gebhart/patrepeval huggingface dataset:
Factor VII deficiency rescues the intrauterine lethality in mice associated with a tissue factor pathway inhibitor deficit (1999)

Mice doubly heterozygous for a modified tissue factor pathway inhibitor (TFPI) allele (tfpi delta) lacking its Kunitz-type domain-1 (TFPI+/delta) and for a deficiency of the factor VII gene (FVII+/-) were mated to generate 309 postnatal and 205 embryonic day 17.5 (E17. 5) offspring having all the predicted genotypic combinations. Progeny singly homozygous for the tfpidelta modification but with the wild-type fVII allele (FVII+/+/TFPIdelta/delta), and mice singly homozygous for the fVII deficiency and possessing the wild-type tfpi allele (FVII-/-/TFPI+/+), displayed previously detailed phenotypes (i.e., a high percentage of early embryonic lethality at E9.5 or normal development with severe perinatal bleeding, respectively). Surprisingly, mice of the combined FVII-/-/TFPIdelta/delta genotype were born at the expected mendelian frequency but suffered the fatal perinatal bleeding associated with the FVII-/- genotype. Mice carrying the FVII+/-/TFPIdelta/delta genotype were also rescued from the lethality associated with the FVII+/+/TFPIdelta/delta genotype but succumbed to perinatal consumptive coagulopathy. Thus, the rescue of TFPIdelta/delta embryos, either by an accompanying homozygous or heterozygous FVII deficiency, suggests that diminishment of FVII activity precludes the need for TFPI-mediated inhibition of the FVIIa/tissue factor coagulation pathway during embryogenesis. Furthermore, the phenotypes of these combined deficiency states suggest that embryonic FVII is produced in mice as early as E9.5 and that any level of maternal FVII in early-stage embryos is insufficient to cause a coagulopathy in TFPIdelta/delta mice.
Autocorrespondence: feature-based match estimation and image metamorphosis (2002)

This paper addresses the problem of matching distinct but related objects across images, for applications such as view-based model capture, virtual presence, and morphing special effects. A new approach to match estimation is presented for estimating correspondences between distinct objects. This approach minimizes the effects of lighting variations and nonrigid deformations. A sparse set of features are used for alignment, followed by image-plane warping, or morphing, based on these constraints.
Elastic Optical Path Network Architecture: Framework for Spectrally-Efficient and Scalable Future Optical Networks (2012)

This paper presents an elastic optical path network architecture as a novel networking framework to address the looming capacity crunch problem in internet protocol (IP) and optical networks. The basic idea is to introduce elasticity and adaptation into the optical domain to yield spectrally-efficient optical path accommodation, heightened network scalability through IP traffic offloading to the elastic optical layer, and enhanced survivability for serious disasters.
Pressure-Transient Analysis of Dual Packer-Probe Wireline Formation Testers in Slanted Wells (2004)

Abstract This paper examines the use of spatial pressure transient measurements acquired by packer-probe wireline formation testers (WFT) in slanted (deviated) wells for estimating formation parameters; e.g., horizontal and vertical permeabilities, skin, tool storage coefficient as well as initial formation pressures. The well's inclination angle ranges from 0 to 90°, covering vertical and horizontal wells as limiting cases. New approximate analytical equations for spherical flow, which is often exhibited by dual-packer interval and observation probe(s), are presented. These analytical equations are valid for all inclination angles and provide a technique for determining formation parameters from spherical and/or radial flow exhibited by packer and probe(s) pressure transient measurements in slanted wells for single layer systems. These equations also provide a useful set of good initial parameter estimates when nonlinear regression analysis is employed for parameter estimation. It is shown that nonlinear regression provides a useful analysis procedure to identify the formation parameters that can be uniquely determined from different sets of spatial pressures measurements of packer/probe WFTs. A field dual-packer/probe test example is provided to illustrate the methodology and procedures developed in this work.
The Effect of Muscle Loading on Skeletal Muscle Regenerative Potential (2009)

