gebhart/patrepeval huggingface dataset:
Plastid Lysophosphatidyl Acyltransferase Is Essential for Embryo Development in Arabidopsis (2004)

Lysophosphatidyl acyltransferase (LPAAT) is a pivotal enzyme controlling the metabolic flow of lysophosphatidic acid into different phosphatidic acids in diverse tissues. A search of the Arabidopsis genome database revealed five genes that could encode LPAAT-like proteins. We identified one of them, LPAAT1, to be the lone gene that encodes the plastid LPAAT. LPAAT1 could functionally complement a bacterial mutant that has defective LPAAT. Bacteria transformed with LPAAT1 produced LPAAT that had in vitro enzyme activity much higher on 16:0-coenzyme A than on 18:1-coenzyme A in the presence of 18:1-lysophosphatidic acid. LPAAT1 transcript was present in diverse organs, with the highest level in green leaves. A mutant having a T-DNA inserted into LPAAT1 was identified. The heterozygous mutant has no overt phenotype, and its leaf acyl composition is similar to that of the wild type. Selfing of a heterozygous mutant produced normal-sized and shrunken seeds in the Mendelian ratio of 3:1, and the shrunken seeds could not germinate. The shrunken seeds apparently were homozygous of the T-DNA-inserted LPAAT1, and development of the embryo within them was arrested at the heart-torpedo stage. This embryo lethality could be rescued by transformation of the heterozygous mutant with a 35S:LPAAT1 construct. The current findings of embryo death in the homozygous knockout mutant of the plastid LPAAT contrasts with earlier findings of a normal phenotype in the homozygous mutant deficient of the plastid glycerol-3-phosphate acyltransferase; both mutations block the synthesis of plastid phosphatidic acid. Reasons for the discrepancy between the contrasting phenotypes of the two mutants are discussed.
Mid-Trimester Cervical Consistency Index and Cervical Length to Predict Spontaneous Preterm Birth in a High-Risk Population (2018)

<b>Background</b> Short cervical length (CL) has not been shown to be adequate as a single predictor of spontaneous preterm birth (sPTB) in high-risk pregnancies. <b>Objective</b> The objective of this study was to evaluate the performance of the mid-trimester cervical consistency index (CCI) to predict sPTB in a cohort of high-risk pregnancies and to compare the results with those obtained with the CL. <b>Study Design</b> Prospective cohort study including high-risk singleton pregnancies between 19 <sup>+0</sup> and 24 <sup>+6</sup> weeks. The ratio between the anteroposterior diameter of the uterine cervix at maximum compression and at rest was calculated offline to obtain the CCI. <b>Results</b> Eighty-two high sPTB risk women were included. CCI (%) was significantly reduced in women who delivered <37 <sup>+0</sup> weeks compared with those who delivered at term, while CL was not. The area under the curve (AUC) of the CCI to predict sPTB <37 <sup>+0</sup> weeks was 0.73 (95% confidence interval [CI], 0.61-0.85), being 0.51 (95% CI, 0.35-0.67), <i>p</i> = 0.03 for CL. The AUC of the CCI to predict sPTB <34 <sup>+0</sup> weeks was 0.68 (95% CI, 0.54-0.82), being 0.49 (95% CI, 0.29-0.69), <i>p</i> = 0.06 for CL. <b>Conclusion</b> CCI performed better than sonographic CL to predict sPTB. Due to the limited predictive capacity of these two measurements, other tools are still needed to better identify women at increased risk.
An exploratory study of the extent of information technology adoption in SMEs: an application of upper echelon theory (2009)

