gebhart/patrepeval huggingface dataset:
Identification of target promoters for the Bacillus subtilis extracytoplasmic function σ factor, σW (1999)

The Bacillus subtilis sigW gene encodes an extracytoplasmic function (ECF) sigma factor that is expressed in early stationary phase from a sigW-dependent autoregulatory promoter, PW. Using a consensus-based search procedure, we have identified 15 operons preceded by promoters similar in sequence to PW. At least 14 of these promoters are dependent on sigma W both in vivo and in vitro as judged by lacZ reporter fusions, run-off transcription assays and nucleotide resolution start site mapping. We conclude that sigma W controls a regulon of more than 30 genes, many of which encode membrane proteins of unknown function. The sigma W regulon includes a penicillin binding protein (PBP4*) and a co-transcribed amino acid racemase (RacX), homologues of signal peptide peptidase (YteI), flotillin (YuaG), ABC transporters (YknXYZ), non-haem bromoperoxidase (YdjP), epoxide hydrolase (YfhM) and three small peptides with structural similarities to bacteriocin precursor polypeptides. We suggest that sigma W activates a large stationary-phase regulon that functions in detoxification, production of anti-microbial compounds or both.
Autohydrolysis of aspen milled wood lignin (1980)

In order to obtain further understanding of the nature of lignin reactions during autocatalysed hydrolysis (autohydrolysis) of wood, milled wood lignin (MWL) was isolated from aspen (Populus tremuloides) and treated under autohydrolysis conditions. By this means reactions of the lignin itself could be distinguished from those taking place between lignin and the carbohydrate or other components of the wood. The material after the reaction was separated into a dioxane insoluble fraction (DI), a dioxane soluble but ether insoluble fraction (DSEI), and an ether soluble fraction (ES). Studies were carried out on the DI and DSEI fractions; no direct study was made of the small ES fraction.The formation of DI material increased linearly during the first 7.5 min at 170 °C and then levelled off. At the same time DSEI decreased and then levelled off. Gel permeation chromatography of the DSEI fraction suggested that during autohydrolysis there is an initial generation of low molecular weight fragments which recombine to form first a high molecular weight soluble fraction and from this the insoluble product. The DSEI fraction contained increased conjugated and unconjugated keto groups. Carboxylic acids were also detected; they have been attributed to the reincorporation of low molecular weight aromatic acids generated by the hydrolysis of the corresponding esters. The dioxane insoluble (DI) fraction had fewer unconjugated keto groups than the DSEI fraction, indicating that these groups participated in the condensation reactions leading to the formation of insoluble material. These probably involve position 6 of the aromatic ring.
Dendritic cells: Immunological sentinels with a central role in health and disease (2000)

Immunological effector cells must be sensitive to the antigens or environmental signals that indicate that a pathogen is present. To this end, a group of cells known as the professional antigen-presenting cells have the ability to educate T, B and NK cells as to the fingerprints of specific infections. The most adept of these cells are a closely related family termed dendritic cells (DC). A subset of these act as peripheral sentinels, specializing in the uptake, processing and presentation of antigenic material combined with an ability to detect a wide variety of 'danger' signals. These 'danger' or activation signals induce profound changes in dendritic cell physiology, facilitating the efficient stimulation of both adaptive and innate immunity. In the present review, a number of recent advances in the understanding of DC biology are discussed. These advances offer insights into the pathogenesis of a wide variety of diseases and point towards future strategies for immunotherapy.
Regioselective cyclodehydration of chiral diols with diethoxytriphenylphosphorane, triphenylphosphine-tetrachloromethane-potassium carbonate, and triphenylphosphine-diethyl azodicarboxylate reagents. A comparative study (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRegioselective cyclodehydration of chiral diols with diethoxytriphenylphosphorane, triphenylphosphine-tetrachloromethane-potassium carbonate, and triphenylphosphine-diethyl azodicarboxylate reagents. A comparative studyPhilip L. Robinson, Carey N. Barry, S. Woody Bass, Susan E. Jarvis, and Slayton A. Evans Jr.Cite this: J. Org. Chem. 1983, 48, 26, 5396–5398Publication Date (Print):December 1, 1983Publication History Published online1 May 2002Published inissue 1 December 1983https://pubs.acs.org/doi/10.1021/jo00174a059https://doi.org/10.1021/jo00174a059research-articleACS PublicationsRequest reuse permissionsArticle Views631Altmetric-Citations45LEARN 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 Get e-Alerts
Characterization of Bacterial Communities in Feces from Healthy Elderly Volunteers and Hospitalized Elderly Patients by Using Real-Time PCR and Effects of Antibiotic Treatment on the Fecal Microbiota (2004)

