gebhart/patrepeval huggingface dataset:
Semiautomatic video database system (1995)

We present a prototype video database system designed to accept video sequences as well as still images. The system indexes these sequences based on scene changes, creates a primitive structure of these sequences, and searches this structure for queried objects using specific color features. A video sequence input to the database is first indexed into subsequences using a color histogram difference method. A hierarchical structure is created by thresholding the sequences at various levels of inter-frame difference. For every subsequence that is identified, the first frame in that subsequence, the representative frame, is entered into the database. The system then automatically generates a description for the frame in terms of its color histogram features. Subsequently, the video sequence may be searched for objects (specified as regions of other video sequence frames or still images) using color similarity matching.
Search for long-lived neutral particles decaying to quark-antiquark pairs in proton-proton collisions ats=8  TeV (2015)

A search is performed for long-lived massive neutral particles decaying to quark-antiquark pairs. The experimental signature is a distinctive topology of a pair of jets, originating at a secondary vertex. Events were collected with the CMS detector at the CERN LHC in proton-proton collisions at a center-of-mass energy of 8 TeV. The data analyzed correspond to an integrated luminosity of $18.5\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$. No significant excess is observed above standard model expectations. Upper limits at 95% confidence level are set on the production cross section of a heavy neutral scalar particle, $H$, in the mass range of 200 to 1000 GeV, decaying promptly into a pair of long-lived neutral $X$ particles in the mass range of 50 to 350 GeV, each in turn decaying into a quark-antiquark pair. For $X$ with mean proper decay lengths of 0.4 to 200 cm, the upper limits are typically $0.5--200\text{ }\text{ }\mathrm{fb}$. The results are also interpreted in the context of an R-parity-violating supersymmetric model with long-lived neutralinos decaying into a quark-antiquark pair and a muon. For pair production of squarks that promptly decay to neutralinos with mean proper decay lengths of $2--40\text{ }\text{ }\mathrm{cm}$, the upper limits on the cross section are typically $0.5--3\text{ }\text{ }\mathrm{fb}$. The above limits are the most stringent on these channels to date.
Faster Multipoint Linkage Analysis Using Fourier Transforms (1998)

Genetic linkage analysis of human pedigrees using many linked markers simultaneously is a difficult computational problem. We have previously described an approach to this problem that uses hidden Markov models (HMMs) and is quite efficient for pedigrees of moderate size. Here, we describe a new, faster algorithm for the key step in the HMM calculation. The algorithm employs a fast Fourier transform on the group of pedigree inheritance patterns. It substantially improves the overall performance of the software package GENEHUNTER for performing linkage analysis. The Fourier representation opens up new research directions for pedigree analysis.
The Softer and More Hydrophobic the Better: Influence of the Side Chain of Polymethacrylate Nanoparticles for Cellular Uptake (2010)

Intracellular uptake of nanoparticles is highly interesting for labeling of cells, drug delivery, or non-viral gene delivery. In this study we have synthesized a wide variety of poly(alkyl methacrylate) nanoparticles with the same size and investigated their uptake into cells. The nanoparticles were prepared from alkylmethacrylates with different linear and branched ester chains as well as from benzylmethacrylate using the miniemulsion polymerizaiton technique. By adding a fluorescent dye as a marker, the internalization of the nanoparticles could be investigated quantitatively with flow cytometry and qualitatively with confocal laser scanning microscopy. With increasing side chain of the ester and therefore increasing hydrophobicity and at glass transition temperature (T(g)), below the incubation temperature of 37 degrees C the uptake of the nanoparticles into cells is favored.
Soluble prefusion-closed HIV-envelope trimers with glycan-covered bases (2023)

Soluble HIV-1-envelope (Env) trimers elicit immune responses that target their solvent-exposed protein bases, the result of removing these trimers from their native membrane-bound context. To assess whether glycosylation could limit these base responses, we introduced sequons encoding potential <i>N</i>-linked glycosylation sites (PNGSs) into base-proximal regions. Expression and antigenic analyses indicated trimers bearing six-introduced PNGSs to have reduced base recognition. Cryo-EM analysis revealed trimers with introduced PNGSs to be prone to disassembly and introduced PNGS to be disordered. Protein-base and glycan-base trimers induced reciprocally symmetric ELISA responses, in which only a small fraction of the antibody response to glycan-base trimers recognized protein-base trimers and vice versa. EM polyclonal epitope mapping revealed glycan-base trimers -even those that were stable biochemically- to elicit antibodies that recognized disassembled trimers. Introduced glycans can thus mask the protein base but their introduction may yield neo-epitopes that dominate the immune response.
Tricalcium phosphate nanoparticles enable rapid purification, increase transduction kinetics, and modify the tropism of mammalian viruses (2008)

