gebhart/patrepeval huggingface dataset:
Reovirus type 3 genome segment S4: nucleotide sequence of the gene encoding a major virion surface protein (1984)

A full-length cDNA copy of reovirus double-stranded RNA genome segment S4 which codes for a major virion structural polypeptide, sigma 3, has been completely sequenced. The 1,196-nucleotide cDNA contains a single long open reading frame in the plus strand extending 1,095 nucleotides from the 5'-proximal A-T-G to a single stop codon. This corresponds to translation of 92% of the S4 gene. The inferred sigma 3 polypeptide is hydrophilic and consists of 365 amino acids, totalling 41,164 daltons.
Timing the Origin of New World Monkeys (2003)

The origin of New World monkeys (Infraorder Platyrrhini) has been an extensively debated issue. In this study, we analyzed mitochondrial genomes from Cebus (Platyrrhini), Homo, Hylobates, Pan, Pongo (Hominoids), Macaca, Papio (Cercopithecoids), and Tarsius (outgroup) to investigate this matter. Two distinct methodologies were employed on mitochondrial genes to estimate divergence times: the traditional likelihood ratio test performed in ML analyses of individual and concatenated gene sequences and the recent multigene Bayesian approach. Using the Cercopithecoid-Hominoid split as calibration point (25 MYA), our results show consistently that Platyrrhines split from Catarrhines at around 35 MYA. Although the main focus of the study is New World monkey origins, we have also estimated other primate divergence times: Homo-Pan at 5-7 MYA; Pongo-(Homo/Pan) at 13-16 MYA; Hylobates-(Pongo/Homo/Pan) at 15-19 MYA; and Macaca-Papio at 10-12 MYA. Our estimate for the origin of New World monkeys is in agreement with the hypothesis of a transatlantic journey from Africa to South America, as suggested by the fossil record.
[Updates on rickets and osteomalacia: anti-FGF23 antibody, a new therapeutic approach for hypophosphatemic rickets/osteomalacia]. (2013)

In the last decade, Fibroblast growth factor (FGF) 23 has been shown to be a causative factor of hypophosphatemic rickets/osteomalacia, and considered as potential therapeutic target for this disease. Now the most attention is paid to FGF23 blockades as a new category of therapy that may replace the current supplementation of phosphate and active vitamin D. In this chapter, pharmacological actions of the FGF23-neutralizing antibodies in murine hypophosphatemic rickets/osteomalacia model are reviewed. In addition, other types of FGF23 blockades are also briefly discussed.
A cross-species comparison of the apolipoprotein B domain that binds to the LDL receptor. (1990)

Apolipoprotein (apo)-B-100 is the ligand that mediates the clearance of low density lipoprotein (LDL) from the circulation by the apoB,E (LDL) receptor pathway. Clearance is mediated by the interaction of a domain enriched in basic amino acid residues on apoB-100 with clusters of acidic residues on the apoB,E (LDL) receptor. A model has been proposed for the LDL receptor binding domain of apoB-100 based on the primary amino acid sequence (Knott, T. J., et al. 1986. Nature. 323: 734-738). Two clusters of basic residues (A: 3147-3157 and B: 3359-3367) are apposed on the surface of the LDL particle by a disulfide bridge between Cys 3167 and 3297. Support for this single domain model has been obtained from the mapping of epitopes for anti-apoB monoclonal antibodies that block the binding of apoB to the LDL receptor. Here we test this model by comparing the nucleotide (from 9623 to 10,442) and amino acid sequence (from 3139 to 3411) of apoB-100 in seven species (human, pig, rabbit, rat, Syrian hamster, mouse, and chicken). Overall, this region is highly conserved. Cluster B maintains a strong net positive charge and is homologous across species in both primary and secondary structure. However, the net positive charge of region A is not conserved across these species, but the region remains strongly hydrophilic. The secondary structure of the region between clusters A and B is preserved, but the disulfide bond is unique to the human sequence. This study suggests that the basic region B is primarily involved in the binding of apoB-100 to the apoB,E (LDL) receptor.
Extremely high transconductance Ge/Si/sub 0.4/Ge/sub 0.6/ p-MODFET's grown by UHV-CVD (2000)