Fecal bacteria were studied in healthy elderly volunteers (age, 63 to 90 years; n = 35) living in the local community, elderly hospitalized patients (age, 66 to 103; n = 38), and elderly hospitalized patients receiving antibiotic treatment (age, 65 to 100; n = 21). Group- and species-specific primer sets targeting 16S rRNA genes were used to quantitate intestinal bacteria by using DNA extracted from feces and real-time PCR. The principal difference between healthy elderly volunteers and both patient cohorts was a marked reduction in the Bacteroides-Prevotella group following hospitalization. Reductions in bifidobacteria, Desulfovibrio spp., Clostridium clostridiiforme, and Faecalibacterium prausnitzii were also found in the hospitalized patients. However, total 16S rRNA gene copy numbers (per gram of wet weight of feces) were generally lower in the stool samples of the two groups of hospitalized patients compared to the number in the stool samples of elderly volunteers living in the community, so the relative abundance (percentage of the group- and species-specific rRNA gene copies in relation to total bacterial rRNA gene copies) of bifidobacteria, Desulfovibrio spp., C. clostridiiforme, and F. prausnitzii did not change. Antibiotic treatment resulted in further reductions in the numbers of bacteria and their prevalence and, in some patients, complete elimination of certain bacterial communities. Conversely, the numbers of enterobacteria increased in the hospitalized patients who did not receive antibiotics, and due to profound changes in fecal microbiotas during antibiotic treatment, the opportunistic species Enterococcus faecalis proliferated.
Complex autoregressive model for shape recognition (1992)

A complex autoregressive model for invariant feature extraction to recognize arbitrary shapes on a plane is presented. A fast algorithm to calculate complex autoregressive coefficients and complex PARCOR coefficients of the model is also shown. The coefficients are invariant to rotation around the origin and to choice of the starting point in tracing a boundary. It is possible to make them invariant to scale and translation. Experimental results that the complicated shapes like nonconvex boundaries can be recognized in high accuracy, even in the low-order model. It is seen that the complex PARCOR coefficients tend to provide more accurate classification than the complex AR coefficients.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Irradiation with a diode at 820 nm induces changes in circular dichroism spectra (250-780 nm) of living cells (2001)

A sensitive method for measuring the circular dichroism (CD) of living cells in visible-near IR region is developed. The changes in CD spectra from 250 to 780 nm of HeLa cell suspension after the first and second irradiation at 820 nm in dose 9 J/cm<SUP>2</SUP> are investigated. The CD spectrum of the intact cells is well structured and characterized by a positive signal in the UV (250-290 nm) and visible-near IR (500-780 nm) regions as well as by a negative signal in 300-450 nm region. Distinct maxima in the visible-near IR region are recorded at 566, 634, 680, 712, and 741 nm. As a rule, the peak circular dichroism signals decrease in the irradiated cells except of the area 750-770 nm. Peak positions (exception: the peak at 680 nm) shift as a rule to the long-wavelength direction. The most remarkable changes in peak positions as well as in CD signals are recorded in the region 750-770 nm: an appearance of the new peak at 767 nm after the first irradiation and its shift to 752 nm after the second irradiation. The peaks at 712 and 741 nm disappear after the irradiation. A new peak appears at 601 nm. It is assumed that the changes in the degree of oxidation of the chromophores of cytochrome c oxidase caused by the irradiation are accompanied by conformational changes in their vicinity. It can be suggested that these changes are occurring in Cu<SUB>B</SUB> environment.
Surface Modification of Poly(ethylene terephthalate) To Prepare Surfaces with Silica-Like Reactivity (1998)

