gebhart/patrepeval huggingface dataset:
Transcriptional Repression of the Anti-apoptoticsurvivin Gene by Wild Type p53 (2002)

Survivin is a member of the inhibitor of apoptosis family. This apoptosis inhibitor also has an evolutionarily conserved role as a mitotic spindle checkpoint protein. Previous studies on p53-repressed genes have implicated several genes involved in the G(2)/M transition of the cell cycle as targets of negative regulation by p53. However, few targets of p53 repression that are anti-apoptotic have been identified. This study identifies the anti-apoptotic survivin gene as a p53-repressed gene. Notably, Survivin repression by p53 is shown to be distinct from p53-dependent growth arrest. Chromatin immunoprecipitations indicate that p53 binds the survivin promoter in vivo; immunobinding studies indicate that this site overlaps with a binding site for E2F transcription factors and is subtly distinct from a canonical p53-transactivating element. The survivin-binding site contains a 3-nucleotide spacer between the two decamer "half-sites" of the p53 consensus element; deletion of this spacer is sufficient to convert the survivin site into a transactivating element. Finally, we show that overexpression of Survivin in cells sensitive to p53-dependent cell death markedly inhibits apoptosis induced by ultraviolet light. The identification of survivin as a p53 repressed gene should aid in the elucidation of the contribution of transcriptional repression to p53-dependent apoptosis.
Micro-objective manipulated with optical tweezers (1997)

A microscope is described that uses a μm-sized ball lens, which is here termed micro-objective, manipulated with optical tweezers to image the side view of the arbitrary region of a sample. Since this micro-objective is small in size, it can go into a concave region to produce a local image of the inside which the conventional microscope cannot observe. Preliminary results show good lens performance from the micro-objective when combined with optical tweezers.
Pitfalls in the Use of DNA Microarray Data for Diagnostic and Prognostic Classification (2003)

DNA microarrays have made it possible to estimate the level of expression of thousands of genes for a sample of cells. Although biomedical investigators have been quick to adopt this powerful new research tool, accurate analysis and interpretation of the data have provided unique challenges. Indeed, many investigators are not experienced in the analytical steps needed to convert tens of thousands of noisy data points into reliable and interpretable biologic information. Although some investigators recognize the importance of collaborating with experienced biostatisticians to analyze microarray data, the number and availability of experienced biostatisticians is inadequate. Consequently, investigators are using available software to analyze their data, many seemingly without knowledge of potential pitfalls. Because of serious problems associated with the analysis and reporting of some DNA microarray studies, there is great interest in guidance on valid and effective methods for analysis of DNA microarray data. The design and analysis strategy for a DNA microarray experiment should be determined in light of the overall objectives of the study. Because DNA microarrays are used for a wide variety of objectives, it is not feasible to address the entire range of design and analysis issues in this commentary. Here, we address statistical issues that arise from the use of DNA microarrays for an important group of objectives that has been called “class prediction” (1). Class prediction includes derivation of predictors of prognosis, response to therapy, or any phenotype or genotype defined independently of the gene expression profile.
Photoisomerization of Cyanines. A Comparative Study of Oxygen- and Sulfur-Containing Species (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotoisomerization of Cyanines. A Comparative Study of Oxygen- and Sulfur-Containing SpeciesM. M. Awad, P. K. McCarthy, and G. J. BlanchardCite this: J. Phys. Chem. 1994, 98, 5, 1454–1458Publication Date (Print):February 1, 1994Publication History Published online1 May 2002Published inissue 1 February 1994https://pubs.acs.org/doi/10.1021/j100056a014https://doi.org/10.1021/j100056a014research-articleACS PublicationsRequest reuse permissionsArticle Views197Altmetric-Citations37LEARN 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
Comparing Clinical Features of the Nebulizer, Metered-Dose Inhaler, and Dry Powder Inhaler (2005)

