gebhart/patrepeval huggingface dataset:
A Novel Molecular and Functional Stemness Signature Assessing Human Cord Blood-Derived Endothelial Progenitor Cell Immaturity (2016)

Endothelial Colony Forming Cells (ECFCs), a distinct population of Endothelial Progenitor Cells (EPCs) progeny, display phenotypic and functional characteristics of endothelial cells while retaining features of stem/progenitor cells. Cord blood-derived ECFCs (CB-ECFCs) have a high clonogenic and proliferative potentials and they can acquire different endothelial phenotypes, this requiring some plasticity. These properties provide angiogenic and vascular repair capabilities to CB-ECFCs for ischemic cell therapies. However, the degree of immaturity retained by EPCs is still confused and poorly defined. Consequently, to better characterize CB-ECFC stemness, we quantified their clonogenic potential and demonstrated that they were reprogrammed into induced pluripotent stem cells (iPSCs) more efficiently and rapidly than adult endothelial cells. Moreover, we analyzed the transcriptional profile of a broad gene panel known to be related to stem cells. We showed that, unlike mature endothelial cells, CB-ECFCs expressed genes involved in the maintenance of embryonic stem cell properties such as DNMT3B, GDF3 or SOX2. Thus, these results provide further evidence and tools to appreciate EPC-derived cell stemness. Moreover this novel stem cell transcriptional signature of ECFCs could help better characterizing and ranging EPCs according to their immaturity profile.
Novel image-based LSI diagnostic method using E-beam without CAD database (2003)

Novel voltage contrast image-based methods have been developed concerning voltage contrast image acquisition using electron beam tester and concerning fault searching on a VLSI chip, and have been applied to real faults of passivated VLSI devices. The developed voltage contrast image acquisition methods have shorten the acquisition time about 1200 times faster than that of the conventional stroboscopic methods and have given better image quality that that of conventional method. The method employed continuous e-beam scanning and gated sampling image signal technique (CGFI) technique. The continuous e-beam scanning may prevent the fading voltage contrast and give good voltage contrast image. The method also employed test vector shortening technique, which has a merit in shortening testing time and avoiding wrong fault tracing back.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Abstract 402: HDL Mimetic Peptides ATI-5261 and CS-6253 Induce ABCA1 Oligomerization, Cellular Cholesterol Efflux and Generate Nascent HDL-Like Lipoproteins (2013)

Novel approaches that target HDL biogenesis may increase nascent HDL-like particle formation that can be used for therapeutic purposes. Here, we evaluated two 26-amino acid apoA-I mimetic peptides designed from c-terminus of apoE, ATI-5261 and CS-6253 in their ability to promote cellular cholesterol efflux via the ABCA1 transporter. Using mifepristone-inducible ABCA1 BHK cells and cAMP-stimulated J774 macrophages, we examined ABCA1 oligomerization with dithiobis[succinimidyl propionate] (DSP) as a cross linker. Like native apoA-I, ATI-5261 and CS-6253 induced ABCA1 oligomerization at equimolar concentrations, and appear to interact with native oligomers of ABCA1, similar to apoA-I, as judged by crosslinking revealed by SDS-PAGE. By sucrose density gradient fractionation, we show that ABCA1 oligomerization occurs in non-raft domains. ATI-5261 and CS-6253 promoted cellular cholesterol efflux in a dose-dependent saturable manner. In BHK cells, the efficiency of cholesterol efflux (Km) on an equimolar basis was: apoA-I (0.16±0.02), ATI-5261 (0.45±0.08) and CS-6253 (0.68±0.15) and the efflux capacity (Vmax) (% in 24h) was: apoA-I (14.54±0.61), ATI-5261 (11.98±0.51) and CS-6253 (10.87±0.66), indicating a higher efflux efficiency for the apoA-I mimetics but with less capacity than native apoA-I. A similar trend was observed in J774 cells. Desorption of cellular cholesterol at 45 min occurred in both non-raft and raft-like membrane domains. We then examined by HPLC and 2-dimentional PAGGE the size and types of HDL-like particles formed. In 3[H]-cholesterol loaded BHK-ABCA1 cells, incubation with ATI-5261 and CS-6253 for 45 min and 12 hours yielded α-migrating particles with an apparent size ranging between 9 and 17 nm, as revealed by specific antibodies directed against ATI-5261 and CS-6253. Taken together, these observations suggest that ATI-5261 and CS-6253 induce cellular cholesterol efflux via ABCA1 oligomerization at molar concentrations similar to apoA-I and with higher efficiency. The particles generated by ATI-5261 and CS-6253 have α-migrating mobility with a size ranging between 9 and 17 nm and contain cholesterol, similar to nascent HDL particles.
The evolution of systems analysis and control: a personal perspective (1996)

