gebhart/patrepeval huggingface dataset:
Abstract 3497: A novel method of active paraffin removal and efficient extraction of NGS-quality DNA from FFPE tissues (2014)

Abstract Formalin Fixation and Paraffin Embedding (FFPE) of tissues remains a routine histology practice by pathologists due to the quality and stability of structural information preserved. The method was conceived primarily to facilitate histological analysis rather than molecular approaches increasingly common in clinical oncology settings such as targeted sequencing and whole genome sequencing. Chemical crosslinks and the paraffin matrix of FFPE-preserved samples present significant challenges for the robust extraction of nucleic acids. To address this and provide reliable access to clinical samples, we present a novel method for consistent and reproducible extraction and purification of DNA from FFPE samples using Covaris Adaptive Focused Acoustics (AFA). Use of focused ultrasonic energy to emulsify embedding paraffin. The method is predicated on the use of highly controlled acoustic energy to efficiently remove paraffin from FFPE cores, sections, and slides enabling efficient tissue rehydration, tissue digestion, crosslink reversal, and nucleic acid release. In addition, this critical step is carried out without the use of organic solvents or mineral oils. We present quantitative fluorescent microscopy illustrating the efficiency of paraffin removal from tissues utilizing this novel approach. Better data quality as a consequence of improved DNA yield and quality. Having established reproducible sample processing we sought to explore benefits in downstream applications and analyses. Results, utilizing replicates of several different tissue types, indicate high dsDNA yields, controllable fragment sizes and excellent DNA quality as indicated by commercial qPCR based kits designed to assess DNA quality. Improved sequencing coverage as a consequence of improved DNA yield and quality. The quality of the extracted DNA, as a function of consistent sequence coverage across the entire genome, was then confirmed using whole genome sequencing of the FFPE samples as compared to sequence data obtained from matched fresh frozen tissue. Our data also indicate that the high quality controllable DNA extraction allows for preparation of large insert (1-6kb) libraries previously considered very difficult from FFPE stabilized tissues. Method suitable for automation. The simple workflow allows for the parallel processing of up to 8 FFPE samples in a 96 well plate format. We present data showing highly reproducible results while processing a large number of FFPE samples. Citation Format: Hamid Khoja, Edwin Rudd, Austin Purdy, James Han, Srikanth Kakumanu, Adrian Palmer, Guillaume Durin, Jim Laugharn. A novel method of active paraffin removal and efficient extraction of NGS-quality DNA from FFPE tissues. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3497. doi:10.1158/1538-7445.AM2014-3497
Searching for Extraterrestrial Intelligence with the Square Kilometre Array (2015)

The vast collecting area of the Square Kilometre Array (SKA), harnessed by sensitive receivers, flexible digital electronics and increased computational capacity, could permit the most sensitive and exhaustive search for technologically-produced radio emission from advanced extraterrestrial intelligence (SETI) ever performed. For example, SKA1-MID will be capable of detecting a source roughly analogous to terrestrial high-power radars (e.g. air route surveillance or ballistic missile warning radars, EIRP 10 17 erg sec -1 ) at 10 pc in less than 15 minutes, and with a modest four beam SETI observing system could, in one minute, search every star in the primary beam out to 100 pc for radio emission comparable to that emitted by the Arecibo Planetary Radar (EIRP 2 x 10 20 erg sec -1 ) . The flexibility of the signal detection systems used for SETI searches with the SKA will allow new algorithms to be employed that will provide sensitivity to a much wider variety of signal types than previously searched for.
Spirosoma fluviale sp. nov., isolated from river water (2015)

A bacterial strain, designated MSd3T, was isolated from a freshwater sample collected from the Hosoda River in Japan. The cells of strain MSd3T were Gram-stain-negative, non-spore-forming, aerobic, non-motile, curved rods forming rings, coils and undulating filaments. The 16S rRNA gene sequence of strain MSd3T showed closest similarity to that of Spirosoma linguale DSM 74T (97.6 % similarity) and similarity to other members of the genus Spirosoma ranged from 90.3 to 95.9 %. Strain MSd3T contained menaquinone 7 as the sole respiratory quinone. The major cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C16 : 1ω5c. The polar lipids were phosphatidylethanolamine, three unidentified aminophospholipids and three unidentified polar lipids. The DNA G+C content was 53.3 mol%. The DNA-DNA relatedness between strain MSd3T and S. linguale DSM 74T was 19 % or 25 % (reciprocal value). From the chemotaxonomic and physiological data and the levels of DNA-DNA relatedness, strain MSd3T should be classified as the representative of a novel species of the genus Spirosoma, for which the name Spirosoma fluviale sp. nov. (type strain MSd3T = JCM 30659T = DSM 29961T) is proposed.
Subspace based approaches for Wiener system identification (2005)

