gebhart/patrepeval huggingface dataset:
Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel (2006)

Chromosome rearrangement, a hallmark of cancer, has profound effects on carcinogenesis and tumor phenotype. We used a panel of 60 human cancer cell lines (the NCI-60) as a model system to identify relationships among DNA copy number, mRNA expression level, and drug sensitivity. For each of 64 cancer-relevant genes, we calculated all 4,096 possible Pearson's correlation coefficients relating DNA copy number (assessed by comparative genomic hybridization using bacterial artificial chromosome microarrays) and mRNA expression level (determined using both cDNA and Affymetrix oligonucleotide microarrays). The analysis identified an association of ERBB2 overexpression with 3p copy number, a finding supported by data from human tumors and a mouse model of ERBB2-induced carcinogenesis. When we examined the correlation between DNA copy number for all 353 unique loci on the bacterial artificial chromosome microarray and drug sensitivity for 118 drugs with putatively known mechanisms of action, we found a striking negative correlation (-0.983; 95% bootstrap confidence interval, -0.999 to -0.899) between activity of the enzyme drug L-asparaginase and DNA copy number of genes near asparagine synthetase in the ovarian cancer cells. Previous analysis of drug sensitivity and mRNA expression had suggested an inverse relationship between mRNA levels of asparagine synthetase and L-asparaginase sensitivity in the NCI-60. The concordance of pharmacogenomic findings at the DNA and mRNA levels strongly suggests further study of L-asparaginase for possible treatment of a low-synthetase subset of clinical ovarian cancers. The DNA copy number database presented here will enable other investigators to explore DNA transcript-drug relationships in their own domains of research focus.
Chemical Synthesis of Highly Congested gp120 V1V2 N-Glycopeptide Antigens for Potential HIV-1-Directed Vaccines (2013)

Critical to the search for an effective HIV-1 vaccine is the development of immunogens capable of inducing broadly neutralizing antibodies (BnAbs). A key first step in this process is to design immunogens that can be recognized by known BnAbs. The monoclonal antibody PG9 is a BnAb that neutralizes diverse strains of HIV-1 by targeting a conserved carbohydrate-protein epitope in the variable 1 and 2 (V1V2) region of the viral envelope. Important for recognition are two closely spaced N-glycans at Asn(160) and Asn(156). Glycopeptides containing this synthetically challenging bis-N-glycosylated motif were prepared by convergent assembly, and were shown to be antigenic for PG9. Synthetic glycopeptides such as these may be useful for the development of HIV-1 vaccines based on the envelope V1V2 BnAb epitope.
ChemInform Abstract: An Efficient Approach to the Synthesis of 1,1‐Diphenyl‐1‐ silacycloheptan‐4‐one. (1995)

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.
High-resolution 13C NMR studies of cellulose and cellulose oligomers in ionic liquid solutions (2005)

High-resolution 13C NMR studies of cellulose and cellulose oligomers dissolved in the ionic liquid (IL) 1-butyl-3-methylimidazolium chloride ([C4mim]Cl) show that the beta-(1-->4)-linked glucose oligomers are disordered in this medium and have a conformational behavior which parallels the one observed in water, and thus, reveal that the polymer is disordered in IL solution as well.
Galangin (3,5,7-Trihydroxyflavone) Shields Human Keratinocytes from Ultraviolet B-Induced Oxidative Stress (2015)

