gebhart/patrepeval huggingface dataset:
Epidermal Growth Factor Treatment Enhances the Kinase Activity of Kinase Suppressor of Ras (2000)

In Drosophila melanogaster and Caenorhabditis elegans, kinase suppressor of Ras (KSR) functions as a positive modulator of Ras-dependent signaling either upstream of or parallel to Raf. Attempts to characterize the biochemical and biological properties of mammalian KSR, however, have had limited success. Although some studies demonstrated a requirement of KSR kinase activity for its action, others indicated the kinase function of KSR is dispensable and suggested that KSR acts primarily as a scaffold protein. Interpretations of KSR function are further hampered by the lack of a standardized assay for its kinase activity in vitro. To address this issue, we established a two-stage in vitro kinase assay in which KSR never comes in contact with any recombinant kinases other than c-Raf-1. Using this assay, we show that KSR immunoprecipitated from quiescent COS-7 cells overexpressing Flag-tagged KSR was inactive, but its activity was rapidly and markedly induced upon epidermal growth factor treatment. Moreover, KSR-reconstituted mitogen-activated protein kinase activation was detected in KSR immunoprecipitates depleted of all contaminating kinases (c-Raf-1, MEK1, ERK2) by multiple high salt washes. Only full-length kinase-active KSR was capable of signaling c-Raf-1-dependent activity as kinase inactive and C- and N-terminal deletion mutants were without effect. Furthermore, endogenous KSR isolated from A431 cells, which contain high levels of activated EGF receptor, displays constitutively enhanced kinase activity. Hence, KSR kinase activity is not an artifact of overexpression but a property intrinsic to this protein. The recognition of EGF as a potent activator of KSR kinase activity and the availability of a well defined in vitro kinase assay should facilitate the definition of the function of KSR as a Ras-effector molecule.
High-quality speech coding at 2.4 to 4.0 kbit/s based on time-frequency interpolation (1993)

The author presents a novel algorithm for high-quality coding and demonstrates the advantage of the proposed coder over the conventional CELP (code-excited linear prediction) algorithm for low rate coding. He proposes an empirical but perceptually advantageous framework for voice speech processing, called time-frequency interpolation (TFI). The general formulation of the TFI technique is given and then a TFI speech coder is described. The performance of this coder at 4.05 and 2.5 kbit/s is demonstrated in terms of formal MOS (mean opinion score) scores. It is shown that the 4.05 kbit/s TFI coder is comparable in performance with the 8 kbit/s European standard GSM (Group Special Mobile) coder. It is also shown that reducing the bit rate to 2.50 kbit/s only gracefully degrades the performance and the coder delivers good-quality speech at this rate.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Deep learning for lung cancer prognostication: A retrospective multi-cohort radiomics study (2018)

Our results provide evidence that deep learning networks may be used for mortality risk stratification based on standard-of-care CT images from NSCLC patients. This evidence motivates future research into better deciphering the clinical and biological basis of deep learning networks as well as validation in prospective data.
SEU mitigation testing of Xilinx Virtex II FPGAs (2004)

SRAM-based reconfigurable programmable logic is widely used in commercial applications and occasionally used in space flight applications because of susceptibility to single-event upset (SEU). Upset detection and mitigation schemes have been tested on the Xilinx Virtex II X-2V1000 in heavy-ion and proton irradiation to control the accumulation of SEUs and to mitigate their effects on the intended operation. Non-intrusive upset detection and partial reconfiguration in combination with TMR can repair the design to maintain state information. In-beam results on a simple test design demonstrate the effectiveness of these methods when used together.
Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing (2021)