Topically inhaled bronchodilators and corticosteroids are the mainstay of treatment for asthma and chronic obstructive pulmonary disease. These medications are delivered via jet or ultrasonic nebulizer, metered-dose inhaler (MDI), or dry powder inhaler (DPI). While the number of devices may be confusing to patients and clinicians, each device has distinct advantages and disadvantages. Most clinical evidence shows that any of these devices will work for most situations, including exacerbations and in the stable outpatient setting. There is a high rate of errors in device use with all these devices, especially the MDI. In choosing a drug/device combination for a patient, the clinician must take into account several factors, including the cognitive and physical ability of the patient, ease of use, convenience, costs, and patient preferences. Clinicians should also have a rudimentary understanding of aerosol principles in order to be able to teach appropriate use of aerosol devices to their patients.
Kinetic parameter estimation from SPECT cone-beam projection measurements (1998)

Kinetic parameters are commonly estimated from dynamically acquired nuclear medicine data by first reconstructing a dynamic sequence of images and subsequently fitting the parameters to time-activity curves generated from regions of interest overlaid upon the image sequence. Biased estimates can result from images reconstructed using inconsistent projections of a time-varying distribution of radiopharmaceutical acquired by a rotating SPECT system. If the SPECT data are acquired using cone-beam collimators wherein the gantry rotates so that the focal point of the collimators always remains in a plane, additional biases can arise from images reconstructed using insufficient, as well as truncated, projection samples. To overcome these problems we have investigated the estimation of kinetic parameters directly from SPECT cone-beam projection data by modelling the data acquisition process. To accomplish this it was necessary to parametrize the spatial and temporal distribution of the radiopharmaceutical within the SPECT field of view. In a simulated chest image volume, kinetic parameters were estimated for simple one-compartment models for four myocardial regions of interest. Myocardial uptake and washout parameters estimated by conventional analysis of noiseless simulated cone-beam data had biases ranging between 3-26% and 0-28%, respectively. Parameters estimated directly from the noiseless projection data were unbiased as expected, since the model used for fitting was faithful to the simulation. Statistical uncertainties of parameter estimates for 10,000,000 events ranged between 0.2-9% for the uptake parameters and between 0.3-6% for the washout parameters.
Tea Polyphenols: Selective Growth Inhibitors of<i>Clostridium</i>spp. (1991)

Journal Article Tea Polyphenols: Selective Growth Inhibitors of Clostridium spp. Get access Young-Joon Ahn, Young-Joon Ahn Frontier Research Program, Laboratory for Intestinal Flora, RIKEN, Wako-shi, Saitama 351–01, Japan Present address: Department of Agrobiology, College of Seoul Nat'l University, Suwon 441–744, Korea Search for other works by this author on: Oxford Academic Google Scholar Toshiya Kawamura, Toshiya Kawamura Central Research Laboratories, Taiyo Kagaku Co., Ltd., Yokkaichi, Mie 510, Japan Search for other works by this author on: Oxford Academic Google Scholar Mujo Kim, Mujo Kim Central Research Laboratories, Taiyo Kagaku Co., Ltd., Yokkaichi, Mie 510, Japan Search for other works by this author on: Oxford Academic Google Scholar Takehiko Yamamoto, Takehiko Yamamoto Department of Biotechnology, Fukuyama University, Fukuyama 729–02, Japan Search for other works by this author on: Oxford Academic Google Scholar Tomotari Mitsuoka Tomotari Mitsuoka Frontier Research Program, Laboratory for Intestinal Flora, RIKEN, Wako-shi, Saitama 351–01, JapanFaculty of Agriculture, The University of Tokyo and The Institute of Physical & Chemical Research, Wako-shi, Saitama 351–01, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 55, Issue 5, 1 May 1991, Pages 1425–1426, https://doi.org/10.1080/00021369.1991.10870770 Published: 01 May 1991 Article history Received: 19 November 1990 Published: 01 May 1991
Genetics of dark skin in mice (2003)

