bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive analysis of The Cancer Genome Atlas reveals a unique gene and non-coding RNA signature of fibrolamellar carcinoma
Authors: Dinh Timothy A. , Vitucci Eva C. M. , Wauthier Eliane , Graham Rondell P. , Pitman Wendy A. , Oikawa Tsunekazu , Chen Mengjie , Silva Grace O. , Greene Kevin G. , Torbenson Michael S. , Reid Lola M. , Sethupathy Praveen 
Published: March 2017

AbstractFibrolamellar carcinoma (FLC) is a unique liver cancer primarily affecting young adults and characterized by a fusion event between DNAJB1 and PRKACA. By analyzing RNA-sequencing data from The Cancer Genome Atlas (TCGA) for >9,100 tumors across ~30 cancer types, we show that the DNAJB1-PRKACA fusion is specific to FLCs. We demonstrate that FLC tumors (n = 6) exhibit distinct messenger RNA (mRNA) and long intergenic non-coding RNA (lincRNA) profiles compared to hepatocellular carcinoma (n = 263) and cholangiocarcinoma (n = 36), the two most common liver cancers. We also identify a set of mRNAs (n = 16) and lincRNAs (n = 4), including LINC00473, that distinguish FLC from ~25 other liver and non-liver cancer types. We confirm this unique FLC signature by analysis of two independent FLC cohorts (n = 20 and 34). Lastly, we validate the overexpression of one specific gene in the FLC signature, carbonic anhydrase XII (CA12), at the protein level by western blot and immunohistochemistry. Both the mRNA and lincRNA signatures support a major role for protein kinase A (PKA) signaling in shaping the FLC gene expression landscape, and present novel candidate FLC oncogenes that merit further investigation.
Chemical profiling analysis of Maca using UHPLC-ESI-Orbitrap MS coupled with UHPLC-ESI-QqQ MS and the neuroprotective study on its active ingredients
Authors: Zhou Yanyan , Li Peng , Brantner Adelheid , Wang Hongjie , Shu Xinbin , Yang Jian , Si Nan , Han Lingyu , Zhao Haiyu , Bian Baolin 
Published: March 2017

AbstractLepidium meyenii (Maca), originated from Peru, has been cultivated widely in China as a popular health care food. However, the chemical and effective studies of Maca were less in-depth, which restricted its application seriously. To ensure the quality of Maca, a feasible and accurate strategy was established. One hundred and sixty compounds including 30 reference standards were identified in 6 fractions of methanol extract of Maca by UHPLC-ESI-Orbitrap MS. Among them, 15 representative active compounds were simultaneously determined in 17 samples by UHPLC-ESI-QqQ MS. The results suggested that Maca from Yunnan province was the potential substitute for the one from Peru. Meanwhile, the neuroprotective effects of Maca were investigated. Three fractions and two pure compounds showed strong activities in the 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine (MPTP)-induced zebrafish model. Among them, 80% methanol elution fraction (Fr5) showed significant neuroprotective activity, followed by 100% part (Fr6). The inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) was a possible mechanism of its neuroprotective effect.
HCMV-encoded miR-UL112-3p promotes glioblastoma progression via tumour suppressor candidate 3
Authors: Liang Qing , Wang Kejia , Wang Bin , Cai Qiliang 
Published: March 2017

AbstractGlioblastoma (GBM) is the most prevalent and lethal type of primary malignant brain tumour. Recent studies suggest that the discovery of human cytomegalovirus (HCMV)-encoded microRNAs (miRNAs) might play a role in the pathogenesis of diseases, including GBM. In this study, we aimed to analyse the expression and function of HCMV-encoded miRNAs in GBM. We found that miR-UL112-3p expression was significantly elevated in GBM, and its expression levels were highly associated with glioma size, differentiation, WHO stage and the overall and disease-free survival of patients. The overexpression of miR-UL112-3p in the GBM cells promoted cell proliferation, clone formation, migration and invasion. In contrast, the down-regulation of miR-UL112-3p exerted an inverse effects. Tumour suppressor candidate 3 (TUSC3), a potential target gene of miR-UL112-3p, was inversely correlated with miR-UL112-3p expression in GBM tissues and cell lines. Furthermore, we demonstrated that TUSC3 was directly regulated by miR-UL112-3p, and the ectopic expression of TUSC3 reversed the effects of miR-UL112-3p on GBM progression via the AKT signalling pathway. Taken together, these findings collectively demonstrate that miR-UL112-3p exerts its oncogene function by directly targeting TUSC3 in GBM, indicating a potential novel therapeutic target for GBM.
Magnetowetting of Ferrofluidic Thin Liquid Films
Authors: Tenneti Srinivas , Subramanian Sri Ganesh , Chakraborty Monojit , Soni Gaurav , DasGupta Sunando 
Published: March 2017

