bluuebunny/crossref_metadata_2025_split huggingface dataset:
BBS4 and BBS5 show functional redundancy in the BBSome to regulate the degradative sorting of ciliary sensory receptors
Authors: Xu Qingwen , Zhang Yuxia , Wei Qing , Huang Yan , Li Yan , Ling Kun , Hu Jinghua 
Published: July 2015

AbstractCilia harbor sensory receptors for various signaling cascades critical for vertebrate development. However, the mechanisms underlying the ciliary homeostasis of sensory receptors remain elusive. Here, we demonstrate that BBS-4 and BBS-5, two distinct BBSome components, show unexpected functional redundancy in the context of cilia in C. elegans. BBS-4 directly interacts with BBS-5 and the interaction can be disrupted by a conserved mutation identified in human BBS4. Surprisingly, we found that BBS-4 and BBS-5 act redundantly in the BBSome to regulate the ciliary removal, rather than the ciliary entry or retrograde IFT transport, of various sensory receptors. Further analyses indicate that co-depletion of BBS-4 and BBS-5 disrupts the lysosome-targeted degradative sorting of ciliary sensory receptors. Moreover, mammalian BBS4 and BBS5 also interact directly and coordinate the ciliary removal of polycystin 2. Hence, we reveal a novel and highly conserved role for the BBSome in fine-tuning ciliary signaling by regulating the ciliary removal of sensory receptors for lysosomal degradation.
Hui and Walter’s latent-class model extended to estimate diagnostic test properties from surveillance data: a latent model for latent data
Authors: Bermingham Mairead L. , Handel Ian G. , Glass Elizabeth J. , Woolliams John A. , Bronsvoort B. Mark de Clare , McBride Stewart H. , Skuce Robin A. , Allen Adrian R. , McDowell Stanley W. J. , Bishop Stephen C. 
Published: July 2015

AbstractDiagnostic test sensitivity and specificity are probabilistic estimates with far reaching implications for disease control, management and genetic studies. In the absence of ‘gold standard’ tests, traditional Bayesian latent class models may be used to assess diagnostic test accuracies through the comparison of two or more tests performed on the same groups of individuals. The aim of this study was to extend such models to estimate diagnostic test parameters and true cohort-specific prevalence, using disease surveillance data. The traditional Hui-Walter latent class methodology was extended to allow for features seen in such data, including (i) unrecorded data (i.e. data for a second test available only on a subset of the sampled population) and (ii) cohort-specific sensitivities and specificities. The model was applied with and without the modelling of conditional dependence between tests. The utility of the extended model was demonstrated through application to bovine tuberculosis surveillance data from Northern and the Republic of Ireland. Simulation coupled with re-sampling techniques, demonstrated that the extended model has good predictive power to estimate the diagnostic parameters and true herd-level prevalence from surveillance data. Our methodology can aid in the interpretation of disease surveillance data and the results can potentially refine disease control strategies.
Revealing Three Stages of DNA-Cisplatin Reaction by a Solid-State Nanopore
Authors: Zhou Zhi , Hu Ying , Shan Xinyan , Li Wei , Bai Xuedong , Wang Pengye , Lu Xinghua 
Published: July 2015

AbstractThe dynamic structural behavior in DNA due to interaction with cisplatin is essential for the functionality of platinum-based anti-cancer drugs. Here we report a novel method to monitor the interaction progress in DNA-cisplatin reaction in real time with a solid-state nanopore. The interaction processes are found to be well elucidated by the evolution of the capture rate of DNA-cisplatin complex, which is defined as the number of their translocation events through the nanopore in unit time. In the first stage, the capture rate decreases rapidly due to DNA discharging as the positive-charged hydrated cisplatin molecules initially bond to the negative-charged DNA and form mono-adducts. In the second stage, by forming di-adducts, the capture rate increases as DNA molecules are softened, appears as the reduced persistence length of the DNA-cisplatin adducts. In the third stage, the capture rate decreases again as a result of DNA aggregation. Our study demonstrates a new single-molecule tool in exploring dynamic behaviors during drug-DNA reactions and may have future application in fast drug screening.
Function of a p24 Heterodimer in Morphogenesis and Protein Transport in Penicillium oxalicum
Authors: Wang Fangzhong , Liu Kuimei , Han Lijuan , Jiang Baojie , Wang Mingyu , Fang Xu 
Published: July 2015

