gebhart/patrepeval huggingface dataset:
Whole-slide Imaging (2012)

Digital pathology systems offer pathologists an alternate, emerging mechanism to manage and interpret information. They offer increasingly fast and scalable hardware platforms for slide scanning and software that facilitates remote viewing, slide conferencing, archiving, and image analysis. Deployed initially and validated largely within the research and biopharmaceutical industries, WSI is increasingly being implemented for direct patient care. Improvements in image quality, scan times, and imageviewing browsers will hopefully allow pathologists to more seamlessly convert to digital pathology, much like our radiology colleagues have done before us. However, WSI creates both opportunities and challenges. Although niche applications of WSI technology for clinical, educational, and research purposes are clearly successful, it is evident that several areas still require attention and careful consideration before more widespread clinical adoption of WSI takes place. These include regulatory issues, development of standards of practice and validation guidelines, workflow modifications, as well as defining situations where WSI technology will really improve practice in a cost-effective way. Current progress on these and other issues, along with improving technology, will no doubt pave the way for increased adoption over the next decade, allowing the pathology community as a whole to harness the true potential of WSI for patient care. The digital decade will likely redefine how pathology is practiced and the role of the pathologist.
Glycosphingolipids in Cellular Interaction, Differentiation, and Oncogenesis (1981)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Attenuation stem-loop lesions in the 5' noncoding region of poliovirus RNA: neuronal cell-specific translation defects (1996)

The nucleotide at position 480 in the 5' noncoding region of the viral RNA genome plays an important role in directing the attenuation phenotype of the Sabin vaccine strain of poliovirus type 1. In vitro translation studies have shown that the attenuated viral genomes of the Sabin strains direct levels of viral protein synthesis lower than those of their neurovirulent counterparts. We previously described the isolation of pseudorevertant polioviruses derived from transfections of HeLa cells with genome-length RNA harboring an eight-nucleotide lesion in a stem-loop structure (stem-loop V) that contains the attenuation determinant at position 480 (A. A. Haller and B. L. Semler, J. Virol. 66:5075-5086, 1992). This stem-loop structure is a major component of the poliovirus internal ribosome entry site required for initiation of viral protein synthesis. The eight-nucleotide lesion (X472) was lethal for virus growth and gave rise only to viruses which had partially reverted nucleotides within the original substituted sequences. In this study, we analyzed two of the poliovirus revertants (X472RI and X472R2) for cell-type-specific growth properties. The X472RI and X472R2 RNA templates directed protein synthesis to wild-type levels in in vitro translation reaction mixtures supplemented with crude cytoplasmic HeLa cell extracts. In contrast, the same X472 revertant RNAs displayed a decreased translation initiation efficiency when translated in a cell-free system supplemented with extracts from neuronal cells. This translation initiation defect of the X472R templates correlated with reduced yields of infectious virus particles in neuronal cells compared with those obtained from HeLa cells infected with the X472 poliovirus revertants. Our results underscore the important of RNA secondary structures within the poliovirus internal ribosome entry site in directing translation initiation and suggest that such structures interact with neuronal cell factors in a specific manner.
Increasing Throughput for Robotic Cells With Parallel Machines and Multiple Robots (2004)

We address the problem of scheduling robots' moves in a robotic cell that is used by a Dallas-area semiconductor equipment manufacturer. The cell has parallel machines, multiple robots, and Euclidean travel times. We describe a plan of operation that allows the robots to operate concurrently, efficiently, and with no risk of colliding. We propose a set of sequences of robot moves, analytically determine this scheme's throughput, and determine problem instances for which it is optimal. Through simulation, we demonstrate that our scheme is superior to the heuristic dispatching rule currently in use by the manufacturer.<br><br>Note to Practitioners-Efficient scheduling of a robotic cell can greatly increase productivity and revenue for manufacturers in many different industries. This increase becomes more pronounced for larger cells that employ multiple robots and parallel machines at various production stages. This paper describes a schedule of robotic actions that is optimal under a common set of conditions for such large cells, in addition to many other types of cells. When this set of conditions does not hold, even though optimality could not be proven, this schedule is shown to be superior to one currently in use by some semiconductor manufacturers. We also present a scheme that allows the robots to operate concurrently, efficiently, and with no risk of colliding. Additionally, an approximation to the improvement in revenues realized by using this schedule is provided.
Study of the defect elimination mechanisms in aspect ratio trapping Ge growth (2007)

