gebhart/patrepeval huggingface dataset:
Contribution of Conserved Amino Acids at the Dimeric Interface to the Conformational Stability and the Structural Integrity of the Active Site in Ketosteroid Isomerase from Pseudomonas putida Biotype B (2003)

Ketosteroid isomerase (KSI) from Pseudomonas putida biotype B is a homodimeric enzyme catalyzing an allylic isomerization of Delta(5)-3-ketosteroids at a rate of the diffusion-controlled limit. The dimeric interactions mediated by Arg72, Glu118, and Asn120, which are conserved in the homologous KSIs, have been characterized in an effort to investigate the roles of the conserved interface residues in stability, function and structure of the enzyme. The interface residues were replaced with alanine to generate the interface mutants R72A, E118A, N120A and E118A/N120A. Equilibrium unfolding analysis revealed that the AG(U)(H 2 O) values for the R72A, E118A, N120A, and E118A/N120A mutants were decreased by about 3.8, 3.9, 7.8, and 9.5 kcal/mol, respectively, relative to that of the wild-type enzyme. The interface mutations not only decreased the k(cat)/K-M value by about 8- to 96-fold, but also increased the K-D value for d-equilenin, a reaction intermediate analogue, by about 7- to 17.5-fold. The crystal structure of R72A determined at 2.5 Angstrom resolution and the fluorescence spectra of all the mutants indicated that the interface mutations altered the active-site geometry and resulted in the decreases of the conformational stability as well as the catalytic activity of KSI. Taken together, our results strongly suggest that the conserved interface residues contribute to stabilization and structural integrity of the active site in the dimeric KSI.
A Joint Initiative to Support the Semantic Interoperability within the GIIDA Project (2010)

The GIIDA project aims to develop a digital infrastructure for the spatial information within CNR. It is foreseen to use semantic-oriented technologies to ease information modeling and connecting, according to international standards like the ISO/IEC 11179. Complex information management systems, like GIIDA, will take benefit from the use of terminological tools like thesauri that make available a reference lexicon for the indexing and retrieval of information. Within GIIDA the goal is to make available the EARTh thesaurus (Environmental Applications Reference Thesaurus), developed by the CNR-IIA-EKOLab. A web-based software, developed by the CNR-Water Research Institute (IRSA) was implemented to allow consultation and utilization of thesaurus through the web. This service is a useful tool to ensure interoperability between thesaurus and other systems of the indexing, with, the idea of cooperating to develop a comprehensive system of knowledge organization, that could be defined integrated, open, multi-functional and multilingual. Currently the system is available in multiple languages mode (Italian - English) and navigation can be done in the following ways: Alphabetical, Hierarchical and for Themes. A full search allows to find any term by searching for the whole term or a part of it and as well as allows to filter the results by themes. Within a collaborative initiative with the CNR-Institute of Applied Mathematics and Information Technology (IMATI) a SKOS (Simple Knowledge Organization System) version of EARTh was developed. This will ensure the possibility to support the use of the thesaurus within the framework of the Semantic Web in order to be used in decentralized metadata applications
Small <i>Demodex</i> populations colonize most parts of the skin of healthy dogs (2013)

Using a real-time PCR technique, Demodex mites, albeit in very low numbers, were found to be normal inhabitants of haired areas of the skin of healthy dogs.
High Q inductors for wireless applications in a complementary silicon bipolar process (1996)

Rectangular spiral inductors with Q's over 12 have been built in a high-speed complementary bipolar process and characterized for use in wireless applications. An accurate broadband model for the inductors has been developed, and a test filter and mixer have been built to verify the performance of the inductors and the accuracy of the model.
Spin-asymmetry function for elastic electron scattering from lead atoms in the energy range 11–14 eV (2009)

We report investigations of the spin-asymmetry function ${S}_{\text{A}}$ in elastic electron scattering from lead atoms. The experimental results are compared to previous measurements as well as to earlier and recent relativistic model-potential and $R$-matrix (close-coupling) calculations. The spin-asymmetry function is found to depend strongly on the incident-electron energy in the region between 11 and 14 eV.
Vibrational Study of the Polymer Electrolyte Poly(ethylene oxide)<sub>6</sub>:LiAsF<sub>6</sub> (2001)

