gebhart/patrepeval huggingface dataset:
NeuNetS: An Automated Synthesis Engine for Neural Network Design (2019)

Application of neural networks to a vast variety of practical applications is transforming the way AI is applied in practice. Pre-trained neural network models available through APIs or capability to custom train pre-built neural network architectures with customer data has made the consumption of AI by developers much simpler and resulted in broad adoption of these complex AI models. While prebuilt network models exist for certain scenarios, to try and meet the constraints that are unique to each application, AI teams need to think about developing custom neural network architectures that can meet the tradeoff between accuracy and memory footprint to achieve the tight constraints of their unique use-cases. However, only a small proportion of data science teams have the skills and experience needed to create a neural network from scratch, and the demand far exceeds the supply. In this paper, we present NeuNetS : An automated Neural Network Synthesis engine for custom neural network design that is available as part of IBM's AI OpenScale's product. NeuNetS is available for both Text and Image domains and can build neural networks for specific tasks in a fraction of the time it takes today with human effort, and with accuracy similar to that of human-designed AI models.
Production of Homozygous Mutant ES Cells with a Single Targeting Construct (1992)

We have developed a simple method for producing embryonic stem (ES) cell lines whereby both alleles have been inactivated by homologous recombination and which requires a single targeting construct. Four different ES cell lines were created that were heterozygous for genes encoding two guanine nucleotide-binding protein subunits, alpha i2 and alpha i3, T-cell receptor alpha, and beta-cardiac myosin heavy chain. When these heterozygous cells were grown in high concentrations of G418, many of the surviving cells were homozygous for the targeted allele and contained two copies of the G418 resistance gene. This scheme provides an easy method for obtaining homozygous mutationally altered cells, i.e., double knockouts, and should be generally applicable to other genes and to cell lines other than ES cells. This method should also enable the production of cell lines in which more than one gene have had both alleles disrupted. These mutant cells should provide useful tools for defining the role of particular genes in cell culture.
Exploring the DNA-binding specificities of zinc fingers with DNA microarrays (2001)

A key step in the regulation of networks that control gene expression is the sequence-specific binding of transcription factors to their DNA recognition sites. A more complete understanding of these DNA-protein interactions will permit a more comprehensive and quantitative mapping of the regulatory pathways within cells, as well as a deeper understanding of the potential functions of individual genes regulated by newly identified DNA-binding sites. Here we describe a DNA microarray-based method to characterize sequence-specific DNA recognition by zinc-finger proteins. A phage display library, prepared by randomizing critical amino acid residues in the second of three fingers of the mouse Zif268 domain, provided a rich source of zinc-finger proteins with variant DNA-binding specificities. Microarrays containing all possible 3-bp binding sites for the variable zinc fingers permitted the quantitation of the binding site preferences of the entire library, pools of zinc fingers corresponding to different rounds of selection from this library, as well as individual Zif268 variants that were isolated from the library by using specific DNA sequences. The results demonstrate the feasibility of using DNA microarrays for genome-wide identification of putative transcription factor-binding sites.
CCR5 or CXCR4 use influences the relationship between CD4 cell depletion, NKp44L expression and NK cytotoxicity in SHIV-infected macaques (2008)

These results highlight the key role played by NK cells in CD4 cell count decline with respect to coreceptor usage, and provided the setting to investigate new strategies for preventive and/or therapeutic immunization to stimulate anti-3S antibodies.
Local additive estimation Series B Statistical methodology (2010)

Additive models are popular in high dimensional regression problems owing to their flexibility in model building and optimality in additive function estimation. Moreover, they do not suffer from the so-called curse of dimensionality generally arising in non-parametric regression settings. Less known is the model bias that is incurred from the restriction to the additive class of models. We introduce a new class of estimators that reduces additive model bias, yet preserves some stability of the additive estimator. The new estimator is constructed by localizing the additivity assumption and thus is named the local additive estimator. It follows the spirit of local linear estimation but is shown to be able to relieve partially the dimensionality problem. Implementation can be easily made with any standard software for additive regression. For detailed analysis we explicitly use the smooth backfitting estimator of Mammen, Linton and Nielsen.
High 1,4‐cis‐polybutadiene by uranium catalysts, 1. Tris(π‐allyl)uranium halide catalysts (1974)

Abstract The synthesis of tris(π‐allyl)uranium halides ( 2a–c ) and their behaviour in the stereospecific polymerization of butadiene are reported. Independently from the nature of the halogen bound to uranium, very high 1,4‐ cis ‐polymer with a fairly good yield is obtained. The catalytic activity of allyluranium derivatives is very much improved when a Lewis acid is added as a co‐catalyst. It is characteristic of the polymer to show a cis ‐content up to 99% and an exceptionally high chain regularity at least for long chain sequencies.
Effects of DNA sequence and structure on binding of RecA to single-stranded DNA (2001)

