gebhart/patrepeval huggingface dataset:
Stimulation of MCM helicase activity by a Cdc6 protein in the archaeon Thermoplasma acidophilum (2006)

Replicative DNA helicases are ring-shaped hexamers that play an essential role in chromosomal DNA replication. They unwind the two strands of the duplex DNA and provide the single-stranded (ss) DNA substrate for the polymerase. The minichromosome maintenance (MCM) proteins are thought to function as the replicative helicases in eukarya and archaea. The proteins of only a few archaeal organisms have been studied and revealed that although all have similar amino acid sequences and overall structures they differ in their biochemical properties. In this report the biochemical properties of the MCM protein from the archaeon Thermoplasma acidophilum is described. The enzyme has weak helicase activity on a substrate containing only a 3'-ssDNA overhang region and the protein requires a forked DNA structure for efficient helicase activity. It was also found that the helicase activity is stimulated by one of the two T.acidophilum Cdc6 homologues. This is an interesting observation as it is in sharp contrast to observations made with MCM and Cdc6 homologues from other archaea in which the helicase activity is inhibited when bound to Cdc6.
Conformationally Restricted Nucleosides. The Reaction of Adenosine Deaminase with Substrates Built on a Bicyclo[3.1.0]hexane Template (1999)

Adenosine deaminase (ADA) can discriminate between two distinct (North and South), conformationally rigid substrate conformers. (N)-methanocarba-2'dA (4) is deaminated 100 times faster than the antipodal (S)-methanocarba-2'dA (5), whereas a non-rigid analogue, aristeromycin (6), is deaminated at an intermediate rate. These results are in agreement with crystallographic data from ADA-ribonucleoside complexes showing the furanose ring of the bound purine in a C3'-endo (North) conformation. The data presented here suggests that 4 and 5 are useful probes to ascertain conformational preferences by purine metabolizing enzymes.
Teaching Cybersecurity Analysis Skills in the Cloud (2015)

This paper reports on the experience of using the EDURange framework, a cloud-based resource for hosting on-demand interactive cybersecurity scenarios. Our framework is designed especially for the needs of teaching faculty. The scenarios we have implemented each are designed specifically to nurture the development of analysis skills in students as a complement to both theoretical security concepts and specific software tools.
Low defect-mediated reverse-bias leakage in (0001) GaN via high-temperature molecular beam epitaxy (2010)

Conductive atomic force microscopy, scanning electron microscopy, and x-ray diffraction were used to determine the effects of Ga/N flux ratio on the conductivity of current leakage paths in GaN grown by molecular beam epitaxy. Our data reveal a band of fluxes near Ga/N≈1 for which these pathways ceased to be observable. We conclude that changes in surface defects surrounding or impurities along screw-component threading dislocations are responsible for their conductive nature. These observations suggest a method for controlling the primary source of reverse-bias Schottky contact leakage in n-type GaN grown by molecular beam epitaxy.
PROTECT-1: A Prospective Randomized Trial of CCX282-B (Traficet-EN), a Novel Oral Therapy Targeting Chemokine Receptor 9 in Crohnʼs Disease (2007)

Purpose: CCX282-B represents a new class of highly specific chemokine receptor antagonists. It targets chemokine receptor 9 (CCR9), a key homing signal for intestine-specific T cells. In a 28-day phase 2 study, CCX282-B induced clinical responses (CDAIΔ70) in 58% of Crohn's disease (CD) patients with a baseline CDAI >250 and elevated CRP, vs. 31% on placebo. CRP decreased 11 mg/L in the CCX282-B group relative to placebo. These results prompted PROTECT-1, a large, randomized, placebo-controlled trial in CD. Methods: This study involves >100 sites in 16 countries. The primary efficacy endpoint is CDAI decrease over 12 weeks. Maintenance of response is assessed over 36 weeks. Adults with moderate to severe CD (CDAI 250–450), are randomized 3:2:2:2 to receive placebo, CCX282-B 250 mg/day, 500 mg/day, or 250 mg twice daily (bid) for 12 weeks followed by a 4-week Active Treatment period (250 mg CCX282-B bid). CDAIΔ70 responders are then re-randomized 2:3 to receive either placebo or 250 mg CCX282-B bid for 36 weeks (Maintenance period). Results: As of May 2007, 163 subjects have been enrolled into the Induction Period. 56 subjects have enrolled into the Active Treatment period. 39 subjects have completed the Active Treatment period, of which 29 (74%) have achieved a CDAIΔ70 response, 27 (69%) a CDAIΔ100 response, and 16 subjects (41%) were in remission (CDAI < 150). No serious unexpected adverse events related to CCX282-B have been observed, and overall more than 250 subjects have received CCX282-B in clinical trials, with no adverse safety concerns. Conclusion: CCX282-B, a highly specific, oral CCR9 antagonist, and the first chemokine-based inhibitor of leukocyte trafficking tested in IBD, shows promise in CD.
Stoichiometric model for evaluating the metabolic capabilities of the facultative methylotroph Methylobacterium extorquens AM1, with application to reconstruction of C3 and C4 metabolism (2002)