A vibrational study of the polymer electrolyte compound poly(ethylene oxide)6:LiAsF6 is reported. A symmetry-based factor group correlation method is applied to interpret the observed bands. The Raman and infrared spectra of the compound are consistent with the reported crystal structure. The ν1 mode, which appears at 685 cm-1, identifies the anions as being “spectroscopically free”. Multiple bands in the ν3 spectral region are interpreted as resulting from the dynamical coupling of the four AsF6- anions in the unit cell. The ρ(CH2) region shows multiple bands that arise from the complex conformations of the polymer backbone.
Influence of antisecretory drugs on Helicobacter pylori eradication rates. (2004)

We read with great interest the article by Sherwood and colleagues ( Gut 2002; 51 :490–5) evaluating the role of acid secretion and gastric luminal pH on the gastric transfer rate of amoxycillin, clarithromycin, and metronidazole. The study showed that metronidazole and clarithromycin but not amoxicillin transfer was increased by acid secretion. Gastric acid suppression, induced by the use of omeprazole, produced the fall in clarithromycin and metronidazole transfer.

These data may help to clarify preliminary results of our study on Helicobacter pylori eradication in a population of 120 H pylori infected dyspeptic patients (63 males and 57 females; mean age 53.2 (12.31) years).1 None of the patients received prior antibiotic treatment with nitroimidazoles or macrolides, or H pylori eradication therapy, nor was there a history of gastrointestinal surgery, alcohol use, or smoking.

Our population was divided in two groups of 60 patients who underwent two different 14 day triple eradicating regimens based on …
Theoretical and experimental analysis links isoform‐ specific ERK signalling to cell fate decisions (2009)

Cell fate decisions are regulated by the coordinated activation of signalling pathways such as the extracellular signal-regulated kinase (ERK) cascade, but contributions of individual kinase isoforms are mostly unknown. By combining quantitative data from erythropoietin-induced pathway activation in primary erythroid progenitor (colony-forming unit erythroid stage, CFU-E) cells with mathematical modelling, we predicted and experimentally confirmed a distributive ERK phosphorylation mechanism in CFU-E cells. Model analysis showed bow-tie-shaped signal processing and inherently transient signalling for cytokine-induced ERK signalling. Sensitivity analysis predicted that, through a feedback-mediated process, increasing one ERK isoform reduces activation of the other isoform, which was verified by protein over-expression. We calculated ERK activation for biochemically not addressable but physiologically relevant ligand concentrations showing that double-phosphorylated ERK1 attenuates proliferation beyond a certain activation level, whereas activated ERK2 enhances proliferation with saturation kinetics. Thus, we provide a quantitative link between earlier unobservable signalling dynamics and cell fate decisions.
Inversion domain boundaries in ZnO: First-principles total-energy calculations (2004)

We present first-principles total-energy calculations of domain wall energies for inversion domain boundaries and their interaction with point defects in ZnO. We find that the inversion domain boundaries (IDB's) with Zn-Zn and O-O wrong bonds are energetically unstable, and they transform into the so-called ${\mathrm{IDB}}^{*}$ structures. Although the ${\mathrm{IDB}}^{*}'\mathrm{s}$ do not induce electronic states in the bandgap, they are very attractive to electrically active compensating point defects. The segregation of such charged point defects builds up electrical potentials for minority carriers in doped ZnO, which are harmful to optoelectronic applications.
Purified apolipoprotein B gene regulatory factor‐3 is DNA topoisomerase I (1999)

