gebhart/patrepeval huggingface dataset:
Nanoporous Thin Films and Binary Nanoparticle Superlattices Created by Directed Self-Assembly of Block Copolymer Hybrid Materials (2015)

The design and development of well-defined, functional nanostructures via self-assembly is one of the key objectives in current nanotechnology. Block copolymer-based hybrid materials are attractive candidates for the fabrication of multifunctional nanostructures, which provide the building blocks for more complex nanoarchitectures and nanodevices. However, one of the major challenges lies in controlling the structure formation in these hybrid materials by guiding the self-assembly of the block copolymer. Here, hierarchical nanoporous structures are fabricated via guided multistep self-assembly of diblock copolymer micellar solutions onto hydrophilic solid substrates. The core of polystyrene-block-poly[4-vinylpyridine] micelles serves as a nanoreactor for the preparation of size-controlled gold nanoparticles. Deposition of thin films of the micellar solution in combination with a nonselective cosolvent (THF), on hydrophilic surfaces leads to the formation of hierarchical nanoporous structures. The micellar films exhibit two different pore diameters and a total pore density of more than 10(10) holes per cm2. Control over the pore diameter is achieved by adapting the molecular weight of the polystyrene-block-poly[4-vinylpyridine] diblock copolymer. Moreover, the porous morphology is used as a template for the fabrication of bimetallic nanostructured thin films. The PS-b-P4VP template is subsequently removed by oxygen plasma etching, leaving behind binary nanoparticle structures that mimic the original thin film morphology.
EYES ABSENT and TIMELESS integrate photoperiodic and temperature cues to regulate seasonal physiology in Drosophila (2020)

Abstract Organisms possess photoperiodic timing mechanisms to anticipate variations in day length and temperature as the seasons progress. The nature of the molecular mechanisms interpreting and signaling these environmental changes to elicit downstream neuroendocrine and physiological responses are just starting to emerge. Here, we demonstrate that in Drosophila melanogaster , EYES ABSENT (EYA) acts as a seasonal sensor by interpreting photoperiodic and temperature changes to trigger appropriate physiological responses. We observed that tissue-specific genetic manipulation of eya expression is sufficient to disrupt the ability of flies to sense seasonal cues, thereby altering the extent of female reproductive dormancy. Specifically we observed that EYA proteins, which peak at night in short photoperiod and accumulate at higher levels in the cold, promote reproductive dormancy in female D. melanogaster . Furthermore, we provide evidence indicating that the role of EYA in photoperiodism and temperature sensing is aided by the stabilizing action of the light-sensitive circadian clock protein TIMELESS (TIM). We postulate that increased stability and level of TIM at night under short photoperiod together with the production of cold-induced and light-insensitive TIM isoforms facilitate EYA accumulation in winter conditions. This is supported by our observations that tim null mutants exhibit reduced incidence of reproductive dormancy in simulated winter conditions, while flies overexpressing tim show an increased incidence of reproductive dormancy even in long photoperiod. Significance Statement Extracting information on calendar time from seasonal changes in photoperiod and temperature is critical for organisms to maintain circannual cycles in physiology and behavior. Here we found that in flies, EYES ABSENT (EYA) protein act as a seasonal sensor by adjusting its abundance and circadian phase in response to changes in photoperiod and temperature. We show that the manipulation of EYA levels is sufficient to impair the ability of female Drosophila to regulate seasonal variation in reproductive dormancy. Finally, our results suggest an important role of the circadian clock protein TIMELESS (TIM) in modulating EYA level through its ability to measure night length, linking the circadian clock to seasonal timing.
FGFR1 is fused to the centrosome-associated proteinCEP110 in the 8p12 stem cell myeloproliferative disorder with t(8;9)(p12;q33) (2000)

