bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cross-cultural measurement invariance of the Revised Child Anxiety and Depression Scale across 11 world-wide societies
Authors: Stevanovic D. , Bagheri Z. , Atilola O. , Vostanis P. , Stupar D. , Moreira P. , Franic T. , Davidovic N. , Knez R. , Nikšić A. , Dodig-Ćurković K. , Avicenna M. , Multazam Noor I. , Nussbaum L. , Deljkovic A. , Aziz Thabet A. , Petrov P. , Ubalde D. , Monteiro L. A. , Ribas R. 
Published: June 2016

Background.In order to compare estimates by one assessment scale across various cultures/ethnic groups, an important aspect that needs to be demonstrated is that its construct across these groups is invariant when measured using a similar and simultaneous approach (i.e., demonstrated cross-cultural measurement invariance). One of the methods for evaluating measurement invariance is testing for differential item functioning (DIF), which assesses whether different groups respond differently to particular items. The aim of this study was to evaluate the cross-cultural measurement invariance of the Revised Child Anxiety and Depression Scale (RCADS) in societies with different socioeconomic, cultural, and religious backgrounds.Methods.The study was organised by the International Child Mental Health Study Group. Self-reported data were collected from adolescents residing in 11 countries: Brazil, Bulgaria, Croatia, Indonesia, Montenegro, Nigeria, Palestinian Territories, the Philippines, Portugal, Romania and Serbia. The multiple-indicators multiple-causes model was used to test the RCADS items for DIF across the countries.Results.Ten items exhibited DIF considering all cross-country comparisons. Only one or two items were flagged with DIF in the head-to-head comparisons, while there were three to five items flagged with DIF, when one country was compared with the others. Even with all cross-culturally non-invariant items removed from nine language versions tested, the original factor model representing six anxiety and depressive symptoms subscales was not significantly violated.Conclusions.There is clear evidence that relatively small number of the RCADS items is non-invariant, especially when comparing two different cultural/ethnic groups, which indicates on its sound cross-cultural validity and suitability for cross-cultural comparisons in adolescent anxiety and depressive symptoms.
Deep sequencing and in silico analyses identify MYB-regulated gene networks and signaling pathways in pancreatic cancer
Authors: Azim Shafquat , Zubair Haseeb , Srivastava Sanjeev K. , Bhardwaj Arun , Zubair Asif , Ahmad Aamir , Singh Seema , Khushman Moh’d. , Singh Ajay P. 
Published: June 2016

AbstractWe have recently demonstrated that the transcription factor MYB can modulate several cancer-associated phenotypes in pancreatic cancer. In order to understand the molecular basis of these MYB-associated changes, we conducted deep-sequencing of transcriptome of MYB-overexpressing and -silenced pancreatic cancer cells, followed by in silico pathway analysis. We identified significant modulation of 774 genes upon MYB-silencing (p < 0.05) that were assigned to 25 gene networks by in silico analysis. Further analyses placed genes in our RNA sequencing-generated dataset to several canonical signalling pathways, such as cell-cycle control, DNA-damage and -repair responses, p53 and HIF1α. Importantly, we observed downregulation of the pancreatic adenocarcinoma signaling pathway in MYB-silenced pancreatic cancer cells exhibiting suppression of EGFR and NF-κB. Decreased expression of EGFR and RELA was validated by both qPCR and immunoblotting and they were both shown to be under direct transcriptional control of MYB. These observations were further confirmed in a converse approach wherein MYB was overexpressed ectopically in a MYB-null pancreatic cancer cell line. Our findings thus suggest that MYB potentially regulates growth and genomic stability of pancreatic cancer cells via targeting complex gene networks and signaling pathways. Further in-depth functional studies are warranted to fully understand MYB signaling in pancreatic cancer.
Network Modeling Identifies Patient-specific Pathways in Glioblastoma
Authors: Tuncbag Nurcan , Milani Pamela , Pokorny Jenny L. , Johnson Hannah , Sio Terence T. , Dalin Simona , Iyekegbe Dennis O. , White Forest M. , Sarkaria Jann N. , Fraenkel Ernest 
Published: June 2016

