gebhart/patrepeval huggingface dataset:
The Genome Organization of Thermotoga maritima Reflects Its Lifestyle (2013)

The generation of genome-scale data is becoming more routine, yet the subsequent analysis of omics data remains a significant challenge. Here, an approach that integrates multiple omics datasets with bioinformatics tools was developed that produces a detailed annotation of several microbial genomic features. This methodology was used to characterize the genome of Thermotoga maritima--a phylogenetically deep-branching, hyperthermophilic bacterium. Experimental data were generated for whole-genome resequencing, transcription start site (TSS) determination, transcriptome profiling, and proteome profiling. These datasets, analyzed in combination with bioinformatics tools, served as a basis for the improvement of gene annotation, the elucidation of transcription units (TUs), the identification of putative non-coding RNAs (ncRNAs), and the determination of promoters and ribosome binding sites. This revealed many distinctive properties of the T. maritima genome organization relative to other bacteria. This genome has a high number of genes per TU (3.3), a paucity of putative ncRNAs (12), and few TUs with multiple TSSs (3.7%). Quantitative analysis of promoters and ribosome binding sites showed increased sequence conservation relative to other bacteria. The 5'UTRs follow an atypical bimodal length distribution comprised of "Short" 5'UTRs (11-17 nt) and "Common" 5'UTRs (26-32 nt). Transcriptional regulation is limited by a lack of intergenic space for the majority of TUs. Lastly, a high fraction of annotated genes are expressed independent of growth state and a linear correlation of mRNA/protein is observed (Pearson r = 0.63, p<2.2 × 10(-16) t-test). These distinctive properties are hypothesized to be a reflection of this organism's hyperthermophilic lifestyle and could yield novel insights into the evolutionary trajectory of microbial life on earth.
Diagnosis and grading of gastritis by non-invasive optical analysis (2004)

The results show that, in a normal clinical setting, the optical in vivo analysis provided by our system detects alterations typical of gastritis, and allow for their graded scoring with a specificity and sensitivity that compare well with those of standard histology, while avoiding the invasiveness of the latter procedure. The method is adaptable to the screening of other types of lesions and mucosae and, hence, should prove useful in improving available diagnostic approaches.
Epitaxial Growth of Wafer-Scale Molybdenum Disulfide/Graphene Heterostructures by Metal–Organic Vapor-Phase Epitaxy and Their Application in Photodetectors (2020)

Van der Waals heterostructures have attracted increasing interest, owing to the combined benefits of their constituents. These hybrid nanostructures can be realized via epitaxial growth, which offers a promising approach for the controlled synthesis of the desired crystal phase and the interface between van der Waals layers. Here, the epitaxial growth of a continuous molybdenum disulfide (MoS<sub>2</sub>) film on large-area graphene, which was directly grown on a sapphire substrate, is reported. Interestingly, the grain size of MoS<sub>2</sub> grown on graphene increases, whereas that of MoS<sub>2</sub> grown on SiO<sub>2</sub> decreases with an increasing amount of hydrogen in the chemical vapor deposition reactor. In addition, to achieve the same quality, MoS<sub>2</sub> grown on graphene requires a much lower growth temperature (400 °C) than that grown on SiO<sub>2</sub> (580 °C). The MoS<sub>2</sub>/graphene heterostructure that was epitaxially grown on a transparent platform was investigated to explore its photosensing properties and was found to exhibit inverse photoresponse with highly uniform photoresponsivity in the photodetector pixels fabricated across a full wafer. The MoS<sub>2</sub>/graphene heterostructure exhibited ultrahigh photoresponsivity (4.3 × 10<sup>4</sup> A W<sup>-1</sup>) upon exposure to visible light of a wide range of wavelengths, confirming the growth of a high-quality MoS<sub>2</sub>/graphene heterostructure with a clean interface.
Moth eye-inspired anti-reflective surfaces for improved IR optical systems & visible LEDs fabricated with colloidal lithography and etching (2018)