Most skin damage caused by ultraviolet B (UVB) radiation is owing to the generation of reactive oxygen species. Phytochemicals can act as antioxidants against UVB-induced oxidative stress. This study investigated the protective effects of the flavone galangin against UVB-induced oxidative damage in human keratinocytes. Galangin efficiently scavenged free radicals and reduced UVB-induced damage to cellular macromolecules, such as DNA, lipids, and proteins. Furthermore, galangin rescued cells undergoing apoptosis induced by UVB radiation via recovering mitochondrial polarization and down-regulating apoptotic proteins. These results showed that galangin protects human keratinocytes against UVB radiation-induced cellular damage and apoptosis via its antioxidant effects.
A Look-Ahead Model Predictive Optimal Control Strategy of a Waste Heat Recovery-Organic Rankine Cycle for Automotive Application (2019)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;The Organic Rankine Cycle (ORC) has proven to be a promising technology for Waste Heat Recovery (WHR) systems in heavy duty diesel engine applications. However, due to the highly transient heat source, controlling the working fluid flow through the ORC system is a challenge for real time application. With advanced knowledge of the heat source dynamics, there is potential to enhance power optimization from the WHR system through predictive optimal control. This paper proposes a look-ahead control strategy to explore the potential of increased power recovery from a simulated WHR system. In the look-ahead control, the future vehicle speed is predicted utilizing road topography and V2V connectivity. The forecasted vehicle speed is utilized to predict the engine speed and torque, which facilitates estimation of the engine exhaust conditions used in the ORC control model. In the simulation study, a reference tracking controller is designed based on the Model Predictive Control (MPC) methodology. Two variants of Non-linear MPC (NMPC) are evaluated: an NMPC with look-ahead exhaust conditions and a baseline NMPC without knowledge of future exhaust conditions. An Extended Kalman Filter (EKF) is used to estimate unmeasurable states inside the ORC evaporators based on exhaust gas and working fluid temperatures. The estimator is augmented with a disturbance model for offset free MPC tracking. Simulation results show no particular improvement to working fluid temperature tracking at the evaporator outlet via the look-ahead strategy. However, the look-ahead control strategy does provide a substantial reduction in system control effort via dampening the heavily transient working fluid pump actuation, enhancing pump longevity, health, and reducing pump power consumption. Furthermore, a simulated sinusoidal exhaust condition shows that evaporator under consideration inherently helps attenuate the fluctuating exhaust conditions due to its thermal inertia.&lt;/div&gt;&lt;/div&gt;
Interleukin-1 restores the impaired cytotoxic T lymphocyte generation in beige mutant mouse. (1984)

Spleen cells from C57BL/6 beige mouse showed significantly lower cytotoxic T lymphocyte (CTL) generation in vitro against allogeneic target cells as compared with spleen cells from the wild type, whereas the heterozygous littermate showed a response similar to that of the wild type. In contrast, the responsiveness of beige spleen cells in the mixed lymphocyte reaction against allogeneic stimulator cells was in the normal range, suggesting that beige spleen cells recognize allogeneic stimulator cells to the same extent as spleen cells from normal mouse, resulting in a significant proliferation. The addition of interleukin 1 (IL-1)-containing supernatant from lipopolysaccharide-stimulated J774.1 cells to the culture of spleen cells from beige mouse stimulated with allogeneic cells restored the impaired CTL generation in a dose-dependent manner. The molecules responsible for restoration of the impaired CTL response co-migrated with IL-1 on gel filtration. The addition of purified interleukin 2(IL-2) also augmented the induction of CTL from beige spleen cells. However, the magnitude of augmentation by IL-2 was appreciably lower than that of augmentation by IL-1. These results suggest that the role of IL-1 in the induction of CTL is not only to provide a signal for activated amplifier T cells to release IL-2, but also to magnify otherwise low responsiveness of CTL-precursors and/or CTL-helpers. Moreover, intraperitoneal injection of IL-1 without allo-antigenic stimulation was able to restore the in vitro CTL responsitivity to allo-antigen but not the natural killer cell activity, indicating that IL-1 has a therapeutic potential in vivo for preferentially correcting impaired CTL generation associated with beige mutation.
SULFINIC ACIDS AND RELATED COMPOUNDS. 15. CONVENIENT METHODS FOR ESTERIFYING SENSITIVE SULFINIC ACID SALTS1 (1985)

Abstract In a study of conversions of sensitive sulfinate salts to esters, a trisulfide bissulfinate, [NaO2S(CH2)4S]2S (1), was esterified with trialkyloxonium fluorborates. This procedure (Method A) was better for ethylation than use of ROH-HC1/BF3 (C2H5)2O (Method B). but Method B was better for methylation. Disodium 3-sulfinopropanoate (7) was best dimethylated with CH3OH/BF3 · (C2H5)2O without HCl (Method C). Method B or C gave satisfactory results with sodium p-toluenesulfinate (3), but ROH/BF3 · (C2H5)2O with the free acid was better than either (Method D). p-Tolylsulfonyldiazomethane did not esterify p-toluenesulfinic acid: only the sulfonate was isolated (10, 15–20% yield).
Providing Instruction Based on Students’ Learning Style Preferences Does Not Improve Learning (2020)

