gebhart/patrepeval huggingface dataset:
Intrinsic immunity against retrotransposons by APOBEC cytidine deaminases (2013)

Over 40% of the human genome is recognizable as having been derived from ancient retroelements, transported by an intracellular copy-and-paste process involving an RNA intermediate, with an additional few percent classified as DNA transposable elements. Endogenous retroviruses are long terminal repeat (LTR)-type retroelements that account for ~8% of human genomic DNA. Non-LTR members are present at extremely high copy numbers, with ~17% of the human genome consisting of long interspersed nuclear elements (LINEs). These LINEs modify vertebrate genomes not only through insertions, but also by the indirect replication of non-autonomous retrotransposons, such as short interspersed nuclear elements. As expected, vertebrate intrinsic immunity has evolved to support a balance between retroelement insertions that confer beneficial genetic diversity and those that cause deleterious gene disruptions. The mammalian cytidine deaminases encoded by the APOBEC3 genes can restrict a broad number of exogenous pathogens, such as exogenous retroviruses, and the mobility of endogenous retroelements. Furthermore, APOBEC1 from a variety of mammalian species, which mediates the cytidine (C) to uridine (U) deamination of apolipoprotein B (apoB) mRNA, a protein involved in lipid transport, also plays a role in controlling mobile elements. These mammalian apoB mRNA-editing, catalytic polypeptide (APOBEC) cytidine deaminases, which can bind to single-stranded DNA (ssDNA) as well as RNA, are able to insert mutations into ssDNA and/or RNA as a result of their ability to deaminate C to U. While these APOBEC cytidine deaminases with DNA mutagenic activity can be deleterious to cells, their biological modifications, such as protein-protein interactions and subcellular localization, in addition to their ability to bind to RNA, appear to have conferred a role for APOBECs as a cellular defense system against retroviruses and retroelements. In support of this notion, the expansion of the single APOBEC3 gene in mice to the seven APOBEC3 genes found in primates apparently correlates with the significant enhancement of the restriction of endogenous retroelements seen in primates, including humans. This review discusses the current understanding of the mechanism of action of APOBEC cytidine deaminases and attempts to summarize their roles in controlling retrotransposons.
Molecular characterization of beet necrotic yellow vein virus in Greece and transgenic approaches towards enhancing rhizomania disease resistance (2010)

Rhizomania disease of sugar beet, caused by Beet necrotic yellow vein virus (BNYVV), is responsible for severe economic losses. Due to the widespread occurrence of BNYVV and the absence of other practical and efficient control measures, economic viability of the crop is to the largest extent dependent on the use of varieties genetically resistant to the disease. Recent reports on the emergence of virus strains capable of compromising the Rz1-based resistance as well as on the spread of highly pathogenic RNA 5-containing BNYVV isolates have necessitated a detailed investigation of the situation as it evolves in Greece. The study revealed the widespread occurrence of BNYVV throughout the country as well as the prevalence of pathotype A isolates in all sugar beet growing regions. Sequence determination of the p25 protein, responsible for symptom development, pointed to the amino acid motifs ACHG/VCHG in the hypervariable amino acid region 67-70. However, the presence of valine (V) in position 67 was not associated with increased pathogenicity and resistance breaking properties. Disease severity appeared mostly dependent on agroclimatic conditions influencing the progress of the disease. A survey for a possible occurrence of Beet Soilborne Virus (BSBV) and Beet Virus Q (BVQ) in rhizomania infested fields revealed the co-existence of both viruses, with BVQ being systematically found in co-infections with BNYVV, while BSBV was in all cases only found in triple infections. Towards the exploitation of the antiviral properties of RNA silencing, three intron hairpin constructs carrying parts of the BNYVV replicase gene, were evaluated for their potential to confer rhizomania resistance in Ri T-DNA-transformed sugar beet roots. The results show that transgenic hairy roots were effectively protected against the virus disease and further indicate that the developed methodology for Agrobacterium rhizogenes-mediated transformation can be employed as a suitable platform to study transgene expression in sugar beet and other transformation recalcitrant crop species. In parallel, the potential to exploit the HrpZPsph protein from Pseudomonas syringae pv. phaseolicola for engineering rhizomania resistance in sugar beet against BNYVV was demonstrated by the successful engineering and protection against BNYVV in the model plant Nicotiana benthamiana
Load sharing of decentralized-controlled multiple mobile robots handling a single object (2002)