AbstractAn extended meniscus of a ferrofluid solution on a silicon surface is subjected to axisymmetric, non-uniform magnetic field resulting in significant forward movement of the thin liquid film. Image analyzing interferometry is used for accurate measurement of the film thickness profile, which in turn, is used to determine the instantaneous slope and the curvature of the moving film. The recorded video, depicting the motion of the film in the Lagrangian frame of reference, is analyzed frame by frame, eliciting accurate information about the velocity and acceleration of the film at any instant of time. The application of the magnetic field has resulted in unique changes of the film profile in terms of significant non-uniform increase in the local film curvature. This was further analyzed by developing a model, taking into account the effect of changes in the magnetic and shape-dependent interfacial force fields.
Preparation of Ho3+/Tm3+ Co-doped Lanthanum Tungsten Germanium Tellurite Glass Fiber and Its Laser Performance for 2.0 μm
Authors: Zhou Dechun , Bai Xuemei , Zhou Hang 
Published: March 2017

AbstractHo3+/Tm3+ co-doped 50TeO2-25GeO2-3WO3-5La2O3-3Nb2O5-5Li2O-9BaF2 glass fiber is prepared with the rod-tube drawing method of 15 μm core diameter and 125 μm inner cladding diameter applied in the 2.0 μm-infrared laser. The 2.0 μm luminescence properties of the core glass are researched and the fluorescence intensity variation for different Tm3+ doping concentration is systematically analyzed. The results show that the 2.0 μm luminescence of Ho3+ is greatly influenced by the doping concentration ratio of Ho3+ to Tm3+ and that the maximum fluorescence intensity of the core glass can be obtained and its emission cross section can reach 0.933 × 10−21 cm2 when the sensitized proportion of holmium to thulium is 0.3 to 0.7 (mol%). Simultaneously, the maximum phonon energy of the core glass sample is 753 cm−1, which is significantly lower than that of silicate, gallate and germanate glass and the smaller matrix phonon energy can be conductive to the increase 2.0 μm-band emission intensity. The continuous laser with the maximum laser output power of 0.993 W and 2051 nm -wavelength of 31.9%-slope efficiency is output within the 0.5 m glass fiber and the experiment adopts 1560 nm erbium-doped fiber laser(EDFL) as the pump source and the self-built all-fiber laser. Therefore, the glass fiber has excellent laser characteristics and it is suitable for the 2.0 μm-band laser.
A conserved inter-domain communication mechanism regulates the ATPase activity of the AAA-protein Drg1
Authors: Prattes Michael , Loibl Mathias , Zisser Gertrude , Luschnig Daniel , Kappel Lisa , Rössler Ingrid , Grassegger Manuela , Hromic Altijana , Krieger Elmar , Gruber Karl , Pertschy Brigitte , Bergler Helmut 
Published: March 2017

AbstractAAA-ATPases fulfil essential roles in different cellular pathways and often act in form of hexameric complexes. Interaction with pathway-specific substrate and adaptor proteins recruits them to their targets and modulates their catalytic activity. This substrate dependent regulation of ATP hydrolysis in the AAA-domains is mediated by a non-catalytic N-terminal domain. The exact mechanisms that transmit the signal from the N-domain and coordinate the individual AAA-domains in the hexameric complex are still the topic of intensive research. Here, we present the characterization of a novel mutant variant of the eukaryotic AAA-ATPase Drg1 that shows dysregulation of ATPase activity and altered interaction with Rlp24, its substrate in ribosome biogenesis. This defective regulation is the consequence of amino acid exchanges at the interface between the regulatory N-domain and the adjacent D1 AAA-domain. The effects caused by these mutations strongly resemble those of pathological mutations of the AAA-ATPase p97 which cause the hereditary proteinopathy IBMPFD (inclusion body myopathy associated with Paget’s disease of the bone and frontotemporal dementia). Our results therefore suggest well conserved mechanisms of regulation between structurally, but not functionally related members of the AAA-family.
Enhancing the sensitivity of magnetic sensors by 3D metamaterial shells
Authors: Navau Carles , Mach-Batlle Rosa , Parra Albert , Prat-Camps Jordi , Laut Sergi , Del-Valle Nuria , Sanchez Alvaro 
Published: March 2017

