gebhart/patrepeval huggingface dataset:
Molecular Cloning of Canine and Feline Flt3 Ligand Reveals High Degree of Similarity to the Human and Mouse Homologue But Uniquely Long Cytoplasmic Domain (2000)

The cDNAs encoding canine and feline flt3 ligand (FL) have been isolated from libraries constructed from canine or feline peripheral blood mononuclear cells and sequenced. A full-length canine FL cDNA encodes a polypeptide of 294 amino acids that shares 52.8% and 71.0% identity with the mouse and human FL protein, respectively. While the feline FL cDNA encodes a polypeptide of 291 amino acids that shares 54.1% and 70.2% identity with the mouse and human FL protein, respectively. The canine and feline FL proteins share 82.8% identity at amino acid level. Besides those encoding the full-length FL protein, several alternatively spliced forms of canine FL transcripts were also isolated. The canine and feline FL proteins have longer cytoplasmic domain than their mouse and human homologue.
Expression profiling of budding cells in colorectal cancer reveals an EMT-like phenotype and molecular subtype switching (2016)

Tumour budding regions are characterised by a phenotype switch compared with the tumour bulk, involving the acquisition of migratory characteristics and a decrease in cell proliferation. In particular, most tumour budding signatures were EMT-positive and switched from an epithelial subtype (CMS2) in the tumour bulk to a mesenchymal subtype (CMS4) in budding cells.
The Synthesis of 2‐Amino‐4‐(4‐imidazolyl)pyridines (1983)

A general synthetic scheme for the preparation of 2‐amino‐4,(4‐imidazolyl)pyridines, potential histamine H 2 antagonists, is described. The synthesis is based on the Neber rearrangement of l,(4‐pyridyl)l‐alkanone oxime 0 ‐tosylates to the appropriate α‐aminoketones or α‐aminoketals, which are then converted to the corresponding imidazoles. The reaction of Grignard reagents with 2‐chloroisonicotinonitrile, as well as nucleophilic displacement of chloride by amines on 2‐chloroisonicotinonitrile and derivatives, are discussed in relation to the preparation of the ketone intermediates.
Use of biochemical markers to monitor changes in bone turnover in cynomolgus monkeys (2003)

The ovariectomized old cynomolgus monkey is a recognized model of human osteoporosis, and the same species can be used for the assessment of the efficacy and potential toxicity of agents intended to prevent or treat osteoporosis. Several assays have been developed that can measure the same biochemical markers of bone turnover as are used in human patients for the diagnosis and treatment follow-up of bone-related diseases, including osteoporosis. The aim of the present study was to describe the results obtained with these assays in normal control monkeys, their variations with age and sex, and their sensitivity in monitoring the bone turnover induced by ovariectomy in old skeletally mature cynomolgus monkeys. Seven old cynomolgus monkeys were bilaterally ovariectomized and 13 age-matched monkeys were sham-operated. Bone mineral density and biochemical markers were measured before and at regular intervals after surgery for up to 20 months. Total alkaline phosphatase (total ALP), bone-specific alkaline phosphatase isoenzyme (bone ALP) and osteocalcin (OC) were highly correlated to the decrease in bone mineral density (BMD) induced by ovariectomy. Deoxypyridinoline (DPD) measured by enzyme-linked immunoassay was insensitive to the bone resorption induced by ovariectomy, but cross-linked N-telopeptide (NTX-I) was higher in ovariectomized monkeys than in control monkeys. These results demonstrate that reliable biochemical parameters are available to adequately monitor and provide insight into osteoclastic bone resorption and osteoblastic bone formation, the two components of bone turnover in this animal model, and can thus be used to assess the efficacy and toxicity of potential therapeutic agents.
Expression of BLIMP1/PRMT5and concurrent histone H2A/H4 arginine 3 dimethylation in fetal germ cells, CIS/IGCNU and germ cell tumors (2008)

These data reveal similarities in marker expression and histone modification between murine and human PGCs. Moreover, we speculate that the histone H2A and H4 arginine 3 dimethylation might be the mechanism by which IGCNU and seminoma maintain the undifferentiated state while loss of these histone modifications leads to somatic differentiation observed in nonseminomatous tumors.
Glucose increases the expression of the ATP/ADP translocator and the glyceraldehyde-3-phosphate dehydrogenase genes in Chlorella. (1991)

