gebhart/patrepeval huggingface dataset:
Mutagenesis analysis of the NS2B determinants of the Alkhurma virus NS2B–NS3 protease activation (2006)

Alkhurma virus (ALKV) is a tick-borne class 4 flavivirus responsible for several human cases of haemorrhagic fever in Saudi Arabia, with no specific treatment currently available. The viral RNA encodes a serine protease (NS2B-NS3), essential for virus replication in infected cells, that constitutes an attractive target for antiviral compounds. In an attempt to identify residues and motifs on NS2B that are necessary for protease activity of the ALKV NS2B-NS3 complex, a series of modified NS2B-NS3 proteins was constructed, with point mutations on particular residues or with the NS2B domain derived from two different viruses. Four mutants and the two chimeric proteins exhibited reduction of protease activity against BAPNA (a p-nitroanilide substrate). The results demonstrate that tight complementarity of the protein sequences is necessary for NS2B-dependent activation of NS3. The results also determine residues in the ALKV NS2B cofactor essential for protease activation, giving new insights into protease function in flaviviruses.
Treadmill training mitigates bone deterioration via inhibiting NLRP3/Caspase1/IL-1β signaling in aged rats (2022)

Treadmill training mitigates the ageing-induced bone loss and reverses the deterioration of bone microarchitecture in hind limbs probably through inhibiting NLRP3/Caspase1/IL-1β signaling to attenuate low-grade inflammation and improve the inflammatory bone microenvironment.
Development of an absorption-based tomographic system for mapping the human microvasculature (2011)

There exist numerous planar imaging methods for mapping the human microvasculature. In medical diagnostics, tomography is preferred over surface imaging for the simple reason that biological organs are 3-dimensional in nature. The aim of this work is to create a novel technique to non-invasively map the concentration of red blood cells in the human microcirculation allowing 3-dimensional image reconstruction. We propose a tomographic system which is based on absorption contrast imaging. A Michelson interferometry method is employed using a broadband, white light source. This work details preliminary results of the calibration procedure of a 'bulk' system. A mirror, reflectance standards, glass-mirror arrangement, and color filter arrangement were used as samples. The resultant interference patterns from each were imaged and analyzed.
Impact of Yttrium-90 Microsphere Density, Flow Dynamics, and Administration Technique on Spatial Distribution: Analysis Using an In Vitro Model (2016)

Glass and resin yttrium-90 surrogates demonstrated similar distribution in a range of clinically relevant flow conditions, suggesting that microsphere density does not have a significant influence on microsphere distribution. Injection parameters that enhanced the mixing of the spheres with the BMF resulted in the most predictable distribution.
Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level (2019)

Folded proteins show a high degree of structural order and undergo (fairly constrained) collective motions related to their functions. On the other hand, intrinsically disordered proteins (IDPs), while lacking a well-defined three-dimensional structure, do exhibit some structural and dynamical ordering, but are less constrained in their motions than folded proteins. The larger structural plasticity of IDPs emphasizes the importance of entropically driven motions. Many IDPs undergo function-related disorder-to-order transitions driven by their interaction with specific binding partners. As experimental techniques become more sensitive and become better integrated with computational simulations, we are beginning to see how the modest structural ordering and large amplitude collective motions of IDPs endow them with an ability to mediate multiple interactions with different partners in the cell. To illustrate these points, here, we use Prostate-associated gene 4 (PAGE4), an IDP implicated in prostate cancer (PCa) as an example. We first review our previous efforts using molecular dynamics simulations based on atomistic AWSEM to study the conformational dynamics of PAGE4 and how its motions change in its different physiologically relevant phosphorylated forms. Our simulations quantitatively reproduced experimental observations and revealed how structural and dynamical ordering are encoded in the sequence of PAGE4 and can be modulated by different extents of phosphorylation by the kinases HIPK1 and CLK2. This ordering is reflected in changing populations of certain secondary structural elements as well as in the regularity of its collective motions. These ordered features are directly correlated with the functional interactions of WT-PAGE4, HIPK1-PAGE4 and CLK2-PAGE4 with the AP-1 signaling axis. These interactions give rise to repeated transitions between (high HIPK1-PAGE4, low CLK2-PAGE4) and (low HIPK1-PAGE4, high CLK2-PAGE4) cell phenotypes, which possess differing sensitivities to the standard PCa therapies, such as androgen deprivation therapy (ADT). We argue that, although the structural plasticity of an IDP is important in promoting promiscuous interactions, the modulation of the structural ordering is important for sculpting its interactions so as to rewire with agility biomolecular interaction networks with significant functional consequences.
Area selective CVD of metallic films from molybdenum, iron, and ruthenium carbonyl precursors: Use of ammonia to inhibit nucleation on oxide surfaces (2018)

