gebhart/patrepeval huggingface dataset:
Synthesis, Characterization and Radical Scavenging Ability of 3,5-di-tert-Butyl-4-hydroxyphenoxy-Functionalized Polynorbornenes Synthesized Using Ring-Opening Metathesis Polymerization (2009)

Novel norbornene derivatives bearing a 3,5-di-tert-butyl-4-hydroxyphenoxy (DBHO) group were synthesized and used as sterically hindered phenol functionalized norbornene monomers (1–4). The ring-opening metathesis polymerization (ROMP) of these functional monomers was carried out with a typical ruthenium catalyst (bis(tricyclohexylphosphine)benzylidene ruthenium (IV) dichloride, a Grubbs first-generation catalyst) to prepare sterically-hindered phenol-functionalized polymers possessing radical scavenging function. The resulting polymers bearing a DBHO side-chain were characterized by means of gel-permeation chromatography, 1H-NMR and 13C-NMR. The radical scavenging ability of polymers was determined using the α,α-diphenyl-β-picrylhydrazyl (DPPH⋅) free radical. Due to the electron-donating effect of the oxygen atom located in the para-position of phenol, the resulting polymers showed high efficiency to scavenge DPPH⋅free radical. The molecular weight of polymers was dependent on the molar ratio of monomer to catalyst ([M]/[C]), and the ROMP activity was dependent on the stereostructure of monomers themselves.
Ultrasound Imaging: Waves, Signals, and Signal Processing (2007)

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A barley polyamine oxidase isoform with distinct structural features and subcellular localization (2001)

Two cDNAs encoding polyamine oxidase (PAO) isoforms (BPAO1 and BPAO2) and the corresponding gene copies were isolated from barley cultivar Aura. Gene organization is not conserved between these two nonallelic coding sequences. Both precursor proteins include a cleavable N-terminal leader of 25 amino acids. N-terminal sequencing of PAO purified from barley seedlings reveals a unique amino-acid sequence corresponding to the BPAO2 N-terminus as predicted from the corresponding cDNA. BPAO2 has been purified, characterized and compared to maize PAO (MPAO), the best characterized member of this enzyme class. The two proteins show different pH optima for catalytic activity, Km and Vmax values with spermidine and spermine as substrates. Molecular modelling of BPAO2 reveals the same global fold as in MPAO. However, substitution of the active site residue Phe403 by a tyrosine, provides a rationale for the different catalytic properties of the two enzymes. In barley leaves PAO-specific activity is higher in isolated mesophyll protoplasts than in the extracellular fluids, whereas in maize the reverse is true. The C-terminus of BPAO2 shows homology with the endoplasmic reticulum retention signal that might be responsible for the subcellular localization observed. We conclude that BPAO2 is a symplastic PAO in barley mesophyll cells. Production of BPAO2 mRNA and the corresponding protein is induced by light, and has a different pattern of accumulation in leaves and coleoptiles.
A facility description language for distributed design integration (1995)

A principal goal of concurrent engineering has been to reduce the development cycle and time to market for new products. The success of such efforts brings about a parallel need for rapid design, evaluation, and reconfiguration of the facilities required to manufacture these products. Traditional facility layout methods rely on a sequence of actions progressing through a series of increasingly detailed analyses. More recent techniques automate and improve this process. However, there is little progress toward an integrated environment that supports the interactions of multidisciplinary facility design teams, similar to those that have enhanced the product design process. This research introduces a generic Facility Description Language (FDL), which provides a common formal base for collaborative work and detailed analysis of process layout, flow geometry, visual aspects of control, and safety. FDL utilizes the capabilities of simulator-emulator design workstations to integrate the physical and logical aspects of manufacturing facility design. Specifically, this research defines the basic functions of FDL and a prototype implementation architecture. This language can serve as a useful structure for the definition and description of a production facility at different levels of abstraction, allowing the same basic design model to be iteratively refined throughout the development process. This research demonstrates how the combination of FDL with an interactive graphical environment provides a powerful modeling tool that permits distributed users to achieve a higher level of design synergy.
Calcineurin Controls Growth, Morphology, and Pathogenicity in Aspergillus fumigatus (2006)

