gebhart/patrepeval huggingface dataset:
Potency and mass of factor VIII in FVIII products (2008)

Several factor (F) VIII products of different origin and structure are being used for haemophilia A treatment worldwide. The assessment of FVIII concentration in these products is done using activity assays, which are dependent upon the assay and its modifications. To evaluate FVIII products for potency and for FVIII concentration and specific activity, three activity-based assays [activated partial thromboplastin time (APTT), intrinsic FXase and synthetic coagulation proteome] and two immunoassays (ELISA and western blotting) were used in this study with albumin-free full-length recombinant (r) FVIII as a standard. In all activity assays, products A and B (both contain full-length rFVIII) at 1 U mL(-1) showed potency similar to that of the 0.7 nm (1 U mL(-1)) rFVIII standard. Product E (contains truncated rFVIII) was less potent in the APTT (83% of standard) and product C (contains plasma FVIII) was less potent in FXase assays (66%). The ELISA immunoassay revealed that the specific activity of FVIII proteins in products A-C and E varied over a wide range (3900-13 200 U mg(-1)) and was higher for most lots when compared with the standard (5000 U mg(-1)), whereas the specific activity of product D (contains plasma FVIII) was lower than expected (3200-4800 U mg(-1)). (i) FVIII potency estimated in different assays gives dissimilar results; (ii) the specific activity of FVIII in various FVIII products is different and inconsistent. Thus, the administration of an equal FVIII potency in units means the administration of different amounts of FVIII protein, which may partly explain apparent discrepancies in product performance.
Chronological Changes in MicroRNA Expression in the Developing Human Brain (2013)

We have constructed a miRNA expression atlas of the developing human brain, and we propose a classification scheme to guide future studies of neurobiological function.
Detection of Elevated Signaling Amino Acids in Human Diabetic Vitreous by Rapid Capillary Electrophoresis (2007)

Elevated glutamate is implicated in the pathology of PDR. The ability to rapidly assess the glutamate and amino acid content of vitreous provides a more complete picture of the chemical changes occurring at the diabetic retina and may lead to a better understanding of the pathology of PDR. Vitreous humor was collected following vitrectomies of patients with PDR and control conditions of macular hole or epiretinal membrane. A capillary electrophoresis method was developed to quantify glutamate and arginine. The analysis is relatively fast (<6 minutes) and utilizes a poly(ethylene)oxide and sodium dodecylsulfate run buffer. Both amino acid levels show significant increases in PDR patients versus controls and are comparable to other reports. The levels of vitreal glutamate vary inversely with the degree of observed hemorrhage. The results demonstrate a rapid method for assessment of a number of amino acids to characterize the chemical changes at the diabetic retina to better understand tissue changes and potentially identify new treatments.
Use of Specific Monoclonal and Polyclonal Antibodies to Define Distinct Antigens of the Porcine Zonae Pellucidae1 (1987)

Specific monoclonal and polyclonal antibodies to solubilized porcine and rabbit zonae pellucidae (ZP) and to purified ZP glycoprotein components have been used to define distinct ZP antigens. These studies demonstrate that the individual ZP glycoproteins contain both unique and shared determinants. One monoclonal antibody (R5) has been used to demonstrate that the major porcine ZP glycoprotein, which has multiple charge species ranging in molecular weight from 42,000 to 120,000, is composed of two distinct polypeptide antigens unique to this glycoprotein class. These distinct antigens can be differentiated by immunoblotting after high-resolution two-dimensional polyacrylamide gel electrophoretic separation of trypsin-treated or deglycosylated glycoproteins. The two polypeptides also differ in their staining properties with the silver-based color stain and in their susceptibility to proteolysis. A second monoclonal antibody (PSI) has been used to define a determinant shared by all three major porcine ZP glycoprotein classes. This determinant appears to involve either a carbohydrate moiety or some other molecular feature related to post-translational modification, since the antibody recognizes only the acidic species of each glycoprotein class, and does not recognize the deglycosylated forms of the proteins. This work demonstrates that there are both unique and shared antigenic determinants present in the individual components of the ZP, but that the immunodominant determinants appear to be unique to each glycoprotein.
Time-dependent decoherence-free subspace (2012)

