gebhart/patrepeval huggingface dataset:
Resveratrol induces autophagy through death‐associated protein kinase 1 (DAPK1) in human dermal fibroblasts under normal culture conditions (2013)

Autophagy is an essential process degrading damaged components. Although resveratrol has various beneficial activities for health, little is known about the effects of resveratrol on autophagy in skin. We investigated whether resveratrol affects autophagy in human dermal fibroblasts grown in complete medium. We found that after the resveratrol treatment, LC3-II reached a maximum level at 8 h and then gradually decreased. By PCR array analysis, we identified death-associated protein kinase 1 (DAPK1) as a new target of resveratrol, and we confirmed that the expression level of DAPK1 was enhanced by resveratrol. We also demonstrated that DAPK1 knock-down by siRNA was sufficient to reduce resveratrol-induced autophagy but did not affect the phosphorylation level of AMP-activated kinase (AMPK), a well-known target of resveratrol. These data indicate that resveratrol-induced autophagy can be mediated by DAPK1, raising the possibility that some of the beneficial effects of resveratrol may be due to its regulation of DAPK1.
Application of flash-lamp post-exposure baking for EUV resist processing (2011)

The reduction of linewidth roughness (LWR) is considered one of the most critical issues in extreme ultraviolet (EUV) photoresists. A possible solution to the LWR issue is shortening the acid-diffusion length of the photoacid via the optimized application of post-exposure bake (PEB) processes. In this study, the development and feasibility of the flash-lamp (FL) PEB process as a replacement for the commonly used hot-plate PEB process is investigated. The results indicate that, using the FL PEB process, the acid-diffusion length is controllable and lithographic patterning results are obtained. Further detailed analysis is necessary to optimize this technology for lithographic patterning applications. However, the present results show the potential of FL PEB for applications in EUV photoresist processing.
The use of two nematic solvents in the determination of molecular structure of systems providing deceptively simple spectra (1984)

Abstract The use of two liquid crystals as solvents in the determination of molecular structure has been demonstrated for systems which do not provide structural information from studies in a single solvent owing to the fact that the spectra are deceptively simple, with the result that all the spectral parameters cannot be derived with reasonable precision. The specific system studied was 2‐( p ‐bromophenyl)‐4,6‐dichloropyrimidine, for which relative inter‐proton discances have been determined from the proton NMR spectra in two nematic solvents.
Upconverting Reporters for Biomedical Diagnostics: Applications in Antibody and DNA Detection (2006)

We describe the properties of near-infrared-excited upconverting phosphor particles for ultrasensitive detection and their application to antibody and DNA diagnostics. Other potential applications include photodynamic therapy, food analysis, and surgical imaging.
Effective management of roles and responsibilities: Driving accountability in software development teams (2010)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Teams differ in the way they define roles and responsibilities and in the level of formalism by which they establish and communicate these definitions. Responsibilities are not always clearly defined, and there is often confusion or mismatch between the individual's perspectives of a role and the expectations of that role by other team members. This lack of shared understanding can lead to issues in performance and lack of accountability. We review the notion of role specification as part of software development governance and present an approach for specifying responsibilities in terms of decisions to be made during the life cycle of software development artifacts. We present evaluation data from software teams as they redefine their roles and shape their responsibilities. We further present a tool for governance specification based on this approach, which can ensure that these specifications are adhered to in the software development platform. We conclude by describing a methodology for how the tool and approach can be implemented to help software development teams understand and evolve the appropriate governance for their needs. </para>
Smooth touch control between position control and force control for industrial robots (2010)

This paper proposes a new smooth touch control for operating industrial robots in unknown environments. The touch control is an useful strategy for the smooth switching from the position control to the force control. Many applications require flexibility to the environments. For example, direct teaching by using a manual control is one of the typical applications. A highperformance force control method is important for meeting this demand. This paper proposes a new sensor-less force control structure based on an I-P force controller and a disturbance observer. The experimental results presented herein confirm that the proposed method provides fine, smooth touch control in unknown environments such as a concrete block, a foamed styrol block and a cardboard box by using the tested structure of an actual industrial robot.
Multifractionated hyperthermia treatment of malignant and normal tissue in vivo. (1980)

Recovery from thermal damage was studied in a methylcholanthrene-induced fibrosarcoma (FSal) and the surrounding normal tissue. Tumors isotransplanted into the feet of C3H mice were treated in a water bath with two equal fractions of heat given at 2-, 6-, or 24-hr intervals and at 42.5–44.5°. The results were analyzed at 120 days as the 50% tumor control dose and as the dose required to achieve a specified level of normal tissue damage in one-half of the treated animals.

