gebhart/patrepeval huggingface dataset:
Inhibition of CUTIN DEFICIENT 2 Causes Defects in Cuticle Function and Structure and Metabolite Changes in Tomato Fruit (2013)

Tomato (Solanum lycopersicum) fruit cuticle has been extensively studied due to its effect on the biochemical and physiological properties of the fruit. To date, several tomato mutants defective in proper cuticle formation have been identified. To gain insight into tomato cuticle formation, we investigated one such mutant, sticky peel/light green (pe lg). We verified the responsible gene by fine mapping and obtained the same conclusion as a previous report. To elucidate the pleiotropic effects of cuticle deficiency caused by the cd2 mutation, CD2 suppression lines were constructed. As found in the pe lg mutant, the suppression lines showed enhanced water permeability and aberrant leaf and fruit cuticles. Water use efficiency of the suppression line was lower than that of the wild type. However, photosynthetic ability was not affected in the suppression line. Since these phenotypes are related to altered deposition of wax and cutin, other lipidic metabolites might be changed, too. To confirm this hypothesis, we conducted metabolite profiling. The metabolite profiling revealed that not only lipid but also sugar, flavonoid and glycoalkaloid metabolites in fruit were changed in the cd2 mutant. These results indicate that CD2 is essential both for normal cutin and wax deposition and for proper accumulation of specific metabolites in tomato fruit.
FhuA–Grubbs–Hoveyda Biohybrid Catalyst Embedded in a Polymer Film Enables Catalysis in Neat Substrates (2020)

Incorporation of metal catalysts into protein scaffolds results in biohybrid catalysts, which have been shown to catalyze various non-natural reactions. Until recently, catalysis with biohybrid catalysts has been performed exclusively in aqueous solutions to maintain the structural integrity of protein scaffolds. Here, we present the incorporation of a biohybrid catalyst into a synthetic polymer film. Ferric hydroxamate uptake protein component A (FhuA), a β-barrel protein, is copolymerized with N-methylpyrrole by electrochemical polymerization. Covalent incorporation of an artificial cofactor into the “stacked barrels” of FhuA gives a catalytic biocomposite enabling ring-closing olefin metathesis in neat substrates.
Stimulation strategies for selective activation of retinal ganglion cell soma and threshold reduction (2018)

Our findings support the possibility of manipulating the responses of RGCs through varying the stimulation waveform. Focal response can be achieved with relative short duration (⩽120 μs) pulses, and can be improved by reversing the standard phase order. The RGCs threshold can be significantly reduced by 33.3%-50% in terms of charge through applying hyperpolarizing pre-pulses with a 20:1 ratio (pre-pulse:stimulus pulse). The results support the future retinal prosthesis design that potentially forms more ideal shape perception with higher spatial resolution and power efficiency.
Gill Ectoparasites of Juvenile Rainbow Trout and Brown Trout in the Upper Colorado River (1999)

During 1996 and 1997, 112 rainbow trout Oncorhynchus mykiss and 204 brown trout Salmo trutta, all young of the year, were sampled from a 40-km study area of the upper Colorado River and were examined for gill parasites. Ambiphrya, Chilodonella, Ichthyobodo, Apiosoma, Trichodina, Trichodinella, Tripartiella, Epistylis, and an unidentified cochliopodid amoeba were the representative protozoan genera observed on fish examined. Significant month–year–species interactions (P = 0.0295) were revealed, reflecting the changes in infestation prevalence among months, years, and species of salmonid. Greater ectoparasite richness was observed in downstream sections of the study area, most notably near Hot Sulphur Springs, Colorado. Peaks of infestation intensity and ectoparasite richness occurred in August and September of both years, presumably because of high mean water temperatures and low flows during that time.
Tecnologías electroquímicas como alternativas en el tratamiento de aguas contaminadas: adsorción por carbón activado. (2010)

&lt;p&gt;A general review about main electrochemical and membranes technologies is presented in this work as alternatives to remove pollutants from waters, such as pesticides, heavy metals, organic matter, and microorganisms. Activated carbon is described as an example in most detail. Also, some advances about studies have been carried out at the National Institute for Scientific Research – Water, Earth, and Environment (INRS – ETE French capital letters) from Quebec, Canada. A project among INRS – ETE and two Mexican Higher Education Institutions is been developing as part of the Quebec-Mexico Work Group activities, they are ITSON and ITESCA.&lt;/p&gt;
Laser-induced material modification in the bulk KDP crystals (2000)

