bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasmonic Gold Decorated MWCNT Nanocomposite for Localized Plasmon Resonance Sensing
Authors: Ozhikandathil J. , Badilescu S. , Packirisamy M. 
Published: August 2015

AbstractThe synergism of excellent properties of carbon nanotubes and gold nanoparticles is used in this work for bio-sensing of recombinant bovine growth hormones (rbST) by making Multi Wall Carbon Nanotubes (MWCNT) locally optically responsive by augmenting it optical properties through Localized Surface Plasmon Resonance (LSPR). To this purpose, locally gold nano particles decorated gold–MWCNT composite was synthesized from a suspension of MWCNT bundles and hydrogen chloroauric acid in an aqueous solution, activated ultrasonically and, then, drop-casted on a glass substrate. The slow drying of the drop produces a “coffee ring” pattern that is found to contain gold–MWCNT nanocomposites, accumulated mostly along the perimeter of the ring. The reaction is studied also at low-temperature, in the vacuum chamber of the Scanning Electron Microscope and is accounted for by the local melting processes that facilitate the contact between the bundle of tubes and the gold ions. Biosensing applications of the gold–MWCNT nanocomposite using their LSPR properties are demonstrated for the plasmonic detection of traces of bovine growth hormone. The sensitivity of the hybrid platform which is found to be 1 ng/ml is much better than that measuring with gold nanoparticles alone which is only 25 ng/ml.
Quick Fabrication of Large-area Organic Semiconductor Single Crystal Arrays with a Rapid Annealing Self-Solution-Shearing Method
Authors: Li Yunze , Ji Deyang , Liu Jie , Yao Yifan , Fu Xiaolong , Zhu Weigang , Xu Chunhui , Dong Huanli , Li Jingze , Hu Wenping 
Published: August 2015

AbstractIn this paper, we developed a new method to produce large-area single crystal arrays by using the organic semiconductor 9, 10-bis (phenylethynyl) anthracene (BPEA). This method involves an easy operation, is efficient, meets the demands of being low-cost and is independent of the substrate for large-area arrays fabrication. Based on these single crystal arrays, the organic field effect transistors exhibit the superior performance with the average mobility extracting from the saturation region of 0.2 cm2V−1s−1(the highest 0.47 cm2V−1s−1) and on/off ratio exceeding 105. In addition, our single crystal arrays also show a very high photoswitch performance with an on/off current ratio up to 4.1 × 105, which is one of the highest values reported for organic materials. It is believed that this method provides a new way to fabricate single crystal arrays and has the potential for application to large area organic electronics.
SRSF1 and hnRNP H antagonistically regulate splicing of COLQ exon 16 in a congenital myasthenic syndrome
Authors: Rahman Mohammad Alinoor , Azuma Yoshiteru , Nasrin Farhana , Takeda Jun-ichi , Nazim Mohammad , Ahsan Khalid Bin , Masuda Akio , Engel Andrew G. , Ohno Kinji 
Published: August 2015

AbstractThe catalytic subunits of acetylcholinesterase (AChE) are anchored in the basal lamina of the neuromuscular junction using a collagen-like tail subunit (ColQ) encoded by COLQ. Mutations in COLQ cause endplate AChE deficiency. An A-to-G mutation predicting p.E415G in COLQ exon 16 identified in a patient with endplate AChE deficiency causes exclusive skipping of exon 16. RNA affinity purification, mass spectrometry and siRNA-mediated gene knocking down disclosed that the mutation disrupts binding of a splicing-enhancing RNA-binding protein, SRSF1 and de novo gains binding of a splicing-suppressing RNA-binding protein, hnRNP H. MS2-mediated artificial tethering of each factor demonstrated that SRSF1 and hnRNP H antagonistically modulate splicing by binding exclusively to the target in exon 16. Further analyses with artificial mutants revealed that SRSF1 is able to bind to degenerative binding motifs, whereas hnRNP H strictly requires an uninterrupted stretch of poly(G). The mutation compromised splicing of the downstream intron. Isolation of early spliceosome complex revealed that the mutation impairs binding of U1-70K (snRNP70) to the downstream 5′ splice site. Global splicing analysis with RNA-seq revealed that exons carrying the hnRNP H-binding GGGGG motif are predisposed to be skipped compared to those carrying the SRSF1-binding GGAGG motif in both human and mouse brains.
Clinicopathological Significance and Potential Drug Target of CDKN2A/p16 in Endometrial Carcinoma
Authors: Su Li , Wang Hanwei , Miao Jingwei , Liang Ying 
Published: August 2015

