gebhart/patrepeval huggingface dataset:
Identification and Characterization of PF4varl, a Human Gene Variant of Platelet Factor 4 (1989)

A synthetic DNA probe designed to detect coding sequences for platelet factor 4 and connective tissue-activating peptide III (two human platelet alpha-granule proteins) was used to identify several similar sequences in total human DNA. Sequence analysis of a corresponding 3,201-base-pair EcoRI fragment isolated from a human genomic library demonstrated the existence of a variant of platelet factor 4, designated PF4var1. The gene for PF4var1 consisted of three exons and two introns. Exon 1 coded for a 34-amino-acid hydrophobic leader sequence that had 70% sequence homology with the leader sequence for PF4 but, in contrast, contained a hydrophilic amino-terminal region with four arginine residues. Exon 2 coded for a 42-amino-acid segment that was 100% identical with the corresponding segment of the mature PF4 sequence containing the amino-terminal and disulfide-bonded core regions. Exon 3 coded for the 28-residue carboxy-terminal region corresponding to a domain specifying heparin-binding and cellular chemotaxis. However, PF4var1 had amino acid differences at three positions in the lysine-rich carboxy-terminal end that were all conserved among human, bovine, and rat PF4s. These differences should significantly affect the secondary structure and heparin-binding properties of the protein based on considerations of the bovine PF4 crystal structure. By comparing the PF4var1 genomic sequence with the known human cDNA and the rat genomic PF4-coding sequences, we identified potential genetic regulatory regions for PF4var1. Rat PF4 and human PF4var1 genes had identical 18-base sequences 5' to the promoter region. The intron positions appeared to correspond approximately to the boundaries of the protein functional domains.
The Coactivator PGC-1 Is Involved in the Regulation of the Liver Carnitine Palmitoyltransferase I Gene Expression by cAMP in Combination with HNF4α and cAMP-response Element-binding Protein (CREB) (2002)

Liver carnitine palmitoyltransferase I catalyzes the transfer of long-chain fatty acids into mitochondria. L-CPT I is considered the rate-controlling enzyme in fatty acid oxidation. Expression of the L-CPT I gene is induced by starvation in response to glucagon secretion from the pancreas, an effect mediated by cAMP. Here, the molecular mechanisms underlying the induction of L-CPT I gene expression by cAMP were characterized. We demonstrate that the cAMP response unit of the L-CPT I gene is composed of a cAMP-response element motif and a DR1 sequence located 3 kb upstream of the transcription start site. Our data strongly suggest that the coactivator PGC-1 is involved in the regulation of this gene expression by cAMP in combination with HNF4 alpha and cAMP-response element-binding protein (CREB). Indeed, (i) cotransfection of CREB or HNF4 alpha dominant negative mutants completely abolishes the effect of cAMP on the L-CPT I promoter, and (ii) the cAMP-responsive unit binds HNF4 alpha and CREB through the DR1 and the cAMP-response element sequences, respectively. Moreover, cotransfection of PGC-1 strongly activates the L-CPT I promoter through HNF4 alpha bound at the DR1 element. Finally, we show that the transcriptional induction of the PGC-1 gene by glucagon through cAMP in hepatocytes precedes that of L-CPT-1. In addition to the key role that PGC-1 plays in glucose homeostasis, it may also be critical for lipid homeostasis. Taken together these observations suggest that PGC-1 acts to coordinate the process of metabolic adaptation in the liver.
A mutation in the TMPRSS6 gene, encoding a transmembrane serine protease that suppresses hepcidin production, in familial iron deficiency anemia refractory to oral iron (2008)

The findings of this study suggest that the observed TMPRSS6 mutation leads to overproduction of hepcidin and, in turn, to defective iron absorption and utilization. More generally, they confirm in humans the inhibitory effect of matriptase-2 on hepcidin synthesis already demonstrated in mice.
Scaling accurate genetic variant discovery to tens of thousands of samples (2017)

