gebhart/patrepeval huggingface dataset:
Adult Stem Cells in the Small Intestine Are Intrinsically Programmed with Their Location‐Specific Function (2014)

Differentiation and specialization of epithelial cells in the small intestine are regulated in two ways. First, there is differentiation along the crypt-villus axis of the intestinal stem cells into absorptive enterocytes, Paneth, goblet, tuft, enteroendocrine, or M cells, which is mainly regulated by WNT. Second, there is specialization along the cephalocaudal axis with different absorptive and digestive functions in duodenum, jejunum, and ileum that is controlled by several transcription factors such as GATA4. However, so far it is unknown whether location-specific functional properties are intrinsically programmed within stem cells or if continuous signaling from mesenchymal cells is necessary to maintain the location-specific identity of the small intestine. Using the pure epithelial organoid technique, we show that region-specific gene expression profiles are conserved throughout long-term cultures of both mouse and human intestinal stem cells and correlated with differential Gata4 expression. Furthermore, the human organoid culture system demonstrates that Gata4-regulated gene expression is only allowed in absence of WNT signaling. These data show that location-specific function is intrinsically programmed in the adult stem cells of the small intestine and that their differentiation fate is independent of location-specific extracellular signals. In light of the potential future clinical application of small intestine-derived organoids, our data imply that it is important to generate GATA4-positive and GATA4-negative cultures to regenerate all essential functions of the small intestine.
The cytokine network and immune functions (1999)

CYTOKINES AND THEIR RECEPTORS: MOLECULAR ASPECTS CYTOKINES AND IMMUNE FUNCTIONS CYTOKINES IN PATHOLOGY
Identification of mycobacteria by high-performance liquid chromatography (1991)

Mycolic acids extracted from saponified mycobacterial cells were examined as p-bromophenacyl esters by high-performance liquid chromatography (HPLC). Standard HPLC patterns were developed for species of Mycobacterium by examination of strains from culture collections and other well-characterized isolates. Relative retention times of peaks and peak height comparisons were used to develop a differentiation scheme that was 98% accurate for the species examined. A rapid, cost-effective HPLC method which offers an alternative approach to the identification of mycobacteria is described.
Calsperin Is a Testis-specific Chaperone Required for Sperm Fertility (2010)

Calnexin (CANX) and calreticulin (CALR) are homologous lectin chaperones located in the endoplasmic reticulum and cooperate to mediate nascent glycoprotein folding. In the testis, calmegin (CLGN) and calsperin (CALR3) are expressed as germ cell-specific counterparts of CANX and CALR, respectively. Here, we show that Calr3(-/-) males produced apparently normal sperm but were infertile because of defective sperm migration from the uterus into the oviduct and defective binding to the zona pellucida. Whereas CLGN was required for ADAM1A/ADAM2 dimerization and subsequent maturation of ADAM3, a sperm membrane protein required for fertilization, we show that CALR3 is a lectin-deficient chaperone directly required for ADAM3 maturation. Our results establish the client specificity of CALR3 and demonstrate that the germ cell-specific CALR-like endoplasmic reticulum chaperones have contrasting functions in the development of male fertility. The identification and understanding of the maturation mechanisms of key sperm proteins will pave the way toward novel approaches for both contraception and treatment of unexplained male infertility.
Advanced oxidation processes. Description of a kinetic model for the oxidation of hazardous materials in aqueous media with ozone and hydrogen peroxide in a semibatch reactor (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAdvanced oxidation processes. Description of a kinetic model for the oxidation of hazardous materials in aqueous media with ozone and hydrogen peroxide in a semibatch reactorWilliam H. Glaze and Joon Wun KangCite this: Ind. Eng. Chem. Res. 1989, 28, 11, 1573–1580Publication Date (Print):November 1, 1989Publication History Published online1 May 2002Published inissue 1 November 1989https://pubs.acs.org/doi/10.1021/ie00095a001https://doi.org/10.1021/ie00095a001research-articleACS PublicationsRequest reuse permissionsArticle Views1926Altmetric-Citations209LEARN 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
Biotinylated Glycopolymers Synthesized by Atom Transfer Radical Polymerization (2006)

