gebhart/patrepeval huggingface dataset:
cDNA sequence of human β-NGF (1990)

Journal Article cDNA sequence of human β-NGF Get access G. Borsani, G. Borsani * * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar A. Pizzuti, A. Pizzuti 1The Institute of Neurology of the University of Milan Medical SchoolVia F. Sforza 35, 20122 Milano, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar E.I. Rugarli, E.I. Rugarli 1The Institute of Neurology of the University of Milan Medical SchoolVia F. Sforza 35, 20122 Milano, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar A. Falini, A. Falini 1The Institute of Neurology of the University of Milan Medical SchoolVia F. Sforza 35, 20122 Milano, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar V. Silani, V. Silani 1The Institute of Neurology of the University of Milan Medical SchoolVia F. Sforza 35, 20122 Milano, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar A. Sidoli, A. Sidoli Search for other works by this author on: Oxford Academic PubMed Google Scholar G. Scarlato, G. Scarlato 1The Institute of Neurology of the University of Milan Medical SchoolVia F. Sforza 35, 20122 Milano, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar F.E. Baralle F.E. Baralle Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 13, 11 July 1990, Page 4020, https://doi.org/10.1093/nar/18.13.4020 Published: 11 July 1990
Canadian best practice recommendations for stroke care (updated 2008) (2008)

The Canadian Stroke Strategy was initiated under the leadership of the Canadian Stroke Network and the Heart and Stroke Foundation of Canada. It brings together a multitude of stakeholders and partners to work toward the common goal of developing and implementing a coordinated and integrated
Hypoglycemia and Diabetes: A Report of a Workgroup of the American Diabetes Association and The Endocrine Society (2013)

The workgroup reconfirmed the previous definitions of hypoglycemia in diabetes, reviewed the implications of hypoglycemia on both short- and long-term outcomes, considered the implications of hypoglycemia on treatment outcomes, presented strategies to prevent hypoglycemia, and identified knowledge gaps that should be addressed by future research. In addition, tools for patients to report hypoglycemia at each visit and for clinicians to document counseling are provided.
The nucleotide sequence of a rat 18 S ribosomal ribonucleic acid gene and a proposal for the secondary structure of 18 S ribosomal ribonucleic acid. (1984)

The nucleotide sequence of a rat 18 S rRNA gene was determined. The 18 S rRNA encoded in the gene contains 1874 nucleotides, and the molecular weight estimated from the sequence is 6.09 X 10(5). The sequences of rat and Xenopus laevis 18 S rRNAs are very similar; the only differences of consequence are the insertions between nucleotides 197 and 206 and between 258 and 279 of the rat nucleic acid of sequences rich in guanine and cytosine. A proposal is presented for the secondary structure of rat 18 S rRNA based on a comparison with the sequences of 17 other small ribosomal subunit RNAs. While the primary sequences of rat and eubacterial RNAs are different, the deduced secondary structures are remarkably similar.
Non-Homologous Sequences of Parathyroid Hormone and the Parathyroid Hormone Related Peptide Bind to a CommonReceptor on ROS 17/2.8 Cells (1989)

We and others have recently shown that amino terminal sequences of parathyroid hormone (PTH) and parathyroid hormone related peptide (PTHrP), which share a 62% homology within the first 13 residues, bind to the same receptor on ROS 17/2.8 cells. The remaining PTHrP sequence is markedly different from PTH, suggesting that receptor binding may be dependent on the first 13 amino acids of either peptide. However, since the amino acid residues 14-34 have previously been recognized as an important binding domain for PTH, conformational similarity within this portion's secondary structure of both peptides could contribute to their capacity to bind to the same receptor. To test this hypothesis, we synthesized [Tyr36,Cys38]PTHrP-(14-38) and [Tyr34]bPTH(14-34)NH2, and studied binding of both peptides to the common PTH/PTHrP receptor on ROS 17/2.8 cells. Radioiodinated, HPLC-purified [Nle8,18, Tyr34]bPTH(1-34)NH2 (NlePTH) and [Tyr36]PTHrP-(1-36)NH2 were used to functionally define receptor binding requirements. [Tyr36,Cys38]PTHrP(14-38) and [Tyr34]bPTH(14-34)NH2 competed with 125I-NlePTH for binding sites on ROS 17/2.8 cells with apparent Kds of 10 microM and 50 microM respectively. Both peptides also competed with 125I-[Tyr36]PTHrP(1-36)NH2 with apparent Kds of 30 microM and 10 microM respectively. In the same assay system, NlePTH and [Tyr36,Cys38]PTHrP(1-38)inhibited binding of either radioiodinated ligand with apparent Kds of 0.3 and 1.0 nM. These studies indicate that although [Tyr34]bPTH(14-34)NH2 and [Tyr36,Cys38]PTHrP(14-38) share virtually no sequence homology, their secondary structures must be sufficiently similar to permit binding to a common PTH/PTHrP receptor.
Animal in vivo models of EBV-associated lymphoproliferative diseases: special references to rabbit models. (2002)