Chemical mutagenesis in the mouse is a powerful approach for phenotype-driven genetics, but questions remain about the efficiency with which new mutations ascertained by their phenotype can be localized and identified, and that knowledge applied to a specific biological problem. During a global screen for dominant phenotypes in about 30,000 animals, a novel class of pigmentation mutants were identified by dark skin (Dsk). We determined the genetic map location, homozygous phenotype, and histology of 10 new Dsk and 2 new dark coat (Dcc) mutations, and identified mutations in Agouti (Met1Leu, Dcc4), Sox18 (Leu220ter, Dcc1), Keratin 2e (Thr500Pro, Dsk2), and Egfr (Leu863Gln, Dsk5). Cutaneous effects of most Dsk mutations are limited to melanocytes, except for the Keratin 2e and Egfr mutations, in which hyperkeratosis and epidermal thickening precede epidermal melanocytosis by 3-6 wk. The Dsk2 mutation is likely to impair intermediate filament assembly, leading to cytolysis of suprabasal keratinocytes and secondary hyperkeratosis and melanocytosis. The Dsk5 mutation causes increased tyrosine kinase activity and a decrease in steady-state receptor levels in vivo. The Dsk mutations represent genes or map locations not implicated previously in pigmentation, and delineate a developmental pathway in which mutations can be classified on the basis of body region, microscopic site, and timing of pigment accumulation.
On the Number of Operations Simultaneously Executable in Fortran-Like Programs and Their Resulting Speedup (1972)

This paper is concerned with the problem of analyzing ordinary Fortran-like programs to determine how many of their operations could be performed simultaneously. Algorithms are presented for handling arithmetic assignment statements, DO loops and IF statement trees. The height of the parse trees of arithmetic expressions is reduced by distribution of multiplication over addition as well as the use of associativity and commutativity. DO loops are analyzed in terms of their index sets and subscript forms. Some general underlying assumptions about machine organization are also given. In terms of several measures which are defined, the results of experimental analyses are presented. About 20 Fortran IV programs consisting of nearly 1000 source cards were analyzed. Evidence is given that for very simple Fortran programs 16 processors could be effectively used operating simultaneously in a parallel or pipeline fashion. Thus, for medium or large size Fortran programs, machines consisting of multiples of a basic 16 processor unit could be used.
Efficient WFST-Based One-Pass Decoding With On-The-Fly Hypothesis Rescoring in Extremely Large Vocabulary Continuous Speech Recognition (2007)

This paper proposes a novel one-pass search algorithm with on-the-fly composition of weighted finite-state transducers (WFSTs) for large-vocabulary continuous-speech recognition. In the standard search method with on-the-fly composition, two or more WFSTs are composed during decoding, and a Viterbi search is performed based on the composed search space. With this new method, a Viterbi search is performed based on the first of the two WFSTs. The second WFST is only used to rescore the hypotheses generated during the search. Since this rescoring is very efficient, the total amount of computation required by the new method is almost the same as when using only the first WFST. In a 65k-word vocabulary spontaneous lecture speech transcription task, our proposed method significantly outperformed the standard search method. Furthermore, our method was faster than decoding with a single fully composed and optimized WFST, where our method used only 38% of the memory required for decoding with the single WFST. Finally, we have achieved high-accuracy one-pass real-time speech recognition with an extremely large vocabulary of 1.8 million words
80 GHz on-chip metamaterial resonator by differential transmission line loaded with split ring resonator (2012)

An on-chip metamaterial resonator is demonstrated in 65 nm CMOS at 80 GHz for millimetre-wave integrated circuit (MMIC) applications. The resonator is based on a differential metamaterial transmission-line (T-line) loaded with a split ring resonator (SRR), which can enhance the EM energy coupling and further improve the quality factor (Q). Measurement results indicate that the proposed differential SRR (DSRR) T-line shows a sharp stopband with maximum 35 dB rejection. Moreover, the metamaterial property of the DSRR T-line is validated from the measurement results. It is the first on-chip demonstration of a millimetre-wave metamaterial resonator in 65 nm CMOS, which can be integrated for a low-noise oscillator and high-Q filter design in a 100 GHz MMIC communication system.
Physicochemical Properties and Antimicrobial Efficacy of Carvacrol Nanoemulsions Formed by Spontaneous Emulsification (2013)