The authors demonstrate that the addition of an ammonia coflow during the chemical vapor deposition of MoCxNy, Fe, or Ru thin films at ≤200 °C from the metal carbonyl precursors Mo(CO)6, Fe(CO)5, or Ru3(CO)12 affords area-selective growth: film grows readily on titanium metal or vanadium nitride substrate surfaces, but no nucleation occurs on air-exposed SiO2, TiO2, Al2O3, or MgO within the investigated times of 1–2 h. By contrast, in the absence of ammonia, nucleation and deposition on these oxide surfaces can either be slow or rapid, depending strongly on the oxide surface preparation. NH3 is also the source of N in MoCxNy, which has a resistivity of 200 μΩ cm and becomes superconducting at a critical temperature of 4 K. The authors hypothesize that the passivating effect of NH3 on oxide surfaces involves site blocking to prevent precursor adsorption, or an acid–base interaction to stabilize surface-bound metal subcarbonyl intermediates, or a combination of these mechanisms. A key finding is that surface selective growth is often crucially dependent on the sample history of the substrate, which must be specified in detail if reproducible results are to be obtained.
Using heat of combustion data to estimate or assess some threshold flammability properties of materials (2003)

Abstract This paper gives a brief summary of recent studies using heat of combustion data to estimate or assess some threshold flammability properties of materials. Heat of combustion data can be used to estimate the lower flammability limit, upper flammability limit and minimum oxygen concentration for flame propagation of organic and organosilicon compounds. The data can also be used to assess the threshold oxygen pressure for the combustion of metal alloys in high‐pressure oxygen environments. Copyright © 2003 John Wiley &amp; Sons, Ltd.
Feasibility of indocyanine green‐guided localization of pulmonary nodules in children with solid tumors (2023)

ICG-guided identification of pulmonary nodules is not feasible for all pediatric solid tumors. However, it may localize most metastatic hepatic tumors and high-grade sarcomas in children.
HEPATOCYTE TRANSPLANTATION (2004)

Isolated hepatocyte transplantation has long been recognized as a potential treatment for life-threatening liver disease. The basis for proceeding with clinical trials has been established by the extensive laboratory work in animal models. Human hepatocyte transplantation has been applied in individual cases and very small, uncontrolled series. Data, although sparse, demonstrate the safety and feasibility of this approach and are supportive, if less than conclusive, of effectiveness. The experience of hepatocyte transplantation in the laboratory and clinical arenas is reviewed and discussion will examine what is believed to be the primary cause for the slow growth of this technology in the clinical setting, namely a severe shortage of usable primary human hepatocytes. The potential of isolated hepatocyte transplantation remains largely untapped and awaits alternate sources of cells for transplantation other than those from discarded human cadaveric livers.
A Metal–Ligand Cooperative Pathway for Intermolecular Oxa‐Michael Additions to Unsaturated Nitriles (2015)

An unprecedented catalytic pathway for oxa-Michael addition reactions of alcohols to unsaturated nitriles has been revealed using a PNN pincer ruthenium catalyst with a dearomatized pyridine backbone. The isolation of a catalytically competent Ru-dieneamido complex from the reaction between the Ru catalyst and pentenenitrile in combination with DFT calculations supports a mechanism in which activation of the nitrile through metal-ligand cooperativity is a key step. The nitrile-derived Ru-N moiety is sufficiently Brønsted basic to activate the alcohol and initiate conjugate addition of the alkoxide to the α,β-unsaturated fragment. This reaction proceeds in a concerted manner and involves a six-membered transition state. These features allow the reaction to proceed at ambient temperature in the absence of external base.
Summary Abstract: GaAs oxidation and the Ga–As–O equilibrium phase diagram (1980)