Recent research has demonstrated the effectiveness of the “aspect ratio trapping” technique for eliminating threading dislocations in Ge grown selectively in submicron trenches on Si substrates. In this letter, analysis of the mechanisms by which dislocation elimination is achieved has been carried out. Detailed transmission electron microscopy studies reveal that facets, when formed early in the growth process, play a dominant role in determining the configurations of threading dislocations in the films. These dislocations are shown to behave as “growth dislocations,” which are replicated during growth approximately along the facet normal and so are deflected out from the center of the selective epitaxial regions.
A Practical Approach for Determining Permeability From Laboratory Pressure-Pulse Decay Measurements (1988)

ABSTRACT A new pressure-pulse decay method is presented to measure permeabilities of tight rock samples. Existing pressure-pulse methods yield pressure decays which are either slow or difficult to analyse. Often approximations are made which may yield considerable errors in the derived permeability values. The new method is simple and enables very fast and accurate permeability measurements. The exact solution of the differential equation describing the decay curve resulting from a pressure-pulse measurement was analysed in detail. This showed how the decay curve is influenced by various parameters in the design of the pressure-pulse permeameter. In this way various existing designs could be compared. Furthermore, the analysis showed how a pressure-pulse permeameter should be designed such that the measured decay is fast and simple to analyse. Also an approximate solution was obtained which is accurate to within 0.3% of the exact solution which is much more difficult to handle. Using this solution a new and simple analysis procedure was developed. Combining the new design with the new analysis method results in an elegant method for fast and accurate pressure-pulse measurements.
Aspirin inhibits interleukin 1-induced prostaglandin H synthase expression in cultured endothelial cells. (1991)

Prostaglandin H (PGH) synthase (EC 1.14.99.1) is a key enzyme in the biosynthesis of prostaglandins, thromboxane, and prostacyclin. In cultured human umbilical vein endothelial cells, interleukin 1 (IL-1) is known to induce the synthesis of this enzyme, thereby raising the level of PGH synthase protein severalfold over the basal level. Pretreatment with aspirin at low concentrations (0.1-1 micrograms/ml) inhibited more than 60% of the enzyme mass and also the cyclooxygenase activity in IL-1-induced cells with only minimal effects on the basal level of the synthase enzyme in cells without IL-1. Sodium salicylate exhibited a similar inhibitory action whereas indomethacin had no apparent effect. Similarly low levels of aspirin inhibited the increased L-[35S]methionine incorporation into PGH synthase that was induced by IL-1 and also suppressed expression of the 2.7-kilobase PGH synthase mRNA. These results suggest that in cultured endothelial cells a potent inhibition of eicosanoid biosynthetic capacity can be effected by aspirin or salicylate at the level of PGH synthase gene expression. The aspirin effect may well be due to degradation of salicylate.
Nitroindoles as Universal Bases (1995)

Abstract Nitroindoles behave as non-discriminatory bases when incorporated into oligodeoxynucleotides, without causing significant destabilisation of the duplex, and exhibit higher melting temperatures than 3-nitropyrrole. When 5-nitroindole and 3-nitropyrrole are incorporated into oligomers for use as primers for sequencing and the polymerase chain reaction, both give products but are not as effective as hypoxanthine.
Recent Advances in Anti-Influenza Agents with Neuraminidase as Target (2006)

Neuraminidase (NA) is the major surface glycoprotein of the influenza virus. It has been considered a suitable target for designing agents against influenza viruses. Rational drug design of NA inhibitors is now in the clinic and is effective for the treatment of influenza. Recently, research of structure-based NA inhibitors is becoming an interesting field, leading to a breakthrough in the control of influenza. Here we review a series of neuraminidase inhibitors and the recent progress in this field.
Plerixafor (AMD3100) and granulocyte colony-stimulating factor (G-CSF) mobilize different CD34+ cell populations based on global gene and microRNA expression signatures (2009)

