gebhart/patrepeval huggingface dataset:
Mapping the Protein Interaction Network of the Human COP9 Signalosome Complex Using a Label-free QTAX Strategy (2012)

The COP9 signalosome (CSN) is a multi-subunit protein complex that performs critical roles in controlling diverse cellular and developmental processes. Aberrant regulation of the CSN complex has been shown to lead to tumorigenesis. Despite its biological significance, our current knowledge of the function and regulation of the CSN complex is very limited. To explore CSN biology, we have developed and employed a new version of the tag team-based QTAX strategy (quantitative analysis of tandem affinity purified in vivo cross-linked (X) protein complexes) by incorporating a label-free MS method for quantitation. Coupled with protein interaction network analysis, this strategy produced a comprehensive and detailed assessment of the protein interaction network of the human CSN complex. In total, we quantitatively characterized 825 putative CSN-interacting proteins, with 270 classified as core interactors (captured by all three bait purifications). Biochemical validation further confirms the validity of selected identified interactors. This work presents the most complete analysis of the CSN interaction network to date, providing an inclusive set of physical interaction data consistent with physiological roles for the CSN. Moreover, the methodology described here is a general proteomic tool for the comprehensive study of protein interaction networks.
Intradialytic Cardiac Magnetic Resonance Imaging to Assess Cardiovascular Responses in a Short-Term Trial of Hemodiafiltration and Hemodialysis (2016)

Hemodynamic stress during hemodialysis (HD) results in recurrent segmental ischemic injury (myocardial stunning) that drives cumulative cardiac damage. We performed a fully comprehensive study of the cardiovascular effect of dialysis sessions using intradialytic cardiac magnetic resonance imaging (MRI) to examine the comparative acute effects of standard HD versus hemodiafiltration (HDF) in stable patients. We randomly allocated 12 patients on HD (ages 32-72 years old) to either HD or HDF. Patients were stabilized on a modality for 2 weeks before undergoing serial cardiac MRI assessment during dialysis. Patients then crossed over to the other modality and were rescanned after 2 weeks. Cardiac MRI measurements included cardiac index, stroke volume index, global and regional contractile function (myocardial strain), coronary artery flow, and myocardial perfusion. Patients had mean±SEM ultrafiltration rates of 3.8±2.9 ml/kg per hour during HD and 4.4±2.5 ml/kg per hour during HDF (<i>P</i>=0.29), and both modalities provided a similar degree of cooling. All measures of systolic contractile function fell during HD and HDF, with partial recovery after dialysis. All patients experienced some degree of segmental left ventricular dysfunction, with severity proportional to ultrafiltration rate and BP reduction. Myocardial perfusion decreased significantly during HD and HDF. Treatment modality did not influence any of the cardiovascular responses to dialysis. In conclusion, in this randomized, crossover study, there was no significant difference in the cardiovascular response to HDF or HD with cooled dialysate as assessed with intradialytic MRI.
Recent advances and new directions in the discovery and development of cyclin-dependent kinase inhibitors. (2001)

The eukaryotic cell division cycle is coordinated by cyclin-dependent protein kinases (CDKs) and cyclin subunits specific for the different phases of the cycle. These complexes phosphorylate target substrates, including the retinoblastoma susceptibility gene product (pRb) and related proteins. Cellular neoplastic transformations are accompanied by loss of regulation of cell cycle checkpoints, frequently through aberrant expression of CDKs and cyclins, as well as loss or mutation of their negative regulators. Consequently, one strategy in the development of mechanism-based anticancer therapeutics has been to halt malignant cellular proliferation through inhibition of the enzymatic activity of CDKs. The development of inhibitors selective for the ATP binding sites of particular protein kinases is a comparatively recent medicinal chemistry endeavor. Advances relevant to CDK inhibition are reviewed critically and alternative approaches to CDK inhibition, as well as applications of CDK inhibitors to therapeutic areas other than oncology, are also discussed.
Design and Development of Optical Packet Switched Network-Element in GE-OSAN (2007)