Near- and sub-wavelength photonic structures are used by numerous organisms (e.g. insects, cephalopods, fish, birds) to create vivid and often dynamically-tunable colors, as well as create, manipulate, or capture light for vision, communication, crypsis, photosynthesis, and defense. This review introduces the physics of moth eye (ME)-like, biomimetic nanostructures and discusses their application to reduce optical losses and improve efficiency of various optoelectronic devices, including photodetectors, photovoltaics, imagers, and light emitting diodes. Light-matter interactions at structured and heterogeneous surfaces over different length scales are discussed, as are the various methods used to create ME-inspired surfaces. Special interest is placed on a simple, scalable, and tunable method, namely colloidal lithography with plasma dry etching, to fabricate ME-inspired nanostructures in a vast suite of materials. Anti-reflective surfaces and coatings for IR devices and enhancing light extraction from visible light emitting diodes are highlighted.
Microparticle Encapsulation of a Prostate-targeted Biologic for the Treatment of Liver Metastases in a Preclinical Model of Castration-resistant Prostate Cancer (2020)

PRX302 is a highly potent, mutant bacterial pore-forming biologic protoxin engineered for selective activation by PSA, a serine protease expressed by benign and malignant prostate epithelial cells. Although being developed as a local therapy for benign prostatic hyperplasia and localized prostate cancer, PRX302 cannot be administered systemically as a treatment for metastatic disease due to binding to ubiquitously expressed glycosylphosphatidylinositol (GPI)-anchored proteins, which leads to poor accumulation within the tumor microenvironment. To overcome this limitation, poly-lactic-co-glycolic acid (PLGA) microparticles encapsulating the protoxin were developed, which are known to accumulate in the liver, a major site of metastasis for prostate cancer and other solid tumors. A highly sensitive and reproducible sandwich ELISA to quantify PRX302 released from microparticles was developed. Utilizing this assay, PRX302 release from different microparticle formulations was assessed over multiple days. Hemolysis assays documented PSA-dependent pore formation and lytic potential (i.e., function) of the released protoxin. MTT assays demonstrated that conditioned supernatant from PRX302-loaded, but not blank (i.e., unloaded), PLGA microparticles was highly cytotoxic to PC3 and DU145 human prostate cancer cells in the presence of exogenous PSA. Microparticle encapsulation prevented PRX302 from immediately interacting with GPI-anchored proteins as demonstrated in a competition assay, which resulted in an increased therapeutic index and significant antitumor efficacy following a single dose of PRX302-loaded microparticles in a preclinical model of prostate cancer liver metastasis with no obvious toxicity. These results document that PRX302 released from PLGA microparticles demonstrate <i>in vivo</i> antitumor efficacy in a clinically relevant preclinical model of metastatic prostate cancer.
Persistence of Decreased T-Helper Cell Function in Industrial Workers 20 Years after Exposure to 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (1996)

In experimentally exposed animals 2,3,7,8-tetrachlorodibenzo-n-dioxin (TCDD) causes severe immunosuppression. However, the overall susceptibility of humans for the different pathological effects of TCDD has remained unclear. We examined the long-term effects of TCDD in 11 industrial workers who were exposed to high doses of TCDD for several years 20 years ago. Current TCDD body burdens were still at least 10 times higher (between 43 and 874 pg/g blood far) in these exposed persons than in the average German population. To evaluate possible TCDD-induced changes in the percentage of different lymphocyte subsets, we determined a large panel of lymphocyte subsets in the blood by flow cytometric analysis. Immunocompetence of T-and B-lymphocytes was tested by nitrogen (phytohemagglutinin, pokeweed mitogen)- induced lymphoproliferation assays and by assays using sensitive mixed-lymphocyte cultures. No significant differences could be detected between the individuals tested and controls for surface marker distribution or mitogen-induced lymphoproliferation TCDD-exposed subjects showed a reduced response to human lymphocyte antigen-allogeneic lymphocytes and interleukin-2-boosted proliferation. Responder cells of the dioxin-exposed persons proliferated less in response to irradiated stimulator cells (p &lt; or = 0.05), and the third-party mixed lymphocyte reaction against unirradiated stimulator cells revealed suppressive activity in the responder cell fraction compared to the controls (p &lt; or = 0.01). Furthermore, the capacity of a pool of T cells isolated from TCDD-exposed subjects to proliferate upon interleukin-2 stimulation was significantly diminished (p &lt; or = 0.05). TCDD has a long-term immunosuppressive-effect on T-helper cell function, which is mediated more likely by a reduced functionality of individual cells rather than by a reduction in absolute cell numbers in the peripheral blood.
Impact of die-to-die and within-die parameter variations on the throughput distribution of multi-core processors (2007)