Laser induced materials modifications in the bulk and on the surface of KDP and DKDP are studied using fluorescence image and spectroscopy. Photoluminescence is observed at damaged regions following above threshold exposure with an emission peak centered at 550-nm. In addition, surfaces exposed to > 100 high power, 355-nm laser pulse reveal a reduced surface finishing quality as evidenced by an associated emission under UV photoexcitation. The emission spectra from the laser-induced damage sites and the laser degraded surfaces are similar suggesting the generation of similar defect species.
A practical method for determining coefficient word length in digital filters (1992)

The author presents a novel method for assessing the sensitivity of recursive digital filters to changes in their coefficients. It is particularly aimed at real-time control applications where continuous filters are being emulated in digital form. The method described enables sensitivity factors to be derived which directly relate the accuracy of the digital filter coefficients to the parameters of the continuous filter. By this means, for a particular percentage accuracy requirement in the parameters of the continuous filter, it is possible to determine directly the percentage accuracy (and hence word length) for the coefficients of the digital filter. Application of the method to typical examples is given, and the sensitivity predictions are confirmed by simulations of the digital filters in response to step inputs. An overview of its use in a design sense is also included.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Combinatorial approaches to signal finding and gene finding in dna sequences (2000)

In this thesis, we develop combinatorial approaches to two important problems in computational biology: signal finding and gene finding in DNA sequences. 
Signal finding (pattern discovery in unaligned DNA sequences) is a fundamental problem in both computer science and molecular biology with important applications in locating regulatory sites and drug target identification. Despite many studies, this problem is far from being solved: most signals in DNA sequences are so complicated that we don't yet have good models or reliable algorithms for their recognition. We complement existing statistical and machine learning approaches to this problem by combinatorial approaches that proved to be successful in identifying very subtle signals. This work appears in “Pevzner P. A. and Sze S.-H. (2000). Combinatorial approaches to finding subtle signals in DNA sequences. In Proc. of the 8th Int. Conf. on Intelligent Systems for Mol. Biol. (ISMB'2000), 269–278.” 
Gene finding (determination of splicing site locations in genomic DNA sequences) is an important problem in molecular biology. We describe three different approaches we have developed to aid the gene finding process. This work appears in “Sze S.-H. and Pevzner P. A. (1997). Las Vegas algorithms for gene recognition: suboptimal and errortolerant spliced alignment. J. Comp. Biol., 4, 297–309”; “Sze S.-H., Roytberg M. A., Gelfand M. S., Mironov A. A., Astakhova T. V. and Pevzner P. A. (1998). Algorithms and software for support of gene identification experiments. Bioinformatics, 14, 14–19”; and “Xu G., Sze S.-H., Liu C.-P., Pevzner P. A. and Arnheim N. (1998). Gene hunting without sequencing genomic clones: finding exon boundaries in cDNAs. Genomics, 47, 171–179.”
SCONE: Surface Coverage Optimization in Unknown Environments by Volumetric Integration (2022)

Next Best View computation (NBV) is a long-standing problem in robotics, and consists in identifying the next most informative sensor position(s) for reconstructing a 3D object or scene efficiently and accurately. Like most current methods, we consider NBV prediction from a depth sensor like Lidar systems. Learning-based methods relying on a volumetric representation of the scene are suitable for path planning, but have lower accuracy than methods using a surface-based representation. However, the latter do not scale well with the size of the scene and constrain the camera to a small number of poses. To obtain the advantages of both representations, we show that we can maximize surface metrics by Monte Carlo integration over a volumetric representation. In particular, we propose an approach, SCONE, that relies on two neural modules: The first module predicts occupancy probability in the entire volume of the scene. Given any new camera pose, the second module samples points in the scene based on their occupancy probability and leverages a self-attention mechanism to predict the visibility of the samples. Finally, we integrate the visibility to evaluate the gain in surface coverage for the new camera pose. NBV is selected as the pose that maximizes the gain in total surface coverage. Our method scales to large scenes and handles free camera motion: It takes as input an arbitrarily large point cloud gathered by a depth sensor as well as camera poses to predict NBV. We demonstrate our approach on a novel dataset made of large and complex 3D scenes.
&lt;title&gt;Holographic grating recorded in photopolymer composed of photosensitive polymer binder&lt;/title&gt; (2002)

