gebhart/patrepeval huggingface dataset:
Two sites of glucose control of insulin release with distinct dependence on the energy state in pancreatic B-cells (1994)

The energy state of pancreatic B-cells may influence insulin release at several steps of stimulus-secretion coupling. By closing ATP-sensitive K+ channels (K(+)-ATP channels), a rise in the ATP/ADP ratio may regulate the membrane potential, and hence Ca2+ influx. It may also modulate the effectiveness of Ca2+ on its intracellular targets. To assess the existence of these two roles and determine their relative importance for insulin release, we tested the effects of azide, a mitochondrial poison, on mouse B-cell function under various conditions. During stimulation by glucose alone, when K(+)-ATP channels are controlled by cellular metabolism, azide caused parallel, concentration-dependent (0.5-5 mM), membrane repolarization, decrease in cytosolic Ca2+ concentration [Ca2+]i and inhibition of insulin release. When K(+)-ATP channels were closed pharmacologically (by tolbutamide in high glucose), azide did not repolarize the membrane or decrease [Ca2+]i, and was much less effective in inhibiting insulin release. A similar resistance to azide was observed when K(+)-ATP channels were opened by diazoxide, and high K+ was used to depolarize the membrane and raise [Ca2+]i. In contrast, azide similarly decreased ATP levels and increased ADP levels, thereby lowering the ATP/ADP ratio under all conditions. In conclusion, lowering the ATP/ADP ratio in B-cells can inhibit insulin release even when [Ca2+]i remains high. However, this distal step is much more resistant to a decrease in the energy state of B-cells than is the control of membrane potential by K(+)-ATP channels. Generation of the signal triggering insulin release, high [Ca2+]i, through metabolic control of membrane potential requires a higher global ATP/ADP ratio than does activation of the secretory process itself.
Sonic hedgehog: a common signal for ventral patterning along the rostrocaudal axis of the neural tube (1995)

The vertebrate hedgehog-related gene, sonic hedgehog, is expressed in ventral domains along the entire rostrocaudal length of the neural tube, including the forebrain. Shh induces the differentiation of ventral neuronal cell types in explants derived from prospective forebrain regions of the neural plate. Neurons induced in explants derived from diencephalic and telencephalic levels of the neural plate express the LIM homeodomain protein Islet-1, but these neurons possess distinct identities that match those of the ventral neurons normally generated in these two subdivisions of the forebrain. These results, together with other studies of neuronal differentiation at caudal levels of the neural tube, suggest that a single inducing molecule, Shh, mediates the induction of distinct ventral neuronal cell types along the entire rostrocaudal extent of the embryonic central nervous system.
Prolonged transcriptional silencing and CpG methylation induced by siRNAs targeted to the HIV-1 promoter region. (2005)

In addition to the degradation of homologous RNAs through the RNA interference (RNAi) pathway, small interfering RNAs (siRNAs) can in some systems induce cytosine methylation and transcriptional silencing of homologous promoters. Targeting of HIV-1 by RNAi results in transient suppression of the virus through degradation of viral transcripts. In an effort to prolong the suppressive effect of siRNAs on productive HIV-1 infection, we targeted conserved tandem NF-kappaB binding motifs in the viral LTR. A 21-nucleotide-RNA duplex induced marked and durable (at least 30 days) suppression of productive HIV-1 infection in chronically infected Magic-5 cells. This suppression is associated with CpG methylation within the 5'LTR and marked reduction of HIV-1 transcription in nuclear run-on assays. We then assessed three additional siRNAs targeting other sites within the HIV-1 promoter region. These siRNAs suppressed HIV-1 infection to different extents and the degree of suppression correlated with the extent of de novo methylation of CpG motifs within the HIV-1 promoter region. These findings indicate that HIV-1 can be silenced by an RNA-directed mechanism that suppresses transcription and induces CpG methylation. In addition to providing evidence that this RNA-directed DNA methylation is active in mammalian cells, this is the first report of prolonged suppression of HIV-1 infection induced by siRNA.
Interface issues in text based chat rooms (1998)

article Free Access Share on Interface issues in text based chat rooms Authors: Brian J. Roddy View Profile , Hernan Epelman-Wang View Profile Authors Info & Claims ACM SIGCHI BulletinVolume 30Issue 2April 1998 pp 119–123https://doi.org/10.1145/279044.279172Published:01 April 1998Publication History 2citation192DownloadsMetricsTotal Citations2Total Downloads192Last 12 Months39Last 6 weeks5 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 SiteeReaderPDF
Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae (2000)

