bluuebunny/crossref_metadata_2025_split huggingface dataset:
BYZANTINE SEAHORSES IN TACITUS' ANNALS, 12.63.2
Authors: Huyck Jefferds 
Published: May 2016

quippe Byzantium fertili solo, fecundo mari, quia uis piscium in metapontum erumpens et obliquis subter undas saxis exterrita omisso alterius litoris flexu hos ad portus defertur.For Byzantium is favoured with fertile soil and teeming seas, since a multitude of fish, bursting out (of the Pontus?) and spooked by rocks slanting beneath the water, leave off the curve of the opposite shore and are wafted to these harbours.
That is the text of the second Medicean and all of its descendants. For centuries now the unfitness of the words in metapontum has been obvious to editors. J. Lipsius conjectured innumera Pontum (1585), G. Brotier innumera Ponto (1771), N. Bach and G.A. Ruperti immensa Pontum (each in 1834). F. Ritter returned to the problem again and again, first proposing immensa Ponto (1834), then immensum Ponto, i.e. ‘immensa multitudine’ (1848), and finally in meatu Ponti (1863). Bach's and Ruperti's remedy is clearly the most efficient. Modern editors agree in printing uis piscium immensa (i.e. inmēsa) Pontum erumpens, ‘an immense multitude of fish, bursting out of the Pontus'. Neat, but perhaps unnecessary. My object here is to defend the text of the manuscripts.
Exopolysaccharide microchannels direct bacterial motility and organize multicellular behavior
Authors: Berleman James E , Zemla Marcin , Remis Jonathan P , Liu Hong , Davis Annie E , Worth Alexandra N , West Zachary , Zhang Angela , Park Hanwool , Bosneaga Elena , van Leer Brandon , Tsai Wenting , Zusman David R , Auer Manfred 
Published: May 2016

Abstract
The myxobacteria are a family of soil bacteria that form biofilms of complex architecture, aligned multilayered swarms or fruiting body structures that are simple or branched aggregates containing myxospores. Here, we examined the structural role of matrix exopolysaccharide (EPS) in the organization of these surface-dwelling bacterial cells. Using time-lapse light and fluorescence microscopy, as well as transmission electron microscopy and focused ion beam/scanning electron microscopy (FIB/SEM) electron microscopy, we found that Myxococcus xanthus cell organization in biofilms is dependent on the formation of EPS microchannels. Cells are highly organized within the three-dimensional structure of EPS microchannels that are required for cell alignment and advancement on surfaces. Mutants lacking EPS showed a lack of cell orientation and poor colony migration. Purified, cell-free EPS retains a channel-like structure, and can complement EPS− mutant motility defects. In addition, EPS provides the cooperative structure for fruiting body formation in both the simple mounds of M. xanthus and the complex, tree-like structures of Chondromyces crocatus. We furthermore investigated the possibility that EPS impacts community structure as a shared resource facilitating cooperative migration among closely related isolates of M. xanthus.
Plate tectonics drive tropical reef biodiversity dynamics
Authors: Leprieur Fabien , Descombes Patrice , Gaboriau Théo , Cowman Peter F. , Parravicini Valeriano , Kulbicki Michel , Melián Carlos J. , de Santana Charles N. , Heine Christian , Mouillot David , Bellwood David R. , Pellissier Loïc 
Published: May 2016

AbstractThe Cretaceous breakup of Gondwana strongly modified the global distribution of shallow tropical seas reshaping the geographic configuration of marine basins. However, the links between tropical reef availability, plate tectonic processes and marine biodiversity distribution patterns are still unknown. Here, we show that a spatial diversification model constrained by absolute plate motions for the past 140 million years predicts the emergence and movement of diversity hotspots on tropical reefs. The spatial dynamics of tropical reefs explains marine fauna diversification in the Tethyan Ocean during the Cretaceous and early Cenozoic, and identifies an eastward movement of ancestral marine lineages towards the Indo-Australian Archipelago in the Miocene. A mechanistic model based only on habitat-driven diversification and dispersal yields realistic predictions of current biodiversity patterns for both corals and fishes. As in terrestrial systems, we demonstrate that plate tectonics played a major role in driving tropical marine shallow reef biodiversity dynamics.
Deregulation of mitochondrial F1FO-ATP synthase via OSCP in Alzheimer’s disease
Authors: Beck Simon J. , Guo Lan , Phensy Aarron , Tian Jing , Wang Lu , Tandon Neha , Gauba Esha , Lu Lin , Pascual Juan M. , Kroener Sven , Du Heng 
Published: May 2016