Calcineurin is implicated in a myriad of human diseases as well as homeostasis and virulence in several major human pathogenic microorganisms. The fungus Aspergillus fumigatus is a leading cause of infectious death in the rapidly expanding immunocompromised patient population. Current antifungal treatments for invasive aspergillosis are often ineffective, and novel therapeutic approaches are urgently needed. We demonstrate that a mutant of A. fumigatus lacking the calcineurin A (cnaA) catalytic subunit exhibited defective hyphal morphology related to apical extension and polarized growth, which resulted in drastically decreased filamentation. The delta cnaA mutant lacked the extensive lattice of invading hyphae seen with the wild-type and complemented strains. Sporulation was also affected in the delta cnaA mutant, including morphological conidial defects with the absence of surface rodlets and the added presence of disjunctors creating long conidial chains. Infection with the delta cnaA mutant in several distinct animal models with different types of immunosuppression and inoculum delivery led to a profound attenuation of pathogenicity compared to infection with the wild-type and complemented strains. Lung tissue from animals infected with the delta cnaA mutant showed a complete absence of hyphae, in contrast to tissue from animals infected with the wild-type and complemented strains. Quantitative fungal burden and pulmonary infarct scoring confirmed these findings. Our results support the clinical observation that substantially decreasing fungal growth can prevent disease establishment and decrease mortality. Our findings reveal that calcineurin appears to play a globally conserved role in the virulence of several pathogenic fungi and yet plays specialized roles in each and can be an excellent target for therapeutic intervention.
DNA Extraction from Archival Formalin-fixed, Paraffin-embedded Tissue Sections Based on the Antigen Retrieval Principle: Heating Under the Influence of pH (2002)

During the course of diagnostic surgical pathology, pathologists have established a large collection of formalin-fixed, paraffin-embedded tissues that form invaluable resources for translational studies of cancer and a variety of other diseases. Accessibility of macromolecules in the fixed tissue specimens is a critical issue as exemplified by heat-induced antigen retrieval (AR) immunohistochemical (IHC) staining. On the basis of observations that heating may also enhance in situ hybridization (ISH) and the similarity of formalin-induced chemical modifications that occur in protein and in DNA, we designed a study to examine the efficiency of DNA extraction from archival formalin-fixed, paraffin-embedded tissues using an adaptation of the basic principles of the AR technique, i.e., heating the tissue under the influence of different pH values. Archival paraffin blocks of lymph nodes, tonsil, and colon were randomly selected. Each paraffin block was prepared in 34 microtubes. For each paraffin block, one tube was used as a control sample, using a non-heating DNA extraction protocol. The other 33 tubes were tested using a heating protocol under 11 variable pH values (pH 2 to 12) under three different heating conditions (80, 100, and 120C). Evaluation of the results of DNA extraction was carried out by measuring yields by photometry and PCR amplification, as well as kinetic thermocycling (KTC)-PCR methods. In general, lower pH (acid) solutions gave inferior results to solutions at higher pH (alkaline). Heating tissues at a higher temperature and at pH 6-9 gave higher yields of DNA. There appeared to be a peak in terms of highest efficiency of extracted DNA at around pH 9. The average ratios 260:280 of extracted DNA also showed better values for samples heated at 120C. PCR products of three primers showed satisfactory results for DNA extracted from archival paraffin-embedded tissues by heating protocols at pH 6-12, with results that were comparable to the control sample subjected to the standard non-heating, enzymatic DNA extraction method. This study is the first to document the use of heating at an alkaline pH for DNA extraction from archival formalin-fixed, paraffin-embedded tissues, a recommendation based on the principles of AR for protein IHC. These findings may lead to a more effective protocol for DNA extraction from archival paraffin-embedded tissues and may also provide enhanced understanding of changes that occur during formalin-induced modification of nucleic acids.
Overcoming Contact Hurdles for Investigating Lower Dimensional Structures in Undoped Heterostructures (2007)