In this paper, we propose a decentralized control algorithm of multiple robots handling a single object in coordination. Different from our previous control algorithm the external force applied to the object, including the inertia force, is shared equally by all of the robots. The proposed control algorithm is experimentally applied to three mobile robots, each of which has one degree of freedom. The experimental results illustrate the validity of the proposed control system.
Influences of Background Noise on Infants and Children (2017)

The goal of this review is to provide a high-level, selected overview of the consequences of background noise on health, perception, cognition, and learning during early development, with a specific focus on how noise may impair speech comprehension and language learning (e.g., via masking). Although much of the existing literature has focused on adults, research shows that infants and young children are relatively disadvantaged at listening in noise. Consequently, a major goal is to consider how background noise may affect young children, who must learn and develop language in noisy environments despite being simultaneously less equipped to do so.
All-optical phase-sensitive waveform sampling at 40 GSymbol/s (2008)

We demonstrate a novel, high-resolution all-optical phase-sensitive sampling method using separate lasers for signal, sampling and mixing. A 40 GBaud DPSK signal was asynchronously sampled and visualized as a constellation diagram including transitions (625 ksamples).
KVZone and the search for a write-optimized key-value store (2010)

Key-value stores are becoming a popular choice for persistent data storage for a wide variety of applications, and multiple implementations are currently available. Deciding which one to use for a specific application requires comparing performance, a daunting task due to the lack of benchmarking tools for such purpose. We present KVZone, a tool specifically designed to evaluate key-value store performance. We used KVZone to search for a key-value store suitable for implementing a low-latency content-addressable store that supports write-intensive workloads. We present a comparative evaluation of three popular key-value stores: Berkeley DB, Tokyo Cabinet, and SQLite, and find that none is capable of approaching the IO rate of our persistent device (a high-throughput SSD). Finally, we present the Alphard key-value store which is optimized for such workloads and devices.
Alternative p38 MAPKs Are Essential for Collagen‐Induced Arthritis (2013)

Reduced disease severity in p38γ/δ(-/-) mice was associated with lower cytokine production and anticollagen antibody responses than in controls, indicating that p38γ and p38δ are crucial regulators of inflammatory joint destruction in CIA. Our findings indicate that p38γ and p38δ are potential therapeutic targets in complex diseases, such as rheumatoid arthritis, that involve innate and adaptive immune responses.
Biosorption: a solution to pollution? (2000)

To solve the water pollution problem by toxic heavy metal contamination resulting from humans technological activities has for long presented a challenge. Biosorption can be a part of the solution. Some types of biosorbents such as seaweeds, molds, yeasts, bacteria or crab shells are examples of biomass tested for metal biosorption with very encouraging results. The uptake of heavy metals by biomass can in some cases reach up to 50% of the biomass dry weight. New biosorbents can be manipulated for better efficiency and multiple re-use to increase their economic attractiveness.
Development of a micromachined THz nanoklystron: a status report (2004)