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Acute otitis media pneumococcal disease burden and nasopharyngeal colonization in children due to serotypes included and not included in current and new pneumococcal conjugate vaccines (2022)

Our review highlights the important epidemiological differences in serotype distribution and coverage by existing and higher valency vaccines to protect against AOM in children. These data provide support for further evaluation of serotype-independent vaccines for optimal control of pneumococcal AOM disease worldwide.
16.7 A 30GHz Digital Sub-Sampling Fractional-N PLL with 198fs<inf>rms</inf> Jitter in 65nm LP CMOS (2019)

Digital phase-locked loops (DPLLs) have been demonstrated to achieve excellent performance as fractional-N frequency synthesizers in the sub-6GHz range, but, when used in the mm-wave range, at 30GHz and above, they typically feature poor jitter-power trade-off. This paper presents a 30GHz fractional-N DPLL in 65nm low-power (LP) CMOS achieving 198fs integrated jitter at 35mW power. The DPLL based on a digital-to-time converter (DTC) combines: (i) sub-sampling bang-bang phase detection to reduce power consumption, (ii) a digital error correction to reduce DTC noise contribution, and (iii) a low-power wide-lock-range divide-by-six circuit to allow operation up to 34GHz.
Foxa1 is essential for development and functional integrity of the subthalamic nucleus (2016)

Inactivation of transcription factor Foxa1 in mice results in neonatal mortality of unknown cause. Here, we report that ablation of Foxa1 causes impaired development and loss of the subthalamic nucleus (STN). Functional deficits in the STN have been implicated in the etiology of Huntington's and Parkinson's disease. We show that neuronal ablation by Synapsin1-Cre-mediated Foxa1 deletion is sufficient to induce hyperlocomotion in mice. Transcriptome profiling of STN neurons in conditional Foxa1 knockout mice revealed changes in gene expression reminiscent of those in neurodegenerative diseases. We identified Ppargc1a, a transcriptional co-activator that is implicated in neurodegeneration, as a Foxa1 target. These findings were substantiated by the observation of Foxa1-dependent demise of STN neurons in conditional models of Foxa1 mutant mice. Finally, we show that the spontaneous firing activity of Foxa1-deficient STN neurons is profoundly impaired. Our data reveal so far elusive roles of Foxa1 in the development and maintenance of STN function.
An injectable supramolecular hydrogel as a self-drug-delivery system for local chemoimmunotherapy against melanoma (2023)

Skin-cancer melanoma caused 57k death in 2020. Some of the available therapies are: topical application of a gel loaded with an anti-skin cancer drug and intravenous injection of immune cytokines; however, both the approaches have drawbacks such as inefficient internalization of the drug in cancer cells and a short half-life with severe side effects, respectively. Interestingly, we observed for the first time that a subcutaneously implanted hydrogel designed and synthesized by coordinating NSAIDs and 5-AP with Zn(II) can effectively combat melanoma cell (B16-F10)-induced tumors in C57BL/6 mice. Both <i>in vitro</i> and <i>in vivo</i> results show that it can effectively reduce PGE<sub>2</sub> expression, consequently upregulating IFN-γ and IL-12 that eventually engage M1-macrophages for activating T cells (CD8<sup>+</sup>), triggering apoptosis. This unique all-in-one self-drug-delivery approach, wherein the hydrogel implant is made from the drug molecules itself providing both chemotherapy and immunotherapy in combating deadly melanoma, highlights the supramolecular chemistry-based bottom-up approach in cancer therapy.
Khalifa University Reachback Program Supporting Prevention of Illicit Nuclear and Radiological Material Smuggling in the United Arab Emirates (2016)