LamPORE is a novel diagnostic platform for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA combining loop-mediated isothermal amplification with nanopore sequencing, which could potentially be used to analyze thousands of samples per day on a single instrument. We evaluated the performance of LamPORE against reverse transcriptase PCR (RT-PCR) using RNA extracted from spiked respiratory samples and stored nose and throat swabs collected at two UK hospitals. The limit of detection of LamPORE was 10 genome copies/μl of extracted RNA, which is above the limit achievable by RT-PCR, but was not associated with a significant reduction of sensitivity in clinical samples. Positive clinical specimens came mostly from patients with acute symptomatic infection, and among them, LamPORE had a diagnostic sensitivity of 99.1% (226/228; 95% confidence interval [CI], 96.9% to 99.9%). Among negative clinical specimens, including 153 with other respiratory pathogens detected, LamPORE had a diagnostic specificity of 99.6% (278/279; 98.0% to 100.0%). Overall, 1.4% (7/514; 0.5% to 2.9%) of samples produced an indeterminate result on first testing, and repeat LamPORE testing on the same RNA extract had a reproducibility of 96.8% (478/494; 94.8% to 98.1%). LamPORE has a similar performance as RT-PCR for the diagnosis of SARS-CoV-2 infection in symptomatic patients and offers a promising approach to high-throughput testing.
Phospholipase D Stimulates Release of Nascent Secretory Vesicles from the <i>trans</i>-Golgi Network (1997)

Phospholipase D (PLD) is a phospholipid hydrolyzing enzyme whose activation has been implicated in mediating signal transduction pathways, cell growth, and membrane trafficking in mammalian cells. Several laboratories have demonstrated that small GTP-binding proteins including ADP-ribosylation factor (ARF) can stimulate PLD activity in vitro and an ARF-activated PLD activity has been found in Golgi membranes. Since ARF-1 has also been shown to enhance release of nascent secretory vesicles from the TGN of endocrine cells, we hypothesized that this reaction occurred via PLD activation. Using a permeabilized cell system derived from growth hormone and prolactin-secreting pituitary GH3 cells, we demonstrate that immunoaffinity-purified human PLD1 stimulated nascent secretory vesicle budding from the TGN approximately twofold. In contrast, a similarly purified but enzymatically inactive mutant form of PLD1, designated Lys898Arg, had no effect on vesicle budding when added to the permeabilized cells. The release of nascent secretory vesicles from the TGN was sensitive to 1% 1-butanol, a concentration that inhibited PLD-catalyzed formation of phosphatidic acid. Furthermore, ARF-1 stimulated endogenous PLD activity in Golgi membranes approximately threefold and this activation correlated with its enhancement of vesicle budding. Our results suggest that ARF regulation of PLD activity plays an important role in the release of nascent secretory vesicles from the TGN.
Deaths: final data for 1999. (2001)

Generally, mortality continued long-term trends. Life expectancy in 1999 was unchanged from 1998 despite a slight increase in the age-adjusted death rate from the record low achieved in 1998. Although statistically unchanged from 1998, the trend in infant mortality has been of a steady but slowing decline. Some mortality measures for women and persons 85 years and over worsened between 1998 and 1999.
Genetic and physical interaction suggest that BARREN STALK1 is a target of BARREN INFLORESCENCE2 in maize inflorescence development (2008)

Organogenesis in plants is controlled by polar auxin transport. In maize (Zea mays), barren inflorescence2 (bif2) encodes a co-ortholog of the serine/threonine protein kinase PINOID (PID), which regulates auxin transport in Arabidopsis. In this paper, we report that the basic helix-loop-helix transcription factor BARREN STALK1 (BA1) is a putative target of BIF2, revealing a previously unknown function of BIF2 in the nucleus. Both bif2 and ba1 are required for axillary meristem initiation during inflorescence and vegetative development in maize. Using a yeast two-hybrid approach, we identified BA1 as an interacting partner with BIF2. We confirmed the interaction by in vitro pull-down assays, and demonstrated that BIF2 phosphorylates BA1 in vitro. Previously, RNA in situ hybridization showed that bif2 and ba1 are both expressed during axillary meristem initiation. Here, we heterologously expressed BIF2 and BA1, and found that they co-localize in the nucleus. Based on these findings, we propose that in addition to regulating auxin transport at the cell periphery, BIF2 also functions in the nucleus by interacting with BA1 to promote axillary meristem initiation. Double mutant analysis is consistent with these results, showing that bif2 and ba1 have overlapping as well as unique roles in inflorescence development.
Tracking State Estimation in Distribution Networks Using Distribution-level Synchrophasor Data (2018)

