bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relationships between functional diversity and aboveground biomass production in the Northern Tibetan alpine grasslands
Authors: Zhu Juntao , Jiang Lin , Zhang Yangjian 
Published: September 2016

AbstractFunctional diversity, the extent of functional differences among species in a community, drives biodiversity–ecosystem function (BEF) relationships. Here, four species traits and aboveground biomass production (ABP) were considered. We used two community-wide measures of plant functional composition, (1) community weighted means of trait values (CWM) and (2) functional trait diversity based on Rao’s quadratic diversity (FDQ) to evaluate the effects of functional diversity on the ABP in the Northern Tibetan alpine grasslands. Both species and functional diversity were positively related to the ABP. Functional trait composition had a larger predictive power for the ABP than species diversity and FDQ, indicating a primary dependence of ecosystem property on the identity of dominant species in our study system. Multivariate functional diversity was ineffective in predicting ecosystem function due to the trade-offs among different traits or traits selection criterions. Our study contributes to a better understanding of the mechanisms driving the BEF relationships in stressed ecosystems and especially emphasizes that abiotic and biotic factors affect the BEF relationships in alpine grasslands.
Controllable Edge Oxidation and Bubbling Exfoliation Enable the Fabrication of High Quality Water Dispersible Graphene
Authors: Tian Suyun , Sun Jing , Yang Siwei , He Peng , Wang Gang , Di Zengfeng , Ding Guqiao , Xie Xiaoming , Jiang Mianheng 
Published: September 2016

AbstractDespite significant progresses made on mass production of chemically exfoliated graphene, the quality, cost and environmental friendliness remain major challenges for its market penetration. Here, we present a fast and green exfoliation strategy for large scale production of high quality water dispersible few layer graphene through a controllable edge oxidation and localized gas bubbling process. Mild edge oxidation guarantees that the pristine sp2 lattice is largely intact and the edges are functionalized with hydrophilic groups, giving rise to high conductivity and good water dispersibility at the same time. The aqueous concentration can be as high as 5.0 mg mL−1, which is an order of magnitude higher than previously reports. The water soluble graphene can be directly spray-coated on various substrates, and the back-gated field effect transistor give hole and electron mobility of ~496 and ~676 cm2 V−1 s−1, respectively. These results achieved are expected to expedite various applications of graphene.
Human and mouse monocytes display distinct signalling and cytokine profiles upon stimulation with FFAR2/FFAR3 short-chain fatty acid receptor agonists
Authors: Ang Zhiwei , Er Jun Zhi , Tan Nguan Soon , Lu Jinhua , Liou Yih-Cherng , Grosse Johannes , Ding Jeak Ling 
Published: September 2016

AbstractKnockout mice studies implicate the mammalian short-chain fatty acid (SCFA) receptors, FFAR2 and FFAR3– in colitis, arthritis and asthma. However, the correlation with human biology is uncertain. Here, we detected FFAR2 and FFAR3 expression in human monocytes via immunohistochemistry. Upon treatment with acetate SCFA or FFAR2- and FFAR3-specific synthetic agonists, human monocytes displayed elevated p38 phosphorylation and attenuated C5, CCL1, CCL2, GM-CSF, IL-1α, IL-1β and ICAM-1 inflammatory cytokine expression. Acetate and FFAR2 agonist treatment also repressed Akt and ERK2 signalling. Surprisingly, mouse monocytes displayed a distinct response to acetate treatment, elevating GM-CSF, IL-1α and IL-1β cytokine expression. This effect persisted in FFAR2/3-knockout mouse monocytes and was not reproduced by synthetic agonists, suggesting a FFAR2/3 independent mechanism in mice. Collectively, we show that SCFAs act via FFAR2/3 to modulate human monocyte inflammatory responses– a pathway that is absent in mouse monocytes.
Highly-stretchable 3D-architected Mechanical Metamaterials
Authors: Jiang Yanhui , Wang Qiming 
Published: September 2016

