gebhart/patrepeval huggingface dataset:
The effects of temperature and pH on the growth of yeast species during the fermentation of grape juice (1988)

The effects of temperature and pH on the survival and growth of Saccharomyces cerevisiae, Kloeckera apiculata, Candida stellata, Candida krusei, Candida pulcherrima and Hansenula anomala were examined during mixed culture in grape juice. At 25°C, pH 3.0 and pH 3.5, S. cerevisiae dominated the fermentation and the other species died off before fermentation was completed. Saccharomyces cerevisiae also dominated the fermentation at 20°C but there was increased growth and survival of the other species. At 10°C the fermentation was dominated by the growth of both S. cerevisiae and K. apiculata and there was extended growth and survival of C. stellata and C. krusei. Juices fermented at 10°C exhibited ethanol concentrations between 7.4 and 13.4% and populations of K. apiculata, C. stellata and C. krusei in the range 10 6 ‐10 8 cells/ml. However, these species produced maximum ethanol concentrations in the range 2.7–6.6% when grown as single cultures in grape juice.
MagNet: a Two-Pronged Defense against Adversarial Examples (2017)

Deep learning has shown promising results on hard perceptual problems in recent years. However, deep learning systems are found to be vulnerable to small adversarial perturbations that are nearly imperceptible to human. Such specially crafted perturbations cause deep learning systems to output incorrect decisions, with potentially disastrous consequences. These vulnerabilities hinder the deployment of deep learning systems where safety or security is important. Attempts to secure deep learning systems either target specific attacks or have been shown to be ineffective. In this paper, we propose MagNet, a framework for defending neural network classifiers against adversarial examples. MagNet does not modify the protected classifier or know the process for generating adversarial examples. MagNet includes one or more separate detector networks and a reformer network. Different from previous work, MagNet learns to differentiate between normal and adversarial examples by approximating the manifold of normal examples. Since it does not rely on any process for generating adversarial examples, it has substantial generalization power. Moreover, MagNet reconstructs adversarial examples by moving them towards the manifold, which is effective for helping classify adversarial examples with small perturbation correctly. We discuss the intrinsic difficulty in defending against whitebox attack and propose a mechanism to defend against graybox attack. Inspired by the use of randomness in cryptography, we propose to use diversity to strengthen MagNet. We show empirically that MagNet is effective against most advanced state-of-the-art attacks in blackbox and graybox scenarios while keeping false positive rate on normal examples very low.
SMAD Proteins Transactivate the Human ApoCIII Promoter by Interacting Physically and Functionally with Hepatocyte Nuclear Factor 4 (2000)

Cotransfection of HepG2 cells with SMADs established that SMAD3 and SMAD3-SMAD4 transactivated (15-70-fold) the -890/+24 apoCIII promoter and shorter promoter segments, whereas cotransfection with a dominant negative SMAD4 mutant repressed the apoCIII promoter activity by 50%, suggesting that SMAD proteins participate in apoCIII gene regulation. Transactivation required the presence of a hormone response element, despite the fact that SMADs could not bind directly to it. Cotransfection of SMAD3-SMAD4 along with hepatocyte nuclear factor-4 resulted in a strong synergistic transactivation of the -890/+24 apoCIII promoter, proximal promoter segments, or synthetic promoters containing either the apoCIII enhancer or the proximal apoCIII hormone response element. Inhibition of endogenous hepatocyte nuclear factor-4 synthesis by an antisense ribozyme construct reduced the constitutive activity of the apoCIII promoter in HepG2 cells to 10% and abolished the SMAD-mediated transactivation. Co-immunoprecipitation and GST pull-down assays provided evidence for physical interactions between SMAD3, SMAD4, and hepatic nuclear factor-4. Our findings indicate that transforming growth factor beta and its signal transducer SMAD proteins can modulate gene transcription by novel mechanisms that involve their physical and functional interaction with hepatocyte nuclear factor-4, suggesting that SMAD proteins may play an important role in apolipoprotein gene expression and lipoprotein metabolism.
3-D Joint Inversion of Magnetic and Gravimetric Data With A Priori Information (1993)

