bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel testate amoebae trait-based approach to infer environmental disturbance in Sphagnum peatlands
Authors: Marcisz Katarzyna , Colombaroli Daniele , Jassey Vincent E. J. , Tinner Willy , Kołaczek Piotr , Gałka Mariusz , Karpińska-Kołaczek Monika , Słowiński Michał , Lamentowicz Mariusz 
Published: September 2016

AbstractSpecies’ functional traits are closely related to ecosystem processes through evolutionary adaptation, and are thus directly connected to environmental changes. Species’ traits are not commonly used in palaeoecology, even though they offer powerful advantages in understanding the impact of environmental disturbances in a mechanistic way over time. Here we show that functional traits of testate amoebae (TA), a common group of palaeoecological indicators, can serve as an early warning signal of ecosystem disturbance and help determine thresholds of ecosystem resilience to disturbances in peatlands. We analysed TA traits from two Sphagnum-dominated mires, which had experienced different kinds of disturbances in the past 2000 years – fire and peat extraction, respectively. We tested the effect of disturbances on the linkages between TA community structure, functional trait composition and functional diversity using structural equation modelling. We found that traits such as mixotrophy and small hidden apertures (plagiostomic apertures) are strongly connected with disturbance, suggesting that these two traits can be used as palaeoecological proxies of peatland disturbance. We show that TA functional traits may serve as a good proxy of past environmental changes, and further analysis of trait-ecosystem relationships could make them valuable indicators of the contemporary ecosystem state.
Flipper strokes can predict energy expenditure and locomotion costs in free-ranging northern and Antarctic fur seals
Authors: Jeanniard-du-Dot Tiphaine , Trites Andrew W. , Arnould John P. Y. , Speakman John R. , Guinet Christophe 
Published: September 2016

AbstractFlipper strokes have been proposed as proxies to estimate the energy expended by marine vertebrates while foraging at sea, but this has never been validated on free-ranging otariids (fur seals and sea lions). Our goal was to investigate how well flipper strokes correlate with energy expenditure in 33 foraging northern and Antarctic fur seals equipped with accelerometers, GPS, and time-depth recorders. We concomitantly measured field metabolic rates with the doubly-labelled water method and derived activity-specific energy expenditures using fine-scale time-activity budgets for each seal. Flipper strokes were detected while diving or surface transiting using dynamic acceleration. Despite some inter-species differences in flipper stroke dynamics or frequencies, both species of fur seals spent 3.79 ± 0.39 J/kg per stroke and had a cost of transport of ~1.6–1.9 J/kg/m while diving. Also, flipper stroke counts were good predictors of energy spent while diving (R2 = 0.76) and to a lesser extent while transiting (R2 = 0.63). However, flipper stroke count was a poor predictor overall of total energy spent during a full foraging trip (R2 = 0.50). Amplitude of flipper strokes (i.e., acceleration amplitude × number of strokes) predicted total energy expenditure (R2 = 0.63) better than flipper stroke counts, but was not as accurate as other acceleration-based proxies, i.e. Overall Dynamic Body Acceleration.
Diversity distribution patterns of Chinese endemic seed plant species and their implications for conservation planning
Authors: Huang Jihong , Huang Jianhua , Lu Xinghui , Ma Keping 
Published: September 2016

AbstractEndemism is an important concept in biogeography and biodiversity conservation. China is one of the richest countries in biodiversity, with very high levels of plant endemism. In this study, we analysed the distribution patterns of diversity, the degree of differentiation and the endemicity of Chinese endemic seed plants using the floristic unit as a basic spatial analysis unit and 11 indices. The analysis was based on distribution data of 24,951 native seed plant species (excluding subspecies and varieties) and 12,980 Chinese endemic seed plant species, which were sourced from both specimen records and published references. The distribution patterns of Chinese endemic flora were generally consistent but disproportionate across China for diversity, degree of differentiation and endemicity. The South Hengduan Mountains Subregion had the highest values for all indices. At the regional level, both the Hengduan Mountains and the Central China regions were highest in diversity and degrees of differentiation. However, both the rate of local endemic to native species and the rate of local to Chinese endemic species were highest in the Taiwan Region and the South Taiwan Region. The Hengduan Mountains Region and the Central China Region are two key conservation priority areas for Chinese endemic seed plants.
Genetic characterization of two fully sequenced multi-drug resistant plasmids pP10164-2 and pP10164-3 from Leclercia adecarboxylata
Authors: Sun Fengjun , Zhou Dongsheng , Sun Qiang , Luo Wenbo , Tong Yigang , Zhang Defu , Wang Qian , Feng Wei , Chen Weijun , Fan Yahan , Xia Peiyuan 
Published: September 2016

