gebhart/patrepeval huggingface dataset:
Biosystems Design. Report from the July 2011 Workshop (2012)

Growing energy demand cannot be met by nonrenewable fossil fuels. Consequently, alternative energy sources are being intensively pursued. Cellulose, a very stable carbohydrate that makes up plant cell walls, is a potential source of renewable fuels. Transforming cellulose into liquid fuels, however, requires substantial chemical and biological processing, first to extract the sugars that comprise the cellulose and then to convert those sugars into fuels. These requirements pose major hurdles to sustainable biofuels production, but overcoming them may be possible by engineering new plants that facilitate the extraction and conversion of their cell walls into liquid fuels. Similarly, newly designed microbes capable of metabolizing plant cell wall components can simplify biomass processing for fuel conversion. Other microorganisms such as microalgae and cyanobacteria can be redesigned to incorporate new functionalities. For example, these photosynthetic organisms, which capture light and convert it into chemical energy, can be re-engineered to produce biofuels, including biodiesel, directly from sunlight. Technological advances enabling the design of new biological systems are already moving biofuels closer to becoming viable, alternative renewable energy resources. Further advances are necessary for developing useful bioenergy crops that not only allow facile conversion of biomass into biofuels, but also do not compete with food crops for arable land. In other words, crops must be rationally redesigned to produce high biomass yields on marginal agricultural lands and under changing weather conditions.
A combined inverse finite element – elastoplastic modelling method to simulate the size-effect in nanoindentation and characterise materials from the nano to micro-scale (2016)

Material properties such as hardness can be dependent on the size of the indentation load when that load is small, a phenomenon known as the indentation size effect (ISE). In this work an inverse finite element method (IFEM) is used to investigate the ISE, with reference to experiments with a Berkovich indenter and an aluminium test material. It was found that the yield stress is highly dependent on indentation depth and in order to simulate this, an elastoplastic constitutive relation in which yielding varies with indentation depth/load was developed. It is shown that whereas Young's modulus and Poisson's ratio are not influenced by the length scale over the range tested, the amplitude portion of yield stress, which is independent of hardening and corresponds to the initial stress for a bulk material, changes radically at small indentation depths. Using the proposed material model and material parameters extracted using IFEM, the indentation depth-time and load-depth plots can be predicted at different loads with excellent agreement to experiment; the relative residual achieved between FE modelling displacement and experiment being less than 0.32%. An improved method of determining hardness from nanoindentation test data is also presented, which shows goof agreement with that determined using the IFEM.
Structure-related properties of sweetpotato critically impact the textural quality of fried chips (2014)

This study sought to define what attributes of sweetpotatoes are most critical to textural qualities of their fried chips for effective selection of specialty cultivars. It compared texture-predicting fracturability of fried chips prepared from either structurally intact or disrupted slices of 13 cultivars; analyzed major attributes of these sweetpotatoes, including starch contents and properties, dry matter contents, and structure-related penetration resistances (measured using an adapted penetration test); and evaluated correlational relationships between these attributes of sweetpotatoes and fracturability of fried chips. The study found that lower dry matter (&lt;22.6% F.W.) and starch contents (&lt;10% F.W.), and lower gelatinization temperatures of starch in sweetpotatoes generally resulted in a more favorable fracturability (lower peak break force) of fried chips. However, contrary to potato, total dry matter content is not the sole determinant of textural qualities of fried sweetpotato chips; instead, structure-related attributes of sweetpotatoes appear to have a greater impact. Partial structural disruptions of sweetpotato slices by blanching effectively improved fracturability of fried chips in all analyzed cultivars, and by ~40% in eight of the 13 cultivars. Furthermore, the degree of structural penetrability of sweetpotatoes, as indexed by penetration resistances, showed very significant correlations with fracturability of fried chips. &nbsp; Key words: Sweetpotato chips, fracturability, puncture test, structure-related attributes, dry matter content, starch.
Titanium Vacancies in TiO2 Nanofibers Enable Highly Efficient Photodriven Seawater Splitting (2021)