Purpose The paper aims to investigate the effect of compositions of managerial/demographic characteristics of the top management team (TMT) on the extent of information technology (IT) adoption in small businesses (SMEs), where such strategic decisions made by TMT have direct and significant influence on all aspects of business operations and its competitive position in a market. Design/methodology/approach Based on the upper echelon theory, the study formulated four hypotheses relating the compositions of TMT characteristics to the extent of IT adoption in different functional areas. Multiple regression analysis was employed to analyze the data. Findings The age average and the education average of TMT in small businesses are significant predictors of the extent of IT adoption. However, the group heterogeneity (either gender or ethnicity), contrary to the prediction, has negative impact on the extent of IT adoption. Practical implications The research findings indicate that the age and education composition of managers as current/future top management is critical to facilitate the extent of IT adoption in SMEs. Originality/value The research contributes to the body of knowledge in IT adoption by complementing the results of prior research with the findings that the characteristic compositions of TMT affect the extent of IT adoption in SMEs, applying the upper echelon theory to examine issues surrounding IT adoption, and suggesting practical implications that SMEs could compose, educate, and rejuvenate their top management teams to achieve a high extent of IT adoption.
Large-scale matrix factorization with distributed stochastic gradient descent (2011)

We provide a novel algorithm to approximately factor large matrices with millions of rows, millions of columns, and billions of nonzero elements. Our approach rests on stochastic gradient descent (SGD), an iterative stochastic optimization algorithm. We first develop a novel "stratified" SGD variant (SSGD) that applies to general loss-minimization problems in which the loss function can be expressed as a weighted sum of "stratum losses." We establish sufficient conditions for convergence of SSGD using results from stochastic approximation theory and regenerative process theory. We then specialize SSGD to obtain a new matrix-factorization algorithm, called DSGD, that can be fully distributed and run on web-scale datasets using, e.g., MapReduce. DSGD can handle a wide variety of matrix factorizations. We describe the practical techniques used to optimize performance in our DSGD implementation. Experiments suggest that DSGD converges significantly faster and has better scalability properties than alternative algorithms.
Self-Organizing Spiking Neural Model for Learning Fault-Tolerant Spatio-Motor Transformations (2012)

In this paper, we present a spiking neural model that learns spatio-motor transformations. The model is in the form of a multilayered architecture consisting of integrate and fire neurons and synapses that employ spike-timing-dependent plasticity learning rule to enable the learning of such transformations. We developed a simple 2-degree-of-freedom robot-based reaching task which involves the learning of a nonlinear function. Computer simulations demonstrate the capability of such a model for learning the forward and inverse kinematics for such a task and hence to learn spatio-motor transformations. The interesting aspect of the model is its capacity to be tolerant to partial absence of sensory or motor inputs at various stages of learning. We believe that such a model lays the foundation for learning other complex functions and transformations in real-world scenarios.
Reliability Assessment on Insertion Mount Assembly under Vibration Conditions (2007)

This paper presents the reliability design-of-experiment and results for an insertion-mount assembly under random vibration loading conditions. The natural frequency and overstress limits were first identified for the test vehicle. The durability of assemblies with Sn37Pb (SnPb) and Sn3.0Ag0.5Cu (SAC) solder joints was compared under aging conditions that vary on temperature and duration: 125degC for 100 hours, 125degC for 350 hours, -55degC for 1000 hours. The effects of aging and printed circuit board pad finishes on solder joint reliability were also investigated. The results show that SnPb solder joints have better performance than SAC solder joints, especially under high-vibration loading conditions and with thermal aging treatment. Pad finishes were also found to contribute to diffusion in assembly reliability but with different trends for differently aged products.
Assembly of G Protein-Coupled Receptors onto Nanosized Bacterial Magnetic Particles Using Mms16 as an Anchor Molecule (2004)