An algorithm which allows the combined 3-D inversion of magnetic total field and gravimetric data is presented. Model parameters which include top and base of vertical rectangular prisms, susceptibility, remanent magnetization with its inclination and declination and density can be given as a priori information. The joint inversion serves to reduce the inherent ambiguity, mainly of gravimetric models, in cases when it can be assumed that a magnetic and a gravimetric anomaly are caused by the same source rock and, in general, allows a fast modelling of potential field data. Different synthetic examples are provided to show some of the possibilities that this algorithm offers. Finally, a couple of anomalies measured in southwestern Germany are modelled using this algorithm.
The DNA-binding domain of two bZIP transcription factors, the Epstein-Barr virus switch gene product EB1 and Jun, is a bipartite nuclear targeting sequence (1993)

The Epstein-Barr virus BZLF1 gene product EB1 (also called ZEBRA and Zta), is a transcription factor belonging to the bZIP (basic domain leucine zipper) family of nuclear proteins. Translocation to the nucleus of EB1 (J. Becker, U. Leser, M. Marschall, A. Langford, W. Jilg, H. Gelderblom, P. Reichart, and H. Wolf, Proc. Natl. Acad. Sci. USA 88:8332-8336, 1991) and of two other bZIP proteins, c-Jun and c-Fos (P. Roux, J.-M. Blanchard, A. Fernandez, N. Lamb, P. Jeanteur, and M. Piechaczyk, Cell 63:341-351, 1990), has been shown to be subject to regulation. We show here that for both EB1 and Jun the nuclear targeting signals (NTS) in the proteins' primary sequences are two clusters of positively charged amino acids. These clusters, called BRA and BRB, are necessary and sufficient to direct beta-galactosidase to the nuclear compartment and act as a bipartite NTS. They are conserved among all the bZIP proteins, and although they are not identical, they probably share the same function. Site-directed mutagenesis studies made on these basic clusters suggest that they also act as a bipartite NTS in the EB1 protein. Our results also demonstrate that in EB1 and Jun, these bipartite NTS are superimposed with bipartite DNA-binding domains, since BRA and BRB are required in vitro for direct and specific contact between these proteins and their DNA-binding sites.
Genotypic Differences in Dengue Virus Neutralization Are Explained by a Single Amino Acid Mutation That Modulates Virus Breathing (2015)

The global burden of dengue virus (DENV) is growing, with recent estimates of ~390 million human infections each year. Antibodies play a crucial role in protection from DENV infection, and vaccines that elicit a robust antibody response are being actively pursued. We report here the identification of a single amino acid residue in the envelope protein of DENV serotype 1 that results in global changes to virus structure and stability when it is changed. Our results indicate that naturally occurring variation at this particular site among virus strains impacts the ensemble of structures sampled by the virus, a process referred to as virus breathing. The finding that such limited and conservative sequence changes can modulate the landscape available for antibody binding has important implications for both vaccine development and the study of DENV-reactive antibodies.
HER2 therapy: Molecular mechanisms of trastuzumab resistance (2006)

Trastuzumab is a monoclonal antibody targeted against the HER2 tyrosine kinase receptor. The majority of patients with metastatic breast cancer who initially respond to trastuzumab develop resistance within one year of treatment initiation, and in the adjuvant setting 15% of patients still relapse despite trastuzumab-based therapy. In this review, we discuss potential mechanisms of antitumor activity by trastuzumab, and how these mechanisms become altered to promote therapeutic resistance. We also discuss novel therapies that may improve the efficacy of trastuzumab, and that offer hope that the survival of breast cancer patients with HER2-overexpressing tumors can be vastly improved.
Analysis of Redox Additive‐Based Overcharge Protection for Rechargeable Lithium Batteries (1991)

