gebhart/patrepeval huggingface dataset:
The rsp5‐domain is shared by proteins of diverse functions (1995)

A novel, unusually small, and highly conserved domain of modular intracellular proteins is described. The domain was first recognized as three repeats in the yeast rsp5 gene product and named thereafter. The rsp5 protein is thought to interact with nuclear proteins but also contains a C2 domain typical for cytoplasmic proteins. Further analyses revealed several additional occurrences of this domain in diverse protein classes, including cytoplasmic signal transduction proteins, gene products interacting with the transcription machinery, structural proteins like dystrophin, and a putative RNA helicase.
Improving orthogonal tRNA-synthetase recognition for efficient unnatural amino acid incorporation and application in mammalian cells (2009)

Optimizing the anticodon recognition between orthogonal tRNA and synthetase significantly increased the incorporation efficiencies of various unnatural amino acids in mammalian cells, and the enhanced incorporation enabled efficient photocrosslinking of interacting proteins in mammalian cells.
MOLECULAR APPROACHES TO AMYOTROPHIC LATERAL SCLEROSIS (1995)

New discoveries are expanding our knowledge of mechanisms involved in amyotrophic lateral sclerosis (ALS) pathogenesis. Some recent advances in our understanding of motoneuron death in familial ALS (fALS) and sporadic ALS (sALS) are reviewed, with emphasis on molecular similarities that may further unite these phenotypically linked diseases.
Understanding Decrements in Knowledge Access Resulting from Increased Fatigue (2007)

Understanding the impact of fatigue on human cognition represents an important challenge in applying research in cognitive science to real-world situations.In this study, we explored the cognitive mechanisms responsible for performance decrements in people doing the Walter Reed Serial Addition/Subtraction Task (SAST) periodically during 88 hrs of total sleep deprivation.In our model, performance on the SAST relies heavily on declarative knowledge of mathematical facts, allowing us to extend fatigue mechanisms associated with procedural knowledge from previous research to include analogous parameters and mechanisms in declarative knowledge in the Adaptive Control of Thought-Rational (ACT-R) cognitive architecture.This research contributes to a comprehensive theory of how the human arousal system impacts cognition and performance.
Tuning direct current streaming dielectrophoresis of proteins (2012)

Dielectrophoresis (DEP) of biomolecules has large potential to serve as a novel selectivity parameter for bioanalytical methods such as (pre)concentration, fractionation, and separation. However, in contrast to well-characterized biological cells and (nano)particles, the mechanism of protein DEP is poorly understood, limiting bioanalytical applications for proteins. Here, we demonstrate a detailed investigation of factors influencing DEP of diagnostically relevant immunoglobulin G (IgG) molecules using insulator-based DEP (iDEP) under DC conditions. We found that the pH range in which concentration of IgG due to streaming iDEP occurs without aggregate formation matches the pH range suitable for immunoreactions. Numerical simulations of the electrokinetic factors pertaining to DEP streaming in this range further suggested that the protein charge and electroosmotic flow significantly influence iDEP streaming. These predictions are in accordance with the experimentally observed pH-dependent iDEP streaming profiles as well as the determined IgG molecular properties. Moreover, we observed a transition in the streaming behavior caused by a change from positive to negative DEP induced through micelle formation for the first time experimentally, which is in excellent qualitative agreement with numerical simulations. Our study thus relates molecular immunoglobulin properties to observed iDEP, which will be useful for the future development of protein (pre)concentration or separation methods based on DEP.
ChemInform Abstract: Preparation and Properties of Methylenebispyridinium Derivatives. (1986)

Abstract Durch Quaternisierung der Pyridine (I) mit Dibrommethan wird eine Reihe von N,N′‐Methylen‐bis‐pyridinium‐dibromiden (II) hergestellt.
Parametric EIT for monitoring cardiac stroke volume (2006)

The bio-impedance technique appears appropriate for non-invasive cardiac stroke volume (SV) measurement, as the thoracic conductivity distribution is altered during the cardiac cycle due to the heart contraction and blood perfusion. In the present work, the feasibility of a parametric electrical impedance tomography (EIT) for assessing the cardiac SV was studied. An impedance model of the thorax was constructed from segmented axial MRI images along 19 phases of the cardiac cycle. The heart was simulated as an ellipsoid, with its axes' lengths set as the reconstruction parameters, while all other tissues' geometry and conductivity values were kept fixed. A Newton-Raphson parametric optimization scheme was utilized, yielding a correlation between the reconstructed and anatomical left ventricular volumes of 0.97 (p = 2 x 10(-11)). An analysis of noise sensitivity showed that the proposed algorithm requires an SNR greater than 65 dB. The simulation results were compared to physical data, collected with a portable EIT system (PulmoTrace, CardioInspect). The validation study was employed for a group of N = 28 healthy patients, and a comparison with impedance cardiography measurements (BioZ, Cardiodynamics) was made, showing a correlation of r = 0.86 (p = 4 x10(-9)). The preliminary results demonstrate that parametric EIT has the potential to measure SV, and may be applicable for both clinical and home environment usage.
Development, construction and analysis of the 'OErsted' fluxgate magnetometer (1995)