Abstract Comprehensive disease gene discovery in both common and rare diseases will require the efficient and accurate detection of all classes of genetic variation across tens to hundreds of thousands of human samples. We describe here a novel assembly-based approach to variant calling, the GATK HaplotypeCaller (HC) and Reference Confidence Model (RCM), that determines genotype likelihoods independently per-sample but performs joint calling across all samples within a project simultaneously. We show by calling over 90,000 samples from the Exome Aggregation Consortium (ExAC) that, in contrast to other algorithms, the HC-RCM scales efficiently to very large sample sizes without loss in accuracy; and that the accuracy of indel variant calling is superior in comparison to other algorithms. More importantly, the HC-RCM produces a fully squared-off matrix of genotypes across all samples at every genomic position being investigated. The HC-RCM is a novel, scalable, assembly-based algorithm with abundant applications for population genetics and clinical studies.
HMDB: A large video database for human motion recognition (2011)

With nearly one billion online videos viewed everyday, an emerging new frontier in computer vision research is recognition and search in video. While much effort has been devoted to the collection and annotation of large scalable static image datasets containing thousands of image categories, human action datasets lag far behind. Current action recognition databases contain on the order of ten different action categories collected under fairly controlled conditions. State-of-the-art performance on these datasets is now near ceiling and thus there is a need for the design and creation of new benchmarks. To address this issue we collected the largest action video database to-date with 51 action categories, which in total contain around 7,000 manually annotated clips extracted from a variety of sources ranging from digitized movies to YouTube. We use this database to evaluate the performance of two representative computer vision systems for action recognition and explore the robustness of these methods under various conditions such as camera motion, viewpoint, video quality and occlusion.
Measurement of directional thermal properties of biomaterials (2001)

This paper presents an experimental technique to measure the directional thermal conductivity and thermal diffusivity of materials. A heated thermistor heats the sample and a sensing thermistor placed about 2.5 mm away measures the temperature rise due the heating pulse at the heated thermistor. An empirical relation between the power delivered by the first thermistor and the temperature rise recorded by the sensing thermistor is used to measure the thermal conductivity of the material along the line joining the thermistors. Diffusivity of the material is determined from the delay between the power pulse in the heated thermistor and the temperature pulse at the sensing thermistor. Signal processing was done to eliminate errors in the measurement due to change of base line temperature. Uncertainty of the measurement technique was found to be 5% when tested in media of known thermal properties. The thermal conductivity and thermal diffusivity of swine left ventricle in normal and ablated conditions were measured using this technique. The thermal conductivity of the tissue dropped significantly from 0.61 to 0.50 W.m(-1).K(-1) after ablation while the diffusivity dropped from 2.1 x 10(-7) to 1.7 x 10(-7)m2.s(-1).
Nuclear Factor-κB and Manganese Superoxide Dismutase Mediate Adaptive Radioresistance in Low-Dose Irradiated Mouse Skin Epithelial Cells (2007)