We consider the problem of Wiener system identification in this note. A Wiener system consists of a linear time invariant block followed by a memoryless nonlinearity. By modeling the inverse of the memoryless nonlinearity as a linear combination of known nonlinear basis functions, we develop two subspace based approaches, namely an alternating projection algorithm and a minimum norm method, to solve for the Wiener system parameters. Based on computer simulations, the algorithms are shown to be robust in the presence of modeling error and noise.
Circulating anti-immunoglobulin antibodies in recent-onset type I diabetic patients (1988)

Human sera from 51 recent-onset insulin-dependent (type I) diabetic patients and 47 unrelated control subjects were screened for the possible presence of circulating factors reacting with several anti-pancreatic islet monoclonal antibodies (MoAb.ISL) in solid-phase radioimmunoassay methods (the original goal being the detection of anti-idiotypic islet cell antibodies and/or specific islet cell antigen-bearing immune complexes). MoAbs from the parental myeloma cell line and purified immunoglobulins (Igs) from different animal species were controls. Type I diabetic sera showed significantly increased binding to MoAb.ISL-coated wells compared with normal subjects (P less than .001). However, the same sera also tended to show a higher binding to the control (non-islet-related) MoAb. Sera from type I diabetic patients also reacted with horse, bovine, pig, rabbit, and goat IgG. Displacement of the binding has been obtained by F(ab')2 and/or Fc fragments of IgG. Evidence has been obtained regarding a similar reaction with human IgM. All the sera were negative when tested for rheumatoid factor by nephelometry. The circulating antibodies described have been proven to be different from islet cell autoantibodies. An anti-Ig antibody is thus present in the sera of recent-onset diabetic patients and represents an additional immunological phenomenon with possible physiopathological and clinical significance.
Solid sorption gas-fired heat pump. (2003)

A solid sorption gas-fired heat pump was designed and developed for residential space heating and cooling applications. The solid sorption technology uses natural gas as the energy source for compressing and circulating the refrigerant in the air-conditioning system. The system adopts a thermal compressor, composed of two cylinders (beds) filled with carbon particles, and employs ammonia as a refrigerant.
Simulation and measurement results of 150 GHz integrated silicon IMPATT diodes (2003)

The integration of IMPATT diodes and their housing in a single technology process is discussed in this paper. The integrated device is designed to improve reliability and reproducibility compared to conventional beam-lead diodes with quartz ring housing. In a single step, the diode with its housing is bonded onto a diamond heat sink. The device can be employed both in a waveguide resonator and in a planar oscillator circuit. Results presented here are obtained in a rectangular, reduced height waveguide resonator. RF-output power levels of more than 100 mW at 135 GHz and 45 mW at 150 GHz are reported.
Estimation of Parent-Offspring Correlation (1990)

When families have different numbers of offspring, Srivastava (1984) provided an easily computable estimator as an alternative to the maximum likelihood estimator of parent-offspring correlation. Some properties of this estimator are discussed vis-à-vis with those of ensemble and pairwise estimators. Further, we derive the small sample distribution of Srivastava's estimator under the assumption of null parent-offspring correlation. In the process, we demonstrate that a certain function of the classical sib-mean estimator has Student's t distribution despite differing sib-ship sizes.
Compact laser module with a high-speed liquid crystal attenuator for see-through display applications (2013)

Many kinds of head mount displays (HMDs) and head up displays (HUDs) have been appeared on the HMD / HUD early adaptor market. Many of them have become equipped with see-through capability and require dimming capability in response to ambient environmental conditions. We fabricated a high-speed liquid crystal (LC) variable attenuator using radially arranged electrodes and evaluated its basic characteristics.
An Evaluation of Bulk Ri-Based Surface Layer Flux Formulas for Stable and Very Stable Conditions with Intermittent Turbulence (2003)

