gebhart/patrepeval huggingface dataset:
Functionally linked resting‐state networks reflect the underlying structural connectivity architecture of the human brain (2009)

During rest, multiple cortical brain regions are functionally linked forming resting-state networks. This high level of functional connectivity within resting-state networks suggests the existence of direct neuroanatomical connections between these functionally linked brain regions to facilitate the ongoing interregional neuronal communication. White matter tracts are the structural highways of our brain, enabling information to travel quickly from one brain region to another region. In this study, we examined both the functional and structural connections of the human brain in a group of 26 healthy subjects, combining 3 Tesla resting-state functional magnetic resonance imaging time-series with diffusion tensor imaging scans. Nine consistently found functionally linked resting-state networks were retrieved from the resting-state data. The diffusion tensor imaging scans were used to reconstruct the white matter pathways between the functionally linked brain areas of these resting-state networks. Our results show that well-known anatomical white matter tracts interconnect at least eight of the nine commonly found resting-state networks, including the default mode network, the core network, primary motor and visual network, and two lateralized parietal-frontal networks. Our results suggest that the functionally linked resting-state networks reflect the underlying structural connectivity architecture of the human brain.
Directed evolution of green fluorescent protein by a new versatile PCR strategy for site-directed and semi-random mutagenesis (2000)

To develop a simple, speedy, economical and widely applicable method for multiple-site mutagenesis, we have substantially modified the Quik-Change Site-Directed Mutagenesis Kit protocol (Stratagene, La Jolla, CA). Our new protocol consists of (i) a PCR reaction using an in vitro technique, LDA (ligation-during-amplification), (ii) a DPN:I treatment to digest parental DNA and to make megaprimers and (iii) a synthesis of double-stranded plasmid DNA for bacterial transformation. While the Quik Change Kit protocol introduces mutations at a single site, requiring two complementary mutagenic oligonucleotides, our new protocol requires only one mutagenic oligonucleotide for a mutation site, and can introduce mutations in a plasmid at multiple sites simultaneously. A targeting efficiency >70% was consistently achieved for multiple-site mutagenesis. Furthermore, the new protocol allows random mutagenesis with degenerative primers, because it does not use two complementary primers. Our mutagenesis strategy was successfully used to alter the fluorescence properties of green fluorescent protein (GFP), creating a new-color GFP mutant, cyan-green fluorescent protein (CGFP). An eminent feature of CGFP is its remarkable stability in a wide pH range (pH 4-12). The use of CGFP would allow us to monitor protein localization quantitatively in acidic organelles in secretory pathways.
Characterization and sequencing of a 40-amino-acid peptide from human thyroglobulin inducing experimental autoimmune thyroiditis (1992)

We previously demonstrated that: a) a cytotoxic T cell hybridoma (HTC2) was able to induce lysis of syngeneic macrophages pulsed with either porcine thyroglobulin (pTg) or the tryptic fragments (TF) from pTg less than 10 kDa (M(r)) and that b) these low M(r) pTg TF included pathogenic epitopes because their injection into CBA/J mice induces thyroid lymphocytic infiltration typical of experimental autoimmune thyroiditis. Therefore the biochemical analysis of the TF preparation from pTg less than 10 kDa M(r) was undertaken and the characterized peptides were tested for their ability to be recognized or not by HTC2 cells. The sequencing of the selected peptides showed a 70% sequence homology with a portion of human thyroglobulin (hTg). The lack of a published sequence of pTg led us to synthesize a 40-amino acid peptide (F40D) similar to that portion of hTg. This F40D peptide was able to generate lymphocytic infiltrations in CBA/J mice thyroid glands, as was the native pTg molecule. Although the lymphocytic infiltrations were similar in the pTg or F40D-immunized mice, auto-antibodies to pTg or to hTg were only detectable in mice immunized with pTg. In contrast, autoantibodies levels to F40D peptide were significantly increased in serum from mice in which EAT had been induced by the F40D peptide. This highly hydrophobic peptide shows a M(r) of 4,492 kDa; it is located at the end of the second-third of the thyroglobulin molecule and up to now represents a unique sequence from the hTg molecule inducing experimental autoimmune thyroiditis.
SELECTIVE CATALYTIC REDUCTION OF DIESEL ENGINE NOX EMISSIONS USING ETHANOL AS A REDUCTANT (2003)