Trafficking of Illicit nuclear or radiological materials is a global threat which can involve and adversely affect any country. Ultimately, it is the responsibility of each state to prevent and combat illicit nuclear trafficking by screening all cargo and travelers entering, exiting, and transiting through its borders. As a part of the national radiation detection infrastructure of the United Arab Emirates (UAE), a reachback program was established at Khalifa University (KU) to provide capabilities for adjudication of radiation alarms at Khalifa Port and other radiation portal monitor (RPM) locations. In addition to the main mission, KU Reachback aims to educate and prepare local talent to lead these vital efforts in the future. This is particularly important because the UAE, similar to other newcomers to the nuclear industry, faces human capital challenges which can be addressed using domestic or regional solutions.
Reputation and Pricing Dynamics in Online Markets (2021)

We study the economic interactions among sellers and buyers in online markets. In such markets, buyers have limited information about the product quality, but can observe the sellers' reputations which depend on their past transaction histories and ratings from past buyers. Sellers compete in the same market through pricing, while considering the impact of their heterogeneous reputations. We consider sellers with limited as well as unlimited capacities, which correspond to different practical market scenarios. In the unlimited seller capacity scenario, buyers prefer the seller with the highest reputation-price ratio. If the gap between the highest and second highest seller reputation levels is large enough, then the highest reputation seller dominates the market as a monopoly. If sellers' reputation levels are relatively close to each other, then those sellers with relatively high reputations will survive at the equilibrium, while the remaining relatively low reputation sellers will get zero market share. In the limited seller capacity scenario, we further consider two different cases. If each seller can only serve one buyer, then it is possible for sellers to set their monopoly prices at the equilibrium while all sellers gain positive market shares; if each seller can serve multiple buyers, then it is possible for sellers to set maximum prices at the equilibrium. Simulation results show that the dynamics of reputations and prices in the longer-term interactions will converge to stable states, and the initial buyer ratings of the sellers play the critical role in determining sellers' reputations and prices at the stable state.
Haemophilus, Antibiotic Therapy and the Airway Microbiome in Chronic Obstructive Pulmonarydisease (2018)

ABSTRACT Chronic obstructive pulmonary disease (COPD) is a smoking-related illness affecting 64 million people worldwide. Airway infection drives recurrent exacerbations and lung function decline. Prophylactic antibiotics may prevent exacerbations but their use is a significant cause of population antimicrobial resistance. We characterised the sputum microbiome by 16S rRNA gene analysis using 138 samples collected during a randomised controlled trial of prophylactic antibiotics in 71 patients with stable COPD. On comparing the profile of the microbiome obtained by sequencing to the isolates grown from samples using standard culture, there were similarities overall, although with a much narrower spectrum of genera on culture with under-representation of certain genera including Veillonella and Prevotella. There was concordance in the most abundant genera within samples and the number of isolates cultured reflected the measured bacterial diversity. We found that at baseline the microbiota of 17 (24%) patients were dominated by Haemophilus influenzae , accompanied by narrowed microbial diversity and higher levels of sputum inflammatory cytokines. Different H. influenzae strains co-existed within individuals. Opportunistic whole genome sequencing of six H. influenzae isolates obtained during the study revealed that all were non-typeable H. influenzae (NTHI), with a range of different antibiotic resistance gene profiles, but an identical complement of virulence genes. Administration of 13 weeks prophylaxis with moxifloxacin, azithromycin or doxycycline revealed distinctive changes in microbial communities for each group. Haemophilus numbers reduced by 90% compared to placebo only after moxifloxacin, and significant reduction in sputum cytokines occurred in patients dominated by Haemophilus at baseline. Haemophilus influenzae dominance defines COPD patients with active disease who may particularly benefit from antibiotics or vaccination.
Gene Transfer into Rat Brain Using Adenoviral Vectors (2010)

