gebhart/patrepeval huggingface dataset:
Insertion Loop 256−268 in Coagulation Factor IX Restricts Enzymatic Activity in the Absence but Not in the Presence of Factor VIII (2000)

Insertions in surface loops bordering the substrate-binding groove have been shown to play a major role in the interaction of serine proteases with their cognate inhibitors and substrates. In the present study, we investigated the functional role of factor IX insertion loop 256-268, and in particular of residues Asn(264) and Lys(265) therein. To this end, the purified and activated mutants des-(N264,K265)-FIX and FIX-K265A were compared to normal factor IXa with regard to a number of functional properties. The catalytic efficiency of des-(N264,K265)-FIXa and FIXa-K265A toward the amide substrate CH(3)SO(2)-Leu-Gly-Arg-pNA was 2-3-fold increased relative to that of normal factor IXa. Comparison of the activities of normal and mutant factor IXa toward a series of closely related amide substrates indicates that mutation of residues Asn(264)-Lys(265) influences the interactions in the S2-binding site. The mutations in loop 256-268 also increased the susceptibility of factor IXa to antithrombin inhibition by approximately 3-fold. Factor X activation experiments in the absence of factor VIIIa revealed that the catalytic efficiency of des-(N264,K265)-FIXa and FIXa-K265A was about 20 times higher than that of normal factor IXa. In the presence of factor VIIIa, however, the activity toward factor X was similar to that of normal factor IXa. The reduced sensitivity of the factor IXa mutants to factor VIIIa was neither due to an increase in factor IXa-dependent inactivation of factor VIIIa, nor to a lower affinity for this cofactor. Overall, these data demonstrate that loop 256-268 restricts the activity of factor IXa toward both synthetic and natural substrates. Complex formation with factor VIIIa alleviates the inhibitory effect of this insertion loop on the activation of FX.
Joint Spatio-Temporal Alignment of Sequences (2013)

Video alignment is important in different areas of computer vision such as wide baseline matching, action recognition, change detection, video copy detection and frame dropping prevention. Current video alignment methods usually deal with a relatively simple case of fixed or rigidly attached cameras or simultaneous acquisition. Therefore, in this paper we propose a joint video alignment for bringing two video sequences into a spatio-temporal alignment. Specifically, the novelty of the paper is to formulate the video alignment to fold the spatial and temporal alignment into a single alignment framework. This simultaneously satisfies a frame-correspondence and frame-alignment similarity; exploiting the knowledge among neighbor frames by a standard pairwise Markov random field (MRF). This new formulation is able to handle the alignment of sequences recorded at different times by independent moving cameras that follows a similar trajectory, and also generalizes the particular cases that of fixed geometric transformation and/or linear temporal mapping. We conduct experiments on different scenarios such as sequences recorded simultaneously or by moving cameras to validate the robustness of the proposed approach. The proposed method provides the highest video alignment accuracy compared to the state-of-the-art methods on sequences recorded from vehicles driving along the same track at different times.
Propofol in subanesthetic doses terminates status epilepticus in a rodent model (2001)

Status epilepticus is commonly refractory to first-line therapy, and thus better treatments are needed. We have investigated an experimental model of drug-resistant self-sustaining status epilepticus (SSSE) induced by 2 hours of perforant path stimulation. Propofol in subanesthetic doses administered shortly after the end of stimulation and also after a further 3 hours of SSSE terminated the SSSE without recurrence. This finding calls for a trial of propofol in refractory status epilepticus and also raises the possibility of using it as first-line therapy.
Evaluation of Long-Term Proppant Stability (1986)