Invited for the cover of this issue are Xiao-Yu Yang and co-workers at Wuhan University of Technology, Heinrich-Heine-Universität Düsseldorf, University of the Witwatersrand, and Ben-Gurion University of the Negev. The image depicts Ti vacancies in TiO<sub>2</sub> as powerful drivers of photo- and photo-electrocatalytic seawater splitting for hydrogen production. Read the full text of the article at 10.1002/chem.202101817.
Cooperative p16 and p21 action protects female astrocytes from transformation (2018)

Mechanisms underlying sex differences in cancer incidence are not defined but likely involve dimorphism (s) in tumor suppressor function at the cellular and organismal levels. As an example, sexual dimorphism in retinoblastoma protein (Rb) activity was shown to block transformation of female, but not male, murine astrocytes in which neurofibromin and p53 function was abrogated (GBM astrocytes). Correlated sex differences in gene expression in the murine GBM astrocytes were found to be highly concordant with sex differences in gene expression in male and female GBM patients, including in the expression of components of the Rb and p53 pathways. To define the basis of this phenomenon, we examined the functions of the cyclin dependent kinase (CDK) inhibitors, p16, p21 and p27 in murine GBM astrocytes under conditions that promote Rb-dependent growth arrest. We found that upon serum deprivation or etoposide-induced DNA damage, female, but not male GBM astrocytes, respond with increased p16 and p21 activity, and cell cycle arrest. In contrast, male GBM astrocytes continue to proliferate, accumulate chromosomal aberrations, exhibit enhanced clonogenic cell activity and in vivo tumorigenesis; all manifestations of broad sex differences in cell cycle regulation and DNA repair. Differences in tumorigenesis disappeared when female GBM astrocytes are also rendered null for p16 and p21. These data elucidate mechanisms underlying sex differences in cancer incidence and demonstrate sex-specific effects of cytotoxic and targeted therapeutics. This has critical implications for lab and clinical research.
1-kHz-Repetition-Rate Millijoule Femtosecond Cryocooled DPSS Yb, Na:CaF2 Regenerative Amplifier (2009)

1-mJ pulses are extracted from cw-diode-pumped Yb3+Na+CaF2 1-kHz regenerative amplifier cooled at −130°C and recompressed to 180 fs FWHM. Further scaling of output energy is currently prevented by AR coating burn of the laser crystal.
Gallium nitride based light emitting diodes (LEDs) for energy efficient lighting and displays (2013)

InGaN based materials have been used to fabricate LEDs fabricated from gallium nitride materials have lead to the realization of high-efficiency white solid-state lighting. Using advanced light extraction structures we have fabricated advanced GaN white LEDs structures which exhibit luminous efficacy greater than 150 lm/Watt, and external quantum efficiencies higher than 60% at low current densities(20A/cm2) on c-plane. New LED structures grown on semipolar orientations of bulk GaN have shown remarkable efficiencies with EQE greater than 45% at high current densities(400A/cm2). Equally impressive are GaN based blue and green laser diodes are displaying high efficiencies at even higher current densities (>2000A/cm2). Further improvements in materials quality and cost reduction are necessary for wide-spread adoption of LEDs for lighting. Solid-state lighting has the potential to achieve 85% energy efficiency, corresponding to 255 lm/watt, and be able to run entirely off sustainable energy sources such as either solar, thermoelectric or wind.
Identification of an Ubinuclein 1 Region Required for Stability and Function of the Human HIRA/UBN1/CABIN1/ASF1a Histone H3.3 Chaperone Complex (2012)

The mammalian HIRA/UBN1/CABIN1/ASF1a (HUCA) histone chaperone complex deposits the histone H3 variant H3.3 into chromatin and is linked to gene activation, repression, and chromatin assembly in diverse cell contexts. We recently reported that a short N-terminal fragment of UBN1 containing amino acids 1-175 is necessary and sufficient for interaction with the WD repeats of HIRA and attributed this interaction to a region from residues 120-175 that is highly conserved with the yeast ortholog Hpc2 and so termed the HRD for Hpc2-related domain. In this report, through a more comprehensive and refined biochemical and mutational analysis, we identify a smaller and more moderately conserved region within residues 41-77 of UBN1, which we term the NHRD, that is essential for interaction with the HIRA WD repeats; we further demonstrate that the HRD is dispensable for this interaction. We employ analytical ultracentrifugation studies to demonstrate that the NHRD of UBN1 and the WD repeats of HIRA form a tight 1:1 complex with a dissociation constant in the nanomolar range. Mutagenesis experiments identify several key residues in the NHRD that are required for interaction with the HIRA WD repeat domain, stability of the HUCA complex in vitro and in vivo, and changes in chromatin organization in primary human cells. Together, these studies implicate the NHRD domain of UBN1 as being an essential region for HIRA interaction and chromatin organization by the HUCA complex.
Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): II. Second-Strand Synthesis and In Vitro Transcription (2008)