Summary form only given. A novel monolithic micro-tube source for submillimeter-wave (0.3 THz, 0.6 THz, 1.2 THz) power generation is being developed at JPL. The tube takes the form of a simple reflex klystron with micrometer range dimensions, nanoklystron, fabricated monolithically in silicon. Nanoklystrons are to be used as local oscillator elements for high-resolution heterodyne spectroscopy instruments and as THz sources for bio-imagers and contraband detectors, high bandwidth communications and atmospheric chemical and biohazard probes. Initial estimates indicate power output in the range of milliwatts at 1.2 THz, which is significantly higher than that possible with other oscillators or multiplier based sources. The device requires an electron gun capable of providing up to a kA/cm/sup 2/. Both cold and hot cathodes are being developed, with cold cathodes being the preferred choice for the eventual stand-alone device. Through a systematic study, "ropes" of multi-walled carbon nanotubes (MWNTs) have been identified as the most suitable candidate for the electron source. Using MWNTs synthesized on e-beam patterned catalyst arrays with varying parameters (bundle diameter and inter-bundle spacing), a suitable arrangement for high emission currents at low fields has been determined. We can repeatedly generate >1.4 A/cm/sup 2/ at fields as low as <3 V//spl mu/m, prior to focusing. The raw emission density can be further increased and this, in combination with beam focusing optics, is expected to achieve the required target current densities. For initial testing, a very high-resolution crossover type hot electron gun has been developed. The gun was designed to deliver /spl sim/0.5 kA/cm/sup 2/ at the repeller of the nanoklystron. The source current density was designed for 16.2 A/cm2. The gun includes three grids, one electrostatic lens and a magnetic lens and is mounted with a 0.6 THz copper constructed nanoklystron with a phosphor screen at the back end. The electron beam was successfully focused onto the phosphor screen behind the device (through the empty repeller hole) in a tunnel of /spl sim/40 /spl mu/m diameter. A current of 3.4 mA was recorded at the phosphor screen amounting to a current density of /spl sim/270 A/cm/sup 2/. This gun will be used for device testing after a shaped repeller electrode has been installed.
Simulation of thin-film growth (1993)

A two-dimensional simulation model of thin-film deposition, which involves the effect of the incident kinetic energy of atoms and the mobility of the substrate temperature, is developed. Lennard-Jones potential and nuclear scattering are used to characterize the atom-atom interaction. The effect of substrate temperature on the relaxation of depositing particles is also considered. Some simulation results are presented and discussed in detail.
Targeting the Ubiquitin-Proteasome Pathway in Cancer Therapy (2007)

The ubiquitin-proteasome pathway plays a central role in the degradation of proteins involved in several pathways including the cell cycle, cellular proliferation and apoptosis. Bortezomib is the first proteasome inhibitor to enter clinical use, and received approval by the Food and Drug Administration (FDA) for the treatment of patients with multiple myeloma, therefore validating inhibition of the proteasome as an anticancer target. The approval of Bortezomib was based on a large, international, multicenter phase III trial showing its efficacy and safety compared with conventional therapy. Preclinical data also demonstrates the synergistic effect of bortezomib with other chemotherapeutic agents and its ability to overcome drug resistance. Since then several other proteasome inhibitors have been developed. The anti-tumor activities of bortezomib have been attributed to its effect on pro-apoptotic pathways including the inhibition of NF-kappaB and induction of endoplasmic reticulum stress. However, the molecular mechanisms are not fully understood. In this review, we will summarize the molecular mechanism of apoptosis by bortezomib.
The Career of Tiberius Claudius Cogidubnus (1979)

By the time that the Romans had become involved in the affairs of Britain the use of client-kings as an instrument of foreign policy and military strategy was well-established. It is hardly surprising, then, that the employment of local chieftains, often against other local chieftains, should have been an important aspect of Caesar's policy. It was also a policy maintained by Claudius nearly a century later when he undertook the final conquest of Britain. The names of some of the rulers who threw in their lots with the Romans, such as Bodvoc(us), Cartimandua, Prasutagus, are of course, familiar, but none is more celebrated than the man generally considered the perfect exemplum of the British client-king, Tiberius Claudius Cogidubnus. We have grown accustomed to thinking of Cogidubnus as a ruler who unreservedly embraced Roman authority and the Roman way of life, and who throughout his career epitomizes the benefits that Roman civilization can bestow on other nations. So prominent a place is he given in general accounts of the conquest, and so vivid a personality has he acquired, that it comes almost as a suprise to realize that there are only two ancient references to Tiberius Claudius Cogidubnus.
Tumor antigen delivered by Salmonella III secretion protein fused with heat shock protein 70 induces protection and eradication against murine melanoma (2010)

