gebhart/patrepeval huggingface dataset:
The study of logarithmic image processing model and its application to image enhancement (1995)

Describes a new implementation of Lee's (1980) image enhancement algorithm. This approach, based on the logarithmic image processing (LIP) model, can simultaneously enhance the overall contrast and the sharpness of an image. A normalized complement transform has been proposed to simplify the analysis and the implementation of the LIP model-based algorithms. This new implementation has been compared with histogram equalization and Lee's original algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Alpha estimation in natural images (2002)

Many boundaries between objects in the world project onto curves in an image. However, boundaries involving natural objects (e.g., trees, hair, water, smoke) are often unworkable under this model because many pixels receive light from more than one object. We propose a technique for estimating alpha, the proportion in which two colors mix to produce a color at the boundary. The technique extends blue screen matting to backgrounds that have almost arbitrary color distributions, though coarse knowledge of the boundary's location is required. Results show a number of different objects moved from one image to another while maintaining naturalism.
Mitochondrial activation chemicals synergize with surface receptor PD-1 blockade for T cell-dependent antitumor activity (2017)

Although immunotherapy by PD-1 blockade has dramatically improved the survival rate of cancer patients, further improvement in efficacy is required to reduce the fraction of less sensitive patients. In mouse models of PD-1 blockade therapy, we found that tumor-reactive cytotoxic T lymphocytes (CTLs) in draining lymph nodes (DLNs) carry increased mitochondrial mass and more reactive oxygen species (ROS). We show that ROS generation by ROS precursors or indirectly by mitochondrial uncouplers synergized the tumoricidal activity of PD-1 blockade by expansion of effector/memory CTLs in DLNs and within the tumor. These CTLs carry not only the activation of mechanistic target of rapamycin (mTOR) and AMP-activated protein kinase (AMPK) but also an increment of their downstream transcription factors such as PPAR-gamma coactivator 1α (PGC-1α) and T-bet. Furthermore, direct activators of mTOR, AMPK, or PGC-1α also synergized the PD-1 blockade therapy whereas none of above-mentioned chemicals alone had any effects on tumor growth. These findings will pave a way to developing novel combinatorial therapies with PD-1 blockade.
T‐cell activation and the dynamic world of rafts: (1999)

Recent evidence, indicates that T-cell receptor (TCR) triggering and T-cell activation are dynamic processes that involve various aspects of T-cell organization. In addition to the interaction between the TCR molecule and its ligand, T-cell activation depends on a combination of many other events involving coreceptor molecules, actin cytoskeleton and plasma membrane lipids. Altogether, these cell structures organize the formation of a specialized junction between the T cell and the antigen-presenting cell (APC), that plays a critical role in sustaining and amplifying TCR signalling.
Bruton's tyrosine kinase as a molecular target in treatment of leukemias and lymphomas as well as inflammatory disorders and autoimmunity (2010)

BTK inhibitors may provide the foundation for therapeutic innovation against B-lineage leukemias/lymphomas, inflammatory disorders and autoimmunity.
A novel adenoviral vector carrying an all-in-one Tet-On system with an autoregulatory loop for tight, inducible transgene expression (2015)

Our novel, single adenoviral vector carrying in its E1 region an all-in-one Tet-On system with an autoregulatory loop displayed tight regulation of transgene expression in vitro. This system has great potential for a variety of applications, including gene therapy and the study of gene function.
DNA sequencing and expression of the formyl coenzyme A transferase gene, frc, from Oxalobacter formigenes (1997)

Oxalic acid, a highly toxic by-product of metabolism, is catabolized by a limited number of bacterial species utilizing an activation-decarboxylation reaction which yields formate and CO2. frc, the gene encoding formyl coenzyme A transferase, an enzyme which transfers a coenzyme A moiety to activate oxalic acid, was cloned from the bacterium Oxalobacter formigenes. DNA sequencing revealed a single open reading frame of 1,284 bp capable of encoding a 428-amino-acid protein. A presumed promoter region and a rho-independent termination sequence suggest that this gene is part of a monocistronic operon. A PCR fragment containing the open reading frame, when overexpressed in Escherichia coli, produced a product exhibiting enzymatic activity similar to the purified native enzyme. With this, the two genes necessary for bacterial catabolism of oxalate, frc and oxc, have now been cloned, sequenced, and expressed.
Interleukin 3 or interleukin 1 abrogates the reconstituting ability of hematopoietic stem cells. (1996)