AbstractMagnetic sensors are key elements in our interconnected smart society. Their sensitivity becomes essential for many applications in fields such as biomedicine, computer memories, geophysics, or space exploration. Here we present a universal way of increasing the sensitivity of magnetic sensors by surrounding them with a spherical metamaterial shell with specially designed anisotropic magnetic properties. We analytically demonstrate that the magnetic field in the sensing area is enhanced by our metamaterial shell by a known factor that depends on the shell radii ratio. When the applied field is non-uniform, as for dipolar magnetic field sources, field gradient is increased as well. A proof-of-concept experimental realization confirms the theoretical predictions. The metamaterial shell is also shown to concentrate time-dependent magnetic fields upto frequencies of 100 kHz.
Suppression of Sin3A activity promotes differentiation of pluripotent cells into functional neurons
Authors: Halder Debasish , Lee Chang-Hee , Hyun Ji Young , Chang Gyeong-Eon , Cheong Eunji , Shin Injae 
Published: March 2017

AbstractSin3 is a transcriptional corepressor for REST silencing machinery that represses multiple neuronal genes in non-neuronal cells. However, functions of Sin3 (Sin3A and Sin3B) in suppression of neuronal phenotypes are not well characterized. Herein we show that Sin3A knockdown impedes the repressive activity of REST and enhances differentiation of pluripotent P19 cells into electrophysiologically active neurons without inducing astrogenesis. It is also found that silencing Sin3B induces neurogenesis of P19 cells with a lower efficiency than Sin3A knockdown. The results suggest that Sin3A has a more profound effect on REST repressive machinery for silencing neuronal genes in P19 cells than Sin3B. Furthermore, we show that a peptide inhibitor of Sin3A-REST interactions promotes differentiation of P19 cells into functional neurons. Observations made in studies using genetic deletion and a synthetic inhibitor suggests that Sin3A plays an important role in the repression of neuronal genes by the REST regulatory mechanism.
Inhibitory role of acyl homoserine lactones in hemolytic activity and viability of Streptococcus pyogenes M6 S165
Authors: Saroj Sunil D. , Holmer Linda , Berengueras Júlia M. , Jonsson Ann-Beth 
Published: March 2017

AbstractStreptococcus pyogenes an adapted human pathogen asymptomatically colonizes the nasopharynx, among other polymicrobial communities. However, information on the events leading to the colonization and expression of virulence markers subject to interspecies and host-bacteria interactions are limited. The interference of acyl homoserine lactones (AHLs) with the hemolytic activity and viability of S. pyogenes M6 S165 was examined. AHLs, with fatty acid side chains ≥12 carbon atoms, inhibited hemolytic activity by downregulating the expression of the sag operon involved in the production of streptolysin S. Inhibitory AHLs upregulated the expression of transcriptional regulator LuxR. Electrophoretic mobility shift assays revealed the interaction of LuxR with the region upstream of sagA. AHL-mediated bactericidal activity observed at higher concentrations (mM range) was an energy-dependent process, constrained by the requirement of glucose and iron. Ferrichrome transporter FtsABCD facilitated transport of AHLs across the streptococcal membrane. The study demonstrates a previously unreported role for AHLs in S. pyogenes virulence.
Imaging of Biliary Infections
Authors: Arellano Ronald , Catalano Onofrio 
Published: March 2017

AbstractBiliary tract infections cover a wide spectrum of etiologies and clinical presentations. Imaging plays an important role in understanding the etiology and as well as the extent of disease. Imaging also plays a vital role in assessing treatment response once a diagnosis is established. This article will review the imaging findings of commonly encountered biliary tract infectious diseases.
Serum Fibroblast Growth Factor 1 is Associated with the Decreased Risk of Obesity in Human
Authors: Zhu Jinzhou , Wang Yuming , Zhu Kefu , Gao Jianguo , Wan Xingyong , Pang Xunlei , Fei Sujuan 
Published: March 2017