Fluorescence anisotropy is used to follow the binding of RecA to short single-stranded DNA (ssDNA) sequences (39 bases) at low DNA and RecA concentration where the initial phase of polymerization occurs. We observe that RecA condensation is extremely sensitive to minute changes in DNA sequences. RecA binds strongly to sequences that are rich in pyrimidines and that lack significant secondary structure and base stacking. We find a correlation between the DNA folding free energy and the onset concentration for RecA binding. These results suggest that the folding of ssDNA and base stacking represent a barrier for RecA binding. The link between secondary structure and binding affinity is further analyzed with two examples: discrimination between two naturally occurring polymorphisms differing by one base and RecA binding on a molecular beacon. A self-assembly model is introduced to explain these observations. We propose that RecA may be used to sense ssDNA sequence and structure.
Roles and mechanisms of the CD38/cyclic adenosine diphosphate ribose/Ca2+signaling pathway (2014)

Mobilization of intracellular Ca(2+) stores is involved in many diverse cell functions, including: cell proliferation; differentiation; fertilization; muscle contraction; secretion of neurotransmitters, hormones and enzymes; and lymphocyte activation and proliferation. Cyclic adenosine diphosphate ribose (cADPR) is an endogenous Ca(2+) mobilizing nucleotide present in many cell types and species, from plants to animals. cADPR is formed by ADP-ribosyl cyclases from nicotinamide adenine dinucleotide. The main ADP-ribosyl cyclase in mammals is CD38, a multi-functional enzyme and a type II membrane protein. It has been shown that many extracellular stimuli can induce cADPR production that leads to calcium release or influx, establishing cADPR as a second messenger. cADPR has been linked to a wide variety of cellular processes, but the molecular mechanisms regarding cADPR signaling remain elusive. The aim of this review is to summarize the CD38/cADPR/Ca(2+) signaling pathway, focusing on the recent advances involving the mechanism and physiological functions of cADPR-mediated Ca(2+) mobilization.
The role of nitric oxide in low level light therapy (2008)

The use of low levels of visible or near infrared light for reducing pain, inflammation and edema, promoting healing of wounds, deeper tissues and nerves, and preventing tissue damage by reducing cellular apoptosis has been known for almost forty years since the invention of lasers. Despite many reports of positive findings from experiments conducted in vitro, in animal models and in randomized controlled clinical trials, LLLT remains controversial. Firstly the biochemical mechanisms underlying the positive effects are incompletely understood, and secondly the complexity of choosing amongst a large number of illumination parameters has led to the publication of a number of negative studies as well as many positive ones. This review will focus on the role of nitric oxide in the cellular and tissue effects of LLLT. Red and near-IR light is primarily absorbed by cytochrome c oxidase (unit four in the mitochondrial respiratory chain). Nitric oxide produced in the mitochondria can inhibit respiration by binding to cytochrome c oxidase and competitively displacing oxygen, especially in stressed or hypoxic cells. If light absorption displaced the nitric oxide and thus allowed the cytochrome c oxidase to recover and cellular respiration to resume, this would explain many of the observations made in LLLT. Why the effect is only seen in hypoxic, stressed or damaged cells or tissues? How the effects can keep working for some time (hours or days) postillumination? Why increased NO concentrations are sometimes measured in cell culture or in animals? How blood flow can be increased? Why angiogenesis is sometimes increased after LLLT in vivo?
Complete cDNA sequence encoding the B subunit of human factor XIII (1990)

Journal Article Complete cDNA sequence encoding the B subunit of human factor XIII Get access Ulrich Grundmann, Ulrich Grundmann Department of Molecular Biology, Research Institutes, Behringwerke AGPostfach 1140, 3550 Marburg, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Claudia Nerlich, Claudia Nerlich Department of Molecular Biology, Research Institutes, Behringwerke AGPostfach 1140, 3550 Marburg, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Thomas Rein, Thomas Rein Department of Molecular Biology, Research Institutes, Behringwerke AGPostfach 1140, 3550 Marburg, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Gerd Zettlmeissl Gerd Zettlmeissl Department of Molecular Biology, Research Institutes, Behringwerke AGPostfach 1140, 3550 Marburg, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 9, 11 May 1990, Pages 2817–2818, https://doi.org/10.1093/nar/18.9.2817 Published: 01 May 1990 Article history Received: 19 March 1990 Published: 01 May 1990
Photophysics of Nanometer Sized Metal Particles:  Electron−Phonon Coupling and Coherent Excitation of Breathing Vibrational Modes (2000)

