gebhart/patrepeval huggingface dataset:
High-Resolution Shape Completion Using Deep Neural Networks for Global Structure and Local Geometry Inference (2017)

We propose a data-driven method for recovering miss-ing parts of 3D shapes. Our method is based on a new deep learning architecture consisting of two sub-networks: a global structure inference network and a local geometry refinement network. The global structure inference network incorporates a long short-term memorized context fusion module (LSTM-CF) that infers the global structure of the shape based on multi-view depth information provided as part of the input. It also includes a 3D fully convolutional (3DFCN) module that further enriches the global structure representation according to volumetric information in the input. Under the guidance of the global structure network, the local geometry refinement network takes as input lo-cal 3D patches around missing regions, and progressively produces a high-resolution, complete surface through a volumetric encoder-decoder architecture. Our method jointly trains the global structure inference and local geometry refinement networks in an end-to-end manner. We perform qualitative and quantitative evaluations on six object categories, demonstrating that our method outperforms existing state-of-the-art work on shape completion.
CD34+ Hematopoietic Progenitors From Human Cord Blood Differentiate Along Two Independent Dendritic Cell Pathways in Response to Granulocyte-Macrophage Colony-Stimulating Factor Plus Tumor Necrosis Factor α: II. Functional Analysis (1997)

In response to granulocyte-macrophage colony-stimulating factor plus tumor necrosis factor alpha, cord blood CD34+ hematopoietic progenitor cells differentiate along two unrelated dendritic cell (DC) pathways: (1) the Langerhans cells (LCs), which are characterized by the expression of CD1a, Birbeck granules, the Lag antigen, and E cadherin; and (2) CD14+ cell-derived DCs, characterized by the expression of CD1a, CD9, CD68, CD2, and factor XIIIa (Caux et al, J Exp Med 184:695, 1996). The present study investigates the functions of each population. Although the two populations are equally potent in stimulating naive CD45RA cord blood T cells through apparently identical mechanisms, each also displays specific activities. In particular CD14-derived DCs show a potent and long-lasting (from day 8 to day 13) antigen uptake activity (fluorescein isothiocyanate dextran or peroxidase) that is about 10-fold higher than that of CD1a+ cells, which is restricted to the immature stage (day 6). The antigen capture is exclusively mediated by receptors for mannose polymers. The high efficiency of antigen capture of CD14-derived cells is coregulated with the expression of nonspecific esterase activity, a tracer of lysosomial compartment. In contrast, the CD1a+ population never expresses nonspecific esterase activity. The most striking difference is the unique capacity of CD14-derived DCs to induce naive B cells to differentiate into IgM-secreting cells, in response to CD40 triggering and interleukin-2. Thus, although the two populations can allow T-cell priming, initiation of humoral responses might be preferentially regulated by the CD14-derived DCs. Altogether, those results show that different pathways of DC development might exist in vivo: (1) the LC type, which might be mainly involved in cellular immune responses, and (2) the CD14-derived DC related to dermal DCs or circulating blood DCs, which could be involved in humoral immune responses.
[Mortality and life span of able-bodied population in Russia: methods and results of studies]. (2010)

The article deals with methods to analyze mortality and life span of able-bodied population, including mathematical modelling methods. These methods helped to analyze changes in mortality, to evaluate life span in able-bodied age interval and damage caused by certain death causes. The authors revealed major trends in mortality of able-bodied population in Russia over the recent decade.
Adenovirus E3/19K Promotes Evasion of NK Cell Recognition by Intracellular Sequestration of the NKG2D Ligands Major Histocompatibility Complex Class I Chain-Related Proteins A and B (2008)

