gebhart/patrepeval huggingface dataset:
Recombinant Nipah Virus Vaccines Protect Pigs against Challenge (2006)

Nipah virus (NiV), of the family Paramyxoviridae, was isolated in 1999 in Malaysia from a human fatality in an outbreak of severe human encephalitis, when human infections were linked to transmission of the virus from pigs. Consequently, a swine vaccine able to abolish virus shedding is of veterinary and human health interest. Canarypox virus-based vaccine vectors carrying the gene for NiV glycoprotein (ALVAC-G) or the fusion protein (ALVAC-F) were used to intramuscularly immunize four pigs per group, either with 10(8) PFU each or in combination. Pigs were boosted 14 days postvaccination and challenged with 2.5 x 10(5) PFU of NiV two weeks later. The combined ALVAC-F/G vaccine induced the highest levels of neutralization antibodies (2,560); despite the low neutralizing antibody levels in the F vaccinees (160), all vaccinated animals appeared to be protected against challenge. Virus was not isolated from the tissues of any of the vaccinated pigs postchallenge, and a real-time reverse transcription (RT)-PCR assay detected only small amounts of viral RNA in several samples. In challenge control pigs, virus was isolated from a number of tissues (10(4.4) PFU/g) or detected by real-time RT-PCR. Vaccination of the ALVAC-F/G vaccinees appeared to stimulate both type 1 and type 2 cytokine responses. Histopathological findings indicated that there was no enhancement of lesions in the vaccinees. No virus shedding was detected in vaccinated animals, in contrast to challenge control pigs, from which virus was isolated from the throat and nose (10(2.9) PFU/ml). Based on the data presented, the combined ALVAC-F/G vaccine appears to be a very promising vaccine candidate for swine.
Vascular Endothelial Growth Factor Transcriptional Activation Is Mediated by Hypoxia-inducible Factor 1α, HDM2, and p70S6K1 in Response to Phosphatidylinositol 3-Kinase/AKT Signaling (2004)

Vascular endothelial growth factor (VEGF) expression is elevated in ovarian and other cancer cells. However, the mechanism that causes the increase in VEGF expression still remains to be elucidated. In this study, we demonstrated that activation of PI3K signaling mediated VEGF protein expression at the transcriptional level through hypoxia-inducible factor 1alpha (HIF-1alpha) expression in human ovarian cancer cells. We found that inhibition of PI3K activity by LY294002 decreased VEGF transcriptional activation and that forced expression of AKT completely reversed the inhibitory effect. HDM2 and p70S6K1 are two downstream targets of AKT that mediate growth factor-induced VEGF transcriptional activation and HIF-1alpha expression. The inhibition of PI3K by LY294002 inhibited p70S6K1 and HDM2 activity in the cells. Forced expression of p70S6K1 or HDM2 reversed LY294002-inhibited VEGF transcriptional activation and HIF-1alpha expression. This study identifies a potential novel mechanism responsible for increased VEGF expression in ovarian cancer cells. It also indicates the important role of VEGF and HIF-1 in ovarian tumorigenesis and angiogenesis, which is mediated by the PI3K/AKT/HDM2 and AKT/p70S6K1 pathways in ovarian cancer cells.
Protein toxins: mode of action and cell entry (1992)