Reactions of semicrystalline poly(ethylene terephthalate) (PET) film with 3-aminopropyltrialkoxysilanes at the film−solution interface and subsequent hydrolysis render silanol (Si−OH) functionality that is attached to the PET surface by amide linkages (PET−CONH(CH2)3Si(OH)3). Toluene was found to be the preferred solvent for the initial amidation reaction, rendering a higher surface concentration of silanol groups than that for other solvents. Polycondensation of tetraethyl orthosilicate on the surface of PET−CONH(CH2)3Si(OH)3 produces thin silica films, the thickness of which can be controlled with reaction time. The surface of this composite film (PET−(SiO2)X−OH) also contains reactive silanol groups. These two reactive surfaces were further modified using other reactive silanes to introduce alkyl, perfluoroalkyl, bromoalkyl, and aminoalkyl functionality to the PET film surface. The surface density of attached groups was assessed by X-ray photoelectron spectroscopy, and wettability of the surfaces was determined using contact angle analysis. The reactivity of these surfaces was compared to that of oxidized silicon wafers, and we conclude that these PET modification procedures (amidation with 3-aminopropyltrialkoxysilanes and polycondensation of tetraethyl orthosilicate) produce surfaces that react with the versatility of oxidized silicon wafers.
The Influence of Age on T Cell Generation and TCR Diversity (2005)

The ability to mount protective immune responses depends on the diversity of T cells. T cell diversity may be compromised by the declining thymic output of new T cells. The aging process imposes a threat to diversity, because thymic function deteriorates. In this study we have examined the relationship between thymic production, homeostatic T cell proliferation and TCR beta-chain diversity in young (approximately 25 years), middle-aged ( approximately 60 years), and elderly adults (approximately 75 years). TCR excision circles (TREC) as a marker of thymic output exponentially decreased by >95% between 25 and 60 years of age. The frequency of Ki67(+) cycling CD4 T cells remained steady, and surprisingly, the diversity of the naive CD4 T cell repertoire was maintained at approximately 2 x 10(7) different TCR beta-chains. After the age of 70 years, TRECs only slightly declined, but homeostatic proliferation doubled. The diversity of the T cell pool drastically contracted to 200,000 TCR beta-chains. Also, the phenotypic distinction between naive and memory CD4 T cells became fuzzy. The collapse in CD4 T cell diversity during the seventh and eighth decades indicates substantial T cell loss and implies that therapeutic measures to improve vaccine responses will have to include strategies for T cell replenishment.
Vanilloid Receptor TRPV1, Sensory C-Fibers, and Vascular Autoregulation (2004)

Myogenic constriction describes the innate ability of resistance arteries to constrict in response to elevations in intraluminal pressure and is a fundamental determinant of peripheral resistance and, hence, organ perfusion and systemic blood pressure. However, the receptor/cell-type that senses changes in pressure on the blood vessel wall and the pathway that couples this to constriction of vascular smooth muscle remain unclear. In this study, we show that elevation of intraluminal transmural pressure of mesenteric small arteries in vitro results in a myogenic response that is profoundly suppressed following ablation of sensory C-fiber activity (using in vitro capsaicin desensitization resulted in 72.8+/-10.3% inhibition, n=8; P<0.05). Activation of C-fiber nerve endings by pressure was attributable to stimulation of neuronal vanilloid receptor, TRPV1, because blockers of this channel, capsazepine (71.9+/-11.1% inhibition, n=9; P<0.001) and ruthenium red (46.1+/-11.7% inhibition, n=4; P<0.05), suppressed the myogenic constriction. In addition, this C-fiber dependency is likely related to neuropeptide substance P release and activity because blockade of tachykinin NK1 receptors (66.3+/-13.7% inhibition, n=6; P<0.001), and not NK2 receptors (n=4, NS), almost abolished the myogenic response. Previous studies support a role for 20-hydroxyeicosatetraenoic acid (20-HETE) in myogenic constriction responses; herein, we show that 20-HETE-induced constriction of mesenteric resistance arteries is blocked by capsazepine. Together, these results suggest that elevation of intraluminal pressure is associated with generation of 20-HETE that, in turn, activates TRPV1 on C-fiber nerve endings resulting in depolarization of nerves and consequent vasoactive neuropeptide release. These findings identify a novel mechanism contributing to Bayliss' myogenic constriction and highlights an alternative pathway that may be targeted in the therapeutics of vascular disease, such as hypertension, where enhanced myogenic constriction plays a role in the pathogenesis.
Effects of nutrition and environment on brain biochemistry and behavior (1983)