ABSTRACT This paper presents initial results of a new testing program initiated to determine the performance of natural and man-made ceramic proppants over extended periods of time (months). The mechanisms involved in proppant performance are related to chemical and crystallographic makeup, as well as to processes used in their manufacture. Definition of the mechanisms controlling proppant behavior will allow future product development work to be concentrated on improving performance characteristics. Data from standarized API permeability/ conductivity testing are presented with a summary of previous long term testing. Results are coupled with new long term permeability data and acid reactivity data. Chemical and crystal structure phase analyses are also reviewed. The various tests were performed on a variety of oxide ceramics (intermediate and high strength proppants) as well as quartz sand. The long term data show that, after an initial period of consolidation, reductions in permeability over time are very slight for the commercial ceramic proppants tested at conditions of 69 MPa stress, 93°C, flowing a 2% KCl brine. Efforts made to correlate long term performance to short term acid reactivity have not been successful. It is unlikely that the long term performance of different classes of proppant can be compared by analyzing standard acid reactivity data.
Diastereoselective Synthesis of New <i>ψ</i>[(<i>E</i>)-CHCMe]- and <i>ψ</i>[(<i>Z</i>)-CHCMe]-type Alkene Dipeptide Isosteres by Organocopper Reagents and Application to Conformationally Restricted Cyclic RGD Peptidomimetics (2002)

Diastereoselective synthesis of new psi[(E)-CH=CMe]- and psi[(Z)-CH=CMe]-type alkene dipeptide isosteres corresponding to dipeptides having one N-methylamino acid, and application to bioactive peptides, are described. In a key reaction introducing the chiral alpha-alkyl group of the isosteres, organocopper-mediated alkylation of syn-beta-methylated gamma-mesyloxy-alpha,beta-enoate 26a afforded E- and Z-isomers of anti-S(N)2' products in a solvent-dependent manner. The resulting two isosteres, D-Phe-psi[(E)-CH=CMe]-L-Val 27a and D-Phe-psi[(Z)-CH=CMe]-L-Val 28b, which corresponded to trans- and cis-conformers of D-Phe-L-MeVal, respectively, were utilized in a structure-activity relationship study on cyclic RGD peptides 1 and 2, in company with a psi[(E)-CH=CH]-type alkene dipeptide isostere, D-Phe-psi[(E)-CH=CH]-L-Val. The cyclic isostere-containing pseudopeptides 3, 4, and 40 were synthesized and biological activity against integrin alpha(V)beta(3) and alpha(IIb)beta(3) receptors were also evaluated.
A Genetic Screen Identifies TCF3/E2A and TRIAP1 as Pathway-Specific Regulators of the Cellular Response to p53 Activation (2013)

The p53 transcription factor participates in diverse cellular responses to stress, including cell-cycle arrest, apoptosis, senescence, and autophagy. The molecular mechanisms defining the ultimate outcome of p53 activation remain poorly characterized. We performed a genome-wide genetic screen in human cells to identify pathway-specific coregulators of the p53 target gene CDKN1A (p21), an inhibitor of cell-cycle progression, versus BBC3 (PUMA), a key mediator of apoptosis. Our screen identified numerous factors whose depletion creates an imbalance in the p21:PUMA ratio upon p53 activation. The transcription factor TCF3, also known as E2A, drives p21 expression while repressing PUMA across cancer cell types of multiple origins. Accordingly, TCF3/E2A depletion impairs the cell-cycle-arrest response and promotes apoptosis upon p53 activation by chemotherapeutic agents. In contrast, TRIAP1 is a specific repressor of p21 whose depletion slows down cell-cycle progression. Our results reveal strategies for driving cells toward specific p53-dependent responses.
Retinoic acid signaling acts via Hox1 to establish the posterior limit of the pharynx in the chordate amphioxus (2004)

In the invertebrate chordate amphioxus, as in vertebrates, retinoic acid (RA) specifies position along the anterior/posterior axis with elevated RA signaling in the middle third of the endoderm setting the posterior limit of the pharynx. Here we show that AmphiHox1 is also expressed in the middle third of the developing amphioxus endoderm and is activated by RA signaling. Knockdown of AmphiHox1 function with an antisense morpholino oligonucleotide shows that AmphiHox1 mediates the role of RA signaling in setting the posterior limit of the pharynx by repressing expression of pharyngeal markers in the posterior foregut/midgut endoderm. The spatiotemporal expression of these endodermal genes in embryos treated with RA or the RA antagonist BMS009 indicates that Pax1/9, Pitx and Notch are probably more upstream than Otx and Nodal in the hierarchy of genes repressed by RA signaling. This work highlights the potential of amphioxus, a genomically simple, vertebrate-like invertebrate chordate, as a paradigm for understanding gene hierarchies similar to the more complex ones of vertebrates.
The CD24hi smooth muscle subpopulation is the predominant fraction in uterine fibroids (2014)