Because of their known myelopoietic activities, both interleukin (IL)-3 and IL-1 are often used in combination with other cytokines for in vitro (ex vivo) expansion of stem cells. We have investigated the effects of IL-3 and IL-1 on in vitro expansion of murine hematopoietic stem cells with long-term engraftment capabilities, using a highly purified progenitor population. Lineage-negative, Ly-6A/E+, c-kit+ bone marrow cells from male mice were cultured in suspension in the presence of stem cell factor, IL-6, IL-11, and erythropoietin with or without IL-3 or IL-1. Kinetic studies revealed an exponential increase in total nucleated cells and about 10-fold enhancement of nucleated cells by IL-3 during the initial 10 days. Addition of IL-3 hastened the development but significantly suppressed the peak production of colony-forming cells. Addition of IL-1 also significantly suppressed the numbers of colony-forming cells. The reconstituting ability of the cultured cells was tested by transplanting the expanded male cells into lethally irradiated female mice. The cells expanded from enriched cells in the absence of IL-3 and IL-1 revealed engraftment at 2, 4, 5, and 6 months, whereas addition of IL-3 or IL-1 to the cultures significantly reduced the reconstituting ability. The results suggest that these cytokines may have a modulatory role on the self-renewal of stem cells and further indicate that the use of IL-3 and IL-1 for in vitro expansion of human stem cells needs to be cautiously evaluated.
Efficacy of Recombinant Human Granulocyte‐macrophage Colony‐stimulating Factor in Rhesus Monkeys (1987)

The glycosylated and the non-glycosylated recombinant human granulocyte-macrophage colony-stimulating factor (rh GM-CSF) expressed in Chinese hamster ovary cells and E. coli, respectively, were administered in rhesus monkeys either by the subcutaneous (three times daily) or intravenous route (6-hr infusions) for seven consecutive days. Within 24 hr peripheral white blood cells (WBC) increased 2-3 fold over normal values. Thereafter, the WBC increased steadily in a dose-dependent manner to reach maximum levels on the last day of or one day after the treatment period. The differential counts showed that neutrophils contributed to 50-80%, eosinophils to 10-20%, monocytes to 2-7%, and lymphocytes to 15-30% of the WBC rise. No effect was found on platelets and erythrocytes. After termination of treatment, WBC counts returned to normal levels within one week. Subcutaneously administered CSF was more effective in inducing leukocytosis than that injected intravenously In addition to the rise in WBC, the administered rh GM-CSF also enhanced the oxidative metabolism and bactericidal activity of the circulating mature granulocytes isolated from the blood of monkeys treated with rh GM-CSF. These results show that glycosylated or non-glycosylated rh GM-CSF is both an effective stimulator of leukocytosis and a potent activator of the functional activity of mature granulocytes in vivo.
Growth of Large-Diameter Single-Walled Carbon Nanotubes (1999)

Single-walled carbon nanotubes (SWNTs) give every indication that they will make a major impact on science and technology. Their unusual physical and chemical properties, which depend on nanotube diameter and helicity, make them particularly attractive for future molecular nanotechnology applications. Production of a variety of nanotubes will be necessary to explore novel properties arising from a variety of detailed atomic structures. We have synthesized large-diameter SWNTs by adding catalyst promoters, using either Co or Fe as primiary catalyst. SWNTs produced by transition metal catalysts alone have a diameter distribution between 1 and 2 nm. Adding catalyst promoter alters the diameter distribution to a much wider range, with a variety of helicities, and dramatically increases the nanotube yields. The results indicate the need for a general growth mechanism that accounts for the effect of catalyst promoters.
The 52 -55 segment of the Bacillus subtilis chromosome: a region devoted to purine uptake and metabolism, and containing the genes cotA, gabP and guaA and the pur gene cluster within a 34960 bp nucleotide sequence (1996)