The experiments and theoretical considerations leading to the construction of a high-performance three-axis fluxgate magnetometer are described. The magnetometer will be used (1996) in the Earth's field mapping satellite named 'OErsted'. The fluxgate sensors are based on stress-annealed metallic glass ribbons as core materials. It is shown that very simple physical models can be used to explain the fluxgate mode of operation, thereby making it easy to calculate the overall sensor performance from first principles. Special attention is drawn to the core excitation current which is analysed on the basis of nonlinear electrical circuitry. It is furthermore shown that the ring-core demagnetizing field obeys a simple cosine law which permits the calculation of the sensor sensitivity with high accuracy. The sensitivity, that is the signal-to-noise ratio, is ultimately determined by the sensor noise which is about 15 pT RMS (0.06-10 Hz), corresponding to a noise power density (1/f noise) of 6.2 pT Hz-1/2 at 1 Hz. The actual magnetometer operating range and sensitivity is determined by the 1 bit resolution of the Earth's field represented by the output from the 18 bit AD converted used in the instrument (+or-65536 nT with 0.5 nT resolution). The maximum attainable bandwidth is half the sensor excitation frequency (1/2*15 kHz) but the OErsted magnetometer bandwidth is limited to 250 Hz. The thermal stability of the sensor has been measured to be better than 1 nT in the temperature range -20 to +60 degrees C.
Chinese Hamster Ovarian Cells Transfected with the Murine lnterleukin-6 Gene cause Hypercalcemia as well as Cachexia, Leukocytosis and Thrombocytosis in Tumor-Bearing Nude Mice (1991)

The effects of interleukin-6 (IL-6) in vivo were assessed by inoculating Chinese hamster ovarian (CHO) cells which were transfected with the murine IL-6 gene in nude mice. Nude mice bearing CHO cells expressing IL-6 developed hypercalcemia. Tumorbearing mice also showed increases in white cell count, platelet count, and decreases in body weight. In nude mice carrying CHO tumors which had not been transfected with the IL-6 gene, there were no changes in these parameters. These results suggest that increased circulating concentrations of IL-6 in patients with malignant disease may contribute to a number of paraneoplastic syndromes including hypercalcemia, cachexia, leukocytosis and thrombocytosis.
[Study on the immune response of mice receiving bone allografts]. (1988)

The immune response of bone allografts has not been well understood. The present study was performed to examine the MLC response, CML activity, and alloantibody production of inbred mice receiving fresh and frozen bone allografts. A) Fresh allografts: High MLC response was observed in an early phase of the culture, suggesting the activation and proliferation of helper T cells. Percent cytotoxicity of CML assay was 24% on the 9th day after grafting, indicating the production of cytotoxic T cells. High alloantibody titer was observed on the 30th day after grafting, further indicating the production of the cytotoxic alloantibody. B) Frozen allografts: No significant difference was observed between frozen allografts and fresh isografts (control group) in these immunological responses. These results indicated that the antigenicity of the frozen bone decreased greatly so that matching of the major histocompatibility complex may not be required.
A LDP Fast Protection Switching Scheme for Concurrent Multiple Failures in MPLS Network (2009)

In this paper, we provide a non route-calculating MPLS LDP fast protection switching scheme called LDPNRC-FPS scheme which is efficient in transient multi-failures in MPLS networks. This scheme makes full use of various working modes and configurable loop detection of LDP protocol.. When network failures happen, the scheme need not to compute routing again. The scheme uses Path Vector TLV and Hop Count TLV in LDP mapping message to avoid loop intransient multi-failure scenario. Furthermore, OAM mechanism has been introduced into LDP NRC-FPS scheme for accelerating fault recovery process. Compared with traditional fast rerouting strategies in IP and MPLS layer, it reduces the failure recovery time of rerouting and has the advantage of more efficient network resource utilization. Performance analysis shows that LDP NRC-FPS scheme outperforms than traditional IP fast reroute scheme and MPLS protection switching scheme at loop ratio , path unreachable ratio and control message overhead aspects.
Induction of leucine aminopeptidase by interferon-gamma. Identification by protein microsequencing after purification by preparative two-dimensional gel electrophoresis. (1992)

