bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disabling Labelling in Indonesia: Invoking WTO Laws in the Wake of Halal Policy Objectives
Authors: LIMENTA MICHELLE , EDIS BAYAN M. , FERNANDO OSCAR 
Published: July 2017

AbstractThe 2014 Halal Product Assurance Act (Halal Act) is the first law in Indonesia requiring mandatory Halal certification and labelling. Local and foreign business entities, while in agreement that Halal assurance through certification and labelling is important for Muslim consumers, have expressed their anxiety over whether such requirements will mean extra costs, particularly for small and medium enterprises. At the same time, the mandatory labelling regime involves several WTO issues under the TBT Agreement, which raise questions regarding Indonesia's compliance with its obligations. As a defence, Indonesia could argue that its mandatory halal labelling measure falls under the exception for protecting ‘public morals’. The WTO panel in theUS–Gamblingdispute noted that the meaning of ‘public morals’ and ‘public order’ varied depending on a range of factors, including prevailing social, cultural, ethical, and religious values. Should the WTO allow all types of moral and religious belief, even if they restrict trade? How can public moral policy objectives be applied in ways that do not violate WTO law? This paper seeks to examine the WTO consistency of the new Indonesian Halal Act, and whether the public moral objective underlying mandatory halal certification/labelling can be defended as an exception in the context of the TBT Agreement.
Autophagosome maturation mediated by Rab7 contributes to neuroprotection of hypoxic preconditioning against global cerebral ischemia in rats
Authors: Zhan Lixuan , Chen Siyuan , Li Kongping , Liang Donghai , Zhu Xinyong , Liu Liu , Lu Zhiwei , Sun Weiwen , Xu En 
Published: July 2017

AbstractAutophagy disruption leads to neuronal damage in hypoxic–ischemic brain injury. Rab7, a member of the Rab GTPase superfamily, has a unique role in the regulation of autophagy. Hypoxic preconditioning (HPC) provides neuroprotection against transient global cerebral ischemia (tGCI). However, the underlying mechanisms remain poorly understood. Thus, the current study explored the potential molecular mechanism of the neuroprotective effect of HPC by investigating how Rab7 mediates autophagosome (AP) maturation after tGCI in adult rats. We found that HPC attenuated AP accumulation in the hippocampal CA1 region after tGCI via restoration of autophagic flux. We also confirmed that this HPC-induced neuroprotection was not caused by the increase in lysosomes or the improvement of lysosomal function after tGCI. Electron microscopic analysis then revealed an increase in autolysosomes in CA1 neurons of HPC rats. Moreover, the inhibition of autophagosome-lysosome fusion by chloroquine significantly aggravated neuronal death in CA1, indicating that AP maturation contributes to HPC-induced neuroprotection against neuronal injury after tGCI. Furthermore, the activation of Rab7 was found to be involved in the neuroprotective effect of AP maturation after HPC. At last, the knockdown of ultraviolet radiation resistance-associated gene (UVRAG) in vivo disrupted the interaction between Vps16 and Rab7, attenuated the activation of Rab7, interrupted autophagic flux, and ultimately abrogated the HPC-induced neuroprotection against tGCI. Our results indicated that AP maturation was enhanced by the activation of Rab7 via UVRAG-Vps16 interaction, which further demonstrated the potential neuroprotective role of Rab7 in HPC against tGCI-induced neuronal injury in adult rats.
Humanin G (HNG) protects age-related macular degeneration (AMD) transmitochondrial ARPE-19 cybrids from mitochondrial and cellular damage
Authors: Nashine Sonali , Cohen Pinchas , Chwa Marilyn , Lu Stephanie , Nesburn Anthony B , Kuppermann Baruch D , Kenney M Cristina 
Published: July 2017