A statistical performance simulator is developed to explore the impact of die-to-die (D2D) and within-die (WID) parameter variations on the distributions of maximum clock frequency (FMAX) and throughput for multi-core processors in a future 22nm technology.allThe simulator integrates a compact analytical throughput model, which captures the key dependencies of multi-core processors, into a statistical simulation framework that models the effects of D2D and WID parameter variations on critical path delays across a die. The salient contributions from this paper are: (1) Product-level variation analysis for multi-core processors must focus on throughput, rather than just FMAX, and (2) Multi-core processors are inherently more variation tolerant than single-core processors due to the larger impact of memory latency and bandwidth on overall throughput. To elucidate these two points, multi-core and single-core processors have a similar chip-level FMAX distribution (mean degradation of 9% and standard deviation of 5%) for multi-threaded applications. In contrast to single-core processors, memory latency and bandwidth constraints significantly limit the throughput dependency on FMAX in multi-core processors, thus reducing the throughput mean degradation and standard deviation by 50%. Since single-threaded applications running on a multi-core processor can execute on the fastest core, mean FMAX and throughput gains of 4% are achieved from the nominal design target.
Stretchable Gas Barrier Achieved with Partially Hydrogen‐Bonded Multilayer Nanocoating (2014)

Super gas barrier nanocoatings are recently demonstrated by combining polyelectrolytes and clay nanoplatelets with layer-by-layer deposition. These nanobrick wall thin films match or exceed the gas barrier of SiOx and metallized films, but they are relatively stiff and lose barrier with significant stretching (≥ 10% strain). In an effort to impart stretchability, hydrogen-bonding polyglycidol (PGD) layers are added to an electrostatically bonded thin film assembly of polyethylenimine (PEI) and montmorillonite (MMT) clay. The oxygen transmission rate of a 125-nm thick PEI-MMT film increases more than 40x after being stretched 10%, while PGD-PEI-MMT trilayers of the same thickness maintain its gas barrier. This stretchable trilayer system has an OTR three times lower than the PEI-MMT bilayer system after stretching. This report marks the first stretchable high gas barrier thin film, which is potentially useful for applications that require pressurized elastomers.
Translating the Simulation of Procedural Drilling Techniques for Interactive Neurosurgical Training (2013)

We have presented our efforts to translate an otologic simulation environment for use in the neurosurgical curriculum. We have demonstrated the initial proof of principles and define the steps to integrate and validate the system as an adjuvant to the neurosurgical curriculum.
Secure broadcasting in cooperative cognitive radio networks (2012)

This paper explores the trade-off between cooperation and secrecy in cognitive radio networks. We consider a scenario consisting of a primary and a secondary system. In the simplest case, each system is represented by a pair of transmitter and receiver. We assume a secrecy constraint on the transmission in the sense that the message of the primary transmitter has to be concealed from the secondary user. Both situations where the secondary transmitter is aware and unaware of the primary message are investigated and compared. Furthermore, we extend our results to the scenario where the secondary system comprises multiple users. For each case we sketch the derivation of the rates that are achievable from an information theoretic perspective. We then investigate the findings by numerical simulations. Our main result is that, in spite of the secrecy constraint, cooperation is beneficial in terms of the achievable rates. The secondary transmitter has the two contradicting tasks of helping the primary system and transmitting its own message. Our results show that both tasks can be accomplished simultaneously, improving both systems' performance. In particular, the secondary system can achieve a significant rate without decreasing the primary rate below the benchmark rate achievable without the help of the secondary transmitter. In the case of multiple secondary users, the rate region reduces, which results in a lower individual rate. However, the linear increase in sumrate counterbalances this effect.
Are redox changes a critical switch for mitotic progression? (2020)

Cell-cycle dependent redox changes result in increased protein oxidation in mitotic cells. We show that oxidative modifications of a conserved cysteine residue within Aurora A kinase (AURKA) can promote its activation during mitosis. Targeting redox-sensitive cysteine residues within AURKA may lead to the development of novel anti-cancer agents with improved clinical efficacy.
Portable Chronic Alcohol Consumption Monitor in Human Sweat through Square-Wave Voltammetry (2017)

