gebhart/patrepeval huggingface dataset:
A Volumetric Approach to Change Detection in Satellite Images (2010)

The increasing availability of very high resolution satellite imagery has spurred interest in automatically detecting very fine detailed changes in an area over time, a particularly useful tool for analyzing activity in dense urban areas. However, attempting automated change detection at this resolution is difficult due to the motion parallax of elevated structures. This paper presents a comprehensive solution to change detection in areas of significant 3D relief using a new framework called volumetric appearance modeling (VAM). This approach can manage the complications of unknown and changing world surfaces by maintaining a 3D voxel-based model, where probability distributions for surface occupancy and image appearance are stored in each voxel. These distributions are continuously updated as new images are received using an adaptive learning procedure. This representation is demonstrated to produce accurate change detection results under conditions of variable illumination and viewpoint as well as haze conditions present in satellite imagery. The volumetric representation also supports automatic sensor model correction to align incoming imagery to a common geographic reference. This registration approach is demonstrated to achieve geo-positioning accuracy on the order of the ground sampling distance (GSD) or better.
Specific reduction of insulin disulfides by macrophage migration inhibitory factor (MIF) with glutathione and dihydrolipoamide: potential role in cellular redox processes (1998)

The molecular mechanism of action of MIF, a cytokine that plays a critical role in the host immune and inflammatory response, has not yet been identified. We recently demonstrated that MIF is an enzyme that exhibits oxidoreductase activity by a cysteine thiol-mediated mechanism. Here we further investigated this function by examining the reduction of insulin disulfides by wild-type human MIF (wtMIF) using various substrates, namely glutathione (GSH), dihydrolipoamide, L-cysteine, beta-mercaptoethanol and dithiothreitol. The activity of wtMIF was compared to that of the relevant cysteine mutants of MIF and to two carboxy-truncated mutants. Only GSH and dihydrolipoamide were found to serve as reductants, whereas the other substrates were not utilized by MIF. Reduction of insulin disulfides by MIF was closely dependent on the presence of the Cys57-Ala-Leu-Cys60 (CALC) motif-forming cysteines C57 and C60, whereas C81 was not involved (activities: 51+/-13%, 14+/-5%, and 70+/-12% of wtMIF, respectively, and 20+/-3% for the double mutant C57S/C60S). Confirming the notion that the activity of MIF was dependent on the CALC motif in the central region of the MIF sequence, the C-terminal deletion mutants MIF(1-105) and MIF(1-110) were found to be fully active. The favored use of GSH and dihydrolipoamide indicated that MIF may be involved in the regulation of cellular redox processes and was supported further by the finding that MIF expression by the cell lines COS-1 and RAW 264.7 was significantly induced upon treatment with the oxidant hydrogen peroxide.
Antibodies specific for distinct Kv subunits unveil a heterooligomeric basis for subtypes of .alpha.-dendrotoxin-sensitive potassium channels in bovine brain (1994)

The authentic subunit compositions of neuronal K+ channels purified from bovine brain were analyzed using a monoclonal antibody (mAb 5), reactive exclusively with the Kv1.2 subunit of the latter and polyclonal antibodies specific for fusion proteins containing C-terminal regions of four mammalian Kv proteins. Western blotting of the K+ channels isolated from several brain regions, employing the selective blocker alpha-dendrotoxin (alpha-DTX), revealed the presence in each of four different Kvs. Variable amounts of Kv1.1 and 1.4 subunits were observed in the K+ channels purified from cerebellum, corpus striatum, hippocampus, cerebral cortex, and brain stem; on the other hand, contents of Kv1.6 and 1.2 subunits appeared uniform throughout. Each Kv-specific antibody precipitated a different proportion (anti-Kv1.2 > 1.1 >> 1.6 > 1.4) of the channels detectable with radioiodinated alpha-DTX in every brain region, consistent with a widespread distribution of these oligomeric subtypes. Such heterooligomeric combinations were further documented by the lack of additivity upon their precipitation with a mixture of antibodies to Kv1.1 and Kv1.2; moreover, cross-blotting of the multimers precipitated by mAb 5 showed that they contain all four Kv proteins. Collectively, these findings demonstrate that subtypes of alpha-DTX-susceptible K+ channels are prevalent throughout mammalian brain which are composed of different Kv proteins assembled in complexes, shown previously to also contain auxiliary beta-subunits [Parcej, D. N., Scott, V. E. S., & Dolly, J.O. (1992) Biochemistry 31, 11084-11088].
Large-Area Atom Interferometry with Frequency-Swept Raman Adiabatic Passage (2015)

