bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA-binding protein LIN28B inhibits apoptosis through regulation of the AKT2/FOXO3A/BIM axis in ovarian cancer cells
Authors: Lin Xiaojuan , Shen Jianfeng , Dan Peng  , He Xinhong , Xu Congjian , Chen Xiaojun , Tanyi Janos L. , Montone Kathleen , Fan Yi , Huang Qihong , Zhang Lin , Zhong Xiaomin 
Published: August 2018

AbstractLIN28B is an evolutionarily conserved RNA-binding protein that regulates mRNA translation and miRNA let-7 maturation in embryonic stem cells and developing tissues. Increasing evidence demonstrates that LIN28B is activated in cancer and serves as a critical oncogene. However, the underlying molecular mechanisms of LIN28B function in tumorigenesis are still largely unknown. Here we report that LIN28B was expressed in over half of the patients with epithelial ovarian cancer who were examined (n = 584). Functional experiments demonstrated that LIN28B inhibited ovarian cancer cell apoptosis. Furthermore, we showed that the proapoptotic factor BIM played an essential role in the antiapoptotic function of LIN28B. RNA-IP microarray analysis suggested that LIN28B binds to mRNAs that are associated with the DNA damage pathway, such as AKT2, in ovarian cancer cells. By binding to AKT2 mRNA and enhancing its protein expression, LIN28B regulated FOXO3A protein phosphorylation and decreased the transcriptional level of BIM, which antagonized the antiapoptosis activity of LIN28B. Taken together, these results mechanistically linked LIN28B and the AKT2/FOXO3A/BIM axis to the apoptosis pathway. The findings may have important implications in the diagnosis and therapeutics of ovarian cancer.
Runx-dependent and silencer-independent repression of a maturation enhancer in the Cd4 gene
Authors: Kojo Satoshi , Yasmin Nighat , Muroi Sawako , Tenno Mari , Taniuchi Ichiro 
Published: August 2018

AbstractAn intronic silencer, S4, in the Cd4 gene has been shown to be responsible for the helper-lineage-specific expression of CD4; S4 requires Runx complex binding to exert its silencer function against the enhancer-mediated Cd4 activation by modulating the epigenetic state of the Cd4 gene. Here we identify a late-acting maturation enhancer. Bcl11b plays essential roles for activation of both the early-acting proximal enhancer and maturation enhancer of Cd4. Notably, Runx complexes suppress these enhancers by distinct mechanisms. Whereas repression of the proximal enhancer depends on the S4 silencer, the maturation enhancer is repressed by Runx in the absence of S4. Moreover, ThPOK, known to antagonize S4-mediated Cd4 repression, assists Runx complexes to restrain maturation enhancer activation. Distinct modes of S4 silencer action upon distinct enhancers thus unravel a pathway that restricts CD4 expression to helper-lineage cells by silencer-independent and Runx-dependent repression of maturation enhancer activity in cytotoxic-lineage cells.
Anomalous twin boundaries in two dimensional materials
Authors: Rooney A. P. , Li Z. , Zhao W. , Gholinia A. , Kozikov A. , Auton G. , Ding F. , Gorbachev R. V. , Young R. J. , Haigh S. J. 
Published: August 2018

AbstractTwin boundary defects form in virtually all crystalline materials as part of their response to applied deformation or thermal stress. For nearly six decades, graphite has been used as a textbook example of twinning with illustrations showing atomically sharp interfaces between parent and twin. Using state-of-the-art high-resolution annular dark-field scanning transmission electron microscopy, we have captured atomic resolution images of graphitic twin boundaries and find that these interfaces are far more complex than previously supposed. Density functional theory calculations confirm that the presence of van der Waals bonding eliminates the requirement for an atomically sharp interface, resulting in long-range bending across multiple unit cells. We show these remarkable structures are common to other van der Waals materials, leading to extraordinary microstructures, Raman-active stacking faults, and sub-surface exfoliation within bulk crystals.
Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea
Authors: Basu Udita , Srivastava Rishi , Bajaj Deepak , Thakro Virevol , Daware Anurag , Malik Naveen , Upadhyaya Hari D. , Parida Swarup K. 
Published: August 2018