Undoped GaAs/AlGaAs heterostructures are attractive systems for studying lower dimensional structures and electron-electron interactions, eliminating or reducing many of the problems that come with the more traditional modulation doped system. A major obstacle involved in using systems where the two dimensional electron gas (2DEG) was induced with a biased top gate was the inability to form a reliable ohmic contact to the 2DEG. We report here a systematic study of the contact system (Au-Ge-Ni), including a discussion of how a various diffusion barriers may prove beneficial, and how the etch depth of the recessed ohmic contact effects the window of success. Yield with the new process approaches 100%, compared to a catastrophically low rate before the system was understood.
A FIBER PROFILE MONITOR FOR LOW BEAM INTENSITIES (2007)

A scintillating Fiber Profile Monitor (FPM) has been prototyped, built and tested for the new low intensity Meson Test (M-Test) beamline at Fermilab. The beamline has the following beam parameters: E = 1-120 GeV, I from a few hundreds to 700,000 particles/spill, the spill length is 4.5 seconds with a cycle time of 1 minute. Segmented Wire Ion Chambers (SWICs) and Proportional Wire Chambers (PWCs) do not display the beam profile accurately below about 10,000 particles. For the prototype FPM detector a modified SWIC vacuum can was used. An (x, y) array of fibers replaced the chamber containing windows, gas, and AuW wires soldered on a ceramic substrate. The fibers were purchased from Saint Gobain and are of the type BCF-12 MC, 420 nm wavelength. They have a diameter of 0.75 mm and are coated with black EMA for optical isolation. The 64 channel fibers are positioned and then epoxied in a vacuum feed-through cookie to match a Burle 64 channel multianode microchannel plate PMT of the type Planacon # 85011-501. The gain of the Planacon PMT is 800,000 at -2400 Volts. Unlike SWICs or PWCs, this device will allow for vacuum continuity. Comparative data with PWCs will be presented. THE BEAMLINE
Machine Learning for Beam Based Mobility Optimization in NR (2017)

One option for enabling mobility between 5G nodes is to use a set of area-fixed reference beams in the downlink direction from each node. To save power these reference beams should be turned on only on demand, i.e. only if a mobile needs it. An User Equipment (UE) moving out of a beam's coverage will require a switch from one beam to another, preferably without having to turn on all possible beams to find out which one is the best. This thesis investigates how to transform the beam selection problem into a format suitable for machine learning and how good such solutions are compared to baseline models. The baseline models considered were beam overlap and average Reference Signal Received Power (RSRP), both building beam-to-beam maps. Emphasis in the thesis was on handovers between nodes and finding the beam with the highest RSRP. Beam-hit-rate and RSRP-difference (selected minus best) were key performance indicators and were compared for different numbers of activated beams. The problem was modeled as a Multiple Output Regression (MOR) problem and as a Multi-Class Classification (MCC) problem. Both problems are possible to solve with the random forest model, which was the learning model of choice during this work. An Ericsson simulator was used to simulate and collect data from a seven-site scenario with 40 UEs. Primary features available were the current serving beam index and its RSRP. Additional features, like position and distance, were suggested, though many ended up being limited either by the simulated scenario or by the cost of acquiring the feature in a real-world scenario. Using primary features only, learned models' performance were equal to or worse than the baseline models' performance. Adding distance improved the performance considerably, beating the baseline models, but still leaving room for more improvements.
<p>Nanomicellar Lenalidomide–Fenretinide Combination Suppresses Tumor Growth in an <em>MYCN</em> Amplified Neuroblastoma Tumor</p> (2020)

