gebhart/patrepeval huggingface dataset:
Characterization of cell wall proteins of yeast and hydrophobic mycelial cells of Candida albicans (1991)

Cell surface hydrophobicity (CSH) of blastoconidia and blastoconidia bearing germ tubes of Candida albicans ATCC 26555 was monitored by assessing attachment of polystyrene microspheres to the cell surface, and we found that mature hyphae were significantly hydrophobic. Treatment of intact cells with low concentrations of beta-glucanase (Zymolyase 20T) or proteases abolished or significantly reduced attachment of latex beads to hyphae. This effect paralleled an obvious reduction in CSH of the entire cell population, as measured by an aqueous-hydrocarbon biphasic partitioning assay. Analysis of the cell wall material released by Zymolyase and adsorbed on polystyrene microspheres indicated that germ tube-specific cell wall proteins and mannoproteins with apparent molecular masses of 20 to 67 kDa may be responsible for the hydrophobicity of hyphae. Zymolyase released from blastoconidia cell walls a different set of proteins and mannoproteins that were able to adsorb to polystyrene microbeads. Such molecular species might in turn be responsible for the CSH exhibited by blastoconidium populations as determined by the biphasic partitioning assay, although these probably hydrophobic components can be masked on the surface of blastoconidia, as the latter had no or very few latex microspheres attached to their surfaces. Treatment of cells of both C. albicans morphologies with 2-mercaptoethanol released qualitatively distinct species of polystyrene-adsorbed proteins and mannoproteins from yeast and mycelial cells. These observations suggested that hydrophobic proteins and mannoproteins that could be associated with CSH are bound to the cell wall structure through diverse types of linkages.
Molecular Characterization of a Type I Quantitative Factor V Deficiency in a Thrombosis Patient that Is “Pseudo Homozygous” for Activated Protein C Resistance (1997)

Resistance to activated protein C (APC), which is associated with the FV Leiden mutation in the large majority of the cases, is the most common genetic risk factor for thrombosis. Several laboratory tests have been developed to detect the APC-resistance phenotype. The result of the APC-resistance test (APC-sensitivity ratio, APC-SR) usually correlates well with the FV Leiden genotype, but recently some discrepancies have been reported. Some thrombosis patients that are heterozygous for FV Leiden show an APC-SR usually found only in homozygotes for the defect. Some of those patients proved to be compound heterozygotes for the FV Leiden mutation and for a type I quantitative factor V deficiency. We have investigated a thrombosis patient characterized by an APC-SR that would predict homozygosity for FV Leiden. DNA analysis showed that he was heterozygous for the mutation. Sequencing analysis of genomic DNA revealed that the patient also is heterozygous for a G5509-->A substitution in exon 16 of the factor V gene. This mutation interferes with the correct splicing of intron 16 and leads to the presence of a null allele, which corresponds to the "non-FV Leiden" allele. The conjunction of these two defects in the patient apparently leads to the same phenotype as observed in homozygotes for the FV Leiden mutation.
Design recovery for maintenance and reuse (1989)

Software maintenance and harvesting reusable components from software both require that an analyst reconstruct the software's design. Design recovery recreates design abstractions from a combination of code, existing design documentation (if available), personal experience and general knowledge about problem and application domains. The author shows how to extend the automated assistance available to the software engineer for this process. He explains the concept of design recovery, proposes an architecture to implement the concept, illustrates how the architecture operates, describes progress toward implementing it, and compares this work with other similar work such as reverse engineering and program understanding. Much of the discussion is based on a model-based design recovery system called Desire.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Epac/Rap1 pathway regulates microvascular hyperpermeability induced by PAF in rat mesentery (2008)