AbstractWe discovered 2150desiand 2199kabuliaccessions-derived SNPs by cultivar-wise individual assembling of sequence-reads generated through genotyping-by-sequencing of 92 chickpea accessions. Subsequent large-scale validation and genotyping of these SNPs discovered 619desiaccessions-derived (DAD) SNPs, 531kabuliaccessions-derived (KAD) SNPs, 884 multiple accessions-derived (MAD) SNPs and 1083 two accessions (desiICC 4958 andkabuliCDC Frontier)-derived (TAD) SNPs that were mapped on eight chromosomes. These informative SNPs were annotated in coding/non-coding regulatory sequence components of genes. The MAD-SNPs were efficient to detect high intra-specific polymorphic potential and wide natural allelic diversity level including high-resolution admixed-population genetic structure and precise phylogenetic relationship among 291desiandkabuliaccessions. This signifies their effectiveness in introgression breeding and varietal improvement studies targeting useful agronomic traits of chickpea. Six trait-associated genes with SNPs including quantitative trait nucleotides (QTNs) in combination explained 27.5% phenotypic variation for seed yield per plant (SYP). A pentatricopeptide repeat (PPR) gene with a synonymous-coding SNP/QTN significantly associated with SYP trait was found most-promising in chickpea. The essential information delineated can be of immense utility in genomics-assisted breeding applications to develop high-yielding chickpea cultivars.
Rapid coupling between gravitational forces and the transcriptome in human myelomonocytic U937 cells
Authors: Thiel Cora S. , Tauber Svantje , Christoffel Swantje , Huge Andreas , Lauber Beatrice A. , Polzer Jennifer , Paulsen Katrin , Lier Hartwin , Engelmann Frank , Schmitz Burkhard , Schütte Andreas , Raig Christiane , Layer Liliana E. , Ullrich Oliver 
Published: August 2018

AbstractThe gravitational force has been constant throughout Earth’s evolutionary history. Since the cell nucleus is subjected to permanent forces induced by Earth’s gravity, we addressed the question, if gene expression homeostasis is constantly shaped by the gravitational force on Earth. We therefore investigated the transcriptome in force-free conditions of microgravity, determined the time frame of initial gravitational force-transduction to the transcriptome and assessed the role of cation channels. We combined a parabolic flight experiment campaign with a suborbital ballistic rocket experiment employing the human myelomonocytic cell line U937 and analyzed the whole gene transcription by microarray, using rigorous controls for exclusion of effects not related to gravitational force and cross-validation through two fully independent research campaigns. Experiments with the wide range ion channel inhibitor SKF-96365 in combination with whole transcriptome analysis were conducted to study the functional role of ion channels in the transduction of gravitational forces at an integrative level. We detected profound alterations in the transcriptome already after 20 s of microgravity or hypergravity. In microgravity, 99.43% of all initially altered transcripts adapted after 5 min. In hypergravity, 98.93% of all initially altered transcripts adapted after 75 s. Only 2.4% of all microgravity-regulated transcripts were sensitive to the cation channel inhibitor SKF-96365. Inter-platform comparison of differentially regulated transcripts revealed 57 annotated gravity-sensitive transcripts. We assume that gravitational forces are rapidly and constantly transduced into the nucleus as omnipresent condition for nuclear and chromatin structure as well as homeostasis of gene expression.
Prescription pattern of alpha-blockers for management of lower urinary tract symptoms/benign prostatic hyperplasia
Authors: Moon Hyong Woo , Yang Jong Hyup , Choi Jin Bong , Bae Woong Jin , Cho Hyuk Jin , Hong Sung-Hoo , Lee Ji Youl , Kim Sae Woong , Park Sang-Hyun , Han Kyungdo , Ha U-Syn 
Published: August 2018