Plerixafor (AMD3100) and granulocyte colony-stimulating factor (G-CSF) mobilize peripheral blood stem cells by different mechanisms. A rhesus macaque model was used to compare plerixafor and G-CSF-mobilized CD34(+) cells. Three peripheral blood stem cell concentrates were collected from 3 macaques treated with G-CSF, plerixafor, or plerixafor plus G-CSF. CD34(+) cells were isolated by immunoselection and were analyzed by global gene and microRNA (miR) expression microarrays. Unsupervised hierarchical clustering of the gene expression data separated the CD34(+) cells into 3 groups based on mobilization regimen. Plerixafor-mobilized cells were enriched for B cells, T cells, and mast cell genes, and G-CSF-mobilized cells were enriched for neutrophils and mononuclear phagocyte genes. Genes up-regulated in plerixafor plus G-CSF-mobilized CD34(+) cells included many that were not up-regulated by either agent alone. Two hematopoietic progenitor cell miR, miR-10 and miR-126, and a dendritic cell miR, miR-155, were up-regulated in G-CSF-mobilized CD34(+) cells. A pre-B-cell acute lymphocytic leukemia miR, miR-143-3p, and a T-cell miR, miR-143-5p, were up-regulated in plerixafor plus G-CSF-mobilized cells. The composition of CD34(+) cells is dependent on the mobilization protocol. Plerixafor-mobilized CD34(+) cells include more B-, T-, and mast cell precursors, whereas G-CSF-mobilized cells have more neutrophil and mononuclear phagocyte precursors.
<title>Determining Image Quality From Electronic Or Digital Signal Characteristics</title> (1980)

Frequency domain measures of image quality have been used successfully for some years to predict human assessment of image quality. These measures were derived from the optical power spectrum. The emphasis in this paper is on utilization of digitally-derived power spectral estimates of image quality computed before hard copy imagery is produced.
Transparent Dielectric Metasurfaces for Spatial Mode Multiplexing (2018)

Abstract Expanding the use of physical degrees of freedom to employ spatial multiplexing of data in optical communication is considered to be the most disruptive and effective solution for meeting the capacity demand of the growing information traffic. Development of space division–multiplexing methods stimulated research on spatial encoding, detection, and processing of data, attracting interest from various fields of science. Here a passive all‐dielectric metasurface with near‐unity transmission is demonstrated that engineers spatial mode profiles, potentially of an arbitrary complexity. The broadband response of the metasurface covers all S, C, and L bands of fiber communications. Unlike conventional phase plates, the metasurface allows for both phase and polarization conversion, providing full flexibility for the mode engineering. The dielectric metasurface is employed for mode multiplexing in a free‐space optical communication system with an extinction ratio in excess of 20 dB over the whole C‐band with negligible penalty even for 100 Gb s −1 data transmission. These results merge two seemingly different fields, optical communication and metamaterials , and they suggest a novel approach for an ultimate miniaturization of mode multiplexers and advanced LiFi technologies.
Identification of a Nuclear Receptor for Bile Acids (1999)

Bile acids are essential for the solubilization and transport of dietary lipids and are the major products of cholesterol catabolism. Results presented here show that bile acids are physiological ligands for the farnesoid X receptor (FXR), an orphan nuclear receptor. When bound to bile acids, FXR repressed transcription of the gene encoding cholesterol 7alpha-hydroxylase, which is the rate-limiting enzyme in bile acid synthesis, and activated the gene encoding intestinal bile acid-binding protein, which is a candidate bile acid transporter. These results demonstrate a mechanism by which bile acids transcriptionally regulate their biosynthesis and enterohepatic transport.
Dihydroartemisinin induces apoptosis in human leukemia cells HL60 via downregulation of transferrin receptor expression (2008)

