gebhart/patrepeval huggingface dataset:
Abstract 4512: Doublecortin-like kinase 1 (DCLK1) correlates with Notch pathway signaling, controls metastatic characteristics in head and neck cancer (2018)

Abstract Despite advancements in the field, the 5 year survival rate of Head and Neck Squamous Cell Carcinoma (HNSCC) still hovers at 60%. In a quest for novel therapy targets for this disease, we performed an extensive and comprehensive quantitative phosphoproteomics scan on 10 HNSCC patient derived xenografts (PDXs) in order to find dysregulated phosphoproteins. DCLK1 is hyperphosphorylated but not over expressed in most of the HNSCC derived PDXs. DCLK1 has been shown to regulate epithelial-to-mesenchymal transition (EMT) as well as serving as a cancer stem cell marker in colon and pancreas cancer. DCLK1 is also associated with bad prognosis in colon, renal and oropharyngeal cancers. We performed a comprehensive transcriptome-based computational analysis on hundreds of HNSCC patients from TCGA and GEO databases. While our results confirm the role of DCLK1 in regulating EMT and focal adhesion kinase (FAK) mediated integrin signaling, we found that high DCLK1 expression also correlates with NOTCH pathway signaling signatures in HNSCC. We have selected 5 cell HNSCC cell lines (JHU-011, JHU-022, JHU-029, FaDu and Cal29) that express DCLK1, and inhibited DCLK1 with LRRK2-in1 inhibitor and siRNA. DCLK1 inhibition resulted in substantially decreased proliferation, migration, and colony formation. Furthermore, these effects paralleled downregulation NOTCH1 signaling in all cell lines tested. Overall, our results demonstrate the novel role of DCLK1 in regulating the NOTCH signaling network and suggest its potential as a therapeutic target in HNSCC. Citation Format: Esther Channah Broner, Tejaswini Subbannayya, Jayshree Advani, Alex Zhavoronkov, Artem Artemov, Ivan Ozerov, Ido Sloma, Harsha Gowda, David Sidransky, Eugene Izumchenko, Aditi Chatterjee. Doublecortin-like kinase 1 (DCLK1) correlates with Notch pathway signaling, controls metastatic characteristics in head and neck cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4512.
Toward a Checklist for Exchange and Interpretation of Data from a Toxicology Study (2007)

Data from toxicology and toxicogenomics studies are valuable, and can be combined for meta-analysis using public data repositories such as Chemical Effects in Biological Systems Knowledgebase, ArrayExpress, and Gene Expression Omnibus. In order to fully utilize the data for secondary analysis, it is necessary to have a description of the study and good annotation of the accompanying data. This study annotation permits sophisticated cross-study comparison and analysis, and allows data from comparable subjects to be identified and fully understood. The Minimal Information About a Microarray Experiment Standard was proposed to permit deposition and sharing of microarray data. We propose the first step toward an analogous standard for a toxicogenomics/toxicology study, by describing a checklist of information that best practices would suggest be included with the study data. When the information in this checklist is deposited together with the study data, the checklist information helps the public explore the study data in context of time, or identify data from similarly treated subjects, and also explore/identify potential sources of experimental variability. The proposed checklist summarizes useful information to include when sharing study data for publication, deposition into a database, or electronic exchange with collaborators. It is not a description of how to carry out an experiment, but a definition of how to describe an experiment. It is anticipated that once a toxicology checklist is accepted and put into use, then toxicology databases can be configured to require and output these fields, making it straightforward to annotate data for interpretation by others.
On the channel-length dependence of the hot-carrier degradation of n-channel MOSFETs (1989)

The channel-length dependence of lifetime plots is analyzed. It is shown that no unique tau *I/sub d/ versus I/sub sub//I/sub d/ relation can be obtained when threshold-voltage shifts are used for measuring the lifetime. In contrast, when using charge pumping as a monitor for the degradation, the lifetime plot for a given technology proves to be independent of the channel length.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Catalytic (transfer) deuterogenation in D2O as deuterium source with H2 and HCO2H as electron sources (2009)

