bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of tectonic burial and temperature on the inversion of inherited extensional basins during collision
Authors: LAFOSSE MANFRED , BOUTOUX ALEXANDRE , BELLAHSEN NICOLAS , LE POURHIET LAETITIA 
Published: June 2016

AbstractThe style of inversion of inherited extensional basins in the Western Alps is investigated through thermo-mechanical modelling. Two-dimensional models consist of a half-graben embedded in a relatively strong crust (basement) and filled with weak syn-rift sediments (cover). We investigate the relative influence of the internal friction (µ) of the basin-bounding normal fault, tectonic burial (h) under an overlying nappe and the geothermal gradient. We use a viscoplastic model with symmetrical shortening. The inherited normal fault is implemented as a curved thin body with a variable friction coefficient (µ) ranging from 0.1 to 0.6. The style of basin inversion is controlled at shallow depth by the internal friction coefficient, whose influence decreases with the increase of both burial depth and geothermal gradient. With increasing burial and/or geothermal gradient, fault reactivation is inhibited and distributed deformation in the basement induces the vertical extrusion of the cover. The basin inversion is accompanied by distributed deformation in the cover and by the shearing of the basin and basement interface. The results are consistent with the style of inversion of inherited half-grabens in the external Western Alps, where no significant fault reactivation occurred owing to tectonic burial underneath the Alpine internal units during the early Alpine collision.
Plantingian theism and the free-will defence
Authors: WIELENBERG ERIK J. 
Published: June 2016

AbstractI advance a challenge to the coherence of Alvin Plantinga's brand of theism that focuses on Plantinga's celebrated free-will defence. This challenge draws on (but goes beyond) some ideas advanced by Wes Morriston. The central claim of my challenge is that Plantinga's free-will defence, together with certain claims that are plausible and/or to which Plantinga is committed, both requires and rules out the claim that it is possible that God is capable of engaging in moral goodness. I then critically evaluate an interesting strategy for responding to my challenge inspired by some recent work by Kevin Timpe, arguing that the response ultimately fails. The upshot of the article is that Plantinga's brand of theism is internally inconsistent; furthermore, because the claims that are in tension with the free-will defence are ones that many theists are likely to find attractive, many theists are not able to appeal to Plantinga's free-will defence in responding to the logical problem of evil.
IHD from copper deficiency: a unified theory
Authors: Klevay Leslie M. 
Published: June 2016

AbstractThe theory, in brief outline here, implicating deficiency of Cu in the aetiology and pathophysiology of IHD explains more attributes of the disease than any other theory. This theory satisfies several of Hill’s criteria of a half-century ago for deducing association between an environmental feature and presence of an illness. Most important is the temporal association between the rise of IHD and the decrease in dietary Cu since the 1930s along with a parallel increase in the supplementation of pregnant women with Fe, a Cu antagonist. There are more than eighty anatomical, chemical and physiological similarities between animals deficient in Cu and individuals with IHD. Few of these similarities have been produced by other dietary manipulations because feeding cholesterol induces Cu deficiency in animals. The most recent of these to be identified is decreased serum dehydroepiandrosterone. Some concomitant aspects of Cu metabolism and utilisation have been identified in other theories about heart disease: fetal programming, homocysteine, and Fe overload.
Clinical and genetic findings in a Chinese family with VDR-associated hereditary vitamin D-resistant rickets
Authors: Pang Qianqian , Qi Xuan , Jiang Yan , Wang Ou , Li Mei , Xing Xiaoping , Dong Jin , Xia Weibo 
Published: June 2016

AbstractHereditary vitamin D-resistant rickets (HVDRR) is a rare autosomal recessive disorder characterized by severe rickets, hypocalcemia, hypophosphatemia, secondary hyperparathyroidism, and elevated alkaline phosphatase. This disorder is caused by homogeneous or heterogeneous mutations affecting the function of the vitamin D receptor (VDR), which lead to complete or partial target organ resistance to the action of 1,25-dihydroxy vitamin D. A non-consanguineous family of Chinese Han origin with one affected individual demonstrating HVDRR was recruited, with the proband evaluated clinically, biochemically and radiographically. To identify the presence of mutations in the VDR gene, all the exons and exon–intron junctions of the VDR gene from all family members were amplified using PCR and sequenced. The proband showed rickets, progressive alopecia, hypocalcemia, hypophosphatemia, secondary hyperparathyroidism, and elevated alkaline phosphatase. She also suffered from epilepsy, which is rarely seen in patients with HVDRR. Direct sequencing analysis revealed a homozygous missense mutation c.122G>A (p.C41Y) in the VDR gene of the proband, which is located in the first zinc finger of the DNA-binding domain. Both parents had a normal phenotype and were found to be heterozygous for this mutation. We report a Chinese Han family with one individual affected with HVDRR. A homozygous missense mutation c.122G>A (p.C41Y) in the VDR gene was found to be responsible for the patient’s syndrome. In contrast to the results of treatment of HVDRR in other patients, our patient responded well to a supplement of oral calcium and a low dose of calcitriol.
Enhancing digestibility and ethanol yield of Populus wood via expression of an engineered monolignol 4-O-methyltransferase
Authors: Cai Yuanheng , Zhang Kewei , Kim Hoon , Hou Guichuan , Zhang Xuebin , Yang Huijun , Feng Huan , Miller Lisa , Ralph John , Liu Chang-Jun 
Published: June 2016

