gebhart/patrepeval huggingface dataset:
Racial/Ethnic Differences in the Role of Childhood Adversities for Mental Disorders Among a Nationally Representative Sample of Adolescents (2016)

Although causal interpretation relies on assumptions, growing work on this topic suggests childhood adversities play an important role in mental disorder development in adolescents.
Reversible Light Switch for Macrocycle Mobility in a DNA Rotaxane (2012)

A recent trend in DNA nanotechnology consists of the assembly of architectures with dynamic properties that can be regulated by employing external stimuli. Reversible processes are important for implementing molecular motion into DNA architectures as they allow for the regeneration of the original state. Here we describe two different approaches for the reversible switching of a double-stranded DNA rotaxane architecture from a stationary pseudorotaxane mode into a state with movable components. Both states only marginally differ in their respective topologies but their mechanical properties are fundamentally different. In the two approaches, the switching operation is based on strand-displacement reactions. One of them employs toehold-extended oligodeoxynucleotides whereas in the other one the switching is achieved by light-irradiation. In both cases, multiple back and forth switching between the stationary and the mobile states was achieved in nearly quantitative fashion. The ability to reversibly operate mechanical motion in an interlocked DNA nanostructure opens exciting new avenues in DNA nanotechnology.
Editorial: The Role of HMGB1 in Immunity (2020)

EDITORIAL article Front. Immunol., 09 September 2020Sec. Inflammation Volume 11 - 2020 | https://doi.org/10.3389/fimmu.2020.594253
Role of the Electrode Material on the RESET Limitation in Oxide ReRAM Devices (2017)

Abstract Metal‐oxide‐based bipolar resistive switching (BRS) redox‐based resistive switching memory (ReRAM) shows many outstanding properties making it of interest as an emerging nonvolatile memory. However, it often suffers from a low R OFF / R ON ratio, while a large ratio is desired to compensate for read margin loss due to the intrinsic variability of the ReRAM cells. Understanding of the physical processes responsible for limitations of the R OFF and R ON in ReRAM cells is therefore of high importance. In this paper a study on the RESET process in BRS Ta 2 O 5 ‐based ReRAM cells is presented. The R OFF is found to be limited by a secondary volatile resistive switching mode that shows an opposite polarity compared to the main BRS mode. Based on results of switching kinetics measurements a physical model is proposed. It involves an oxygen exchange reaction at the metal‐oxide/active electrode interface combined with a drift‐diffusion induced migration of the resulting oxygen vacancy defects within the metal‐oxide. Incorporation of a thin oxygen‐blocking layer at the active interface allows for a suppression of the secondary switching mechanism. The improved RESET characteristic results in a strongly increased maximum R OFF . These results provide new insights into the role of the electrode material on the RESET process in BRS ReRAM cells.
Impact of Xpert MTB/RIF Testing on Tuberculosis Management and Outcomes in Hospitalized Patients in Uganda (2012)

Xpert MTB/RIF facilitated more accurate and earlier TB diagnosis, leading to a higher proportion of TB suspects with a confirmed TB diagnosis prior to hospital discharge in a high HIV/low MDR TB prevalence setting. However, our study did not detect a decrease in two-month mortality following implementation of Xpert MTB/RIF possibly because of insufficient powering, differences in empiric TB treatment rates, and disease severity between study phases.
Binding of Methyltrienolone to Various Androgen-Dependent and Androgen-Responsive Tissues in Four Animal Species (1976)

Comparative sucrose gradient studies of the in vitro binding of dihydrotestosterone (DHT) and of a synthetic androgen, methyltrienolone (R 1881), have been done with the cytosols of various tissues of the rat, mouse, cock and man. With rat prostate cytosol, the amount of R 1881 and DHT binding in the 8-9S region of the gradient was found to be comparable. Specific 8-9S peaks of R 1881 were also found in rat levator ani/bulbocavernosus and skeletal muscles and in the mouse kidney. Only 4-5S peaks could be demonstrated in the cock's comb while DHT under the same conditions showed both 8-9S and 4-5S binding. Binding of R 1881 to the cytosol of the hyperplastic prostate was polydispersed, and showed evidence of the presence of aggregates. Evidence was also found that R 1881 could bind to the progesterone receptor in rat uterus. Our study supports the theory that in a given species the androgen receptors are similar if not identical in all the tissues. The synthetic androgen R 1881 appears to be a useful tool for androgen receptor studies in various animal species provided that the tissue under study contains no progesterone receptor.
Adenoviral-encoded GMCSF-CAIX antigen fusion gene transfer into human peripheral blood monocyte-derived dendritic cells to induce antigen-specific cellular immune responses: preclinical studies (2008)

