gebhart/patrepeval huggingface dataset:
Genotype and Phenotype in Cystic Fibrosis (2000)

Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR) gene which encodes a protein expressed in the apical membrane of exocrine epithelial cells. CFTR functions principally as a cAMP-induced chloride channel and appears capable of regulating other ion channels. Besides the most common mutation, DeltaF508, accounting for about 70% of CF chromosomes worldwide, more than 850 mutant alleles have been reported to the CF Genetic Analysis Consortium. These mutations affect CFTR through a variety of molecular mechanisms which can produce little or no functional CFTR at the apical membrane. This genotypic variation provides a rationale for phenotypic effects of the specific mutations. The extent to which various CFTR alleles contribute to clinical variation in CF is evaluated by genotype-phenotype studies. These demonstrated that the degree of correlation between CFTR genotype and CF phenotype varies between its clinical components and is highest for the pancreatic status and lowest for pulmonary disease. The poor correlation between CFTR genotype and severity of lung disease strongly suggests an influence of environmental and secondary genetic factors (CF modifiers). Several candidate genes related to innate and adaptive immune response have been implicated as pulmonary CF modifiers. In addition, the presence of a genetic CF modifier for meconium ileus has been demonstrated on human chromosome 19q13.2. The phenotypic spectrum associated with mutations in the CFTR gene extends beyond the classically defined CF. Besides patients with atypical CF, there are large numbers of so-called monosymptomatic diseases such as various forms of obstructive azoospermia, idiopathic pancreatitis or disseminated bronchiectasis associated with CFTR mutations uncharacteristic for CF. The composition, frequency and type of CFTR mutations/variants parallel the spectrum of CFTR-associated phenotypes, from classic CF to mild monosymptomatic presentations. Expansion of the spectrum of disease associated with the CFTR mutant genes creates a need for revision of the diagnostic criteria for CF and a dilemma for setting nosologic boundaries between CF and other diseases with CFTR etiology.
Physical properties of apolipoprotein A-I from the chicken, Gallus domesticus (1993)

The amphipathic alpha-helices of exchangeable apolipoproteins (apo) function to simultaneously facilitate interaction with lipid surfaces and the aqueous environment. In contrast to mammalian apoA-I's, which self-associate in the absence of lipid, chicken apoA-I, which shares 66% sequence homology with human apoA-I, exists as a monomeric protein when dissociated from high-density lipoprotein (HDL). Sedimentation equilibrium studies conducted in the analytical ultracentrifuge yielded a weight-average molecular weight of 28,170. Corresponding sedimentation velocity and diffusion experiments gave rise to s0(20,w) = 2.23 S and D0(20,w) = 6.39 x 10(-7) cm2/s. A translational frictional ratio (f/fmin) of 1.18 and an axial ratio of 4.0 were also determined from this data. The Stokes radius (Rs,sed = 2.80 nm) and translational frictional ratio were subsequently used to calculate estimated molecular dimensions of 25.2 x 100.8 A for chicken apoA-I. Circular dichroism (CD) studies revealed a highly alpha-helical structure predicted to be 74% by Provencher-Glöckner analysis. Denaturation studies performed on lipid-free apoA-I and monitored by CD revealed a midpoint of denaturation of 0.64 M guanidine hydrochloride. From plots of delta G(app) versus guanidine hydrochloride concentration, a delta GDH2O of 1.86 kcal/mol was determined. In other studies, a midpoint of temperature-induced denaturation for apoA-I of 57 degrees C was obtained. The effect of solvent pH on the secondary structure content of apoA-I revealed a significant loss of alpha-helix below pH 4.0 and above pH 10, suggesting that lipid-free apoA-I may by partially stabilized by the formation of intra- or interhelix salt bridges between oppositely charged amino acid side chains.(ABSTRACT TRUNCATED AT 250 WORDS)
Sialyl-Tn antigen expression occurs early during human mammary carcinogenesis and is associated with high nuclear grade and aneuploidy. (1994)

Sialyl-Tn (STn) antigen represents an aberrant glycosylation product of cell surface mucin in adenocarcinomas. We studied its expression in 40 breast carcinomas (35 of which included in situ carcinomas) by performing immunostaining with B72.3 monoclonal antibody. STn expression was observed in 50% of cases and was equally frequent in in situ and in invasive carcinomas. Positive STn staining significantly correlated with high nuclear grade (P = 0.001), aneuploidy (P < 0.001) and high S-phase fraction (P = 0.02). No correlation was observed between STn staining and age, menopausal status, presence of invasive component, or hormone receptor positivity. STn staining may provide an objective marker of dedifferentiation of breast tumors and should be investigated further for its prognostic value in breast cancers and as a biomarker of malignant transformation of breast epithelium.
Characterization of Optical Diffraction and Crystal Structure in Monodisperse Polystyrene Colloids (1984)