Hepatic cell-specific expression of the human apolipoprotein B (apoB) gene is controlled by at least four cis-acting elements located between positions -128 and +122 [Chuang, S. S., & Das, H. K. (1996) Biochem. Biophys. Res. Commun. 220, 553-562]. A negative cis-acting element (+20 to +40) is located in the first nontranslated exon of the human apoB gene, and apoB regulatory factor-3 (BRF-3) interacts with this. In this paper, we report the purification and characterization of BRF-3 from rat liver nuclear extracts. BRF-3 has been purified to apparent homogeneity by DEAE-cellulose, heparin-agarose, and DNA-specific affinity chromatography. Purified BRF-3 produced two polypeptide bands with apparent molecular masses of 70 kDa and 67 kDa in SDS/PAGE as detected by silver staining. Both 70-kDa and 67-kDa proteins have been found to hybridize specifically with labeled double-stranded oligonucleotide containing BRF-3 binding site in a South-Western blot. Double-stranded oligonucleotide containing mutations in the BRF-3 binding site was found to abolish DNA binding by these two proteins. Amino acid sequences of tryptic peptides derived from affinity purified 70-kDa and 67-kDa rat BRF-3 proteins were found to have 100% sequence homologies with DNA topoisomerase I. These data suggest that the 70-kDa and 67-kDa forms of BRF-3 are derived by proteolytic cleavage of topoisomerase I, and therefore, topoisomerase I may play an important role in transcriptional regulation of apoB.
Chimerism after Vascularized Limb Versus Bone Marrow Transplantation (2006)

This study used quantitative PCR in the murine model to compare the ability of a limb allograft vs. a comparable dose of marrow suspension to induce chimerism. Female C57Bl/6 mice received a vascularized hindlimb allograft, a comparable dose of 5 x 10 (6) donor bone marrow cells, or a standard dose (20 x 10 (6)) of marrow suspension from male Balb/c donors. All recipients were treated with a regimen based on CD40 costimulation blockade and T cell depletion. Y chromosome-specific quantitative PCR was used to measure chimerism. Most recipients of limb allografts demonstrated low levels of chimerism after 1 week (3/4) and 1 month (3/4). Most recipients of 5 x 10 (6) marrow cells had low levels of chimerism at 1 week (4/6) and only 1/5 after 1 month. All recipients of 20 x 10 (6) cells except one demonstrated either low or high levels of chimerism after 1 week (5/5) and 1 month (5/6). The marrow component of a limb allograft is thus more effective at inducing microchimerism compared to a comparable dose of bone marrow suspension.
Application of multiple path sequential decoding for the intersymbol interference problem (1988)

ABSTRACT: Maximum likelihood sequence estimation -- Viterbi decoding -- Sequential decoding -- Sequential decoding metric for the ISI problem -- Computer simulations -- Error performance and computational effort -- Simplified multiple path sequential decoder -- Error performance of the simplified algorithm.
Chromatic sharing a binary secret within a host image (2010)

A type of Probabilistic Visual Secret Sharing Scheme giving non-expansive and meaningful shadow images is here introduced. A binary secret image is shared from any natural color image by transferring the host content to each shadow and to their combination.
Indexing and retrieval for genomic databases (2002)

Genomic sequence databases are widely used by molecular biologists for homology searching. Amino acid and nucleotide databases are increasing in size exponentially, and mean sequence lengths are also increasing. In searching such databases, it is desirable to use heuristics to perform computationally intensive local alignments on selected sequences and to reduce the costs of the alignments that are attempted. We present an index-based approach for both selecting sequences that display broad similarity to a query and for fast local alignment. We show experimentally that the indexed approach results in significant savings in computationally intensive local alignments and that index-based searching is as accurate as existing exhaustive search schemes.
Effects of plasma treatment on the growth of SnO<sub>2</sub>nanorods from SnO<sub>2</sub>thin films (2006)

SnO2 thin films have been deposited by radio-frequency inductively coupled plasma-enhanced chemical vapour deposition using dibutyltin diacetate as the precursor. The as-deposited SnO2 thin films were post-treated in the inductively coupled plasma. After plasma treatment, uniform SnO2 nanorods were grown on the SnO2 thin films. The nanorods were formed by a sputtering–redeposition mechanism. The effects of the conditions of the plasma treatment on the morphology of plasma-treated SnO2 thin films were studied. The plasma power and the gaseous composition of the plasma had a great effect on the growth of SnO2 nanorods from SnO2 thin films. The type of plasma was also very critical, and no nanorods were grown on the SnO2 thin films treated in capacitively coupled plasma.
Fin whale calls observed with submarine cabled observatories off Kushiro-Tokachi during ten years (2016)