Ge-channel modulation-doped field-effect transistors (MODFET's) with extremely high transconductance are reported. The devices were fabricated on a compressive-strained Ge/Si/sub 0.4/Ge/sub 0.6/ heterostructure with a Hall mobility of 1750 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Vs (30,900 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Vs) at room temperature (77 K). Self-aligned, T-gate p-MODFET's with L/sub g/=0.1 μm displayed an average peak extrinsic transconductance (g(m/sub ext/)) of 439 mS/mm, at a drain-to-source bias voltage (V/sub ds/) of -0.6 V, with the best device having a value of g(m/sub ext/)=488 mS/mm. At 77 K, values as high as g(m/sub ext/)=687 mS/mm were obtained at a bias voltage of only V/sub ds/=-0.2 V. These devices also displayed a unity current gain cutoff frequency (f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> ) of 42 GHz and maximum frequency of oscillation (f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> ) of 86 GHz at V/sub ds/=-0.6 V and -1.0 V, respectively.
Dehydrative Sialylation with C2-Hemiketal Sialyl Donors (2003)

[reaction: see text] A new method for sialylation involving the dehydrative coupling of sialyl donors with the reagent combination of (p-nitrophenyl)(phenyl) sulfoxide and triflic anhydride is reported. This process establishes sialyl C2-hemiketals as viable sialyl donors for complex carbohydrate synthesis.
Colloidal Crystals of Monodisperse FePt Nanoparticles Grown by a Three-Layer Technique of Controlled Oversaturation (2002)

Colloidal crystals of FePt nanocrystals have been produced by a three-layer oversaturation technique. Faceted triangular and hexagonal platelets, pyramids, and tetrahedrons have been obtained (see Figure), consisting of individual monodisperse FePt nanocrystals aligned in a 3D superlattice. Transition from superparamagnetic to ferromagnetic behavior is observed at 14 K.
EVIDENCE FOR ANOMALOUS FLUCTUATIONS IN SUPERCONDUCTING Bi1.75Pb0.25Ca2Sr2Cu3O10 (1988)

We report very precise measurements of the electrical resistivity of granular Bi 1.75 Pb 0.25 - Ca 2 Sr 2 Cu 3 O 10 superconducting ceramics from room temperature down to the superconducting percolating temperature. We analyze the temperature behavior of the excess conductivity and of the temperature derivative variation in electrical resistivity in order to extract the superconductivity fluctuation dimensionality regimes. We obtain unusual power law behaviors which do not correspond to predictions based on Aslamazov and Larkin theory (nor to its generalizations) nor to the regimes found in YBa 2 Cu 3 O 7 , e.g., here, dR/dT≃E −11/6 for ln E in [−4,0] with E=|T−T c |T c , where T c is the critical temperature.
Inhibition of Angiogenesis by HC·HA, a Complex of Hyaluronan and the Heavy Chain of Inter-α-Inhibitor, Purified from Human Amniotic Membrane (2011)

The antiangiogenic activity of HC·HA might explain why AM is developmentally avascular and how AM might exert an antiangiogenic action when transplanted to the ocular surface, and it might indicate a potential therapeutic effect of HC·HA in diseases manifesting pathogenic angiogenesis. Roles of IGFBP-1 and platelet factor 4 in HC·HA antiangiogenic action warrant further investigation.
Carbon-13 NMR studies of the Peptide hormones oxytocin, arginine vasopressin, isotocin, mesotocin, glumitocin, aspartocin, related analogs, and diastereoisomers. Use of specifically deuterated hormone derivatives for assignments and effects of structural changes on carbon-13 NMR chemical shifts in peptides (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCarbon-13 NMR studies of the Peptide hormones oxytocin, arginine vasopressin, isotocin, mesotocin, glumitocin, aspartocin, related analogs, and diastereoisomers. Use of specifically deuterated hormone derivatives for assignments and effects of structural changes on carbon-13 NMR chemical shifts in peptidesVictor J. Hruby, K. K. Deb, Arno F. Spatola, Donald A. Upson, and Diane YamamotoCite this: J. Am. Chem. Soc. 1979, 101, 1, 202–212Publication Date (Print):January 1, 1979Publication History Published online1 May 2002Published inissue 1 January 1979https://doi.org/10.1021/ja00495a033Request reuse permissionsArticle Views118Altmetric-Citations33LEARN 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 InReddit PDF (1 MB) Get e-Alertsclose Get e-Alerts
IgA-affinity purification and characterization of the lectin jacalin. (1986)

