gebhart/patrepeval huggingface dataset:
Ultrabright room-temperature single-photon emission from nanodiamond\n nitrogen-vacancy centers with sub-nanosecond excited-state lifetime (2017)

Ultrafast emission rates obtained from quantum emitters coupled to plasmonic\nnanoantennas have recently opened fundamentally new possibilities in quantum\ninformation and sensing applications. Plasmonic nanoantennas greatly improve\nthe brightness of quantum emitters by dramatically shortening their\nfluorescence lifetimes. Gap plasmonic nanocavities that support strongly\nconfined modes are of particular interest for such applications. We demonstrate\nsingle-photon emission from nitrogen-vacancy (NV) centers in nanodiamonds\ncoupled to nanosized gap plasmonic cavities with internal mode volumes about 10\n000 times smaller than the cubic vacuum wavelength. The resulting structures\nfeatures sub-nanosecond NV excited-state lifetimes and detected photon rates up\nto 50 million counts per second. Analysis of the fluorescence saturation allows\nthe extraction of the multi-order excitation rate enhancement provided by the\nnanoantenna. Efficiency analysis shows that the NV center is producing up to\n0.25 billion photons per second in the far-field.\n
Enhanced In Vitro Protein Synthesis Through Optimal Design of PCR Primers (2006)

The functional stability of mRNA is one of the crucial factors affecting the efficiency of in vitro translation. As the rapid degradation of mRNA in the cell extract (S30 extract) causes early termination of the translational reactions, extending the mRNA half-life will improve the productivity of the in vitro protein synthesis. Thus, a simple PCR-based method is introduced to increase the stability of mRNA in an S30 extract. The target genes are PCR-amplified with primers designed to make the ends of the transcribed mRNA molecule anneal to each other. When compared with normal mRNA, the mRNA with the annealing sequences resulted in an approximately 2-fold increase of protein synthesis in an in vitro translation reaction. In addition, sequential transcription and translation reactions in a single tube enabled direct protein expression from the PCR-amplified genes without any separate purification of the mRNA.
Morphology and structure of ZIF-8 during crystallisation measured by dynamic angle-resolved second harmonic scattering (2018)

Recent developments in nonlinear optical light scattering techniques have opened a window into morphological and structural characteristics for a variety of supramolecular systems. However, for the study of dynamic processes, the current way of measuring is often too slow. Here we present an alternative measurement scheme suitable for following dynamic processes. Fast acquisition times are achieved through Fourier imaging, allowing simultaneous detection at multiple scattering angles for different polarization combinations. This allows us to follow the crystal growth of the metal organic framework ZIF-8 in solution. The angle dependence of the signal provides insight into the growth mechanism by probing the evolution of size, shape and concentration, while polarization analysis yields structural information in terms of point group symmetry. Our findings highlight the potential of dynamic angle-resolved harmonic light scattering to probe crystal growth processes, assembly-disassembly of biological systems, adsorption, transport through membranes and myriad other applications.
A Proteomic and Transcriptomic Approach Reveals New Insight into β-methylthiolation of Escherichia coli Ribosomal Protein S12 (2010)

β-methylthiolation is a novel post-translational modification mapping to a universally conserved Asp 88 of the bacterial ribosomal protein S12. This S12 specific modification has been identified on orthologs from multiple bacterial species. The origin and functional significance was investigated with both a proteomic strategy to identify candidate S12 interactors and expression microarrays to search for phenotypes that result from targeted gene knockouts of select candidates. Utilizing an endogenous recombinant E. coli S12 protein with an affinity tag as bait, mass spectrometric analysis identified candidate S12 binding partners including RimO (previously shown to be required for this post-translational modification) and YcaO, a conserved protein of unknown function. Transcriptomic analysis of bacterial strains with deleted genes for RimO and YcaO identified an overlapping transcriptional phenotype suggesting that YcaO and RimO likely share a common function. As a follow up, quantitative mass spectrometry additionally indicated that both proteins dramatically impacted the modification status of S12. Collectively, these results indicate that the YcaO protein is involved in β-methylthiolation of S12 and its absence impairs the ability of RimO to modify S12. Additionally, the proteomic data from this study provides direct evidence that the E. coli specific β-methylthiolation likely occurs when S12 is assembled as part of a ribosomal subunit.
Geology and mineralogy of the Apex germanium-gallium mine, Washington County, Utah (1986)

