gebhart/patrepeval huggingface dataset:
Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA Sequencing. (2007)

We performed high-throughput cDNA sequencing in colorectal adenocarcinoma and matching normal colorectal epithelium. All six hundred three genes in the UCSC database that were expressed in colon cancers and contained open reading frames of 1000 nucleotides or less were selected for study (total basepairs/bp, 366,686). 304,350 of these 366,686 bp (83.0%) were amplified and sequenced successfully. Seventy-eight sequence variants present in germline (i.e. normal) as well as matching somatic (i.e. tumor) DNA were discovered, yielding a frequency of 1 variant per 3,902 bp. Fifty-one of these sequence variants were homozygous (26 synonymous, 25 non-synonymous), while 27 were heterozygous (11 synonymous, 16 non-synonymous). Cancer tissue contained only one sequence-altered allele of the gene ATP50, which was present heterozygously alongside the wild-type allele in matching normal epithelium. Despite this relatively large number of bp and genes sequenced, no somatic mutations unique to tumor were found. High-throughput cDNA sequencing is a practical approach for detecting novel sequence variations and alterations in human tumors, such as those of the colon.
Transformation of Follicular Lymphoma into CD30-Large Cell Lymphoma with Anaplastic Cytologic Features (1997)

The natural history of follicular lymphoma is to accrue large cells and become diffuse, resulting in progression/transformation to a higher-grade lymphoma. Histologic transformation occurs in approximately 60% of patients. Most often, follicular lymphomas transform into diffuse large cell lymphoma, but transformation to lymphomas classified using the Working Formulation as diffuse mixed, large cell immunoblastic, or small noncleaved cell also have been reported. Evidence of transformation may be found over time in sequential biopsy specimens, or may coexist in the same biopsy specimen. Here, we describe six cases of follicular lymphoma, large cell in five cases and mixed in one case, that transformed into a diffuse or sinusoidal CD30 antigen-positive large cell lymphoma with anaplastic cytologic features. Both the follicular and diffuse/sinusoidal components were of B-cell lineage, positive for the CD20 antigen and negative for the CD3 and CD43 antigens. The neoplastic cells expressed monotypic immunoglobulin light chain in five cases, three kappa and two lambda. BCL-2 protein was positive in four tumors, in both the follicular and diffuse/sinusoidal components in three cases, and only in the latter component in one case. Using the polymerase chain reaction (PCR), three of six cases had monoclonal immunoglobulin heavy chain gene rearrangements. The t(14;18) was not amplified in any case. Using reverse transcriptase (RT)-PCR, the t(2;5) was amplified in one of four tumors. This report highlights the heterogeneity of B-lineage anaplastic large cell lymphomas and indicates the need to consider antecedent follicular lymphoma in any B-cell lymphoma with anaplastic cytologic features.
LPV control of two dimensional wing flutter (2003)

We utilize a standard linear model for the control of a thin airfoil in subsonic flow. The airfoil is modeled by a 2D section with three degrees of freedom: plunge, pitch angle and flap angle. This is a 6D linear system with states: plunge, pitch angle, flap angle and their rates. The system has three inputs: the lift and moment generated by the air flowing over the wing and the torque applied at the flap hinge. This torque consists of two parts: the torque generated by the air flow and the external torque that can be applied by a motor. The goal is to use feedback to stabilize the airfoil at or above its flutter speed. We consider several standard control strategies. The simplest is to assume that all states are measurable and to design a stabilizing state feedback using the linear quadratic regulator theory. A more realistic approach is to assume that only some or all of the six physical states are measurable and to use dynamic state feedback based on the linear quadratic Gaussian approach.
Trehalose accumulation triggers autophagy during plant desiccation (2015)