Bragg diffraction of laser light from crystalline aqueous colloids of polystyrene spheres is examined to determine crystal structure, orientation, and elasticity. A new technique using Kossel rings is described which simultaneously measures structure, lattice spacings, and crystallite orientation. The monodisperse polystyrene sphere latex dispersions crystallize into large single crystals, which, depending on sphere concentration, are either face-centered or body-centered cubic. The interparticle spacings in the crystals are many times larger than the sphere diameter (0.109 μm). The use of tunable lasers to easily determine crystal structure is described, and the technique is further illustrated by the experimental determination of the bulk modulus. The bulk modulus is a macroscopic physical constant which can be used to monitor intersphere potentials and the screening of the particle charges by electrolytes in the solution. Data are presented which suggest that crystallite orientation occurs with the closest packed sphere layers parallel to the sample cell quartz walls.
Stress engineering during metalorganic chemical vapor deposition of AlGaN/GaN distributed Bragg reflectors (2001)

In situ stress monitoring has been employed during metalorganic chemical vapor deposition of AlGaN/GaN distributed Bragg reflectors (DBRs). It was found that the insertion of multiple AlN interlayers is effective in converting the tensile growth stress typically observed in this system into compression, thus alleviating the problem of crack generation. Crack-free growth of a 60 pair Al0.20Ga0.80N/GaN quarter-wavelength DBR was obtained over the entire 2 in. wafer; an accompanying reflectivity of at least 99% was observed near the peak wavelength around 380 nm.
Expression of BMP-7 in human gastric cancer and its clinical significance (2011)

From the data collected, it would be appropriate to conclude on the possible regulation of gastric cancer progression by autocrine or paracrine BMP-7 loops. We can use BMP-7 expression as one of the strong predictors of risk of tumour recurrence in gastric cancer.
Prevalence of HIV Infection in Childbearing Women in the United States (1991)

A national, population-based survey was initiated in 1988 to measure the prevalence of human immunodeficiency virus (HIV) infection in women giving birth to infants in the United States. Following standardized procedures, residual dried-blood specimens collected on filter paper for newborn metabolic screening were tested anonymously in state public health laboratories for maternal antibody to HIV. As of September 1990, annual survey data were available from 38 states and the District of Columbia. The highest HIV seroprevalence rates were observed in New York (5.8 per 1000), the District of Columbia (5.5 per 1000), New Jersey (4.9 per 1000), and Florida (4.5 per 1000). Nationwide, an estimated 1.5 per 1000 women giving birth to infants in 1989 were infected with HIV. Assuming a perinatal transmission rate of 30%, we estimate that approximately 1800 newborns acquired HIV infection during one 12-month period. Preventing transmission of HIV infection to women and infants is an urgent public health priority. (<i>JAMA</i>. 1991;265:1704-1708)
New radiopaque polyHEMA‐based hydrogel particles (1997)

New iodine-containing polymeric hydrogel particles were prepared by suspension radical copolymerization of 2-hydroxyethyl methacrylate (HEMA), 3-(methacryloylamidoacetamido)-2,4,6-triiodobenzoic acid (MABA) and ethylene dimethacrylate (EDMA) in an aqueous medium using azobisisobutyronitrile as an initiator and magnesium hydroxide as a suspension stabilizer. To impart porosity to the product, cyclohexanol and 1-dodecanol were added as inert diluents to the polymerization mixture. Particles containing 27 wt % iodine produced radiopacity sufficient to observe a clearly visible X-ray image. The equilibrium swelling behavior of the particles in water was characterized. Swelling of the particles dramatically increased by converting the acid groups of MABA into their Na+ form. The more MABA the copolymer particle contain, the higher is their swelling in the Na+ form. © 1997 John Wiley & Sons, Inc.
Lack of Interaction Between the HIV Integrase Inhibitor S/GSK1349572 and Tenofovir in Healthy Subjects (2010)

S/GSK1349572 and TDF can be coadministered without dose adjustment.
Adrenergic agents. 1. Synthesis and potential .beta.-adrenergic agonist activity of some catechol amine analogs bearing a substituted amino functionality in the meta position (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAdrenergic agents. 1. Synthesis and potential .beta.-adrenergic agonist activity of some catechol amine analogs bearing a substituted amino functionality in the meta positionCarl Kaiser, Donald F. Colella, Mark S. Schwartz, Eleanor Garvey, and Joe R. Wardell Jr.Cite this: J. Med. Chem. 1974, 17, 1, 49–57Publication Date (Print):January 1, 1974Publication History Published online1 May 2002Published inissue 1 January 1974https://pubs.acs.org/doi/10.1021/jm00247a011https://doi.org/10.1021/jm00247a011research-articleACS PublicationsRequest reuse permissionsArticle Views357Altmetric-Citations29LEARN 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
A personal digital store (2001)

article Share on A personal digital store Author: Gordon Bell Microsoft Bay Area Research Center, San Francisco, CA Microsoft Bay Area Research Center, San Francisco, CAView Profile Authors Info & Claims Communications of the ACMVolume 44Issue 1Jan. 2001 pp 86–91https://doi.org/10.1145/357489.357513Published:01 January 2001Publication History 44citation1,765DownloadsMetricsTotal Citations44Total Downloads1,765Last 12 Months50Last 6 weeks4 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
The tissue engineering of blood vessels and the heart (2004)

