gebhart/patrepeval huggingface dataset:
Mechanical control of stem cell differentiation (2008)

2. What are mechanical signals?................................................................2 3. What are the sources and functional consequences of applied mechanical forces on stem cells in vivo?... 3 4. How do mechanical forces lead to lineage switching?............................................4
Micro(mi) RNA-34a targets protein phosphatase (PP)1γ to regulate DNA damage tolerance (2015)

The DNA damage response (DDR) triggers widespread changes in gene expression, mediated partly by alterations in micro(mi) RNA levels, whose nature and significance remain uncertain. Here, we report that miR-34a, which is upregulated during the DDR, modulates the expression of protein phosphatase 1γ (PP1γ) to regulate cellular tolerance to DNA damage. Multiple bio-informatic algorithms predict that miR-34a targets the PP1CCC gene encoding PP1γ protein. Ionising radiation (IR) decreases cellular expression of PP1γ in a dose-dependent manner. An miR-34a-mimic reduces cellular PP1γ protein. Conversely, an miR-34a inhibitor antagonizes IR-induced decreases in PP1γ protein expression. A wild-type (but not mutant) miR-34a seed match sequence from the 3' untranslated region (UTR) of PP1CCC when transplanted to a luciferase reporter gene makes it responsive to an miR-34a-mimic. Thus, miR-34a upregulation during the DDR targets the 3' UTR of PP1CCC to decrease PP1γ protein expression. PP1γ is known to antagonize DDR signaling via the ataxia-telangiectasia-mutated (ATM) kinase. Interestingly, we find that cells exposed to DNA damage become more sensitive - in an miR-34a-dependent manner - to a second challenge with damage. Increased sensitivity to the second challenge is marked by enhanced phosphorylation of ATM and p53, increased γH2AX formation, and increased cell death. Increased sensitivity can be partly recapitulated by a miR-34a-mimic, or antagonized by an miR-34a-inhibitor. Thus, our findings suggest a model in which damage-induced miR-34a induction reduces PP1γ expression and enhances ATM signaling to decrease tolerance to repeated genotoxic challenges. This mechanism has implications for tumor suppression and the response of cancers to therapeutic radiation.
Zero-moment point determination of worst-case manoeuvres leading to vehicle wheel lift (2012)

Abstract This paper proposes a method to evaluate vehicle rollover propensity based on a frequency-domain representation of the zero-moment point (ZMP). Unlike other rollover metrics such as the static stability factor, which is based on the steady-state behaviour, and the load transfer ratio, which requires the calculation of tyre forces, the ZMP is based on a simplified kinematic model of the vehicle and the analysis of the contact point of the vehicle relative to the edge of the support polygon. Previous work has validated the use of the ZMP experimentally in its ability to predict wheel lift in the time domain. This work explores the use of the ZMP in the frequency domain to allow a chassis designer to understand how operating conditions and vehicle parameters affect rollover propensity. The ZMP analysis is then extended to calculate worst-case sinusoidal manoeuvres that lead to untripped wheel lift, and the analysis is tested across several vehicle configurations and compared with that of the standard Toyota J manoeuvre. Keywords: rolloveroverturningmulti-body system methodskinematic mechanicszero-moment point Acknowledgements The authors thank the Thomas D. Larson Pennsylvania Transportation Institute for the financial support. Sittikorn Lapapong cordially thanks the Ministry of Science and Technology, the Royal Thai Government, for the financial support.
Tracking the Sun VI: An Historical Summary of the Installed Price of Photovoltaics in the United States from 1998 to 2012 (2013)

United States through 2011. The report describes installed price trends for residential and commercial PV systems, and another set of trends for utility-scale PV. In all cases, installed prices are identified in terms of real 2011 dollars per installed watt (DC-STC), prior to receipt of any direct financial incentives or tax credits.
Abstract 4558: Mapping tolerized T cell states to exhaustion phenotypes in NSCLC (2019)

