gebhart/patrepeval huggingface dataset:
Retinoid X receptor beta polymorphisms do not explain functional differences in vitamins D and A response in Antineutrophil cytoplasmic antibody associated vasculitis patients (2009)

It has been suggested that the retinoid X receptor beta (RXRB) gene is a risk factor for Wegener's granulomatosis. We addressed if there is a functional difference in the response to retinoic acid (RA) and vitamin D in Antineutrophil cytoplasmic antibody (ANCA) associated systemic vasculitis (AASV) patients and if this was associated with RXRB genotypes. TNFalpha and IL-10 production were measured in whole blood assay from AASV patients (n = 51) and healthy controls (HC, n = 67). One micromolar of 1,25-(OH)(2) D3, 9-cis RA (9c-RA) or all-trans RA (ATRA) was added to the assay. Genotyping was performed for exons 7 and 2 of the RXRB gene and for a microsatellite in vicinity of the RXRB gene. Lipopolysaccharide (LPS) mediated TNFalpha production and IL-10 were significantly lower in patients. Addition of 1,25-(OH)(2) D3, ATRA or 9c-RA, blunted TNFalpha production, more pronounced in patients. Although all three compounds inhibited IL-10 production significantly in HC, only 1,25-(OH)(2) D3 was found to be effective in patients. Allele distribution of the RXRB microsatellite differed significantly between patients and HC. This was not found for the SNP in exons 2 and 7. Genotype of the latter correlated with the ability of 1,25-(OH)(2) D3 and ATRA to inhibit IL-10 production. We provide immunological evidence for a functional difference in vitamins D and A responsiveness in AASV patients. Since the inhibition of TNFalpha was more effective in patients, vitamin D supplementation might be an additional therapeutical approach.
Genetics of early-onset depression (2003)

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Reasons for revision following stand-alone anterior lumbar interbody fusion and lateral lumbar interbody fusion (2021)

There was a low reoperation rate after anterior or lateral lumbar interbody fusions without direct posterior decompression. The majority of same-level reoperations were due to a need for further decompression. Smaller preoperative canal diameters were associated with the need for revision decompression.
ChemInform Abstract: THE 5‐ALKOXYMETHYL‐, 5‐ALKYLTHIOMETHYL‐, AND 5‐DIALKYLAMINOMETHYLISOXAZOLES (1985)

Abstract Durch dipolare Cycloaddition von Propargylbromid (I) mit den z. Tl.
HIGH CURRENT PROPERTIES OF A MICROSPRING CONTACT FOR FLIP CHIP PACKAGING (2010)

The high current properties of a micro spring pressure contact are characterized. The spring has large compliance (>30 m) compared to other packaging technologies and fits in a 180 m pitch 2d array. At 250 mA and 65 C, daisy chains of 134 spring contacts in a silicon package show stable resistances and hotspot temperature rises of less than a degree. At 1 amp, failure near the spring tip or body is observed. Finite element modeling is performed to study the current distribution and provide failure mode insight. Simultaneous force and resistance measurements suggest there is no spring force softening. The results suggest a 10 mg (100 ) micro spring with large compliance can be reliable for high current applications.
Spin transport, magnetoresistance, and electrically detected magnetic resonance in amorphous hydrogenated silicon nitride (2016)

We report on a study of spin transport via electrically detected magnetic resonance (EDMR) and near-zero field magnetoresistance (MR) in silicon nitride films. Silicon nitrides have long been important materials in solid state electronics. Although electronic transport in these materials is not well understood, electron paramagnetic resonance studies have identified a single dominating paramagnetic defect and have also provided physical and chemical descriptions of the defects, called K centers. Our EDMR and MR measurements clearly link the near-zero field MR response to the K centers and also indicate that K center energy levels are approximately 3.1 eV above the a-SiN:H valence band edge. In addition, our results suggest an approach for the study of defect mediated spin-transport in inorganic amorphous insulators via variable electric field and variable frequency EDMR and MR which may be widely applicable.
Effect of carbazole–oxadiazole excited-state complexes on the efficiency of dye-doped light-emitting diodes (2002)