The hallmark of the 8p12 stem cell myeloproliferative disorder (MPD) is the disruption of the FGFR1 gene, which encodes a tyrosine kinase receptor for members of the fibroblast growth factor family. FGFR1 can be fused to at least 3 partner genes at chromosomal regions 6q27, 9q33, or 13q12. We report here the cloning of the t(8;9)(p12;q33) and the detection of a novel fusion betweenFGFR1 and the CEP110 gene, which codes for a novel centrosome-associated protein with a unique cell-cycle distribution. CEP110 is widely expressed at various levels in different tissues and is predicted to encode a 994-amino acid coiled-coil protein with 4 consensus leucine zippers [L-X(6)-L-X(6)-L-X(6)-L]. Both reciprocal fusion transcripts are expressed in the patient's cells. The CEP110-FGFR1 fusion protein encodes an aberrant tyrosine kinase of circa 150-kd, which retains most of CEP110 with the leucine zipper motifs and the catalytic domain of FGFR1. Transient expression studies show that the CEP110-FGFR1 protein has a constitutive kinase activity and is located within the cell cytoplasm. (Blood. 2000;95:1788-1796)
A Low-Carbohydrate, Ketogenic Diet versus a Low-Fat Diet To Treat Obesity and Hyperlipidemia (2004)

Compared with a low-fat diet, a low-carbohydrate diet program had better participant retention and greater weight loss. During active weight loss, serum triglyceride levels decreased more and high-density lipoprotein cholesterol level increased more with the low-carbohydrate diet than with the low-fat diet.
Supplementary Table 1, Figures 1-8 from Smad2 and Smad3 Phosphorylated at Both Linker and COOH-Terminal Regions Transmit Malignant TGF-β Signal in Later Stages of Human Colorectal Cancer (2023)

Supplementary Table 1, Figures 1-8 from Smad2 and Smad3 Phosphorylated at Both Linker and COOH-Terminal Regions Transmit Malignant TGF-β Signal in Later Stages of Human Colorectal Cancer
Supplementary Figure 1A from Molecular Triage of Premalignant Lesions in Liquid-Based Cervical Cytology and Circulating Cell-Free DNA from Urine, Using a Panel of Methylated Human Papilloma Virus and Host Genes (2023)

&lt;p&gt;Phase 1 Biomarker Development Trial to identify genes or clusters of genes that appear to be differentially methylated in cervical cancer biopsy tissues relative to control cervical brush epithelium tissue taken from women seen in the same hospital. The search for cervical cancer screening methylation biomarkers began with preclinical exploratory studies to identify characteristics unique to tumor tissue that might lead to methylated biomarkers for clinical tests that can discriminate cancer from pre-malignant and normal lesions. We used Methylated DNA Immunoprecipitation (MeDIP) and oligonucleotide sequencing arrays (Nimblegen 385K CpG Island Plus Promoter Arrays) to unveil the cervical cancer promoter region methylome (MeDIP-chip). We then used bisulfite sequencing and quantitative Methylation Specific Polymerase Chain Reaction (qMSP) to identify potential biomarkers of progression from normal cervical mucosa epithelium in cervical brush samples from women with abnormal cytology. MeDIP-chip Discovery identified 2,044 differentially methylated probes associated to total of 444 gene loci differentially methylated when comparing tumor and normal samples. Gene loci were subdivided according to two cutoffs defined for the maximal distance between a methylation peak and the TSS: -1000 to +1000, called the standard cut-off; -500 to +500, called the narrow cut-off. We found 255 unique gene loci that are cancer specific methylated according to the standard cutoff and 189 according to the narrow cutoff. More than half of the methylated gene promoters identified with MeDIP-chip (60%) were hypermethylated in all cancer samples and not in normal samples. One hundred and sixty two (162) genes were jointly identified by the intersection between both lists. These stringent criteria ensured that all 10 genes selected for biomarker validation had methylated peaks within a CPG island located in the promoter region, 500 base pairs upstream from the TSS in all the hybridized tumor samples and none in the normal samples hybridized to the arrays. The top three genes in the list that contained CpG islands in their promoter regions FKBP6, ZNF516 and INTS1) were selected for further analysis with MSP and qMSP in Validation and Prevalence cohorts. Samples were tsted for HPV presence using the reverse line blot assay.&lt;/p&gt;
Concreteness Fading of Algebraic Instruction: Effects on Learning (2016)

