The major specific interactions between the peptide and thrombin are 1) a hydrophobic cage formed by residues Tyr-60A, Trp-60D, Leu-99, Ile-174, Trp-215, Leu-9f, Gly-13f, and Val-15f that surrounds Phe-8f; 2) a hydrogen bond linking Phe-8f NH to Lys-97 O;3) a salt link between Glu-11f and Arg-173; 4) two antiparallel beta-sheet hydrogen bonds between Gly-14f and Gly-216; and 5) the insertion of Arg-16f into the specificity pocket. Binding of the peptide is accompanied by a considerable shift in two of the loops near the active site relative to human D-phenyl-L-prolyl-L-arginyl chloromethyl ketone (PPACK)-thrombin.
Differential space-time multi-block decoding (2003)

In this paper, we consider the maximum-likelihood multi-block decoding in differential space-time block coding systems. Since the computational complexity of the maximum-likelihood multi-block detector increases exponentially as a function of the number of signal blocks used in the decoding, a trellis-based Viterbi algorithm is proposed to implement multi-block space-time decoding without an increase in the computational complexity in each new branch-metric evaluation stage. It is demonstrated that by increasing the number of blocks, one can more efficiently utilize the differential coding relationship in the decoding process. A forgetting factor is further introduced into the maximum-likelihood decoding and the corresponding branch-metric is derived. Numerical results are presented to demonstrate the effects of fading rate, the value of the forgetting factor, and the number of comparative paths on the performance of the proposed approaches.
Somatostatin Acts by Inhibiting the Cyclic 3′,5′-Adenosine Monophosphate (cAMP)/Protein Kinase A Pathway, cAMP Response Element-Binding Protein (CREB) Phosphorylation, and CREB Transcription Potency (1997)

Somatostatin (SRIF) was discovered as an inhibitor of GH secretion from pituitary somatotroph cells. SRIF analogs are very effective agents used to treat neuroendocrine tumors and are now being used with increasing frequency in clinical trials to treat more aggressive malignancies. However, the cellular components mediating SRIF signal transduction remain largely unknown. We have stably overexpressed the SRIF type 2 receptor (SST2) in GH4 rat somatomammotroph cells, establishing a physiologically relevant model system. In this model, the SRIF analog, BIM23014, inhibited forskolin-induced cAMP accumulation, protein kinase A activation, cAMP response element-binding protein phosphorylation, and Pit-1/GHF-1 promoter activation in an okadaic acid-insensitive manner. Pertussis toxin inhibited the effects of BIM23014, documenting that SST2 signaling was coupled to Gi. Moreover, the inhibitory effects of BIM23014 were reversed by overexpression of protein kinase A catalytic subunit, indicating that SRIF does not act via serine/threonine phosphatases, but, rather, by lowering protein kinase A activity. These data define the components of the SRIF/SST2 receptor signaling pathway and provide important mechanistic insights into how SRIF controls neuroendocrine tumors. As SRIF analogs are effective antitumor agents, and many other related compounds are in development, the knowledge gained here will further our understanding of their mechanism of action in other malignancies as well.
Structures of the asparagine-linked sugar chains of human chorionic gonadotropin produced in choriocarcinoma. Appearance of triantennary sugar chains and unique biantennary sugar chains. (1983)