The overcharge condition in secondary lithium batteries employing redox additives for overcharge protection, has been theoretically analyzed in terms of a finite linear diffusion model. The analysis leads to expressions relating the steady‐state overcharge current density and cell voltage to the concentration, diffusion coefficient, standard reduction potential of the redox couple, and interelectrode distance. The model permits the estimation of the maximum permissible overcharge rate for any chosen set of system conditions. Digital simulation of the overcharge experiment leads to numerical representation of the potential transients, and estimate of the influence of diffusion coefficient and interelectrode distance on the transient attainment of the steady state during overcharge. The model has been experimentally verified using 1,1'‐dimethylferrocene as a redox additive. The analysis of the experimental results in terms of the theory allows the calculation of the diffusion coefficient and the formal potential of the redox couple. The model and the theoretical results may be exploited in the design and optimization of overcharge protection by the redox additive approach.
DNA aptamer–micelle as an efficient detection/delivery vehicle toward cancer cells (2009)

We report the design of a self-assembled aptamer-micelle nanostructure that achieves selective and strong binding of otherwise low-affinity aptamers at physiological conditions. Specific recognition ability is directly built into the nanostructures. The attachment of a lipid tail onto the end of nucleic acid aptamers provides these unique nanostructures with an internalization pathway. Other merits include: extremely low off rate once bound with target cells, rapid recognition ability with enhanced sensitivity, low critical micelle concentration values, and dual-drug delivery pathways. To prove the potential detection/delivery application of this aptamer-micelle in biological living systems, we mimicked a tumor site in the blood stream by immobilizing tumor cells onto the surface of a flow channel device. Flushing the aptamer-micelles through the channel demonstrated their selective recognition ability under flow circulation in human whole-blood sample. The aptamer-micelles show great dynamic specificity in flow channel systems that mimic drug delivery in the blood system. Therefore, our DNA aptamer-micelle assembly has shown high potential for cancer cell recognition and for in vivo drug delivery applications.
Exogenous substrate preference of the post-ischaemic myocardium (1986)

Myocardial exogenous substrate preference was studied under conditions of increased plasma lactate concentration before and after a severe (halving of tissue ATP concentration, sixfold increase in tissue lactate concentration) but reversible (less than 1% necrosis on reperfusion) global ischaemic stress produced by continuous hypothermic electromechanical arrest of the heart of four hours' duration by aortic cross clamping and multidose potassium cardioplegia. Fatty acid oxidation was studied using 1-14C-palmitate under steady state conditions and under similar isovolumic fixed pressure conditions with the heart at a constant rate using a left ventricular intracavitary balloon. Exogenous free fatty acid oxidation during the pre-ischaemic period with an increased lactate concentration (3.9-5.8 mmol . litre-1) was 0.62(0.21) mumol . min-1 X 100 g-1 (mean (SEM)). This represented a mean of 32% of the total carbon dioxide produced in contrast to a post-ischaemia free fatty oxidation rate of 2.67(0.87) mumol . min-1 X 100 g-1, in the presence of even further increased plasma lactate concentrations (8.47-11.17 mmol . litre-1), representing a mean of 82% of the total carbon dioxide output. These data suggest that the substrate preference of the myocardium, under conditions of increased plasma lactate concentration, shifts to greater oxidation of exogenous free fatty acids after ischaemic stress.
c-fos gene transcription in murine macrophages is modulated by a calcium-dependent block to elongation in intron 1. (1991)

Cultured mouse thioglycolate-elicited peritoneal macrophages exhibit a strong block to transcriptional elongation beyond the end of the c-fos gene first exon. This block is absent in freshly isolated peritoneal cells, appears slowly during culture, and does not require adherence of the cells. The extent of this block is largely responsible for the levels of c-fos mRNA in cultured macrophages, even after modulation by agents such as the tumor promoter phorbol myristate acetate and increased intracellular cyclic AMP, which also increase the activity of the c-fos promoter. When macrophages are cultured in the absence of mobilizable calcium, the block can no longer be relieved by any inducing agent. Conversely, upon calcium influxes, there is little alteration in the level of transcriptional initiation, but transcription proceeds efficiently through the entire c-fos locus. These results suggest the presence of an intragenic calcium-responsive element in the c-fos gene and illustrate its key role in the control of c-fos gene transcription.
Removal of neutralized model parvoviruses and enteroviruses in human IgG solutions by nanofiltration (2002)