Attenuated Salmonella typhimurium possess the ability to stimulate innate immune responses and preferentially allocate within the solid tumor. These two main characteristics make attenuated Salmonella one of the most attractive vehicles for development of vaccine and also targeted cancer therapies. However, location of Salmonella prevents the process of antigen presentation. Salmonella Type III secretion system can be utilized to circumvent this problem because this system secretes the protein it encoded outside the cells. Heat shock protein 70 (Hsp70) is referred to as an "immunochaperone" for its capacity to elicit tumor-specific adaptive immune responses in the form of Hsp70-TAA (tumor associated antigen) complex. Hsp70 facilitates the cross-presentation of exogenous antigens through its receptor on antigen-presenting cells and therefore activates an antigen-specific cytotoxic T lymphocyte (CTL) response, which can directly contribute to potent anti-tumor immunity. Here, we designed a novel therapeutic vaccine utilizing the type III secretion system and Hsp70 to deliver and present the tumor-specific antigen. This live recombinant bacteria vaccine, when administrated orally, successfully broke the immune tolerance, induced a specific CTL response against tumor cells, and therefore revealed protective and therapeutic effects against generation and growth of B16F10 melanoma in C57BL/6J mice.
Integrated Analyses of Copy Number Variations and Gene Expression in Lung Adenocarcinoma (2011)

Numerous efforts have been made to elucidate the etiology and improve the treatment of lung cancer, but the overall five-year survival rate is still only 15%. Identification of prognostic biomarkers for lung cancer using gene expression microarrays poses a major challenge in that very few overlapping genes have been reported among different studies. To address this issue, we have performed concurrent genome-wide analyses of copy number variation and gene expression to identify genes reproducibly associated with tumorigenesis and survival in non-smoking female lung adenocarcinoma. The genomic landscape of frequent copy number variable regions (CNVRs) in at least 30% of samples was revealed, and their aberration patterns were highly similar to several studies reported previously. Further statistical analysis for genes located in the CNVRs identified 475 genes differentially expressed between tumor and normal tissues (p<10(-5)). We demonstrated the reproducibility of these genes in another lung cancer study (p = 0.0034, Fisher's exact test), and showed the concordance between copy number variations and gene expression changes by elevated Pearson correlation coefficients. Pathway analysis revealed two major dysregulated functions in lung tumorigenesis: survival regulation via AKT signaling and cytoskeleton reorganization. Further validation of these enriched pathways using three independent cohorts demonstrated effective prediction of survival. In conclusion, by integrating gene expression profiles and copy number variations, we identified genes/pathways that may serve as prognostic biomarkers for lung tumorigenesis.
Primary role of sarcoplasmic reticulum in phasic contractile activation of cardiac myocytes with shunted myolemma. (1981)

