gebhart/patrepeval huggingface dataset:
Secretion of theHormoconis resinaeglucoamylase P enzyme fromTrichoderma reeseidirected by the natural and thecbh1gene secretion signal (1993)

Secretion of the Hormoconis resinae glucoamylase P (GAMP) enzyme from Trichoderma reesei using either the natural N-terminal extension of the premature glucoamylase P or the cellobiohydrolase I (CBHI) signal peptide was examined. The expression conditions for the heterologous glucoamylase P (gamP) gene in T. reesei were standardized by targeting one copy of a plasmid fragment, containing the gamP gene, to the cbh1 locus of the host. The results showed that the transient N-terminal extension of the premature GAMP acts as an efficient secretion signal in T. reesei and leads to a higher yield of extracellular glucoamylase activity than does the signal peptide of CBHI.
Real-Time Multispectral Rendering with Complex Illumination (2011)

Techniques for rendering with illumination maps captured from real-world environments have provided the means to produce complex, realistic patterns of reflections in real-time computer graphics simulations. While the directional aspects of light emission and surface reflection are modeled comprehensively with these methods, the spectral component is typically represented with a three-channel RGB workflow. In this paper, we present a multispectral framework for capturing environmental illumination maps and incorporating them into a real-time rendering pipeline. The framework maintains two sets of trichromatic data through a real-time rendering workflow, using a six-channel representation optimized to allow for color-accurate relighting under a range of illuminants. We present the design of an end-to-end computer graphics color pipeline from capture to display, provide simulation results on the pipeline's colorimetric accuracy, and develop a prototype to demonstrate how the framework can be implemented in a GPU-based graphics shader architecture.
Increased local density of states and electromagnetic well effect by using very thin hyperbolic metamaterial (2013)

Hyperbolic material (HM) is proven to dramatically increase the power emitted by a source near its surface or inside it. Moreover, the power emitted by a source is mostly directed into the HM thanks to a very wide spatial wave spectrum that is allowed to propagate, and carry power, inside the HM. These exotic properties of HM gained a great interest for applications such as increased rate of spontaneous emission by dye molecules, or novel and improved absorbers, both at microwave and optic frequencies. Here we show the impact of the thickness of a HM substrate on the power emitted by a source close to its surface in order to explore the principles for decreasing the thickness of HM based designs. We initiate the analysis with vertical and transverse dipoles located at a certain distance from the surface of a homogeneous HM substrate grounded at the bottom. Then the same analysis is extended to a realistic HM design with metal/dielectric multilayers by using transmission line formalism of TE and TM waves (thus taking the heterogeneity of the layered medium into account). The spatial spectrum of the power directed into HM is shown to possess different distributions for HM substrates with different thicknesses; however the amount of the total emitted power and the ratio of power directed towards the HM substrate exhibit little dependence on the thickness of the substrate. This important result proves that very thin HMs are a new promising technology for enabling engineers to design extremely thin absorbers.
Abstract TMP1: Multi-omic Biomarker Development In A Mendelian Neurovascular Disease, Cavernous Angioma (2022)

Introduction: Cavernous Angioma (CA) is a hemorrhagic neurovascular disease characterized by either a familial form with autosomal dominant germline mutations in one of three CCM genes or a sporadic form with somatic mutations of the same genes. Circulating proteins have been previously investigated as possible diagnostic and prognostic biomarkers of disease activity, with up to 86% and 88% sensitivity and specificity, respectively. We hypothesize that differentially expressed (DE) plasma microRNAs and metabolites in CA patients can be integrated with plasma proteins to increase the sensitivity and specificity of circulating CA biomarkers. Methods: Mechanistically relevant homologous DE miRNAs were identified between familial CA patients and preclinical murine models and validated in an independent cohort of patients using real time qPCR. In conjunction, DE metabolites were determined in CA patients using liquid-chromatography mass spectrometry. The interactions of these metabolites with the previously established CA transcriptome, proteome, and microbiome were queried to assess for mechanistic relevance. Optimal diagnostic models of proteins, DE miRNAs, and DE metabolites alone were next established. Plasma metabolites and miRNAs were then separately integrated with protein, using a machine learning-implemented, Bayesian approach to develop diagnostic CA biomarkers. Results: The optimal diagnostic biomarker model with only DE miRNAs performed at up to 68%, while proteins and metabolites achieved up to 68%, and 82% accuracy respectively. The optimal combination for proteins with miRNAs improved the diagnostic association of familial-CA disease to up to 94.7% sensitivity and 100% specificity. Integrating metabolites and proteins improved the diagnosis of CA disease and its clinical manifestations to 100% sensitivity and 100% specificity. Conclusion: Combining plasma proteins with miRNAs or metabolites can improve diagnostic accuracy of CA disease and its disease characteristics above any single molecular modality alone. Future studies should incorporate proteins, miRNAs, and metabolites to further increase diagnostic accuracy, and validate these in a larger cohort with control for demographic and disease features.
ChemInform Abstract: The Study of Glycopeptide Syntheses: Exploring Concise O‐Linked Sialylglycopeptide Synthesis and Glycopeptide Coupling Reaction (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Transient Debris Freezing and Potential Wall Melting During a Severe Reactivity Initiated Accident Experiment (1981)