We demonstrate light-pulse atom interferometry with large-momentum-transfer atom optics based on stimulated Raman transitions and frequency-swept adiabatic rapid passage. Our atom optics have produced momentum splittings of up to 30 photon recoil momenta in an acceleration-sensitive interferometer for laser cooled atoms. We experimentally verify the enhancement of phase shift per unit acceleration and characterize interferometer contrast loss. By forgoing evaporative cooling and velocity selection, this method lowers the atom shot-noise-limited measurement uncertainty and enables large-area atom interferometry at higher data rates.
IES TM-30-15 Is Approved—Now What? (2015)

Address correspondence to Michael P. Royer, Pacific Northwest National Laboratory, 620 SW 5th Ave., Suite 810, Portland, OR 97204, USA. E-mail: michael.royer@pnnl.gov
Glutamate Induces Mitochondrial Dynamic Imbalance and Autophagy Activation: Preventive Effects of Selenium (2012)

Glutamate-induced cytotoxicity is partially mediated by enhanced oxidative stress. The objectives of the present study are to determine the effects of glutamate on mitochondrial membrane potential, oxygen consumption, mitochondrial dynamics and autophagy regulating factors and to explore the protective effects of selenium against glutamate cytotoxicity in murine neuronal HT22 cells. Our results demonstrated that glutamate resulted in cell death in a dose-dependent manner and supplementation of 100 nM sodium selenite prevented the detrimental effects of glutamate on cell survival. The glutamate induced cytotoxicity was associated with mitochondrial hyperpolarization, increased ROS production and enhanced oxygen consumption. Selenium reversed these alterations. Furthermore, glutamate increased the levels of mitochondrial fission protein markers pDrp1 and Fis1 and caused increase in mitochondrial fragmentation. Selenium corrected the glutamate-caused mitochondrial dynamic imbalance and reduced the number of cells with fragmented mitochondria. Finally, glutamate activated autophagy markers Beclin 1 and LC3-II, while selenium prevented the activation. These results suggest that glutamate targets the mitochondria and selenium supplementation within physiological concentration is capable of preventing the detrimental effects of glutamate on the mitochondria. Therefore, adequate selenium supplementation may be an efficient strategy to prevent the detrimental glutamate toxicity and further studies are warranted to define the therapeutic potentials of selenium in animal disease models and in human.
Sternal reconstruction with bone cement block using the rigid plate fixation technique (2019)

Chest computed tomography demonstrated a suspected primary tumor in the upper sternal body of a 48-year-old woman who presented with sternal pain. After being diagnosed with chondrosarcoma, she underwent sternal resection. Subsequent chest wall reconstruction was performed after careful planning using a bone cement block made of polypropylene mesh and polymethylmethacrylate. The block was fixed to the manubrium and ribs using the SternaLock System. She was discharged following an uneventful postoperative recovery, and is currently undergoing follow-up.
Solar Tracking by Plants (1980)

Leaves of many desert and agricultural species have the ability to move diurnally, orienting perpendicular or parallel to the sun's direct rays. This phenomenon is widespread in many plant families and occurs in both C(3) and C(4) photosynthetic pathway plants. In the annual flora of desert communities, solar tracking becomes more frequent as the length of the growing season decreases. Leaves that are perpendicular to the sun's direct rays for tracking appear to have high photosynthetic rates throughout the day, whereas leaves parallel to the sun's rays have reduced leaf temperatures and transpirational water losses.
Polar sampling in k‐space: Reconstruction effects (1998)

Magnetic resonance images are most commonly computed by taking the inverse Fourier transform of the k-space data. This transformation can potentially create artifacts in the image, depending on the reconstruction algorithm used. For equally spaced radial and azimuthal k-space polar sampling, both gridding and convolution backprojection are applicable. However, these algorithms potentially can yield different resolution, signal-to-noise ratio, and aliasing characteristics in the reconstructed image. Here, these effects are analyzed and their tradeoffs are discussed. It is shown that, provided the modulation transfer function and the signal-to-noise ratio are considered together, these algorithms perform similarly. In contrast, their aliasing behavior is different, since their respective point spread functions (PSF) differ. In gridding, the PSF is composed of the mainlobe and ringlobes that lead to aliasing. Conversely, there are no ringlobes in the convolution backprojection PSF, thus radial aliasing effects are minimized. Also, a hybrid gridding and convolution backprojection reconstruction is presented for radially nonequidistant k-space polar sampling.
Frequency agility in a ZigBee network for smart grid application (2010)