A presumably full-length cDNA clone of the mitochondrial ATP/ADP translocator (AAT) of Chlorella kessleri has been isolated and sequenced. The expression of the AAT gene is highly increased in the presence of D-glucose (14 mM). At least nine more genes are activated when autotrophically grown Chlorella cells switch to heterotrophic growth. Among these is the HUP1 gene coding for the hexose transporter (Sauer, N., Caspari, T., Klebl, F., and Tanner, W. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 7949-7952) and, as also shown in this paper, the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene. When glucose or the nonmetabolizable analogue 6-deoxyglucose is added to the cells, an increased expression of GAPDH or AAT is observed after 10 or 30 min, respectively. Hexose uptake mutants (HUP1-) do not respond to sugars in this way, which indicates that either the inducer has to be internalized or that the HUP1 translocator is part of the signal transduction mechanism.
Removal of N‐acetyl groups from blocked peptides with acylpeptide hydrolase (1991)

Acylpeptide hydrolase, an enzyme that removes the modified residue from N-terminally acetylated peptides, has been purified from ovine liver and developed as a tool in sequencing blocked peptides and proteins. Its instability imposes a major limitation on the use of the mammalian enzyme in protein chemistry. Coupling to Sepharose followed by intramolecular cross-linking with dimethyl-suberimidate increased its thermostability and rendered it more resistant to inactivation by either SDS or N,N-dimethylformamide. The resulting enzyme preparation is reusable and more effective at cleaving longer acetylated peptides. It is therefore useful for unblocking acetylated proteins prior to protein sequence analysis. Intact proteins and many isolated peptides are still too large to be cleaved directly, but in this paper we describe a procedure for overcoming this difficulty. The protein is fragmented and non-acetylated peptides are then absorbed out with isothiocyanato-glass. The N-terminal peptide remains in solution and is unblocked with stabilised acylpeptide hydrolase. No chromatographic separation are required. The N-terminal sequence can then be obtained by automated Edman degradation. This procedure has been successfully demonstrated on a large synthetic peptide.
New report of additional enterobacterial species causing wilt in West Bengal, India (2015)

Ralstonia solanacearum is known to be the most prominent causal agent of bacterial wilt worldwide. It has a wide host range comprising solanaceous and nonsolanaceous plants. Typical symptoms of the disease are leaf wilt, browning of vascular tissues, and collapsing of the plant. With the objective of studying the diversity of pathogens causing bacterial wilt in West Bengal, we collected samples of diseased symptomatic crops and adjacent symptomatic and asymptomatic weeds from widespread locations in West Bengal. By means of a routine molecular identification test specific to "R. solanacearum species complex", the majority of these strains (68 out of 71) were found to not be R. solanacearum. Presumptive identification of these isolates with conventional biochemicals, extensive testing of pathogenicity of a subset involving greenhouse trials fulfilling Koch's postulate test, and scanning electron microscopic analysis for the presence of pathogen in diseased plants were done. 16S rDNA sequencing of a subset of these strains (GenBank accession Nos. JX880249-JX880251) and analysis of sequences with the nBLAST programme showed a high similarity (97%-99%) to sequences of the Enterobacteriaceae group available in GenBank. Molecular phylogeny further established the taxonomic position of the strains. The 3 bacterial strain cultures have been submitted to MTCC, Institute of Microbial Technology, Chandigarh, India, and were identified as Klebsiella oxytoca, Enterobacter cowanii, and Klebsiella oxytoca, respectively. Although Enterobacter sp. has previously been reported to cause wilt in many plants, susceptibility of most of the dedicated hosts of R. solanacearum to wilt caused by Enterobacter and other bacteria from Enterobacteriaceae is being reported for the first time in this work.
Fifty-million-year-old polymorphism at an immunoglobulin variable region gene locus in the rabbit evolutionary lineage (1999)