Introduction 1 Germanium and gallium 1 Apex Mine 1 Acknowledgments 3 Methods 3 Geologic setting 3 Regional geology 3 Local geology 3 Ore geology 4 Mineralogy 5 Primary ore 5 Supergene ore 5 Discussion and conclusions 7 Primary ore deposition 7. Supergene alteration 8 Implications 8 References 8 FIGURES 1. Map showing location of Apex Mine and generalized geology of surrounding region 2 2. Photograph showing main adit of Apex Mine and gently dipping beds of the Callville Limestone 3 3. Geologic map showing locations of Apex and Paymaster mines and Apex fault zone 4 4. Scanning electron photomicrograph showing plumbian jarosite crystals from the 1,601-m level, Apex Mine 6 TABLES 1. Chemical analyses of some representative ore samples from the Apex Mine 5 2. Chemical analyses of some nearly monomineralic samples from the Apex Mine 6 lll
Bifunctional MnOx electrocatalysts for zinc–air batteries in alkaline electrolytes (2021)

The growing need for rechargeable zinc–air batteries has led researchers to look for low-cost and robust catalytic candidates. Manganese oxides are promising for their low toxicity, natural abundance and low cost. In this review, we summarize the versatility of manganese oxides which is achievable by adjusting synthetic parameters. In addition, we highlight how manganese oxides impact zinc–air electrochemistry.
Screen Printable Boron Doping Paste and Its Process for n-Type PERT Solar Cells (2018)

We have developed new boron paste materials for the process of diffusing crystalline silicon solar cells. The boron paste promotes pattern-forming, long carrier lifetime, and allows good sheet resistance uniformity. The cell efficiency achieved when applying boron paste to an n-type PERT cell was practically excellent. A high efficiency was also obtained under a codiffusion process with POCl3 gas for a simplifying process. We reported on the diffusion characteristic and process details of the boron paste in this paper.
NEMO: movilidad de redes en IPv6 (2005)

en la actualidad, los usuarios solicitan el acceso a Internet en escenarios cada vez mas heterogeneos. Particularmente ha surgido como necesidad el poder acceder a Internet desde plataformas moviles como pueden ser trenes, autobuses, o aviones. En el seno del IETF (Internet Engineering Task Force) se ha formado el grupo de trabajo NEMO (NEtwork MObility Working Group) que tiene como objetivo el proponer mecanismos que permitan gestionar la movilidad de una red como un todo, permitiendo que vaya cambiando su punto de conexion a una infraestructura fija basada en IP (Internet Protocol), sin que con ello se interrumpan las comunicaciones ya establecidas. En este articulo se describe la solucion basica para el soporte de movilidad en redes IPv6 (Internet Protocol version 6) desarrollada por el grupo NEMO y se analizan sus limitaciones. Asimismo se presentan las diversas aportaciones a la problematica de movilidad de redes desarrolladas en el marco del proyecto europeo DAIDALOS (Designing Advanced network Interfaces for the Delivery and Administration of Location independent, Optimised personal Services).
Executive Summary: Diagnosis and Management of Prosthetic Joint Infection: Clinical Practice Guidelines by the Infectious Diseases Society of Americaa (2012)

These guidelines are intended for use by infectious disease specialists, orthopedists, and other healthcare professionals who care for patients with prosthetic joint infection (PJI). They include evidence-based and opinion-based recommendations for the diagnosis and management of patients with PJI treated with debridement and retention of the prosthesis, resection arthroplasty with or without subsequent staged reimplantation, 1-stage reimplantation, and amputation.
Cell-Active Small Molecule Inhibitors of the DNA-Damage Repair Enzyme Poly(ADP-ribose) Glycohydrolase (PARG): Discovery and Optimization of Orally Bioavailable Quinazolinedione Sulfonamides (2018)

