bluuebunny/crossref_metadata_2025_split huggingface dataset:
HDAC1 and Klf4 interplay critically regulates human myeloid leukemia cell proliferation
Authors: Huang Y , Chen J , Lu C , Han J , Wang G , Song C , Zhu S , Wang C , Li G , Kang J , Wang J 
Published: October 2014

AbstractAcute myeloid leukemia (AML) is recognized as a complex disease of hematopoietic stem cell disorders, but its pathogenesis mechanisms, diagnosis, and treatment remain unclear. General histone deacetylase (HDAC) inhibitors have been used in blood cancers including AML, but the lack of gene specificity greatly limits their anti-cancer effects and clinical applications. Here, we found that HDAC1 expression was negatively correlated with that of Krüppel-like factor 4 (Klf4) and that AML patients with lower HDAC1 level had better prognosis. Further, knockdown of HDAC1 in leukemia cells K562, HL-60, and U937 significantly increased Klf4 expression and inhibited cell cycle progression and cell proliferation, similar results were found for HDAC inhibitors (VPA and mocetinostat). Moreover, overexpression or knockdown of Klf4 could markedly block the effects of HDAC1 overexpression or knockdown on leukemia cells in vitro and in vivo, respectively. Mechanistic analyses demonstrated that HDAC1 and Klf4 competitively bound to the promoter region of Klf4 and oppositely regulated Klf4 expression in myeloid leukemia. We identified HDAC1 as a potential specific target for repressing cell proliferation and inducing cell cycle arrest through interplay and modulation of Klf4 expression, suggests that HDAC1 and Klf4 are potential new molecular markers and targets for clinical diagnosis, prognosis, and treatment of myeloid leukemia.
Pro-oxidant/antioxidant balance controls pancreatic β-cell differentiation through the ERK1/2 pathway
Authors: Hoarau E , Chandra V , Rustin P , Scharfmann R , Duvillie B 
Published: October 2014

AbstractDuring embryogenesis, the intrauterine milieu affects cell proliferation, differentiation, and function by modifying gene expression in susceptible cells, such as the pancreatic β-cells. In this limited energy environment, mitochondrial dysfunction can lead to overproduction of reactive oxygen species (ROS) and to a decline in β-cell function. In opposition to this toxicity, ROS are also required for insulin secretion. Here we investigated the role of ROS in β-cell development. Surprisingly, decreasing ROS production in vivo reduced β-cell differentiation. Moreover, in cultures of pancreatic explants, progenitors were highly sensitive to ROS stimulation and responded by generating β-cells. ROS enhanced β-cell differentiation through modulation of ERK1/2 signaling. Gene transfer and pharmacological manipulations, which diminish cellular ROS levels, also interfered with normal β-cell differentiation. This study highlights the role of the redox balance on β-cell development and provides information that will be useful for improving β-cell production from embryonic stem cells, a step in cell therapy for diabetes.
Polycomb protein EZH2 suppresses apoptosis by silencing the proapoptotic miR-31
Authors: Zhang Q , Padi S K R , Tindall D J , Guo B 
Published: October 2014

AbstractEnhancer of zeste homolog 2 (EZH2) is the catalytic subunit of the polycomb repressive complex 2 and suppresses gene expression by catalyzing histone H3 methylation on lysine 27. EZH2 is overexpressed in metastatic prostate cancer and has been shown to promote cell proliferation and metastasis. Here we show that EZH2 also suppresses prostate cancer apoptosis by coordinating the epigenetic silencing of two proapoptotic microRNAs (miRNA), miR-205 and miR-31. We previously reported that miR-205 promotes apoptosis by targeting antiapoptotic protein Bcl-w and miR-205 is silenced in prostate cancer through promoter methylation. In this study, we found that EZH2 suppresses miR-31 expression by trimethylation of lysine 27 on histone 3 on the miR-31 promoter. SiRNA knockdown of EZH2 increased miR-31 expression and decreased the antiapoptotic protein E2F6 (E2F transcription factor 6) (a target of miR-31), resulting in the sensitization of prostate cancer cells to docetaxel-induced apoptosis. Conversely, overexpression of EZH2 blocked docetaxel-induced apoptosis. We further demonstrated that miR-205 silencing is linked to miR-31 silencing through EZH2. Suppression of miR-205 with an miRNA inhibitor caused an increase of EZH2 protein, which in turn inhibited miR-31 expression. Conversely, overexpression of miR-205 decreased EZH2 protein and increased miR-31 expression. In paired human prostate cancer specimens and adjacent normal tissues, we observed that the decrease of miR-205 expression correlated with EZH2 overexpression and miR-31 silencing. Thus, EZH2 integrates the epigenetic silencing of miR-205 and miR-31 to confer resistance to chemotherapy-induced apoptosis.
Arrest defective 1 regulates the oxidative stress response in human cells and mice by acetylating methionine sulfoxide reductase A
Authors: Shin S-H , Yoon H , Chun Y-S , Shin H-W , Lee M-N , Oh G T , Park J-W 
Published: October 2014