The engineering of biological substitutes and strategies for the replacement and/or repair of blood vessels and the components of the heart represents an important challenge for tissue engineering. In this review, the progress to date and the barriers remaining are addressed. Even though the progress has been considerable and there are even some approaches that have entered clinical trials, we are still a ways off from having FDA-approved replacements and/or repair strategies. The engineering of biological substitutes and strategies for the replacement and/or repair of blood vessels and the components of the heart represents an important challenge for tissue engineering. In this review, the progress to date and the barriers remaining are addressed. Even though the progress has been considerable and there are even some approaches that have entered clinical trials, we are still a ways off from having FDA-approved replacements and/or repair strategies.
PHONEME-TO-VISEME MAPPING FOR VISUAL SPEECH RECOGNITION (2012)

Phonemes are the standard modelling unit in HMM-based continuous speech recognition systems. Visemes are the equivalent unit in the visual domain, but there is less agreement on precisely what visemes are, or how many to model on the visual side in audio-visual speech recognition systems. This paper compares the use of 5 viseme maps in a continuous speech recognition task. The focus of the study is visual-only recognition to examine the choice of viseme map. All the maps are based on the phoneme-to-viseme approach, created either using a linguistic method or a data driven method. DCT, PCA and optical flow are used as the visual features. The best visual-only recognition on the VidTIMIT database is achieved using a linguistically motivated viseme set. These initial experiments demonstrate that the choice of visual unit requires more careful attention in audio-visual speech recognition system development.
Vaccination with DNA Encoding an Immunodominant Myelin Basic Protein Peptide Targeted to Fc of Immunoglobulin G Suppresses Experimental Autoimmune Encephalomyelitis (1998)

We explore here if vaccination with DNA encoding an autoantigenic peptide can suppress autoimmune disease. For this purpose we used experimental autoimmune encephalomyelitis (EAE), which is an autoaggressive disease in the central nervous system and an animal model for multiple sclerosis. Lewis rats were vaccinated with DNA encoding an encephalitogenic T cell epitope, guinea pig myelin basic protein peptide 68-85 (MBP68-85), before induction of EAE with MBP68-85 in complete Freund's adjuvant. Compared to vaccination with a control DNA construct, the vaccination suppressed clinical and histopathological signs of EAE, and reduced the interferon gamma production after challenge with MBP68-85. Targeting of the gene product to Fc of IgG was essential for this effect. There were no signs of a Th2 cytokine bias. Our data suggest that DNA vaccines encoding autoantigenic peptides may be useful tools in controlling autoimmune disease.
Structural Biology of the T-cell Receptor: Insights into Receptor Assembly, Ligand Recognition, and Initiation of Signaling (2010)

The T-cell receptor (TCR)-CD3 complex serves as a central paradigm for general principles of receptor assembly, ligand recognition, and signaling in the immune system. There is no other receptor system that matches the diversity of both receptor and ligand components. The recent expansion of the immunological structural database is beginning to identify key principles of MHC and peptide recognition. The multicomponent assembly of the TCR complex illustrates general principles used by many receptors in the immune system, which rely on basic and acidic transmembrane residues to guide assembly. The intrinsic binding of the cytoplasmic domains of the CD3epsilon and zeta chains to the inner leaflet of the plasma membrane represents a novel mechanism for control of receptor activation: Insertion of critical CD3epsilon tyrosines into the hydrophobic membrane core prevents their phosphorylation before receptor engagement.
The SMR family: a novel family of multidrug efflux proteins involved with the efflux of lipophilic drugs (1996)

The sequenced members of a novel family of small, hydrophobic, bacterial multidrug-resistance efflux proteins, which we have designated the small multidrug resistance (SMR) protein family, are identified and analysed. Two distinct clusters of proteins were identified within this family: (i) small multidrug efflux systems; and (ii) Sug proteins, potentially involved in the suppression of groEL mutations. Hydropathy and residue distribution analyses of this family suggest a structural model in which the polypeptide chain spans the membrane four times as mildly amphipathic alpha-helices. The roles of specific residues, a possible mechanistic model of drug efflux, and the primary physiological role(s) of the SMR proteins are discussed.
Suppression of RAD21 gene expression decreases cell growth and enhances cytotoxicity of etoposide and bleomycin in human breast cancer cells (2005)