AbstractSoft materials featuring both 3D free-form architectures and high stretchability are highly desirable for a number of engineering applications ranging from cushion modulators, soft robots to stretchable electronics; however, both the manufacturing and fundamental mechanics are largely elusive. Here, we overcome the manufacturing difficulties and report a class of mechanical metamaterials that not only features 3D free-form lattice architectures but also poses ultrahigh reversible stretchability (strain > 414%), 4 times higher than that of the existing counterparts with the similar complexity of 3D architectures. The microarchitected metamaterials, made of highly stretchable elastomers, are realized through an additive manufacturing technique, projection microstereolithography and its postprocessing. With the fabricated metamaterials, we reveal their exotic mechanical behaviors: Under large-strain tension, their moduli follow a linear scaling relationship with their densities regardless of architecture types, in sharp contrast to the architecture-dependent modulus power-law of the existing engineering materials; under large-strain compression, they present tunable negative-stiffness that enables ultrahigh energy absorption efficiencies. To harness their extraordinary stretchability and microstructures, we demonstrate that the metamaterials open a number of application avenues in lightweight and flexible structure connectors, ultraefficient dampers, 3D meshed rehabilitation structures and stretchable electronics with designed 3D anisotropic conductivity.
G9a inhibits MEF2C activity to control sarcomere assembly
Authors: Ow Jin Rong , Palanichamy Kala Monica , Rao Vinay Kumar , Choi Min Hee , Bharathy Narendra , Taneja Reshma 
Published: September 2016

AbstractIn this study, we demonstrate that the lysine methyltransferase G9a inhibits sarcomere organization through regulation of the MEF2C-HDAC5 regulatory axis. Sarcomeres are essential for muscle contractile function. Presently, skeletal muscle disease and dysfunction at the sarcomere level has been associated with mutations of sarcomere proteins. This study provides evidence that G9a represses expression of several sarcomere genes and its over-expression disrupts sarcomere integrity of skeletal muscle cells. G9a inhibits MEF2C transcriptional activity that is essential for expression of sarcomere genes. Through protein interaction assays, we demonstrate that G9a interacts with MEF2C and its co-repressor HDAC5. In the presence of G9a, calcium signaling-dependent phosphorylation and export of HDAC5 to the cytoplasm is blocked which likely results in enhanced MEF2C-HDAC5 association. Activation of calcium signaling or expression of constitutively active CaMK rescues G9a-mediated repression of HDAC5 shuttling as well as sarcomere gene expression. Our results demonstrate a novel epigenetic control of sarcomere assembly and identifies new therapeutic avenues to treat skeletal and cardiac myopathies arising from compromised muscle function.
Coxsackievirus A16 induced neurological disorders in young gerbils which could serve as a new animal model for vaccine evaluation
Authors: Sun Yi-Sheng , Li Ya-jing , Xia Yong , Xu Fang , Wang Wei-wei , Yang Zhang-Nv , Lu Hang-Jing , Chen Zhi-Ping , Miao Zi-Ping , Liang Wei-Feng , Xu Zhi-Yao , Dong Hong-Jun , Qiu Dan-Hong , Zhu Zhi-Yong , van der Veen Stijn , Qian Jie , Zhou Bin , Yao Ping-Ping , Zhu Han-Ping 
Published: September 2016

AbstractCoxsackievirus A16 (CA16) is one of the major pathogens associated with human hand, foot, and mouth disease (HFMD) in the Asia-pacific region. Although CA16 infections are generally mild, severe neurological manifestations or even death has been reported. Studies on CA16 pathogenesis and vaccine development are severely hampered because the small animal models that are currently available show major limitations. In this study, gerbils (Meriones unguiculatus) were investigated for their suitability as an animal model to study CA16 pathogenesis and vaccine development. Our results showed that gerbils up to the age of 21 days were fully susceptible to CA16 and all died within five days post-infection. CA16 showed a tropism towards the skeletal muscle, spinal cord and brainstem of gerbils, and severe lesions, including necrosis, were observed. In addition, an inactivated CA16 whole-virus vaccine administrated to gerbils was able to provide full protection to the gerbils against lethal doses of CA16 strains. These results demonstrate that gerbils are a suitable animal model to study CA16 infection and vaccine development.
Low‐power time‐based ADC with alternating time‐residue amplification
Authors: Jung J. , Shin S. 
Published: September 2016