Mechanisms governing inducible resistance to ionizing radiation in untransformed epithelial cells pre-exposed to low-dose ionizing radiation (LDIR; </=10 cGy) are not well understood. The present study provides evidence that pre-exposure to 10 cGy X-rays increases clonogenic survival of mouse skin JB6P+ epithelial cells subsequently exposed to 2 Gy doses of gamma-rays. To elucidate the molecular pathways of LDIR-induced adaptive radioresistance, the transcription factor nuclear factor-kappaB (NF-kappaB) and a group of NF-kappaB-related proteins [i.e., p65, manganese superoxide dismutase (MnSOD), phosphorylated extracellular signal-regulated kinase, cyclin B1, and 14-3-3zeta] were identified to be activated as early as 15 min after LDIR. Further analysis revealed that a substantial amount of both 14-3-3zeta and cyclin B1 accumulated in the cytoplasm at 4 to 8 h when cell survival was enhanced. The nuclear 14-3-3zeta and cyclin B1 were reduced and increased at 4 and 24 h, respectively, after LDIR. Using YFP-fusion gene expression vectors, interaction between 14-3-3zeta and cyclin B1 was visualized in living cells, and LDIR enhanced the nuclear translocation of the 14-3-3zeta/cyclin B1 complex. Treatment of JB6P+ cells with the NF-kappaB inhibitor IMD-0354 suppressed LDIR-induced expression of MnSOD, 14-3-3zeta, and cyclin B1 and diminished the adaptive radioresistance. In addition, treatment with small interfering RNA against mouse MnSOD was shown to inhibit the development of LDIR-induced radioresistance. Together, these results show that NF-kappaB, MnSOD, 14-3-3zeta, and cyclin B1 contribute to LDIR-induced adaptive radioresistance in mouse skin epithelial cells.
New Family of Base- and Nucleophile-Sensitive Amino-Protecting Groups. A Michael-Acceptor-Based Deblocking Process. Practical Utilization of the 1,1-Dioxobenzo[<i>b</i>]thiophene-2-ylmethyloxycarbonyl (Bsmoc) Group (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTNew Family of Base- and Nucleophile-Sensitive Amino-Protecting Groups. A Michael-Acceptor-Based Deblocking Process. Practical Utilization of the 1,1-Dioxobenzo[b]thiophene-2-ylmethyloxycarbonyl (Bsmoc)† GroupLouis A. Carpino, Michael Philbin, Mohamed Ismail, George A. Truran, E. M. E. Mansour, Shin Iguchi, Dumitru Ionescu, Ayman El-Faham, Christoph Riemer, Ralf Warrass, and Manfred S. WeissView Author Information Department of Chemistry, University of Massachusetts Amherst, Massachusetts 01003 Cite this: J. Am. Chem. Soc. 1997, 119, 41, 9915–9916Publication Date (Web):October 15, 1997Publication History Received30 April 1997Published online15 October 1997Published inissue 1 October 1997https://pubs.acs.org/doi/10.1021/ja9713690https://doi.org/10.1021/ja9713690rapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views1149Altmetric-Citations44LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Adducts,Monomers,Peptides and proteins,Piperidines,Reactivity Get e-Alerts
Pregnancy Prevents Hypertensive Remodeling of Cerebral Arteries (2005)

We investigated how hypertension during pregnancy affected passive structural (wall:lumen, wall stress) and active (myogenic activity) responses of the cerebral circulation. Female nonpregnant (NP; n=8) Sprague Dawley rats were compared with late-pregnant (LP; day 19 to 20, n=6) rats. Some animals were treated with the NO synthase inhibitor nitro-L-arginine in their drinking water to raise blood pressure. LP rats (n=6) were treated for the last 7 days of pregnancy (last trimester) to mimic preeclampsia and compared with NP rats treated for the same duration (n=8). Active and passive responses were determined on isolated and pressurized third-order posterior cerebral arteries. Nitro-L-arginine treatment significantly raised blood pressure in both groups of animals that was associated with increased wall thickness and wall:lumen ratio in the NP hypertensive animals versus controls (P<0.05). In contrast, this response to pressure was absent in LP animals, which had similar wall measurements. In addition, arteries from NP hypertensive animals had increased myogenic tone and pressure of forced dilatation compared with NP control animals (P<0.01). Again, this response was lacking in the LP hypertensive animals that had similar tone and pressure of forced dilatation as normotensive controls. The increased tone and wall thickness decreased wall stress in the NP hypertensive animals, a response that did not occur in LP hypertensive animals. Because medial hypertrophy is considered a protective response to elevated blood pressure, these results suggest that hypertension in pregnancy may predispose the cerebral circulation to autoregulatory breakthrough and blood-brain-barrier disruption when blood pressure is elevated, as during eclampsia.
Elastic registration of 3D cartilage surfaces from MR image data for detecting local changes in cartilage thickness (2000)

The objective of this work was to develop and validate a computational method for the registration (matching) of 3D cartilage plates from MR image data sets. The technique tracks local cartilage thickness changes over time. A 3D elastic registration technique was applied that identifies corresponding points of the bone-cartilage interface in MR data sets of 3D-reconstructed cartilage plates. In a first rigid preregistration step, the surfaces are aligned, using the principal axes decomposition to correct for different joint positions and orientations in the MR scanner. In a second step, the surfaces are deformed elastically, based on geometric surface features, until they are sufficiently similar to identify corresponding surface points. The method was validated against artificially corrupted cartilage surfaces and MR data obtained from in vivo and in vitro compression experiments. The in vivo reproducibility was tested on patellar data sets of volunteers, with repositioning of the joint in between replicate acquisitions.
Targeting kallikrein 6‐proteolysis attenuates CNS inflammatory disease (2004)

