gebhart/patrepeval huggingface dataset:
Alpha 5, alpha 3, and non-alpha 3. Three clustered avian genes encoding neuronal nicotinic acetylcholine receptor-related subunits. (1990)

In vertebrates, neuronal nicotinic acetylcholine receptors (nAChRs) assemble in an unknown stoichiometry from two homologous subunits, an alpha and a non-alpha. How large is the repertoire of these subunits and how many subtypes of functionally different nAChRs can they constitute? We found in the avian genome a cluster of three closely linked genes spanning 28 kilobase pairs and encoding three proteins, n alpha 3, alpha 3, and alpha 5, that have the features expected of neuronal nAChR subunits. Gene n alpha 3 lies 5' of alpha 3 (whose role in cholinoception has already been established) and is transcribed from the same DNA strand, whereas alpha 5 lies 3' of alpha 3 and is transcribed from the opposite DNA strand. The structure of the n alpha 3 and alpha 5 genes consists of six exons with precisely conserved splice sites and is identical to the structure of the previously characterized avian neuronal receptor subunit genes alpha 2, alpha 3, alpha 4, and n alpha 1. alpha 3, n alpha 3, and alpha 5 transcripts are rare in the central nervous system, but alpha 3 and n alpha 3 are readily detectable in embryonic superior cervical and ciliary ganglia. In order to assay function, the gene encoding n alpha 3 and the cDNAs encoding alpha 3, alpha 4, alpha 5, and n alpha 1 were subcloned into an expression vector, and the constructs were injected into Xenopus oocyte nuclei, either singly or in pairwise combinations of one alpha and one non-alpha. One to five days later, ACh sensitivity of the injected oocytes was examined in voltage clamp. The n alpha 3 gene and n alpha 1 cDNA elicited assembly of nAChRs when coinjected with alpha 3 or alpha 4 cDNA and the electrophysiological properties of the four pairwise combinations were significantly different. alpha 5, however, did not direct the assembly of functional nAChRs when injected alone or in combination with n alpha 1 or n alpha 3.
β‐Peptides: Synthesis by Arndt‐Eistert homologation with concomitant peptide coupling. Structure determination by NMR and CD spectroscopy and by X‐ray crystallography. Helical secondary structure of a β‐hexapeptide in solution and its stability towards pepsin (1996)

Abstract The β‐hexapeptide (H‐β‐HVal‐β‐HAla‐β‐HLeu) 2 ‐OH ( 2 ) was prepared from the component L ‐β‐amino acids by conventional peptide synthesis, including fragment coupling. A cyclo‐β‐tri‐ and a cyclo‐β‐hexapeptide were also prepared. The β‐amino acids were obtained from α‐amino acids by Arndt‐Eistert homologation. All reactions leading to the β‐peptides occur smoothly and in high yields. The β‐peptides were characterized by their CD and NMR spectra (COSY, ROESY, TOCSY, and NOE‐restricted modelling), and by an X‐ray crystal‐structure analysis. β‐Sheet‐type structures (in the solid state) and a compact, left‐handed or ( M ) 3 1 helix of 5‐Å pitch (in solution) were discovered. Comparison with the analogous secondary structures of α‐peptides shows fundamental differences, the most surprising one at this point being the greater stability of β‐peptide helices. There are structural relationships of β‐peptides with oligomers of β‐hydroxyalkanoic acids, and dissimilarities between the two classes of compounds are a demonstration of the power of H‐bonding. The β‐hexapeptide 2 is stable to cleavage by pepsin at pH 2 in H 2 O for at least 60 h at 37°, while the corresponding α‐peptide H‐(Val‐Ala‐Leu) 2 ‐OH is cleaved instantaneously under these conditions. The implication of the described results are discussed.
Epidermal nerve fiber density, axonal swellings and QST as predictors of HIV distal sensory neuropathy (2004)