AbstractThe safe containment of molten core debris following a hypothetical meltdown accident in a light water reactor depends on the post-accident distribution and freezing of the debris on cold core structures. A one-dimensional physical model was developed to study the transient freezing of the molten debris on the inner surface of the test shroud wall in a severe, reactivity initiated accident in-pile experiment, and to assess the potential for wall melting upon being contacted by the molten debris. The conditions of finite wall thickness, convective cooling at the wall outer surface, radiative cooling of the debris, temperature-dependent thermophysical properties, and internal heat generation in the debris were considered. It is concluded that the shroud wall should not melt upon contact by the molten debris, which agreed with the experimental observations, because of the initial low temperature of the wall (538 K) and of the molten debris (∼3500 K) at the time of contact. Should wall melting occur, however, the wall molten layer would be unstable because of the small thickness of the wall and the continuous cooling at the wall outer surface by coolant bypass flow. The agreement between the calculations and experimental results indicated that considering the molten debris during the freezing process as a homogeneous mixture of the constituents (UO2 and Zircaloy) was a reasonable assumption.
Colorectal endoscopy (1994)

Literature highlights from the past year pertaining to endoscopy of the colorectum are discussed. As most journal articles have dealt with applications in the screening, diagnosis, and management of colorectal neoplasia, the critique reflects this emphasis. Diagnostic and therapeutic advances, safety and monitoring information, and training issues in colonoscopy are also covered.
Optical and Electrical Properties of Inner Tubes in Outer Wall-Selectively Functionalized Double-Wall Carbon Nanotubes (2011)

Atom-thick materials such as single-wall carbon nanotubes (SWNTs) and graphene are prone to chemical attacks because all constituent atoms are exposed. Here we report the retention of optical and electrical properties of inner tubes in heavily functionalized double-wall carbon nanotubes (DWNTs). Correlated optical absorption spectroscopy, Raman scattering, and thin film electrical conductivity all suggest that an inner tube behaves strikingly similar to a pristine SWNT; however, because of the protection of the outer wall, the inner tube can survive aggressive chemical attacks (e.g., by diazonium chemistry) without compromising physical properties. At the saturation limit of the diazonium functionalization, an SWNT network becomes electrically insulating; in stark contrast, the double-walled structure retains ∼50% of the initial conductivity, owing to the intact inner tube pathway. These results suggest the possibility of high-performance DWNT electronic devices with important capabilities for tailored surface chemistry on the outer walls, whereas the inner tubes are chemically protected.
Continuous Glucose Monitoring in a Healthy Population: Understanding the Post-Prandial Glycemic Response in Individuals without Diabetes Mellitus (2023)

Continuous glucose monitoring has become a common adjunct in the management of Diabetes Mellitus. However, there has been a recent trend among individuals without diabetes using these devices as a means of monitoring their health. The increased visibility of glucose data has allowed users to study the effect lifestyle has upon post-prandial glucose levels. Although post-prandial hyperglycemia is well understood in the setting of diabetes, its impact in individuals without diabetes is less well defined. This article reviews those factors which contribute to post-prandial hyperglycemia in individuals without diabetes and how the data obtained from continuous glucose monitoring can be used to improve an individual’s metabolic health.
Osteogenic effect of low‐temperature‐heated porcine bone particles in a rat calvarial defect model (2013)

