gebhart/patrepeval huggingface dataset:
FOVEA: a foveated vergent active stereo vision system for dynamic three-dimensional scene recovery (1998)

We introduce FOVEA: a foveated vergent active stereo vision system. FOVEA actively directs a pair of vergent stereo cameras to fixate on surfaces in a scene, performing multiresolution surface depth recovery at each fixation point, and accumulating and integrating a multiresolution map of surface depth over multiple successive fixations. Several features of the system are novel: an active foveated image sampling and processing strategy is shown to greatly simplify the problem of establishing correspondence; a probabilistic fixation strategy is developed that is driven by the scene structure; the system uses the fixation strategy to recover local depth maps at a high resolution at multiple fixation points, eventually mapping the entire scene; and finally, the local maps are integrated as they are acquired into a global depth map.
Discarded stem cells with a future? (2006)

Although embryonic stem cells hold the promise for tissue and organ generation, stem cells with early mesenchymal character, which can be obtained at the time of birth from extra-embryonic tissue, may have similar capabilities if manipulated appropriately. These 'perinatal' tissues, such as the umbilical cord or the placenta, which are generally discarded after delivery, contain early mesenchymal stem cells that are believed to have a greater potential for plasticity than postnatal mesenchymal cells, such as those from bone marrow. They express early transcriptional genes, and emerging technologies, such as nuclear reprogramming, could direct their development into tissues of embryonic origin. Hence, these cells, generally discarded after birth, could become a valuable source for future tissue generation.
Defective Antitumor Function of Monocyte-Derived Macrophages from Epithelial Ovarian Cancer Patients (2006)

These findings highlight for the first time the defective antibody-dependent cell-mediated cytotoxicity and phagocyte functions of epithelial ovarian cancer-associated MO/MA, which could have implications for immunobiotherapeutic strategies.
Sequence and Characterization of a Coactivator for the Steroid Hormone Receptor Superfamily (1995)

A yeast two-hybrid system was used to identify a protein that interacts with and enhances the human progesterone receptor (hPR) transcriptional activity without altering the basal activity of the promoter. Because the protein stimulated transactivation of all the steroid receptors tested, it has been termed steroid receptor coactivator-1 (SRC-1). Coexpression of SRC-1 reversed the ability of the estrogen receptor to squelch activation by hPR. Also, the amino terminal truncated form of SRC-1 acted as a dominant-negative repressor. Together, these results indicate that SRC-1 encodes a coactivator that is required for full transcriptional activity of the steroid receptor superfamily.
Contextual Dominant Color Name Extraction for Web Image Search (2012)

This paper addresses the problem of extracting perceptually dominant color names of images. Our approach is motivated by the principle that the pixels corresponding to one dominant color name identified by human are often context dependent, spatially connected and form a perceptually meaningful region. Our algorithm first learns the probabilistic mapping from a RGB color to a color name. Then, a double-threshold approach is utilized to determine the color name of a RGB pixel in a specific image by considering its neighboring pixels. This scheme effectively deals with the pixels ambiguously belonging to several dominant color names. Last, the saliency information is combined to extract perceptually dominant colors. Experiments on our labeled image data set and the Ebay image set demonstrate the effectiveness of our approach.
Thiazole Orange−Peptide Conjugates:  Sensitivity of DNA Binding to Chemical Structure (2004)

[structure: see text] Derivatives of the highly fluorescent and DNA-binding dye thiazole orange (TO) are described that feature appended peptides. Functionalization of TO can be achieved at either of the endocyclic nitrogens, and the photophysical properties and DNA-binding modes are sensitive to the position of the tethered peptide. A series of TO-peptide conjugates are described, demonstrating the utility of a solid-phase synthesis approach to their preparation and illustrating how the photophysical and DNA-binding properties of the compounds are influenced by chemical structure.
Function and solution structure of huwentoxin-IV, a potent neuronal tetrodotoxin (TTX)-sensitive sodium channel antagonist from Chinese bird spiderSelenocosmia huwena. (2003)

Page 47567, Fig. 4 legend: The following sentence is missing from the figure legend. “An asterisk indicates that the C-terminal carboxyl group is amidated.” The figure with the corrected legend is shown below.
Comparison of the Effects of Early Pregnancy with Human Interferon, Alpha 2 (IFNA2), on Gene Expression in Bovine Endometrium1 (2011)