Interactions between hole-transporting carbazole groups and electron-transporting 1,3,4-oxadiazole groups were studied by photoluminescence and electroluminescence (EL) spectroscopy, in blends of poly(N-vinylcarbazole) with 2-tert-butylphenyl-5-biphenyl-1,3,4-oxadiazole (PVK:PBD) and in random copolymers with carbazole and oxadiazole groups attached as side chains. Different excited-state complexes form in the blends, which exhibit exciplexes, and in the copolymers, which manifest electroplexes, due to topological constraints on the position of carbazole and oxadiazole units in the polymer. Both types of complex red-shift the EL spectra of the matrices compared with pure PVK homopolymer, although the shift is significantly greater for the electroplex. The presence of these complexes has a profound effect on the external quantum efficiency of dye-doped organic light-emitting diodes employing the blends or copolymers as matrices, as it strongly affects the efficiency of Förster energy transfer from the matrix to the dye. Single-layer devices doped with either coumarin 47 (C47), coumarin 6 (C6), or nile red (NR) were compared. Among the three dye-doped PVK:PBD devices, C6 doping yields the highest efficiency, while NR doping produced the most efficient copolymer devices, consistent with the degree of overlap between the EL spectrum of the matrix material and the absorption spectrum of the dye.
Characterization of insulin-stimulated seryl/threonyl protein kinases in rat skeletal muscle (1993)

Post-insulin receptor signal transduction is mediated by a cascade of seryl/threonyl protein kinases which includes a family of mitogen-activated protein (MAP) kinases, ribosomal protein S6 kinases, and casein kinase-2. Previous studies have characterized these kinases primarily in cultured or isolated cells. We have demonstrated that intravenous injection of insulin into fasted rats significantly stimulated the activities of MAP kinases and S6 kinases in skeletal muscle, independently of the blood glucose levels in these animals. Anion exchange chromatography on Mono Q afforded the resolution of at least five peaks of insulin-stimulated myelin basic protein kinase activity. By immunological criteria, these myelin basic protein kinases included the p42mapk and p44erk1 as well as other potentially novel 44-kDa MAP kinases. Insulin-activated ribosomal S6 kinases were resolved into two major peaks by Mono Q chromatography, the latter of which contained a 100-kDa isoform of p90rsk as revealed by immunoblotting with an anti-rsk-peptide antibody. A 32-kDa S6 kinase in the earlier peak may represent a novel protein kinase in this tissue. Skeletal muscle casein kinase-2 was not significantly stimulated following insulin injection into rats under our experimental conditions. These results indicate that the intact rat can serve as a useful model system to investigate the mechanisms of insulin signal transduction.
The Nature of Ligand Efficiency (2018)

Ligand efficiency is a widely used design parameter in drug discovery. It is calculated by scaling affinity by molecular size and has a nontrivial dependency on the concentration unit used to express affinity that stems from the inability of the logarithm function to take dimensioned arguments. Consequently, perception of efficiency varies with the choice of concentration unit and it is argued that the ligand efficiency metric is not physically meaningful nor should it be considered to be a metric. The dependence of ligand efficiency on the concentration unit can be eliminated by defining efficiency in terms of sensitivity of affinity to molecular size and this is illustrated with reference to fragment-to-lead optimizations. An alternative to ligand efficiency for normalization of affinity with respect to molecular size is presented. Group efficiency and fit quality are also examined in detail from a physicochemical perspective. The importance of examining relationships between affinity and molecular size directly is stressed throughout this study.
Development of high-Q embedded passive library for RF-SOP module applications (2005)

Scalable broadband modeling techniques have been developed for the high-Q passive components buried into the organic laminate package substrate. Based on modified-T equivalent circuits, the developed models can achieve an effective bandwidth several times larger than the conventional PI models. For scalability, the fundamental reactive elements in a modified-T model can be converted directly from those in an existing scalable PI model. Curve-fitting techniques are particularly applied for the peak Q factors and the resonant frequencies that can be further converted into the resistive elements and the higher-order reactive elements, respectively, to form a complete modified-T model. In this paper, the proposed scalable modeling techniques have accomplished the automatic generation of broadband lumped models for designing the embedded passives in a 4-layer BT (Bismaleimide Triazine) laminate, one of today's most popular package substrate, quite successfully.
Proof of principle: An HIV p24 microsphere immunoassay with potential application to HIV clinical diagnosis (2008)