High-rate near-surface overnight atmospheric data taken during the Cooperative Atmosphere–Surface Exchange Study-1999 (CASES-99) is used to quantify the representativeness of surface layer formulations under statically stable conditions. Combined with weak wind shear, such conditions generate large dynamic stability (Ri > 1.0), intermittency, and nonstationarity, which violate the underlying assumptions of surface layer theory. Still, such parameterizations are applied in atmospheric numerical models from large-eddy to global circulation. To investigate two formulas, their parameterized sensible heat flux and friction velocity (u∗) values are compared, when driven by CASES-99 measurements, to CASES-99 measurements of the same from various heights. Significant inaccuracies in the magnitude and sign of flux are found with 1) a frequent, large underprediction of heat flux for Rib > ∼1.0, 2) an overprediction of negative sensible heat flux and u∗ for ∼0.2 < Rib < ∼0.8, 3) a systematic underprediction of u∗ for Rib > 1.0 for one of the schemes tested, and 4) a misrepresentation of natural heat and u∗ intermittency by both schemes for Ri > ∼1.0. Failures of the “constant flux assumption” for a given height are proposed as a partial source for the errors. Using experimental data, a surface layer of O[1–10] m is found during dynamically stable conditions. Rather than suggest a revised algebraic fit to the observations, an alternate approach to surface layer parameterization is proposed.
A study on the automation of scanner matching (2013)

Scanner matching based on CD or patterning contours has been demonstrated in past works. All of these published works require extensive wafer metrology. In contrast, this work extends a previously proposed optical pattern matching method that requires little metrology by adding the component requirements and the procedure for creating an automation flow. In a test case, we matched an ASML XT:1900i using a DOE to an ASML NXT:1950i scanner using FlexRay. The matching was conducted on a 4x nm process test layer as a development vehicle for the 2x nm product nodes. The paper summarizes the before and after matching data and analysis, with future opportunities for improvements suggested.
Peak Caspase‐1 p20 Levels During Acute Myocardial Infarction Correlate with Pre‐Existing Hypertension, Age and Post‐Infarction Cardiac Dysfunction (2017)

Background Increased inflammation contributes to the development of myocardial infarction (MI) and adversely impacts infarct healing. Caspase‐1 is an end effector of inflammasome activation and is an important mediator of systemic inflammation. Caspase‐1 is cleaved to produce a 20 kDa (p20) peptide upon activation. Activated Caspase‐1 activates downstream cytokines IL‐1β and IL‐18. Previous work demonstrated that the p20 is elevated in patient serum during and after acute MI. Objective The aim of this study was to further elucidate the relationship of Caspase‐1 p20 and risk factors for MI. Between 12/10/2007 and 3/28/2016, 170 eligible patients with acute MI were enrolled that had complete information on p20 levels. Method Using a solid phase enzyme‐linked immunosorbent assay, the 20 kDa peptide was detected in serum during ST elevation (STEMI) and non‐ST elevation (NSTEMI) MI as well as after MI. Cardiac function post‐MI was evaluated via standard‐of‐care echocardiography. Results There is a positive correlation between age and peak p20 level during acute MI (P=0.01, linear regression, n=170). In STEMI but not in NSTEMI subjects, pre‐existing hypertension (HTN) was associated with a 50.3% higher average circulating peak p20 level during acute MI than those without HTN (P=0.0056, Wilcoxon, n=31 for both groups‐those with HTN and without HTN), suggesting a greater degree of inflammasome activation in HTN patients during STEMI. In these STEMI subjects, the existence of diabetes mellitus or smoking was not associated with a higher peak p20 level during acute MI. There is a trend for all acute MI patients to have a reduced post‐MI cardiac function as quantified by LV fractional shortening in echocardiography (P=0.05, Spearman correlation, r=−0.35, n=31). Conclusion Older subjects had more elevated peak p20 levels during acute MI, consistent with the concept of a larger inflammasome response to MI as age increases. Inflammasome activation is more pronounced in HTN patients during STEMI, implying a greater degree of inflammatory response in the presence of HTN. A greater extent of inflammasome activation during STEMI may be associated with a worse LV function subsequently. Support or Funding Information The study is supported by the Pat and Jim Calhoun Cardiology Endowment Fund.
Influence of injection gate definition on the flow‐front approximation in numerical simulations of mold‐filling processes (2003)

