gebhart/patrepeval huggingface dataset:
2,3-Dihydrobenzofuran analogs of hallucinogenic phenethylamines (1991)

Two 2,3-dihydrobenzofuran analogues of hallucinogenic amphetamines were prepared and evaluated for activity in the two-lever drug-discrimination paradigm in rats trained to discriminate saline from LSD tartrate (0.08 mg/kg) and for the ability to displace [125I]-(R)-DOI [( 125I]-(R)-1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropane) from rat cortical homogenate 5-HT2 receptors. The compounds, 1-(5-methoxy-2,3-dihydrobenzofuran-4-yl)-2-aminopropane (6a) and its 7-brominated analogue 6b, possessed activity comparable to their conformationally flexible counterparts 1-(2,5-dimethoxyphenyl)-2-aminopropane (3) and its 4-bromo derivative DOB (5), respectively. The results suggest that the dihydrofuran ring in 6a and 6b models the active conformation of the 5-methoxy groups in 3 and 5. Free energy of binding, derived from radioligand displacement KA values, indicated that addition of the bromine in either series contributes 2.4-3.2 kcal/mol of binding energy. On the basis of surface area of the bromine atom, this value is 2-3 times higher than would be expected on the basis of hydrophobic binding. Thus, hydrophobicity of the para substituent alone cannot account for the dramatic enhancement of hallucinogenic activity. Although this substituent may play a minor role in orienting the conformation of the 5-methoxy group in derivatives such as 4 and 5, there appears to be some other, as yet unknown, critical receptor interaction.
Isolation of Dysprosium and Yttrium Complexes of a Three-Electron Reduction Product in the Activation of Dinitrogen, the (N2)3− Radical (2009)

DyI(2) reacts with 2 equiv of KOAr (OAr = OC(6)H(3)(CMe(3))(2)-2,6) under nitrogen to form not only the (N(2))(2-) complex, [(ArO)(2)(THF)(2)Dy](2)(mu-eta(2):eta(2)-N(2)), 1, but also complexes of similar formula with an added potassium ion, [(ArO)(2)(THF)Dy](2)(mu-eta(2):eta(2)-N(2))[K(THF)(6)], 2, and [(ArO)(2)(THF)Dy](2)(mu(3)-eta(2):eta(2):eta(2)-N(2))K(THF), 3. The 1.396(7) and 1.402(7) A N-N bond distances in 2 and 3, respectively, are consistent with an (N(2))(3-) ligand, but the high magnetic moment of 4f(9) Dy(3+) precluded definitive identification. The Y[N(SiMe(3))(2)](3)/K reduction system was used to synthesize yttrium analogues of 2 and 3, {[(Me(3)Si)(2)N](2)(THF)Y}(2)(mu-eta(2):eta(2)-N(2))[K(THF)(6)] and {[(Me(3)Si)(2)N](2)(THF)Y}(2)(mu(3)-eta(2):eta(2):eta(2)-N(2))K, that had similar N-N distances and allowed full characterization. EPR, Raman, and DFT studies are all consistent with the presence of (N(2))(3-) in these complexes. (15)N analogues were also prepared to confirm the spectroscopic assignments. The DFT studies suggest that the unpaired electron is localized primarily in a dinitrogen pi orbital isolated spatially, energetically, and by symmetry from the metal orbitals.
SAMSON (2016)

This paper introduces SAMSON (Self-Adaptive Middleware for wireless SensOr Networks), an instance of a Reference Architecture (RA) that was designed to manage wireless sensor networks (WSN) in an autonomic way by enabling runtime adaptation of nodes' behavior according to context changes, application requirements, and predefined adaptation policies. In this paper, we propose a process, supported by model-driven transformations to generate SAMSON from the RA specification. The model-driven transformations are used to map each element of the RA specification to software components and to generate the source code to be deployed in a target WSN platform. We evaluate our proposal by presenting four application scenarios where SAMSON was employed to optimize the network lifetime and to react to runtime events according to adaptation policies previously defined by software architects and network administrators. Evaluation results shown that SAMSON was able to dynamically adapt the behavior of sensor nodes, to efficiently use the hardware resources, and to increase the WSN lifetime.
Characterization of microsatellite primers for Bembidion lampros through 454-sequencing of the genome (2012)