The Saccharomyces cerevisiae Snf/Swi complex has been previously demonstrated to control transcription and chromatin structure of particular genes in vivo and to remodel nucleosomes in vitro. We have performed whole-genome expression analysis, using DNA microarrays, to study mutants deleted for a gene encoding one conserved (Snf2) or one unconserved (Swi1) Snf/Swi component. This analysis was performed on cells grown in both rich and minimal media. The microarray results, combined with Northern blot, computational, and genetic analyses, show that snf2Delta and swi1Delta mutations cause similar effects on mRNA levels, that Snf/Swi controls some genes differently in rich and minimal media, and that Snf/Swi control is exerted at the level of individual genes rather than over larger chromosomal domains. In addition, this work shows that Snf/Swi controls mRNA levels of MATalpha-specific genes, likely via controlling transcription of the regulators MATalpha1 and MCM1. Finally, we provide evidence that Snf/Swi acts both as an activator and as a repressor of transcription, and that neither mode of control is an indirect effect of the other.
Anti-inflammatory properties of the short-chain fatty acids acetate and propionate: A study with relevance to inflammatory bowel disease (2007)

In the present study propionate and butyrate were equipotent, whereas acetate was less effective, at suppressing NF-kappaB reporter activity, immune-related gene expression and cytokine release in vitro. Our findings suggest that propionate and acetate, in addition to butyrate, could be useful in the treatment of inflammatory disorders, including IBD.
Prepro-alpha-factor has a cleavable signal sequence. (1988)

MAT alpha Saccharomyces cerevisiae secrete a small peptide mating pheromone termed alpha-factor. Its precursor, prepro-alpha-factor, is translocated into the endoplasmic reticulum and glycosylated at three sites. The glycosylated form is the major product in a yeast in vitro translation/translocation system. However, there is another translocated, nonglycosylated product that contains a previously unidentified modification. Contrary to previous results suggesting that the signal sequence of prepro-alpha-factor is not cleaved, amino-terminal radiosequencing has identified this product as prepro-alpha-factor without its signal sequence, that is, pro-alpha-factor. The translocated, glycosylated proteins are also processed by signal peptidase. Moreover, we have found that both purified eukaryotic and prokaryotic signal peptidase can process prepro-alpha-factor. Experiments using a yeast secretory mutant (sec 18) blocked in transport from the endoplasmic reticulum to the Golgi indicate that the protein is also cleaved in vivo. Finally, characterization of the Asn-linked oligosaccharide present on pro-alpha-factor in the yeast in vitro system by use of specific glucosidase and mannosidase inhibitors indicates that they have had the three terminal glucoses and probably one mannose removed. Therefore they most likely consist of Man8GlcNAc2 structures, identical to those found in the endoplasmic reticulum in vivo.
Availability in globally distributed storage systems (2010)

Highly available cloud storage is often implemented with complex, multi-tiered distributed systems built on top of clusters of commodity servers and disk drives. Sophisticated management, load balancing and recovery techniques are needed to achieve high performance and availability amidst an abundance of failure sources that include software, hardware, network connectivity, and power issues. While there is a relative wealth of failure studies of individual components of storage systems, such as disk drives, relatively little has been reported so far on the overall availability behavior of large cloudbased storage services.We characterize the availability properties of cloud storage systems based on an extensive one year study of Google's main storage infrastructure and present statistical models that enable further insight into the impact of multiple design choices, such as data placement and replication strategies. With these models we compare data availability under a variety of system parameters given the real patterns of failures observed in our fleet.
Genetic diversity of the envelope glycoprotein from human immunodeficiency virus type 1 isolates of African origin (1995)

The genetic diversity of the envelope glycoprotein of human immunodeficiency virus type 1 (HIV-1) isolates was studied. HIV-1 isolates were obtained from eight countries in Africa: Djibouti, Gabon, Kenya, Senegal, Somalia, Uganda, Zaire, and Zambia. The DNA sequences encoding the complete HIV-1 envelope protein were PCR amplified and sequenced. Phylogenetic relationships among the 21 sequences from this study and the 32 previously published full-length env HIV-1 sequences were determined. Twenty of the newly sequenced African isolates could be assigned to envelope subtypes A, C, D, and G. One isolate, collected in Zambia, did not belong to any of the eight previously described subtypes and may represent a prototype sequence of its envelope subtype. The phylogenetic classification of these isolates was strongly supported by bootstrapping and the congruence of trees generated by either distance methods or maximum parsimony analysis. The data presented in this study confirm the existence of several genetic subtypes within the global HIV epidemic and broaden the genetic variability previously observed for envelope subtypes. The geographic spread of different subtypes was shown to be substantial, and the notion of cocirculation of subtypes was reinforced.
A Structural View of Tyrosine Recombinase Site‐Specific Recombination (2007)