AbstractAge-related macular degeneration (AMD) ranks third among the leading causes of visual impairment with a blindness prevalence rate of 8.7%. Despite several treatment regimens, such as anti-angiogenic drugs, laser therapy, and vitamin supplementation, being available for wet AMD, to date there are no FDA-approved therapies for dry AMD. Substantial evidence implicates mitochondrial damage and retinal pigment epithelium (RPE) cell death in the pathogenesis of AMD. However, the effects of AMD mitochondria and Humanin G (HNG), a more potent variant of the mitochondrial-derived peptide (MDP) Humanin, on retinal cell survival have not been elucidated. In this study, we characterized mitochondrial and cellular damage in transmitochondrial cybrid cell lines that contain identical nuclei but possess mitochondria from either AMD or age-matched normal (Older-normal (NL)) subjects. AMD cybrids showed (1) reduced levels of cell viability, lower mtDNA copy numbers, and downregulation of mitochondrial replication/transcription genes and antioxidant enzyme genes; and (2) elevated levels of genes related to apoptosis, autophagy and ER-stress along with increased mtDNA fragmentation and higher susceptibility to amyloid-β-induced toxicity compared to NL cybrids. In AMD cybrids, HNG protected the AMD mitochondria, reduced pro-apoptosis gene and protein levels, upregulated gp130 (a component of the HN receptor complex), and increased the protection against amyloid-β-induced damage. In summary, in cybrids, damaged AMD mitochondria mediate cell death that can be reversed by HNG treatment. Our results also provide evidence of Humanin playing a pivotal role in protecting cells with AMD mitochondria. In the future, it may be possible that AMD patient’s blood samples containing damaged mitochondria may be useful as biomarkers for this condition. In conclusion, HNG may be a potential therapeutic target for treatment of dry AMD, a debilitating eye disease that currently has no available treatment. Further studies are needed to establish HNG as a viable mitochondria-targeting therapy for dry AMD.
A role for the cell-wall protein silacidin in cell size of the diatomThalassiosira pseudonana
Authors: Kirkham Amy R , Richthammer Patrick , Schmidt Katrin , Wustmann Martin , Maeda Yoshiaki , Hedrich René , Brunner Eike , Tanaka Tsuyoshi , van Pée Karl-Heinz , Falciatore Angela , Mock Thomas 
Published: July 2017

AbstractDiatoms contribute 20% of global primary production and form the basis of many marine food webs. Although their species diversity correlates with broad diversity in cell size, there is also an intraspecific cell-size plasticity owing to sexual reproduction and varying environmental conditions. However, despite the ecological significance of the diatom cell size for food-web structure and global biogeochemical cycles, our knowledge about genes underpinning the size of diatom cells remains elusive. Here, a combination of reverse genetics, experimental evolution and comparative RNA-sequencing analyses enabled us to identify a previously unknown genetic control of cell size in the diatom Thalassiosira pseudonana. In particular, the targeted deregulation of the expression of the cell-wall protein silacidin caused a significant increase in valve diameter. Remarkably, the natural downregulation of the silacidin gene transcript due to experimental evolution under low temperature also correlated with cell-size increase. Our data give first evidence for a genetically controlled regulation of cell size in T. pseudonana and possibly other centric diatoms as they also encode the silacidin gene in their genomes.
Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars
Authors: Suzuki Shino , Ishii Shun’ichi , Hoshino Tatsuhiko , Rietze Amanda , Tenney Aaron , Morrill Penny L , Inagaki Fumio , Kuenen J Gijs , Nealson Kenneth H 
Published: July 2017

Abstract
Water from The Cedars springs that discharge from serpentinized ultramafic rocks feature highly basic (pH=~12), highly reducing (Eh&lt;−550 mV) conditions with low ionic concentrations. These conditions make the springs exceptionally challenging for life. Here, we report the metagenomic data and recovered draft genomes from two different springs, GPS1 and BS5. GPS1, which was fed solely by a deep groundwater source within the serpentinizing system, was dominated by several bacterial taxa from the phyla OD1 (‘Parcubacteria’) and Chloroflexi. Members of the GPS1 community had, for the most part, the smallest genomes reported for their respective taxa, and encoded only archaeal (A-type) ATP synthases or no ATP synthases at all. Furthermore, none of the members encoded respiration-related genes and some of the members also did not encode key biosynthesis-related genes. In contrast, BS5, fed by shallow water, appears to have a community driven by hydrogen metabolism and was dominated by a diverse group of Proteobacteria similar to those seen in many terrestrial serpentinization sites. Our findings indicated that the harsh ultrabasic geological setting supported unexpectedly diverse microbial metabolic strategies and that the deep-water-fed springs supported a community that was remarkable in its unusual metagenomic and genomic constitution.
Role of plant–fungal nutrient trading and host control in determining the competitive success of ectomycorrhizal fungi
Authors: Hortal Sara , Plett Krista Lynn , Plett Jonathan Michael , Cresswell Tom , Johansen Mathew , Pendall Elise , Anderson Ian Charles 
Published: July 2017