Abstract Adenoviral, adeno‐associated viral, and retroviral particles are chosen as gene delivery shuttles in more than 50% of all gene therapy clinical trials. Bulk availability of clinical‐grade viral particles and their efficiency to transduce the therapeutic cargo into specific target cells remain the most critical bottlenecks in gene therapy applications to date. Capitalizing on the flame‐spray technology for the reproducible economic large‐scale production of amorphous tricalcium phosphate nanoparticulate powders (ATCP), we designed a scalable ready‐to‐use gravity‐flow column set‐up for the straightforward concentration and purification of transgenic adenoviral, adeno‐associated viral, and lentiviral particles. Specific elution buffers enabled rapid release of viral particles from the ATCP matrix of the column and provided high‐titer virus preparations in an unsurpassed period of time. The interaction of ATCP with adenoviral, adeno‐associated viral, and lentiviral particles in solution increased the transduction kinetics of several mammalian cell lines in culture. The nanoparticles were also able to modify the tropism of murine leukemia virus (MLV) towards transduction of human cells. Based on these findings, we believe that the use of flame‐spray tricalcium phosphate nanoparticles will lead to important progress in the development of future gene therapy initiatives. Biotechnol. Bioeng. 2009;102: 1197–1208. © 2008 Wiley Periodicals, Inc.
Identification of IEX-1 as a Biomechanically Controlled Nuclear Factor-κB Target Gene That Inhibits Cardiomyocyte Hypertrophy (2002)

Biomechanical strain is a stimulus for cardiomyocyte hypertrophy and heart failure, but the underlying molecular mechanisms remain incompletely understood. Using an in vivo murine model of pressure overload and an in vitro model of mechanical stimulation of primary cardiomyocytes, we identified iex-1 as a gene activated during the early response of cardiomyocytes to hypertrophic stimuli and as a gene product that inhibits hypertrophy without affecting cardiomyocyte viability. On stimulation of cardiomyocytes, iex-1 mRNA and protein expression increased and translocation of the gene product to the cardiomyocyte nucleus occurred. iex-1 has previously been proposed as a mediator of NF-kappaB-dependent cell survival and growth in tumor cells. Here, we demonstrate that the biomechanical induction of iex-1 in cardiomyocytes was NF-kappaB-dependent, as overexpression of the NF-kappaB inhibitor IkappaBalpha completely inhibited strain-mediated iex-1 mRNA accumulation. The functional role of iex-1 was investigated by overexpressing wild-type iex-1 with replication-defective adenoviral gene transfer. Overexpression of iex-1 abolished cardiomyocyte hypertrophy by mechanical strain, phenylephrine, or endothelin-1 at levels that did not affect cell viability. These studies identify iex-1 as a biomechanical stress-inducible and NF-kappaB-dependent gene in cardiac muscle cells during the acute phase of hypertrophy with negative growth regulatory effects that may counterbalance early hypertrophic responses in activated cardiomyocytes.
Design Methodology for High Brightness Projectors (2008)

The low luminance levels of light-emitting diodes (LEDs) compared to arc lamps make it difficult to design high-brightness LED-based projectors. Besides, the specificities of LEDs do not always allow using the same design schemes as with arc lamp-based projection displays. This paper performs a taxonomy of the techniques that can be used to increase the brightness of LED-based projection displays. We show that, in etendue-limited systems, the perceived brightness depends on the system etendue limit, the efficiency of the light engine, and the source luminance. The ability to improve each of these parameters depends on the design constraints. The system etendue limit can be increased at the expense of bulkier, more complex, and more expensive designs. The light engine efficiency can be increased by using free-form shape components adapted to the shapes and the emission patterns of the considered LEDs. The apparent source luminance can be increased at the expense of the flux by either recycling light or restricting the light collection to a smaller etendue with higher average luminance. Luminance can also be increased by using multiple color primaries (spatial multiplexing) or pulsed LEDs (temporal multiplexing). Finally, we review how light recycling can be implemented to convert polarization without increasing etendue.
Q-Learning Based Joint Energy-Spectral Efficiency Optimization in Multi-Hop Device-to-Device Communication (2020)

In scenarios, like critical public safety communication networks, On-Scene Available (OSA) user equipment (UE) may be only partially connected with the network infrastructure, e.g., due to physical damages or on-purpose deactivation by the authorities. In this work, we consider multi-hop Device-to-Device (D2D) communication in a hybrid infrastructure where OSA UEs connect to each other in a seamless manner in order to disseminate critical information to a deployed command center. The challenge that we address is to simultaneously keep the OSA UEs alive as long as possible and send the critical information to a final destination (e.g., a command center) as rapidly as possible, while considering the heterogeneous characteristics of the OSA UEs. We propose a dynamic adaptation approach based on machine learning to improve a joint energy-spectral efficiency (ESE). We apply a Q-learning scheme in a hybrid fashion (partially distributed and centralized) in learner agents (distributed OSA UEs) and scheduler agents (remote radio heads or RRHs), for which the next hop selection and RRH selection algorithms are proposed. Our simulation results show that the proposed dynamic adaptation approach outperforms the baseline system by approximately 67% in terms of joint energy-spectral efficiency, wherein the energy efficiency of the OSA UEs benefit from a gain of approximately 30%. Finally, the results show also that our proposed framework with C-RAN reduces latency by approximately 50% w.r.t. the baseline.
Prediction of movement intention using connectivity within motor-related network: An electrocorticography study (2018)

