gebhart/patrepeval huggingface dataset:
Cryo-EM-guided engineering of T-box-tRNA modules with enhanced selectivity and sensitivity in translational regulation (2023)

Riboswitches are non-coding RNA elements that play vital roles in regulating gene expression. Their specific ligand-dependent structural reorganization facilitates their use as templates for design of engineered RNA switches for therapeutics, nanotechnology and synthetic biology. T-box riboswitches bind tRNAs to sense aminoacylation and control gene expression via transcription attenuation or translation inhibition. Here we determine the cryo-EM structure of the wild-type <i>Mycobacterium smegmatis ileS</i> T-box in complex with its cognate tRNA <sup>Ile</sup> . This structure shows a very flexible antisequestrator region that tolerates both 3'-OH and 2',3'-cyclic phosphate modification at the 3' end of tRNA <sup>Ile</sup> . Elongation of one helical turn (11-base pair) in both the tRNA acceptor arm and T-box Stem III maintains T-box-tRNA complex formation and increases the selectivity for tRNA 3' end modification. Moreover, elongation of Stem III results in ∼6-fold tighter binding to tRNA, which leads to increased sensitivity of downstream translational regulation indicated by precedent translation. Our results demonstrate that cryo-EM can guide RNA engineering to design improved riboswitch modules for translational regulation, and potentially a variety of additional functions.
Development of local strontium ranelate delivery systems and long term in vitro drug release studies in osteogenic medium (2018)

It has been recognized that the operative stabilization of osteoporotic fractures should be followed up with an appropriate osteoporosis treatment in order to decrease the risk of repeated fractures. Despite the good clinical results of strontium ranelate (SrRan) towards the osteoporosis treatment, high drug doses and long treatment period cause an increased risk of serious side effects. Novel local SrRan/poly(lactic acid) (SrRan/PLA) delivery systems containing from 3.57 ± 0.28 wt% to 24.39 ± 0.91 wt% of active substance were developed. In order to resemble the naturally occurring processes, osteogenic media (OM) was used as a release medium for long term (121 days) in vitro drug release studies and UV/VIS method for the determination of SrRan content in OM was developed and validated. Biomimetic calcium phosphate precipitates were found on the surface and in the pores of prepared delivery system after microcapsule exposure to OM for 121 days as well as SrRan particles, indicating that the release of the drug have not been completed within 121 days. In vitro cell viability evaluation approved no cytotoxic effects of microcapsule suspensions and extracts.
Use of Contact Angle Hysteresis in Estimating Thin Polymer Film Surface Energy and Wettability (2006)

A recent surface energy estimation method [1] interpreting contact angle hysteresis measurements was used to estimate surface energy of various commercially important polymer films including UV radiation cross-linked acrylic based monomer systems. The validity of the method was tested on highly hydrophobic non-polar amorphous fluoro-polymers using a number of polar and low surface tension liquids. Contact angle hysteresis was present on these surfaces even though surface morphology of the solution processed fluoro-polymers is close to ideal. Estimated surface energies using such probe liquids were consistent varying slightly with the probe liquid type. On such highly ordered and non-polar polymer surfaces use of polar and low surface tension liquids results in accurate surface energy estimation. However, use of polar probe liquids commonly employed in surface energy estimation methods, such as, Harmonic mean (HM), Geometric mean (GM) or Lewis Acid-Base method (LWAB) on polar surfaces such as polyester resulted in inconsistent surface energy values. To strengthen this observation, the ASTM surface energy estimation procedure (ASTM D2578 04a) developed for polyethylene and polypropylene surfaces (both non-polar) was employed on a sample polar polyester surface using the ASTM probe liquids. Results showed inconsistent surface energy values supporting the conclusion that care must be exercised during use of polar probe liquids in estimating surface energy on polar polymers with the contact angle hysteresis method. Finally, UV radiation cross-linkable acrylic polymer surface energies were estimated with the hysteresis method. Surface energy results were consistent based on five different probe liquids. It was observed that surface energy of the cross-linked monomer networks decreased slightly with increasing UV curing time.
Effect of N-Acetylcysteine in Combination with Antibiotics on the Biofilms of Three Cystic Fibrosis Pathogens of Emerging Importance (2021)