In this research, the automatically analyzation method which detect acoustic events such as fin whale calls and its locations is embedded in cable observatory system. This system has detection method about fin whale calls using spectrogram correlation, and the localization of fin whale calls using two hydrophones and a three-axis seismometer. This observation at off Kushiro-Tokachi has been continuously performed for more than 10 years. The detection and tracking analysis for fin whale calls are carried out about the archive data in parallel with the real-time data. The results of the past 10 years including the latest information is reported.
An integrated GaAs n-p-n-p thyristor/JFET memory cell exhibiting nondestructive read (1992)

An integrated GaAs n-p-n-p thyristor-junction field effect transistor (JFET) structure displays memory by storing charge on the thyristor reverse-biased junctions. The device can be electrically programmed and erased through a single terminal. A buried p-channel, which also functions as the thyristor anode, is used to read stored charge nondestructively over a small range of applied drain voltages (+or-1.5 V). Measured storage times exceeded 10 s at room temperature with an activation energy of approximately 0.6 eV.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
ChemInform Abstract: A Simple and Expedient Method for the Preparation of N‐Chlorohydantoins. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
This Journal feature begins with a case vignette highlighting a common clinical problem. Evidence supporting various strategies is then presented, followed by a review of formal guidelines, when they exist. The article ends with the authors' clinical recommendations. Colony-Stimulating Factors for Febrile Neutropenia during Cancer Therapy (2013)

A 55-year-old, previously healthy woman received a diagnosis of diffuse large-B-cell lymphoma after the evaluation of an enlarged left axillary lymph node obtained on biopsy. She had been asymptomatic except for the presence of enlarged axillary lymph nodes, which she had found while bathing. She was referred to an oncologist, who performed a staging evaluation. A complete blood count and test results for liver and renal function and serum lactate dehydrogenase were normal. Positronemission tomography and computed tomography (PET–CT) identified enlarged lymph nodes with abnormal uptake in the left axilla, mediastinum, and retroperitoneum. Results on bone marrow biopsy were normal. The patient’s oncologist recom mends treatment with six cycles of cyclophosphamide, doxorubicin, vincristine, and prednisone with rituximab (CHOP-R) at 21-day intervals. Is the administration of prophylactic granulocyte colony-stimulating factor (G-CSF) with the first cycle of chemotherapy indicated? T h e C l i nic a l Probl e m Cycling cells in the bone marrow are sensitive to some forms of chemotherapy, including DNA-damaging agents and agents that inhibit cell-cycle progression. Therefore, in patients who are treated with chemotherapy regimens that include such agents, normal hematopoietic cells undergo damage that is both immediate and cumulative. The most serious immediate consequence of chemotherapy is febrile neutropenia, which is defined as an absolute neutrophil count of less than 500 cells per cubic millimeter and a temperature of more than 38.5°C. Most stan dard-dose chemotherapy regimens are associated with 6 to 8 days of neutropenia. 1-3 Data from the National Cancer Institute (NCI) suggest that more than 60,000 patients are admitted for the treatment of febrile neutropenia annually, or approximately 8 cases per 1000 patients receiving cancer chemotherapy. 4 Febrile neutropenia predisposes patients to serious infections and even death, particularly if severe neutropenia persists for longer than 10 to 14 days. 4-6 In the study of NCI data, the in-hospital rate of death was 6.8%. 4 In another analysis, the overall in-hospital rate of death was 9.5% (and 15.3% for patients with documented infection). 6 The mean costs per hospitalization in these two studies were $13,372 and $19,110, respectively. 4,6
ChemInform Abstract: REACTION BETWEEN 8‐BROMOADENOSINE AND AMINES. CHEMISTRY OF 8‐HYDRAZINOADENOSINE (1978)