The results show a slow and nearly parallel recovery in tumor and normal tissue for split treatments with intervals up to 24 hr. For an intertreatment interval of 6 hr, 50% tumor control dose and 50% response dose values were not different from those for single heat exposure. In fact, for a 2-hr interval, the 50% tumor control dose and 50% response dose values were lower than those for single treatments. This is probably due to short-term physiological changes induced by the first heat exposure. For split time intervals of 24 hr, a moderate degree of repair was noted with recovery ratios between 1.27 and 1.56. Owing to parallel recovery found in tumors and normal tissue, no significant variations in the therapeutic ratio could be obtained by use of the two fraction schedules studied here. The time-temperature relationship for fractionated thermal damage was not different from that seen after a single treatment.

The effect of multifractionated hyperthermia was studied at a temperature of 43.5°. Daily treatments resulted in a pronounced recovery, with recovery ratios for tumor and two different levels of normal tissue damage at 2.6 to 2.9 for heating in five fractions and 4.2 to 6.3 for heating in the ten-fraction schedule. Although an increasing number of fractions tended to result in a greater recovery ratio for normal tissue damage than for tumor, this finding was not statistically significant.
Dopant Precursor Adsorption into Single-Dimer Windows: Towards Guided Self-Assembly of Dopant Arrays on Si(100) (2021)

Atomically precise dopant arrays in Si are being pursued for solid-state quantum computing applications. We propose a guided self-assembly process to produce atomically precise arrays of single dopant atoms in lieu of lithographic patterning. We leverage the self-assembled c(4x2) structure formed on Br- and I-Si(100) and investigate molecular precursor adsorption into the generated array of single-dimer window (SDW) adsorption sites with density functional theory (DFT). The adsorption of several technologically relevant dopant precursors (PH$_3$, BCl$_3$, AlCl$_3$, GaCl$_3$) into SDWs formed with various resists (H, Cl, Br, I) are explored to identify the effects of steric interactions. PH$_3$ adsorbed without barrier on all resists studied, while BCl$_3$ exhibited the largest adsorption barrier, 0.34 eV, with an I resist. Dense arrays of AlCl$_3$ were found to form within experimentally realizable conditions demonstrating the potential for the proposed use of guided self-assembly for atomically precise fabrication of dopant-based devices.
Cleaning Aspects of Novel Materials after CMP (2011)

High mobility channel materials such as Ge and III-V compound semiconductors, are explored for the sub-22nm technology node. In order to allow process integration and full scale manufacturing of these materials, they need to be introduced by epitaxial growth in narrow trenches on silicon carrier wafers. Consequently, CMP is needed to flatten the surface before constructing the gate stack. Similarly to silicon, trace contamination is expected to have a detrimental effect on the devices and therefore, an appropriate cleaning of the wafer consisting of areas with mixed substrates is an absolute requisite. This involves the removal of particulate, metallic and organic contamination while controlling surface etching of these novel materials integrated on the silicon wafer. This will be addressed in this paper and allows the development of efficient post-CMP cleaning strategies.
The Chemokine, CCL3, and Its Receptor, CCR1, Mediate Thoracic Radiation–Induced Pulmonary Fibrosis (2010)

