gebhart/patrepeval huggingface dataset:
A Novel Level Shifter Employing IGZO TFT (2010)

A new level shifter employing indium-gallium-zinc-oxide thin-film transistor (IGZO TFT) for a display panel was proposed and successfully fabricated. Two clock signals with 180° out of phase and a discharging TFT were employed to obtain a full-swing output. The IGZO level shifter has successfully exhibited a wide swing output from <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">VDD</i> to <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">VSS</i> without any additional power sources and input signals. The power consumption is 0.30 mW at a clock frequency of 12.5 kHz. The proposed level shifter with a depletion-mode device would be an important building block for an oxide TFT display.
Interference avoidance for capacity optimization in mutually interfering wireless systems (2006)

In this paper we present application of greedy interference avoidance to capacity optimization of wireless sys- tems with multiple transmitters and receivers which interfere with each other. We start with a simple system consisting of two transmitters and two receivers for which we formally state a greedy interference avoidance algorithm, and show that its application converges to a simultaneous water filling solution. We discuss generalization of the algorithm to systems with more than two transmitters and receivers which interfere with each other, and present also numerical results obtained from simulations.
A tight binding study of the electronic structure of MnTe (1987)

A tight-binding version of the itinerant spin-fluctuation theory is used to describe the electronic structure of MnTe in both magnetically ordered and disordered phases. The static model of disordered local moments is shown to be sufficiently accurate to form the basis for a quantitative description of semiconducting behaviour of paramagnetic MnTe. A new type of disorder-induced metal-insulator transition is found.
Identification and Characterization of a Novel Heme-Associated Cell Surface Protein Made by <i>Streptococcus pyogenes</i> (2002)

Analysis of the genome sequence of a serotype M1 group A Streptococcus (GAS) strain identified a gene encoding a previously undescribed putative cell surface protein. The gene was cloned from a serotype M1 strain, and the recombinant protein was overexpressed in Escherichia coli and purified to homogeneity. The purified protein was associated with heme in a 1:1 stoichiometry. This streptococcal heme-associated protein, designated Shp, was produced in vitro by GAS, located on the bacterial cell surface, and accessible to specific antibody raised against the purified recombinant protein. Mice inoculated subcutaneously with GAS and humans with invasive infections and pharyngitis caused by GAS seroconverted to Shp, indicating that Shp was produced in vivo. The blood of mice actively immunized with Shp had significantly higher bactericidal activity than the blood of unimmunized mice. The shp gene was cotranscribed with eight contiguous genes, including homologues of an ABC transporter involved in iron uptake in gram-negative bacteria. Our results indicate that Shp is a novel cell surface heme-associated protein.
A bilateral tumor model identifies transcriptional programs associated with patient response to immune checkpoint blockade (2020)

Significance Immune checkpoint blockade (ICB) has revolutionized treatment of many cancer types, but the majority of treated patients still do not respond to ICB. There is an urgent need to identify predictive biomarkers of response prior to or shortly after therapy initiation, as well as the underlying mechanisms. Here we utilize a model of bilateral tumor implantations followed by resection and immunotherapy-response assessment to study the tumor microenvironment shortly following treatment, identifying biomarkers for response or resistance at early time points. Our biomarker gene signatures derived from CD8 + T cells significantly segregate patients by survival and associate with patient response to ICB. Our findings provide a general approach for studying mechanisms of resistance to ICB and discovering predictive biomarkers of response.
IC Specification Language (1979)

This paper explores the use of computer languages for specifying ICs. Many different aspects of an IC may be specified via language such as logical function and layout. The logic function of an IC may be specified via boolean equations and the layout may be specified via shapes expressed with cartesian coordinates. With such specification, the computer can simulate the behavior of the IC and generate layouts with great precision.
Laser writing of optical waveguides in sol-gel films (1994)