Conference Article| November 01 1992 Protein toxins: mode of action and cell entry Kirsten Sandvig; Kirsten Sandvig 1Institute for Cancer Research at The Norwegian Radium Hospital, Montebello, 0310 Oslo 3, Norway Search for other works by this author on: This Site PubMed Google Scholar Elena Dubinina; Elena Dubinina *WA Engelhardt Institute for Molecular Biology, Academy of Sciences of Russia, Vavilov str 32, Moscow, Russia Search for other works by this author on: This Site PubMed Google Scholar Garred Øystein; Garred Øystein 1Institute for Cancer Research at The Norwegian Radium Hospital, Montebello, 0310 Oslo 3, Norway Search for other works by this author on: This Site PubMed Google Scholar Kristian Prydz; Kristian Prydz 1Institute for Cancer Research at The Norwegian Radium Hospital, Montebello, 0310 Oslo 3, Norway Search for other works by this author on: This Site PubMed Google Scholar Juri V. Kozlov; Juri V. Kozlov *WA Engelhardt Institute for Molecular Biology, Academy of Sciences of Russia, Vavilov str 32, Moscow, Russia Search for other works by this author on: This Site PubMed Google Scholar Steen H. Hansen; Steen H. Hansen †Structural Cell Biology Unit, Department of Anatomy, The Panum Institute, University of Copenhagen, DK-2200 Copenhagen N, Denmark Search for other works by this author on: This Site PubMed Google Scholar Bo van Deurs Bo van Deurs †Structural Cell Biology Unit, Department of Anatomy, The Panum Institute, University of Copenhagen, DK-2200 Copenhagen N, Denmark Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1992) 20 (4): 724–727. https://doi.org/10.1042/bst0200724 Article history Received: July 10 1992 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation Kirsten Sandvig, Elena Dubinina, Garred Øystein, Kristian Prydz, Juri V. Kozlov, Steen H. Hansen, Bo van Deurs; Protein toxins: mode of action and cell entry. Biochem Soc Trans 1 November 1992; 20 (4): 724–727. doi: https://doi.org/10.1042/bst0200724 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: HRP, horseradish peroxidase, TGN, trans-Golgi network This content is only available as a PDF. © 1992 Biochemical Society1992 Article PDF first page preview Close Modal You do not currently have access to this content.
Frustulins: Domain Conservation in a Protein Family Associated with Diatom Cell Walls (1996)

The outstanding feature of a diatom is the species-specific design and ornamentation of the silica-based cell wall, termed frustulum. A new frustulum is shaped in a specialized organelle (silica deposition vesicle) and secreted. Proteins in the lumen of this organelle may control the biomineralization process and are likely to remain associated with the mature cell wall. Therefore a study of the structures of proteins associated with the diatom cell wall was initiated. The complete primary structures of three cell wall proteins (denoted as frustulins) have been determined. In addition, partial amino acid sequences from two more cell wall components were obtained. From these data, a highly conserved domain has been identified as a common building block of diatom cell wall proteins that is repeated several times per polypeptide chain together with polyproline/hydroxyproline or polyglycine spacers. All frustulins characterized so far, are synthesized as preproteins with a novel type of N-terminal presequence.
Plasma sphingolipids are biomarkers of metabolic syndrome in non-human primates maintained on a Western-style diet (2012)

Together, these data indicate that HFFD induces de novo synthesis of ceramides in non-human primates, and that increased production of plasma ceramides is significantly correlated with the decline in insulin sensitivity.
Göran Sonesson; Bildbetydelser - inledning till bildsemiotiken som vetenskap. Studemtlitteratur, Lund : (en recension) (1992)

Goran Sonesson; Bildbetydelser - inledning till bildsemiotiken som vetenskap. Studemtlitteratur, Lund : (en recension)
Effect of dietary seaweed extracts and fish oil supplementation in sows on performance, intestinal microflora, intestinal morphology, volatile fatty acid concentrations and immune status of weaned pigs (2010)

A 2 × 2 factorial experiment (ten sows per treatment) was conducted to investigate the effect of maternal dietary supplementation with a seaweed extract (SWE; 0 v. 10·0 g/d) and fish oil (FO; 0 v. 100 g/d) inclusion from day 109 of gestation until weaning (day 26) on pig performance post-weaning (PW) and intestinal morphology, selected microflora and immune status of pigs 9 d PW. The SWE contained laminarin (10 %), fucoidan (8 %) and ash (82 %) and the FO contained 40 % EPA and 25 % DHA. Pigs weaned from SWE-supplemented sows had higher daily gain ( P = 0·063) between days 0 and 21 PW and pigs weaned from FO-supplemented sows had higher daily gain ( P &lt; 0·05) and gain to feed ratio ( P &lt; 0·01) between days 7 and 14 PW. There was an interaction between maternal SWE and FO supplementation on caecal Escherichia coli numbers ( P &lt; 0·05) and the villous height to crypt depth ratio in the ileum ( P &lt; 0·01) and jejunum ( P &lt; 0·05) in pigs 9 d PW. Pigs weaned from SWE-supplemented sows had lower caecal E . coli and a higher villous height to crypt depth ratio in the ileum and jejunum compared with non-SWE-supplemented sows ( P &lt; 0·05). There was no effect of SWE on E . coli numbers and villous height to crypt depth ratio with FO inclusion. Maternal FO supplementation induced an increase in colonic mRNA abundance of IL-1α and IL-6 ( P &lt; 0·05), while SWE supplementation induced an increase in ileal TNF-α ( P &lt; 0·01) and colonic TFF3 mRNA expression ( P &lt; 0·05). In conclusion, these results demonstrate that SWE and FO supplementation to the maternal diet influenced the gastrointestinal environment and performance of the weaned pig.
A gas-liquid solid phase peptide and protein sequenator. (1981)