Abstract The promise of checkpoint blockade treatment has yet to be fully realized in part due to a lack of knowledge of immune exhaustion and its efficient characterization, especially in the context of immunosuppressive tumor microenvironments which effectively tolerize the immune system. We hypothesized that mapping expression signatures defining regulatory T-cell states to previously studied and characterized exhaustion phenotypes of infiltrating T cells in NSCLC would reveal points of contact between T cell tolerization and exhaustion. Concretely, we profiled the gene expression and directly inferred CDR3/1 clonality between tolerized and immunized states in purified CD4+ T-Cells from 10 patients with ovarian or peritoneal and non-small cell lung cancer. The samples were taken before and during immunization therapy for the antigens MAGE-A3 or NY-ESO-1 over a period of 13 weeks, in the presence and absence of adjuvant to emulate the tolerized and immunized states. Further, by modeling the regulatory T-cell states as an interaction between the tolerized and immunized with time and type of antigen allowed us to identify significant differentially expressed gene clusters and their correlation to clonality. We then projected these signatures onto single cell RNAseq data from NSCLC-TCGA to compare the identified clusters to previously identified exhaustion phenotypes. We show that antigen vaccination is immunostimulating and induces lymphocyte activation, leading to a proinflammatory environment. During an immunized stated an increase in cytokine activity, including IL2, 4, 9, 10, 13 and 17, whereas tolerized T Cells, we observe an increase in clonality, BIRC6 and IL20 apart from alterations in chromosome organization pathways and cell cycle including senescence. In conclusion, we detail how the differences between tolerized and immunized states help unravel exhaustion mechanisms, which will ultimately identify molecular markers for exhaustion to assist during treatment and prognosis in clinical settings. Citation Format: Edgar Kozlova, Shingo Eikawa, Sacha Gnjatic, Bojan Losic. Mapping tolerized T cell states to exhaustion phenotypes in NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4558.
MOLECULAR SHOCK RESPONSE OF EXPLOSIVES: ELECTRONIC ABSORPTION SPECTROSCOPY (2009)

Electronic absorption spectroscopy in the range 400–800 nm was coupled to ultrafast laser generated shocks to begin addressing the extent to which electronic excitations are involved in shock induced reactions. Data are presented on shocked polymethylmethacrylate (PMMA) thin films and single crystal pentaerythritol tetranitrate (PETN). Shocked PMMA exhibited thin film interference effects from the shock front. Shocked PETN exhibited interference as well as broadband increased absorption. Relation to shock initiation and the need for time dependent absorption (future experiments) is briefly discussed.
Epoxidation of 2-Alkenylimidazolines (1964)

For the purpose of effective utilization of higher unsaturated fatty acids, epoxidized 2-alkenylimidazolines were prepared. Olive and safflower oil fatty acids of which lower fractions were considerably eliminated by means of rectification were converted into 2-alkenylimidazolines by E. Waldmann's method. These two 2-alkenylimidazolines were epoxidized respectively with 7.5% peracetic acid-acetic acid solution at 30 C. Oxiran oxygen content of epoxidized olive imidazoline was 4.3% (epoxidation degree : 90%) and that of epoxidized safflower imidazoline was 3.5% (epoxidation degree : 46%).
A 3D Stacked Memory Integrated on a Logic Device Using SMAFTI Technology (2007)

A general-purpose 3D-LSI platform technology for a high-capacity stacked memory integrated on a logic device was developed for high-performance, power-efficient, and scalable computing. SMAFTI technology, featuring an ultra-thin organic interposer with high-density feedthrough conductive vias, was introduced for interconnecting the 3D stacked memory and the logic device. A DRAM-compatible manufacturing process was realized through the use of a "via-first" process and highly doped poly-Si through-silicon-vias (TSVs) for vertical traces inside memory dice. A multilayer ultra-thin die stacking process using micro-bump interconnection technology was developed, and Sn-Ag/Cu pillar bumps and Au/Ni backside bumps for memory dice were used for this technology. The vertical integration of stacked DRAM with TSVs and a logic device in a BGA package has been successfully achieved, and actual device operation has been demonstrated for the first time as a 3D-LSI with the DRAM introducing TSVs on the logic device.
Identification and Cloning of Differentially Expressed Genes by DDRT-PCR (2003)