The adenovirus (Ad) early transcription unit 3 (E3) encodes multiple immunosubversive functions that are presumed to facilitate the establishment and persistence of infection. Indeed, the capacity of E3/19K to inhibit transport of HLA class I (HLA-I) to the cell surface, thereby preventing peptide presentation to CD8(+) T cells, has long been recognized as a paradigm for viral immune evasion. However, HLA-I downregulation has the potential to render Ad-infected cells vulnerable to natural killer (NK) cell recognition. Furthermore, expression of the immediate-early Ad gene E1A is associated with efficient induction of ligands for the key NK cell-activating receptor NKG2D. Here we show that while infection with wild-type Ad enhances synthesis of the NKG2D ligands, major histocompatibility complex class I chain-related proteins A and B (MICA and MICB), their expression on the cell surface is actively suppressed. Both MICA and MICB are retained within the endoplasmic reticulum as immature endoglycosidase H-sensitive forms. By analyzing a range of cell lines and viruses carrying mutated versions of the E3 gene region, E3/19K was identified as the gene responsible for this activity. The structural requirements within E3/19K necessary to sequester MICA/B and HLA-I are similar. In functional assays, deletion of E3/19K rendered Ad-infected cells more sensitive to NK cell recognition. We report the first NK evasion function in the Adenoviridae and describe a novel function for E3/19K. Thus, E3/19K has a dual function: inhibition of T-cell recognition and NK cell activation.
Designer aminoglycosides: the race to develop improved antibiotics and compounds for the treatment of human genetic diseases (2007)

Aminoglycosides are highly potent, broad-spectrum antibiotics that exert their bactericidal therapeutic effect by selectively binding to the decoding aminoacyl site (A-site) of the bacterial 16 S rRNA, thereby interfering with translational fidelity during protein synthesis. The appearance of bacterial strains resistant to these drugs, as well as their relative toxicity, have inspired extensive searches towards the goal of obtaining novel molecular designs with improved antibacterial activity and reduced toxicity. In the last few years, a new, aminoglycoside dependent therapeutic approach for the treatment of certain human genetic diseases has been identified. These treatments rely on the ability of certain aminoglycosides to induce mammalian ribosomes to readthrough premature stop codon mutations. This new and challenging task has introduced fresh research avenues in the field of aminoglycoside research. Recent observations and current challenges in the design of aminoglycosides with improved antibacterial activity and the treatment of human genetic diseases are discussed.
JAK3 Janus kinase is involved in interleukin 7 signal pathway (1994)

Interleukin (IL) 7 is an important cytokine regulating both T and B cell development and inducing the formation of lymphokine-activated killer cells and cytolytic T lymphocytes. This study reports the role of JAK family kinases in the IL-7 signalling pathway in a T cell clone. The results have shown that out of 4 members of JAK family tyrosine kinases (JAK1, JAK2, JAK3 and Tyk2), only JAK3 was tyrosine-phosphorylated and activated in cells of a T cell clone by stimulation with IL-7. Furthermore, STAT1 alpha (STAT, the signal transducers and activators of transcription) and p44 of MAPK (mitogen-activated protein kinases) were tyrosine phosphorylated by IL-7 stimulation, indicating that the two signal pathways might be involved in IL-7 signal transduction.
TNFα receptor expression in rat cardiac myocytes: TNFα inhibition of L‐type Ca2+ current and Ca2+ transients (1995)

Tumor necrosis factor-alpha (TNF alpha) is a potentially powerful anti-neoplastic agent; however, its therapeutic usefulness is limited by its cardiotoxic and negative inotropic effects. Accordingly, studies were undertaken to gain a better understanding of the mechanisms of TNF alpha-mediated cardiodepression. Single cell RT-PCR, [125I]TNF alpha ligand binding and Western immunoblotting experiments demonstrated that rat cardiac cells predominantly express type I TNF alpha receptors (TNFRI or p60). TNF alpha inhibited cardiac L-type Ca2+ channel current (ICa) and contractile Ca2+ transients. Thus, it is possible that the negative inotropic effects of TNF alpha are the result of TNFRI-mediated blockade of cardiac excitation-contraction coupling.
Lack of responses to a beta3-adrenergic agonist in lipoatrophic A-ZIP/F-1 mice. (2000)