AbstractThe lignocellulose degradation capacity of filamentous fungi has been widely studied because of their cellulase hypersecretion. The p24 proteins in eukaryotes serve important functions in this secretory pathway. However, little is known about the functions of the p24 proteins in filamentous fungi. In this study, four p24 proteins were identified in Penicillium oxalicum. Six p24 double-deletion strains were constructed and further studies were carried out with the ΔerpΔpδ strain. The experimental results suggested that Erp and Pδ form a p24 heterodimer in vivo. This p24 heterodimer participates in important morphogenetic events, including sporulation, hyphal growth and lateral branching. The results suggested that the p24 heterodimer mediates protein transport, particularly that of cellobiohydrolase. Analysis of the intracellular proteome revealed that the ΔerpΔpδ double mutant is under secretion stress due to attempts to remove proteins that are jammed in the endomembrane system. These results suggest that the p24 heterodimer participates in morphogenesis and protein transport. Compared with P. oxalicum Δerp, a greater number of cellular physiological pathways were impaired in ΔerpΔpδ. This finding may provide new insights into the secretory pathways of filamentous fungi.
Association of relative telomere length with progression of chronic kidney disease in two cohorts: effect modification by smoking and diabetes
Authors: Raschenberger Julia , Kollerits Barbara , Ritchie James , Lane Beverley , Kalra Philip A. , Ritz Eberhard , Kronenberg Florian 
Published: July 2015

AbstractChronic kidney disease (CKD) is a highly progressive disease. We studied the association between relative telomere length (RTL) and CKD progression and tested whether this association is modified by smoking and diabetes mellitus. RTL was measured by qPCR in two prospective cohort studies, the MMKD-Study (n = 166) and the CRISIS-Study (n = 889) with a median follow-up of 4.5 and 2.8 years, respectively. Progression was defined as doubling of baseline serum creatinine (MMKD-Study) and/or end stage renal disease (both studies). 59 and 105 of the patients from MMKD and CRISIS experienced a progression of CKD. Mean standardized pooled RTL was 0.74 ± 0.29. In the meta-analysis shorter RTL at baseline showed a borderline association with CKD progression (HR = 1.07 [95%CI 1.00–1.15]; p = 0.06). We observed an effect modification of RTL and CKD progression by smoking and diabetes (p-values of interaction p = 0.02 and p = 0.09, respectively). Each 0.1 unit shorter RTL was significantly associated with an increased hazard for CKD progression in active-smokers by 44% (HR = 1.44 [1.16–1.81]; p = 0.001) and in patients with diabetes mellitus by 16% (HR = 1.16 [1.01–1.34]; p = 0.03). Estimates were adjusted for baseline age, sex, proteinuria and GFR. This study in two independent cohorts reinforces that RTL is a marker and potentially a pathogenetic factor for CKD progression.
Functional characterization of the principal sigma factor RpoD of phytoplasmas via an in vitro transcription assay
Authors: Miura Chihiro , Komatsu Ken , Maejima Kensaku , Nijo Takamichi , Kitazawa Yugo , Tomomitsu Tatsuya , Yusa Akira , Himeno Misako , Oshima Kenro , Namba Shigetou 
Published: July 2015

AbstractPhytoplasmas (class, Mollicutes) are insect-transmissible and plant-pathogenic bacteria that multiply intracellularly in both plants and insects through host switching. Our previous study revealed that phytoplasmal sigma factor rpoD of OY-M strain (rpoDOY) could be a key regulator of host switching, because the expression level of rpoDOY was higher in insect hosts than in plant hosts. In this study, we developed an in vitro transcription assay system to identify RpoDOY-dependent genes and the consensus promoter elements. The assay revealed that RpoDOY regulated some housekeeping, virulence and host–phytoplasma interaction genes of OY-M strain. The upstream region of the transcription start sites of these genes contained conserved –35 and –10 promoter sequences, which were similar to the typical bacterial RpoD-dependent promoter elements, while the –35 promoter elements were variable. In addition, we searched putative RpoD-dependent genes based on these promoter elements on the whole genome sequence of phytoplasmas using in silico tools. The phytoplasmal RpoD seems to mediate the transcription of not only many housekeeping genes as the principal sigma factor, but also the virulence- and host-phytoplasma interaction-related genes exhibiting host-specific expression patterns. These results indicate that more complex mechanisms exist than previously thought regarding gene regulation enabling phytoplasmas to switch hosts.
miR-125a-3p and miR-483-5p promote adipogenesis via suppressing the RhoA/ROCK1/ERK1/2 pathway in multiple symmetric lipomatosis
Authors: Chen Ke , He Honghui , Xie Yanhong , Zhao Liling , Zhao Shaoli , Wan Xinxing , Yang Wenjun , Mo Zhaohui 
Published: July 2015

