gebhart/patrepeval huggingface dataset:
Intercodon dinucleotides affect codon choice in plant genes (2000)

In this work, 710 CDSs corresponding to over 290 000 codons equally distributed between Brassica napus, Arabidopsis thaliana, Lycopersicon esculentum, Nicotiana tabacum, Pisum sativum, Glycine max, Oryza sativa, Triticum aestivum, Hordeum vulgare and Zea mays were considered. For each amino acid, synonymous codon choice was determined in the presence of A, G, C or T as the initial nucleotide of the subsequent triplet; data were statistically analysed under the hypothesis of an independent assortment of codons. In 33.4% of cases, a frequency significantly (P: = 0.01) different from that expected was recorded. This was mainly due to a pervasive intercodon TpA and CpG deficiency. As a general rule, intercodon TpAs and CpGs were preferably replaced by CpAs and TpGs, respectively. In several instances, codon frequencies were also modified to avoid homotetramer and homotrimer formation, to reduce intercodon ApCs downstream (1,2) GG or AG dinucleotides, as well as to increase GpA or ApG intercodons under certain contexts. Since TpA, CpG and homotetra(tri)mer deficiency directly or indirectly accounted for 77% of significant variation in the codon frequency, it can be concluded that codon usage mirrors precise needs at the DNA structure level. Plant species exhibited a phylogenetically-related adaptation to structural constraints. Codon usage flexibility was reflected in strikingly different arrays of optimum codons for probe design.
Plasmons and optical properties of carbon nanotubes (1994)

The optical properties of carbon nanotubes are studied within the gradient approximation. The calculated dielectric function exhibits many divergent structures, due to the divergencies in its density of states. As a result, the electron-energy-loss spectrum has many peak structures, including a prominent one at \ensuremath{\sim}6 eV, which is identified as the collective excitations of the \ensuremath{\pi}-band electrons. This plasmon is found to be insensitive to both radius and chiral angle, due to the unique one-dimensional band structure of carbon nanotubes. The result is consistent with the experimental measurements. The reflectance also exhibits many interesting features, including a weak but sharp plasmon edge at \ensuremath{\sim}6 eV.
Homo- and Hetero-oligomerization of β-Arrestins in Living Cells (2005)

Arrestins are important proteins, which regulate the function of serpentine heptahelical receptors and contribute to multiple signaling pathways downstream of receptors. The ubiquitous beta-arrestins are believed to function exclusively as monomers, although self-association is assumed to control the activity of visual arrestin in the retina, where this isoform is particularly abundant. Here the oligomerization status of beta-arrestins was investigated using different approaches, including co-immunoprecipitation of epitope-tagged beta-arrestins and resonance energy transfer (BRET and FRET) in living cells. At steady state and at physiological concentrations, beta-arrestins constitutively form both homo- and hetero-oligomers. Co-expression of beta-arrestin2 and beta-arrestin1 prevented beta-arrestin1 accumulation into the nucleus, suggesting that hetero-oligomerization may have functional consequences. Our data clearly indicate that beta-arrestins can exist as homo- and hetero-oligomers in living cells and raise the hypothesis that the oligomeric state may regulate their subcellular distribution and functions.
Cerebrospinal Fluid and Blood Cytokines as Biomarkers for Multiple Sclerosis: A Systematic Review and Meta-Analysis of 226 Studies With 13,526 Multiple Sclerosis Patients (2019)