A genome-wide case-control association study done in our laboratory has identified a single nucleotide polymorphism located in RAD21 as being significantly associated with breast cancer susceptibility. RAD21 is believed to function in sister chromatid alignment as part of the cohesin complex and also in double-strand break (DSB) repair. Following our initial finding, expression studies revealed a 1.25- to 2.5-fold increased expression of this gene in several human breast cancer cell lines as compared with normal breast tissue. To determine whether suppression of RAD21 expression influences cellular proliferation, RNA interference technology was used in breast cancer cell lines MCF-7 and T-47D. Proliferation of cells treated with RAD21-specific small inhibitory RNA (siRNA) was significantly reduced as compared with mock-transfected cells and cells transfected with a control siRNA (Lamin A/C). This inhibition of proliferation correlated with a significant reduction in the expression of RAD21 mRNA and with an increased level of apoptosis. Moreover, MCF-7 cell sensitivity to two DNA-damaging chemotherapeutic agents, etoposide and bleomycin, was increased after inhibition of RAD21 expression with a dose reduction factor 50 (DRF50) of 1.42 and 3.71, respectively. At the highest concentrations of etoposide and bleomycin administered, cells transfected with a single siRNA duplex targeted against RAD21 showed 57% and 60% survival as compared with control cells, respectively. Based on these findings, we conclude that RAD21 is a novel target for developing cancer therapeutics that can potentially enhance the antitumor activity of chemotherapeutic agents acting via induction of DNA damage.
Steroids. CLXXV. Further Steroidal Anabolic Agents (1962)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSteroids. CLXXV. Further Steroidal Anabolic AgentsP. G. Holton and E. NecoecheaCite this: J. Med. Chem. 1962, 5, 6, 1352–1357Publication Date (Print):November 1, 1962Publication History Published online1 May 2002Published inissue 1 November 1962https://pubs.acs.org/doi/10.1021/jm01241a027https://doi.org/10.1021/jm01241a027research-articleACS PublicationsRequest reuse permissionsArticle Views70Altmetric-Citations6LEARN 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 options Get e-Alerts
Current concepts in the assessment and treatment of Hepatic Encephalopathy (2009)

Hepatic encephalopathy (HE) is defined as a metabolically induced, potentially reversible, functional disturbance of the brain that may occur in acute or chronic liver disease. Standardized nomenclature has been proposed but a standardized approach to the treatment, particularly of persistent, episodic and recurrent encephalopathy associated with liver cirrhosis has not been proposed. This review focuses on the pathogenesis and treatment of HE in patients with cirrhosis. The pathogenesis and treatment of hepatic encephalopathy in fulminant hepatic failure is quite different and is reviewed elsewhere.
Diversity, vitality and activities of intestinal lactic acid bacteria and bifidobacteria assessed by molecular approaches (2005)

While lactic acid bacteria and bifidobacteria have been scientifically important for over a century, many of these are marketed today as probiotics and have become a valuable and rapidly expanding sector of the food market that is leading functional foods in many countries. The human gastro-intestinal tract with its various compartments and complex microbiota is the primary target of most of these functional foods containing lactic acid bacteria and bifidobacteria (LAB&B). In addition, their use as vectors for delivery of molecules with therapeutic value to the host via the intestinal tract is being studied. This review focuses on molecular approaches for the investigation of the diversity of lactic acid bacteria and bifidobacteria in the human intestine, as well as tracking of probiotic bacteria within this complex ecosystem. Moreover, methodologies to determine the viability of the lactic acid bacteria and bifidobacteria and molecular approaches to study the mechanisms by which they adapt, establish and interact with the human host via the digestive tract, are described.
TSC1 and TSC2 tumor suppressors antagonize insulin signaling in cell growth (2001)

Tuberous sclerosis is a human disease caused by mutations in the TSC1 or the TSC2 tumor suppressor gene. Previous studies of a Drosophila TSC2 homolog suggested a role for the TSC genes in maintaining DNA content, with loss of TSC2 leading to polyploidy and increased cell size. We have isolated mutations in the Drosophila homolog of the TSC1 gene. We show that TSC1 and TSC2 form a complex and function in a common pathway to control cellular growth. Unlike previous studies, our work shows that TSC1(-) or TSC2(-) cells are diploid. We find that, strikingly, the heterozygosity of TSC1 or TSC2 is sufficient to rescue the lethality of loss-of-function insulin receptor mutants. Further genetic analyses suggest that the TSC genes act in a parallel pathway that converges on the insulin pathway downstream from Akt. Taken together, our studies identified the TSC tumor suppressors as novel negative regulators of insulin signaling.