Most brain-machine interface (BMI) studies have focused only on the active state of which a BMI user performs specific movement tasks. Therefore, models developed for predicting movements were optimized only for the active state. The models may not be suitable in the idle state during resting. This potential maladaptation could lead to a sudden accident or unintended movement resulting from prediction error. Prediction of movement intention is important to develop a more efficient and reasonable BMI system which could be selectively operated depending on the user's intention. Physical movement is performed through the serial change of brain states: idle, planning, execution, and recovery. The motor networks in the primary motor cortex and the dorsolateral prefrontal cortex are involved in these movement states. Neuronal communication differs between the states. Therefore, connectivity may change depending on the states. In this study, we investigated the temporal dynamics of connectivity in dorsolateral prefrontal cortex and primary motor cortex to predict movement intention. Movement intention was successfully predicted by connectivity dynamics which may reflect changes in movement states. Furthermore, dorsolateral prefrontal cortex is crucial in predicting movement intention to which primary motor cortex contributes. These results suggest that brain connectivity is an excellent approach in predicting movement intention.
Detection of Shigella in Feces Using DNA Amplification (1990)

A rapid diagnostic method employing a polymerase chain reaction procedure (PCR) was used to identify Shigella and enteroinvasive Escherichia coli. This procedure amplified a region of the invasive-associated locus (ial) from a crude DNA extract of feces. A synthetic 21-base oligonucleotide corresponding to the ial gene sequence was shown to specifically hybridize only with enteroinvasive E. coli (EIEC) strains and Shigella species. Upon PCR amplification, a 320-base pair fragment was generated in DNA extracted from feces reconstituted with EIEC or Shigella flexneri but not in DNA from 70 normal stools lacking these organisms and could be readily detected by the ial probe. For identifying Shigella and EIEC, the PCR assay was 10(5)- and 10(2)-fold more sensitive than standard biochemical tests and the macrocolony hybridization assay, respectively. These findings demonstrate a novel methodology for rapid, sensitive, and culture-independent diagnosis of diarrhea caused by these pathogens and underscores the utility of PCR in the diagnostic laboratory.
Correction: An ATP-competitive mammalian target of rapamycin inhibitor reveals rapamycin-resistant functions of mTORC1. (2020)

VOLUME 284 (2009) PAGES 8023–8032 There was an error in Fig. 4A. The immunoblot for total levels of S6K was mistakenly duplicated for both WT and rictor−/− MEFs. This error has now been corrected and does not affect the results or conclusions of this work.
Cryo automated electron tomography: Towards high‐resolution reconstructions of plastic‐embedded structures (1994)

The use of fully automated data collection methods for electron tomography allows a substantial reduction in beam dose. The goal has been to develop new protocols for data collection defining optimal approaches for maintaining data self-consistency and maximizing the useful resolution of the reconstruction. The effects of irradiation and post-cure microwaving were examined for a variety of embedding media (Epon, Epox, Lowicryl) in order to quantify beam damage with the goal of identifying the most beam stable embedding medium. Surprisingly, the substantial dose reduction made possible by automated data collection did not result in a significant decrease in specimen shrinkage even for samples stabilized by pre-irradiation. We believe that the accelerated shrinkage is a direct consequence of the stroboscopic illumination patterns inherent to automated data collection. Furthermore neither the choice of embedding resin nor microwave post-curing greatly affected shrinkage. Finally, cryogenic data collection was investigated as a means to minimize the effects of secondary radiation damage. Minimal pre-irradiation coupled with low-temperature automated data collection greatly reduces shrinkage and should result in high-quality data for three-dimensional reconstructions.
Quantifying the Value of a Future Pressure Transient Well Test with Reservoir and Measurement Uncertainty (2009)