G protein-coupled receptors (GPCRs) play a central role in a wide range of biological processes and are prime targets for drug discovery. GPCRs have large hydrophobic domains, and therefore purification of GPCRs from cells is frequently time-consuming and typically results in loss of native conformation. In this work, GPCRs have been successfully assembled into the lipid membrane of nanosized bacterial magnetic particles (BMPs) produced by the magnetic bacterium Magnetospirillum magneticum AMB-1. A BMP-specific protein, Mms16, was used as an anchor molecule, and localization of heterologous Mms16 on BMPs was confirmed by luciferase fusion studies. Stable luminescence was obtained from BMPs bearing Mms16 fused with luciferase at the C-terminal region. D1 dopamine receptor (D1R), a GPCR, was also efficiently assembled onto BMPs by using Mms16 as an anchor molecule. D1R-BMP complexes were simply extracted by magnetic separation from ruptured AMB-1 transformants. After washing, the complexes were ready to use for analysis. This system conveniently refines the native conformation of GPCRs without the need for detergent solubilization, purification, and reconstitution after cell disruption.
Automated AC Voltammetric Sensor for Early Fault Detection and Diagnosis in Monitoring of Electroplating Processes (2012)

Abstract An in situ sensor employing AC‐voltammetry techniques was designed to provide a response strongly affected by the presence of specific disturbances like foreign contaminants, accumulated degradation products, severely out‐of‐target concentrations of electroplating bath constituents and out‐of‐target physical conditions of the plating process (i.e. temperature). Soft Independent Modelling of Class Analogy (SIMCA) is a pattern recognition method which describes each class separately in eigenvector space. In this supervised classification technique the projected new measurements are evaluated to determine whether they belong to a certain class or not. An automated analytical system was developed capable of collecting on‐line AC voltammetric data and investigating similarities between measurements in proper conditions and measurements with upset behavior with known disturbances which can be utilized to recognize a likely pattern of behavior. The shape differences between deformed and reference set voltammograms are quantified by Mahalanobis Distance (MD)‐SIMCA. In addition to the numerical approach, a graphical projection is utilized to diagnose the root cause of the detected process disturbances.
Variation of the Adhesive Properties of an Epoxy Resin Modified by End-Functionalized Liquid Polybutadiene as a Function of Temperature and Water Absorption (2007)

The adhesive behavior of a diglycidyl ether of bisphenol-A epoxy resin modified by end-functionalyzed liquid polybutadiene was evaluated as a function of the temperature and of the time of immersion in distilled water. The neat epoxy and three modified systems were analyzed. Butt joints and single-lap joints were tested using an API X60 steel as substrate. The monophasic system obtained by reacting the epoxy monomer with hydroxyl-terminated polybutadiene (HTPB) functionalyzed with isocyanate groups (EPI) showed the best performance. The results show that this system is stable in respect to water degradation, but changes when exposed to temperature. Under the set of experimental parameters of time and temperature used, however, the adhesive strength increased with the temperature. For all epoxy formulations analyzed the fracture mode observed was of the adhesive type.
Evaluation of a symmetry-based strategy for assembling protein complexes (2011)

We evaluate a strategy for assembling proteins into large cage-like structures, based on the symmetry associated with the native protein's quaternary structure. Using a trimeric protein, KDPG aldolase, as a building block, two fusion proteins were designed that could assemble together upon mixing. The fusion proteins, designated A-(+) and A-(-), comprise the aldolase domain, a short, flexible spacer sequence, and a sequence designed to form a heterodimeric antiparallel coiled-coil between A-(+) and A-(-). The flexible spacer is included to minimize constraints on the ability of the fusion proteins to assemble into larger structures. On incubating together, A-(+) and A-(-) assembled into a mixture of complexes that were analyzed by size exclusion chromatography coupled to multi-angle laser light scattering, analytical ultracentrifugation, transmission electron microscopy and atomic force microscopy. Our analysis indicates that, despite the inherent flexibility of the assembly strategy, the proteins assemble into a limited number of globular structures. Dimeric and tetrameric complexes of A-(+) and A-(-) predominate, with some evidence for the formation of larger assemblies; e.g. octameric A-(+): A-(-) complexes.
Stereoselective Synthesis of Neu5Acα(2→5)Neu5Gc:  The Building Block of Oligo/Poly(→5-OglycolylNeu5Gcα2→) Chains in Sea Urchin Egg Cell Surface Glycoprotein (2002)