The measurement of CD4 counts and viral loads on a single instrument such as an affordable flow cytometer could considerably reduce the cost related to the follow-up of antiretroviral therapy in resource-poor settings. The aim of this study was to assess whether the HIV-1 p24 antigen could be measured using a microsphere-based flow cytometric (FC) assay and the experimental conditions necessary for processing plasma samples. A commercial anti-p24 antibody pair from Biomaric was used to develop a p24 microsphere immunoassay (MIA) using HIV culture supernatant as the source of antigen. The ultrasensitive Perkin Elmer enzyme immunoassay (EIA) served as a reference assay. Quantification of HIV p24 using the heat-mediated immune complex disruption format described for plasma samples was feasible using the Biomaric MIA and applicable to a broad range of HIV-1 Group M subtypes. The inclusion of a tyramide amplification step was successful and increased the fluorescence signal up to 3 logs as compared with the MIA without amplification. The analytical sensitivity of this ultrasensitive Biomaric assay reached 1 pg/mL, whereas the ultrasensitive Perkin Elmer EIA was sensitive to less than 0.17 pg/mL. Our data indicate, for the first time, that the principle of p24 detection using the heat-denatured ultrasensitive format can be applied to FC.
Structure of human ADAM-8 catalytic domain complexed with batimastat (2012)

The role of ADAM-8 in cancer and inflammatory diseases such as allergy, arthritis and asthma makes it an attractive target for drug development. Therefore, the catalytic domain of human ADAM-8 was expressed, purified and crystallized in complex with a hydroxamic acid inhibitor, batimastat. The crystal structure of the enzyme-inhibitor complex was refined to 2.1 Å resolution. ADAM-8 has an overall fold similar to those of other ADAM members, including a central five-stranded β-sheet and a catalytic Zn(2+) ion. However, unique differences within the S1' binding loop of ADAM-8 are observed which might be exploited to confer specificity and selectivity to ADAM-8 competitive inhibitors for the treatment of diseases involving this enzyme.
High Performance Liquid Chromatography/Electrochemistry/High Resolution Electrospray Ionization‐Mass Spectrometry (HPLC/EC/HR ESI‐MS) Characterization of Selected Cytokinins Oxidation Products (2015)

Abstract Electrochemistry combined with mass spectrometry represents an emerging analytical technique used to study the oxidation pathway of various drugs and in vivo occurring compounds, continuously showing a capability to generate many known metabolites or new oxidation products. An on‐line HPLC/EC/HR ESI‐MS method had been used to investigate the oxidation of selected cytokinin compounds. This setup allowed rapid identification and general structure elucidation of the obtained products. An electrochemical oxidation of isopentenyladenine resulted in five products, including hydroxylated and dehydrogenated products, which correlates very well with its in vivo metabolism. Electrochemical conversion of trans‐ zeatin revealed six products, with two dehydrogenation products corresponding to its in vivo occurring metabolites. cis‐ Zeatin oxidation in the electrochemical cell gave rise to eight products, resembling similarity to trans ‐zeatin oxidation. All three compounds underwent a complete turnover mainly through two oxidation reactions occurring in the electrochemical celldehydrogenation and a less typical aliphatic hydroxylation. The resulting products are in correlation with their known in vivo metabolism.
The utilization of time-resolved dielectric loss to probe the role of the surface in heterogeneous photochemistry (1986)

The measurement of time-resolved (or transient) dielectric loss in semiconductors using an e.p.r. spectrometer interfaced to a flash-photolysis system is discussed. In particular, it is demonstrated that aqueous dispersions of pigments can readily be studied using this technique. In this way, the system can be monitored in the presence of donors and acceptors where dynamic interfacial redox reactions are occurring. A flow system was utilized to avoid setting problems as well as providing the potential for the acquisition of first-flash kinetic data. Finally, surface modified pigments are contrasted to their corresponding starting materials.
DASON: Dependability Assessment Framework for Imperfect Distributed SDN Implementations (2020)