A new miniaturized protein and peptide sequenator has been constructed which uses gas phase reagents at the coupling and cleavage steps of the Edman degradation. The sample is embedded in a matrix of Polybrene dried onto a porous glass fiber disc located in a small cartridge-style reaction cell. The protein or peptide, though not covalently attached to the support, is essentially immobile throughout the degradative cycle, since only relatively apolar, liquid phase solvents pass through the cell. This instrument can give useful sequence data on as little as 5 pmol or protein, can perform extended sequence runs (greater than 30 residues) on subnanomole quantities of proteins purified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and can sequence hydrophobic peptides to completion. The sequenator is characterized by a high repetitive yield during the degradation, low reagent consumption, low maintenance requirements, and a degradative cycle time of only 50 min using a complete double cleavage program.
Aberrant dimerization of von Willebrand factor as the result of mutations in the carboxy-terminal region: identification of 3 mutations in members of 3 different families with type 2A (phenotype IID) von Willebrand disease (2001)

The 3' end of the VWF gene was screened in the affected members of 3 different families with type 2A (phenotype IID) von Willebrand disease (vWD). Exons 49 to 52 of the VWF gene were amplified and screened for mutations by chemical cleavage mismatch detection. Mismatched bands were detected in exon 52 of 2 patients and in exon 51 of a third patient. Using direct DNA sequencing, a heterozygous G8562A transition leading to a Cys2008Tyr substitution was found in all the patients in family 1, and a T8561A transversion leading to a Cys2008Ser substitution was found in both patients from family 2. In a patient from a third family, an 8-base deletion from nucleotide 8437 to 8444 was identified in exon 51. The 2 mutations in exon 52 were reproduced by in vitro site-directed mutagenesis of full-length von Willebrand factor (vWF) cDNA and transiently expressed in COS-7 cells. The corresponding recombinant VWFs for these 2 mutations exhibited the typical aberrant vWF:Ag multimer pattern seen in the plasma of the patients. These 3 mutations demonstrate the importance of other carboxy-terminal cysteines in addition to the reported Cys2010 residue, in the normal dimerization of vWF, and their essential role in the assembly of normal multimeric vWF. (Blood. 2001;98:674-680)
Deletion Analysis of the Imprinting Center Region in Patients with Angelman Syndrome and Prader-Willi Syndrome by Real-Time Quantitative PCR (2004)

The molecular basis of Angelman syndrome and Prader-Willi syndrome is well established, and genetic testing for these disorders is clinically available. Imprinting abnormalities account for up to 4% of patients with Angelman and Prader-Willi syndromes. Deletions of the imprinting center region are the molecular abnormality observed in a subset of Angelman and Prader-Willi syndrome cases with imprinting defects. Genetic testing of imprinting center deletions in patients with Angelman and Prader-Willi syndrome is not readily available. Such testing is important for the diagnostics of Angelman and Prader-Willi syndrome because it allows for more accurate diagnosis and recurrence risk prediction in families. Here we describe the development, validation, and implementation of a real time quantitative polymerase chain reaction (PCR)-based assay for imprinting center deletion detection in patients with Angelman and Prader-Willi syndrome, which we have incorporated into our genetic testing strategy for these disorders. To date we have tested, on a clinical basis, five patients with either Angelman or Prader-Willi syndrome in whom an imprinting center defect was implicated and found a deletion in one patient that was determined to be familial.
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data (2010)