Global climate change, increasingly erratic weather and a burgeoning global population are significant threats to the sustainability of future crop production. There is an urgent need for the development of robust measures that enable crops to withstand the uncertainty of climate change whilst still producing maximum yields. Resurrection plants possess the unique ability to withstand desiccation for prolonged periods, can be restored upon watering and represent great potential for the development of stress tolerant crops. Here, we describe the remarkable stress characteristics of Tripogon loliiformis, an uncharacterised resurrection grass and close relative of the economically important cereals, rice, sorghum, and maize. We show that T. loliiformis survives extreme environmental stress by implementing autophagy to prevent Programmed Cell Death. Notably, we identified a novel role for trehalose in the regulation of autophagy in T.loliiformis. Transcriptome, Gas Chromatography Mass Spectrometry, immunoblotting and confocal microscopy analyses directly linked the accumulation of trehalose with the onset of autophagy in dehydrating and desiccated T. loliiformis shoots. These results were supported in vitro with the observation of autophagosomes in trehalose treated T. loliiformis leaves; autophagosomes were not detected in untreated samples. Presumably, once induced, autophagy promotes desiccation tolerance in T.loliiformis , by removal of cellular toxins to suppress programmed cell death and the recycling of nutrients to delay the onset of senescence. These findings illustrate how resurrection plants manipulate sugar metabolism to promote desiccation tolerance and may provide candidate genes that are potentially useful for the development of stress tolerant crops.
Problems Modeling Web Sites and User Behavior (2006)

As the World Wide Web has grown in size and scope, so too has the demand for analysis tools that can help Web site providers determine how their sites are being used. Early analysis approaches focused primarily on accesses to Web documents as recorded in Web server logs. More recent techniques create a model of a site, and the natural modeling approach is to use a directed graph, where pages are denoted by nodes and links are modeled by edges. The process of creating the model and then analyzing the corresponding visitor traffic, however, is fraught with difficulties. The contribution of this paper is a catalog of problems gathered from extensive experience modeling Web sites to determine site structure and analyze user behavior
Control of Linear Dichroism in Metamaterial-Twisted Nematics Structure via Photo-Isomerization (2010)

Linear dichroism in metamaterial-twisted nematics structure of nano meta surface is controlled via photoisomerization process. Azo twisted nematic cell structure enables the switching on-off of meta-induced resonance by trans-cis-trans isomerization when irradiated by UV light.
Chromatographic Studies of Rat Kidney Lysozyme. (1958)

SummaryChromatography of rat kidney lysozyme with Amberlite XE-64 ion-exchange resin by direct and gradient elution procedures have been described. Three peaks of enzyme activity have been resolved by either procedure. Separate rechromatography of each peak by direct elution substantiated that none of the peaks was an artifact. The central peak contains the major portion of enzyme activity and after rechromatography the enzyme is spectrophotometrically free of cytochrome c. Cytochrome c appeared, after direct elution, as 4 peaks closely associated with the enzyme due to similar physical-chemical properties. Two peaks of reduced and oxidized cytochrome were found by gradient elution. Total purification of the specific enzyme activity was about 100-fold over the original supernatant.
Measurement of Serum Complement During Homograft Rejection in Man and Rat (1964)

In the rat, active homograft rejection of skin, whether first set, second set, or “white” does not alter the serum whole complement titer (CH50). During renal homograft rejection in man there is a small reduction in the CH50 titer, and a pronounced diminution in the titer of the second component of human complement (C'2hu), presumably reflecting in vivo complement fixation.
Access to phenolic fungal metabolites via the acid-catalysed Claisen rearrangement. The total synthesis of (±)-mellein, aurocitrin, and 5′,6′-dihydroaurocitrin (1984)

Regioselective trifluoroacetic acid catalysed rearrangement of allyl 5-allyloxy-2-hydroxybenzoate (2b) with concomitant cyclisation of the initial product permits the simple preparation of 3,4-dihydro-5,8-dihydroxy-3-methylisocoumarin (5). Hydrogenolysis of the non-hydrogen bonded hydroxy group yields (±)-mellein (7) whereas elaboration of the lactone moiety of compound (5) provides access to aurocitrin (8b) and its side chain analogues.
Optimal direct torque control for PMSM based on model predictive control (2011)

In this paper, we propose a novel direct torque control (DTC) system for permanent magnet synchronous motors (PMSM) based on model predictive control (MPC). The proposed method achieves a comparable torque ripple with lower inverter switching frequency than a conventional DTC.
Performance analysis for chipsets and systems (1999)

Plasma is a new tool for modeling the timing of chipsets and other system components. Modeling chipsets is in some ways more difficult than modeling processors: the interfaces are more complex and more numerous, the internal queues and buffers are larger, and the traces are much more complicated. We have used Plasma to create a timing model for a modern chipset. The resulting model is fast, flexible, and useful for both design and verification.
Macrocycles polyoxygénés à structure benzodioxinique. Synthèse et étude de la complexation du sodium et du potassium dans le methanol (1989)