AbstractMethionine sulfoxide reductase A (MSRA) protects proteins from oxidation, and also helps remove reactive oxygen species (ROS) by recovering antioxidant enzymes inactivated by oxidation. Although its functions have been investigated extensively, little is known about the mechanism by which MSRA is regulated. Arrest defective 1 (ARD1) is an enzyme that catalyzes not only N-terminal acetylation as a cotranslational modification but also lysine acetylation as a posttranslational modification. ARD1, which is expressed in most cell types, is believed to participate in diverse biological processes, but its roles are poorly understood. Given that MSRA was hunted in a yeast two-hybrid screen with ARD1 as the bait, we here investigated whether ARD1 is a novel regulator of MSRA. ARD1 was shown to interact with and acetylate MSRA in both cells and test tubes. It specifically acetylated the K49 residue of MSRA, and by doing so repressed the enzymatic function of MSRA. ARD1 increased cellular levels of ROS, carbonylated proteins and DNA breaks under oxidative stress. Moreover, it promoted cell death induced by pro-oxidants, which was attenuated in MSRA-deficient cells. When mice were exposed to hyperoxic conditions for 2 days, their livers and kidneys were injured and protein carbonylation was increased. The oxidative tissue injury was more severe in ARD1 transgenic mice than in their wild-type littermates. In conclusion, ARD1 has a crucial role in the cellular response to oxidative stress as a bona fide regulator of MSRA. ARD1 is a potential target for ameliorating oxidative injury or for potentiating ROS-producing anticancer agents.
Bottom‐inlet‐type micro‐electro‐mechanical system acoustic sensors based on two polyimide/amorphous‐Si sacrificial layers
Authors: Lee Jaewoo , Je Changhan , Kim Yi‐Gyeong , Lee Sung Q , Yang Woo‐Seok , Lee Sang‐Gug 
Published: October 2014

A bottom‐inlet‐type micro‐electro‐mechanical system acoustic sensor based on two polyimide/a‐Si sacrificial layers is presented. A diaphragm was adapted to be on the top side of the sacrificial layers, showing the bottom‐inlet structure for the package, which has the sensitivity of more than 3 dB compared with that of the top‐inlet type. Also, the fundamental CMOS process implemented with Al electrodes was applied to have simple releasing steps by O2 ashing and XeF2 isotropic etching because of their material etching selectivity. The sensor module had a sensitivity of −38.9 dBV/Pa at 1 kHz with a bias of 9.2 V in the sweep range from 100 Hz to 16 kHz. In addition, to evaluate the open‐circuit sensitivity, structure‐based equivalent circuit modelling was performed with lumped parameters. The modelled sensitivity was in good agreement with the measured sensitivity in the error rate of 4.3% under 8 kHz, demonstrating the validity of the modelling. The modelled open‐circuit sensitivity was determined to be −37.2 dBV/Pa at 1 kHz using the proposed lumped model.
Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing
Authors: Lee Mei-Chong Wendy , Lopez-Diaz Fernando J. , Khan Shahid Yar , Tariq Muhammad Akram , Dayn Yelena , Vaske Charles Joseph , Radenbaugh Amie J. , Kim Hyunsung John , Emerson Beverly M. , Pourmand Nader 
Published: October 2014