<b>Background:</b> Multiple sclerosis (MS) biomarker identification is important for pathogenesis research and diagnosis in routine clinical practice. Cerebrospinal fluid (CSF) and blood cytokines as potential biomarkers that can inform MS pathogenesis, diagnosis and response to treatment have been assessed in numerous studies. However, there have been no comprehensive meta-analyses to pool cytokine data and to address their diagnostic performance. We systematically reviewed literature with meta-analyses to assess the alteration levels of cytokines and chemokines in MS. <b>Methods:</b> We searched PubMed and Web of Science for articles published between January 1, 1990 and April 30, 2018 for this systematic review and meta-analysis. Data were extracted from 226 included studies encompassing 13,526 MS patients and 8,428 controls. Biomarker performance was rated by a random-effects meta-analysis based on the standard mean difference between cytokine concentration in patients with MS and controls, or patients before and after treatments. <b>Results:</b> Of the 26 CSF cytokines and 37 blood cytokines for potential differentiation between MS patients and controls, the random-effects meta-analysis showed that 13 CSF cytokines and 21 blood cytokines were significantly increased in MS patients in comparison to the controls. Interestingly, TNF-α, CXCL8, IL-15, IL-12p40, and CXCL13 were increased in both blood and CSF of MS patients. For those cytokines analyzed in at least 10 studies, differentiation between case and control was strong for CSF CXCL13, blood IL-2R, and blood IL-23; CSF CXCL8, blood IL-2, and blood IL-17 also performed well in differentiating between MS patients and controls, whereas those of CSF TNF-α and blood TNF-α, CXCL8, IL-12, IFN-γ were moderate. Furthermore, CSF IL-15, CCL19, CCL11, CCL-3, and blood CCL20, IL-12p40, IL-21, IL-17F, IL-22 had large effective sizes when differentiating between MS patients and controls but had a relatively small number of studies (three to seven studies). <b>Conclusion:</b> Our findings clarified the circulating cytokine profile in MS, which provide targets for disease modifying treatments, and suggest that cytokines have the potential to be used as biomarkers for MS.
Collagen in Wound Healing: Are We Onto Something New or Just Repeating the Past? (2009)

The Foot and Ankle Online Journal 2 (9): 3 Lower extremity amputations in patients living with diabetes have significant morbidity and mortality. Given the obvious link between lower extremity amputations and the ulcerations that precede them, it is incumbent upon the wound care provider to become familiar with advanced wound care products. The importance of reestablishing a functional extracellular matrix (ECM) in chronic wounds has led to a renewed interest in collagen-based wound healing products. These products can be applied either in the surgical or clinical setting. An intact functional ECM will seek to promote normal progression through the stages of wound healing. This article presents several representative collagen-based advanced wound care products utilized in wound healing, discusses their mechanism of action, and the appropriate indication for each product's usage.
Stepwise mechanism of HIV reverse transcriptase: primer function of phosphorothioate oligodeoxynucleotide (1989)

Primer recognition by purified HIV reverse transcriptase has been investigated. Earlier we found that the reaction pathway for DNA synthesis is ordered, with template-primer and free enzyme combining to form the first complex in the reaction sequence (Majumdar et al., 1988). We now find that d(C)28 is a linear competitive inhibitor of DNA synthesis against poly[r(A)].oligo[d(T)] as template.primer, indicating that d(C)28 and the template.primer combine with the same form of the enzyme in the reaction scheme, i.e., the free enzyme. The phosphorothioate oligodeoxynucleotide Sd(C)28 also is a linear competitive inhibitor against template.primer. However, the Ki for inhibition (approximately 2.8 nM) is approximately 200-fold lower than the Ki for inhibition by d(C)28. Since the inhibition is linear competitive, the dissociation constant is equal to the Ki for inhibition. Filter binding assays confirmed high-affinity binding between Sd(C)28 and the enzyme and yielded a KD similar to the Ki for inhibition. Substrate kinetic studies of DNA synthesis using Sd(C)28 as primer, and poly[r(I)] as template, revealed that the Km for Sd(C)28 is 24 nM. The Km for this primer is, therefore, 8-fold higher than the KD for enzyme-primer binding (2.8 nM). These results enable calculation of real time rate values for the enzyme-primer association (kon = 5.7 x 10(8) M-1 s-1) and dissociation (koff = 1.6 s-1).
Heat Shock Protein 27: Developmental Regulation and Expression after Peripheral Nerve Injury (1998)

