gebhart/patrepeval huggingface dataset:
Multi-View Fusion-Based 3D Object Detection for Robot Indoor Scene Perception (2019)

To autonomously move and operate objects in cluttered indoor environments, a service robot requires the ability of 3D scene perception. Though 3D object detection can provide an object-level environmental description to fill this gap, a robot always encounters incomplete object observation, recurring detections of the same object, error in detection, or intersection between objects when conducting detection continuously in a cluttered room. To solve these problems, we propose a two-stage 3D object detection algorithm which is to fuse multiple views of 3D object point clouds in the first stage and to eliminate unreasonable and intersection detections in the second stage. For each view, the robot performs a 2D object semantic segmentation and obtains 3D object point clouds. Then, an unsupervised segmentation method called Locally Convex Connected Patches (LCCP) is utilized to segment the object accurately from the background. Subsequently, the Manhattan Frame estimation is implemented to calculate the main orientation of the object and subsequently, the 3D object bounding box can be obtained. To deal with the detected objects in multiple views, we construct an object database and propose an object fusion criterion to maintain it automatically. Thus, the same object observed in multi-view is fused together and a more accurate bounding box can be calculated. Finally, we propose an object filtering approach based on prior knowledge to remove incorrect and intersecting objects in the object dataset. Experiments are carried out on both SceneNN dataset and a real indoor environment to verify the stability and accuracy of 3D semantic segmentation and bounding box detection of the object with multi-view fusion.
Impact of down-regulation of starch branching enzyme IIb in rice by artificial microRNA- and hairpin RNA-mediated RNA silencing (2011)

The inactivation of starch branching IIb (SBEIIb) in rice is traditionally associated with elevated apparent amylose content, increased peak gelatinization temperature, and a decreased proportion of short amylopectin branches. To elucidate further the structural and functional role of this enzyme, the phenotypic effects of down-regulating SBEIIb expression in rice endosperm were characterized by artificial microRNA (amiRNA) and hairpin RNA (hp-RNA) gene silencing. The results showed that RNA silencing of SBEIIb expression in rice grains did not affect the expression of other major isoforms of starch branching enzymes or starch synthases. Structural analyses of debranched starch showed that the doubling of apparent amylose content was not due to an increase in the relative proportion of amylose chains but instead was due to significantly elevated levels of long amylopectin and intermediate chains. Rices altered by the amiRNA technique produced a more extreme starch phenotype than those modified using the hp-RNA technique, with a greater increase in the proportion of long amylopectin and intermediate chains. The more pronounced starch structural modifications produced in the amiRNA lines led to more severe alterations in starch granule morphology and crystallinity as well as digestibility of freshly cooked grains. The potential role of attenuating SBEIIb expression in generating starch with elevated levels of resistant starch and lower glycaemic index is discussed.
Renal Tissue Engineering with Decellularized Rhesus Monkey Kidneys: Age-Related Differences (2011)

New therapies for severely damaged kidneys are needed due to limited regenerative capacity and organ donor shortages. The goal of this study was to repopulate decellularized kidney sections in vitro and to determine the impact of donor age on recellularization. This was addressed by generating decellularized kidney scaffolds from fetal, juvenile, and adult rhesus monkey kidney sections using a procedure that removes cellular components while preserving the structural and functional properties of the native extracellular matrix (ECM). Kidney scaffolds were recellularized using explants from different age groups (fetal, juvenile, adult) and fetal renal cell fractions. Results showed vimentin+ cytokeratin+ calbindin+ cell infiltration and organization around the scaffold ECM. The extent of cellular repopulation was greatest with scaffolds from the youngest donors, and with seeding of mixed fetal renal aggregates that formed tubular structures within the kidney scaffolds. These findings suggest that decellularized kidney sections from different age groups can be effectively repopulated with donor cells and the age of the donor is a critical factor in repopulation efficiency.
Dissecting the hematopoietic microenvironment. IX. Further characterization of murine bone marrow stromal cells (1993)

