gebhart/patrepeval huggingface dataset:
Charge Transport in DNA Oligonucleotides with Various Base-Pairing Patterns (2010)

We combined various experimental (scanning tunneling microscopy and Raman spectroscopy) and theoretical (density functional theory and molecular dynamics) approaches to study the relationships between the base-pairing patterns and the charge transfer properties in DNA 32-mer duplexes that may be relevant for identification and repair of defects in base pairing of the genetic DNA and for DNA use in nanotechnologies. Studied were two fully Watson-Crick (W-C)-paired duplexes, one mismatched (containing three non-W-C pairs), and three with base pairs chemically removed. The results show that the charge transport varies strongly between these duplexes. The conductivity of the mismatched duplex is considerably lower than that of the W-C-paired one despite the fact that their structural integrities and thermal stabilities are comparable. Structurally and thermally much less stable abasic duplexes have still lower conductivity but not markedly different from the mismatched duplex. All duplexes are likely to conduct by the hole mechanism, and water orbitals increase the charge transport probability.
Basic Studies for Continuous Production of L-Aspartic Acid by Immobilized <i>Escherichia coli</i> Cells (1974)

By using a column packed with immobilized Escherichia coli cells entrapped in a polyacrylamide gel lattice, conditions for continuous production of L-aspartic acid from ammonium fumarate were investigated. When a solution of 1 M ammonium fumarate (pH 8.5) containing 1 mM Mg 2+ was passed through the immobilized cell column at a flow rate of space velocity (SV) = 0.8 at 37 C, the highest rate of reaction was attained. From the column effluents, L-aspartic acid was obtained in good yield. The immobilized cell column was very stable.
Comparison of Botulinum Toxins A and B in the Aesthetic Treatment of Facial Rhytides (2003)

Botulinum toxin injections have become a popular treatment for minimizing or eliminating facial wrinkles. After injection, the toxin acts to paralyze or weaken facial mimetic muscles. Two antigenically distinct serotypes, botulinum toxin type A (BTX-A) and botulinum toxin type B (BTX-B), are currently available. BTX-A is a lyophilized powder preparation requiring reconstitution; BTX-B is a ready-to-use liquid formulation. Both agents produce the same resultant clinical effect (i.e., muscle weakening). However, in addition to differences with respect to formulation, they are pharmacologically distinct in terms of molecular size, cellular mechanism of action, and species sensitivity. BTX-A has been used for aesthetic purposes for more than 10 years. Clinical studies and observations have shown that it is an effective agent for treating hyperkinetic facial lines. BTX-B was approved for use in cervical dystonia in 2000, but it has been used off-label to treat facial wrinkles as reported in several open-label studies. These preliminary dose-ranging studies have demonstrated that BTX-B is also effective. Both agents are extremely safe nonsurgical modalities for hyperkinetic facial lines. This article reviews the pharmacology and molecular features of BTX-A and BTX-B and highlights some of the key clinical studies that have been published to date with these two agents.
Towards supported catalyst models: the synthesis, characterization, redox chemistry, and structures of the complexes Ti(OAr′)<sub>4</sub> (Ar′ = C<sub>6</sub>H<sub>4</sub>(2-<i>t</i>-Bu), C<sub>6</sub>H(2,3,5,6-Me)<sub>4</sub>) (1991)