Biotinylated glycopolymers that bind to the protein streptavidin were synthesized by atom transfer radical polymerization (ATRP). Poly(methacrylate)s with pendent N-acetyl-d-glucosamines were prepared by polymerizing the protected monomer, followed by deprotection. Alternatively, the unprotected monomer was directly polymerized. Both paths provided well-defined glycopolymers with narrow molecular weight distributions (PDI = 1.07-1.23). The number-average molecular weights determined by gel permeation chromatography increased with increasing initial monomer-to-initiator ratios. The polymers were synthesized using a biotin-functionalized initiator for ATRP. Confirmation of the end group and binding to the protein streptavidin was achieved by (1)H NMR and surface plamon resonance.
Gadd45a Functions as a Promoter or Suppressor of Breast Cancer Dependent on the Oncogenic Stress (2010)

Gadd45a plays a pivotal role as a stress sensor that modulates cellular responses to various stress stimuli including oncogenic stress. We reported that the stress sensor Gadd45a gene functions as a tumor suppressor in Ras-driven breast tumorigenesis via increasing JNK-mediated apoptosis and p38-mediated senescence. In contrast, here, we show that Gadd45a promotes Myc-driven breast cancer by negatively regulating MMP10 via GSK3 β/β-catenin signaling, resulting in increased tumor vascularization and growth. These novel findings indicate that Gadd45a functions as either tumor promoter or suppressor, is dependent on the oncogenic stress, and is mediated via distinct signaling pathways. Collectively, these novel findings highlight the significance of the type of oncogenic alteration on how stress response genes function during initiation and progression of tumorigenesis. Because Gadd45a is a target for BRCA1 and p53, these findings have implications regarding BRCA1/p53 tumor suppressor functions.
Defective sperm–zona pellucida interaction: a major cause of failure of fertilization in clinical in-vitro fertilization (2000)

Sperm-zona pellucida binding and penetration were assessed on the oocytes that failed to fertilize from couples with >/=3 oocytes treated by standard in-vitro fertilization (IVF). There were four groups: fertilization rate 0% (n = 369), 1-25% (n = 194), 26-50% (n = 81) and 51-95% (n = 100). Of the couples with zero fertilization rate 70% had </=5 spermatozoa bound per zona pellucida and 42% had no spermatozoa penetrating the zona pellucida of any oocyte. In contrast, in the 51-95% fertilization rate group, only 17% had </= 5 spermatozoa bound per zona pellucida and 6% had no spermatozoa penetrating the zona pellucida. There was a significantly higher frequency of poor sperm morphology (</= 5% normal) in couples with zero fertilization rate (36%) than in the fertilization rate group 51-95% (7%). Incubation of oocytes from 68 couples with zero fertilization rate and low sperm-zonae pellucidae binding with fertile donor spermatozoa resulted in normal sperm-zona pellucida binding and most zonae pellucidae being penetrated. In conclusion, defective sperm-zona pellucida interaction was the major cause for low fertilization rates in standard IVF. This was usually because of defects of the spermatozoa rather than defects of the oocytes. Sperm defects likely to cause failure of fertilization should be diagnosed before commencing IVF and the patients directed to intracytoplasmic sperm injection.
The Ovine Cathelicidin SMAP29 Kills Ovine Respiratory Pathogens In Vitro and in an Ovine Model of Pulmonary Infection (2001)