454-sequencing of the genome was used to isolate and characterize nuclear 22 microsatellite sequences from the ground beetle Bembidion lampros (Carabidae). A 23 total of 4502 contigs containing di- to penta-nucleotide microsatellite repeats were 24 found (4211 perfect and 289 non-perfect repeats). Primers were developed and tested 25 for 34 microsatellite sequences. Of these 15 were tested on 1140 individual samples 26 amplifying on average 89% of samples and they did not deviate significantly from 27 Hardy-Weinberg and linkage equilibrium. These microsatellite sequences will be useful 28 in studying the effect of agricultural management techniques and various environmental 29 factors on a beneficial agricultural species.
Shock-wave–inertial-bubble interaction near an elastic boundary (2006)

The interaction of laser-generated single cavitation bubbles (maximum diameter Dmax=1.34 mm) near a silicon rubber membrane with a shock wave (39–75 MPa in peak pressure and 1.7 μs in compressive pulse duration) is investigated. The interaction leads to directional, forced collapse of the bubble with microjet formation along shock wave propagation direction. Maximum jet penetration into the membrane is produced during the bubble collapse phase with optimal shock wave arrival time and stand-off distance s, a condition that ensures that the forced collapse time of the bubble matches with the compressive duration of the shock wave to generate presumably the maximum axial jet velocity toward the boundary. A maximum penetration depth of 0.5 mm is observed at dimensionless proximity γ (=2s/Dmax)=0.7 when the bubble establishes contact with the boundary during expansion. At larger γ (≥1.2), jet impact is significantly attenuated by the interposing water layer separating the collapsing bubble and the membrane surface. Such interaction may provide a novel acoustic means for in vivo microinjection, applicable to targeted delivery of macromolecules and gene vectors to biological tissues.
Validation of a risk prediction score for proximal neoplasia in colorectal cancer screening: a prospective colonoscopy study (2016)

This study developed a clinical scoring system to predict the risks of PN among screening participants for colorectal cancer. We recruited 5,789 Chinese asymptomatic screening participants who received colonoscopy in Hong Kong (2008-2014). From random sampling of 2,000 participants, the independent risk factors were evaluated for PN using binary regression analysis. The odds ratios for significant risk factors were used to develop a scoring system, with scores stratified into 'average risk' (AR):0-2 and 'high risk' (HR):3-5. The other 3,789 subjects formed an independent validation cohort. Each participant received a score calculated based on their risk factors. The performance of the scoring system was evaluated. The proportion of PN in the derivation and validation cohorts was 12.6% and 12.9%, respectively. Based on age, gender, family history, body mass index and self-reported ischaemic heart disease, 85.0% and 15.0% in the validation cohort were classified as AR and HR, respectively. Their prevalence of PN was 12.0% and 18.1%, respectively. Participants in the HR group had 1.51-fold (95% CI = 1.24-1.84, p < 0.001) higher risk of PN than the AR group. The overall c-statistics of the prediction model was 0.71(0.02). The scoring system is useful in predicting the risk of PN to prioritize patients for colonoscopy.
Chromosomal profiles of high‐grade cervical intraepithelial neoplasia relate to duration of preceding high‐risk human papillomavirus infection (2011)

High-grade cervical intraepithelial neoplasia (CIN2/3) represents a heterogeneous disease both with respect to clinical behavior and chromosomal aberrations detected. We hypothesized that the extent of chromosomal aberrations reflects the duration of their existence. Chromosomal profiles were determined of CIN3 of women with a known 5-year history of high-risk human papillomavirus virus (hrHPV) infection, in which duration of prior hrHPV infection was considered a proxy for duration of CIN3 existence. Eleven women had a <5 year preceding hrHPV infection (CIN3<5yrPHI) and 24 had a PHI lasting ≥5 years (CIN3≥5yrPHI). For comparison, six CIN3 adjacent to squamous cell carcinomas (CIN3-SCC), the corresponding SCCs, and six CIN1 were included. Unsupervised hierarchical clustering analysis of the chromosomal profiles revealed two clusters. One was characterized by a low number of chromosomal aberrations and included all CIN1, 81.8% of CIN3<5yrPHI and 33.3% of CIN3≥5yrPHI. Samples in the second cluster, displaying multiple aberrations, included 18.2% of CIN3<5yrPHI, 66.7% CIN3≥5yrPHI, all except one CIN3-SCC and all SCCs. The number of genomic aberrations increased according to lesion grade and also with longer duration of PHI. The increase in aberrations in CIN3≥5yrPHI compared to <5yrPHI was highly significant (p = 0.001), suggesting that CIN3≥5yrPHI represent more severe lesions. In conclusion, longer duration of preceding hrHPV infection is associated with an increased number of chromosomal aberrations. Hence, CIN3 with a longer duration of existence are likely more prone to have an increased short-term risk of cervical cancer.
Simulations and Experiments on Low-Pressure Permeation of Fabrics: Part I—3D Modeling of Unbalanced Fabric (2001)