Abstract We present a consistent and functional methodology for conducting value-of-information (VoI) analysis on proposed well tests in the presence of multiple critical uncertainties associated with the reservoir and the measurement/interpretation. Such uncertainties can impact asset economics acutely when they influence recoverable hydrocarbons. A key feature of this analysis is that the value of the measurement is determined before the measurement is made. Our demonstration uses an example of a marginal offshore asset where severe compartmentalization is possible. In this example, the VoI is a critical deciding factor because it is not obvious a priori that this value will justify the cost of the test in this marginal asset. Our analysis uses a novel approach to standard decision trees by introducing new decision tree nodes in the form of "uncertainty" and "transformation uncertainty" nodes that can accommodate single or numerous continuous and discrete uncertainties. Without such novel tree components, a standard decision tree would become far too cumbersome for practical purposes and may even result in sub-optimal (uneconomic) development decisions from being made because of the discretized nature of the existing decision tree constructs. We also consider, in addition to the reservoir uncertainties, the uncertainty in the well test measurement and/or the interpretation itself. We present expected asset net present value as a function of measurement uncertainty. Since well-test uncertainty can be related to the well-test duration, we show how the optimum well-test duration can be determined by identifying the time at which the difference between VoI and test cost is maximized. The cost of running the test longer than this optimal duration will only serve to reduce the net present value of the asset. Introduction The problem of establishing meaningful value-of-information (VoI) metrics for a well test when faced with multiple significant uncertainties is examined. Such uncertainties can impact asset economics acutely when they influence recoverable hydrocarbons. We examine this VoI through an example of a small, marginal, offshore asset where the primary reservoir uncertainties relate to the degree of possible compartmentalization as well as permeability and porosity. The underlying driver of this study was to devise and test a consistent and functional methodology that can compute meaningful VoI for a well test such that all significant uncertainties are considered, including measurement uncertainty.
Biochemical characterization of recombinant β-carbonic anhydrase (PgiCAb) identified in the genome of the oral pathogenic bacteriumPorphyromonas gingivalis (2014)

Carbonic anhydrases (CAs, EC 4.2.1.1) belonging to the α-, β-, γ-, δ- and ζ-CAs are ubiquitous metalloenzymes present in prokaryotes and eukaryotes. CAs started to be investigated in detail only recently in pathogenic bacteria, in the search for antibiotics with a novel mechanism of action, since it has been demonstrated that in many such organisms they are essential for the life cycle of the organism. CA inhibition leads to growth impairment or growth defects in several pathogenic bacteria. The microbiota of the human oral mucosa consists of a myriad of bacterial species, Porphyromonas gingivalis being one of them and the major pathogen responsible for the development of chronic periodontitis. The genome of P. gingivalis encodes for a β- and a γ-CAs. Recently, our group purified the recombinant γ-CA (named PgiCA) which was shown to possess a significant catalytic activity for the reaction that converts CO2 to bicarbonate and protons, with a kcat of 4.1 × 10(5 )s(-1) and a kcat/Km of 5.4 × 10(7 )M(-1 )× s(-1). We have also investigated its inhibition profile with a range of inorganic anions such as thiocyanate, cyanide, azide, hydrogen sulfide, sulfamate and trithiocarbonate. Here, we describe the cloning, purification and kinetic parameters of the other class of CA identified in the genome of P. gingivalis, the β-CA, named PgiCAb. This enzyme has a good catalytic activity, with a kcat of 2.8 × 10(5 )s(-1) and a kcat/Km of 1.5 × 10(7 )M(-1 )× s(-1). PgiCAb was also inhibited by the clinically used sulfonamide acetazolamide, with an inhibition constant of 214 nM. The role of CAs as possible virulence factors of P. gingivalis is poorly understood at the moment but their good catalytic activity and the fact that they might be inhibited by a large number of compounds, which may pave the way for finding inhibitors with antibacterial activity that may elucidate these phenomena and lead to novel antibiotics.
The genomic basis of adaptive evolution in threespine sticklebacks (2012)

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.
Data from Fibulin-5 Blocks Microenvironmental ROS in Pancreatic Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;Elevated oxidative stress is an aberration seen in many solid tumors, and exploiting this biochemical difference has the potential to enhance the efficacy of anticancer agents. Homeostasis of reactive oxygen species (ROS) is important for normal cell function, but excessive production of ROS can result in cellular toxicity, and therefore ROS levels must be balanced finely. Here, we highlight the relationship between the extracellular matrix and ROS production by reporting a novel function of the matricellular protein Fibulin-5 (Fbln5). We used genetically engineered mouse models of pancreatic ductal adenocarcinoma (PDAC) and found that mutation of the integrin-binding domain of Fbln5 led to decreased tumor growth, increased survival, and enhanced chemoresponse to standard PDAC therapies. Through mechanistic investigations, we found that improved survival was due to increased levels of oxidative stress in Fbln5-mutant tumors. Furthermore, loss of the Fbln5–integrin interaction augmented fibronectin signaling, driving integrin-induced ROS production in a 5-lipooxygenase–dependent manner. These data indicate that Fbln5 promotes PDAC progression by functioning as a molecular rheostat that modulates cell–ECM interactions to reduce ROS production, and thus tip the balance in favor of tumor cell survival and treatment-refractory disease. &lt;i&gt;Cancer Res; 75(23); 5058–69. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;