A stoichiometric model of central metabolism was developed based on new information regarding metabolism in this bacterium to evaluate the steady-state growth capabilities of the serine cycle facultative methylotroph Methylobacterium extorquens AM1 during growth on methanol, succinate, and pyruvate. The model incorporates 20 reversible and 47 irreversible reactions, 65 intracellular metabolites, and experimentally-determined biomass composition. The flux space for this underdetermined system of equations was defined by finding the elementary modes, and constraints based on experimental observations were applied to determine which of these elementary modes give a reasonable description of the flux distribution for each growth substrate. The predicted biomass yield, on a carbon atom basis, is 49.8%, which agrees well with the range of published experimental yield measurements (37-50%). The model predicts the cell to be limited by reduced pyridine nucleotide availability during methylotrophic growth, but energy-limited when growing on multicarbon substrates. Mutation and phenotypic analysis was used to explore a previously unknown region of the metabolic map and to confirm the stoichiometry of the pathways in this region used in the metabolic model. Based on genome sequence data and simulation results, three enzymes involved in C(3)-C(4) interconversion pathways were predicted to be mutually redundant: malic enzyme, phosphoenolpyruvate carboxykinase, and phosphoenolpyruvate synthase. Insertion mutations in the genes predicted to encode these enzymes were made and these mutants were capable of growing on all substrates tested, confirming the redundancy of these pathways. Likewise, pathway analysis suggests that the TCA cycle enzymes citrate synthase and succinate dehydrogenase are essential for all growth substrates. In keeping with these predictions, null mutants could not be obtained in these genes. Finally, a similar model was developed for the ribulose monophosphate pathway obligate methylotroph Methylobacillus flagellatum KT to compare the efficiency of carbon utilization in the two types of methylotrophic carbon utilization pathways. The predicted yield for this organism on methanol is 65.9%.
Investigation of Indium Phosphide Nanocrystal Synthesis Using a High‐Temperature and High‐Pressure Continuous Flow Microreactor (2010)

Die relevanten Parameter für die Synthese von Indiumphosphid-Nanokristallen wurden mit dem gezeigten Mikrofluidiksystem ermittelt. Das Wachstum der InP-Nanokristalle ist weitgehend unabhängig von vielen experimentellen Parametern, die bei der Synthese von CdSe-Nanokristallen wichtig sind, z. B. Mischtemperatur und Reagentienkonzentration. Dagegen spielt die Konzentration der Myristinsäure (MA) eine wichtige Rolle beim Wachstum von InP-Nanokristallen. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Conformation-dependent degradation of thermally activated delayed fluorescence materials bearing cycloamino donors (2020)

Organic light-emitting devices (OLEDs) containing organic molecules that exhibit thermally activated delayed fluorescence (TADF) produce high efficiencies. One challenge to the commercialization of the TADF OLEDs that remains to be addressed is their operational stability. Here we investigate the molecular factors that govern the stability of various archetypal TADF molecules based on a cycloamino donor-acceptor platform. Our results reveal that the intrinsic stability depends sensitively on the identity of the cycloamino donors in the TADF compounds. The rates and photochemical quantum yields of the degradation are positively correlated with the operation lifetimes of the devices. Our research shows that the stability is governed by the conformeric heterogeneity between the pseudo-axial and pseudo-equatorial forms of the cycloamino donor. Spontaneous bond dissociation occurs in the former (i.e., the pseudo-axial form), but the cleavage is disfavored in the pseudo-equatorial form. These findings provide valuable insights into the design of stable TADF molecules.
Claudin3 is localized outside the tight junctions in human carcinomas (2018)