Cystic fibrosis (CF) is a genetic disorder causing dysfunctional ion transport resulting in accumulation of viscous mucus that fosters chronic bacterial biofilm-associated infection in the airways. <i>Achromobacter xylosoxidans</i> and <i>Stenotrophomonas maltophilia</i> are increasingly prevalent CF pathogens and while <i>Burkholderia cencocepacia</i> is slowly decreasing; all are complicated by multidrug resistance that is enhanced by biofilm formation. This study investigates potential synergy between the antibiotics ciprofloxacin (0.5-128 µg/mL), colistin (0.5-128 µg/mL) and tobramycin (0.5-128 µg/mL) when combined with the neutral pH form of <i>N</i>-Acetylcysteine (NAC<sub>neutral</sub>) (0.5-16.3 mg/mL) against 11 cystic fibrosis strains of <i>Burkholderia, Stenotrophomonas</i> and <i>Achromobacter</i> sp. in planktonic and biofilm cultures. We screened for potential synergism using checkerboard assays from which fraction inhibitory concentration indices (FICI) were calculated. Synergistic (FICI ≤ 0.5) and additive (0.5 > FICI ≥ 1) combinations were tested on irreversibly attached bacteria and 48 h mature biofilms via time-course and colony forming units (CFU/mL) assays. This study suggests that planktonic FICI analysis does not necessarily translate to reduction in bacterial loads in a biofilm model. Future directions include refining synergy testing and determining further mechanisms of action of NAC to understand how it may interact with antibiotics to better predict synergy.
Increased expression of glial cell line‐derived neurotrophic factor protects against oxidative damage‐induced retinal degeneration (2007)

Oxidative damage contributes to retinal cell death in patients with age-related macular degeneration or retinitis pigmentosa. One approach to treatment is to identify and eliminate the sources of oxidative damage. Another approach is to identify treatments that protect cells from multiple sources of oxidative damage. In this study, we investigated the effect of increased expression of glial cell line-derived neurotrophic factor (GDNF) in three models of oxidative damage-induced retinal degeneration. Double transgenic mice with doxycycline-inducible expression of GDNF in the retina were exposed to paraquat, FeSO(4), or hyperoxia, all sources of oxidative damage and retinal cell death. Compared to controls, mice with increased expression of GDNF in the retina showed significant preservation of retinal function measured by electroretinograms, reduced thinning of retinal cell layers, and fewer TUNEL-positive cells indicating less retinal cell death. Mice over-expressing GDNF also showed less staining for acrolein, nitrotyrosine, and 8-hydroxydeoxyguanosine, indicating less oxidative damage to lipids, proteins, and DNA. This suggests that GDNF did not act solely to allow cells to tolerate higher levels of oxidative damage before initiation of apoptosis, but also reduced damage from oxidative stress to critical macromolecules. These data suggest that gene transfer of Gdnf should be considered as a component of therapy for retinal degenerations in which oxidative damage plays a role.
Full characterization of modern transmission fibers for Raman amplified-based communication systems (2007)

Telecommunication carriers have to estimate the Raman parameters of the fibers installed on their optical transport networks in order to facilitate the design of the next generation of high bit-rate Raman amplified-based transmission systems. This paper reports a very complete characterization of the most popular modern transmission fibers in terms of Raman efficiency, noise figure and double Rayleigh backscattering crosstalk. Our experiment is based on an averaged power analysis, applied to a counter-pumped long-haul distributed fiber Raman amplifier. We evaluate as well at 40 Gb/s for these different fiber types the double Rayleigh backscattering impact in terms of Q-factor penalty for various Raman gains and RZ modulation formats with different duty cycles.
Strong Bragg gratings for WDM devices in non-sensitised low-loss Ge-doped waveguides (1996)

Bragg gratings have been written with 193 nm UV-light through a phase mask in low-loss germanium-doped buried waveguides. Without any kind of sensitisation, reflectivities of up to 99.98% and background rejection better than 22 dB have been obtained for 20 mm long Bragg gratings.
Lipofuscin-like autofluorescence within microglia and its impact on studying microglial engulfment (2023)