AbstractThis study investigated trends in the prescription of α-blockers for patients with BPH, focusing on changing patterns of prescriptions during 2002–2013 using National Health Insurance Service-National Sample Cohort data. A total of 65,596 Korean males over 50 years old diagnosed with BPH were identified from the NHIS-NSC database between 2002–2013. Patterns of each α -blocker prescription were analyzed and persistence rate, switch rate, and return rate during a follow-up period of 3 years after the first prescription were calculated. A total of 28,318 men over 50 years old (64.95 ± 9.12), changed medication within six months following the first prescription of α -blocker. (1) Tamsulosin showed the highest persistence rate when compared with other α-blockers (2) Among patients who switched to a second α-blocker, tamsulosin showed the highest return rate when compared with other α-blockers. Tamsulosin has been the most commonly prescribed α1-blocker since the mid-2000s, in line with its demonstrated highest persistence and return rates. These data probably reflect patient satisfaction with α1-blockers in the management of BPH, in which the decision to stop and switch pharmacological treatments is primarily based on changes in symptoms or side effects.
TiHo-0906: a new feline mammary cancer cell line with molecular, morphological, and immunocytological characteristics of epithelial to mesenchymal transition
Authors: Granados-Soler José Luis , Junginger Johannes , Hewicker-Trautwein Marion , Bornemann-Kolatzki Kirsten , Beck Julia , Brenig Bertram , Betz Daniela , Schille Jan Torben , Murua Escobar Hugo , Nolte Ingo 
Published: August 2018

AbstractFeline mammary carcinomas (FMCs) with anaplastic and malignant spindle cells histologically resemble the human metaplastic breast carcinoma (hMBC), spindle-cell subtype. hMBCs display epithelial-to-mesenchymal transition (EMT) characteristics. Herein we report the establishment and characterization of a cell line (TiHoCMglAdcar0906; TiHo-0906) exhibiting EMT-like properties derived from an FMC with anaplastic and malignant spindle cells. Copy-number variations (CNVs) by next-generation sequencing and immunohistochemical characteristics of the cell line and the tumour were compared. The absolute qPCR expression of EMT-related markers HMGA2 and CD44 was determined. The growth, migration, and sensitivity to doxorubicin were assessed. TiHo-0906 CNVs affect several genomic regions harbouring known EMT-, breast cancer-, and hMBCs-associated genes as AKT1, GATA3, CCND2, CDK4, ZEB1, KRAS, HMGA2, ESRP1, MTDH, YWHAZ, and MYC. Most of them were located in amplified regions of feline chromosomes (FCAs) B4 and F2. TiHo-0906 cells displayed an epithelial/mesenchymal phenotype, and high HMGA2 and CD44 expression. Growth and migration remained comparable during subculturing. Low-passaged cells were two-fold more resistant to doxorubicin than high-passaged cells (IC50: 99.97 nM, and 41.22 nM, respectively). The TiHo-0906 cell line was derived from a poorly differentiated cellular subpopulation of the tumour consistently displaying EMT traits. The cell line presents excellent opportunities for studying EMT on FMCs.
A Simple Method to Obtain Basic Acoustic Measures From Video Recordings as Subtitles
Authors: Kumar S. Pravin , Švec Jan G. 
Published: August 2018

Purpose

Sound pressure level (SPL) and fundamental frequency (f
o
) are very basic and important measures in the acoustical assessment of voice quality, and their variation influences also the vocal fold vibration characteristics. Most sophisticated laryngeal videostroboscopic systems therefore also measure and display the SPL and f
o
values directly over the video frames by means of a rather expensive special hardware setup. An alternative simple software-based method is presented here to obtain these measures as video subtitles.

Method

The software extracts acoustic data from the video recording, calculates the SPL and f
o
parameters, and saves their values in a separate subtitle file. To ensure the correct SPL values, the microphone signal is calibrated beforehand with a sound level meter.