The Ig heavy chain variable region (V(H)) genes encode the antigen-binding regions of antibodies. The rabbit genome contains more than 100 V(H) genes, but only one (V(H)1) is preferentially used in the VDJ gene rearrangement. Three highly divergent alleles occur at this V(H)1 locus in most rabbit populations. These three V(H) alleles are also present in snowshoe hare populations, indicating that the polymorphism of the V(H)1 alleles is trans-specific. Here we report the results of a phylogenetic analysis of rabbit Ig germ-line V(H) genes (alleles) together with V(H) genes from humans and mice. We have found that all rabbit V(H) genes belong to one mammalian V(H) group (group C), which also includes various human and mouse V(H) genes. Using the rate of nucleotide substitution obtained from human and mouse V(H) sequences, we have estimated that the V(H)1 polymorphism in the rabbit lineage has been maintained for about 50 million years. This extremely long persistence of V(H)1 polymorphism is apparently caused by overdominant selection, though the real mechanism is unclear.
Lipid emulsions in parenteral nutrition of intensive care patients: current thinking and future directions (2010)

Ongoing research using adequately designed and well-controlled studies that characterize the biologic properties of LEs should assist clinicians in selecting LEs within the critical care setting. Prescription of PN containing LEs should be based on available clinical data, while considering the individual patient's physiologic profile and therapeutic requirements.
E-cadherin Mediates Aggregation-dependent Survival of Prostate and Mammary Epithelial Cells through the Retinoblastoma Cell Cycle Control Pathway (1999)

E-cadherin and the retinoblastoma tumor suppressor (Rb) are traditionally associated with diverse regulatory aspects of cell growth and differentiation. However, we have discovered new evidence, which suggests that these proteins are functionally linked in a physiologic pathway required for cell survival and programmed cell death. Pharmacological activation of protein kinase C (PKC) or inducible overexpression and activation of the alpha isozyme of PKC (PKCalpha) resulted in approximately 60% apoptosis of mammary and prostate epithelial cells. Interestingly, the surviving cells had undergone dramatic aggregation concurrent with increased E-cadherin expression. When aggregation was inhibited by the addition of an E-cadherin-blocking antibody, apoptosis increased synergistically. We hypothesized that survival of the aggregated population was associated with contact-inhibited growth and that apoptosis might result from aberrant growth regulatory signals in non-aggregated, cycling cells. This hypothesis was confirmed by experiments that demonstrated that E-cadherin-dependent aggregation resulted in Rb-mediated G1 arrest and survival. Immunoblot analysis and flow cytometry revealed that hypophosphorylated Rb was present in non-aggregated, S phase cultures concurrent with synergistic cell death. We have also determined that the loss of membrane E-cadherin and subsequent hypophosphorylation of Rb in luminal epithelial cells preceded apoptosis induced by castration. These findings provide compelling evidence that suggests that E-cadherin-mediated aggregation results in Rb activation and G1 arrest that is critical for survival of prostate and mammary epithelial cells. These data also indicate that Rb can initiate a fatal growth signal conflict in non-aggregated, cycling cells when the protein is hypophosphorylated as these epithelial cells enter S phase.
Expression and Characterisation of Plasmepsin I from Plasmodium falciparum (1997)

Two aspartic proteinases, plasmepsins I and II, are present in the digestive vacuole of the human malarial parasite Plasmodium falciparum and are believed to be essential for parasite degradation of haemoglobin. Here we report the expression and kinetic characterisation of functional recombinant plasmepsin I. In order to generate active plasmepsin I from its precursor, an autocatalytic cleavage site was introduced into the propart of the zymogen by mutation of Lys110P to Val (P indicates a propart residue). Appropriate refolding of the mutated zymogen then permitted pH-dependent autocatalytic processing of the zymogen to the active mature proteinase. A purification scheme was devised that removed aggregated and misfolded protein to yield pure, fully processable, proplasmepsin I. Kinetic constants for two synthetic peptide substrates and four inhibitors were determined for both recombinant plasmepsin I and recombinant plasmepsin II. Plasmepsin I had 5-10-fold lower k(cat)/Km values than plasmepsin II for the peptide substrates, while the aspartic proteinase inhibitors, selected for their ability to inhibit P. falciparum growth, were found to have up to 80-fold lower inhibition constants for plasmepsin I compared to plasmepsin II. The most active plasmepsin I inhibitors were antagonistic to the antimalarial action of chloroquine on cultured parasites. Northern blot analysis of RNA, isolated from specific stages of the erythrocytic cycle of P. falciparum, showed that the proplasmepsin I gene is expressed in the ring stages whereas the proplasmepsin II gene is not transcribed until the later trophozoite stage of parasite growth. The differences in kinetic properties and temporal expression of the two plasmepsins suggest they are not functionally redundant but play distinct roles in the parasite.
A convenient Synthesis of 6-amino-1-β-D-ribofuranosylpyrazolo[3,4-

d

] Pyrimidin-4-one and related 4,6-disubstltuted pyrazodopyrimidine nucleosldes (1983)