Teachers commonly categorize students as visual or auditory learners. Despite a lack of empirical evidence, teaching to a student's perceived learning style remains common practice in education (Pashler et al., 2009). Having conducted an extensive review of the literature, Pashler et al. (2009) noted, "...very few studies have even used an experimental methodology capable of testing the validity of learning styles applied to education" (p. 105). Rogowsky et al. (2015) published the first study following the experimental design prescribed by Pashler et al. Focusing specifically on the visual/auditory dichotomy, Rogowsky et al. (2015) examined the extent to which learning style predicts comprehension and retention based on mode of instruction. Their study has been noted as "The only study located through the systematic literature search across six different databases and the screening of more than 1000 records that was totally aligned with Pashler's criteria" (Aslaksen and Loras, 2018, p. 3). The caveat to the 2015 study is that it was conducted with adult learners. The current study uses the same design and methodology as its predecessor, but on a school-aged population, making it the first of its kind. Consistent with earlier findings with adults, results failed to find a significant relationship between auditory or visual learning style preference and comprehension. Fifth graders with a visual learning style scored higher than those with an auditory learning style on listening and reading comprehension measures. As such, and counter to current educational beliefs and practices, teachers may actually be doing a disservice to students by using resources to determine their learning style and then tailoring the curriculum to match that learning style.
A Study of Hydraulic Fracturing Clean-up Efficiency in Unconventional Gas Reservoirs Using Statistical Approaches (2014)

Summary Hydraulic fracturing is widely used to improve well productivity especially in unconventional reservoirs. This costly operation, however, sometimes underperforms. One of the main reasons for this poor performance is poor clean-up efficiency of injected fracturing fluid (FF). In this work, a parametric study of FF clean-up efficiency of hydraulic fractured vertical wells was performed with 49152 simulations (in 12 sets) consisting of injection, soaking and production periods. Due to the large number of required simulations, that were conducted using a commercial reservoir simulator, a developed computer code was used to automatically read input data, run simulations and creates output data. In each set (consisting of 4096 runs), simultaneous impacts of 12 parameters (fracture permeability, matrix permeability and capillary pressure, end points and exponents of Corey gas and FF relative permeability curve in both matrix and fracture)were studied. To sample the variables domain and analyse results, two-level full factorial experimental design and linear surface model describing dependency of gas production loss (GPL), compared to 100% clean-up, to pertinent parameters at three production periods (10, 30 and 365 days) were considered and supported by the tornado charts of fitted equations, frequency of simulations with given GPL and FF saturation maps. Results indicate that generally parameters controlling FF mobility within fracture had greatest impact on GPL reduction. However in sets with very low matrix permeability especially when applied pressure drop during production is low, the effect of fluid mobility in the matrix on GPL is more pronounced, in other words, it is important how gas and FF flow within matrix rather than how fast fracture is cleaned. In tighter gas formations, generally more GPL and slower clean-up was observed. The effect of matrix capillary pressure on GPL reduction was more pronounced when drawdown was very low and/or soaking time was extended. This observation was more profound in tighter formations, i.e. for these formations, the effect of a change in drawdown and/or soaking time on matrix capillary pressure and GPL was more pronounced. These findings can be used to make better decisions on the performance and optimised design of hydraulic fracturing, which is a costly but widely used stimulation technique for unconventional low permeability gas reservoirs.
P-A9 Transformation of Darunavir into a long acting nanoformulated prodrug (2018)