AbstractF1FO-ATP synthase is critical for mitochondrial functions. The deregulation of this enzyme results in dampened mitochondrial oxidative phosphorylation (OXPHOS) and activated mitochondrial permeability transition (mPT), defects which accompany Alzheimer’s disease (AD). However, the molecular mechanisms that connect F1FO-ATP synthase dysfunction and AD remain unclear. Here, we observe selective loss of the oligomycin sensitivity conferring protein (OSCP) subunit of the F1FO-ATP synthase and the physical interaction of OSCP with amyloid beta (Aβ) in the brains of AD individuals and in an AD mouse model. Changes in OSCP levels are more pronounced in neuronal mitochondria. OSCP loss and its interplay with Aβ disrupt F1FO-ATP synthase, leading to reduced ATP production, elevated oxidative stress and activated mPT. The restoration of OSCP ameliorates Aβ-mediated mouse and human neuronal mitochondrial impairments and the resultant synaptic injury. Therefore, mitochondrial F1FO-ATP synthase dysfunction associated with AD progression could potentially be prevented by OSCP stabilization.
Simplified quantification method for in vivo SPECT/CT imaging of asialoglycoprotein receptor with 99mTc-p(VLA-co-VNI) to assess and stage hepatic fibrosis in mice
Authors: Zhang Deliang , Guo Zhide , Zhang Pu , Li Yesen , Su Xinhui , You Linyi , Gao Mengna , Liu Chang , Wu Hua , Zhang Xianzhong 
Published: May 2016

AbstractThe goal of this study is to develop a noninvasive method of SPECT imaging to quantify and stage liver fibrosis with an Asialoglycoprotein receptor (ASGP-R) targeting tracer—99mTc-p(VLA-co-VNI). ASGP-Rs are well known to specifically express in the mammalian liver. Here, we demonstrated ASGP-R expression decreased in carbon tetrachloride (CCl4)-induced mouse model. ASGP-R expression correlated with liver fibrosis progression. ASGP-R could be a useful marker in the stage of liver fibrosis. Liver uptake value (LUV) derived by SPECT imaging was used to assess liver fibrosis in the CCl4-induced mouse model. LUV = [radioactivity (liver uptake)/radioactivity (injected)] × 100/liver volume. The LUV decreased along with the disease progression. The relationships between LUV and liver hydroxyproline (i.e. collagen), as well as Sirius Red were established and verified. A strong negative linear correlation was found between LUV and hydroxyproline levels (r = −0.83) as well as LUV and Sirius Red quantification (r = −0.83). In conclusion, SPECT imaging with 99mTc-p(VLA-co-VNI) is useful in evaluating and staging liver fibrosis in vivo.
Identification of side- and shear-dependent microRNAs regulating porcine aortic valve pathogenesis
Authors: Rathan Swetha , Ankeny Casey J. , Arjunon Sivakkumar , Ferdous Zannatul , Kumar Sandeep , Fernandez Esmerats Joan , Heath Jack M. , Nerem Robert M. , Yoganathan Ajit P. , Jo Hanjoong 
Published: May 2016

AbstractAortic valve (AV) calcification is an inflammation driven process that occurs preferentially in the fibrosa. To explore the underlying mechanisms, we investigated if key microRNAs (miRNA) in the AV are differentially expressed due to disturbed blood flow (oscillatory shear (OS)) experienced by the fibrosa compared to the ventricularis. To identify the miRNAs involved, endothelial-enriched RNA was isolated from either side of healthy porcine AVs for microarray analysis. Validation using qPCR confirmed significantly higher expression of 7 miRNAs (miR-100, -130a, -181a/b, -199a-3p, -199a-5p, and -214) in the fibrosa versus the ventricularis. Upon bioinformatics analysis, miR-214 was selected for further investigation using porcine AV leaflets in an ex vivo shear system. Fibrosa and ventricularis sides were exposed to either oscillatory or unidirectional pulsatile shear for 2 days and 3 & 7 days in regular and osteogenic media, respectively. Higher expression of miR-214, increased thickness of the fibrosa, and calcification was observed when the fibrosa was exposed to OS compared to the ventricularis. Silencing of miR-214 by anti-miR-214 in whole AV leaflets with the fibrosa exposed to OS significantly increased the protein expression of TGFβ1 and moderately increased collagen content but did not affect AV calcification. Thus, miR-214 is identified as a side- and shear-dependent miRNA that regulates key mechanosensitive gene in AV such as TGFβ1.
Ultrapure laser-synthesized Si-based nanomaterials for biomedical applications: in vivo assessment of safety and biodistribution
Authors: Baati Tarek , Al-Kattan Ahmed , Esteve Marie-Anne , Njim Leila , Ryabchikov Yury , Chaspoul Florence , Hammami Mohamed , Sentis Marc , Kabashin Andrei V. , Braguer Diane 
Published: May 2016

