bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climate warming and atmospheric deposition affect seed viability of common juniper (Juniperus communis) via their impact on the nutrient status of the plant
Authors: Gruwez Robert , De Frenne Pieter , De Schrijver An , Vangansbeke Pieter , Verheyen Kris 
Published: December 2016

AbstractGlobal environmental change is increasingly affecting species worldwide. One of the emblematic casualties among plants in several European countries is common juniper (Juniperus communis). Many populations of common juniper throughout its distribution range are declining. The relative lack of viable seed production, resulting in low probabilities for successful natural regeneration, is one of the main reasons for this decline. Climate warming and elevated atmospheric depositions have been shown to negatively affect seed viability of common juniper, but our understanding of the underlying mechanisms remains scarce. One possible pathway is via changes in the plant nutrient status that, in turn, may affect seed viability. Here we took advantage of large‐scale gradients in climate and atmospheric depositions between central Sweden and northern Spain, and analysed foliar nutrient concentrations and stoichiometry and seed viability in 20 juniper populations spread across Europe. Our results show that increasing temperatures can negatively affect needle N and P concentrations while enhanced potentially acidifying depositions resulted in lower foliar N and Ca concentrations. Needle C:N ratios increased with higher temperature, acidifying depositions and precipitation. By linking these patterns to seed viability, we found that low needle P, Ca and Mg concentrations were related to low seed viability. Thus, a shortage of these key elements during seed development and seed nutrient storage, can lead to anomalies and seed abortion. These findings help to explain the low seed viability of juniper in Europe and may help to assist land managers to take urgently needed conservation actions.
Eicosapentaenoic Acid‐Enriched Phosphatidylcholine Attenuated Hepatic Steatosis Through Regulation of Cholesterol Metabolism in Rats with Nonalcoholic Fatty Liver Disease
Authors: Liu Yanjun , Shi Di , Tian Yingying , Liu Yuntao , Zhan Qiping , Xu Jie , Wang Jingfeng , Xue Changhu 
Published: December 2016

AbstractNonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in the world. Disturbed cholesterol metabolism plays a crucial role in the development of NAFLD. The present study was conducted to evaluate the effects of EPA‐PC extracted from sea cucumber on liver steatosis and cholesterol metabolism in NAFLD. Male Wistar rats were randomly divided into seven groups (normal control group, model group, lovastatin group, low‐ and high‐dose EPA groups, and low‐ and high‐dose EPA‐PC groups). Model rats were established by administering a diet containing 1% orotic acid. To determine the possible cholesterol metabolism promoting mechanism of EPA‐PC, we analyzed the transcription of key genes and transcriptional factors involved in hepatic cholesterol metabolism. EPA‐PC dramatically alleviated hepatic lipid accumulation, reduced the serum TC concentration, and elevated HDLC levels in NAFLD rats. Fecal neutral cholesterol excretion was also promoted by EPA‐PC administration. Additionally, EPA‐PC decreased the mRNA expression of hydroxymethyl glutaric acid acyl (HMGR) and cholesterol 7α‐hydroxylase (CYP7A), and increased the transcription of sterol carrying protein 2 (SCP2). Moreover, EPA‐PC stimulated the transcription of peroxisome proliferators‐activated receptor α (PPARα) and adenosine monophosphate activated protein kinase (AMPK) as well as its modulators, liver kinase B1 (LKB1) and Ca2+/calmodulin‐dependent kinase kinase (CAMKK). Based on the results, the promoting effects of EPA‐PC on NAFLD may be partly associated with the suppression of cholesterol synthesis via HMGR inhibition and the enhancement of fecal cholesterol excretion through increased SCP2 transcription. The underlying mechanism may involve stimulation of PPARα and AMPK.
On the possibility of identifying human subjects using behavioural complexity analyses
Authors: Kloucek Petr , von Gunten Armin 
Published: December 2016