The invention of polymerase chain reaction (PCR) and its application to amplification of reverse transcribed cDNA copies of mRNA has opened new possibilities for the development of techniques for identification of changes in gene expression patterns. Two very similar variants of the same strategy were published in 1992 that were named mRNA differential display () and RNA arbitrary primed PCR (). In contrast to the standard RT-PCR technique, where individual mRNAs are detected in a qualitative and sometimes also quantitative manner using gene-specific primers, in these new techniques a set of short primers with arbitrary sequences is used to generate amplified cDNA fragments from a large number of mRNAs used before for DNA fingerprinting (). Basically, the identification of every individual mRNA species expressed should be possible provided a sufficiently large number of primer pairs is used (). The method of differential display (DDRT-PCR) has already been described in detail in a number of reviews (, , , , , ). Therefore, we give only a very brief description of the principle. First, RNA is prepared from the different cell types of interest. Second, RNA is reverse transcribed in 12 (,), 4 (), or 3 () fractions using anchored oligo-dT primers (e.g., T11VV in Fig. 1) to generate single-stranded cDNA. Third, every cDNA fraction is amplified in a number of independent PCR reactions using various 10-mer upstream primers. Fourth, products of individual PCR reactions are separated on standard sequencing gels (,) or on nondenaturing polyacrylamide gels (,,) and visualized, normally by autoradiography. Fifth, fragments differing in their intensities between the parallel samples from different cells are cut out of the gel, reamplified, cloned into a suitable vector, and sequenced. Sixth, differential expression of the genes corresponding to the identified sequence tags is confirmed by an independent analysis. We have previously recommended nuclear run-on analysis (,). However, this method is not easy to apply to small amounts of cells and tissues. Therefore, we have recently optimized conditions for RNase protection analysis that we will describe here. Finally, if cloning of full-length cDNAs is the ultimate goal, simultaneous isolation of a larger number of cDNA clones from a suitable library can be carried out using a biotinylated fragment mix as probes and streptavidin-coated magnetic beads to purify specifically hybridizing cDNA clones. The cloning step is not an essential part of DDRT-PCR and it is usually omitted if only diagnosis of gene expression patterns is required. Open image in new window Fig. 1. Scheme of DDRT-PCR.
Anterior vascularized rib strut graft in the treatment of Pott's disease in the young child. (1993)

Two young children suffering from acute thoracic kyphosis due to vertebral tuberculosis (Pott's disease) are described. One patient presented with recent onset spastic paraplegia due to cord compression. Anterior decompression and stabilization with a vascularized rib strut graft was performed in both patients. The neurological recovery in the compromised patient was remarkable; spinal stability was achieved in both patients, thus avoiding the necessity for a posterior spinal fusion.
Single−photon and two−photon absorption induced charge model calibration (2017)

International audience
Multimodal method for the identification of multiphoton cancer biomarkers using 3D tumor spheroids (Conference Presentation) (2020)

Endoscopes and other optical, non-invasive diagnostic instruments require measurable parameters (biomarkers) that reliably represent early signs of cancer. These biomarkers are challenging to identify in complex tissues due to their dependence on environmental and disease specific influences. In Multiphoton Microscopy (MPM), signals are commonly separated into channels using optical filters. The choice of channels typically relies on generalized prior knowledge. In order to establish more disease specific biomarkers, a reliable cancer model is desired. We present a method to study biomarkers using spheroids as a cancer model. The spheroid development and harvesting are monitored using Optical Coherence Tomography (OCT). We further introduce a hyperspectral MPM system to investigate biomarkers in the autofluorescence of cancerous and normal cell lines. To improve the detection of the selected biomarkers, an algorithm suggests corresponding filters for diagnostic or research purposes.
Induced Protic Behaviour in Aprotonic Ionic Liquids by Anion Basicity for Efficient Carbon Dioxide Capture (2020)