Deuterium-labelled compounds were prepared by (transfer) deuterogenation of unsaturated compounds using H(2) or HCO(2)H in acidic D(2)O as deuterium source with almost quantitative yields and high deuterium contents under mild reaction conditions via heterolytic cleavage of H(2) (or decomposition of HCO(2)H) and rapid H(+)/D(+) exchange using iridium catalysts with 4,4'-dihydroxy-2,2'-bipyridine.
ChemInform Abstract: Extremely Fast Gas/Liquid Reactions in Flow Microreactors: Carboxylation of Short‐Lived Organolithiums. (2014)

Abstract Carboxylation of organolithium compounds bearing electrophilic functional groups such as nitro, cyano, and alkoxycarbonyl groups, with CO 2 to give carboxylic acids and active esters is accomplished in a flow microreactor system consisting of three micromixers and three microtube reactors.
Spin-orbit coupling as a source of long-range triplet proximity effect in superconductor-ferromagnet hybrid structures (2014)

We investigate the proximity effect in diffusive superconducting hybrid structures with a spin-orbit (SO) coupling. Our study is focused on the singlet-triplet conversion and the generation of long-range superconducting correlations in ferromagnetic elements. We derive the quasiclassical equations for the Green's functions including the SO coupling terms in form of a background SU(2) field. With the help of these equations, we first present an interesting complete analogy between the spin diffusion process in normal metals and the generation of the triplet components of the condensate in a diffusive superconducting structure in the presence of SO coupling. From this analogy it turns out naturally that the SO coupling is an additional source of the long-range triplet component (LRTC) besides the magnetic inhomogeneities studied in the past. This analogy opens a range of possibilities for the generation and manipulation of the triplet condensate in hybrid structures. In particular we demonstrate that a normal metal with SO coupling can be used as source of LRTC if attached to a superconductor-ferromagnet bilayer. We also demonstrate an explicit connection between an inhomogeneous exchange field and SO coupling mechanisms for the generation of the LRTC and establish the conditions for the appearance of the LRTC in different geometries. Our work gives a global description of the singlet-triplet conversion in hybrid structures in terms of generic spin fields and our results are particularly important for the understanding of the physics underlying spintronic devices with superconductors.
<title>Stray light characterization of optical systems</title> (1996)

A new stray light test facility developed by SODERN for space instruments characterization is described. The main purpose of this instrumentation is to measure the point source transmittance (PST) and non-uniformity for attenuations up to 10 degrees but the instrumentation design, capacities and performances have been sized to perform tests on a broad variety of instruments or sub- assemblies. The test and checking process to achieve a perfect instrument reliability will be discussed. The limiting factors of the bench performances, including cleanliness level, air, source and light trap scattering have been estimated and measured to determine the level of unwanted stray-light.
DISCRIMINATIVE-STIMULUS EFFECTS OF DOPAMINERGIC DRUGS (1998)

Behavioral Pharmacology Program'ADARC, McLean Hospital/Harvard Medical School, Belmont, Massachusetts, USA
Preliminary Convective-Radiative Heating Environments for a Neptune Aerocapture Mission (2004)

Convective and radiative heating environments have been computed for a three-dimensional ellipsled configuration which would perform an aerocapture maneuver at Neptune. This work was performed as part of a one-year Neptune aerocapture spacecraft systems study that also included analyses of trajectories, atmospheric modeling, aerodynamics, structural design, and other disciplines. Complementary heating analyses were conducted by separate teams using independent sets of aerothermodynamic modeling tools (i.e. Navier-Stokes and radiation transport codes). Environments were generated for a large 5.50 m length ellipsled and a small 2.88 m length ellipsled. Radiative heating was found to contribute up to 80% of the total heating rate at the ellipsled nose depending on the trajectory point. Good agreement between convective heating predictions from the two Navier-Stokes solvers was obtained. However, the radiation analysis revealed several uncertainties in the computational models employed in both sets of codes, as well as large differences between the predicted radiative heating rates.
Virtual Sensor Design of Particulate and Nitric Oxide Emissions in a DI Diesel Engine (2005)