2871 Metastatic renal cell carcinoma (mRCC) is resistant to conventional modes of therapy. Carbonic anhydrase IX (CAIX), a cell surface tumor-associated antigen, is expressed by most clear cell renal cell carcinomas (RCC) and has implications in RCC diagnosis, prognosis, and response to immunotherapy, and represents a novel approach to tumor-specific targeted therapy. Adenoviral-mediated, tumor-associated antigen transfer is a promising strategy to manipulate the immunostimulatory properties of DCs to create tumor vaccines.  In the present study, we constructed a recombinant adenovirus encoding GMCSF-CAIX fusion gene (Ad-GMCAIX) using the AdEasy system. Human immature dendritic cells (DCs) were generated from CD14+ monocycles derived from peripheral blood mononuclear cells (PBMC) of healthy donors. DCs were infected with Ad-GMCAIX to raise specific CTLs responses from autologous peripheral blood lymphocytes. The expression level of CAIX in the DCs was confirmed by RT-PCR, flow cytometric assay and western blot analysis. Lymphocytes from the same donors were repeatedly stimulated by genetically modified DCs to generate CAIX-specific cytotoxic T lymphocytes (CTLs). ELISA was used to measure the secretion of IFN-gamma in the supernatants containing effectors cells stimulated with modified DCs. The ability of CTLs to lyse target cells expressing CAIX was performed in vitro by quantitative measurements of release of lactate dehydrogenase (LDH). Our results demonstrated that DCs were efficiently transduced with Ad-GMCAIX and the expression of CAIX was significantly increased. The Ad-GMCAIX significantly increased the number of mature DCs via up-regulation of CD83, CD86 and HLA-DR as compared to unstimulated DCs. Ad-GMCAIX transduced DCs were able to induce CAIX -specific CTLs against RCC cancer cells expressing CAIX in vitro. Moreover, the DCs modified by Ad-GMCAIX produced higher levels of interferon gamma when compared with unstitumated DCs.  Our results suggest that Ad-GMCAIX critically alters DC immune function and leads to the generation of CAIX specific CTLs, critical to the development of CAIX-based immunotherapy strategies. This finding demonstrates the exciting potential of CAIX to serve as an effective treatment modality for advanced RCC patients. These studies form the foundation for a planned clinical trial using dendritic cells pulsed with GMCAIX in patients with advanced kidney cancer.
Cryogenic performance of ultrathin oxide MOS capacitors within situdoped p poly-Si1 xGexand poly-Si gate materials (2002)

A low-temperature electrical characterization of ultrathin oxide MOS capacitors with p+ poly-Si1−xGex and poly-Si gate is performed. The investigated structures are suitable for future nano-scaled high speed MOSFETs. The aim of this study is to compare the low-temperature performance of poly-Si1−xGex and poly-Si gate MOS structures in the nanoscale channel length regime. Apart from the significant change in the flat band voltage, the result shows that all the poly-Si and poly-Si1−xGex gated MOS structures exhibit two centres of polarity change (zero-temperature coefficients) in capacitance. The second polarity change leads to an exclusive phenomenon in these structures. The low-temperature capacitance is found to be less than high-temperature capacitance at strong accumulation and this is in contrast to what has been observed so far in metal-gated capacitors. It is also observed that the temperature dependence of the tunnelling current is only on the oxide thickness and not on the gate material used.
ChemInform Abstract: Enzymatic Preparation of Homochiral 2‐Isobutyl Succinic Acid Derivatives. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Enzyme relaxation in the reaction catalyzed by triosephosphate isomerase: detection and kinetic characterization of two unliganded forms of the enzyme (1987)