Kallikrein 6 (K6, MSP) is a newly identified member of the Kallikrein family of serine proteases that is preferentially expressed in the adult central nervous system (CNS). We have previously demonstrated that K6 is abundantly expressed by inflammatory cells at sites of CNS inflammation and demyelination in animal models of multiple sclerosis (MS) and in human MS lesions. To test the hypothesis that this novel enzyme is a mediator of pathogenesis in CNS inflammatory disease, we have evaluated whether autonomously generated K6 antibodies alter the clinicopathological course of disease in murine proteolipid protein139-151-induced experimental autoimmune encephalomyelitis (PLP139-151 EAE). We demonstrate that immunization of mice with recombinant K6 generates antibodies that block K6 enzymatic activity in vitro, including the breakdown of myelin basic protein (MBP), and that K6-immunized mice exhibit significantly delayed onset and severity of clinical deficits. Reduced clinical deficits were reflected in significantly less spinal cord pathology and meningeal inflammation and in reduced Th1 cellular responses in vivo and in vitro. These data demonstrate for the first time that K6 participates in enzymatic cascades mediating CNS inflammatory disease and that this unique enzyme may represent a novel therapeutic target for the treatment of progressive inflammatory disorders, including MS.
Malrecognition of Taste in Uremia (1980)

Impaired cognitive functions were reported in uremia. The purpose of this study was to quantify the functional state of taste in various stages of chronic renal failure. Taste sensitivity was assessed by asking the subjects to identify test solutions of sucrose ('sweet'), NaCl ('salty'), citric acid ('sour'), quinine ('bitter') and water presented randomly in five concentrations. The number of recognition errors was statistically analyzed as a measure of taste acuity. Four groups of subjects were examined: 20 nondialyzed uremic patients, 23 patients on regular hemodialysis, 20 patients suffering from chronic diseases with normal renal functions and 22 healthy volunteers. Non dialyzed and dialyzed uremic patients younger than 55 years had a significant impairment of recognition in all taste modalities when compared to both control groups. This was less obvious in patients older than 55 years. No differences in taste recognition were found between dialyzed and nondialyzed uremics of all ages. In the younger age group, however, there was imrpovement in the recognition of 'sour' and 'bitter' when tested before and immediately after the dialysis session. As zinc deficiency was excluded in all of the uremic patients we conclude that the impaired taste perception is another subtle facet of the uremic neuropathy.
An overview of molecular marker methods for plants (2006)

The development and use of molecular markers for the detection and exploitation of DNA polymorphism is one of the most significant developments in the field of molecular genetics. The presence of various types of molecular markers, and differences in their principles, methodologies, and applications require careful consideration in choosing one or more of such methods. No molecular markers are available yet that fulfill all requirements needed by researchers. According to the kind of study to be undertaken, one can choose among the variety of molecular techniques, each of which combines at least some desirable properties. This article provides detail review for 11 different molecular marker methods: restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), inter-simple sequence repeats (ISSRs), sequence characterized regions (SCARs), sequence tag sites (STSs), cleaved amplified polymorphic sequences (CAPS), microsatellites or simple sequence repeats (SSRs), expressed sequence tags (ESTs), single nucleotide polymorphisms (SNPs), and diversity arrays technology (DArT).
Architectural design for next generation heterogeneous memory systems (2010)

New enterprise workloads requiring fast, reliable access to increasing amounts of data have pushed today's memory systems to power and capacity limits while creating bottlenecks as they ensure transactions are persistently tracked for reliability. New storage class memory technologies (such as phase change memory) have the potential to offer high capacity within latency and bandwidth ranges acceptable for a computer memory system and persistence which may help ease the system-level burden of balancing performance and reliability. This paper describes architectural options for addressing the challenges of future, heterogeneous memory systems as well as the attributes required of the next generation memory devices.
<i>Lidocaine Patches Reduce Pain in Trauma Patients with Rib Fractures</i> (2011)