The foundations of systems analysis and control as we know them today were laid for the most part at MIT's Radiation Laboratory during World War II and a period thereafter. Most of the founders-both in the United States and abroad-are no longer with us. As one who had the privilege of knowing Wiener, Bode, Nyquist, Guillemin, Gordon Brown, Sam Mason, John Coales, Aizerman, Pontryagin, Letov, Bellman, and many others, I present some personal perceptions and reminiscences in this paper. However, in view of the vastness of the subject, I touch upon only a small subset of the issues and events that were at the center of attention.
Texture and neural network for road segmentation (2002)

Road recognition is a main component in autonomous vehicle guidance system. We aim to determine whether an image element is part of the road or not, by using information from the element's proximity. The wide range of situations have to be processed is a problem, and they impose on the system a capacity of self-adaptation to new cases. A neural network based architecture has been chosen to implement the texture analysis. By applying a local texture recognition process to the whole image, we obtain a segmented image of the road.
Busaliol and Busalicifol, Two New Tetrahydrofuran Lignans from Bupleurum salicifolium (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBusaliol and Busalicifol, Two New Tetrahydrofuran Lignans from Bupleurum salicifoliumA. Estévez-Braun, R. Estévez-Reyes, J. A. González-Pérez, and A. G. GonzálezCite this: J. Nat. Prod. 1995, 58, 6, 887–892Publication Date (Print):June 1, 1995Publication History Published online1 July 2004Published inissue 1 June 1995https://doi.org/10.1021/np50120a010RIGHTS & PERMISSIONSArticle Views414Altmetric-Citations20LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (366 KB) Get e-Alertsclose Get e-Alerts
Crossing fitness valleys via double substitutions within codons (2019)

Abstract Single nucleotide substitutions in protein-coding genes can be divided into synonymous (S), with little fitness effect, and non-synonymous (N) ones that alter amino acids and thus generally have a greater effect. Most of the N substitutions are affected by purifying selection that eliminates them from evolving populations. However, additional mutations of nearby bases can modulate the deleterious effect of single substitutions and thus might be subject to positive selection. To elucidate the effects of selection on double substitutions in all codons, it is critical to differentiate selection from mutational biases. We approached this problem by comparing the fractions of double substitutions within codons to those of the equivalent double S substitutions in adjacent codons. Under the assumption that substitutions occur one at a time, all within-codon double substitutions can be represented as “ancestral-intermediate-final” sequences and can be partitioned into 4 classes: 1) SS: S intermediate – S final, 2) SN: S intermediate – N final, 3) NS: N intermediate – S final, 4) NN: N intermediate – N final. We found that the selective pressure on the second substitution markedly differs among these classes of double substitutions. Analogous to single S substitutions, SS evolve neutrally whereas, analogous to single N substitutions, SN are subject to purifying selection. In contrast, NS show positive selection on the second step because the original amino acid is recovered. The NN double substitutions are heterogeneous and can be subject to either purifying or positive selection, or evolve neutrally, depending on the amino acid similarity between the final or intermediate and the ancestral states. The general trend is that the second mutation compensates for the deleterious effect of the first one, resulting in frequent crossing of valleys on the fitness landscape.
THEORETICAL MODELING OF ELECTRICALLY OPERATED AMMONIUM NITRATE PROPELLANT COMBUSTION (2019)