The wide variety of applications of metal nanoparticles has motivated many studies of their properties. Some important practical issues are how the size, composition and structure of these materials affect their catalytic and optical properties. In this article we review our recent work on the photophysics of metal nanoparticles. The systems that have been investigated include Au particles with sizes ranging from 2 nm diameter (several hundred atoms) to 120 nm diameter, and bimetallic core−shell particles composed of Au, Ag, Pt and/or Pb. These particles, which have a rather narrow size distribution, are prepared by radiolytic techniques. By performing time-resolved laser measurements we have been able to investigate the coupling between the electrons and phonons in the particles, and their low frequency “breathing” modes. These experiments show that for Au the time scale for electron−phonon coupling does not depend on size, in contrast to metals such as Ga and Ag. On the other hand, the frequency of the acoustic breathing modes strongly depends on the size of the particles, as well as their composition. These modes are impulsively excited by the rapid lattice heating that accompanies ultrafast laser excitation. The subsequent coherent nuclear motion modulates the transmitted probe laser intensity, giving a “beat” signal in our experiments. Unlike quantum-beats in molecules or semiconductors, this signal can be completely understood by classical mechanics.
Bioactive marine metabolites. 33. Cyclotheonamides, potent thrombin inhibitors, from a marine sponge Theonella sp (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBioactive marine metabolites. 33. Cyclotheonamides, potent thrombin inhibitors, from a marine sponge Theonella spNobuhiro Fusetani, Shigeki Matsunaga, Hisao Matsumoto, and Yukihiro TakebayashiCite this: J. Am. Chem. Soc. 1990, 112, 19, 7053–7054Publication Date (Print):September 1, 1990Publication History Published online1 May 2002Published inissue 1 September 1990https://pubs.acs.org/doi/10.1021/ja00175a045https://doi.org/10.1021/ja00175a045research-articleACS PublicationsRequest reuse permissionsArticle Views708Altmetric-Citations216LEARN 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 (1)»Supporting Information Supporting Information Get e-Alerts
Functional Production of a Soluble and Secreted Single-Chain Antibody by a Bacterial Secretion System (2014)

Single-chain variable fragments (scFvs) serve as an alternative to full-length monoclonal antibodies used in research and therapeutic and diagnostic applications. However, when recombinant scFvs are overexpressed in bacteria, they often form inclusion bodies and exhibit loss of function. To overcome this problem, we developed an scFv secretion system in which scFv was fused with osmotically inducible protein Y (osmY), a bacterial secretory carrier protein, for efficient protein secretion. Anti-EGFR scFv (aEGFR) was fused with osmY (N-and C-termini) and periplasmic leader sequence (pelB) to generate aEGFR-osmY, osmY-aEGFR, and pelB-aEGFR (control), respectively. In comparison with the control, both the osmYfused aEGFR scFvs were soluble and secreted into the LB medium. Furthermore, the yield of soluble aEGFR-osmY was 20fold higher, and the amount of secreted protein was 250-fold higher than that of osmY-aEGFR. In addition, the antigenbinding activity of both the osmY-fused aEGFRs was 2-fold higher than that of the refolded pelB-aEGFR from inclusion bodies. Similar results were observed with aTAG72-osmY and aHer2-osmY. These results suggest that the N-terminus of osmY fused with scFv produces a high yield of soluble, functional, and secreted scFv, and the osmY-based bacterial secretion system may be used for the large-scale industrial production of low-cost aEGFR protein.
Polyglutamine length-dependent interaction of Hsp40 and Hsp70 family chaperones with truncated N-terminal huntingtin: their role in suppression of aggregation and cellular toxicity (2000)

Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by polyglutamine expansion in the disease protein, huntingtin. In HD patients and transgenic mice, the affected neurons form characteristic ubiquitin-positive nuclear inclusions (NIs). We have established ecdysone-inducible stable mouse Neuro2a cell lines that express truncated N-terminal huntingtin (tNhtt) with different polyglutamine lengths which form both cytoplasmic and nuclear aggregates in a polyglutamine length- and inducer dose-dependent manner. Here we demonstrate that newly synthesized polyglutamine-expanded truncated huntingtin interacts with members of Hsp40 and Hsp70 families of chaperones in a polyglutamine length-dependent manner. Of these interacting chaperones, only Hdj-2 and Hsc70 frequently (Hdj-2 > Hsc70) co-localize with both the aggregates in the cellular model and with the NIs in the brains of HD exon 1 transgenic mice. However, Hdj-2 and Hsc70 do not co-localize with cytoplasmic aggregates in the brains of transgenic mice despite these chaperones being primarily localized in the cytoplasmic compartment. This strongly suggests that the chaperone interaction and their redistribution to the aggregates are two completely different phenomena of the cellular unfolded protein response. This unfolded protein response is also evident from the dramatic induction of Hsp70 on expression of polyglutamine-expanded protein in the cellular model. Transient overexpression of either Hdj-1 or Hsc70 suppresses the aggregate formation; however, suppression efficiency is much higher in Hdj-1 compared with Hsc70. Overexpression of Hdj-1 and Hsc70 is also able to protect cell death caused by polyglutamine-expanded tNhtt and their combination proved to be most effective.
Intraocular lens calculations after refractive surgery (2005)