&lt;div class="htmlview paragraph"&gt;As a physical description of the emissions of a specific engine is seldom possible, we present here a method to design an online dynamic estimator for PM and NOx based on data. The design method is based on a systematic search of function candidates performed using genetic programming after data have been pre-treated in an adequate fashion. While data and a simple data pretreatment prove enough for NOx, some basic physical understanding is necessary to preset the method and obtain the required precision in the case of PM. The method has been applied for raw emissions of a production DI diesel engine and shows a remarkable prediction performance. While the method is not able to replace the insight in the design process given by physical understanding, the authors expect substantial advantages in all those cases in which the prediction of overall behavior is required, as virtual sensors, and also expect that the suitable introduction of additional physical knowledge can strongly improve the results.&lt;/div&gt;
Oxide layer phase structure of MCrAIY coatings (1997)

During operation, stationary blades and vanes of gas turbines are subjected to high thermal and mechanical stresses and severe oxidation. This situation can only be controlled by a composite approach in which the base material provides the necessary mechanical properties and coatings provide protection against oxidation, corrosion and, in the case of thermal barrier coatings, a part of the heat flux. For a better understanding of the oxidation processes on standalone MCrAIY overlays as well as MCr AIY used as a bond coat, in situ X-ray diffraction measurements of the formation and composition of the oxide scale at high temperatures are presented. The phase changes during oxide scale formation are discussed. Data are presented for MCrAlY coatings with 12%AI and 3%Re at three different temperatures versus time. At 950, 1000, and 1050°C a three phase oxide layer of Cr 2 0 3 ‘ A1 2 0 3 , and NiCr 2 O 4 was detectable. Rhenium could not be found in the oxide layer at any of the three temperatures.
Improving Malicious URL Re-Evaluation Scheduling Through an Empirical Study of Malware Download Centers (2011)

The retrieval and analysis of malicious content is an essential task for security researchers. At the same time, the distrib- utors of malicious files deploy countermeasures to evade the scrutiny of security researchers. This paper investigates two techniques used by malware download centers: frequently updating the malicious payload, and blacklisting (i.e., re- fusing HTTP requests from researchers based on their IP). To this end, we sent HTTP requests to malware download centers over a period of four months. The requests are dis- tributed across two pools of IPs, one exhibiting high volume research behaviour and another exhibiting semi-random, low volume behaviour. We identify several distinct update pat- terns, including sites that do not update the binary at all, sites that update the binary for each new client but then repeatedly serve a specific binary to the same client, sites that periodically update the binary with periods ranging from one hour to 84 days, and server-side polymorphic sites, that deliver new binaries for each HTTP request. From this classification we identify several guidelines for crawlers that re-query malware download centers looking for binary updates. We propose a scheduling algorithm that incorpo- rates these guidelines, and perform a limited evaluation of the algorithm using the data we collected. We analyze our data for evidence of blacklisting and find strong evidence that a small minority of URLs blacklisted our high volume IPs, but for the majority of malicious URLs studied, there was no observable blacklisting response, despite issuing over over 1.5 million requests to 5001 different malware download centers.
Vertical profiles of environmental parameters measured from physical, optical and imaging sensors during station TARA_023 of the Tara Oceans expedition 2009-2013 (2014)

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set includes properties of seawater, particulate matter and dissolved matter from physical, optical and imaging sensors mounted on a vertical sampling system (Rosette) used during the 2009-2013 tara Oceans Expedition. It comprised 2 pairs of conductivity and temperature sensors (SEABIRD components), and a complete set of WEtLabs optical sensors, including chrorophyll and CDOM fluorometers, a 25 cm transmissiometer, and a one-wavelength backscatter meter. In addition, a SATLANTIC ISUS nitrate sensor and a Hydroptic Underwater Vision Profiler (UVP) were mounted on the rosette. In the Arctic Ocean and Arctic Seas (2013), a second oxygen sensor (SBE43) and a four frequency Aquascat acoustic profiler were added. The system was powered on specific Li-Ion batteries and data were self-recorded at 24HZ. Sensors have all been factory calibrated before, during and after the four year program. Oxygen was validated using climatologies (WOA09). Nitrate and Fluorescence data were adjusted with discrete measurements from Niskin bottles mounted on the Rosette, and optical darks were performed monthly on board. A total of 839 quality checked vertical profiles were made during the tara Oceans expedition 2009-2013.
In vitro-reassembled plant virus-like particles for loading of polyacids (2006)