Dihydroartemisinin (DHA), a water-soluble active metabolite of artemisinin derivatives, is the safest and most effective antimalarial analog of artemisinin. In the present investigation, we assessed the apoptotic effect of DHA on leukemia HL60 cells and its regulation of transferrin receptor (TfR). Cell growth inhibition was assessed by Trypan blue exclusive staining; the expression of caspase-3, Bcl-2, and Bax in HL60 cells was evaluated by Western blotting; DHA-induced apoptosis was determined by AO/EB double staining, DNA fragmentation assay, and flow cytometric analysis; the expression of TfR in HL60 cells was examined by real-time PCR assays, Western blotting, and flow cytometric analysis. DHA could specifically reduce the mRNA and protein expression of TfR in HL60 cells, and the flow cytometric analysis presented the unity tendency that the TfR content decreased progressively in a dose-dependent manner. Consequently, DHA exhibited high anticancer activity in HL60 cells; MTT assay and growth inhibition assay showed that DHA could specifically inhibit the growth of HL60 cells in a dose-dependent (0.25-8 micromol/l) and time-dependent (12-72 h) manner. DHA-induced DNA fragmentation also induced the activation of caspase-3 and influenced the expression of Bcl-2 and Bax. Taken together, these data from our study show that DHA can induce HL60 cell apoptosis via the effect of downregulation TfR expression resulting in an induction of apoptosis through the mitochondrial pathway, and it might be a potential antileukemia strategy for leukemia therapy.
Relationship between immune gene signatures and clinical response to PD-1 blockade with pembrolizumab (MK-3475) in patients with advanced solid tumors (2015)

Meeting abstracts Immune checkpoint inhibition with anti–PD-1 monoclonal antibodies such as pembrolizumab has demonstrated robust, durable anti-tumor activity against many advanced malignancies. We analyzed immune-related gene expression profiles in pembrolizumab-treated patients with advanced
Magnetic resonance imaging and model prediction for thermal ablation of tissue (2007)

For normal tissue in vivo, the dynamics of tissue temperature distribution and lesion size during RF thermal ablation can be 1) monitored with GRE phase and magnitude images, and 2) simulated for prediction with a thermal model.
Early detection and treatment of neovascular age-related macular degeneration. (2002)

Primary care physicians can effect good treatment outcomes by detecting early signs of AMD and educating patients about the necessity of prompt referral to an ophthalmologist. Immediate referral is increasingly important because, compared with laser photocoagulation, current photodynamic therapy with verteporfin is applicable to more patients. Greater patient awareness of neovascular AMD and the importance of self-testing of vision can also be communicated to patients in primary care.
Relationship of endothelial function to birth weight in humans. (1999)

The finding of elevated von Willebrand factor in low birth weight subjects is suggestive of endothelial cell injury but does not appear to be associated with dysfunction of the L-arginine-nitric oxide pathway.
Self-referencing spectral interferometry for measuring ultrashort optical pulses (1999)

This paper describes a novel self-referencing interferometric method for measuring the time-dependent intensity and phase of ultrashort optical pulses. The technique, spectral phase interferometry for direct electric-field reconstruction (SPIDER), measures the interference between a pair of spectrally sheared replicas of the input pulse. Direct (noniterative) inversion of the interferogram yields the electric field of the input pulse without ambiguity. The interferogram, which is solely a function of frequency, is resolved with a spectrometer and recorded with a slow detector. Moreover, the geometry is entirely collinear and requires no moving components. This paper describes in detail the principle of operation, apparatus, and calibration of SPIDER and gives experimental examples of reconstructed pulses.
Effect of Material Properties on Cracking in Bridge Decks (1999)

The effect of concrete material properties on cracking in bridge decks is evaluated based on field surveys of 40 continuous steel girder bridges, representative of construction throughout the State of Kansas. Information collected from construction documents and field books is compared with observed levels of cracking to identify correlations between cracking and the variables studied. The results of the evaluation indicate that cracking in monolithic bridge decks increases with increasing values of concrete slump, percent of concrete volume occupied by water and cement, water content, cement content, and compressive strength, and decreasing values of air content (especially below 6.0%). Bridge deck overlays placed with zero slump concrete exhibit consistently higher levels of cracking than overlays with measurable slumps.
Altered Tau and Neurofilament Proteins in Neuro‐Degenerative Diseases: Diagnostic Implications for Alzheimer's Disease and Lewy Body Dementias (1993)