Skeletal muscle is a dynamic tissue with a remarkable ability to continuously respond to environmental stimuli. Among its adaptive responses is the widely investigated ability of skeletal muscle to regenerate after loading or injury or both. Although significant basic science efforts have been dedicated to better understand the underlying mechanism controlling skeletal muscle regeneration, there has been relatively little impact in the clinical approaches used to treat skeletal muscle injuries and wasting. The purpose of this review article is to provide an overview of the basic biology of satellite cell function in response to muscle loading and to relate these findings in the context of aging and neuromuscular pathology for the rehabilitation medicine specialist.
Seasonal below‐ground metabolism in switchgrass (2017)

Switchgrass (Panicum virgatum), a perennial, polyploid, C4 warm-season grass is among the foremost herbaceous species being advanced as a source of biomass for biofuel end uses. At the end of every growing season, the aerial tissues senesce, and the below-ground rhizomes become dormant. Future growth is dependent on the successful over-wintering of the rhizomes. Although the importance of rhizome health to overall year-upon-year plant productivity has been long recognized, there is limited information on seasonal changes occurring during dormancy at both the transcriptome and metabolite levels. Here, global changes in transcriptomes and metabolites were investigated over two growing seasons in rhizomes harvested from field-grown plants. The objectives were: (a) synthesize information on cellular processes that lead to dormancy; and (b) provide models that could account for major metabolic pathways present in dormant switchgrass rhizomes. Overall, metabolism during dormancy appeared to involve discrete but interrelated events. One was a response to abscisic acid that resulted in dehydration, increases in osmolytes and upregulation of autophagic processes, likely through the target of rapamycin complex and sucrose non-fermentative-related kinase-based signaling cascades. Another was a recalibration of energy transduction through apparent reductions in mitochondrial oxidative phosphorylation, increases in substrate level generation of ATP and reducing equivalents, and recycling of N and possibly CO<sub>2</sub> through refixation. Lastly, transcript abundances indicated that cold-related signaling was also occurring. Altogether, these data provide a detailed overview of rhizome metabolism, especially during dormancy, which can be exploited in the future to improve winter survival in switchgrass.
System Level Simulations of an Open Photo-Acoustic Gas Sensor (2018)

This document deals with a new approach to the system level modeling of open photo-acoustic gas sensors (PAS) for CO2 sensing applications. The complex nature of the sensor calls for a flexible co-simulation environment which combines diverse domains and physical quantities such as pressure, temperature, voltage and electrical power. After validation against laboratory measurements, the system model can be used to investigate different package or hardware options, to evaluate the impact of different types of coupling (e.g., electrical or acoustic) and explore new algorithms and signal processing methods for more accurate gas concentration estimates.
Processability‐enhanced bimodal high‐density polyethylene with comb‐branched high‐density polyethylene (2017)

ABSTRACT Two solution reactors in series were utilized to synthesize comb‐branched high‐density polyethylene (HDPE), cbHDPE, where the first reactor prepares vinyl‐terminated HDPE macromers catalyzed by an organometallic catalyst favoring beta hydride transfer and the second reactor copolymerizes HDPE macromers with ethylene using a different organometallic catalyst capable of incorporating macromers. A bimodal HDPE, biHDPE with bimodalities in molecular weight, and hexene content of the desired composition distribution was also prepared in a gas phase reactor using silica supported dual organometallic catalysts. By blending 3% solution‐made cbHDPE into the gas‐phase biHDPE, the resulting trimodal HDPE preserves the excellent stiffness and toughness of the bimodal HDPE while having exceptional melt strength and processability. © 2017 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2018 , 135 , 45755.
Specific Cross-reaction of IgG Anti-phospholipid Antibody with Platelet Glycoprotein IIIa (1996)

