gebhart/patrepeval huggingface dataset:
Rescue of the 1947 Zika Virus Prototype Strain with a Cytomegalovirus Promoter-Driven cDNA Clone (2016)

The recent Zika virus (ZIKV) outbreak has been linked to severe pathogenesis. Here, we report the construction of a plasmid carrying a cytomegalovirus (CMV) promoter-expressed prototype 1947 Uganda MR766 ZIKV cDNA that can initiate infection following direct plasmid DNA transfection of mammalian cells. Incorporation of a synthetic intron in the nonstructural protein 1 (NS1) region of the ZIKV polyprotein reduced viral cDNA-associated toxicity in bacteria. High levels of infectious virus were produced following transfection of the plasmid bearing the wild-type MR766 ZIKV genome, but not one with a disruption to the viral nonstructural protein 5 (NS5) polymerase active site. Multicycle growth curve and plaque assay experiments indicated that the MR766 virus resulting from plasmid transfection exhibited growth characteristics that were more similar to its parental isolate than previously published 2010 Cambodia and 2015 Brazil cDNA-rescued ZIKV. This ZIKV infectious clone will be useful for investigating the genetic determinants of ZIKV infection and pathogenesis and should be amenable to construction of diverse infectious clones expressing reporter proteins and representing a range of ZIKV isolates. <b>IMPORTANCE</b> The study of ZIKV, which has become increasingly important with the recent association of this virus with microcephaly and Guillain-Barré syndrome, would benefit from an efficient strategy to genetically manipulate the virus. This work describes a model system to produce infectious virus in cell culture. We created a plasmid carrying the prototype 1947 Uganda MR766 ZIKV genome that both was stable in bacteria and could produce high levels of infectious virus in mammalian cells through direct delivery of this DNA. Furthermore, growth properties of this rescued virus closely resembled those of the viral isolate from which it was derived. This model system will provide a simple and effective means to study how ZIKV genetics impact viral replication and pathogenesis.
The positive and negative consequences of stressors during early life (2015)

We discuss the long-term effects of stress exposure in pre- and early postnal life. We present an evolutionary framework within which such effects can be viewed, and describe how the outcomes might vary with species life histories. We focus on stressors that induce increases in glucocorticoid hormones and discuss the advantages of an experimental approach. We describe a number of studies demonstrating how exposure to these hormones in early life can influence stress responsiveness and have substantial long-term, negative consequences for adult longevity. We also describe how early life exposure to mild levels of stressors can have beneficial effects on resilience to stress in later life, and discuss how the balance of costs and benefits is likely dependent on the nature of the adult environment.
PP2A Regulates BCL-2 Phosphorylation and Proteasome-mediated Degradation at the Endoplasmic Reticulum (2006)

Anti-apoptotic activity of BCL-2 is mediated by phosphorylation at the endoplasmic reticulum (ER), but how this phosphorylation is regulated and the mechanism(s) by which it regulates apoptosis are unknown. We purified macromolecular complexes containing BCL-2 from ER membranes and found that BCL-2 co-purified with the main two subunits of the serine/threonine phosphatase, PP2A. The association of endogenous PP2A and BCL-2 at the ER was verified by co-immunoprecipitation and microcystin affinity purification. Knock down or pharmacological inhibition of PP2A caused degradation of phosphorylated BCL-2 and led to an overall reduction in BCL-2 levels. We found that this degradation was due to the action of the proteasome acting selectively at the ER. Conversely, overexpression of PP2A caused elevation in endogenous BCL-2. Most importantly, we found that PP2A knock down sensitized cells to several classes of death stimuli (including ER stress), but this effect was abolished in a genetic background featuring knock in of a non-phosphorylatable BCL-2 allele. These studies support the hypothesis that PP2A-mediated dephosphorylation of BCL-2 is required to protect BCL-2 from proteasome-dependent degradation, affecting resistance to ER stress.
Review: Rotations in Structural Response (2009)

