gebhart/patrepeval huggingface dataset:
The use of entropy to characterize coding genes for translation of proteins from DNA (2005)

The entropies of protein genes froin E. Coli were calculated according to Bolhmann's formula. Entropies of the coding regions were compared to the entropies of noncoding or miscoding ones using first nucleotides, and then triplets of nucleotides as coding units. Biologically functional proteins had significantly higher entropies than proteins translated from the frameshifted sequences, while with triplets of nucleotides as code units, the results were opposite. We attempt to explain this paradox with the hypothesis that the Results: The entropies of protein coding genes have been calculated, compared and related to the infomation content and biological significance. The analysis initially covered the total of 42,353 base pairs organized in 20 sequences of protein coding genes from E. coli and together they represented approximately 1% of its genome. The average entropy of a complete gene expressed in binary units with nucleotide as a code unit was 1.99225 bits per nucleotide, only slightly different from the entropy.of only the coding region. With triplets as code units, the entropies of biologically functional sequences were compared to the entropies of frameshifted sequences. The sequences containing biological information had a lower entropy than the frameshifted sequences which lack that information. Observed were average differences of 0.21474 bits and 0.28872 bits between entropy of the reading frame and frameshifts +I and -1, respectively. The analogous analysis with amino acids as code units gave opposite results: protein sequences which are biologically functional have shown higher entropies than protein sequences which are products of the frameshift and hence lack any biological function. Conclusion: Results of this analysis support the idea that entropy calculated could be used as an indicator for the functional information contained in DNA. The entropies of correct and reading frames using triplets as coding units were significantly lower thaa those of frameshifted units. This reflects the expectation that sequences containing a definite biological information should have a lower entropy than those which lack any that information. However, biologically functional proteins that originate from the correct reading frame showed significantly higher entropies than sequences unable to yield functional proteins. We assume that the genetic code may have the ability OC increasing entropy of proteins while translating them from the DNA sequence. This ability might be beneficial to orgai~isms'~ because it would make the functionaI proteins more probable (having a higher entropy) than nonfunctional ones produced by frameshifted translation (mutation) of the genetic information. References:
Parameter Screening in Dynamic Computer Model Calibration Using Global Sensitivities (2010)

Sensitivity analysis and computer model calibration are generally treated as two separate topics. In sensitivity analysis one quantifies the effect of each input factor on outputs, whereas in calibration one finds the values of input factors that provide the best match to a set of field data. In this paper we show a connection between these two seemingly separate concepts, and illustrate it with an automotive industry application involving a Road Load Acquisition Data (RLDA) computer model. We use global sensitivity analysis for computer models with transient responses to screen out inactive input parameters and make the calibration algorithm numerically more stable. Because the computer model can be computationally intensive, we construct a fast statistical surrogate for the computer model with transient responses. This fast surrogate is used for both sensitivity analysis and RLDA computer model calibration.
Influence of Solution Treatment under (Unrecrystallizing Condition for Austenite Unrecrystallization Solution Treatment) on Martensite Structure of 18% Ni Maraging Steel (1987)

逆変態オーステナイト(γ)の再結晶温度の高いボロン添加18%Niマルエージ鋼において,γの未再結晶温度域での溶体化処理(未再結晶溶体化処理)のマルテンサイト(α')組織の形態におよぼす影響と,強度との関係を検討し,次のことを明らかにした.未再結晶溶体化処理の加熱温度の変化によるラスマルテンサイト組織の形態変化は,γ中の転位密度の変化に対応している.また,この形態変化は炭素量を変化させた場合の変化とよく符合している.すなわち,低温域の未再結晶溶体化処理で得られる高密度の転位を含む逆変態γからの変態では,パケット,ブロックという階層的な紐織構成が失われて,0.4% C以上の中,高炭素鋼,合金鋼のラスマルテンサイトとよく似た組織となる.γの中の回復が進行する高温域での未再結晶溶体化処理では,0.1%～0.3% Cの低炭素鋼と類似の組織となり,ブロックは微細化するが,階層的な構成は保たれた組織となる.未再結晶溶体化処理によるα'の強度上昇は,この組織の細分化によって支えられている.γ中の回復の進行に伴つて,α'の強度は低下するが,高温域での未再結晶溶体化処理でも,ブロックの微細化により,再結晶γより生じたα'よりも高い値となる.
Interactive Slice WIM: Navigating and Interrogating Volume Data Sets Using a Multisurface, Multitouch VR Interface (2011)