AbstractWe previously reported the complete sequence of the resistance plasmid pP10164-NDM, harboring blaNDM (conferring carbapenem resistance) and bleMBL (conferring bleomycin resistance), which is recovered from a clinical Leclercia adecarboxylata isolate P10164 from China. This follow-up work disclosed that there were still two multidrug-resistant (MDR) plasmids pP10164-2 and pP10164-3 coexisting in this strain. pP10164-2 and pP10164-3 were completely sequenced and shown to carry a wealth of resistance genes, which encoded the resistance to at least 10 classes of antibiotics (β-lactams. macrolides, quinolones, aminoglycosides, tetracyclines, amphenicols, quaternary ammonium compounds, sulphonamides, trimethoprim and rifampicin) and 7 kinds of heavy mental (mercury, silver, copper, nickel, chromate, arsenic and tellurium). All of these antibiotic resistance genes are associated with mobile elements such as transposons, integrons and insertion sequence-based transposable units, constituting a total of three novel MDR regions, two in pP10164-2 and the other one in pP10164-3. Coexistence of three resistance plasmids pP10164-NDM, pP10164-2 and pP10164-3 makes L. adecarboxylata P10164 tend to become extensively drug-resistant.
The Healthy Infant Nasal Transcriptome: A Benchmark Study
Authors: Chu Chin-Yi , Qiu Xing , Wang Lu , Bhattacharya Soumyaroop , Lofthus Gerry , Corbett Anthony , Holden-Wiltse Jeanne , Grier Alex , Tesini Brenda , Gill Steven R. , Falsey Ann R. , Caserta Mary T. , Walsh Edward E. , Mariani Thomas J. 
Published: September 2016

AbstractResponses by resident cells are likely to play a key role in determining the severity of respiratory disease. However, sampling of the airways poses a significant challenge, particularly in infants and children. Here, we report a reliable method for obtaining nasal epithelial cell RNA from infants for genome-wide transcriptomic analysis and describe baseline expression characteristics in an asymptomatic cohort. Nasal epithelial cells were collected by brushing of the inferior turbinates and gene expression was interrogated by RNA-seq analysis. Reliable recovery of RNA occurred in the absence of adverse events. We observed high expression of epithelial cell markers and similarity to the transcriptome for intrapulmonary airway epithelial cells. We identified genes displaying low and high expression variability, both inherently and in response to environmental exposures. The greatest gene expression differences in this asymptomatic cohort were associated with the presence of known pathogenic viruses and/or bacteria. Robust bacteria-associated gene expression patterns were significantly associated with the presence of Moraxella. In summary, we have developed a reliable method for interrogating the infant airway transcriptome by sampling the nasal epithelium. Our data demonstrates both the fidelity and feasibility of our methodology and describes normal gene expression and variation within a healthy infant cohort.
Region-specific growth restriction of brain following preterm birth
Authors: Iwata Sachiko , Katayama Reiji , Kinoshita Masahiro , Saikusa Mamoru , Araki Yuko , Takashima Sachio , Abe Toshi , Iwata Osuke 
Published: September 2016

