gebhart/patrepeval huggingface dataset:
Secondary Metabolites from Endophytic Fungus Penicillium pinophilum Induce ROS-Mediated Apoptosis through Mitochondrial Pathway in Pancreatic Cancer Cells (2016)

The endophytic fungus strain MRCJ-326, isolated from Allium schoenoprasum, which is also known as Snow Mountain Garlic or Kashmiri garlic, was identified as Penicillium pinophilum on the basis of morphological characteristics and internal transcribed spacer region nucleotide sequence analysis. The endophytic fungus extract was subjected to 2D-SEPBOX bioactivity-guided fractionation and purification. The anthraquinone class of the bioactive secondary metabolites were isolated and characterized as oxyskyrin (1), skyrin (2), dicatenarin (3), and 1,6,8-trihydroxy-3-hydroxy methylanthraquinone (4) by spectral analysis. Dicatenarin and skyrin showed marked growth inhibition against the NCI60/ATCC panel of human cancer cell lines with least IC50 values of 12 µg/mL and 27 µg/mL, respectively, against the human pancreatic cancer (MIA PaCa-2) cell line. The phenolic hydroxyl group in anthraquinones plays a crucial role in the oxidative process and bioactivity. Mechanistically, these compounds, i.e., dicatenarin and skyrin, significantly induce apoptosis and transmit the apoptotic signal via intracellular reactive oxygen species generation, thereby inducing a change in the mitochondrial transmembrane potential and induction of the mitochondrial-mediated apoptotic pathway. Our data indicated that dicatenarin and skyrin induce reactive oxygen species-mediated mitochondrial permeability transition and resulted in an increased induction of caspase-3 apoptotic proteins in human pancreatic cancer (MIA PaCa-2) cells. Dicatenarin showed a more pronounced cytotoxic/proapopotic effect than skyrin due to the presence of an additional phenolic hydroxyl group at C-4, which increases oxidative reactive oxygen species generation. This is the first report from P. pinophilum secreating these cytotoxic/proapoptotic secondary metabolites.
Programming in the medical real-time environment (1970)

The Shock Research Unit (SRU) is a specialized clinical research facility developed for the triple purposes of rendering intensive care to seriously ill patients, studying underlying mechanisms of the disease process of circulatory shock, and developing new technologies for evaluating the status and treatment of seriously ill patients.
<title>Ultrasonic waves for fabricating lattice structure in composite materials</title> (1999)

Ultrasonic waves are useful for arranging small particles in liquid, since the acoustic pressure exerts a sufficient trapping force on the particles. A composite material with layered structure can be fabricated by solidifying a particle suspension during the process of ultrasonic standing wave excitation. Fabrication of a 2D or 3D lattice structure is also possible by simultaneous excitation of two or three orthogonal ultrasonic standing waves. A polysiloxane resin is appropriate as a host material of such composite materials, since it is easily synthesized from a solution and its yields a small-periodicity structure due to its low sound velocity. Acrylic spheres, glass rods, and metal particles have been successfully arranged in polysiloxane resin forming layers or lattice structures. The spacing of particles was approximately 60 micrometers , which was half of the ultrasonic wavelength used. For heavy particles, a sample cell was continually rotated during the solidification process in order to prevent sedimentation.
Anti-melanoma effect of intra-tumoral injection of recombinant Salmonella typhimurium (2004)

