gebhart/patrepeval huggingface dataset:
6 Bacterial Sigma Factors (1992)

OVERVIEW Sigma factors confer promoter specificity to bacterial core RNA polymerase (E). There are two major families of sigmas, one related in protein sequence to σ 70 , the primary Escherichia coli sigma, and a second related to σ 54 , an alternative E. coli sigma involved in transcribing nitrogen-regulated genes. We present an updated analysis of the sequence conservation among σ 70 -related sigmas, contrast transcription initiation at Eσ 70 and Eσ 54 promoters, and discuss the role of σ 70 -like and σ 54 -like sigmas in binding to core RNA polymerase and promoter recognition. The existence of alternative sigma subunits provides a way to coordinately regulate gene expression. We discuss how the synthesis, stability, and activity of alternative sigmas are regulated to achieve elaborate control of the expression of a variety of regulons in response to environmental stimuli and developmental signals. INTRODUCTION In a groundbreaking study published in 1969, Burgess and Travers at Harvard, and Dunn and Bautz working independently at Rutgers, discovered that bacterial RNA polymerase could be split into two components (Burgess et al. 1969). Transcription of a phage T4 DNA template required not only core RNA polymerase (E), which remains bound to a phosphocellulose column, but also a new stimulatory factor called sigma (σ), which flows through the phosphocellulose column. The function of sigma was clarified in short order (Dunn and Bautz 1969; Travers and Burgess 1969). It was found to promote initiation of transcription in a catalytic manner; that is, one sigma molecule permitted many core RNA polymerases to initiate transcription (for review, see Burgess...
Do effector and memory T helper cells also need B7 ligand costimulatory signals? (1997)

Blocking B7 ligand-costimulatory molecules can inhibit a primary T-dependent immune response, but whether these interactions also mediate ongoing or memory immune responses is less clear. Development of immunotherapies based on blocking B7 ligand interactions would be limited if they were effective only at the initiation of an immune response. We discuss the conditions under which T helper effector and memory cells may or may not require B7 ligand interactions for their function.
Substrate specificity of Pasteurella multocida toxin for α subunits of heterotrimeric G proteins (2012)

Pasteurella multocida is the causative agent of a number of epizootic and zoonotic diseases. Its major virulence factor associated with atrophic rhinitis in animals and dermonecrosis in bite wounds is P. multocida toxin (PMT). PMT stimulates signal transduction pathways downstream of heterotrimeric G proteins, leading to effects such as mitogenicity, blockade of apoptosis, or inhibition of osteoblast differentiation. On the basis of Gα(i2), it was demonstrated that the toxin deamidates an essential glutamine residue of the Gα(i2) subunit, leading to constitutive activation of the G protein. Here, we studied the specificity of PMT for its G-protein targets by mass spectrometric analyses and by utilizing a monoclonal antibody, which recognizes specifically G proteins deamidated by PMT. The studies revealed deamidation of 3 of 4 families of heterotrimeric G proteins (Gα(q/11), Gα(i1,2,3), and Gα(12/13) of mouse or human origin) by PMT but not by a catalytic inactive toxin mutant. With the use of G-protein fragments and chimeras of responsive or unresponsive G proteins, the structural basis for the discrimination of heterotrimeric G proteins was studied. Our results elucidate substrate specificity of PMT on the molecular level and provide evidence for the underlying structural reasons of substrate discrimination.
PCR-Sequence-Specific Oligonucleotide Probe Typing for HLA-A, -B, and -DR (2003)

The advantages of using molecular methods instead of serological typing to define the human leukocyte antigen (HLA) system have been well shown in transplantation and disease association studies (1,2). There are many molecular methods available to define the HLA alleles. Described in this chapter is the sequencespecific oligonucleotide probe (SSOP) method. The basis of this method is the HLA locus-specific amplification by polymerase chain reaction (PCR) and the subsequent probing of this product by SSOP. Most of the vast polymorphism of the HLA system results from conversion events whereby small nucleotide sections of one allele (usually no more that 100 bases long) are transferred to another allele. Thus many of the sequences tend to be shared by alleles and not to be allele-specific. Therefore probes are used which are sequence-specific. In order to differentiate the alleles, a battery of probes is required, and it is the pattern of reaction of these probes that distinguishes the HLA alleles.
Overexpression of the UGT73C6 alters brassinosteroid glucoside formation in Arabidopsis thaliana (2011)