The heat shock protein (HSP) 27 is constitutively expressed at low levels in medium-sized lumbar dorsal root ganglion (DRG) cells in adult rats. Transection of the sciatic nerve results in a ninefold upregulation of HSP27 mRNA and protein in axotomized neurons in the ipsilateral DRG at 48 hr, without equivalent changes in the mRNAs encoding HSP56, HSP60, HSP70, and HSP90. Dorsal rhizotomy, injuring the central axon of the DRG neuron, does not upregulate HSP27 mRNA levels. After peripheral axotomy, HSP27 mRNA and protein are present in small, medium, and large DRG neurons, and HSP27 protein is transported anterogradely, accumulating in the dorsal horn and dorsal columns of the spinal cord, where it persists for several months. Axotomized motor neurons also upregulate HSP27. Only a minority of cultured adult DRG neurons are HSP27-immunoreactive soon after dissociation, but all express HSP27 after 24 hr in culture with prominent label throughout the neuron, including the growth cone. HSP27 differs from most axonal injury-regulated and growth-associated genes, which are typically present at high levels in early development and downregulated on innervation of their targets, in that its mRNA is first detectable in the DRG late in development and only approaches adult levels by postnatal day 21. In non-neuronal cells, HSP27 has been shown to be involved both in actin filament dynamics and in protection against necrotic and apoptotic cell death. Therefore, its upregulation after adult peripheral nerve injury may both promote survival of the injured neurons and contribute to alterations in the cytoskeleton associated with axonal growth.
A Potent and Broad Neutralizing Antibody Recognizes and Penetrates the HIV Glycan Shield (2011)

The HIV envelope (Env) protein gp120 is protected from antibody recognition by a dense glycan shield. However, several of the recently identified PGT broadly neutralizing antibodies appear to interact directly with the HIV glycan coat. Crystal structures of antigen-binding fragments (Fabs) PGT 127 and 128 with Man(9) at 1.65 and 1.29 angstrom resolution, respectively, and glycan binding data delineate a specific high mannose-binding site. Fab PGT 128 complexed with a fully glycosylated gp120 outer domain at 3.25 angstroms reveals that the antibody penetrates the glycan shield and recognizes two conserved glycans as well as a short β-strand segment of the gp120 V3 loop, accounting for its high binding affinity and broad specificity. Furthermore, our data suggest that the high neutralization potency of PGT 127 and 128 immunoglobulin Gs may be mediated by cross-linking Env trimers on the viral surface.
Caspase Inhibition Protects against Reovirus-Induced Myocardial Injury In Vitro and In Vivo (2004)

Viral myocarditis is a disease with a high morbidity and mortality. The pathogenesis of this disease remains poorly characterized, with components of both direct virus-mediated and secondary inflammatory and immune responses contributing to disease. Apoptosis has increasingly been viewed as an important mechanism of myocardial injury in noninfectious models of cardiac disease, including ischemia and failure. Using a reovirus murine model of viral myocarditis, we characterized and targeted apoptosis as a key mechanism of virus-associated myocardial injury in vitro and in vivo. We demonstrated caspase-3 activation, in conjunction with terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling and annexin binding, in cardiac myocytes after myocarditic viral infection in vitro. We also demonstrated a tight temporal and geographical correlation between caspase-3 activation, histologic injury, and viral load in cardiac tissue after myocarditic viral infection in vivo. Two pharmacologic agents that broadly inhibit caspase activity, Q-VD-OPH and Z-VAD(OMe)-FMK, effectively inhibited virus-induced cellular death in vitro. The inhibition of caspase activity in vivo by the use of pharmacologic agents as well as genetic manipulation reduced virus-induced myocardial injury by 40 to 60% and dramatically improved survival in infected caspase-3-deficient animals. This study indicates that apoptosis plays a critical role in mediating cardiac injury in the setting of viral myocarditis and is the first demonstration that caspase inhibition may serve as a novel therapeutic strategy for this devastating disease.
Insulin‐and insulin‐like growth‐factor‐I receptor tyrosine‐kinase activities in human renal carcinoma (1995)