Engulfment of cellular material and proteins is a key function for microglia, a resident macrophage of the central nervous system (CNS). Among the techniques used to measure microglial engulfment, confocal light microscopy has been used the most extensively. Here, we show that autofluorescence (AF), likely due to lipofuscin and typically associated with aging, can also be detected within microglial lysosomes in the young mouse brain by light microscopy. This lipofuscin-AF signal accumulates first within microglia and increases with age, but it is not exacerbated by amyloid beta-related neurodegeneration. We further show that this lipofuscin-AF signal within microglia can confound the interpretation of antibody-labeled synaptic material within microglia in young adult mice. Finally, we implement a robust strategy to quench AF in mouse, marmoset, and human brain tissue.
Plasma Sputtering Deposition of PEMFC Porous Carbon Platinum Electrodes (2007)

Abstract A novel method is proposed to fabricate the active catalytic layers of proton exchange membrane fuel cells (PEMFC). A plasma sputtering technique is used to deposit a porous columnar carbon film (column diameter of 20 nm) followed by the catalyst (platinum) deposition directly on the proton‐conducting membrane. The study of Pt diffusion shows that the optimised catalysed layers correspond to low plasma pressure operation (0.5 Pa) below a platinum loading limit of about 90 μg cm –2 . The initial carbon porosity is then maintained and Pt nanoparticles are present in all parts of the carbon layer. A membrane electrode assembly (MEA) is then achieved by alternate depositions of carbon and platinum onto both sides of the membrane. The results show the importance of the porous carbon structure. A significant increase in the catalyst efficiency is observed compared to a commercial fuel cell when measuring open circuit voltage.
Experiences From the Joint Development of the GTX100 Turbine Blading (1998)

The GTX100 is the most recent industrial gas turbine in the ABB fleet. The development of the GTX100 turbine blading was a joint project involving four companies. A thorough evaluation of various design requirements resulted in the selection of a single shaft three-stage turbine configuration. The cooling techniques employed for the blading are based on the knowledge from the Russian school of design for gas turbines. These techniques have been verified by a considerable amount of experimental data and field experience over a number of years. To incorporate western manufacturing methods, western suppliers were introduced at an early stage in the development. Most of the engineering development of the turbine blading was carried out in Russia. In order to achieve efficient cooperation between Russia and Sweden, specialists from both companies were stationed at alternating companies. The verification of the turbine design is divided into two steps. The first step is cold and hot component testing and the second is the overall engine testing.
Classification with invariant scattering representations (2011)

A scattering transform defines a signal representation which is invariant to translations and Lipschitz continuous relatively to deformations. It is implemented with a non-linear convolution network that iterates over wavelet and modulus operators. Lipschitz continuity locally linearizes deformations. Complex classes of signals and textures can be modeled with low-dimensional affine spaces, computed with a PCA in the scattering domain. Classification is performed with a penalized model selection. State of the art results are obtained for handwritten digit recognition over small training sets, and for texture classification.
Data from Efficacy and Determinants of Response to HER Kinase Inhibition in <i>HER2</i>-Mutant Metastatic Breast Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;i&gt;HER2&lt;/i&gt; mutations define a subset of metastatic breast cancers with a unique mechanism of oncogenic addiction to HER2 signaling. We explored activity of the irreversible pan-HER kinase inhibitor neratinib, alone or with fulvestrant, in 81 patients with &lt;i&gt;HER2&lt;/i&gt;-mutant metastatic breast cancer. Overall response rate was similar with or without estrogen receptor (ER) blockade. By comparison, progression-free survival and duration of response appeared longer in ER&lt;sup&gt;+&lt;/sup&gt; patients receiving combination therapy, although the study was not designed for direct comparison. Preexistent concurrent activating &lt;i&gt;HER2&lt;/i&gt; or &lt;i&gt;HER3&lt;/i&gt; alterations were associated with poor treatment outcome. Similarly, acquisition of multiple &lt;i&gt;HER2&lt;/i&gt;-activating events, as well as gatekeeper alterations, were observed at disease progression in a high proportion of patients deriving clinical benefit from neratinib. Collectively, these data define &lt;i&gt;HER2&lt;/i&gt; mutations as a therapeutic target in breast cancer and suggest that coexistence of additional HER signaling alterations may promote both &lt;i&gt;de novo&lt;/i&gt; and acquired resistance to neratinib.&lt;/p&gt;Significance:&lt;p&gt;&lt;i&gt;HER2&lt;/i&gt; mutations define a targetable breast cancer subset, although sensitivity to irreversible HER kinase inhibition appears to be modified by the presence of concurrent activating genomic events in the pathway. These findings have implications for potential future combinatorial approaches and broader therapeutic development for this genomically defined subset of breast cancer.&lt;/p&gt;&lt;p&gt;&lt;i&gt;This article is highlighted in the In This Issue feature, p. 161&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Diagnostics (2016)

