gebhart/patrepeval huggingface dataset:
Function of the Diiron Cluster of Escherichia coli Class Ia Ribonucleotide Reductase in Proton-Coupled Electron Transfer (2013)

The class Ia ribonucleotide reductase (RNR) from Escherichia coli employs a free-radical mechanism, which involves bidirectional translocation of a radical equivalent or “hole” over a distance of ~35 Å from the stable diferric/tyrosyl-radical (Y[subscript 122]•) cofactor in the β subunit to cysteine 439 (C[subscript 439]) in the active site of the α subunit. This long-range, intersubunit electron transfer occurs by a multistep “hopping” mechanism via formation of transient amino acid radicals along a specific pathway and is thought to be conformationally gated and coupled to local proton transfers. Whereas constituent amino acids of the hopping pathway have been identified, details of the proton-transfer steps and conformational gating within the β sununit have remained obscure; specific proton couples have been proposed, but no direct evidence has been provided. In the key first step, the reduction of Y[subscript 122]• by the first residue in the hopping pathway, a water ligand to Fe[subscript 1] of the diferric cluster was suggested to donate a proton to yield the neutral Y[subscript 122]. Here we show that forward radical translocation is associated with perturbation of the Mössbauer spectrum of the diferric cluster, especially the quadrupole doublet associated with Fe[subscript 1]. Density functional theory (DFT) calculations verify the consistency of the experimentally observed perturbation with that expected for deprotonation of the Fe[subscript 1]-coordinated water ligand. The results thus provide the first evidence that the diiron cluster of this prototypical class Ia RNR functions not only in its well-known role as generator of the enzyme’s essential Y[subscript 122]•, but also directly in catalysis.
[18F]D3FSP ([18F]D3AV-45) as a PET imaging agent for Abeta plaques in the brain. (2018)

1031 Objectives: Replacement of the carbon hydrogen bond (C-H) with a carbon-deuterium (C-D) bond often increases in vivo metabolic stability through a reduction in drug metabolism. FDA has recently approved a new deuterated drug, deuterated tetrabenazine (SD-809, Austedo) for treatment of Huntington’s disease. Amyvid (florbetapir, [18F]AV-45) is currently a commercially available PET imaging agent targeting Aβ plaques in the brain for assisting the diagnosis of Alzheimer’s disease. A deuterated analog, [18F]D3FSP ([18F]D3AV-45), was prepared and tested for mapping Aβ plaques in the brain. Methods: [18F]D3FSP, a potential PET imaging agent targeting amyloid plaques in the brain, was prepared using a reaction sequence similar to that of [18F]AV-45. [18F]D3FSP was tested by in vitro binding, autoradiography and in vivo biodistribution studies in normal mice. Results: Binding studies, using either [18F]D3FSP or [18F]AV-45 as the hot ligand, showed that hydrogen to deuterium substitution (AV-45 vs D3FSP) showed the same excellent binding affinity to Aβ aggregate binding sites (Ki = 3 to 4 nM). Within statistical errors the biodistribution of [18F]-AV-45 and [18F]D3FSP in normal mice showed very similar results. [18F]D3FSP and [18F]AV-45 showed comparable initial brain penetration at 2 min after an iv injection with rapid washout in the normal mice brain as shown at later time points (60 and 120 min). Autoradiography of AD brain sections using these two ligands showed very similar binding pattern confirming the high binding affinity to Aβ aggregates. Conclusion: The preliminary results suggest that [18F]D3FSP is a potential PET imaging agent for mapping Aβ plaques in the brain.
Effects of In composition on ultraviolet emission efficiency in quaternary InAlGaN light-emitting diodes on freestanding GaN substrates and sapphire substrates (2005)