Results

The new approach was tested on videokymographic recordings obtained laryngoscopically. The results of SPL and f
o
values calculated from the videokymographic recording, subtitles creation, and their display are presented.

Conclusions
This method is useful in integrating the acoustic measures with any kind of video recordings containing audio data when inbuilt hardware means are not available. However, calibration and other technical aspects related to data acquisition and synchronization described in this article should be properly taken care of during the recording.
Franck–Condon picture of incoherent neutron scattering
Authors: Kneller Gerald R. 
Published: August 2018

Significance
Despite the long history of neutron scattering studies on complex condensed matter systems, there is still a need for appropriate analysis concepts beyond the classical Van Hove theory, which is commonly used to interpret the experimental spectra in terms of trajectory-based dynamical models. The approach presented in this paper, which is based on quantum mechanical transition rather than on classical displacement probabilities, accounts by construction for the scattering kinematics and opens perspectives for the interpretation of quasielastic neutron scattering experiments from complex systems.
Transcategoriality and right periphery
Authors: Hancil Sylvie 
Published: August 2018

Abstract
Among the various syntactic functions that transcategorial but can take, it is the final particle that is the focus of our attention. As it is a characteristic feature of Northern English colloquial conversations, the semantic-pragmatic analysis is pursued in the spoken section of the Scottish Corpus of Texts and Speech. Moreover, particular attention is paid to the relationship between final but and information structure in order to account for the strategy of organizing information. In addition, it is shown that its status as a post-rheme element, which takes into account the position of this particle, does not pay tribute to its main function of textual cohesion. Finally, its potential status as an Antitopic is discussed.
Accounting for transcategorial morphemes
Authors: Nemo François , Horchani Binène 
Published: August 2018

AbstractThe article presents a morphemic account of transcategoriality, with detailed illustrations (e.g. Englishbutandeven, Frenchencore,tout, meme, Latin to French morpheme /tant/) of the approach. After making explicit the paradigmatic differences between exoskeletal and endoskeletal approaches, and showing that ultimately it can be summarized in terms of existence or not of grammar-free morphemes becoming lexemes through grammatical and contextual insertion, it turns to the issue of knowing what an exoskeletal non-categorial meaning can be. It introduces at this stage the notion of fractality, before making explicit and detailing the method which allows isolation of a morpheme’s indicational semantics. The whole approach is finally illustrated with the study of the whole distribution of French /tant/, first semantically in synchrony before extending the tests to Latin data, showing that polysemy, transcategoriality and plurisemy are various forms of the same issue.
Study on three major effects and guarantee system for quality management of edible mushroom products
Authors: Zhou L , Guo S , Shu M , Liang L , Li Y 
Published: August 2018

Abstract
In order to provide consumers with more safe and edible fungus products and to create a faithful social environment of food quality, the edible fungus products quality safety events, as well as their evoked factors and effects on edible fungus industry were discussed in depth in this paper. The performance of edible fungus products quality management is a comprehensive reflection of technical effect, control effect and implementation effect. Among them, the implementation effect is the most important, which refers to the actual implementation effect of quality and safety rules by practitioners of edible fungus industry. Thus, the initiative implementation effect in quality management will be improved, and a quality assurance system in which practitioners are volunteered to participate and implement initiatively the quality standards and regulations so as to provide safe and high-quality products will be established, thereby achieving the best actual implementation effect in quality management.
Can Intraindividual Variability in Cognitive Speed Be Reduced by Physical Exercise? Results From the LIFE Study
Authors: Bielak Allison A M , Brydges Christopher R 
Published: August 2018

Abstract

Objectives
Findings are mixed regarding the potential to improve older adults’ cognitive ability via training and activity interventions. One novel sensitive outcome may be intraindividual variability (IIV) in cognitive speed, or moment-to-moment changes in a person’s performance. The present article evaluated if participants who participated in a moderate physical activity intervention showed a reduction in IIV, compared with a successful aging education control group.

