gebhart/patrepeval huggingface dataset:
A Survey of the Genome of the Hyperthermophilic Archaeon, Pyrococcus furiosus (1996)

Pyrococcus furiosus is a marine microorganism with the unusual ability to grow optimally at 100°C. It is classified as a member of the domain Archaea (Archaebacteria). We present studies on the genome of P. furiosus, consisting of a precise determination of the size of the chromosome, 2.05 mb, and an analysis of sequence data from cDNA and genomic libraries. The sequence analysis included a total of 1176 sequences, representing 14.7% of the genome, which were compared with the current databases using the BLAST X algorithm. Expressed sequence tag (EST) analysis is skewed toward the repeated detection of highly expressed genes, for example, ribosomal RNA, in P. furiosus. The relatively small size of the genome implies a high coding density, and randomly chosen genomic sequences provide good performance in gene discovery with relatively fewer identical hits compared with the EST database. The recovery of database matches with P(n) ≤ 1.0e−05 was 30% of the total sequences tested. We estimate that the genome contains approximately 1800 genes, and this study has provided evidence for 309 genes. The average G+C content of the sequences obtained was 41.2%, and no repetitive sequences were detected. Genes from Eukarya and Bacteria are almost equally represented in the matches obtained in this study. The homologs representing central metabolism exhibit preferential similarity to their homologs from bacteria, despite the availability of eukaryotic homologs in the databases. Several characteristically eukaryotic protein homologs were found with functions in transcription, translation, and membrane transport. We propose that the archaeal genome is a mosaic, consisting of ancient gene sequences related to eukaryal homologs and more recently acquired genes, many of which are related to bacterial metabolic functions. Further sequencing and phylogenetic studies are needed to confirm this hypothesis, which predicts that there was extensive lateral genetic transfer among Bacteria, Eukarya, and Archaea during a period when the original gene pool was expanding into the early lineages of life.
Studying the fragmentation behavior of peptides with arginine phosphorylation and its influence on phospho‐site localization (2012)

Phospho-proteomic studies opened a broad view onto the main mechanisms of regulating cellular processes. Our recent discovery of a protein arginine kinase and its target in bacteria added a previously undescribed type of phosphorylation to control protein activity. Several challenges arise from large in vivo studies of this and other types of phosphorylations. The main factors impeding correct localization are low spectral quality, neutral loss of phosphoric acid, and gas-phase rearrangements, which have recently been described for phospho-serine, -threonine, and -tyrosine. Studies on histidine-phosphorylated peptides, a nitrogen-bound phosphorylation, also reported loss of phosphoric acid upon collision-induced dissociation. We were interested in studying the behaviour of arginine phosphorylation under different fragmentation conditions and its influence on site localization. First, we determined the percentage of false localizations obtained by three different search engines and a software tool dedicated for phospho-site determination. Next, we demonstrate that application of collisional activation for analysis of arginine-phosphorylated peptides leads to extensive elimination of phosphoric acid and increases the numbers of false localizations, while the modification is maintained on the arginine side chain upon electron-transfer dissociation. Furthermore, we also observed a rearrangement of the phosphorylation onto serine and glutamic acid side chains upon collisional activation.
Stabilization of Rice Bran with Extruder Cookers and Recovery of Edible Oil: A Preliminary Analysis of Operational and Financial Feasibility (1981)

This report, which describes technical and economic aspects of edible oil recovery from bran stabilized by extrusion cooking, is based upon 1979 site visits to India, Egypt, and Burma, and interaction with persons involved in those phases of rice delivery systems expected to impinge upon rice bran oil production. Models are described in which bran produced at small or large two-stage rice mills is stabilized either in centralized or decentralized operations and is then subjected to oil extraction and refining. The effects upon return on investment of variable stabilization and bran costs and oil extraction and refining yields are examined. Edible oil recovery from rice bran is shown to be economically feasible under a wide range of technical and economic conditions. Data used to arrive at this conclusion should be applicable to situations in other countries. This project was carried out by the Office of International Cooperation and Development, and the Western Regional Research Center, U.S. Department of Agriculture, on behalf of the Office of Nutrition, U.S. Agency for International Development.
Search for nonstandard neutrino interactions with IceCube DeepCore (2018)