We have previously shown the adherent nontransformed, nonimmortalized murine bone marrow stromal cell (BMSC) population to consist of phagocytic macrophage and endothelial-like cells and nonphagocytic fibroblasts. Both colonial and near confluent growth of each cell type was obtained following magnetic bead separation, subsequent passaging, and sustained culture with fetal bovine serum and cytokines. Monoclonal antibody staining of antigenic determinants was used to characterize the phenotype of the stromal cell population in primary platings of murine colony-forming unit fibroblast and long-term bone marrow cultures. The antibodies MECA-99, MECA-32, and MJ7–18, raised against murine vascular endothelial antigenic determinants, and von Willebrand's factor all stained selectively for the rounded endothelial- like cells. Endothelial-like cells as well as macrophages expressed the myeloid surface antigens F4/80, 7/4, and Mac-1 under our culture conditions. The cytoskeleton of the stromal fibroblasts in culture was shown to express smooth muscle-specific actin isoforms, as evidenced by positive staining of stress fibers for alpha smooth muscle-1, CGA-7 (alpha/gamma isoforms), and HHF-35 (recognizes all muscle-specific actins). Under culture conditions, stromal fibroblasts were also found to be positive for a polyclonal smooth muscle myosin. It was found that these fibroblasts stained for collagens type I, III, and IV in our cultures. Although collagen type IV is considered a by-product of endothelial cells, endothelial-like cells in our cultures did not stain for any of the collagen types. We propose a classification listing for murine BMSCs as macrophages, endotheliallike cells, and fibroblasts that display smooth muscle-like characteristics in culture.
A Single Ser-180 Mutation Desensitizes Feedback Inhibition of the Phenylalanine-Sensitive 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate (DAHP) Synthetase in Escherichia coli1 (1994)

The Escherichia coli phenylalanine-sensitive DAHP (3-deoxy-D-arabino-heptulosonate 7-phosphate) synthetase (aroG product) is one of the DAHP synthetase isozymes that catalyze the first committed step in the biosynthesis of aromatic amino acids and vitamins. Through target-directed mutagenesis of the cloned aroG on a plasmid vector, followed by screening of phenylalanine-resistant colonies, we isolated a clone (pG908) showing feedback-insensitive mutation of DAHP synthetase. The mutations were identified as a T-->A mutation at nucleotide 22, and a C-->T mutation at nucleotide 539, causing a Leu-8 to Ile-8 mutation and a Ser-180 to Phe-180 substitution, respectively. The resulting enzyme exhibited comparable enzymatic activity to the wild type, but the degree of feedback inhibition had declined from approximately 60% to less than 10% in the presence of 20 mM phenylalanine in the assay medium. Replacement of Ile-8 by Leu, and substitution of Phe-180 with Ser, Asn and Cys, using site-directed mutagenesis, demonstrated that Ser-180 is a critical residue in the feedback inhibition of AroG. The result suggests that the major role played by Ser-180 may not involve a simple charge-size effect in the Phe-binding site of the enzyme molecule, but rather may involve more complicated molecular interactions occurring in the feedback inhibition mechanisms.
Application of Associative Neural Networks for Prediction of Lipophilicity in ALOGPS 2.1 Program (2002)

This article provides a systematic study of several important parameters of the Associative Neural Network (ASNN), such as the number of networks in the ensemble, distance measures, neighbor functions, selection of smoothing parameters, and strategies for the user-training feature of the algorithm. The performance of the different methods is assessed with several training/test sets used to predict lipophilicity of chemical compounds. The Spearman rank-order correlation coefficient and Parzen-window regression methods provide the best performance of the algorithm. If additional user data is available, an improved prediction of lipophilicity of chemicals up to 2-5 times can be calculated when the appropriate smoothing parameters for the neural network are selected. The detected best combinations of parameters and strategies are implemented in the ALOGPS 2.1 program that is publicly available at http://www.vcclab.org/lab/alogps.
[Biochemical markers in bone metastasis]. (2004)

Certain types of cancers have a strong propensity to metastasize to bone, which requires combination of multiple factors responsible for the different steps of metastasis. Bone metabolic markers are now widely used in clinical practice and give useful information on the ongoing bone metabolism, reflecting the activity of bone-resorbing osteoclasts and bone-forming osteoblasts. Bone markers have a potential as diagnostic tools for bone metastasis, and are useful in monitoring the response to anticancer as well as antiresorptive therapies. Since bone metabolic markers alone are insufficient for the diagnosis and assessment of bone metastasis, it is important to combine bone markers with tumor-related markers and imaging studies such as scintigraphy and MRI. More recently, soluble receptor activator of nuclear factor-kappaB ligand (RANKL) and osteoprotegerin (OPG) have been implicated as markers for osteoclastogenic activity. Serum levels of these factors and/or their ratios may provide additional information on the severity of bone disease and the prognosis.
Three-dimensional optical memory with a photorefractive crystal (1995)

