gebhart/patrepeval huggingface dataset:
Single Unpurified Breast Tumor-Initiating Cells from Multiple Mouse Models Efficiently Elicit Tumors in Immune-Competent Hosts (2013)

The tumor-initiating cell (TIC) frequency of bulk tumor cell populations is one of the criteria used to distinguish malignancies that follow the cancer stem cell model from those that do not. However, tumor-initiating cell frequencies may be influenced by experimental conditions and the extent to which tumors have progressed, parameters that are not always addressed in studies of these cells. We employed limiting dilution cell transplantation of minimally manipulated tumor cells from mammary tumors of several transgenic mouse models to determine their tumor-initiating cell frequency. We determined whether the tumors that formed following tumor cell transplantation phenocopied the primary tumors from which they were isolated and whether they could be serially transplanted. Finally we investigated whether propagating primary tumor cells in different tissue culture conditions affected their resident tumor-initiating cell frequency. We found that tumor-initiating cells comprised between 15% and 50% of the bulk tumor cell population in multiple independent mammary tumors from three different transgenic mouse models of breast cancer. Culture of primary mammary tumor cells in chemically-defined, serum-free medium as non-adherent tumorspheres preserved TIC frequency to levels similar to that of the primary tumors from which they were established. By contrast, propagating the primary tumor cells in serum-containing medium as adherent populations resulted in a several thousand-fold reduction in their tumor-initiating cell fraction. Our findings suggest that experimental conditions, including the sensitivity of the transplantation assay, can dramatically affect estimates of tumor initiating cell frequency. Moreover, conditional on cell culture conditions, the tumor-initiating cell fraction of bulk mouse mammary tumor cell preparations can either be maintained at high or low frequency in vitro thus permitting comparative studies of tumorigenic and non-tumorigenic cancer cells.
Lipid Autacoids in Inflammation and Injury Responses: A Matter of Privilege (2008)

Host defense is essential to all vertebrates, and programs of inflammation and wound healing must be highly integrated in tissue and organ structures, such as the skin, cornea, and mucosa, that provide crucial barriers and interfaces with the external environment. Certain aspects of inflammation and wound healing have posed a conundrum for biologists, especially to the extent that the two programs may appear to operate in opposition to each other. The recruitment of neutrophils to injured tissue, for example, is essential to inflammation and defense against infection, but can at the same time impair wound healing. One mechanism for regulating this duality is provided by lipid autacoids, which act to restrain leukocyte activation and to promote the resolution of inflammation. Emerging evidence indicates that lipid autacoids also have a central role in wound healing and in fact mediate a privileged injury response, as is observed in the cornea, characterized by rapid healing as well as effective host defense.
Abstract 553: Scavenging Reactive Aldehydes With 5'-o-pentyl-pyridoxamine (PPM) Improves HDL Function and Reduces Atherosclerosis in Ldlr Deficient Mice (2018)

Background: Lipid peroxidation products impair the cholesterol efflux capacity of high-density lipoprotein (HDL) and contribute to the development of atherosclerosis. The effect of inhibition of HDL dysfunction by scavengers on HDL function and whether scavenging reactive aldehydes with PPM protects against the development of atherosclerosis was examined. Methods and Results: HDL of familial hypercholesterolemia (FH) subjects have impaired ability to promote cholesterol efflux and FH-HDL contain 5-fold more malondialdehyde adducts (MDA) than control HDL. In vitro studies revealed that reactive aldehyde MDA crosslinks apolipoprotein AI (apoAI) and impairs the ability of HDL to promote cholesterol efflux from Apoe -/- macrophages. 5'-O-pentyl-pyridoxamine (PPM), a potent scavenger of reactive aldehydes, abolished MDA-mediated crosslinking of apoA-I in HDL by 80 % (P&lt;0.05). PPM prevents the reduction in cholesterol efflux capacity of MDA treated HDL in Apoe-/- macrophages. Furthermore, PPM significantly improved the cholesterol efflux capacity of HDL from Ldlr -/- mice fed a Western diet (WD) for 16 weeks (P&lt;0.05), indicating that PPM protects HDL from modifications by reactive aldehydes and maintains HDL function in vivo. Importantly, administration of 1 mg/mL of the reactive aldehyde scavenger PPM, versus 1 mg/mL of the nonreactive analogue PPO, to Ldlr -/- mice consuming a WD for 16 weeks reduced the extent of proximal aortic atherosclerosis by 45% (P&lt;0.05). Immunohistochemistry studies revealed that PPM reduced the macrophage content and the number of TUNEL positive cells by 55% (P&lt;0.05) and by 60% (P&lt;0.01) in advanced atherosclerotic lesions of Ldlr -/- mice, respectively. In addition, the necrotic core area was reduced by 52% (P&lt;0.05) in advanced atherosclerotic lesions in Ldlr -/- mice treated with PPM compared to the control group. Conclusions: Treatment with PPM, a reactive aldehyde scavenger: 1) inhibits MDA-ApoA1 adduct formation thereby preserving HDL cholesterol efflux capacity in Ldlr -/- mice; 2) reduces the number of apoptotic cells in atherosclerotic lesions and the necrotic core area in lesions of Ldlr -/- mice. These results support the therapeutic potential of PPM in the treatment of atherosclerotic cardiovascular disease.
Three-dimensional piezoelectric MEMS actuator by using sputtering deposition of Pb(Zr,Ti)O3 on microstructure sidewalls (2017)