As atmospheric neutrinos propagate through the Earth, vacuumlike oscillations are modified by Standard Model neutral- and charged-current interactions with electrons. Theories beyond the Standard Model introduce heavy, TeV-scale bosons that can produce nonstandard neutrino interactions. These additional interactions may modify the Standard Model matter effect producing a measurable deviation from the prediction for atmospheric neutrino oscillations. The result described in this paper constrains nonstandard interaction parameters, building upon a previous analysis of atmospheric muon-neutrino disappearance with three years of IceCube DeepCore data. The best fit for the muon to tau flavor changing term is ${\ensuremath{\epsilon}}_{\ensuremath{\mu}\ensuremath{\tau}}=\ensuremath{-}0.0005$, with a 90% C.L. allowed range of $\ensuremath{-}0.0067&lt;{\ensuremath{\epsilon}}_{\ensuremath{\mu}\ensuremath{\tau}}&lt;0.0081$. This result is more restrictive than recent limits from other experiments for ${\ensuremath{\epsilon}}_{\ensuremath{\mu}\ensuremath{\tau}}$. Furthermore, our result is complementary to a recent constraint on ${\ensuremath{\epsilon}}_{\ensuremath{\mu}\ensuremath{\tau}}$ using another publicly available IceCube high-energy event selection. Together, they constitute the world's best limits on nonstandard interactions in the $\ensuremath{\mu}\ensuremath{-}\ensuremath{\tau}$ sector.
Cascadability and fanout of semiconductor optical amplifier wavelength shifter (1992)

Data at bit rates of 1 or 2 Gb/s are transferred through two cascaded, broadband wavelength shifters, which operate using gain saturation in semiconductor optical amplifiers. Such devices copy data from a modulated pump signal, in which the intensity of the marks is sufficient to significantly compress the gain of the amplifier, to a CW probe signal, producing the complement of the data. Furthermore, fanout (multicasting) is demonstrated in a single device by using two input CW probe signals. Such devices may find importance in wavelength division multiplexed systems requiring wavelength reuse and reassignment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
TU-FG-BRC-03: Current Clinical Trials Using Radiation and Immunomodulatory Agents (2016)

There is substantial current interest in the potential of radiation therapy for synergizing with novel immunotherapies to transform irradiated tumor into an immunogenic hub with capacity to ignite a powerful and adaptive longterm anti-cancer response. Interest stems from new insights into fundamental mechanisms underlying interactions between cancer, radiation and the immune system. Radically new immunotherapy approaches have been proposed, which target the immune system, rather than the cancer itself. Promising preliminary results on subsets of patients have led to a surge in research and clinical trials investigating the potential for combining new immunomodulatory agents with radiation therapy. In this symposia, we undertake a basic review of key topics and questions relating to the potential for combining radiation therapy and new immunotherapy approaches, including a focus on opportunities for medical physicists. Learning Objectives: 1. Gain insight into approaches to combining immunotherapy and radiation therapy. 2. Review latest clinical trial data investigating radiation and immunotherapy. 3. Consider how radiation therapy can better stimulate immunogenicity. 4. Explore opportunities for medical physicists in radiation and immunotherapy M Oldham has funding support from Immunolioght Llc
Pulsed amperometric detection of carbohydrates at gold electrodes with a two-step potential waveform (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPulsed amperometric detection of carbohydrates at gold electrodes with a two-step potential waveformGlen G. Neuburger and Dennis C. JohnsonCite this: Anal. Chem. 1987, 59, 1, 150–154Publication Date (Print):January 1, 1987Publication History Published online1 May 2002Published inissue 1 January 1987https://pubs.acs.org/doi/10.1021/ac00128a031https://doi.org/10.1021/ac00128a031research-articleACS PublicationsRequest reuse permissionsArticle Views340Altmetric-Citations68LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Shaft Seal Compensates for Cold Flow (1985)

Seal components easy to install. Ring seal for rotating or reciprocating shafts spring-loaded to compensate for slow yielding (cold flow) of sealing material. New seal relatively easy to install because components preassembled, then installed in one piece.
Enhancement of third-order nonlinearity of thermally evaporated GeSbSe waveguides through annealing (2019)

Chalcogenides are a promising platform for infrared nonlinear optics but are susceptible to structural changes during fabrication that affect their linear and nonlinear optical properties. We analyze the structure and optical properties of thermally evaporated and annealed chalcogenide films. Thermally evaporated Ge<sub>28</sub>Sb<sub>12</sub>Se<sub>60</sub> has an increased selenium content, bandgap, and concentration of heteropolar bonds. The concentration of heteropolar bonds can be reduced by annealing above the glass transition temperature, resulting in improved optical nonlinearity. We demonstrate a 4-fold enhancement of third-order nonlinearity in Ge<sub>28</sub>Sb<sub>12</sub>Se<sub>60</sub> chalcogenide waveguides by thermal annealing and a decrease in propagation loss from 2.5 dB/cm to 1 dB/cm as an added benefit.
Visual signals: color and light production (2012)