High-throughput sequencing platforms are generating massive amounts of genetic variation data for diverse genomes, but it remains a challenge to pinpoint a small subset of functionally important variants. To fill these unmet needs, we developed the ANNOVAR tool to annotate single nucleotide variants (SNVs) and insertions/deletions, such as examining their functional consequence on genes, inferring cytogenetic bands, reporting functional importance scores, finding variants in conserved regions, or identifying variants reported in the 1000 Genomes Project and dbSNP. ANNOVAR can utilize annotation databases from the UCSC Genome Browser or any annotation data set conforming to Generic Feature Format version 3 (GFF3). We also illustrate a 'variants reduction' protocol on 4.7 million SNVs and indels from a human genome, including two causal mutations for Miller syndrome, a rare recessive disease. Through a stepwise procedure, we excluded variants that are unlikely to be causal, and identified 20 candidate genes including the causal gene. Using a desktop computer, ANNOVAR requires ∼4 min to perform gene-based annotation and ∼15 min to perform variants reduction on 4.7 million variants, making it practical to handle hundreds of human genomes in a day. ANNOVAR is freely available at http://www.openbioinformatics.org/annovar/.
A cannabinoid derived prototypical analgesic (1984)

The synthesis and analgesic testing of 3-[4-(1,1-dimethylheptyl)-2-hydroxyphenyl]cyclohexanol (1) are described. Prior (SAR) studies led us to conclude that the pyran ring of 9-nor-9 beta-hydroxyhexahydrocannabinol (HHC) was not necessary for the expression of biological activity in this series of cannabinoids. Analysis of models and the use of molecular mechanics calculations suggested that a simpler compound, such as 1, would possess the biological activity of HHC. Compound 1 was prepared in nine steps from [3-(benzyloxy)phenyl]acetonitrile (2). Biological testing in five models of pain shows that compound 1 and morphine are equally potent as analgesics and demonstrates that the pyran ring of HHC is not necessary for biological activity. Further simplification of 1 was pursued by the synthesis of 4-[4-(1,1-dimethylheptyl)-2-hydroxyphenyl]-2-pentanol (17), but this derivative exhibits significantly reduced analgesic activity.
At concentrations that inhibit mTOR, resveratrol suppresses cellular senescence (2009)

Here we demonstrated that, at cytostatic, near-toxic concentrations, resveratrol inhibited S6 phosphorylation and prevented the senescence morphology in human cells. Using a sensitive functional assay, we found that resveratrol partially prevented loss of the proliferative potential associated with cellular senescence. Resveratrol was less effective than rapamycin, because aging-suppression by resveratrol was limited by its toxicity at high concentrations. We discuss whether concentrations of resveratrol that inhibit mTOR (target of rapamycin) and suppress cellular senescence are clinically achievable and whether partial inhibition of mTOR by resveratrol might be sufficient to affect organismal aging.
Effects of ghrelin administration during chemotherapy with advanced esophageal cancer patients (2012)

Short-term administration of exogenous ghrelin at the start of cisplatin-based chemotherapy stimulated food intake and minimized adverse events.
Gradient-based Hyperparameter Optimization through Reversible Learning (2015)

Tuning hyperparameters of learning algorithms is hard because gradients are usually unavailable. We compute exact gradients of cross-validation performance with respect to all hyperparameters by chaining derivatives backwards through the entire training procedure. These gradients allow us to optimize thousands of hyperparameters, including step-size and momentum schedules, weight initialization distributions, richly parameterized regularization schemes, and neural network architectures. We compute hyperparameter gradients by exactly reversing the dynamics of stochastic gradient descent with momentum.
Basic Cell Culture (2003)

This article describes the basic techniques required for successful cell culture. It also acts to introduce some of the other chapters in this volume. It is not intended to describe the establishment of a tissue culture laboratory, nor to provide a historical or theoretical survey of cell culture. There are several books that adequately cover these areas, including the now somewhat dated, but still valuable volume by Paul (1), that of Freshney (2), and the multi-authored volumes edited by Jakoby and Pastan (3), Davis (4), and Celis (5). Instead, this chapter focuses on the techniques for establishing primary rodent cell cultures from embryos and adult skin, maintaining and subculturing these fibroblasts and their transformed derivatives, and the isolation of genetically pure strains. The cells described are all derived from Chinese hamsters since to date, these cells have proved to be the most useful for somatic cell genetics (6,7). The techniques, however, are generally applicable to most fibroblast cell types.
Mutations in the Primer Grip Region of HIV Reverse Transcriptase Can Increase Replication Fidelity (1999)