Triosephosphate isomerase has been shown to exist in two unliganded forms, one of which binds and isomerizes (R)-glyceraldehyde 3-phosphate and the other of which binds and isomerizes dihydroxyacetone 3-phosphate. The tracer perturbation method of Britton demonstrates the kinetic significance of the interconversion of these two enzyme forms at high substrate concentrations and yields a rate constant of about 10(6) s-1 for the interconversion. Although the molecular nature of the two forms of unliganded enzyme is not defined by these experiments, a shuffling of protons among active site residues, or a protein conformational change, or both, may be involved. This study, coupled with the known rate constants for the substrate-handling steps of triosephosphate isomerase catalysis, completes the kinetic characterization of the catalytic cycle for this enzyme.
Non‐Hodgkin lymphoma after treatment for classical Hodgkin lymphoma: a report from the German Hodgkin Study Group (2021)

Data on non-Hodgkin lymphoma (NHL) after classical Hodgkin lymphoma (cHL) are scarce. We therefore performed a retrospective analysis comprising 11·841 cHL patients who had first-line treatment within the randomized German Hodgkin Study Group (GHSG) HD7-HD15 studies. After a median follow-up of 106 months, 175 patients (1·5%) had developed NHL. The median time to NHL was 44 months, the median age at NHL diagnosis was 54 years. The five-year event-free survival and overall survival estimates from the diagnosis of NHL were 36·9% and 44·2%, respectively. Thus, NHL after cHL is a rare event primarily affecting older individuals and often resulting in the patient´s death.
High-resolution matrix-assisted laser desorption/ionization mass spectrometry of biomolecules in an quadrupole ion trap (1993)

Mass resolution as high as 1 part in 12,000 is reported that has been obtained using a novel method for trapping MALDI ions by controlled gating of the trapping RF field. The method has been implemented on a Finnigan ITD modified for MALDI experiments inside an ion trap with axial introduction of the sample probe.
Dynamic Response of Mycobacterium vanbaalenii PYR-1 to BP Deepwater Horizon Crude Oil (2015)

We investigated the response of the hydrocarbon-degrading Mycobacterium vanbaalenii PYR-1 to crude oil from the BP Deepwater Horizon (DWH) spill, using substrate depletion, genomic, and proteome analyses. M. vanbaalenii PYR-1 cultures were incubated with BP DWH crude oil, and proteomes and degradation of alkanes and polycyclic aromatic hydrocarbons (PAHs) were analyzed at four time points over 30 days. Gas chromatography-mass spectrometry (GC-MS) analysis showed a chain length-dependent pattern of alkane degradation, with C12 and C13 being degraded at the highest rate, although alkanes up to C28 were degraded. Whereas phenanthrene and pyrene were completely degraded, a significantly smaller amount of fluoranthene was degraded. Proteome analysis identified 3,948 proteins, with 876 and 1,859 proteins up- and downregulated, respectively. We observed dynamic changes in protein expression during BP crude oil incubation, including transcriptional factors and transporters potentially involved in adaptation to crude oil. The proteome also provided a molecular basis for the metabolism of the aliphatic and aromatic hydrocarbon components in the BP DWH crude oil, which included upregulation of AlkB alkane hydroxylase and an expression pattern of PAH-metabolizing enzymes different from those in previous proteome expression studies of strain PYR-1 incubated with pure or mixed PAHs, particularly the ring-hydroxylating oxygenase (RHO) responsible for the initial oxidation of aromatic hydrocarbons. Based on these results, a comprehensive cellular response of M. vanbaalenii PYR-1 to BP crude oil was proposed. This study increases our fundamental understanding of the impact of crude oil on the cellular response of bacteria and provides data needed for development of practical bioremediation applications.
The Synthesis of Chiral Myo-Inositol Trisphosphate Analogues (1996)

Abstract d- And l-Ins(1,4,6)P3 and d-Ins(1,4,6)PS3 were synthesised and evaluated for their ability to mobilise Ca2+.
ReviewArticle Role of Peroxisome Proliferator-Activated Receptor Gamma and Its Ligands in the Treatment of Hematological Malignancies (2008)

ligands is crucial for the development of new therapeutic approaches for hematological malignancies.Copyright © 2008 Tatiana M. Garcia-Bates et al. This is an open access article distributed under the Creative CommonsAttribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work isproperly cited.
What do people ask their social networks, and why? (2010)