With time-dependent Lindblad operators, an open system may have a time-dependent decoherence-free subspace (t-DFS). In this paper, we define the t-DFS and present a necessary and sufficient condition for the t-DFS. Two examples are presented to illustrate the t-DFS, showing that this t-DFS is not trivial, when the dimension of the t-DFS varies.
A proximal gradient splitting method for solving convex vector optimization problems (2020)

In this paper, a proximal gradient splitting method for solving nondifferentiable vector optimization problems is proposed. The convergence analysis is carried out when the objective function is the sum of two convex functions where one of them is assumed to be continuously differentiable. The proposed splitting method exhibits full convergence to a weakly efficient solution without assuming the Lipschitz continuity of the Jacobian of the differentiable component. To carry this analysis, the popular Beck–Teboulle's line-search procedure is extended to the vectorial setting under mild assumptions. It is also shown that the proposed scheme obtains an ϵ-approximate solution to the vector optimization problem in at most O(1/ε) iterations.
Fusion of the tissue factor extracellular domain to a tumour stroma specific single-chain fragment variable antibody results in an antigen-specific coagulation-promoting molecule (2000)

Solid tumours growing beyond a size of 1-2 mm in diameter induce supporting connective tissue structures, the tumour stroma, comprising activated fibroblasts and newly formed blood vessels, embedded in an extracellular matrix. The selective destruction of this tissue or the inhibition of its function (e.g. tumour neoangiogenesis) may result in the destruction of tumour nodules, thus providing novel opportunities for tumour therapy. Our approach aims at an antibody-mediated induction of coagulation in tumour nodules to cut off their blood supply. As a target structure the fibroblast activation protein (FAP) is used, which is specifically and abundantly expressed on the activated fibroblasts of the tumour stroma. We constructed a fusion protein comprising a single-chain module of a FAP-specific humanized antibody [single-chain fragment variable (scFv) OS4] and the extracellular domain of human tissue factor. The fusion protein, designated TFOS4, was produced in the Proteus mirabilis protoplast expression system with a yield of 15 microg/ml. Biochemical characterization of TFOS4 revealed high-affinity binding to cellular FAP. Further, TFOS4 bound to factor VIIa and also exerted allosteric activation of factor VIIa. A complex of TFOS4 and factor VIIa bound to FAP-expressing cells efficiently generated activated factor X. Finally, cell-bound TFOS4 selectively induced plasma coagulation, implying its activity under physiological conditions, notably with relevant concentrations of coagulation factors and their natural inhibitors. These findings suggest that TFOS4 has the potential to increase the procoagulant state in a cell-type-specific fashion. No systemic coagulation or side effects were observed when TFOS4 was injected intravenously into normal mice, indicating the biosafety and specificity of the recombinant protein.
Seasonal Occurrence and Impact of <I>Halyomorpha halys</I> (Hemiptera: Pentatomidae) in Tree Fruit (2009)

Halyomorpha halys is an introduced stink bug species from Asia that is spreading throughout the Mid-Atlantic United States. It is native to South Korea, Japan, and eastern China, where it is an occasional pest of tree fruit, including apple and pear. Cage experiments with adults placed on apple and peach during critical plant growth stages demonstrate that it can cause damage to developing fruit during mid- and late season growth periods and that feeding occurs on all regions of the fruit. Feeding that occurred during pit hardening/mid-season and final swell periods were apparent as damage at harvest, whereas feeding at shuck split/petal fall in peaches and apples caused fruit abscission. Tree fruit at two commercial farms were sampled weekly in 2006-2007 to determine H. halys seasonality. Low densities of nymphs in apple suggest that it is an unsuitable developmental host. Both nymphs and adults were found on pear fruits with peak populations occurring in early July and mid-August, the time when pit hardening/mid-season and swell period damage occurs. At both farms, stink bug damage was greater than 25% damaged fruit per tree. We attribute this to H. halys because population densities were significantly higher than native pentatomids at both locations in both beat samples and blacklight trap captures. The data presented here documents the potential for H. halys to cause damage in orchards throughout the Mid-Atlantic United States and shows the need for development of appropriate control strategies.
Geminivirus Replication Origins Have a Modular Organization (1994)

