jimnoneill/paper-to-field-training huggingface dataset:
Supplementary Table 2 from Integrative Array-Based Approach Identifies MZB1 as a Frequently Methylated Putative Tumor Suppressor in Hepatocellular Carcinoma

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

<p>PDF file, 60KB, Eleven candidates for epigenetically silenced genes in HCC cells identified through our integrated array-based approach.</p>
On effective classification of strings with wavelets

Field: Computer Science (Physical Sciences)

In recent years, the technological advances in mapping genes have made it increasingly easy to store and use a wide variety of biological data. Such data are usually in the form of very long strings for which it is difficult to determine the most relevant features for a classification task. For example, a typical DNA string may be millions of characters long, and there may be thousands of such strings in a database. In many cases, the classification behavior of the data may be hidden in the compositional behavior of certain segments of the string which cannot be easily determined apriori. Another problem which complicates the classification task is that in some cases the classification behavior is reflected in global behavior of the string, whereas in others it is reflected in local patterns. Given the enormous variation in the behavior of the strings over different data sets, it is useful to develop an approach which is sensitive to both the global and local behavior of the strings for the purpose of classification. For this purpose, we will exploit the multi-resolution property of wavelet decomposition in order to create a scheme which can mine classification characteristics at different levels of granularity. The resulting scheme turns out to be very effective in practice on a wide range of problems.
Quadratic Programs for High Relative Degree Spatial Constraints and Spatiotemporal Specifications with Spacecraft Applications

Field: Computer Science (Physical Sciences)

This paper presents a new methodology for ensuring forward invariance of sublevel sets of high relative degree functions, and convergence of the state to these sets. We introduce the notion of the boundary layer of a set defined by multiple constraints, and develop polynomially-derived trajectory constraints as means to enforce set invariance by redirecting trajectories that enter this boundary layer. This strategy is then extended to achieve convergence to and invariance of goal sets that are specified using Signal Temporal Logic. A quadratic program computes control inputs online that yield trajectories that achieve high level objectives specified by these sets, such as obstacle avoidance and target observation. We present a case study utilizing this controller for a spacecraft position and attitude control problem requiring observation of targets on the surface of a small body.
Materials Data on Na3BSbAsO7 by Materials Project

Field: Materials Science (Physical Sciences)

Na3BSbAsO7 crystallizes in the monoclinic P2_1/m space group. The structure is three-dimensional. there are two inequivalent Na1+ sites. In the first Na1+ site, Na1+ is bonded in a 6-coordinate geometry to six O2- atoms. There are a spread of Na–O bond distances ranging from 2.51–2.78 Å. In the second Na1+ site, Na1+ is bonded in a 6-coordinate geometry to six O2- atoms. There are a spread of Na–O bond distances ranging from 2.34–2.58 Å. B3+ is bonded in a trigonal planar geometry to three O2- atoms. There are a spread of B–O bond distances ranging from 1.33–1.44 Å. Sb3+ is bonded in a 6-coordinate geometry to six O2- atoms. There are a spread of Sb–O bond distances ranging from 2.08–2.82 Å. As5+ is bonded in a tetrahedral geometry to four O2- atoms. There are a spread of As–O bond distances ranging from 1.69–1.75 Å. There are six inequivalent O2- sites. In the first O2- site, O2- is bonded in a 5-coordinate geometry to four Na1+ and one B3+ atom. In the second O2- site, O2- is bonded in a 5-coordinate geometry to three Na1+, one B3+, and one Sb3+ atom. In the third O2- site, O2- is bonded in a distorted trigonal bipyramidal geometry to three Na1+, one B3+, and one Sb3+ atom. In the fourth O2- site, O2- is bonded in a 4-coordinate geometry to two Na1+, one Sb3+, and one As5+ atom. In the fifth O2- site, O2- is bonded in a 3-coordinate geometry to two equivalent Na1+, one Sb3+, and one As5+ atom. In the sixth O2- site, O2- is bonded in a distorted rectangular see-saw-like geometry to two equivalent Na1+, one Sb3+, and one As5+ atom.
Dual mode fibre bundle confocal endomicroscopy: combining reflectance and fluorescence imaging

Field: Engineering (Physical Sciences)