The goal of tumor immunotherapy is to induce a specific anti-tumor immune response to prevent disease in healthy high-risk individuals or to eradicate an already established tumor mass. However, achievement of an effective anti-tumor immune response is often hampered by the difficulty to overcome tumor immune escape mechanisms. It is well established for example that in response to active immunotherapy many patients develop tumor-specific CTLs, which, however, are either excluded from the tumor site or are downsized by the tumor microenvironment, rendering the immunotherapeutical approach particularly inefficient. We have previously shown that subcutaneous injection of bacteria induces a local inflammatory response that facilitates the infiltration and activation of immune system cells. Thus, in order to overcome tumor escape mechanisms, we propose here the use of recombinant bacteria injected directly in the tumor site. To address this issue we set up a mice melanoma model, in which B16 melanoma cells are injected subcutaneously and give rise to a rapidly growing aggressive tumor mass. We chose an attenuated Salmonella tiphymurium strain, which is unable to replicate more than two or three times in vivo, to induce local inflammatory response. This bacterial strain is very well tolerated in mice even at high doses and should be totally safe in humans. Our data confirm the proposed hypothesis, showing that intra-tumoral injection of attenuated Salmonella severely affects tumor growth. Even more effective was the injection of attenuated recombinant Salmonella expressing TRP2, a melanoma associated antigen, leading to complete regression of the tumor mass in 20% of treated mice, probably due to the in situ restimulation of pre-existing CTLs. Moreover we were able to demonstrate that this type of treatment induced a massive recruitment of different subpopulations of immune cells, which are probably responsible for the observed therapeutic effect and for the direct elimination of tumor cells. In fact, in vitro apoptotic assays argue against the possibility that the bacteria exert a direct and intrinsic toxic effect toward tumor cells. Granulocytes were the most representative recruited cell types, but we could detect also macrophages, NK cells and T lymphocytes. We are currently investigating the role of each cell type in tumor regression.
Persistent use of “false” cell lines (2007)

From HeLa and its multiple identities, to MDA-MB-435, erroneously and widely used as breast cancer cells, the history of cancer cell lines is rich in misidentification and cross-contamination events. Despite the fact that these problems were regularly signaled during the last decades, many actors of research still seem to ignore them. A never-ending story? Solutions exist, notably based on recent technical advances in cell line authentication (short tandem repeat analysis). However, a collaborative action involving users of cell lines, cell banks, journals and funding agencies is needed to achieve success.
Suture-Mediated Patent Foramen Ovale Closure Using the NobleStitch EL: Results from a Hospital-Based HTA (2022)

(1) Background: Patent foramen ovale (PFO) is a congenital abnormality present in up to 25% of the general population, and it is a relevant cause of cryptogenic stroke. We applied the hospital-based HTA model (AdHopHTA) to conduct a multidimensional assessment of NobleStitch EL, an innovative suture-mediated PFO closure device. We compared it to Amplatzer PFO Occluder (APO) to provide evidence to inform technologies' governance in hospital settings. (2) Methods: For each AdHopHTA dimension we: systematically retrieved available evidence from the literature applying the PRISMA guidelines and then analyzed original clinical and cost data of a NobleStitch EL device at San Raffaele research hospital in Milan (Italy). The economic dimension was analyzed through activity-based costing and a cost analysis. We conducted semi-structured interviews with selected healthcare professionals to explore the organizational, legal, social, and ethical impact. (3) Results: A single study was included for the NobleStitch EL, with 10 for APO. Both literature data and original data showed comparable safety. Efficacy data analysis found that the PFO closure was at 89% for NobleStitch EL vs. 89-97% for APO. APO has a better impact on the budget and minor process costs. Consulted experts reported that the organizational impact of NobleStitch EL in the short and the long run as null, albeit a better impact under the social and the ethical aspects. (4) Conclusion: We suggest that there is inadequate evidence to conclude the relative efficacy of NobleStitch EL as compared to APO. Nevertheless, this report shows a good safety profile and higher costs for NobleStitch EL, with no organizational or legal impact. Further studies in selected population are recommended.
Histone Acetyltransferase 1 Promotes Homologous Recombination in DNA Repair by Facilitating Histone Turnover (2013)

Faithful repair of DNA double-strand breaks is vital to the maintenance of genome integrity and proper cell functions. Histone modifications, such as reversible acetylation, phosphorylation, methylation, and ubiquitination, which collectively contribute to the establishment of distinct chromatin states, play important roles in the recruitment of repair factors to the sites of double-strand breaks. Here we report that histone acetyltransferase 1 (HAT1), a classical B type histone acetyltransferase responsible for acetylating the N-terminal tail of newly synthesized histone H4 in the cytoplasm, is a key regulator of DNA repair by homologous recombination in the nucleus. We found that HAT1 is required for the incorporation of H4K5/K12-acetylated H3.3 at sites of double-strand breaks through its HIRA-dependent histone turnover activity. Incorporated histones with specific chemical modifications facilitate subsequent recruitment of RAD51, a key repair factor in mammalian cells, to promote efficient homologous recombination. Significantly, depletion of HAT1 sensitized cells to DNA damage compromised the global chromatin structure, inhibited cell proliferation, and induced cell apoptosis. Our experiments uncovered a role for HAT1 in DNA repair in higher eukaryotic organisms and provide a mechanistic insight into the regulation of histone dynamics by HAT1.
Deletion of Nrip1 Extends Female Mice Longevity, Increases Autophagy, and Delays Cell Senescence (2018)