We present Interactive Slice World-in-Miniature (WIM), a framework for navigating and interrogating volumetric data sets using an interface enabled by a virtual reality environment made of two display surfaces: an interactive multitouch table, and a stereoscopic display wall. The framework addresses two current challenges in immersive visualization: 1) providing an appropriate overview+detail style of visualization while navigating through volume data, and 2) supporting interactive querying and data exploration, i.e., interrogating volume data. The approach extends the WIM metaphor, simultaneously displaying a large-scale detailed data visualization and an interactive miniature. Leveraging the table+wall hardware, horizontal slices are projected (like a shadow) down onto the table surface, providing a useful 2D data overview to complement the 3D views as well as a data context for interpreting 2D multitouch gestures made on the table. In addition to enabling effective navigation through complex geometries, extensions to the core Slice WIM technique support interacting with a set of multiple slices that persist on the table even as the user navigates around a scene and annotating and measuring data via points, paths, and volumes specified using interactive slices. Applications of the interface to two volume data sets are presented, and design decisions, limitations, and user feedback are discussed.
Cervical cancer control in HIV-infected women: Past, present and future (2017)

Since the initial recognition of acquired immunodeficiency syndrome (AIDS) in 1981, an increased burden of cervical cancer was identified among human immunodeficiency virus (HIV)-positive women. Introduction of antiretroviral therapy (ART) decreased risks of opportunistic infections and improved overall survival. HIV-infected women are living longer. Introduction of the human papillomavirus (HPV) vaccine, cervical cancer screening and early diagnosis provide opportunities to reduce cervical cancer associated mortality. In line with 2030 Sustainable Development Goals to reduce mortality from non-communicable diseases, increased efforts need to focus on high burden countries within sub-Saharan Africa (SSA). Despite limitations of resources in SSA, opportunities exist to improve cancer control. This article reviews advancements in cervical cancer control in HIV-positive women.
Toward Reducing Fault Fix Time: Understanding Developer Behavior for the Design of Automated Fault Detection Tools (2007)

The longer a fault remains in the code from the time it was injected, the more time it will take to fix the fault. Increasingly, automated fault detection (AFD) tools are providing developers with prompt feedback on recently-introduced faults to reduce fault fix time. If however, the frequency and content of this feedback does not match the developer's goals and/or workflow, the developer may ignore the information. We conducted a controlled study with 18 developers to explore what factors are used by developers to decide whether or not to address a fault when notified of the error. The findings of our study lead to several conjectures about the design of AFD tools to effectively notify developers of faults in the coding phase. The AFD tools should present fault information that is relevant to the primary programming task with accurate and precise descriptions. The fault severity and the specific timing of fault notification should be customizable. Finally, the AFD tool must be accurate and reliable to build trust with the developer.
Dietary Influences on the Antiparkinsonian Response to Levodopa (1987)

The ability of dietary factors to modify the response to levodopa was evaluated in six patients with idiopathic Parkinson's disease who manifested fluctuations in motor performance. The single oral administration of a high-protein formula substantially elevated plasma large neutral amino acid levels, and prematurely terminated the antiparkinsonian response to levodopa/carbidopa. In contrast, during oral or intravenous administration of levodopa, the ingestion of diets meeting the recommended daily allowance (RDA) for protein had no significant effect on plasma levodopa or large neutral amino acid levels or variance, nor on parkinsonian scores or variance. The results suggest that while protein intake in excess of the RDA can diminish the antiparkinsonian response to orally administered levodopa/carbidopa in patients with advanced disease, diets adhering to RDA protein guidelines have no clinically appreciable effect.
Toward automatic 3d modeling of scenes using a generic camera model (2011)

maxime.lhuillier.free.fr The automatic reconstruction of 3D models from image sequences is still a very active field of research. All existing methods are designed for a given camera model, and a new (and ambitious) challenge is 3D modeling with a method which is exploitable for any kind of camera. A similar approach was recently suggested for structure-frommotion thanks to the use of generic camera models. In this paper, we first introduce geometric tools designed for 3D scene modeling with a generic camera model. Then, these tools are used to solve many issues: matching errors, wide range of point depths, depth discontinuities, and view-point selection for reconstruction. Experiments are provided for perspective and catadioptric cameras. 1.
Activation of ERBB4 in Glioblastoma Can Contribute to Increased Tumorigenicity and Influence Therapeutic Response (2018)