Within the framework of the international project for sequencing the entire Bacillus subtilis genome, we have determined the complete sequence of the segment flanking the purE-D gene cluster (55 degrees) as far as cotA (52 degrees). This segment (34960 bp) contains, as well as 12 genes already identified as part of the pur operon, 17 putative ORFs and one partial one. Two of them (gabP and guaA) are known B. subtilis genes. The gene product of cotA (formerly pig) shows significant similarity to oxidoreductases (phenoxazine synthase and bilirubin oxidase). The putative products of ORFs yeaB (Czd protein), yeaC (MoxR), yebA (CNG-channel and cGMP-channel proteins from eukaryotes), yebB (hypothetical 32.9 kDa protein of Escherichia coli), yecA (amino acid permease) and yecB (adenine deaminase) were similar to proteins in data banks.
Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes (1999)

Comparing patterns of gene expression in cell lines and tissues has important applications in a variety of biological systems. In this study we have examined whether the emerging technology of cDNA microarrays will allow a high throughput analysis of expression of cDNA clones generated by suppression subtractive hybridization (SSH). A set of cDNA clones including 332 SSH inserts amplified by PCR was arrayed using robotic printing. The cDNA arrays were hybridized with fluorescent labeled probes prepared from RNA from ER-positive (MCF7 and T47D) and ER-negative (MDA-MB-231 and HBL-100) breast cancer cell lines. Ten clones were identified that were over-expressed by at least a factor of five in the ER-positive cell lines. Northern blot analysis confirmed over-expression of these 10 cDNAs. Sequence analysis identified four of these clones as cytokeratin 19, GATA-3, CD24 and glutathione-S-transferase mu-3. Of the remaining six cDNA clones, four clones matched EST sequences from two different genes and two clones were novel sequences. Flow cytometry and immunofluorescence confirmed that CD24 protein was over-expressed in the ER-positive cell lines. We conclude that SSH and microarray technology can be successfully applied to identify differentially expressed genes. This approach allowed the identification of differentially expressed genes without the need to obtain previously cloned cDNAs.
Interaction in a collaborative augmented reality environment (2002)

In this paper we describe an Augmented Reality (AR) system which allows multiple participants to interact with two- and three-dimensional data using tangible user interfaces. Interactively controllable 2D and 3D information is seamless integrated into the system.
Principles of communications (1976)

Ziemer and Tranter provide a thorough treatment of the principles of communications at the physical layer suitable for college seniors, beginning graduate students, and practicing engineers. This is accomplished by providing overviews of the necessary background in signal, system, probability, and random process theory required for the analog and digital communications topics covered in the book. In addition to stressing fundamental concepts, sections on currently important areas such as spread spectrum, cellular communications, and orthogonal frequency-division multiplexing are provided. While the book is aimed at a two-semester course, more than enough material is provided for structuring courses according to the needs of the students and the preferences of the instructor.
Feasibility Study of a Mini, Bone-Attached, Robotic System for Spinal Operations (2004)

The given results support the theoretical model developed. Moreover, a miniature robotic guiding system can be attached to the spinous process of a given vertebra. The deflection and system error resulting from the forces and moments acting during operation are within the allowable errors.
Expression of the mdr (P-glycoprotein) Gene in Chinese Hamster Digestive Tracts1 (1988)

P-glycoprotein has been shown to be responsible for multidrug resistance in mammalian cells. However, its physiological roles in normal cells are not known. The gene encoding this protein has been shown to express at a relatively high level in human digestive tracts. In the present study, in situ hybridizations were employed to determine the expression of this gene in gastrointestinal tissues. Epithelial cells in the villi of small intestine, colon, and stomach were rich in the P-glycoprotein gene transcript. Observations were consistent with the idea that the P-glycoprotein plays a role in detoxification by pumping potentially harmful compounds into the lumen of digestive tracts in animals.
Altered Distribution of Nicotinamide-Adenine Dinucleotide Phosphate—Diaphorase Cells in Frontal Lobe of Schizophrenics Implies Disturbances of Cortical Development (1993)