Interferon tau (IFNT), a type I IFN similar to alpha IFNs (IFNA), is the pregnancy recognition signal produced by the ruminant conceptus. To elucidate specific effects of bovine IFNT and of other conceptus-derived factors, endometrial gene expression changes during early pregnancy were compared to gene expression changes after intrauterine application of human IFNA2. In experiment 1, endometrial tissue samples were obtained on Day (D) 12, D15, and D18 postmating from nonpregnant or pregnant heifers. In experiment 2, heifers were treated from D14 to D16 of the estrous cycle with an intrauterine device releasing IFNA2 or, as controls, placebo lipid extrudates or PBS only. Endometrial biopsies were performed after flushing the uterus. All samples from both experiments were analyzed with an Affymetrix Bovine Genome Array. Experiment 1 revealed differential gene expression between pregnant and nonpregnant endometria on D15 and D18. In experiment 2, IFNA2 treatment resulted in differential gene expression in the bovine endometrium. Comparison of the data sets from both studies identified genes that were differentially expressed in response to IFNA2 but not in response to pregnancy on D15 or D18. In addition, genes were found that were differentially expressed during pregnancy but not after IFNA2 treatment. In experiment 3, spatiotemporal alterations in expression of selected genes were determined in uteri from nonpregnant and early pregnant heifers using in situ hybridization. The overall findings of this study suggest differential effects of bovine IFNT compared to human IFNA2 and that some pregnancy-specific changes in the endometrium are elicited by conceptus-derived factors other than IFNT.
Point-of-Care Support for Error-Free Medication Process (2007)

Technological advances and critical needs have led to medication administration devices and tools designed to prevent and reduce medication errors. They include smart medication carts, robots and dispensers for professionals and smart dispensers for naive users. This paper describes architectures and interfaces of these devices. It also discusses support environment that is needed to increase their effectiveness and missing standards that will enable their integration into medication process tool chain.
Notch-1 signaling facilitates survivin expression in human non-small cell lung cancer cells (2011)

The oncogenic potential of Notch activation is observed in many instances including lung tumorigenesis, but the associated molecular regulatory mechanism has not been thoroughly defined. It has been demonstrated that hypoxia can act as one of the major stimuli in the progression of many types of tumorigenesis. This study was designed to examine the activation of Notch-1 signaling by hypoxia and its contribution to survivin expression in human lung carcinomas. Western-blot and PCR analysis showed that Notch-1 signaling is activated by hypoxia in the human non-small cell lung cancer (NSCLC) cell line, A549, through the upregulation of Notch-1, along with its intracellular domain (N1ICD). The activity of Hes-1, a crucial target molecule of N1ICD, was also increased under hypoxia. Interestingly, blockade of the Notch-1 pathway by a γ-secretase inhibitor or small interfering RNA (siRNA) inhibited survivin expression. Conversely, activation of Notch-1 signaling by N1ICD or stimulation with the Jagged1 ligand enhanced survivin levels in A549 cells. Notably, HIF-1α cooperated with Notch-1 signaling to increase survivin expression through its direct association with N1ICD, consequently accelerating survivin transcription. Overall, our findings suggest that Notch-1 signaling is involved in the upregulation of survivin expression in lung cancer cells, which is synergized by HIF-1α.
Allelic loss of the retinoblastoma gene in primary human prostatic adenocarcinomas (1995)

Inactivation of the retinoblastoma (Rb) gene has been implicated in the genesis and progression of a number of tumor types, including prostatic adenocarcinomas. We have analyzed a series of 46 surgically-resected human prostatic adenocarcinomas for allelic loss of the Rb gene with PCR amplification of a highly polymorphic region of the gene. 41 of 46 tumors (89%) were informative and 11 of these (27%) had lost one Rb allele. The relative frequency of this occurrence suggests that inactivation of the retinoblastoma gene may be an important event in prostate carcinogenesis.
Tyrosine kinase JAK1 is associated with the granulocyte-colony-stimulating factor receptor and both become tyrosine-phosphorylated after receptor activation. (1994)