Elizabeth P. B. Fontes, Heather J. Gladfelter, Reenah L. Schaffer, Ian T. D. Petty, Linda Hanley-Bowdoin, Geminivirus Replication Origins Have a Modular Organization, The Plant Cell, Vol. 6, No. 3 (Mar., 1994), pp. 405-416
Tryptase is a candidate autoantigen in rheumatoid arthritis (2014)

Autoimmune processes have been implicated in the development of rheumatoid arthritis (RA); however, specific autoantigens that play a role in the aetiology of RA have been lacking. In this study, we found that sera from RA patients were particularly immunoreactive against the protein tryptase. Compared with osteoarthritis (OA) patients and healthy controls, RA patients had relatively higher levels of tryptase and concomitant anti-tryptase antibodies in their synovial tissues and sera. Similarly, synovial fluid from RA patients, but not from OA patients, contained antibodies that recognized tryptase in vitro. In addition, serum tryptase levels in both early and late RA patients significantly correlated with clinical indices usually used to diagnose RA, such as rheumatoid factor, Disease Activity Score using 28 joint counts and autoantibodies against cyclic citrullinated peptide. Our results identify tryptase as a candidate autoantigen involved in the pathogenesis of RA and monitoring its levels may have diagnostic and prognostic value.
Test–retest reliability and practice effects of Expanded Halstead–Reitan Neuropsychological Test Battery (1999)

Test-retest reliabilities and practice effects of a broad range of neuropsychological measures were examined in 384 normal or neurologically stable adults. Median test-retest interval was 11 months (range 3-16 months). The reliability estimates for most of the measures are reasonably good, ranging from .70 to low .90s. An exception is the relatively poor reliabilities of most memory measures. For all test measures, the value on initial testing is a strong determinant of the value on the second examination. Practice effects are seen on most measures. The magnitude of the practice effects, however, varies as a function of type of measure, test-retest interval, age, and overall competency level of the participant. This study provides several types of retest information that may be useful for future research and clinical work: comparative reliabilities of the various measures, estimate of error variability associated with each administration, standard deviation of the change, and comparative magnitude of practice effects on various tests.
Proinflammatory cytokine responses induced by influenza A (H5N1) viruses in primary human alveolar and bronchial epithelial cells (2005)

The H5N1/97 and H5N1/04 subtype influenza A viruses are more potent inducers of proinflammatory cytokines and chemokines in primary human respiratory epithelial cells than subtype H1N1 virus. We suggest that this hyper-induction of cytokines may be relevant to the pathogenesis of human H5N1 disease.
An integrated view of the activities of defibrotide. (1996)

Defibrotide is a polydeoxyribonucleotide sodium salt extracted from mammalian organs. Its mean molecular weight is 15,000-30,000 daltons. Defibrotide contains aptamers, i.e., single-stranded polynucleotides with a well-defined base sequence and composition (5'-GGTTGG-ATT-GGTTGG-3' and 5'-GGTTGG-ATC-GGTTGG-3') that bind thrombin. For the time being, these aptamers are the only ones that have been identified in defibrotide, but there may also be other aptamers that bind proteins other than thrombin. Defibrotide has no anticoagulant activity, but in some other aspects it probably parallels heparin. Heparin is a sulfated polysaccharide sodium salt with a mean molecular weight ranging from 5,000 to 40,000 daltons extracted from mammalian organs. It contains disaccharide sequences of well-defined structure and frequency. Heparin binds an array of proteins, enzymes, and growth factors and shows inhibitory or stimulatory or protective activity. Defibrotide has a spectrum of interesting pharmacological properties that make this drug very useful for the treatment of arterial and venous thrombotic diseases. In fact, defibrotide has profibrinolytic, antithrombotic-thrombolytic, anti-ischemic, and antiatherosclerotic activity and protective activity in shock. What have all the above activities to do with a single drug? The explanation is that atherosclerosis, myocardial, renal, and liver ischemia, hemorrhagic and septic shock, and shock induced by occlusion of splanchnic artery and thrombosis are different facets of the same entity: the polyhedric inflammatory process.
CDD: a curated Entrez database of conserved domain alignments (2003)