Assertions are Boolean expressions that are expected to be true at a given point in the code. The assert macro of <cassert> is defined similar to this.
Immunofluorescent study for pathogenesis of skin eruption of Gianotti's disease (1980)

病因としてB型肝炎ウイルス(以下HBV)が確認されているGianotti病皮膚病変の発生病理については未だ不明であり,体液性免疫もしくは細胞性免疫の両方面からの検討が加えられているが,著者らはその発生機序に皮膚組織へのHBs抗原抗体複合物の沈着が密接に関与している可能性を想定しその実証を目的として9例のGianotti病患者皮膚生検材料を用い蛍光抗体法を実施し,HBs抗原,IgG, IgM, C3の皮膚組織内局在を観察した.その結果真皮乳頭層および網状層の血管周囲性リンパ球,組織球性炎症細胞浸潤を伴った毛細血管,細静脈壁にHBs抗原,IgG, IgM, C3の特異蛍光が微細穎粒状,一部線状に認められた症例は9例中4例であった.対照のGianotti症候群は全例陰性所見であった.したがって以上の検索結果よりその結合比,分子量は不明であるが抗原過剰域HBs抗原抗体複合物の皮膚血管壁への一過性沈着がGianotti病皮膚病変形成に重要な因子であり得ることが示唆された.
Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome (2017)

In addition to mutations in genes, aberrant enhancer element activity at non-coding regions of the genome is a key driver of tumorigenesis. Here, we perform epigenomic enhancer profiling of a cohort of more than forty genetically diverse human colorectal cancer (CRC) specimens. Using normal colonic crypt epithelium as a comparator, we identify enhancers with recurrently gained or lost activity across CRC specimens. Of the enhancers highly recurrently activated in CRC, most are constituents of super enhancers, are occupied by AP-1 and cohesin complex members, and originate from primed chromatin. Many activate known oncogenes, and CRC growth can be mitigated through pharmacologic inhibition or genome editing of these loci. Nearly half of all GWAS CRC risk loci co-localize to recurrently activated enhancers. These findings indicate that the CRC epigenome is defined by highly recurrent epigenetic alterations at enhancers which activate a common, aberrant transcriptional programme critical for CRC growth and survival.
Identifying robot parameters using partial pose information (1993)

A simple radial-distance linear transducer (LVDT) that measures the distance from several fixed points in the workspace to the robot's endpoint has been used to infer the kinematic parameters of a robot. The motivation, theory, implementation, and performance of this particularly easy calibration and parameter identification method are discussed. A disagreement in the literature about the type of measuring system (in particular, the dimensionality of the pose measurements) needed to fully identify a robot's kinematic parameters is addressed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The 2017 IUIS Phenotypic Classification for Primary Immunodeficiencies (2017)

Since the 1990s, the International Union of Immunological Societies (IUIS) PID expert committee (EC), now called Inborn Errors of Immunity Committee, has published every other year a classification of the inborn errors of immunity. This complete catalog serves as a reference for immunologists and researchers worldwide. However, it was unadapted for clinicians at the bedside. For those, the IUIS PID EC is now publishing a phenotypical classification since 2013, which proved to be more user-friendly. There are now 320 single-gene inborn errors of immunity underlying phenotypes as diverse as infection, malignancy, allergy, auto-immunity, and auto-inflammation. We herein propose the revised 2017 phenotypic classification, based on the accompanying 2017 IUIS Inborn Errors of Immunity Committee classification.
Hybrid Distributed Video Coding Using SCA Codes (2006)