A key network-element for the gigabit Ethernet-optical switched access network that achieves higher security and longer span than PON is introduced. Its feasibility is confirmed when implemented by optical packet switches.
Design considerations for high power high frequency transformers (2002)

Various design considerations for high-power (multikilowatt), high-frequency transformers for DC-DC power converters are investigated. Although Ferrite (PC40) is lossier than Permalloy80 (0.5 mil) at the frequencies of interest (25-50 kHz) the use of the former is justified on the basis of cost, weight, and wide ranges of shapes. The influence of the leakage flux distribution in the window region on the copper losses has been demonstrated for various conventional winding arrangements. However, it is seen that in conventionally wound transformers a considerable amount of leakage flux enters the core, resulting in localized core saturation and hot-spots. This becomes a very critical issue for high-power, high-frequency transformers. Coaxially wound transformers are seen to be a viable alternative, in that the leakage flux is contained with the interwinding space, with very little or none of it permeating the core. Such transformers can also realize multiple benefits of a low distributed and controllable leakage inductance, robust construction, low electromechanical forces, and low core and copper losses. Test results on two coaxially wound transformers with different tube geometries, designed for 50 kW, 50 kHz, primary voltage of 200 V, and secondary voltage of 1000 V (two windings), are presented. Finally the concept of coaxial winding technique for three-phase transformers is also presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Determination and speciation of selenium in end products from a garbage incinerator (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination and speciation of selenium in end products from a garbage incineratorChristina Ericzon, Jean Pettersson, Marit Andersson, and Aake OlinCite this: Environ. Sci. Technol. 1989, 23, 12, 1524–1528Publication Date (Print):December 1, 1989Publication History Published online1 May 2002Published inissue 1 December 1989https://pubs.acs.org/doi/10.1021/es00070a012https://doi.org/10.1021/es00070a012research-articleACS PublicationsRequest reuse permissionsArticle Views72Altmetric-Citations15LEARN 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
Phosphinate Inhibitors of UDP‐<i>N</i>‐Acetylmuramoyl‐<scp>L</scp>‐Alanyl‐<scp>D</scp>‐Glutamate: <scp>L</scp>‐Lysine Ligase (MurE) (2007)

The increasing emergence of pathogenic bacterial strains with high resistance to antibiotic therapy has created an urgent need for the development of new antibacterial agents that are directed towards novel targets. We have focused our attention on the Mur ligases (MurC-F), which catalyze the early steps of bacterial peptidoglycan biosynthesis, and which to date represent under-exploited targets for antibacterial drug design. We show that some of our phosphinate inhibitors of UDP-N-acetylmuramoyl-L-alanyl:D-glutamate ligase (MurD) also inhibits UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:L-lysine ligase (MurE). To obtain new information on their structure-activity relationships, three new, structurally related phosphinates were synthesized and evaluated for inhibition of MurD and MurE.
Comparison of Lateral and Medial Orbital Decompression for the Treatment of Compressive Optic Neuropathy in Thyroid Eye Disease (2010)

Lateral orbital decompression and medial orbital decompression are both efficacious for the treatment of TED-associated CON. Lateral decompression also results in a greater proptosis reduction than medial decompression.
Active site similarities of glucose dehydrogenase, glucose oxidase, and glucoamylase probed by deoxygenated substrates (1992)