The diffraction gratings in novel photopolymer were fabricated by optical interference method. Holographic recording in new polymer layers can be applied for optical information storage. The hydrophilic and hydrophobic polymers are used with the monomer of acrylamide, which are well miscible with the sensitizing dye of yellow eosin and the charge transfer agent of triethanolamine. Addition of the crosslinking agent bisacrylamide stabilizes the formed structures against thermal and environmental relaxations. We compared the diffraction efficiencies of new polymer samples with that of the conventional photopolymer. Relatively high diffraction efficiency can be obtained from LPOMPP-02 series. The influence of the UV curing on the diffraction grating is also studied when the diffraction efficiency becomes stable. The diffraction efficiency under UV irradiation shows slight decrement and becomes stable at a lower value. The surface topographical change of the photopolymer layer was observed after irradiation of the two polarized lights. The actual periodicity of the surface relief grating is about 1.95-1.98 ?m according to the AFM profiles close to the theoretical value of 1.92 ?m .
Abstract 2498: Differential rapamycin sensitivity distinguishes two distinct populations of tumor cells in murine glioma (2012)

Abstract Solid tumors are complex ecosystems, composed of a heterogeneous ensemble of cells that comprise the tumor mass (neoplastic compartment) and the surrounding stroma (non-neoplastic compartment). Currently, research efforts are aimed at defining the individual contributions of each cell type to tumor development and maintenance. Previous studies using a genetically-engineered mouse model of Neurofibromatosis type 1 (NF1)-associated optic glioma have underscored the critical role of one stromal cell type (microglia) in the growth of these tumors. In the current study, we analyze neoplastic cell heterogeneity and demonstrate that two distinct proliferating populations of neoplastic cells exist in the tumor. These distinct cell types, neuroglial progenitors and differentiated astrocytes, are distinguished by their sensitivity to rapamycin. The molecular basis for this differential sensitivity to rapamycin reflects dramatic differences in mammalian target of rapamycin (mTOR) complex protein expression and basal mTOR activation. We leverage this cell type-specific sensitivity to target neuroglial progenitor cells in the tumor and inhibit optic glioma formation in vivo. Collectively, these findings emphasize the importance of cellular diversity in glioma formation and growth, and highlight the importance of developing novel treatment strategies that co-target multiple cell populations for maximal therapeutic benefit. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2498. doi:1538-7445.AM2012-2498
Whole genome sequencing of Caribbean Hispanic families with late‐onset Alzheimer's disease (2018)

Rare variants in multiple genes influence the risk of LOAD disease in multiplex families. These results suggest that rare variants may underlie loci identified in genome wide association studies.
Use of serum biomarkers in a diagnostic test for irritable bowel syndrome (2009)

Assessing serum biomarker patterns can differentiate IBS from non-IBS with reasonable sensitivity and specificity. Assessing serum biomarkers in an overall diagnostic strategy may allow earlier diagnosis and treatment for patients with IBS.
Wavelets in Chemistry and Cheminformatics (2006)

Chapter 5 covers the topic of wavelet transforms, a general technique that can be used in protein-related research as well as for a multitude of other needs in computational chemistry, informatics, engineering and biology. Unlike traditional signal processing methods, the wavelet transform offers simultaneous localization of information in both frequency and time (or property) domains and is well suited to processing data containing complex and irregular property distributions or waveforms into simple, yet meaningful components. The method developed quickly in the 1990s with many applications in spectroscopy, chemometrics, quantum chemistry and more recently in chemoinformatics. This pedagogically driven review begins with an introduction to wavelets. The Fourier transform, continuous- and short-time Fourier transforms are described using simple mathematics as are the wavelet transform, the continuous-, discrete-, and wavelet packet transforms. The chapter is replete with illustrations describing the concepts and the mathematics associated with each technique. Following this introductory tutorial the authors provide examples of wavelet applications in chemistry with an emphasis in smoothing and denoising, signal feature isolation, signal compression, and quantum chemistry. Their chapter ends with a survey of how wavelets are used in classification, regression, and in QSAR/QSPR. The authors provide a simple tutorial for the novice molecular modeler and create a compelling rationale for why wavelets are so useful to computational scientists in chemistry and informatics. The chapter consists of: Preface Introduction to Wavelets Fourier Transform Continuous Fourier Transform Short Time Fourier Transformation Wavelet Transform Continuous Wavelet Transform Discrete Wavelet Transform Wavelet Packet Transform Wavelets vs. Fourier Transforms: A Summary Application of Wavelets in Chemistry Smoothing and Denoising Signal Feature Isolation Signal Compression Quantum Chemistry Classification, Regression and QSAR/QSPR Summary References
Early Region 1 Transforming Functions Are Dispensable for Mammary Tumorigenesis by Human Adenovirus Type 9 (1999)