NOx emissions from a heavy-duty diesel engine were reduced by more than 90% and 80% utilizing a full-scale ethanol-SCR system for space velocities of 21000/h and 57000/h respectively. These results were achieved for catalyst temperatures between 360 and 400 C and for C1:NOx ratios of 4-6. The SCR process appears to rapidly convert ethanol to acetaldehyde, which subsequently slipped past the catalyst at appreciable levels at a space velocity of 57000/h. Ammonia and N2O were produced during conversion; the concentrations of each were higher for the low space velocity condition. However, the concentration of N2O did not exceed 10 ppm. In contrast to other catalyst technologies, NOx reduction appeared to be enhanced by initial catalyst aging, with the presumed mechanism being sulfate accumulation within the catalyst. A concept for utilizing ethanol (distilled from an E-diesel fuel) as the SCR reductant was demonstrated.
Selective Area Metallization by Electron-Beam Controlled Direct Metallic Deposition (1973)

Direct metallic deposition exploits the advantages of electron-beam exposure for the production of fine structures and avoids the use of resists and chemical etching. The process involves the electron-induced decomposition of metallic compounds in areas precisely defined by an electron probe. In principle, the resistivity of the deposits formed by direct metallic deposition can be controlled by regulating the amount of molecular dissociation which takes place. To date, in experiments with silver chloride, deposits with submicron dimensions have been obtained. Typical sheet-resistance values of the deposits range from 10 to 1000 Ω/square for exposures varied from 3×10−2 to 5×10−3 C/cm2. A Monte Carlo simulation of electron scattering in thin films on a supporting substrate has shown that the minimum deposit dimensions which can be expected from the process vary directly with film thickness and inversely with accelerating voltage. Experimental evidence is in agreement with the theoretical predictions.
Toxicity, pharmacokinetics, and dose-finding study of repetitive treatment with the humanized anti-interleukin 6 receptor antibody MRA in rheumatoid arthritis. Phase I/II clinical study. (2003)

Repetitive treatment with MRA was safe and normalized acute phase response in patients with RA. Optimal dosing schedule was not defined in this small study, but maintenance of serum MRA concentration seemed important to achieve efficacy.
Load research for fault location in distribution feeders (1999)

Load behaviour needs to be considered in the algorithms for distribution systems fault locations to reduce the resulting error to practical limits. The restrictions imposed by the load models proposed so far are discussed in the paper, and a new modelling methodology, referred to as the ‘fast response model‘ is proposed. New models for load elements, experimentally based and suitable for that application, are presented and aggregated at the distribution transformer level. The behaviour of the proposed models is compared with the methodologies used for that purpose, through the evaluation of their response under unbalanced abnormal voltage situations. As shown in the paper, the consideration of these models in fault location algorithms can enhance the accuracy of the location process.
A Molecular Signature of the Nottingham Prognostic Index in Breast Cancer (2004)

The Nottingham prognostic index (NPI) is a widely used clinicopathological staging system for breast cancer prognostication. Using a step-wise classification approach where breast tumor expression profiles were first divided into general "molecular subtypes" [estrogen receptor (ER)+, ER-, ERBB2+], followed by an independent analysis of each subtype, we identified a 62-gene expression signature (NPI-ES) highly correlated to the NPI in ER+ tumors. The NPI-ES classified the majority of ER+ tumors into two distinct groups with high confidence and was significantly correlated to NPI status in two independent sets of ER+ tumors derived from different centers. The NPI-ES is comparable to the classical NPI in identifying patients likely to exhibit a poor clinical prognosis, as well as to a recently described "prognosis signature" for breast cancer. Our findings demonstrate how expression profiling can complement classical staging systems employing histopathological parameters scored over a continuous range of values.
High-speed direct single-frequency modulation with large tuning rate and frequency excursion in cleaved-coupled-cavity semiconductor lasers (1983)