Certain propellants exhibit combustion zone properties that allow burn rate manipulation by application of a transverse electric field, perpendicular to the axis of flame propagation. In the configuration of interest, the solid propellant is dielectric, but its melt layer underneath the gaseous flame region is electrically conductive. The applied electric field imparts ohmic heating to the subsurface region adjacent to the flame. The advantages of ammonium nitrate (AN) propellants for this method of burn-rate control have been known for some time; a clear effect, on the order of 100% of normal burn-rate amplification, could be possible using moderate voltages. Whereas AN is dielectric in all its known solid phase variants, its melt phase is electrically conductive. The objective of this study is to provide a theory for this mode of electrically enhanced combustion. A quasi one-dimensional model of the solid/melt/gas combustion zone is derived at steady state. The resulting two-point boundary value formulation for the melt layer is based on variable electrical conductivity as a function of temperature. This leads to a unique Sturm-Liouville formulation for which eigenvalues and associated eigenfunctions are solved. The two parameters of physical significance are the Péclét number and the eigenvalue. The analysis herein offers physical insight into this electrically augmented combustion process at steady state, which explains the dependence of burn rate and apparent melt layer resistance upon the applied electrical voltage. These functional dependences are verified by correlating the available experimental results.
On-Demand Virtual Optical Network Access Using 100 Gb/s Ethernet (2011)

Our Terabit LAN challenges are to enhance the scalability and utilization of lambda resources. Bandwidth-on-demand virtualized 100GE access to WDM networks on a field fiber test-bed using multi-domain optical-path provisioning is described.
Ca2+ influx via T-type channels modulates PDGF-induced replication of mouse fibroblasts (1993)

The role of low-threshold voltage-gated calcium channels (VGCC) in modulating extracellular calcium influx and proliferation was investigated in platelet-derived growth factor (PDGF)-stimulated C3H/10T1/2 mouse fibroblasts. Previous studies demonstrated that cell cycle progression after PDGF stimulation was dependent on extracellular calcium influx producing a sustained increase in the intracellular calcium concentration. In this study, PDGF-induced calcium influx, the sustained intracellular calcium increase, and progression to S phase were inhibited by nordihydroguariaretic acid (NDGA), an inhibitor of calcium influx through VGCC. With the use of the whole cell patch-clamp technique to measure calcium currents, NDGA inhibited inward calcium current through low-threshold VGCC, the only VGCC expressed in C3H/10T1/2 fibroblasts. The inhibitory effects of NDGA on calcium influx and cell proliferation each had a mean inhibitory dose of 2-3 microM. Although NDGA also effectively inhibits cyclooxygenase and lipoxygenase, the addition of prostaglandins or leukotrienes could not reverse this inhibition nor could it be replicated by other antioxidants. These data support the hypothesis that low-threshold VGCC can mediate extracellular calcium influx on the stimulation of cell proliferation by PDGF.
Optical properties of extended and localized states in m-plane InGaN quantum wells (2013)

Scanning near-field and time-resolved photoluminescence spectroscopy were applied to study potential fluctuations and photoexcited carrier dynamics in single m-plane InGaN quantum well structures. The far- and near-field spectra were found to have contributions from transitions to the first and second hole levels in the extended states, and transitions in the localized states. Correlations between parameters of the near-field spectra confirmed that extended state luminescence was prevailing. The localized states, which were found to be separated from the extended states by ∼10 meV barriers, were attributed to regions of a higher In content.
Caffeine Confinement into a Series of Functionalized Porous Zirconium MOFs: A Joint Experimental/Modeling Exploration (2013)

A multitechnique approach was conducted to investigate the confinement of caffeine in a series of UiO-66(Zr)-type MOFs, functionalized with −H, −NH2, −Br, and −2OH groups. DFT calculations were first undertaken to elucidate the preferential geometries of the drug within the pores and the resulting drug/host framework interactions. It was shown that the caffeine molecules are preferentially located in the smaller cages, giving rise to only weak interactions with the function groups grafted on the organic linker. These host/guest interactions were concomitantly probed by advanced 1D and 2D high-field/ultrafast MAS NMR and FTIR spectroscopies, which allowed us to not only validate the DFT predictions but also to bring complementary insight into the nature of the interacting sites of both the caffeine and the MOFs. Dielectric relaxation measurements further revealed significant modifications of the ligand dynamics upon the drug encapsulation for all UiO-66(Zr) solids. It was demonstrated that the perturbation of the ligand flip strongly depends on the nature of the grafted function. While the dynamics of the ligand is slightly enhanced in the case of the −NH2 form, it is significantly slower for the −Br analogue. Such specific behaviors were then interpreted in light of the conclusions drawn from the DFT calculations and NMR observations.
Reconstructing ancient mitochondrial DNA links between Africa and Europe (2012)