The Insects has been the standard textbook in the field since the first edition published over forty years ago. Building on the strengths of Chapman's original text, this long-awaited 5th edition has been revised and expanded by a team of eminent insect physiologists, bringing it fully up-to-date for the molecular era. The chapters retain the successful structure of the earlier editions, focusing on particular functional systems rather than taxonomic groups and making it easy for students to delve into topics without extensive knowledge of taxonomy. The focus is on form and function, bringing together basic anatomy and physiology and examining how these relate to behaviour. This, combined with nearly 600 clear illustrations, provides a comprehensive understanding of how insects work. Now also featuring a richly illustrated prologue by George McGavin, this is an essential text for students, researchers and applied entomologists alike.
Gas-Lift Valve Performance Testing (1993)

Abstract Gas lift valves are used in many producing wells to increase or maintain production. The spacing of valves in the well, calculation of opening or closing pressures, and selection of port size all play an integral role in the success of unloading and lifting operations. The design procedures that have been developed through the years include many safety factors; however, some of these were based on erroneous assumptions concerning the flow performance of gas lift valves; subsequently, many problems resulted. Now that recent developments in gas lift valve mechanics have addressed the importance of using gas lift valve performance testing in predicting a valve's true flow performance, considerably more interest is being shown in this topic. One gas lift valve manufacturer has been furnishing gas lift valve performance data and using the data to perform gas lift valve spacing designs since 1962. This paper will answer the questions of what constitutes performance data, why there is a need for this data and what types of testing techniques must be conducted to obtain a valve's true flow performance when subjected to subsurface conditions. The methods for performing the tests will also be discussed.
Common-base intermodulation characteristics of advanced SiGe HBTs (2008)

Common-base (CB) linearity performance of insensitive to these various parameters. However, at high currents, these factors each play a significant role in determining overall CB linearity. We show that CB linearity performance of SiGe HBTs can be well-predicted by the standard VBIC model.
Optimization of data-independent acquisition using predicted libraries for deep and accurate proteome profiling (2020)

ABSTRACT In silico spectral library prediction of all possible peptides from whole organisms has a great potential for improving proteome profiling by data-independent acquisition (DIA) and extending its scope of application. In combination with other recent improvements in the field of mass spectrometry (MS)-based proteomics, including sample preparation, peptide separation and data analysis, we aimed to uncover the full potential of such an advanced DIA strategy by optimization of the data acquisition. The results demonstrate that the combination of high-quality in silico libraries, reproducible and high-resolution peptide separation using micro-pillar array columns as well as neural network supported data analysis enables the use of long MS scan cycles without impairing the quantification performance. The study demonstrates that mean coefficient of variations of 4 % were obtained even at only 1.5 data points per peak (full width at half maximum) across different gradient lengths, which in turn improved proteome coverage up to more than 8000 proteins from HeLa cells using empirically-corrected libraries and more than 7000 proteins using a whole human in silico predicted library. These data were obtained using a Q Exactive orbitrap mass spectrometer with moderate scanning speed (12 Hz) and perform very well in comparison to recent studies using more advanced MS instruments, which underline the high potential of this optimization strategy for various applications in clinical proteomics, microbiology and molecular biology.
A lineage-tracing tool to map the fate of hypoxic tumour cells (2020)

Abstract Intratumoural hypoxia is a common characteristic of malignant treatment-resistant cancers. However, hypoxia-modification strategies for the clinic remain elusive. To date little is known on the behaviour of individual hypoxic tumour cells in their microenvironment. To explore this issue in a spatial and temporally-controlled manner we developed a genetically encoded sensor by fusing the O 2 -labile Hypoxia-Inducible Factor 1α to eGFP and a tamoxifen-regulated Cre recombinase. Under normoxic conditions HIF-1α is degraded but under hypoxia, the HIF-1α-GFP-Cre-ER T2 fusion protein is stabilised and in the presence of tamoxifen activates a tdTomato reporter gene that is constitutively expressed in hypoxic progeny. We visualise the random distribution of hypoxic tumour cells from hypoxic or necrotic regions and vascularised areas using immunofluorescence and intravital microscopy. Once tdTomato expression is induced, it is stable for at least 4 weeks. Using this system, we could show that the post-hypoxic cells were more proliferative in vivo than non-labelled cells. Our results demonstrate that single-cell lineage tracing of hypoxic tumour cells can allow visualisation of their behaviour in living tumours using intravital microscopy. This tool should prove valuable for the study of dissemination and treatment response of post-hypoxic tumour cells in vivo at single-cell resolution. Summary Statement Here we developed and characterised a novel HIF-1α-Cre fusion gene to trace the progeny of hypoxic tumour cells in a temporal and spatially resolved manner using intravital microscopy.
An eigenvalue characterization of multivariable system zeros (1977)