The synthesis of two new series of polyoxygenated macrocyclic derivatives, 1 and 2, was realised. All these compounds have a 1,4-benzodioxinic moiety and are related to crown ethers, benzocrown ethers, and lariat ethers. The complexing properties of sodium and potassium ions were studied using potentiometry in methanol; results thus obtained are compared to data, previously reported in the literature, for classical polyoxygenated macrocyclic compounds. Keywords: polyoxygenated macrocycles, 1,4-benzodioxin, lariat ethers, sodium and potassium complexes, solvent methanol.
Design of tunable silicon metasurfaces with cross-polarization transmittance over 80% (2018)

We designed highly efficient, mechanically tunable metasurfaces based on an array of crystalline silicon nanoposts on stretchable substrates. The metasurface can continuously tune the wavefront of light by changing the lattice constant of the silicon nanoposts with a high transmission efficiency at all tuning ranges. Systematic numerical simulations were performed to determine the optimized structural parameters of the nanoposts, in which the cross-polarization transmittance was maximized. Transmission efficiency was maintained at over 80% with a maximum stretch ratio of ∼137% (2.9× flat zoom lens) and at over 75% with a maximum stretch ratio of ∼171% (1.9× flat zoom lens) in the tunable metasurface at λ = 680 nm. The simulation also showed that the tunable metasurface could be optimized at other wavelengths between 580 and 730 nm. We believe that the tunable metasurfaces will be useful for a variety of applications including information technology, biomedical sciences, integrated optics, optical communications, imaging, flat displays, or wearable consumer electronics.
Mucopolysaccharide Production By Fibroblasts Derived from Human Buffy-Coat Cultures in vitro (1964)

Grossfeld(l) has shown that fibroblasts from different tissues cultivated in vitro are able to produce acid mucopolysaccharides (AMPS) and release them into the medium. AMPS belong to the group of hyaluronic acid and chondroitin sulphates A and C, are highly polymerized, and give positive mucin clot and hyaluronidase tests(2). Since fibroblast-like cells are known to originate in cultures of buffy-coat and hemapoie-tic tissues(3,4), it seems of interest to study the AMPS production in human white blood cell cultures undergoing fibroblastic transformation. Materials and methods. Peripheral human blood buffycoat was obtained by venipuncture and centrifugation at 600 × g with 0.1 mg/ml of heparin (Liquemine Roche) for each 5 ml of blood and phytoagglutinine (Difco), 0.25 ml for each 10 ml of blood. The first 1 or 2 ml extracted from the vein was discarded to avoid contamination with tissue cells. Buffycoats from 10 ml of blood were explanted in Earle's flasks with a layer of isologous plasma and 5 ml of liquid medium containing yeast extract Eagle mediumlactalbumin hydrolysate peptone (5) and 5% chicken embryo extract. Turbidimetric tests of hyaluronidase according to Seastone and Kass(6) were performed as previously described(7) in samples of culture media taken every 4 days. The medium was centrifuged to eliminate cells and debris that might interfere with the turbidimetric tests. Incubated medium without explants was used as a blank. Determinations were also made on aliquots of homogenized cells before and after cultivation. The cells were homogenized in phosphate buffer pH 6.5 (0.1 M) with Potter Elvehjem homogenizer and centrifuged at 800 × g The supernatant was taken, for analysis. Hyaluronidase from Benger Lab. Lt. was used (Hyalase Benger). It was found that 500 U Benger was the optimum necessary to reduce turbidity to 50%. Standard curves were made with pure hyaluronic acid prepared at Prof. Karl hIeyerls Laboratory.
Assessment of T1rho relaxation times after reperfused myocardial infarction (2016)

Background T1r MRI is an emerging method for high spatial resolution tissue characterization of myocardial infarct (MI), but the evolution of T1r in the first month after reperfused MI is uncertain. We conducted a study of reperfused MI in pigs to serially monitor T1r relaxation times at baseline, 1 and 4 weeks post-MI and correlated these results with T2, native T1, and histological findings.
Energetics of heterometal substitution in  -Keggin [MO4Al12(OH)24(OH2)12]6/7/8+ ions (2014)