Mutations in the primer grip region of human immunodeficiency virus reverse transcriptase (HIV-RT) affect its replication fidelity. The primer grip region (residues 227-235) correctly positions the 3'-ends of primers. Point mutations were created by alanine substitution at positions 224-235. Error frequencies were measured by extension of a dG:dA primer-template mismatch. Mutants E224A, P225A, P226A, L228A, and E233A were approximately equal to the wild type in their ability to extend the mismatch. Mutants F227A, W229A, M230A, G231A, and Y232A extended 40, 66, 54, 72, and 76% less efficiently past a dG:dA mismatch compared with the wild type. We also examined the misinsertion rates of dG, dC, or dA across from a DNA template dA using RT mutants F227A and W229A. Mutant W229A exhibited high fidelity and did not produce a dG:dA or dC:dA mismatch. Interestingly, mutant F227A displayed high fidelity for dG:dA and dC:dA mismatches but low fidelity for dA:dA misinsertions. This indicates that F227A discriminates against particular base substitutions. However, a primer extension assay with three dNTPs showed that F227A generally displays higher fidelity than the wild type RT. Clearly, primer grip mutations can improve or worsen either the overall or base-specific fidelity of HIV-RT. We hypothesize that wild type RT has evolved to a fidelity that allows genetic variation without compromising yield of viable viruses.
Nearly single-mode Raman lasing at 954  nm in a graded-index fiber directly pumped by a multimode laser diode (2016)

High beam quality and narrow spectrum have been obtained in a Raman fiber laser based on a 1.1 km long graded-index fiber directly pumped by a multimode 915 nm laser diode. The generation of a near-diffraction-limited beam at 954 nm with M<sup>2</sup>≤1.27 and Δλ=0.42 nm at an output power above 10 W is enabled by a cavity mirror made of a special fiber Bragg grating inscribed by a femtosecond technique in the central part of the graded-index fiber core.
What is Around the Camera? (2017)

How much does a single image reveal about the environment it was taken in? In this paper, we investigate how much of that information can be retrieved from a foreground object, combined with the background (i.e. the visible part of the environment). Assuming it is not perfectly diffuse, the foreground object acts as a complexly shaped and far-from-perfect mirror An additional challenge is that its appearance confounds the light coming from the environment with the unknown materials it is made of. We propose a learning-based approach to predict the environment from multiple reflectance maps that are computed from approximate surface normals. The proposed method allows us to jointly model the statistics of environments and material properties. We train our system from synthesized training data, but demonstrate its applicability to real-world data. Interestingly, our analysis shows that the information obtained from objects made out of multiple materials often is complementary and leads to better performance.
Secreted LOXL2 is a novel therapeutic target that promotes gastric cancer metastasis via the Src/FAK pathway (2009)

The purpose of this study was to investigate invasion- and metastasis-related genes in gastric cancer. To this end, we used the transwell system to select a highly invasive subcell line from minimally invasive parent cells and compared gene expression in paired cell lines with high- and low-invasive potentials. Lysyl oxidase-like 2 (LOXL2) was overexpressed in the highly invasive subcell line. Immunohistochemical analysis revealed that LOXL2 expression was markedly increased in carcinoma relative to normal epithelia, and this overexpression in primary tumor was significantly associated with depth of tumor invasion, lymph node metastasis and poorer overall survival. Moreover, LOXL2 expression was further increased in lymph node metastases compared with primary cancer tissues. RNA interference-mediated knockdown and ectopic expression of LOXL2 showed that LOXL2 promoted tumor cell invasion in vitro and increased gastric carcinoma metastasis in vivo. Subsequent mechanistic studies showed that LOXL2 could activate both the Snail/E-cadherin and Src kinase/Focal adhesion kinase (Src/FAK) pathways. However, secreted LOXL2 induced gastric tumor cell invasion and metastasis exclusively via the Src/FAK pathway. Expression correlation analysis in gastric carcinoma tissues also revealed that LOXL2 promoted invasion via the Src/FAK pathway but not the Snail/E-cadherin pathway. We then evaluated secreted LOXL2 as a target for gastric carcinoma treatment and found that an antibody against LOXL2 significantly inhibited tumor growth and metastasis. Overall, our data revealed that LOXL2 overexpression, a frequent event in gastric carcinoma progression, contributes to tumor cell invasion and metastasis, and LOXL2 may be a therapeutic target for preventing and treating metastases.