Commercial endomicroscopes operate in fluorescence mode only and so require the application of contrast agents. As an alternative, we describe a fibre bundle confocal endomicroscope which acquires simultaneous and co-registered fluorescence and reflectance mode images. A combination of polarisation selection and refractive index matching is used to minimise back-reflections from the fibre bundle. We show preliminary results from the system using phantoms and tissue samples. © (2013) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.
Evaluation of Mismatch Repair Gene Polymorphisms and their Contribution to Colorectal Cancer and its Subsets

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Colorectal cancer (CRC) is a major source of morbidity and mortality in the Western world. Approximately 15% of all CRCs develop via the mutator pathway, which results from a deficiency of mismatch repair (MMR) system and leads to genome-wide microsatellite instability (MSI). MLH1 promoter hypermethylation accounts for the majority of MSI CRCs. Numerous single nucleotide polymorphisms have been identified in MMR genes, however their functional roles in affecting MMR system, and therefore susceptibility to MSI CRCs, are unknown. This study uses a multidisciplinary approach combining molecular genetics, epigenetics, and epidemiology to examine the contribution of MMR gene polymorphisms in CRC. Among a panel of MMR SNPs examined, the MLH1 (-93G>A) promoter polymorphism (rs1800734) was shown to be associated with increased risk of MSI CRCs in two Canadian populations, Ontario and Newfoundland. Functional studies of the MLH1-93G>A polymorphism indicate that it has weak effects on the core promoter activity, although it dramatically reduces activity of the shorter promoter constructs in a panel of cell lines. Furthermore, MLH1 gene shares a bi-directional promoter with EMP2AIP1 gene, and the MLH1-93G>A polymorphism increases the activity of the reverse, EPM2AIP1 promoter. Examination of alternative role of the MLH1-93G>A polymorphism in MSI-H CRCs led to evaluation of a 500-kilobase pair chromosome 3 region around the MLH1 gene and identification of two additional SNPs, rs749072 and rs13098279, which are in strong linkage disequilibrium with rs1800734. All three SNPs showed strong associations with MLH1 promoter methylation, loss of MLH1 protein expression, and MSI-H CRCs in three populations, Ontario, Newfoundland, and Seattle. Such findings potentially implicate genetic susceptibility to DNA methylation. Logistic regression models for MSI-H versus non-MSI-H CRCs demonstrate that models including MLH1 IHC status and MLH1 promoter methylation status fit the data most parsimoniously in all three populations combined, however, when rs1800734/rs749072/rs13098279 was added to this model, polymorphisms no longer remained significant indicating that the observed associations of these polymorphisms with the MSI-H CRCs occur through their effect on DNA methylation. This study identified a novel mechanism in which common missense alterations may contribute to complex disease.
PCR-SSCP and Isoelectric Focusing as Screening Methods for Identification of (Sub-) Tropical Fish Species

Field: Agricultural and Biological Sciences (Life Sciences)

To ensure the authentication of fishery products lacking biological characters, rapid species identification methods are required. Two DNA- and protein-based methods, PCR-SSCP (polymerase chain reaction - single strand conformation polymorphism) of a 464 bp segment of the cytochrome b – gene and isoelectric focusing (IEF) of water-soluble proteins from fish fillets, were applied to identify fillets of (sub-) tropical fish species available on the European market. Among the samples analysed weretwo taxonomically identified species from the family Sciaenidae and one from Sphyraenidae. By comparison of DNA- and protein patterns of different samples, information about intra-species variability of patterns,and homogeneity of batches (e.g. fillet blocks or bags) can be obtained. PCR-SSCP and IEF may be useful for pre-checking of a large number of samples by food control laboratories.ZusammenfassungZur Sicherstellung der Authentizität von Fischerei-Erzeugnissen ohne biologische Merkmale sind schnelle Verfahren zur Speziesidentifizierung hilfreich. Zwei Methoden der DNA- bzw. Protein-Analyse wurden eingesetzt, um Filets (sub-) tropischer Fischarten, die auf dem europäischen Markt angeboten werden, zu identifizieren. Bei diesen Methoden handelt es sich um die PCR-SSCP (Polymerase-Kettenreaktion – Einzelstrang-Konformationspolymorphismus) – Analyse der PCR-Produkte und die IEF (isoelektrische Fokussierung) der wasserlöslichen Fischmuskelproteine. Unter den untersuchten Proben waren zwei taxonomisch bestimmte Arten aus der Familie Sciaenidae und eine Spezies aus der Familie Sphyraenidae. Durch Vergleich der DNA- bzw. Proteinmuster lassen sich Informationen über die intra-spezifische Variabilität solcher Muster und die Einheitlichkeit von Partien (beispielsweise Filetblöcke oder Filetbeutel) gewinnen. PCR-SSCP und IEF könnenin Laboratorien der Lebensmittelüberwachung als Vortest gerade bei hohen Probenzahlen sinnvoll eingesetzt werden.
Abstract 4903: AXL inhibition overcomes erlotinib resistance in AXL-activated non-small cell lung cancer cells