The specificity constants, kcat/KM, were determined for glucose oxidase and glucose dehydrogenase using deoxy-D-glucose derivatives and for glucoamylase using deoxy-D-maltose derivatives as substrates. Transition-state interactions between the substrate intermediates and the enzymes were characterized by the observed kcat/Km values and found to be very similar. The binding energy contributions of individual sugar hydroxyl groups in the enzyme/substrate complexes were calculated using the relationship delta(delta G) = -RT ln [(kcat/KM)deoxy/(kcat/KM)hydroxyl] for the series of analogues. The activity of all three enzymes was found to depend heavily on the 4- and 6-OH groups (4'- and 6'-OH in maltose), where changes in binding energies from 10 to 18 kJ/mol suggested strong hydrogen bonds between the enzymes and these substrate OH groups. The 3-OH (3'-OH in maltose) was involved in weaker interactions, while the 2-OH (2'-OH in maltose) had a very small if any role in transition-state binding. The three enzyme-substrate transition-state interactions were compared using linear free energy relationships (Withers, S. G., & Rupitz, K. (1990) Biochemistry 29, 6405-6409) in which the set of kcat/KM values obtained with substrate analogues for one enzyme is plotted against the corresponding values for a second enzyme. The high linear correlation coefficients (rho) obtained, 0.916, 0.958, and 0.981, indicate significant similarity in transition-state interactions, although the three enzymes lack overall sequence homology.(ABSTRACT TRUNCATED AT 250 WORDS)
A Streptococcal Collagen-like Protein Interacts with the α2β1 Integrin and Induces Intracellular Signaling (2005)

The streptococcal collagen-like proteins Scl1 and Scl2 are prokaryotic members of a large protein family with domains containing the repeating amino acid sequence (Gly-Xaa-Yaa)(n) that form a collagen-like triple-helical structure. Here, we test the hypothesis that Scl variant might interact with mammalian collagen-binding integrins. We show that the recombinant Scl protein p176 promotes adhesion and spreading of human lung fibroblast cells through an alpha2beta1 integrin-mediated interaction as shown in cell adhesion inhibition assays using anti-alpha2beta1 and anti-beta1 integrins monoclonal antibodies. Accordingly, C2C12 cells stably expressing alpha2beta1 integrin as the only collagen-binding integrin show productive cell adhesion activities on p176 that can be blocked by an anti-alpha2beta1 integrin antibody. In addition, p176 promotes tyrosine phosphorylation of p125(FAK) of C2C12 cells expressing alpha2beta1 integrin, whereas parental cells do not. Furthermore, C2C12 adhesion of human lung fibroblast cells to p176 induces phosphorylation of p125FAK, p130CAS, and p68Paxillin proteins. In a domain swapping experiment, we show that integrin binds to the collagenous domain of the Scl protein. Moreover, the recombinant inserted domain of the alpha2 integrin interacts with p176 with a relatively high affinity (K(D) = 17 nm). Attempts to identify the integrin sites in p176 suggest that more than one site may be involved. These studies, for the first time, suggest that the collagen-like proteins of prokaryotes retained not only structural but also functional characteristics of their eukaryotic counterparts.
Self-organization (2013)

Heterogeneous cellular network (HCN) deployments may imply an order of magnitude more network nodes than conventional homogenous macrocell deployments. Therefore, it is important that the integration and operation of these new nodes require minimal manual efforts from operators. Self-organizing network (SON) features can be seen as essential enablers to facilitate service as well as network deployment and management. The main objectives of SONs are to reduce the deployment costs, simplify network management (managing a plethora of radio access technologies (RATs) without significantly increasing operational expenses) and enhance network performance.
BRAF, GNAQ, and GNA11 mutations and copy number in pediatric low‐grade glioma (2012)

Fifty-two samples of pediatric low-grade glioma (48 primary, 4 recurrent) were analyzed for BRAF copy number variation (digital PCR analysis, CopyCaller) and point mutations of BRAF V600E, and exon 5 Q209 in GNAQ, and GNA11, using the MALDI-TOF mass spectrometer with validation by direct sequencing. An increased BRAF copy number was found in 18/47 primary samples tested; 15 of them (83.3%) were pilocytic astrocytomas. A BRAF mutation was found in 3/48 primary tumors, all with a normal BRAF copy number and no GNAQ mutation. One sample had a GNAQ209 mutation (Q209P626) with a normal BRAF gene; none of the tumors had a GNA11Q209 mutation. Recurrent or progressive tumors, analyzed in four patients, had the same molecular genotype as their primary. Increased BRAF copy number and activating BRAF mutations may be involved in the development of low-grade glioma via overactivation of the Ras/Raf pathway. This is the first report of a mutation in GNAQ209 in pediatric low-grade glioma. Understanding the molecular mechanisms underlying glioma initiation and growth may assist in the development of targeted therapies.
Obstacle avoidance and speed control in a mobile vehicle equipped with a compound eye (2005)