Learning algebra is difficult for many students in part because of an emphasis on the memorization of abstract rules. Algebraic reasoners across expertise levels often rely on perceptual-motor strategies to make these rules meaningful and memorable. However, in many cases, rules are provided as patterns to be memorized verbally, with little overt perceptual support. Although most work on concreteness focuses on conceptual support through examples or analogies, here we consider notational concreteness—perceptual-motor supports that provide access into the dynamic structure of a representation itself. We hypothesize that perceptual support may be maximally beneficial as an initial scaffold to learning so that later static symbol use may be interpreted using a dynamic perspective. This hypothesis meshes with other findings using concrete analogies or examples, which often find that fading these supports over time leads to stronger learning outcomes. In an experiment exploring this hypothesis, we compared gains from the fading out of dynamic concrete physical motion of symbols during instruction with the introduction of motion over the course of instruction. In line with our theoretical perspective, concreteness fading led to significantly better achievement than concreteness introduction after Day 2 of the intervention.
The Transformation of Enterovirus Replication Structures: a Three-Dimensional Study of Single- and Double-Membrane Compartments (2011)

Positive-strand RNA viruses hijack specific intracellular membranes and remodel them into special structures that support viral RNA synthesis. The ultrastructural characterization of these "replication structures" is key to understanding their precise role. Here, we resolved the three-dimensional architecture of enterovirus-induced membranous compartments and their transformation in time by applying electron tomography to cells infected with coxsackievirus B3 (CVB3). Our results show that closed single-membrane tubules are the predominant initial virus-induced structure, whereas double-membrane vesicles (DMVs) become increasingly abundant at the expense of these tubules as infection progresses. Additionally, more complex multilamellar structures appear late in infection. Based on compelling intermediate structures in our tomograms, we propose a model for transformation from the tubules to DMVs and multilamellar structures via enwrapping events. Our work provides an in-depth analysis of the development of an unsuspected variety of distinct replication structures during the course of CVB3 infection.
A compact 5&#x2013;6 GHz T/R module based on SiGe BiCMOS and SOI that enhances 256 QAM 802.11ac WLAN radio front-end designs (2014)

A compact high linearity 4.9–5.9 GHz T/R FEM is presented, which consists of a SiGe BiCMOS PA and a SOI switched LNA realized in an ultra-compact 2.3 × 2.3 × 0.33 mm3 QFN package. The Tx chain has > 30 dB gain and meets −35 dB DEVM up to 17 dBm at 3.3 V and 20 dBm at 5V, insensitive to modulation bandwidths and transmission data length up to 4 mS. With digital pre-distortion (DPD), the PA can be down-biased to save 30 mA while maintaining its linearity. The Rx chain features <2.5 dB NF and 12 dB gain with 4 dBm IIP3 and 8 dB bypass attenuator with 29 dBm IIP3. All the unique features enhance the front-end circuit designs of complex 802.11ac radios.
Nonlinear Optical Properties (2004)

Abstract In the presence of a sufficiently intense light, the optical properties of a polymer may become measurably nonlinear, leading to field‐dependent changes in the frequency response, the refractive index, and/or the absorption coefficient of the polymer. This article introduces nonlinear optical phenomena and the structural properties that enhance a material's nonlinear optical response. Second‐and third‐order nonlinear optical (NLO) phenomena are discussed, with a primary emphasis on harmonic generation, intensity‐dependent refractive index, and nonlinear, multiphoton, absorption. Macroscopic nonlinear phenomena are related to the molecular properties of the materials. Sum‐over‐states models are used to understand the fundamental molecular parameters affecting the nonlinear response, particularly π‐electron conjugation, bond length alternation, and donor–acceptor substitution. Measurement techniques used to characterize a material's nonlinear response are surveyed.
Benchmark Testing for Plane Elasticity Non-linear Analysis (1987)

Since the development of the first finite element structural codes benchmark testing has been a significant part of their validation phase prior to public use. A recent publication has proposed a set of benchmark tests for static linear analysis. Such tests are designed to demonstrate that codes are capable of emulating basic deformation and stress states in solid bodies, and where structural approximations are made, as in shell theory, that elements are performing to the same level of approximation. Benchmark tests examine when things do not work well and expose weaknesses in any code. A potential user of a code can subject it to such benchmark tests to satisfy him or herself as to its quality. Non-linear material behaviour is present in many areas of structural deformation especially in cyclic loading and work hardening or cold working. This work lays down some possible guidelines for establishing benchmark tests for material non-linearity and presents suggestions for four such tests.
Measurements of Isoprene-Derived Organosulfates in Ambient Aerosols by Aerosol Time-of-Flight Mass Spectrometry - Part 1: Single Particle Atmospheric Observations in Atlanta (2011)