Smart grid is an intelligent power generation, distribution and control system. ZigBee, as wireless mesh networking scheme low in cost, power, data rate, and complexity, is ideal for smart grid applications. Unfortunately, almost all ZigBee channels are overlapped with wireless local area networks (WLAN) based on 802.11 specifications, resulting in significant service degradations in interference scenarios. We propose a frequency agility-based interference avoidance algorithm, which utilizes Energy Detection (ED) and active scan to perform smart channel selection. This algorithm can detect interference and adaptively switch nodes to “safe” channels to dynamically avoid WLAN interference. Our proposed scheme was empirically evaluated in terms of the packet error rate (PER) using a ZigBee and Wifi coexistence testbed, and the results were compared with our analytical results. The measurement results show the algorithm efficiently mitigates the effect of WiFi interference upon ZigBee networks.
Comprehensive Proteome Analysis of an Apc Mouse Model Uncovers Proteins Associated with Intestinal Tumorigenesis (2009)

Tumor-derived proteins may occur in the circulation as a result of secretion, shedding from the cell surface, or cell turnover. We have applied an in-depth comprehensive proteomic strategy to plasma from intestinal tumor-bearing Apc mutant mice to identify proteins associated with tumor development. We used quantitative tandem mass spectrometry of fractionated mouse plasma to identify differentially expressed proteins in plasma from intestinal tumor-bearing Apc mutant mice relative to matched controls. Up-regulated proteins were assessed for the expression of corresponding genes in tumor tissue. A subset of proteins implicated in colorectal cancer were selected for further analysis at the tissue level using antibody microarrays, Western blotting, tumor immunohistochemistry, and novel fluorescent imaging. We identified 51 proteins that were elevated in plasma with concordant up-regulation at the RNA level in tumor tissue. The list included multiple proteins involved in colon cancer pathogenesis: cathepsin B and cathepsin D, cullin 1, Parkinson disease 7, muscle pyruvate kinase, and Ran. Of these, Parkinson disease 7, muscle pyruvate kinase, and Ran were also found to be up-regulated in human colon adenoma samples. We have identified proteins with direct relevance to colorectal carcinogenesis that are present both in plasma and in tumor tissue in intestinal tumor-bearing mice. Our results show that integrated analysis of the plasma proteome and tumor transcriptome of genetically engineered mouse models is a powerful approach for the identification of tumor-related plasma proteins.
Amplified Transmural Dispersion of Repolarization as the Basis for Arrhythmogenesis in a Canine Ventricular-Wedge Model of Short-QT Syndrome (2004)

Our data suggest that heterogeneous abbreviation of the action potential duration among different cell types spanning the ventricular wall creates the substrate for the genesis of VT under conditions associated with short QT intervals.
Low-Complexity Watermarking Based on Entropy Coding in H.264/AVC (2008)

This paper is to propose a digital watermarking to protect the ownership of a video content which is compressed by H.264/AVC main profile. This scheme intends to be performed during the CABAC (Context-based Adaptive Binary Arithmetic Coding) process which is the entropy coding of the main profile. It uses the contexts extracted during the context modeling process of CABAC to position the watermark bits by simply checking the context values and determining the coefficients. The watermarking process is also as simple as replacing the watermark bit with the LSB (Least Significant Bit) of the corresponding coefficient to be watermarked. Experimental results from applying this scheme and attacking in various ways such as blurring, sharpening, cropping, Gaussian noise addition, and geometrical modification showed that the watermark embedded by this scheme has very high imperceptibility and robustness to the attacks. Thus, we expect it to be used as a good watermarking scheme, especially in the area that the watermarking should be performed during the compression process with requiring minimal amount of process for watermarking.
<i>Francisella tularensis:</i>Taxonomy, Genetics, and Immunopathogenesis of a Potential Agent of Biowarfare (2006)