Animal models of human EBV-associated diseases are essential to elucidate the pathogenesis of EBV-associated diseases. Here we review those previous models using EBV or EBV-like herpesviruses and describe the details on our two newly-developed rabbit models of lymphoproliferative diseases (LPD) induced by simian EBV-like viruses. The first is Cynomolgus-EBV-induced T-cell lymphomas in rabbits inoculated intravenously (77-90%) and orally (82-89%) during 2-5 months. EBV-DNA was detected in peripheral blood by PCR from 2 days after oral inoculation, while anti-EBV-VCA IgG was raised 3 weeks later. Rabbit lymphomas and their cell lines contained EBV-DNA and expressed EBV-encoded RNA-1 (EBER-1). Rabbit lymphoma cell lines, most of which have specific chromosomal abnormality, showed tumorigenicity in nude mice. The second is the first animal model for EBV-infected T-cell LPD with virus-associated hemophagocytic syndrome (VAHS), using rabbits infected with an EBV-like herpesvirus, Herpesvirus papio (HVP). Rabbits inoculated intravenously with HVP-producing cells showed increased anti-EBV-VCA-IgG titers, and most (85%) subsequently died of fatal LPD and VAHS, with bleeding and hepatosplenomegaly, during 22-105 days. Peroral spray of cell-free HVP induced viral infection with seroconversion in 3 out of 5 rabbits, with 2 of the 3 infected rabbits dying of LPD with VAHS. Atypical T lymphocytes containing HVP-DNA and expressing EBER-1 were observed in many organs. Hemophagocytic histiocytosis was observed in the lymph nodes, spleen, bone marrow, and thymus. These rabbit models are also useful and inexpensive alternative experimental model systems for studying the biology and pathogenesis of EBV, and prophylactic and therapeutic regimens.
Fabry kidney disease. (2012)

Fabry disease (FD), the second most common type of lysosomal storage disease (LSD), is one of 41 disorders characterized by accumulation of substances normally degraded within lysosomes. It is an X-linked recessive disorder characterized by a deficiency of lysosomal alpha-galactosidase A (alpha-Gal A). The locus for human alpha-Gal A is located on the Xq22 chromosome. Most FD mutations are confined to a single family. Although FD is an X-linked disorder, up to one third of female carriers develop clinical manifestations of the disease. It typically presents during infancy or adolescence with crisis of neuropathic pain (acroparesthesia), angiokeratomas, and asymptomatic corneal lesions. As Gb3 deposition progresses, clinical manifestations occur in other organs. Patients typically die in the fourth or fifth decade of life due to cardiac, renal or cerebrovascular complications. Usually, there is diffuse deposition of glycosphingolipid in the renal glomeruli, tubules, interstitium, and vasculature. Clinically, the renal disease manifests with hypertension, microscopic hematuria (rare), moderate proteinuria, which can be in the nephrotic range, and lipiduria. End-stage renal disease can be treated with either dialysis or transplantation. Thegene for (x-Gal A was cloned and sequenced, which eventually led to production of enzyme for therapeutic use by either recombinant DNA technology or gene activation.
Addition of a C-Terminal Extension Sequence to Transforming Growth Factor-pl Interferes with Biosynthetic Processing and Abolishes Biological Activity (1991)