Granulocyte-colony-stimulating factor (G-CSF) stimulates the proliferation and differentiation of cells of the neutrophil lineage by interaction with a specific receptor. Early signal transduction events following G-CSF receptor activation were studied. We detected tyrosine phosphorylation of both the G-CSF receptor and the protein tyrosine kinase JAK1 following G-CSF binding to the human G-CSF receptor. In vitro, the kinase activity of JAK1 was increased by G-CSF stimulation. Coimmunoprecipitation of JAK1 with the G-CSF receptor suggested a physical association which existed prior to G-CSF stimulation.
Exon-skipping and mRNA decay in human liver tissue: molecular consequences of pathogenic bile salt export pump mutations (2016)

The bile salt export pump BSEP mediates bile formation. Over 150 BSEP mutations are associated with progressive familial intrahepatic cholestasis type 2 (PFIC-2), with few characterised specifically. We examined liver tissues from two PFIC-2 patients compound heterozygous for the splice-site mutation c.150 + 3A > C and either c.2783_2787dup5 resulting in a frameshift with a premature termination codon (child 1) or p.R832C (child 2). Splicing was analysed with a minigene system and mRNA sequencing from patients' livers. Protein expression was shown by immunofluorescence. Using the minigene, c.150 + 3A > C causes complete skipping of exon 3. In liver tissue of child 1, c.2783_2787dup5 was found on DNA but not on mRNA level, implying nonsense-mediated mRNA decay (NMD) when c.2783_2787dup5 is present. Still, BSEP protein as well as mRNA with and without exon 3 were detectable and can be assigned to the c.150 + 3A > C allele. Correctly spliced transcripts despite c.150 + 3A > C were also confirmed in liver of child 2. In conclusion, we provide evidence (1) for effective NMD due to a BSEP frameshift mutation and (2) partial exon-skipping due to c.150 + 3A > C. The results illustrate that the extent of exon-skipping depends on the genomic and cellular context and that regulation of splicing may have therapeutic potential.
Mouse Dll3: a novel divergent Delta gene which may complement the function of other Delta homologues during early pattern formation in the mouse embryo (1997)

Mouse delta-like 3 (Dll3), a novel vertebrate homologue of the Drosophila gene Delta was isolated by a subtracted library screen. In Drosphila, the Delta/Notch signalling pathway functions in many situations in both embryonic and adult life where cell fate specification occurs. In addition, a patterning role has been described in the establishment of the dorsoventral compartment boundary in the wing imaginal disc. Dll3 is the most divergent Delta homologue identified to date. We confirm that Dll3 can inhibit primary neurogenesis when ectopically expressed in Xenopus, suggesting that it can activate the Notch receptor and therefore is a functional Delta homologue. An extensive expression study during gastrulation and early organogenesis in the mouse reveals a diverse and dynamic pattern of expression. The three major sites of expression implicate Dll3 in somitogenesis and neurogenesis and in the production of tissue from the primitive streak and tailbud. A careful comparison of Dll3 and Dll1 expression by double RNA in situ hybridisation demonstrates that these genes have distinct patterns of expression, but implies that together they operate in many of the same processes. We postulate that during somitogenesis Dll3 and Dll1 coordinate in establishing the intersomitic boundaries. We confirm that, during neurogenesis in the spinal cord, Dll1 and Dll3 are expressed by postmitotic cells and suggest that expression is sequential such that cells express Dll1 first followed by Dll3. We hypothesise that Dll1 is involved in the release of cells from the precursor population and that Dll3 is required later to divert neurons along a specific differentiation pathway.
Contrast agents for MRA: Future directions (1999)

The purpose of this review is to outline recent developments in contrast agents for magnetic resonance angiography (MRA) and to give some idea of what the future might hold. Up to now, non-binding gadolinium (Gd) chelates have been the agents used for MRA. Modified paramagnetic Gd-based agents with varying degrees of protein interaction have been developed, and these, together with new superparamagnetic compounds, are currently under clinical evaluation. It is likely that two different types of contrast agent will soon be available: extracellular agents for first-pass MRA and intravascular agents mainly for steady-state MRA. Several agents also exhibit certain tissue specific properties in addition to conventional extracellular properties. This will lead to more comprehensive imaging approaches.J. Magn. Reson. Imaging 10:314–316, 1999. © 1999 Wiley-Liss, Inc.
DNA binding proteins explore multiple local configurations during docking via rapid rebinding (2016)