The current study was designed to investigate the chemical and physical properties of porcine-derived xenografts of different crystallinity (low and high) and to evaluate their osteogenic potential. Porcine femur bone underwent a heat treatment process at 400°C (P400) and 1200°C (P1200) and was then milled into particles of 1 mm or less. In X-ray diffraction, P400 exhibited a low crystallinity compared with that of P1200, as indicated by the relatively wide diffraction peaks. Brunauer-Emmett-Teller analysis revealed that P400 also had a wider surface area than P1200. In micro-CT scan analysis of specimens in a rat calvarial defect model, bone mineral density of the P400 group was significantly higher than that of the P1200 group (p < 0.01). New bone formation was also remarkably higher at 8 weeks in the P400 group, which showed more new osteocytes in the lacuna compared with the P1200 group. In this study, low crystalline bone particles were obtained at low processing temperature (at temperature of 400°C) and achieved superior new bone formation compared with the high crystalline bone particles created at a higher process temperature (1200°C). It can be concluded that lower process temperature bone particles might provide a more effective graft material for enhancing bone formation. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 102A: 3609-3617, 2014.
Coxsackievirus B4 and type 1 diabetes pathogenesis: contribution of animal models (2009)

The role of enteroviruses, in particular type B coxsackieviruses (CV-B), in type 1 diabetes (T1D) pathogenesis is supported by epidemiological, clinical and experimental observations.The investigation of T1D pathogenesis benefits from the contribution of animal models called spontaneously diabetic. Among these animals the non-obese diabetic (NOD) mouse and the bio-breeding diabetes-prone (BBDP) rat present a genetic susceptibility manifested by the expression of an autoimmune diabetes similar to the pathology observed in human beings. Other models whose genetic predisposition is less known are of considerable contribution as well. Numerous major observations relative to several aspects of T1D pathogenesis in the context of CV-B infections, such as susceptibility, diabetogenicity, pancreatotropism, mechanisms of beta cells destruction and others, have been deduced thanks to investigations with animal models. Despite their limits, these models are necessary in improving our knowledge of the role of enteroviruses, like CV-B4, in the pathogenesis of T1D, and the recent advances ensuing from their contribution may have important therapeutic and preventive spin-offs.
Effect of residual H2O2 from advanced oxidation processes on subsequent biological water treatment: A laboratory batch study (2017)

H<sub>2</sub>O<sub>2</sub> residuals from advanced oxidation processes (AOPs) may have critical impacts on the microbial ecology and performance of subsequent biological treatment processes, but little is known. The objective of this study was to evaluate how H<sub>2</sub>O<sub>2</sub> residuals influence sand systems with an emphasis on dissolved organic carbon (DOC) removal, microbial activity change and bacterial community evolution. The results from laboratory batch studies showed that 0.25 mg/L H<sub>2</sub>O<sub>2</sub> lowered DOC removal by 10% while higher H<sub>2</sub>O<sub>2</sub> concentrations at 3 and 5 mg/L promoted DOC removal by 8% and 28%. A H<sub>2</sub>O<sub>2</sub> dosage of 0.25 mg/L did not impact microbial activity (as measured by ATP) while high H<sub>2</sub>O<sub>2</sub> dosages, 1, 3 and 5 mg/L, resulted in reduced microbial activity of 23%, 37% and 37% respectively. Therefore, DOC removal was promoted by the increase of H<sub>2</sub>O<sub>2</sub> dosage while microbial activity was reduced. The pyrosequencing results illustrated that bacterial communities were dominated by Proteobacteria. The presence of H<sub>2</sub>O<sub>2</sub> showed clear influence on the diversity and composition of bacterial communities, which became more diverse under 0.25 mg/L H<sub>2</sub>O<sub>2</sub> but conversely less diverse when the dosage increased to 5 mg/L H<sub>2</sub>O<sub>2</sub>. Anaerobic bacteria were found to be most sensitive to H<sub>2</sub>O<sub>2</sub> as their growth in batch reactors was limited by both 0.25 and 5 mg/L H<sub>2</sub>O<sub>2</sub> (17-88% reduction). In conclusion, special attention should be given to effects of AOPs residuals on microbial ecology before introducing AOPs as a pre-treatment to biological (sand) processes. Additionally, the guideline on the maximum allowable H<sub>2</sub>O<sub>2</sub> concentration should be properly evaluated.
Several micron-range measurements with sub-nanometric resolution by the use of dual-wavelength digital holography and vertical scanning (2009)