Transforming growth factor-beta 1 (TGF-beta 1) is synthesized and secreted as a biologically latent complex. It has been proposed that one role of the latent complex is to prevent premature interaction of ligand and receptor intracellularly during biosynthesis (Wakefield et al., J. Cell Biol. (1987) 105, 965-975). To test this hypothesis, the endoplasmic reticulum retention sequence Lys-Asp-Glu-Leu (KDEL) was added to the C-terminus of the wildtype TGF-beta 1 coding sequence, and to a construct in which mutagenesis of two cysteine residues in the precursor pro region results in the synthesis and secretion of active, as opposed to latent, TGF-beta. Addition of either SEKDEL, or the control sequence SEKDVS to the TGF-beta 1 protein abolished biological activity. Western blot analysis indicated that the extended gene products are synthesized, but that the extension sequence partially interferes with the normal dimerization of the protein product, and totally inhibits the normal proteolytic processing and glycosylation of the precursor protein. The data suggest that correct folding of the highly conserved C terminus of TGF-beta 1 is critical for subsequent proteolytic cleavage and glycosylation at sites that are quite distant in the primary sequence. Thus molecular strategies for the generation of TGF-beta antagonists or superagonists should avoid extensive modification of this region of the molecule. Since synthesis of the endogenous TGF-beta 1 is unaffected by the presence of the mutated analog, the data further indicate that transfection with the KDEL-extended TGF-beta 1 sequence cannot be used as a dominant negative mutation to prevent secretion of the endogenous TGF-beta protein.
Molecular cloning and expression of early T cell costimulatory molecule-1 and its characterization as B7-2 molecule. (1994)

The interaction of T cell CD28/CTLA-4 receptors with B7-1 activation Ag on APC represents an important costimulatory pathway in T cell activation. However, it is now evident that this costimulatory pathway is neither unique nor universal for the activation of T cells. Our previous study indicated that a 60-kDa membrane protein, recognized by mAb 2D10, was expressed before B7 by activated murine B cells. This molecule was critically involved in activation of T cells in response to auto- and alloantigens. In the present study, we report on the isolation of a cDNA for this early T cell costimulatory molecule (ETC-1). ETC-1, like B7-1, is a member of the Ig supergene family and is composed of 303 amino acids. Nucleic acid sequence comparison indicated that ETC-1 is identical to the B7-2 molecule. When expressed in Chinese hamster ovary cells, ETC-1 showed profound T cell costimulatory activity as demonstrated by its ability to enhance CD4 T cell proliferation in response to Con A or anti-CD3 stimulation. Furthermore, ETC-1 also bound to both CD28-Ig and CTLA4-Ig fusion proteins. These results strongly support the notion that the interaction of ETC-1/B7-2 with CD28 or CTLA-4 receptors represents an alternative T cell costimulatory pathway.
Aberrant DNA methylation is a dominant mechanism in MDS progression to AML (2008)

Myelodysplastic syndromes (MDSs) are clonal hematologic disorders that frequently represent an intermediate disease stage before progression to acute myeloid leukemia (AML). As such, study of MDS/AML can provide insight into the mechanisms of neoplastic evolution. In 184 patients with MDS and AML, DNA methylation microarray and high-density single nucleotide polymorphism array (SNP-A) karyotyping were used to assess the relative contributions of aberrant DNA methylation and chromosomal deletions to tumor-suppressor gene (TSG) silencing during disease progression. Aberrant methylation was seen in every sample, on average affecting 91 of 1505 CpG loci in early MDS and 179 of 1505 loci after blast transformation (refractory anemia with excess blasts [RAEB]/AML). In contrast, chromosome aberrations were seen in 79% of early MDS samples and 90% of RAEB/AML samples, and were not as widely distributed over the genome. Analysis of the most frequently aberrantly methylated genes identified FZD9 as a candidate TSG on chromosome 7. In patients with chromosome deletion at the FZD9 locus, aberrant methylation of the remaining allele was associated with the poorest clinical outcome. These results indicate that aberrant methylation can cooperate with chromosome deletions to silence TSG. However, the ubiquity, extent, and correlation with disease progression suggest that aberrant DNA methylation is the dominant mechanism for TSG silencing and clonal variation in MDS evolution to AML.
Chemical Stabilization of Unnatural Nucleotide Triphosphates for the in Vivo Expansion of the Genetic Alphabet (2017)