Claudin3 is an integral component of the tight junction proteins in polarized epithelia. The expression of claudin3 was assessed in epithelial-derived tumors using Oncomine database. To determine the gene alteration during carcinogenesis, copy number alterations and mutations of claudin3 were evaluated using cBioPortal database. Claudin3 is overexpressed in several tumors including gynecological, bladder, breast and prostate carcinomas. 38% of the 163 evaluated studies show mutations and/or amplification of claudin3. 3D reconstruction of tissue samples following immunofluorescence analysis clearly demonstrated that, unlike in healthy tissues, claudin3 is mislocalized and unengaged in the formation of tight junction in tumor samples. These data strongly support the evaluation of unengaged claudin3 as a target for the development of novel diagnostic probes, optical approaches for real time detection of tumoral tissues during surgery, and target therapeutic drugs.
Positive working photosensitive polymers for semiconductor surface coating (2002)

A positive working photosensitive polymer for semiconductor surface coating has been developed. Two types of thermal stable polymers, polyimide with hydroxyl groups and polybenzoxazole (PBO) precursor, were examined. It was confirmed that PBO precursor is superior to polyimide with hydroxyl groups with respect to solvent and humidity resistance. But PBO precursor had only poor adhesion to silicon wafers, and their patterns were stripped easily from substrates in developing with alkaline solution. The effect of the addition of silane coupling agents and the modification of PBO precursor with silicone compound in order to improve their adhesion properties is discussed. As a result, it was found that they had excellent adhesion to silicon wafer during development when they are modified with some silicone polyimides. Through these results, a positive working photosensitive polymer with practical sensitivity and resolution was developed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Simultaneous Quantification of Cells and Nanomaterials by Inductive-Coupled Plasma Techniques (2013)

We demonstrate that endogenous cellular magnesium levels can be used as an accurate determinant of total cell number by inductively coupled plasma techniques, increasing the throughput and reproducibility of nanoparticle-uptake studies. Uptake of either gold nanoparticles or quantum dots did not affect intracellular concentration of Mg. To demonstrate this technique, we show the decreased uptake of nano-urchins in A549 cells compared with gold nanospheres.
Experimental and Computational Studies on Saltation of Metal Powders Used in Laser Powder Bed Fusion Systems for Metal Additive Manufacturing (2021)

Abstract The ability of Powder Bed Fusion (PBF) to create complex geometries across a wide range of materials makes PBF a widely used powder-based metal additive manufacturing (AM) process in various industries for advanced applications. However, compared to conventional manufacturing processes, the metal parts printed by PBF exhibit lower surface quality due to soot and spatter particles arising from laser-powder interaction. To minimize spatter and soot generation during the build, PBF systems are equipped with cross-flow nozzles that are designed to flow inert gas across the build platform. It is desired that these gas flow systems have the ability to remove most of the spattered powder from the build chamber, but do not erode the freshly spread layer of powder on the to-be-printed surface to ensure high-quality manufactured parts. The onset of particle bed erosion can be characterized by the critical Shields number. Once the critical Shields number is known for the metal powders and system of interest, the flow of inert gas in the build chamber can be optimized to ensure the build process is efficient and clean. This work proposes a Shields number-based method for obtaining engineering design guidance for PBF gas flow systems to optimize the spatter removal process. A combined experimental and Computational Fluid Dynamics (CFD) study was performed to provide design guidance for these cross-flow systems. All experiments were conducted using a small, closed-loop wind tunnel, with built-in flexibility, capable of testing a number of cross-flow configurations. A high-speed camera captured the threshold of particle movement at a variety of operating conditions for various metal powders used in metal AM including aluminum alloy AlSi10Mg, nickel-based superalloy Inconel 718, titanium alloy Ti-6Al-4V, steel alloy 4340, and 316L stainless steel. Time-averaged flowfield measurements of the gas flow inside the test section were made using particle tracking velocimetry (PTV) and a hot-wire air flow meter at the same conditions. Using these experimental measurements and attendant CFD simulations, CFD predictions of wall shear stress can be used to calculate the Shields number at the condition of incipient movement as identified experimentally.
Electroluminescence Efficiency Enhancement in Quantum Dot Light‐Emitting Diodes by Embedding a Silver Nanoisland Layer (2015)