Reflection digital holographic microscopy (DHM) is a very powerful technique allowing measuring topography with a sub-nanometer axial resolution from a single hologram acquisition. But as most of interferometer methods, the vertical range is limited to half the wavelength if numerical unwrapping procedure could not be applied (very high aspect ratio specimen). Nevertheless, it was already demonstrated that the use of dual-wavelength DHM allows increasing the vertical range up to several microns by saving the single wavelength resolution if conditions about phase noise are fulfilled (the higher the synthetic wavelength, the smaller the phase noise has to be). In this paper, we will demonstrate that the choice of a synthetic wavelength of about 17 microns allows measuring precisely a 4.463&mu;m certified step. Furthermore, we will show the feasibility of a sub-nanometer resolution on a range higher than the synthetic wavelength by being able to map the dual-wavelength measurement on data acquired from a vertical scanning process, which precision is about 1 &mu;m.
Synthesis and mesomorphic properties of novel phenacylpyridines and their copper (II) complexes (1996)

Abstract The synthesis, characterization and liquid crystal properties of a homologous series of a new class of alkoxyphenacylpyridine ligands and their copper(II) complexes are reported. According to textural observations and calorimetric data, ligands with n = m ≧ 8 and copper complexes with n = m ≧ 6, where n, m denote the number of carbon atoms in the alkoxy chains, exhibit liquid crystal properties. The mesogenic ligands display monotropic nematic phases, while the mesogenic copper(II) complexes give enantiotropic smectic A phases.
A 409 GOPS/W Adaptive and Resilient Domino Register File in 22 nm Tri-Gate CMOS Featuring In-Situ Timing Margin and Error Detection for Tolerance to Within-Die Variation, Voltage Droop, Temperature and Aging (2015)

This paper presents an adaptive and resilient domino register file design featuring in-situ timing margin and error detection for the performance-critical domino read path. Voltage/frequency is adapted for slow-changing variations such as low-frequency supply noise, temperature fluctuation, and aging-induced degradation. Dynamic adaptation is combined with error detection and recovery for fast voltage droops and random data access patterns in the presence of within-die process variations. Throughput and energy efficiency gains are higher than the replica/canary based critical path approach. Timing margin is tracked by double-sampling the read output and its delayed version at the same clock edge. Timing errors are detected by double-sampling and comparing the read output within a clock window. The sensing errors in the precharge/evaluate domino read path are converted into timing errors using a conditional delayed-bitline precharge technique that does not impact the subsequent precharge operation. The proposed techniques incur 6-13% area overhead and 0.2-0.3% power overhead for a 4 Kb sub-array. The measurement results from a 22 nm tri-gate CMOS testchip demonstrate 21% throughput and 67% energy efficiency improvement with a peak energy efficiency of 409 GOPS/W.
Induction of Multi-Functional T Cells in a Phase I Clinical Trial of Dendritic Cell Immunotherapy in Hepatitis C Virus Infected Individuals (2012)

We have previously reported a world-first phase I clinical trial to treat HCV patients using monocyte-derived dendritic cells (Mo-DC) loaded with HCV-specific lipopeptides. While the brief treatment proved to be safe, it failed to reduce the viral load and induced only transient cell-mediated immune responses, measured by IFNγ ELIspot. Here we reanalysed the PBMC samples from this trial to further elucidate the immunological events associated with the Mo-DC therapy. We found that HCV-specific single- and multi-cytokine secreting T cells were induced by the Mo-DC immunotherapy in some patients, although at irregular intervals and not consistently directed to the same HCV antigen. Despite the vaccination, the responses were generally poor in quality and comprised of primarily single-cytokine secreting cells. The frequency of FOXP3(+) regulatory T cells (Treg) fluctuated following DC infusion and eventually dropped to below baseline by week 12, an interesting trend suggesting that the vaccination may have resulted in a more subtle outcome than was initially apparent. Our data suggested that Mo-DC therapy induced complex immune responses in vivo that may or may not lead to clinical benefit.
Unrepeatered 100G Transmission Over 520.6 km of G.652 Fiber and 556.7 km of G.654 Fiber With Commercial Raman DWDM System and Enhanced ROPA (2014)