Cathelicidins are antimicrobial peptides from sheep (SMAP29 and SMAP34), rabbits (CAP11 and CAP18), rodents (CRAMP), and humans (FALL39, LL37, and h/CAP18). In a broth microdilution assay against nine ovine pathogens, SMAP29, SMAP34, mouse CRAMP, CAP18, CAP18(31), CAP18(28), CAP18(22), and CAP18(21a) were the most active, with MICs as low as 0.6 microg/ml. Other cathelicidins were less active. In lambs with pneumonia, 0.5 mg of SMAP29 reduced the concentration of bacteria in both bronchoalveolar lavage fluid and consolidated pulmonary tissues. Hence, the antimicrobial activity of SMAP29 suggests that it has applications in the treatment of respiratory tract infections.
Speed of Heart Rate Recovery in Response to Orthostatic Challenge (2016)

Speed of orthostatic HRR predicts mortality and may aid clinical decision making. Attenuated orthostatic HRR may reflect dysregulation of the parasympathetic branch of the autonomic nervous system.
SPECTROSCOPY ANDHOTELECTRONRELAXATIONDYNAMICS INSEMICONDUCTORQUANTUMWELLS ANDQUANTUMDOTS (2001)

Photoexcitation of a semiconductor with photons above the semiconductor band gap creates electrons and holes that are out of equilibrium. The rates at which the photogenerated charge carriers return to equilibrium via thermalization through carrier scattering, cooling by phonon emission, and radiative and nonradiative recombination are important issues. The relaxation processes can be greatly affected by quantization effects that arise when the carriers are confined to regions of space that are small compared with their deBroglie wavelength or the Bohr radius of bulk excitons. The effects of size quantization in semiconductor quantum wells (carrier confinement in one dimension) and quantum dots (carrier confinement in three dimensions) on the respective carrier relaxation processes are reviewed, with emphasis on electron cooling dynamics. The implications of these effects for applications involving radiant energy conversion are also discussed.
Do physiological data relate to traditional usability indexes (2005)

Task performance data and subjective assessment data are widely used as usability measures in the human-computer interaction (HCI) field. Recently, physiology has also been explored as a metric for evaluating usability. However, it is not clear how physiological measures relate to traditional usability evaluation measures. In this paper, we investigated the relationships among three kinds of data: task performance, subjective assessment and physiological measures. We found evidence that physiological data correlate with task performance data in a video game: with a decrease of the task performance level, the normalized galvanic skin response (GSR) increases. In addition, physiological data are mirrored in subjective reports assessing stress level. The research provides an initial step toward establishing a new usability method using physiology as a complementary measure for traditional HCI evaluation.
Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood (2008)

We directly sequenced cell-free DNA with high-throughput shotgun sequencing technology from plasma of pregnant women, obtaining, on average, 5 million sequence tags per patient sample. This enabled us to measure the over- and underrepresentation of chromosomes from an aneuploid fetus. The sequencing approach is polymorphism-independent and therefore universally applicable for the noninvasive detection of fetal aneuploidy. Using this method, we successfully identified all nine cases of trisomy 21 (Down syndrome), two cases of trisomy 18 (Edward syndrome), and one case of trisomy 13 (Patau syndrome) in a cohort of 18 normal and aneuploid pregnancies; trisomy was detected at gestational ages as early as the 14th week. Direct sequencing also allowed us to study the characteristics of cell-free plasma DNA, and we found evidence that this DNA is enriched for sequences from nucleosomes.
Present and future therapy for hepatitis C virus (2006)

The treatment of hepatitis C virus (HCV) infection has developed enormously over recent years. Early treatment of acute HCV infection with interferon-alpha can prevent chronicity and a significant proportion of patients with chronic HCV can be cured with the current standard therapy consisting of pegylated interferon-alpha and ribavirin. However, the improvement of current treatment regimens and the development of new antiviral drugs will be essential within the next few years. This review focuses on the present and future concepts for treating HCV infection, including prevention of infection, antiviral therapy of acute and chronic HCV and the management of patients after liver transplantation.
Cone-beam CT: Applications in image-guided external beam radiotherapy and brachytherapy (2000)