BackgroundIdentification of human subjects using a geometric approach to complexity analysis of behavioural data is designed to provide a basis for a more precise diagnosis leading towards personalised medicine.MethodsThe approach is based on capturing behavioural time‐series that can be characterized by a fractional dimension using non‐invasive longer‐time acquisitions of heart rate, perfusion, blood oxygenation, skin temperature, relative movement and steps frequency. The geometry based approach consists in the analysis of the area and centroid of convex hulls encapsulating the behavioural data represented in Euclidian index spaces based on the scaling properties of the self‐similar normally distributed behavioural time‐series of the above mentioned quantities.ResultsAn example demonstrating the presented approach of behavioural fingerprinting is provided using sensory data of eight healthy human subjects based on approximately fifteen hours of data acquisition. Our results show that healthy subjects can be factorized to different similarity groups based on a particular choice of a convex hull in the corresponding Euclidian space. One of the results indicates that healthy subjects share only a small part of the convex hull pertaining to a highly trained individual from the geometric comparison point of view. Similarly, the presented pair‐wise individual geometric similarity measure indicates large differences among the subjects suggesting the possibility of neuro‐fingerprinting.ConclusionsRecently introduced multi‐channel body‐attached sensors provide a possibility to acquire behavioural time‐series that can be mathematically analysed to obtain various objective measures of behavioural patterns yielding behavioural diagnoses favouring personalised treatments of, e.g., neuropathologies or aging.
Differential expression analyses for single‐cell RNA‐Seq: old questions on new data
Authors: Miao Zhun , Zhang Xuegong 
Published: December 2016

BackgroundSingle‐cell RNA sequencing (scRNA‐seq) is an emerging technology that enables high resolution detection of heterogeneities between cells. One important application of scRNA‐seq data is to detect differential expression (DE) of genes. Currently, some researchers still use DE analysis methods developed for bulk RNA‐Seq data on single‐cell data, and some new methods for scRNA‐seq data have also been developed. Bulk and single‐cell RNA‐seq data have different characteristics. A systematic evaluation of the two types of methods on scRNA‐seq data is needed.ResultsIn this study, we conducted a series of experiments on scRNA‐seq data to quantitatively evaluate 14 popular DE analysis methods, including both of traditional methods developed for bulk RNA‐seq data and new methods specifically designed for scRNA‐seq data. We obtained observations and recommendations for the methods under different situations.ConclusionsDE analysis methods should be chosen for scRNA‐seq data with great caution with regard to different situations of data. Different strategies should be taken for data with different sample sizes and/or different strengths of the expected signals. Several methods for scRNA‐seq data show advantages in some aspects, and DEGSeq tends to outperform other methods with respect to consistency, reproducibility and accuracy of predictions on scRNA‐seq data.
Comorbidity, family history and personality traits in pathological gamblers compared with healthy controls
Authors: Mann K. , Lemenager T. , Zois E. , Hoffmann S. , Nakovics H. , Beutel M. , Vogelgesang M. , Wölfling K. , Kiefer F. , Fauth-Bühler M. 
Published: December 2016

AbstractBackgroundWhile DSM-5 classified pathological gambling as an addictive disorder, there is debate as to whether ICD-11 should follow suit. The debate hinges on scientific evidence such as neurobiological findings, family history of psychiatric disorders, psychiatric comorbidity, and personality variables.MethodsIn the “Baden-Württemberg Study of Pathological Gambling”, we compared a group of 515 male pathological gamblers receiving treatment with 269 matched healthy controls. We studied differences in sociodemographic characteristics, gambling-related variables, psychiatric comorbidity (lifetime), family history of psychiatric conditions, as well as personality traits such as impulsivity (Barratt Impulsiveness Scale), sensation seeking (Zuckerman's Sensation Seeking Scale) and the NEO-FFI big five. Personality traits were validated in an age- and ethnicity-matched subsample of “pure” gamblers without any psychiatric comorbidity (including nicotine dependence). Data were analyzed using two-sample t-tests, Chi2 analyses, Fisher's exact test and Pearson correlation analysis, as appropriate. Bonferroni correction was applied to correct for multiple comparisons.ResultsOnly 1% of the gamblers had been diagnosed with an impulse control disorder other than gambling (ICD-10). Notably, 88% of the gamblers in our sample had a comorbid diagnosis of substance dependence. The highest axis I comorbidity rate was for nicotine dependence (80%), followed by alcohol dependence (28%). Early age of first gambling experience was correlated with gambling severity. Compared to first-degree relatives of controls, first-degree relatives of pathological gamblers were more likely to suffer from alcohol dependence (27.0% vs. 7.4%), pathological gambling (8.3% vs. 0.7%) and suicide attempts (2.7% vs. 0.4%). Significant group differences were observed for the NEO-FFI factors neuroticism, agreeableness and conscientiousness. Gamblers were also more impulsive than controls, but did not differ from controls in terms of sensation seeking.ConclusionsOur findings support classifying pathological gambling as a behavioural addiction in the ICD-11. This decision will have a significant impact on the approaches available for prevention (e.g. age limits) and treatment.
Preclinical Alzheimer's disease and longitudinal driving decline
Authors: Roe Catherine M. , Babulal Ganesh M. , Head Denise M. , Stout Sarah H. , Vernon Elizabeth K. , Ghoshal Nupur , Garland Brad , Barco Peggy P. , Williams Monique M. , Johnson Ann , Fierberg Rebecca , Fague M. Scot , Xiong Chengjie , Mormino Elizabeth , Grant Elizabeth A. , Holtzman David M. , Benzinger Tammie L.S. , Fagan Anne M. , Ott Brian R. , Carr David B. , Morris John C. 
Published: December 2016