AbstractMultiple symmetric lipomatosis (MSL) is a rare disease characterized by symmetric and abnormal distribution of subcutaneous adipose tissue (SAT); however, the etiology is largely unknown. We report here that miR-125a-3p and miR-483-5p are upregulated in the SAT of MSL patients, promoting adipogenesis through suppressing the RhoA/ROCK1/ERK1/2 pathway. TaqMan microRNA (miR) array analysis revealed that 18 miRs were upregulated in the SAT of MSL patients. Transfection of human adipose-derived mesenchymal stem cells (hADSCs) with the individual agomirs of these 18 miRs showed that miR-125a-3p and miR-483-5p significantly promoted adipogenesis. A dual-luciferase assay showed that RhoA and ERK1 were the targets of miR-125a-3p and miR-483-5p, respectively. Moreover, transfection of hADSCs with mimics of miR-125a-3p and miR-483-5p resulted in a pronounced decrease of ERK1/2 phosphorylation in the nucleus; conversely, transfection of hADSCs with inhibitors of miR-125a-3p and miR-483-5p led to a significant increase of ERK1/2 phosphorylation in the nucleus. Most importantly, we found that miR-125a-3p and miR-483-5p promotedde novoadipose tissue formation in nude mice. These results demonstrated that miR-125a-3p and miR-483-5p coordinately promoted adipogenesis through suppressing the RhoA/ROCK1/ERK1/2 pathway. Our findings may provide novel strategies for the management and treatment of MSL or obesity.
Crystal structure of a COG4313 outer membrane channel
Authors: Berg Bert van den , Bhamidimarri Satya Prathyusha , Winterhalter Mathias 
Published: July 2015

AbstractCOG4313 proteins form a large and widespread family of outer membrane channels and have been implicated in the uptake of a variety of hydrophobic molecules. Structure-function studies of this protein family have so far been hampered by a lack of structural information. Here we present the X-ray crystal structure of Pput2725 from the biodegrader Pseudomonas putida F1, a COG4313 channel of unknown function, using data to 2.3 Å resolution. The structure shows a 12-stranded barrel with an N-terminal segment preceding the first β-strand occluding the lumen of the barrel. Single channel electrophysiology and liposome swelling experiments suggest that while the narrow channel visible in the crystal structure does allow passage of ions and certain small molecules in vitro, Pput2725 is unlikely to function as a channel for hydrophilic molecules. Instead, the presence of bound detergent molecules inside the barrel suggests that Pput2725 mediates uptake of hydrophobic molecules. Sequence alignments and the locations of highly conserved residues suggest the presence of a dynamic lateral opening through which hydrophobic molecules might gain entry into the cell. Our results provide the basis for structure-function studies of COG4313 family members with known function, such as the SphA sphingosine uptake channel of Pseudomonas aeruginosa.
An optimization solution of a laser plane in vision measurement with the distance object between global origin and calibration points
Authors: Xu Guan , Hao Zhaobing , Li Xiaotao , Su Jian , Liu Huanping , Sun Lina 
Published: July 2015

AbstractEquation construction of a laser plane demonstrates a remarkable importance for vision measurement systems based on the structured light. Here we create a simple 1D target with a cone at the bottom and a checkered pattern on the top to calibrate the equation of the laser plane in the view field of a camera. A group of 2D coordinates of the intersection points are extracted from the images with the 1D target at different positions. The objective function is constructed to optimize the coefficients of the laser plane by minimizing the difference between the distance from the feature point to the the origin point and the length of the 1D target. The projective lines of the optimized laser plane on the 3D calibration board overlap the real intersection lines in the experimental images. Finally, the comparison work about the influences of the non-Gaussian noise and point number is investigated experimentally. The experiments show that the method of the distance optimal object from the feature point to the origin point provides an accurate and robust calibration for the laser plane in structured light measurement.
A High Throughput Micro-Chamber Array Device for Single Cell Clonal Cultivation and Tumor Heterogeneity Analysis
Authors: Shen Feng-Min , Zhu Lian , Ye Heng , Yang Yu-Jun , Pang Dai-Wen , Zhang Zhi-Ling 
Published: July 2015