We propose a three-dimensional optical-memory device in which refractive dot data are recorded directly into a photorefractive crystal. To record a single bit of datum, one focuses a laser beam with an objective lens onto a specific spot in a crystal, thereby changing its refractive index locally as a result of photorefraction. To record in three dimensions, one keeps the objective lens stationary while the crystal is translated. The beam-spot intensity is modulated with a beam shutter according to the logic state of the data point. The recorded data points are read with a phase-contrast microscope objective lens. We present experimental results of three-dimensional recording and reading with a LiNbO(3) crystal. The distribution of the refractive index formed by a focused beam is also analyzed with the charge-transport model.
Big returns from small fibers: A review of polymer/carbon nanotube composites (2004)

Abstract This paper reviews recent studies conducted on carbon nanotube/polymer composites. Carbon nanotubes are promising new materials for blending with polymers with potential to obtain low‐weight nanocomposites of extraordinary mechanical, electrical, thermal and multifunctional properties. The size scale, aspect ratio and properties of nanotubes provide advantages in a variety of applications, including electrostatically dissipative materials; advanced materials with combined stiffness, strength and impact for aerospace or sporting goods; composite mirrors; automotive parts that require electrostatic painting and automotive components with enhanced mechanical properties. The various processing methods for producing these nanocomposites are discussed, in particular melt mixing, solution processing and in‐situ polymerization. Some key results are summarized, relating to the mechanical, electrical, thermal, optical and surface properties. Finally, the challenges for the future are discussed in terms of processing, characterization, nanotube availability, nanotube tailoring, and the mechanisms governing the behavior of these remarkable nanoscale composites. Polym. Compos. 25:630–645, 2004. © 2004 Society of Plastics Engineers.
Complete Nucleotide Sequence and Analysis of the Locus of Enterocyte Effacement from Rabbit Diarrheagenic Escherichia coli RDEC-1 (2001)

The pathogenicity island termed the locus of enterocyte effacement (LEE) is found in diverse attaching and effacing pathogens associated with diarrhea in humans and other animal species. To explore the relation of variation in LEE sequences to host specificity and genetic lineage, we determined the nucleotide sequence of the LEE region from a rabbit diarrheagenic Escherichia coli strain RDEC-1 (O15:H-) and compared it with those from human enteropathogenic E. coli (EPEC, O127:H6) and enterohemorrhagic E. coli (EHEC, O157:H7) strains. Differing from EPEC and EHEC LEEs, the RDEC-1 LEE is not inserted at selC and is flanked by an IS2 element and the lifA toxin gene. The RDEC-1 LEE contains a core region of 40 open reading frames, all of which are shared with the LEE of EPEC and EHEC. orf3 and the ERIC (enteric repetitive intergenic consensus) sequence present in the LEEs of EHEC and EPEC are absent from the RDEC-1 LEE. The predicted promoters of LEE1, LEE2, LEE3, tir, and LEE4 operons are highly conserved among the LEEs, although the upstream regions varied considerably for tir and the crucial LEE1 promoter, suggesting differences in regulation. Among the shared genes, high homology (>95% identity) between the RDEC-1 and the EPEC and EHEC LEEs at the predicted amino acid level was observed for the components of the type III secretion apparatus, the Ces chaperones, and the Ler regulator. In contrast, more divergence (66 to 88% identity) was observed in genes encoding proteins involved in host interaction, such as intimin (Eae) and the secreted proteins (Tir and Esps). A comparison of the highly variable genes from RDEC-1 with those from a number of attaching and effacing pathogens infecting different species and of different evolutionary lineages was performed. Although RDEC-1 diverges from some human-infecting EPEC and EHEC, most of the variation observed appeared to be due to evolutionary lineage rather than host specificity. Therefore, much of the observed hypervariability in genes involved in pathogenesis may not represent specific adaptation to different host species.
Synthetic factor VIII peptides with amino acid sequences contained within the C2 domain of factor VIII inhibit factor VIII binding to phosphatidylserine (1990)