Antiretroviral therapy (ART) has improved the quality and longevity of HIV-1 patients. Despite such advances limitations in drug bioavailability, resistance, and secondary toxicities abound affecting regimen adherence. We posit that such pharmaceutical limitations may be overcome by drug transformation into long acting slow effective release ART (LASER ART); a pharmaceutical approach that improves cell and tissue drug penetrance and depot formation leading to extended dosing intervals and improved antiretroviral responses. To this end, a hydrophobic bioreversible derivative prodrug of darunavir (DRV) was synthesized by medicinal chemistry. Modified DRV (MDRV) was synthesized by covalent linkage of a 14-carbon hydrophobic fatty acid moiety to the parent drug through a hemiaminal bond. A stable poloxamer 407 coated prodrug DRV nanoformulations (NMDRV) produced by high-pressure homogenization. Physicochemical properties of NMDRV and resultant particle cell uptake, antiretroviral efficacy pharmacokinetic and biodistribution studies were performed with subsequent comparisons made between prodrug and native drug formulations. Laboratory and pharmacokinetic tests were performed in monocyte derived macrophages (MDM) and BALB/c mice, respectively. NMDRV displayed up to 86 mg per 106 cells in 24 hours and retention up to 2 weeks compared to undetectable levels in the native DRV treatment. Effective plasma DRV concentration was detected in the prodrug arm through day 7 following a single dose of 40 mg/kg compared to undetectable levels in the parent drug treatment arm. The results highlight opportunities for LASER ART to achieve improved ART distribution and dissolution with limited toxicity for long-term HIV/AIDS treatments.
Three Cases of Idiopathic “Multiple-Parallel-line” Endotheliitis (2008)

This series of cases presented a unique type of idiopathic endotheliitis with the clinical appearance of multiple and parallel lines of keratic precipitates. The expression patterns of the keratic precipitates were distinct from those of previously reported linear endotheliitis.
Murine Tumor Models for Oncolytic Rhabdo-Virotherapy (2016)

The preclinical optimization and validation of novel treatments for cancer therapy requires the use of laboratory animals. Although in vitro experiments using tumor cell lines and ex vivo treatment of patient tumor samples provide a remarkable first-line tool for the initial study of tumoricidal potential, tumor-bearing animals remain the primary option to study delivery, efficacy, and safety of therapies in the context of a complete tumor microenvironment and functional immune system. In this review, we will describe the use of murine tumor models for oncolytic virotherapy using vesicular stomatitis virus. We will discuss studies using immunocompetent and immunodeficient models with respect to toxicity and therapeutic treatments, as well as the various techniques and tools available to study cancer therapy with Rhabdoviruses.
Transmit power optimization for multiantenna decode-and-forward relays with loopback self-interference from full-duplex operation (2011)

We develop transmit power control schemes for a regenerative full-duplex relay link. The focus is on MIMO scenarios with multiple antennas at all communicating nodes. As a new aspect for the optimization problem, we note that practical full-duplex relays are subject to unavoidable self-interference propagating from the transmit antenna array to the receive antenna array. Thus, residual interference remaining after mitigation needs to be explicitly modelled. Multiantenna techniques facilitate performance improvement by directing the interference to the least harmful spatial dimensions. As a result of transmit power optimization, the end-to-end transmission rate is maximized while, at the same time, the relay transmit power may be decreased. Finally, we compare full-duplex relaying to half-duplex relaying, i.e., we illustrate the benefit of choosing one over the other and the conditions where each one is preferred.
Antiphospholipid Antibodies are Associated with Low Levels of Complement C3 and C4 in Patients with Systemic Lupus Erythematosus (2016)

Complement activation and low complement levels are common in systemic lupus erythematosus (SLE). Antiphospholipid antibodies (aPL) are found in about 30-40% of patients with SLE. This study aimed to investigate the association between aPL and complement levels in patients with SLE. Serum samples were collected from 269 patients with SLE enrolled in the Norwegian Systemic Connective Tissue and Vasculitis Registry (NOSVAR) during 2003-2009, and from 353 controls. All samples were analysed for anti-β2 glycoprotein 1 (anti-β2GP1) and anticardiolipin antibodies (aCL), C-reactive protein (CRP) and complement components C3 and C4. Median CRP level was significantly higher in cases than in controls (2.06 versus 0.90 mg/l; P < 0.0001). No significant difference in CRP was found between SLE patients with or without aPL (2.09 versus 1.89; P = 0.665). Median C3 levels were similar in cases (1.03 g/l) and controls (1.00 g/l), whereas median C4 levels were 0.16 g/l in cases versus. 0.19 in controls (P < 0.0001). However, aPL-positive SLE patients had significantly lower median C3 levels (0.92 versus. 1.07 g/l; P = 0.001) and C4 levels (0.11 versus 0.16 g/l; P < 0.0001) compared to aPL-negative patients. Lower C3 and C4 values in aPL-positive SLE patients may reflect a higher consumption of C3 and C4 due to more pronounced complement activation in aPL-positive SLE patients compared to SLE patients without aPL.
Straight Hemming of Aluminum Sheet Panels Using the Electromagnetic Forming Technology: First Approach (2007)