AbstractIntroductionLinks between preclinical Alzheimer's disease (AD) and driving difficulty onset would support the use of driving performance as an outcome in primary and secondary prevention trials among older adults (OAs). We examined whether AD biomarkers predicted the onset of driving difficulties among OAs.MethodsOne hundred four OAs (65+ years) with normal cognition took part in biomarker measurements, a road test, clinical and psychometric batteries, and self‐reported their driving habits.ResultsHigher values of cerebrospinal fluid (CSF) tau/Aβ42 and phosphorylated tau (ptau181)/Aβ42 ratios, but not uptake on Pittsburgh compound B amyloid imaging (P = .12), predicted time to a rating of marginal or fail on the driving test using Cox proportional hazards models. Hazards ratios (95% confidence interval) were 5.75 (1.70–19.53), P = .005 for CSF tau/Aβ42; 6.19 (1.75–21.88), and P = .005 for CSF ptau181/Aβ42.DiscussionPreclinical AD predicted time to receiving a marginal or fail rating on an on‐road driving test. Driving performance shows promise as a functional outcome in AD prevention trials.
Alex Halliday Receives 2016 Harry H. Hess Medal
Authors:   AGU
Published: December 2016

Alex Halliday was awarded the 2016 Harry H. Hess Medal at the American Geophysical Union Fall Meeting Honors Ceremony, held on 14 December 2016 in San Francisco, Calif. The medal is for "outstanding achievements in research on the constitution and evolution of the Earth and other planets."
Pleckstrin homology domain-containing protein PHLDB3 supports cancer growth via a negative feedback loop involving p53
Authors: Chao Tengfei , Zhou Xiang , Cao Bo , Liao Peng , Liu Hongbing , Chen Yun , Park Hee-Won , Zeng Shelya X. , Lu Hua 
Published: December 2016

AbstractThe tumour suppressor p53 transactivates the expression of its target genes to exert its functions. Here, we identify a pleckstrin homology domain-containing protein (PHLDB3)-encoding gene as a p53 target. PHLDB3 overexpression increases proliferation and restrains apoptosis of wild-type p53-harboring cancer cells by reducing p53 protein levels. PHLDB3 binds to MDM2 (mouse double minute 2 homolog) and facilitates MDM2-mediated ubiquitination and degradation of p53. Knockdown of PHLDB3 more efficiently inhibits the growth of mouse xenograft tumours derived from human colon cancer HCT116 cells that contain wild type p53 compared with p53-deficient HCT116 cells, and also sensitizes tumour cells to doxorubicin and 5-Fluorouracil. Analysis of cancer genomic databases reveals that PHLDB3 is amplified and/or highly expressed in numerous human cancers. Altogether, these results demonstrate that PHLDB3 promotes tumour growth by inactivating p53 in a negative feedback fashion and suggest PHLDB3 as a potential therapeutic target in various human cancers.
The overexpressed functional transient receptor potential channel TRPM2 in oral squamous cell carcinoma
Authors: Zhao Ling-Yan , Xu Wan-Lin , Xu Zeng-Qi , Qi Cui , Li Yang , Cheng Jie , Liu Lai-Kui , Wu Yu-Nong , Gao Jun , Ye Jin-Hai 
Published: December 2016