Human chorionic gonadotropin (hCG) highly purified from urine of the patient with choriocarcinoma contains four asparagine-linked sugar chains in one molecule. The sugar chains were quantitatively liberated as radioactive oligosaccharides from polypeptide portion by hydrazinolysis followed by N-acetylation and NaB3H4 reduction. The structures of these sugar chains were determined by the combination of sequential glycosidase digestion, periodate oxidation, and methylation analysis. As compared with the sugar chains of normal urinary and placental hCG reported previously, they include several prominent structural differences. More than 97% of the sugar chains of choriocarcinoma hCG was free from sialic acid, while the sugar chains of normal hCG were mostly sialylated. Choriocarcinoma hCG contains unusual biantennary complex-type sugar chains in addition to regular tri-, bi-, and monoantennary sugar chains. These sugar chains have two outer chains linked at the C-2 and C-4 positions of the same alpha-mannosyl residue of the trimannosyl core. Since normal hCG does not contain any triantennary sugar chains, occurrence of Gal beta 1 leads to 4GlcNAc beta 1 leads to 4Man alpha 1 leads to group is another characteristic feature of the sugar chains of choriocarcinoma hCG. The evidence that the monoantennary sugar chain of Man alpha 1 leads to 6(Gal beta 1 leads to 4GlcNAc beta 1 leads to 2Man alpha 1 leads to 3)Man beta 1 leads to 4GlcNAc beta 1 leads to 4(Fuc alpha 1 leads to 6)GlcNAc leads to Asn is not found in normal hCG and the sum total of fucosylated sugar chains is 50%, which is twice as much as normal hCG, indicated that fucosylation is also modified in choriocarcinoma tissue.
Optimal transmission modes by simulated annealing (2011)

We address the problem of finding efficient combinations of transmitting links between nodes distributed as a spatial Poisson process in an infinite plane using a stochastic optimization method called simulated annealing. A simple Boolean interference model with the interference radius equaling the transmission radius is used to verify the operation of the method. The same approach is then applied to SINR-determined data rates. The obtained numerical results shed light on the spatial reuse problem in wireless multihop networks. In particular, for the SINR-based interference model we obtain new results. We characterize the asymptotic behavior of the sum capacity of the optimal combination of transmitting links and the fraction of transmitting nodes in the low and high interference regimes. Additionally, the numerical results establish, in the interference-limited case of high node densities, the sum capacity (spectral efficiency) to be approximately equal to 1.2 bit/s/Hz per node.
Regulatory Properties and Subunit Structure of Chick Embryo Deoxycytidylate Deaminase (1968)

Abstract Evidence has been presented that chick embryo deoxycytidylate deaminase (EC 3.5.4.12) is capable of undergoing structural changes under a variety of conditions. Rate studies revealed that inhibition of the enzyme by ethylenediaminetetraacetate markedly diminishes at 10° and below. Although EDTA does not inhibit the deaminase at 10°, the inhibition by urea, N-ethylmaleimide, and 5,5'-dithiobis(2-nitrobenzoic acid) is dramatically enhanced in its presence. End product inhibition by deoxythymidine 5'-triphosphate, shown to be both pH and concentration dependent, is completely eliminated at 10° by EDTA. The reversal of deoxythymidine 5'-triphosphate inhibition by deoxycytidine 5'-triphosphate is markedly sigmoidal, emphasizing the regulatory interaction of these ligands. Hill constants for the reaction of the enzyme with substrate in the presence of deoxycytidine 5'-triphosphate and deoxythymidine 5'-triphosphate are 1.0 and 4.0, respectively. The Hill constant for the homotropic reaction of deoxycytidine 5'-monophosphate with the deaminase at 30° is 4.0, whereas that at 10° is 2.8. The apparent Km value for the activation of the deaminase by deoxycytidine 5'-triphosphate is 2.12 x 10-4 mm. The subunit structure of the deaminase is emphasized by its conversion from an s0.72520,w value of 6.78 in the presence of deoxycytidine 5'-triphosphate to a value of 3.63 S in the presence of deoxythymidine 5'-triphosphate. The latter form of the enzyme is inactive when assayed in the absence of mercaptoethanol. Deoxycytidine 5'-triphosphate and, to a lesser extent, deoxythymidine 5'-triphosphate and deoxyguanosine 5'-monophosphate protect the deaminase rather strikingly from inactivation by trypsin. The low molecular weight, inactive form, of the enzyme is not protected under similar circumstances.
T-cell and natural killer cell therapies for hematologic malignancies after hematopoietic stem cell transplantation: enhancing the graft-versus-leukemia effect (2015)