The effective activation of factor X by factor IXa requires the co- factor activity of activated factor VIII (FVIII). Factor Xa formation is also dependent on the presence of negatively charged phospholipid. A phospholipid binding domain of FVIII has been reported to be present on the FVIII light chain. Recent observations on a subset of human FVIII inhibitors have implicated the carboxyl-terminal C2 domain of FVIII as containing a possible phospholipid binding site. The purpose of this study was to investigate directly the role of the C2 domain in phospholipid binding. Twenty-six overlapping peptides, which span the entire C2 domain of FVIII, were synthesized. The ability of these peptides to inhibit the binding of purified human FVIII to immobilized phosphatidylserine was evaluated in an enzyme-linked immunosorbent assay. Three overlapping synthetic FVIII peptides, 2303–2317, 2305- 2332, and 2308–2322, inhibited FVIII binding to phosphatidylserine by greater than 90% when tested at a concentration of 100 mumols/L. A fourth partially overlapping peptide, 2318–2332, inhibited FVIII binding by 65%. These results suggest that the area described by these peptides, residues 2303 to 2332, may play an important role in the mediation of FVIII binding to phospholipid.
Charles S. Mott prize papillomaviruses in human cancer (1987)

Twelve types of human papillomaviruses (HPV) have been isolated thus far from papillomatous and Bowenoid lesions of the human genital tract. Four type, HPV 6, 11, 16 and 18 are most frequently found. HPV 6 and 11 cause the typical genital warts (condylomata acuminata) and mild dysplastic lesions of the cervix characterized by a high degree of koilocytotic atypia. HPV 16 and 18 are preferentially found in Bowenoid papulosis and Bowen's disease at external genital sites. Moderate and severe cervical dysplasias with little or no koilocytosis appear to be common manifestations of these infections at cervical sites. HPV 16 is found in approximately 50% of all cervical, penile and vulvar cancers, HPV 18 in close to 20%. The majority of the remaining tumors reveals evidence for infections with additional types of HPV. Several cell lines have been identified containing either HPV 18 or HPV 16 genomes. The state of viral DNA in Bowenoid precursor lesions differs from that of cervical carcinomas. The former contain episomal DNA whereas integration seems to be a regular event in carcinomas. Integration regularly affects the E1-E2 open reading frames of HPV 16 or HPV 18 DNA. Fusion transcripts from the integrated HPV DNA (E6-E7 region) and adjacent host cell DNA have been documented. The available data support a causative role of specific HPV infections in the etiology of human genital cancer.
Cancer gene discovery using digital differential display. (2000)

The Cancer Gene Anatomy Project database of the National Cancer Institute has thousands of expressed sequences, both known and novel, in the form of expressed sequence tags (ESTs). These ESTs, derived from diverse normal and tumor cDNA libraries, offer an attractive starting point for cancer gene discovery. Using a data-mining tool called Digital Differential Display (DDD) from the Cancer Gene Anatomy Project database, ESTs from six different solid tumor types (breast, colon, lung, ovary, pancreas, and prostate) were analyzed for differential expression. An electronic expression profile and chromosomal map position of these hits were generated from the Unigene database. The hits were categorized into major classes of genes including ribosomal proteins, enzymes, cell surface molecules, secretory proteins, adhesion molecules, and immunoglobulins and were found to be differentially expressed in these tumorderived libraries. Genes known to be up-regulated in prostate, breast, and pancreatic carcinomas were discovered by DDD, demonstrating the utility of this technique. Two hundred known genes and 500 novel sequences were discovered to be differentially expressed in these select tumor-derived libraries. Test genes were validated for expression specificity by reverse transcription-PCR, providing a proof of concept for gene discovery by DDD. A comprehensive database of hits can be accessed at http:// www.fau.edu/cmbb/publications/cancergenes. htm. This solid tumor DDD database should facilitate target identification for cancer diagnostics and therapeutics.
Immunohistochemical characterization of histiocytic tumours. (1981)

Immunohistochemical labelling of histiocytic tumour cells in formalin-fixed paraffin-embedded material was usefully applied to malignant fibrous histiocytoma (MFH) and to malignant histiocytosis (MH). Not all cases of MFH showed a positive reaction, in contrast with the obligatory positive staining in MH. In general, histiocytic tumour cells stained more intensively with alpha 1-antichymotrypsin than with lysozyme. False positive results can be due to intermingled non-neoplastic histiocytes or degenerating neoplastic cells in any mesenchymal tumour.
Digital cameras and electronic color image acquisition (2002)