A factorial design was used to explore the influence of malnutrition and environmental enrichment on brain development and adult behavior. Malnutrition in suckling rats was produced by restricting the intake of their dams to 40% of normal food consumption. Environment was enriched using combined preweaning handling and a postweaning complex environment treatment. Malnutrition produced lasting effects upon brain biochemical composition and behavior. The environmental manipulation had no ameliorative effect on the brain parameters measured but it had pronounced effects on behavior, decreasing latency to move in the open field and increasing some measures of activity while it enhanced passive-avoidance performance. There was little evidence for any interaction between the nutritional and environmental variables, but all trends were in the direction of the environmental treatment having more effect on the well-nourished rats.
Survey of the Effect of Biotin on Glycemic Control and Plasma Lipid Concentrations in Type 1 Diabetic Patients in Kermanshah in Iran (2008-2009) (2013)

Results of this study showed that biotin administration as an adjuvant in addition to insulin regimen can improve glycemic management and decrease plasma lipids concentrations in poorly controlled type 1 diabetic patients.
Rapid Identification of Monospecific Monoclonal Antibodies Using a Human Proteome Microarray (2012)

To broaden the range of tools available for proteomic research, we generated a library of 16,368 unique full-length human ORFs that are expressible as N-terminal GST-His(6) fusion proteins. Following expression in yeast, these proteins were then individually purified and used to construct a human proteome microarray. To demonstrate the usefulness of this reagent, we developed a streamlined strategy for the production of monospecific monoclonal antibodies that used immunization with live human cells and microarray-based analysis of antibody specificity as its central components. We showed that microarray-based analysis of antibody specificity can be performed efficiently using a two-dimensional pooling strategy. We also demonstrated that our immunization and selection strategies result in a large fraction of monospecific monoclonal antibodies that are both immunoblot and immunoprecipitation grade. Our data indicate that the pipeline provides a robust platform for the generation of monoclonal antibodies of exceptional specificity.
Induction of somatic embryogenesis in immature seeds of guavatree cv. Paluma (2009)

The biotechnological techniques may help solve many problems of guava culture, such as the high perishability of fruits. Somatic embryogenesis can generate highly multiplicative cell cultures and with high regenerative potential, serving as basis for genetic transformation. The aim of this work was to obtain somatic embryogenesis of guava (Psidium guajava L.) cv. Paluma. Immature seeds were used, and they were inoculated in MS environment containing 400 mg L-1 of L-glutamine, 100 mg L-1 myo-inositol, 60 g L-1 sucrose, 100 mg L-1 ascorbic acid and supplemented with different types and concentrations of growth regulators. Embryogenic callus appeared after 37 days of culture in an environment containing 1.0 mg L-1 2.4-D + 2.0 mg L-1 2-ip, in 7% of the explants. After 65 days of culture, the treatment containing 0.5 mg L-1 CPA showed 20% of explants with direct embryos, while the treatment with 1 mg L-1 had 14% of explants with direct embryos and 7% of explants with embryogenic callus. In 66.6% of embryos regenerated with 0.5 mg L¹ CPA there was the formation of secondary embryos. The use of IASP and BAP, aiming embryogenesis proliferation, led to an increase in the cellular proliferation, but calli apparently lost their embryogenic potential.
The New Genomics: Global Views of Biology (1996)

What will happen after a complete sequence of the human genome is available? Eric Lander argues that it will be the beginning of a new phase of research. He presents 10 goals for the future that are related to a global view of biology. The author is at the Whitehead Institute for Biomedical Research and the Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
Examining the Role of Mitochondrial Respiration in Vanilloid-Induced Apoptosis (2002)