People often turn to their friends, families, and colleagues when they have questions. The recent, rapid rise of online social networking tools has made doing this on a large scale easy and efficient. In this paper we explore the phenomenon of using social network status messages to ask questions. We conducted a survey of 624 people, asking them to share the questions they have asked and answered of their online social networks. We present detailed data on the frequency of this type of question asking, the types of questions asked, and respondents' motivations for asking their social networks rather than using more traditional search tools like Web search engines. We report on the perceived speed and quality of the answers received, as well as what motivates people to respond to questions seen in their friends' status messages. We then discuss the implications of our findings for the design of next-generation search tools.
ChemInform Abstract: Rational Design, Synthesis, and Biological Evaluation of Rigid Pyrrolidone Analogues as Potential Inhibitors of Prostate Cancer Cell Growth. (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.
Current status of the SR stepper development (1997)

We describe some results of exposure experiments using the present prototype SR stepper which Canon has developed and also describe the novel technology development which is necessary to establish the next generation SR stepper for volume production. In the evaluation of the prototype machine, alignment performance, stage accuracy, and printing performance were examined, and we found the SR lithography can be applied to manufacturing devices beyond 0.15 micrometer level. In the technology development for the production machine, we have examined methods related to masks; they are reduction of thermal expansion, suppression out-of-plane displacement of mask membrane, and magnification correction. As a result of the examinations, we have a good perspective in development of a high-throughput SR stepper which is suitable for the production beyond 1 G-bit DRAM.
A Recursive Least-Squares Algorithm for the Identification of Trilinear Forms (2020)

High-dimensional system identification problems can be efficiently addressed based on tensor decompositions and modelling. In this paper, we design a recursive least-squares (RLS) algorithm tailored for the identification of trilinear forms, namely RLS-TF. In our framework, the trilinear form is related to the decomposition of a third-order tensor (of rank one). The proposed RLS-TF algorithm acts on the individual components of the global impulse response, thus being efficient in terms of both performance and complexity. Simulation results indicate that the proposed solution outperforms the conventional RLS algorithm (which handles only the global impulse response), but also the previously developed trilinear counterparts based on the least-mean- squares algorithm.
Abstract 4952: A novel smoothened antagonist, TAK-441, delays castration-resistant progression in prostate cancer by disrupting paracrine hedgehog signaling. (2013)

Abstract Hedgehog (Hh) signaling is a highly conserved inter- and intracellular communication mechanism that governs organogenesis and is dysregulated in cancers of numerous tissues, including prostate. Up-regulated expression of the Hh ligands, Sonic (Shh) and Desert (Dhh), has been reported in androgen-deprived and castration-resistant prostate cancer (CRPC). In a cohort of therapy naive, short- and long-term neoadjuvant hormone therapy-treated (NHT), and CRPC specimens, we observed elevated Dhh expression predominantly in long-term NHT specimens and elevated Shh expression predominantly in CRPC specimens. Together with previously demonstrated reciprocal signaling between Shh-producing prostate cancer (PCa) cells and urogenital mesenchymal fibroblasts, these results suggest that castration-induced Hh expression promotes CRPC progression through reciprocal paracrine signaling within the tumor microenvironment. We tested whether the orally available Smoothened (Smo) antagonist, TAK-441, could impair castration-resistant progression of LNCaP PCa xenografts by disrupting paracrine Hh signaling. While TAK-441 or cyclopamine did not affect androgen withdrawal-induced Shh up-regulation or viability of LNCaP cells, castration-resistant progression of LNCaP xenografts was significantly delayed in animals treated with TAK-441. In TAK-441-treated xenografts, expression of murine orthologues of the Hh-activated genes, Gli1, Gli2, and Ptch1, was substantially suppressed, while expression of the corresponding human orthologues was unaffected. Since androgen-deprived LNCaP cells up-regulate Shh expression, but are not sensitive to Smo antagonists, these studies indicate that TAK-441 leads to delayed castration-resistant progression of LNCaP xenografts by disrupting paracrine Hh signaling with the tumor stroma. Thus, paracrine Hh signaling may offer unique opportunities for prognostic biomarker development, drug targeting and therapeutic response monitoring of PCa progression. Citation Format: Mazyar Ghaffari, Naokazu Ibuki, Irene Iu, Mitali Pandey, Ladan Fazli, Masahide Kashiwagi, Hideaki Tojo, Osamu Nakanishi, Martin E. Gleave, Michael E. Cox. A novel smoothened antagonist, TAK-441, delays castration-resistant progression in prostate cancer by disrupting paracrine hedgehog signaling. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4952. doi:10.1158/1538-7445.AM2013-4952
Effect of Na on Cu(In,Ga)Se<inf>2</inf> in-plane conductance and Seebeck coefficient (2014)