For the realization of piezoelectric microelectromechanical systems (MEMS) with multiple degrees-of-freedom, lead zirconate titanate thin films were deposited and micropatterned on the sidewalls of a pre-etched substrate with a feature depth of several hundred micrometers. The piezoelectric test structures, consisting of concave geometries and cantilevers with vertical and sloped sidewalls were successfully fabricated onto a 4 inch full sized wafer. Characterization of the fundamental properties of the lead zirconate titanate thin films indicated values comparable to those deposited on flat substrates. Actuation tests demonstrated that the triangular column cantilevers can be driven both in-plane and out-of-plane. The deposition of lead zironate titanate thin films onto a vertical sidewall created bimorph cantilevers composed of piezo/non-piezo/piezo structures in the horizontal direction. The use of microfabrication techniques to deposit lead zironate titanate thin films on pre-etched substrates gives MEMS actuators with multiple degrees-of-freedom and batch process compatibility.
High Intensity Molecular Beam Apparatus (1963)

A high intensity molecular beam apparatus is described which is based on a supersonic stream gas source. Intensities of the order of 1017 molecules/cm2/sec have been achieved with nitrogen. The effects on performance of Mach number, source pressure, and geometry are summarized. Results are compared with theory.
Gallium nitride epitaxy on (0001) sapphire (2002)

Abstract Two-step epitaxy consisting of low-temperature GaN nucleation layers (NLs) and high temperature (HT) GaN overgrowths, deposited on sapphire (0001) by metal-organic chemical vapour deposition, has been examined by transmission electron microscopy and atomic force microscopy. Results indicate that NLs consist of faceted crystalline islands that exhibit a spread in rotation about the (0001) axis. These islands undergo a metamorphosis on annealing and become rounded. The lateral growth during HT deposition of GaN occurs by the attachment of atomic species to steps associated with the rounded islands, resulting in faceted flat-topped islands. Furthermore, growth occurs preferentially in certain regions which evolve into ‘growth patches’. These patches then grow vertically and laterally over the underlying subgrains. The coalescence of these patches produces a continuous GaN layer. The origins of threading dislocations (TDs) in GaN layers have also been investigated. Results show that the majority of TDs do not form during the coalescence of islands as was assumed previously. Instead, two possible sources of TDs have been identified: firstly, growth faults in NLs and, secondly, point defects. Partial dislocations associated with the faults in the NLs constitute the major source of basal plane dislocations, which may develop into TDs by self-glide and climb. It has also been suggested that the mosaic structure observed in fully grown GaN layers is due to elastic interactions between TDs, which glide and climb to form subgrain boundaries.
CuO/Graphene Nanohybrids: Preparation and Enhancement on Thermal Stability and Smoke Suppression of Polypropylene (2013)

Cu/graphene nanohybrids were successfully prepared using a simultaneous chemical reduction method. Successful oxidation of Cu nanoparticles was carried out by the melt blending during preparation of the nanocomposites. Cu nanoparticles were well dispersed on graphene with a diameter of 3–7 nm. XRD and TGA results revealed successful oxidation of Cu nanoparticles during processing. TEM results indicated that PP nanocomposites decorated with CuO/graphene were better dispersed than those added with graphene because the CuO acted as a spacer to keep graphene layers separated. The thermal property of the PP/G-Cu-1 and PP/G-Cu-2 was efficiently improved by around 30 °C compared with native PP. Moreover, the smoke suppression property of PP/graphene, PP/G-Cu-1, and PP/G-Cu-2 nanocomposites were also improved by 28.9%, 35.8%, and 47.2%, respectively. The main reasons for the improvements were due to two factors: the good mass barrier effect of graphene and being easily reduced or the catalytic charring effect of CuO. This work represents a novel and simple process to synthesize CuO/graphene nanohybrids to reduce the fire hazards of polypropylene, indicating further application in research and industrial areas.
A taxonomic note on the genus Prevotella: Description of four novel genera and emended description of the genera Hallella and Xylanibacter (2022)