To study the pathological functions of anti-phospholipid (anti-PL) antibodies, we have analyzed their effect on platelet function. We identified an IgG anti-PL mAb, designated PSG3, which cross-reacted specifically with glycoprotein (GP) IIIa in human platelets and inhibited platelet aggregation. PSG3 bound also to certain polyanionic substances, such as double-stranded DNA, heparan sulfate, dextran sulfate and acetylated-LDL, but not to other polyanionic substances. The binding of PSG3 to GPIIIa was completely inhibited by heparan sulfate and dextran sulfate, indicating that PSG3 recognizes a particular array of negative charges expressed on both GPIIIa and the specified polyanionic substances. Since neither neuraminidase- nor endoglycopeptidase F-treatment of GPIIIa had any significant effect on the binding of PSG3, this array must be located within the amino acid sequence of GPIIIa but not in the carbohydrate moiety. Reduction of the disulfide bonds in GPIIIa greatly reduced its reactivity, suggesting that the negative charges in the epitope are arranged in a particular conformation. PSG3 inhibited platelet aggregation induced by either ADP or collagen, it also inhibited fibrinogen binding to activated platelets in a dose-dependent fashion. PSG3, however, did not inhibit the binding of GRGDSP peptide to activated platelets. These results suggest that the PSG3 epitope on GPIIIa contains a particular array of negative charges, and possibly affects the fibrinogen binding to GPIIb/IIIa complex necessary for platelet aggregation.
Supplementary Materials and Methods from Delta-Like Ligand–Notch1 Signaling Is Selectively Modulated by HPV16 E6 to Promote Squamous Cell Proliferation and Correlates with Cervical Cancer Prognosis (2023)

&lt;p&gt;The Supplementary materials and methods provide more detail on cell culture; antibodies; scratch assay; immunofluorescence and immunohistochemistry; TMA analysis; Western blots and statistical analysis.&lt;/p&gt;
ChemInform Abstract: Advantages of Culture Models Utilizing Substrata Made of TOSHI (Tissue/Organ Sections for Histopathology) or Collagen Vitrigel Membrane and Their Application Concept for Drug Development Researches (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Establishment of reference standards for multifaceted mosaic variant analysis (2022)

Detection of somatic mosaicism in non-proliferative cells is a new challenge in genome research, however, the accuracy of current detection strategies remains uncertain due to the lack of a ground truth. Herein, we sought to present a set of ultra-deep sequenced WES data based on reference standards generated by cell line mixtures, providing a total of 386,613 mosaic single-nucleotide variants (SNVs) and insertion-deletion mutations (INDELs) with variant allele frequencies (VAFs) ranging from 0.5% to 56%, as well as 35,113,417 non-variant and 19,936 germline variant sites as a negative control. The whole reference standard set mimics the cumulative aspect of mosaic variant acquisition such as in the early developmental stage owing to the progressive mixing of cell lines with established genotypes, ultimately unveiling 741 possible inter-sample relationships with respect to variant sharing and asymmetry in VAFs. We expect that our reference data will be essential for optimizing the current use of mosaic variant detection strategies and for developing algorithms to enable future improvements.
History Erase Effect in a Non-Volatile Memristor (2016)

This work presents a detailed study of the nonlinear dynamics of a tantalum oxide memristor recently fabricated at Hewlett Packard Labs. Our investigations uncover direct current, quasi-static, and alternating current behavior of the nanodevice. A thorough study of the dynamics emerging in the nanoscale element under various input/initial condition combinations reveals a fundamental property of the tantalum oxide device, which was unnoticed so far. The initial condition has no effect on the steady-state operation of the memristor under non-zero input. This property, known as fading memory in system theory, implies the uniqueness of asymptotic behavior of the memristor. The progressive input-induced memory erase phenomenon is solely determined by the switching dynamics of the nanodevice, mathematically described by the state evolution function, which governs the rate of evolution of the memristor state. A constant-sign DC input will activate on or off switching dynamics only. Consequently, due to the limited on/off memductance ratio, the memristor will asymptotically attain a fully-conducting or highly-resistive state, irrespective of the initial condition. Most interestingly, under AC periodic excitations, it is the pronounced asymmetry in the state dependence of on and off switching processes which is at the basis of the reported history erase effect. It is important to point out that this novel fading memory phenomenon does not compromise the nonvolatile behavior of the nanostructure. In fact, despite the device may be stimulated so as to forget its past history, it still has a continuum of analog nonvolatile memory states.
Development and Characterization of Micro Arc Oxidation Process for Vacuum Equipment (2020)

We have developed a method of micro arc oxidation treatment as a surface treatment of aluminum alloy used for vacuum equipment using corrosive gas such as chemical vapor deposition (CVD) equipment. The oxide layer formed by the micro arc oxidation (MAO) treatment was evaluated. The oxide layer formed by MAO had a three layer structure of crystalline γ-alumina. Moreover, it turned out that the oxide layer does not contain other than the element derived from a base material. It was found that the outgassing amount of the aluminum alloy covered with this oxide layer was 1/10 compared to the sulfuric acid alumite treatment.
Antiangiogenic Effect of Interleukin-10 in Ischemia-Induced Angiogenesis in Mice Hindlimb (2000)