We report a new mechanism of direct frequency modulation, the cavity-mode enhanced frequency modulation (CME-FM), using the newly developed cleaved-coupled-cavity (C3) semiconductor laser. In this operation, one of the diode of the C3 laser was operated as a laser, while the other diode was operated as a frequency modulator. It was shown that a very large frequency excursion of 150 Å and frequency tuning rate of 10 Å/mA have been obtained with a C3 GaInAsP crescent laser operating at 1.3 μm. Time-resolved spectral and spectral-resolved pulse response measurements also showed that such C3 lasers operated in highly stable single-longitudinal mode at all times even under high-speed direct frequency modulation. In addition to the important application as the optical source in FM optical communication systems, the present CME-FM C3 laser can also be used as the optical source in wavelength-division multiplexing systems. Further, it opens the possibility of ultrahigh capacity multilevel optical FM information transmission systems.
Cyclometalated complexes of platinum(II): homoleptic compounds with aromatic C,N ligands (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCyclometalated complexes of platinum(II): homoleptic compounds with aromatic C,N ligandsL. Chassot and A. Von ZelewskyCite this: Inorg. Chem. 1987, 26, 17, 2814–2818Publication Date (Print):August 1, 1987Publication History Published online1 May 2002Published inissue 1 August 1987https://pubs.acs.org/doi/10.1021/ic00264a018https://doi.org/10.1021/ic00264a018research-articleACS PublicationsRequest reuse permissionsArticle Views1255Altmetric-Citations141LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Stability of annular equilibrium of energetic large orbit ion beam (1991)

The low-frequency stability of a long thin annular layer of energetic ions in a background plasma with finite axial and zero azimuthal magnetic field is studied analytically. It is found that although the equilibrium is susceptible to the kink instability, low mode number perturbations can be stabilized in the limit of Ni/Nb→0 when the current layer is close to the maximum field-reversal parameter. A brief discussion of the tearing mode stability criteria of such strong current layers with respect to the placement of conducting walls is also presented.
Unraveling the Difference between Invertases and Fructan Exohydrolases: A Single Amino Acid (Asp-239) Substitution Transforms Arabidopsis Cell Wall Invertase1 into a Fructan 1-Exohydrolase (2007)

Plant cell wall invertases and fructan exohydrolases (FEHs) are very closely related enzymes at the molecular and structural level (family 32 of glycoside hydrolases), but they are functionally different and are believed to fulfill distinct roles in plants. Invertases preferentially hydrolyze the glucose (Glc)-fructose (Fru) linkage in sucrose (Suc), whereas plant FEHs have no invertase activity and only split terminal Fru-Fru linkages in fructans. Recently, the three-dimensional structures of Arabidopsis (Arabidopsis thaliana) cell wall Invertase1 (AtcwINV1) and chicory (Cichorium intybus) 1-FEH IIa were resolved. Until now, it remained unknown which amino acid residues determine whether Suc or fructan is used as a donor substrate in the hydrolysis reaction of the glycosidic bond. In this article, we present site-directed mutagenesis-based data on AtcwINV1 showing that the aspartate (Asp)-239 residue fulfills an important role in both binding and hydrolysis of Suc. Moreover, it was found that the presence of a hydrophobic zone at the rim of the active site is important for optimal and stable binding of Suc. Surprisingly, a D239A mutant acted as a 1-FEH, preferentially degrading 1-kestose, indicating that plant FEHs lacking invertase activity could have evolved from a cell wall invertase-type ancestor by a few mutational changes. In general, family 32 and 68 enzymes containing an Asp-239 functional homolog have Suc as a preferential substrate, whereas enzymes lacking this homolog use fructans as a donor substrate. The presence or absence of such an Asp-239 homolog is proposed as a reliable determinant to discriminate between real invertases and defective invertases/FEHs.
Functional mimetics of neurotrophins and their receptors (2006)