Field: Medicine (Health Sciences)

Abstract Mutations in the tyrosine kinase domain of epidermal growth factor receptor (EGFR) are present in 10-35% patients with NSCLC. In patients with EGFR-mutated NSCLC, EGFR tyrosine kinase inhibitors, including erlotinib, have demonstrated excellent initial responses. However, despite improved outcomes observed in patients treated with EGFR TKIs, most patients eventually develop drug resistance. We and others recently demonstrated that the activation of oncogene AXL is necessary to confers erlotinib resistance in both cell and mouse models as well as in human tumor tissues. While genetic aberrations affecting AXL appear rare, we recently identified two patients with EGFR-mutated lung cancer who simultaneously harbor AXL A273V or AXL V289M mutation. Both patients were resistant to erlotinib treatment (one case of primary and one case of acquired resistance). In this study, we first evaluated whether these AXL mutations conferred resistance to erlotinib treatment. Using HCC827 and PC-9 NSCLC cell lines stably expressing the AXL A273V or V289M mutation, we confirmed that AXL A273V significantly increased resistance to erlotinib treatment. Subsequently we also conducted a preclinical study to test if a new AXL inhibitor MGCD265 could overcome such erlotinib resistance in NSCLC cells. Using an in vitro MTS assay, we first validated that administration of MGCD265 in combination with erlotinib significantly inhibited the viability of erlotinib-resistant HCC827-ER cells, compared to erlotinib- or MGCD265-alone treatment. Through conducting an array of cell functional studies, we found that combination of MGCD265 and erlotinib significantly decreased cell cycle progression in S phase, enhanced apoptosis, and repressed cell migration relative to single-agent erlotinib or MGCD265 treatment in HCC827-ER cells. We further performed RNA-sequencing to evaluate the gene expression profile and the cellular pathways altered in cells treated with erlotinib alone, MGCD265 alone or a combination of erlotinib and MGCD265. RNA-sequencing analysis identified that several groups of genes involved in cell survival inhibition or apoptosis promotion were upregulated, whereas genes involved in cell cycle process, DNA replication or cancer metabolism were downregulated in cells treated with the combination of erlotinib and MGCD265. Taken together, our results indicated that AXL mutations may confer resistance to EGFR TKI treatment, and effective blockade of the AXL pathway may represent a novel strategy to overcome erlotinib resistance for the treatment of NSCLC patients. Citation Format: Feng Wang. AXL inhibition overcomes erlotinib resistance in AXL-activated non-small cell lung cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4903.
Isolation and characterization of bacterium with ACC deaminase activity and its effect on salt tolerance of eggplant

Field: Agricultural and Biological Sciences (Life Sciences)

A bacterium, named strain DW1 with 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, was isolated from saline soil in Shangyu, Zhejiang Province. Based on the results of phenotypic features, phylogenetic similarity of 16S rDNA gene sequences, DNA G+C content, strain DW1 was identified as Pseudomonas sp. The response of eggplant seeds and seedlings treated with strain DW1 to salt stress was assessed. The results show that strain DW1 was capable of promoting eggplant seed germination percentage and seedling root elongation compared with control. Interestingly, the strain DW1 significantly increased the fresh weights of eggplant seedlings in saline soil and slightly influenced the uptake of calcium ions while reduced the uptake of sodium ions. This may suggest strain DW1 can increase resistance in eggplant to salt stress.
Label-free in vivo imaging of Drosophila melanogaster by multiphoton microscopy