We describe the use of IgA-Sepharose 4B affinity chromatography to purify the lectin jacalin from saline extracts of Artocarpus integrifolia L. seeds. Elution with 0.8 M D-galactose provides 10-15 mg lectin/50 mg seed protein. Jacalin behaved like a single component on immunoelectrophoresis and a single, somewhat diffuse band was obtained by polyacrylamide gel electrophoresis (PAGE) at pH 4.5. A single peak corresponding to an apparent molecular weight of 43 kDa was obtained by gel filtration on Sephadex G-75 (10 mM phosphate buffered saline (PBS), pH 7.4). On SDS-PAGE +/- 2-mercaptoethanol two bands of apparent molecular weights 11.8 and 14.7 kDa were detected. Jacalin behaved like a protein of apparent molecular weight of 13-14 kDa on Sephadex G-50 eluted with PBS containing 0.2% SDS. These data indicate that the jacalin molecule consists of 3-4 non-identical polypeptide subunits not connected by disulfide bridges. The amino acid composition of IgA affinity-purified jacalin (mol/405 mol amino acids) is Lys (24), His (5), Arg (4), Trp (6), Asx (36), Thr (35), Ser (48), Glx (31), Pro (18), Gly (53), Ala (13), Val (25), Met (3), Ile (23), Leu (25), Tyr (30), Phe (26), which corresponds to a molecular weight of 44.163 kDa.
Principal components null space analysis for image and video classification (2006)

We present a new classification algorithm, principal component null space analysis (PCNSA), which is designed for classification problems like object recognition where different classes have unequal and nonwhite noise covariance matrices. PCNSA first obtains a principal components subspace (PCA space) for the entire data. In this PCA space, it finds for each class "i," an Mi-dimensional subspace along which the class' intraclass variance is the smallest. We call this subspace an approximate null space (ANS) since the lowest variance is usually "much smaller" than the highest. A query is classified into class "i" if its distance from the class' mean in the class' ANS is a minimum. We derive upper bounds on classification error probability of PCNSA and use these expressions to compare classification performance of PCNSA with that of subspace linear discriminant analysis (SLDA). We propose a practical modification of PCNSA called progressive-PCNSA that also detects "new" (untrained classes). Finally, we provide an experimental comparison of PCNSA and progressive PCNSA with SLDA and PCA and also with other classification algorithms-linear SVMs, kernel PCA, kernel discriminant analysis, and kernel SLDA, for object recognition and face recognition under large pose/expression variation. We also show applications of PCNSA to two classification problems in video--an action retrieval problem and abnormal activity detection.
An Epstein-Barr virus deletion mutant associated with fatal lymphoproliferative disease unresponsive to therapy with virus-specific CTLs (2001)

There is a growing interest in using antigen-specific T cells for the treatment of human malignancy. For example, adoptive transfer of Epstein-Barr virus (EBV)-specific cytotoxic T lymphocytes (CTLs) has been effective prophylaxis and treatment of EBV-associated lymphoproliferative disease in immunocompromised patients. For all immunotherapies, however, there has been a hypothetical concern that mutations in tumor-specific antigens may lead to tumor escape. We now demonstrate that such events may indeed occur, with lethal outcome. A patient who developed lymphoma after marrow transplantation received donor-derived, EBV-specific CTLs but died with progressive disease. The tumor cells proved substantially less sensitive to cytolysis than the EBV-transformed B-cell line used for CTL generation. The major cytolytic activity of the donor CTL was directed against 2 HLA-A11-restricted epitopes in the viral EBNA-3B antigen. Sequence analysis of this gene in the tumor virus revealed a 245-base pair deletion, which removed these 2 CTL epitopes. Hence, the viral antigen in the tumor had mutated in a way that allowed escape from CTLs. Analysis of EBV polymorphisms demonstrated that before CTL infusion, more than one virus was present, including a virus with wild-type EBNA-3B. After CTL infusion, only the virus with the EBNA-3B deletion could be detected, suggesting that the infused CTLs had selected a resistant strain in vivo. Such an occurrence, even when polyclonal CTL lines are used against genetically stable virus antigens, suggests that escape mutants may be a serious problem when CTL therapy is directed against more unstable tumor cell-derived targets.
An adaptive center of mass detection system employing a 2-D dynamic element matching algorithm for object tracking (2003)