Abstract
Multiple ectomycorrhizal fungi (EMF) compete to colonise the roots of a host plant, but it is not known whether their success is under plant or fungal control, or a combination of both. We assessed whether plants control EMF colonisation by preferentially allocating more carbon to more beneficial partners in terms of nitrogen supply or if other factors drive competitive success. We combined stable isotope labelling and RNA-sequencing approaches to characterise nutrient exchange between the plant host Eucalyptus grandis and three Pisolithus isolates when growing alone and when competing either indirectly (with a physical barrier) or directly. Overall, we found that nitrogen provision to the plant does not explain the amount of carbon that an isolate receives nor the number of roots that it colonises. Differences in nutrient exchange among isolates were related to differences in expression of key fungal and plant nitrogen and carbon transporter genes. When given a choice of partners, the plant was able to limit colonisation by the least cooperative isolate. This was not explained by a reduction in allocated carbon. Instead, our results suggest that partner choice in EMF could operate through the upregulation of defence-related genes against those fungi providing fewer nutrients.
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
Authors: Callahan Benjamin J , McMurdie Paul J , Holmes Susan P 
Published: July 2017

Abstract
Recent advances have made it possible to analyze high-throughput marker-gene sequencing data without resorting to the customary construction of molecular operational taxonomic units (OTUs): clusters of sequencing reads that differ by less than a fixed dissimilarity threshold. New methods control errors sufficiently such that amplicon sequence variants (ASVs) can be resolved exactly, down to the level of single-nucleotide differences over the sequenced gene region. The benefits of finer resolution are immediately apparent, and arguments for ASV methods have focused on their improved resolution. Less obvious, but we believe more important, are the broad benefits that derive from the status of ASVs as consistent labels with intrinsic biological meaning identified independently from a reference database. Here we discuss how these features grant ASVs the combined advantages of closed-reference OTUs—including computational costs that scale linearly with study size, simple merging between independently processed data sets, and forward prediction—and of de novo OTUs—including accurate measurement of diversity and applicability to communities lacking deep coverage in reference databases. We argue that the improvements in reusability, reproducibility and comprehensiveness are sufficiently great that ASVs should replace OTUs as the standard unit of marker-gene analysis and reporting.
Slow conformational exchange and overall rocking motion in ubiquitin protein crystals
Authors: Kurauskas Vilius , Izmailov Sergei A. , Rogacheva Olga N. , Hessel Audrey , Ayala Isabel , Woodhouse Joyce , Shilova Anastasya , Xue Yi , Yuwen Tairan , Coquelle Nicolas , Colletier Jacques-Philippe , Skrynnikov Nikolai R. , Schanda Paul 
Published: July 2017

AbstractProteins perform their functions in solution but their structures are most frequently studied inside crystals. Here we probe how the crystal packing alters microsecond dynamics, using solid-state NMR measurements and multi-microsecond MD simulations of different crystal forms of ubiquitin. In particular, near-rotary-resonance relaxation dispersion (NERRD) experiments probe angular backbone motion, while Bloch–McConnell relaxation dispersion data report on fluctuations of the local electronic environment. These experiments and simulations reveal that the packing of the protein can significantly alter the thermodynamics and kinetics of local conformational exchange. Moreover, we report small-amplitude reorientational motion of protein molecules in the crystal lattice with an ~3–5° amplitude on a tens-of-microseconds time scale in one of the crystals, but not in others. An intriguing possibility arises that overall motion is to some extent coupled to local dynamics. Our study highlights the importance of considering the packing when analyzing dynamics of crystalline proteins.
Dynamical sensitivity control of a single-spin quantum sensor
Authors: Lazariev Andrii , Arroyo-Camejo Silvia , Rahane Ganesh , Kavatamane Vinaya Kumar , Balasubramanian Gopalakrishnan 
Published: July 2017