The genus Prevotella comprises 55 species with validly published, and correct, names (at June 2021) that are phenotypically, ecologically and functionally diverse. This study used a range of comparative genome approaches (marker gene-based genome phylogeny, core genome phylogeny, average amino acid identity, percentage of conserved proteins and clade-specific marker genes) to identify large differences between the 53 species for which genomes are available, as well as two effectively published yet not validly named species and four novel species. These differences were consistent between the various analysis methods and justify the separation of Prevotella into multiple genera. While the distribution across 19 ecosystem types was unique for each species and inconsistent within clades, the functional repertoire based on the presence/absence of both PFAMs and CAZy families revealed distinct clustering based on the proposed genera. Based on the integration of all results, we propose the reclassification of species previously assigned to the genus Prevotella into seven genera, including four novel genera for which the names Segatella, Hoylesella, Leyella and Palleniella are proposed. In addition to the reclassification of Prevotella, this work describes four novel species, Hallella faecis, Xylanibacter rodentium, Xylanibacter muris, and Palleniella intestinalis.
Have London's Roads Become more Dangerous for Cyclists? (2013)

Abstract Cities are dangerous places to cycle – and a sudden spike in deaths has brought a media furore. But do they mean that something on the streets has changed? Jody Aberdein and David Spiegelhalter investigate.
Anodic nitridation of silicon and silicon dioxide (1985)

Anodic nitridation of Si wafers and SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> films in an ammonia plasma was investigated. Compositions of the anodic nitride and the anodic nitrided-oxide films were analyzed with Auger electron spectroscopy and Rutherford backscattering techniques. The etching and oxidation behavior as well as the interfacial, electrical conduction, and charge trapping properties were studied.
Supplementary Figure 1 from A Peptide-Based Positron Emission Tomography Probe for <i>In Vivo</i> Detection of Caspase Activity in Apoptotic Cells (2023)

&lt;p&gt;PDF file - 79KB, 19FFB-VAD-FMK and parent peptide enzyme selectivity. Biochemistry, fluorescence measured IC50 values, collected as duplicates, of the parent peptide, VAD-FMK, and 19FFB-VAD-FMK against caspases-3/6/7/8.&lt;/p&gt;
The meeting of meanings (1999)

The context in which supervision occurs powerfully influences the supervisory process and bestows both advantages and limitations. In this article Susan Lewis outlines what the process of supervision should involve. (editor abstract)
Accuracy of whole slide image based image analysis is adversely affected by preanalytical factors such as stained tissue slide and paraffin block age (2022)

WSIs of aged H&E slides and stained paraffin block re-cuts produce different tumor quantification compared to those of original scanned sslides most likely due to pre-analytical factors. The difference in tumor area detected between original and rescanned WSIs trended upward in the period between 2012 and 2014. Less tumor area was detected as the slides age. Recut and H&E-stained tissues from stored paraffin blocks may detect more tumor due to excess eosinophilia. These results highlights the value of documenting archives of H&E WSIs collected at the procurement time. Such images provide a superior archive over glass slides and Formalin-Fixed Paraffin-Embedded (FFPE) blocks and contribute betterg to WSIs analysis application.
Adaptive Arrays Can Be Used to Separate Communication Signals (1981)

Using eigentheory, it is shown how up to n unknown independent narrowband signals arriving from different directions at an array of n antenna elements can be separated into n channels where each channel contains primarily one signal. An expression for the signal-to-interference ratio (SIR) on eachoutput channel is determined analytically and evaluated for many illustrative cases. The results show that in most cases the SIR is + 10 dB or greater; only when two signals arrive within a few degrees of each other does the SIR fall substantially below 0 dB.
Synthesis of Enantiopure Reversed Structured Ether Lipids of the 1-O-Alkyl-sn-2,3-diacylglycerol Type (2015)