Homogeneous populations of single myocytes showing good preservation of ultrastructure were obtained by enzymatic digestion of rabbit and rat hearts, and maintained in a relaxed state in the presence of free Ca2+ concentrations less than 10(-7) M. Ultrastructural details such as a cytoskeleton of 100-A filaments connected to the sarcolemma at the Z lines were demonstrated especially well in these preparations. In spite of seemingly normal structure, electron probe analysis of cryosections reveals similar concentrations of electrolytes in the medium and in the cytoplasm, indicating the presence of electrochemical shunting across the external membrane. The dissociated myocytes display Ca uptake and phasic contractions that are apparently dependent on mitochondrial respiration, but are not affected by mitochondrial uncouplers when ATP and phosphocreatine are added. The uptake is augmented by oxalate and, based on identification of calcium oxalate crystals by electron microscopy and electron probe analysis, is localized to the sarcoplasmic reticulum (SR). An advantageous feature of the dissociated myocytes is that they are suitable for experiments using large numbers of cells in suspension. Thereby, velocities of calcium transport were measured directly by isotopic tracer and filtration methods. It was then found that the lowest CA2+ concentrations (5 x 10(-7) M for the rabbit and 1 x 10(-7) M for the rat) sustaining Ca transport also induce phasic contractile activity in all myocytes, even though the external membrane is electrochemically shunted. A stepwise rise in the Ca2+ concentration of up to one order of magnitude, increases transport velocities in parallel with the rates of phasic contractions. Both these parameters are affected by Mg2+, temperature, cyclic-AMP, and methylxanthines, even though the Ca2+ concentration is maintained constant in the medium. Therefore, Ca transport by SR is a requirement and a rate limiting factor for the occurrence of phasic contractile activation in dissociated cardiac cells retaining an electrochemically shunted external membrane. It is suggested that transient Ca release required for phasic contractile activation is due to equilibrium oscillations across the SR membrane. The sequential pattern of sarcomere activation is consistent with a self propagating mechanism of calcium release. SR in dissociated skeletal muscle cells sustains a greater Ca transport activity than in dissociated heart cells. However, the heart cells display a much higher phasic contractile activity, indicating that cardiac SR has a greater tendency to release accumulated calcium. If free Ca2+ in the medium is raised above 10(-6) M, both cardiac and skeletal myocytes undergo contractures and degenerative phenomena, accompanied by Ca, Mg, and phosphate accumulation in cardiac mitochondria.
A quartz crystal microbalance dew point sensor without frequency measurement (2014)

This work deals with the design of a dew point sensor based on Quartz Crystal Microbalance (QCM) without measuring the frequency. This idea is inspired by the fact that the Colpitts oscillation circuit will stop oscillating when the QCM works in the liquid media. The quartz crystal and the electrode are designed through the finite element simulation and the stop oscillating experiment is conducted to verify the sensibility. Moreover, the measurement result is calibrated to approach the true value. At last a series of dew points at the same temperature is measured with the designed sensor. Results show that the designed dew point sensor is able to detect the dew point with the proper accuracy.
Rotavirus Vaccination and the Global Burden of Rotavirus Diarrhea Among Children Younger Than 5 Years (2018)

Rotavirus-associated mortality has decreased markedly over time in part because of the introduction of the rotavirus vaccine. This study suggests that prioritizing vaccine introduction and interventions to reduce diarrhea-associated morbidity and mortality is necessary in the continued global reduction of rotavirus infection.
Feedback-directed instrumentation for deployed JavaScript applications (2016)

Many bugs in JavaScript applications manifest themselves as objects that have incorrect property values when a failure occurs. For this type of error, stack traces and log files are often insufficient for diagnosing problems. In such cases, it is helpful for developers to know the control flow path from the creation of an object to a crashing statement. Such crash paths are useful for understanding where the object originated and whether any properties of the object were corrupted since its creation.
Isotope ratio characteristics and sensitivity for uranium determinations using a liquid sampling-atmospheric pressure glow discharge ion source coupled to an Orbitrap mass analyzer (2016)

The coupling of an LS-APGD microplasma with an Orbitrap analyzer is applied to the isotope ratio analysis of uranium.
Stm1p alters the ribosome association of eukaryotic elongation factor 3 and affects translation elongation (2009)

Stm1p is a Saccharomyces cerevisiae protein that is primarily associated with cytosolic 80S ribosomes and polysomes. Several lines of evidence suggest that Stm1p plays a role in translation under nutrient stress conditions, although its mechanism of action is not yet known. In this study, we show that yeast lacking Stm1p (stm1Delta) are hypersensitive to the translation inhibitor anisomycin, which affects the peptidyl transferase reaction in translation elongation, but show little hypersensitivity to other translation inhibitors such as paromomycin and hygromycin B, which affect translation fidelity. Ribosomes isolated from stm1Delta yeast have intrinsically elevated levels of eukaryotic elongation factor 3 (eEF3) associated with them. Overexpression of eEF3 in cells lacking Stm1p results in a growth defect phenotype and increased anisomycin sensitivity. In addition, ribosomes with increased levels of Stm1p exhibit decreased association with eEF3. Taken together, our data indicate that Stm1p plays a complementary role to eEF3 in translation.