An adaptive high precision image object centroid - center of mass (COM) detection system employing a 2-D dynamic element matching (DEM) algorithm for object tracking is presented. This proposed system outputs a high resolution COM location of the most salient object in the field of view for tracking and navigation purposes and is suitable for real time applications. Precomputation object detection is performed by a low resolution mixed signal winner-take-all (WTA) circuit. In this work, the COM computation algorithm parameters are adaptively changed according to the object size, enabling lowering object scanning frequency, but still providing a high precision in the object COM location. Simulation results prove the concept and demonstrate the high precision COM detection result. In addition, a possible hardware implementation is described.
Murine B Cell Leukemia Line with Inducible Surface Immunoglobulin Expression (1978)

Abstract A chemically induced leukemia of BDF1 mice, designated 70Z/3, was adapted to tissue culture in our laboratory. A minority of these cells displayed surface immunoglobulin (sIg) as detected by immunofluorescence with rhodamine-labeled class (IgM)-specific antibodies. Addition of the B cell mitogen, LPS, to the cultures induced sIg expression on all of these cells. The kinetics of this transition were dependent on the dose of LPS. As little as 0.1 µg/ml induced sIg on &amp;gt;97% of the cells within 36 hr. DxS also induced sIg whereas other mitogens (Con A, PPD) or inducing agents (DMSO, dimethyl formamide, butyric acid), tested over a wide range of concentrations, failed to induce sIg expression. The cells bear H-2 antigens but lack IgD, IgG, IgA, Ia, and Thy 1.2. Exposure to LPS had no effect on the presence or absence of these structures. A small percentage of cells possessed receptors for complement and for the Fc portion of immunoglobulin. Cytoplasmic IgM was detectable within all of the cells, and constitutive production of small quantities of IgM was confirmed by SDS-polyacrylamide gel electrophoresis of serologic precipitates of cell lysates after pulsing with radioactive amino acids. Using similar methods, we failed to detect active secretion of immunoglobulin. Thus, this cell line has properties similar to cytoplasmic Ig+, surface Ig- cells found in immature tissues and in bone marrow of mice and humans that are thought to be immediate precursors of sIg+ B lymphocytes. It may provide a model for studying the mechanism of LPS activation and the molecular events associated with externalization of cell surface receptors.
New saxitoxin analogues from the freshwater filamentous cyanobacteriumLyngbya wollei (1997)

Along with decarbamoylsaxitoxin and decarbamoylgonyautoxin-2 and -3, six new saxitoxin analogues were isolated from the freshwater mat-forming filamentous cyanobacterium Lyngbya wollei collected from Guntersville Reservoir on the Tennessee River in Alabama. Their structures were determined by electrospray ionization mass spectrometry and several NMR techniques. Five of the toxins contain an acetyl moiety attached to the side chain, which is the first report of these saxitoxin analogues. In three of the toxins a hydrated ketone at C-12 was reduced to alpha-alcohol. The presence of acetate in the side chain resulted in a sevenfold to 17-fold times decrease in mouse toxicity compared to their carbamoyl counterparts, while the reduction at C-12 resulted in a complete loss of mouse toxicity.
Previous Experience as a Confounding Factor in Comparing Cochlear-Implant Processing Schemes (1986)