The DNA recombination sequences where recombinase binding and strand exchange take place are referred to as the core recombination sites. These sites are composed of two recombinase binding elements (RBEs) arranged as inverted repeats surrounding a central strand exchange or crossover region. A parallel alignment of sites is defined as one in which the DNA helical axes of the crossover regions form an angle less than 90° with respect to the crossover sequence directions. The helices, which carry the tyrosine nucleophiles, are provided in trans to the neighboring subunits, where they participate in the formation of shared active sites between pairs of adjacent subunits. The mechanistic implications of this alternative arrangement are discussed in this chapter. The author summarizes what one has learned from the crystal structures of recombinase-HJ intermediates and then relates the structural models to recent experimental data in the tyrosine recombinase family. A study by Arciszewska et al. demonstrated using permanganate oxidation sensitivity of thymine bases that the recombinase-bound form of the junction is clearly distinct from the stacked-X conformation. Voziyanov et al. presented a thorough geometric treatment of the tyrosine recombinase reaction pathway model that focuses on the relative rotation and positioning of the reaction components as the reaction proceeds. The current understanding of the tyrosine recombinase site-specific recombination pathway in the three-dimensional sense has been guided primarily by structures of reaction intermediates in the Cre- lox P system.
Bladder and Upper Tract Urothelial Cancer (2007)

The costs of treating bladder cancer increased steadily during a 6-year period despite a decrease in inpatient care. Coupled with a lack of substantial change in transurethral resection and cystectomy rates, this suggests that the primary cost drivers are increased outpatient testing, eg computerized tomography and cystoscopy, and an increase in the number of diagnosed cases. Greater focus on selective use of testing modalities, preventive care such as smoking cessation and earlier identification of patients at risk may help curtail further expenditure with regard to managing bladder and upper urinary tract cancers.
Reversal of multidrug resistance by RU 486. (1994)

P-Glycoproteins represent a family of drug efflux proteins that convey multidrug resistance to cells in which they are expressed. This phenomenon can lower the efficacy of drugs used in chemotherapy. The steroid progesterone has been shown to bind P-glycoproteins and inhibit their drug efflux. We report that the antiprogestin RU 486 can reverse multidrug resistance in cells overexpressing the mouse mdr1 gene. Using flow cytometry to measure inhibition of P-glycoprotein-dependent efflux of rhodamine 123, RU 486 was found to be considerably more effective than progesterone and one-half as effective as verapamil. The results suggest a valuable new use for RU 486.
Homology Dependence of UvsX Protein-catalyzed Joint Molecule Formation (1995)

The bacteriophage UvsX protein is a "strand transferase" that promotes the pairing of homologous single and double-stranded DNAs. The efficiency of UvsX protein-mediated joint molecule formation between supercoiled duplex DNA and oligonucleotides is shown to have a sharp dependence on the degree of homology. The reaction proceeded efficiently with oligonucleotides containing 32 homologous positions but not with oligonucleotides containing only 24 homologous bases. This was shown to reflect an intrinsic homology requirement for the formation of stable joint molecules and was not caused by poor binding of the protein to short single-stranded DNAs. Even a single mismatch located in the middle of a region of 40 homologous nucleotides had a detectable effect on the efficiency of pairing. An in vitro recombinationally initiated DNA synthesis reaction that mimics the "secondary mode" of phage T4 DNA replication exhibited the same homology dependence.
Lucid touch (2007)

Touch is a compelling input modality for interactive devices; however, touch input on the small screen of a mobile device is problematic because a user's fingers occlude the graphical elements he wishes to work with. In this paper, we present LucidTouch, a mobile device that addresses this limitation by allowing the user to control the application by touching the back of the device. The key to making this usable is what we call pseudo-transparency: by overlaying an image of the user's hands onto the screen, we create the illusion of the mobile device itself being semi-transparent. This pseudo-transparency allows users to accurately acquire targets while not occluding the screen with their fingers and hand. Lucid Touch also supports multi-touch input, allowing users to operate the device simultaneously with all 10 fingers. We present initial study results that indicate that many users found touching on the back to be preferable to touching on the front, due to reduced occlusion, higher precision, and the ability to make multi-finger input.
Polysomy of chromosome 17 in breast cancer tumors showing an overexpression of ERBB2: a study of 175 cases using fluorescence in situhybridization and immunohistochemistry (2005)

The determination of the copy number of chromosome 17 should be incorporated into the assesment of ERBB2 status. It might also be helpful to differentiate a subgroup of breast cancer patients with polysomy of chromosome 17 and overexpression of ERBB2 protein that probably have genetic and clinical differences.
Integration of Outcrop and Modern Analogs in Reservoir Modeling (2004)