In Software Defined Networking (SDN), network programmability is enabled through a logically centralized control plane. Production networks deploy multiple controllers for scalability and reliability reasons, which in turn rely on distributed consensus protocols to operate in a logically centralized manner. However, bugs in distributed control plane can have disastrous effects on the data plane, e.g., losing traffic by installing paths containing blackholes. In this paper we study the prevalence of issues in state-of-the-art distributed frameworks in SDN, by analyzing 500+ issues reported in two of the largest open source SDN controller platforms: Open Network Operating System (ONOS) and OpenDaylight (ODL), during the period between 2014-2019. We identify system vulnerabilities, localize dependability bottlenecks, and provide stochastic models for a holistic assessment of system dependability.
A Framework for Detecting Selfish Misbehavior in Wireless Mesh Community Networks (2009)

Wireless Mesh Networks (WMNs) have recently emerged as a flexible and low-cost extension of wired infrastructure networks. They consist of mesh routers and clients, where mesh routers are almost static and form the backbone of the WMN. The complete absence of an infrastructure and the flexibility provided by the wireless mesh technology has fostered the development of new network paradigms like Wireless Mesh Community Networks. Such networks are usually composed of heterogeneous mesh routers managed by different users (a subset of participants to the community), that collaborate to extend the network coverage. However, in such environment some participants can exhibit selfish behaviors, by dropping selectively the packets sent by other mesh routers, in order to prioritize their own traffic and increase their network utilization. In this paper we propose a complete scheme to detect selfish behavior of the mesh routers that participate to the community network. Each node evaluates the trustworthiness of the other mesh routers by combining the direct observations on the relaying behavior of neighbor nodes with the trust information provided by other mesh routers. The proposed scheme has been integrated in the AODV routing protocol, and tested in several network scenarios. The numerical results show that our scheme provides a high detection accuracy, even when a high percentage of network nodes provide false trust values (bad-mouthing attack).
Concussion in Professional Football: Epidemiological Features of Game Injuries and Review of the Literature—Part 3 (2004)

The professional football players most vulnerable to concussions are quarterbacks, wide receivers, and defensive secondaries. Concussions involved 2.74 symptoms/injury, and players were generally removed from the game. More than one-half of the players returned to play within 1 day, and symptoms resolved in a short time in the vast majority of cases.
Abstract LB-389: Antitumor activity of HM781–36B, a highly effective pan-HER inhibitor in erlotinib-resistant NSCLC and other EGFR-dependent cancer models (2011)

Abstract The epidermal growth factor receptor (EGFR) family of receptor tyrosine kinases has been implicated in a variety of cancers. In particular, activating mutations such as the L858R point mutation in exon 21 and the small in-frame deletions in exon 19 of the EGFR tyrosine kinase domain are correlated with sensitivity to EGFR tyrosine kinase inhibitors in non-small cell lung cancer (NSCLC) patients. But clinical treatment is limited by the development of drug resistance resulting mainly from an acquired mutation (T790M). In this study, we evaluated the therapeutic potential of a novel, irreversible pan-HER inhibitor, HM781–36B. We demonstrated that HM781–36B is a potent EGFR inhibitor including the EGFR-acquired resistance mutation (IC50 4.2 nM in EGFR T790M and IC50 2.2 nM in EGFR L858R/T790M), as well as EGFR, HER-2 and HER-4 (IC50 3.2 nM, 5.3 nM and 23.5 nM, respectively), compared to other EGFR tyrosine kinases inhibitors (erlotinib, lapatinib and BIBW-2992), with kinase selectivity confirmed by 77 kinases panel assay except for Blk, Bmx and Btk. Strong growth inhibitory activity by the treatment of HM781–36B was confirmed with the range of IC50 0.6–6nM in NSCLC (HCC827, H358, H1975, Calu-3, and H1781), breast cancer (SK-Br3, BT474, MDA-175, and MDA-453), and gastric cancer (N87 and SNU-216) cell lines. HM781–36B showed 400–4,000 fold low growth inhibitory effect against normal cell lines (Hs-27 and Balb/c 3T3) relative to cancer cell lines. HM781–36B treatment results in the inhibition of EGFR phosphorylation and the subsequent deactivation of downstream signaling proteins in EGFR DelE746_A750-harboring erlotinib-sensitive HCC827 and EGFR L858R/T790M-harboring erlotinib-resistant NCI-H1975 NSCLC cells. HM781–36B interacts directly with its target enzyme (EGFR WT, EGFR T790M, HER-2), which was confirmed through prolongation study of phosphorylation inhibitory effect in A431 and SK-Br3 cells and direct fluorescence-based SDS-PAGE analysis by the incubation of Cy3-labeled HM781–36B probe. This irreversible occupation at the kinase domain leads to excellent in vivo efficacy of HM781–36B (1mg/kg – 5mg/kg) toward various xenograft models with EGFR-dependent cancers cells, including erlotinib-sensitive HCC827 NSCLC cells, erlotinib-resistant H1975 NSCLC cells, HER-2 overexpressing Calu-3 NSCLC cells, N87 gastric cancer cells, and SK-Ov3 ovarian cancer cells, and EGFR-overexpressing A431 epidermoid carcinoma cancer cells. On the basis of these preclinical results, HM781–36B was selected as a candidate for clinical development and a phase I study of HM781–36B is currently undergoing in South Korea. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-389. doi:10.1158/1538-7445.AM2011-LB-389
Comparative analysis of innate immune responses following infection of newborn calves with bovine rotavirus and bovine coronavirus (2007)