Geometric uncertainties in radiotherapy result in the use of margins as a means to guarantee target coverage and normal tissue avoidance. The advantages of reducing these uncertainties are significant. Here, the authors report on the application of a new imaging technology to image-guidance in external beam radiotherapy and brachytherapy. Results are summarized.
7-Deazapurine containing DNA: efficiency of c7GdTP, c7AdTP and c7ldTP incorporation during PCR amplification and protection from endodeoxyribonuclease hydrolysis (1992)

The enzymatic synthesis of 7-deazapurine nucleoside containing DNA (501 bp) is performed by PCR-amplification (Taq polymerase) using a pUC18 plasmid DNA as template and the triphosphates of 7-deaza-2'-deoxyguanosine (c7Gd), -adenosine (c7Ad) and -inosine (c7Id). c7GdTP can fully replace dGTP resulting in a completely modified DNA-fragment of defined size and sequence. The other two 7-deazapurine triphosphates (c7AdTP) and (c7IdTP) require the presence of the parent purine 2'-deoxyribonucleotides. In purine/7-deazapurine nucleotide mixtures Taq polymerase prefers purine over 7-deazapurine nucleotides but accepts c7GdTP much better than c7AdTP or c7IdTP. As incorporation of 7-deazapurine nucleotides represents a modification of the major groove of DNA it can be used to probe DNA/protein interaction. Regioselective phosphodiester hydrolysis of the modified DNA-fragments was studied with 28 endodeoxyribonucleases. c7Gd is able to protect the DNA from the phosphodiester hydrolysis in more than 20 cases, only a few enzymes (Mae III, Rsa I, Hind III, Pvu II or Taq I) do still hydrolyze the modified DNA. c7Ad protects DNA less efficiently, as this DNA could only be modified in part. The absence of N-7 as potential binding position or a geometric distortion of the recognition duplex caused by the 7-deazapurine base can account for protection of hydrolysis.
Topical Omega-3 and Omega-6 Fatty Acids for Treatment of Dry Eye (2008)

Topical application of ALA omega-3 fatty acid may be a novel therapy to treat the clinical signs and inflammatory changes accompanying dry eye syndrome.
Isoform-specific Localization of Voltage-gated K+Channels to Distinct Lipid Raft Populations (2001)

The precise subcellular localization of ion channels is often necessary to ensure rapid and efficient integration of both intracellular and extracellular signaling events. Recently, we have identified lipid raft association as a novel mechanism for the subcellular sorting of specific voltage-gated K(+) channels to regions of the membrane rich in signaling complexes. Here, we demonstrate isoform-specific targeting of voltage-gated K(+) (Kv) channels to distinct lipid raft populations with the finding that Kv1.5 specifically targets to caveolae. Multiple lines of evidence indicate that Kv1.5 and Kv2.1 exist in distinct raft domains: 1) channel/raft association shows differential sensitivity to increasing concentrations of Triton X-100; 2) unlike Kv2.1, Kv1.5 colocalizes with caveolin on the cell surface and redistributes with caveolin following microtubule disruption; and 3) immunoisolation of caveolae copurifies Kv1.5 channel. Both depletion of cellular cholesterol and inhibition of sphingolipid synthesis alter Kv1.5 channel function by inducing a hyperpolarizing shift in the voltage dependence of activation and inactivation. The differential targeting of Kv channel subtypes to caveolar and noncaveolar rafts within a single membrane represents a unique mechanism of compartmentalization, which may permit isoform-specific modulation of K(+) channel function.
Game-Console Makers Battle over Motion-Sensitive Controllers (2009)