The coat protein (CP) of certain plant viruses may reassemble into empty virus-like particles (VLPs) and these protein cages may serve as potential drug delivery platforms. In this paper, the production of novel VLPs from the Hibiscus chlorotic ringspot virus (HCRSV) is reported and the capacity to load foreign materials was characterized. VLPs were readily produced by destabilizing the HCRSV in 8 M urea or Tris buffer pH 8, in the absence of calcium ions, followed by removal of viral RNA by ultrahigh-speed centrifugation and the reassembly of the CP in sodium acetate buffer pH 5. The loading of foreign materials into the VLPs was dependent on electrostatic interactions. Anionic polyacids, such as polystyrenesulfonic acid and polyacrylic acid, were successfully loaded but neutrally charged dextran molecules were not. The molecular-mass threshold for the polyacid cargo was about 13 kDa, due to the poor retention of smaller molecules, which readily diffused through the holes between the S domains present on the surface of the VLPs. These holes precluded the entry of large molecules, but allowed smaller molecules to enter or exit. The polyacid-loaded VLPs had comparable size, morphology and surface-charge density to the native HCRSV, and the amount of polyacids loaded was comparable to the weight of the native genomic materials. The conditions applied to disassembly-reassembly of the virions did not change the structural conformation of the CP. HCRSV-derived VLPs may provide a promising nano-sized protein cage for delivery of anionic drug molecules.
Effect of pH on Toxicity of Copper to Scytalidium sp., a Copper-tolerant Fungus, and Some Other Fungi (1973)

SUMMARY: Scytalidium sp. grew in acidic media (pH 2·0 to 0·3) saturated with copper sulphate (approx. 1 M) but was sensitive to low concentrations of copper (4 × 10−5 M) near neutrality. Eleven other fungi differed in that they tolerated relatively high concentrations of copper near neutrality; nine tolerated high concentrations from pH 3·0 to 7·0, and six tolerated 4 × 10−3 M-copper sulphate at pH 2·0 to 7·0. Oxine was more toxic to Scytalidium sp. at neutrality than it was at an acid pH and in the presence of relatively large amounts of copper. EDTA had no appreciable effect on toxicity of copper. The fungus was relatively tolerant to chlorides of iron, cobalt and chromium at both neutral and acid pH.
IFAST: Implicit Function as Squashing Time for EEG Analysis* - Theory (2009)

This chapter presents the innovative use of special types of Artificial Neural Networks assembled in a novel methodology, capable of compressing the temporal sequence of EEG data into spatial invariants. The spatial content of the EEG voltage recorded from 19 channels along 60 seconds is extracted by a stepwise procedure using ANNs (SEMEION©). The core of the procedure is that the ANNs do not classify individuals by directly using the EEG data as an input. Rather, the data inputs for the classification are the weights of the connections within a non linear Auto-Associative ANN trained to generate the recorded EEG data. These connection weights represent an optimal model of the peculiar spatial features of the EEG patterns at scalp surface. The classification based on these weights is then performed by a supervised ANN. Half of the EEG database is used for the ANN training and the remaining EEG database serves for the automatic classification phase (testing). The best results distinguishing between mild Alzheimer patients and Mild Cognitive Impairment patient were equal to 92.33%. The comparative results obtained with the best method so far described in the literature, based on blind source separation and Wavelet pre-processing, were 80.43% ( p &lt; 0.001). These results confirmed the working hypothesis and represent the basis for research aimed at integrating spatial and temporal information content of the EEG.
Electrophoretic cell separation using microspheres (1980)

Methods of cell separation based on the electrokinetic properties of the cell membrane offer a degree of discrimination among cell populations which is not available with methods based on cell size or density alone. Studies aimed at extending red cell separations using microspheres to purification of lymphocytes.
Bias Temperature Instability (BTI) of High-Voltage Devices for Memory Periphery (2022)

This paper reports BTI trends in high-voltage transistors for memory periphery devices with SiO2/Poly-Si and High-K/Metal gate stacks. For PBTI, we present an extension to the typical power law kinetics that is related to the creation of interface states due to hot electrons transported through the gate oxide. This extension enables a good fit of accelerated test data and, thereby, lifetime extrapolation. We then explore EOT and gate stack trends in PBTI. For NBTI, we report gate stack, EOT, and thermal budget trends.
A Highly Efficient Catalyst for the Synthesis of Alternating Copolymers with Thieno[3,4-c]pyrrole-4,6-dione Units via Direct Arylation Polymerization (2014)