We have developed an unnatural base pair (UBP) and a semisynthetic organism (SSO) that imports the constituent unnatural nucleoside triphosphates and uses them to replicate DNA containing the UBP. However, propagation of the UBP is at least in part limited by the stability of the unnatural triphosphates, which are degraded by cellular and secreted phosphatases. To circumvent this problem, we now report the synthesis and evaluation of unnatural triphosphates with their β,γ-bridging oxygen replaced with a difluoromethylene moiety, yielding dNaMTP<sup>CF2</sup> and dTPT3TP<sup>CF2</sup>. We find that although dNaMTP<sup>CF2</sup> cannot support in vivo replication, likely due to poor polymerase recognition, dTPT3TP<sup>CF2</sup> can, and moreover, its increased stability can contribute to increased UBP retention. The data demonstrate the promise of this chemical approach to SSO optimization, and suggest that other modifications should be sought that confer phosphatase resistance without interfering with polymerase recognition.
Investigation of the TCA cycle and the glyoxylate shunt in Escherichia coli BL21 and JM109 using 13C-NMR/MS (2000)

Acetate accumulation is a common problem observed in aerobic high cell density Escherichia coli cultures. A previous report has hypothesized that the glyoxylate shunt is active in a low acetate producer, E. coli BL21, and inactive in a high acetate producer, JM109. To further investigate this hypothesis, we now develop a model for the incorporation of 13C from uniformly labeled glucose into key TCA cycle intermediates. The 13C isotopomer distributions of oxaloacetate and acetyl-CoA are first determined using NMR and MS techniques. These distributions are next validated by predicting the NMR spectrum of glutamate. Under steady state isotopic conditions, and with knowledge of the full isotopomer distributions of oxaloacetate and acetyl-CoA, the flux ratios through the TCA cycle and the glycoxylate shunt are obtained with respect to the flux through the PPC anaplerotic shunt. We conclude that in BL21, the glyoxylate shunt is active at 22% of the flux through the TCA cycle, and is inactive in JM109. Further, in BL21, the flux through the TCA cycle equals the flux through the PPC shunt, while in JM109 the TCA cycle flux is only third of the flux through the PPC shunt. © 2000 John Wiley & Sons, Inc. Biotechnol Bioeng 68: 316–327, 2000.
Current and emerging commercial optical biosensors (2001)

The field of commercial optical biosensors is rapidly evolving, with new systems and detection methods being developed each year. This review outlines the currently available biosensor hardware and highlights unique features of each platform. Affinity-based biosensor technology, with its high sensitivity, wide versatility and high throughput, is playing a significant role in basic research, pharmaceutical development, and the food and environmental sciences. Likewise, the increasing popularity of biosensors is prompting manufacturers to develop new instrumentation for dedicated applications. We provide a preview of some of the emerging commercial systems that are dedicated to drug discovery, proteomics, clinical diagnostics and routine biomolecular interaction analysis.
ECG and navigator‐free four‐dimensional whole‐heart coronary MRA for simultaneous visualization of cardiac anatomy and function (2014)

A fully self-gated 4D whole-heart imaging technique was developed, potentially allowing cardiac anatomy and function assessment from a single measurement.
Estimating Phred scores of Illumina base calls by logistic regression and sparse modeling (2017)