A simple cost-effective method (spontaneous emulsification) for fabricating physically stable antimicrobial nanoemulsions from essential oils is described. These nanoemulsions (10 wt % total oil phase) were formed by titration of a mixture of essential oil (carvacrol), carrier oil (medium chain triglyceride, MCT), and nonionic surfactant (Tween) into an aqueous solution with continuous stirring. Oil phase composition (carvacrol-to-MCT mass ratio) had a major impact on initial droplet diameter, with the smallest droplets (d ≈ 55 nm) being formed at 2.5 wt % carvacrol and 7.5 wt % MCT. Surfactant type also had an appreciable impact on mean droplet diameter, with Tween 80 giving the smallest droplets (d ≈ 55 nm) from a group of food-grade nonionic surfactants (Tween 20, 40, 60, 80, and 85). The droplet size also decreased (from >5000 to <25 nm) as the total surfactant concentration was increased (from 5 to 20 wt %). The long-term stability and antimicrobial efficacy of selected nanoemulsions was examined at ambient temperature. The stability of the nanoemulsions to droplet growth during storage decreased as the carvacrol concentration in the oil phase increased. Conversely, the antimicrobial efficacy of the nanoemulsions increased as the carvacrol concentration increased. These results have important implications for the design and utilization of nanoemulsions as antimicrobial delivery systems in the food and other industries. They suggest that the carrier oil concentration must be carefully controlled to obtain good physical stability and antimicrobial efficacy.
Syndecan-3 and the Control of Chondrocyte Proliferation during Endochondral Ossification (1996)

During endochondral ossification, chondrocytes progress through several stages of maturation before they are replaced by bone cells. Chondrocyte proliferation, the first step in this complex multistage process, is strictly controlled both spatially and temporally but its underlying mechanisms of regulation remain unclear. In this study we asked whether chondrocytes produce syndecan-3, a cell surface receptor for growth factors such as fibroblast growth factor 2 (FGF-2), and whether syndecan-3 may play a role in proliferation during chondrocyte maturation. We found that proliferating immature cartilage from chick embryo tibia and sternum contained significant amounts of syndecan-3 mRNA, whereas mature hypertrophic cartilage contained markedly lower transcript levels. Immunohistochemical analyses on sections of Day 18 chick embryo tibia revealed that syndecan-3 was spatially restricted and indeed detectable only in immature proliferating chondrocytes in the top zone of growth plate. These syndecan-3-rich proliferating chondrocytes lay beneath developing articular chondrocytes rich in their typical matrix protein tenascin-C, resulting in a striking boundary between these two populations of chondrocytes. Immature proliferating chondrocyte populations reared in growth-promoting culture conditions displayed strong continuous syndecan-3 gene expression; upon induction of maturation by vitamin C treatment, syndecan-3 gene expression was markedly down-regulated. Treatment with FGF-2 for 24 h stimulated both syndecan-3 gene expression and chondrocyte proliferation; this growth stimulation was counteracted by cotreatment with heparinase I or III. The results of the study indicate that syndecan-3 participates in the maturation of chondrocytes during endochondral ossification and represents a regulator of the proliferative phase of this multistage process.
Thin topological insulator film in a perpendicular magnetic field (2011)

We report on a study of an ultrathin topological insulator film with hybridization between the top and bottom surfaces, placed in a quantizing perpendicular magnetic field. We calculate the full Landau-level spectrum of the film as a function of the applied magnetic field and the magnitude of the hybridization matrix element, taking into account both the orbital and the Zeeman spin splitting effects of the field. For an undoped film, we find a quantum phase transition between a state with a zero Hall conductivity and a state with a quantized Hall conductivity equal to ${e}^{2}/h$, as a function of the magnitude of the applied field. The transition is driven by the competition between the Zeeman and the hybridization energies.
A new bipolar transistor&amp;#8212;GAT (1980)