The Conserved Domain Database (CDD) is now indexed as a separate database within the Entrez system and linked to other Entrez databases such as MEDLINE(R). This allows users to search for domain types by name, for example, or to view the domain architecture of any protein in Entrez's sequence database. CDD can be accessed on the WorldWideWeb at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. Users may also employ the CD-Search service to identify conserved domains in new sequences, at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. CD-Search results, and pre-computed links from Entrez's protein database, are calculated using the RPS-BLAST algorithm and Position Specific Score Matrices (PSSMs) derived from CDD alignments. CD-Searches are also run by default for protein-protein queries submitted to BLAST(R) at http://www.ncbi.nlm.nih.gov/BLAST. CDD mirrors the publicly available domain alignment collections SMART and PFAM, and now also contains alignment models curated at NCBI. Structure information is used to identify the core substructure likely to be present in all family members, and to produce sequence alignments consistent with structure conservation. This alignment model allows NCBI curators to annotate 'columns' corresponding to functional sites conserved among family members.
Epigenetic and genetic dissections of UV-induced global gene dysregulation in skin cells through multi-omics analyses (2017)

To elucidate the complex molecular mechanisms underlying the adverse effects UV radiation (UVR) on skin homeostasis, we performed multi-omics studies to characterize UV-induced genetic and epigenetic changes. Human keratinocytes from a single donor treated with or without UVR were analyzed by RNA-seq, exome-seq, and H3K27ac ChIP-seq at 4 h and 72 h following UVR. Compared to the relatively moderate mutagenic effects of UVR, acute UV exposure induced substantial epigenomic and transcriptomic alterations, illuminating a previously underappreciated role of epigenomic and transcriptomic instability in skin pathogenesis. Integration of the multi-omics data revealed that UVR-induced transcriptional dysregulation of a subset of genes was attributable to either genetic mutations or global redistribution of H3K27ac. H3K27ac redistribution further led to the formation of distinctive super enhancers in UV-irradiated cells. Our analysis also identified several new UV target genes, including CYP24A1, GJA5, SLAMF7 and ETV1, which were frequently dysregulated in human squamous cell carcinomas, highlighting their potential as new molecular targets for prevention or treatment of UVR-induced skin cancers. Taken together, our concurrent multi-omics analyses provide new mechanistic insights into the complex molecular networks underlying UV photobiological effects, which have important implications in understanding its impact on skin homeostasis and pathogenesis.
Effects of Mechanical Forces on Signal Transduction and Gene Expression in Endothelial Cells (1998)

Fluid shear stress and circumferential stretch play important roles in maintaining the homeostasis of the blood vessel, and they can also be pathophysiological factors in cardiovascular diseases such as atherosclerosis and hypertension. The uses of flow channels and stretch devices as in vitro models have helped to elucidate the mechanisms of signal transduction and gene expression in cultured endothelial cells in response to shear stress, which is a function of blood flow and vascular geometry, or mechanical strain, which is a function of transmural pressure and the mechanical properties and geometry of the vessel. Shear stress has been found to increase the activities of a number of kinases to modulate the phosphorylation of many signaling proteins in endothelial cells, eg, the proteins in focal adhesion sites and the proteins in the mitogen-activated protein kinase pathways. Downstream to such signaling cascades, multiple transcription factors such as AP-1, NF-kappaB, Sp-1, and Egr-1 are activated. The actions of these transcription factors on the corresponding cis-elements result in the induction of genes encoding for vasoactivators, adhesion molecules, monocyte chemoattractants, and growth factors in endothelial cells, thus modulating vascular structure and function. Some of the effects of mechanical strain on endothelial cells are similar to those by shear stress, eg, the signaling pathways and the genes activated, but there are differences, eg, the time course of the responses. Studies on the effects of mechanical forces on signal transduction and gene expression provide insights into the molecular mechanisms by which hemodynamic factors regulate vascular physiology, and pathophysiology.
Privacy-Enabled Global Threat Monitoring (2006)