We investigated the associations of baseline epidermal nerve fiber (ENF) densities and morphology (percent ENF swellings) and quantitative sensory testing (QST) with clinically defined human immunodeficiency virus (HIV)-associated distal polyneuropathy (DSP) and whether these measures are predictive of development of symptomatic DSP over time. Fifty-seven HIV-infected subjects with and without DSP and 19 controls participated. Mean ENF densities were lower at the distal leg and proximal thigh in asymptomatic or symptomatic DSP than in controls. Mean ENF densities did not differ significantly among the HIV groups. Percent ENF swellings was higher in patients with symptomatic DSP than controls at the distal leg, and was also greater at the proximal thigh in patients with asymptomatic or symptomatic DSP than in controls. The percent ENF swellings at the distal leg correlated with the thresholds for both minimal (HP 0.5) and intermediate (HP 5.0) heat pain (HP) intensity. A higher percent ENF swellings in the distal leg [hazard ratio (HR) 1.16, 95% CI 1.02-1.31] and HP 0.5 thresholds (HR 1.03, 95% CI 1.01-1.05) were the only two measures associated with a shorter time to development of symptomatic DSP. Quantitation of ENF swellings and heat pain thresholds deserve further study as predictors of symptomatic neuropathy.
An HLA-A*02:01-B*13:01-DRB1*14:01:03 haplotype conserved in Taiwanese and a possible close relationship between DRB1*14:01:03 and DRB1*14:54 (2010)

We here report sequence confirmation and analysis of the variant HLA-DRB1*14:01:03 on three voluntary bone marrow donors and the conserved haplotype carrying DRB1*14:01:03 allele in Taiwanese population. In exon 2, the DNA sequence of DRB1*14:01:03 is identical to HLA-DRB1*14:01:01 except a silent nucleotide substitution at position 192. However, sequence specific primer (SSP) reaction pattern of DRB1*14:01:03 matched with the pattern of DRB1*14:54 instead of DRB1*14:01:01, 14:01:02 or 14:01:03. In exon 3, at position 421, DRB1*14:01:03 has an identical nucleotide as DRB1*14:54 but differs from DRB1*14:01:01. We think the discrepancy of the allele assignment by SSP typing protocol and by sequence-specific oligonucleotide probe (SSO) and sequence-based typing methods should be addressed. We assume DRB1*14:54 is probably the parental allele for DRB1*14:01:03.
Structural mutations in the constant region of the T-cell antigen receptor (TCR)beta chain and their effect on TCR alpha and beta chain interaction. (1996)

The region responsible for T-cell receptor (TCR)alpha and beta chain assembly has previously been shown to reside in their extracellular domains. In an attempt to delineate further the structural requirements for TCR alpha and beta chain assembly, chimeric TCR beta chains with increasing length of constant (C) region and mutant TCR beta chains with C-domain point mutations were constructed. Their ability to assemble with wild-type TCR alpha chain was evaluated in non-T (COS cells) or T cells. The results reveal that the C beta domain is the binding region to TCR alpha chain, whereas the intact variable (V), diversity (D) and joining (J) regions with a short C-domain of beta chain are not sufficient for the TCR alpha and beta chain assembly. The unique interchain disulphide bond between TCR alpha and beta chains is not required for the TCR alpha beta heterodimer formation.
Thermal gelation of oat globulin (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThermal gelation of oat globulinChing Yung Ma, Ghanikhan Khanzada, and Venktesh R. HarwalkarCite this: J. Agric. Food Chem. 1988, 36, 2, 275–280Publication Date (Print):March 1, 1988Publication History Published online1 May 2002Published inissue 1 March 1988https://pubs.acs.org/doi/10.1021/jf00080a009https://doi.org/10.1021/jf00080a009research-articleACS PublicationsRequest reuse permissionsArticle Views394Altmetric-Citations30LEARN 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-Alertsclose Get e-Alerts
Relationship among oxidative stress, growth cycle, and sporulation in Bacillus subtilis (1987)

The sensitivity of Bacillus subtilis to hydrogen peroxide (oxidative stress) was found to vary with the position of the culture in the growth cycle. The most dramatic change occurred at the stationary phase, when the cells became totally resistant to 10 mM H2O2, in contrast to the loss of 3 to 4 log units of viability when treated at the early log phase. Two of the eight proteins induced by a protective concentration of H2O2 (50 muM) were also induced (in the absence of oxidative stress) on entry into the late log phase of growth. The response of five isogenic spo0 mutants (spo0B, spo0E, spo0F, spo0H, and spo0J) to oxidative stress was identical to that of the wild-type parental strain. In an isogenic spo0A strain, mid-log-phase cells were 100-fold less sensitive to 10 mM H2O2 than was the wild type. Pretreatment with 50 microM H2O2 induced little further protection, suggesting that the response is constitutive in this strain. By comparison of proteins induced by 50 microM H2O2 in the wild-type, spo0A, spo0H, and spo0J strains, four proteins were identified that may be essential for protection against lethal concentrations of H2O2. The presence of multiple copies of the spo0H gene in a spo0A background converted the stress phenotype of the spo0A mutant to that of the wild type but left the sporulation phenotype unaltered.
Electrical characterisation of high-k materials prepared by atomic layer CVD (2002)