The synthesis of a sialic acid dimer derivative, Neu5Acalpha(2-->5)Neu5Gc, is described. The synthetic strategy is based on the use of allyl alcohol to achieve an exclusive alpha-sialylation product. The allyloxy group is also a latent glycolic acid that provides the subsequent coupling with neuraminate with minimal protection-deprotection manipulations.
Antithrombotic effect of recombinant truncated tissue factor pathway inhibitor (TFPI1-161) in experimental venous thrombosis--a comparison with low molecular weight heparin. (1994)

The aim was to investigate whether a truncated recombinant Tissue Factor Pathway Inhibitor (TFPI1-161), which lacked the third Kunitz-type domain and the basic c-terminal region, had an antithrombotic effect comparable to LMWH in a randomised double-dummy study. The experimental thrombosis was induced in jugular veins, in a total of 40 rabbits by a combination of destruction of the endothelium and restricted blood flow. Group 1: placebo, gr 2: LMWH 60 anti-FXa IU/kg, gr 3-5: 0.1, 1.0 and 10.0 mg/kg TFPI1-161. TFPI1-161 reduced the thrombus weights in all treated groups, significantly in doses of 1.0 and 10.0 mg/kg compared to placebo. The frequency of thrombosis and occlusive thrombosis were also significantly reduced in those doses. The antithrombotic properties of TFPI1-161 (1.0-10.0 mg/kg) measured as thrombus weight, frequency of thrombosis and frequency of occlusive thrombosis was equivalent to the anti-thrombotic properties of LMWH. In the anti-FXa, APTT and PT-assays TFPI1-161 displayed a dose dependent increase of activity. Recombinant-TFPI1-161 did not influence the anti-FIIa-assay. No haemorrhagic side effects were noted.
P‐167: FDTD and Elastic Continuum Analysis of the Liquid Crystal Polarization Grating (2006)

Abstract The liquid crystal polarization grating (LCPG) has advantages of polarization independence of the zero diffraction order, nearly 100% diffraction efficiency in the first orders, and higher resolution capability over previously reported binary LC gratings. Here we analyze the LCPG, an electrically controlled, polarization‐independent light modulator using the finite‐difference time‐domain (FDTD) method and the elastic continuum theory. The optical performance is studied and critical electrical parameters for a LCPG cell are presented.
A Convex Approach to Frisch-Kalman Problem (2019)

This paper proposes a convex approach to the Frisch-Kalman problem that identifies the linear relations among variables from noisy observations. The problem was proposed by Ragnar Frisch in 1930s, and was promoted and further developed by Rudolf Kalman later in 1980s. It is essentially a rank minimization problem with convex constraints. Regarding this problem, analytical results and heuristic methods have been pursued over a half century. The proposed convex method in this paper is demonstrated to outperform several commonly adopted heuristics when the noise components are relatively small compared with the underlying data.
Determination of the Potential Tumor-Suppressive Effects of Gsdme in a Chemically Induced and in a Genetically Modified Intestinal Cancer Mouse Model (2019)

<i>Gasdermin E</i> (<i>GSDME</i>), also known as <i>deafness autosomal dominant 5</i> (<i>DFNA5</i>) and previously identified to be an inducer of regulated cell death, is frequently epigenetically inactivated in different cancer types, suggesting that <i>GSDME</i> is a tumor suppressor gene. In this study, we aimed to evaluate the tumor-suppressive effects of GSDME in two intestinal cancer mouse models. To mimic the silencing of <i>GSDME</i> by methylation as observed in human cancers, a <i>Gsdme</i> knockout (KO) mouse was developed. The effect of GSDME on tumorigenesis was studied both in a chemically induced and in a genetic intestinal cancer mouse model, as strong evidence shows that GSDME plays a role in human colorectal cancer and representative mouse models for intestinal cancer are available. Azoxymethane (AOM) was used to induce colorectal tumors in the chemically induced intestinal cancer model (<i>n</i> = 100). For the genetic intestinal cancer model, <i>Apc<sup>1638N/+</sup></i> mice were used (<i>n</i> = 37). In both experiments, the number of mice bearing microscopic proliferative lesions, the number and type of lesions per mouse and the histopathological features of the adenocarcinomas were compared between <i>Gsdme</i> KO and wild type (WT) mice. Unfortunately, we found no major differences between <i>Gsdme</i> KO and WT mice, neither for the number of affected mice nor for the multiplicity of proliferative lesions in the mice. However, recent breakthroughs on gasdermin function indicate that GSDME is an executioner of necrotic cell death. Therefore, it is possible that GSDME may be important for creating an inflammatory microenvironment around the tumor. This is in line with the trend towards more severe inflammation in WT compared to <i>Gsdme</i> KO mice, that we observed in our study. We conclude that the effect of GSDME in tumor biology is probably more subtle than previously thought.
Preliminary report of brain activities during active and passive gait-like motion (2013)