AbstractRegional brain sizes of very-preterm infants at term-equivalent age differ from those of term-born peers, which have been linked with later cognitive impairments. However, dependence of regional brain volume loss on gestational age has not been studied in detail. To investigate the spatial pattern of brain growth in neonates without destructive brain lesions, head MRI of 189 neonates with a wide range of gestational age (24–42 weeks gestation) was assessed using simple metrics measurements. Dependence of MRI findings on gestational age at birth (Agebirth) and the corrected age at MRI scan (AgeMRI) were assessed. The head circumference was positively correlated with AgeMRI, but not Agebirth. The bi-parietal width, deep grey matter area and the trans-cerebellar diameter were positively correlated with both Agebirth and AgeMRI. The callosal thickness (positive), atrial width of lateral ventricle (negative) and the inter-hemispheric distance (negative) were exclusively correlated with Agebirth. The callosal thickness and cerebral/cerebellar transverse diameters showed predominant dependence on Agebirth over AgeMRI, suggesting that brain growth after preterm-birth was considerably restricted or even became negligible compared with that in utero. Such growth restriction after preterm birth may extensively affect relatively more matured infants, considering the linear relationships observed between brain sizes and Agebirth.
Expression of immunoproteasome genes is regulated by cell-intrinsic and –extrinsic factors in human cancers
Authors: Rouette Alexandre , Trofimov Assya , Haberl David , Boucher Geneviève , Lavallée Vincent-Philippe , D’Angelo Giovanni , Hébert Josée , Sauvageau Guy , Lemieux Sébastien , Perreault Claude 
Published: September 2016

AbstractBased on transcriptomic analyses of thousands of samples from The Cancer Genome Atlas, we report that expression of constitutive proteasome (CP) genes (PSMB5, PSMB6, PSMB7) and immunoproteasome (IP) genes (PSMB8, PSMB9, PSMB10) is increased in most cancer types. In breast cancer, expression of IP genes was determined by the abundance of tumor infiltrating lymphocytes and high expression of IP genes was associated with longer survival. In contrast, IP upregulation in acute myeloid leukemia (AML) was a cell-intrinsic feature that was not associated with longer survival. Expression of IP genes in AML was IFN-independent, correlated with the methylation status of IP genes, and was particularly high in AML with an M5 phenotype and/or MLL rearrangement. Notably, PSMB8 inhibition led to accumulation of polyubiquitinated proteins and cell death in IPhigh but not IPlow AML cells. Co-clustering analysis revealed that genes correlated with IP subunits in non-M5 AMLs were primarily implicated in immune processes. However, in M5 AML, IP genes were primarily co-regulated with genes involved in cell metabolism and proliferation, mitochondrial activity and stress responses. We conclude that M5 AML cells can upregulate IP genes in a cell-intrinsic manner in order to resist cell stress.
The Capacity of Cognitive Control Estimated from a Perceptual Decision Making Task
Authors: Wu Tingting , Dufford Alexander J. , Mackie Melissa-Ann , Egan Laura J. , Fan Jin 
Published: September 2016

AbstractCognitive control refers to the processes that permit selection and prioritization of information processing in different cognitive domains to reach the capacity-limited conscious mind. Although previous studies have suggested that the capacity of cognitive control itself is limited, a direct quantification of this capacity has not been attempted. In this behavioral study, we manipulated the information rate of cognitive control by parametrically varying both the uncertainty of stimul measured as information entropy and the exposure time of the stimuli. We used the relationship between the participants’ response accuracy and the information rate of cognitive control (in bits per second, bps) in the model fitting to estimate the capacity of cognitive control. We found that the capacity of cognitive control was approximately 3 to 4 bps, demonstrating that cognitive control as a higher-level function has a remarkably low capacity. This quantification of the capacity of cognitive control may have significant theoretical and clinical implications.
Flavonoids are determinants of freezing tolerance and cold acclimation in Arabidopsis thaliana
Authors: Schulz Elisa , Tohge Takayuki , Zuther Ellen , Fernie Alisdair R. , Hincha Dirk K. 
Published: September 2016