Mitochondrial DNA (mtDNA) lineages of macro-haplogroup L (excluding the derived L3 branches M and N) represent the majority of the typical sub-Saharan mtDNA variability. In Europe, these mtDNAs account for <1% of the total but, when analyzed at the level of control region, they show no signals of having evolved within the European continent, an observation that is compatible with a recent arrival from the African continent. To further evaluate this issue, we analyzed 69 mitochondrial genomes belonging to various L sublineages from a wide range of European populations. Phylogeographic analyses showed that ~65% of the European L lineages most likely arrived in rather recent historical times, including the Romanization period, the Arab conquest of the Iberian Peninsula and Sicily, and during the period of the Atlantic slave trade. However, the remaining 35% of L mtDNAs form European-specific subclades, revealing that there was gene flow from sub-Saharan Africa toward Europe as early as 11,000 yr ago.
Diffusivity of Binary and Ternary Concrete Mixture Blends (2014)

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Data from Distinguishing Tumor from Associated Fibrosis to Increase Diagnostic Biopsy Yield with Polarization-Sensitive Optical Coherence Tomography (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;With recent advancements in personalized medicine, biopsies must contain sufficient tumor for histologic diagnosis and molecular testing. However, inadvertent biopsy of tumor-associated fibrosis compromises tumor yield, resulting in delayed diagnoses and/or repeat procedures when additional tumor is needed. The ability to differentiate tumor from fibrosis intraprocedurally during biopsy could significantly increase tumor yield. Polarization-sensitive optical coherence tomography (PS-OCT) is an imaging modality that is endoscope- and/or needle-compatible, and provides large volumetric views of tissue microstructure with high resolution (∼10 μm) while simultaneously measuring birefringence of organized tissues such as collagen. We aim to determine whether PS-OCT can accurately detect and distinguish tumor-associated fibrosis from tumor.&lt;/p&gt;Experimental Design:&lt;p&gt;PS-OCT was obtained &lt;i&gt;ex vivo&lt;/i&gt; in 64 lung nodule samples. PS-OCT birefringence was measured and correlated to collagen content in precisely matched histology, quantified on picrosirius red (PSR) staining.&lt;/p&gt;Results:&lt;p&gt;There was a strong positive correlation between PS-OCT measurement of birefringent fibrosis and total collagen content by PSR (&lt;i&gt;r&lt;/i&gt; = 0.793; &lt;i&gt;P&lt;/i&gt; &lt; 0.001). In addition, PS-OCT was able to accurately classify tumor regions with &gt;20% fibrosis from those with low fibrosis (≤20%) that would likely yield higher tumor content (&lt;i&gt;P&lt;/i&gt; &lt; 0.0001).&lt;/p&gt;Conclusions:&lt;p&gt;PS-OCT enables accurate fibrosis detection and can distinguish tumor regions with low fibrosis. PS-OCT has significant potential for clinical impact, as the ability to differentiate tumor from fibrosis could be used to guide intraprocedural tissue sampling &lt;i&gt;in vivo&lt;/i&gt;, or for rapid biopsy adequacy assessment &lt;i&gt;ex vivo&lt;/i&gt;, to increase diagnostic tumor yield essential for patient care and research.&lt;/p&gt;&lt;/div&gt;
Vacuum tightness down to the 10−15 mbar l s−1 range, measured with a spinning rotor viscosity gauge (1987)

The pressure rise in small systems (∼10 cm3) evacuated and baked before sealing was measured. The intention was to measure the tightness of glass and ceramic to metal seals, below 10−12 mbar l s−1, that is, below the lowest detectable leak rate of commercial helium leak detectors. Different influences on measurements, like outgassing rate after bakeout, penetration of helium through glass, and environmental conditions like temperature, were evaluated. We determined the lowest pressure rise rate, during a week, including outgassing and all possible leaks, in the 10−15 mbar l s−1 range at total pressure of ∼1.10−6 mbar. The advantages of pressure rise leak detection using the spinning rotor gauge are (1) no gas evolution, (2) no gas pumping, (3) isothermic measurement at 25 °C, and (4) small dead volume and high sensitivity.
High Density Lipoprotein Subfractions during Oral and Cutaneous Administration of 17β-Estradiol to Menopausal Women* (1983)