This report describes the synthesis of reversed structured 1-O-alkyl-2,3-diacyl-sn-glycerols (DAGEs) possessing a pure saturated even number fatty acid (C6:0-C16:0) at the sn-2 position along with a pure EPA or DHA located at the terminal sn-3 position of the glycerol backbone of chimyl, batyl and selachyl alcohols. These adducts were synthesized by a highly efficient two-step chemoenzymatic process involving an immobilized Candida antarctica lipase to introduce pure EPA and DHA activated as oxime esters exclusively to the sn-3 terminal position of enantiopure chimyl, batyl and selachyl alcohols in excellent yields. The saturated fatty acids were subsequently incorporated to the remaining sn-2 position of the resulting 3-monoacylglyceryl ethers (3-MAGEs) using EDAC coupling agent in the presence of DMAP in very high to excellent yields (85%-98%). No losses of enantiomeric composition were observed during these processes. The multiple utilities of the resulting focused library of reversed structured DAGEs are discussed including how such compounds may possibly be utilized within the pharmaceutical area.
Analyse du génome des espèces d’élevage : projet d’établissement de la carte génétique du porc et des bovins (1991)

Comparées à celles de l’homme et de la souris, les cartes génétiques des espèces d’élevage sont encore très rudimentaires. Toutefois, la gamme des techniques actuellement disponibles permet désormais de progresser rapidement dans l’établissement de ces cartes. L’objectif immédiat des équipes de génétique moléculaire et cytogénétique de l’INRA est d’identifier, pour les génomes bovin (à Jouy-en-Josas) et porcin (à Toulouse essentiellement), un premier réseau de marqueurs distants d’environ 20 centimorgans, soit un ensemble d’environ 150 marqueurs. Compte tenu du fait que l’organisation du génome est relativement conservée d’une espèce de mammifères à l’autre, les connaissances acquises chez l’homme et la souris permettront, dans une certaine mesure, de guider les travaux de cartographie des espèces d’élevage. On attend de ces recherches : 1) la mise en évidence des régions du génome intervenant dans la variabilité des caractères quantitatifs ; 2) des bases de départ pour le clonage des gènes d’intérêt zootechnique ; 3) le repérage précoce de gènes majeurs à l’aide de gènes marqueurs proches ; 4) une meilleure appréciation de la diversité génétique des races et 5) une précision accrue dans l’identification des animaux et le contrôle des filiations. Des collaborations internationales se mettent en place, notamment dans le cadre de la CEE.
Spectral tilt change in stop consonant perception (2008)

There exists no clear understanding of the importance of spectral tilt for perception of stop consonants. It is hypothesized that spectral tilt may be particularly salient when formant patterns are ambiguous or degraded. Here, it is demonstrated that relative change in spectral tilt over time, not absolute tilt, significantly influences perception of /b/ vs /d/. Experiments consisted of burstless synthesized stimuli that varied in spectral tilt and onset frequency of the second formant. In Experiment 1, tilt of the consonant at voice onset was varied. In Experiment 2, tilt of the vowel steady state was varied. Results of these experiments were complementary and revealed a significant contribution of relative spectral tilt change only when formant information was ambiguous. Experiments 3 and 4 replicated Experiments 1 and 2 in an /aba/-/ada/ context. The additional tilt contrast provided by the initial vowel modestly enhanced effects. In Experiment 5, there was no effect for absolute tilt when consonant and vowel tilts were identical. Consistent with earlier studies demonstrating contrast between successive local spectral features, perceptual effects of gross spectral characteristics are likewise relative. These findings have implications for perception in nonlaboratory environments and for listeners with hearing impairment.
Preparation and characterization of asymmetric α-alkoxy dipyrrin ligands and their metal complexes (2007)