AbstractThe Nitrogen-Vacancy (NV) defect in diamond is a unique quantum system that offers precision sensing of nanoscale physical quantities at room temperature beyond the current state-of-the-art. The benchmark parameters for nanoscale magnetometry applications are sensitivity, spectral resolution, and dynamic range. Under realistic conditions the NV sensors controlled by conventional sensing schemes suffer from limitations of these parameters. Here we experimentally show a new method called dynamical sensitivity control (DYSCO) that boost the benchmark parameters and thus extends the practical applicability of the NV spin for nanoscale sensing. In contrast to conventional dynamical decoupling schemes, where π pulse trains toggle the spin precession abruptly, the DYSCO method allows for a smooth, analog modulation of the quantum probe’s sensitivity. Our method decouples frequency selectivity and spectral resolution unconstrained over the bandwidth (1.85 MHz–392 Hz in our experiments). Using DYSCO we demonstrate high-accuracy NV magnetometry without |2π| ambiguities, an enhancement of the dynamic range by a factor of 4 · 103, and interrogation times exceeding 2 ms in off-the-shelf diamond. In a broader perspective the DYSCO method provides a handle on the inherent dynamics of quantum systems offering decisive advantages for NV centre based applications notably in quantum information and single molecule NMR/MRI.
An Integrative Computational Approach to Evaluate Genetic Markers for Bipolar Disorder
Authors: Xu Yong , Wang Jun , Rao Shuquan , Ritter McKenzie , Manor Lydia C. , Backer Robert , Cao Hongbao , Cheng Zaohuo , Liu Sha , Liu Yansong , Tian Lin , Dong Kunlun , Yao Shugart Yin , Wang Guoqiang , Zhang Fuquan 
Published: July 2017

AbstractStudies to date have reported hundreds of genes connected to bipolar disorder (BP). However, many studies identifying candidate genes have lacked replication, and their results have, at times, been inconsistent with one another. This paper, therefore, offers a computational workflow that can curate and evaluate BP-related genetic data. Our method integrated large-scale literature data and gene expression data that were acquired from both postmortem human brain regions (BP case/control: 45/50) and peripheral blood mononuclear cells (BP case/control: 193/593). To assess the pathogenic profiles of candidate genes, we conducted Pathway Enrichment, Sub-Network Enrichment, and Gene-Gene Interaction analyses, with 4 metrics proposed and validated for each gene. Our approach developed a scalable BP genetic database (BP_GD), including BP related genes, drugs, pathways, diseases and supporting references. The 4 metrics successfully identified frequently-studied BP genes (e.g. GRIN2A, DRD1, DRD2, HTR2A, CACNA1C, TH, BDNF, SLC6A3, P2RX7, DRD3, and DRD4) and also highlighted several recently reported BP genes (e.g. GRIK5, GRM1 and CACNA1A). The computational biology approach and the BP database developed in this study could contribute to a better understanding of the current stage of BP genetic research and assist further studies in the field.
Elucidation of the biosynthetic pathway of cis-jasmone in Lasiodiplodia theobromae
Authors: Matsui Ryo , Amano Naruki , Takahashi Kosaku , Taguchi Yodai , Saburi Wataru , Mori Hideharu , Kondo Norio , Matsuda Kazuhiko , Matsuura Hideyuki 
Published: July 2017

AbstractIn plants, cis-jasmone (CJ) is synthesized from α-linolenic acid (LA) via two biosynthetic pathways using jasmonic acid (JA) and iso-12-oxo-phytodienoic acid (iso-OPDA) as key intermediates. However, there have been no reports documenting CJ production by microorganisms. In the present study, the production of fungal-derived CJ by Lasiodiplodia theobromae was observed for the first time, although this production was not observed for Botrytis cinerea, Verticillium longisporum, Fusarium oxysporum, Gibberella fujikuroi, and Cochliobolus heterostrophus. To investigate the biosynthetic pathway of CJ in L. theobromae, administration experiments using [18,18,18-2H3, 17,17-2H2]LA (LA-d5), [18,18,18-2H3, 17,17-2H2]12-oxo-phytodienoic acid (cis-OPDA-d5), [5′,5′,5′-2H3, 4′,4′-2H2, 3′-2H1]OPC 8:0 (OPC8-d6), [5′,5′,5′-2H3, 4′,4′-2H2, 3′-2H1]OPC 6:0 (OPC6-d6), [5′,5′,5′-2H3, 4′,4′-2H2, 3′-2H1]OPC 4:0 (OPC4-d6), and [11,11-2H2, 10,10-2H2, 8,8-2H2, 2,2-2H2]methyl iso-12-oxo-phytodienoate (iso-MeOPDA-d8) were carried out, revealing that the fungus produced CJ through a single biosynthetic pathway via iso-OPDA. Interestingly, it was suggested that the previously predicted decarboxylation step of 3,7-didehydroJA to afford CJ might not be involved in CJ biosynthesis in L. theobromae.
Radiocesium concentrations in wild mushrooms after the accident at the Fukushima Daiichi Nuclear Power Station: Follow-up study in Kawauchi village
Authors: Orita Makiko , Nakashima Kanami , Taira Yasuyuki , Fukuda Toshiki , Fukushima Yoshiko , Kudo Takashi , Endo Yuko , Yamashita Shunichi , Takamura Noboru 
Published: July 2017