Aluminum hydroxide ions in the e-Keggin structure provide geochemical models for how structure affects reactivity, and consequently, how aqueous ions evolve to bulk precipitates. Here we report a systematic comparison of heterometal substitution into the MAl12 e-Keggin structure, where M = Ga<sup>III</sup>, Al<sup>III</sup>, or Ge<sup>IV</sup>. We use direct solution calorimetric techniques to compare the energetics of these substituted structures and complement these measurements with density functional theory (DFT) calculations to further examine this structure as a host to alternative heterometals. The measured enthalpy of solution (DHsoln) at 28 °C in 5 N HCl for the selenate salts of GaAl<sub>12</sub> 7+ and AlAl<sub>12</sub><sup>7+</sup>, was measured as -869.71 ± 5.18 and -958.04 ± 2.79 kJ/mol, respectively. The enthalpies of formation from the elements, DH°f,el, for the selenate salts of GaAl<sub>12</sub><sup>7+</sup> and AlAl<sub>12</sub>7+, are -23 075.02 ± 61.68 and -23 334.18 ± 60.38 kJ/mol, respectively, supplanting previous values. We compare structural relationships to both experimental and calculated energies to identify the driving forces that control these substitutions and stability, and establish that tetrahedral M-O bond lengths are closely related to the strain and stability of the structure. Furthermore, we show that substitution depends on the size and valence of the heterometal through energetics, and we extend our thermodynamic and structural relationships to other not yet synthesized MAl<sub>12</sub> clusters (M = Si<sup>IV</sup>, Fe<sup>III</sup>, Be<sup>II</sup>, Mg<sup>II</sup>, or Zn<sup>II</sup>).
Iterative Soft-Input Soft-Output Decoding with Ordered Reliability Bits GRAND (2022)

Guessing Random Additive Noise Decoding (GRAND) is a universal decoding algorithm that can be used to perform maximum likelihood decoding. It attempts to find the errors introduced by the channel by generating a sequence of possible error vectors in order of likelihood of occurrence and applying them to the received vector. Ordered reliability bits GRAND (ORBGRAND) integrates soft information received from the channel to refine the error vector sequence. In this work, ORBGRAND is modified to produce a soft output, to enable its use as an iterative soft-input soft-output (SISO) decoder. Three techniques specific to iterative GRAND-based decoding are then proposed to improve the error-correction performance and decrease computational complexity and latency. Using the OFEC code as a case study, the proposed techniques are evaluated, yielding substantial performance gain and astounding complexity reduction of 48% to 85% with respect to the baseline SISO ORBGRAND.
Prudent Practices for Designing Malware Experiments: Status Quo and Outlook (2012)

Malware researchers rely on the observation of malicious code in execution to collect datasets for a wide array of experiments, including generation of detection models, study of longitudinal behavior, and validation of prior research. For such research to reflect prudent science, the work needs to address a number of concerns relating to the correct and representative use of the datasets, presentation of methodology in a fashion sufficiently transparent to enable reproducibility, and due consideration of the need not to harm others. In this paper we study the methodological rigor and prudence in 36 academic publications from 2006 -- 2011 that rely on malware execution. 40% of these papers appeared in the 6 highest-ranked academic security conferences. We find frequent shortcomings, including problematic assumptions regarding the use of execution-driven datasets (25% of the papers), absence of description of security precautions taken during experiments (71% of the articles), and oftentimes insufficient description of the experimental setup. Deficiencies occur in top-tier venues and elsewhere alike, highlighting a need for the community to improve its handling of malware datasets. In the hope of aiding authors, reviewers, and readers, we frame guidelines regarding transparency, realism, correctness, and safety for collecting and using malware datasets.
Lipid and fatty acid composition of the mantle and digestive gland of four Southern Ocean squid species: implications for food-web studies (2002)

Lipid content, lipid class and fatty acid composition of four Southern Ocean cephalopod species – the myopsid Sepioteuthis australis and three oegopsids, Gonatus antarcticus , Moroteuthis robsoni and Todarodes spp. – were analysed. The lipid content of the digestive gland was consistently greater than that of the mantle, and was an order of magnitude greater in oegopsid species. The lipid class and fatty acid composition of the mantle and digestive gland also differed markedly in each species. Digestive gland lipid is likely to be of dietary origin, and large amounts of lipid in the digestive gland of oegopsids may accumulate over time. Thus the digestive gland is a rich source of fatty acid dietary tracers and may provide a history of dietary intake. However, the absolute amount of dietary lipid in the digestive gland of oegopsid species exceeds the absolute lipid content of mantle tissue. Therefore the overall lipid “signature” of an oegopsid may more closely resemble its prey species rather than its mantle tissue. When lipid techniques are used in dietary analysis of teuthophagous predators, squid may not be represented by a unique signature in analyses and their importance in the diets of predators may be underestimated.
Full Field Nondestructive Techniques For Imaging Composite Fiber Volume Fraction (1996)