FLM treatment induced a superior antitumor response than FM in NLF xenografts, presumably due to the combined effects of fenretinide cytotoxicity and lenalidomide antiangiogenic activity. The ability of FLM to penetrate tumor cells, transporting the encapsulated drugs, substantially improved the therapeutic efficiency of this system. Moreover, the enhancement of GD2 expression in FLM treated tumors offers the possibility to further increase the antitumor effect by the use of anti-GD2 CAR-T cells and anti-GD2 antibodies in combination with FLM in multimodal therapies.
Interim results of the SLATS concentrator experiment on LIPS-II (space vehicle power plants) (1988)

An analysis of four months of data from SLATS concentrator experiments on LIPS-III is presented. The array panel includes three mirrors, each focusing on two different linear solar cell strings. Small changes in current, voltage, and temperature have been observed in all six experiments. The use of unglassed solar cells on four of the six strings does not seem to affect these performance trends, confirming that the surrounding mirror and cell assembly components can be used as cell shielding. Analysis of current output during off-pointed periods allows a determination of concentrator pointing tolerances. Results show the ability of the design to withstand launch and deployment forces and maintain the accuracy needed for optical efficiency.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Trait Repertoire Enabling Cyanobacteria to Bloom Assessed through Comparative Genomic Complexity and Metatranscriptomics (2020)

Water bloom development due to eutrophication constitutes a case of niche specialization among planktonic cyanobacteria, but the genomic repertoire allowing bloom formation in only some species has not been fully characterized. We posited that the habitat relevance of a trait begets its underlying genomic complexity, so that traits within the repertoire would be differentially more complex in species successfully thriving in that habitat than in close species that cannot. To test this for the case of bloom-forming cyanobacteria, we curated 17 potentially relevant query metabolic pathways and five core pathways selected according to existing ecophysiological literature. The available 113 genomes were split into those of blooming (45) or nonblooming (68) strains, and an index of genomic complexity for each strain's version of each pathway was derived. We show that strain versions of all query pathways were significantly more complex in bloomers, with complexity in fact correlating positively with strain blooming incidence in 14 of those pathways. Five core pathways, relevant everywhere, showed no differential complexity or correlations. Gas vesicle, toxin and fatty acid synthesis, amino acid uptake, and C, N, and S acquisition systems were most strikingly relevant in the blooming repertoire. Further, we validated our findings using metagenomic gene expression analyses of blooming and nonblooming cyanobacteria in natural settings, where pathways in the repertoire were differentially overexpressed according to their relative complexity in bloomers, but not in nonbloomers. We expect that this approach may find applications to other habitats and organismal groups.<b>IMPORTANCE</b> We pragmatically delineate the trait repertoire that enables organismal niche specialization. We based our approach on the tenet, derived from evolutionary and complex-system considerations, that genomic units that can significantly contribute to fitness in a certain habitat will be comparatively more complex in organisms specialized to that habitat than their genomic homologs found in organisms from other habitats. We tested this in cyanobacteria forming harmful water blooms, for which decades-long efforts in ecological physiology and genomics exist. Our results essentially confirm that genomics and ecology can be linked through comparative complexity analyses, providing a tool that should be of general applicability for any group of organisms and any habitat, and enabling the posing of grounded hypotheses regarding the ecogenomic basis for diversification.
Comparison of Cloud Top Altitudes from Passive and Active Remote Sensors onboard ER‐2 during TC4 (2009)

Cloud altitude is one of the key properties for the Earth radiation budget. There still exist large uncertainties on cloud altitude as well as optical and microphysical properties for high altitude clouds, in particular. Targeting the high altitude clouds around tropical tropopause transition layer (TTL), the Tropical Composition, Clouds and Climate Coupling (TC4) Experiment was carried out, based on Costa Rica during July and August 2007. In this campaign, NASA’s high altitude airplane, ER‐2, made remote sensing observation, and we obtained precious data with both passive and active remote sensors, such as Imager, Sounder, LIDAR, Radar, and so on. In this study, we compare cloud top altitudes using colocated datasets with Imager, LIDAR, and Sounder onboard the high altitude airplane. We have preliminary results, which are generally consistent with the former field campaign based on Hawaii during February and March 2003. We discuss the consistency between IR sounding and LIDAR backscattering measurements, and also show a result with respect to cloud optical and microphysical properties.
Repair of bone defect using bioglass-chitosan as a pharmaceutical drug: An experimental study in an ovariectomised rat model (2012)