A characterization of multivariable system zeros as the common eigenvalues of certain matrices is obtained. Major differences are noted between this and other approaches, including implementation and interpretation of results. In addition, a useful determinantal identity is proven.
High Frequency Performance of Graphene Transistors Grown by Chemical Vapor Deposition for Mixed Signal Applications (2011)

This paper demonstrates high frequency performance of graphene transistors grown by chemical vapor deposition on copper foils. Using Ti/Pd/Au-based ohmic contacts and a hybrid gate dielectric stack of 5 nm SiO 2 and 15 nm Al 2 O 3 grown by atomic layer deposition, graphene transistors with an extrinsic current-gain cut-off frequency ( f T ) of 2 GHz and power-gain cut-off frequency, f max , of 5.6 GHz were obtained for a gate length of L g = 1.6 µm. By applying a bias to the Si substrate the access resistances are reduced, which improved the f T and f max in the devices to 3.5 and 6.5 GHz, respectively. Finally we demonstrate these devices in a real-application circuit for binary-phase shift keying.
Anterior mitral valve aneurysm perforation secondary to aortic valve endocarditis detected by Doppler colour flow mapping (1989)

We report a case of mitral valve aneurysm formation and perforation, secondary to Streptococcus sanguis endocarditis of the aortic valve. Aneurysm formation was documented by cross-sectional echocardiography and its perforation was established by Doppler colour flow mapping, and subsequently confirmed at surgery.
Influence of a Specialized Trigonella foenum‐graecum Seed Extract (Libifem), on Testosterone, Estradiol and Sexual Function in Healthy Menstruating Women, a Randomised Placebo Controlled Study (2015)

The aim of the study was to evaluate the effect of Trigonella foenum-graecum (fenugreek) seed extract on sex hormones and sexual function in healthy menstruating women who reported low sexual drive. This short term, single site, double blind, randomised, placebo-controlled study was conducted on 80 women, aged 20 to 49 years. Participants were randomised to either an oral dose of a standardised T. foenum-graecum seed extract (libifem) at a dose of 600 mg/day or placebo over two menstrual cycles. Dehydroepiandrosterone sulfate, progesterone, androstenedione, total and free testosterone, estradiol (E2), luteinizing hormone, follicle stimulating hormone, sex hormone binding globulin and cholesterol were measured at baseline and 8 weeks. The individual aspects of sexual function were measured using the Derogatis interview for sexual functioning and female sexual function index self-administered questionnaires. Stress, fatigue and quality of the relationship with partner were also measured using the PSS (Perceived Stress Scale), MFI-20 (Multidimensional Fatigue Inventory) and DAS (Dyadic Adjustment Scale) quality of life measures, respectively. There was a significant increase in free testosterone and E2 in the active group as well as sexual desire and arousal compared with the placebo group. The results indicate that this extract of T. foenum-graecum may be a useful treatment for increasing sexual arousal and desire in women.
Insulin, C-Peptide, and Leptin Concentrations Predict Increased Visceral Adiposity at 5- and 10-Year Follow-Ups in Nondiabetic Japanese Americans (2005)

We prospectively examined the relationship between leptin and markers of insulin resistance and secretion and future visceral adipose tissue accumulation. In this study, 518 nondiabetic Japanese-American men and women underwent the following measurements at baseline and at 5- and 10-year follow-ups: plasma glucose and insulin measured after an overnight fast and during a 75-g oral glucose tolerance test, insulin secretion ratio (ISR) [(30-min insulin - fasting insulin)/30-min glucose], fasting C-peptide levels, plasma leptin (baseline only), and fat areas (intra-abdominal and subcutaneous) measured by computed tomography. Predictors of future intra-abdominal fat (IAF) were determined using multiple linear regression. Fasting insulin and C-peptide levels at baseline were significantly associated with IAF area at 5 years (coefficient = 0.041, P = 0.001 and coefficient = 1.283, P < 0.001, respectively) and 10 years (coefficient = 0.031, P = 0.020 and coefficient = 0.221, P = 0.035, respectively). ISR was not significantly associated with IAF at 5 or 10 years. Leptin level at baseline was positively associated with IAF at 5 years (coefficient = 0.055, P = 0.002) and 10 years (coefficient = 0.059, P = 0.003). In conclusion, higher levels of fasting insulin, C-peptide, and circulating leptin level predicted visceral fat accumulation independent from subcutaneous fat accumulation in nondiabetic Japanese-American men and women in both short-term (5 years) and long-term (10 years) follow-up.