A time‐based analogue‐to‐digital converter (ADC) that can exhibit both low power and high resolution is introduced. By amplifying alternate time residues and successively subtracting the comparator‐induced timing offset, both fast conversion speed of 2N cycles for an N‐bit converter and very small input‐referred timing offset are achieved. For a 12‐bit ADC implemented in a 0.18 µm CMOS process, an effective number of bits of 10.8 has been measured at a sampling frequency of 100 kHz, while consuming 30 µW of total power.
Potential and challenges of conservation agriculture in sequestration of atmospheric CO
2
for enhancing climate-resilience and improving productivity of soil of small landholder farms.
Authors: Rattan Lal Rattan Lal 
Published: September 2016

Abstract
The projected climate change, caused by emissions from fossil fuel combustion and land use change, may adversely impact the agronomic yields and aggravate food insecurity of small landholder farms. About 500 million small landholder farms have depleted and degraded soils, while having low soil organic carbon (SOC) pools, low plant nutrient reserves, low plant-available water capacity and low agronomic yield, yet high vulnerability to changing and uncertain climate. Projected climate change may reduce rice yield by 10% for every 1°C increase in temperature, and total maize production may decline by 10% by 2050. Agronomic yield of wheat in South Asia may be adversely affected by increase in temperature during spring. Yield of other cereals (sorghum, millet) and root crops (cassava, yam) may be adversely affected by aggravation of other biotic stresses (smut, fungi, viruses, etc.). Thus, climate-resilience may be a key component of sustainable intensification of small landholder agriculture. It is in this context that conservation agriculture (CA) can be an important option. With fine-tuning for adaptation to site-specific conditions, CA has numerous benefits including erosion control, water conservation, SOC sequestration and increase in profitability and farm income. Further, CA can be implemented in synergism with other practices such as forestry and forest plantations (during early stages of tree establishment), and integrated crop-livestock (ley farming). In several farm operations, CA builds upon the traditional systems and indigenous technology. Widespread adoption of CA could sequester 1 Pg C/year globally, which could create another income stream for small landholders. Further, CA fits in with the '4 per Thousand' programme proposed at the COP-21 in Paris.
Effects of Passive Integrated Transponder Tags on the Physiology and Swimming Performance of a Small‐Bodied Stream Fish
Authors: Clark Scott R. 
Published: September 2016

AbstractWithin the past few decades, telemetry has proven to be a valuable tool for tracking and monitoring fish. Although the advent of smaller transmitters has made these methods increasingly applicable to small‐bodied fishes, limited information currently exists regarding the efficacy of these transmitters or their putative effects on small‐bodied fishes. I evaluated the physiological and performance consequences of PIT tag implantation in a small‐bodied, sexually dimorphic stream fish, the Blackspotted Topminnow Fundulus olivaceus. First, I used a common‐garden experiment in an outdoor mesocosm setting to assess the long‐term effects (184 d) of PIT tag implantation on a suite of physiological and phenotypic metrics. I randomly assigned 216 individuals (50–73 mm SL; equal sex ratio) to one of three tagging treatments: control (no PIT tag), small (8 mm) PIT tag, or large (12 mm) PIT tag. Survivorship did not vary among treatment groups, and the presence of the tags had no apparent effects on the condition or development of the intraperitoneal organs relative to that observed in control fish. Fish that received large PIT tags showed reduced growth rates relative to fish that received small PIT tags; however, this appeared to result in a trade‐off that prioritized reproductive output. Second, I evaluated fish swimming performance (kinematics and endurance) to assess potential hydrodynamic consequences of PIT tag implantation. Kinematics (tail‐beat frequency, amplitude, and total displacement) and endurance swimming were similar across all treatments and between sexes, with only slight idiosyncratic effects observed. These results indicate that 8‐mm and 12‐mm PIT tags are appropriate for use in adult Blackspotted Topminnow as no detrimental long‐term effects were observed.Received February 26, 2016; accepted July 12, 2016 Published online September 26, 2016
Protoplast mutant selection of Glarea Lozoyensis and statistical optimization of medium for pneumocandin B0 yield-up
Authors: Qin Tingting , Song Ping , Wang Xiaoting , Ji Xiaojun , Ren Lujing , Huang He 
Published: September 2016