The interactions between aprotonic tetrabutylphosphonium carboxylate ionic liquids (ILs), [P<sub>4 4 4 4</sub> ][C<sub>n</sub> COO] (n=1, 2 and 7), and water were investigated. The cation-anion interactions occur via the α-<sup>1</sup> H on [P<sub>4 4 4 4</sub> ]<sup>+</sup> and the carboxylate headgroup of the anion. Upon addition, H<sub>2</sub> O localises around the carboxylate headgroups, inducing an electron inductive effect towards the oxygens, leading to ion-pair separation. Studies with D<sub>2</sub> O and [P<sub>4 4 4 4</sub> ][C<sub>n</sub> COO] revealed protic behaviour of the systems, with proton/deuterium exchange occurring at the α-<sup>1</sup> H of the cation, promoted by the basicity of the anion, forming an intermediate ylide. The greater influence of van der Waals forces of the [P<sub>4 4 4 4</sub> ][C<sub>7</sub> COO] system allows for re-orientation of the ions through larger interdigitation. The protic behaviour of the neat ILs allows for CO<sub>2</sub> to be chemically absorbed on the ylide intermediate, forming a phosphonium-carboxylate zwitterion, signifying proton exchange occurs even in the absence of H<sub>2</sub> O. The absorption of CO<sub>2</sub> in equimolar IL-H<sub>2</sub> O mixtures forms a hydrogen carbonate, through a proposed reaction of the CO<sub>2</sub> with an intermediate hydroxide, and carboxylic acid.
Differential Actions of a Mammalian Gonadotropin-Releasing Hormone Antagonist on Gonadotropin-ll and Growth Hormone Release in Goldfish, <i>Carassius auratus</i> (1994)

In goldfish the two native forms of gonadotropin-releasing hormone (GnRH), salmon GnRH (sGnRH) and chicken GnRH-II (cGnRH-II), stimulate both gonadotropin-II (GTH-II) and growth hormone (GH) release. Modifications of GnRH structure at positions 1, 2, 3, and 6 often result in an antagonist in goldfish, an observation well documented in mammalian studies. In a preliminary study in goldfish, a mammalian GnRH antagonist, [Ac-D(2)Nal1, 4Cl-D-Phe2, D(3)-Pal3,6, Arg5, D-Ala10]-mGnRH (analog L) weakly stimulated GTH-II release, and strongly inhibited GH release. The objectives of the present study were to study the dose-related actions of analog L on GTH-II and GH release in the goldfish, the specificity of inhibition of native GnRH actions, and to test whether analog L can act directly on goldfish pituitary cells. In a goldfish pituitary fragments perifusion system, analog L at different concentrations, given as 2-min pulses or as 30-min prolonged treatments, stimulated GTH-II and inhibited GH release in a dose-dependent manner. Analog L at 2 microM concentration (45 min) significantly suppressed sGnRH- and cGnRH-II-stimulated GTH-II as well as GH release. Analog L specifically inhibited GnRH-stimulated GH release, without having any significant effects on the GH release induced by either SKF38393, a dopamine D1 receptor agonist, or thyrotropin-releasing hormone. The GTH-II stimulatory and GH-inhibitory actions of analog L were significantly suppressed by a 'true' GnRH antagonist (Ac-delta 3-Pro1, 4FD-Phe2, D-Trp3,6)-mGnRH. Further, analog L stimulated GTH-II release and suppressed GH release from the enzymatically dispersed goldfish pituitary cells, indicating the direct actions of analog L at the pituitary cell level. Analog L also displaced 125I-(D-Arg6, Pro9 NHEt)-sGnRH bound to crude goldfish pituitary membrane preparations in a dose-related manner. In conclusion, contrary to its action as a potent GnRH antagonist in mammals, analog L has GTH-II stimulatory action in goldfish. Analog L by acting via GnRH receptors at the pituitary cell level differentially acts on GTH-II and GH release, suggesting functional differences in the properties of the GnRH receptors on GTH and GH cells. Analog L also specifically inhibits sGnRH and cGnRH-II actions on GTH-II and GH release.
A 16b 125MS/s 385mW 78.7dB SNR CMOS pipeline ADC (2009)

Today's communication systems require high-performance low-cost ADCs with emphasis on low power, and the ability to IF-sample to reduce receiver complexity. Further, the often-overlooked metric of small-signal linearity quantified by SFDR for less-than-full-scale inputs is important, especially in the presence of large interferers. This 16 b pipeline ADC achieves 78.7 dB SNR, 78.6 dB SNDR and 96 dB SFDR at 125 MS/s with a 30 MHz input, while dissipating 385 mW from a 1.8 V supply. The ADC quantizes inputs up to 150 MHz with an SNR >76 dB and an SFDR >85 dB, has a jitter of 65 fs and accepts 2 V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">pp-diff</sub> , inputs. Further, with dithering enabled the worst spur is <-98 dB for inputs below -4 dBFS at 100 MHz IF. The ADC is fabricated in a 1P5M 0.18mum CMOS process.
Adapting Multichip Module Foundries for MEMS Packaging (2016)