Reaction of substituted phenoxides with TiCl 4 affords the species Ti(OAr′) 4 (Ar′ = C 6 H 4 (2-t-Bu), 1; Ar′ = C 6 H(2,3,5,6-Me) 4 , 2). The compound Ti(OC 6 H 4 (2-t-Bu)) 4 , 1, crystallizes in the tetragonal space group [Formula: see text], with a = 15.203(4) Å, c = 8.026(3) Å, Z = 2, and V = 1855(2) Å 3 . The compound Ti(OC 6 H(2,3,5,6-Me) 4 ) 4 , 2, crystallizes in the orthorhombic space group Pbcn, with a = 16.539(7) Å, b = 16.136(6) Å, c = 27.716(12) Å, Z = 8, and V = 7397(9) Å 3 . The geometry of the Ti coordination sphere in these complexes is best described as pseudo-tetrahedral. In the case of 1 strict crystallographic [Formula: see text] symmetry is imposed. The complex 2 exhibits reversible cyclic voltammetric behaviour consistent with a one electron reduction to the Ti(III) analogue. Chemical reduction of 2 employing sodium amalgam affords the quantitative formation of (C 6 H(2,3,5,6-Me) 4 O) 2 Ti(μ-OC 6 H(2,3,5,6-Me) 4 ) 2 Na(THF) 2 , 3. The reaction of 3 with [(COD)Rh(μ-Cl)] 2 does not afford the Ti(III)/Rh(I) early–late heterobimetallic (ELHB) complex (C 6 H(2,3,5,6-Me) 4 O) 2 Ti(μ-OC 6 H(2,3,5,6-Me) 4 ) 2 Rh(COD). The nature of all products is not known; however, redox chemistry, in which electron transfer from Ti(III) to Rh(I) occurs is evidenced by the generation of 2 and Rh(0). In addition, ligand transfer reactions giving uncharacterized Rh-alkoxides are suggested by the spectral data. The implications and ramifications for the synthesis of alkoxide bridged ELHB models of bimetallic heterogeneous catalyst systems are discussed. Key words: titanium phenoxides, redox chemistry, structures.
A multiresolution color clustering approach to image indexing and retrieval (2002)

We propose a multiresolution color feature extraction scheme based on octree data structure to achieve efficient and robust image retrieval. With the proposed method, multiple color features, including the dominant color, the number of distinctive colors and the color histogram, can be naturally integrated into one framework. A selective filtering strategy is also described to speed up the retrieval process. Retrieval examples are given to illustrate the performance of the proposed approach.
Synthesis of Fulleropyrrolidines under Microwave Irradiation (2004)

In recent years, considerable efforts have been devoted to the development of systems in which C60 is covalently linked to an electron donor.[1] Studies[2] on intermolecular photoinduced electron transfer between C60 and triphenyl amine show that triphenyl amine is a good donor. It is envisaged that the use of donor segments consisting of either pyrrole/aniline may extend the lifetime of charge-separated state.[3] Since Gedye[4] demonstrated that many organic reactions can be conducted rapidly under microwave irradiation, here we have successfully synthesized five new fulleropyrrolidines containing triphenyl amine or thiophene dyads under microwave irradiation, which are different from traditional heating. The determination of structures of these fulleropyrrolidines is in progress. On the other hand, we have studied the geometry, electronic structures and frontier orbitals of these N-methyl-pyrrolo[3,4]C60 derivatives by using AM1semiempirical quantum calculation method. The results indicate that there exists strong intramolecular electron transfer in them.……
Coordinated regulation of platelet actin filament barbed ends by gelsolin and capping protein. (1996)

Exposure of cryptic actin filament fast growing ends (barbed ends) initiates actin polymerization in stimulated human and mouse platelets. Gelsolin amplifies platelet actin assembly by severing F-actin and increasing the number of barbed ends. Actin filaments in stimulated platelets from transgenic gelsolin-null mice elongate their actin without severing. F-actin barbed end capping activity persists in human platelet extracts, depleted of gelsolin, and the heterodimeric capping protein (CP) accounts for this residual activity. 35% of the approximately 5 microM CP is associated with the insoluble actin cytoskeleton of the resting platelet. Since resting platelets have an F-actin barbed end concentration of approximately 0.5 microM, sufficient CP is bound to cap these ends. CP is released from OG-permeabilized platelets by treatment with phosphatidylinositol 4,5-bisphosphate or through activation of the thrombin receptor. However, the fraction of CP bound to the actin cytoskeleton of thrombin-stimulated mouse and human platelets increases rapidly to approximately 60% within 30 s. In resting platelets from transgenic mice lacking gelsolin, which have 33% more F-actin than gelsolin-positive cells, there is a corresponding increase in the amount of CP associated with the resting cytoskeleton but no change with stimulation. These findings demonstrate an interaction between the two major F-actin barbed end capping proteins of the platelet: gelsolin-dependent severing produces barbed ends that are capped by CP. Phosphatidylinositol 4,5-bisphosphate release of gelsolin and CP from platelet cytoskeleton provides a mechanism for mediating barbed end exposure. After actin assembly, CP reassociates with the new actin cytoskeleton.
Implementing TMB measurement in clinical practice: considerations on assay requirements (2019)