350 - nm -band quaternary InAlGaN quantum-well (QW) structures have been fabricated on low-dislocation-density GaN substrates and sapphire substrates, and the impact of the In composition on ultraviolet emission efficiency has been investigated. Photoluminescence, cathodoluminescence, and atomic force microscopy measurements have revealed that with increasing In concentration, band-gap inhomogeneity in InAlGaN layers is promoted and quantum efficiency becomes less sensitive to dislocation densities. However, this does not necessarily result in the enhancement of QW emission efficiency, because both a decrease in growth temperature and an increase in Al concentration degrade the InAlGaN crystalline quality. It is found that improving the InAlGaN crystalline quality by increasing the growth temperature while maintaining an In fluctuation effect with minimal In composition is essential for highly efficient InAlGaN QWs. The utilization of the optimized InAlGaN growth condition significantly improves the output power of 350-nm-band light-emitting diodes on GaN and sapphire substrates to 7.4mW at 400mA and 2.9mW at 200mA, respectively.
Generation of alkali-free and high-proton concentration layer in a soda lime glass using non-contact corona discharge (2013)

Formation mechanisms of alkali-free and high-proton concentration surfaces were investigated for a soda lime glass using a corona discharge treatment under an atmospheric pressure. Protons produced by high DC voltage around an anode needle electrode were incorporated into a sodium ion site in the anode side glass. The sodium ion was swept away to the cathode side as a charge carrier. Then it was discharged. The precipitated sodium was transformed to a Na2CO3 powder when the surface contacted with air. The sodium ion in the glass surface layer of the anode side was replaced completely by protons. The concentration of OH groups in the layer was balanced with the amount of excluded sodium ions. The substitution reaction of sodium ions with protons tends to be saturated according to a square root function of time. The alkali depletion layer formation rate was affected by the large difference in mobility between sodium ions and protons in the glass.
Influence of the bonding front propagation on the wafer stack curvature (2014)

The influence of the dynamics of the direct wafer bonding process on the curvature of the final wafer stack is investigated. An analytical model for the final curvature of the bonded wafers is developed, as a function of the different load components acting during the bonding front propagation, using thin plate theory and considering a strain discontinuity locked at the bonding interface. Experimental profiles are measured for different bonding conditions and wafer thicknesses. A very good agreement with the model prediction is obtained and the influence of the thin air layer trapped in-between the two wafers is demonstrated. The proposed model contributes to further improvement of the bonding process, in particular, for the stacking of layers of electronic devices, which requires a high accuracy of wafer-to-wafer alignment and a very low distortion level.
ChemInform Abstract: Analogues of Polyamine Alkaloids and Their Synthetic Advantages (2001)

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.
The Effect of Select Personal Care Ingredients and Simple Formulations on the Attachment of Bacteria on Polystyrene (2018)

The human body is covered with bacteria that are required for health and wellbeing. Additionally, there are pathogenic bacteria that are unwanted. It is therefore important to understand how personal care ingredients interact with these bacteria. To help understand these interactions, a high-throughput assay was developed to study the effect of personal care ingredients on attachment. Seventeen personal care ingredients were assayed singly and in simple alcohol based formulations. Three of the ingredients decreased the attachment of both bacteria tested by 90% singly and in formulation. Personal care ingredients singly and in simple formulations can prevent the attachment of bacteria. Further research is needed to better understand how personal care ingredients affect bacterial attachment and how these effects can be used to create new hygiene products for consumers.
Proof-of-concept of flexible massive MIMO beamforming at 2.4 GHz (2017)

The next wireless communication system will support flexible beamforming and beam-sweeping to realize high capacity demands. This can be achieved with Massive MIMO systems realizing high beamforming gains as well as higher order multi-user multiplexing. Real proof-of-concepts are required to evaluate algorithms and show performance gains. In general, prototyping of M-MIMO systems is challenging, since many transceiver chains have to be calibrated and data streams synchronized. In this paper, we perform measurements in an indoor environment using a real M-MIMO SDR system with 16 active antenna ports. System-level simulations on recorded measurement data highlight downlink throughput results for individual users.
A Synthetic Influenza Virus Vaccine Induces a Cellular Immune Response That Correlates with Reduction in Symptomatology and Virus Shedding in a Randomized Phase Ib Live-Virus Challenge in Humans (2015)