The glycosylation of 4,6-dichloropyTazolo[3,4-d]pyrinidine and 4-chloro-6-nethylthiopyrazolo[3,4-d]pyrimidine via the corresponding trlmethylsilyl intermediate and tetra-O-acetyl-β-D-rlbofuranose in the presence of trinethyl-silyl trlflate as a catalyst, gave selective glycosylation at N1 as the only nucleoslde product. The intermediates 4,6-dichloro-l-(2,3,5-tri-(acetyl-β-D-ribofuranosyl)pyraEolo[3,4-d]pyripidine 7 and 4-chloro-6-methylthio-l-(2,3,5-tri-(acetyl-β-D-rlbofurano8yl)pyTarolo[3,4-d]pyrimidine 13 gave new and convenient synthetic routes to the inosine analog 1 the guanosine analog 2, the adenosine analog 3, and the isoguanosine analog 16. Glycosylation of the tri-methylsilyl derivative of 6-chloropyraEolo[3,4-d]pyTimidin-4-one unexpectedly gave the N2-glycosyl lsomer 20 as the major product. A number of new 4,6-disubstituted pyrarolo[3,4-d]pyrimidine nucleosides were prepared from these glycosyl intermediates.
Indium Isoelectronic Doping Influence on Etch Pit Density in GaAs Layers Grown by Vapour Phase Epitaxy (1986)

In this letter we report the In doping of GaAs layers grown by VPE (chloride method) using a Ga/In alloyed source. This work also aims to contribute to an understanding of the influence of isoelectronic doping on etch pit density (EPD) reduction. With a 4.5×10 19 at.cm -3 optimum doping and a 8 µm optimum thickness, a 50-fold EPD reduction has been obtained. Buffer layers assure considerable EPD reductions to In concentration values of 4.5×10 20 at.cm -3 .
Understanding the Significance and Implications of Antibody Numbering and Antigen-Binding Surface/Residue Definition (2018)

Monoclonal antibodies are playing an increasing role in both human and animal health. Different strategies of protein and chemical engineering, including humanization techniques of non-human antibodies were applied successfully to optimize clinical performances of antibodies. Despite the emergence of techniques allowing the development of fully human antibodies such as transgenic Xeno-mice, antibody humanization remains a standard procedure for therapeutic antibodies. An important prerequisite for antibody humanization requires standardized numbering methods to define precisely complementary determining regions (CDR), frameworks and residues from the light and heavy chains that affect the binding affinity and/or specificity of the antibody-antigen interaction. The recently generated deep-sequencing data and the increasing number of solved three-dimensional structures of antibodies from human and non-human origins have led to the emergence of numerous databases. However, these different databases use different numbering conventions and CDR definitions. In addition, the large fluctuation of the variable chain lengths, especially in CDR3 of heavy chains (CDRH3), hardly complicates the comparison and analysis of antibody sequences and the identification of the antigen binding residues. This review compares and discusses the different numbering schemes and "CDR" definition that were established up to date. Furthermore, it summarizes concepts and strategies used for numbering residues of antibodies and CDR residues identification. Finally, it discusses the importance of specific sets of residues in the binding affinity and/or specificity of immunoglobulins.
Efficacy and Safety of Inhaled Insulin (Exubera) Compared With Subcutaneous Insulin Therapy in Patients With Type 2 Diabetes (2004)