Glioblastoma (GBM) is often resistant to conventional and targeted therapeutics. ErbB2 Receptor Tyrosine Kinase 4 (ERBB4) is expressed throughout normal brain and is an oncogene in several pediatric brain cancers; therefore, we investigated ERBB4 as a prognostic marker and therapeutic target in GBM. Using RT-qPCR, we quantified mRNA encoding total ERBB4 and known ERBB4 variants in GBM and non-neoplastic normal brain (NNB) samples. Using immunohistochemistry, we characterized the localization of total and phosphorylated ERBB4 (p-ERBB4) and EGFR protein in archived GBM samples and assessed their association with patient survival. Furthermore, we evaluated the effect of ERBB4 phosphorylation on angiogenesis and tumorigenicity in GBM xenograft models. Total <i>ERBB4</i> mRNA was significantly lower in GBM than NNB samples, with the juxtamembrane JM-a and cytoplasmic CYT-2 variants predominating. ERBB4 protein was ubiquitously expressed in GBM but was not associated with patient survival. However, high p-ERBB4 in 11% of archived GBM samples, independent of p-EGFR, was associated with shorter patient survival (12.0 ± 3.2 months) than was no p-ERBB4 (22.5 ± 9.5 months). Increased ERBB4 activation was also associated with increased proliferation, angiogenesis, tumorigenicity and reduced sensitivity to anti-EGFR treatment in xenograft models. Despite low <i>ERBB4</i> mRNA in GBM, the functional effects of increased ERBB4 activation identify ERBB4 as a potential prognostic and therapeutic target.
Signatures of adaptation in the field (2015)

Plant Genomics![Figure][1] 

Sorghum genomes show signs of adaptation

PHOTO: DSZC/ISTOCKPHOTO

Adaptation to the environment is critical for the survival of all species. For crops, this can be confounded or enhanced by farmers and breeders selecting for particular traits. To determine the
Mesobaculum littorinae gen. nov., sp. nov., a novel bacterium isolated from a sea snail Littorina scabra (2021)

Members within the family <i>Rhodbacteraceae</i> are morphologically and genetically highly diverse, and originate mostly from coastal marine environments. In this study, a novel species of this family, designated M0103<sup>T</sup>, was isolated from the surface of a sea snail <i>Littorina scabra</i>. Strain M0103<sup>T</sup> is Gram-stain-negative, halophilic, non-motile and non-Bacteriochlorophyll <i>a</i>-producing bacterium. Several phenotypic characteristics of the isolate were similar to other species within this family, such as the sole respiratory quinone Q-10 and major fatty acid components C<sub>18 : 1</sub> <i> ω</i>7c, C<sub>18 : 0</sub> and C<sub>16 : 0</sub>. Strain M0103<sup>T</sup> contains a diphosphatidylglycerol, a phosphatidylglycerol, a phosphatidylcholine, a phosphatidy ethanolamine, a phosphatidylinositol, five unidentified phospholipids and four unidentified polar lipids. Based on the 16S rRNA gene sequence analysis, this isolate showed the closest phylogenetic relationship with '<i>Palleronia pontilimi</i>' GH1-23<sup>T</sup> (95.1 %). Values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) of genome sequences were of 70.1-76.4 % and 18.3-20.9 % between the isolate and 24 closely related type strains. Analysis the 4.0 Mb genome of strain M0103<sup>T</sup> revealed several putative genes associated with cellular stress resistance, which may play protective roles for the isolate in the adaptation to a marine environment. Phylogenetic, phenotypic and chemotaxonomic analyses suggested that strain M0103<sup>T</sup> represents a novel genus and novel species of the family <i>Rhodobacteraceae</i>, for which the name <i>Mesobaculum littorinae</i> gen. nov., sp. nov. is proposed. The type strain is M0103<sup>T</sup> (=MCCC 1K03619<sup>T</sup>=KCTC 62358<sup>T</sup>).
Electro-active polymer transduction for distributed netted sensing (2008)