Hematopoietic stem cell transplantation has revolutionized the treatment of hematologic malignancies, but infection, graft-versus-host disease and relapse are still important problems. Calcineurin inhibitors, T-cell depletion strategies, and immunomodulators have helped to prevent graft-versus-host disease, but have a negative impact on the graft-versus-leukemia effect. T cells and natural killer cells are both thought to be important in the graft-versus-leukemia effect, and both cell types are amenable to ex vivo manipulation and clinical manufacture, making them versatile immunotherapeutics. We provide an overview of these immunotherapeutic strategies following hematopoietic stem cell transplantation, with discussions centered on natural killer and T-cell biology. We discuss the contributions of each cell type to graft-versus-leukemia effects, as well as the current research directions in the field as related to adoptive cell therapy after hematopoietic stem cell transplantation.
The Efficacy and Safety of Lixivaptan in Outpatients with Heart Failure and Volume Overload: Results of a Multicentre, Randomized, Double-Blind, Placebo-Controlled, Parallel-Group Study (2012)

NCT01055912.
Fabrication and characterization of a nanoelectromechanical switch with 15-nm-thick suspension air gap (2008)

We developed titanium nitride (TiN) based nanoelectromechanical (NEM) switch with the smallest suspension air-gap thickness ever made to date by a “top-down” complementary metal-oxide semiconductor fabrication methods. Cantilever-type NEM switch with a 15-nm-thick suspension air gap and a 35-nm-thick TiN beam was successfully fabricated and characterized. The fabricated cantilever-type NEM switch showed an essentially zero off current, an abrupt switching with less than 3mV/decade, and an on/off current ratio exceeding 105 in air ambient. Also achieved was an endurance of over several hundreds of switching cycles under dc and ac biases in air ambient.
Further evidence that 5‐HT‐induced relaxation of pig pulmonary artery is mediated by endothelial 5‐HT<sub>2B</sub> receptors (2000)

The endothelial 5-HT receptor mediating relaxation of pig pulmonary artery has been characterized using the selective 5-HT(2B) receptor agonist BW 723C86 and a variety of structurally diverse 5-HT receptor antagonists. If arterial rings with intact endothelium were precontracted with prostaglandin F(2alpha) (3 microM), BW 723C86 caused concentration-dependent relaxation with a pEC(50)=8.21+/-0.03 and E(max)=89+/-4% relative to 5-HT. The relaxant responses to BW 723C86 were inhibited by the 5-HT(2B) receptor antagonist SB 204741, the 5-HT(2B/2C) receptor antagonist SB 206553 and the antimigraine drug pizotifen, yielding pA(2) values of 6.68, 7.20 and 8.32, respectively. The pA(2) values against BW 723C86 were similar to those determined against 5-HT. The relaxant effect of 5-HT was antagonized by a variety of 22 compounds of diverse chemical structures. Based on the calculated mean pA(2) values the order of the most potent antagonists was ritanserin (9.38) > methysergide (8. 86) > pizotifen (8.47) >/= methiothepin (8.32) > LY 53857 (7.84) >/= amoxapine (7.80) >/= loxapine (7.73) >/= metergoline (7.64) >/= mianserin (7.51) >/= rauwolscine (7.39). Compounds with weak blocking potency were yohimbine (6.37), spiperone (5.88) and ketanserin (5.85). Correlation analysis between the affinities of the antagonists in pig pulmonary artery and those from radioligand binding studies at human and rat 5-HT(2B) receptors showed a highly significant correlation (r=0.95 and 0.84, P<0.002 and <0.005). Correlation with 5-HT(2C) receptors was much lower (r=0.57, P=0.035), and no correlations were obtained with 5-ht(6) and 5-HT(7) receptors. It is concluded that the 5-HT receptor mediating endothelium-dependent relaxation of pig pulmonary artery is of the 5-HT(2B) subtype.
Design of locally stable sliding modes in bidirectional switching converters (2002)

A method to select the coefficients of a sliding surface for a specified dynamic response of a bidirectional switching converter is presented. After obtaining the coordinates of the equilibrium point, poles assignment for the desired sliding dynamics provides the control parameters. A boost structure and a Cuk converter illustrate the application of the procedure.
Theory of the Dynamic Vibration Neutralizer With Motion-Limiting Stops (1972)