Significance
Tumor cells are heterogeneous, and much variation occurs at the single-cell level, which may contribute to therapeutic response. Here, we studied drug resistance dynamics in a model of tolerance with a metastatic breast cancer cell line by leveraging the power of single-cell RNA-Seq technology. Drug-tolerant cells within a single clone rapidly express high cell-to-cell transcript variability, with a gene expression profile similar to untreated cells, and the population reacquires paclitaxel sensitivity. Our gene expression and single nucleotide variants analyses suggest that equivalent phenotypes are achieved without relying on a unique molecular event or fixed transcriptional programs. Thus, transcriptional heterogeneity might ensure survival of cancer cells with equivalent combinations of gene expression programs and/or single nucleotide variants.
Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis
Authors: Lohman Danielle C. , Forouhar Farhad , Beebe Emily T. , Stefely Matthew S. , Minogue Catherine E. , Ulbrich Arne , Stefely Jonathan A. , Sukumar Shravan , Luna-Sánchez Marta , Jochem Adam , Lew Scott , Seetharaman Jayaraman , Xiao Rong , Wang Huang , Westphall Michael S. , Wrobel Russell L. , Everett John K. , Mitchell Julie C. , López Luis C. , Coon Joshua J. , Tong Liang , Pagliarini David J. 
Published: October 2014

Significance
Coenzyme Q (CoQ) is a requisite component of the mitochondrial oxidative phosphorylation machinery that produces more than 90% of cellular ATP. Despite the discovery of CoQ more than 50 years ago, many aspects of its biosynthesis remain obscure. These include the functions of uncharacterized CoQ-related proteins whose disruption can cause human diseases. Our work reveals that one such protein, COQ9, is a lipid-binding protein that enables CoQ biosynthesis through its physical and functional interaction with COQ7, and via its stabilization of the entire CoQ biosynthetic complex. Unexpectedly, COQ9 achieves these functions by repurposing an ancient bacterial fold typically used for transcriptional regulation. Collectively, our work adds new insight into a core component of the CoQ biosynthesis process.
Monitoring the enzyme expression in a respiratory chain of Corynebacterium glutamicum in a copper ion-supplemented culture medium
Authors: Kusumoto Tomoichirou , Aoyagi Makoto , Sugiyama Takahiko , Sakamoto Junshi 
Published: October 2014

Abstract
Corynebacterium glutamicum has a branched respiratory chain: one of the branches is cytochrome bcc complex and cytochrome aa3-type cytochrome c oxidase, and the other is cytochrome bd-type menaquinol oxidase. The factors that influence the expression patterns of these respiratory enzymes remain unclear. To investigate the expressional control mechanism of the enzymes, we have previously constructed a promoter assay system utilizing enhanced green fluorescence protein. Here, we monitored respiratory enzymes’ expression by using this system during growth in various culture media, with and without Cu2+ ion supplementation. The promoter activities of cytochrome aa3 oxidase in the early stationary phase in the media supplemented with Cu2+ ion at 40 or 400 μM were significantly increased 1.49-fold or 1.99-fold, respectively, as compared to the control. Moreover, the H+/O ratio, or the proton-pumping activity of the cells, increased about 1.6 times by the Cu2+ supplementation. These facts indicate that copper ions can switch the branches.
Evaluation of Hydrogenated Soybean Oil in Feeds for Hybrid Striped Bass Fed in Conjunction with Finishing Periods of Different Durations
Authors: Kanczuzewski Kenson , Trushenski Jesse T 
Published: October 2014

Abstract
We evaluated the production performance and tissue composition of hybrid striped bass, i.e., sunshine bass (female White Bass Morone chrysops × male Striped Bass M. saxatilis (initial weight = 110.6 g) raised to a marketable size (final weight = 575 g) on grow-out feeds containing graded levels of fish oil and hydrogenated soybean oil (100% fish oil, 50% fish oil and 50% soybean oil, 25% fish oil and 75% soybean oil, or 100% soybean oil) in conjunction with finishing periods of different durations (4, 8, or 12 weeks of feeding the 100% fish oil feed prior to harvest). Production performance varied significantly among the feeding regimens, but none of the experimental groups were significantly different from the 100% fish oil control group. However, performance tended to follow fish oil consumption, with regimens providing more fish oil during grow-out yielding marginally superior growth and growth efficiency. Fillet fatty acid profiles varied considerably among the regimens prior to finishing. Fillets of fish fed diets containing increasing amounts of hydrogenated soybean oil contained more monounsaturated fatty acids (18:1[n-9]) and (n-6) and fatty acids (18:2[n-6]) and less long-chain polyunsaturated fatty acids and (n-3) fatty acids (20:5[n-3] and 22:6[n-3]). Despite major differences in dietary levels of saturated fatty acids (SFAs), fillet levels of SFAs did not vary appreciably. Profile differences arising during grow out were reversed by finishing, to a greater or lesser extent, depending on the magnitude of prefinishing profile distortion and the duration of the finishing period. Utilization of hydrogenated soybean oil merits further consideration and research, but our results suggest that this feedstuff has value as a supplemental lipid source, if not a complete fish oil substitute, in feeds for hybrid striped bass.
Climate Change: A Very Short Introduction
Authors: Maslin Mark 
Published: October 2014