State estimation is often a challenging task in distribution systems due to numerous nodes and limited number of measurement sources. As a result, distribution system state estimation is often not real-time; instead, it is done once every 5 to 15 minutes, e.g., when smart meter measurements are available. Accordingly, this paper proposes a novel method for tracking state estimation in distribution systems to update the system states following an event, e.g., a sudden load change, that occurs in between the 5 to 15 minutes intervals of a typical distribution system state estimation cycle, without the need to rerun the whole state estimation. This method is of great interest for real-time monitoring and control applications. The proposed method uses measurements from as few as only two distribution-level phasor measurement units, a.k.a., micro-PMUs, that are installed at the substation and at the end of the main feeder or laterals. The method is developed based on the compensation theorem in circuit theory to generate an equivalent circuit according to the pre-event and post-event feeder data in order to update the state estimation results. The effectiveness of the proposed method is demonstrated through simulating the IEEE 33-bus test system.
Ecolabels: boon for the environment or confusion for the consumer? (1999)

The rise of green consumerism led to a proliferation of products claiming to be environmentally friendly, however consumers often found the statements given in support of these claims confusing. `Ecolabels' are intended to help consumers recognise products which have been manufactured and which perform their intended function in an environmentally friendly way. This article gives an overview of the current position regarding ecolabelling within the Member States of the European Union (EU) and proposals for strengthening the EU Ecolable Regulations.
Optimization of the expression of recombinant human activin A in the yeast <i>Pichia pastoris</i> (2010)

We report a new procedure to express recombinant human activin A using the methanolic yeast, Pichia pastoris. Optimization of culture procedures has involved comprehensive examination of the effects of culture vessel shape, volume of broth in the induction and expression cultures, methanol concentration, culturing temperature, and pH of the expression cultures. After this optimization, as well as modification of the native cleavage sites, a laboratory scale procedure has been established which routinely produced 2-10 mg/L amounts of this vital growth factor in the highly efficient, eukaryotic yeast system. This system avoids the need to produce this protein and similar TGF-beta proteins in mammalian cell lines which, in addition to being costly, produce many native binding partners of these cystine knot proteins, a factor which can dramatically affect yields of the target protein.
A Comparative Study of Static Analysis Tools for AUTOSAR Automotive Software Components Development (2017)

The use of static analysis is clearly recommended in automotive safety standard ISO26262 to reduce software runtime errors. A comparative study of top performance tools is provided by analyzing production code of AUTOSAR application software components for an Instrument Panel Cluster. A quantitative analysis based on an alert classification model and performance metrics has been carried out. The goal of this paper is to identify the best combination of commercial static analysis tools to minimize defects of AUTOSAR software components in a context of automatic code generation. Finally, the results analysis has suggested some improvements of static analysis tools.
Increased Adherence and Expression of Virulence Genes in a Lineage of Escherichia coli O157:H7 Commonly Associated with Human Infections (2010)

These findings demonstrate that the EHEC O157:H7 lineage associated with HUS expresses higher levels of virulence genes and has an enhanced ability to attach to epithelial cells relative to another common lineage.
Learning Near Duplicate Image Pairs using Convolutional Neural Networks (2018)

In this paper, we illustrate how to learn a general straightforward similarity function from raw image pairs, which is a fundamental task in computer vision. To encode the function, inspired by the recent achievements of deep learning methods, we explore several deep neural networks and adopt one of the suitable networks to our task encoding implementation with several models on benchmark datasets UKBench and Holidays. The adopted network achieves comparable overall results and especially presents the excellent learning ability for global-similar data. Compared to previous approaches, this function eliminates the complex handcrafted features extraction, and utilizes pairwise correlation information by the jointly processing.
Convolutional neural networks with multi-valued neurons (2017)