The exact solution for the steady-state motion of a dynamic vibration neutralizer with motion-limiting stops attached to a sinusoidally excited primary system is derived analytically, and its asymptotically stable regions are determined. Simulated motion on a digital computer and experimental studies with an analog computer corroborate the predictions of the theory. Results of the analysis are applied to modified vibration neutralizers, Lanchester dampers, and impact dampers. It is shown that the incorporation of properly designed motion-limiting stops into the auxiliary mass system will enhance the performance of the foregoing dampers.
Quantum theory of human communication (2004)

We use notions and techniques of Quantum Field Theory to formulate and investigate basic concepts and mechanisms of human communication. We start with attitudes which correspond to photons frequencies, then we introduce states-of-mind which correspond to wave functions. Finally, by way of the second quantization, we come to states-of-opinions which correspond to states of quantized radiation fields. In the present paper we shall only investigate superpositions of pairs of coherent states (e.g. the government and the opposition in a democratic country).
On the Editing Standardization of Sci-tech Journal Papers (2010)

The editing standardization of sci-tech journal papers has played an important role in improving the scientific and technical interchange and information propaganda.This paper summarizes contents of the editing standardization of sci-tech journals papers,and,expounds the details in editing sci-tech journals papers for more standardization.
Histologic Evaluation of Autogenous Connective Tissue and Acellular Dermal Matrix Grafts in Humans (2005)

Although CT and ADM have a slightly different histological appearance, both can successfully be used to cover denuded roots with similar attachments and no adverse healing.
Microwave photon counting at room temperature (2008)

We demonstrate efficient upconversion of sub-THz radiation into the optical domain in a high-Q whispering gallery mode resonator with quadratic optical nonlinearity. The 5x10^{-3} power conversion efficiency of continuous wave 100GHz signal is achieved with only 16 mW of optical pump.
Synthesis of the First α‐Methylene‐β‐peroxylactone—Regiospecific Ene Reaction of <sup>1</sup>O<sub>2</sub> with α,β‐Unsaturated Carboxylic Acids (1985)

5-Methyl-4-methylene-1,2-dioxolane-3-one 2 exhibits unexpectedly high thermal stability. The first α-methylene-β-peroxylactone was obtained by regiospecific photooxygenation of the α,β-unsaturated carboxylic acid 1 to give the hydroperoxide followed by acid-catalyzed dehydration.
Determination of the amino acid sequence of an intramolecular disulfide linkage‐containing sperm‐activating peptide by tandem mass spectrometry (1991)

A sperm-activating peptide (SAP) was isolated from the egg jelly of the sea urchin Stomopneustes variolaris. The presence of an intramolecular disulfide linkage in the peptide was demonstrated by fast atom bombardment (FAB) mass spectrometry with the intact and reduced peptides. The amino acid sequence of the reduced peptide was determined to be Lys-Phe-Cys-Pro-Glu-Gly-Lys-Cys-Val by tandem mass spectrometry from the spectrum produced by a collision-induced decomposition method. Furthermore, it was also demonstrated that SAPs obtained from sea urchins Arbacia punctulata and Glyptocidaris crenularis are cyclic peptides containing one cystine residue by FAB mass spectrometry.
Pretreatments for enhancing clarification efficiency of depth filtration during production of monoclonal antibody therapeutics (2020)

High cell density, high product titer mammalian cell culture is the new paradigm for production of recombinant proteins. While the typical motivation is to get a high product titer, additional undesirable outcomes often include an increase in percentage solids in the cell culture fluid (cellular debris and sub-micron colloids), thereby offering new challenges to downstream processing. This article focuses on scouting and comparison of different approaches used for clarification of cell culture fluid. The approaches include centrifugation followed by depth filtration, direct depth filtration without centrifugation and feed pretreatment with use of specially designed density gradient filtration to improve efficiency of clarification and removal of process contaminants from feed stream. The work also evaluates impact of three different pretreatment approaches, namely pH adjustment to acidic condition, metal cation (calcium phosphate) flocculation, and polycationic polymer flocculation (using polymer-I and polymer-II). The results obtained indicate that the use of pretreatment significantly improves the clarification efficiency of depth filtration. Pretreatment options like polycationic polymer-I based flocculation resulted in a >5 fold reduction in filter area requirement as well as >6 fold reduction in HCDNA while retaining acceptable recovery of the IgG (>98%). Thus, pretreatment offers a significant reduction in the depth filtration footprint (~5-6 fold decrease in filter area requirement). However, one must take into consideration the process development time required, capital cost, consumable cost, cost of the pretreatment chemical, cost of testing to demonstrate clearance of treatment agent, ease of scale-ability, and process robustness when finalizing the optimal clarification approach.
Applying Empirical Data on Upper Torso Movement to Real-time Collision-free Reach Tasks (2005)