Abstract
Climate change is still, arguably, the most critical and controversial issue facing the world in the twenty-first century. Previously published as Global Warming: A Very Short Introduction, the new title of this VSI reflects an important change in the terminology of the last decade. Climate Change: A Very Short introduction includes crucial updates from the last few years, including the results of the 2013 IPCC Fifth Assessment Report, the effects of ocean acidification, and the impact of changes to global population and health. Exploring all of the key topics in the debate, it makes sense of the complexities climate change involves, from political and social issues to environmental and scientific. Looking at the predicted impacts of climate change, it explores all of the controversies, and also explains the various proposed solutions.
A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data
Authors: Coil David , Jospin Guillaume , Darling Aaron E. 
Published: October 2014

Motivation: Open-source bacterial genome assembly remains inaccessible to many biologists because of its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina data.
Results: A5-miseq can produce high-quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation and includes several improvements to read trimming. Together, these changes result in substantially improved assemblies that recover a more complete set of reference genes than previous methods.
Availability: A5-miseq is licensed under the GPL open-source license. Source code and precompiled binaries for Mac OS X 10.6+ and Linux 2.6.15+ are available from http://sourceforge.net/projects/ngopt
Contact: aaron.darling@uts.edu.au
Supplementary information: Supplementary Data are available at Bioinformatics online.
A model for the expression of gap genes based on the Jeffreys-type equation
Authors: Gula Igor A. , Samsonov Alexander M. 
Published: October 2014

Motivation: We propose the third-order model equation of the Jeffreys type for concentrations of gap gene proteins in order to take into account particle inertia. Gap genes are responsible for formation of body segments in Drosophila melanogaster embryo during its early development. Usually the expression of the genes is described by the model of protein transport based on conventional diffusion equation. However, the model is known to govern the Brownian (non-inertial) motion of particles; hence, it is hardly applicable to the description of protein transport.
Results: Analysis of the Jeffreys-type equation results in the necessary condition for the problem to be well-posed. Application of the Jeffreys-type equation with non-linear terms to description of the dynamics of gap gene network demonstrates better fitting to experimental data than the conventional model.
Availability and implementation: Implementation of solver algorithms and the software are freely available from: https://github.com/wswgG/solver-for-the-Jeffreys-type-equations-system
Contact: gula@mail.ioffe.ru
Supplementary information: Supplementary Data are available at Bioinformatics online.
DANN: a deep learning approach for annotating the pathogenicity of genetic variants
Authors: Quang Daniel , Chen Yifei , Xie Xiaohui 
Published: October 2014

Summary: Annotating genetic variants, especially non-coding variants, for the purpose of identifying pathogenic variants remains a challenge. Combined annotation-dependent depletion (CADD) is an algorithm designed to annotate both coding and non-coding variants, and has been shown to outperform other annotation algorithms. CADD trains a linear kernel support vector machine (SVM) to differentiate evolutionarily derived, likely benign, alleles from simulated, likely deleterious, variants. However, SVMs cannot capture non-linear relationships among the features, which can limit performance. To address this issue, we have developed DANN. DANN uses the same feature set and training data as CADD to train a deep neural network (DNN). DNNs can capture non-linear relationships among features and are better suited than SVMs for problems with a large number of samples and features. We exploit Compute Unified Device Architecture-compatible graphics processing units and deep learning techniques such as dropout and momentum training to accelerate the DNN training. DANN achieves about a 19% relative reduction in the error rate and about a 14% relative increase in the area under the curve (AUC) metric over CADD’s SVM methodology.
Availability and implementation: All data and source code are available at https://cbcl.ics.uci.edu/public_data/DANN/.
Contact: xhx@ics.uci.edu
Linear spectropolarimetry: a new diagnostic tool for the classification and characterization of asteroids
Authors: Bagnulo S. , Cellino A. , Sterzik M. F. 
Published: October 2014