INTRODUCTIONT7-based linear amplification of DNA (TLAD) uses a linear amplification approach based on in vitro transcription (IVT) of template DNA by RNA polymerase from the T7 phage. TLAD was designed primarily for use with the ChIP-chip method (whereby DNA recovered from chromatin immunoprecipitation [ChIP] of cell lysate is used for subsequent analysis on DNA microarrays) and requires nanogram quantities of dsDNA to generate microgram amounts of amplified RNA. Briefly, the strategy is to add a 3' conserved end to the template dsDNA, using terminal deoxynucleotidyl transferase (TdT) tailing, which permits the addition of a T7 promoter sequence in the subsequent second-strand synthesis step, described here. At this stage, the strand-displacement activity of the Klenow fragment polymerase separates the two strands of the template DNA, after which the enzyme performs fill-in 5' → 3' polymerization. Its 3' → 5' exonuclease activity may also remove the 3' overhanging poly(dT) tails, although the efficiency of this activity will vary based on the length of the poly(dT) tail. IVT can then use this newly appended T7 promoter. Because the T7-based IVT proceeds as an isothermal reaction, it linearly amplifies the template DNA, producing antisense RNA (aRNA) (i.e., each strand of RNA produced is antisense to the original template strand). Since both strands are amplified, this distinction is usually not important and is affected only by the location of the T7 promoter and poly(A) tract on the aRNA.
Sol-Gel-Assisted Microwave-Derived Synthesis of Anatase Ag/TiO2/GO Nanohybrids toward Efficient Visible Light Phenol Degradation (2017)

Abstract: A simple microwave-assisted (MWI) wet chemical route to synthesize pure anatase phase titanium dioxide (TiO2) nanoparticles (NPs) is reported here using titanium tetrachloride (TiCl4) as starting material. The as-prepared TiO2 NPs were characterized by electron microscopy, X-ray diffraction, UV/visible absorption spectroscopy, and infrared and Raman spectroscopic techniques. Further modification of the anatase TiO2 NPs was carried out by incorporating plasmonic silver (Ag) NPs and graphene oxide (GO) in order to enhance the visible light absorption. The photocatalytic activities of the anatase TiO2, Ag/TiO2, and Ag/TiO2/GO nanocomposites were evaluated under both ultraviolet (UV) and visible light irradiation using phenol as a model contaminant. The presence of Ag NPs was found to play a significant role to define the photocatalytic activity of the Ag/TiO2/GO nanocomposite. It was found that the Ag performed like a sink under UV excitation and stored photo-generated electrons from TiO2, whereas, under visible light excitation, the Ag acted as a photosensitizer enhancing the photocatalytic activity of the nanocomposite. The detailed mechanism was studied based on photocatalytic activities of Ag/TiO2/GO nanocomposites. Therefore, the as-prepared Ag/TiO2/GO nanocomposite was used as photocatalytic materials under both UV and visible light irradiation toward degradation of organic molecules.
Heterogeneity of commercial timothy grass pollen extracts (2008)

Timothy grass pollen extracts from different manufacturers exhibit a considerable heterogeneity regarding the presence of individual allergens and hence yield varying in vivo test results. Problems related to the use of natural grass pollen allergen extracts may be circumvented by using defined recombinant grass pollen allergens.
Stability of Sodium Couple in Organic and Inorganic Molten Salt Electrolytes Investigated with Electrochemical Quartz Crystal Microbalance (2001)