Shows that the use of onboard visual motion sensors has advantages in visually guided navigation. An agent equipped with a given array of motion detectors detects obstacles all the more distant when it is running faster. Its "radius of vision" becomes simply proportional to speed, with the interesting consequence that the agent can easily adapt its speed to the environmental context. The simulation study presented shows that the newly designed visuomotor system allows the robot to reach a target while avoiding obstacles in cluttered environments, adapt its own speed to the situation, follow walls, retreat from dead-ends and bypass impenetrable clusters of obstacles. These performances result all from one and the same visuomotor algorithm and do not require any "arbitration" between different "behaviors" as is the case with the subsumption architecture. Nor do they require any kind of high level reasoning, world model and long term memory. The described system could be part of a hierarchical system and carry out the basic and reputedly difficult task of fast piloting in uncertain environments, for example, between intermediary waypoints that would be specified by a high level mission planner.
Approximate Record Matching Using Hash Grams (2011)

Accurately identifying duplicate records between multiple data sources is a persistent problem that continues to plague organizations and researchers alike. Small inconsistencies between records can prevent detection between two otherwise identical records. In this paper, we present a new probabilistic h-gram (hash gram) record matching technique by extending traditional n-grams and utilizing scale based hashing for equality testing. h-gram matching highly reduces the number of comparisons to be performed for duplicate record detection applicable to a variety of data types and data sizes by transforming data into its equivalent numerical realities. One of the key features of h-gram matching is that it is highly extensible providing more intuitive and flexible results. With the sampling technique in place, our method can be applied on variable size databases to perform data linkage and probabilistic results can be quickly obtained. We have extensively evaluated h-gram matching on large samples of real-world data and the results show higher level of accuracy as well as reduction in required time when compared with existing techniques.
Relationship between Virucidal Efficacy and Free Iodine Concentration of Povidone-Iodine in Buffer Solution (2016)

Povidone-iodine solutions prepared to various concentrations (0.01, 0.1, 1 and 10%) with 0.2M phosphate buffer (pH 7.0) (PVP-I PB) were analyzed to determine their free iodine concentrations using membrane permeation cells, and their inactivation effects on three viruses (influenza A virus, poliovirus type 1 and adenovirus type 3) were examined. The free iodine concentrations in the 0.01-10% PVP-I PB were determined to be 1.84, 4.88, 1.58 and 0.17 ppm (approximate values), respectively, with the maximum obtained for the 0.1% solution. The virucidal efficacy of these PVP-I PB against poliovirus type 1 and adenovirus type 3 was found to be generally dependent on free iodine concentration, with the 0.1% solution being the most effective. Influenza A virus was inactivated with an action time of 15 s at all four concentrations examined. The results of this study suggested an association between free iodine concentration and virucidal efficacy for the 0.01-10% PVP-I PB.
Linear and Nonlinear Processes in the Erosion of H_{2}O Ice by Fast Light Ions (1980)

The erosion of water ice films by fast H and He ions has been found to depend on the electronic energy loss of the ion. At low temperatures the erosion yield is temperature independent and varies quadratically with the electronic stopping power, consistent with a Coulomb repulsion model of ejection. At temperatures above \ensuremath{\sim}100 \ifmmode^\circ\else\textdegree\fi{}K the erosion is found to be temperature dependent and linear with the electronic stopping power. The erosion in this regime can be associated with defect formation and migration in the ice.
Positive Reinforcement Training As a Technique to Alter Nonhuman Primate Behavior: Quantitative Assessments of Effectiveness (2003)