Abstract Measurements of point rotations in full-scale structures during earthquake excitation do not exist at present, but average rotations can be computed from pairs of parallel transducers. The examples presented illustrate rotations in the range from 10 -6 to 10 -3 rad and angular accelerations from 10 -4 to 10 -1 rad/sec 2 . Measurements of rotations in the structures for excitation by microtremors are also described. It is argued that recording the rotational components of motion contributes significantly to the overall volume and quality of information. It is recommended that the development and deployment of instruments to measure rotational components of motion in free-field conditions and in full-scale structures will open a new frontier for advanced experimental identification of structural properties and for structural health monitoring.
Mapping XML to Key-Value Database (2013)

XML is a popular data format used in many software applications. Native XML databases can be used for persistence of XML documents or the document can be stored in a relational database. In this paper we propose an alternative storage for XML documents based on key-value databases. We propose three general algorithms for XML to key-value database mapping. The algorithms are optimized using specific features of key- value database Redis. Finally a performance comparison of implemented algorithms and common native XML databases is provided. Keywords-XML; key-value database; Redis; RedXML; XML mapping
Estimation of Socioeconomic Attributes from Location Information (2020)

Abstract Timely estimation of the distribution of socioeconomic attributes and their movement is crucial for academic as well as administrative and marketing purposes. During the fight against the COVID-19 pandemic, for example, it has been revealed that collecting information on where elderly people, who are most vulnerable to the virus, are and how the young, who are susceptible to transmitting it, move is valuable to find routes and potential clusters of infection. In this study, assuming personal attributes affect human behavior and movement, we predict these attributes from location information. First, we predict the socioeconomic characteristics of individuals by supervised learning methods, i.e., logistic Lasso regression, Gaussian Naive Bayes, random forest, XGBoost, LightGBM, and support vector machine, using survey data we collected of personal attributes and frequency of visits to specific facilities, to test our conjecture. We find that gender, a crucial attribute, is as highly predictable from locations as from other sources such as social networking services, as done by existing studies. Second, we apply the model trained with the survey data to actual GPS log data to check the performance of our approach in a real-world setting. Though our approach does not perform as well as for the survey data, the results suggest that we can infer gender from a GPS log.
Quantum Dot-Size Variation and Its Impact on Emission and Absorption Characteristics: An Experimental and Theoretical Modeling Investigation (2002)

This paper presents a study of electronic carrier redistribution in doped (In, Ga)As/GaAs quantum dots due to size variation. The dots in our samples fall roughly into "large" and "small" size clusters. At low temperatures, the carriers predominantly occupy the large-size dots. As the sample temperature is raised, thermal energy redistributes the carriers so that some begin to occupy energy states in the small-size dots. At room-temperature, the photoluminescence emission spectrum exhibits two distinct peaks due to transitions from the large- and small-size dots. This carrier redistribution can also be followed by observing the integrated absorbance as a function of temperature. The transition energy levels extracted from photoluminescence data compare favorably with theoretically calculated values for dots with truncated pyramidal shapes.
A CMOS up-conversion receiver front-end for cable and terrestrial DTV applications (2003)

A CMOS up-conversion receiver front end consists of a low-noise variable-gain amplifier with an input-frequency range from 48 to 860MHz and a mixer with an output frequency of 1.1GHz. The IC exhibits a gain range of 55dB, noise figure of 6.2dB at a gain of 19dB, and a maximum IIP3 of 26dBm. The chip consumes 125mW and is fabricated in a 0.18/spl mu/m 5M process.
Interprocedural parallelization analysis in SUIF (2005)