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

The fruit fly Drosophila melanogaster is one of the most valuable organisms in genetic and developmental biology studies. Drosophila is a small organism with a short life cycle, and is inexpensive and easy to maintain. The entire genome of Drosophila has recently been sequenced (cite the reference). These advantages make fruit fly an attractive model organism for biomedical researches. Unlike humans, Drosophila can be subjected to genetic manipulation with relative ease. Originally, Drosophila was mostly used in classical genetics studies. In the model era of molecular biology, the fruit fly has become a model organ for developmental biology researches. In the past, numerous molecularly modified mutants with well defined genetic defects affecting different aspects of the developmental processes have been identified and studied. However, traditionally, the developmental defects of the mutant flies are mostly examined in isolated fixed tissues which preclude the observation of the dynamic interaction of the different cell types and the extracellular matrix. Therefore, the ability to image different organelles of the fruit fly without extrinsic labeling is invaluable for Drosophila biology. In this work, we successfully acquire in vivo images of both developing muscles and axons of motor neurons in the three larval stages by using the minimially invasive imaging modality of multiphoton (SHG) microscopy. We found that while SHG imaging is useful in revealing the muscular architecture of the developing larva, it is the autofluorescence signal that allows label-free imaging of various organelles to be achieved. Our results demonstrate that multiphoton imaging is a powerful technique for investigation the development of Drosophila.
Supplemental Table 1. Supplemental Table 2. Supplemental Table 3. from Inhibition of ABCB1 Overcomes Cancer Stem Cell–like Properties and Acquired Resistance to MET Inhibitors in Non–Small Cell Lung Cancer

Field: Medicine (Health Sciences)

<p>Supplemental Table 1. Gene copy numbers of MET, EGFR and KRAS in EBC-1R cells Supplemental Table 2. MiRNAs correlated with the sensitivity to PHA665752 Supplemental Table 3. ABCB1 protein expression in 50 lung squamous cell cancer patientsã€€</p>
Techno-Globalism and Techno-Nationalism: an Interpretative Framework

Field: Social Sciences (Social Sciences)

This paper adopts a “geography of innovation” approach to test for France the hypothesis that patent activity within each administrative region is related to corporate expenditures in R&D in that territory, as well as research expenditures undertaken in universities located in the same area. It emerges that French manufacturing firms (both private and state-owned) benefit significantly from knowledge produced within the geographical area in which they are located, although the coefficient estimated for the university R&D variable is equally significant but higher than that for the industry R&D one. At the reginal level, university research therefore turns out to be the most crucial source of knowledge spillovers for the innovative activities of manufacturing firms.
Dual inoculation of peanut withGlomussp. andBradyrhizobiumsp. enhanced the symbiotic nitrogen fixation as assessed by15N-Technique

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract The response of peanut (Arachis hypogaea L.) to inoculation with vesicular-arbuscular mycorrhizal (VAM) fungi (Glomus etunicatum) and Bradyrhizobiurn sp. was studied in pots by the acetylene reduction activity (ARA) and ‘A-value’ methods. The soil used was a Light-coloured Andosol and the treatments consisted of the inoculation of VAM fungi only, inoculation of Bradyrhizobium only, dual inoculation of VAM fungi and Bradyrhizobium and control, under non-sterilized and sterilized soil conditions. In the non-sterilized soil the ARA and nitrogen fixation determined by the ‘A-value’ method increased significantly only by dual inoculation of VAM fungi and Bradyrhizobium at 100 days after planting (DAP), but no significant difference was observed at 70 DAP. In the case of dual inoculation, 75% of the nitrogen of the plant was derived from fixation whereas the plants inoculated only with Bradyrhizobium derived 68% of their nitrogen from fixation and the control plants, 64%. Amount of P in plant increased significantly only by dual inoculation with VAM fungi and Bradyrhizobium. In the sterilized soil a highly significant increase in the ARA was observed of the dual inoculation at all the sampling times. Nitrogen fixation determined by the A-value technique and N and P contents in plant also increased significantly by dual inoculation. Results obtained by the A-value method showed that plants with dual inoculation derived 68% of their nitrogen from fixation while the plants inoculated only with Bradyrhizobium, 38%. From our this study we conclude that nitrogen fixation as well as N and P contents in peanut increased significantly only by dual inoculation with VAM fungi and Bradyrhizobium.
Bone age is the best predictor of growth response to recombinant human growth hormone in Turner′s syndrome