The aggressive scaling of MOS devices is quickly reaching the fundamental limits of SiO/sub 2/ as the gate dielectric. Replacement of SiO/sub 2/ with a high dielectric constant material allows an increase in the physical oxide thickness, while maintaining a low equivalent oxide thickness (EOT) and low direct tunnelling current. The high-k gate dielectric of choice will most likely be a deposited film, which makes the replacement of SiO/sub 2/, a thermally grown layer, even more challenging. Atomic layer CVD (ALCVD/sup TM/) is a well-controlled surface saturating process using gas-solid interactions to deposit thin films. The technique results in covalent bonding between the gaseous precursors and the surface bonding sites. ALCVD/sup TM/ provides highly uniform layers and the possibility to deposit many materials, including mixed oxide layers and nano-laminates. Some of the challenges facing high-k materials include achieving a high quality Si/high-k interface, film stability and solving reliability and integration issues. In this paper, we use MOS capacitors to investigate these challenges for Al/sub 2/O/sub 3/-TiN and Al/sub 2/O/sub 3/-ZrO/sub 2/-TiN gate stacks.
Lack of mitochondrial trifunctional protein in mice causes neonatal hypoglycemia and sudden death (2001)

Mitochondrial trifunctional protein (MTP) is a hetero-octamer of four alpha and four beta subunits that catalyzes the final three steps of mitochondrial long chain fatty acid beta-oxidation. Human MTP deficiency causes Reye-like syndrome, cardiomyopathy, or sudden unexpected death. We used gene targeting to generate an MTP alpha subunit null allele and to produce mice that lack MTP alpha and beta subunits. The Mtpa(-/-) fetuses accumulate long chain fatty acid metabolites and have low birth weight compared with the Mtpa(+/-) and Mtpa(+/+) littermates. Mtpa(-/-) mice suffer neonatal hypoglycemia and sudden death 6-36 hours after birth. Analysis of the histopathological changes in the Mtpa(-/-) pups revealed rapid development of hepatic steatosis after birth and, later, significant necrosis and acute degeneration of the cardiac and diaphragmatic myocytes. This mouse model documents that intact mitochondrial long chain fatty acid oxidation is essential for fetal development and for survival after birth. Deficiency of MTP causes fetal growth retardation, neonatal hypoglycemia, and sudden death.
Bayesian Inference in Cyclical Component Dynamic Linear Models (1995)

Abstract Dynamic linear models (DLM's) with time-varying cyclical components are developed for the analysis of time series with persistent though time-varying cyclical behavior. The development covers inference on wavelengths of possibly several persistent cycles in nonstationary time series, permitting explicit time variation in amplitudes and phases of component waveforms, decomposition of stochastic inputs into purely observational noise and innovations that impact on the waveform characteristics, with extensions to incorporate ranges of (time-varying) time series and regression terms wihin the standard DLM context. Bayesian inference via iterative stochastic simulation methods is developed and illustrated. Some indications of model extensions and generalizations are given. In addition to the specific focus on cyclical component models, the development provides the basis for Bayesian inference, via stochastic simulation, for state evolution matrix parameters and variance components in DLM's, building on recent work on Gibbs sampling for state vectors in such models by other authors. Key Words: Autoregressive component dynamic linear modelCyclical time seriesDynamic linear modelMarkov chain Monte Carlo
The vaccine potential of cell surface glycoproteins from Trypanosoma cruzi (1984)

An experimental Trypanosoma cruzi 90 kDa cell surface glycoprotein (GP90) vaccine, previously shown to be protective in mice is similarly effective in marmosets (Callithrix jacchus jacchus). Protection in the mouse is completely dependent on the adjuvant saponin and immunological studies confirm that GP90 is intrisically poorly immunogenic. Both specific antibody and cell mediated immunity are potentiated strongly by saponin and the resulting protective immunity is long lasting (six months). It is effective against the naturally infective, insect-metacyclic, form and a range of heterologous T. cruzi strains including a low mouse passage human isolate. Sterile immunity (that is, complete elimination of parasites) was not however, achieved. Evidence is presented that the levels of tissue damage associated with acute infection, as measured by production of auto anti-tissue immunoglobulins, are significantly reduced in GP90-immunized mice. These and other results are discussed in terms of the desired characteristics for vaccine use of T. cruzi antigens.
Human T-cell lymphotropic virus (HTLV)-related endogenous sequence, HRES-1, encodes a 28-kDa protein: a possible autoantigen for HTLV-I gag-reactive autoantibodies. (1992)