A colloidal quantum dot light‐emitting diode (QLED) is reported with substantially enhanced electroluminescence by embedding a thin layer of Ag nanoislands into hole transport layer. The maximum external quantum efficiency (EQE) of 7.1% achieved in the present work is the highest efficiency value reported for green‐emitting QLEDs with a similar structure, which corresponds to 46% enhancement compared with the reference device. The relevant mechanisms enabling the EQE enhancement are associated with the near‐field enhancement via an effective coupling between excitons of the quantum dot emitters and localized surface plasmons around Ag nano­islands, which are found to lead to good agreement between the simulation results and the experimental data, providing us with a useful insight important for plasmonic QLEDs.
Selective surface functionalization at regions of high local curvature in graphene (2012)

Monolayer graphene was deposited on a Si wafer substrate decorated with SiO(2) nanoparticles (NPs) and then exposed to aryl radicals that were generated in situ from their diazonium precursors. Using micro-Raman mapping, the aryl radicals were found to selectively react with the regions of graphene that covered the NPs. The enhanced chemical reactivity was attributed to the increased strain energy induced by the local mechanical deformation of the graphene.
Indoor massive MIMO deployments for uniformly high wireless capacity (2018)

Providing consistently high wireless capacity is becoming increasingly important to support the applications required by future digital enterprises. In this paper, we propose Eigen-direction-aware ZF (EDA-ZF) with partial coordination among base stations (BSs) and distributed interference suppression as a practical approach to achieve this objective. We compare our solution with Zero Forcing (ZF), entailing neither BS coordination or inter-cell interference mitigation, and Network MIMO (NeMIMO), where full BS coordination enables centralized inter-cell interference management. We also evaluate the performance of said schemes for three sub-6 GHz deployments with varying BS densities — sparse, intermediate, and dense — all with fixed total number of antennas and radiated power. Extensive simulations show that: (i) indoor massive MIMO implementing the proposed EDA-ZF provides uniformly good rates for all users; (ii) indoor network densification is detrimental unless full coordination is implemented; (iii) deploying NeMIMO pays off under strong outdoor interference, especially for cell-edge users.
Life Cycle Costing (LCC) Based Decision Making for Reactor Effluent Air Coolers in Refineries (2002)

Abstract This paper addresses the applicability of Activity Based Costing(ABC) methodology for Life Cycle Cost (LCC) based decision making in refinery facilities. In process plant facilities suffering wet corrosion problem, LCC assessment is quite difficult because the parameters influencing LCC are very complicated and have synergistic effects of both process and metallurgical aspects on facility life. This paper presents the case study of LCC assessment using ABC for Reactor Effluent Air Coolers(REAC) of hydroprocessing units in refineries, which suffer wet ammonium bisulfide(NH4HS) corrosion. As the result of the assessment, it was found that ABC could lead to usable options to support decision making to minimize LCC of REAC by analyzing operation parameters and maintenance activities affecting wet NH4HS corrosion.
Suppression of non-prompt J/ψ, prompt J/ψ, and $ \Upsilon $(1S) in PbPb collisions at $ \sqrt {{{s_{\text{NN}}}}} = 2.76 $ TeV (2012)