Laser heating can be used to fully densify selected areas of a partially densified sol-gel film deposited onto a glass substrate, thus substituting the conventional heat treatment in an oven. Here the topographic and optical characteristics of strip waveguides produced in a SiO<SUB>2</SUB>-TiO<SUB>2</SUB> film by direct writing with a focused CO<SUB>2</SUB> laser are presented, and the critical parameters of the process discussed.
Adverse Effects of Poor Mudcake Quality: A Supercharging and Fluid Sampling Study (2000)

Summary Wireline formation testers are routinely used at discrete depths of a well to collect reservoir fluid samples and to estimate undisturbed reservoir pressures, near-wellbore formation permeabilities, fluid compressibilities, and saturation pressures. A pressure profile in the vertical direction yields fluid densities and fluid contacts (gas/oil and water/oil contacts) in the reservoir. Reliable results are obtained when the mudcake isolates the wellbore from the formation. When the mudcake cannot provide isolation, mud filtrate invasion continues and supercharging occurs. The issue of sample quality becomes critical when using oil-based muds because the filtrate is also oil and is difficult to separate from the formation oil, a pure sample of which is needed for fluid characterization studies. This study investigated the effects of poor mudcake seal on sample quality and formation test data and its analysis when oil-based muds are used. Modeling studies were conducted using a finite-element simulator. The results of the study indicate that mudcake permeabilities must be less than 1 μd and mudcake-to-formation permeability ratios must be less than 10−4 to achieve sample qualities higher than 90%. Such conditions as high pumpout rates, low overbalance pressures, and shallow filtrate invasion depths improve sample quality. The presence of a permeability-damaged zone around the mudcake improves the sample quality but reduces the sampling pressure. The formation rate analysis (FRASM)† technique estimates formation permeability accurately in the presence or absence of supercharging. The formation pressure estimated using the buildup data is the pressure at the mudcake-formation interface. The supercharged pressure must be subtracted from the apparent formation pressure to obtain the true formation pressure. A simple procedure is developed for estimating the mudcake permeability and the supercharged pressure. Supercharged pressure is shown to be a product of the apparent overbalance pressure, mudcake-to-formation permeability ratio, and an invasion factor representing the distance up to which supercharging extends.
Impacts of transient voltage clamp on CPU power delivery (2004)

Transient voltage clamp (TVC) can be used in modern microprocessor power delivery loop to reduce passive decoupling elements. Where to put the TVC and how to control it are the objects of this paper. A microprocessor power supply design without bulk cap on motherboard by using TVC is proposed, which offers adaptive voltage position function and can meet Intel's VRD10.0 specifications.
Measuring the lesion load of multiple sclerosis patients within the corticospinal tract (2015)

In this paper we present a framework for reliable determination of the lesion load within the corticospinal tract (CST) of multiple sclerosis patients. The basis constitutes a probabilistic fiber tracking approach which checks possible parameter intervals on the fly using an anatomical brain atlas. By exploiting the range of those intervals, the algorithm is able to resolve fiber crossings and to determine the CST in its full entity although it can use a simple diffusion tensor model. Another advantage is its short running time, tracking the CST takes less than a minute. For segmenting the lesions we developed a semi-automatic approach. First, a trained classifier is applied to multimodal MRI data (T1/FLAIR) where the spectrum of lesions has been determined in advance by a clustering algorithm. This leads to an automatic detection of the lesions which can be manually corrected afterwards using a threshold-based approach. For evaluation we scanned 46 MS patients and 16 healthy controls. Fiber tracking has been performed using our novel fiber tracking and a standard defection based algorithm. Regression analysis of the old and new version of the algorithm showed a highly significant superiority of the new algorithm for disease duration. Additionally, a low correlation between old and new approach supports the observation that standard DTI fiber tracking is not always able to track and quantify the CST reliably.
Alport syndrome caused by a <i>COL4A5</i> deletion and exonization of an adjacent <i>AluY</i> (2014)