A new bipolar transistor named Gate Associated Transistor (GAT) was proposed and the operating mechanisms were verified. The structure of the GAT has a unique base region consisting of an FET merged into the base of a standard bipolar transistor. The operating mechanisms and characteristics of the GAT were investigated and compared with those of standard power transistors. The most outstanding feature of the GAT was a large area for safe operation.
Fibroblast Growth Factor 23 (2005)

Although phosphate is important in skeletal mineralization, energy metabolism, and multiple enzymatic processes, little has been understood about the regulation of phosphate in health and disease until recently. Genetic and acquired disorders of phosphate homeostasis have begun to reveal important
Substituent effects on stability of oxiranes, oxirenes, and dioxiranes (2000)

Homodesmotic reactions were designed to study substituent effects on stability of oxiranes, oxirenes, and dioxiranes. Good or fair correlation between their homodesmotic stabilization energies and Taft's dual-substituent-parameters has been found. Oxiranes are stabilized by σ-donating and π-donating substituents but destabilized by σ-accepting and π-accepting substituents. The π-effects on oxiranes are comparable to σ-effects for π-acceptor substituents and are much stronger than σ-effects for π-donor substituents. Oxirenes are stabilized by σ-donating, π-donating, and π-accepting substituents but destabilized by σ-accepting substituents. The π-effects on oxirenes are stronger than σ-effects. Oxirenes with strong π-donor substituents such as F, OH, and NH 2 , or strong σ-donor substituents such as Li and Na are neither real molecules nor transition states. Dioxiranes are stabilized by σ-donating and π-donating substituents but destabilized by σ-accepting and π-accepting substituents. The π-effects on dioxiranes are stronger than σ-effects for π-donor substituents, but weaker than σ-effects for π-acceptor substituentsKey words: oxirane, oxirene, dioxirane, homodesmotic reaction, substituent effect.
Conformance of ECD wafer bumping to future demands on CSP, 3D integration, and MEMS (2006)

A bumping technique which is based on electrochemical deposition (ECD) of various metals and metal alloys on wafer level will be presented and characterized in this paper. The machining of the single process steps principally origins from front-end technology widely using standard equipment, but mainly differing in structure sizes and layer thicknesses. Photosensitive polymers have been coated to repassivate the IC wafer and to serve as dielectric layers for I/O redistribution. Sputtering of the under-bump metallization (UBM), lithographical printing of resist pattern, electroplating of the bump metal, and selective etching of the plating base will be treated in detail. Different kinds of UBMs are used for the various bump metals. A sputtered Ti:W(N)/Au thin-film layer is used for the electroplating of Au and Au/Sn, and a Ti:W/Cu metallization acts as the seed layer for Cu and Ni/Au deposition as well as for the solder (SnPb37, PbSn5, SnAg3.5, SnCu0.7). Alternatively, other UBMs such as Ti/Ti:Ni/Ni, Ti/Au, and Cr/Cr:Cu/Cu has been qualified to generate several reliable solder bump metallurgies. Both spin-coating and spray-coating are used as a method to deposit the liquid photoresist onto the wafer. By applying a highly viscous system, layer thicknesses from 5 mum up to 90 mum with excellent thickness homogeneity and a precise pattern resolution for all standard wafer sizes can be achieved. A high standard of bump geometry as well as a high process quality and long term reliability can be obtained by carefully chosen electrolytes, well defined plating conditions, and specially developed microgalvanic equipment. Adequate wet etching solutions had to be formulated to get a neglectable corrosion affect on the bump surface and a minimum bump undercut. Thermal, mechanical, and electrical tests were performed to get statements about the reliability of the bumped devices
Medical accelerator projects at Michigan State University (2003)

The authors report on three medical accelerator projects at Michigan State University. One involves construction of a 100-MeV superconducting cyclotron for neutron therapy. In the second, a conceptual design has been prepared for a 250-MeV superconducting synchrocyclotron for proton therapy. The third consists of preliminary studies of a compact 1600-MeV superconducting cyclotron system for heavy ion therapy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>