It is of great importance to compare the relative merits of different cochlear-implant speech-processing strategies. Some groups have compared different strategies within single subjects, but usually the subject has prior experience with one strategy, and no allowance is made for this prior experience. We show in the present study that this is inappropriate. We tested one subject using the Melbourne (Cochlear Corp.) multichannel implant with the device set to process sounds in two different ways. In the first processing scheme, the device functioned normally, extracting information about voicing frequency, amplitude and second-formant frequency. This information activated the 21-channel device, determining pulse rate, pulse amplitude and electrode position (respectively). In the second processing scheme, a single electrode (with the largest dynamic range) was activated. This electrode coded overall amplitude and voicing frequency. The subject was tested on an audiovisual test of a 14-choice consonant recognition in the form /iCi/ over a period of over 4 months. During this time the subject used the 21-channel processor outside of the laboratory. Upon initial connection, there was little difference between the results obtained with the two schemes when tested in sound alone or in sound plus vision. However, after about 4 months, scores obtained with the 21-channel processor in sound plus vision were superior to the scores obtained with the one channel. This advantage came from a superiority in the features of voicing and nasality, but not place. Scores for sound-alone conditions between the two processing schemes remained similar for the 4-month period.(ABSTRACT TRUNCATED AT 250 WORDS)
681. Non-Viral DNA and mRNA Gene Delivery to the CNS Pre-Operatively for Neuroprotection and Following Neurotrauma (2004)

Introduction. The consequences of Central Nervous System (CNS) injury due to ischemic insult, stroke, or neurotrauma are so severe that novel methods of preventing or minimizing these deficits must be investigated. Gene delivery has the potential to provide both pre-operative neuroprotection before procedures with a predictable high risk, as well as an effective therapy after post-traumatic or ischemic CNS or spinal cord injury. Although viral methods are currently the predominant form of gene delivery, both DNA and mRNA can be delivered by non-viral, cationic lipid-mediated methods.
Mutation that blocks ATP binding creates a pseudokinase stabilizing the scaffolding function of kinase suppressor of Ras, CRAF and BRAF (2011)

Because mutations in RAS and BRAF represent the most common mutations found in human tumors, identification of inhibitors has been a major goal. Surprisingly, new oncogenic BRAF specific inhibitors inhibit cells transformed with mutated BRAF but paradoxically stimulate the growth of cells transformed with RAS. Here, we show that the mechanism for activation is via drug-induced dimer formation between CRAF and kinase suppressor of Ras (KSR)1. To understand the function of KSR1, we generated a KSR1 mutant that cannot bind ATP but stabilizes the closed, active conformation of KSR1. Molecular modeling suggested that the mutant stabilizes the two hydrophobic spines critical for the closed active conformation. We, therefore, could use the mutant to discriminate between the scaffold versus kinase functions of KSR1. The KSR1 mutant bound constitutively to RAF and mitogen-activated protein kinase kinase (MEK) but could not reconstitute activity suggesting that the catalytic activity of KSR1 is required for its function. Analogous mutations in BRAF and CRAF allowed us to test the generality of the model. The mutation induced changes consistent with the active, closed conformation of both kinases and confirmed that BRAF functions distinctly from CRAF in the MAP kinase pathway. Not only does this work suggest that KSR1 may function as a kinase, we anticipate that the mutation that we generated may be broadly applicable to stabilize the closed conformation of other kinases many of which may also form dimers.
Immune Tolerance After Delivery of Dying Cells to Dendritic Cells In Situ (2002)

Peripheral immune tolerance is believed to be induced by the processing and presentation of self-tissues that die during physiologic tissue turnover. To examine the mechanism that mediates tolerance, we injected mice with dying syngeneic TAP(-/-) splenocytes loaded with small amounts of the protein antigen, ovalbumin (OVA). After ingestion and presentation of cell-associated OVA by the CD8(+) subset of dendritic cells in situ, large numbers of antigen-reactive, CD8(+) T cell receptor (TCR) transgenic T lymphocytes were driven into cell cycle, but then the T cells were deleted. The animals were also tolerant to challenge with OVA in complete Freund's adjuvant. An agonistic anti-CD40 monoclonal antibody was then administered together with the OVA-loaded splenocytes, so that the dendritic cells in the recipient mice would mature. In contrast to observations made in the steady state, the antigen-reactive T cells expanded in numbers for 1-2 wk and produced large amounts of interleukin 2 and interferon gamma, while the animals retained responsiveness to antigen rechallenge. The specific tolerance that develops when dendritic cells process self tissues in the steady state should prevent or reduce the development of autoimmunity when dying cells are subsequently processed during infection.