Rib fracture pain is notoriously difficult to manage. The lidocaine patch is effective in other pain scenarios with an excellent safety profile. This study assesses the efficacy of lidocaine patches for treating rib fracture pain. A prospectively gathered cohort of patients with rib fracture was retrospectively analyzed for use of lidocaine patches. Patients treated with lidocaine patches were matched to control subjects treated without patches. Subjective pain reports and narcotic use before and after patch placement, or equivalent time points for control subjects, were gathered from the chart. All patients underwent long-term follow-up, including a McGill Pain Questionnaire (MPQ). Twenty-nine patients with lidocaine patches (LP) and 29 matched control subjects (C) were analyzed. During the 24 hours before patch placement, pain scores and narcotic use were similar (LP 5.3, C 4.6, P = 0.19 and LP 51, C 32 mg morphine, P = 0.17). In the 24 hours after patch placement, LP patients had a greater decrease in pain scores (LP 1.2, C 0.0, P = 0.01) with no change in narcotic use (LP -8.4, C 0.5-mg change in morphine, P = 0.25). At 60 days, LP patients had a lower MPQ pain score (LP 7.7, C 12.2, P < 0.01), although only one patient was still using a patch. There was no difference in time to return to baseline activity (LP 73, C 105 days, P = 0.16) and no adverse events. Lidocaine patches are a safe, effective adjunct for rib fracture pain. Lidocaine patches resulted in a sustained reduction in pain, outlasting the duration of therapy.
Sustained improvement over two years in physical function, structural damage, and signs and symptoms among patients with rheumatoid arthritis treated with infliximab and methotrexate (2004)

Throughout 102 weeks of therapy, infliximab plus MTX provided significant, clinically relevant improvement in physical function and quality of life, accompanied by inhibition of progressive joint damage and sustained improvement in the signs and symptoms of RA among patients who previously had an incomplete response to MTX alone.
Calix[4]arenes as Molecular Platforms for Magnetic Resonance Imaging (MRI) Contrast Agents (2009)

The novel amphipilic conjugate of a calix[4]arene with four Gd-1,4,7,10- tetra(carboxymethyl)-1,4,7,10-tetraazacyclododecane (DOTA) chelates has potential as a magnetic resonance imaging contrast agent, both in its monomeric and in its micellar form. The system, illustrated here with its nuclear magnetic relaxation profile, shows good relaxivities, thanks to its high rigidity.An amphiphilic conjugate 1 of a calix[4]arene with four Gd-DOTA chelates (DOTA=1,4,7,10-tetra(carboxymethyl)-1,4,7,10-tetraazacyclododecane) was prepared and the properties relevant to its application as a magnetic resonance imaging (MRI) contrast agent were investigated by NMR, dynamic light scattering (DLS), and cryo-electron microscopy (cryo-TEM). The compound aggregates in water; its critical micelle concentration (cmc) is 0.21 mM (or 0.84 mM for Gd) at 37 degrees C. The relaxivity of the aggregates at 37 degrees C and 20 MHz (18.3 s(-1) per mM Gd or 73.2 s(-1) per mM 1) is about twice that of the monomer. Nuclear magnetic relaxation dispersion (NMRD) profiles show the relaxivity of the monomer to be almost independent of the magnetic field strength up to 60 MHz. At higher concentrations, the NMRD profiles exhibit a maximum at about 20 MHz, which is typical for high molecular volumes. The average water residence lifetime is 1.20 mus at 298 K as determined by (17)O NMR. The rotational correlation time of the monomer (390 ns at 37 degrees C) is very close to the optimal value predicted for high-field contrast agents. Monomer as well as micelles are very rigid systems with negligible local contributions to the overall rotational dynamics. The binding to human serum albumin (HSA) is significant (K(A)=1.2x10(3) M(-1)) and the relaxivity of the HSA adduct at 20 MHz is 24.6 s(-1) per mM Gd or 98.5 s(-1) per mM 1.