Abstract Flow through porous media has been used to model resin impregnation in composites manufacturing processes such as resin transfer molding. Many numerical schemes have been used to explore the efficiency and accuracy in description of the movement of the liquid front when it is introduced through injection gates into a mold containing stationary and compacted fibrous porous media. In all numerical schemes, injection gates are modelled with a single node. Mathematically, a single node definition for a finite radius injection gate imparts a singularity. In this paper, an approach to avoid this singularity by modelling the injection gate with more than one node is presented. An analytical solution relating the fill time to the injection gate radius is developed for a constant pressure injection from a spherical injection gate into an isotropic media. A new parameter ‘mesh density level’, defined as the ratio of the injection radius to the element size, is used to investigate the accuracy and the convergence of the numerical results. It is shown that the numerical results converge when the mesh density level is increased. The accuracy of the results depends on the ratio of the flow‐front radius to the injection gate radius as well as on the mesh density level. In many situations, a spherical injection gate may not represent the correct physics and model simplification may be necessary. The impact of such simplifications is also quantified. The systematic analysis presented in this paper should prove useful to the modeller in taking the decision whether to select the proper, geometric definition for the injection gate to obtain accurate results or to define the injection gate using a single node and be aware of the errors introduced due to the singularity. Copyright © 2003 John Wiley & Sons, Ltd.
Les variations climatiques récentes (1951)

Nicod Jean. Les variations climatiques recentes. In: L'information geographique, volume 15, n°4, 1951. pp. 156-157.
Geospace Environment Modeling Program (1992)

The geospace environment encompasses the highest and largest of the four physical geospheres—lithosphere, hydrosphere, atmosphere, and magnetosphere. Despite its size, its far‐reaching structures interconnect and move together in a choreography of organized dynamics, whose complexity is reflected in the intricate movements of the northern lights. The vastness and inaccessibility of geospace, encompassing the plasma environment of the magnetosphere/ionosphere system, and the invisibility of its structures pose great challenges to scientists who want to study its dynamics by obtaining, in effect, video tapes of its globally organized motions. A key component of their strategy is the ability to see nearly all of geospace imaged onto the top of the atmosphere. The geomagnetic field threads the volume of geospace and transmits action, TV‐like, from the magnetospheric stage down its lines of force onto the atmospheric screen.
Seasonal fluctuations in ascospore concentrations of Didymella applanata in relation to raspberry spur blight incidence (1975)

SUMMARY Ascospores of Didymella applanata were released in rain and dew throughout the summer, the highest concentrations occurring in May when new raspberry canes were emerging. Infections on new canes did not develop until later in the season, when ascospore concentrations were low although pycnospores were present. Lesions first appeared near the base of the green canes just below the point of attachment of the petioles; they were not associated with obvious leaf, petiole or bud infections. Once maturation of the canes occurred, further infection was prevented.
Imidazolinone Herbicide Systems for Peanut (<i>Arachis hypogaea</i> L.) (1994)

Abstract Field studies conducted in 1990 and 1991 at five locations in Georgia and one location in Virginia in 1991 evaluated imazethapyr [2-[4,5-dihydro-4-methyl-4-(l-methylethyl)-5-oxo-1H-imidazol-2-yl]-5-ethyl-3-pyridinecarboxylic acid] and AC 263,222 [(±)-2[4,5-dihydro-4-methyl-4-(l-methylethyl)-5-oxo-1H-imidazol-2-yl]-5-methyl-3-pyridinecarboxylic acid] for weed control, peanut tolerance, and yield. Imazethapyr and AC 263,222 applied early postemergence (EPOST) controlled smallflower morningglory [Jacquemontia tamnifolia (L.) Griseb], Ipomoea morningglory species, prickly sida (Sida spinosa L.), and coffee senna (Cassia occidentalis L.) greater than 90%. Imazethapyr did not control Florida beggarweed [Desmodium tortuosum (SW.) DC.] or sicklepod (Cassia obtusifolia L.) adequately, with control generally less than 40%. AC 263,222 controlled Florida beggarweed greater than 92% when applied EPOST and from 54 to 100% when applied postemergence (POST). Imazethapyr applied preplant incorporated (PPI) controlled bristly starbur (Acanthospermum hispidium DC.) 89% and imazethapyr and AC 263,222 applied EPOST controlled at least 96%. Imazethapyr controlled yellow nutsedge (Cyperus esculentus L.) 83% when applied PPI and 93% as an EPOST application. AC 263,222 controlled yellow nutsedge at least 90%. Peanut yields were higher with AC 263,222 than with imazethapyr. Imazethapyr systems that included alachlor (2-chloro-N-(2,6-diethylphenyl)-N-(methoxymethyl)acetamide), lactofen ([(±)2-ethoxy-l-methyl-2-oxoethyl 5-[2-chloro-4-(trifluoromethyl)phenoxy]-2-nitrobenzoate] + 2,4-DB [4-(2,4-dichlorophenoxy)butanoic acid], paraquat [1,1′-dimethyl-4,4′-bipyridinium ion] + 2,4-DB, pyridate [O-(6-chloro-3-phenyl-4-pyridazinyl)-S-octyl carbonothioate] + 2,4-DB, metolachlor [2-chloro-N-(2-ethyl-6-methylphenyl)-N-(2-methoxy-l-methylethyl)acetamide], or 2,4-DB provided yields equivalent to AC 263,222.
Caracterisation des fonctions distinctes generees par les recepteurs tnf-r55 et tnf-r75 du facteur tnf (tumor necrosis factor) (1994)