Convolutional neural network (CNN) has been successfully used in many fields including image recognition. CNN is composed of input, convolution, pooling, hidden and output layers, and the weights and biases between layers except the ones between convolution and pooling layers are acquired by learning. In comparison to the conventional neural networks, the learning cost of CNN is higher, and the learning time is longer especially when hidden layer(s) are added. Recently, complex- and quaternion-valued neural networks have drawn much attention. In complex-valued neural networks, inputs, weights, biases and outputs are complex numbers, and in quaternion-valued neural networks, these parameters are quaternions. It has been shown that both methods exhibit excellent accuracy in various applications such as classification and function approximation problems with less computational burden. In this study, we propose CNNs with complex- and quaternion-valued neurons where complex and quaternion numbers are used between pooling, hidden and output layers. We here show that CNNs with complex- and quaternion-valued neurons have higher learning ability in handwritten digit image classification with the MNIST data than the real-valued counterpart.
ADS-B based Trajectory Prediction and Conflict Detection for Air Traffic Management (2012)

The Automatic Dependent Surveillance Broadcast (ADS-B) system is a key component of CNS/ATM recommended by the International Civil Aviation Organization (ICAO) as the next generation air traffic control system. ADS-B broadcasts identification, positional data, and operation information of an aircraft to other aircraft, ground vehicles and ground stations in the nearby region. This paper explores the ADS-B based trajectory prediction and the conflict detection algorithm. The multiple-model based trajectory prediction algorithm leads accurate predicted conflict probability at a future forecast time. We propose an efficient and accurate algorithm to calculate conflict probability based on approximation of the conflict zone by a set of blocks. The performance of proposed algorithms is demonstrated by a numerical simulation of two aircraft encounter scenarios.
Magnetic resonance imaging image intensity correction with extrapolation and adaptive smoothing (2006)

A significant problem in magnetic resonance imaging (MRI) is the inhomogeneity of the image resulting from a number of factors that are hardware related. The obtained image can be treated as the true image multiplied by a signal modulator, which is usually smooth across the image. A class of MR image intensity correction methods extracts the slowly varying component from the image with low-pass filtering or smoothing to approximate the signal modulator. This usually causes the edge enhancement artifact in the corrected image. A novel method of extrapolating the image in advance is proposed to reduce this effect significantly. Closest point algorithm is implemented to minimize the calculation time for extrapolation. To remove bright spots caused by nonuniform sensitivity profiles, a gradient-weighted smoothing method is discussed in this work. The partial differential equations based model is applied for locally adaptive smoothing. The filtered gradient of the corrupted image is used as the weight for smoothing. Phantom and clinical data collected on various MRI systems are used for evaluation of our method. These experimental results show that the proposed method solves the edge enhancement and bright spots problem effectively and robustly.
Spinal 2-chloroprocaine: Minimum effective dose (2005)

Spinal 2-CP 40 mg and 60 mg provide rapid and reliable sensory and motor block. Although the 20-mg and 30-mg doses can produce sensory anesthesia adequate for brief surgical procedures, less motor block and some sacral sparing should be anticipated. Because the 10-mg dose produces only brief and inconsistent sensory anesthesia, it can be considered a no-effect dose.
Application of High-Density DNA Microarray to Study Smoke- and Hydrogen Peroxide–Induced Injury and Repair in Human Bronchial Epithelial Cells (2003)