Chronic alcohol consumption is a significant financial and physical burden in the United States each year. Alcohol consumption monitors focus on establishing a state of intoxication, not assessing a user's health risks as a function of consumed alcohol. This work demonstrates a biosensor for a chronic alcohol consumption monitor through the electrochemical detection of ethyl glucuronide (EtG) in human sweat using square-wave voltammetry (SWV). A novel affinity assay was demonstrated in which monoclonal antibodies were chemically coabsorbed onto a gold electrode surface in parallel with thiolated charge transfer molecule. Concentration-dependent EtG binding was detected by measuring a reduction in the charge transfer of the sensor, manifesting as a current response during SWV measurement. A companion compact electronic reader was constructed, demonstrating comparable sensitivity to a conventional lab instrument. Both tools demonstrated a limit of detection of 0.1 µg/L and a linear dynamic range of 0.1-100 µg/L corresponding to the physiologically relevant range of EtG expression in human sweat. This device can address the need for a chronic alcohol consumption monitor toward establishing a user's long-term consumption habits to assess the risk of developing specific diseases and conditions associated with regular alcohol consumption, through integration with existing technologies.
Transmission of HBV DNA Mediated by Ceramide-Triggered Extracellular Vesicles (2016)

These findings suggest that EVs harbor a DNA cargo capable of transmitting viral DNA into hepatocytes during HBV infection, representing an additional antibody-neutralization-resistant route of HBV infection.
Instruction of myeloid cells by the tumor microenvironment: Open questions on the dynamics and plasticity of different tumor-associated myeloid cell populations (2012)

The versatility and plasticity of myeloid cell polarization/differentiation has turned out to be crucial in health and disease, and has become the subject of intense investigation during the last years. On one hand, myeloid cells provide a critical contribution to tissue homeostasis and repair. On the other hand, myeloid cells not only play an important role as first line defense against pathogens but also they are involved in a broad array of inflammation-related diseases such as cancer. Recent studies show that macrophages can exist in different activation states within the same tumor, underlining their plasticity and heterogeneity. In this review, we will discuss recent evidence on how the tumor microenvironment, as it evolves, shapes the recruitment, function, polarization and differentiation of the myeloid cell compartment, leading to the selection of myeloid cells with immunosuppressive and angiogenic functions that facilitate tumor progression and dissemination.
In vitro and in vivo assessment of oxygenator blood volume for the prediction of clot formation in an ECMO circuit (theory and validation) (2018)

Dilution technology has the ability to accurately and reproducibly assess the clotting process in the oxygenator. Larger studies are needed to establish guidelines for the prediction of imminent clotting and may help to avoid unnecessary circuit changes.
Cover Picture: Macromol. Rapid Commun. 3/2006 (2006)

Cover: The cover picture shows a strategy used to synthesize new functional polyethylenes (PE). A neodymium based complex catalyzes ethylene chain growth reaction on MgR 2 producing Mg(PE) 2 . Those are excellent candidates to react with disulfides of thiocarbonylated compounds (RC(S)SSC‐(S)R). Further details can be found in the Communication by R. Godoy Lopez, C. Boisson, F. D'Agosto, * R. Spitz, F. Boisson, D. Gigmes, and D. Bertin on page 173.
Enhanced osteogenesis by collagen‐binding peptide from bone sialoprotein in vitro and in vivo (2012)

Bone sialoprotein (BSP) is a mineralized, tissue-specific, and noncollagenous protein. The binding of BSP to collagen is thought to be important for the initiation of bone mineralization and formation. In this study, we elucidated the osteogenic efficiency of the collagen-binding (CB) peptide derived from BSP in vitro and in vivo. The CB peptide increased osteoblastic differentiation marker gene and protein expression without affecting cell proliferation. The osteoblastic differentiation by the CB peptide is performed by the activation of extracellular signal-regulated kinase (ERK1/2) and protein kinase B (Akt). Notably, the activation of CB peptide-induced osteogenic differentiation was completely blocked to the basal level by the specific inhibitors for ERK1/2 (U0126) and Akt (LY294002). In vivo results further demonstrated that the CB peptide-coated hydroxyapatite scaffold was able to induce bone formation in the bone defect. Taken together, the CB peptide can be developed as an osteoblastic differentiation agent as well as a fusion biomaterial for bone regeneration therapy.
Low-Concentration Ethanol Vapor Sensing With Nanostructured Porous Silicon Interferometers Using Interferogram Average Over Wavelength Reflectance Spectroscopy (2018)