The Naval Undersea Warfare Center in Newport, RI is developing an electro-active polymer-based sensing node for use in a persistent distributed underwater surveillance system. Persistence demands extreme energy conservation measures. The node will resemble a jellyfish in form, complete with tentacles housing a volumetric array of light-weight piezoelectric polyvinylidene fluoride trifluoroethylene (PVDF-TrFE) copolymer cylindrical hydrophones designed for an ultra-low power acoustic receiver. Each cylinder has conductive silver electrodes on the inside and outside surfaces, a length of 2.5 cm, an outside diameter of 11 mm, a 1 mm wall thickness, and a mass less than 2 g. Operating in the hydrostatic mode, the hydrophone sensitivity is typically -195 dB//1 V/μPa and is stable with both hydrostatic pressure (50 to 1000 psi) and temperature (-1 to 35°C). [Work supported by the Office of Naval Research.]
3 nJ, 100 ps laser pulses generated with an asymmetric waveguide laser diode for a single-photon avalanche diode time-of-flight (SPAD TOF) rangefinder application (2012)

An asymmetric waveguide laser diode with a thick active layer operated with enhanced gain switching is shown to be able to produce ∼100 ps, ∼25 W optical pulses in fundamental transverse mode with ∼15 A, ∼1.5 ns injection current pulses. A pulsed time-of-flight distance measurement demonstration utilizing this laser diode and a SPAD detector indicates centimetre-level precision and compensated accuracy from uncooperative targets at tens to hundreds of metres in a measurement time of a fraction of a second.
Calicheamicins: discovery, structure, chemistry, and interaction with DNA (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCalicheamicins: discovery, structure, chemistry, and interaction with DNAMay D. Lee, George A. Ellestad, and Donald B. BordersCite this: Acc. Chem. Res. 1991, 24, 8, 235–243Publication Date (Print):August 1, 1991Publication History Published online1 May 2002Published inissue 1 August 1991https://pubs.acs.org/doi/10.1021/ar00008a003https://doi.org/10.1021/ar00008a003research-articleACS PublicationsRequest reuse permissionsArticle Views1067Altmetric-Citations195LEARN 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
Effect of Annealing Temperature on the Anode Properties of TiO2Nanotubes for Rechargeable Lithium Batteries (2012)

루타일(rutile) <TEX>$TiO_2$</TEX> 분말의 알칼리 수열합성과 <TEX>$300{\sim}500^{\circ}C$</TEX> 열처리를 통해 <TEX>$TiO_2$</TEX> 나노튜브를 제조하고, 이를 리튬이 차전지의 음극 활물질로 채택하여 그 물성과 전기화학적 특성을 조사하였다. 수열반응 직후의 정제과정에서 불순물인 미세분진을 완전히 제거하여 제조된 <TEX>$TiO_2$</TEX> 나노튜브는 고비표면적과 확연한 나노튜브 결정상을 보였다. 또한 열처리 온도가 증가함에 따라 등방적으로 분산된 나노튜브들이 서로 응집되어 비표면적의 감소를 초래하였다. <TEX>$300^{\circ}C$</TEX> 열처리한 <TEX>$TiO_2$</TEX> 나노튜브가 250 mAh <TEX>$g^{-1}$</TEX>의 가장 높은 초기 방전용량을 나타내었으며, 사이클과 고율 특성은 <TEX>$400^{\circ}C$</TEX> 열처리한 시료가 가장 우수한 성능을 보였다. <TEX>$TiO_2$</TEX> nanotubes are prepared from rutile prticles via an alkaline hydrothermal synthesis and the consequent heat treatment at <TEX>$300{\sim}500^{\circ}C$</TEX>. The physical and electrochemical properties of the <TEX>$TiO_2$</TEX> nanotubes are characterized for use as a anode material of rechargeable lithium battery. In particular, the microscale dusts as an impurity component occurred in the purification step after the hydrothermal reaction are completely removed to yield <TEX>$TiO_2$</TEX> nanotube with a higher specific surface area and more obvious crystalline phases. As the annealing temperature increases, the specific surface area is slightly decreased due to some aggregation between the isotropically dispersed nanotubes. Highest initial discharge capacity of 250 mAh <TEX>$g^{-1}$</TEX> is achieved for the <TEX>$TiO_2$</TEX> nanotube annealed at <TEX>$300^{\circ}C$</TEX>, whereas the <TEX>$400^{\circ}C$</TEX> <TEX>$TiO_2$</TEX> nanotube shows the superior cycle performance and high-rate capability.
Electromagnetic fields and DNA damage (2009)