Experiments in cultured endothelial cell monolayers demonstrate that increased intracellular cAMP strongly inhibits the acute permeability responses by both protein kinase A (PKA)-dependent and -independent pathways. The contribution of the PKA-independent pathways to the anti-inflammatory mechanisms of cAMP in intact mammalian microvessels has not been systematically investigated. We evaluated the role of the cAMP-dependent activation of the exchange protein activated by cAMP (Epac), a guanine nucleotide exchange factor for the small GTPase Rap1, in rat venular microvessels exposed to the platelet-activating factor (PAF). The cAMP analog 8-pCPT-2'-O-methyl-cAMP (O-Me-cAMP), which stimulates the Epac/Rap1 pathway but has no effect on PKA, significantly attenuated the PAF increase in microvessel permeability as measured by hydraulic conductivity (Lp). We also demonstrated that PAF induced a rearrangement of vascular endothelial (VE)-cadherin seen as numerous lateral spikes and frequent short breaks in the otherwise continuous peripheral immunofluorescent label. Pretreatment with O-Me-cAMP completely prevented the PAF-induced rearrangement of VE-cadherin. We conclude that the action of the Epac/Rap1 pathway to stabilize cell-cell adhesion is a significant component of the activity of cAMP to attenuate an acute increase in vascular permeability. Our results indicate that increased permeability in intact microvessels by acute inflammatory agents such as PAF is the result of the decreased effectiveness of the Epac/Rap1 pathway modulation of cell-cell adhesion.
Developing next generation of electric grids for fulfilling deficiencies of conventional grids in supporting today's requirements (2011)

From the initial days of establishment of power system in the late 20 century up to now, no fundamental improvement has been taken place in power distribution systems; on the other hand many innovations have taken place in both demand and generation sides of power systems. These innovations have introduced new requirements which electric grids should be able to support. The majority of these innovations have held during recent decades. All these have made conventional electric grids somehow deficient. Our aim of this presentation is to develop the next generation of electric grids which fulfills conventional grids and support all new requirements. So at first we investigate innovations and also new requirements which conventional electric grids are not able to support. Then we obtain semantics which next generation of electric grids should be able to support. For implementation of these semantics some infrastructures should be developed, the result is obtaining required pragmatic functions. Finally we investigate achievements. These achievements satisfy the requirements that we introduced firstly which today's grids should be able to support.
Slurry reactor design studies (1990)

The objective of these studies was to perform a realistic evaluation of the relative costs of tublar-fixed-bed and slurry reactors for methanol, mixed alcohols and Fischer-Tropsch syntheses under conditions where they would realistically be expected to operate. The slurry Fischer-Tropsch reactor was, therefore, operated at low H{sub 2}/CO ratio on gas directly from a Shell gasifier. The fixed-bed reactor was operated on 2.0 H{sub 2}/CO ratio gas after adjustment by shift and CO{sub 2} removal. Every attempt was made to give each reactor the benefit of its optimum design condition and correlations were developed to extend the models beyond the range of the experimental pilot plant data. For the methanol design, comparisons were made for a recycle plant with high methanol yield, this being the standard design condition. It is recognized that this is not necessarily the optimum application for the slurry reactor, which is being proposed for a once-through operation, coproducing methanol and power. Consideration is also given to the applicability of the slurry reactor to mixed alcohols, based on conditions provided by Lurgi for an Octamix{trademark} plant using their standard tubular-fixed reactor technology. 7 figs., 26 tabs.
Pea leaf mitochondrial pyruvate dehydrogenase complex is inactivated in vivo in a light-dependent manner. (1990)

We examined the effect of light on the activity of the mitochondrial pyruvate dehydrogenase complex (mt-PDC) by using intact green pea (Pisum sativum) seedlings. Upon illumination there is an initial drop in mtPDC activity followed by oscillations that dampen during the initial period of photosynthesis to a steady-state level of one-fourth or less of the mtPDC activity measured in the dark. The initial light-dependent decrease in mtPDC activity is inhibited by 3-(3,4-dichlorophenyl)-1,1-dimethylurea (an inhibitor of photosystem II of photosynthesis) and does not occur in etiolated seedlings. Therefore, the effect of light is indirect and most likely associated with photosynthesis and/or photorespiration. Conditions that would be unfavorable for photorespiration also inhibited the light-dependent decrease in mtPDC activity.
cDNA Cloning of Androgen-Stimulated mRNAs in Rat Seminal Vesicles: Partial Characterization of Newly Isolated cDNA Clones, pSv-1 and pSv-2. (1990)