Neurotrophins regulate cell survival, death, differentiation and growth. Neurotrophins and their receptors have been validated for pathologies including neurodegenerative disorders of the central nervous system and the peripheral nervous system, certain types of cancers, asthma, inflammation and others. Development of neurotrophin-based therapeutics is important due to the limitations of using whole neurotrophins as pharmacological agents. The use of mimicry has proven to be an alternative. Mimetics can be developed through a number of different approaches. To develop receptor-binding agents, we have used anti-receptor antibody mimicry and neurotrophin mimicry. To develop ligand-binding agents, we have used antiligand antibody mimicry and receptor mimicry. High-throughput screening can be incorporated to complement any of these approaches. The end result is small molecule peptidomimetics with properties favourable over proteins. The present review will offer a general overview of these strategies with a few proven examples from our laboratory.
Study of three weekly nab-paclitaxel regimens in combination with carboplatin as first-line therapy in advanced non-small cell lung cancer (NSCLC) (2007)

7659 Background: We previously reported that 130-nM albumin-bound form of paclitaxel (ABI-007, nab paclitaxel) 225 - 340 mg/m 2 and carboplatin AUC of 6 mg/min·ml (C6), both administered on day (d) 1 every 3 weeks (q3w), produced an objective (PR/CR) response rate (ORR) of 27% in first line patients (pts) with NSCLC with median progression-free (PFS) and overall survivals of 6.0 and &gt;10.3 months respectively [Hawkins et al., ASCO, 2006]. Grade 2 and 3 sensory neuropathy (SN) was 36–56%. The aim of the current study was to obtain clinical experience with weekly schedules of nab- paclitaxel in combination with C6 in NSCLC prior to initiating large scale clinical trials. Methods: 75 Pts with previously untreated, stage IIIB or IV NSCLC with measurable disease and a life expectancy of over 12 weeks were recruited into 3 cohorts (n = 25 each) of successive pts and received nab paclitaxel weekly using 3 different regimens (see table ). Results: Patient Characteristics: 75 pts (100% Caucasian; 84% male; median age, 60; performance status score: 0 [16%], 1 [84%]. Accrual was completed in each cohort and serious adverse events reviewed prior to accrual at the next dose level. The primary efficacy endpoints are provided in the table . Grade 3/4 hematologic toxicities were: neutropenia 32%/35%; thrombocytopenia, 19%/11%; anemia, 24%/3%. The most common non- hematologic toxicities (any grade) were fatigue, 48%; SN, 48%; nausea, 37%; alopecia, 40%; and vomiting, 26%. Grade 2 and 3 SN was 12–28%. Graded toxicity data by regimen will be presented. Conclusions: When combined with C6, the ORR was higher and there was less peripheral neuropathy for weekly nab-paclitaxel compared to our previous experience using q3w administration. [Table: see text] [Table: see text]
Quantitative analysis of idiotypic mimicry and allelic exclusion in mice with a mu Ig transgene. (1989)

Analysis of C57BL/6 mice (IgM allotype, Igh-6b or mu b) that carry an Ig H chain transgene of a different allotype (mu a) shows that IgM molecules of mixed allotype (mu a mu b) are present among serum antibodies. The finding was extended to hybridomas prepared from nonimmune transgenic mice, many of which also failed to exhibit allelic exclusion. The proportions of mu a and mu b secreted by individual hybridomas varied markedly, and the product of an individual hybridoma was found to be heterogeneous with respect to the allotype content of individual molecules. The ratio of mu a:mu b chains secreted by individual hybridomas was found to correlate with the number of transgene copies remaining in each hybridoma, and several hybridomas that secrete only mu b-positive molecules had apparently lost all but one copy of the transgene. An idiotype characteristic of the transgene was found to be present only in association with the transgenic (mu a) allotype, and indirect evidence strongly suggests that the idiotype was present only on mu a polypeptide chains. Thus, there is no evidence in this system for the induction of idiotypically cross-reactive endogenous molecules.
Activity-Modulating Monoclonal Antibodies to the Human Serine Protease HtrA3 Provide Novel Insights into Regulating HtrA Proteolytic Activities (2014)