A major concern of the adverse effects of exposure to non-ionizing electromagnetic field (EMF) is cancer induction. Since the majority of cancers are initiated by damage to a cell's genome, studies have been carried out to investigate the effects of electromagnetic fields on DNA and chromosomal structure. Additionally, DNA damage can lead to changes in cellular functions and cell death. Single cell gel electrophoresis, also known as the 'comet assay', has been widely used in EMF research to determine DNA damage, reflected as single-strand breaks, double-strand breaks, and crosslinks. Studies have also been carried out to investigate chromosomal conformational changes and micronucleus formation in cells after exposure to EMF. This review describes the comet assay and its utility to qualitatively and quantitatively assess DNA damage, reviews studies that have investigated DNA strand breaks and other changes in DNA structure, and then discusses important lessons learned from our work in this area.
Nanoscale Capacitance and Capacitance-Voltage Curves for Advanced Characterization of Electrical Properties of Silicon and GaN Structures Using Scanning Microwave Impedance Microscopy (sMIM) (2017)

Abstract Scanning microwave impedance microscopy (sMIM) is a relatively new method for making electrical measurements on test samples in AFMs. This article presents examples in which sMIM technology is used to measure dielectric coefficients, doping concentrations, and nanoscale C-V curves for different semiconductor and dielectric materials. It also explains how measured results compare with theoretical models, confirming the validity of each approach.
Gel filtration and quasielastic light scattering studies of human bile. (1990)

Analyses of cholesterol carriers in the extremely variable biliary samples were performed by chromatography under standard conditions. Sephacryl columns were eluted with buffer containing 10 mmol/L sodium cholate, 150 mmol/L sodium chloride, 50 mmol/L Tris(hydroxymethyl)aminomethane-hydrochloride, pH 8.0, and 1.5 mmol/L ethylenediaminetetraacetate. Moderate changes in temperature, flow rate or sample size produced only minor differences in the results. Increments in bile salt concentration in the elution buffer caused progressive disappearance of vesicles and a rise in their cholesterol/phospholipid ratio. Using the standard chromatographic technique, analyses of the same bile gave reproducible results, and comparisons among various biles were possible. Quantitative light scattering measurements of bile showed that the amount of vesicular cholesterol in whole unprocessed bile was similar to that measured by Sephacryl chromatography. Analyses of human gallbladder biles using a high-resolution Sephacryl column showed four cholesterol-containing peaks: vesicles, lamellae, mixed micelles and an undefined carrier. This long chromatographic column separated the lamellar from the micellar peaks (which had merged on the short column). Phospholipid lamellae solubilized most of the biliary cholesterol. These findings were confirmed by ultracentrifugation of bile.
Solubility study of silver halides in molten calcium nitrate tetrahydrate (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSolubility study of silver halides in molten calcium nitrate tetrahydrateBrian Burrows and Soefjan NoersjamsiCite this: J. Phys. Chem. 1972, 76, 19, 2759–2764Publication Date (Print):September 1, 1972Publication History Published online1 May 2002Published inissue 1 September 1972https://pubs.acs.org/doi/10.1021/j100663a024https://doi.org/10.1021/j100663a024research-articleACS PublicationsRequest reuse permissionsArticle Views43Altmetric-Citations2LEARN 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 optionsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Über die Bildung von Melanin in Muskelzellen nach der direkten Übertragung von RNA aus HARDING-PASSEY-Melanomzellen (1971)

Article Über die Bildung von Melanin in Muskelzellen nach der direkten Übertragung von RNA aus HARDING-PASSEY-Melanomzellen was published on January 1, 1971 in the journal Biological Chemistry (volume 352, issue 1).
Role of p38 protein kinase in heat-induced Raw cells apoptosis. (2000)

p38 activation is required for heat-induced apoptosis in Raw264.7 cells, and stimulation of the p38 signaling pathway contributes to cell death.