As the first step in surveying the molecular mechanism of androgen-responsive gene expression in rat seminal vesicles, the effect of androgen on the mRNAs was examined by in vitro translation assay. When the in vitro translation products of mRNAs from castrated animals (48 h) were compared with those from castrated and testosterone-treated animals (48 h) by SDS-PAGE, several discrete bands which were stimulated or repressed in response to androgen were observed in addition to major peptide bands of SVS IV and SVS V. From these findings, we constructed a partial cDNA library from the seminal vesicle poly(A +)RNAs of androgen-treated rats and screened by differential colony hybridization. Two distinct cDNA clones, pSv-1 and pSv-2, whose mRNAs were differentially stimulated in response to androgen and seemed to be expressed specifically in the seminal vesicles, were isolated. pSv-1 and pSv-2 hybridized to mRNAs of 1,600 and 3,500 nucleotides in length, respectively. These cDNA sequences, newly isolated in the present study, may provide useful probes for the study of molecular mechanism of androgen-responsive gene expression.
Topology design optimization of dielectric substrates for bandwidth improvement of a patch antenna (2003)

Most literature studies dealing with design optimization for RF applications focused to a large extend on size and shape optimization. So far, material and topology optimization has not been pursued primarily due to the challenges associated with the fabrication of inhomogeneous materials and the limited access to analysis tools. In this paper, we focus on optimum topology/material design of dielectric substrates for bandwidth enhancement of a simple patch antenna. First, the possibility of designing arbitrary dielectric constant materials using off-the-shelf dielectrics is presented as is necessary for the practical fabrication of inhomogeneous substrates. Then, a formal design optimization procedure is conducted using the solid isotropic material with penalization (SIMP) method by relying on a fast full wave finite element-boundary integral (FE-BI) simulator. The SIMP method is a mathematically well-posed topology optimization algorithm because a continuous density function is used to relate the cell variable to the actual material properties. This also allows for a formulation in a versatile optimization framework. Sequential linear programming (SLP) is used to solve the nonlinear optimization procedure with the sensitivity analysis based on the adjoint variable method. An important advantage of the proposed design optimization approach is its generality to handle multiple objectives and multidisciplinary problems. Using the proposed automated design procedure, inhomogeneous substrates are designed which allow for 250% bandwidth enhancement of the square patch antenna. Typically, only a few iterations are needed to reach convergence. Finally, the designed substrate is post-processed with image processing and fabricated using thermoplastic green machining.
PGRMC1: a new biomarker for the estrogen receptor in breast cancer (2008)

Estrogen receptor (ER) status is a critical biomarker in breast cancer, in large part because the ER is the target of tamoxifen and similar drugs. In the previous issue of Breast Cancer Research, Neubauer and colleagues used a proteomic approach to identify proteins that are differentially regulated by ER in breast tumors. The authors showed that ER-negative tumors have elevated levels of PGRMC1 (progesterone receptor membrane component-1), a hormone receptor component and binding partner for P450 proteins. In contrast, PGRMC1 was phosphorylated in ER-positive tumors. The staining patterns of ER and PGRMC1 were mutually exclusive in breast tumor sections, and PGRMC1 staining was sharply increased in hypoxic areas of the tumor. The results suggest that PGRMC1 is a candidate biomarker for ER status and hypoxia in breast cancer.
Detecting error-related negativity for interaction design (2012)

This paper examines the ability to detect a characteristic brain potential called the Error-Related Negativity (ERN) using off-the-shelf headsets and explores its applicability to HCI. ERN is triggered when a user either makes a mistake or the application behaves differently from their expectation. We first show that ERN can be seen on signals captured by EEG headsets like Emotiv™ when doing a typical multiple choice reaction time (RT) task -- Flanker task. We then present a single-trial online ERN algorithm that works by pre-computing the coefficient matrix of a logistic regression classifier using some data from a multiple choice reaction time task and uses it to classify incoming signals of that task on a single trial of data. We apply it to an interactive selection task that involved users selecting an object under time pressure. Furthermore the study was conducted in a typical office environment with ambient noise. Our results show that online single trial ERN detection is possible using off-the-shelf headsets during tasks that are typical of interactive applications. We then design a Superflick experiment with an integrated module mimicking an ERN detector to evaluate the accuracy of detecting ERN in the context of assisting users in interactive tasks. Based on these results we discuss and present several HCI scenarios for use of ERN.
<i>PIN1</i> Is an E2F Target Gene Essential for <i>Neu</i>/<i>Ras</i>-Induced Transformation of Mammary Epithelial Cells (2002)