Abstract
As a transducer of PPARγ signaling, recent evidence supports that fibroblast growth factor 1 (FGF1) mediates adipose tissue remodeling and insulin sensitivity.
This study is to assess the role of serum FGF1 in obesity.
A hospital-based case-control study of 154 subjects was conducted. Serum level of FGF1 was measured by enzyme-linked immunosorbent assay.
The serum level of FGF1 in the lean (119.0 [103.1–146.1] pg/ml) was higher than it in the subjects with overweight/obesity (111.9 [80.3–127.4] pg/ml, P=0.009). Binary logistic regression models found a reverse association between serum FGF1 level and the risk of overweight/obesity (adjusted odds ratio=0.990, 95% confidence interval [0.981–0.998], P=0.019). Furthermore, serum FGF1 reversely correlated with body mass index (r=−0.176, P=0.029), systolic blood pressure (r=−0.224, P=0.005), diastolic blood pressure (r=−0.185, P=0.022) and triglycerides (r=−0.162, P=0.044). Multiple stepwise linear regression analysis found serum level of FGF1 was dependent on anti-diabetic drugs, hemoglobin A1C, body mass index and sex.
Serum level of FGF1 is associated with the decreased risk of obesity in human.
Flowering phenology shifts in response to biodiversity loss
Authors: Wolf Amelia A. , Zavaleta Erika S. , Selmants Paul C. 
Published: March 2017

Significance
Advanced spring flowering has been described as a fingerprint of climate change—a public, visible display of the detrimental effects of global warming. However, warming experiments fail to account for the full magnitude of observed changes in phenology, suggesting that other factors may play important roles. We show that peak flowering time shifts earlier for most species when we experimentally reduce plant diversity. Additionally, peak flowering times of plant species are more evenly distributed across the season in high-diversity plots. Overall, these results demonstrate the importance of biotic interactions in influencing flowering times and indicate that advancing phenology, one of the most well-described and well-publicized phenomena linking global warming to plant communities, may result equally from biodiversity declines.
Host immunity to
Plasmodium falciparum
and the assessment of emerging artemisinin resistance in a multinational cohort
Authors: Ataide Ricardo , Ashley Elizabeth A. , Powell Rosanna , Chan Jo-Anne , Malloy Michael J. , O’Flaherty Katherine , Takashima Eizo , Langer Christine , Tsuboi Takafumi , Dondorp Arjen M. , Day Nicholas P. , Dhorda Mehul , Fairhurst Rick M. , Lim Pharath , Amaratunga Chanaki , Pukrittayakamee Sasithon , Hien Tran Tinh , Htut Ye , Mayxay Mayfong , Faiz M. Abul , Beeson James G. , Nosten Francois , Simpson Julie A. , White Nicholas J. , Fowkes Freya J. I. 
Published: March 2017

Significance
Slow-clearing artemisinin-resistant malaria parasites are now well established in the Greater Mekong Subregion. This large multinational therapy efficacy study incorporating clinical data, molecular drug-resistance markers, and immune profiling aimed to understand how variations in population levels of naturally acquired malarial immunity affect the slow-clearing phenotype, emergence of artemisinin resistance-associated mutations, and assessment of the geographical spread of artemisinin resistance. We found that slow-clearing mutant parasites occur at higher frequencies in areas where immunity is lowest, patients with higher immunity have faster clearance times, and immunity has the greatest effect on clearance in patients with slow-clearing mutant parasites. Immunity plays an important role in the emergence of resistant parasites and can confound the World Health Organization’s phenotype and genotype definitions of artemisinin resistance.
Photocyclic behavior of rhodopsin induced by an atypical isomerization mechanism
Authors: Gulati Sahil , Jastrzebska Beata , Banerjee Surajit , Placeres Ángel L. , Miszta Przemyslaw , Gao Songqi , Gunderson Karl , Tochtrop Gregory P. , Filipek Sławomir , Katayama Kota , Kiser Philip D. , Mogi Muneto , Stewart Phoebe L. , Palczewski Krzysztof 
Published: March 2017