Despite numerous studies, there is still no definitive explanation on how Na improves Cu(In,Ga)Se <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> (CIGS) device efficiency. This paper investigates how the electrical transport properties of CIGS films are affected by the amount of Na at grain boundaries. The controlled removal of Na from CIGS grain boundaries is achieved by rinsing in a water bath at 70°C. Periodically during the rinse, the in-plane conductance and the Seebeck coefficient are measured, and both are found to decrease as Na is removed by the bath. Assuming carrier mobility remains unaffected, a simultaneous decrease in conductivity and Seebeck effect can only be caused by an increase in compensating donor-like defects.
Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein–Protein Interface (2011)

Protein-protein interfaces are considered difficult targets for small-molecule protein-protein interaction modulators (PPIMs ). Here, we present for the first time a computational strategy that simultaneously considers aspects of energetics and plasticity in the context of PPIM binding to a protein interface. The strategy aims at identifying the determinants of small-molecule binding, hot spots, and transient pockets, in a protein-protein interface in order to make use of this knowledge for predicting binding modes of and ranking PPIMs with respect to their affinity. When applied to interleukin-2 (IL-2), the computationally inexpensive constrained geometric simulation method FRODA outperforms molecular dynamics simulations in sampling hydrophobic transient pockets. We introduce the PPIAnalyzer approach for identifying transient pockets on the basis of geometrical criteria only. A sequence of docking to identified transient pockets, starting structure selection based on hot spot information, RMSD clustering and intermolecular docking energies, and MM-PBSA calculations allows one to enrich IL-2 PPIMs from a set of decoys and to discriminate between subgroups of IL-2 PPIMs with low and high affinity. Our strategy will be applicable in a prospective manner where nothing else than a protein-protein complex structure is known; hence, it can well be the first step in a structure-based endeavor to identify PPIMs.
The Endothelial Protein C Receptor Supports Tissue Factor Ternary Coagulation Initiation Complex Signaling through Protease-activated Receptors (2010)

Protease-activated receptor (PAR) signaling is closely linked to the cellular activation of the pro- and anticoagulant pathways. The endothelial protein C receptor (EPCR) is crucial for signaling by activated protein C through PAR1, but EPCR may have additional roles by interacting with the 4-carboxyglutamic acid domains of procoagulant coagulation factors VII (FVII) and X (FX). Here we show that soluble EPCR regulates the interaction of FX with human or mouse tissue factor (TF)-FVIIa complexes. Mutagenesis of the FVIIa 4-carboxyglutamic acid domain and dose titrations with FX showed that EPCR interacted primarily with FX to attenuate FX activation in lipid-free assay systems. In human cell models of TF signaling, antibody inhibition of EPCR selectively blocked PAR activation by the ternary TF-FVIIa-FXa complex but not by the non-coagulant TF-FVIIa binary complex. Heterologous expression of EPCR promoted PAR1 and PAR2 cleavage by FXa in the ternary complex but did not alter PAR2 cleavage by TF-FVIIa. In murine smooth muscle cells that constitutively express EPCR and TF, thrombin and FVIIa/FX but not FVIIa alone induced PAR1-dependent signaling. Although thrombin signaling was unchanged, cells with genetically reduced levels of EPCR no longer showed a signaling response to the ternary complex. These results demonstrate that EPCR interacts with the ternary TF coagulation initiation complex to enable PAR signaling and suggest that EPCR may play a role in regulating the biology of TF-expressing extravascular and vessel wall cells that are exposed to limited concentrations of FVIIa and FX provided by ectopic synthesis or vascular leakage.