Oncogenes Neu/HER2/ErbB2 and Ras can induce mammary tumorigenesis via upregulation of cyclin D1. One major regulatory mechanism in these oncogenic signaling pathways is phosphorylation of serines or threonines preceding proline (pSer/Thr-Pro). Interestingly, the pSer/Thr-Pro motifs in proteins exist in two completely distinct cis and trans conformations, whose conversion is catalyzed specifically by the essential prolyl isomerase Pin1. By isomerizing pSer/Thr-Pro bonds, Pin1 can regulate the conformation and function of certain phosphorylated proteins. We have previously shown that Pin1 is overexpressed in breast tumors and positively regulates cyclin D1 by transcriptional activation and posttranslational stabilization. Moreover, in Pin1 knockout mice, mammary epithelial cells fail to undergo massive proliferation during pregnancy, as is the case in cyclin D1 null mice. These results indicate that Pin1 is upregulated in breast cancer and may be involved in mammary tumors. However, the mechanism of Pin1 overexpression in cancer and its significance in cell transformation remain largely unknown. Here we demonstrate that PIN1 expression is mediated by the transcription factor E2F and enhanced by c-Neu and Ha-Ras via E2F. Furthermore, overexpression of Pin1 not only confers transforming properties on mammary epithelial cells but also enhances the transformed phenotypes of Neu/Ras-transformed mammary epithelial cells. In contrast, inhibition of Pin1 suppresses Neu- and Ras-induced transformed phenotypes, which can be fully rescued by overexpression of a constitutively active cyclin D1 mutant that is refractory to the Pin1 inhibition. Thus, Pin1 is an E2F target gene that is essential for the Neu/Ras-induced transformation of mammary epithelial cells through activation of cyclin D1.
3D Morphology Prediction of Progressive Spinal Deformities from Probabilistic Modeling of Discriminant Manifolds (2017)

We introduce a novel approach for predicting the progression of adolescent idiopathic scoliosis from 3D spine models reconstructed from biplanar X-ray images. Recent progress in machine learning have allowed to improve classification and prognosis rates, but lack a probabilistic framework to measure uncertainty in the data. We propose a discriminative probabilistic manifold embedding where locally linear mappings transform data points from high-dimensional space to corresponding low-dimensional coordinates. A discriminant adjacency matrix is constructed to maximize the separation between progressive and non-progressive groups of patients diagnosed with scoliosis, while minimizing the distance in latent variables belonging to the same class. To predict the evolution of deformation, a baseline reconstruction is projected onto the manifold, from which a spatiotemporal regression model is built from parallel transport curves inferred from neighboring exemplars. Rate of progression is modulated from the spine flexibility and curve magnitude of the 3D spine deformation. The method was tested on 745 reconstructions from 133 subjects using longitudinal 3D reconstructions of the spine, with results demonstrating the discriminatory framework can identify between progressive and non-progressive of scoliotic patients with a classification rate of 81% and prediction differences of 2.1$^{o}$ in main curve angulation, outperforming other manifold learning methods. Our method achieved a higher prediction accuracy and improved the modeling of spatiotemporal morphological changes in highly deformed spines compared to other learning methods.
A 3-V 5.4-mW BiCMOS track & hold circuit with sampling frequency up to 150 MHz (1997)

A track & hold circuit to be used in front of a high-speed analog-to-digital converter (ADC) is proposed. In order to achieve the required resolution with a single 3-V supply, a fully differential closed-loop architecture is used. The track & hold circuit processes a differential 1-Vpp output signal swing and achieves more than 8-b linearity with sampling frequency up to 150 MHz. In these conditions, the total power consumption is 5.4 mW from a single 3-V supply. The circuit has been realized in a 0.7 /spl mu/m BiCMOS technology, and its active area is about 0.15 mm/sup 2/.
The optics of semiconductor diode lasers (2009)