Ischemia induces both hypoxia and inflammation that trigger angiogenesis. The inflammatory reaction is modulated by production of anti-inflammatory cytokines. This study examined the potential role of a major anti-inflammatory cytokine, interleukin (IL)-10, on angiogenesis in a model of surgically induced hindlimb ischemia. Ischemia was produced by artery femoral occlusion in both C57BL/6J IL-10(+/+) and IL-10(-/-) mice. After 28 days, angiogenesis was quantified by microangiography, capillary, and arteriole density measurement and laser Doppler perfusion imaging. The protein levels of IL-10 and vascular endothelial growth factor (VEGF) were determined by Western blot analysis in hindlimbs. IL-10 was markedly expressed in the ischemic hindlimb of IL-10(+/+) mice. Angiogenesis in the ischemic hindlimb was significantly increased in IL-10(-/-) compared with IL-10(+/+) mice. Indeed, angiographic data showed that vessel density in the ischemic leg was 10.2+/-0.1% and 5.7+/-0.4% in IL-10(-/-) and IL-10(+/+) mice, respectively (P:<0.01). This corresponded to improved ischemic/nonischemic leg perfusion ratio by 1.4-fold in IL-10(-/-) mice compared with IL-10(+/+) mice (0.87+/-0. 05 versus 0.63+/-0.01, respectively; P:<0.01). Revascularization was associated with a 1.8-fold increase in tissue VEGF protein level in IL-10(-/-) mice compared with IL-10(+/+) mice (P:<0.01). In vivo electrotransfer of murine IL-10 cDNA in IL-10(-/-) mice significantly inhibited both the angiogenic process and the rise in VEGF protein level observed in IL-10(-/-) mice. No changes in vessel density or VEGF content were observed in the nonischemic hindlimb. These findings underscore the antiangiogenic effect of IL-10 associated with the downregulation of VEGF expression and suggest a role for the inflammatory balance in the modulation of ischemia-induced angiogenesis.
Chamber Walls Coatings during hard mask patterning of Ultra Low-k Materials: Consequences on Cleaning Strategies (2007)

International audience
A phase I study of a p53MVA vaccine in combination with gemcitabine (GEM) in recurrent ovarian cancer (OC). (2016)

e17040 Background: We developed a modified vaccinia Ankara virus containing the wild-type p53 transgene (p53MVA) to stimulate immunity to over-expressed p53 in tumor cells. This approach is applicable to OC, in which p53 mutation is common. We previously reported that p53MVA was well tolerated at a dose of 5.6 x 108 pfu in patients (pts) with gastro-intestinal malignancies. GEM, a standard chemotherapy agent in OC, may potentiate the action of immunotherapies. Numerous early phase trials of cancer vaccines and GEM in pancreatic cancer report encouraging immunological and clinical responses. We conducted a de-escalation Phase I trial of p53MVA and GEM in pts with recurrent OC. Methods: OC pts with a platinum free interval ≤ 12 months, ≤ 2 chemotherapy lines for recurrent disease and histology showing p53 involvement were eligible. All pts received GEM at 1000mg/m2 on days 1 and 8 every 3 weeks and p53MVA at 5.6 x 108 pfu, sq on day 15 of the first 3 cycles of GEM. Dose-limiting toxicities (DLTs) were evaluable during the first 2 cycles of therapy. Results: A total of 7 pts have been enrolled [median age 63, platinum free interval ≤ 6 months 7/7, serous or mixed adenocarcinoma 6/7, carcinosarcoma (CS) 1/7]. The number of prior lines of therapy for recurrent OC was 0 in 1/7 pts, 1 in 4/7 pts and 2 in 2/7 pts. Five pts are evaluable for DLT. Two pts were inevaluable; one due to GEM allergy requiring steroids and another (with CS of the ovary) due to rapidly progressive disease and early death. No DLTs were observed, establishing the starting dose as the recommended Phase II dose. GEM related grade 3/4 AEs, not meeting DLT definition included: neutropenia (grade 3 in 1 pt, grade 4 in 1 pt), anemia (grade 3, 2pts), hyperuricemia (grade 4, 1pt) hyponatremia (grade 3, 1pt), leukopenia (grade 3, 1pt). Additional pts are being recruited at the recommended Phase II dose. Conclusions: Combination therapy of p53MVA and GEM is well tolerated with expected toxicities relating to GEM alone and no evidence of autoimmunity. To our knowledge this is the first trial combining a viral based cancer vaccine and GEM in OC. Support: NCI/NIH grant P30CA033572. Clinical trial information: NCT02275039.
Feasibility and Process Alternatives for Reactive Distillation (2002)