Inhaled insulin appears to be effective, well tolerated, and well accepted in patients with type 2 diabetes and provides glycemic control comparable to a conventional subcutaneous regimen.
Stoichiometric and Catalytic B−C Bond Formation from Unactivated Hydrocarbons and Boranes (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTStoichiometric and Catalytic B−C Bond Formation from Unactivated Hydrocarbons and BoranesCarl N. Iverson and Milton R. SmithView Author Information Department of Chemistry, Michigan State University East Lansing, Michigan 48824 Cite this: J. Am. Chem. Soc. 1999, 121, 33, 7696–7697Publication Date (Web):August 6, 1999Publication History Received20 April 1999Published online6 August 1999Published inissue 1 August 1999https://pubs.acs.org/doi/10.1021/ja991258whttps://doi.org/10.1021/ja991258wrapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views6072Altmetric-Citations321LEARN 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:Chemical reactions,Group 13 compounds,Hydrocarbons,Inorganic compounds,Reagents Get e-Alerts
Development of a panel of recombinase polymerase amplification assays for detection of common bacterial urinary tract infection pathogens (2017)

Rapid identification of the causative pathogens of UTIs can be valuable in preventing serious complications by helping avoid the empirical treatment necessitated by traditional urine culture's 48-72-h turnaround time. The routine and widespread use of RPA to supplement or replace culture-based methods could profoundly impact UTI management and the emergence of multidrug-resistant pathogens.
Handbook of 3D Integration (2014)

Edited by key figures in 3D integration and written by top authors from high-tech companies and renowned research institutions, this book covers the intricate details of 3D process technology. As such, the main focus is on silicon via formation, bonding and debonding, thinning, via reveal and backside processing, both from a technological and a materials science perspective. The last part of the book is concerned with assessing and enhancing the reliability of the 3D integrated devices, which is a prerequisite for the large-scale implementation of this emerging technology. Invaluable reading for materials scientists, semiconductor physicists, and those working in the semiconductor industry, as well as IT and electrical engineers.
TLR2- and Dectin 1–Associated Innate Immune Response Modulates T-Cell Response to Pancreatic β-Cell Antigen and Prevents Type 1 Diabetes (2014)

The progression of autoimmune diseases is dictated by deviations in the fine balance between proinflammatory versus regulatory responses, and pathogen recognition receptors (PRRs) play a key role in maintaining this balance. Previously, we have reported that ligation of Toll-like receptor 2 (TLR2) and Dectin 1 on antigen-presenting cells by zymosan results in a regulatory immune response that prevents type 1 diabetes (T1D). Here, we show that TLR2 and Dectin 1 engagement by zymosan promotes regulatory T-cell (Treg) responses against the pancreatic β-cell-specific antigen (Ag). Unlike the TLR4 ligand, bacterial lipopolysaccharide, which induced proinflammatory cytokines and pathogenic T cells, zymosan induced a mixture of pro- and anti-inflammatory factors and Tregs, both in vitro and in vivo. Ag-specific T cells that are activated using zymosan-exposed dendritic cells (DCs) expressed Foxp3 and produced large amounts of IL-10, TGF-β1, and IL-17. NOD mice that received β-cell-Ag-loaded, zymosan-exposed DCs showed delayed hyperglycemia. Injection of NOD mice at the prediabetic age and early hyperglycemic stage with β-cell-Ag, along with zymosan, results in a superior protection of the NOD mice from diabetes as compared with mice that received zymosan alone. This therapeutic effect was associated with increased frequencies of IL-10-, IL-17-, IL-4-, and Foxp3-positive T cells, especially in the pancreatic lymph nodes. These results show that zymosan can be used as an immune regulatory adjuvant for modulating the T-cell response to pancreatic β-cell-Ag and reversing early-stage hyperglycemia in T1D.
Reducing the immunostimulatory activity of CpG-containing plasmid DNA vectors for non-viral gene therapy (2004)

The mammalian innate immune system has the ability to recognise and direct a response against incoming foreign DNA. The primary signal that triggers this response is unmethylated CpG motifs present in the DNA sequence of various disease-causing pathogens. These motifs are rare in vertebrate DNA, but abundant in bacterial and some viral DNAs. Because gene therapy generally involves the delivery of DNA from either plasmids of bacterial origin or recombinant viruses, an acute inflammatory response of variable severity inevitably results. The response is most serious for non-viral gene delivery vectors composed of cationic lipid-DNA complexes, producing adverse effects at lower doses and lethality at higher doses of complex. This review examines the role of immunostimulatory CpG motifs in the acute inflammatory response to non-viral gene therapy vectors. Strategies to neutralise or eliminate CpG motifs within plasmid DNA vectors, and the existing limitations of CpG reduction on improving the safety profile of non-viral vectors, will be discussed.