Abstract
A combination of microbial strain improvement and statistical optimization is investigated to maximize pneumocandin B0 production from Glarea lozoyensis ATCC 74030. Atmospheric and room temperature plasma (ARTP) was used to enhance G. lozoyensis ATCC 74030 in pneumocandin B0 yield. Mutant strain G. lozoyensis Q1 exhibited 1.39-fold increase in pneumocandin B0 production to 1134 mg/L when compared with the parent strain (810 mg/L). Further, the optimized medium provided another 1.65-fold in final pneumocandin B0 concentration to 1873 mg/L compared to the original medium. The results of this study indicated the combined application of a classical mutation and medium optimization can improve effectively pneumocandin B0 production from G. lozoyensis and could be a tool to improve other secondary metabolites production by fungal strains.
LongISLND: in silico sequencing of lengthy and noisy datatypes
Authors: Lau Bayo , Mohiyuddin Marghoob , Mu John C. , Fang Li Tai , Bani Asadi Narges , Dallett Carolina , Lam Hugo Y. K. 
Published: September 2016

Summary: LongISLND is a software package designed to simulate sequencing data according to the characteristics of third generation, single-molecule sequencing technologies. The general software architecture is easily extendable, as demonstrated by the emulation of Pacific Biosciences (PacBio) multi-pass sequencing with P5 and P6 chemistries, producing data in FASTQ, H5, and the latest PacBio BAM format. We demonstrate its utility by downstream processing with consensus building and variant calling.
Availability and Implementation: LongISLND is implemented in Java and available at http://bioinform.github.io/longislnd
Contact: hugo.lam@roche.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Site of metabolism prediction for oxidation reactions mediated by oxidoreductases based on chemical bond
Authors: He Shuaibing , Li Manman , Ye Xiaotong , Wang Hongyu , Yu Wenkang , He Wenjing , Wang Yun , Qiao Yanjiang 
Published: September 2016

Abstract

Motivation
The metabolites of exogenous and endogenous compounds play a pivotal role in the domain of metabolism research. However, they are still unclear for most chemicals in our environment. The in silico methods for predicting the site of metabolism (SOM) are considered to be efficient and low-cost in SOM discovery. However, many in silico methods are focused on metabolism processes catalyzed by several specified Cytochromes P450s, and only apply to substrates with special skeleton. A SOM prediction model always deserves more attention, which demands no special requirements to structures of substrates and applies to more metabolic enzymes.

Results
By incorporating the use of hybrid feature selection techniques (CHI, IG, GR, Relief) and multiple classification procedures (KStar, BN, IBK, J48, RF, SVM, AdaBoostM1, Bagging), SOM prediction models for six oxidation reactions mediated by oxidoreductases were established by the integration of enzyme data and chemical bond information. The advantage of the method is the introduction of unlabeled SOM. We defined the SOM which not reported in the literature as unlabeled SOM, where negative SOM was filtered. Consequently, for each type of reaction, a series of SOM prediction models were built based on information about metabolism of 1237 heterogeneous chemicals. Then optimal models were attained through comparisons among these models. Finally, independent test set was used to validate optimal models. It demonstrated that all models gave accuracies above 0.90. For receiver operating characteristic analysis, the area under curve values of all these models over 0.906. The results suggested that these models showed good predicting power.

Availability and implementation
All the models will be available when contact with wangyun@bucm.edu.cn

Supplementary information
Supplementary data are available at Bioinformatics online.
Postoperative excessive gain in visceral adipose tissue as well as body mass index are associated with adverse outcomes of an ileal pouch
Authors: Liu Ganglei , Wu Xianrui , Li Yi , Rui Yuanyi , Stocchi Luca , Remzi Feza H. , Shen Bo 
Published: September 2016