Viral vector-mediated gene delivery is an attractive procedure for introducing genes into the brain, both for purposes of basic neuroscience research and to develop gene therapy for neurological diseases. Replication-defective adenoviruses possess many features which make them ideal vectors for this purpose-efficiently transducing terminally differentiated cells such as neurons and glial cells, resulting in high levels of transgene expression in vivo. Also, in the absence of anti-adenovirus immunity, these vectors can sustain very long-term transgene expression within the brain parenchyma. This unit provides protocols for the stereotactic injection of adenoviral vectors into the brain, followed by protocols to detect transgene expression or infiltrates of immune cells by immunocytochemistry or immunofluorescence. ELISPOT and neutralizing antibody assay methodologies are provided to quantitate the levels of cellular and humoral immune responses against adenoviruses. Quantitation of adenoviral vector genomes within the rat brain using qPCR is also described.
Nitric Oxide Regulates Monocyte Chemotactic Protein-1 (1997)

These studies indicate that the antiatherogenic effect of NO may be mediated in part by its inhibition of MCP-1 expression.
Optimizing color performance for LCD computer monitors (2005)

Despite the fact that the LCD computer monitors have undergone a tremendous technology improvement in recent years, their color performance may still be enhanced through image processing. This paper presents few correction algorithms for improving color performance of the LCD computer monitors in the area of gray tracking, viewing angle performance and response time. The implementation of each algorithm does not require special hardware additions or alterations or architecture changes, but it uses the existent resources of a modern computer system.
Efficient geometry-based similarity search of 3D spatial databases (1999)

Searching a database of 3D-volume objects for objects which are similar to a given 3D search object is an important problem which arises in number of database applications — for example, in Medicine and CAD. In this paper, we present a new geometry-based solution to the problem of searching for similar 3D-volume objects. The problem is motivated from a real application in the medical domain where volume similarity is used as a basis for surgery decisions. Our solution for an efficient similarity search on large databases of 3D volume objects is based on a new geometric index structure. The basic idea of our new approach is to use the concept of hierarchical approximations of the 3D objects to speed up the search process. We formally show the correctness of our new approach and introduce two instantiations of our general idea, which are based on cuboid and octree approximations. We finally provide a performance evaluation of our new index structure revealing significant performance improvements over existing approaches.
Hydrolysis of Benzopyrylium Dyes - An Application of the Concept of Chemical Hardness (1996)

A systematic study on the relationship between the substitution pattern, the pKa values, and spectral properties of flavylium cations and the respective–(CH2)2–bridged analoga (5,6-dihydrobenzo[c]xanthylium cations) is given in order to find rules concerning their spectral behaviour and their chemical reactivity. Our results show that the concept of chemical hardness can explain the different reactivity of 4′- and 7-substituted flavylium ions against HO−. The pKa values of these species, which can act as a measure of reactivity with respect to a nucleophile, correlate linearly with the absolute hardness calculated from half the energy gap between the frontier orbitals. Since the longest-wavelength UV/VIS absorption maximum is mainly determined by the HOMO-LUMO transition, an analogous linear correlation is obtained between the spectral 0–0 transition and the pKa value. Deviations from these correlations are assumed to be due to steric effects.
Wideband Predistortion Technique With Dual-Parallel Schottky Diodes for Low Power RoF Systems (2021)

Radio-over-fiber (RoF)-based front haul architecture has attracted considerable attention for fifth-generation (5G) cellular systems because of its cost effectiveness, however, it is susceptible to harmonic frequency distortion and intermodulation products (IMs) arising from the nonlinearity of the laser diode. To overcome this limitation, an asymmetric electrical predistortion method, using a single Schottky diode with nonlinear characteristics similar to those of a laser diode, was previously proposed. However, its asymmetric structure causes a phase mismatch, which limits the system bandwidth. In this study, we propose an enhanced electrical predistortion technique using dual-parallel Schottky diode blocks. The proposed technique was validated by experiments involving an IM3 drop of approximately 27 dB, and by using identical dual Schottky diode blocks, the phase mismatch in the previously proposed method is completely eliminated. Thus, the applicable bandwidth is extended to 1.8 GHz. This technique can be used to improve the linearity and increase the bandwidth of RoF systems. Additionally, the simple structure is attractive for low-power applications.