AbstractTRPM2, one member of the transient receptor potential (TRP) protein super-family, is a Ca2+-permeable channel that is activated by oxidative stress and confers susceptibility to cell death. In the human tongue specimens of carcinoma and the tongue carcinoma SCC cell lines, we observed the enhanced expression of TRPM2. By means of the whole-cell electrophysiological recording, the ADPR-induced currents mediated by TRPM2 were recorded in cultured SCC9 cells. Moreover, after H2O2 treatment for 24 hours, the apoptotic number of SCC9 cells was significantly increased. However, the selectively knocked-down TRPM2 with the small interfering RNA technique inhibited the survival and migration of the SCC9 cancer cells, which was independent of the p53-p21 pathway, since the expression of p21 was enhanced after TRPM2 knockdown. Furthermore, the sub-cellular localization of TRPM2 was remarkably different between cancerous and non-cancerous cells. A significant amount of the TRPM2 proteins were located in the nuclei in cancer cells. All these data suggest that TRPM2 is essential for the survival and migration of SCC cancer cells and may be a potential target for the selective treatment of tongue cancer.
Collisional cross-section of water molecules in vapour studied by means of 1H relaxation in NMR
Authors: Mammoli Daniele , Canet Estel , Buratto Roberto , Miéville Pascal , Helm Lothar , Bodenhausen Geoffrey 
Published: December 2016

AbstractIn gas phase, collisions that affect the rotational angular momentum lead to the return of the magnetization to its equilibrium (relaxation) in Nuclear Magnetic Resonance (NMR). To the best of our knowledge, the longitudinal relaxation rates R1 = 1/T1 of protons in H2O and HDO have never been measured in gas phase. We report R1 in gas phase in a field of 18.8 T, i.e., at a proton Larmor frequency ν0 = 800 MHz, at temperatures between 353 and 373 K and pressures between 9 and 101 kPa. By assuming that spin rotation is the dominant relaxation mechanism, we estimated the effective cross-section σJ for the transfer of angular momentum due to H2O-H2O and HDO-D2O collisions. Our results allow one to test theoretical predictions of the intermolecular potential of water in gas phase.
Acoustic micro-tapping for non-contact 4D imaging of tissue elasticity
Authors: Ambroziński Łukasz , Song Shaozhen , Yoon Soon Joon , Pelivanov Ivan , Li David , Gao Liang , Shen Tueng T. , Wang Ruikang K. , O’Donnell Matthew 
Published: December 2016

AbstractElastography plays a key role in characterizing soft media such as biological tissue. Although this technology has found widespread use in both clinical diagnostics and basic science research, nearly all methods require direct physical contact with the object of interest and can even be invasive. For a number of applications, such as diagnostic measurements on the anterior segment of the eye, physical contact is not desired and may even be prohibited. Here we present a fundamentally new approach to dynamic elastography using non-contact mechanical stimulation of soft media with precise spatial and temporal shaping. We call it acoustic micro-tapping (AμT) because it employs focused, air-coupled ultrasound to induce significant mechanical displacement at the boundary of a soft material using reflection-based radiation force. Combining it with high-speed, four-dimensional (three space dimensions plus time) phase-sensitive optical coherence tomography creates a non-contact tool for high-resolution and quantitative dynamic elastography of soft tissue at near real-time imaging rates. The overall approach is demonstrated in ex-vivo porcine cornea.
Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin-regulating proteins
Authors: Waks Zeev , Weissbrod Omer , Carmeli Boaz , Norel Raquel , Utro Filippo , Goldschmidt Yaara 
Published: December 2016