AbstractSi/SiOx nanoparticles (NPs) produced by laser ablation in deionized water or aqueous biocompatible solutions present a novel extremely promising object for biomedical applications, but the interaction of these NPs with biological systems has not yet been systematically examined. Here, we present the first comprehensive study of biodistribution, biodegradability and toxicity of laser-synthesized Si-SiOx nanoparticles using a small animal model. Despite a relatively high dose of Si-NPs (20 mg/kg) administered intravenously in mice, all controlled parameters (serum, enzymatic, histological etc.) were found to be within safe limits 3 h, 24 h, 48 h and 7 days after the administration. We also determined that the nanoparticles are rapidly sequestered by the liver and spleen, then further biodegraded and directly eliminated in urine without any toxicity effects. Finally, we found that intracellular accumulation of Si-NPs does not induce any oxidative stress damage. Our results evidence a huge potential in using these safe and biodegradable NPs in biomedical applications, in particular as vectors, contrast agents and sensitizers in cancer therapy and diagnostics (theranostics).
Convergent Transcription of Interferon-stimulated Genes by TNF-α and IFN-α Augments Antiviral Activity against HCV and HEV
Authors: Wang Wenshi , Xu Lei , Brandsma Johannes H. , Wang Yijin , Hakim Mohamad S. , Zhou Xinying , Yin Yuebang , Fuhler Gwenny M. , van der Laan Luc J. W. , van der Woude C. Janneke , Sprengers Dave , Metselaar Herold J. , Smits Ron , Poot Raymond A. , Peppelenbosch Maikel P. , Pan Qiuwei 
Published: May 2016

AbstractIFN-α has been used for decades to treat chronic hepatitis B and C and as an off-label treatment for some cases of hepatitis E virus (HEV) infection. TNF-α is another important cytokine involved in inflammatory disease, which can interact with interferon signaling. Because interferon-stimulated genes (ISGs) are the ultimate antiviral effectors of the interferon signaling, this study aimed to understand the regulation of ISG transcription and the antiviral activity by IFN-α and TNF-α. In this study, treatment of TNF-α inhibited replication of HCV by 71 ± 2.4% and HEV by 41 ± 4.9%. Interestingly, TNF-α induced the expression of a panel of antiviral ISGs (2-11 fold). Blocking the TNF-α signaling by Humira abrogated ISG induction and its antiviral activity. Chip-seq data analysis and mutagenesis assay further revealed that the NF-κB protein complex, a key downstream element of TNF-α signaling, directly binds to the ISRE motif in the ISG promoters and thereby drives their transcription. This process is independent of interferons and JAK-STAT cascade. Importantly, when combined with IFN-α, TNF-α works cooperatively on ISG induction, explaining their additive antiviral effects. Thus, our study reveals a novel mechanism of convergent transcription of ISGs by TNF-α and IFN-α, which augments their antiviral activity against HCV and HEV.
Orderly progression through S-phase requires dynamic ubiquitylation and deubiquitylation of PCNA
Authors: Álvarez Vanesa , Viñas Laura , Gallego-Sánchez Alfonso , Andrés Sonia , Sacristán María P. , Bueno Avelino 
Published: May 2016