Many suggest that operant conditioning techniques can be applied successfully to improve the behavioral management of nonhuman primates in research settings. However, relatively little empirical data exist to support this claim. This article is a review of several studies that discussed applied positive reinforcement training techniques (PRT) on breeding/research colonies of rhesus macaques (Macaca mulatta) and chimpanzees (Pan troglodytes) at The University of Texas M. D. Anderson Cancer Center and measured their effectiveness. Empirical analyses quantified the amount of time required to train rhesus monkeys to come up, station, target, and stay. Additionally, a study found that time spent affiliating by female rhesus was changed as a function of training low affiliators to affiliate more and high affiliators to affiliate less. Another study successfully trained chimpanzees to feed without fighting and to come inside on command. PRT is an important behavioral management tool that can improve the care and welfare of primates in captivity. Published empirical findings are essential for managers to assess objectively the utility of positive reinforcement training techniques in enhancing captive management and research procedures.
Application Of Inexpensive Liquid Crystal TV To Optical Parallel Logic (1988)

The optical implementation of all parallel logic gates using inexpensive LCTVs is demonstrated and basic experimental results are presented.
ChemInform Abstract: PREPARATION OF ISOPROPYL AND TERT.‐BUTYL DIFLUOROPHOSPHITES (1974)

Abstract Die beiden Titelverbindungen wurden durch Umsetzen von PF 3 mit den betreffenden Alkoholen in 25 bzw. 50%iger Ausbeute dargestellt.
Facile Proton Conduction via Ordered Water Molecules in a Phosphonate Metal−Organic Framework (2010)

A new phosphonate metal-organic framework (MOF) with a layered motif but not that of the classical hybrid inorganic-organic solid is presented. Zn(3)(L)(H(2)O)(2)·2H(2)O (L = [1,3,5-benzenetriphosphonate](6-)), henceforth denoted as PCMOF-3, contains a polar interlayer lined with Zn-ligated water molecules and phosphonate oxygen atoms. These groups serve to anchor free water molecules into ordered chains, as observed by X-ray crystallography. The potential for proton conduction via the well-defined interlayer was studied by (2)H solid-state NMR spectroscopy and AC impedance spectroscopy. The proton conductivity in H(2) was measured as 3.5 × 10(-5) S cm(-1) at 25 °C and 98% relative humidity. More interestingly, an Arrhenius plot gave a low activation energy of 0.17 eV for proton transfer, corroborating the solid-state NMR data that showed exchange between all deuterium sites in the D(2)O analogue of PCMOF-3, even at -20 °C.
Grf40, A Novel Grb2 Family Member, Is Involved in T Cell Signaling through Interaction with SLP-76 and LAT (1999)

We molecularly cloned a new Grb2 family member, named Grf40, containing the common SH3-SH2-SH3 motif. Expression of Grf40 is predominant in hematopoietic cells, particularly T cells. Grf40 binds to the SH2 domain-containing leukocyte protein of 76 kD (SLP-76) via its SH3 domain more tightly than Grb2. Incidentally, Grf40 binds to linker for activation of T cells (LAT) possibly via its SH2 domain. Overexpression of wild-type Grf40 in Jurkat cells induced a significant increase of SLP-76-dependent interleukin (IL)-2 promoter and nuclear factor of activated T cell (NF-AT) activation upon T cell receptor (TCR) stimulation, whereas the COOH-terminal SH3-deleted Grf40 mutant lacked any recognizable increase in IL-2 promoter activity. Furthermore, the SH2-deleted Grf40 mutant led to a marked inhibition of these regulatory activities, the effect of which is apparently stronger than that of the SH2-deleted Grb2 mutant. Our data suggest that Grf40 is an adaptor molecule involved in TCR-mediated signaling through a more efficient interaction than Grb2 with SLP-76 and LAT.
Model of current pathways in electrical water bath stunners used for poultry (1992)

Abstract 1. The paper explains the use and method of operation of electrical water bath stunners, and explains the possible current pathways through a single bird and through a number of birds. 2. A mathematical model has been formulated to demonstrate the effects of bird resistance and physical attitude of the bird on the current received by individual birds in a water bath stunner. 3. The model shows that readings from ammeters installed in series with commercial stunners, or the values shown on voltmeters, are not an accurate indicator or a guarantee that individual birds are effectively stunned. 4. The model demonstrates the need for a stunner to supply a constant current to each bird, rather than operate at a constant voltage where the current which the bird receives is dependant upon its own resistance.