Asymmetric alpha-substituted dipyrrins have been synthesized and characterized. The compounds were formed by a metal mediated reaction involving a single alkoxy group substituted into the alpha-position of an alpha,beta-unsubstituted dipyrrin. An alpha-methoxy dipyrrin, 5-(4-cyanophenyl)-1-methoxydipyrrin (alpha-OMe-4-cydpm), was prepared from 5-(4-cyanophenyl)-4,6-dipyrromethane. Methoxy, ethoxy, and propoxy derivatives (alpha-OMe-4-mecdpm, alpha-OEt-4-mecdpm, alpha-OPr-4-mecdpm) of 5-(4-methoxycarbonylphenyl)-4,6-dipyrromethane have also been prepared. A homoleptic, bis(1-methoxy)dipyrrinato zinc(II) complex, [Zn(alpha-OMe-4-mecdpm)(2)], has been synthesized, as has a heteroleptic cobalt(III) complex with one alpha-OMe-4-cydpm ligand and two unsubstituted 5-(4-cyanophenyl)dipyrrin (4-cydpm) ligands ([Co(alpha-OMe-4-cydpm)(4-cydpm)(2)]). The rotational barrier of the meso-aryl substituent of [Zn(alpha-OMe-4-mecdpm)(2)] was found to be 17.3 kcal mol(-1) by variable-temperature NMR spectroscopy. The compounds alpha-OMe-4-cydpm and [Zn(alpha-OMe-4-mecdpm)(2)] have also been characterized by X-ray diffraction. The formation of the new dipyrrin derivatives is shown to be general and can be performed on dipyrrins with various meso-aryl substitutents, with a variety of alcohols, and can be promoted by several metal salts.
Mitochondrial Release of Pro-apoptotic Proteins (2004)

A key step in the initiation of apoptosis is the release from the mitochondrial intermembrane space of cytochrome c and other pro-apoptotic proteins such as Smac/DIABLO, Omi/HtrA2, apoptosis-inducing factor (AIF), and endonuclease G (EndoG). Discrepancies have arisen, however, as to whether all these proteins are released in different systems. Our results suggest that failure to observe cytochrome c release may be due to the use of different buffers because after permeabilization by caspase-8 cleaved human Bid (tBid), cytochrome c dissociation from mitochondria was highly dependent on ionic strength and required 50-80 mm KCl, NaCl, or LiCl. In addition, mitochondria isolated from apoptotic cells using low ionic strength buffer bound a greater proportion of endogenous cytochrome c. In contrast to cytochrome c, Smac/DIABLO and Omi/HtrA2 were released independent of ionic strength, and AIF and EndoG behaved as if they are exposed to the intermembrane space but tethered to or within the inner membrane. AIF and EndoG were also not released by active caspases, which suggests their involvement in apoptosis may be limited. In summary, whereas tBid permeabilizes the outer membrane to cytochrome c, Smac/DIABLO, and Omi/HtrA2, the release of cytochrome c during apoptosis will be underestimated unless sufficient ionic strength is maintained to overcome the electrostatic association of cytochrome c with membranes.
Systematic Development of Sandwich Immunoassays for the Plasma Secretome (2019)

The plasma proteome offers a clinically useful window into human health. Recent advances from highly multiplexed assays now call for appropriate pipelines to validate individual candidates. Here, a workflow is developed to build dual binder sandwich immunoassays (SIA) and for proteins predicted to be secreted into plasma. Utilizing suspension bead arrays, ≈1800 unique antibody pairs are first screened against 209 proteins with recombinant proteins as well as EDTA plasma. Employing 624 unique antibodies, dilution-dependent curves in plasma and concentration-dependent curves of full-length proteins for 102 (49%) of the targets are obtained. For 22 protein assays, the longitudinal, interindividual, and technical performance is determined in a set of plasma samples collected from 18 healthy subjects every third month over 1 year. Finally, 14 of these assays are compared with with SIAs composed of other binders, proximity extension assays, and affinity-free targeted mass spectrometry. The workflow provides a multiplexed approach to screen for SIA pairs that suggests using at least three antibodies per target. This design is applicable for a wider range of targets of the plasma proteome, and the assays can be applied for discovery but also to validate emerging candidates derived from other platforms.
Ultrasonic sensing of powder densification (1992)

An independent scattering theory has been applied to the interpretation of ultrasonic velocity measurements made on porous metal samples produced either by a cold or a high-temperature compaction process. The results suggest that the pores in both processes are not spherical, an aspect ration of 1:3 fitting best with the data for low (&amp;lt;4%) pore volume fractions. For the hot compacted powders, the pores are smooth due to active diffusional processes during processing. For these types of voids, the results can be extended to a pore fraction of 10%, at which point voids form an interconnected network that violates the model assumptions. The cold pressed samples are not as well predicted by the theory because of poor particle bonding.
Melioidosis: advances in diagnosis and treatment (2010)

In endemic areas, empiric antibiotics should include agents active against melioidosis as well as the other common causes of severe sepsis. It is likely that future improvements in mortality will be the result of efforts to improve on the early recognition and management of severe sepsis generally.