Significance
Vertebrate rhodopsin (Rh) has been a model system for many G protein-coupled receptors for over a decade. However, due to its thus-far limited repertoire of active ligands, its use in assisting the development of new therapeutic modalities and drugs has been limited. This study elucidates a photocyclic G protein activation by Rh bound with a six-carbon ring retinal (Rh6mr), and thus broadens the diversity of such Rh signaling modulators. Rh6mr does not release its chromophore after light activation, but instead the resulting photoproduct is thermally reisomerized back to its inactive state, abrogating the necessity for a complex retinoid cycle to renew its chromophore. This photocyclic behavior of Rh6mr opens up several avenues for using optogenetic tools based on vertebrate Rhs.
Transcriptional landscape of the human cell cycle
Authors: Liu Yin , Chen Sujun , Wang Su , Soares Fraser , Fischer Martin , Meng Feilong , Du Zhou , Lin Charles , Meyer Clifford , DeCaprio James A. , Brown Myles , Liu X. Shirley , He Housheng Hansen 
Published: March 2017

Significance
Our study provided a comprehensive view of the transcriptional landscape across the cell cycle. We revealed lag between transcription and steady-state RNA expression at the cell-cycle level and characterized a large amount of active transcription during early mitosis. In addition, our analysis identified thousands of enhancer RNAs and related transcription factors that are highly correlated with cell-cycle–regulated transcription but not with steady-state expression, thus highlighting the importance of transcriptional and epigenetic dynamics during cell-cycle progression.
In vivo diagnostics of early abiotic plant stress response via Raman spectroscopy
Authors: Altangerel Narangerel , Ariunbold Gombojav O. , Gorman Connor , Alkahtani Masfer H. , Borrego Eli J. , Bohlmeyer Dwight , Hemmer Philip , Kolomiets Michael V. , Yuan Joshua S. , Scully Marlan O. 
Published: March 2017

Significance
Feeding a population of 9 billion in 2050 coupled with the changing climate and environmental stresses motivate us to develop advances in plant science and technology. We present a high-throughput plant phenotyping platform for detection of abiotic stress. The proposed Raman spectroscopic technique for high-throughput stress phenotyping and early stress detection in vivo improves sensitivity with the ability to interrogate individual molecules simultaneously in plants. This technology holds promise for mobile automated systems and precision agriculture.
Persistence of the mitochondrial permeability transition in the absence of subunit c of human ATP synthase
Authors: He Jiuya , Ford Holly C. , Carroll Joe , Ding Shujing , Fearnley Ian M. , Walker John E. 
Published: March 2017

Significance
Cellular powerhouses called mitochondria generate fuel known as adenosine triphosphate, or ATP, to sustain complex life. The capacity of mitochondria to do so depends on a supply of energy from oxidation of energy-rich compounds in foodstuffs to generate a chemical potential difference for hydrogen ions, called the proton motive force (pmf), across the inner mitochondrial membrane. Disruption of this membrane dissipates the pmf, and the cells die for lack of fuel. This event happens, for example, when the concentration of calcium ions inside human mitochondria is increased. The mitochondria respond by opening a pore, water enters, and the mitochondria swell and burst. The molecular identity of the pore is disputed, and we have disproved one proposal.
‘Only the people can defend this struggle’: the politics of the everyday, extrajudicial executions and civil society in Mathare, Kenya
Authors: Jones Peris S. , Kimari Wangui , Ramakrishnan Kavita 
Published: March 2017

ABSTRACT
Though a perennial problem in postcolonial Kenya, extrajudicial executions (EJE) show few signs of ending and in recent years are even accelerating amongst young men in informal settlements. Avenues for legal, institutional and civil society redress, nominally expanded in recent years, display an ongoing tendency towards disconnection from the grassroots. A case study from Mathare, Nairobi, seeks explanations for the lack of urgency in addressing EJE and also the limited effectiveness of responses to them that are rooted in the political economy of interests of civil society actors, which tends to perpetuate these ‘excluded spaces’ of the slum. The authors do so, however, by exploring one particular struggle to show how frustration with civil society is being used by social justice activists to articulate ideas of ‘everyday’ violence to mobilise for change that disrupts the apparent normalisation of EJE.
ConKit: a python interface to contact predictions
Authors: Simkovic Felix , Thomas Jens M H , Rigden Daniel J 
Published: March 2017

Abstract

Summary
Recent advances in protein residue contact prediction algorithms have led to the emergence of many new methods and a variety of file formats. We present ConKit, an open source, modular and extensible Python interface which allows facile conversion between formats and provides an interface to analyses of sequence alignments and sets of contact predictions.

Availability and Implementation
ConKit is available via the Python Package Index. The documentation can be found at http://www.conkit.org. ConKit is licensed under the BSD 3-Clause.

Supplementary information
Supplementary data are available at Bioinformatics online.