Conformation of fabrics to complex molds during composite processing induces significant fabric deformation and local shear, which in turn alter the processability of these preforms from their unsheared, flat configuration. The present work (Parts I and II) establishes that although composite mold processing can often be described generally by a percolation flow assumption (e.g., Darcy or Poiseuille flow), changes in microarchitecture of fabric in shear result in markedly different flow fronts. We reiterate our earlier finding that use of a transformed Darcy law (i.e., mathematical transformation of tensor of undeformed permeability, to the sheared configuration) does not accurately predict permeability for sheared fabrics. In essence, the effect of the change in microarchitecture of the fabric is not captured by mathematical transformation of the tensorial permeability. Wealso point out the deficiencies of semi-empirical approaches in determining sheared fabric permeability. We then develop a 3D fabric model, which is used to quantify the effects of nesting and changes in gap architecture with shear angle. We show that nesting produces gaps in molds in commonly-used permeability experiments which easily exceed single-layer fabric thicknesses when more than a few layers are used, but that this condition is easily detectable in an experiment (i.e., Poiseuille flow between topmost layer and mold top is easily detected). We also show that shear angle (in our case,. = 0°, 15°, and 30°) produces little difference in nesting, though it significantly alters fabric microstructure and the sizes and shapes of intralayer gaps. In Part II of this paper, we use this fabric model to predict fabric permeability. Our work suggests that departure from the more traditional approach of generation of a large suite of data from permeation experiments to determine manufacturability of preforms, in favor of computational simulation of fabric geometries, is well-justified.
A distributed consensus approach to synchronization of RF signals (2012)

We propose a consensus-based algorithm for the synchronization of carrier signals in a wireless network. This work is motivated by recent progress on distributed beamforming and other cooperative MIMO techniques that require synchronized RF signals among all the cooperating nodes in a network and is aimed at addressing the limitations of the centralized master-slave approach used in previous work in this area. Our proposed algorithm is based on a variation of the classic Kuramoto model for the synchronization of coupled oscillators and is well-suited for a digital baseband implementation. We describe our proposed algorithm in detail and present initial results that show that this algorithm achieves global frequency lock given only that the network is connected i.e. there exists (possibly multi-hop) paths for every node to transmit and receive a signal from every other node.
HTN Planning for the Composition of Stream Processing Applications (2013)

Goal-driven automated composition of software components is an important problem with applications in Web service composition and stream processing systems. The popular approach to address this problem is to build the composition automatically using AI planning. However, it is shown that some of these planning approaches may neither be feasible nor scalable for many large-scale flow-based applications. Recent advances have proven that the automated composition problem can take advantage of expert knowledge describing the many ways in which different reusable components can be composed. This knowledge can be represented using an extensible composition template or pattern. In prior work, a flow pattern language called Cascade and its corresponding specialized planner have shown the best performance in these domains. In this paper, we propose the use of Hierarchical Task Network (HTN) planning for the composition of stream processing applications. To this end, we propose an automated approach of creating an HTN-based problem from the Cascade representation of the flow patterns. The resulting technique not only allows us to use the HTN planning paradigm and its many advantages including added expressivity but also enables optimization and customization of composition with respect to preferences and constraints. Further, we propose and develop a lookahead heuristic and show that it significantly reduces the planning time. We have performed extensive experimentation with stream processing applications and evaluated applicability and performance of our approach.
Hepatocyte Growth Factor, but not Vascular Endothelial Growth Factor, Attenuates Angiotensin II–Induced Endothelial Progenitor Cell Senescence (2008)