The present study generates essential knowledge and molecular and biochemical tools, that will allow for the verification of a potential physiological role of UGT73C6 in BR glucosylation and will facilitate the investigation of the functional significance of BR glucoside formation in plants.
Preexisting BCG-Specific T Cells Improve Intravesical Immunotherapy for Bladder Cancer (2012)

Therapeutic intravesical instillation of bacillus Calmette-Guérin (BCG) is effective at triggering inflammation and eliciting successful tumor immunity in patients with non-muscle invasive bladder cancer, with 50 to 70% clinical response. Therapeutic success relies on repeated instillations of live BCG administered as adjuvant therapy shortly after tumor resection; however, the precise mechanisms remain unclear. Using an experimental model, we demonstrate that after a single instillation, BCG could disseminate to bladder draining lymph nodes and prime interferon-γ-producing T cells. Nonetheless, repeated instillations with live BCG were necessary for a robust T cell infiltration into the bladder. Parenteral exposure to BCG before instillation overcame this requirement; after the first intravesical instillation, BCG triggered a more robust acute inflammatory process and accelerated T cell entry into the bladder, as compared to the standard protocol. Moreover, parenteral exposure to BCG before intravesical treatment of an orthotopic tumor markedly improved response to therapy. Indeed, patients with sustained preexisting immunity to BCG showed a significant improvement in recurrence-free survival. Together, these data suggest that monitoring patients' response to purified protein derivative, and, in their absence, boosting BCG responses by parenteral exposure before intravesical treatment initiation, may be a safe and effective means of improving intravesical BCG-induced clinical responses.
Estrogen, Menopause, and the Aging Brain: How Basic Neuroscience Can Inform Hormone Therapy in Women (2006)

As neuroscientists, we can be so taken by the complexity and unique capabilities of the brain that we occasionally forget that it is part of a larger integrated biological system reliant on signaling and communication throughout the organism. The interactions between key organs that release hormones
Interaction of D-amino acid incorporated analogs of pardaxin with membranes (1992)

The influence of specific L- to D-amino acid substitutions on the interaction of pardaxin, a shark repellent neurotoxin polypeptide, with phospholipid vesicles and human erythrocytes is described. Twelve modified, truncated, or fluorescently labeled [with the fluorophore 7-nitrobenz-2-oxa-1,3-diazole-4-yl (NBD) at their N-terminal amino acid] analogues of pardaxin were synthesized by a solid-phase method. Fluorescence measurements were used to monitor the interaction of the analogues with membranes [Rapaport, D., & Shai, Y. (1991) J. Biol. Chem. 266, 23769-23775]. Upon titration of solutions containing the NBD-labeled peptides with small unilamellar vesicles, the fluorescent emission spectra of all NBD-labeled peptides displayed similar blue-shifts, in addition to enhanced intensities, upon relocation of the probe to the more apolar environment. Binding isotherms were constructed from which surface partition constants, in the range of 10(4) M-1, were derived. The existence of an aggregation process, suggested by the shape of the binding isotherms, could be associated only with those analogues in which the N-helix (residues 1-9) was not perturbed. The alpha-helical content of the analogues was estimated by circular dichroism (CD) spectroscopy, both before and after binding to vesicles at neutral pH. The ability of the peptides to dissipate a diffusion potential and to cause calcein release, as well as to lyse human erythrocytes, served to functionally characterize the peptides. The results support a two alpha-helix model, with a bend at position 13, as best describing pardaxin in its membrane-bound state.(ABSTRACT TRUNCATED AT 250 WORDS)
Timing of Insemination for Dairy Cows Identified in Estrus by a Radiotelemetric Estrus Detection System (1998)