DNA damage repair enzymes are promising targets in the development of new therapeutic agents for a wide range of cancers and potentially other diseases. The enzyme poly(ADP-ribose) glycohydrolase (PARG) plays a pivotal role in the regulation of DNA repair mechanisms; however, the lack of potent drug-like inhibitors for use in cellular and in vivo models has limited the investigation of its potential as a novel therapeutic target. Using the crystal structure of human PARG in complex with the weakly active and cytotoxic anthraquinone 8a, novel quinazolinedione sulfonamides PARG inhibitors have been identified by means of structure-based virtual screening and library design. 1-Oxetan-3-ylmethyl derivatives 33d and 35d were selected for preliminary investigations in vivo. X-ray crystal structures help rationalize the observed structure-activity relationships of these novel inhibitors.
Computational Studies of Catechol and Water Interactions with Titanium Oxide Nanoparticles (2003)

The interaction of catechol and water with titanium oxide nanoparticles was investigated using ab initio molecular orbital theory and density functional theory. Hydrogen-terminated TiO2 clusters were used to model the surface of anatase nanoparticles. The calculations indicate that catechol reacts with a TiO defect site on the surface to form a bidentate structure that is favored over dissociative or molecular adsorption on the (101) anatase surface. The dissociative adsorption of catechol at the defect site leads to a much larger red shift in the TiO2 excitation energy than molecular adsorption on the (101) anatase surface on the basis of ZINDO/S calculations. This is consistent with recent experimental results on small (<2 nm) titania nanoparticles. The calculations on water adsorption indicate that it can also add to the TiO double bond site. However, molecular adsorption of water on the (101) anatase surface is more favorable.
Cryptography with right-angled Artin groups (2016)

In this paper we propose right-angled Artin groups as a platform for secret sharing schemes based on the efficiency (linear time) of the word problem. Inspired by previous work of Grigoriev-Shpilrain in the context of graphs, we define two new problems: Subgroup Isomorphism Problem and Group Homomorphism Problem. Based on them, we also propose two new authentication schemes. For right-angled Artin groups, the Group Homomorphism and Graph Homomorphism problems are equivalent, and the later is known to be NP-complete. In the case of the Subgroup Isomorphism problem, we bring some results due to Bridson who shows there are right-angled Artin groups in which this problem is unsolvable.
Multiplicity of enzymatic functions in the CAZy AA3 family (2018)

The CAZy auxiliary activity family 3 (AA3) comprises enzymes from the glucose-methanol-choline (GMC) family of oxidoreductases, which assist the activity of other AA family enzymes via their reaction products or support the action of glycoside hydrolases in lignocellulose degradation. The AA3 family is further divided into four subfamilies, which include cellobiose dehydrogenase, glucose oxidoreductases, aryl-alcohol oxidase, alcohol (methanol) oxidase, and pyranose oxidoreductases. These different enzymes catalyze a wide variety of redox reactions with respect to substrates and co-substrates. The common feature of AA3 family members is the formation of key metabolites such as H<sub>2</sub>O<sub>2</sub> or hydroquinones, which are required by other AA enzymes. The multiplicity of enzymatic functions in the AA3 family is reflected by the multigenicity of AA3 genes in fungi, which also depends on their lifestyle. We provide an overview of the phylogenetic, molecular, and catalytic properties of AA3 enzymes and discuss their interactions with other carbohydrate-active enzymes.
A Novel Chemical Compound, NK026680, Targets Dendritic Cells to Prolong Recipient Survival After Rat Liver Grafting (2007)

These results demonstrate that NK026680 may have therapeutic potential for preventing allo-rejection in organ transplantation, acting at the step of immune response through inhibiting BMDC differentiation and maturation into potent antigen-presenting cells.
Anti-Apoptotic Bfl-1 Is the Major Effector in Activation-Induced Human Mast Cell Survival (2012)