AbstractPrevious studies demonstrated that the loss of function of the CDKN2A/p16/INK4A gene is mainly caused by the hypermethylation of CDKN2A, however, whether or not it is associated with the incidence and clinicopathological characteristics of endometrial carcinoma (EC) remains unclear. In this study, we conducted a meta-analysis aiming to comprehensively assess the role of CDKN2A hypermethylation in the pathogenesis of EC. A detailed literature search was made to identify the related research publications. Analysis of pooled data was performed. Odds ratio (OR) was calculated and summarized. Final analysis of 638 EC patients from 12 eligible studies was performed. The results showed that CDKN2A hypermethylation was significantly higher in EC than in normal control tissue, the pooled OR from 8 studies including 400 EC patients and 131 controls, OR = 8.39 with 95% CI 4.03–17.45, test for overall effect, Z = 5.69, P < 0.00001. Further analysis showed that CDKN2A hypermethylation was not significantly associated with tumor differentiation and clinical stage status in EC patients. The results of this meta-analysis suggest that CDKN2A hypermethylation may be implicated in the pathogenesis of EC. CDKN2A hypermethylation was not significantly associated with tumor differentiation and clinical stage status in EC patients, indicating that CDKN2A hypermethylation might be early event of EC.
OLA1 regulates protein synthesis and integrated stress response by inhibiting eIF2 ternary complex formation
Authors: Chen Huarong , Song Renduo , Wang Guohui , Ding Zonghui , Yang Chunying , Zhang Jiawei , Zeng Zihua , Rubio Valentina , Wang Luchang , Zu Nancy , Weiskoff Amanda M. , Minze Laurie J. , Jeyabal Prince V.S. , Mansour Oula C. , Bai Li , Merrick William C. , Zheng Shu , Shi Zheng-Zheng 
Published: August 2015

AbstractTranslation is a fundamental cellular process and its dysregulation can contribute to human diseases such as cancer. During translation initiation the eukaryotic initiation factor 2 (eIF2) forms a ternary complex (TC) with GTP and the initiator methionyl-tRNA (tRNAi), mediating ribosomal recruitment of tRNAi. Limiting TC availability is a central mechanism for triggering the integrated stress response (ISR), which suppresses global translation in response to various cellular stresses, but induces specific proteins such as ATF4. This study shows that OLA1, a member of the ancient Obg family of GTPases, is an eIF2-regulatory protein that inhibits protein synthesis and promotes ISR by binding eIF2, hydrolyzing GTP and interfering with TC formation. OLA1 thus represents a novel mechanism of translational control affecting de novo TC formation, different from the traditional model in which phosphorylation of eIF2α blocks the regeneration of TC. Depletion of OLA1 caused a hypoactive ISR and greater survival in stressed cells. In vivo, OLA1-knockdown rendered cancer cells deficient in ISR and the downstream proapoptotic effector, CHOP, promoting tumor growth and metastasis. Our work suggests that OLA1 is a novel translational GTPase and plays a suppressive role in translation and cell survival, as well as cancer growth and progression.
CaMKII regulates the strength of the epithelial barrier
Authors: Shiomi Ryo , Shigetomi Kenta , Inai Tetsuichiro , Sakai Masami , Ikenouchi Junichi 
Published: August 2015

AbstractEpithelial cells define the boundary between the outside and the inside of our body by constructing the diffusion barrier. Tight junctions (TJs) of epithelial cells function as barriers against invasion of harmful microorganisms into the human body and free diffusion of water or ions from the body. Therefore, formation of TJs has to be strictly controlled in epithelial cells. However, the molecular mechanisms governing this regulation are largely unknown. In this study, we identified Ca2+/calmodulin-dependent protein kinase II (CaMKII) as a regulator of the barrier function of TJs. CaMKII inhibition led to enlargement of TJ-areas and up-regulation of the barrier function. CaMKII inhibition induced excess TJ formation in part by the activation of AMP-activated protein kinase (AMPK) and subsequent phosphorylation of claudin-1. As up-regulation of epithelial barriers is essential for the prevention of chronic inflammatory diseases, the identification of CaMKII as a modulator of TJ function paves the way for the development of new drugs to treat these diseases.
Imaging Cells in Flow Cytometer Using Spatial-Temporal Transformation
Authors: Han Yuanyuan , Lo Yu-Hwa 
Published: August 2015