AbstractGlioblastoma is the most aggressive type of malignant human brain tumor. Molecular profiling experiments have revealed that these tumors are extremely heterogeneous. This heterogeneity is one of the principal challenges for developing targeted therapies. We hypothesize that despite the diverse molecular profiles, it might still be possible to identify common signaling changes that could be targeted in some or all tumors. Using a network modeling approach, we reconstruct the altered signaling pathways from tumor-specific phosphoproteomic data and known protein-protein interactions. We then develop a network-based strategy for identifying tumor specific proteins and pathways that were predicted by the models but not directly observed in the experiments. Among these hidden targets, we show that the ERK activator kinase1 (MEK1) displays increased phosphorylation in all tumors. By contrast, protein numb homolog (NUMB) is present only in the subset of the tumors that are the most invasive. Additionally, increased S100A4 is associated with only one of the tumors. Overall, our results demonstrate that despite the heterogeneity of the proteomic data, network models can identify common or tumor specific pathway-level changes. These results represent an important proof of principle that can improve the target selection process for tumor specific treatments.
Transcriptome profiling of the rat retina after optic nerve transection
Authors: Yasuda Masayuki , Tanaka Yuji , Omodaka Kazuko , Nishiguchi Koji M. , Nakamura Orie , Tsuda Satoru , Nakazawa Toru 
Published: June 2016

AbstractGlaucoma is a group of eye diseases characterized by alterations in the contour of the optic nerve head (ONH), with corresponding visual field defects and progressive loss of retinal ganglion cells (RGCs). This progressive RGC death is considered to originate in axonal injury caused by compression of the axon bundles in the ONH. However, the molecular pathomechanisms of axonal injury-induced RGC death are not yet well understood. Here, we used RNA sequencing (RNA-seq) to examine transcriptome changes in rat retinas 2 days after optic nerve transection (ONT) and then used computational techniques to predict the resulting alterations in the transcriptional regulatory network. RNA-seq revealed 267 differentially expressed genes after ONT, 218 of which were annotated and 49 unannotated. We also identified differentially expressed transcripts, including potentially novel isoforms. Anin silicopathway analysis predicted that CREB1 was the most significant upstream regulator. Thus, this study identified genes and pathways that may be involved in the pathomechanisms of axonal injury. We believe that our data should serve as a valuable resource to understand the molecular processes that define axonal injury-driven RGC death and to discover novel therapeutic targets for glaucoma.
Comparative genomics analysis of the companion mechanisms of Bacillus thuringiensis Bc601 and Bacillus endophyticus Hbe603 in bacterial consortium
Authors: Jia Nan , Ding Ming-Zhu , Gao Feng , Yuan Ying-Jin 
Published: June 2016

AbstractBacillus thuringiensis and Bacillus endophyticus both act as the companion bacteria, which cooperate with Ketogulonigenium vulgare in vitamin C two-step fermentation. Two Bacillus species have different morphologies, swarming motility and 2-keto-L-gulonic acid productivities when they co-culture with K. vulgare. Here, we report the complete genome sequencing of B. thuringiensis Bc601 and eight plasmids of B. endophyticus Hbe603, and carry out the comparative genomics analysis. Consequently, B. thuringiensis Bc601, with greater ability of response to the external environment, has been found more two-component system, sporulation coat and peptidoglycan biosynthesis related proteins than B. endophyticus Hbe603, and B. endophyticus Hbe603, with greater ability of nutrients biosynthesis, has been found more alpha-galactosidase, propanoate, glutathione and inositol phosphate metabolism, and amino acid degradation related proteins than B. thuringiensis Bc601. Different ability of swarming motility, response to the external environment and nutrients biosynthesis may reflect different companion mechanisms of two Bacillus species. Comparative genomic analysis of B. endophyticus and B. thuringiensis enables us to further understand the cooperative mechanism with K. vulgare, and facilitate the optimization of bacterial consortium.
Mantle Subduction and Uplift of Intracontinental Mountains: A Case Study from the Chinese Tianshan Mountains within Eurasia
Authors: Li Jinyi , Zhang Jin , Zhao Xixi , Jiang Mei , Li Yaping , Zhu Zhixin , Feng Qianwen , Wang Lijia , Sun Guihua , Liu Jianfeng , Yang Tiannan 
Published: June 2016