Some human adenoviruses are tumorigenic in rodents. Subgroup A and B human adenoviruses generally induce sarcomas in both male and female animals, and the gene products encoded within viral early region 1 (E1 region) are both necessary and sufficient for this tumorigenicity. In contrast, subgroup D human adenovirus type 9 (Ad9) induces estrogen-dependent mammary tumors in female rats and requires the E4 region-encoded ORF1 oncoprotein for its tumorigenicity. Considering the established importance of the viral E1 region for tumorigenesis by adenoviruses, we investigated whether this viral transcription unit is also necessary for Ad9 to generate mammary tumors. The nucleotide sequence of the Ad9 E1 region indicated that the gene organization and predicted E1A and E1B polypeptides of Ad9 are closely related to those of other human adenovirus E1 regions. In addition, an Ad9 E1 region plasmid demonstrated focus-forming activity in both low-passage-number and established rat embryo fibroblasts, whereas a large deletion within either the E1A or E1B gene of this plasmid diminished transforming activity. Surprisingly, we found that introducing the same transformation-inactivating E1A and E1B deletions into Ad9 results in mutant viruses that retain the ability to elicit mammary tumors in rats. These results are novel in showing that Ad9 represents a unique oncogenic adenovirus in which the E4 region, rather than the E1 region, encodes the major oncogenic determinant in the rat.
EmoconLite: Bridging the Gap Between Emotiv and Play for Children With\n Severe Disabilities (2021)

Brain-computer interfaces (BCIs) allow users to control computer applications\nby modulating their brain activity. Since BCIs rely solely on brain activity,\nthey have enormous potential as an alternative access method for engaging\nchildren with severe disabilities and/or medical complexities in therapeutic\nrecreation and leisure. In particular, one commercially available BCI platform\nis the Emotiv EPOC headset, which is a portable and affordable\nelectroencephalography (EEG) device. Combined with the EmotivBCI software, the\nEmotiv system can generate a model to discern between different mental tasks\nbased on the user's EEG signals in real-time. While the Emotiv system shows\npromise for use by the pediatric population in the setting of a BCI clinic, it\nlacks integrated support that allows users to directly control computer\napplications using the generated classification output. To achieve this, users\nwould have to create their own program, which can be challenging for those who\nmay not be technologically inclined. To address this gap, we developed a freely\navailable and user-friendly BCI software application called EmoconLite. Using\nthe classification output from EmotivBCI, EmoconLite allows users to play\nYouTube video clips and a variety of video games from multiple platforms,\nultimately creating an end-to-end solution for users. Through its deployment in\nthe Holland Bloorview Kids Rehabilitation Hospital's BCI clinic, EmoconLite is\nbridging the gap between research and clinical practice, providing children\nwith access to BCI technology and supporting BCI-enabled play.\n
Implementing a Processor-in-the-loop with a Universal Controller in the Virtual Test Bed (2007)

As digital processor technology has rapidly developed, researchers have proposed various methodologies to design, develop, implement, and test digital control systems. A testing procedure, called processor-in-the-loop (PIL), allows designers to verify the actual control software running in a dedicated processor which controls a virtual prototype of a plant. In this paper, we focus on the demonstration of how to implement PIL technology in the virtual test bed (VTB) with a hybrid DSP/FPGA-based control platform; PIL system structure and simulation results are presented. Based on this example, we can extend the PIL procedure in VTB to other control hardware platforms easily.
Bacteroidetocins Target the Essential Outer Membrane Protein BamA of <i>Bacteroidales</i> Symbionts and Pathogens (2021)