Bovine rotavirus (BRV) and bovine coronavirus (BCV) are important causes of diarrhoea and death in newborn calves. Although these viruses belong to distinct viral classes, they both infect intestinal epithelial cells and induce similar clinical symptoms. Rotavirus usually causes an acute infection, but coronavirus infection can persist and reoccur in adults. Differences in viral structure and clinical outcome prompted us to postulate that innate mucosal immune responses would be markedly different following rotavirus and coronavirus infections. To address this hypothesis, gene expression following BRV and BCV infection was analysed in surgically prepared intestinal loops from 1-day-old colostrum-deprived calves. Gene expression was profiled at 18 h post-infection using bovine cDNA microarrays; the majority of differentially expressed significant genes were associated with the cell cycle and innate immune responses. A select group of these genes was validated by quantitative real-time PCR (qRT-PCR). The expression of genes associated with interferons (IFNs), cytokines and Toll-like receptors, which were not present on the microarray, was analysed further by qRT-PCR. Strong activation of TLR3, IL-6 and p65 was observed in BRV-infected host tissues, but not in tissues infected with BCV. Both viruses also downregulated IFN- and pro-inflammatory cytokine-associated pathways. In vitro studies confirmed that IFN inhibited viral replication. All of these results together suggested either that very early events of host responses at 18 h post-infection were being observed, or that both viruses have unique effective strategies to evade host immune responses.
Signal Processing for Advanced Materials [From the Guest Editors] (2021)

The development of new materials has been a hallmark of technological advancement since at least the Bronze Age, when copper and tin were alloyed to create tools that had properties favorable to those made from stone. For thousands of years, until the development of microscope imaging, new materials continued to be developed “blindly,” without any understanding of the effects of the structure at the micro- or nanoscale on the observable properties of a material. With the advent of sensing modalities, such as electron microscopy and X-ray tomography, huge amounts of microstructural data of many different classes of materials have become available.
Atomically resolved electronic properties in single layer graphene on α-Al2O3 (0001) by chemical vapor deposition (2022)

Metal-free chemical vapor deposition (CVD) of single-layer graphene (SLG) on c-plane sapphire has recently been demonstrated for wafer diameters of up to 300 mm, and the high quality of the SLG layers is generally characterized by integral methods. By applying a comprehensive analysis approach, distinct interactions at the graphene-sapphire interface and local variations caused by the substrate topography are revealed. Regions near the sapphire step edges show tiny wrinkles with a height of about 0.2 nm, framed by delaminated graphene as identified by the typical Dirac cone of free graphene. In contrast, adsorption of CVD SLG on the hydroxyl-terminated α-Al<sub>2</sub>O<sub>3</sub> (0001) terraces results in a superstructure with a periodicity of (2.66 ± 0.03) nm. Weak hydrogen bonds formed between the hydroxylated sapphire surface and the π-electron system of SLG result in a clean interface. The charge injection induces a band gap in the adsorbed graphene layer of about (73 ± 3) meV at the Dirac point. The good agreement with the predictions of a theoretical analysis underlines the potential of this hybrid system for emerging electronic applications.