Clinical evidence demonstrates that treatment with immune checkpoint inhibitor immunotherapy agents can have considerable benefit across multiple tumours. However, there is a need for the development of predictive biomarkers that identify patients who are most likely to respond to immunotherapy. Comprehensive characterisation of tumours using genomic, transcriptomic, and proteomic approaches continues to lead the way in advancing precision medicine. Genetic correlates of response to therapy have been known for some time, but recent clinical evidence has strengthened the significance of high tumour mutational burden (TMB) as a biomarker of response and hence a rational target for immunotherapy. Concordantly, immune checkpoint inhibitors have changed clinical practice for lung cancer and melanoma, which are tumour types with some of the highest mutational burdens. TMB is an implementable approach for molecular biology and/or pathology laboratories that provides a quantitative measure of the total number of mutations in tumour tissue of patients and can be assessed by whole genome, whole exome, or large targeted gene panel sequencing of biopsied material. Currently, TMB assessment is not standardised across research and clinical studies. As a biomarker that affects treatment decisions, it is essential to unify TMB assessment approaches to allow for reliable, comparable results across studies. When implementing TMB measurement assays, it is important to consider factors that may impact the method workflow, the results of the assay, and the interpretation of the data. Such factors include biopsy sample type, sample quality and quantity, genome coverage, sequencing platform, bioinformatic pipeline, and the definitions of the final threshold that determines high TMB. This review outlines the factors for adoption of TMB measurement into clinical practice, providing an understanding of TMB assay considerations throughout the sample journey, and suggests principles to effectively implement TMB assays in a clinical setting to aid and optimise treatment decisions.
Incoherent acquisition of DSSS signals in presence of Doppler shifts (2002)

Code synchronization in direct-sequence spread-spectrum (DSSS) receivers can be divided into the acquisition and the tracking phases. Here we assume that the acquisition is performed with a periodic pseudo-random signal of period N. Acquisition of pseudo-random signals is similar to target detection with a pulse compression radar. The appropriate tool for the description of a pulse compression radars behaviour is the ambiguity function. The present paper describes the code acquisition in DSSS receivers in terms of cross ambiguity functions. Moreover the importance of the merit factor for incoherent acquisition is represented. The signal to interference ratio and an equation giving the optimum matched filter length as a function of the Doppler shift is derived.
A decision-directed symbol timing recovery circuit for ATSC digital TV receivers (1999)

We present and analyze a full-digital decision-directed symbol timing recovery circuit based on the double-sampling maximum-likelihood estimator. Intended for the ATSC digital TV system, the proposed scheme works independently of the segment synchronization by extracting timing information from the randomized data symbols even in the extremely small roll-off case. With the proposed method we get not only quick synchronization, but also robust timing recovery with reduced timing jitter compared to the conventional correlation method. The simulation is performed using the 8-level PAM signal, and evaluated in terms of the steady-state timing jitter under AWGN and multipath ghost channels. Additionally, initial timing acquisition and segment synchronization performance are also shown.
Adaptive ground bounce removal (2001)

An adaptive ground bounce (GB) removal algorithm is presented for landmine detection with a downward looking stepped frequency ground penetrating radar (GPR). The main idea is to estimate and eliminate the GB from a given scan as a shifted and scaled version of an adaptively estimated reference GB. Experimental results are provided to demonstrate that the new algorithm outperforms existing approaches.
Pulmonary vascular resistance and compliance relationship in pulmonary hypertension (2015)

Right ventricular adaptation to the increased pulmonary arterial load is a key determinant of outcomes in pulmonary hypertension (PH). Pulmonary vascular resistance (PVR) and total arterial compliance (C) quantify resistive and elastic properties of pulmonary arteries that modulate the steady and pulsatile components of pulmonary arterial load, respectively. PVR is commonly calculated as transpulmonary pressure gradient over pulmonary flow and total arterial compliance as stroke volume over pulmonary arterial pulse pressure (SV/PApp). Assuming that there is an inverse, hyperbolic relationship between PVR and C, recent studies have popularised the concept that their product (RC-time of the pulmonary circulation, in seconds) is "constant" in health and diseases. However, emerging evidence suggests that this concept should be challenged, with shortened RC-times documented in post-capillary PH and normotensive subjects. Furthermore, reported RC-times in the literature have consistently demonstrated significant scatter around the mean. In precapillary PH, the true PVR can be overestimated if one uses the standard PVR equation because the zero-flow pressure may be significantly higher than pulmonary arterial wedge pressure. Furthermore, SV/PApp may also overestimate true C. Further studies are needed to clarify some of the inconsistencies of pulmonary RC-time, as this has major implications for our understanding of the arterial load in diseases of the pulmonary circulation.
Modeling and simulation of the assembly of snap joints (2002)