We studied expression and functional characteristics of the insulin- and insulin-like-growth-factor-I (IGF-I) receptors in human renal carcinoma. Ligand-binding properties and tyrosine-kinase activity of both receptors, as well as the expression of the 2 isoforms of the human insulin receptor (HIR-A and -B) were analyzed in renal carcinoma and normal adjacent kidney tissue of 8 adult patients. Partially purified insulin- and IGF-I receptors from normal and renal cell carcinoma tissue possessed identical affinities for their ligands. Renal cell carcinoma, however, contained 3- to 4-fold more specific insulin-binding sites and 2-fold more IGF-I binding sites than adjacent normal kidney tissue. In addition, we determined the relative content of insulin/IGF-I receptor hybrids in both tissues. Renal cell carcinoma and adjacent normal tissue revealed similar amounts of insulin/IGF-I receptor hybrids, i.e., 44 +/- 8.2% of tracer IGF-I binding in normal tissue and 46 +/- 12.0% in renal cell carcinoma. When equal amounts of insulin- and IGF-I receptor protein were studied, we found significantly increased receptor autophosphorylation and elevated substrate phosphorylation in carcinoma tissue. To assess whether the differences in insulin-receptor tyrosine-kinase activity were caused by an altered pattern of insulin receptor isoform expression, we determined mRNA levels for HIR-A and -B. The 2 insulin receptor isoforms were, however, expressed in highly variable ratios in both normal and tumor tissue. Our experiments show that renal carcinoma expresses an elevated amount of insulin- and IGF-I receptor protein with increased specific autophosphorylation and tyrosine-kinase activity each. The increase of insulin-receptor tyrosine-kinase activity in renal carcinoma cannot be explained by an altered expression pattern of insulin receptor isoforms.
Fluoxetine, placebo, and tricyclic antidepressants in major depression with and without anxious features. (1994)

Anxiety in major depression does not appear to affect response to an antidepressant. Therefore, antidepressant selection should be determined by an agent's overall risk:benefit ratio, not the presence or absence of anxiety.
Handbook of industrial cell culture: mammalian, microbial, and plant cells (2003)

The advent of molecular genetics, the progression of transgenic animal and plant methodologies from the laboratory to industrial-scale production, and the development of powerful analytical techniques have each helped standardize the culturing of cells to produce desirable commercial products. In Handbook of Industrial Cell Culture: Mammalian, Microbial, and Plant Cells, a diverse team of researchers, technologists, and engineers describe, in simple and practical language, the major current and evolving technologies for improving the biocatalytic capabilities of mammalian, microbial, and plant cells. The authors present state-of-the-art techniques, proven methods, and strategies for industrial screening, cultivation, and scale-up of these cells, and describe their biotechnological and industrial uses. Special emphasis is given to solving the critical issues encountered during the discovery of new drugs, process development, and the manufacture of new and existing compounds. Other topics include recombinant protein expression, bioinformatics, high throughput screening, analytical tools in biotechnology, DNA shuffling, and genomics discovery. The authors all have proven track records in the successful implementation of commercial-scale processes. Cutting-edge and highly practical, the Handbook of Industrial Cell Culture: Mammalian, Microbial, and Plant Cells not only surveys the best current practices in the art of industrial cell culture across cell types, but also delineates today's evolving technologies with examples of proven practical applications, as well as projections of their future potential
Reactions of b-Aminoenones with Acetylhydrazine, Semicarbazide and Methoxycarbonylhydrazine. Synthesis of 1-Acetyl-, 1-Carboxamide- or Methyl 1-Carboxylated Pyrazole Derivatives (1999)

Acetylhydrazine, semicarbazide and methoxycarbonylhydrazine react with p-aminoenones to give regioselectively the corresponding N-acetyl-or Ncarhoxypyrazole derivatives.The reaction are highly regioselective and occurs via 5-hydroxypyrazolines which in several case can be isolated and characterized.
Sialylation of the B lymphocyte molecule CD22 by alpha 2,6-sialyltransferase is implicated in the regulation of CD22-mediated adhesion. (1994)

The B cell surface receptor CD22 binds several sialoglycoproteins containing sialic acid in alpha 2,6 linkage, on the surface of B and T lymphocytes. Because lymphocytes adhere tightly to fibroblasts transfected with CD22 cDNA, it would appear reasonable to suggest that regulatory mechanisms might have evolved which prevent undesired CD22-mediated leukocyte aggregation. Here we provide evidence for the existence of at least one mechanism that might regulate CD22 interaction with ligands on adjacent cells. We demonstrate that sialylation of CD22 by beta-galactoside alpha 2,6-sialyltransferase abrogates CD22-mediated lymphocyte adhesion, and that adhesion can be restored by removal of alpha 2,6-linked sialic acid residues from the CD22 molecule. Taken together, our results suggest that alpha 2,6-sialyltransferase can both promote and inhibit CD22-ligand interactions. These observations provide the first direct evidence that receptor-ligand interactions mediated by an Ig superfamily molecule are under the control of a specific glycosyltransferase.
Engineering Target-Responsive Hydrogels Based on Aptamer−Target Interactions (2008)