Bacteroidetocins are a family of antibacterial peptide toxins that are produced by and target members of the phylum <i>Bacteroidetes</i>. To date, 19 bacteroidetocins have been identified, and four have been tested and shown to kill diverse <i>Bacteroidales</i> species (M. J. Coyne, N. Béchon, L. M. Matano, V. L. McEneany, et al., Nat Commun 10:3460, 2019, https://doi.org/10.1038/s41467-019-11494-1). Here, we identify the target and likely mechanism of action of the bacteroidetocins. We selected seven spontaneous mutants of four different genera, all resistant to bacteroidetocin A (Bd-A) and found that all contained mutations in a single gene, <i>bamA</i>. Construction of three of these <i>bamA</i> mutants in the wild-type (WT) strains confirmed they confer resistance to Bd-A as well as to other bacteroidetocins. We identified an aspartate residue of BamA at the beginning of exterior loop 3 (eL3) that, when altered, renders strains resistant to Bd-A. Analysis of a panel of diverse <i>Bacteroidales</i> strains showed a correlation between the presence of this aspartate residue and Bd-A sensitivity. Fluorescence microscopy and transmission electron microscopy (TEM) analysis of Bd-A-treated cells showed cellular morphological changes consistent with a BamA defect. Transcriptomic analysis of Bd-A-treated cells revealed gene expression changes indicative of cell envelope stress. Studies in mice revealed that bacteroidetocin-resistant mutants are outcompeted by their WT strain <i>in vivo</i>. Analyses of longitudinal human gut isolates showed that <i>bamA</i> mutations leading to bacteroidetocin resistance do not become fixed in the human gut, even in bacteroidetocin-producing strains and nonproducing coresident strains. Together, these data lend further support to the applicability of the bacteroidetocins as therapeutic peptides in the treatment of maladies involving <i>Bacteroidales</i> species. <b>IMPORTANCE</b> The bacteroidetocins are a newly discovered class of bacteriocins specific to <i>Bacteroidetes</i> with a spectrum of targets extending from symbiotic gut <i>Bacteroides</i>, <i>Parabacteroides</i>, and <i>Prevotella</i> species to pathogenic oral and vaginal <i>Prevotella</i> species. We previously showed that one such bacteroidetocin, Bd-A, is active at nanomolar concentrations, is water soluble, and is bactericidal, all desirable features in a therapeutic antibacterial peptide. Here, we identify the target of several of the bacteroidetocins as the essential outer membrane protein BamA. Although mutations in <i>bamA</i> can be selected in bacteria grown <i>in vitro</i>, we show both in a mouse model and in human gut ecosystems that <i>bamA</i> mutants leading to Bd-A resistance are fitness attenuated and are not selected. These features further support the potential usefulness of the bacteroidetocins as therapeutics for maladies associated with pathogenic <i>Prevotella</i> species, such as recurrent bacterial vaginosis, for which there are few effective treatments.
Spiral Scan In Video Compression (2005)

Publication in the conference proceedings of EUSIPCO, Antalya, Turkey, 2005
Performance Enhancement Of Mems-Based Microbial Fuel Cells (μMFC) For Microscale Power Generation (2016)

This paper reports the design, fabrication, and testing of a microliter scale Microbial Fuel Cell (mu mu MFC) based on silicon MEMS fabrication technology. mu MFC systems are operated under different loads or open circuit to compare the effect of different acclimatization conditions on start-up time. Shewanella oneidensis MR-1 is preferred to be the biocatalyst. The internal resistance is calculated as 20 k Omega under these conditions. Acclimatization of mu MFC under a finite load resulted in shorter start-up time (30 hours) when compared to the open load case. Power and current densities normalized to anode area are 2 mu W/cm(2) and 12 mu A/cm(2) respectively. When the load resistance value is closer to the internal resistance of the mu MFC, higher power and current densities are achieved as expected, and it resulted in a shorter start-up time. Further studies focusing on the different acclimatization techniques for mu MFC could pave the way to use mu MFCs as fast and efficient portable power sources.