Using age of female sexual maturation as a biomarker, we previously identified nuclear receptor interacting protein 1 (Nrip1) as a candidate gene that may regulate aging and longevity. In the current report, we found that the deletion of Nrip1 can significantly extend longevity of female mice (log-rank test, p = .0004). We also found that Nrip1 expression is altered differently in various tissues during aging and under diet restriction. Remarkably, Nrip1 expression is elevated with aging in visceral white adipose tissue (WAT), but significantly reduced after 4 months of diet restriction. However, in gastrocnemius muscle, Nrip1 expression is significantly upregulated after the diet restriction. In mouse embryonic fibroblasts, we found that the deletion of Nrip1 can suppress fibroblast proliferation, enhance autophagy under normal culture or amino acid starvation conditions, as well as delay oxidative and replicative senescence. Importantly, in WAT of old animals, the deletion of the Nrip could significantly upregulate autophagy and reduce the number of senescent cells. These results suggest that deleting Nrip1 can extend female longevity, but tissue-specific deletion may have varying effects on health span. The deletion of Nrip1 in WAT may delay senescence in WAT and extend health span.
Using latent semantic analysis to improve access to textual information (1988)

This paper describes a new approach for dealing with the vocabulary problem in human-computer interaction. Most approaches to retrieving textual materials depend on a lexical match between words in users' requests and those in or assigned to database objects. Because of the tremendous diversity in the words people use to describe the same object, lexical matching methods are necessarily incomplete and imprecise [5]. The latent semantic indexing approach tries to overcome these problems by automatically organizing text objects into a semantic structure more appropriate for matching user requests. This is done by taking advantage of implicit higher-order structure in the association of terms with text objects. The particular technique used is singular-value decomposition, in which a large term by text-object matrix is decomposed into a set of about 50 to 150 orthogonal factors from which the original matrix can be approximated by linear combination. Terms and objects are represented by 50 to 150 dimensional vectors and matched against user queries in this “semantic” space. Initial tests find this completely automatic method widely applicable and a promising way to improve users' access to many kinds of textual materials, or to objects and services for which textual descriptions are available.
ChemInform Abstract: S‐NUCLEOSIDE PHOTOREARRANGEMENT. ACCESS TO PYRIDINE PSEUDONUCLEOSIDES (1979)

Abstract Bei der Photolyse und nachfolgenden Behandlung mit Diazomethan erhält man aus den 2‐Mercapto‐pyridinen (Ia) und (Ic) in allerdings nur niederen Ausbeuten die Umlagerungsprodukte (III)‐(V).
THE ADAPTATION OF DUNALIELLA SALINA CELLS TO HIGH SALT CONCENTRATION. ISOLATION OF 63 AND 28 KDA SALT-INDUCED POLYPEPTIDES (1996)

Conference Abstract| November 01 1996 THE ADAPTATION OF DUNALIELLA SALINA CELLS TO HIGH SALT CONCENTRATION. ISOLATION OF 63 AND 28 KDA SALT-INDUCED POLYPEPTIDES V.A. Ajalov; V.A. Ajalov 1Institute of Botany, Academy of Sciences, Patamdar shosse 40, Baku 370073, Azerbaijan Search for other works by this author on: This Site PubMed Google Scholar T.V. Savchenko; T.V. Savchenko 1Institute of Botany, Academy of Sciences, Patamdar shosse 40, Baku 370073, Azerbaijan Search for other works by this author on: This Site PubMed Google Scholar J.A. Aliev J.A. Aliev 1Institute of Botany, Academy of Sciences, Patamdar shosse 40, Baku 370073, Azerbaijan Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1996) 24 (4): 534S. https://doi.org/10.1042/bst024534sc Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation V.A. Ajalov, T.V. Savchenko, J.A. Aliev; THE ADAPTATION OF DUNALIELLA SALINA CELLS TO HIGH SALT CONCENTRATION. ISOLATION OF 63 AND 28 KDA SALT-INDUCED POLYPEPTIDES. Biochem Soc Trans 1 November 1996; 24 (4): 534S. doi: https://doi.org/10.1042/bst024534sc 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 This content is only available as a PDF. © 1996 Biochemical Society1996 Article PDF first page preview Close Modal You do not currently have access to this content.
Evolution of pathogen response genes associated with increased disease susceptibility during adaptation to an extreme drought in a Brassica rapa plant population (2020)