Mast cells are best known for their role in allergic reactions, where aggregation of FcεRI leads to the release of mast cell mediators causing allergic symptoms. The activation also induces a survival program in the cells, i.e., activation-induced mast cell survival. The aim of the present study was to investigate how the activation-induced survival is mediated. Cord blood-derived mast cells and the mast cell line LAD-2 were activated through FcεRI crosslinking, with or without addition of chemicals that inhibit the activity or expression of selected Bcl-2 family members (ABT-737; roscovitine). Cell viability was assessed using staining and flow cytometry. The expression and function of Bcl-2 family members BFL-1 and MCL-1 were investigated using real-time quantitative PCR and siRNA treatment. The mast cell expression of Bfl-1 was investigated in skin biopsies. FcεRI crosslinking promotes activation-induced survival of human mast cells and this is associated with an upregulation of the anti-apoptotic Bcl-2 family member Bfl-1. ABT-737 alone or in combination with roscovitine decreases viability of human mast cells although activation-induced survival is sustained, indicating a minor role for Bcl-X(L), Bcl-2, Bcl-w and Mcl-1. Reducing BFL-1 but not MCL-1 levels by siRNA inhibited activation-induced mast cell survival. We also demonstrate that mast cell expression of Bfl-1 is elevated in birch-pollen-provocated skin and in lesions of atopic dermatitis and psoriasis patients. Taken together, our results highlight Bfl-1 as a major effector in activation-induced human mast cell survival.
Comparing American and Palestinian Perceptions of Charisma UsingAcoustic-Prosodic and Lexical Analysis: Presentation Powerpoint Poster (2007)

Charisma, the ability to lead by virtue of personality alone, is difﬁcult to deﬁne but relatively easy to identify. However, cultural factors clearly affect perceptions of charisma. In this paper we compare results from parallel perception studies investigating charismatic speech in Palestinian Arabic and American English. We examine acoustic/prosodic and lexical correlates of charisma ratings to determine how the two cultures differ with respect to their views of charismatic speech.
Design, Synthesis and Structure—Activity Relationships of a Series of 9‐Substituted Adenine Derivatives as Selective Phosphodiesterase Type‐4 Inhibitors. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Feasibility of Dual-Energy CT in the Arterial Phase: Imaging After Endovascular Aortic Repair (2010)

Virtual unenhanced and arterial phase images derived from dual-energy CT can replace true unenhanced and arterial phase single-energy CT images in follow-up after endovascular aneurysm repair (except immediately after the procedure), providing comparable diagnostic information with substantial dose savings.
Optically pumped 13  μm room-temperature InAs quantum-dot micro-disk lasers directly grown on (001) silicon (2016)

Direct integration of high-performance laser diodes on silicon will dramatically transform the world of photonics, expediting the progress toward low-cost and compact photonic integrated circuits (PICs) on the mainstream silicon platform. Here, we report, to the best of our knowledge, the first 1.3 μm room-temperature continuous-wave InAs quantum-dot micro-disk lasers epitaxially grown on industrial-compatible Si (001) substrates without offcut. The lasing threshold is as low as hundreds of microwatts, similar to the thresholds of identical lasers grown on a GaAs substrate. The heteroepitaxial structure employed here does not require the use of an absorptive germanium buffer and/or dislocation filter layers, both of which impede the efficient coupling of light from the laser active regions to silicon waveguides. This allows for full compatibility with the extensive silicon-on-insulator (SOI) technology. The large-area virtual GaAs (on Si) substrates can be directly adopted in various mature in-plane laser configurations, both optically and electrically. Thus, this demonstration represents a major advancement toward the commercial success of fully integrated silicon photonics.
Antibodies and antibody‐drug conjugates in the treatment of Hodgkin lymphoma (2014)

Abstract Hodgkin lymphoma ( HL ) is a B cell‐derived lymphoid malignancy most often affecting young adults. More than 80% of HL patients achieve long‐term remission after appropriate first‐line treatment consisting of multiagent chemotherapy and/or radiotherapy ( RT ). In addition, approximately 50% of patients with disease recurrence remain relapse‐free after salvage therapy with high‐dose chemotherapy followed by autologous stem cell transplantation ( ASCT ). However, patients with multiple relapses are mostly in a palliative situation, and novel drugs for this patient group are needed. Furthermore, novel less toxic but equally effective first‐line and second‐line approaches are required as therapy‐related late sequelae represent a relevant cause of morbidity and mortality in HL survivors. Several antibodies and antibody‐drug conjugates ( ADC ) targeting CD 30 and CD 20 have recently been evaluated in HL . Excellent response rates in heavily pretreated patients were observed with the ADC brentuximab vedotin directed against CD 30. Thus, ongoing trials investigate brentuximab vedotin in different additional indications. One example is the first‐line treatment of advanced HL where the drug is currently being evaluated in combination with variants of the first‐line protocols ABVD (adriamycin, bleomycin, vinblastine, dacarbazine) and escalated BEACOPP (bleomycin, etoposide, adriamycin, cyclophosphamide, vincristine, procarbazine, prednisone). Anti‐ CD 20 antibodies given either as single agent or in combination with conventional chemotherapy have also been investigated and still undergo investigation in prospective studies including HL patients. This article reviews the available data on treatment approaches including antibodies and ADC in HL patients.
Introduction to the Special Issue on Music Signal Processing (2011)