Abstract 8‐Bromadenosin (I) reagiert mit primären und sekundären Aminen (II) zu den entsprechenden Aminen (III), mit Hydrazin zum 8‐Hydrazinoadenosin (IV).
[Determination of gestational age using crown-rump length and the biparietal diameter in the 1st half of pregnancy--comparison of 2 methods]. (1984)

In the first half of pregnancy ultrasound investigations was made on women with known gestational age by regular menstruation or conception. In 221 cases of single pregnancies fetal crownrump length was measured. Biparietal cephalometry was performed in 198 single fetuses. All examinations were done with a Kranzbühler Linearscanner using an ADR 3.5 MHZ transducer. Growth curves and the velocity of growth from biparietal diameter and from crown-rump length were determined and compared. The accuracy of the estimation of gestational age was observed to be +/- 10 days (2 SD) with both methods. A difference in accuracy could not be found. Even if the first half of pregnancy was separated in an early and a late part there wasn't any improvement of accuracy.
Cytokines as cellular communicators (1996)

Cytokines and their receptors are involved in the pathophysiology of many diseases. Here we present a detailed review on cytokines, receptors and signalling routes, and show that one important lesson from cytokine biology is the complex and diverse regulation of cytokine activity. The activity of cytokines is controlled at the level of transcription, translation, storage, processing, posttranslational modification, trapping, binding by soluble proteins, and receptor number and/or function. Translation of this diverse regulation in strategies aimed at the control of cytokine activity will result in the development of more specific and selective drugs to treat diseases.
Natriuretic Peptide Testing for Predicting Adverse Events Following Heart Failure Hospitalization (2012)

Concentrations of both B-type natriuretic peptide (BNP) and amino-terminal pro-BNP (NT-proBNP) are useful for diagnostic evaluation of patients with acute decompensated heart failure (ADHF), providing important information regarding presence and severity of heart failure. In addition, levels of both BNP and NT-proBNP are strongly prognostic for adverse outcomes in this setting. While values for BNP and NT-proBNP at hospital admission predict impending risk for adverse outcome, their measurement following HF treatment provides incremental prognostic information, even more accurately identifying patients at highest risk for death or rehospitalization in the short term. Thus, changes in BNP or NT-proBNP following treatment should be considered an important part of the pre-discharge decision making for patients hospitalized with ADHF.
Efficient Chirp Diagnosis Algorithms for Femtosecond Laser Pulses (2004)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text D. A. Bender, M. P. Hasselbeck, and M. Sheik-Bahae, "Efficient Chirp Diagnosis Algorithms for Femtosecond Laser Pulses," in Nonlinear Optics: Materials, Fundamentals and Applications, Technical Digest (CD) (Optica Publishing Group, 2004), paper WD10. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
A single WW domain is the predominant mediator of the interaction between the human ubiquitin-protein ligase Nedd4 and the human epithelial sodium channel (2002)

The activity of the epithelial Na(+) channel (ENaC) is required for the maintenance of salt and water balance in the body. Channel activity is regulated by the ubiquitin-protein ligase Nedd4 ['neuronal precursor cell-expressed developmentally down-regulated (gene 4)'] that interacts with the channel via its WW domains. Mutations in channel subunits that disrupt this interaction cause Liddle's syndrome, a severe inherited form of hypertension. In previous studies we showed that WW domains 2, 3 and 4 of human Nedd4 bound to the human ENaC (hENaC) subunits, whereas WW domain 1 did not. Here we extend this observation to determine the binding affinities of the human Nedd4 WW domains for hENaC C-terminal peptides. We show that WW domains 2, 3 and 4 bind with differing affinities to Na(+) channel subunit peptides. WW domain 3 has the highest affinity and we predict that WW domain 3 contributes most of the binding because a construct containing the three WW domains bound no better than WW domain 3 alone. Further, a single amino acid change (Arg(165)-->Thr) in WW domain 1 enables binding to the alpha subunit of the channel to occur, with an affinity comparable with that of WW domain 4. Differential binding propensities between the various WW domains and Na(+) channel subunit peptides are explained on the basis of quantitative structural modelling of the complexes and their isolated components.