AbstractThe driving mechanism that is responsible for the uplift of intracontinental mountains has puzzled geologists for decades. This study addresses this issue by using receiver function images across the Chinese Tianshan Mountains and available data from both deep seismic profiles and surface structural deformation. The near-surface structural deformation shows that the Tianshan crust experienced strong shortening during the Cenozoic. The receiver function image across the Tianshan Mountains reveals that the lithosphere of the Junggar Basin to the north became uncoupled along the Moho and the mantle below the Moho subducted southwards beneath the northern part of the Tianshan Mountains, thereby thickening the overlying crust. Similar deep structures, however, are not observed under the Tarim Basin and the adjacent southern Tianshan Mountains. This difference in the deep structures correlates with geomorphological features in the region. Thus, a new model of mantle subduction, herein termed M-type subduction, is proposed for the mountain-building processes in intracontinental compressional settings. The available geomorphological, geological and seismic data in the literatures show that this model is probably suitable for other high, linear mountains within the continent.
Informational laws of genome structures
Authors: Bonnici Vincenzo , Manca Vincenzo 
Published: June 2016

AbstractIn recent years, the analysis of genomes by means of strings of lengthkoccurring in the genomes, calledk-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value ofkfor applying information theoretic concepts that express intrinsic aspects of genomes. The valuek = lg2(n), wherenis the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balancesentropicandanti-entropiccomponents of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.
Steady State Ocean Response to Wind Forcing in Extratropical Frontal Regions
Authors: Cronin Meghan F. , Tozuka Tomoki 
Published: June 2016

AbstractIn regions of strong sea surface temperature (SST) gradients, the surface “geostrophic” currents have a vertical shear aligned with the surface density front defined by the temperature. This surface geostrophic (“thermal wind”) shear can balance a portion of the surface wind stress, altering the classic Ekman response to wind forcing. Here we show that these frontal effects cannot be ignored in the Tropics or in strong frontal regions in the extratropics, such as found in coastal regions and in western boundary currents of all basins. Frontal effects also dominate the classic Ekman response in the regions of both hemispheres where Trade winds change to westerlies. Implications for vertical motion and global heat transport are discussed.
Modelling how incorporation of divalent cations affects calcite wettability–implications for biomineralisation and oil recovery
Authors: Andersson M. P. , Dideriksen K. , Sakuma H. , Stipp S. L. S. 
Published: June 2016

AbstractUsing density functional theory and geochemical speciation modelling, we predicted how solid-fluid interfacial energy is changed, when divalent cations substitute into a calcite surface. The effect on wettability can be dramatic. Trace metal uptake can impact organic compound adsorption, with effects for example, on the ability of organisms to control crystal growth and our ability to predict the wettability of pore surfaces. Wettability influences how easily an organic phase can be removed from a surface, either organic compounds from contaminated soil or crude oil from a reservoir. In our simulations, transition metals substituted exothermically into calcite and more favourably into sites at the surface than in the bulk, meaning that surface properties are more strongly affected than results from bulk experiments imply. As a result of divalent cation substitution, calcite-fluid interfacial energy is significantly altered, enough to change macroscopic contact angle by tens of degrees. Substitution of Sr, Ba and Pb makes surfaces more hydrophobic. With substitution of Mg and the transition metals, calcite becomes more hydrophilic, weakening organic compound adsorption. For biomineralisation, this provides a switch for turning on and off the activity of organic crystal growth inhibitors, thereby controlling the shape of the associated mineral phase.
Non-canonical NFκB activation promotes chemokine expression in podocytes
Authors: Valiño-Rivas Lara , Gonzalez-Lafuente Laura , Sanz Ana B. , Ruiz-Ortega Marta , Ortiz Alberto , Sanchez-Niño Maria D. 
Published: June 2016