Organosulfate species have recently been identified as a potentially significant class of secondary organic aerosol (SOA) species, yet little is known about their behavior in the atmosphere. In this work, organosulfates were observed in individual ambient aerosols using single particle mass spectrometry in Atlanta, GA during the 2002 Aerosol Nucleation and Characterization Experiment (ANARChE) and the 2008 August Mini-Intensive Gas and Aerosol Study (AMIGAS). Organosulfates derived from biogenically produced isoprene were detected as deprotonated molecular ions in negative-ion spectra measured by aerosol time-of-flight mass spectrometry; comparison to high-resolution mass spectrometry data obtained from filter samples corroborated the peak assignments. The size-resolved chemical composition measurements revealed that organosulfate species were mostly detected in submicrometer aerosols and across a range of aerosols from different sources, consistent with secondary reaction products. Detection of organosulfates in a large fraction of negative-ion ambient spectra - ca. 90-95% during ANARChE and ~65% of submicrometer particles in AMIGAS - highlights the ubiquity of organosulfate species in the ambient aerosols of biogenically influenced urban environments.
Meteosat Third Generation: presentation of the video detection chains (2021)

Meteosat Third Generation (MTG) is the next challenging mission for accurate observation of the Earth dedicated to meteorology forecast. MTG encompasses two different missions: MTG-I (Imaging) and MTG-S (Sounding). MTG-I optical payload counts the FCI (Flexible Combined Imager), a multi-spectral imager in the continuity of Meteosat Second Generation (MSG) with improved performance and additional spectral bands. MTG-S transports the IRS instrument which is an Infrared Fourier Transform Spectrometer dedicated to the sounding of the atmosphere inspired by the previous IASI mission. Located in a geostationary orbit, the satellites are covering the full hemisphere for imaging (FCI) in less than 10 minutes in 16 different spectral bands from Visible to Very Long Wave IR at a resolution of 0.5-2 km and make a complete IR sounding of the atmosphere (IRS) in less than 1h at a spatial resolution of 4 km and a spectral resolution of 0.625 cm<sup>-1</sup>. In this article, we describe the detection chains of FCI and IRS instruments which give accurate sight to the remote sensing and afford the capability to reach the objectives of MTG-I and S missions. Some particularities of designs and key performance are presented. MTG on ground tests have provided interesting results which are therefore presented. These results have been obtained after 10 years of intensive research and development at Thales Alenia Space (Prime FCI) and OHB(Prime IRS), with the support and supervision of ESA and EUMETSAT. This research and development work has been performed under an ESA contract.
Role of Clp Proteins in Expression of Virulence Properties ofStreptococcus mutans (2009)

Mutational analysis revealed that members of the Clp system, specifically the ClpL chaperone and the ClpXP proteolytic complex, modulate the expression of important virulence attributes of Streptococcus mutans. Compared to its parent, the DeltaclpL strain displayed an enhanced capacity to form biofilms in the presence of sucrose, had reduced viability, and was more sensitive to acid killing. The DeltaclpP and DeltaclpX strains displayed several phenotypes in common: slow growth, tendency to aggregate in culture, reduced autolysis, and reduced ability to grow under stress, including acidic pH. Unexpectedly, the DeltaclpP and DeltaclpX mutants were more resistant to acid killing and demonstrated enhanced viability in long-term survival assays. Biofilm formation by the DeltaclpP and DeltaclpX strains was impaired when grown in glucose but enhanced in sucrose. In an animal study, the average number of S. mutans colonies recovered from the teeth of rats infected with the DeltaclpP or DeltaclpX strain was slightly lower than that of the parent strain. In Bacillus subtilis, the accumulation of the Spx global regulator, a substrate of ClpXP, has accounted for the DeltaclpXP phenotypes. Searching the S. mutans genome, we identified two putative spx genes, designated spxA and spxB. The inactivation of either of these genes bypassed phenotypes of the clpP and clpX mutants. Western blotting demonstrated that Spx accumulates in the DeltaclpP and DeltaclpX strains. Our results reveal that the proteolysis of ClpL and ClpXP plays a role in the expression of key virulence traits of S. mutans and indicates that the underlying mechanisms by which ClpXP affect virulence traits are associated with the accumulation of two Spx orthologues.
Synthesis, Characterization, and Biological Activities of Some 3,5,6‐Trichloropyridine Derivatives. (2007)