Vanilloid-induced apoptosis in the parental SCC cells appears to involve the inhibition of mitochondrial respiration. The apoptogenic effects promoted by vanilloid treatment in parental SCC cells, as well as the antiproliferative effects observed in their respiration-deficient clones, suggest that vanilloids may be useful for preventing or treating skin cancers or other hyperproliferative skin disorders.
Turning point in the design of linkage studies of schizophrenia (1994)

Despite extensive genomic scans, linkage studies of multiplex pedigrees have been unable to produce replicable evidence of genes predisposing to schizophrenia. This indicates that it is unlikely that a single gene accounts for a majority of cases of schizophrenia, even in multiplex pedigrees. It is most likely that schizophrenia is caused by the nonlinear interaction of multiple genetic and environmental factors influencing brain development and function. This conclusion has strong implications for the design of linkage and association studies. Recently designed linkage studies involve several improvements to deal with extensive locus heterogeneity and multiplicative interaction. These improvements include much larger samples of pedigrees, systematic ascertainment and sequential extension rules, and standardized procedures at multiple sites to facilitate collaboration and replication. Future improvements are likely to require advances in the assessment of clinical and neurobiological variability in multiplex pedigrees, more systematic environmental assessment, and advances in analytic methods to deal with multiplicative interaction. Rather than focusing only on schizophrenia as one or more discrete disorders, future linkage efforts should also consider the etiology of individual clinical syndromes or dimensional components of risk that interact to cause the complex pattern of syndromal comorbidity observed within schizophrenics and their families.
NKG2D-mediated Natural Killer Cell Protection Against Cytomegalovirus Is Impaired by Viral gp40 Modulation of Retinoic Acid Early Inducible 1 Gene Molecules (2003)

Natural killer (NK) cells play a critical role in the innate immune response against cytomegalovirus (CMV) infections. Although CMV encodes several gene products committed to evasion of adaptive immunity, viral modulation of NK cell activity is only beginning to be appreciated. A previous study demonstrated that the mouse CMV m152-encoded gp40 glycoprotein diminished expression of ligands for the activating NK cell receptor NKG2D on the surface of virus-infected cells. Here we have defined the precise ligands that are affected and have directly implicated NKG2D in immune responses to CMV infection in vitro and in vivo. Murine CMV (MCMV) infection potently induced transcription of all five known retinoic acid early inducible 1 (RAE-1) genes (RAE-1alpha, RAE-1beta, RAE-1delta, RAE-1 epsilon, and RAE-1gamma), but not H-60. gp40 specifically down-regulated the cell surface expression of all RAE-1 proteins, but not H-60, and diminished NK cell interferon gamma production against CMV-infected cells. Consistent with previous findings, a m152 deletion mutant virus (Deltam152) was less virulent in vivo than the wild-type Smith strain of MCMV. Treatment of BALB/c mice with a neutralizing anti-NKG2D antibody before infection increased titers of Deltam152 virus in the spleen and liver to levels seen with wild-type virus. These experiments demonstrate that gp40 impairs NK cell recognition of virus-infected cells through disrupting the RAE-1-NKG2D interaction.
Lithographic Properties of Poly(tert-butyl methacrylate)-Based Block and Random Copolymer Resists Designed for 193 nm Wavelength Exposure Tools (1996)

Block and random copolymers were prepared using the monomers tert-butyl methacrylate and [3-(methacryloxy)propyl]pentamethyldisiloxane. The polymers have low absorption at 193 nm wavelength, making them attractive candidates for 193 nm wavelength imaging. The resists have a high resistance to oxygen reactive ion etching, making them suitable for the imagable layer of a bilevel resist system. After exposure, the block copolymers have better development behavior in aqueous base than that of the corresponding random copolymers even though they have a long hydrophobic siloxane block.
Functional Characterization of FLT3 Receptor Signaling Deregulation in Acute Myeloid Leukemia by Single Cell Network Profiling (SCNP) (2010)

These studies show the feasibility of SCNP to assess modulated intracellular signaling pathways and characterize the biology of individual AML samples in the context of genetic alterations.