The presence of a human T-cell lymphotropic virus (HTLV)-related endogenous sequence, HRES-1, in the human genome has been documented. The HRES-1 genomic locus is transcriptionally active and contains open reading frames. Antibodies 232 and 233, specific for synthetic peptides pep14-24 and pep117-127, corresponding to two nonoverlapping HTLV-related regions in the longer open reading frame of HRES-1, recognize an identical 28-kDa protein in H9 human T cells. Thus, HRES-1 is a human endogenous retroviral sequence capable of protein expression. HRES-1/p28 is localized to the cytoplasm and nuclear bodies. While HTLV-I-specific antibodies react with HRES-1 peptides, antibody 233 cross-reacts with HTLV-I gag p24 protein. Three consecutive highly charged amino acid residues, Arg-Arg-Glu, present in both HRES-1 pep117-127 and HTLV-I gag p24 are likely to be the core of cross-reactive epitopes. The prevalence of antibodies to HRES-1 peptides pep14-24 and pep117-127 was determined in 65 normal blood donors and 146 patients with immunological disorders. Sera of patients with multiple sclerosis (19 out of 65, 29%), progressive systemic sclerosis (4 out of 17, 23%), systemic lupus erythematosus (4 out of 19, 21%), and Sjogren syndrome (2 out of 19, 10%) contained significantly higher HRES-1 peptide binding activity than sera of normal donors. Sera of patients with AIDS showed no specific binding to HRES-1 peptides. Nine of 30 HRES-1-seropositive patients showed immunoreactivity to HTLV-I gag p24. The data indicate that HRES-1/p28 may serve as an autoantigen eliciting autoantibodies cross-reactive with HTLV-I gag antigens.
Thermosensation and pain (2004)

We feel a wide range of temperatures spanning from cold to heat. Within this range, temperatures over about 43 degrees C and below about 15 degrees C evoke not only a thermal sensation, but also a feeling of pain. In mammals, six thermosensitive ion channels have been reported, all of which belong to the TRP (transient receptor potential) superfamily. These include TRPV1 (VR1), TRPV2 (VRL-1), TRPV3, TRPV4, TRPM8 (CMR1), and TRPA1 (ANKTM1). These channels exhibit distinct thermal activation thresholds (>43 degrees C for TRPV1, >52 degrees C for TRPV2, > approximately 34-38 degrees C for TRPV3, > approximately 27-35 degrees C for TRPV4, < approximately 25-28 degrees C for TRPM8 and <17 degrees C for TRPA1), and are expressed in primary sensory neurons as well as other tissues. The involvement of TRPV1 in thermal nociception has been demonstrated by multiple methods, including the analysis of TRPV1-deficient mice. TRPV2, TRPM8, and TRPA1 are also very likely to be involved in thermal nociception, because their activation thresholds are within the noxious range of temperatures.
Novel Innate Immune Functions for Galectin-1: Galectin-1 Inhibits Cell Fusion by Nipah Virus Envelope Glycoproteins and Augments Dendritic Cell Secretion of Proinflammatory Cytokines (2005)

Galectin-1 (gal-1), an endogenous lectin secreted by a variety of cell types, has pleiotropic immunomodulatory functions, including regulation of lymphocyte survival and cytokine secretion in autoimmune, transplant disease, and parasitic infection models. However, the role of gal-1 in viral infections is unknown. Nipah virus (NiV) is an emerging pathogen that causes severe, often fatal, febrile encephalitis. The primary targets of NiV are endothelial cells. NiV infection of endothelial cells results in cell-cell fusion and syncytia formation triggered by the fusion (F) and attachment (G) envelope glycoproteins of NiV that bear glycan structures recognized by gal-1. In the present study, we report that NiV envelope-mediated cell-cell fusion is blocked by gal-1. This inhibition is specific to the Paramyxoviridae family because gal-1 did not inhibit fusion triggered by envelope glycoproteins of other viruses, including two retroviruses and a pox virus, but inhibited fusion triggered by envelope glycoproteins of the related Hendra virus and another paramyxovirus. The physiologic dimeric form of gal-1 is required for fusion inhibition because a monomeric gal-1 mutant had no inhibitory effect on cell fusion. gal-1 binds to specific N-glycans on NiV glycoproteins and aberrantly oligomerizes NiV-F and NiV-G, indicating a mechanism for fusion inhibition. gal-1 also increases dendritic cell production of proinflammatory cytokines such as IL-6, known to be protective in the setting of other viral diseases such as Ebola infections. Thus, gal-1 may have direct antiviral effects and may also augment the innate immune response against this emerging pathogen.
Robotic folding of 2D and 3D structures from a ribbon (2016)