Epidemiological and anatomical studies support the theory that disturbances of brain development may play a contributory role in the etiology of schizophrenia. Anatomical findings suggest that the normal pattern of neuronal migration during development of the cerebral cortex may be affected in the brains of schizophrenics, with the implication that cortical connectivity and associative function will be disrupted. In the present investigation in matched schizophrenic and control brains, we examined a particular population of neurons found in the prefrontal cortex and underlying white matter and characterized by histochemical staining for the enzyme nicotinamide-adenine dinucleotide phosphate-diaphorase. In normal brains, these neurons are found in highest numbers in the white matter immediately deep to layer VI of the cortex where they remain from the subplate, an early formed, but transitory structure that plays a key role in cortical development and connection formation. The dorsolateral prefrontal area of schizophrenics showed a significant decline in nicotinamide-adenine dinucleotide phosphate-diaphorase neurons in the superficial white matter and in the overlying cortex but a significant increase in these neurons in white matter deeper than 3 mm from the cortex. These findings are consistent with a disturbance of the subplate during development in which the normal pattern of programmed cell death is compromised and accompanied by a defect in the normal orderly migration of neurons toward the cortical plate. These are likely to have serious consequences for the establishment of a normal pattern of cortical connections leading to a potential breakdown of frontal lobe function in schizophrenics.
Toward deciphering proteomes of formalin‐fixed paraffin‐embedded (FFPE) tissues (2012)

Formalin-fixed paraffin-embedded (FFPE) tissue specimens comprise a potentially valuable resource for both prospective and retrospective biomarker discovery. Unlocking the proteomic profile of clinicopathological FFPE tissues is a critically essential step for annotating clinical findings and predicting biomarkers for ultimate disease prognosis and therapeutic follow-up.
Breaking down bone: new insight into site-specific mechanisms of breast cancer osteolysis mediated by metalloproteinases: Figure 1. (2009)

Bone metastases are the most common skeletal complication of malignancy. Tumor cells disrupt normal bone remodeling to promote bone destruction and its associated morbidity. In the August 15, 2009, issue of Genes & Development, Lu and colleagues (pp. 1882-1894) propose a novel molecular mechanism by which tumor-produced metalloproteinases release epidermal growth factor (EGF) ligands to activate the central osteoclastogenic pathway receptor activator of NF-kappaB ligand (RANKL) to promote breast cancer osteolysis. This work has important therapeutic applications that may quickly translate to more effective treatment for bone metastases.
An intermediate-risk multiple myeloma subgroup is defined by sIL-6r: levels synergistically increase with incidence of SNP rs2228145 and 1q21 amplification (2011)

IL-6 signaling can be enhanced through transsignaling by the soluble IL-6 receptor (sIL-6r), allowing for the pleiotropic cytokine to affect cells it would not ordinarily have an effect on. Serum levels of sIL-6r can be used as an independent prognostic indicator and further stratify the GEP 70-gene low-risk group to identify an intermediate-risk group in multiple myeloma (MM). By analyzing more than 600 MM patients with ELISA, genotyping, and gene expression profiling tools, we show how the combination of 2 independent molecular genetic events is related to synergistic increases in sIL-6r levels. We also show that the rs2228145 minor allele is related to increased expression levels of an IL-6r splice variant that purportedly codes exclusively for a sIL-6r isoform. Together, the SNP rs2228145 minor allele C and amplification of chromosome 1q21 are significantly correlated to an increase in sIL-6r levels, which are associated with lower overall survival in 70-gene low-risk disease, and aid in identification of the intermediate-risk MM group.
P2‐121: Senescent Neurons in the Alzheimer's Brain Kill Nearby Healthy Neurons by Blocking their WNT Lifeline: The Continuing Saga of the Zombie Apocalypse (2016)