Abstract BACKGROUND Pathogens are key components in natural and agricultural plant systems. There is evidence of evolutionary changes in disease susceptibility as a consequence of climate change, but we know little about the underlying genetic basis of this evolution. To address this, we took advantage of a historical seed collection of a Brassica rapa population, which we previously demonstrated evolved an increase in disease susceptibility to a necrotrophic fungal pathogen following a drought. RESULTS Previously, we combined a resurrection experiment with genome-wide sequencing of 124 pooled ancestral and descendant plants. Here, using these previously generated sequence data (Franks et al, 2016), we show that well-characterized necrotrophic fungal pathogen response (NFPR) genes have evolved, as indicated by changes in allele frequency, between ancestors and descendants, with several of them identified as extreme F ST outliers. The jasmonic acid (JA) signaling pathway in particular seems to underlie the evolution of disease susceptibility, in addition to its well characterized role in plastic disease response. We identify a list of 260 genes that are both NFPR genes and are differentially expressed in response to drought, based on publicly available data. We present evidence that five of these genes evolved between ancestors and descendants, suggesting that the drought acted as the evolutionary driver, and that the accompanying increase in disease susceptibility may have been a consequence of genetic pleiotropy. CONCLUSIONS Our study provides evidence that for this population, standing variation in NFPR genes is affected by natural selection related to climate change. Our results reveal potentially important candidates that may underlie trait evolution in both crops and natural systems. Additionally, this trade-off between adaptation to biotic and abiotic stresses is an example of how climate change can have diverse and unexpected consequences.
Characterization and Optimization of a Novel Protein–Protein Interaction Biosensor High-Content Screening Assay to Identify Disruptors of the Interactions Between p53 and hDM2 (2010)

We present here the characterization and optimization of a novel imaging-based positional biosensor high-content screening (HCS) assay to identify disruptors of p53-hDM2 protein-protein interactions (PPIs). The chimeric proteins of the biosensor incorporated the N-terminal PPI domains of p53 and hDM2, protein targeting sequences (nuclear localization and nuclear export sequence), and fluorescent reporters, which when expressed in cells could be used to monitor p53-hDM2 PPIs through changes in the subcellular localization of the hDM2 component of the biosensor. Coinfection with the recombinant adenovirus biosensors was used to express the NH-terminal domains of p53 and hDM2, fused to green fluorescent protein and red fluorescent protein, respectively, in U-2 OS cells. We validated the p53-hDM2 PPI biosensor (PPIB) HCS assay with Nutlin-3, a compound that occupies the hydrophobic pocket on the surface of the N-terminus of hDM2 and blocks the binding interactions with the N-terminus of p53. Nutlin-3 disrupted the p53-hDM2 PPIB in a concentration-dependent manner and provided a robust, reproducible, and stable assay signal window that was compatible with HCS. The p53-hDM2 PPIB assay was readily implemented in HCS and we identified four (4) compounds in the 1,280-compound Library of Pharmacologically Active Compounds that activated the p53 signaling pathway and elicited biosensor signals that were clearly distinct from the responses of inactive compounds. Anthracycline (topoisomerase II inhibitors such as mitoxantrone and ellipticine) and camptothecin (topoisomerase I inhibitor) derivatives including topotecan induce DNA double strand breaks, which activate the p53 pathway through the ataxia telangiectasia mutated-checkpoint kinase 2 (ATM-CHK2) DNA damage response pathway. Although mitoxantrone, ellipticine, camptothecin, and topotecan all exhibited concentration-dependent disruption of the p53-hDM2 PPIB, they were much less potent than Nutlin-3. Further, their corresponding cellular images and quantitative HCS data did not completely match the Nutlin-3 phenotypic profile.
Probabilistic estimates of attribute statistics and match likelihood for people entity resolution (2014)