Snap fasteners are being increasingly used as joints for parts mating. Due to their simple fitting, the application of snap joints has become widespread in automated assembly. Two aspects are important concerning the design of snap joints, mating forces during the assembly and forces during the disassembly. The former have to be applied for the insertion and the latter are responsible for the function of the snap fit. In this paper the authors present the modeling and the simulation of the insertion and the extraction of snap fasteners. Therefore the authors are able to predict the forces and moments acting during the assembly and the maximum force which can be carried by the snap joint. The approach is verified experimentally.
Abatement of Cutaneous Kaposi's Sarcoma Associated with Cidofovir Treatment (1998)

static lesions of pyogenic liver abscess. Their association with Klebsiella
Formation of Isoamylase by <i>Pseudomonas</i> (1968)

We have isolated a Pseudomonas sp. (strain SB15) which produces an isoamylase (EC 3.2.1.9). Highest yields of this enzyme were obtained when the bacterium was grown in shaken culture in a medium containing maltose, dextrin, starch, or isomaltose. Specific carbon and nitrogen sources were required for growth. The most satisfactory medium consisted of 2% maltose, 0.4% sodium glutamate, 0.3% diammonium hydrogen phosphate, and other inorganic salts. The optimal pH for enzyme production was 5 to 6. The enzyme is stable between pH 3 and 6 but is extremely labile above pH 7. It splits amylopectin completely by combined action with beta-amylase but does not attack pullulan.
Heat shock protein 90 mediates cytoprotection by H<sub>2</sub>S against chemical hypoxia‐induced injury in PC12 cells (2010)

1. Increasing evidence indicates that hydrogen sulphide (H₂S) may serve as an important biological cytoprotective agent. Heat shock protein (Hsp) 90 can attenuate stress-induced injury. However, whether Hsp90 mediates the cytoprotective effect of H₂S against chemical hypoxia-induced injury in PC12 cells is not known. 2. In the present study, CoCl₂ (a chemical hypoxia mimetic) was used to treat PC12 cells to create a model of chemical hypoxia. To explore the role of Hsp90 in the cytoprotection afforded by H₂S against chemical hypoxia-induced injury, 2 μmol/L 17-allylaminogeldanamycin (17-AAG), a selective inhibitor of Hsp90, was administered for 30 min prior to preconditioning with 400 μmol/L NaHS, followed by chemical hypoxia. 3. Cobalt chloride reduced cell viability (by 52.7 ± 1.5%), increased PC12 cell apoptosis (by 42.1 ± 1.5%), induced reactive oxygen species (ROS) by 3.79% compared with control and induced the dissipation of mitochondrial membrane potential (MMP) by 2.56% compared with control. 4. Pretreatment of PC12 cells with 100-400 μmol/L sodium hydrosulphide (NaHS), an H₂S donor, for 3 h prior to exposure to 600 μmol/L CoCl₂ provided significant, concentration-dependant protection to PC12 cells against CoCl₂-induced cytotoxicity. Specifically, pretreatment of PC12 cells with 400 μmol/L NaHS decreased apoptosis to 16.77 ± 1.77% and blocked the CoCl₂-induced increase in ROS production and loss of MMP. 5. At 400 μmol/L, NaHS upregulated Hsp90 in a time-dependant manner (over the period 0-180 min). In addition to its effects on Hsp90 expression, NaHS pretreatment of PC12 cells augmented the overexpression of Hsp90 induced by 600 μmol/L CoCl₂ by 1.38-fold (P < 0.01). 6. Treatment of PC12 cells with 2 μmol/L 17-AAG for 30 min prior to NaHS pretreatment blocked the overexpression of Hsp90 induced by NaHS preconditioning, as evidenced by decreased cell viability (by 54.2 + 1.2%; P < 0.01), increased PC12 cell apoptosis (by 36.6 ± 1.2%; P < 0.01) and increasing ROS production. 7. The findings of the present study provide novel evidence that Hsp90 mediates H₂S-induced neuroprotection against chemical hypoxia-induced injury via anti-oxidant and anti-apoptotic effects.
Resin-Based Cement Alternatives for Deepwater Well Construction (2012)