Finding the target site and associating in a specific orientation are essential tasks for DNA-binding proteins. In order to make the target search process as efficient as possible, proteins should not only rapidly diffuse to the target site but also dynamically explore multiple local configurations before diffusing away. Protein flipping is an example of this second process that has been observed previously, but the underlying mechanism of flipping remains unclear. Here, we probed the mechanism of protein flipping at the single molecule level, using HIV-1 reverse transcriptase (RT) as a model system. In order to test the effects of long-range attractive forces on flipping efficiency, we varied the salt concentration and macromolecular crowding conditions. As expected, increased salt concentrations weaken the binding of RT to DNA while increased crowding strengthens the binding. Moreover, when we analyzed the flipping kinetics, i.e. the rate and probability of flipping, at each condition we found that flipping was more efficient when RT bound more strongly. Our data are consistent with a view that DNA bound proteins undergo multiple rapid re-binding events, or short hops, that allow the protein to explore other configurations without completely dissociating from the DNA.
Superantigens Associated with Staphylococcal and Streptococcal Toxic Shock Syndrome are Potent Inducers of Tumor Necrosis Factor- Synthesis (1993)

The role of tumor necrosis factor-alpha (TNF alpha) in the pathogenesis of severe bacterial infections has been studied extensively. However, the role of TNF beta, a lymphokine with biologic activities similar to those of TNF alpha, has received little attention. Therefore, the purpose of this study was to examine the production of TNF beta by peripheral blood mononuclear cells in response to lipopolysaccharide (LPS) and the superantigens staphylococcal toxic shock syndrome toxin 1 (TSST-1) and streptococcal pyrogenic exotoxin A (SPEA). Though LPS was a more potent inducer of TNF alpha than was TSST-1 or SPEA, TSST-1 and SPEA were both more potent inducers of TNF beta. The superantigens TSST-1 and SPEA were more potent inducers of total TNF (TNF alpha and TNF beta) than was LPS. These data suggest that the induction of TNF beta synthesis may be a unique pathway by which superantigens associated with severe streptococcal and staphylococcal infections mediate shock and multiorgan failure characteristic of toxic shock syndrome.
Discovery of a Novel Non-Peptide Somatostatin Agonist with SST4 Selectivity (1998)

The discovery of novel non-peptide compounds with a high affinity for the peptide hormone somatostatin (SST) receptor is described. The compounds were tested for affinity at five human SST receptor subtypes individually expressed in mammalian cells. The compound NNC 26-9100 showed a Ki of 6 nM at SST4 and more than 100 fold selectivity for SST4 over SST1, SST2, SST3, or SST5. Competition binding studies and Scatchard analysis of the interaction by NNC 26-9100 with SST showed specificity at SST4. Furthermore, NNC 26-9100 was highly selective for SST4 over a variety of other G protein-coupled receptors, having affinities for M1 muscarinic acetylcholin and D3 dopamine receptors of around 500 and 1000 nM, respectively. Finally, NNC 26-9100 was found to fully inhibit forskolin-induced accumulation of adenosine 3‘,5‘-cyclic monophosphate in baby hamster kidney cells, expressing the human SST4 receptor with an EC50 of 2 nM.
Transcriptional regulation of p90 with sequence homology to Escherichia coli glycerol-3-phosphate acyltransferase. (1991)

We have previously isolated cDNA clones for several mRNAs that are dramatically increased in livers of fasted mice refed a high carbohydrate diet. We report here the sequence and regulation of one such mRNA; the 6.8-kilobase mRNA has an open reading frame of 2481 nucleotides, and the coded protein contains 827 amino acid residues (Mr of 90,000) with a 30% identity and an additional 42% similarity in an approximately 300-amino acid stretch to Escherichia coli glycerol-3-phosphate acyltransferase. The p90 mRNA is highly expressed in liver and in adipose tissue. When previously fasted mice were refed a high carbohydrate, fat-free diet, the liver mRNA level for p90 was increased about 20-fold at 8 h. Administration of dibutyryl cAMP at the time of refeeding prevented the increase in the p90 mRNA by 70%. In addition, there was no increase in the p90 mRNA level when previously starved streptozotocin-diabetic mice were refed. In diabetic animals, the p90 mRNA level increased by 2-fold 1 h after insulin injection and reached a maximum of 19-fold after 6 h. The increase in transcription rate of the p90 gene preceded that of steady state mRNA level caused by fasting/refeeding, and cAMP abolished the increase in transcription. Transcription of the p90 gene was not detectable in either fasted or refed streptozotocin-diabetic mice, but increased 4-fold 30 min after insulin administration and further increased up to 8-fold at 2 h. On-going protein synthesis was necessary for this increase.
Multivariable model predictive control of a novel rapid pressure swing adsorption system (2017)