Stimulation of beta3-adrenergic receptors increases metabolic rate via lipolysis in white adipose tissue (WAT) and thermogenesis in brown adipose tissue (BAT). Other acute effects include decreased gastrointestinal motility and food intake and increased insulin secretion. Chronic treatment with a beta3 agonist ameliorates diabetes and obesity in rodents. We studied the effects of beta3 stimulation in A-ZIP/F-1 mice, which have virtually no WAT, a reduced amount of BAT, severe insulin resistance, and diabetes. In contrast with wild-type mice, treatment of A-ZIP/F-1 mice with CL316243, a beta3-adrenergic agonist, did not increase O2 consumption. A single dose of CL316243 produced a 2-fold increase in serum free fatty acids, a 53-fold increase in insulin, and a 2.4-fold decrease in glucose levels in wild-type mice but no change in A-ZIP/F-1 animals. The A-ZIP/F-1 mice also did not show reduced gastrointestinal motility or 24-h food intake during beta3 stimulation. Chronic administration of CL316243 to the A-ZIP/F-1 mice did not improve their thermogenesis, hyperglycemia, or hyperinsulinemia. Thus, all of the beta3 effects studied were absent in the lipoatrophic A-ZIP/F-1 mice, including the effects on nonadipose tissues. From these results, we suggest that all of the effects of beta3 agonists are initiated at the adipocyte with the nonadipose effects being secondary events presumably mediated by signals from adipose tissue.
Induction of experimental bone metastasis in mice by transfection of integrin alpha 4 beta 1 into tumor cells. (1996)

Cell adhesion receptors (eg, integrins and CD44) play an important role in invasion and metastasis during tumor progression. The increase in integrin alpha 4 beta 1 expression on primary melanomas has been reported to significantly correlate with the development of metastases. alpha 4 beta 1 is a cell surface heterodimer that mediates cell-cell and cell-extracellular matrix interactions through adhesion to vascular cell adhesion molecule (VCAM)-1 and to the IIICS region of fibronectin. To test the effects of alpha 4 beta 1 expression on tumor cell metastasis, Chinese hamster ovary cells were transfected with human alpha 4 cDNA. Whereas alpha 4-negative Chinese hamster ovary cells developed only pulmonary metastasis, alpha 4-positive Chinese hamster ovary cells developed bone and pulmonary metastasis in 3 to 4 weeks when injected intravenously into nude mice. Bone metastasis was inhibited by antibody against alpha 4 or VCAM-1. Expression of alpha 3 beta 1, alpha 6 beta 1, or alpha V beta 1 did not induce bone metastasis. Expression of alpha 4 beta 1 also induced bone metastasis in K562 human erythroleukemia cells injected into SCID mice. These results demonstrate that alpha 4 beta 1 can induce tumor cell trafficking to bone, probably via interaction with VCAM-1 that is constitutively expressed on bone marrow stromal cells.
A single base substitution in the coding region for neurophysin II associated with familial central diabetes insipidus. (1991)

To elucidate the molecular mechanism of familial central diabetes insipidus (FDI), we sequenced the arginine vasopressin-neurophysin II (AVP-NPII) gene in 2 patients belonging to a pedigree that is consistent with an autosomal dominant mode of inheritance. 10 patients with idiopathic central diabetes insipidus (IDI) and 5 normals were also studied. The AVP-NPII gene, locating on chromosome 20, consists of three exons that encode putative signal peptide, AVP, NPII, and glycoprotein. Using polymerase chain reaction, fragments including the promoter region and all coding regions were amplified from genomic DNA and subjected to direct sequencing. Sequences of 10 patients with IDI were identical with those of normals, while in 2 patients with FDI, a single base substitution was detected in one of two alleles of the AVP-NPII gene, indicating they were heterozygotes for this mutation. It was a G----A transition at nucleotide position 1859 in the second exon, resulting in a substitution of Gly for Ser at amino acid position 57 in the NPII moiety. It was speculated that the mutated AVP-NPII precursor or the mutated NPII molecule, through their conformational changes, might be responsible for AVP deficiency.
CpG Oligodeoxynucleotides Adsorbed onto Polylactide-Co-Glycolide Microparticles Improve the Immunogenicity and Protective Activity of the Licensed Anthrax Vaccine (2005)