Quantitative comparison of different thermal models.36 2 Material properties used for thermal calculations.37 3 Material property values used in the ultrasound model 49 4 Calculated mean square difference values for FVF.60 5 Calculated mean square difference values for porosity and thermal/ultrasound FVF.61 v 4.22 Comparison of thermal/ultrasonic measured FVF for 65B.83 viii 4.23 Comparison of thermal/ultrasonic measured FVF for 70A.84 4.24 Comparison of thermal/ultrasonic measured FVF for 70A2.85 5.1 Comparison of techniques for measuring FVF.88 ix
Severe shot peening of AISI 321 with 1 000 % and 1 300 % coverages: A comparative study on the surface nanocrystallization, phase transformation, sub-surface microcracks, and microhardness (2018)

Abstract In this study, AISI 321 austenitic stainless steel samples were surface treated using severe shot peening (SSP) with 1 000 % and 1 300 % coverages. Microstructural features including the grain size, phase transformation, and formation of sub-surface microcracks were investigated at the rough top surface and about 40 μm depth (top surface after grinding and removal of initial rough surface layer created by SSP). In addition, microhardness variations were thoroughly analyzed in-depth. Experimental results demonstrated that for both 1 000 % and 1 300 % coverages, the microstructures of top surface and 40 μm depth are respectively composed of equiaxed nano-grains and lamella-shaped cells; however, enhanced imparted strain in the case of 1 300 % coverage leads to the formation of considerable amounts of strain-induced martensite (α′) phase in the surface layers and consequently, due to strength increase and lack of deformability, some microcracks are created in the sub-surface layers (up to 20 μm depth).
Use of PCR-restriction fragment length polymorphism of inlA for rapid screening of Listeria monocytogenes strains deficient in the ability to invade Caco-2 cells (2004)

International audience
Fast Converging Minimum Probability of Error Neural Network Receivers for DS-CDMA Communications (2004)

We consider a multilayer perceptron neural network (NN) receiver architecture for the recovery of the information bits of a direct-sequence code-division-multiple-access (DS-CDMA) user. We develop a fast converging adaptive training algorithm that minimizes the bit-error rate (BER) at the output of the receiver. The adaptive algorithm has three key features: i) it incorporates the BER, i.e., the ultimate performance evaluation measure, directly into the learning process, ii) it utilizes constraints that are derived from the properties of the optimum single-user decision boundary for additive white Gaussian noise (AWGN) multiple-access channels, and iii) it embeds importance sampling (IS) principles directly into the receiver optimization process. Simulation studies illustrate the BER performance of the proposed scheme.
Elastic constants, viscosity and response time in nematic liquid crystals doped with ferroelectric nanoparticles (2014)

We report on the role of ferroelectricity on the physical and electro-optic parameters in suspensions of nanoparticles in cyclohexane based, fluorinated nematic liquid crystals. The dielectric and elastic constants, response time, and viscosity of the suspensions were analyzed experimentally and compared with the undoped samples. Our study shows a decrease in the splay elastic constant and an increase in the dielectric constants, together with an increase in the average rotational viscosity.
The role of amino acid profiles in diabetes risk assessment (2016)

Plasma-free amino acid profiles have potential as biomarkers for both assessing diabetes risk and monitoring the effects of strategies designed to lower that risk. In addition, the methodology for measuring amino acids has been refined, with the goal of routine clinical application.
ChemInform Abstract: Lanthanides in Organic Synthesis. Part 4. Reduction of αβ‐Epoxy Ketones with Samarium Diiodide. A Route to Chiral, Nonracemic Aldols. (1987)

Abstract The αβ‐epoxyketones (I), (IV) and (VI) are reduced with freshly prepared samarium diiodide (II) to give the β‐hydroxy ketones (III), (V) and (VII) respectively.