The optimal time of artificial insemination (AI) was determined from data for 2661 AI in 17 herds utilizing a radiotelemetric system for estrus detection that has the potential for continuous 24-h surveillance to monitor behavioral events associated with estrus. The system consisted of pressure-sensitive radio frequency transmitters affixed over the sacrum region of cows. The activation of the sensor sent a radiotelemetric signal to a microcomputer via a fixed antenna. Cow identification, date, time, and duration of each standing event were recorded in the software program provided with the system. Each farm selected a 3-h interval to AI for cows that were identified in estrus during the previous 24 h. Pregnancy status was determined from data for return to estrus and palpation of the uterus 35 to 75 d following AI. Standing events during estrus averaged (+/- SD) 8.5 +/- 6.6 per cow, and the number of events per estrus across herds averaged from 6.2 +/- 5.1 to 12.8 +/- 9.9 per cow. The duration of estrus ranged from 5.1 +/- 3.8 to 10.6 +/- 6.8 h across herds; the mean was 7.1 +/- 5.4 h. The interval from the first standing event to AI affected the probability of pregnancy; the highest conception rates for AI occurred between 4 and 12 h after the onset of standing activity. The probability of pregnancy was higher for cows > 100 d in milk, exhibiting > 2 standing events during estrus, and inseminated during March, April or May.
Approaching the Secrets of N-Glycosylation in Aspergillus fumigatus: Characterization of the AfOch1 Protein (2010)

The mannosyltransferase Och1 is the key enzyme for synthesis of elaborated protein N-glycans in yeast. In filamentous fungi genes implicated in outer chain formation are present, but their function is unclear. In this study we have analyzed the Och1 protein of Aspergillus fumigatus. We provide first evidence that poly-mannosylated N-glycans exist in A. fumigatus and that their synthesis requires AfOch1 activity. This implies that AfOch1 plays a similar role as S. cerevisiae ScOch1 in the initiation of an N-glycan outer chain. A Δafoch1 mutant showed normal growth under standard and various stress conditions including elevated temperature, cell wall and oxidative stress. However, sporulation of this mutant was dramatically reduced in the presence of high calcium concentrations, suggesting that certain proteins engaged in sporulation require N-glycan outer chains to be fully functional. A characteristic feature of AfOch1 and Och1 homologues from other filamentous fungi is a signal peptide that clearly distinguishes them from their yeast counterparts. However, this difference does not appear to have consequences for its localization in the Golgi. Replacing the signal peptide of AfOch1 by a membrane anchor had no impact on its ability to complement the sporulation defect of the Δafoch1 strain. The mutant triggered a normal cytokine response in infected murine macrophages, arguing against a role of outer chains as relevant Aspergillus pathogen associated molecular patterns. Infection experiments provided no evidence for attenuation in virulence; in fact, according to our data the Δafoch1 mutant may even be slightly more virulent than the control strains.
All-trans-Retinoic Acid Ameliorated High Fat Diet-Induced Atherosclerosis in Rabbits by Inhibiting Platelet Activation and Inflammation (2012)

AtRA can ameliorate HFD-induced AS in rabbits by inhibiting platelet activation and inflammation.
Structure-Activity Relationship and Molecular Action Mechanism in the Family of Antidiabetic bis(Picolinato)oxovanadium(IV) Complexes (2007)

Trials for the use of vanadium in treating diabetes mellitus (DM) was reported in 1899, which was 23 years before Banting and Best discovered insulin and used it to treat diabetic patients. However, pharmaceutical interest in vanadium as an insulin substitute started in 1980. Ten years after, in 1990, orally active insulin substitutes were found as chelated oxovanadium(IV) complexes such as bis(methylcysteinato)oxovanadium(IV) and bis(malonato)oxovanadium(IV). Since these findings, a wide variety of antidiabetic oxovanadium(IV) complexes have been proposed. In 1995, bis(picolinato)oxovanadium(IV) complexes [VO(pa)2] was found to have excellent in vitro insulinomimetic and in vivo antidiabetic activities in type 1—like diabetic rats. This VO(pa)2 complex has an advantage to study structure-activity relationships in both in vitro and in vivo levels, and produce many interesting results. This article reviews the recent new progress in our research groups on the structure-activity relationship and the molecular action mechanism in the family of VO(pa)2 complex.
Design, Synthesis, and Evaluation of Coumarin-Based Molecular Probes for Imaging of Myelination (2011)