As shared-memory multiprocessor systems become widely available, there is an increasing need for tools to simplify the task of developing parallel programs. This paper describes one such tool, the automatic parallelization system in the Stanford SUIF compiler. This article represents a culmination of a several-year research effort aimed at making parallelizing compilers significantly more effective. We have developed a system that performs full interprocedural parallelization analyses, including array privatization analysis, array reduction recognition, and a suite of scalar data-flow analyses including symbolic analysis. These analyses collaborate in an integrated fashion to exploit coarse-grain parallel loops, computationally intensive loops that can execute on multiple processors independently with no cross-processor synchronization or communication. The system has successfully parallelized large interprocedural loops over a thousand lines of code completely automatically from sequential applications.This article provides a comprehensive description of the analyses in the SUIF system. We also present extensive empirical results on four benchmark suites, showing the contribution of individual analysis techniques both in executing more of the computation in parallel, and in increasing the granularity of the parallel computations. These results demonstrate the importance of interprocedural array data-flow analysis, array privatization and array reduction recognition; a third of the programs spend more than 50% of their execution time in computations that are parallelized with these techniques. Overall, these results indicate that automatic parallelization can be effective on sequential scientific computations, but only if the compiler incorporates all of these analyses.
The THAP-Zinc Finger Protein THAP1 Associates with Coactivator HCF-1 and O-GlcNAc Transferase (2010)

THAP1 is a sequence-specific DNA binding factor that regulates cell proliferation through modulation of target genes such as the cell cycle-specific gene RRM1. Mutations in the THAP1 DNA binding domain, an atypical zinc finger (THAP-zf), have recently been found to cause DYT6 dystonia, a neurological disease characterized by twisting movements and abnormal postures. In this study, we report that THAP1 shares sequence characteristics, in vivo expression patterns and protein partners with THAP3, another THAP-zf protein. Proteomic analyses identified HCF-1, a potent transcriptional coactivator and cell cycle regulator, and O-GlcNAc transferase (OGT), the enzyme that catalyzes the addition of O-GlcNAc, as major cellular partners of THAP3. THAP3 interacts with HCF-1 through a consensus HCF-1-binding motif (HBM), a motif that is also present in THAP1. Accordingly, THAP1 was found to bind HCF-1 in vitro and to associate with HCF-1 and OGT in vivo. THAP1 and THAP3 belong to a large family of HCF-1 binding factors since seven other members of the human THAP-zf protein family were identified, which harbor evolutionary conserved HBMs and bind to HCF-1. Chromatin immunoprecipitation (ChIP) assays and RNA interference experiments showed that endogenous THAP1 mediates the recruitment of HCF-1 to the RRM1 promoter during endothelial cell proliferation and that HCF-1 is essential for transcriptional activation of RRM1. Together, our findings suggest HCF-1 is an important cofactor for THAP1. Interestingly, our results also provide an unexpected link between DYT6 and DYT3 (X-linked dystonia-parkinsonism) dystonias because the gene encoding the THAP1/DYT6 protein partner OGT maps within the DYT3 critical region on Xq13.1.
Reordering Schemes for Multiple-Rotation Fan-Beam CT Scanner (1985)

The number of detectors in a fan-beam CT scanner can be substantially decreased if a multiple-rotation data collection mode is used to provide appropriate spatial resolution. The efficiency of multiple-rotation schemes using a detector offset combined with angular shift of the detectors in each cycle for projection space filling is examined. It is shown that in reordering into parallel projections, angular interpolation can be avoided if an appropriate angular offset of the source with respect to the axis of a fan can be made in each cycle. To achieve even spacing of rays at the ends of the reordered parallel projections, the shifted positions of each detector must be symmetrical with respect to the position of the detector in the original symmetric fan. Results of the computer simulation are presented.
Palladium-Induced Lateral Crystallization of Amorphous-Germanium Thin Film on Insulating Substrate (2009)

In this article, metal (palladium, Pd)-induced lateral crystallization (MILC) of amorphous-germanium films prepared by room-temperature sputtering on an insulating material is observed and investigated using micro-Raman microscopy and transmission electron microscopy. The planar thin films were annealed at 300, 350, and in a ambient. The MILC phenomenon is not observed for the samples annealed at for 2 h, while the MILC phenomenon is observed for films annealed at 350 and for 2 h with a lateral growth rate of and , respectively. A poly-Ge film with a annealing temperature exhibits a smaller full width at half-maximum and a higher intensity of the sharp c-Ge peak than that annealed at , which can be the promising material candidate for Si-based three-dimensional integrated circuit applications.
Worldwide Genomic Diversity of the High-Risk Human Papillomavirus Types 31, 35, 52, and 58, Four Close Relatives of Human Papillomavirus Type 16 (2005)