Tularemia is a zoonosis of humans caused by infection with the facultative intracellular bacterium Francisella tularensis. Interest in F. tularensis has increased markedly in the past few years because of its potential use as an agent of bioterrorism. Five subspecies of this organism are found in the Northern hemisphere, but only F. tularensis subsp. tularensis and subsp. holarctica cause disease in humans. This review summarizes what is known about the pathogenesis of tularemia with a focus on bacterial surface components such as lipopolysaccharide and capsule as well as information obtained from the F. tularensis subsp. tularensis SCHU S4 genome. In particular, the mechanisms of action of recently identified virulence factors are discussed in the context of bacterial replication in macrophages and manipulation of the host inflammatory response. Throughout this report, shared and unique features of F. tularensis subsp. tularensis, subsp. holarctica, and subsp. novicida are discussed.
Oxidative Metabolism of Combretastatin A-1 Produces Quinone Intermediates with the Potential To Bind to Nucleophiles and To Enhance Oxidative Stress via Free Radicals (2007)

Combretastatins are stilbene-based, tubulin depolymerization agents with selective activity against the tumor vasculature; two variants (A-1 and A-4) are currently undergoing clinical trials. Combretastatin A-1 (CA1) has a greater antitumor effect than combretastatin A-4 (CA4). We hypothesized that this reflects the enhanced reactivity conferred by the second (ortho) phenolic moiety in CA1. Oxidation of CA1 by peroxidase, tyrosinase, or Fe(III) generates a species with mass characteristics of the corresponding ortho-quinone Q1. After administration of CA1-bis(phosphate) to mice, the hydroquinone-thioether conjugate Q1H2-SG, formed from the nucleophilic addition of GSH to Q1, was detected in liver. In competition, electrocyclic ring closure of Q1, over a few minutes at pH 7.4, leads to a second ortho-quinone product Q2, characterized by exact mass and NMR. This product was also generated by human promyelocytic leukemia (HL-60) cells in vitro, provided that superoxide dismutase was added. Q2 is highly reactive toward glutathione (GSH) and ascorbate, stimulating oxygen consumption in a catalytic manner. Free radical intermediates formed during autoxidation of CA1 were characterized by EPR, and the effects of GSH and ascorbate on the signals were studied. Pulse radiolysis was used to initiate selective one-electron oxidation or reduction and provided further evidence, from the differing absorption spectra of the radicals formed on oxidation of CA1 or reduction of Q2, that two different quinones were formed on oxidation of CA1. The results demonstrate fundamental differences between the pharmacological properties of CA1 and CA4 that provide two possible explanations for their differential activities in vivo: oxidative activation to a quinone intermediate likely to bind to protein thiols and possibly to nucleic acids and stimulation of oxidative stress by enhancing superoxide/hydrogen peroxide production. The observation of the GSH conjugate Q1H2-SG in vivo provides a new marker for oxidative metabolism of relevance to current clinical trials of CA1-bis(phosphate) (OXi4503).
Negative Regulation of Prolactin Receptor Stability and Signaling Mediated by SCF<sup>β-TrCP</sup> E3 Ubiquitin Ligase (2004)

Ubiquitin-dependent degradation of hormone receptors is emerging as a key mechanism that regulates the magnitude and duration of hormonal effects on cells and tissues. The pituitary hormone prolactin (PRL) is involved in regulating cell differentiation, proliferation, and survival. PRL engages its receptor (PRLR) to initiate various signaling cascades, including the phosphorylation and activation of Stat5. We found that PRL promotes interaction between PRLR and the F-box protein beta-TrCP2, which functions as a substrate recognition subunit of the SCF(beta-TrCP) E3 ubiquitin ligase. This interaction requires PRLR phosphorylation and the integrity of serine 349 within a conserved motif, which is similar to conserved motifs present in other substrates of SCF(beta-TrCP). The PRLR(S349A) mutant is resistant to ubiquitination and is more stable than its wild-type counterpart. Phosphorylated PRLR undergoes ubiquitination by SCF(beta-TrCP) in vitro. Knockdown of beta-TrCP expression inhibits the ubiquitination and degradation of PRLR and promotes PRL-dependent phosphorylation of Stat5 as well as Stat5-dependent transcription in cells. Furthermore, the activation of Stat5 and the stimulation of cell growth by PRL are augmented in cells expressing the PRLR(S349A) mutant. These data indicate that PRLR is a novel SCF(beta-TrCP) substrate and implicate beta-TrCP as an important negative regulator of PRL signaling and cellular responses to this hormone.
SSG1, a gene encoding a sporulation-specific 1,3-beta-glucanase in Saccharomyces cerevisiae (1993)