AbstractIn plants from temperate climates such asArabidopsis thalianalow, non-freezing temperatures lead to increased freezing tolerance in a process termed cold acclimation. This process is accompanied by massive changes in gene expression and in the content of primary metabolites and lipids. In addition, most flavonols and anthocyanins accumulate upon cold exposure, along with most transcripts encoding transcription factors and enzymes of the flavonoid biosynthetic pathway. However, no evidence for a functional role of flavonoids in plant freezing tolerance has been shown. Here, we present a comprehensive analysis using qRT-PCR for transcript, LC-MS for flavonoid and GC-MS for primary metabolite measurements and an electrolyte leakage assay to determine freezing tolerance of 20 mutant lines in twoArabidopsisaccessions that are affected in different steps of the flavonoid biosynthetic pathway. This analysis provides evidence for a functional role of flavonoids in plant cold acclimation. The accumulation of flavonoids in the activation tagging mutant linepap1-Dimproved, while reduced flavonoid content in different knock-out mutants impaired leaf freezing tolerance. Analysis of the different knock-out mutants suggests redundancy of flavonoid structures, as the lack of flavonols or anthocyanins could be compensated by other compound classes.
Tooth wear as a means to quantify intra-specific variations in diet and chewing movements
Authors: Calandra Ivan , Labonne Gaëlle , Schulz-Kornas Ellen , Kaiser Thomas M. , Montuire Sophie 
Published: September 2016

AbstractIn mammals, tooth function, and its efficiency, depends both on the mechanical properties of the food and on chewing dynamics. These aspects have rarely been studied in combination and/or at the intra-specific level. Here we applied 3D dental surface texture analysis to a sample of field voles (Microtus agrestis) trapped from Finnish Lapland at different seasons and localities to test for inter-population variations. We also explored intra-individual variation in chewing dynamics by analysing two facets on the second upper molars. Our results confirm that the two localities have similar environments and that the voles feed on the same items there. On the other hand, the texture data suggest that diets are seasonally variable, probably due to varying concentrations of abrasives. Lastly, the textures on the buccal facets are more isotropic and their direction deviates more from the mesial chewing direction than the lingual facets. We interpret these results as reflecting food, rather than chewing, movements, where food particles are more guided on the lingual side of the molars. This has implications for the application of dental microwear analysis to fossils: only homologous facets can be compared, even when the molar row seems to constitute a functional unit.
Stereological analyses of the whole human pancreas
Authors: Poudel Ananta , Fowler Jonas L. , Zielinski Mark C. , Kilimnik German , Hara Manami 
Published: September 2016

AbstractThe large size of human tissues requires a practical stereological approach to perform a comprehensive analysis of the whole organ. We have developed a method to quantitatively analyze the whole human pancreas, as one of the challenging organs to study, in which endocrine cells form various sizes of islets that are scattered unevenly throughout the exocrine pancreas. Furthermore, the human pancreas possesses intrinsic characteristics of intra-individual variability, i.e. regional differences in endocrine cell/islet distribution, and marked inter-individual heterogeneity regardless of age, sex and disease conditions including obesity and diabetes. The method is built based on large-scale image capture, computer-assisted unbiased image analysis and quantification, and further mathematical analyses, using widely-used software such as Fiji/ImageJ and MATLAB. The present study includes detailed protocols of every procedure as well as all the custom-written computer scripts, which can be modified according to specific experimental plans and specimens of interest.
Modulation of yeast telomerase activity by Cdc13 and Est1 in vitro
Authors: Chen Yu-Fan , Lu Chia-Ying , Lin Yi-Chien , Yu Tai-Yuan , Chang Chun-Ping , Li Jing-Ru , Li Hung-Wen , Lin Jing-Jer 
Published: September 2016

AbstractTelomerase is the enzyme involved in extending telomeric DNA. Control of telomerase activity by modulating its access to chromosome ends is one of the most important fundamental mechanisms. This study established an in vitro yeast telomerase reconstitution system that resembles telomere replication in vivo. In this system, a tailed-duplex DNA formed by telomeric DNA was employed to mimic the structure of telomeres. The core catalytic components of telomerase Est2/Tlc1 RNA were used as the telomeric DNA extension machinery. Using the reconstituted systems, this study found that binding of Cdc13 to telomeric DNA inhibited the access of telomerase to its substrate. The result was further confirmed by a single-molecule approach using the tethered-particle motion (TPM)-based telomerase assay. The findings also showed that the inhibitory effect can be relieved by telomerase-associated protein Est1, consistent with the role of Cdc13 and Est1 in regulating telomere extension in vivo. Significantly, this study found that the DNA binding property of Cdc13 was altered by Est1, providing the first mechanistic evidence of Est1 regulating the access of telomerase to its substrate. Thus, the roles of Cdc13 and Est1 in modulating telomerase activity were clearly defined using the in vitro reconstituted system.
Transmembrane Helices Tilt, Bend, Slide, Torque, and Unwind between Functional States of Rhodopsin
Authors: Ren Zhong , Ren Peter X. , Balusu Rohith , Yang Xiaojing 
Published: September 2016