AbstractTNF-like weak inducer of apoptosis (TWEAK) receptor Fn14 is expressed by podocytes and Fn14 deficiency protects from experimental proteinuric kidney disease. However, the downstream effectors of TWEAK/Fn14 in podocytes are poorly characterized. We have explored TWEAK activation of non-canonical NFκB signaling in cultured podocytes. In cultured podocytes, TWEAK increased the expression of the chemokines CCL21, CCL19 and RANTES in a time-dependent manner. The inhibitor of canonical NFκB activation parthenolide inhibited the CCL19 and the early RANTES responses, but not the CCL21 or late RANTES responses. In this regard, TWEAK induced non-canonical NFκB activation in podocytes, characterized by NFκB2/p100 processing to NFκB2/p52 and nuclear migration of RelB/p52. Silencing by a specific siRNA of NIK, the upstream kinase of the non-canonical NFκB pathway, prevented CCL21 upregulation but did not modulate CCL19 or RANTES expression in response to TWEAK, thus establishing CCL21 as a non-canonical NFκB target in podocytes. Increased kidney Fn14 and CCL21 expression was also observed in rat proteinuric kidney disease induced by puromycin and was localized to podocytes. In conclusion, TWEAK activates the non-canonical NFκB pathway in podocytes, leading to upregulation of CCL21 expression. The non-canonical NFκB pathway should be explored as a potential therapeutic target in proteinuric kidney disease.
Membrane protein assembly: two cytoplasmic phosphorylated serine sites of Vpu from HIV-1 affect oligomerization
Authors: Chen Chin-Pei , Lin Meng-Han , Chan Ya-Ting , Chen Li-Chyong , Ma Che , Fischer Wolfgang B. 
Published: June 2016

AbstractViral protein U (Vpu) encoded by human immunodeficiency virus type 1 (HIV-1) is a short integral membrane protein which is known to self-assemble within the lipid membrane and associate with host factors during the HIV-1 infectivity cycle. In this study, full-length Vpu (M group) from clone NL4-3 was over-expressed in human cells and purified in an oligomeric state. Various single and double mutations were constructed on its phosphorylation sites to mimic different degrees of phosphorylation. Size exclusion chromatography of wild-type Vpu and mutants indicated that the smallest assembly unit of Vpu was a dimer and over time Vpu formed higher oligomers. The rate of oligomerization increased when (i) the degree of phosphorylation at serines 52 and 56 was decreased and (ii) when the ionic strength was increased indicating that the cytoplasmic domain of Vpu affects oligomerization. Coarse-grained molecular dynamic simulations with models of wild-type and mutant Vpu in a hydrated lipid bilayer supported the experimental data in demonstrating that, in addition to a previously known role in downregulation of host factors, the phosphorylation sites of Vpu also modulate oligomerization.
Optofluidic UV-Vis spectrophotometer for online monitoring of photocatalytic reactions
Authors: Wang Ning , Tan Furui , Zhao Yu , Tsoi Chi Chung , Fan Xudong , Yu Weixing , Zhang Xuming 
Published: June 2016

AbstractOn-chip integration of optical detection units into the microfluidic systems for online monitoring is highly desirable for many applications and is also well in line with the spirit of optofluidics technology–fusion of optics and microfluidics for advanced functionalities. This paper reports the construction of a UV-Vis spectrophotometer on a microreactor, and demonstrates the online monitoring of the photocatalytic degradations of methylene blue and methyl orange under different flow rates and different pH values by detecting the intensity change and/or the peak shift. The integrated device consists of a TiO2-coated glass substrate, a PDMS micro-sized reaction chamber and two flow cells. By comparing with the results of commercial equipment, we have found that the measuring range and the sensitivity are acceptable, especially when the transmittance is in the range of 0.01–0.9. This integrated optofluidic device can significantly cut down the test time and the sample volume, and would provide a versatile platform for real-time characterization of photochemical performance. Moreover, its online monitoring capability may enable to access the usually hidden information in biochemical reactions like intermediate products, time-dependent processes and reaction kinetics.
Genome-wide characterization of the β-1,3-glucanase gene family in Gossypium by comparative analysis
Authors: Xu Xiaoyang , Feng Yue , Fang Shuai , Xu Jun , Wang Xinyu , Guo Wangzhen 
Published: June 2016