International audience
A Pipeline VLSI Architecture for High-Speed Computation of the 1-D Discrete Wavelet Transform (2010)

In this paper, a scheme for the design of a high-speed pipeline VLSI architecture for the computation of the 1-D discrete wavelet transform (DWT) is proposed. The main focus of the scheme is on reducing the number and period of clock cycles for the DWT computation with little or no overhead on the hardware resources by maximizing the inter- and intrastage parallelisms of the pipeline. The interstage parallelism is enhanced by optimally mapping the computational load associated with the various DWT decomposition levels to the stages of the pipeline and by synchronizing their operations. The intrastage parallelism is enhanced by decomposing the filtering operation equally into two subtasks that can be performed independently in parallel and by optimally organizing the bitwise operations for performing each subtask so that the delay of the critical data path from a partial-product bit to a bit of the output sample for the filtering operation is minimized. It is shown that an architecture designed based on the proposed scheme requires a smaller number of clock cycles compared to that of the architectures employing comparable hardware resources. In fact, the requirement on the hardware resources of the architecture designed by using the proposed scheme also gets improved due to a smaller number of registers that need to be employed. Based on the proposed scheme, a specific example of designing an architecture for the DWT computation is considered. In order to assess the feasibility and the efficiency of the proposed scheme, the architecture thus designed is simulated and implemented on a field-programmable gate-array board. It is seen that the simulation and implementation results conform to the stated goals of the proposed scheme, thus making the scheme a viable approach for designing a practical and realizable architecture for real-time DWT computation.
Chemoselective synthesis and analysis of naturally occurring phosphorylated cysteine peptides (2016)

In contrast to protein O-phosphorylation, studying the function of the less frequent N- and S-phosphorylation events have lagged behind because they have chemical features that prevent their manipulation through standard synthetic and analytical methods. Here we report on the development of a chemoselective synthetic method to phosphorylate Cys side-chains in unprotected peptides. This approach makes use of a reaction between nucleophilic phosphites and electrophilic disulfides accessible by standard methods. We achieve the stereochemically defined phosphorylation of a Cys residue and verify the modification using electron-transfer higher-energy dissociation (EThcD) mass spectrometry. To demonstrate the use of the approach in resolving biological questions, we identify an endogenous Cys phosphorylation site in IICB(Glc), which is known to be involved in the carbohydrate uptake from the bacterial phosphotransferase system (PTS). This new chemical and analytical approach finally allows further investigating the functions and significance of Cys phosphorylation in a wide range of crucial cellular processes.
High-speed modulation of quantum-dot lasers (1999)

The formation of nanostructures through the Stranski-Krastanow growth mode has proven to be an excellent method of forming damage-free quantum dots and has demonstrated laser operation and some improved characteristics expected for quantum dots. However, due to the complex nature of the bandstructure, quantum dot array formation, and carrier interactions in the dots, the understanding of self-assembled quantum dot lasers is still in the early stages. In order to meet a wide range of applications, the dynamic properties of the lasers have to be characterized, understood and, if necessary, improved. These properties impact small- and large-signal modulation phenomena and associated gain switching and chirp. We present our observations on the dynamic properties of self-assembled quantum dot lasers. In addition to improving laser performance, the discrete energy levels in quantum dots provide for unique laser applications. The lasing in self-assembled quantum dot devices has been shown to exist for ground and excited state transitions, depending on the gain in the active region. Through use of a cavity-coupled saturable absorber region, the gain may be altered to provide lasing in either the ground or excited state in a quantum dot laser, providing controlled wavelength switching, useful for optoelectronic integrated circuit applications and wavelength division multiplexing. Laser heterostructures with self-assembled In/sub 0.4/Ga/sub 0.6/As quantum dots as the gain medium were grown by molecular beam epitaxy (MBE).