Robert N. Hall, born in New Haven, Connecticut in 1919, joined General Electric's Research and Development Center after graduating from the California Institute of Technology. In 1962, having realized that a semiconductor junction could support population inversion, Hall built the first semiconductor injection laser. This device, based on a specially designed p-n junction, operated when an electric current injected the electrons directly into the junction, thus allowing for highly efficient generation of coherent light from a compact source. Today, diode lasers based on Hall's original idea are used, among other places, in CD and DVD players, laser printers, and fiber-optic communication systems.
Solid-phase-supported synthesis of morpholinoglycine oligonucleotide mimics (2014)

An efficient solid-phase-supported peptide synthesis (SPPS) of morpholinoglycine oligonucleotide (MorGly) mimics has been developed. The proposed strategy includes a novel specially designed labile linker group containing the oxalyl residue and the 2-aminomethylmorpholino nucleoside analogues as first subunits.
Responsive Polymer‐Protein Bioconjugates Prepared by RAFT Polymerization and Copper‐Catalyzed Azide‐Alkyne Click Chemistry (2008)

Abstract Responsive polymer‐protein conjugates were synthesized by combination of reversible addition‐fragmentation chain transfer (RAFT) polymerization and a grafting‐to approach by a highly efficient “click chemistry” strategy. A model protein, bovine serum albumin (BSA), was functionalized with an alkyne moiety by reaction of its free cysteine residue with propargyl maleimide. Azido‐terminated poly( N ‐isopropylacrylamide) (PNIPAM‐N 3 ) was prepared via RAFT, and polymer‐protein coupling was accomplished by copper‐catalyzed azide‐alkyne cycloaddition. In aqueous solution, the conjugates were observed by dynamic light scattering to be larger than the free polymer or the unmodified protein. Upon heating above the PNIPAM lower critical solution temperature (LCST), the PNIPAM‐BSA bioconjugates formed stable nanoparticles composed of dehydrated polymer and hydrophilic protein. magnified image
32-Mb 2T1R SPRAM with localized bi-directional write driver and ‘1’/‘0’ dual-array equalized reference cell (2009)

A 32-Mb SPin-transfer torque RAM (SPRAM) chip was demonstrated with an access time of 32 ns and a cell write-time of 40 ns at a supply voltage of 1.8 V. The chip was fabricated with 150-nm CMOS and a 100 × 200 nm tunnel magnetoresistive device element. This chip features three circuit technologies suitable for a large-scale array: 1) a two-transistor, one-resistor (2T1R) type memory cell for achieving a sufficiently large writing current despite the small cell size, 2) a compact read/write separated hierarchy bit/source-line structure with a localized bi-directional write driver for efficiently distributing writing current, and 3) a ‘1’/‘0’ dual-array equalized reference cell for stable read operation.
Sensitivity of MR diffusion measurements to variations in intracellular structure: Effects of nuclear size (2009)

Magnetic resonance imaging measurements of the apparent rate of water diffusion in tumors are sensitive to variations in tissue cellularity, which have been shown useful for characterizing tumors and their responses to treatments. However, because of technical limitations on most MRI systems, conventional pulse gradient spin echo (PGSE) methods measure relatively long time scales, during which water molecules may encounter diffusion barriers at multiple spatial scales, including those much greater than typical cell dimensions. As such they cannot distinguish changes on subcellular scales from gross changes in cell density. Oscillating gradient spin echo (OGSE) methods have the potential to distinguish effects on restriction at much shorter time and length scales. Both PGSE and OGSE methods have been studied numerically by simulating diffusion in a three-dimensional, multicompartment tissue model. The results show that conventional measurements with the PGSE method cannot selectively probe variations over short length scales and, therefore, are relatively insensitive to intracellular structure, whereas results using OGSE methods at moderate gradient frequencies are affected by variations in cell nuclear sizes and can distinguish tissues that differ only over subcellular length scales. This additional sensitivity suggests that OGSE imaging may have significant advantages over conventional PGSE methods for characterizing tumors.
New Equations for Computing Vapor Pressure and Enhancement Factor (1981)

Equations are presented which relate saturation vapor pressure to temperature for moist air. The equations are designed to be easily implemented on a calculator or computer and can be used to convert in either direction. They are more accurate than the commonly used Goff-Gratch equations for the meteorologically interesting region of −80 to +50°C. Equations also are given for the enhancement factor.