AbstractProliferating-cell nuclear antigen (PCNA) is a DNA sliding clamp with an essential function in DNA replication and a key role in tolerance to DNA damage by ensuring the bypass of lesions. In eukaryotes, DNA damage tolerance is regulated by ubiquitylation of lysine 164 of PCNA through a well-known control mechanism; however, the regulation of PCNA deubiquitylation remains poorly understood. Our work is a systematic and functional study on PCNA deubiquitylating enzymes (DUBs) in Schizosaccharomyces pombe. Our study reveals that the deubiquitylation of PCNA in fission yeast cells is a complex process that requires several ubiquitin proteases dedicated to the deubiquitylation of a specific subnuclear fraction of mono- and di-ubiquitylated PCNA or a particular type of poly-ubiquitylated PCNA and that there is little redundancy among these enzymes. To understand how DUB activity regulates the oscillatory pattern of ubiquitylated PCNA in fission yeast, we assembled multiple DUB mutants and found that a quadruple mutation of ubp2+, ubp12+, ubp15+ and ubp16+ leads to the stable accumulation of mono-, di- and poly-ubiquitylated forms of PCNA, increases S-phase duration and sensitizes cells to DNA damage. Our data suggest that the dynamic ubiquitylation and deubiquitylation of PCNA occurs during S-phase to ensure processive DNA replication.
Prokineticin receptor-1 signaling promotes Epicardial to Mesenchymal Transition during heart development
Authors: Arora Himanshu , Boulberdaa Mounia , Qureshi Rehana , Bitirim Verda , Gasser Adeline , Messaddeq Nadia , Dolle Pascal , Nebigil Canan G. 
Published: May 2016

AbstractThe epicardium plays an essential role in coronary artery formation and myocardial development. However, signals controlling the developing epicardium and epicardial-mesenchymal transition (EMT) in the normal and diseased adult heart are studied less rigorously. Here we investigated the role of angiogenic hormone, prokineticin-2 and its receptor PKR1 in the epicardium of developing and adult heart. Genetic ablation of PKR1 in epicardium leads to partial embryonic and postnatal lethality with abnormal heart development. Cardiac developmental defects are manifested in the adult stage as ischemic cardiomyopathy with systolic dysfunction. We discovered that PKR1 regulates epicardial-mesenchymal transition (EMT) for epicardial-derived progenitor cell (EPDC), formation. This event affects at least three consequential steps during heart development: (i) EPDC and cardiomyocyte proliferation involved in thickening of an outer compact ventricular chamber wall, (ii) rhythmicity, (iii) formation of coronary circulation. In isolated embryonic EPDCs, overexpression or activation of PKR1 alters cell morphology and EMT markers via activating Akt signaling. Lack of PKR1 signal in epicardium leads to defective heart development and underlies the origin of congenital heart disease in adult mice. Our mice provide genetic models for congenital dysfunction of the heart and should facilitate studies of both pathogenesis and therapy of cardiac disorders in humans.
Quantitative Study of Cell Invasion Process under Extracellular Stimulation of Cytokine in a Microfluidic Device
Authors: Lei Kin Fong , Tseng Hsueh-Peng , Lee Chia-Yi , Tsang Ngan-Ming 
Published: May 2016

AbstractCell invasion is the first step of cancer metastasis that is the primary cause of death for cancer patients and defined as cell movement through extracellular matrix (ECM). Investigation of the correlation between cell invasive and extracellular stimulation is critical for the inhabitation of metastatic dissemination. Conventional cell invasion assay is based on Boyden chamber assay, which has a number of limitations. In this work, a microfluidic device incorporating with impedance measurement technique was developed for quantitative investigation of cell invasion process. The device consisted of 2 reservoirs connecting with a microchannel filled with hydrogel. Malignant cells invaded along the microchannel and impedance measurement was concurrently conducted by measuring across electrodes located at the bottom of the microchannel. Therefore, cell invasion process could be monitored in real-time and non-invasive manner. Also, cell invasion rate was then calculated to study the correlation between cell invasion and extracellular stimulation, i.e., IL-6 cytokine. Results showed that cell invasion rate was directly proportional to the IL-6 concentration. The microfluidic device provides a reliable and convenient platform for cell-based assays to facilitate more quantitative assessments in cancer research.
Exploring a Phonological Process Approach to Adult Pronunciation Training
Authors: Franklin Amber , McDaniel Lana 
Published: May 2016

Purpose
The production of speech sound classes in adult language learners is affected by (a) interference between the native language and the target language and (b) speaker variables such as time speaking English. In this article, we demonstrate how phonological process analysis, an approach typically used in child speech, can be used to characterize adult target language phonological learning.

Method
Sentences produced by 2 adult Japanese English language learners were transcribed and coded for phoneme accuracy and analyzed according to the percent occurrence of phonological processes. The results were interpreted relative to a contrastive analysis between Japanese and English phonetic inventories and developmental norms for monolingual English children.

Results
In this pilot study, common consonant processes included vocalization, final consonant devoicing, and cluster reduction. These are processes commonly observed in the speech of children who are typically developing.