A multivariable model predictive control (MPC) algorithm is developed for the control and operation of a rapid pressure swing adsorption (RPSA)‐based medical oxygen concentrator. The novelty of the approach is the use of all four step durations in the RPSA cycle as independent manipulated variables in a truly multivariable context. The RPSA has a complex, cyclic, nonlinear multivariable operation that requires feedback control, and MPC provides a suitable framework for controlling such a multivariable system. The multivariable MPC presented here uses a quadratic optimization program with integral action and a linear model identified using subspace system identification techniques. The controller was designed and tested in simulation using a complex, highly coupled, nonlinear RPSA process model. The model was developed with the least restrictive assumptions compared to those reported in the literature, thereby providing a more realistic representation of the underlying physical phenomena. The resulting MPC effectively tracks set points, rejects realistic process disturbances and is shown to outperform conventional PID control. © 2017 American Institute of Chemical Engineers AIChE J , 64: 1234–1245, 2018
Targeting the complement system for the management of retinal inflammatory and degenerative diseases (2016)

The retina, an immune privileged tissue, has specialized immune defense mechanisms against noxious insults that may exist in diseases such as age-related macular degeneration (AMD), diabetic retinopathy (DR), uveoretinitis and glaucoma. The defense system consists of retinal innate immune cells (including microglia, perivascular macrophages, and a small population of dendritic cells) and the complement system. Under normal aging conditions, retinal innate immune cells and the complement system undergo a low-grade activation (parainflammation) which is important for retinal homeostasis. In disease states such as AMD and DR, the parainflammatory response is dysregulated and develops into detrimental chronic inflammation. Complement activation in the retina is an important part of chronic inflammation and may contribute to retinal pathology in these disease states. Here, we review the evidence that supports the role of uncontrolled or dysregulated complement activation in various retinal degenerative and angiogenic conditions. We also discuss current strategies that are used to develop complement-based therapies for retinal diseases such as AMD. The potential benefits of complement inhibition in DR, uveoretinitis and glaucoma are also discussed, as well as the need for further research to better understand the mechanisms of complement-mediated retinal damage in these disease states.
Nod2 Is a General Sensor of Peptidoglycan through Muramyl Dipeptide (MDP) Detection (2003)

Nod2 activates the NF-kappaB pathway following intracellular stimulation by bacterial products. Recently, mutations in Nod2 have been shown to be associated with Crohn's disease, suggesting a role for bacteria-host interactions in the etiology of this disorder. We show here that Nod2 is a general sensor of peptidoglycan through the recognition of muramyl dipeptide (MDP), the minimal bioactive peptidoglycan motif common to all bacteria. Moreover, the 3020insC frameshift mutation, the most frequent Nod2 variant associated with Crohn's disease patients, fully abrogates Nod2-dependent detection of peptidoglycan and MDP. Together, these results impact on the understanding of Crohn's disease development. Additionally, the characterization of Nod2 as the first pathogen-recognition molecule that detects MDP will help to unravel the well known biological activities of this immunomodulatory compound.
Improved Marine 4D Repeatability Using an Automated Vessel, Source and Receiver Positioning System (2008)

A new automated and integrated, vessel, source, and receiver control system has been developed to improve the accuracy and repeatability of 4D surveys. The new control system replaces operator intervention with automated updates to vessel, source, and streamer steering devices from positioning information from all in-sea equipment. This has lead to a step change in the accuracy of source repeatability (2.5-m repeat accuracy for 95% of shotpoints), and has also improved the ability to repeat receiver positions.