Patients receiving thoracic radiation often develop pulmonary injury and fibrosis. Currently, there are no effective measures to prevent or treat these conditions. We tested whether blockade of the chemokine, CC chemokine ligand (CCL) 3, and its receptors, CC chemokine receptor (CCR) 1 and CCR5, can prevent radiation-induced lung inflammation and fibrosis. C57BL/6J mice received thoracic radiation, and the interaction of CCL3 with CCR1 or CCR5 was blocked using genetic techniques, or by pharmacologic intervention. Lung inflammation was assessed by histochemical staining of lung tissue and by flow cytometry. Fibrosis was measured by hydroxyproline assays and collagen staining, and lung function was studied by invasive procedures. Irradiated mice lacking CCL3 or its receptor, CCR1, did not develop the lung inflammation, fibrosis, and decline in lung function seen in irradiated wild-type mice. Pharmacologic treatment of wild-type mice with a small molecule inhibitor of CCR1 also prevented lung inflammation and fibrosis. By contrast, mice lacking CCR5 were not protected from radiation-induced injury and fibrosis. The selective interaction of CCL3 with its receptor, CCR1, is critical for radiation-induced lung inflammation and fibrosis, and these conditions can be largely prevented by a small molecule inhibitor of CCR1.
The Techno-Economic Basis for Coproduct Manufacturing To Enable Hydrocarbon Fuel Production from Lignocellulosic Biomass (2016)

Biorefinery process development relies on techno-economic analysis (TEA) to identify primary cost drivers, prioritize research directions, and mitigate technical risk for scale-up through development of detailed process designs. Here, we conduct TEA of a model 2000 dry metric ton-per-day lignocellulosic biorefinery that employs a two-step pretreatment and enzymatic hydrolysis to produce biomass-derived sugars, followed by biological lipid production, lipid recovery, and catalytic hydrotreating to produce renewable diesel blendstock (RDB). On the basis of projected near-term technical feasibility of these steps, we predict that RDB could be produced at a minimum fuel selling price (MFSP) of USD $9.55/gasoline-gallon-equivalent (GGE), predicated on the need for improvements in the lipid productivity and yield beyond current benchmark performance. This cost is significant given the limitations in scale and high costs for aerobic cultivation of oleaginous microbes and subsequent lipid extraction/recovery. In light of this predicted cost, we developed an alternative pathway which demonstrates that RDB costs could be substantially reduced in the near term if upgradeable fractions of biomass, in this case hemicellulose-derived sugars, are diverted to coproducts of sufficient value and market size; here, we use succinic acid as an example coproduct. The coproduction model predicts an MFSP of USD $5.28/GGE when leaving conversion and yield parameters unchanged for the fuel production pathway, leading to a change in biorefinery RDB capacity from 24 to 15 MM GGE/year and 0.13 MM tons of succinic acid per year. Additional analysis demonstrates that beyond the near-term projections assumed in the models here, further reductions in the MFSP toward $2–3/GGE (which would be competitive with fossil-based hydrocarbon fuels) are possible with additional transformational improvements in the fuel and coproduct trains, especially in terms of carbon efficiency to both fuels and coproducts, recovery and purification of fuels and coproducts, and coproduct selection and price. Overall, this analysis documents potential economics for both a hydrocarbon fuel and bioproduct process pathway and highlights prioritized research directions beyond the current benchmark to enable hydrocarbon fuel production via an oleaginous microbial platform with simultaneous coproduct manufacturing from lignocellulosic biomass.
Symmetry of Cerebral Hemodynamic Indices Derived from Bilateral Transcranial Doppler (2003)

Objective. The authors evaluated with bilateral transcranial Doppler (TCD) ultrasonography the norm of interhemispheric difference for several cerebrovascular hemodynamic parameters. Methods. Forty-four volunteers (33 male, 11 female; average age = 21 years; range, 20–23 years) were studied. The authors recorded bilateral systolic, diastolic, and mean flow velocity (FV) and noninvasive systolic, diastolic, and mean arterial blood pressure. Calculated indices included Gosling's pulsatility index (GPI), an index of autoregulation (Mx), critical closing pressure (CCP), and a noninvasive estimator of cerebral perfusion pressure (nCPP). All indices were averaged per side and patient. For each parameter, the left-right correlation coefficient (r2) and the 95% confidence limit of the left-right differences were calculated. Results. All TCD-derived indices displayed significant correlations between the left and right sides: r2=0.49 for mean FV (FVm), r2=0.66 for GPI, r2=0.79 for Mx, r2=0.93 for CCP, and r2=0.94 for nCPP. The 95% confidence intervals for the left-right differences were 20 cm/s for FVm, 0.16 for GPI, 0.18 for Mx, 13 mm Hg for CCP, and 4.6 mm Hg for nCPP. Conclusions. This study gives the reference values for the assessment of left-right symmetry of cerebral hemodynamics using various TCD-derived indices. These reference values should be useful for clinical studies assessing the left-right asymmetry of cerebral hemodynamics on a daily basis.
Single-phase grid interface for home energy storage (2023)