The protein previously called "Mr approximately 50/pI approximately 6.9," which we observed to be induced by the immunoregulatory cytokine interferon (IFN)-gamma in human fibroblasts, was purified from a total cell lysate by preparative two-dimensional gel electrophoresis and identified by partial amino-terminal sequencing as leucine aminopeptidase (LAP), a 53-kDa cytosolic exopeptidase. Induction of LAP protein by IFN-gamma, confirmed by immunoblotting with an antiserum raised against bovine lens LAP, is a consequence of induction of LAP mRNA and occurs in all four human cell lines examined: HS153 fibroblasts, ACHN renal carcinoma, A549 lung carcinoma, and A375 melanoma. Induction of LAP mRNA is a secondary response to IFN-gamma, blocked by inhibition of protein synthesis with cycloheximide.
DNA Ligases:  Structure, Reaction Mechanism, and Function (2006)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDNA Ligases: Structure, Reaction Mechanism, and FunctionAlan E. Tomkinson, Sangeetha Vijayakumar, John M. Pascal, and Tom EllenbergerView Author Information Radiation Oncology Research Laboratory and Marlene and Stewart Greenebaum Cancer Center, Molecular and Cellular Biology Graduate Program, University of Maryland School of Medicine, Baltimore, Maryland 21201, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115 Cite this: Chem. Rev. 2006, 106, 2, 687–699Publication Date (Web):January 24, 2006Publication History Received26 April 2005Published online24 January 2006Published inissue 1 February 2006https://pubs.acs.org/doi/10.1021/cr040498dhttps://doi.org/10.1021/cr040498dresearch-articleACS PublicationsCopyright © 2006 American Chemical SocietyRequest reuse permissionsArticle Views8049Altmetric-Citations210LEARN 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 SUBJECTS:Conformation,Genetics,Ligation,Monomers,Peptides and proteins Get e-Alerts
Identification and Isolation of a Receptor for N-Methyl Alkylammonium Salts: Molecular Amplification in a Pseudo-peptide Dynamic Combinatorial Library (2001)

A cyclic pseudo-peptide receptor for acetylcholine has been amplified and isolated from a dynamic combinatorial library by virtue of templated stabilization under thermodynamic control (see scheme, TFA=trifluoroacetic acid). This is a demonstration of significant molecular amplification in dynamic systems to evolve a novel receptor.
A near-optimal algorithm for differentially-private principal components (2013)

The principal components analysis (PCA) algorithm is a standard tool for identifying good low-dimensional approximations to high-dimensional data. Many data sets of interest contain private or sensitive information about individuals. Algorithms which operate on such data should be sensitive to the privacy risks in publishing their outputs. Differential privacy is a framework for developing tradeoffs between privacy and the utility of these outputs. In this paper we investigate the theory and empirical performance of differentially private approximations to PCA and propose a new method which explicitly optimizes the utility of the output. We show that the sample complexity of the proposed method differs from the existing procedure in the scaling with the data dimension, and that our method is nearly optimal in terms of this scaling. We furthermore illustrate our results, showing that on real data there is a large performance gap between the existing method and our method.
V617F mutation in JAK2 is associated with poorer survival in idiopathic myelofibrosis (2005)

International audience
Inactivation of Naturally Grown Microorganisms in Orange Juice Using Pulsed Electric Fields (2006)

In this paper, the effect of pulsed electric fields (PEFs) on naturally contaminated orange juice was investigated. A 2-log reduction in a colony count for the naturally grown microorganisms was achieved after application of 120 pulses/mL at a PEF level of 46 kV/cm. Also, the effect of the PEF on microorganisms inoculated in orange juice was studied. Compared to the naturally grown microorganisms, about 1-log more reduction was observed with inoculated microorganisms that were subjected to the same PEF conditions. The results suggest that other factors like the increased temperature and antimicrobial additives might be required to enhance the killing efficiency. A 20 degC increase in temperature prior to the application of the PEF resulted in about 1-log more reduction in microorganisms
Post-transcriptional nucleotide addition is responsible for the formation of the 5' terminus of histidine tRNA. (1982)

All sequenced histidine tRNAs have one additional nucleotide at the 5' end when compared to other tRNA species. Sequence analysis of histidine tRNA genes from Drosophila melanogaster and Schizosaccharomyces pombe showed that the terminal guanylate residue of the mature tRNAs is not encoded by the genes. Analysis of the products from in vitro transcription of these genes in extracts from Drosophila Kc cells demonstrated that the 5'-terminal nucleotide present in the mature tRNA is added post-transcriptionally. The addition reaction requires ATP. A portion of the mature tRNAs are then modified at the 5'-terminal pG. Analysis of the RNA species formed during the in vitro maturation of the Drosophila histidine tRNA primary transcript uncovered the following maturation scheme: (i) the primary transcript is processed by RNase P at the 5' end to form an intermediate precursor; (ii) the 3'-flanking sequence is endonucleolytically removed, and a guanylate moiety is added to the 5' end to form mature-sized histidine tRNA; and (iii) a fraction of the 5'-terminal guanylate residues then undergoes modification. In contrast to the capping of eukaryotic mRNA, the guanylate addition to histidine tRNA results in the formation of a (3'-5')-phosphodiester bond. There are no precedents for the post-transcriptional addition of nucleotides (in phosphodiester linkage) to the 5' end of RNA precursors.
Purification and Properties of a Phospholipase C that has High Activity Toward Sphingomyelin from Aspergillus Saitoi (1987)