To reduce the biothreat posed by anthrax, efforts are under way to improve the protection afforded by vaccination. This work examines the ability of immunostimulatory CpG oligodeoxynucleotides (ODN) adsorbed onto cationic polylactide-co-glycolide (PLG) microparticles (CpG ODN-PLG) to accelerate and boost the protective immunity elicited by Anthrax Vaccine Adsorbed (AVA, the licensed human anthrax vaccine). The results indicate that coadministering CpG ODN-PLG with AVA induces a stronger and faster immunoglobulin G response against the protective antigen of anthrax than AVA alone. Immunized mice were protected from lethal anthrax challenge within 1 week of vaccination with CpG ODN-PLG plus AVA, with the level of protection correlating with serum immunoglobulin G anti-protective antigen titers.
Monte Carlo Simulation of Pulse Pile Up (1999)

The Monte Carlo simulation code CEARPPU has been developed to simulate pulse piledup spectra for high counting rates from given true spectra. In this simulation, the exponential pulse interval distribution is used and the multichannel analyzer (MCA) is assumed to operate perfectly in obtaining and scoring the first local maximum from a sum pulse. Forcing and other variance reduction techniques are used to accelerate the simulation process. An accurate simulated spectrum can be obtained in two or three minutes with this code when it is run on a Sun Ultra I work station. Simulation results showed excellent agreement with benchmark measurements with an Fe-55 source and a Si(Li) detector. Use of this code in conjunction with a Monte Carlo code that simulates true spectral responses will allow one to simulate the actual pulse height spectra obtained for radiation analyzer systems. This, in turn, will allow the use of a suitable nonlinear approach for the routine analysis of in viva medical or on-line process samples at very high counting rates. 1.
New Tactics in Heterocycles Synthesis (1984)

syntheses of the antitumor quinones s t r e p t o n i g r i n and lavendamycin and the a l k a l o i d selagine are described.
Aminobenzoic acid diuretics. 8. 3,4-Disubstituted 5-methylsulfonylbenzoic acids and related compounds (1976)

Various 2, 4- and 3, 4-disubstituted 5-methylsulfonylbenzoic acids were synthesized as methylsulfonyl analogues of previously described 5-sulfamoylbenzoic acid diuretics. The results of the diuretic screening in dogs reveal that substitution of the sulfamoyl group by the spatially and sterically similar methylsulfonyl group does not affect the diuretic pattern but leads generally to somewhat decreased potency. For the highly potent 3-benzylamino-4-phenoxy-5-methylsulfonylbenzoic acid the corresponding 5-methylthio and 5-methylsulfinyl analogs were prepared and found still to exhibit diuretic activity. Internal aldol condensation and subsequent dehydration of 3-benzylamino-and 3-n-butylamino-4-benzoyl-5-methylsulfonylbenzoic acid provided the corresponding inactive 4-alkylamino-6-carboxy-2, 3-dihydro-3-hydroxy-3-phenylbenzo[b]thiophene 1, 1-dioxides and 4-alkylamino-6-carboxy-3-phenyl-benzo[b]thiophene 1,1-dioxides.
Glutathione S-transferase in humans in health and disease. (1991)

Most biological processes are catalysed by means of enzymes and study of these in health and disease is important for our understanding of both biology and disturbed function. The glutathione S-transferases (GST:E.C.2.5.1.18) are a complex multigene family of enzymes that are widely distributed in the animal kingdom. ' These enzymes possess many biological functions, the most important of which is detoxification, conjugating reduced glutathione with a large number of electrophiles.2 Such conjugation reactions result in the synthesis of mercapturic acids and represent an important excretory route for xenobiotics including carcinogens, toxins, and drugs.' As well as being concerned in the metabolism of xenobiotics, GST are involved in the metabolism of endogenous substances such as leukotriene A4 and prostaglandin A1.3 GST are also involved in non-substrate binding to such substances as bilirubin and bile acids and have an important role in hepatic anion transport. Several GST isoenzymes possess selenium-independent glutathione peroxidase activity with certain organic hydroperoxides such as linoleic and arachidonic hydroperoxide but not with hydrogen peroxide.5 In humans the cytosolic GST isoenzymes are dimeric and can be subdivided on the basis of their physicochemical and immunological properties into three major groups, namely pi, alpha, and mu class GST (Table6). In humans
Enhanced Humoral Immunity in Mice Infected with Attenuated Venezuelan Equine Encephalitis Virus (1969)