Abstract In this paper, an overview of a novel home energy storage system is presented. The aim of the system is the utilization of community solar panels in urban environments with decentralized energy storage at the household level. An increase in the total energy production from renewable energy sources as well as a reduction in energy costs for the consumer are the obvious benefits of such a system. The key focus of the paper presented is to model, design, and optimize a Dual Active Bridge that serves as a low-voltage grid-battery interface for the proposed storage system. A state-of-the-art loss model of the Dual Active Bridge is presented along with a novel optimization method intended for total power loss minimization.
Development of a second generation linkage map for almond using RAPD and SSR markers (2000)

Fifty-four RAPD (random amplified polymorphic DNA) markers and 6 SSRs (simple sequence repeats) were included in a molecular marker map with 120 RFLPs (restriction fragment length polymorphisms) and 7 isozyme genes previously constructed using the offspring of a cross between the almond (Prunus amygdalus) cultivars 'Ferragnès' and 'Tuono'. Only highly reproducible RAPDs segregating 1:1 were used. To identify these markers, a total of 325 primers were screened, from which 41 produced RAPDs useful for mapping. Polymorphism was detected in six of the eight Prunus SSRs (simple sequence repeats) studied, thus enabling these to be mapped. All markers were placed on the 8 linkage groups previously identified. The number of new markers included in the map of 'Ferragnès' was 33 for a total of 126, and 30 in the map of 'Tuono' for a total of 99. The sizes of the maps of 'Ferragnès' (415 cM) and 'Tuono' (416 cM) were similar, representing a 5% increase over the maps constructed solely with isozymes and RFLPs. The estimated total size of the almond map was of 457 cM. Some markers were placed in zones with low density of markers and others in the extreme of linkage groups. The use of RAPD markers to complete genetic maps constructed with transferable markers is discussed.Key words: almond, Prunus amygdalus, RAPD, SSR, mapping.
A Framework for MIMO Capacity Bounds Based on the Cramer-Rao Bound on the Channel Estimation Error (2006)

This paper provides n framework for deriving MIMO capacity bounds that takes channel estimation error into account by using the Cramer-Rao bound (CRB). Combining the CRB with capacity analysis allows for studies of the trade-off between estimation performance and throughput. The framework is used to investigate the impact of the spatio-temporal structure found in practical channel sounding experiments. Numerical evaluations indicate that higher capacities are possible and the optimum number of training symbols and transmit antennas are different when exploiting the structure in the channel compared to previous unstructured approaches
Accelerating HMMER on GPUs by implementing hybrid data and task parallelism (2010)

Many biologically motivated problems are expressed as dynamic programming recurrences and are difficult to parallelize due to the intrinsic data dependencies in their algorithms. Therefore their solutions have been sped up using task level parallelism only. Emerging platforms such as GPUs are appealing parallel architectures for high-performance; at the same time they are a motivation to rethink the algorithms associated with these problems, to extract finer-grained parallelism such as data parallelism.In this paper, we consider the hmmersearch program as a representative of these problems and we re-design its computational algorithm to extract data parallelism for a more efficient execution on emerging platforms, despite the fact that hmmersearch has data dependencies. Our approach outperforms other existing methods when searching a very large database of unsorted sequences on GPUs.
Protein Dimerization on a Phosphonated Calix[6]arene Disc (2017)

Abstract Complex formation between cationic cytochrome c and the water‐soluble, poly‐anionic p ‐phosphonatocalix[6]arene (pclx 6 ) was investigated. A crystal structure (at 1.8 Å resolution) revealed a remarkable dimeric disc of pclx 6 that acts like glue to mediate a symmetric ( C 2 ) protein dimer. The calixarene disc has a diameter of about 1.5 nm and masks about 360 Å 2 of protein surface. The key protein–calixarene contacts occur via two linchpin lysines, with additional contacts provided by a small hydrophobic patch. The protein–calixarene supramolecular assemblies were observed in solution by size‐exclusion chromatography with multi‐angle light scattering and NMR spectroscopy. Using isothermal titration calorimetry and NMR data, an apparent K d in the low micromolar range was determined for the charge‐rich protein–calixarene complex. In contrast to p ‐sulfonatocalix[4]arene, the larger pclx 6 has a single, well‐defined binding site that mediates the assembly of cytochrome c in solution.
ChemInform Abstract: Incorporation of Alkylthiol Chains at C‐5 of Deoxyuridine. (1993)