Recent advances in high-density DNA microarray technique allow the possibility to analyze thousands of genes simultaneously for their differential gene expression patterns in various biologic processes. Through clustering analysis and pattern recognition, the significance of these differentially expressed genes can be recognized and correlated with the biologic events that may take place inside the cell and tissue. High-density DNA microarray nylon membranes were used to explore gene expression and regulation associated with smoke- and hydrogen peroxide-induced injury and repair in differentiated human bronchial epithelial cells in vitro. At least three phases of change in gene expression could be recognized. The first phase seems to be an immediate event in response to oxidant injury. This phase includes the induction of bcl-2 and mdm2 genes that are involved in the regulation of apoptosis, and the mitogen-activated protein kinase phosphatase 1 that functions as a regulator for various mitogen-activated protein kinase activities. The second phase, usually 5 h later, includes the induction of various stress proteins and ubiquitin, which are important in providing the chaperone mechanism and the turnover of damaged macromolecules. The third phase, which is 5 to 10 h later, includes the induction of genes that seem to be involved in reducing oxidative stress by metabolizing the cellular level of reactive oxygen species. In this phase, enzymes associated with tissue and cell remodeling are also elevated. These results demonstrated a complex gene expression array by bronchial epithelial cells in response to a single insult of oxidants that are relevant to environmental pollutants.
Uganda - Country-level savings assessment CGAP savings initiative (2006)

This report summarizes the results of the fifth test of the Country-Level Savings Assessment Toolkit under development as part of CGAP's Savings Initiative. The purpose of the toolkit is to help government agencies, donors, and others identify opportunities and constraints in increasing poor people's access to high-quality deposit services. The methodology examines client demand for deposit services and the capacity of the financial system to meet that demand at three levels: financial institutions (micro), supporting infrastructure (meso), and policy (macro). It concludes with suggestions for strategies to improve the quality and quantity of deposit services available to low income households.
Comparative distribution patterns of type I and III collagens and fibronectin in human arteriosclerotic aorta. (1985)

The distribution patterns of type I and III collagens and fibronectin were studied in arteriosclerotic lesions of human aortas as well as in the regions devoid of any macroscopic lesions of the same aortas. Frozen sections were analyzed for fibronectin and collagens by indirect immunofluorescence or immunoperoxidase analysis with specific antisera prepared in rabbits against human plasma fibronectin and against human type I and III collagens. Tissue samples were also stained for type I and III collagen distribution using Picro Sirius red according to the method described by Junqueira et al. (1979). In the regions devoid of any visible macroscopic lesions, there is a co-distribution in the media of the aortic wall of type I and III collagens, with a predominance of type I collagen. Type I collagen is also visible in the intima, as a continuous layer. This is attributed to an age-dependent change of the aorta (arteriosclerosis). Fibronectin can be demonstrated as a thin layer in the subendothelium and as a weak immunofluorescence over the media. In recent or evolutive arteriosclerotic plaques, fibronectin and type III collagen appear to be strongly increased and superimposed. There is also an increase of type I collagen in the intimal region of the plaque. The co-distribution of type III collagen and fibronectin in the arteriosclerotic plaques may suggest a tissue-repair-type of process, analogous to that which can be observed during wound healing. Our results suggest that in arteriosclerotic lesions, type III collagen and fibronectin are predominantly synthesized.(ABSTRACT TRUNCATED AT 250 WORDS)
Peak-to-average power ratio reduction in space–time block coded multi-input multi-output orthogonal frequency division multiplexing systems using a small overhead selective mapping scheme (2009)

The selective mapping (SLM) scheme is one of the most popular peak-to-average power ratio (PAPR) reduction techniques proposed for multi-input multi-output orthogonal frequency division multiplexing (MIMO-OFDM) systems. One of the major disadvantages of this scheme is the need for the transmission of side information (SI) bits to enable the receiver to recover the transmitted data. The authors present a small overhead SLM (s-SLM) scheme for space–time block coded (STBC) MIMO-OFDM systems. This proposed scheme improves the system bandwidth efficiency and achieves a significantly lower bit error rate (BER) than the individual SLM (i-SLM) and direct SLM (d-SLM) schemes. In addition, approximate expressions for the complementary cumulative distribution function (CCDF) of the PAPR and the average BER of the proposed s-SLM scheme are derived. The simulation results show that the proposed s-SLM scheme improves the detection probability of the SI bits and hence gives a better performance than the i-SLM and the d-SLM schemes.