Myelination represents one of the most fundamental biological processes in the vertebrate nervous system. Abnormalities and changes in myelination in the central nervous system (CNS) are seen in many neurodegenerative disorders, such as multiple sclerosis (MS). A long-standing goal has been to directly detect and quantify myelin content in order to facilitate diagnosis and therapeutic treatments of myelin-related diseases. In the course of our studies, we have developed a series of small-molecule probes (SMP) as myelin-imaging agents. Among them are coumarin derivatives, which exhibit promising brain permeability and myelin-binding properties. Herein we report a full account of the design and synthesis of coumarin-based SMPs as myelin-imaging agents. Systematic evaluation of these SMPs in both the CNS and peripheral nervous system (PNS) allowed us to identify some lead agents for potential use as fluorescent dyes for intraoperative nerve mapping in surgical operations or as radiotracers for positron emission tomography (PET) imaging of myelination.
PMA-activated neutrophils decrease pulmonary endothelial ectoenzyme activities in perfused rabbit lungs (1992)

We have studied the effects of phorbol 12-myristate 13-acetate (PMA, 15 micrograms) on pulmonary endothelial ectoenzyme [angiotensin-converting enzyme (ACE) and 5'-nucleotidase (NCT)] function in isolated rabbit lungs perfused in situ with platelet-poor (PPP) or platelet-rich (PRP) plasma in the presence or absence of neutrophils. Enzyme activities were estimated from the hydrolysis of the substrates [3H]benzoyl-Phe-Ala-Pro ([3H]BPAP) by ACE and 14C-labeled AMP by NCT during a single transpulmonary passage, using indicator-dilution techniques. In all treatment groups PMA produced a delayed increase in pulmonary vascular resistance to about three times the control value. PMA alone [in lungs perfused with PPP (n = 5 animals) or PRP (n = 6)] or neutrophils alone (in PPP-perfused lungs, n = 5) had no effect on enzyme activity. However, PMA-activated neutrophils (n = 5) decreased percent metabolism (%M) of [3H]BPAP from 87 +/- 3 to 77 +/- 4% (30 min after PMA), and the apparent first-order parameter [ratio of maximum activity to Michaelis constant (Amax/Km)] for ACE from 821 +/- 114 to 613 +/- 61 ml/min (30 min after PMA). At the same time, Km values of BPAP for ACE and AMP for NCT were elevated from 9.2 +/- 2.2 to 19.3 +/- 3 microM and 6.7 +/- 1.2 to 15.1 +/- 3.6 microM, respectively, whereas Amax (product of enzyme mass and rate of product formation, thus an index of perfused microvascular surface area) did not change.(ABSTRACT TRUNCATED AT 250 WORDS)
<title>Edge-based block matching technique for video motion estimation</title> (1991)

An important part of most video compression techniques is displacement vector estimation, which in many situations is achieved by Block Matching Algorithms (BMA). Traditional BMA uses costly integer arithmetic on 8-bit images to minimize a Mean Absolute Error (MAE) criterion that determines the displacement estimate. In this paper, we present an approach for motion estimation based on binary edge images. Specifically, we assign an intensity gradient vector to each edge pixel and apply BMA to the gradient vector. Our approach can potentially reduce the complexity of the VLSI implementation of motion estimation algorithms. We present simulation results comparing this technique to traditional BMA over several 50-frame sequences.
The effect of membrane cholesterol content on ion transport processes in plasma membranes (1997)

Cholesterol is a prominent component of mammalian plasma membranes and is one of the factors that determine membrane function. In this review the effects of cholesterol content on transport processes in biological membranes are summarized. Membrane cholesterol affects a variety of membrane proteins, including ion channels, transporters, and receptors. Present concepts concerning the mechanistic basis of lipid-induced modulation of transport protein function range between two extremes: modulation by bulk properties or by specific interactions. Interest in bulk properties has been focussed mainly on membrane fluidity. The fluidity of biomembranes is diminished particularly by enrichment with cholesterol. As a change in membrane composition alters the environment in which the proteins are dissolved, any process which depends on membrane protein function may be affected by alterations in membrane composition, such as a change in cholesterol content. This review emphasizes the inhibitory effect of cholesterol enrichment on all membrane ATPases studied, and the stimulating effect of cholesterol enrichment on most other membrane transport proteins. Together with the intriguing feature that the cholesterol content of plasma membranes is considerably higher than that of subcellular membranes, there is ample evidence for a significant role of plasma membrane cholesterol in transmembrane protein function.
Identification of Residues in the 558-Loop of Factor VIIIa A2 Subunit That Interact with Factor IXa (2009)