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.
Abstract 464: Novel role of xpo1 in regulating MicroRNAs related to pancreatic ductal adenocarcinoma invasion and metastasis (2017)

Abstract Objective: There are no known reports on the role of exportin 1 (XPO1; also known as chromosome maintenance region 1 [CRM1]) in microRNA biology. In this study, we for the first time demonstrate that interfering with XPO1 machinery can influence miRNA signaling leading to suppression of pancreatic ductal adenocarcinoma (PDAC) proliferation, invasion and metastasis. Methods: miRNA arrays (LCSciences, Houston, TX) were performed on total RNA samples from PDAC cell lines (HPAC, MiaPaCa-2, AsPc-1 and L3.6pl) and normal human pancreatic ductal epithelial (HPDE) cells. PDAC cells were treated with XPO1 inhibitor (Selinexor) or transfected with control siRNA, XPO1 siRNA (Santa Cruz), miR-control or miR-145 mimic (Applied biosystems) all at a final concentration of 20 nM using DharmaFact Transfection Reagent (Dharmacon, Lafayette. CO). The total RNA and total protein from treated or transfected cells were subjected to real-time PCR or immunoblot analysis in order to measure expression level of miR-145, let-7d, miR-34c, miR-320, miR-205, and miR-145 target or downstream genes including EGFR, MMP1, MT-MMP, c-Myc, Sox-2, and PAK4. The impact of XPO1 inhibitor Selinexor on PDAC growth, proliferation, invasion and migrations was also evaluated using MTT and scratch assay. Results: In this study, we show that PDAC cells have significantly reduced expression of miR-145 when compared to normal pancreatic duct epithelial cells. Similarly, forced expression of miR-145 in PDAC cells inhibited cell proliferation and migration. Conversely, we demonstrate that RNAi of XPO1 by siRNA knockdown or chemical inhibition of XPO1 by selective inhibitor of nuclear export compound (Selinexor) restores miR-145 expression in PDAC cells ultimately leading to inhibition of cell proliferation and migration. In addition, we show that the inhibition of cell proliferation and migration by Selinexor is mediated through the down-regulation of known miR-145 signals including EGFR, MMP1, MT-MMP, c-Myc, PAK4 and Sox-2. Selinexor also induced the expression of two important tumor suppressive miRNAs, miR-34c and let-7d, leading to the up-regulation of p21WAF1. We also observed the down-regulation of oncomir mir-205. Conclusions: These results are the first to show that targeted inhibition of the nuclear exporter protein XPO1 by RNAi or Selinexor could restore tumor suppressive miRs in PDAC. Citation Format: Asfar S. Azmi, Yiwei Li, Irfana Muqbil, Amro Aboukameel, William Senapedis, Erkan Baloglu, Yosef Landesman, Michael Kauffman, Sharon Shacham, Philip A. Philip, Ramzi M. Mohammad. Novel role of xpo1 in regulating MicroRNAs related to pancreatic ductal adenocarcinoma invasion and metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 464. doi:10.1158/1538-7445.AM2017-464
Supplementary Table S7 from Detection of Promoter DNA Methylation in Urine and Plasma Aids the Detection of Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Univariate and multivariate logistic regression analysis for risk of having NSCLC in late stages (n=53)&lt;/p&gt;
Synthesis and characterization of new poly(thienylenevinylene)s with thioether side chains (1998)

The first poly(thienylene vinylene)s with alkylthio side chains are synthesized by the McMurry reductive polymerisation of the corresponding 2,5-dialdehydes. The polymers PTVa and b show good solubility and comparable optical properties, with the exception of the CD effect, present in PTVb due to its chiral side chains. Furthermore the polymers have optical properties that change upon modification of different parameters, such as the solvent and the temperature.