Current influenza vaccines elicit primarily antibody-based immunity. They require yearly revaccination and cannot be manufactured until the identification of the circulating viral strain(s). These issues remain to be addressed. Here we report a phase Ib trial of a vaccine candidate (FLU-v) eliciting cellular immunity. Thirty-two males seronegative for the challenge virus by hemagglutination inhibition assay participated in this single-center, randomized, double-blind study. Volunteers received one dose of either the adjuvant alone (placebo, n = 16) or FLU-v (500 μg) and the adjuvant (n = 16), both in saline. Twenty-one days later, FLU-v (n = 15) and placebo (n = 13) volunteers were challenged with influenza virus A/Wisconsin/67/2005 (H3N2) and monitored for 7 days. Safety, tolerability, and cellular responses were assessed pre- and postvaccination. Virus shedding and clinical signs were assessed postchallenge. FLU-v was safe and well tolerated. No difference in the prevaccination FLU-v-specific gamma interferon (IFN-γ) response was seen between groups (average ± the standard error of the mean [SEM] for the placebo and FLU-v, respectively, 1.4-fold ± 0.2-fold and 1.6-fold ± 0.5-fold higher than the negative-control value). Nineteen days postvaccination, the FLU-v group, but not the placebo group, developed FLU-v-specific IFN-γ responses (8.2-fold ± 3.9-fold versus 1.3-fold ± 0.1-fold higher than the negative-control value [average ± SEM] for FLU-v versus the placebo [P = 0.0005]). FLU-v-specific cellular responses also correlated with reductions in both viral titers (P = 0.01) and symptom scores (P = 0.02) postchallenge. Increased cellular immunity specific to FLU-v correlates with reductions in both symptom scores and virus loads. (This study has been registered at ClinicalTrials.gov under registration no. NCT01226758 and at hra.nhs.uk under EudraCT no. 2009-014716-35.).
Waldenström macroglobulinemia: from biology to treatment (2014)

Waldenström macroglobulinemia (WM) is distinct B-cell lymphoproliferative disorder primarily characterized by bone marrow infiltration of lymphoplasmacytic cells along with production of a serum monoclonal (IgM). In this review, we describe the biology of WM, the diagnostic evaluation for WM with a discussion of other conditions that are in the differential diagnosis and clinical manifestations of the disease as well as current treatment options. Within the novel agents discussed are everolimus, perifosine, enzastaurin, panobinostat, bortezomib and carfilzomib, pomalidomide and ibrutinib. Many of the novel agents have shown good responses and have a better toxicity profile compared to traditional chemotherapeutic agents, which makes them good candidates to be used as primary therapies for WM in the future.
A widespread family of WYL-domain transcriptional regulators co-localises with diverse phage defence systems and islands (2021)

A bstract Bacteria are under constant assault by bacteriophages and other mobile genetic elements. As a result, bacteria have evolved a multitude of systems that protect from attack. Genes encoding bacterial defence mechanisms can be clustered into “defence islands”, providing a potentially synergistic level of protection against a wider range of assailants. However, there is a comparative paucity of information on how expression of these defence systems is controlled. Here, we functionally characterise a transcriptional regulator, BrxR, encoded within a recently described phage defence island from a multidrug resistant plasmid of the emerging pathogen Escherichia fergusonii . Using a combination of reporters and electrophoretic mobility shift assays, we discovered that BrxR acts as a repressor. We present the structure of BrxR to 2.15 Å, the first structure of this family of transcription factors, and pinpoint a likely binding site for ligands within the WYL-domain. Bioinformatic analyses demonstrated that BrxR homologues are widespread amongst bacteria. About half (48%) of identified BrxR homologues were co-localised with a diverse array of known phage defence systems, either alone or clustered into defence islands. BrxR is a novel regulator that reveals a common mechanism for controlling the expression of the bacterial phage defence arsenal.
Focused Ion Beam Structuring of Exposed-Core Microstructured Optical Fibers (2015)