An electrochemical quartz crystal microbalance (EQCM) was used to examine the sodium plating-stripping reactions in two room- temperature molten salts: buffered-neutral 1-methyl-3-propylimidazolium chloride and methanesulfonyl-aluminum chloride. In cyclic voltammetry scans on melt slightly more mass was plated on the electrode than required by the charge passed for sodium reduction. The excess mass deposition suggests coreduction of either electrolytes or impurities and formation of protective layers; this results in irreversible deposition and less than 100% coulombic efficiency. In chronoamperometry scans, the mass deposition rate was lower than the equivalent charge passed for pure sodium. This indicates possible reaction between sodium metal and the electrolytes or impurities at the electrode surface after depletion of sodium ions. The inorganic molten salt melts, were made of aluminum chloride, methanesulfonyl chloride, and sodium chloride. The amount of sodium chloride added to melts was critical to the stability of the sodium deposited. The highest coulombic efficiency for the sodium couple in these melts was 97%, and the self-discharge rate was 3 The EQCM results showed reduction of the electrolyte or reaction with sodium metal forming irreversible products. © 2001 The Electrochemical Society. All rights reserved.
Transcriptomic Description of an Endogenous Female State in C. elegans (2016)

Understanding genome and gene function in a whole organism requires us to fully comprehend the life cycle and the physiology of the organism in question. Although C. elegans is traditionally though of as a hermaphrodite, XX animals exhaust their sperm and become (endogenous) females after 3 days of egg-laying. The molecular physiology of this state has not been studied as intensely as other parts of the life cycle, in spite of documented changes in behavior and metabolism that occur at this stage. To study the female state of C. elegans, we designed an experiment to measure the transcriptomes of 1st day adult females; endogenous, 6th day adult females; and at the same time points, mutant feminized worms. At these time points, we were able to separate the effects of biological aging from the transition into the female state.
We find that spermless young adult animals partially phenocopy 6 day old wild-type animals that have depleted their sperm after egg-laying, and that spermless animals also exhibit fewer differentially expressed genes as they age throughout these 6 days. Our results indicate that sperm loss is responsible for some of the naturally occuring transcriptomic changes that occur during the life cycle of these animals.
These changes are enriched in transcription factors canonically associated with neuronal development and differentiation. Our data provide a high-quality picture of the changes that happen in global gene expression throughout the period of early aging in the worm
Interview. Les collectivités ne forment pas un monde à part (2017)

Pour les collectivités, le grand enjeu du quinquennat qui s’ouvre est avant tout budgétaire. Telle est l'analyse du politologue Patrick Le Lidec qui décrypte la stratégie d’Emmanuel Macron de baisse de la dépense publique locale. Entretien avec le chercheur au centre d'études européennes de Sciences Po.
Model coverage as a quality measure and teaching Tool for embedded control system design (2007)

To systematically establish that a design satisfies its requirements, the design model is analyzed with respect to a set of test cases to establish a measure of so-called model coverage. If less than 100% coverage of model behavior is achieved, the design contains unintended functionality or there may be lacking test cases, which in turn may be because of missing requirements. This paper presents the use of model coverage in education, illustrated by the design of an aircraft attitude control system. Model coverage provides a measure of quality of a design task performed by a student while it can help obtain insight into details of critical behavior of a design and how to correct problems discovered.
A Polygon to Ellipse Transformation Enabling Fingerprinting and Emergency Localization in GSM (2011)

Cellular location-based services need to use a variety of positioning methods to meet requirements on availability, response time, and accuracy. Due to the geometrical properties of the different positioning methods, the number of standardized reporting formats is large. Because the user requirements on the reporting formats are as scattered as the geometrical properties of the positioning methods, there is a need for shape conversion algorithms that transform between different formats. This paper discusses a case that transforms between a polygon and an ellipse while preserving the confidence between the two shapes. The transformation is required for emergency positioning outside North America, and when fingerprinting, localization is used in the Global System for Mobile Communications (GSM). The algorithm has a number of technically interesting properties, e.g., with regard to the selection of the optimization criterion and the fact that the solution is computed by an analytical solution of a cubic equation.
Instrument Comparison for Dna Genotyping by Amplicon Melting (2006)