Mutation-induced activation of splice sites in intronic repetitive sequences has contributed significantly to the evolution of exon-intron structure and genetic disease. Such events have been associated with mutations within transposable elements, most frequently in mutation hot-spots of Alus. Here, we report a case of Alu exonization resulting from a 367-nt genomic COL4A5 deletion that did not encompass any recognizable transposed element, leading to the Alport syndrome. The deletion brought to proximity the 5' splice site of COL4A5 exon 33 and a cryptic 3' splice site in an antisense AluY copy in intron 32. The fusion exon was depleted of purines and purine-rich splicing enhancers, but had low levels of intramolecular secondary structure, was flanked by short introns and had strong 5' and Alu-derived 3' splice sites, apparently compensating poor composition and context of the new exon. This case demonstrates that Alu splice sites can be activated by outlying deletions, highlighting Alu versatility in shaping the exon-intron organization and expanding the spectrum of mutational mechanisms that introduce repetitive sequences in mRNAs.
A rapid and facile method for the general synthesis of 3-aryl substituted 4,5,6,7-tetrahydro[1,2,3]triazolo[1,5-a]pyrazines and their ring fused analogues (2011)

We report a general and facile method that provides rapid entry into 3-aryl substituted 4,5,6,7-tetrahydro[1,2,3]triazolo[1,5-a]pyrazines and their ring fused analogues in one-pot under palladium-copper catalysis. The methodology utilises simple and easily available substrates of broad range. The applicability of this reaction for the synthesis of optically active products has been demonstrated. A plausible reaction mechanism has also been proposed.
A kit formulation for preparation of iodine-123-IBZM: a new CNS D-2 dopamine receptor imaging agent. (1991)

A method for the preparation of iodine-123IBZM, a central nervous system D-2 imaging agent, is reported. By using a rapid filtration technique to remove the unreacted iodide, the preparation can be completed in less than 20 min (overall yield greater than 60%). The product, with high purity (greater than or equal to 95%) and specific activity, is suitable for human use.
Aberrant expression of cAMP-response-element-binding protein (‘CREB’) induces apoptosis (1999)

We have reported previously that cAMP-response-element-binding protein (CREB) was phosphorylated in a cell-cycle-dependent manner, showing that it was phosphorylated at early S-phase at casein kinase II target sites. To assess the possible involvement of CREB in cell cycle progression, CREB expression vector was transiently transfected into various cells. Unexpectedly we found that transfection with CREB expression vector resulted in an abundance of dead cells. Morphological examination revealed that these cells had undergone apoptosis. The coincidence of CREB overexpression and apoptosis induction at the individual cell level was confirmed by a immunohistochemical study. To confirm that overexpression of CREB was the cause of apoptosis, a dominant-negative mutant of CREB, KCREB, was co-expressed with the wild type. The co-existence of KCREB effectively rescued CREB-mediated apoptosis in a dose-dependent manner, verifying that apoptosis was truly a specific effect of overexpressed CREB and not an artifact of the transfection procedure. Deletion analysis indicates that neither the Q1 transactivation domain, which functions in transcription, nor the kinase-inducible domain, in which a cluster of various kinase targets exists, is necessary; however, the Q2 transactivation domain is required for the induction of apoptosis. A more precise study indicates that the four-residue stretch Glu-Glu-Ala-Ala at the most C-terminal region of the Q2 domain is especially important for the induction of apoptosis. Thus overexpressed CREB induces apoptosis by transmitting certain signals from the C-terminal portion of the Q2 domain. Possible roles of cell-cycle-regulated phosphorylation and also an elevation of the intracellular cAMP level in CREB-induced apoptosis are suggested.
Modulation of extracellular matrix proteins by endothelial cells undergoing angiogenesis in vitro. (1991)