AbstractFlow cytometers measure fluorescence and light scattering and analyze multiple physical characteristics of a large population of single cells as cells flow in a fluid stream through an excitation light beam. Although flow cytometers have massive statistical power due to their single cell resolution and high throughput, they produce no information about cell morphology or spatial resolution offered by microscopy, which is a much wanted feature missing in almost all flow cytometers. In this paper, we invent a method of spatial-temporal transformation to provide flow cytometers with cell imaging capabilities. The method uses mathematical algorithms and a spatial filter as the only hardware needed to give flow cytometers imaging capabilities. Instead of CCDs or any megapixel cameras found in any imaging systems, we obtain high quality image of fast moving cells in a flow cytometer using PMT detectors, thus obtaining high throughput in manners fully compatible with existing cytometers. To prove the concept, we demonstrate cell imaging for cells travelling at a velocity of 0.2 m/s in a microfluidic channel, corresponding to a throughput of approximately 1,000 cells per second.
Multichannel OADM using cascaded Bragg grating/Mach–Zehnder interferometers in SOI
Authors: Wang J. , Chen L.R. 
Published: August 2015

Multichannel optical add–drop multiplexers (OADMs) based on cascaded Bragg grating/Mach–Zehnder interferometers in silicon‐on‐insulator are reported. The OADMs are fabricated using electron beam lithography with a single etch. Three add–drop channels at wavelengths of 1542.5, 1557.0, and 1570.4 nm, each with a 3 dB bandwidth (BW) of 4 nm are obtained. All channels exhibit a transmission isolation of >20 dB, an interferometric crosstalk of <−30 dB, and a bandwidth utilisation factor of >0.5.
Increasing disparities between resource inputs and outcomes, as measured by certain health deliverables, in biomedical research
Authors: Bowen Anthony , Casadevall Arturo 
Published: August 2015

Significance
The general public funds the vast majority of biomedical research and is also the major intended beneficiary of biomedical breakthroughs. We show that increasing research investments, resulting in an increasing knowledge base, have not yielded comparative gains in certain health outcomes over the last five decades. We demonstrate that monitoring scientific inputs, outputs, and outcomes can be used to estimate the productivity of the biomedical research enterprise and may be useful in assessing future reforms and policy changes. A wide variety of negative pressures on the scientific enterprise may be contributing to a relative slowing of biomedical therapeutic innovation. Slowed biomedical research outcomes have the potential to undermine confidence in science, with widespread implications for research funding and public health.
IRF5 controls both acute and chronic inflammation
Authors: Weiss Miriam , Byrne Adam J. , Blazek Katrina , Saliba David G. , Pease James E. , Perocheau Dany , Feldmann Marc , Udalova Irina A. 
Published: August 2015

SignificanceMany of the world’s major chronic diseases are driven by inflammation. The most abundant inflammatory cells in these diseases are myeloid cells, such as macrophages and neutrophils. Both cell types show remarkable phenotypic diversity among tissues. Defining molecular factors that control this diversity provides abundant scope for the generation of more specific and effective therapeutics, as the lack of specificity of the current most widely used antiinflammatory approaches, such as glucocorticoids and nonsteroidal antiinflammatory molecules, leads to widespread problems if used long term, even at relatively low doses. In this study we demonstrate that a transcription factor called IFN regulatory factor 5 controls macrophage and neutrophil aspects of inflammation, and thus its blockade might be an effective therapeutic strategy for multiple indications.
Neural systems supporting linguistic structure, linguistic experience, and symbolic communication in sign language and gesture
Authors: Newman Aaron J. , Supalla Ted , Fernandez Nina , Newport Elissa L. , Bavelier Daphne 
Published: August 2015