We describe the architecture for our distributed video coding (DVC) system. Some key differences between our work and previous systems include a new method of enabling decoder motion compensation, and the use of serially concatenated accumulate syndrome codes for distributed source coding. To evaluate performance, we compare our system to the H.263+ and H.264/AVC video codecs. Experiments show that our system is comparable to DVC systems from Stanford and Berkeley in the sense that our system performs better than H.263+Intra, but worse than H.263+Inter and H.264/AVC
Association of atherogenic serum lipids and platelet activation with changes in arterial stiffness in patients with type 2 diabetes (2022)

Pulse wave velocity (PWV) is a potential marker for atherosclerosis severity and/or predictor of future atherosclerotic cardiovascular events. PWV is significantly correlated with carotid-intimal media thickness in patients with diabetes. However, its significance as a surrogate marker for the treatment of atherosclerotic cardiovascular risk in the management of type 2 diabetes has not been fully established. To elucidate the factors that determine the improvement or deterioration of PWV, we studied the association of clinical parameters, parameters for glucose metabolism, serum lipids including each lipoprotein fraction, serotonin as a marker for platelet activation, and change in PWV in 54 patients with type 2 diabetes. Systolic blood pressure and serum levels of non-high-density lipoprotein-cholesterol, low-density lipoprotein-cholesterol (LDL-C), and intermediate-density lipoprotein-cholesterol significantly decreased in the PWV-improved group after 2 months compared with those in the PWV-deteriorated group. The serotonin levels at baseline were significantly lower in the PWV-improved group than in the PWV-deteriorated group. The changes in systolic blood pressure and LDL-C levels were significantly and positively correlated with those in PWV. The serotonin levels at baseline were significantly and positively correlated with changes in PWV. Therefore, amelioration of blood pressure, serum lipid level, and platelet activation might be beneficially associated with PWV change. PWV-guided clinical practice for cardiovascular risk stratification could be useful in type 2 diabetes management.
Abscisic Acid and Gibberellin Differentially Regulate Expression of Genes of the SNF1-Related Kinase Complex in Tomato Seeds (2003)

The SNF1/AMP-activated protein kinase subfamily plays central roles in metabolic and transcriptional responses to nutritional or environmental stresses. In yeast (Saccharomyces cerevisiae) and mammals, activating and anchoring subunits associate with and regulate the activity, substrate specificity, and cellular localization of the kinase subunit in response to changing nutrient sources or energy demands, and homologous SNF1-related kinase (SnRK1) proteins are present in plants. We isolated cDNAs corresponding to the kinase (LeSNF1), regulatory (LeSNF4), and localization (LeSIP1 and LeGAL83) subunits of the SnRK1 complex from tomato (Lycopersicon esculentum Mill.). LeSNF1 and LeSNF4 complemented yeast snf1 and snf4 mutants and physically interacted with each other and with LeSIP1 in a glucose-dependent manner in yeast two-hybrid assays. LeSNF4 mRNA became abundant at maximum dry weight accumulation during seed development and remained high when radicle protrusion was blocked by abscisic acid (ABA), water stress, far-red light, or dormancy, but was low or undetected in seeds that had completed germination or in gibberellin (GA)-deficient seeds stimulated to germinate by GA. In leaves, LeSNF4 was induced in response to ABA or dehydration. In contrast, LeSNF1 and LeGAL83 genes were essentially constitutively expressed in both seeds and leaves regardless of the developmental, hormonal, or environmental conditions. Regulation of LeSNF4 expression by ABA and GA provides a potential link between hormonal and sugar-sensing pathways controlling seed development, dormancy, and germination.
Field evaluation of the sulfur chemiluminescence detector (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTField evaluation of the sulfur chemiluminescence detectorRichard L. Benner and Donald H. StedmanCite this: Environ. Sci. Technol. 1990, 24, 10, 1592–1596Publication Date (Print):October 1, 1990Publication History Published online1 May 2002Published inissue 1 October 1990https://pubs.acs.org/doi/10.1021/es00080a021https://doi.org/10.1021/es00080a021research-articleACS PublicationsRequest reuse permissionsArticle Views169Altmetric-Citations29LEARN 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