AbstractCompiling a comprehensive list of cancer driver genes is imperative for oncology diagnostics and drug development. While driver genes are typically discovered by analysis of tumor genomes, infrequently mutated driver genes often evade detection due to limited sample sizes. Here, we address sample size limitations by integrating tumor genomics data with a wide spectrum of gene-specific properties to search for rare drivers, functionally classify them, and detect features characteristic of driver genes. We show that our approach, CAnceR geNe similarity-based Annotator and Finder (CARNAF), enables detection of potentially novel drivers that eluded over a dozen pan-cancer/multi-tumor type studies. In particular, feature analysis reveals a highly concentrated pool of known and putative tumor suppressors among the <1% of genes that encode very large, chromatin-regulating proteins. Thus, our study highlights the need for deeper characterization of very large, epigenetic regulators in the context of cancer causality.
Lotus Base: An integrated information portal for the model legume Lotus japonicus
Authors: Mun Terry , Bachmann Asger , Gupta Vikas , Stougaard Jens , Andersen Stig U. 
Published: December 2016

AbstractLotus japonicus is a well-characterized model legume widely used in the study of plant-microbe interactions. However, datasets from various Lotus studies are poorly integrated and lack interoperability. We recognize the need for a comprehensive repository that allows comprehensive and dynamic exploration of Lotus genomic and transcriptomic data. Equally important are user-friendly in-browser tools designed for data visualization and interpretation. Here, we present Lotus Base, which opens to the research community a large, established LORE1 insertion mutant population containing an excess of 120,000 lines, and serves the end-user tightly integrated data from Lotus, such as the reference genome, annotated proteins, and expression profiling data. We report the integration of expression data from the L. japonicus gene expression atlas project, and the development of tools to cluster and export such data, allowing users to construct, visualize, and annotate co-expression gene networks. Lotus Base takes advantage of modern advances in browser technology to deliver powerful data interpretation for biologists. Its modular construction and publicly available application programming interface enable developers to tap into the wealth of integrated Lotus data. Lotus Base is freely accessible at: https://lotus.au.dk.
Development of a high-density genetic linkage map and identification of flowering time QTLs in adzuki bean (Vigna angularis)
Authors: Liu Changyou , Fan Baojie , Cao Zhimin , Su Qiuzhu , Wang Yan , Zhang Zhixiao , Tian Jing 
Published: December 2016

AbstractA high-density linkage map is crucial for the identification of quantitative trait loci (QTLs), positional cloning, and physical map assembly. Here, we report the development of a high-density linkage map based on specific length amplified fragment sequencing (SLAF-seq) for adzuki bean and the identification of flowering time-related QTLs. Through SLAF library construction and Illumina sequencing of a recombinant inbred line (RIL) population, a total of 4425 SLAF markers were developed and assigned to 11 linkage groups (LGs). After binning the SLAF markers that represented the same genotype, the final linkage map of 1628.15 cM contained 2032 markers, with an average marker density of 0.80 cM. Comparative analysis showed high collinearity with two adzuki bean physical maps and a high degree of synteny with the reference genome of common bean (Phaseolus vulgaris). Using this map, one major QTL on LG03 and two minor QTLs on LG05 associated with first flowering time (FLD) were consistently identified in tests over a two-year period. These results provide a foundation that will be useful for future genomic research, such as identifying QTLs for other important traits, positional cloning, and comparative mapping in legumes.
Formation of equiaxed crystal structures in directionally solidified Al-Si alloys using Nb-based heterogeneous nuclei
Authors: Bolzoni Leandro , Xia Mingxu , Babu Nadendla Hari 
Published: December 2016

AbstractThe design of chemical compositions containing potent nuclei for the enhancement of heterogeneous nucleation in aluminium, especially cast alloys such as Al-Si alloys, is a matter of importance in order to achieve homogeneous properties in castings with complex geometries. We identified that Al3Nb/NbB2 compounds are effective heterogeneous nuclei and are successfully produced in the form of Al-2Nb-xB (x = 0.5, 1 and 2) master alloys. Our study shows that the inoculation of Al-10Si braze alloy with these compounds effectively promotes the heterogeneous nucleation of primary α-Al crystals and reduces the undercooling needed for solidification to take place. Moreover, we present evidences that these Nb-based compounds prevent the growth of columnar crystals and permit to obtain, for the first time, fine and equiaxed crystals in directionally solidified Al-10Si braze alloy. As a consequence of the potent heterogeneous particles, the size of the α-Al crystals was found to be less dependent on the processing conditions, especially the thermal gradient. Finally, we also demonstrate that the enhanced nucleation leads to the refinement of secondary phases such as eutectic silicon and primary silicon particles.