Focused ion beam milling has been employed to create micro-structured features onto an exposed-core microstructured optical fiber. Here we detail results for fabricating and characterizing Fabry-Perot cavities using this method.
Analog-Based Drug Discovery Edited by Janos Fischer and C. Robin Ganellin. Wiley/VCH Verlag GmbH, Weinheim, Germany. 2006. xxi + 575 pp. 17.5 × 42.5 cm. ISBN 3527312579. $180.00. (2006)

ADVERTISEMENT RETURN TO ISSUEPREVBook ReviewNEXTAnalog-Based Drug Discovery Edited by Janos Fischer and C. Robin Ganellin. Wiley/VCH Verlag GmbH, Weinheim, Germany. 2006. xxi + 575 pp. 17.5 × 42.5 cm. ISBN 3527312579. $180.00.Marlon CowartView Author Information Department of Neuroscience Research Abbott Laboratories Abbott Park, Illinois 60064-6123Cite this: J. Med. Chem. 2006, 49, 15, 4799Publication Date (Web):June 15, 2006Publication History Published online15 June 2006Published inissue 1 July 2006https://pubs.acs.org/doi/10.1021/jm068024phttps://doi.org/10.1021/jm068024pbook-reviewACS PublicationsCopyright © 2006 American Chemical SocietyRequest reuse permissionsArticle Views266Altmetric-Citations1LEARN 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 SUBJECTS:Antagonists,Chemical structure,Drug discovery,Peptides and proteins,Pharmaceuticals Get e-Alerts
Design Optimization with Uncertain Application Knowledge (2020)

Designing modern electro-mechanical devices is a non-trivial task, due to their versatility, their increasing performance requirements, and the integration of software and hardware. Competition in the market place motivates additional requirements, such as high performance and low cost, and an important part of design is often to optimize conflicting objectives. In this paper, we present model-based techniques for design optimization. We develop a parameterized machine model in the form of design, scheduling and cost constraints and present a tool that determines values for design variables that optimize the performance and cost of the machine. Furthermore, we present a method for analyzing design solutions in the absence of precise workload knowledge. A qualitative method for classifying optimal sets of machine parameter values with respect to workload distribution, helps the designer to understand the interaction between potential application contexts and optimal solutions, and may be used to generate configurable designs.
ChemInform Abstract: Triplet‐State Phosphoryl Diradicals. (1995)

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.
Investigating Determinants and Evaluating Deep Learning Training Approaches for Visual Acuity in Foveal Hypoplasia (2022)

Nystagmus and foveal anatomy impact visual outcomes in patients with FH, and computational algorithms reliably estimate FH grading and visual acuity.
A Pilot Trial to Assess Potential Effects of Selective Intracoronary Bone Marrow–Derived Progenitor Cell Infusion in Patients With Nonischemic Dilated Cardiomyopathy (2009)

Intracoronary administration of BMC seems to be associated with improvements in cardiac contractile and microvascular function in patients with DCM. Thus, randomized blinded studies are warranted to evaluate potential clinical benefits of intracoronary BMC administration in patients with DCM.
The Benign Cystic Lymphoepithelial Lesion of the Parotid Gland Is a Viral Reservoir in HIV Type 1-Infected Patients (1999)