For IOL power selection in previously myopic patients, a predictive formula to calculate IOL power based only on the pre-refractive surgery SEQ(m) and current flattest keratometry readings was not statistically different from IOL(exact). The IOL(HisKs), which was also not statistically different from IOL(exact), requires pre-refractive surgery keratometry readings that are often not available to the cataract surgeon.
Sézary T-cell-activating factor induces functional interleukin 2 receptors on T-cells derived from patients with Sézary syndrome. (1993)

Sézary syndrome is the leukemic form of cutaneous T-cell lymphoma characterized by circulating neoplastic CD4+ T-cells. Although peripheral blood mononuclear cells from patients with Sézary syndrome have been shown to respond poorly to mitogens, we found that mitogen-activated peripheral blood mononuclear cells from four of five patients with Sézary syndrome produce a 28 kDa protein termed Sézary T-cell activating factor (SAF). SAF renders nonproliferating "resting" T-cells from leukemic patients or healthy donors responsive to interleukin 2 in the absence of a costimulator. We demonstrate that SAF induces functional, high-affinity interleukin 2 receptors on T-cells from Sézary syndrome patients and provide evidence that SAF may be a novel cytokine.
Imaging thermally damaged tissue by Polarization Sensitive Optical Coherence Tomography (1998)

Polarization Sensitive Optical Coherence Tomography (PS- OCT) was used to image the reduction of birefringence in biological tissue due to thermal damage. Through simultaneous detection of the amplitude of signal fringes in orthogonal polarization states formed by interference of light backscattered from turbid media and a mirror in the reference arm of a Michelson interferometer, changes in the polarization due to the optical phase delay between light propagating along the fast and slow axes of birefringent media were measured. Inasmuch as fibrous structures in many biological tissues in uence the polarization state of light backscattered, PS-OCT is a potentially useful technique to image the structural properties of turbid biological materials. Birefringence of collagen, a constituent of many biological tissues, is reduced by denaturation that takes place at a temperature between 56-65 0 C, thus providing an "optical marker" for thermal damage. Images showing reduction of birefringence due to thermal damage in porcine tendon and skin are presented and demonstrate the potential of PS-OCT for burn depth assessment.
Face Recognition Based on Gabor Feature Extraction and Fractal Coding (2010)

A face recognition method that based on Gabor wavelet transform and fractal is proposed, Since Gabor feature is robust to illumination and expression variations and has been successfully used in face recognition area. First, the proposed method decomposes the normalized face image by convolving the face image with multi-scale and multi-orientation Gabor filters to extract their corresponding Gabor magnitude maps. Then, link each piece of Gabor feature image according to rows and columns, and wavelet transform is used in these linked Gabor feature image for dimensionality reduction, finally, fractal code is calculated in dimension reduction of Gabor feature image. Experiments show the new method works well.
흑지마(黑芝麻)가 Leydig cell의 항산화에 미치는 영향 (2011)

Objectives: The purpose of this study was to estimate the antioxidant activity of Sesami Semen Nigrum extract (SSN) on mouse Leydig cells, TM3. Methods: Cell viability assays were performed. The protective effects of SSN against hydrogen peroxide-induced oxidative stress in Leydig cells were examined by measuring cell viability. Lipid peroxidation levels and antioxidant enzyme concentrations such as SOD and catalase were measured. Results: Cell viability of Leydig cells increased with SSN concentration. Cell viability of Leydig cells was 136.66% when SSN concentration was 50 μg/ml. Cell viability of the hydrogen peroxide group was statistically decreased (p<0.01) compared with the control group. Antioxidant effect of SSN was measured and the protective effect of SSN concentration were 5, 10, 50 μg/ml. LPO were decreased significantly at 5, 50 μg/ml of SSN concentrations. SOD activity was increased at 1, 10, 50 ug/ml of SSN concentrations. Catalase activity was significantly increased at 123.7, 133.3 and 131.9 units/mg protein when SSN concentrations were 5, 10 and 50 μg/ml, respectively. Conclusions: In conclusion, Sesami Semen Nigrum extract has antioxidant activities in Leydig cells against oxidative stress.