π-Conjugated polymers with a donor–acceptor (DA) combination of repeating units possess a narrow HOMO–LUMO gap, thus resulting in a high device performance in solar cells. This paper reports an improved catalytic system for the synthesis of DA polymers containing 5-(2-hexyldecyl)-5H-thieno[3,4-c]pyrrole-4,6-dione-1,3-diyl (TPD) group as the acceptor unit via palladium-catalyzed direct arylation polymerization. Although a related study has been reported (Angew. Chem. Int. Ed. 2012, 51, 2068), we attempted to reduce the catalyst loading because the palladium residue in π-conjugated polymers has been known to produce a detrimental effect on device performance. As a result, the amount of palladium could be reduced to 1/8 by using PdCl2(MeCN)2 and P(C6H4-o-OMe)3 (L1) as catalyst precursors. The polymerization smoothly proceeds at 100 °C in THF in the presence of pivalic acid and Cs2CO3 to afford TPD-based DA polymers 3a–3d containing the following donor units in almost quantitative yields: 4,4′-dioctyl-2,2′-bithiophene-5,5′-diyl (3a, Mn = 36800, Mw/Mn = 2.20), 4,8-bis(2-ethylhexyloxy)benzo[1,2-b:4,5-b′]dithiophene-2,6-diyl (3b, Mn = 31100, Mw/Mn = 2.44), 3,4-(2,2′-dioctylpropylenedioxy)thiophene-2,5-diyl (3c, Mn = 68200, Mw/Mn = 3.04), and 2,5-bis(2-ethylhexyloxy)-1,4-phenylene (3d, Mn = 65500, Mw/Mn = 2.21). A detailed analysis of the structure of 3a is reported.
SET-PP2A complex as a new therapeutic target in KMT2A (MLL) rearranged AML. (2023)

Abstract Background KMT2A -rearranged (KMT2A-R) is an aggressive and chemo-refractory acute leukemia which mostly affects children. Transcriptomics-based characterization and chemical interrogation identified kinases as key drivers of survival and drug resistance in KMT2A -R leukemia. In contrast, the contribution and regulation of phosphatases is unknown. We explored the role of SET, the endogenous inhibitor of SER/THR phosphatase PP2A in KMT2A -R leukemia. Material and Methods The expression of SET was analysed in a large acute myeloid leukemia (AML)- RNA-seq dataset and in primary KMT2A -R samples and aged matched-controls. Stable SET knockdown (KD) was established by RNA interference in three KMT2A wild-type (wt) and four KMT2A -R leukemic cell lines. Gene and protein expression were analysed by RT-qPCR, ChiP, IP and western blot. RNA-seq and phospho-proteomics were employed to evaluate the effect of the SET-PP2A inhibitor FTY720 on global protein phosphorylation and gene expression. The cellular impact of FTY720 was evaluated by analysing proliferation, cell cycle and apoptosis in leukemic cell lines and by colony formation assay in two patient-derived xenograft (PDX). Results SET mRNA was found expressed in blasts from KMT2A -R-patients and in leukemic stem cells. SET protein interacted with both KMT2A wt and fusion proteins. Knockdown of SET inhibited the transcription of KMT2A target genes HOXA9 and HOXA10 and abolished the self-renewal of KMT2A -R leukemic cells. Pharmacological inhibition of SET by FTY720 disrupted SET-PP2A interaction leading to cell cycle arrest, apoptosis and increased sensitivity to chemotherapy in KMT2A -R-leukemic models. Phospho-proteomic and western blot analyses revealed that FTY720 reduced the activity of kinases regulated by PP2A, including ERK1, GSK3b, ARKB, and led to degradation of MYC, supporting the hypothesis of a feedback loop among SET, PP2A and MYC. The RNA-seq indicated that FTY720 reduced the activity of signalling pathways implicated in gene transcription and it compromised the expression of several genes belonging to the KMT2A -R leukemia signature. Conclusions Taken together our results identify SET as a novel player in KMT2A -R leukemia and provide evidence that SET antagonism could serve as a novel strategy to treat this aggressive leukemia.