This paper describes a preliminary report of the brain activity during active and passive gait-like motions simulated by our novel lower-extremity motion simulator. Our motion simulator provides a wearer with physical supports to move their lower extremities or physical constrains during gait-like motion within lying posture in a magnetic resonance imaging (MRI) room so that brain activities could be simultaneously measured. To be employed in MRI room, the simulator fulfill MRI compatibility by being consisted from nonmagnetic materials and actuator. The pilot functional MRI measurement of the brain activities during active and passive gait-like motions shows the difference of the brain activation in the sensory area between during the active motion and the passive motion.
Damage detection in plate-like structures based on mode-conversion sensing with 3D laser vibrometer (2017)

Interpretation of Lamb waves signals raises serious difficulties due to their multi-modal nature. Various modes propagating with different velocities can be confused and erroneously treated as damage reflected components. Both S0 and A0 Lamb modes exhibit elliptical polarization, therefore, their in-plane and out-of plane motion components are shifted by ± 90°. Also, the ratios of in-plane and out-of-plane displacements between these components vary and the direction of particle motion is opposite for both modes. Using a 3D scanning laser vibrometer it is possible to capture the in-plane and out-of-plane motion. The modes differ not only in polarization parameters but also in group velocities, therefore, normally they are well separated in time. Two modes can occur simultaneously only close to the wave source or to a defect that leads to mode conversion. Since the in-plane and out-of plane motion components are generally out-of-phase, a comparison of these components permits detection of mode conversion, which leads to superior and reliable damage detection. Here, we present a damage imaging method based on mode-conversion indicator (MCI).
Search for the smallest random forest (2009)

Random forests have emerged as one of the most commonly used nonparametric statistical methods in many scientific areas, particularly in analysis of high throughput genomic data. A general practice in using random forests is to generate a sufficiently large number of trees, although it is subjective as to how large is sufficient. Furthermore, random forests are viewed as "black-box" because of its sheer size. In this work, we address a fundamental issue in the use of random forests: how large does a random forest have to be? To this end, we propose a specific method to find a sub-forest (e.g., in a single digit number of trees) that can achieve the prediction accuracy of a large random forest (in the order of thousands of trees). We tested it on extensive simulation studies and a real study on prognosis of breast cancer. The results show that such sub-forests usually exist and most of them are very small, suggesting they are actually the "representatives" of the whole random forests. We conclude that the sub-forests are indeed the core of a random forest. Thus it is not necessary to use the whole forest for satisfying prediction performance. Also, by reducing the size of a random forest to a manageable size, the random forest is no longer a black-box.
Design and implementation of cloud API access control based on OAuth (2013)

As the popularity of cloud computing increases, cloud services can provide rich functionality by means of standardized APIs based on open technology. More and more web services offer APIs for application developers to use. APIs act as the intermediate between application developers and web services. The security of cloud computing depends largely on the management of APIs. Hence a strong API access control model is required. In this paper, we design and implement an API access control mechanism based on OAuth which simplifies its process flow under different application scenarios. We also show how access control mechanism can be realized as REST-style web services.