Although both hepatocyte growth factor (HGF) and vascular endothelial growth factor (VEGF) are potent angiogenic growth factors in animal models of ischemia, their characteristics are not the same in animal experiments and clinical trials. To elucidate the discrepancy between HGF and VEGF, we compared the effects of HGF and VEGF on endothelial progenitor cells under angiotensin II stimulation, which is a well-known risk factor for atherosclerosis. Here, we demonstrated that HGF, but not VEGF, attenuated angiotensin II-induced senescence of endothelial progenitor cells through a reduction of oxidative stress by inhibition of the phosphatidylinositol-3,4,5-triphosphate/rac1 pathway. Potent induction of neovascularization of endothelial progenitor cells by HGF, but not VEGF, under angiotensin II was also confirmed by in vivo experiments using several models, including HGF transgenic mice.
Deep Learning for Dialogue Systems (2018)

In the past decade, goal-oriented spoken dialogue systems have been the most prominent component in today’s virtual personal assistants. The classic dialogue systems have rather complex and/or modular pipelines. The advance of deep learning technologies has recently risen the applications of neural models to dialogue modeling. However, how to successfully apply deep learning based approaches to a dialogue system is still challenging. Hence, this tutorial is designed to focus on an overview of the dialogue system development while describing most recent research for building dialogue systems and summarizing the challenges, in order to allow researchers to study the potential improvements of the state-of-the-art dialogue systems. The tutorial material is available at http://deepdialogue. miulab.tw.
Flat Fresnel doublets made of PMMA and PC: combining low cost production and very high concentration ratio for CPV (2011)

The linear chromatic aberration (LCA) of several combinations of polycarbonates (PCs) and poly (methyl methacrylates) (PMMAs) as singlet, hybrid (refractive/diffractive) lenses and doublets operating with wavelengths between 380 and 1600 nm - corresponding to a typical zone of interest of concentrated photovoltaics (CPV) - are compared. Those comparisons show that the maximum theoretical concentration factor for singlets is limited to about 1000 × at normal incidence and that hybrid lenses and refractive doublets present a smaller LCA increasing the concentration factor up to 5000 × and 2 × 10(6) respectively. A new achromatization equation more useful than the Abbé equation is also presented. Finally we determined the ideal position of the focal point as a function of the LCA and the geometric concentration which maximizes the flux on the solar cell.
Epitaxial growth of a monolayer WSe 2 -MoS 2 lateral p-n junction with an atomically sharp interface (2015)

Two-dimensional transition metal dichalcogenides (TMDCs) such as molybdenum sulfide MoS2 and tungsten sulfide WSe2 have potential applications in electronics because they exhibit high on-off current ratios and distinctive electro-optical properties. Spatially connected TMDC lateral heterojunctions are key components for constructing monolayer p-n rectifying diodes, light-emitting diodes, photovoltaic devices, and bipolar junction transistors. However, such structures are not readily prepared via the layer-stacking techniques, and direct growth favors the thermodynamically preferred TMDC alloys. We report the two-step epitaxial growth of lateral WSe2-MoS2 heterojunction, where the edge of WSe2 induces the epitaxial MoS2 growth despite a large lattice mismatch. The epitaxial growth process offers a controllable method to obtain lateral heterojunction with an atomically sharp interface.
R753Q Polymorphism Inhibits Toll-like Receptor (TLR) 2 Tyrosine Phosphorylation, Dimerization with TLR6, and Recruitment of Myeloid Differentiation Primary Response Protein 88 (2012)

The R753Q polymorphism in the Toll-IL-1 receptor domain of Toll-like receptor 2 (TLR2) has been linked to increased incidence of tuberculosis and other infectious diseases, but the mechanisms by which it affects TLR2 functions are unclear. Here, we studied the impact of the R753Q polymorphism on TLR2 expression, hetero-dimerization with TLR6, tyrosine phosphorylation, and recruitment of myeloid differentiation primary response protein (MyD) 88 and MyD88 adapter-like (Mal). Complementation of HEK293 cells with transfected WT or R753Q TLR2 revealed their comparable total levels and only minimal changes in cell surface expression of the mutant species. Notably, even a 100-fold increase in amounts of transfected R753Q TLR2 versus WT variant did not overcome the compromised ability of the mutant TLR2 to activate nuclear factor κB (NF-κB), indicating that a minimal decrease in cell surface levels of the R753Q TLR2 cannot account for the signaling deficiency. Molecular modeling studies suggested that the R753Q mutation changes the electrostatic potential of the DD loop and results in a discrete movement of the residues critical for protein-protein interactions. Confirming these predictions, biochemical assays demonstrated that R753Q TLR2 exhibits deficient agonist-induced tyrosine phosphorylation, hetero-dimerization with TLR6, and recruitment of Mal and MyD88. These proximal signaling deficiencies correlated with impaired capacities of the R753Q TLR2 to mediate p38 phosphorylation, NF-κB activation, and induction of IL-8 mRNA in transfected HEK293 cells challenged with inactivated Mycobacterium tuberculosis or mycobacterial components. Thus, the R753Q polymorphism renders TLR2 signaling-incompetent by impairing its tyrosine phosphorylation, dimerization with TLR6, and recruitment of Mal and MyD88.
Disruption of proteostasis causes IRE1 mediated reprogramming of alveolar epithelial cells (2022)