SignificanceAlthough sign languages and nonlinguistic gesture use the same modalities, only sign languages have established vocabularies and follow grammatical principles. This is the first study (to our knowledge) to ask how the brain systems engaged by sign language differ from those used for nonlinguistic gesture matched in content, using appropriate visual controls. Signers engaged classic left-lateralized language centers when viewing both sign language and gesture; nonsigners showed activation only in areas attuned to human movement, indicating that sign language experience influences gesture perception. In signers, sign language activated left hemisphere language areas more strongly than gestural sequences. Thus, sign language constructions—even those similar to gesture—engage language-related brain systems and are not processed in the same ways that nonsigners interpret gesture.
aRrayLasso: a network-based approach to microarray interconversion
Authors: Brown Adam S. , Patel Chirag J. 
Published: August 2015

Abstract
Summary: Robust conversion between microarray platforms is needed to leverage the wide variety of microarray expression studies that have been conducted to date. Currently available conversion methods rely on manufacturer annotations, which are often incomplete, or on direct alignment of probes from different platforms, which often fail to yield acceptable genewise correlation. Here, we describe aRrayLasso, which uses the Lasso-penalized generalized linear model to model the relationships between individual probes in different probe sets. We have implemented aRrayLasso in a set of five open-source R functions that allow the user to acquire data from public sources such as Gene Expression Omnibus, train a set of Lasso models on that data and directly map one microarray platform to another. aRrayLasso significantly predicts expression levels with similar fidelity to technical replicates of the same RNA pool, demonstrating its utility in the integration of datasets from different platforms.
Availability and implementation: All functions are available, along with descriptions, at https://github.com/adam-sam-brown/aRrayLasso.
Contact: chirag_patel@hms.harvard.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Correcting gene expression data when neither the unwanted variation nor the
factor of interest are observed
Authors: Jacob Laurent , Gagnon-Bartsch Johann A. , Speed Terence P. 
Published: August 2015

Abstract
When dealing with large scale gene expression studies, observations are commonly contaminated by sources of unwanted variation such as platforms or batches. Not taking this unwanted variation into account when analyzing the data can lead to spurious associations and to missing important signals. When the analysis is unsupervised, e.g. when the goal is to cluster the samples or to build a corrected version of the dataset—as opposed to the study of an observed factor of interest—taking unwanted variation into account can become a difficult task. The factors driving unwanted variation may be correlated with the unobserved factor of interest, so that correcting for the former can remove the latter if not done carefully. We show how negative control genes and replicate samples can be used to estimate unwanted variation in gene expression, and discuss how this information can be used to correct the expression data. The proposed methods are then evaluated on synthetic data and three gene expression datasets. They generally manage to remove unwanted variation without losing the signal of interest and compare favorably to state-of-the-art corrections. All proposed methods are implemented in the bioconductor package RUVnormalize.
A proposed chemical scheme for HCCO formation in cold dense clouds
Authors: Wakelam V. , Loison J.-C. , Hickson K. M. , Ruaud M. 
Published: August 2015

Abstract
The ketenyl radical (HCCO) has recently been discovered in two cold dense clouds with a non-negligible abundance of a few 10−11 (compared to H2). Until now, no chemical network has been able to reproduce this observation. We propose here a chemical scheme that can reproduce HCCO abundances together with HCO, H2CCO and CH3CHO in the dark clouds Lupus-1A and L486. The main formation pathway for HCCO is the OH + CCH → HCCO + H reaction as suggested by Agúndez et al. but with a much larger rate coefficient than used in current models. Since this reaction has never been studied experimentally or theoretically, this larger value is based on a comparison with other similar systems.
TET1 Modulates H4K16 Acetylation by Interacting with hMOF to Regulate Expression of DNA Repair Genes and Oncogenic Transformation
Authors: Zhong Jianing , Li Xianfeng , Cai Wanshi , Wang Yan , Dong Shanshan , Zhang Jian’an , Yang Jie , Wang Kangli , Mao Fengbiao , Zeng Cheng , Li Yuanyuan , Wu Jinyu , Yang Huanming , Xu Xingzhi , Sun Zhong Sheng 
Published: August 2015