Uterine fibroids are the most common gynecological tumors affecting women in their reproductive age. Despite this high incidence the pathogenesis of fibroids is widely unsolved. Whereas formerly only imbalances in hormonal levels were considered to account for tumor development, the identification of genetic changes likely to affect myometrial stem cell reservoirs provided a novel approach to fibroid genesis. Here, we identified a certain subset of cells by the surface marker CD24 with increased abundance in fibroids compared with myometrial tissue. Fibroid cells expressing CD24 shared certain features of immature or progenitor-like cells such as quiescence, reduced expression of smooth muscle differentiation markers and elevated expression of genes involved in the wingless-type (WNT)-pathway such as beta-catenin. In addition, a positive correlation between CD24 and wingless-type family member 4 (WNT4) expression was observed in uterine fibroids with mediator subcomplex 12 gene (MED12) mutations. Our findings suggest that cells highly expressing CD24 represent a type of immature smooth muscle progenitor cells. Their accumulation might be driven by disturbed differentiation processes caused by genetic changes possibly involving MED12 mutations or high mobility group AT-hook (HMGA)2 rearrangements.
[Ru(bpy)<sub>2</sub>(5-cyanouracil)<sub>2</sub>]<sup>2+</sup> as a Potential Light-Activated Dual-Action Therapeutic Agent (2011)

The cation cis-[Ru(bpy)(2)(5CNU)(2)](2+) (bpy = 2,2'-bipyridine; 5CNU = 5-cyanouracil) was synthesized and investigated for use as a potential light-activated dual-action therapeutic agent. The complex undergoes efficient photoinduced 5CNU ligand exchange for solvent water molecules, thus simultaneously releasing biologically active 5CNU and generating [Ru(bpy)(2)(H(2)O)(2)](2+). The latter binds covalently to ds-DNA, such that photolysis results in the generation of 3 equiv of potential therapeutic agents from a single molecule.
Animal Models of Diabetes (2007)

As the incidence of diabetes increases worldwide, the need for recommendations on how to prevent and treat the condition grows exponentially, and so does the need for an authoritative source for information on the appropriate models to study the condition. The new edition of Animal Models of Diabetes is that source. The book presents updated
The retroviral oncogene qin belongs to the transcription factor family that includes the homeotic gene fork head. (1993)

Avian sarcoma virus 31 contains an oncogene that we have named qin. qin codes for a nuclear protein, Qin, that is a member of the HNF-3/fork head family of transcriptional regulators. Within this family Qin is particularly closely related to rat brain factor 1 (BF-1), a telencephalon-specific gene presumed to play an important role in the development of the mammalian brain.
Cloning of a Ca2+-ATPase gene of <i>Plasmodium falciparum</i> and comparison with vertebrate Ca2+-ATPases (1993)