Angiogenesis results in part from the response of endothelial cells to the integrated action of morphogenic factors and extracellular matrix proteins. In this study we identified specific components of the extracellular matrix that were modulated in endothelial cells derived from bovine aorta and rat cerebral microvessels, both of which spontaneously form cords and tubes under standard culture conditions. SPARC (secreted protein, acidic and rich in cysteine) was upregulated 4.2-fold in aortic and 10-fold in microvascular cultures that had organized into cords and/or tubes. This Ca(2+)-binding glycoprotein was synthesized primarily by endothelial cells in the process of cord formation. Transcription of type I collagen was initiated in aortic endothelial cells undergoing angiogenesis in vitro and showed a 12-fold increase in similar cultures of microvascular cells. Type VIII collagen protein was upregulated to a lesser degree (4.3-fold in aortic and 1.8-fold in microvascular cells). Dense cytoplasmic staining for these two collagen types was seen in cells directly participating in the organization of cords. In contrast, the disparate levels of fibronectin observed in both types of endothelium indicated an indirect or secondary role for this glycoprotein in cord/tube formation in vitro. These results identify SPARC, type I collagen, and type VIII collagen as extracellular matrix components that are actively synthesized by endothelial cells undergoing angiogenesis in vitro. Moreover, expression of these proteins during the formation of tubes and cords appears to follow a biosynthetic program that is common to endothelial cells from both the macrovasculature and microvasculature.
Location of the alkali metal ion in gas-phase peptide complexes (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLocation of the alkali metal ion in gas-phase peptide complexesLynn M. Teesch, Ronald C. Orlando, and Jeanette AdamsCite this: J. Am. Chem. Soc. 1991, 113, 10, 3668–3675Publication Date (Print):May 1, 1991Publication History Published online1 May 2002Published inissue 1 May 1991https://pubs.acs.org/doi/10.1021/ja00010a006https://doi.org/10.1021/ja00010a006research-articleACS PublicationsRequest reuse permissionsArticle Views318Altmetric-Citations121LEARN 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
Next-generation transcriptome sequencing of the premenopausal breast epithelium using specimens from a normal human breast tissue bank (2014)

Abstract Introduction Our efforts to prevent and treat breast cancer are significantly impeded by a lack of knowledge of the biology and developmental genetics of the normal mammary gland. In order to provide the specimens that will facilitate such an understanding, The Susan G. Komen for the Cure Tissue Bank at the IU Simon Cancer Center (KTB) was established. The KTB is, to our knowledge, the only biorepository in the world prospectively established to collect normal, healthy breast tissue from volunteer donors. As a first initiative toward a molecular understanding of the biology and developmental genetics of the normal mammary gland, the effect of the menstrual cycle and hormonal contraceptives on DNA expression in the normal breast epithelium was examined. Methods Using normal breast tissue from 20 premenopausal donors to KTB, the changes in the mRNA of the normal breast epithelium as a function of phase of the menstrual cycle and hormonal contraception were assayed using next-generation whole transcriptome sequencing (RNA-Seq). Results In total, 255 genes representing 1.4% of all genes were deemed to have statistically significant differential expression between the two phases of the menstrual cycle. The overwhelming majority (221; 87%) of the genes have higher expression during the luteal phase. These data provide important insights into the processes occurring during each phase of the menstrual cycle. There was only a single gene significantly differentially expressed when comparing the epithelium of women using hormonal contraception to those in the luteal phase. Conclusions We have taken advantage of a unique research resource, the KTB, to complete the first-ever next-generation transcriptome sequencing of the epithelial compartment of 20 normal human breast specimens. This work has produced a comprehensive catalog of the differences in the expression of protein-coding genes as a function of the phase of the menstrual cycle. These data constitute the beginning of a reference data set of the normal mammary gland, which can be consulted for comparison with data developed from malignant specimens, or to mine the effects of the hormonal flux that occurs during the menstrual cycle.
Intracellular Bacteria Differentially Regulated Endothelial Cytokine Release by MAPK-Dependent Histone Modification (2005)