AbstractSince the accident at the Chernobyl Nuclear Power Plant, it has become well known that radiocesium tends to concentrate in wild mushrooms. During the recovery process after the accident at the Fukushima Daiichi Nuclear Power Station (FDNPS), it is important to perform follow-up measurements of the activity concentrations of radiocesium in mushrooms. We evaluated the activity concentrations of the detected artificial radionuclides (radiocesium) in wild mushrooms collected from Kawauchi village, which is within 30 km of the FDNPS, in 2015, four years after the accident. We found that the radiocesium was determined in 147 of 159 mushroom samples (92.4%). Based on the average mushroom consumption of Japanese citizens (6.28 kg per year), we calculated committed effective doses ranging from <0.001 to 0.6 mSv. Although committed effective doses are relatively limited, even if residents have consumed mushrooms several times, continuous monitoring of the radiocesium in mushrooms in Fukushima is needed for sustained recovery from the nuclear disaster.
Associations of statin use with motor performance and myalgia may be modified by 25-hydroxyvitamin D: findings from a British birth cohort
Authors: Sharma Nikhil , Cooper Rachel , Kuh Diana , Shah Imran 
Published: July 2017

AbstractThe objective was to examine whether: (1) statin use was associated with muscle related outcomes at age 60–64, (2) these associations were modified by 25-hydroxyvitamin D (25(OH)D) status and explained by inflammation, body-size or lifestyle in a British birth cohort. Markers of myalgia (intrusive body pain) and myopathy (self-reported and performance-based measures) were examined in 734 men and 822 women (MRC National Survey of Health and Development). Statin use was associated with intrusive body pain, difficulty climbing stairs and slower chair rise speed. Some associations were modified by 25(OH)D e.g. the association with intrusive body pain was evident in the insufficient (13–20 ng/l) and deficient (<13 ng/l) 25(OH)D status groups (OR = 2.6,95% CI 1.7–1.1; OR = 1.8,95% CI 1.2–2.8, respectively) but not in those with status >20 ng/l (OR = 0.8,95% CI 0.5–1.4) (p = 0.003 for interaction). Associations were maintained in fully adjusted models of intrusive body pain and difficulty climbing stairs, but for chair rise speed they were fully accounted for by inflammation, body-size and lifestyle. In a nationally representative British population in early old age, statin use was associated with lower limb muscle-related outcomes, and some were only apparent in those with 25(OH)D status below 20 ng/l. Given 25(OH)D is modifiable in clinical practice, future studies should consider the links between 25(OH)D status and muscle related outcomes.
Anti-obesity and anti-inflammatory effects of synthetic acetic acid vinegar and Nipa vinegar on high-fat-diet-induced obese mice
Authors: Beh Boon Kee , Mohamad Nurul Elyani , Yeap Swee Keong , Ky Huynh , Boo Sook Yee , Chua Joelle Yi Heng , Tan Sheau Wei , Ho Wan Yong , Sharifuddin Shaiful Adzni , Long Kamariah , Alitheen Noorjahan Banu 
Published: July 2017

AbstractRecently, food-based bioactive ingredients, such as vinegar, have been proposed as a potential solution to overcome the global obesity epidemic. Although acetic acid has been identified as the main component in vinegar that contributes to its anti-obesity effect, reports have shown that vinegar produced from different starting materials possess different degrees of bioactivity. This study was performed to compare the anti-obesity and anti-inflammatory effects of synthetic acetic acid vinegar and Nipa vinegar in mice fed a high-fat diet. In this work, mice were fed a high-fat diet for 33 weeks. At the start of week 24, obese mice were orally fed synthetic acetic acid vinegar or Nipa vinegar (0.08 and 2 ml/kg BW) until the end of week 33. Mice fed a standard pellet diet served as a control. Although both synthetic acetic acid vinegar and Nipa vinegar effectively reduced food intake and body weight, a high dose of Nipa vinegar more effectively reduced lipid deposition, improved the serum lipid profile, increased adipokine expression and suppressed inflammation in the obese mice. Thus, a high dose of Nipa vinegar may potentially alleviate obesity by altering the lipid metabolism, inflammation and gut microbe composition in high-fat-diet-induced obese mice.