Abstract Building robust 3-D reservoir models is a major challenge that requires incorporation of geologically defined input parameters. This publication provides an overview of current approaches used in the development of geologically constrained and integrated reservoir models. Each of the 18 papers addresses various stages in the process of creating a reservoir model through the development and incorporation of an analog, extracting the quantitative input parameters on lateral and vertical variability, and the development and modification of a 3-D reservoir model based upon geologically constrained data. This applied volume is divided into two sections. The first is a set of papers illustrating the value and methodology of acquiring geometrical data on the lateral and vertical distribution of reservoir facies, within a sequence stratigraphic framework, using both outcrop analogs and detailed study of modern depositional systems. The second section includes both case studies where outcrop and modern analog data have been incorporated into subsurface reservoir models, as well as papers that illustrate recent advances in simulation and geostatistical methodologies. Together, the two sections provide a comprehensive look at integrated reservoir modeling.
Thin-film-technology-based micro-Fourier spectrometer (2003)

A novel Fourier spectrometer using thin film technology was developed. The spectrometer based on a semi transparent thin film detector in combination with a tunable micro machined mirror. The semi transparent detector is introduced into a standing wave created in front of the mirror to sample the profile of the standing wave. Varying the position of the mirror results in a shift of the phase of the standing waves and thus in a change of the optical generation profile within the semi transparent detector. The active region of the sensor (thickness-absorption) is thinner than the wavelength of the incoming light, so that the modulation of the intensity results in a modulation of the overall photocurrent. The spectral information of the incoming light can be determined by the Fourier transformation of the sensor signal. Based on the linear arrangement of the sensor and the mirror, the spectrometer facilitates the realization of 1D and 2D arrays of spectrometers combining medium range spectral resolution with medium range spatial resolution. The novel device is filling the gap between solid-state camera technology with only three-color channels (red, green and blue) but high spatial resolution on one hand and precision spectrometers with high spectral resolution but no spatial resolution on the other hand. An analytical optical model of the spectrometer was applied to evaluate different detector concepts. The model was used to study the performance of different device designs regarding the spectral resolution of the spectrometer, the spectral range and the linearity of the response. The calculations will be compared with experimental results of semi transparent amorphous silicon detectors.
CD44 crosslinking-mediated matrix metalloproteinase-9 relocation in breast tumor cells leads to enhanced metastasis (2007)

CD44 plays a major role in multiple physiological processes, including cell-cell adhesion, cell-substrate interaction, lymphocyte homing, and tumor metastasis. It has been reported that highly expressed CD44 in certain types of tumors is associated with the hematogenic spread of tumor cells. The ability of CD44 to bind hyaluronan has been shown to correlate with tumor cell invasiveness, and it is likely that this ability may enhance tumor cell migration at several points during metastasis. However, the mechanism as to how CD44 stimulates metastasis remains unknown. The human breast tumor cell line, MDA-MB-435s, was used to investigate the effect of antibody-mediated CD44 crosslinking on the cellular level and localization of matrix metalloproteinase-9 (MMP-9). Confocal microscopy and immunocytochemical analyses were performed to demonstrate colocalization of CD44 and MMP-9 after CD44 crosslinking. Furthermore, the CD44-MMP-9 complex was purified by immunoprecipitation. G8 myoblast monolayers were employed to evaluate the invasiveness of human breast tumor cells after CD44 crosslinking in the presence or absence of protease inhibitors. CD44 crosslinking augmented the level of MMP-9 in the membrane of human breast tumor cells and clustering of CD44 serves as an MMP-9 docking molecule allowing MMP-9 to retain its concentrated proteolytic activity on the cell surface. Furthermore, crosslinking of CD44 enhances the ability of breast tumor cells to invade G8 myoblast monolayers and migrate through the basal membranes which was inhibited in the presence of anti-MMP-9 antibody or the MMP inhibitors GM6001 or 1,10-phenanthroline. This study demonstrates for the first time that CD44 crosslinking leads to an enhanced level and relocation of MMP-9 in human breast tumor cells accompanied by increased tumor invasion and metastasis.
The basic principles of wound care. (1998)

A chronic wound should prompt a search for the underlying causes. Knowledge of the physiology of the normal wound healing trajectory through the stages of hemostasis, inflammation, granulation, and maturation provides a framework for understanding the advantages of moist interactive wound healing. Good chronic wound care is patient-centered, holistic, interdisciplinary, and evidence-based.
Tight‐binding inhibitory sequences against pp60c−src identified using a random 15‐amino‐acid peptide library (1996)

A bacteriophage peptide library containing a random 15-amino-acid insert was screened for identification of peptide sequence(s) that bind pp60(c-src). Sequencing the random insert from more than 100 virions indicated that more than 60% of the phage virions that bound to this enzyme contained a GXXG sequence motif in which X was frequently a hydrophobic residue. The GXXG sequence was often repeated as GXXGXXG. Two nonameric peptides were synthesized to determine whether or not the peptide inhibits pp60(c-src) tyrosine kinase activity and the importance of the glycine residues within this sequence. The peptide containing glycine had a Ki of 24 microM, whereas replacing the glycines with proline increased the Ki value to 3.1 mM.