The history of intrusion detection research gives a nice example of a community in a perpetual race to stay relevant. While we once focused on detecting user account misuse in mainframes, we then moved on to local area network abuse, and then to address the scalability problems in enterprise-wide detection. With the rise of e-commerce in the late 1990s, we intrusion detection developers have had to react to the emergence of script kiddies and Web defacements. Distributed denial-of-service attacks and wide-scale virus propagation soon followed, as did a new term, malware research, to address the growing concern about viruses and self-replicating worms spreading across the Internet at alarming speeds. More recently, we've had to consider the problem of botnets, which can organize and maintain illicit control of thousands of machines for months at a time to spread spam, conduct phishing attacks, or steal data or computing resources. Over the past decade, intrusion detection research has rarely been boring
Single amino acid substitution in the Fc region of chimeric TNT-3 antibody accelerates clearance and improves immunoscintigraphy of solid tumors. (2000)

The accelerated clearance produced by a single amino acid substitution in the Fc region of chTNT-3 leads to improved imaging in tumor-bearing mice. These studies suggest that a rapidly clearing antibody generated by this approach may be useful for the immunoscintigraphy of human tumors.
Wavefield separation using hydrophone and particle velocity components with arbitrary orientation (2014)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 2014Wavefield separation using hydrophone and particle velocity components with arbitrary orientationAuthors: Gordon PooleGordon PooleCGGhttps://doi.org/10.1190/segam2014-0756.1 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Abstract A strategy for wavefield separation by deriving a 3D tau-p model of the up-going wavefield is proposed. The model is solved to simultaneously satisfy hydrophone and particle velocity recordings. The equations respect the unique orientation of each individual particle velocity sensor so as to obtain optimal wavefield separation and maximize amplitude preservation. The algorithm is applied to a variable depth multi-component streamer dataset. Keywords: 3D, multicomponent, prestack, separation, broadbandPermalink: https://doi.org/10.1190/segam2014-0756.1FiguresReferencesRelatedDetailsCited byThree-dimensional receiver deghosting of seismic streamer data using L1 inversion and redundant extended radon dictionary10 April 2018 | Geophysical Prospecting, Vol. 66, No. 5Wave height guided multishot receiver deghostingGordon Poole and Simon King1 September 2016Inversion-driven free surface multiple modelling using multi-order Green's functionsGordon Poole* and James Cooper19 August 2015Interpolation of multicomponent streamer data using extended structure tensors. Part 2: Interpolating the pressure field's depth derivative.Fredrik Andersson, Adriana Citlali Ramírez, and Torgeir Wiik19 August 2015Hydrophone-only receiver deghosting using a variable sea surface datumSimon King* and Gordon Poole19 August 2015 SEG Technical Program Expanded Abstracts 2014ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 2014 Pages: 5183 publication data© 2014 Published in electronic format with permission by the Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 05 Aug 2014 CITATION INFORMATION Gordon Poole, (2014), "Wavefield separation using hydrophone and particle velocity components with arbitrary orientation," SEG Technical Program Expanded Abstracts : 1858-1862. https://doi.org/10.1190/segam2014-0756.1 Plain-Language Summary Keywords3DmulticomponentprestackseparationbroadbandPDF DownloadLoading ...
Regulation of Adaptive Immunity by the Innate Immune System (2010)

Twenty years after the proposal that pattern recognition receptors detect invasion by microbial pathogens, the field of immunology has witnessed several discoveries that have elucidated receptors and signaling pathways of microbial recognition systems and how they control the generation of T and B lymphocyte-mediated immune responses. However, there are still many fundamental questions that remain poorly understood, even though sometimes the answers are assumed to be known. Here, we discuss some of these questions, including the mechanisms by which pathogen-specific innate immune recognition activates antigen-specific adaptive immune responses and the roles of different types of innate immune recognition in host defense from infection and injury.