For big data practitioners, data integration/entity resolution/record linkage is one of the key challenges we face from day to day. Entity resolution/record linkage with high precision and recall on a large graph with billions of nodes, and hundreds of times more edges poses significant scalability challenges. Similarity based graph partition is still the most scalable method available. This paper presents a probabilistic method to approximate the match likelihood of a pair of records by incorporating values of different attributes and their aggregates/statistics. The quality of the approximates depend on the accuracy of the estimates of the aggregated values. The paper adapts the GTM model described in [1] to obtain the estimates. We present experimental results based on real world commercial data sources to show that the estimates obtained via GTM model is better than the baseline. Our experimental results also showed that the approximate match likelihood can improve the recall of the similarity function.
GENOME SCANNING USING ENDOGENOUS LTR-LIKE ELEMENTS FOR RAPID DNA-FINGERPRINTING OF BREAST-CANCER AND TRANSFORMED HUMAN BREAST EPITHELIAL-CELLS (1995)

In the present work genomic DNAs from nine primary breast cancers and transformed human breast epithelial cell lines obtained by treatment of MCF 10F, a spontaneously immortalized human breast epithelial cell line, with benzo(a)pyrene (BP) or 7,12 dimethyl benz(a)anthracene (DMBA), were used for genomic scanning. The treatment of MCF 10F with BP gave rise to different clones designated BP1 and BP1E, the latter being a tumorigenic cell line. Treatment with DMBA gave rise to D3 and D3-1 clones. The clones D3-1 and BP1 have been transfected with the plasmid pH06T1 containing the mutated c-Ha-ras oncogene resulting in the D3-1Tras and BP1T-ras cell lines, that are highly tumorigenic in SCID mice. Genomic DNA are separately hybridized to two different probes representing different families of human endogenous retrovirus like sequences (RTLV-H and HERV-K LTR). The technique of genomic scanning allows the mapping of each tumor or cell line and comparison with its counterpart obtained from the adjacent normal tissue of the same patient or with the untreated MCF 10F cells. DNA changes such as deletions, amplifications and/or rearrangements were detected in 5 of the tumor pairs studied. We have identified genomic alterations that involved amplification of a 10 kb band in the transformed cell lines. The cell lines D3-1Tras and BP1T-ras show, in addition, the presence of a second band of 4.5 kb in size. A third band of 500 bp size was found in clones D3-1 and BP1E that have a more aggressive behavior in vitro than their precursors D3 and BP1 cells respectively. In conclusion the present report indicates that genomic scanning detects DNA aberrations in primary primary tumors and in human breast epithelial cells transformed with chemical carcinogens and/or oncogene transfection that are not present in their normal counterpart. These results further indicate that detection of endogenous retrovirus elements may help in genome mapping and can be a useful tool for detecting genomic changes in the preliminary screening of DNA extracted from primary breast cancer and transformed cells.
Data Cube Materialization and Mining over MapReduce (2011)

Computing interesting measures for data cubes and subsequent mining of interesting cube groups over massive data sets are critical for many important analyses done in the real world. Previous studies have focused on algebraic measures such as SUM that are amenable to parallel computation and can easily benefit from the recent advancement of parallel computing infrastructure such as MapReduce. Dealing with holistic measures such as TOP-K, however, is nontrivial. In this paper, we detail real-world challenges in cube materialization and mining tasks on web-scale data sets. Specifically, we identify an important subset of holistic measures and introduce MR-Cube, a MapReduce-based framework for efficient cube computation and identification of interesting cube groups on holistic measures. We provide extensive experimental analyses over both real and synthetic data. We demonstrate that, unlike existing techniques which cannot scale to the 100 million tuple mark for our data sets, MR-Cube successfully and efficiently computes cubes with holistic measures over billion-tuple data sets.