The L <sub>1</sub>-regularized logistic regression improves the empirical discrimination power by as large as 14 and 25% respectively for two kinds of preprocessed sequencing signals, compared to the Illumina scoring method. Namely, the L <sub>1</sub> method identifies more base calls of high fidelity. Computationally, the L <sub>1</sub> method can handle large dataset and is efficient enough for daily sequencing. Meanwhile, the logistic model resulted from BIC is more interpretable. The modeling suggested that the most prominent quenching pattern in the current chemistry of Illumina occurred at the dinucleotide "GT". Besides, nucleotides were more likely to be miscalled as the previous bases if the preceding ones were not "G". It suggested that the phasing effect of bases after "G" was somewhat different from those after other nucleotide types.
Synthesis and Utilization of Monodisperse Hollow Polymeric Particles in Photonic Crystals (2004)

We developed a process to fabricate 150-700 nm monodisperse polymer particles with 100-500 nm hollow cores. These hollow particles were fabricated via dispersion polymerization to synthesize a polymer shell around monodisperse SiO(2) particles. The SiO(2) cores were then removed by HF etching to produce monodisperse hollow polymeric particle shells. The hollow core size and the polymer shell thickness, can be easily varied over significant size ranges. These hollow polymeric particles are sufficiently monodisperse that upon centrifugation from ethanol they form well-ordered close-packed colloidal crystals that diffract light. After the surfaces are functionalized with sulfonates, these particles self-assemble into crystalline colloidal arrays in deionized water. This synthetic method can also be used to create monodisperse particles with complex and unusual morphologies. For example, we synthesized hollow particles containing two concentric-independent, spherical polymer shells, and hollow silica particles which contain a central spherical silica core. In addition, these hollow spheres can be used as template microreactors. For example, we were able to fabricate monodisperse polymer spheres containing high concentrations of magnetic nanospheres formed by direct precipitation within the hollow cores.
Cytokines and Chemokines in T-Cell Development (1998)

The history of T-cell development is highly connected to the physiology of the thymus. Following the pioneering observations of J. F. A. P. Miller on the role of the thymus in T lymphocyte production, many laboratories have studied the events that take place in this gland. As shall be reviewed in this chapter and elsewhere in this book, the events known to take place in the thymus have remained fundamentally unchanged and include: colonization of the thymus by bone-marrow derived precursors; commitment to the T-cell lineage; rearrangement of the TCR genes; selection of T-cells according to their MHC and antigenic specificity, and finally, export from the thymus to the periphery. However, new molecular insights obtained more recently have reaffirmed these events. During the 1980s, the main interest of most T-cell development labs focused on the selection mechanisms that resulted in the T-cell repertoire. This was prompted by the molecular characterization of the T-cell receptor, as well as the availability of reagents (monoclonal antibodies, and so forth), which allowed the demonstration of positive and negative selection. Only a few labs focused instead on the earlier events of T-cell development, before positive and negative selection take place. More recently, this situation has changed with more labs studying the early events of T-cell development in the thymus. We have really only begun to understand the basic events that take place before the CD4+CD8+ (double positive [DP]) stage. This situation means that many basic and important developments await to be discovered and understood in early T-cell development.
Coding categorical and coordinate spatial relations in visual–spatial short-term memory (2009)

Four experiments explored the coding of categorical and coordinate spatial relations in visual-spatial short-term memory (VSSTM). Participants judged whether two stimuli presented successively on a computer screen were the same or different. On positional change trials the two stimuli differed in the position of one element. Positional changes were of two types, coordinate and categorical. On coordinate trials the position of one element changed by a small amount, but retained the categorical relationships (above, below, left of, right of) to all other elements. On categorical trials one element moved by the same amount but additionally changed its categorical relationship to one of the other elements (e.g., changed from below to above). Participants detected categorical changes more accurately than coordinate changes when the elements were independent locations marked by squares, indicating that the categorical relationships amongst the squares were encoded in memory. Furthermore, this categorical advantage was unmodulated by either the suppression of articulation (Experiment 2) or by the requirement to retain either colour-position associations or positions only (Experiment 3). When the elements to be remembered were the vertices of simple outline polygons (Experiment 4) there was no categorical advantage, establishing the effect as spatial in nature. Contrary to predictions derived from Postma and De Haan (1996), the employment of categorical relations appears not to be specifically linked to either verbal coding or to the requirement to associate objects with positions. The results suggest that the categorical relations are an intrinsic property of the representation of spatial configurations.