Automatic folding has drawn increasing attention in robotics research in the past ten years. The focus has been on folding two-dimensional (2D) sheets into three-dimensional (3D) structures, but little work has been done on how structures may be formed by folding ribbons. Here we propose the concept of robotic ribbon folding including a general workflow from shape design to ribbon folding and shape retention. We also propose a method to realize robotic ribbon folding on the macroscopic scale. The method consists of minimally engineered ribbons with patterned flexures, a folding robot, and a folding scheme that relates the orientation of flexures, the type of folds and the type of structural elements. By using this method we demonstrate robotic ribbon folding into 2D static structures such as triangles and squares, 3D static structures, and planar kinematic linkages such as a simple non-crossing four-bar mechanism. Burn-in result shows a four-bar mechanism with all bars' length of 5 cm could move for over 660 cycles.
Variation in the decision to terminate pregnancy in the setting of fetal aneuploidy (2006)

Type and severity of aneuploidy, type of diagnostic procedure, maternal age, and ethnicity contribute to patients' decision-making in the setting of fetal aneuploidy.
Comparison of Canine and Non‐Human Primate Animal Models for Periodontal Regenerative Therapy: Results Following a Single Administration of PDGF/IGF‐I (1994)

Two commonly used animal models for evaluating putative periodontal regenerative therapies are the beagle dog model with natural periodontal disease and the non-human primate with ligature-induced attachment loss. The host response, microbiology, and skeletal rates of remodeling of these two models are summarized. In addition, the results of experiments comparing the healing response to periodontal surgery with and without concurrent use of the combination of platelet-derived growth factor (PDGF) and insulin-like growth factor-I (IGF-I) in these models are presented. At 1 month, PDGF/IGF-I administration resulted in a 64.1% and 51.4% increase in new attachment formation in the non-human primate and canine, respectively, while controls (surgery plus placebo) demonstrated 34.1% and 8.6% increases in new attachment formation in the non-human primate and canine models, respectively. Further, application of PDGF/IGF-I stimulated 21.6% and 65% osseous defect fill in the non-human primate and canine, respectively, while controls demonstrated 8.5% and 14.5% osseous defect fill in the non-human primate and canine, respectively. The osseous response in the canine appears greater than that of the non-human primate, and the new attachment formation was more substantial in the non-human primate than the canine. However, in general these data demonstrate a high degree of consistency in the effects of PDGF/IGF-I in promoting periodontal regeneration. Positive results in these two models--the dog with natural periodontal disease and the non-human primate with ligature-induced attachment loss--justify human clinical trial testing of a putative regenerative therapy.
How to study lipidomes (2008)

Lipidome is loosely defined as the entire spectrum of lipids in a biological system. Given the modern lipidomics platforms for the first time empower us with the ability to obtain a snapshot of complete cellular/organismal lipidome, many surprises and discoveries are likely awaiting us in the area of lipids as related to cellular/organismal physiology. The lipidomics approaches can be applied both as the phenotyping platform and for the hypothesis-driven research aiming to elucidate, e.g., a specific pathway or gene function. Modern lipidomics methods combine the latest mass spectrometry technology and bioinformatics methods with traditional methods such as for sample preparation and lipid extraction.
Structural and evolutionary divergence of eukaryotic protein kinases in Apicomplexa (2011)

We pinpoint key conserved residues that can be predicted to mediate functional differences from eukaryotic homologs in three identified kinase families. We discuss the structural, functional and evolutionary implications of these lineage-specific variations and propose specific hypotheses for experimental investigation. The apicomplexan-specific kinase features reported in this study can be used in the design of selective kinase inhibitors.