Abstract
We explore the use of spectropolarimetry as a remote sensing tool for asteroids in addition to traditional reflectance measurements. In particular, we are interested in possible relationships between the wavelength-dependent variation of linear polarization and the properties of the surfaces, including albedo and composition. We have obtained optical spectropolarimetric measurements of a dozen asteroids of different albedo and taxonomic classes and of two small regions at the limb of the Moon. We found that objects with marginally different relative reflectance spectra (in the optical) may have totally different polarization spectra. This suggests that spectropolarimetry may be used to refine the classification of asteroids. We also found that in some cases the Umov law may be violated, that is, in contrast to what is expected from basic physical considerations, the fraction of linear polarization and the reflectance may be positively correlated. In agreement with a few previous studies based on multicolour broad-band polarimetry, we found that the variation of linear polarization with wavelength and with phase-angle is correlated with the albedo and taxonomic class of the objects. Finally, we have serendipitously discovered that spinel-rich asteroid (599) Luisa, located very close to the Watsonia family, is a member of the rare class of Barbarian asteroids. We suggest that future modelling attempts of the surface structure of asteroids should be aimed at explaining both reflectance and polarization spectra.
Deciphering the genetic and transcriptional basis of cross-stress responses inEscherichia coliunder complex evolutionary scenarios
Authors: Zorraquino-Salvo Violeta , Quinones-Soto Semarhy , Kim Minseung , Rai Navneet , Tagkopoulos Ilias 
Published: October 2014

AbstractA tantalizing question in microbial physiology is the inter-dependence and evolutionary potential of cellular stress response across multiple environmental dimensions. To address this question, we comprehensively characterized the cross-stress behavior of wild-type and evolved Escherichia coli populations in five abiotic stresses (n-butanol, osmotic, alkaline, acidic, and oxidative) by performing genome-scale genetic, transcriptional and growth profiling, thus identifying 18 cases of cross-stress protection and one case of cross-stress vulnerability. We identified 18 cases of cross-stress protection and one case of cross-stress vulnerability, along with core and stress-specific networks. We tested several hypotheses regarding the effect of the stress order, stress combinations, mutation reversal and varying environments to the evolution and final cellular fitness of the respective populations. Our results argue of a common systems-level core of the stress response with several crucial implicated pathways that include metal ion binding and glycolysis/gluconeogenesis that is further complemented by a stress-specific expression program.
The role of NGOs in building sustainable community resilience
Authors: Fitzpatrick Tal , Molloy Julie 
Published: October 2014

Purpose
– This case study aims to explore the findings and documented impacts of Volunteering Qld’s “Step Up” programme which is the largest community resilience building programme led by a non-government organisation (NGO) in Australia.

Design/methodology/approach
– It will describe the programme design and systems that support this type of qualitative work using evidence-based data collected by the project coordinators over the duration of the programme and contextualising these within a broader resilience framework.

Findings
– This case study will demonstrate and advocate for the need to create stronger partnerships and more significant opportunities for the sector to engage in resilience-building activities.

Research limitations/implications
– The scope of this project was limited by organisational capacity to conduct research into its own programme, as it was being delivered and with limited resourcing. There is a significant need for further research into the work of NGOs in the emergency management and disaster resilience and the impacts of these programmes on communities.

Practical implications
– The practical implications of this case study is a recognition that there are inherent challenges for disaster management agencies trying to engage communities in dialogue around planning risk-informed response and recovery plans for disasters.

Social implications
– However, NGOs are ideally placed to work in and with the communities which they service, to educate and support them at all stages of disaster management.

Originality/value
– This is a unique first-hand account of the experience of a NGO delivering community resilience programme in Australia and provides an important insight for practitioners and researchers alike.