Mammalian HtrA (high temperature requirement factor A) proteases, comprising 4 multi-domain members HtrA1-4, play important roles in a number of normal cellular processes as well as pathological conditions such as cancer, arthritis, neurodegenerative diseases and pregnancy disorders. However, how HtrA activities are regulated is not well understood, and to date no inhibitors specific to individual HtrA proteins have been identified. Here we investigated five HtrA3 monoclonal antibodies (mAbs) that we have previously produced, and demonstrated that two of them regulated HtrA3 activity in an opposing fashion: one inhibited while the other stimulated. The inhibitory mAb also blocked HtrA3 activity in trophoblast cells and enhanced migration and invasion, confirming its potential in vivo utility. To understand how the binding of these mAbs modulated HtrA3 protease activity, their epitopes were visualized in relation to a 3-dimensional HtrA3 homology model. This model suggests that the inhibitory HtrA3 mAb blocks substrate access to the protease catalytic site, whereas the stimulatory mAb may bind to the PDZ domain alone or in combination with the N-terminal and protease domains. Since HtrA1, HtrA3 and HtrA4 share identical domain organization, our results establish important foundations for developing potential therapeutics to target these HtrA proteins specifically for the treatment of a number of diseases, including cancer and pregnancy disorders.
Differential Effects Of Hepatocyte Growth Factor Isoforms On Epithelial And Endothelial Tubulogenesis (1998)

Hepatocyte growth factor (HGF)/scatter factor (SF) is a pleiotropic cytokine that acts as a mitogen, motogen, and morphogen for a variety of cell types. HGF/NK1 and HGF/NK2 are two naturally occurring truncated variants of HGF/SF, which extend from the NH2 terminus through the first and second kringle domain, respectively. Although these variants have been reported to have agonistic or antagonistic activity relative to HGF/SF in assays of cell proliferation and motility, their potential morphogenic activity has not been investigated. To address this issue, we assessed the ability of HGF/NK1 and HGF/NK2 to induce tube formation by (a) MCF-10A mammary epithelial cells grown within collagen gels and (b) human umbilical vein endothelial (HUVE) cells grown on Matrigel. We found that HGF/NK1 stimulated tubulogenesis by both MCF-10A and HUVE cells, whereas HGF/NK2 did not stimulate tubulogenesis, but efficiently antagonized the morphogenic effect of full-length HGF/SF. HGF/NK1 and HGF/NK2 also had agonistic and antagonistic effects, respectively, on MCF-10A cell proliferation and HUVE cell migration. These results demonstrate that HGF/NK1, which only consists of the NH2-terminal hairpin and first kringle domain, is sufficient to activate the intracellular signaling pathways required to induce morphogenic responses in epithelial and endothelial cells. In contrast, HGF/NK2, which differs from HGF/ NK1 by the presence of the second kringle domain, is devoid of intrinsic activity but opposes the effects of HGF/SF. The differential properties of the two HGF/SF isoforms provide a basis for the design of more potent HGF/SF agonists and antagonists.
Enzyme-immunoassay. (1976)

Abstract The bases of the different enzyme-immunoassay techniques are described and their applications to the identification and quantification of antigens, haptens, and antibodies in biological fluids are discussed. Substances for which enzyme-immunoassays have been developed are listed. The enzymes used as labels, the methods of linking them to proteins, and the methods for separating free and bound labeled material are described. The reliability and practicality of the enzyme-immunoassay methods are reviewed.
Identification of elastic-plastic material parameters from pyramidal indentation of thin films (2002)

The indentation experiment is a popular method for the investigation of mechanical properties of thin films. By application of conventional methods, the hardness and the stiffness of the film material can be determined by limiting the indentation depth to well below the film thickness so that the substrate effects can be eliminated. In this work a new method is proposed, which allows for a determination of the reduced modulus as well as the nonlinear hardening behaviour of both the film and substrate materials. To this end, comparable deep indentations are made on the film/substrate composite to obtain sufficient information on the mechanical properties of both materials. The inverse problem is solved by training neural networks on the basis of finite–element simulations using only the easily measurable hardness and stiffness behaviour as input data. It is shown that the neural networks are very robust against noise in the load and depth. The identification of the material parameters of aluminium films on different substrates results in a significant increase in yield stress and initial work–hardening rate for a reduction of the film thickness from 1.5 to 0.5 µm, while the elastic modulus and the extent of work hardening remain constant.