Conclusions
The process analysis can inform clinical approaches to pronunciation training in adult English language learners. For example, the cycles approach (Hodson & Paden, 1981) may provide more clinical efficacy than an articulatory approach in which phonemes are targeted individually. In addition, a process analysis can enable clinicians to examine the principles of within-class and across-class generalization in adult pronunciation instruction.
Joint modulation format/bit‐rate classification and signal‐to‐noise ratio estimation in multipath fading channels using deep machine learning
Authors: Khan F.N. , Lu C. , Lau A.P.T. 
Published: May 2016

A novel algorithm for simultaneous modulation format/bit‐rate classification and non‐data‐aided (NDA) signal‐to‐noise ratio (SNR) estimation in multipath fading channels by applying deep machine learning‐based pattern recognition on signals’ asynchronous delay‐tap plots (ADTPs) is proposed. The results for three widely‐used modulation formats at two different bit‐rates demonstrate classification accuracy of 99.8%. In addition, NDA SNR estimation over a wide range of 0−30 dB is shown with mean error of 1 dB. The proposed method requires low‐speed, asynchronous sampling of signal and is thus ideal for low‐cost multiparameter estimation under real‐world channel conditions.
Bandwidth improvement of a circularly polarised printed monopole antenna using a lumped capacitor
Authors: Hoang T.V. , Le T.T. , Park H.C. 
Published: May 2016

Axial‐ratio bandwidth (ARBW) improvement of a circularly polarised printed monopole antenna using a lumped capacitor is presented. To demonstrate the effectiveness of this approach, a lumped capacitor is attached in the gap of an inverted‐U‐shaped patch antenna having a narrow 3 dB ARBW. Simulation shows that the ARBW improves from 4.1% (5.68–5.92 GHz) to 30.7% (4.33–5.9 GHz) with the use of a 0.5 pF capacitor. The measured results show a −10 dB reflection bandwidth of 60.5% (3.75–7 GHz), and a 3 dB ARBW of 33.3% (4.25–5.95 GHz). The advantage of the proposed design is that the 3 dB ARBW of an antenna can be easily tuned and extended with the use of only one lumped capacitor.
Effects of thickness on switching current for (Pb0.97La0.02)(Zr0.95Ti0.05)O3 antiferroelectric films under thermo‐electric coupled field
Authors: An Kun , Wang Erwei , He Jian , Chou Xiujian , Xue Chenyang , Zhang Wendong 
Published: May 2016

Homogeneous and compact antiferroelectric (AFE) (Pb, La)(Zr, Ti)O3 thick films in large area with different thicknesses were successfully fabricated by the sol–gel processing on Pt(111)/Ti/SiO2/Si(100) substrates. The characteristics of switching current of samples with different thicknesses under thermo‐electric coupled field were investigated in detail. The experimental result shows that the peak of switching current density increased with the increase of temperature in three samples. Moreover, it is found that the thickness of the films has a big effect on the current density. Therefore, the peak of switching current density increased with increasing in the thickness at the same temperatures. The maximum switching current density of film with the thickness of 2254 nm is 4.35 × 10−5A/cm2. These results are quite important and necessary for design and preparation of the AFE materials applied on high sensitivity and intelligent micro‐sensors and micro‐actuators.
DOGMA: domain-based transcriptome and proteome quality assessment
Authors: Dohmen Elias , Kremer Lukas P.M. , Bornberg-Bauer Erich , Kemena Carsten 
Published: May 2016

Abstract
Motivation: Genome studies have become cheaper and easier than ever before, due to the decreased costs of high-throughput sequencing and the free availability of analysis software. However, the quality of genome or transcriptome assemblies can vary a lot. Therefore, quality assessment of assemblies and annotations are crucial aspects of genome analysis pipelines.
Results: We developed DOGMA, a program for fast and easy quality assessment of transcriptome and proteome data based on conserved protein domains. DOGMA measures the completeness of a given transcriptome or proteome and provides information about domain content for further analysis. DOGMA provides a very fast way to do quality assessment within seconds.
Availability and Implementation: DOGMA is implemented in Python and published under GNU GPL v.3 license. The source code is available on https://ebbgit.uni-muenster.de/domainWorld/DOGMA/ .
Contacts: e.dohmen@wwu.de or c.kemena@wwu.de
Supplementary information: Supplementary data are available at Bioinformatics online.