The neuronal cytoskeleton is one of the most profoundly altered organelles in late life neuro-degenerative disorders that are characterized by progressive impairments in cognitive abilities. The elucidation of the protein building blocks of these organelles as well as advances in understanding how these proteins become altered in Alzheimer's disease (AD) and other less common dementing illnesses, i.e., diffuse Lewy body disease (DLBD) or the Lewy body variant of AD (LBVAD), will provide insights into the molecular basis of these disorders. Within, we review evidence that normal adult human tau is abnormally phosphorylated and converted into the subunits of AD paired helical filaments (PHFs), and that Lewy bodies (LBs) represent accumulation of altered neurofilament (NF) triplet subunits. Although the precise biological consequences of PHF and LB formation in neurons is unknown, growing evidence suggests that the formation of PHFs and LBs from normal neuronal cytoskeletal proteins could have deleterious effects on neuronal function and survival. Finally, insights into the composition of PHFs and LBs could lead to the development of novel strategies for the timely and accurate diagnosis of AD, DLBD and the LBVAD.
Functions of the adenovirus E4 proteins and their impact on viral vectors (2005)

Viral vectors based on recombinant adenoviruses (rAd) are used extensively as gene delivery systems for investigations of gene function and gene therapy applications. In both cases, the desire is for efficient expression of a transgene without substantial toxicity to the target cell. The first generation of rAd vectors were deleted of early region E1 and sometimes additionally early region E3. Evaluation of these vectors in preclinical animal models revealed transient gene expression, accompanied by cytotoxicity and immune responses. Expression of remaining viral genes, even in the absence of the E1 region, contributes to these effects and therefore it is important to have an appreciation of the functions of these viral genes. In particular, the early region E4 has been shown to affect transgene persistence, vector toxicity and immunogenicity. Proteins from the E4 genes can modulate transcription, the cell-cycle, cell signaling and DNA repair. In addition, some of these proteins also cause oncogenic transformation. Therefore interactions of these viral genes with key cell regulators should be taken into account when engineering rAd vectors. This review will summarize our knowledge of E4 functions and the implications of recent findings on the development of rAd vectors.
Using Self-Assembled Monolayers Exposed to X-rays To Control the Wetting Behavior of Thin Films of Diblock Copolymers (2000)

The wetting behavior of thin films of symmetric poly(styrene-block-methyl methacrylate) was investigated on self-assembled monolayers (SAMs) of octadecyltrichlorosilane (OTS) that were chemically modified by exposure to X-rays in the presence of air. The concentration of aldehyde and hydroxyl groups on the surface of exposed OTS increases with increasing dose. The polarity and surface tension of the SAMs were tuned to control the wetting behavior of the polymer films. Symmetric, neutral, and asymmetric wetting of the films were observed for doses of 400−1000, 1200, and 1400−2000 mJ/cm2, respectively. The wetting behavior was qualitatively described by estimating the interfacial energies between each block of the copolymer and exposed SAMs and the surface tensions of both blocks using the Fowkes−van Oss−Chaudhury−Good model of surface tension. These results lay the foundation for controlling the morphology of thin films of block copolymers over macroscopic dimensions by nanopatterning substrates with regions of different wetting behavior using advanced lithography.
Enantioselective Reduction of α,β‐Unsaturated Carboxylates with NaBH4 and Catalytic Amounts of Chiral Cobalt Semicorrin Complexes (1989)

High enantioselectivities (up to 96% ee), almost quantitative chemical yields, and mild reaction conditions characterize the title reaction. It is suitable, for example, for the synthesis of isoprenoid chains as occur in the vitamins E and K1. An example is reaction (a), R  CH2OSiMe2tBu.