Among the more than one hundred formally described human papillomavirus (HPV) types, 18 are referred to as high-risk HPV types due to their association with anogenital cancer. Despite pathogenic similarities, these types form three remotely related taxonomic groups. One of these groups is called HPV species 9 and is formed by HPV-16, the most common and best-studied type, together with HPV-31, -33, -35, -52, -58, and -67. Previous worldwide comparisons of HPV-16 samples showed about 2% nucleotide diversity between isolates, which were subsequently termed variants. The distribution of divergent variants has been found to correlate frequently with the geographic origin and the ethnicity of the infected patients and led to the concept of unique African, European, Asian, and Native American HPV-16 variants. In the current study, we address the question of whether geography and ethnicity also correlate with sequence variations found for HPV-31, -35, -52, and -58. This was done by sequencing the long control region in samples derived from Europe, Asia, and Africa, and from immigrant populations in North and South America. We observed maximal divergence between any two variants within each of these four HPV types ranging from 1.8 to 3.6% based on nucleotide exchanges and, occasionally, on insertions and deletions. Similar to the case with HPV-16, these mutations are not random but indicate a relationship between the variants in form of phylogenetic trees. An interesting example is presented by a 16-bp insert in select variants of HPV-35, which appears to have given rise to additional variants by nucleotide exchanges within the insert. All trees showed distinct phylogenetic topologies, ranging from dichotomic branching in the case of HPV-31 to star phylogenies of the other three types. No clear similarities between these types or between these types and HPV-16 exist. While variant branches in some types were specific for Europe, Africa, or East Asia, none of the four trees reflected human evolution and spread to the extent illustrated by HPV-16. One possible explanation is that the rare HPV types that we studied spread and thereby diversified more slowly than the more abundant HPV-16 and may have established much of today's variant diversity already before the worldwide spread of humans 100,000 years ago. Most variants had prototypic amino acid sequences within the E6 oncoprotein and a segment of the L1 capsid protein. Some had one, two, or three amino acid substitutions in these regions, which might indicate biological and pathogenic diversity between the variants of each HPV type.
Impaired Vasodilation in the Pathogenesis of Hypertension: Focus on Nitric Oxide, Endothelial‐Derived Hyperpolarizing Factors, and Prostaglandins (2012)

Under resting conditions the arterial vasculature exists in a vasoconstricted state referred to as vascular tone. Physiological dilatation in response to increased flow, a function of normal endothelium is necessary to maintain normal blood pressure. Endothelial dysfunction in vascular smooth muscle cells thus results in loss of normal vasorelaxant function and the inability of arteries to appropriately dilate in response to increased blood flow in either a systemic or regional vascular bed, resulting in increased blood pressure, a sequence that may represent a common pathway to hypertension. Normal vasorelaxation is mediated by a number of endothelial systems including nitric oxide (NO), prostaglandins (PGI2 and PGE2), and a family of endothelial-derived hyperpolarizing factors (EDHF). In response to hemodynamic shear stress, endothelium continuously releases NO, EDHF, and PGI2 to provide vasodilatation. EDHF, not a single molecule but rather a group of molecules that includes epoxyeicosatrienoic acids, hydrogen peroxide, carbon monoxide, hydrogen sulfide, C-natriuretic peptide, and K+ itself, causes vasodilatation by activation of vascular smooth muscle cell K+ channels, resulting in hyperpolarization and thus vasorelaxation. The understanding and effective management of blood pressure requires an understanding of both physiologic and pathophysiologic regulation of vascular tone. This review describes molecular mechanisms underlying normal endothelial regulation and pathological states, such as increased oxidative stress, which cause loss of vasorelaxation. Possible pharmacological interventions to restore normal function are suggested.
Cellulases from Penicillium funiculosum: production, properties and application to cellulose hydrolysis (2009)