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, please click on HTML or PDF.
Role of Outer Membrane Vesicles in Bacterial Physiology and Host Cell Interactions (2020)

Abstract Outer membrane vesicles (OMVs) are spherical particles shed from the outer membrane of Gram-negative bacteria, which contain the typical components present in the outer membrane, although enrichment of specific molecules may occur, and furthermore a variety of periplasmic components and occasionally some inner membrane or cytoplasmic fractions. Although the detailed mechanisms of OMV biogenesis are not fully illuminated yet, several models have been proposed that demonstrate OMV biogenesis is an orchestrated well-regulated process. OMV secretion offers a way for both intra- and inter-species bacterial communication and for interaction or modulation of the bacterial environment. Therefore, OMVs have proven to be functionally versatile and important for bacterial physiology and survival of the host environment. In the host, OMVs are internalized via host cell endocytosis pathways, allowing them to subsequently trigger a variety of cellular responses. In this review, we discuss the recent advances in establishing the mechanisms involved in OMV biogenesis and the impact of OMVs on bacterial physiology and intracellular modulation of the host.
Maintenance-optimized Modular Robotic Concepts for Planetary Surface ISRU Excavators (2020)

Modular robotic concepts are identified and evaluated over the design and operations/maintenance lifecycle for autonomous Lunar, Mars, and partial gravity planetary surface excavation and in-situ earthworks equipment. In-Situ Resource Utilization (ISRU) is the exploitation of available resources at the site of a landed spacecraft on the surface of another planetary body. It is intended that this ISRU excavator concept be capable of material extraction from native regolith, and will be able to operate in a variety of planetary surface environments after initial shakedown on the moon. Using heritage from highly multi-functional, reconfigurable robotic systems like the All-Terrain Hex-Limbed Extra-Terrestrial Explorer (ATHLETE), Regolith Advanced Surface Systems Operations Robot (RASSOR), and Mars exploration rovers, we propose a flexible maintenance-optimized mobility platform concept with quick-connect/disconnect features for robotically swappable excavation implements. Dust tolerant torque transmission, power & data docking, thermal fluid connectors, and modular avionics and instrumentation will allow for autonomous swapping of tools, replacement of spares, and longterm maintenance of robotic excavators. The architecture includes modular tools for conventional excavate / scoop / haul / dump / process functions of a terrestrial mining operation on Earth, but also will have the capability to operate and robotically maintain itself without human intervention. The concepts described in this study will provide a suite of technologies, configurations, and operations ready for inclusion into a final flight-ready excavator system.
Specific Binding of Nisin to the Peptidoglycan Precursor Lipid II Combines Pore Formation and Inhibition of Cell Wall Biosynthesis for Potent Antibiotic Activity (2001)

Unlike numerous pore-forming amphiphilic peptide antibiotics, the lantibiotic nisin is active in nanomolar concentrations, which results from its ability to use the lipid-bound cell wall precursor lipid II as a docking molecule for subsequent pore formation. Here we use genetically engineered nisin variants to identify the structural requirements for the interaction of the peptide with lipid II. Mutations affecting the conformation of the N-terminal part of nisin comprising rings A through C, e.g. [S3T]nisin, led to reduced binding and increased the peptide concentration necessary for pore formation. The binding constant for the S3T mutant was 0.043 10 7 M 1 compared with 2 10 7 M 1 for the wildtype peptide, and the minimum concentration for pore formation increased from the 1 nM to the 50 nM range. In contrast, peptides mutated in the flexible hinge region, e.g. [N20/M21]nisin, were completely inactive in the pore formation assay, but were reduced to some extent in their in vivo activity. We found the remaining in vivo activity to result from the unaltered capacity of the mutated peptide to bind to lipid II and thus to inhibit its incorporation into the peptidoglycan network. Therefore, through interaction with the membrane-bound cell wall precursor lipid II, nisin inhibits peptidoglycan synthesis and forms highly specific pores. The combination of two killing mechanisms in one molecule potentiates antibiotic activity and results in nanomolar MIC values, a strategy that may well be worth considering for the construction of novel antibiotics.