AbstractRecently, single cell cloning techniques have been gradually developed benefited from their important roles in monoclonal antibody screening, tumor heterogeneity research fields, etc. In this study, we developed a high throughput device containing 1400 lateral chambers to efficiently isolate single cells and carry out long-term single cell clonal cultivation as well as tumor heterogeneity studies. Most of the isolated single cells could proliferate normally nearly as long as three weeks and hundreds of clones could be formed once with one device, which made it possible to study tumor heterogeneity at single cell level. The device was further used to examine tumor heterogeneity such as morphology, growth rate, anti-cancer drug tolerance as well as adenosine triphosphate-binding cassette (ABC) transporter ABCG2 protein expression level. Except for the single cell isolation and tumor heterogeneity studies, the device is expected to be used as an excellent platform for drug screening, tumor biomarker discovering and tumor metastasis assay.
Transcriptome analysis of mRNA and miRNA in skeletal muscle indicates an important network for differential Residual Feed Intake in pigs
Authors: Jing Lu , Hou Ye , Wu Hui , Miao Yuanxin , Li Xinyun , Cao Jianhua , Michael Brameld John , Parr Tim , Zhao Shuhong 
Published: July 2015

AbstractFeed efficiency (FE) can be measured by feed conversion ratio (FCR) or residual feed intake (RFI). In this study, we measured the FE related phenotypes of 236 castrated purebred Yorkshire boars and selected 10 extreme individuals with high and low RFI for transcriptome analysis. We used RNA-seq analyses to determine the differential expression of genes and miRNAs in skeletal muscle. There were 99 differentially expressed genes identified (q ≤ 0.05). The down-regulated genes were mainly involved in mitochondrial energy metabolism, including FABP3, RCAN, PPARGC1 (PGC-1A), HK2 and PRKAG2. The up-regulated genes were mainly involved in skeletal muscle differentiation and proliferation, including IGF2, PDE7A, CEBPD, PIK3R1 and MYH6. Moreover, 15 differentially expressed miRNAs (|log2FC| ≥ 1, total reads count ≥ 20, p ≤ 0.05) were identified. Among them, miR-136, miR-30e-5p, miR-1, miR-208b, miR-199a, miR-101 and miR-29c were up-regulated, while miR-215, miR-365-5p, miR-486, miR-1271, miR-145, miR-99b, miR-191 and miR-10b were down-regulated in low RFI pigs. We conclude that decreasing mitochondrial energy metabolism, possibly through AMPK - PGC-1A pathways and increasing muscle growth, through IGF-1/2 and TGF-β signaling pathways, are potential strategies for the improvement of FE in pigs (and possibly other livestock). This study provides new insights into the molecular mechanisms that determine RFI and FE in pigs.
Insulin sensitivity index (ISI0, 120) potentially linked to carbon isotopes of breath CO2 for pre-diabetes and type 2 diabetes
Authors: Ghosh Chiranjit , Mukhopadhyay Prabuddha , Ghosh Shibendu , Pradhan Manik 
Published: July 2015

AbstractNew strategies for an accurate and early detection of insulin resistance are important to delay or prevent the acute onset of type 2 diabetes (T2D). Currently, insulin sensitivity index (ISI0,120) is considered to be a viable invasive method of whole-body insulin resistance for use in clinical settings in comparison with other invasive sensitivity indexes like homeostasis model assessment (HOMA) and quantitative insulin sensitivity check index (QUICKI). To investigate how these sensitivity indexes link the 13C/12C-carbon isotopes of exhaled breath CO2 to pre-diabetes (PD) and type 2 diabetes in response to glucose ingestion, we studied excretion dynamics of 13C/12C-isotopic fractionations of breath CO2. Here, we show that 13C/12C-isotope ratios of breath CO2 were well correlated with blood glucose, insulin, glycosylated-hemoglobin as well as with HOMA-IR and 1/QUICKI. Conversely, the strongest correlation was observed between 1/ISI0,120 and breath CO2 isotopes. Consequently, we determined several optimal diagnostic cut-off points of 1/ISI0,120 and 13CO2/12CO2-isotope ratios to distinctively track the evolution of PD prior to the onset of T2D. Our findings suggest that isotopic breath CO2 is a novel method for accurate estimation of ISI0,120 and thus may open new perspectives into the isotope-specific non-invasive evaluation of insulin resistance for large-scale real-time diabetes screening purposes.
Wide Carbon Nanopores as Efficient Sites for the Separation of SF6 from N2
Authors: Takase Atsushi , Kanoh Hirofumi , Ohba Tomonori 
Published: July 2015