A bstract Yields of prompt and non-prompt J/ ψ , as well as $ \Upsilon $ (1S) mesons, are measured by the CMS experiment via their μ + μ − decays in PbPb and pp collisions at $ \sqrt {{{s_{\text{NN}}}}} = 2.76 $ TeV for quarkonium rapidity | y | &lt; 2.4. Differential cross sections and nuclear modification factors are reported as functions of y and transverse momentum p T , as well as collision centrality. For prompt J/ ψ with relatively high p T (6.5 &lt; p T &lt; 30 GeV/ c ), a strong, centrality-dependent suppression is observed in PbPb collisions, compared to the yield in pp collisions scaled by the number of inelastic nucleon-nucleon collisions. In the same kinematic range, a suppression of non-prompt J/ ψ , which is sensitive to the in-medium b-quark energy loss, is measured for the first time. Also the low- p T $ \Upsilon $ (1S) mesons are suppressed in PbPb collisions.
Monitoring blood flow and photobleaching during topical ALA PDT treatment (2009)

Photodynamic therapy (PDT) using topical aminolevulinic acid (ALA) is currently used as a clinical treatment for nonmelanoma skin cancers. In order to optimize PDT treatment, vascular shutdown early in treatment must be identified and prevented. This is especially important for topical ALA PDT where vascular shutdown is only temporary and is not a primary method of cell death. Shutdown in vasculature would limit the delivery of oxygen which is necessary for effective PDT treatment. Diffuse correlation spectroscopy (DCS) was used to monitor relative blood flow changes in Balb/C mice undergoing PDT at fluence rates of 10mW/cm<sup>2</sup> and 75mW/cm<sup>2</sup> for colon-26 tumors implanted intradermally. DCS is a preferable method to monitor the blood flow during PDT of lesions due to its ability to be used noninvasively throughout treatment, returning data from differing depths of tissue. Photobleaching of the photosensitizer was also monitored during treatment as an indirect manner of monitoring singlet oxygen production. In this paper, we show the conditions that cause vascular shutdown in our tumor model and its effects on the photobleaching rate.
Experimentally Determined Plasma Parameters in a 30 cm Ion Engine (2004)

Single planar Langmuir probes and fiber optic probes are used to concurrently measure the plasma properties and neutral density variation in a 30cm diameter ion engine discharge chamber, from the immediate vicinity of the keeper to the near grid plasma region. The fiber optic probe consists of a collimated optical fiber recessed into a double bore ceramic tube fitted with a stainless steel light-limiting window. The optical fiber probe is used to measure the emission intensity of excited neutral xenon for a small volume of plasma, at various radial and axial locations. The single Langmuir probes, are used to generate current-voltage
Assessing the Impact of Nonspecific Binding on Oligonucleotide Bioanalysis (2021)

<b>Aim:</b> Accurate and reliable quantification of oligonucleotides can be difficult, which has led to an increased focus on bioanalytical methods for more robust analyses. Recent advances toward mitigating sample losses on liquid chromatography (LC) systems have produced recovery advantages for oligonucleotide separations. <b>Results & methodology:</b> LC instruments and columns constructed from MP35N metal alloy and stainless steel columns were compared against LC hardware modified with hybrid inorganic-organic silica surfaces. Designed to minimize metal-analyte adsorption, these surfaces demonstrated a 73% increase in 25-mer phosphorothioate oligonucleotide recovery using ion-pairing reversed-phase LC versus standard LC surfaces, most particularly upon initial use. <b>Conclusion:</b> Hybrid silica chromatographic surfaces improve the performance, detection limits and reproducibility of oligonucleotide bioanalytical assays.
Behavior Negotiation in Link Management Protocol (2010)

The Link Management Protocol (LMP) is used to coordinate the
properties, use, and faults of data links in Generalized Multiprotocol
Label Switching (GMPLS) networks. Various proposals have been advanced
to provide extensions to the base LMP specification. This document
provides a generic procedure for LMP implementations that do not
recognize or do not support any one of these extensions.
ChemInform Abstract: A Facile Synthesis of 3‐Substituted Pipecolic Acids, Chimeric Amino Acids. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Classification of cognitive performance in bipolar disorder (2017)

Whereas the majority of patients performed similar to controls, a subgroup of patients with bipolar disorder differed substantially from healthy controls in the correlation pattern of low-level cognitive abilities. This suggests that cognitive impairment is not a general trait in bipolar disorder but characteristic of a cognitive subgroup. This has important clinical implications for cognitive rehabilitation and remediation.