Digital photography is quickly becoming a viable alternative to conventional photographic imaging in several existing imaging applications. The future extrapolation of this trend depends on the development of improvements to existing digital cameras. Several image processing approaches to improving image quality generated from digital cameras are discussed.
Expression of Functional CXCR4 by Muscle Satellite Cells and Secretion of SDF-1 by Muscle-Derived Fibroblasts is Associated with the Presence of Both Muscle Progenitors in Bone Marrow and Hematopoietic Stem/Progenitor Cells in Muscles (2003)

We found that the murine cell lines C2C12 and G7 derived from muscle satellite cells, which are essential for muscle regeneration, express the functional CXCR4 receptor on their surface and that the specific ligand for this receptor, alpha-chemokine stromal-derived factor 1 (SDF-1), is secreted in muscle tissue. These cell lines responded to SDF-1 stimulation by chemotaxis, phosphorylation of mitogen-activated protein kinase (MAPK) p42/44 and AKT serine-threonine kinase, and calcium flux, confirming the functionality of the CXCR4 receptor. Moreover, supernatants derived from muscle fibroblasts chemoattracted both satellite cells and human CD34(+) hematopoietic stem/progenitor cells. In a similar set of experiments, supernatants from bone marrow fibroblasts were found to chemoattract CXCR4(+) satellite cells just as they chemoattract CD34(+) cells. Moreover, preincubation of both muscle satellite cells and hematopoietic stem/progenitor CD34(+) cells before chemotaxis with T140, a specific CXCR4 inhibitor, resulted in a significantly lower chemotaxis to media conditioned by either muscle- or bone marrow-derived fibroblasts. Based on these observations, we postulate that the SDF-1-CXCR4 axis is involved in chemoattracting circulating CXCR4(+) muscle stem/progenitor and circulating CXCR4(+) hematopoietic CD34(+) cells to both muscle and bone marrow tissues. Thus, it appears that tissue-specific stem cells circulating in peripheral blood could compete for SDF-1(+) niches, and this would explain, without invoking the concept of stem cell plasticity, why hematopoietic colonies can be cultured from muscles and early muscle progenitors can be cultured from bone marrow.
Chemical synthesis of β-D-GlcpA(2SO4)-(1→3)-D-GalpNAc(6SO4), the disaccharide repeating unit of shark cartilage chondroitin sulfate D, and of its methyl β-D-glycoside derivative (2000)

The syntheses of sodium O-(disodium 2-O-sulfonato-β-D-glucopyranosyluronate)-(1→3)-2-acetamido-2-deoxy-6-O-sulfonato-D-galactopyranose 1, which represents a structural element of shark cartilage chondroitin sulfate D, and of its methyl β-D-glycoside derivative 2 are reported for the first time. The glucuronyl donor 10 is prepared in a straightforward manner from D-glucose, whereas the glycosyl acceptors 20 and 21 are obtained from known 3,4,6-tri-O-acetyl-2-deoxy-2-trichloroacetamido-1-O-trichloroacetimidoyl-α-D-glucopyranose through glycosylation with benzyl alcohol and methanol, respectively, and subsequent transformation into D-galacto synthons by selective inversion of configuration at C-4. Unexpected pyranose → furanose ring contraction as well as 3,6-anhydro-derivative formation in the D-galacto series are also reported. Stereocontrolled coupling of the imidate 10 with the alcohols 20 and 21 afforded the corresponding β-linked disaccharide derivatives 24 and 25, respectively, which are submitted to radical reduction of the N-trichloroacetyl groups, O-desilylation, saponification, O-sulfonation, and catalytic hydrogenation to provide the target molecules 1 and 2, respectively, in high yields.
PPAR-β/δ agonists for Type 2 diabetes and dyslipidemia: an adopted orphan still looking for a home (2008)

Thus far, the activities of the agonists seen in the clinic are broadly similar to those seen in preclinical models. However, it is still not known if PPAR-beta/delta agonists will truly be differentiated enough from current treatments to justify their use in treating dyslipidemia or Type 2 diabetes. Major challenges for the development of PPAR-beta/delta agonists exist and the path forward is as yet undefined.