Method
For approximately 2.6 years, sedentary adults aged 70–90 years participated in the Lifestyle Interventions and Independence for Elders (LIFE) Study (n = 1,635), a multisite Phase 3 randomized controlled trial to reduce major mobility disability. They completed 4 reaction time tests at baseline and at approximately 24 months post-test.

Results
Analyses were conducted following both the intent-to-treat principle and complier average casual effect modeling. Results indicated that participants in the physical activity group did not show a reduction in their IIV.

Discussion
The lack of a significant reduction in IIV may be due to the mild nature of the physical activity program and the cognitively healthy sample. It is also possible that other types of lifestyle activity interventions (e.g., social and cognitive engagement) can elicit reductions in IIV for older adults.
Prediction of delayed mortality using vitality scores and reflexes, as well as catch, processing, and post-release conditions: evidence from discarded flatfish in the Western Baltic trawl fishery
Authors: Kraak S B M , Velasco A , Fröse U , Krumme U 
Published: August 2018

Abstract
The EU discard ban and its high-survival exemption exposed our lack of scientific evidence on discard survival in the fisheries. Discard survival is known to be highly variable and influenced by numerous factors, including conditions during the catch, on-board the fishing vessels, and post-discard. Therefore, obtaining unambiguous results in discard survival experiments is challenging. We conducted the first systematic year-round discard survival study of flatfish in the Western Baltic Sea on-board a commercial stern trawler under realistic fishing conditions (13 monthly hauls from May 2015 to May 2016) to test whether delayed mortality can be predicted by vitality scores and reflex action mortality predictor (RAMP) scores in combination with variable conditions during catch, processing, and post-release. The factors vessel type, gear, haul duration, fishing ground, depth, handling time, and processing procedures were kept constant as much as possible. On-board, live individual flatfish were tested for vitality and the presence of reflexes for RAMP, then “discarded” and kept in cages on the bottom of the seafloor for about a week after which the delayed mortality was determined. The proportions of “discarded” plaice, flounder, and dab that were dead after being kept in the cages ranged from 5% to 100%, 0% to 96%, and 33% to 100%, respectively. Higher mortalities occurred in summer-autumn when air and water temperatures were higher, catches smaller, and catches contained smaller proportions of roundfish. Relationships between RAMP scores and mortality probabilities varied substantially across the monthly trials. Indeed, in addition to RAMP or vitality scores and individual reflexes, the factors air and water temperature and catch weight and catch composition were significant in logistic GLMs explaining delayed mortality. Cross-validations indicated that delayed mortality could be predicted by these models with a reasonable accuracy. Nevertheless, the presence of possible confounding effects calls for caution in inferring causality and extrapolating the conclusions on predictability.
Pricing American Options under High-Dimensional Models with Recursive Adaptive Sparse Expectations*
Authors: Scheidegger Simon , Treccani Adrien 
Published: August 2018

AbstractWe introduce a novel numerical framework for pricing American options in high dimensions. Our scheme manages to alleviate the problem of dimension scaling through the use of adaptive sparse grids. We approximate the value function with a low number of points and recursively apply fast approximations of the expectation operator from an exercise period to the previous period. Given that available option databases gather several thousands of prices, there is a clear need for fast approaches in empirical work. Our method processes an entire cross section of options in a single execution and offers an immediate solution to the estimation of hedging coefficients through finite differences. It thereby brings valuable advantages over Monte Carlo simulations, which are usually considered to be the tool of choice in high dimensions, and satisfies the need for fast computation in empirical work with current databases containing thousands of prices. We benchmark our algorithm under the canonical model of Black and Scholes and the stochastic volatility model of Heston, the latter in the presence of discrete dividends. We illustrate the massive improvement of complexity scaling over dense grids with a basket option study including up to eight underlying assets. We show how the high degree of parallelism of our scheme makes it suitable for deployment on massively parallel computing units to scale to higher dimensions or further speed up the solution process.