Background: There are no published studies on the impact of visceral adipose tissue (VAT) change on outcomes of restorative proctocolectomy and ileal pouch-anal anastomosis (IPAA). The aim of this historic cohort study was to evaluate the impact of excessive VAT gain on the outcomes of inflammatory bowel disease (IBD) patients with IPAA.Methods: We evaluated all eligible patients with at least two sequential CT scans after pouch construction from our prospectively maintained Pouchitis Registry between 2002 and 2014. The visceral fat area (VFA) was measured on CT images. The study group comprised patients with a significant VAT gain (&gt; 15%), and the control group was those without. The adverse outcomes of the pouch were defined as the new development of chronic pouch inflammation (chronic pouchitis, chronic cuffitis or Crohn’s disease of the pouch), anastomotic sinus and the combination of above (the composite adverse outcome) or pouch failure, after the inception CT.Results: Of 1564 patients in the Registry, 59 (3.8%) with at least 2 CT scans after pouch surgery were included. Twenty-nine patients (49.2%) were in the study group, and 30 (50.8%) were in the control group. The median duration from the inception to the latest CT was 552 (range: 31–2598) days for the entire cohort. We compared the frequency of new chronic pouch inflammation (13.8% vs 3.3%, P = 0.195), new pouch sinus (10.3% vs 0%, P = 0.112), composite adverse pouch outcome (24.1% vs 3.3%, P = 0.026) or pouch failure (10.3% vs 6.7%, P = 0.671) between the two groups. Kaplan-Meier plot for time-to-pouch failure between the pouch patients with or without excessive body mass index (BMI) gain (&gt; 10%) showed statistical difference (P = 0.011). Limited stepwise multivariate analysis showed that excessive VAT gain (odds ratio = 12.608, 95% confidence interval: 1.190–133.538, P = 0.035) was an independent risk factor for the adverse pouch comes.Conclusions: In this cohort of ileal pouch patients, excessive VAT gain as well as gain in BMI after pouch construction was found to be associated with poor long-term outcomes.
EU Competition Law
Authors: Jones Alison , Sufrin Brenda 
Published: September 2016

Abstract
EU Competition Law: Text, Cases, and Materials provides a complete guide to European competition law in a single authoritative volume. Carefully selected extracts from key cases, academic articles, and statutory materials are accompanied by in-depth author commentary from two experienced academics in the field. Thorough footnoting and referencing give a tour of the available literature, making this an ideal text and stand-alone resource for undergraduate and postgraduate students, as well as for competition law scholars engaged in specialized study. This sixth edition has been fully updated with detailed coverage and commentary on recent developments. These include the EU Courts’ judgments on Articles 101, 102 and 106 including Groupement des Cartes Bancaires, SIA ‘Maxima Latvija’, MasterCard, ‘Eturas’ UAB, Post Danmark II,Intel,Huawei and DEI; cases on the Commission’s enforcement powers and judicial review; new legislation and guidelines on technology transfer; the revised de minimis notice; Commission actions in the digital economy, including the Google case; the directive on damages; and thorough discussion of ongoing developments in competition law such as the Commission's enforcement policy against cartels, the appraisal of mergers, the use of commitments decisions and the compatibility of EU competition procedures with human rights provisions.
Article 102 TFEU
Authors: Jones Alison , Sufrin Brenda 
Published: September 2016

Abstract
This chapter discusses the difficult concept of what constitutes an ‘abuse’ of a dominant position for the purposes of Article 102 and whether conduct should be condemned on account of the form it takes or only for its effects. It considers the case law of the EU Courts, the decisional practice of the Commission, and the Commission’s Guidance Paper on enforcement priorities, and the problem of distinguishing competition on the merits from illegimate conduct. The chapter looks at the different classifications of abuse, particularly exclusionary and exploitative abuses; dominance and abuse in different markets; the objective justification defence; and general issues in respect of abuses concerning prices, including the ‘as efficient competitor’ test.The chapter examines the application of Article 102 to various forms of conduct, including: price discrimination; predatory pricing; selective pricing; margin squeeze; exclusive dealing; discounts and rebates; tying and bundling; refusal to supply; pursuit of legal proceedings; misuse of intellectual property rights, including standard-essential patents; search engine practices; discrimination abuses; unfairly high and low pricing; and hindering inter-Member State trade. It considers the abuse of collective dominance.
Public Enforcement by the Commission and the National Competition Authorities of the Antitrust Provisions
Authors: Jones Alison , Sufrin Brenda 
Published: September 2016

Abstract
This chapter discusses the public enforcement regime for the application of Article 101 and Article 102 under Regulation 1/2003. It explains briefly the system under Regulation 17 that previously applied, and the reasons for, and salient features of, the ‘modernisation’ in Regulation 1/2003. The chapter then examines; the powers of the Commission, including the investigation and inter partes stages of the Commission's procedure; the decisions which the Commission may take, including decisions imposing fines and commitments decisions; judicial review by the EU Courts; the European Competition Network (ECN) and enforcement by national competition authorities; the possibility of sanctions against individuals; and the procedure for making complaints about alleged infringements of the competition rules. The chapter also considers the application of fundamental rights provisions in EU competition proceedings.