These results indicate that viruses with bound antibodies are efficiently eliminated by nanofiltration by use of filters having nominal pore sizes larger than the diameter of the respective free virions.
Stages of embryonic development of the zebrafish (1995)

We describe a series of stages for development of the embryo of the zebrafish, Danio (Brachydanio) rerio. We define seven broad periods of embryogenesis--the zygote, cleavage, blastula, gastrula, segmentation, pharyngula, and hatching periods. These divisions highlight the changing spectrum of major developmental processes that occur during the first 3 days after fertilization, and we review some of what is known about morphogenesis and other significant events that occur during each of the periods. Stages subdivide the periods. Stages are named, not numbered as in most other series, providing for flexibility and continued evolution of the staging series as we learn more about development in this species. The stages, and their names, are based on morphological features, generally readily identified by examination of the live embryo with the dissecting stereomicroscope. The descriptions also fully utilize the optical transparancy of the live embryo, which provides for visibility of even very deep structures when the embryo is examined with the compound microscope and Nomarski interference contrast illumination. Photomicrographs and composite camera lucida line drawings characterize the stages pictorially. Other figures chart the development of distinctive characters used as staging aid signposts.
Stabilization of the Tau Exon 10 Stem Loop Alters Pre-mRNA Splicing (2006)

Neurofibrillary tangles containing filaments of the microtubule-associated protein tau are found in a variety of neurodegenerative diseases. Mutations in the tau gene itself cause frontotemporal dementia with parkinsonism, demonstrating the critical role of tau in pathogenesis. Many of these mutations in tau are silent, are found at the 5'-splice site of exon 10, and lead to increased inclusion of exon 10. These silent mutations are predicted to destabilize a stem loop structure at the exon 10 5'-splice site; however, the existence of this stem loop under physiological conditions and its role in splice regulation are controversial. Here we show that base changes that stabilize this stem loop in vitro substantially decrease exon 10 inclusion in a wild type tau minigene and rescue the increase in exon 10 splicing caused by a dementia-causing point mutation. Moreover, we probed the intracellular structure of the tau stem loop with antisense RNA and demonstrate that the stability of the stem loop dictates antisense effectiveness. Together these results validate the stem loop as a bona fide structure regulating tau exon 10 splicing.
A Novel Protein with Homology to the Junctional Adhesion Molecule (2000)

We have cloned a novel cDNA belonging to the Ig superfamily that shows 44% similarity to the junctional adhesion molecule (JAM) and maps to chromosome 21q21.2. The open reading frame of JAM2 predicts a 34-kDa type I integral membrane protein that features two Ig-like folds and three N-linked glycosylation sites in the extracellular domain. A single protein kinase C phosphorylation consensus site and a PDZ-binding motif are present in the short intracellular tail. Heterologous expression of JAM2 in Chinese hamster ovary cells defined a 48-kDa protein that localizes predominantly to the intercellular borders. Northern blot analysis showed that JAM2 is preferentially expressed in the heart. JAM2 homotypic interactions were demonstrated by the ability of JAM2-Fc to capture JAM2-expressing Chinese hamster ovary cells. We further showed that JAM2, but not JAM1, is capable of adhering to the HSB and HPB-ALL lymphocyte cell lines. Neutralizing mouse anti-JAM2 polyclonal antibodies provided evidence against homotypic interactions in this assay. Biotinylation of HSB cell membranes revealed a 43-kDa counter-receptor that precipitates specifically with JAM2-Fc. These characteristics of JAM2 led us to hypothesize a role for this novel protein in adhesion events associated with cardiac inflammatory conditions.
Gate-capacitance characteristics of deep-submicron LATID (large-angle-tilt implanted drain) MOSFETs (2002)