We report the results of 100G unrepeatered transmission aimed at achieving the longest distance without any inline active elements. The unrepeatered transmission system uses commercial distributed Raman pump modules, enhanced ROPA, and real-time processing coherent 100G transceivers (PM-QPSK) with soft-decision FEC. Two types of ultra-low loss fibers, G.652B and G.654B compliant, are fully characterized and used as span fiber. First, a single 100G channel is successfully transmitted over 520.6 km of G.652B fiber (86.2 dB) in a lab trial. Second, cabled large effective area, ultra-low loss G.654B fiber in a field environment is used as span fiber. A single 100G channel and four 100G channels are transmitted over 556.7 km (90.2 dB) and 523.2 km (84.8 dB), respectively.
Selective CDK9 Inhibition by Natural Compound Toyocamycin in Cancer Cells (2022)

Aberrant transcription in cancer cells involves the silencing of tumor suppressor genes (TSGs) and activation of oncogenes. Transcriptomic changes are associated with epigenomic alterations such as DNA-hypermethylation, histone deacetylation, and chromatin condensation in promoter regions of silenced TSGs. To discover novel drugs that trigger TSG reactivation in cancer cells, we used a GFP-reporter system whose expression is silenced by promoter DNA hypermethylation and histone deacetylation. After screening a natural product drug library, we identified that toyocamycin, an adenosine-analog, induces potent GFP reactivation and loss of clonogenicity in human colon cancer cells. Connectivity-mapping analysis revealed that toyocamycin produces a pharmacological signature mimicking cyclin-dependent kinase (CDK) inhibitors. RNA-sequencing revealed that the toyocamycin transcriptomic signature resembles that of a specific CDK9 inhibitor (HH1). Specific inhibition of RNA Pol II phosphorylation level and kinase assays confirmed that toyocamycin specifically inhibits CDK9 (IC<sub>50</sub> = 79 nM) with a greater efficacy than other CDKs (IC<sub>50</sub> values between 0.67 and 15 µM). Molecular docking showed that toyocamycin efficiently binds the CDK9 catalytic site in a conformation that differs from other CDKs, explained by the binding contribution of specific amino acids within the catalytic pocket and protein backbone. Altogether, we demonstrated that toyocamycin exhibits specific CDK9 inhibition in cancer cells, highlighting its potential for cancer chemotherapy.
Distinct Roles of IL-23 and IL-17 in the Development of Psoriasis-Like Lesions in a Mouse Model (2011)

Psoriasis is an inflammatory disease with dynamic interactions between the immune system and the skin. The IL-23/Th17 axis plays an important role in the pathogenesis of psoriasis, although the exact contributions of IL-23 and IL-17 in vivo remain unclear. K5.Stat3C transgenic mice constitutively express activated Stat3 within keratinocytes, and these animals develop skin lesions with histological and cytokine profiles similar to those of human plaque psoriasis. In this study, we characterized the effects of anti-mouse IL-17A, anti-mouse IL-12/23p40, and anti-mouse IL-23p19 Abs on the development of psoriasis-like lesions in K5.Stat3C transgenic mice. Treatment with anti-IL-12/23p40 or anti-IL-23p19 Abs greatly inhibited 12-O-tetradecanoylphorbol-13-acetate-induced epidermal hyperplasia in the ears of K5.Stat3C mice, whereas the inhibitory effect of an anti-IL-17A Ab was relatively less prominent. Treatment with anti-IL-12/23p40 or anti-IL-23p19 Abs markedly lowered transcript levels of Th17 cytokines (e.g., IL-17 and IL-22), β-defensins, and S100A family members in skin lesions. However, anti-IL-17A Ab treatment did not affect mRNA levels of Th17 cytokines. Crossing IL-17A-deficient mice with K5.Stat3C mice resulted in partial attenuation of 12-O-tetradecanoylphorbol-13-acetate-induced lesions, which were further attenuated by anti-IL-12/23p40 Ab treatment. FACS analysis of skin-draining lymph node cells from mice that were intradermally injected with IL-23 revealed an increase in both IL-22-producing T cells and NK-22 cells. Taken together, this system provides a useful mouse model for psoriasis and demonstrates distinct roles for IL-23 and IL-17.