The presence of HIV-1 in cystic fluid aspirates from six cases of benign cystic lymphoepithelial lesion (BLL) of the parotid gland, a rare disorder affecting HIV-1-infected patients, has been investigated. HIV-1 p24 protein was present at a concentration ranging from 3 to 15 ng/ml, while it was undetectable in the peripheral blood of the same patients. The number of RNA copies of HIV-1 in the cystic fluids was high, ranging from 0.5 x 10(7) to 7.2 x 10(7) RNA copies/ml. BLL cystic fluid aspirates, despite the high level of HIV-1 RNA, were found to contain only a few infectious virions. The low infectivity correlated with the infrequent detection by electron microscopy of complete HIV-1 particles. The pathogenic mechanism leading to virus accumulation in the cystic fluid was studied by immunohistochemistry of tissue sections. p24 protein was associated with DRC-1+/S-100+ follicular dendritic reticulum cells, which were also present within the cystic cavities. Our findings are consistent with the possibility that the large amounts of virus present in the fluid derive from continuous shedding of HIV-1-infected cells from the surrounding lymphoid tissue.
Few-layer bismuth selenide cathode for low-temperature quasi-solid-state aqueous zinc metal batteries (2022)

The performances of rechargeable batteries are strongly affected by the operating environmental temperature. In particular, low temperatures (e.g., ≤0 °C) are detrimental to efficient cell cycling. To circumvent this issue, we propose a few-layer Bi<sub>2</sub>Se<sub>3</sub> (a topological insulator) as cathode material for Zn metal batteries. When the few-layer Bi<sub>2</sub>Se<sub>3</sub> is used in combination with an anti-freeze hydrogel electrolyte, the capacity delivered by the cell at -20 °C and 1 A g<sup>-1</sup> is 1.3 larger than the capacity at 25 °C for the same specific current. Also, at 0 °C the Zn | |few-layer Bi<sub>2</sub>Se<sub>3</sub> cell shows capacity retention of 94.6% after 2000 cycles at 1 A g<sup>-1</sup>. This behaviour is related to the fact that the Zn-ion uptake in the few-layer Bi<sub>2</sub>Se<sub>3</sub> is higher at low temperatures, e.g., almost four Zn<sup>2+</sup> at 25 °C and six Zn<sup>2+</sup> at -20 °C. We demonstrate that the unusual performance improvements at low temperatures are only achievable with the few-layer Bi<sub>2</sub>Se<sub>3</sub> rather than bulk Bi<sub>2</sub>Se<sub>3</sub>. We also show that the favourable low-temperature conductivity and ion diffusion capability of few-layer Bi<sub>2</sub>Se<sub>3</sub> are linked with the presence of topological surface states and weaker lattice vibrations, respectively.
<title>Chemical Vapor deposition (CVD) TiN: a barrier metallization for submicron via and contact applications</title> (1994)

A new technique for low temperature CVD TiN is introduced as a barrier/glue layer for sub 0.5 micron applications. Excellent conformity (&gt; 70%) is achieved while maintaining good electrical performance and reliability. The films are shown to be polycrystalline TiN with no preferred grain orientation. In addition compositional analysis shows significant amounts of carbon in the film presumably between the grains. The electrical properties of the CVD film were evaluated at the via and contact level. The contact and via resistances of tungsten plugs using CVD TiN glue layers are shown to be comparable to plugs using sputtered TiN. The barrier performance of the film was also evaluated at the contact level. The superior junction leakage data indicate that the CVD TiN film should have wide application as a barrier metal for sub 0.5 mm applications.
The neuroendocrine polypeptide 7B2 is an endogenous inhibitor of prohormone convertase PC2. (1994)

The subtilisin-like prohormone convertase PC2 and the polypeptide 7B2 (an intracellularly cleaved protein of unknown function) are both selectively present in the regulated secretory pathway of neurons and endocrine cells. Here we demonstrate that intact recombinant 7B2 is a potent inhibitor of PC2 and prevents proPC2 cleavage in vitro, whereas the 7B2 cleavage product is virtually inactive. The PC2-related proteinase PC1/PC3 is not inhibited by 7B2. Furthermore, the carboxyl-terminal half of the 7B2 protein sequence is distantly related to the so-called potato inhibitor I family (which includes subtilisin inhibitors). Our findings indicate that 7B2 is a physiological inhibitor of PC2 and may provide alternative avenues for the manipulation of peptide hormone levels.