<div class="htmlview paragraph">Simulating human reach is still challenging when considering complex interactions with the environment. Standard approaches involve inverse kinematics (IK) methods and usually require a complete but exponential cost search in configuration space. In ergonomic applications, both “naturalness” and interactive performance are important. We describe a real-time, collision-free, sternum-rooted IK solution for an articulated human figure based on motion capture data, human strength models, and multi-joint coordination functions. Movement paths are discovered through spatial search in a partitioned workspace. The system generates natural collision-free reach motions in real-time. The resulting animations and statistics demonstrate the efficacy of this approach.</div>
Optimization of scannable latches for low energy (2003)

This paper covers a range of issues in the design of latches and flip-flops for low-power applications. First it revisits, extends, and improves the energy-performance optimization methodology, attempting to make it more formal and comprehensive. The data-switching factor and the glitching activity are taken into consideration, using a formal analytical approach, then a notion of an energy-efficient family of configurations is introduced to make the comparison of different latch styles in the energy-performance space more fair. A recently proposed methodology for balancing hardware intensity in processor pipelines is applied to latch design to facilitate the selection of the objective function for tuning transistor sizes. The power dissipation of the clock distribution is taken into account, supported by simulations of extracted netlists for multibit datapath registers. Practical issues of building a low overhead scan mechanism are considered, and the power overhead of the scannable design is analyzed. A low-power level-sensitive scan mechanism is proposed, and results of a comparative study of scannable latches are shown. The applicability of the proposed scan mechanism to a wide variety of latches is demonstrated.
Real-Space Observation of Short-Period Cubic Lattice of Skyrmions in MnGe (2015)

Three-dimensional forms of skyrmion aggregate, such as a cubic lattice of skyrmions, are anticipated to exist, yet their direct observations remain elusive. Here, we report real-space observations of spin configurations of the skyrmion-antiskyrmion cubic-lattice in MnGe with a very short period (∼3 nm) and hence endowed with the largest skyrmion number density. The skyrmion lattices parallel to the {100} atomic lattices are directly observed using high-resolution Lorentz transmission electron microscopes, simultaneously with underlying atomic-lattice fringes.
Genomic Object Net: Object Oriented Representation of Biological Systems (2000)

One of the most important and interesting topic in the field of bioinformatics is to develop the tool simulating biological phenomenon such as gene expressions and biochemical reactions. The required conditions for realizing the effective simulation tool are 1) Acceptable technical expression of the tool to biologists, 2) Easy to describe biological facts and biological phenomenon on computers, 3) Easy to get the tool through Internet, and 4) Easy to simulate the biological phenomenon on the tool. Our solution to the problems is “exploiting hybrid Petri net (HPN) technique for describing biological systems”. In [1], we showed that, by using HPN, the genetic switch mechanism of λ phage can be realized on computer in a natural manner, and protein and mRNA concentrations of the mechanism can be successfully simulated by using Visual Object Net++ (Figure 1) [2] which is a general purpose system description tool based on HPN technique. The evaluation version of Visual Object Net++ can be downloaded from the site [2]. In this software demonstration, we will show the following examples of biological systems describing and simulating on Visual Object Net++; 1) Circadian rhythms in Drosophila, 2) Delta-Notch lateral inhibitory, and 3) Apoptosis induced by protein Fas. We then introduce our next strategy “Genomic Object Net Project” which may lead us to the development of new efficient bio-simulation tools.