Disruption of alveolar type 2 cell (AEC2) protein quality control has been implicated in chronic lung diseases, including pulmonary fibrosis (PF). We previously reported the in vivo modeling of a clinical surfactant protein C (SP-C) mutation that led to AEC2 endoplasmic reticulum (ER) stress and spontaneous lung fibrosis, providing proof of concept for disruption to proteostasis as a proximal driver of PF. Using two clinical SP-C mutation models, we have now discovered that AEC2s experiencing significant ER stress lose quintessential AEC2 features and develop a reprogrammed cell state that heretofore has been seen only as a response to lung injury. Using single-cell RNA sequencing in vivo and organoid-based modeling, we show that this state arises de novo from intrinsic AEC2 dysfunction. The cell-autonomous AEC2 reprogramming can be attenuated through inhibition of inositol-requiring enzyme 1 (IRE1α) signaling as the use of an IRE1α inhibitor reduced the development of the reprogrammed cell state and also diminished AEC2-driven recruitment of granulocytes, alveolitis, and lung injury. These findings identify AEC2 proteostasis, and specifically IRE1α signaling through its major product XBP-1, as a driver of a key AEC2 phenotypic change that has been identified in lung fibrosis.
Motexafin Gadolinium Mobilizes Zinc and Inhibits Thioredoxin Reductase in Human Lymphoma Cell Lines. (2004)

Abstract Motexafin gadolinium (MGd, Xcytrin®) is an anti-cancer agent that selectively localizes in tumors and promotes redox stress by oxidizing intracellular reducing species. MGd, at low concentrations, induces expression of metallothioneins (MT) and zinc transporter 1 (ZnT-1) transcripts in vitro. In the present study, we describe the effects of MGd on zinc ion homeostasis, thioredoxin reductase activity and cytotoxicity in lymphoma cell lines. Human lymphoma (Ramos, DHL-4, HF-1) cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum. Zinc (0–100 μM) and 0–25 μM MGd were added for 4–6 hr. Medium was exchanged and thioredoxin reductase activity was assessed by measuring the rate of lipoate reduction (Biaglow, Anal. Biochem.281:77, 2000). In other experiments, cells were treated with MGd and zinc, and analyzed by flow cytometry using annexin-V, propidium iodide, and the ion-specific fluorescent probe, FluoZin-3-AM™. RNA from treated cultures was harvested and metallothionein and ZnT-1 induction assessed by Northern blotting. Treatment with MGd and zinc led to synergistic increases in free intracellular zinc levels, inhibition of lipoate reduction, MT and ZnT-1 induction, and cytotoxicity. In DHL-4, exposure to 10 μM MGd and 50 μM zinc for 3 hr led to a 2.5-fold increase in FluoZn-3 fluorescence, relative to treatment with zinc alone. In Ramos, this treatment led to 1.4, 2.6, 5.2, and 30-fold increase in FluoZn-3 fluorescence after 2, 4, 6, or 24 hr. There was a 2-fold increase in annexin-V positive Ramos cells after 6 hr, and an 11-fold increase in propidium iodide permeable cells by 24 hr. The rate of lipoate reduction decreased to 69%, 47%, and 58% of control in Ramos, DHL-4, and HF-1 cell lines after 5 hr under these conditions. MT and ZnT-1 transcript levels were elevated within 4 hr after treatment with MGd, zinc, or the combination, and remained elevated for at least 24 hr. For example, in HF-1, MT transcript levels were increased 20, 40, and 173-fold by MGd, zinc, or the combined treatment after 8 hr. These observations support the characterization of MGd as a redox cycling agent that increases the intracellular availability of free zinc. This activity leads to inhibition of thioredoxin reductase and, ultimately, induction of cell death. The proposed mechanism of action supports the use of this agent alone or in combination with various chemotherapy agents that induce redox stress.