New controllers promise to enable more intuitive game playing based on natural body movements, rather than on button pushing.
A Concise and Traceless Linker Strategy toward Combinatorial Libraries of 2,6,9-Substituted Purines (2001)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTA Concise and Traceless Linker Strategy toward Combinatorial Libraries of 2,6,9-Substituted PurinesSheng Ding, Nathanael S. Gray, Qiang Ding, and Peter G. SchultzView Author Information Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, and Genomics Institute of the Novartis Research Foundation, 3115 Merryfield Row, San Diego, California 92121 [email protected]Cite this: J. Org. Chem. 2001, 66, 24, 8273–8276Publication Date (Web):October 31, 2001Publication History Received6 August 2001Published online31 October 2001Published inissue 1 November 2001https://pubs.acs.org/doi/10.1021/jo016010fhttps://doi.org/10.1021/jo016010fbrief-reportACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views813Altmetric-Citations41LEARN 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 (2)»Supporting Information Supporting Information SUBJECTS:Alcohols,Amines,Aromatic compounds,Peptides and proteins,Substituents Get e-Alerts
Investigation of physical properties of porous rocks and fluid flow phenomena in porous media using computer assisted tomography (1990)

Computer assisted tomography is becoming a very attractive tool for petroleum engineers. The method can give an image of a core in two or three dimensions with a very fine resolution and high accuracy. The image data can be processed to give information about the physical properties of the core (density, porosity, mineralogy, heterogeneities) and the fluids within the core (saturation and saturation profiles). This paper presents a software package that uses the CAT scanner output data as input for petrographic and dynamic modelling of a porous rock. Core samples up to 10 cm in diameter are scanned at different x-ray energy levels using an EMI CT5005 full body scanner. The scanner computer is producing an array of normalized linear attenuation coefficients per scanned slice. The resolution is 0.75 mm {times} 0.75 mm while the slice thickness can vary from 15 mm down to 1 mm depending on the bulk density and size of the sample. The developed package analyzes the CAT scanner data for bulk and grain density, effective atomic number, static and dynamic porosity and fluid saturations for up to three fluids present. The capabilities and limitations of the presented algorithm are discussed and characteristic examples are presented.
Assembly of functional Escherichia coli RNA polymerase containing beta subunit fragments. (1995)

The Escherichia coli rpoB gene, which codes for the 1342-residue beta subunit of RNA polymerase (RNAP), contains two dispensable regions centered around codons 300 and 1000. To test whether these regions demarcate domains of the RNAP beta subunit, fragments encoded by segments of rpoB flanking the dispensable regions were individually overexpressed and purified. We show that these beta-subunit polypeptide fragments, when added with purified recombinant beta', sigma, and alpha subunits of RNAP, reconstitute a functional enzyme in vitro. These results demonstrate that the beta subunit is composed of at least three distinct domains and open another avenue for in vitro studies of RNAP assembly and structure.
Induction of tenascin in healing wounds. (1988)

The distribution of the extracellular matrix glycoprotein, tenascin, in normal skin and healing skin wounds in rats, has been investigated by immunohistochemistry. In normal skin, tenascin was sparsely distributed, predominantly in association with basement membranes. In wounds, there was a marked increase in the expression of tenascin at the wound edge in all levels of the skin. There was also particularly strong tenascin staining at the dermal-epidermal junction beneath migrating, proliferating epidermis. Tenascin was present throughout the matrix of the granulation tissue, which filled full-thickness wounds, but was not detectable in the scar after wound contraction was complete. The distribution of tenascin was spatially and temporally different from that of fibronectin, and tenascin appeared before laminin beneath migrating epidermis. Tenascin was not entirely codistributed with myofibroblasts, the contractile wound fibroblasts. In EM studies of wounds, tenascin was localized in the basal lamina at the dermal-epidermal junction, as well as in the extracellular matrix of the adjacent dermal stroma, where it was either distributed homogeneously or bound to the surface of collagen fibers. In cultured skin explants, in which epidermis migrated over the cut edge of the dermis, tenascin, but not fibronectin, appeared in the dermis underlying the migrating epithelium. This demonstrates that migrating, proliferating epidermis induces the production of tenascin. The results presented here suggest that tenascin is important in wound healing and is subject to quite different regulatory mechanisms than is fibronectin.