Methods of packaging micro-electro-mechanical systems (MEMS) using advanced multichip module (MCM) foundry processes are described. MCM packaging provides an efficient solution for integration of MEMS with other microelectronic technologies. The MCM foundries investigated for MEMS packaging were the General Electric high density interconnect (HDI) and Chip-on-Flex (COF) as well as the Micro Module Systems (MMS) MCM-D process. Bulk and surface micromachined test di were packaged with CMOS electronics using these MCM foundries. Procedures were developed to successfully release and assemble the MEMS devices without degrading the MCM package or other die in the module. The use of MCM foundries enables the cost-effective development of microsystems in situations for which monolithic integration of MEMS and microelectronics is not suitable.
Figure S4 from Excessive Costimulation Leads to Dysfunction of Adoptively Transferred T Cells (2023)

&lt;p&gt;(A) CAR T cells, day 5 after infusion, were characterized by flow cytometry in terms of percentage and representative plots. m1928ï�ºIL-12 CAR T cells expressed higher levels of inhibitory receptors, PD-1 (*p=0.0015) and LAG-3 (*p=0.0491) and showed a trend toward higher levels of TIM-3 (*p=0.1715). Data obtained is mean +/- s.e.m. of three independent experiments analyzed by unpaired t test. (B) Representative flow cytometry plots of PD-1, LAG-3, and TIM-3 inhibitory receptor expression of CAR T cells referenced in Figure 2B.&lt;/p&gt;
Retinal, anterior segment and full eye imaging using ultrahigh speed swept source OCT with vertical-cavity surface emitting lasers (2012)

We demonstrate swept source OCT utilizing vertical-cavity surface emitting laser (VCSEL) technology for in vivo high speed retinal, anterior segment and full eye imaging. The MEMS tunable VCSEL enables long coherence length, adjustable spectral sweep range and adjustable high sweeping rate (50-580 kHz axial scan rate). These features enable integration of multiple ophthalmic applications into one instrument. The operating modes of the device include: ultrahigh speed, high resolution retinal imaging (up to 580 kHz); high speed, long depth range anterior segment imaging (100 kHz) and ultralong range full eye imaging (50 kHz). High speed imaging enables wide-field retinal scanning, while increased light penetration at 1060 nm enables visualization of choroidal vasculature. Comprehensive volumetric data sets of the anterior segment from the cornea to posterior crystalline lens surface are also shown. The adjustable VCSEL sweep range and rate make it possible to achieve an extremely long imaging depth range of ~50 mm, and to demonstrate the first in vivo 3D OCT imaging spanning the entire eye for non-contact measurement of intraocular distances including axial eye length. Swept source OCT with VCSEL technology may be attractive for next generation integrated ophthalmic OCT instruments.
REGULATION OF LUNG INFLAMMATION IN THE MODEL OF IGG IMMUNE-COMPLEX INJURY (2006)

Modern techniques of cell and molecular biology have rapidly uncovered the mechanisms underlying inflammatory injury of the lung. This expanding knowledge (which includes an understanding of complement, cell surface receptors, cytokines and chemokines, transcription factors, oxidants, proteinases, and endogenous inhibitors, as well as the role of leukocyte adhesion-promoting molecules) has provided new insights into the inflammatory system in general, as well as in the context of lung injury. In this review, we summarize recent progress in understanding the regulation of lung inflammation by using immunoglobulin G (IgG) immune complex–induced lung injury as a model. These studies have provided information on the role of various inflammatory mediators and their sequence of engagement. Insights into potential interventional approaches for the suppression of inflammatory processes in humans have emerged from those studies.
Towards foundry approach for silicon photonics: silicon photonics platform ePIXfab (2009)

Fabless access to wafer-scale silicon photonics technology is moving silicon photonics closer to becoming a mainstream technology and opens up new exciting areas for research at the same time. It is only by using wafer-scale technology that this emerging field will be able to realise its promise: to become a disruptive technology. At the basis of the rationale for silicon photonics is a complex of photonic functions integrated on a single chip, coupled to a stable, high-yield volume fabrication technology base. ePIXfab is a service platform offering R&amp;D oriented access to state-of-the-art 200 mm wafer-scale CMOS technology optimised for silicon photonics purposes.