Abstract Attenuated Venezuelan equine encephalitis virus (VEE) infection increased the antibody response to human γ globulin (HGG) in adult Balb/c mice. Mice infected 1 or 11 days before but not 29 days before immunization with 1 mg HGG showed increased rates of elimination of 131I-HGG and elevated hemagglutination titers to HGG. In addition, VEE infection prevented the induction of tolerance to HGG and converted a tolerance-inducing stimulus into an immunizing stimulus. However, VEE infection did not prolong the survival of skin allografts across weak or strong histocompatibility barriers. Two to 6 days after infection, mice showed increased rates of clearance of colloidal carbon. This may have been related to the proliferation of reticuloendothelial cells, since VEE infection caused a proliferation of these cells in germfree mice. In addition, germfree mice infected with VEE had increased spleen weights, and germinal centers appeared in histologic sections of spleens. Increased γ globulin concentrations were seen in the sera of infected germfree mice, which could be attributed only partially to antivirus antibody. Thus, VEE behaves as an adjuvant for humoral antibody responses.
Oncolytic potential of E1B 55 kDa-deleted YKL-1 recombinant adenovirus: Correlation with p53 functional status (2000)

YKL-1, E1B 55 kDa-deleted recombinant adenovirus vector, capable of harboring a transgene casette of up to 4.9 kb, was newly constructed by reintroducing E1A and E1B 19 kDa into E1/E3-deleted adenoviral vector with a homologous recombination in E. coli. Virus replication and cytotoxicity were dramatically attenuated in all 3 different types of normal human cells. In contrast, YKL-1 efficiently replicated and induced cytotoxicity in most cancer cells, especially Hep3B and C33A cells with an inactivating p53 mutation. However, both H460 and HepG2 exhibited intermediate sensitivity to YKL-1, which was between that of Hep3B or C33A and normal human cells. The YKL-1 and DNA damaging agent, camptothecin effectively induced p53 in H460 and HepG2 as well as in normal cells. Furthermore, YKL-1 effectively prohibited both Hep3B and C33A tumor growth in nu/nu mice in a dose-dependent manner. H/E staining and TUNEL assay indicated a largely distributed necrotic area and apoptosis on its periphery. This study, therefore, indicates that YKL-1, possesses promising potential as an oncolytic adenoviral vector, which acts partially in a p53-dependent manner.
Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains (2018)

The recent emergence of Zika virus (ZIKV) has been concentrated in the Caribbean, Southeastern United States, and South- and Central America; resulting in travel-based cases being reported around the globe. As multi-disciplinary collaborations are combatting the ZIKV outbreak, the need to validate the sequence of existing strains has become apparent. Here, we report high-quality sequence data for multiple ZIKV strains made publicly available through the National Institutes of Health- (NIH) funded biorepository, BEI Resources (www.beiresources.org). Next-generation sequencing, 3' rapid amplification of cDNA ends (RACE), and viral genome annotation pipelines generated GenBank sequence records for 16 BEI Resources strains. Minor variants, consensus mutations, and consensus insertions/deletions were identified within the viral stocks using next-generation sequencing (NGS) and consensus changes were confirmed with Sanger sequencing. Bioinformatics analyses of the sequencing results confirm that the virus stocks available to the scientific research community through BEI Resources adequately represent the viral population diversity of ZIKV.
KEKE motifs (1994)

A stretch of 28 'alternating' lysine (K) and glutamate (E) residues is found in an activator of the multicatalytic protease. Such 'KEKE sequences' are also present in subunits of the multicatalytic protease, in subunits of the 26S protease and in a variety of chaperonins. We propose that KEKE regions promote association between protein complexes. Furthermore, they may contribute to the selection of peptides presented on MHC Class I receptors.