The 15 papers in this special issue are devoted to the merging field of music signal processing.
Influence of Sialoadenectomy on Capsaicin-Sensitive “Gastric Defense Mechanism” in Rats (1991)

Chemical ablation of sensory afferents produced by the treatment with the neurotoxin capsaicin worsened gastric ulcers induced by 50% ethanol in sham- and sialoadenectomized (SALX)-operated rats. Conversely, capsaicin worsened water immersion stress (WIS)-ulcers in SALX, but not those in sham-operated animals. The concomitant removal of two potent antisecretory factors, such as salivary gland containing epidermal growth factor and neuropeptides contained in the sensory afferents, is probably responsible for the enhanced vulnerability of the mucosa in WIS-ulcers.
Validation of optical properties quantification with a dual-step technique for biological tissue analysis (2018)

To approach wide-field optical properties quantification in real heterogeneous biological tissue, we developed a Dual-Step setup that couples a punctual diffuse reflectance spectroscopy (DRS) technique with multispectral imaging (MSI). The setup achieves wide-field optical properties assessment through an initial estimation of scattering with DRS, which is used to estimate absorption with MSI. The absolute quantification of optical properties is based on the ACA-Pro algorithm that has been adapted both for DRS and for MSI. This paper validates the Dual-Step system not only on homogeneous Intralipid phantoms but also on a heterogeneous gelatine phantom with different scattering and absorbing properties.
A Scalable Mobility-Centric Architecture for Named Data Networking (2014)

Information-centric networking (ICN) proposes to redesign the Internet by replacing its host centric design with an information centric one, by establishing communication at the naming level, with the receiver side acting as the driving force behind content delivery. Such design promises great advantages for the delivery of content to and from mobile hosts. This, however, is at the expense of increased networking overhead, specifically in the case of Named-data Networking (NDN) due to use of flooding for path recovery. In this paper, we propose a mobility centric solution to address the overhead and scalability problems in NDN by introducing a novel forwarding architecture that leverages decentralized server-assisted routing over flooding based strategies. We present an in-depth study of the proposed architecture and provide demonstrative results on its throughput and overhead performance at different levels of mobility proving its scalability and effectiveness, when compared to the current NDN based forwarding strategies.
MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape (2020)

Convergent evolution dictates that diverse groups of viruses will target both similar and distinct host pathways to manipulate the immune response and improve infection. In this study, we sought to leverage this uneven viral antagonism to identify critical host factors that govern disease outcome. Utilizing a systems-based approach, we examined differential regulation of IFN-γ–dependent genes following infection with robust respiratory viruses including influenza viruses [A/influenza/Vietnam/1203/2004 (H5N1-VN1203) and A/influenza/California/04/2009 (H1N1-CA04)] and coronaviruses [severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV)]. Categorizing by function, we observed down-regulation of gene expression associated with antigen presentation following both H5N1-VN1203 and MERS-CoV infection. Further examination revealed global down-regulation of antigen-presentation gene expression, which was confirmed by proteomics for both H5N1-VN1203 and MERS-CoV infection. Importantly, epigenetic analysis suggested that DNA methylation, rather than histone modification, plays a crucial role in MERS-CoV–mediated antagonism of antigen-presentation gene expression; in contrast, H5N1-VN1203 likely utilizes a combination of epigenetic mechanisms to target antigen presentation. Together, the results indicate a common mechanism utilized by H5N1-VN1203 and MERS-CoV to modulate antigen presentation and the host adaptive immune response.