Le facteur tnf alpha (tumor necrosis factor-alpha) est une cytokine pluripotente qui stimule les cellules a l'aide de deux recepteurs membranaires distincts, tnf-r55 et tnf-r75. Cette these a eu pour objectif de definir le role de chaque recepteur du tnf, en particulier sur les cellules endotheliales et les fibroblastes. L'activation des cellules endotheliales et des fibroblastes par le tnf alpha, est essentiellement orchestree par le recepteur tnf-r55. Ce recepteur controle l'induction des proprietes adhesives de ces cellules a l'egard des leucocytes en stimulant l'expression de molecules d'adhesion a leur surface; il stimule leur activite secretoire, influence leur vitesse de proliferation et declenche l'activation du facteur nucleaire nf-kappab. A l'inverse, bien que demontree, la fonction du tnf-r75 s'integre mal au sein d'un processus biologique. Cependant, plusieurs resultats suggerent une collaboration entre les recepteurs tnf-r55 et tnf-r75, qu'elle soit de type ligand passing a la surface des cellules ou intracellulaire au niveau de la transduction du signal. L'activation du recepteur tnf-r75 peut egalement etre conditionnelle, dependant d'une costimulation avec l'interferon-gamma. De maniere generale, la fonction du recepteur tnf-r75 est tres specifique du type cellulaire considere. En conclusion, c'est le recepteur tnf-r55 qui apparait comme le plus important au niveau du processus inflammatoire et probablement aussi lors de maladies inflammatoires
Assessment of iris recognition reliability for eyes affected by ocular pathologies (2015)

This paper presents an analysis of how the iris recognition is impacted by eye diseases and an appropriate dataset comprising 2996 iris images of 230 distinct eyes (including 184 illness-affected eyes representing more than 20 different eye conditions). The images were collected in near infrared and visible light during a routine ophthalmological practice. The experimental study shows four valuable results. First, the enrollment process is highly sensitive to those eye conditions that make the iris obstructed or introduce geometrical distortions. Second, even those conditions that do not produce visible changes to the iris structure may increase the dissimilarity among samples of the same eyes. Third, eye conditions affecting iris geometry, its tissue structure or producing obstructions significantly decrease the iris recognition reliability. Fourth, for eyes afflicted by a disease, the most prominent effect of the disease on iris recognition is to cause segmentation errors. To our knowledge this is the first database of iris images for disease-affected eyes made publicly available to researchers, and the most comprehensive study of what we can expect when the iris recognition is deployed for non-healthy eyes.
Atomic Force Microscopy Study of the Pressure-Dependent Structural and Frictional Properties of <i>n</i>-Alkanethiols on Gold (1997)

Atomic force microscopy (AFM) has been used to study the effect of pressure on the structural and frictional properties of self-assembled monolayers of n-octadecanethiol on Au(111). Sharp microfabricated silicon nitride tips (tip radii 100−300 Å) were used. At low load, the periodicity of the thiol layer is imaged. At higher load, the layer is observed to become disordered. At a critical contact pressure of ∼2.3 GPa, a transition from the thiol overlayer to the Au(111) substrate periodicity is observed in the lattice resolution images. This transition is gradual and reversible. During the transition, frictional forces first increase and then decrease as the tip−sample separation decreases by a distance approximately equivalent to the thickness of the thiol layer.