Two types of cellular senescence are known. Replicative senescence is associated with shortened telomeres and the process of aging and thus would be expected to play a role in the AD neurodegenerative process. Oncogene induced senescence, by contrast is a cellular defense against cancer; it produces a persistent abnormal state of cell cycle arrest and cytokine secretion. The latter have deleterious effects on bystander cells and thus help a tumor invade its surroundings. Human material was obtained from the NIH NeuroBioBank. Wild type and AD transgenic mice, bred from stock obtained from JAX, were sacrificed by perfusion. All tissue was cryostat sectioned at 10 μm and immunostained. In both human AD and its mouse models, cells in at-risk populations show elevated nuclear levels of the known oncogene, β-catenin. This was associated with ectopic expression of genes such as cyclin D, p53 and c-Myc and, predictably, neuronal cell cycle re-entry and cellular senescence. The senescence is marked by the presence of senescence associated β-galactosidase and elevated levels of Wnt inhibitors such as Dickkopf (DKK1). As adult neurons require Wnt signaling for survival, this rise in DKK1 levels triggers apoptosis in nearby healthy neurons. The central role of DKK1 has been validated by in vitro studies using function-blocking antibody as well as in AD mouse models. The bystander effect can be documented in human AD brain where sporadic groups of b-catenin-positive cells are surrounded by an area containing dying (caspase-3+) cells. The senescent cells themselves are caspase-3–, protected from DKK1 by the presence the modified cyclin-like protein, p25, that blocks the association of GSK3β with its b-catenin substrate. This prevents the degradation of b-catenin, facilitating its nuclear accumulation and thus short-circuiting the normal Wnt signaling pathway. These findings have unexpected implications for AD treatment. The emergence of senescent neurons means the AD brain contains zombie-like cells that kill healthy bystander neurons. We do not know what creates the zombies, but to fully treat AD they must be destroyed. This presents a paradox: to cure a neurodegenerative disease, we have to kill more neurons.
Targeted Delivery of siRNA to Hepatocytes and Hepatic Stellate Cells by Bioconjugation (2010)

Previously, we successfully conjugated galactosylated poly(ethylene glycol) (Gal-PEG) to oligonucleotides (ODNs) via an acid labile ester linker (Zhu et al., Bioconjugate Chem. 2008, 19, 290-8). In this study, sense strands of siRNA were conjugated to Gal-PEG and mannose 6-phosphate poly(ethylene glycol) (M6P-PEG) for targeted delivery of siRNAs to hepatocytes and hepatic stellate cells (HSCs), respectively. These siRNA conjugates were purified by ion exchange chromatography and verified by gel retardation assay. To evaluate their RNAi functions, the validated siRNA duplexes targeting firefly luciferase and transforming growth factor beta 1 (TGF-β1) mRNA were conjugated to Gal-PEG and M6P-PEG, and their gene silencing efficiencies were determined after transfection into HepG2 and HSC-T6 cells. The disulfide bond between PEG and siRNA was cleaved by dithiothreitol, leading to the release of intact siRNA. Both Gal-PEG-siRNA and M6P-PEG-siRNA conjugates could silence luciferase gene expression by about 40% without any transfection reagents, while the gene silencing effects reached more than 98% with the help of cationic liposomes at the same dose. Conjugation of TGF-β1 siRNA with Gal-PEG and M6P-PEG could silence endogenous TGF-β1 gene expression as well. In conclusion, these siRNA conjugates have the potential for targeted delivery of siRNAs to hepatocytes and hepatic stellate cells for efficient gene silencing in vivo.
The generation of natural killer (NK) cells from NK precursor cells in rat long-term bone marrow cultures. (1990)

In this report, we describe a novel long-term bone marrow culture (LTBMC) system to study the origin and generation of natural killer (NK) cells from NK precursors. Rat bone marrow was cultured for 4 wk in RPMI 1640 with 5% fetal calf serum and 2-mercaptoethanol to allow the formation of an adherent stromal cell layer containing NK precursor cells. After addition of interleukin 2 (IL-2), the LTBMC generated high numbers (up to 100-fold expansion in 7 d) of pure 3.2.3+ large granular lymphocytes with lytic activity against NK-sensitive and -resistant tumor targets, as well as antibody-dependent cellular cytotoxicity. NK activity in LTBMC could be detected 3 d after addition of as little as 1 U/ml rIL-2, whereas lymphokine-activated killer activity was found 5 d after addition of at least 10 U/ml rIL-2. In vivo depletion and in vitro complement lysis studies showed that the NK precursor cells in LTBMC did not express the NK-associated surface markers asialo GM1 or 3.2.3. We also found that LTBMC cells did not exhibit colony growth in granulocyte/macrophage or spleen colony-forming unit assays. The generation of NK cells from NK precursors required, in addition to IL-2, a second growth/maturation factor(s), which was present in the conditioned medium of the LTBMC. This LTBMC system provides a unique in vitro model to study the development of NK cells from precursor cells, the role of the bone marrow stromal microenvironment in this development, and the lineage relationship of NK cells to other hematopoietic cells.
Interferon‐alpha in lupus psychosis (1992)

These findings support the hypothesis that IFN alpha, possibly synthesized in the brain, is the cause of the manifestation of psychosis in patients with SLE.