An enzyme hydrolyzing sphingomyelin was purified from extracts of solid cultures of Aspergillus saitoi 7041 by fractionation with isopropanol followed by successive column chromatographies on DEAE-Sepharose CL-6B, butyl-Toyopearl 650 M, and phenyl-Sepharose CL-4B. The preparation of purified enzyme was homogeneous and had an activity increased 81-fold over that of the isopropanol fraction. The yield was about 65%. The molecular weight was estimated to be 54,000 by sodium dodecyl sulfate-gel electrophoresis. The enzyme solution had a violet color and contained iron atoms. The enzyme catalyzed the hydrolysis of sphingomyelin to N-acylsphingosine and phosphorylcholine. The optimum pH for hydrolytic activity was around 3.5. The Km values for sphingomyelin and 2-hexadecanoylamino-4-nitrophenylphosphorylcholine were 0.11 and 0.33 mM, respectively. The enzyme also catalyzed the hydrolysis of other phospholipids; the order of its hydrolytic activity at a substrate concentration of 2.5 mM was phosphatidylcholine greater than or equal to sphingomyelin = phosphatidylethanolamine = lysophosphatidylethanolamine greater than phosphatidyl DL-glycerol = phosphatidyl L-serine greater than phosphatidylinositol. From these results, this enzyme appears to be a new type of phospholipase C(phosphatidylcholine cholinephosphohydrolase, EC 3.1.4.3).
1980 CRC Fuel Rating Program - The Effects of Heavy Aromatics and Ethanol on Gasoline Road Octane Ratings (1982)

&lt;div class="htmlview paragraph"&gt;A gasoline Road Octane study was conducted by the Coordinating Research Council (CRC) to evaluate the effects of heavy aromatics (C&lt;sub&gt;9&lt;/sub&gt; and heavier) and ethanol content on Road Octane performance independent of Research Octane Number (RON) and Motor Octane Number (MON). Maximum-throttle and part-throttle Road ON’s were found to be well predicted by equations containing only RON and MON terms. Heavier aromatics were found to have a small adverse effect on both maximum-throttle and part-throttle Road ON independent of its direct effects on RON and MON.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The all-car data did not show a significant ethanol-content effect, but eight of the thirty-seven cars did show significant effects for ethanol content.&lt;/div&gt;
Coding for a network coded fountain (2011)

Batched sparse (BATS) codes are proposed for transmitting a collection of packets through communication networks employing linear network coding. BATS codes generalize fountain codes and preserve the properties such as ratelessness and low encoding/decoding complexity. Moreover, the buffer size and the computation capability of the intermediate network nodes required to apply BATS codes are independent of the number of packets for transmission. It is verified theoretically for certain cases and demonstrated numerically for the general cases that BATS codes achieve rates very close to the capacity of linear operator channels.
Late results of a prospective study of direct intra-arterial urokinase infusion for peripheral arterial and bypass graft occlusions (1995)

The outcome of 72 direct intra-arterial urokinase infusions was studied prospectively. Thirty four were performed for native arterial occlusion and 38 for bypass graft occlusion; the immediate success rates were 67.5 and 84% respectively. The overall incidence of complications was 26%. Median follow-up was 36 (range 1-60) months. Seventeen patients (27%) died during follow-up; nine (14%) required a major amputation. Among patients with native arterial occlusion, 29% had no adjunctive procedure after thrombolysis; of these patients, 85% remained patent at a median of 21 (range 3-42) months. Among bypass occluded patients, only two (6%) had no lesion revealed after successful lysis; both bypasses remain patent at 54 and 58 months respectively. For patients treated with balloon angioplasty immediately after successful thrombolysis, 62% with native arterial occlusion remained patent at a median of 39 (range 2-60) months, whereas only 27% of bypass occlusion patients were patent at a median of 11 (range 2-40) months. Of patients requiring a surgical procedure after thrombolysis, 23 new bypasses (15 vein, eight prosthetic) were placed (nine in native arterial occlusion patients, 14 in bypass occlusion patients). In addition, there were 15 other surgical procedures, including six thrombectomies, four vein patch angioplasties, four vein jump grafts and one endarterectomy. The primary and secondary patencies for the 15 new vein bypasses placed were 81 and 88% respectively at a median follow-up of 36 months. Good immediate results were experienced with urokinase thrombolysis for peripheral arterial and graft occlusions. However, multiple adjunctive procedures were required to maintain patency.(ABSTRACT TRUNCATED AT 250 WORDS)