The objective of this work is to investigate the utilization of two abundant agricultural residues in Brazil for the production and application of cellulolytic enzymes. Different materials obtained after pretreatment of sugarcane bagasse, as well as pure synthetic substrates, were considered for cellulase production by Penicillium funiculosum. The best results for FPase (354 U L(-1)) and beta-glucosidase (1,835 U L(-1)) production were observed when sugarcane bagasse partially delignified cellulignin (PDC) was used. The crude extract obtained from PDC fermentation was then partially characterized. Optimal temperatures for cellulase action ranged from 52 to 58 degrees C and pH values of around 4.9 contributed to maximum enzyme activity. At 37 degrees C, the cellulases were highly stable, losing less than 15% of their initial activity after 23 h of incubation. There was no detection of proteases in the P. funiculosum extract, but other hydrolases, such as endoxylanases, were identified (147 U L(-1)). Finally, when compared to commercial preparations, the cellulolytic complex from P. funiculosum showed more well-balanced amounts of beta-glucosidase, endo- and exoglucanase, resulting in the desired performance in the presence of a lignocellulosic material. Cellulases from this filamentous fungus had a higher glucose production rate (470 mg L(-1) h(-1)) when incubated with corn cob than with Celluclast, GC 220 and Spezyme (312, 454 and 400 mg L(-1) h(-1), respectively).
Progressive Data Hiding in Integer Wavelet Transform of Electrocardiogram by Using Simple Decision Rule and Coefficient Calibration (2020)

Based on one dimensional (1D) integer wavelet transform (IWT) domain, patient's data can be effectively embedded in electrocardiogram (ECG) via the proposed criterion and coefficient alignment.Multiple data bits can be sequentially hidden in host bundles (with different lengths) of the low and high subbands of IWT coefficients.Simulations indicated that the average signal-to-noise ratio (SNR) and the payload of the proposed method are superior to those of existing techniques.Additionally, the proposed method exhibited a robustness that has rarely been observed in conventional ECG steganography.Our method is capable of resisting attacks such as cropping, inversion, scaling, translation, truncation, and Gaussian noise addition.Because bit embedding and extraction procedures are quite simple, our method can be applied in portable biometric devices.
Energy-Efficient Neighbor Discovery in Mobile Ad Hoc and Wireless Sensor Networks: A Survey (2014)

Due to slow advance in battery technology, power remains a bottleneck to limit wide applications of mobile ad hoc and wireless sensor networks. Among all extensive studies on minimizing power consumption, neighbor discovery is one of the fundamental components focusing on communication and access. This work surveys research literature on neighbor discovery protocols (NDPs). In general, they can be roughly classified by four underlying principles: randomness, over-half occupation, rotation-resistant intersection, and coprime cycles. The Birthday protocols act as representatives of NDPs using randomness, in which a node decides to listen, transmit, or sleep with probabilities. The original idea of over-half occupation is to be active over at least half of each period, though several refinements have been proposed to decrease its high duty cycle. Methods of rotation-resistant intersection formulate the problem of discovery using combinatorial characteristics of discrete time slots, and guarantee discovery at least once per period. Moreover, neighbor discovery can also be guaranteed within a worst-case bound, as shown by methods adopting coprime cycles. In this paper, we elaborate on these ideas and present several representative protocols, respectively. In particular, we give an integrative analysis of deterministic protocols via a generic framework. A qualitative comparison incorporating multiple criteria and a quantitative evaluation on energy efficiency are also included. Finally, we point out promising research directions towards energy-efficient neighbor discovery.
Electronic transport in chemical vapor deposited graphene synthesized on Cu: Quantum\n Hall effect and weak localization (2010)

We report on electronic properties of graphene synthesized by chemical vapor deposition (CVD) on copper then transferred to SiO2/Si. Wafer-scale (up to 4 in.) graphene films have been synthesized, consisting dominantly of monolayer graphene as indicated by spectroscopic Raman mapping. Low temperature transport measurements are performed on microdevices fabricated from such CVD graphene, displaying ambipolar field effect (with on/off ratio similar to 5 and carrier mobilities up to similar to 3000 cm(2)/V s) and "half-integer" quantum Hall effect, a hall-mark of intrinsic electronic properties of monolayer graphene. We also observe weak localization and extract information about phase coherence and scattering of carriers.