Thirty eight women with menopausal vasomotor symptoms were randomly allocated to 6 months treatment with either 2-4 mg micronized estradiol given orally or 3 mg estradiol applied cutaneously. The concentrations of cholesterol (C) and phospholipids (PL) were determined in high density lipoprotein (HDL) and its subfractions HDL2 and HDL3 twice before treatment and after 2, 4, and 6 months of medication. Oral estradiol increased the C and PL concentration in the HDL2 fraction in a dose-dependent way. With 2 mg estradiol orally the HDL3 fraction did not change, whereas 4 mg estradiol orally increased the C and PL concentrations in the HDL3 fraction. Cutaneous treatment with estradiol did not influence the lipid level in HDL or its subfractions. It is concluded that the rise of HDL during estrogen treatment is mainly caused by an elevation of the HDL2 fraction. Furthermore, the route of administration of estrogens has a profound influence on the metabolism of the HDL subfractions.
The Ordered Queue and the Optimality of the Watershed Approaches (2005)

This work reviews the watershed in the graph framework of a shortest-path forest problem using a lexicographic path cost formulation. This formulation reflects the behavior of the ordered queue-based watershed algorithm. This algorithm is compared with our proposed shortest-path forest (IFT-Image Foresting Transform), concluding that the watershed is a special case of that. Recently many different watershed approaches are being used. We point out that in some cases the watershed algorithm does not keep the optimality of the shortest-path forest solution unless the IFT algorithm is used. The main difference between the algorithms is related to permanently labeling a pixel when inserting or removing it from the queue. The watershed based on the pixel dissimilarity using IFT can segment one-pixel width regions while keeping the optimality of the shortest-path forest solution.
Targeting and limiting surgery for patients with node-positive breast cancer (2015)

The presence of axillary nodal metastases has a significant impact on locoregional and systemic treatment decisions. Historically, all node-positive patients underwent complete axillary lymph node dissection; however, this paradigm has changed over the last 10 years. The use of sentinel lymph node dissection has expanded from its initial role as a surgical staging procedure in clinically node-negative patients. Clinically node-negative patients with small volume disease found on sentinel lymph node dissection now commonly avoid more extensive axillary surgery. There is interest in expanding this role to node-positive patients who receive neoadjuvant chemotherapy as a way to restage the axilla in hopes of sparing women who convert to node-negative status from the morbidity of complete nodal clearance. While sentinel lymph node dissection alone may not accomplish this goal, there are novel techniques, such as targeted axillary dissection, that may now allow for reliable nodal staging after chemotherapy.
Purification of Porcine Brain Protein Phosphatase 2A Leucine Carboxyl Methyltransferase and Cloning of the Human Homologue, (1999)

The carboxyl methyltransferase, which is claimed to exclusively methylate the carboxyl group of the C-terminal leucine residue of the catalytic subunit of protein phosphatase 2A (Leu(309)), was purified from porcine brain. On the basis of tryptic peptides, the cDNA encoding the human homologue was cloned. The cDNA of this gene encodes for a protein of 334 amino acids with a calculated M(r) of 38 305 and a predicted pI of 5.72. Database screening reveals the presence of this protein in diverse phyla. Sequence analysis shows that the novel methyltransferase is distinct from other known protein methyltransferases, sharing only sequence motifs supposedly involved in the binding of adenosylmethionine. The recombinant protein expressed in bacteria is soluble and the biophysical, catalytic, and immunological properties are indistinguishable from the native enzyme. The methylation of PP2A by the recombinant protein is restricted to Leu(309) of PP2A(C). No direct effects on phosphatase activity changes were observed upon methylation of the dimeric or trimeric forms of PP2A.
Table S8 from Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia (2023)

&lt;p&gt;Overlap with aging signatures&lt;/p&gt;