AbstractThe β-1,3-glucanase gene family is involved in a wide range of plant developmental processes as well as pathogen defense mechanisms. Comprehensive analyses of β-1,3-glucanase genes (GLUs) have not been reported in cotton. Here, we identified 67, 68, 130 and 158 GLUs in four sequenced cotton species, G. raimondii (D5), G. arboreum (A2), G. hirsutum acc. TM-1 (AD1) and G. barbadense acc. 3–79 (AD2), respectively. Cotton GLUs can be classified into the eight subfamilies (A–H) and their protein domain architecture and intron/exon structure are relatively conserved within each subfamily. Sixty-seven GLUs in G. raimondii were anchored onto 13 chromosomes, with 27 genes involved in segmental duplications and 13 in tandem duplications. Expression patterns showed highly developmental and spatial regulation of GLUs in TM-1. In particular, the expression of individual member of GLUs in subfamily E was limited to roots, leaves, floral organs or fibers. Members of subfamily E also showed more protein evolution and subgenome expression bias compared with members of other subfamilies. We clarified that GLU42 and GLU43 in subfamily E were preferentially expressed in root and leaf tissues and significantly upregulated after Verticillium dahliae inoculation. Silencing of GLU42 and GLU43 significantly increased the susceptibility of cotton to V. dahliae.
Clear Speech Variants: An Acoustic Study in Parkinson's Disease
Authors: Lam Jennifer , Tjaden Kris 
Published: June 2016

Purpose
The authors investigated how different variants of clear speech affect segmental and suprasegmental acoustic measures of speech in speakers with Parkinson's disease and a healthy control group.

Method
A total of 14 participants with Parkinson's disease and 14 control participants served as speakers. Each speaker produced 18 different sentences selected from the Sentence Intelligibility Test (Yorkston & Beukelman, 1996). All speakers produced stimuli in 4 speaking conditions (habitual, clear, overenunciate, and hearing impaired). Segmental acoustic measures included vowel space area and first moment (M1) coefficient difference measures for consonant pairs. Second formant slope of diphthongs and measures of vowel and fricative durations were also obtained. Suprasegmental measures included fundamental frequency, sound pressure level, and articulation rate.

Results
For the majority of adjustments, all variants of clear speech instruction differed from the habitual condition. The overenunciate condition elicited the greatest magnitude of change for segmental measures (vowel space area, vowel durations) and the slowest articulation rates. The hearing impaired condition elicited the greatest fricative durations and suprasegmental adjustments (fundamental frequency, sound pressure level).

Conclusions
Findings have implications for a model of speech production for healthy speakers as well as for speakers with dysarthria. Findings also suggest that particular clear speech instructions may target distinct speech subsystems.
Comparison of Physical Activity Levels in Rheumatic Diseases
Authors: Acar M. , Tonga E. , Daskapan A. , Karataş M. , Tekindal A. 
Published: June 2016

Abstract
Objectives: The aim of this study was to evaluate levels of physical activity in patients with rheumatoid arthritis, osteoarthritis and fibromyalgia and to compare the results with both healthy subjects and each other.
Methods: A group of 50 rheumatoid arthritis patients, 95 osteoarthritis patients, 82 fibromyalgia patients and 110 healthy subjects were included in this study. Physical activity levels were assessed by the International Physical Activity Questionnaire (IPAQ).
Results: There were significant differences in walking and total physical activity scores in IPAQ between the rheumatoid arthritis (RA), osteoarthritis (OA), fibromyalgia (FMS) patients and the control group (p<0.05). 36.6% of the fibromyalgia group, 28.4% of the osteoarthritis group, 38% of the rheumatoid arthritis group and 22.7% of the healthy subjects were found to be inactive. 45.1% of the fibromyalgia group, 42.1% of the osteoarthritis group, 46% of the rheumatoid arthritis group and 36.4% of the healthy subjects were found to be insufficiently active.
Conclusion: As a result, when compared to healthy people, physical activity levels were significantly decreased in patients with rheumatoid arthritis, osteoarthritis, fibromyalgia. The decreases in the physical activity levels were clearer in patients with rheumatoid arthritis than in patients with osteoarthritis and fibromyalgia. Recommending regular physical activity should be integral to rheumatic disease management and walking offers a potentially accessible, inexpensive, and acceptable physical activity intervention.