AbstractThe seven-helical bundle of rhodopsin and other G-protein coupled receptors undergoes structural rearrangements as the transmembrane receptor protein is activated. These structural changes are known to involve tilting and bending of various transmembrane helices. However, the cause and effect relationship among structural events leading to a cytoplasmic crevasse for G-protein binding is less well defined. Here we present a mathematical model of the protein helix and a simple procedure to determine multiple parameters that offer precise depiction of a helical conformation. A comprehensive survey of bovine rhodopsin structures shows that the helical rearrangements during the activation of rhodopsin involve a variety of angular and linear motions such as torsion, unwinding, and sliding in addition to the previously reported tilting and bending. These hitherto undefined motion components unify the results obtained from different experimental approaches, and demonstrate conformational similarity between the active opsin structure and the photoactivated structures in crystallo near the retinal anchor despite their marked differences.
Time to lowest postoperative carcinoembryonic antigen level is predictive on survival outcome in rectal cancer
Authors: Yu Huichuan , Luo Yanxin , Wang Xiaolin , Bai Liangliang , Huang Pinzhu , Wang Lei , Huang Meijin , Deng Yanhong , Wang Jianping 
Published: September 2016

AbstractThis study was to investigate whether the time to the lowest postoperative CEA can predict cancer survival. We enrolled 155 rectal cancer patients in this retrospective and longitudinal cohort study. Deepness of response (DpR) of CEA refers to the relative change of the lowest postoperative CEA level from baseline and time to DpR (TTDpR) refers to the time from surgery to the lowest postoperative CEA level. The median of TTDpR and DpR was 4.5 (range, 3.0–18.0) weeks and −67% (range, −99% to 114%) respectively. Patients with TTDpR </ = 4.5 weeks had better 3-year DFS (81.4% vs. 76.2%; P = 0.059) and OS (95.8% vs. 87.9%; P = 0.047) rate than patients with TTDpR >4.5 weeks. Using TTDpR as a continuous variable, the HR of DFS and OS was 1.13 (95% CI 1.06–1.22, P = 0.001) and 1.17 (95% CI 1.07–1.29, P = 0.001) respectively. On multivariate analysis, the predictive value of prolonged TTDpR remained [adjusted HRs: 1.12 (95% CI 1.03–1.21, P = 0.006) and 1.17 (95% CI 1.06–1.28, P = 0.001)]. These findings remained significant in patients with normal preoperative CEA. Our results showed prolonged TTDpR of CEA independently predicted unfavorable survival outcomes, regardless of whether preoperative CEA was elevated or not.
Interleukin-25 Induces Resistance Against Intestinal Trematodes
Authors: Muñoz-Antoli Carla , Cortés Alba , Santano Rebeca , Sotillo Javier , Esteban J. Guillermo , Toledo Rafael 
Published: September 2016

AbstractEchinostoma caproni is an intestinal trematode that has been extensively used as an experimental model to investigate the factors determining the resistance to intestinal helminths or the development of chronic infections. ICR mice are permissive hosts for E. caproni in which chronic infections are developed, concomitantly with local Th1 responses, elevated levels of local IFN-γ, inflammation and antibody responses. However, mice develop partial resistance to homologous challenge infections after cure of a primary infection, which converts this subject into an adequate model for the study of the mechanisms generating resistance against intestinal helminths. The purpose of the present study was to compare the immune response induced in primary and secondary infections to elucidate the factors determining the different outcome of the infection in each type of infection. The results obtained indicate that susceptibility is determined by the lack of IL-25 expression in response to primary infection. In contrast, infection in an environment with elevated levels of IL-25, as occurs in challenge infection, results in a Th2 phenotype impairing parasite survival. This was confirmed by treatment of naïve mice with exogenous IL-25 and subsequent infection. Changes induced in goblet cell populations and mucin glycosylation could be implicated in resistance to infection.