Factor VIIIa is comprised of A1, A2, and A3C1C2 subunits. Several lines of evidence have identified the A2 558-loop as interacting with factor IXa. The contributions of individual residues within this region to inter-protein affinity and cofactor activity were assessed following alanine scanning mutagenesis of residues 555-571 that border or are contained within the loop. Variants were expressed as isolated A2 domains in Sf9 cells using a baculovirus construct and purified to >90%. Two reconstitution assays were employed to determine affinity and activity parameters. The first assay reconstituted factor Xase using varying concentrations of A2 mutant and fixed levels of A1/A3C1C2 dimer purified from wild type (WT), baby hamster kidney cell-expressed factor VIII, factor IXa, and phospholipid vesicles to determine the inter-molecular K(d) for A2. The second assay determined the K(d) for A2 in factor VIIIa by reconstituting various A2 and fixed levels of A1/A3C1C2. Parameter values were determined by factor Xa generation assays. WT A2 expressed in insect cells yielded similar K(d) and k(cat) values following reconstitution as WT A2 purified from baby hamster kidney cell-expressed factor VIII. All A2 variants exhibited modest if any increases in K(d) values for factor VIIIa assembly. However, variants S558A, V559A, D560A, G563A, and I566A showed >9-fold increases in K(d) for factor Xase assembly, implicating these residues in stabilizing A2 association with factor IXa. Furthermore, variants Y555A, V559A, D560A, G563A, I566A, and D569A showed >80% reduction in k(cat) for factor Xa generation. These results identify residues in the 558-loop critical to interaction with factor IXa in Xase.
Gallium Imide, {Ga(NH)3/2}n, a New Polymeric Precursor for Gallium Nitride Powders (1996)

The efficient preparation of the new polymeric gallium imide {Ga(NH)3/2}n from the reaction between [Ga(NMe2)3]2 and NH3 at ambient temperatures is described. The gallium imide precursor is shown by TEM and XRD studies to yield upon pyrolysis a rare cubic/hexagonal variety of gallium nitride, GaN. Some control over the average particle size of GaN in the nanosized region is achieved by application of various pyrolysis schemes.
Biological Effects of Short-Chain Fatty Acids in Nonruminant Mammals (1993)

The objective of this review is to provide an overview of intermittent fasting regimens, summarize the evidence on the health benefits of intermittent fasting, and discuss physiological mechanisms by which intermittent fasting might lead to improved ...Read More
Bone Lengthening in the Craniofacial Skeleton (1990)

The process of bone lengthening by cortical fracture and gradual distraction of callus has become well established in the enchondral bones of the extremities. In this study the principles of bone lengthening were applied to the membranous bone of the craniofacial skeleton using the growing dog mandible as a model. Six mongrel dogs five months of age were studied. A unilateral, periosteal-preserving angular corticotomy was performed, and an external minilengthening device was fixed to the mandible perpendicular to the corticotomy. After 10 days of external fixation, the mandible was lengthened 1 mm/day for 20 days and then held in external fixation for 56 days (8 weeks) after which all dogs were killed. Anthropometric measurements and histological analysis of the specimens confirmed that bone lengthening had occurred and that new cortical bone was formed in the expanded areas.
Synthesis of 5-substituted pyrimidines. II (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of 5-substituted pyrimidines. IIWady Asbun and Stephen B. BinkleyCite this: J. Org. Chem. 1968, 33, 1, 140–142Publication Date (Print):January 1, 1968Publication History Published online1 May 2002Published inissue 1 January 1968https://pubs.acs.org/doi/10.1021/jo01265a026https://doi.org/10.1021/jo01265a026research-articleACS PublicationsRequest reuse permissionsArticle Views205Altmetric-Citations25LEARN 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