DNA melting analysis for the identification of sequence is increasingly used in molecular diagnostics. Recent advances in DNA melting analysis, including high-resolution instrumentation and specialized fluorescent DNA-binding dyes, allow genotyping by whole amplicon melting without probes. With the popularity of melting analysis as a diagnostic tool, there is a need to characterize the ability of commercially available real-time PCR instruments to perform high-resolution amplicon melting analyses. Four real-time instruments varying in sample format, throughput, and heat transfer (Cepheid's SmartCycler, Idaho Technology's HR-1, and Roche's LightCycler 1.2 and LightCycler 2.0) were evaluated for their ability to differentiate homozygous genotypes at the human β-globin sickle cell locus. The melting transition was monitored by including the dye LCGreen Plus in the PCR, and the data were uniformly analyzed with custom in-house software. The wild-type and mutant homozygous genotypes differed by a theoretical T m of 0.09°C and were best discriminated by the high-resolution HR-1 instrument. All instruments could identify a double single nucleotide polymorphism heterozygote by the heteroduplexes formed. However, signal-to-noise ratios varied from 260 to 3500, suggesting that melting instrument design (data acquisition, data density, thermal control) determines the accuracy of genotyping by amplicon melting. (JALA 2006;11:273-7)
<title>Status of the IS&amp;C Project in Japan</title> (1994)

A prototype IS&C (Image Save and Carry) system is under development at the National Cancer Center Hospital in Japan as a project of the Ministry of International Trade and Industry. The purpose of the project is to develop a medical information filing system for personal health care using the IS&C system. This paper describes the outline and present status of the project.
Approximate distribution of capacity of Rayleigh fading MIMO channels (2004)

Approximate closed-form density and distribution functions for the capacity of multiple-input multiple-output (MIMO) radio systems in spatially semi-correlated Rayleigh fading channels are derived. The approximations are given in terms of the Meijer G-function, hence allowing easy numerical evaluation of capacity outage probabilities with, for example, Maple or Mathematica.
Flexible Graphene Electrode-Based Organic Photovoltaics with Record-High Efficiency (2015)

Advancements in the field of flexible high-efficiency solar cells and other optoelectronic devices will strongly depend on the development of electrode materials with good conductivity and flexibility. To address chemical and mechanical instability of currently used indium tin oxide (ITO), graphene has been suggested as a promising flexible transparent electrode, but challenges remain in achieving high efficiency of grahene-based polymer solar cells (PSCs) compared to their ITO-based counterparts. Here we demonstrate graphene anode- and cathode-based flexible PSCs with record-high power conversion efficiencies of 6.1% and 7.1%, respectively. The high efficiencies were achieved via thermal treatment of MoO 3 electron blocking layer and direct deposition of ZnO electron transporting layer on graphene. We also demonstrate graphene-based flexible PSCs on polyethylene naphthalate substrates and show the device stability under different bending conditions. Our work paves a way to fully graphene electrode-based flexible solar cells using a simple and reproducible process
Apelin stimulates glucose uptake but not lipolysis in human adipose tissue ex vivo (2010)

Apelin is a peptide present in different cell types and secreted by adipocytes in humans and rodents. Apelin exerts its effects through a G-protein-coupled receptor called APJ. During the past years, a role of apelin/APJ in energy metabolism has emerged. Apelin was shown to stimulate glucose uptake in skeletal muscle through an AMP-activated protein kinase (AMPK)-dependent pathway in mice. So far, no metabolic effects of apelin have been reported on human adipose tissue (AT). Thus, the effect of apelin on AMPK in AT was measured as well as AMPK-mediated effects such as inhibition of lipolysis and stimulation of glucose uptake. AMPK and acetyl-CoA carboxylase phosphorylation were measured by western blot to reflect the AMPK activity. Lipolysis and glucose uptake were measured, ex vivo, in response to apelin on isolated adipocytes and explants from AT of the subcutaneous region of healthy subjects (body mass index: 25.6 ± 0.8 kg/m(2), n = 30 in total). APJ mRNA and protein are present in human AT and isolated adipocytes. Apelin stimulated AMPK phosphorylation at Thr-172 in a dose-dependent manner in human AT, which was associated with increased glucose uptake since C compound (20 μM), an AMPK inhibitor, completely prevented apelin-induced glucose uptake. However, in isolated adipocytes or AT explants, apelin had no significant effect on basal and isoprenaline-stimulated lipolysis. Thus, these results reveal, for the first time, that apelin is able to act on human AT in order to stimulate AMPK and glucose uptake.