This chapter contains sections titled: Introduction Motivation Flash Cascade Model Feasibility Hypothesis Bifurcation Analysis of the Flash Cascade Model Conclusions Notation
Polarized Light Microscopy for Analyzing Tissue Mechanics During In Vitro Acupuncture (2008)

Acupuncture is a traditional therapy originating in China almost 2000 years ago. Acupuncture has slowly been growing in popularity in the West, and clinical evidence has shown the potential for acupuncture as a low-cost ‘alternative’ therapy for an assortment of ailments [1]. The practice of acupuncture involves inserting fine needles into the skin followed by needle manipulation, usually by rotation. Recent studies by Langevin et al demonstrate that this rotation causes the subcutaneous connective tissue to couple to and wind around the needle [2–4], which suggests that mechanotransduction in the connective tissue might play a role in the therapeutic mechanisms that underlay acupuncture [2, 3]. To begin to decompose and quantify this complex mechanism at the tissue level in a controlled setting, we have simulated acupuncture in type I collagen gels in vitro, and have developed algorithms to quantify the tissue response following imaging with polarized light microscopy (PLM).
A conserved cysteine‐based redox mechanism sustains TFEB/HLH‐30 activity under persistent stress (2020)

Mammalian TFEB and TFE3, as well as their ortholog in Caenorhabditis elegans HLH-30, play an important role in mediating cellular response to a variety of stress conditions, including nutrient deprivation, oxidative stress, and pathogen infection. In this study, we identify a novel mechanism of TFEB/HLH-30 regulation through a cysteine-mediated redox switch. Under stress conditions, TFEB-C212 undergoes oxidation, allowing the formation of intermolecular disulfide bonds that result in TFEB oligomerization. TFEB oligomers display increased resistance to mTORC1-mediated inactivation and are more stable under prolonged stress conditions. Mutation of the only cysteine residue present in HLH-30 (C284) significantly reduced its activity, resulting in developmental defects and increased pathogen susceptibility in worms. Therefore, cysteine oxidation represents a new type of TFEB post-translational modification that functions as a molecular switch to link changes in redox balance with expression of TFEB/HLH-30 target genes.
Labeling Point Features on Maps and Diagrams (1992)

A major factor affecting the clarity of graphical displays that include text labels is the degree to which labels obscure display features (including other labels) as a result of spatial overlap. Point-feature label placement (PFLP) is the problem of placing text labels adjacent to point features on a map or diagram so as to maximize legibility. This problem occurs frequently in the production of many types of informational graphics, though it arises most often in automated cartography. In this paper we present a comprehensive treatment of the PFLP problem, viewed as a type of combinatorial optimization problem. Complexity analysis reveals that the basic PFLP problem and most interesting variants of it are NP-hard. These negative results help inform a survey of previously reported algorithms for PFLP; not surprisingly, all such algorithms either have exponential time complexity or are incomplete. To solve the PFLP problem in practice, then, we must rely on good heuristic methods. We propose two new methods, one based on a discrete form of gradient descent, the other on simulated annealing, and report on a series of empirical tests comparing these and the other known algorithms for the problem. Based on this study, the first to be conducted, we identify the best approaches as a function of available computation time.
Architecture optimization of nanobridge-based field-programmable gate array and its evaluation (2017)

Logic cell architecture on nanobridge-based field-programmable gate array (NB-FPGA) is investigated in terms of cell area and signal delay. Area-delay product is minimized when the cluster size is 4 and the segment length is 4, because of small area and small capacitance of nanobridge (NB). 1.34× logic density improvement and 15% energy saving, compared to the previous NB-FPGA with cluster size = 2, are demonstrated by implementing an application of a lightweight block cipher.