Hemming is the last or one of the latest stage operations for the stamped parts. For this reason it has a critical importance on the performance and perceived quality of assembled vehicles. It is used to attach two sheet metal parts together or to improve appearance creating a smooth edge rather than a razor edge with burrs. However, designing the hemmed union is not always easy and is deeply influenced by the mechanical properties of the material of the bended part. Main problems for the automotive industry arise when bending aluminum alloys. Aluminum sheet is more difficult to hem due to its susceptibility to strain localization during the hemming process. This phenomenon produces cracking on the hemmed edge [1]. In order to avoid this problem and due to the limitations of conventional flanging and hemming technologies, the flange radii must be increased and a rope hem used (instead of the flat hem used with steels) when working with aluminum alloys. These changes on the design of the hem union give as a result a lower quality final product [2]. Dies and tools used for the hemming process are designed based on experience and on lengthy and costly die tryouts. Continuing with the development of new applications for the Electromagnetic Forming (EMF) technology, LABEIN-Tecnalia and Professor Glenn Daehn’s group from The Ohio State University carried out some first straight flat hemming experiments using the AA 6016 T4 aluminum alloy. The results obtained from these first trials are presented in this paper giving a first sight of the possibilities, advantages and disadvantages of using the Electromagnetic Forming technology for the hemming of aluminum sheet panels. Using a non-clouped FEM simulation method, the experimental results are compared to the ones obtained with the simulations. The future working line in developing this new application for the Electromagnetic Forming technology will be based on the results obtained by this study.
Analyzing Bipolar Carrier Transport Characteristics of Diarylamino-Substituted Heterocyclic Compounds in Organic Light-Emitting Diodes by Probing Electroluminescence Spectra (2008)

We analyzed bipolar carrier transport characteristics of diarylamino-substituted heterocyclic compounds (DAHCs) having benzene, pyridine, pyrimidine, or triazine electron-accepting core units and carbazole or β-naphthylamine as electron-donating substituents. The highest occupied molecular and lowest unoccupied molecular orbital levels, carrier injection, and transport characteristics were systematically controlled by changing combinations of the core and substituent units. By analyzing electroluminescence spectra as a probe in four kinds of organic light emitting diode (OLED) structures, we found that the carrier transport characteristics of DAHCs significantly change depending on device structure. We concluded that all DAHCs have bipolar carrier transport characteristics, that is, DAHCs intrinsically possess both hole and electron mobilities that are based on unique molecular structures having both electron-donating and -accepting units. We also demonstrated that carrier injection barriers between DAHCs and adjacent carrier transport layers virtually control the appearance of bipolar characteristics in OLEDs.
CODEMINE: Building a Software Development Data Analytics Platform at Microsoft (2013)

The scale and speed of today's software development efforts impose unprecedented constraints on the pace and quality of decisions made during planning, implementation, and postrelease maintenance and support for software. Decisions during the planning process include level of staffing and choosing a development model given the scope of a project and timelines. Tracking progress, course correcting, and identifying and mitigating risks are key in the development phase, as are monitoring aspects of and improving overall customer satisfaction in the maintenance and support phase. Availability of relevant data can greatly increase both the speed and likelihood of making a decision that leads to a successful software system. This article outlines the process Microsoft has gone through developing CODEMINE--a software development data analytics platform for collecting and analyzing engineering process data—its constraints, and pivotal organizational and technical choices.