In this communication, we report a simple, but highly adaptable, method of constructing selective target-responsive hydrogels using DNA aptamers. The simplicity of the design is accomplished by using linear polymer chains as the hydrogel backbone and a DNA aptamer as the cross-linker. In this design, competitive binding of target to the aptamer causes the decrease of cross-linking density and, hence, dissolution of the hydrogel. The adaptability of this strategy for therapeutic applications was demonstrated using two different types of targets, small molecules and proteins. Our results indicated that this molecular engineering provides a highly selective and controllable release system whereby efficient release of therapeutic agents can occur at specific environments in which the target biomarker is found.
Heterotypic recognition of foot-and-mouth disease virus by cattle lymphocytes (1990)

Lymphoproliferation against foot-and-mouth disease (FMD) virus was examined using peripheral blood mononuclear cells from vaccinated cattle. Ten weeks after revaccination the optimum conditions for proliferation were obtained with 1 microgram/ml of purified virus after 5 to 6 days in culture. This contrasted with the response at 20 months post-revaccination, when the response required less antigen and showed a peak response after 3 to 4 days in culture. Proliferation was specific for FMD virus, but was cross-reactive between serotypically distinct strains of the virus. The proliferative response to isolated virus proteins (VP) involved all three major capsid proteins (VP1, -2 and -3), although the proliferation of lymphocytes from heterotypically vaccinated cattle was due to VP3. Furthermore, the response induced by purified virus, chemically fixed virus and subunit virus particles was indistinguishable and thus it is likely that processing was required for the induction of proliferation. Together these data strongly suggest that FMD virus-induced lymphoproliferation is T cell-mediated and that VP3 may contain dominant, cross-reactive sequences.
Relevance of Chlamydia pneumoniae murine pneumonitis model to evaluation of antimicrobial agents (1995)

A mouse model of Chlamydia pneumoniae pneumonitis was established in outbred MF1 mice immunosuppressed with cyclophosphamide. Following intranasal inoculation with 2.2 x 10(3) inclusion-forming units of C. pneumoniae TW-183 per mouse, chlamydiae were culturable from the lungs for at least 29 days. Progressive subacute pneumonitis with perivascular and peribronchial lymphoid cell hyperplasia was observed, and C. pneumoniae organisms were located in consolidated areas of tissue by immunocytochemistry. Mice were treated orally, commencing at 8 days after infection, with clinically achievable concentrations of amoxicillin-clavulanate or ciprofloxacin (three times daily for 7 days), ofloxacin, doxycycline, or erythromycin (twice daily for 7 days), or azithromycin (once daily for 4 days). Despite disparate antichlamydial activity in cell culture and different pharmacokinetic properties in infected animals, all treatments reduced the chlamydial load in the lungs (P < 0.05) when the loads were evaluated by culture at 1 and 10 days after the cessation of dosing, and this was reflected in the histopathological and immunocytochemistry scores. There was no significant difference between these treatments, and C. pneumoniae TW-183 was eradicated from the majority but not from all mice. These results confirm the limited clinical data available to date. In conclusion, a range of oral antimicrobial agents commonly used for the treatment of community-acquired respiratory infection was found to be efficacious in this experimental model of C. pneumoniae pneumonitis, which may therefore be of utility in chemotherapy and follow-up studies.
TheEscherichia colimetal-binding chaperone SlyD interacts with the large subunit of [NiFe]-hydrogenase 3 (2010)

The multi-step biosynthesis of the [NiFe]-hydrogenase enzyme involves a variety of accessory proteins. To further understand this process, a Strep-tag II variant of the large subunit of Escherichia coli hydrogenase 3, HycE, was constructed to enable isolation of protein complexes. A complex with SlyD, a chaperone protein implicated in hydrogenase production through association with the nickel-binding accessory protein HypB, was observed. A SlyD-HycE interaction preceding both iron and nickel insertion to the enzyme was detected, mediated by the chaperone domain of SlyD, and independent of HypB. These results support a model of several roles for SlyD during hydrogenase maturation.