Abstract Well construction in deepwater environments poses many challenges from a cementing perspective. Limited options for controlling cement density and rheological profile can present significant risks to wellbore stability, especially in narrow fracture gradient wells. In addition, poor compatibility between traditional aqueous-based cement and synthetic-based drilling fluids (SBFs) commonly used in deepwater drilling can lead to issues with cement-to-casing and cement-to-formation bond integrity. To address these issues, a new epoxy-resin based cement alternative has been developed with highly tunable specific gravity and drilling fluid-like rheology. The combination of a highly tunable specific gravity and maintenance of drilling fluid-like rheology yields minimal equivalent circulating density (ECD) increases upon placement of the resin in the wellbore and enhanced management of narrow fracture-gradients. Furthermore, the new resin formulations have been shown to provide excellent compatibility with SBFs used in deepwater applications. The resin shows applicability over the broad temperature range of 90 to 225°F, with resin densities of 7.0 to 18.0 lb/gal. In addition, elevated shear bond strengths with minimal shrinkage upon cure were observed for the resins. The paper presents detailed studies of the new resin systems at 90°F, 160°F, and 225°F with 9.0 to 14.0 lb/gal densities. It also discusses set time/pump time issues and the control of resin rheological properties and density by means of a judicious choice of added particle types and particle sizes. The resin systems tolerated a high volume percentage of SBF contamination, and excellent compressive strengths were observed with and without SBF contamination. Combined, the data indicates that the new resin potentially provides substantial advantages over traditional cement and mitigates many of the challenges associated with the application of cement in deepwater well construction.
The insidious nature and presentation of oral squamous cell carcinoma in the low-risk population. (2008)

Oral squamous cell carcinoma is found predominantly in patients who have a history of smoking, alcohol consumption, or betel quid use. However, some of these patients have no known risk factors for development of the lesion and sometimes are diagnosed later in life due to low clinical suspicion of squamous cell carcinoma. This article presents three such cases, including their history and treatment.
A novel crystalline soft magnetic intermediate layer for perpendicular recording media (2009)

In order to improve the recording efficiency in current perpendicular recording media, it is important to reduce the distance from the head to soft underlayer. In this paper, a soft magnetic intermediate layer is proposed to partially replace the presently used Ru intermediate layer. The new soft magnetic intermediate layer serves two purposes, which are as follows: (1) to decrease the thickness of the nonmagnetic Ru intermediate layer by providing a proper crystalline texture and surface morphology for the optimal crystalline grain growth of the magnetic storage layer on top and (2) to act as an additional soft magnetic underlayer that is closer to the head air bearing surface to enhance the recording performance. The prototypes of the soft magnetic intermediate layer consists of CoIr:SiO2/CoPt:SiO2/NiW multilayer structure. CoIr and CoPt were chosen because both have the hcp structure but the opposite sign for K1. A zero effective magnetoanisotropy of a composite grain is accomplished by varying the thickness ratio of each layer of CoIr and CoPt. The developed multilayer film shows the hcp (00.2) orientation with a dome morphology for facilitating the growth of the top magnetic storage layer as well as soft magnetic properties (K1=6.8×105 erg/cc).
Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein–Protein Interfaces (2012)

In the context of protein-protein interactions, the term "hot spot" refers to a residue or cluster of residues that makes a major contribution to the binding free energy, as determined by alanine scanning mutagenesis. In contrast, in pharmaceutical research, a hot spot is a site on a target protein that has high propensity for ligand binding and hence is potentially important for drug discovery. Here we examine the relationship between these two hot spot concepts by comparing alanine scanning data for a set of 15 proteins with results from mapping the protein surfaces for sites that can bind fragment-sized small molecules. We find the two types of hot spots are largely complementary; the residues protruding into hot spot regions identified by computational mapping or experimental fragment screening are almost always themselves hot spot residues as defined by alanine scanning experiments. Conversely, a residue that is found by alanine scanning to contribute little to binding rarely interacts with hot spot regions on the partner protein identified by fragment mapping. In spite of the strong correlation between the two hot spot concepts, they fundamentally differ, however. In particular, while identification of a hot spot by alanine scanning establishes the potential to generate substantial interaction energy with a binding partner, there are additional topological requirements to be a hot spot for small molecule binding. Hence, only a minority of hot spots identified by alanine scanning represent sites that are potentially useful for small inhibitor binding, and it is this subset that is identified by experimental or computational fragment screening.