Field: Medicine (Health Sciences)

Recombinant human growth hormone (rhGH) is approved for use in children with Turner's syndrome (TS) in most industrialized countries and is recommended in the recently issued guidelines. We determined the growth responses of girls who are treated with rhGH for TS, with an aim to identify the predictors of growth response.Fifty-six prepubertal girls with TS, documented by peripheral blood karyotype, were enrolled. All the patients received biosynthetic growth hormone therapy with a standard dose of 30 IU/m(2)/week. The calculated dose per week was divided for 6 days and given subcutaneously at night.This study showed that rhGH therapy provides satisfactory auxological results. Bone age delay is to be considered as a predictive factor which may negatively influence the effect of rhGH therapy on final height. The growth velocity in the preceding year is the most important predictor of rhGH therapy response.These observations help us to guide rhGH prescription, to reduce the risks and costs.
Adoption of Umar Bin Abdul Aziz's Principles of Social Justice and Welfare in the Start-up Business Ecosystem

Field: Business, Management and Accounting (Social Sciences)

This article examines the adaptability and application of Umar bin Abdul Aziz's social justice and welfare principles in modern startup business strategies. Umar bin Abdul Aziz is known as one of the fair leaders and focuses on the welfare of society. Through this approach, this article explores how startups can integrate these principles into their business models. This study contributes by providing an ethical framework for startups in Indonesia to not only focus on financial gain but also play an active role in promoting social justice and public welfare. This research is descriptive qualitative research. The sources used are secondary sources. The study uses documentation to find and collect elements or variables related to the study. The analysis method in this study uses descriptive qualitative analysis. The results show that the adoption of the principles of social justice and welfare of Umar bin Abdul Aziz in startup businesses shows that these values are very relevant. Startups can implement a profit-sharing system, establish partnerships with MSMEs, and implement CSR programs to improve community welfare. Financial transparency is also important to prevent corruption, while attention to the welfare of society by offering affordable products can strengthen their contribution to social justice. In this way, business startups gain an ethical framework that not only focuses on financial gain but also plays an active role in the welfare of society, so that public trust in startups can increase.
Auctions Versus Posted-Price Selling

Field: Economics, Econometrics and Finance (Social Sciences)

wo most popular selling methods -- posted-price selling and auctions -- are compared in this paper. We confirm the common belief that auctions are most often used when the distribution of the object's value is widely dispersed. The choice of selling methods usually depends on the costs of displaying, storing and auctioning. In the absence of auctioning costs, auctioning at every instant is optimal. The 'dispersion' of a distribution is then formally defined and developed. Using the definition of dispersion, we prove that auctions becomes preferable when a potential buyer's valuation becomes more dispersed. Finally, the optimization of a social planner is studied and we find that the monopoly seller's price can be higher or lower than that of the social optimum.
Modular Pore-Forming Immunotoxins with Caged Cytotoxicity\nTailored by Directed Evolution

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Immunotoxins are proteins containing\na cell-targeting element linked\nto a toxin that are under investigation for next-generation cancer\ntreatment. However, these agents are difficult to synthesize, chemically\nheterogeneous, expensive, and show toxicity toward healthy cells.\nIn this work, we describe the synthesis and characterization of a\nnew type of immunotoxin that showed exquisite selectivity toward\ntargeted cells. In our construct, targeting molecules were covalently\nattached or genetically fused to oligomeric pore-forming toxins. The\nactivity of the immunotoxin was then caged by fusing a soluble protein\nto the transmembrane domain and activated via cleavage with furin,\nwhich is a protease that is overexpressed in many cancer cells. During\nthe several coupling steps, directed evolution allowed the efficient\nsynthesis of the molecules in <i>E. coli</i> cells, as well\nas selection for further specificity toward targeted cells. The final\nconstruct showed no off-target activity, while acquiring an additional\ndegree of specificity toward the targeted cells upon activation. The\npore-forming toxins described here do not require internalization\nto operate, while the many protomeric subunits can be individually\nmodified to refine target specificity.