AbstractSF6 and SF6-N2 mixed gases are used widely as insulators, but such gases have high greenhouse gas potential. The separation of SF6 from SF6-N2 mixed gases is an inevitable result of their use. Single-walled carbon nanohorns (CNHs) were used here for a fundamental study of the separation of SF6 and N2. The diameters of the interstitial and internal nanopores of the CNHs were 0.7 and 2.9 nm, respectively. The high selectivity of SF6 over N2 was observed only in the low-pressure regime in the interstitial 0.7 nm nanopores; the selectively was significantly decreased at higher pressures. In contrast, the high selectivity was maintained over the entire pressure range in the internal 2.9-nm nanopores. These results showed that the wide carbon nanopores were efficient for the separation of SF6 from the mixed gas.
Scaffolding of a bacterial genome using MinION nanopore sequencing
Authors: Karlsson E. , Lärkeryd A. , Sjödin A. , Forsman M. , Stenberg P. 
Published: July 2015

AbstractSecond generation sequencing has revolutionized genomic studies. However, most genomes contain repeated DNA elements that are longer than the read lengths achievable with typical sequencers, so the genomic order of several generated contigs cannot be easily resolved. A new generation of sequencers offering substantially longer reads is emerging, notably the Pacific Biosciences (PacBio) RS II system and the MinION system, released in early 2014 by Oxford Nanopore Technologies through an early access program. The latter has highly advantageous portability and sequences samples by measuring changes in ionic current when single-stranded DNA molecules are translocated through nanopores. We show that the MinION system produces long reads with high mapability that can be used for scaffolding bacterial genomes, despite currently producing substantially higher error rates than PacBio reads. With further development we anticipate that MinION will be useful not only for assembling genomes, but also for rapid detection of organisms, potentially in the field.
Increased neurokinin-1 receptor availability in the amygdala in social anxiety disorder: a positron emission tomography study with [11C]GR205171
Authors: Frick A , Ahs F , Linnman C , Jonasson M , Appel L , Lubberink M , Långström B , Fredrikson M , Furmark T 
Published: July 2015

AbstractThe neurokinin-1 (NK1) receptor is abundantly expressed in the fear circuitry of the brain, including the amygdala, where it modulates stress and anxiety. Despite its proposed involvement in psychopathology, only a few studies of NK1 receptor availability in human subjects with anxiety disorders exist. Here, we compared NK1 receptor availability in patients with social anxiety disorder (SAD; n=17) and healthy controls (n=17) using positron emission tomography and the radiotracer [11C]GR205171. The Patlak Graphical plot using a cerebellar reference region was used to model the influx parameter, Ki measuring NK1 receptor availability. Voxel-wise statistical parametric mapping analyses revealed increased NK1 receptor availability specifically in the right amygdala in SAD patients relative to controls. Thus, we demonstrate that exaggerated social anxiety is related to enhanced NK1 receptor availability in the amygdala. This finding supports the contribution of NK1 receptors not only in animal models of stress and anxiety but also in humans with anxiety disorders.
Stability of Word-Retrieval Errors With the AphasiaBank Stimuli
Authors: Boyle Mary 
Published: July 2015

Purpose
This study examined the test–retest reliability of select measures of word-retrieval errors in narrative discourses of individuals with aphasia assessed with the AphasiaBank stimuli.

Method
Ten participants with aphasia were video recorded during 2 sessions producing narratives elicited with pictures. Discourses were transcribed and coded using AphasiaBank procedures, then analyzed for the stability of rates of phonological errors, semantic errors, false starts, time fillers, and repetitions per minute. Values for correlation coefficients and the minimal detectable change score were used to assess stability for research and clinical decision making.

Results
There was poor test–retest reliability when the discourses were analyzed by each narrative subgenre. When the narrative discourses were combined for analysis, several measures appeared to be sufficiently stable across sessions for use in group studies, and 1 could be adequately stable for making clinical decisions about an individual.

Conclusions
Because the short speech samples yielded by the subgenre narrative analyses demonstrated poor test–retest reliability, it is recommended that all of the picture-based narrative discourse tasks be combined for analysis of word-retrieval impairments when the AphasiaBank stimuli are used. However, the confidence intervals associated with the reliability coefficients obtained in this study suggest caution in using the measures if they are based on performance in a single session. More investigations of the test–retest reliability of measures used to study language impairment in discourse contexts are essential.