ABSTRACTThe Ten Eleven Translocation 1 (TET1) protein is a DNA demethylase that regulates gene expression through alteration of DNA methylation. Recent studies have demonstrated that TET1 could modulate transcriptional expression independent of its DNA demethylation activity; however, the detailed mechanisms underlying TET1’s role in such transcriptional regulation remain not well understood. Here, we uncovered that Tet1 formed a chromatin complex with histone acetyltransferase Mof and scaffold protein Sin3a in mouse embryonic stem cells by integrative genomic analysis using publicly available ChIP-seq data sets. Specifically, the TET1/SIN3A/hMOF complex mediates acetylation of histone H4 at lysine 16,viafacilitating the binding of hMOF on chromatin, to regulate expression of important DNA repair genes in DNA double strand breaks, includingTP53BP1,RAD50,RAD51, andBRCA1, for homologous recombination and non-homologous end joining repairs. Under hydrogen peroxide-induced DNA damage, dissociation of TET1 and hMOF from chromatin, concurrent with increased binding of SIRT1 on chromatin, led to hypo-acetylation of H4K16, reduced expression of these DNA repair genes, and DNA repair defects in a DNA methylation independent manner. A similar epigenetic dynamic alteration was also observed in H-RASV12oncogenic-transformed cells, supporting the notion that suppression of TET1 downregulates DNA repair genes through modifying H4K16ac, instead of its demethylation function, and therefore contribute to tumorigenesis. Taken together, our results suggested a mechanistic link between a novel TET1 complex and H4K16ac, DNA repair genes expression, and genomic instability.
Antithetic Integral Feedback: A new motif for robust perfect adaptation in noisy biomolecular networks
Authors: Briat Corentin , Gupta Ankit , Khammash Mustafa 
Published: August 2015

AbstractHomeostasis is a running theme in biology. Often achieved through feedback regulation strategies, homeostasis allows living cells to control their internal environment as a means for surviving changing and unfavourable environments. While many endogenous homeostatic motifs have been studied in living cells, some other motifs may remain under-explored or even undiscovered. At the same time, known regulatory motifs have been mostly analyzed at the deterministic level, and the effect of noise on their regulatory function has received low attention. Here we lay the foundation for a regulation theory at the molecular level that explicitly takes into account the noisy nature of biochemical reactions and provides novel tools for the analysis and design of robust homeostatic circuits. Using these ideas, we propose a new regulation motif, which we refer to asantithetic integral feedback,and demonstrate its effectiveness as a strategy for generically regulating a wide class of reaction networks. By combining tools from probability and control theory, we show that the proposed motif preserves the stability of the overall network, steers the population of any regulated species to a desired set point, and achieves robust perfect adaptation – all with low prior knowledge of reaction rates. Moreover, our proposed regulatory motif can be implemented using a very small number of molecules and hence has a negligible metabolic load. Strikingly, the regulatory motif exploits stochastic noise, leading to enhanced regulation in scenarios where noise-free implementations result in dysregulation. Finally, we discuss the possible manifestation of the proposed antithetic integral feedback motif in endogenous biological circuits and its realization in synthetic circuits.
Multiple obstacles to psychological care from the viewpoint of addiction service users
Authors: Gore Stuart , Mendoza Julio , Delgadillo Jaime 
Published: August 2015

Purpose
– The purpose of this paper is to explore addiction service users’ experiences of psychological interventions for depression symptoms, with an emphasis on understanding obstacles to engage with treatment.

Design/methodology/approach
– This was a thematic analysis of semi-structured interviews with ten people who took part in a randomised controlled trial of cognitive and behavioural interventions; four of whom never engaged with treatment.

Findings
– Five prominent obstacles to access therapy were: memory deficits, becoming overwhelmed by multiple demands and appointments, being housebound due to fluctuations in mental health problems, tendency to avoid the unfamiliar, and contextual life problems related to deprivation and social conflict.

Research limitations/implications
– The authors note some possible limitations related to overreliance on telephone interviews and interviewers’ field notes. The authors discuss the findings in light of epidemiological research, cognitive, behavioural and motivational enhancement theories.

Practical implications
– The authors propose it is important to recognise and address multiple obstacles to therapy. Offering therapy appointments that are co-located within addiction services and time-contingent to other social/medical interventions may help to address some of these obstacles.

Originality/value
– The present qualitative results complement the prior experimental research and enrich the understanding of how to maximise engagement with psychological interventions.