A Ca(2+)-ATPase gene was cloned from the genomic libraries of Plasmodium falciparum. From the deduced amino acid sequence of the gene, a 139 kDa protein with a total of 1228 amino acids was predicted. Sequence of a partial cDNA clone of the gene identified two introns near the 3'-end at the regions identical to the regions assumed for the Ca(2+)-ATPase gene of P. yoelii, a rodent malaria species. As compared with a variety of Ca(2+)-ATPases, the P. falciparum Ca(2+)-ATPase had the highest amino acid sequence homology (78%) to the P. yoelii Ca(2+)-ATPase, moderate homology (45-50%) to vertebrate sarcoplasmic/endoplasmic reticulum Ca(2+)-ATPases (SERCAs), and lowest homology (20%) to a plasma membrane Ca(2+)-ATPase. The P. falciparum protein conserved sequences and residues that are important for the function and/or structure of the organellar type Ca(2+)-ATPase, such as high affinity Ca(2+)-binding sites, fluorescein isothiocyanate (FITC)-binding regions, and the phosphorylation site, but the protein did not contain calmodulin-binding regions that occur in the plasma membrane type Ca(2+)-ATPase. Thus we concluded the cloned gene was the organellar type Ca(2+)-ATPase of P. falciparum. In a region between the phosphorylation site and FITC-binding region, the P. falciparum protein was about 200 residues longer than the rabbit SERCA and lacked a sequence that binds to phospholamban, a protein that regulates the activity of the rabbit SERCA.(ABSTRACT TRUNCATED AT 250 WORDS)
Finite element analysis of sucker rod couplings with guidelines for improving fatigue life (1997)

The response of a variety of sucker rod couplings to an applied axial load was simulated using axisymmetric finite element models. The calculations investigated three sucker rod sizes and various combinations of the slimhole, Spiralock, and Flexbar modifications to the coupling. In addition, the effect of various make-ups (assembly tightness) on the performance of coupling was investigated. An axial load was applied to the sucker rod ranging from {minus}5 ksi to 40 ksi, encompassing three load cycles identified on a modified Goodman diagram as acceptable for indefinite service life of the sucker rods. The simulations of the various coupling geometries and make-ups were evaluated with respect to how well they accomplish the two primary objectives of preloading threaded couplings: (1) to lock the threaded coupling together so that it will not loosen and eventually uncouple, and (2) to improve the fatigue resistance of the threaded connection by reducing the stress amplitude in the coupling when subjected to cyclic loading. Perhaps the most significant finding in this study was the characterization of the coupling parameters which affect two stress measures. The mean hydrostatic stress, which determines the permissible effective alternating stress, is a function of the coupling make-up. Whereas, the alternating effective stress is a function of the relative stiffnesses of the pin and box sections of the coupling and, as long as the coupling does not separate, is unaffected by the amount of circumferential displacement applied during make-up. The results of this study suggest approaches for improving the fatigue resistance of sucker rod couplings.
Amino Acid Metabolism in Acute Renal Failure (1974)

A solution of 8 essential I-amino acids and hypertonic dextrose was administered to 5 patients in acute postoperative renal failure in a program of hyperalimentation designed to decrease the patient's catabolic state and to accrue certain metabolic benefits. A sixth patient receiving intravenous glucose alone served as a control. The pretreatment plasma concentrations of amino acids in all 6 patients did not differ significantly from normal; following intravenous essential amino acids at a dose of approximately 12.6 gm/24 hours, no significant elevations out of the normal range of these substances occurred. Since urinary excretion rates did not dramatically increase, urinary loss was excluded as a possible cause for the failure of increase of plasma concentrations. The results suggest that the administration of an intravenous solution of 1-amino acids and hypertonic dextrose is associated with rapid clearance from the blood of these substances and, with a failure of increased urinary excretion, indirect evidence of amino acid utilization for protein synthesis has been obtained. Histidine supplementation in patients with acute renal failure is probably unnecessary based on the lack of significant decreases in histidine concentrations in these patients.
Electrical Transport Properties of p-GaN (1996)

Electrical transport properties of Mg-doped p-GaN grown by organometallic vapor phase epitaxy were studied between 100 and 700 K. Calculations using Fermi-Dirac statistigs were carried out, identifying the majority carrier to be holes over the whole temperature range considered. The acceptor level is 0.17 ± 0.01 eV. The hole mobility is 10 cm 2 /V·s and is almost temperature independent from 160 to 300 K. The detailed analysis employing Fermi-Dirac statistics was then extended to determine the temperature dependence of the Fermi level.
Transferring genes for arcelin protein from wild to cultivated beans: implications for bruchid resistance (1988)