In Saccharomyces cerevisiae, the meiotic process is accompanied by a large increase in 1,3-beta-glucan-degradative activity. The molecular cloning of the gene (SSG1) encoding a sporulation-specific exo-1,3-beta-glucanase was achieved by screening a genomic library with a DNA probe obtained by polymerase chain reaction amplification using synthetic oligonucleotides designed according to the nucleotide sequence predicted from the amino-terminal region of the purified protein. DNA sequencing indicates that the SSG1 gene specifies a 445-amino-acid polypeptide (calculated molecular mass, 51.8 kDa) showing extensive similarity to the extracellular exo-1,3-beta-glucanases encoded by the EXG1 gene (C. R. Vazquez de Aldana, J. Correa, P. San Segundo, A. Bueno, A. R. Nebreda, E. Mendez, and F. del Rey, Gene 97:173-182, 1991). The N-terminal domain of the putative precursor is a very hydrophobic segment with structural features resembling those of signal peptides of secreted proteins. Northern (RNA) analysis reveals a unique SSG1-specific transcript, 1.7 kb long, which can be detected only in sporulating diploids (MATa/MAT alpha) but does not appear in vegetatively growing cells or in nonsporulating diploids (MAT alpha/MAT alpha) when incubated under nitrogen starvation conditions. The meiotic time course of SSG1 induction indicates that the gene is transcribed only in the late stages of the process, beginning at the time of meiosis I and reaching a maximum during spore formation. Homozygous ssg1/ssg1 mutant diploids are able to complete sporulation, although with a significant delay in the appearance of mature asci.
Visualising File-Systems Using ENCCON Model. (2003)

This paper describes a new approach for visualising the file structures.Our technique uses an enclosure + connection (ENCCON) approach that provides an overall view of the entire file/directory hierarchy that gives a better understanding of the folder-folder and folder-file relationships, and therefore makes easier for the navigation.We firstly use the rectangular regions to present the folders.This allows the user to immediately percept the location, size (number of files contained) and other properties of any particular folder.To enrich the visual attributes of the file structure, we also use a nodelink diagram to present the "belonging" relationships.This "belonging" relationship includes folder-folder and folder-file relationships.We use a semantic zooming technique to enlarge the display of files and folders in a particular focused area.The animation is also accommodated in order to preserve the mental map [Bartram 1997] during the navigation.
"Critical Fat" (1993)

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Dynamic genetic regulation of gene expression during cellular differentiation (2019)

Genetic regulation of gene expression is dynamic, as transcription can change during cell differentiation and across cell types. We mapped expression quantitative trait loci (eQTLs) throughout differentiation to elucidate the dynamics of genetic effects on cell type-specific gene expression. We generated time-series RNA sequencing data, capturing 16 time points during the differentiation of induced pluripotent stem cells to cardiomyocytes, in 19 human cell lines. We identified hundreds of dynamic eQTLs that change over time, with enrichment in enhancers of relevant cell types. We also found nonlinear dynamic eQTLs, which affect only intermediate stages of differentiation and cannot be found by using data from mature tissues. These fleeting genetic associations with gene regulation may explain some of the components of complex traits and disease. We highlight one example of a nonlinear eQTL that is associated with body mass index.
Olfactomedin 4 defines a subset of human neutrophils (2011)

OLFM4 was identified initially as a gene highly induced in myeloid stem cells by G-CSF treatment. A bioinformatics method using a global meta-analysis of microarray data predicted that OLFM4 would be associated with specific granules in human neutrophils. Subcellular fractionation of peripheral blood neutrophils demonstrated complete colocalization of OLFM4 with the specific granule protein NGAL, and stimulation of neutrophils with PMA resulted in corelease of NGAL and OLFM4, proving that OLFM4 is a genuine constituent of neutrophil-specific granules. In accordance with this, OLFM4 mRNA peaked at the MY/MM stage of maturation. OLFM4 was, however, present in only 20-25% of peripheral blood neutrophils, as determined by immunocytochemistry and flow cytometry, whereas mRNA for OLFM4 was present in all MY/MM, indicating post-transcriptional regulation as a basis for the heterogeneous expression of OLFM4 protein.