Gate-capacitance characteristics for LATID (large-angle-tilt implanted drain) devices are studied using high-resolution measurements and device simulation. As compared with single-S/D (source/drain), a deep-submicron LATID FET, developed to introduce sidewall spacers for reducing overlap length to approximately 0.09 mu m, is found to suppress gate-to-drain capacitance C/sub GD/ at 3.3 V operation by approximately 40%, to almost the same level as LDDs (lightly doped drains), while a LATID without spacers suffers from a >25% larger C/sub GD/. To suppress C/sub GD/, offsetting the n/sup +/ region by spacers is crucial, while the n/sup -/ region should remain fully overlapped with the gate to improve current drivability. Following this design guideline, the circuit speed of LATID can be improved by approximately 15% compared to LDDs. The deep-submicron LATID technology, with spacers, is promising for high-speed ULSI circuits.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comparative Study of Si, Ge and InAs based Steep SubThreshold Slope Tunnel Transistors for 0.25V Supply Voltage Logic Applications (2008)

This paper examines the potential of double gate (DG) inter-band tunnel FETs (TFET) in 3 different material systems, Si, Ge and InAs, for logic circuit applications down to 0.25 V supply voltage (V<sub>CC</sub>). Based on two-dimensional numerical drift-diffusion simulations, we show that 30 nm gate length (LG) InAs (indium arsenide) based TFETs can achieve I<sub>on</sub>/I<sub>off</sub> of >4x10<sup>4</sup> with <1 ps intrinsic delay at 0.25 V V<sub>CC</sub>. The key features of the InAs TFETs are: (a) asymmetric source drain design to suppress the ambipolar leakage (b) use of a lower dielectric constant gate oxide (non high-K) and (c) high source side injection velocity at moderate electric fields. Thus, narrow bandgap semiconductor based DG TFETs provide a promising device option for ultra-low standby and dynamic power high-speed logic circuits operating under quarter volt supply voltages.
Homozygous loss of the cyclin-dependent kinase 4-inhibitor (p16) gene in human leukemias (1994)

Recently, it has been shown that the homozygous deletion of the cyclin-dependent kinase-4 inhibitor (CDK4I;p16) gene, which is mapped to chromosome 9p21, is frequently observed in a wide spectrum of human cancers, including leukemias. Therefore, the CDK4I gene is thought to be a putative tumor-suppressor gene. We report here that both alleles of the CDK4I gene were completely or partially deleted in human leukemia cells derived from both patients and established cell lines. Thirty-seven hematopoietic cell lines and samples from 72 patients with leukemias were examined for homozygous loss of the CDK4I gene locus by Southern blot analysis. We found that a part or the whole of the CDK4I gene was homozygously deleted in 14 of the 37 (38%) cell lines and 4 of 72 (6%) samples from leukemia patients, including 45 with acute myelocytic leukemia, 14 with acute lymphocytic leukemia (ALL), and 13 with chronic myelocytic leukemia in blastic crisis. In the cell lines, the homozygous deletion of the CDK4I gene was detected in a variety of cell lineages, whereas all 4 cases showing the homozygous deletion were confined to ALL. It should be noted that 2 of them had no cytogenetic abnormalities of chromosome 9. Our results suggest that loss of the CDK4I function may contribute to immortalization of human leukemia cells and play a causative role at least in development of human lymphocytic leukemias.
Anomalously increased effective thermal conductivities of ethylene glycol-based nanofluids containing copper nanoparticles (2001)

It is shown that a “nanofluid” consisting of copper nanometer-sized particles dispersed in ethylene glycol has a much higher effective thermal conductivity than either pure ethylene glycol or ethylene glycol containing the same volume fraction of dispersed oxide nanoparticles. The effective thermal conductivity of ethylene glycol is shown to be increased by up to 40% for a nanofluid consisting of ethylene glycol containing approximately 0.3 vol % Cu nanoparticles of mean diameter &amp;lt;10 nm. The results are anomalous based on previous theoretical calculations that had predicted a strong effect of particle shape on effective nanofluid thermal conductivity, but no effect of either particle size or particle thermal conductivity.
Department of Surgery (2006)

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