Four different types of arcelin, a protein that plays an important role in resistance to bruchids such as Zabrotes subfasciatus, were identified in wild accessions of Phaseolus vulgaris. Isogenic lines with cultivated black- (Porrillo 70) and white- (Sanilac) seeded parents were obtained by normal backcrossing of wild lines. The presence of arcelin hihgly affects the resistance parameters in lines derived both from Porrillo 70 and Sanilac. In lines derived from Sanilac, the life table of Zabrotes subfasciatus increased approx. 16 days, while in those from Porrillo 70, it increased 9 days. The strongest restriction effect was associated with the presence of arcelin-1, which decreased percentage of emergence up to 80 percent in both types of lines. Although the results are highly consistent in all Porrillo and Sanilac lines, the effect can vary given the difference observed in the levels of resistance to each arcelin type and because the lines differ in their degree of arcelin concn. in the seed, which is closely related with resistance to Zabrotes subfasciatus. (CIAT)
Kappa Free Light Chains in Cerebrospinal Fluid as Markers of Intrathecal Immunoglobulin Synthesis (2004)

Our data indicate that the nephelometric assay for kappaFLCs in CSF reliably detects intrathecal immunoglobulin synthesis. This automated and quantitative method could simplify the diagnostic procedure for CSF analysis in the routine laboratory.
Immersed electrokinetic finite element method (2006)

Abstract A new method is proposed for modelling the electrokinetic‐induced mechanical motion of particles in a fluid domain under an applied electric field. In this method, independent solid meshes move in a fixed background field mesh that models the fluid and the electric field. This simple strategy removes the need for expensive mesh updates. Furthermore, the reproducing kernel particle functions enable efficient coupling of various immersed deformable solids with the surrounding viscous fluid in the presence of an applied electric field. The electric force on a particle is calculated by the Maxwell stress tensor method. For the first time, three‐dimensional assembly of nano/biomaterials of various geometries and electrical properties have been comprehensively studied using the new method. Simulation of the dynamic process of electro‐manipulation of individual and multiple cells agrees well with experimental data. Preliminary results for selective deposition of viruses and stretching of a DNA molecule are also presented. Copyright © 2006 John Wiley & Sons, Ltd.
Understanding the Heart of the 5G Air Interface: An Overview of Physical Downlink Control Channel for 5G New Radio (2020)

New Radio (NR) is a new radio air interface developed by the 3rd Generation Partnership Project for the fifth generation (5G) mobile communications system. With great flexibility, scalability, and efficiency, 5G is expected to address a wide range of use cases including enhanced mobile broadband, ultra-reliable low-latency communications, and massive machine type communications. The physical downlink control channel (PDCCH) in NR carries downlink control information. Understanding how PDCCH operates is key to developing a good understanding of how information is communicated over NR. This article provides an overview of the 5G NR PDCCH by describing its physical layer structure, monitoring mechanisms, beamforming operation, and the carried information. We also share various design rationales that influenced NR standardization.
Characteristics of the Vold-Kalman order tracking filter (1999)

In this paper the filter characteristics of the Vold-Kalman Order Tracking Filter are presented. Both frequency response as well as time response and their time-frequency relationship have been investigated. Some guidelines for optimum choice of filter parameters are presented. The Vold-Kalman filter allows for the high performance simultaneous tracking of orders in systems with multiple independent shafts. With this new filter and using multiple tacho references, waveforms, as well as amplitude and phase may be extracted without the beating interactions that are associated with conventional methods. The Vold-Kalman filter provides several filter shapes for optimum resolution and stopband suppression. Orders extracted as waveforms have no phase bias, and may hence be used for playback, synthesis and tailoring.
Genetic and structural analysis of the protein stability problem (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGenetic and structural analysis of the protein stability problemBrian W. MatthewsCite this: Biochemistry 1987, 26, 22, 6885–6888Publication Date (Print):November 1, 1987Publication History Published online1 May 2002Published inissue 1 November 1987https://pubs.acs.org/doi/10.1021/bi00396a001https://doi.org/10.1021/bi00396a001research-articleACS PublicationsRequest reuse permissionsArticle Views416Altmetric-Citations183LEARN 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