Herein, we report low-concentration ethanol vapor detection with nanostructured porous silicon (PSi) interferometers using interferogram average over wavelength reflectance spectroscopy (IAWRS), a novel interferometric technique recently developed for ultrasensitive (bio)sensing applications in liquid using miniaturized integrated interferometers. Ethanol vapors at concentrations of 100, 500, and 1000 ppm (in synthetic dry air) are reliably monitored in real-time using IAWRS by monitoring changes on the reflectance spectrum of PSi interferometers after ethanol physisorption onto the nanopore surface. Good signal-to-noise ratio, high sensitivity, and low resolution are achieved at any of the tested concentrations, leading to a theoretical detection limit (DL) of 0.9 ppm. Fast response times of a few tens of seconds are estimated from time-resolved sensorgrams, both for adsorption and desorption, which confirm that physisorption takes place into the nanopores. Capillary condensation of ethanol in the pores of our PSi interferometers is further ruled out using the Kelvin theory, at least at the concentrations tested in this paper. These results represent a remarkable improvement compared to the state-of-the-art literature on gas/vapor optical sensing using nanostructured PSi, according to which sub-ppm DLs can only be achieved exploiting either capillary condensation in the nanopores or through the assembling PSi-polymer composites.
Superparamagnetic Gadonanotubes Are High‐Performance MRI Contrast Agents. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Cover Picture: Fast mapping of inhomogeneities in the popular metallic perovskite Nb:SrTiO3 by confocal Raman microscopy (Phys. Status Solidi RRL 9/2014) (2014)

No abstract is available for this article.
Counting networks are practically linearizable (1996)

Counting networks are a class of concurrent structures that allow the design of highly scalable concurrent data structures in a way that eliminates sequential bottlenecks and contention. Linearizable counting networks assure that the order of the values returned by the network reflects the real-time order in which they were requested. We argue that in many concurrent systems the worst case scenarios that violate linearizability require a form of timing anomaly that is uncommon in practice. The linear time cost of designing networks that achieve linearizability under all circumstances may thus prove an unnecessary burden on applications that are willing to trade-off occasional non-linearizability for speed and parallelism.
Alkyl‐linked diquinolines are monofunctional AT‐selective DNA‐intercalating agents (1988)

The binding of a homologous series of alkyl-linked 4-aminodiquinolines to circular and linear DNAs was studied using viscometric titrations and equilibrium dialysis. The compounds are monofunctional intercalators with the capacity for intercalative binding reaching a peak for the heptane homologue. They show marked AT-base pair selectivity, which suggests that the non-intercalated quinoline ring may lie in the DNA minor groove. Affinities for calf thymus DNA increase as the alkyl chain is lengthened, falling in the range 6 to greater than 250 X 10(4) M-1 in a buffer of I 0.01. The association constant of the heptane diquinoline decreases with increasing ionic strength, 2.1 cations being released per bound dipositive ligand molecule. All the agents are growth inhibitory towards mouse leukemia cells in culture with IC50 values in the range 0.06-18 microM.
An accessory role for Escherichia coli integration host factor: characterization of a lambda mutant dependent upon integration host factor for DNA packaging (1984)

Bacteriophage lambda grows lytically on Escherichia coli defective for integration host factor, a protein involved in lambda site-specific recombination and the regulation of gene expression. We report the characterization of a mutant, lambda cos154, that, unlike wild-type lambda, is defective for growth in integration host factor-defective E. coli. The cis-dominant mutation in lambda cos154 is a single base pair change in a region of hyphenated dyad symmetry close to the lambda left cohesive end; this mutation prevents DNA packaging. We propose the following two alternative roles for this site in lambda DNA packaging: (i) to bind an E. coli accessory protein required in the absence of integration host factor or (ii) to bind the phage-encoded terminase protein that is essential for DNA packaging.