Epigenetic histone modifications contribute to the regulation of eukaryotic gene transcription. The role of epigenetic regulation in immunity to intracellular pathogens is poorly understood. We tested the hypothesis that epigenetic histone modifications influence cytokine expression by intracellular bacteria. Intracellular Listeria monocytogenes, but not noninvasive Listeria innocua, induced release of distinct CC and CXC chemokines, as well as Th1 and Th2 cytokines and growth factors by endothelial cells. Cytokine expression was in part dependent on p38 MAPK and MEK1. We analyzed global histone modification and modifications in detail at the gene promoter of IL-8, which depended on both kinase pathways, and of IFN-gamma, which was not blocked by kinase inhibition. Intracellular Listeria induced time-dependent acetylation (lysine 8) of histone H4 and phosphorylation/acetylation (serine 10/lysine 14) of histone H3 globally and at the il8 promoter in HUVEC, as well as recruitment of the histone acetylase CREB-binding protein. Inhibitors of p38 MAPK and MEK1 reduced lysine 8 acetylation of histone H4 and serine 10/lysine 14 phosphorylation/acetylation of histone H3 in Listeria-infected endothelial cells and disappearance of histone deacetylase 1 at the il8 promoter in HUVEC. In contrast, IFN-gamma gene transcription was activated by Listeria monocytogenes independent of p38 MAPK and MEK1, and histone phosphorylation/acetylation remained unchanged in infected cells at the IFN-gamma promoter. Specific inhibition of histone deacetylases by trichostatin A increased Listeria-induced expression of IL-8, but not of IFN-gamma, underlining the specific physiological impact of histone acetylation. In conclusion, MAPK-dependent epigenetic modifications differentially contributed to L. monocytogenes-induced cytokine expression by human endothelial cells.
A CTD function linking transcription to splicing (1997)

Since its discovery in 1985, the function of the C-terminal domain (CTD) of RNA polymerase II has been a puzzle. Recent studies suggest that the CTD functions as a linear platform for assembly of complexes that splice, cleave and polyadenylate pre-mRNA. A new set of CTD-associated SR-like proteins (CASPs) have been implicated in pre-mRNA processing and transcription elongation as a component of the emerging 'transcriptosome'.
Angiomodulin, a marker of cancer vasculature, is upregulated by vascular endothelial growth factor and increases vascular permeability as a ligand of integrin <i>α</i>v<i>β</i>3 (2014)

Angiomodulin (AGM) is a member of insulin-like growth factor binding protein (IGFBP) superfamily and often called IGFBP-rP1 or IGFBP-7. AGM was originally identified as a tumor-derived cell adhesion factor, which was highly accumulated in blood vessels of human cancer tissues. AGM is also overexpressed in cancer-associated fibroblasts (CAFs) and activates fibroblasts. However, some studies have shown tumor-suppressing activity of AGM. To understand the roles of AGM in cancer progression, we here investigated the expression of AGM in benign and invasive breast cancers and its functions in cancer vasculature. Immunohistochemical analysis showed that AGM was highly expressed in cancer vasculature even in ductal carcinoma in situ (DCIS) as compared to normal vasculature, while its expression in CAFs was more prominent in invasive carcinomas than DCIS. In vitro analyses showed that AGM was strongly induced by vascular endothelial cell growth factor (VEGF) in vascular endothelial cells. Although AGM stimulated neither the growth nor migration of endothelial cells, it supported efficient adhesion of endothelial cells. Integrin αvβ3 was identified as a novel major receptor for AGM in vascular endothelial cells. AGM retracted endothelial cells by inducing actin stress fibers and loosened their VE-cadherin-mediated intercellular junction. Consequently, AGM increased vascular permeability both in vitro and in vivo. Furthermore, AGM and integrin αvβ3 were highly expressed and colocalized in cancer vasculature. These results suggest that AGM cooperates with VEGF to induce the aberrant functions of cancer vasculature as a ligand of integrin αvβ3.