AbstractProducing cellulosic biofuels and bio-based chemicals from woody biomass is impeded by the presence of lignin polymer in the plant cell wall. Manipulating the monolignol biosynthetic pathway offers a promising approach to improved processability, but often impairs plant growth and development. Here, we show that expressing an engineered 4-O-methyltransferase that chemically modifies the phenolic moiety of lignin monomeric precursors, thus preventing their incorporation into the lignin polymer, substantially alters hybrid aspens’ lignin content and structure. Woody biomass derived from the transgenic aspens shows a 62% increase in the release of simple sugars and up to a 49% increase in the yield of ethanol when the woody biomass is subjected to enzymatic digestion and yeast-mediated fermentation. Moreover, the cell wall structural changes do not affect growth and biomass production of the trees. Our study provides a useful strategy for tailoring woody biomass for bio-based applications.
Alterations of the human gut microbiome in multiple sclerosis
Authors: Jangi Sushrut , Gandhi Roopali , Cox Laura M. , Li Ning , von Glehn Felipe , Yan Raymond , Patel Bonny , Mazzola Maria Antonietta , Liu Shirong , Glanz Bonnie L. , Cook Sandra , Tankou Stephanie , Stuart Fiona , Melo Kirsy , Nejad Parham , Smith Kathleen , Topçuolu Begüm D. , Holden James , Kivisäkk Pia , Chitnis Tanuja , De Jager Philip L. , Quintana Francisco J. , Gerber Georg K. , Bry Lynn , Weiner Howard L. 
Published: June 2016

AbstractThe gut microbiome plays an important role in immune function and has been implicated in several autoimmune disorders. Here we use 16S rRNA sequencing to investigate the gut microbiome in subjects with multiple sclerosis (MS,n=60) and healthy controls (n=43). Microbiome alterations in MS include increases inMethanobrevibacterandAkkermansiaand decreases inButyricimonas, and correlate with variations in the expression of genes involved in dendritic cell maturation, interferon signalling and NF-kB signalling pathways in circulating T cells and monocytes. Patients on disease-modifying treatment show increased abundances ofPrevotellaandSutterella, and decreasedSarcina, compared with untreated patients. MS patients of a second cohort show elevated breath methane compared with controls, consistent with our observation of increased gutMethanobrevibacterin MS in the first cohort. Further study is required to assess whether the observed alterations in the gut microbiome play a role in, or are a consequence of, MS pathogenesis.
Microglia and monocytes synergistically promote the transition from acute to chronic pain after nerve injury
Authors: Peng Jiyun , Gu Nan , Zhou Lijun , B Eyo Ukpong , Murugan Madhuvika , Gan Wen-Biao , Wu Long-Jun 
Published: June 2016

AbstractMicroglia and peripheral monocytes contribute to hypersensitivity in rodent models of neuropathic pain. However, the precise respective function of microglia and peripheral monocytes has not been investigated in these models. To address this question, here we combined transgenic mice and pharmacological tools to specifically and temporally control the depletion of microglia and monocytes in a mouse model of spinal nerve transection (SNT). We found that although microglia and monocytes are required during the initiation of mechanical allodynia or thermal hyperalgesia, these cells may not be as important for the maintenance of hypersensitivity. Moreover, we demonstrated that either resident microglia or peripheral monocytes are sufficient in gating neuropathic pain after SNT. We propose that resident microglia and peripheral monocytes act synergistically to initiate hypersensitivity and promote the transition from acute to chronic pain after peripheral nerve injury.
Structural lubricity under ambient conditions
Authors: Cihan Ebru , İpek Semran , Durgun Engin , Baykara Mehmet Z. 
Published: June 2016

AbstractDespite its fundamental importance, physical mechanisms that govern friction are poorly understood. While a state of ultra-low friction, termed structural lubricity, is expected for any clean, atomically flat interface consisting of two different materials with incommensurate structures, some associated predictions could only be quantitatively confirmed under ultra-high vacuum (UHV) conditions so far. Here, we report structurally lubric sliding under ambient conditions at mesoscopic (∼4,000–130,000 nm2) interfaces formed by gold islands on graphite. Ab initio calculations reveal that the gold–graphite interface is expected to remain largely free from contaminant molecules, leading to structurally lubric sliding. The experiments reported here demonstrate the potential for practical lubrication schemes for micro- and nano-electromechanical systems, which would mainly rely on an atomic-scale structural mismatch between the slider and substrate components, via the utilization of material systems featuring clean, atomically flat interfaces under ambient conditions.
Industrial-scale separation of high-purity single-chirality single-wall carbon nanotubes for biological imaging
Authors: Yomogida Yohei , Tanaka Takeshi , Zhang Minfang , Yudasaka Masako , Wei Xiaojun , Kataura Hiromichi 
Published: June 2016

AbstractSingle-chirality, single-wall carbon nanotubes are desired due to their inherent physical properties and performance characteristics. Here, we demonstrate a chromatographic separation method based on a newly discovered chirality-selective affinity between carbon nanotubes and a gel containing a mixture of the surfactants. In this system, two different selectivities are found: chiral-angle selectivity and diameter selectivity. Since the chirality of nanotubes is determined by the chiral angle and diameter, combining these independent selectivities leads to high-resolution single-chirality separation with milligram-scale throughput and high purity. Furthermore, we present efficient vascular imaging of mice using separated single-chirality (9,4) nanotubes. Due to efficient absorption and emission, blood vessels can be recognized even with the use of ∼100-fold lower injected dose than the reported value for pristine nanotubes. Thus, 1 day of separation provides material for up to 15,000 imaging experiments, which is acceptable for industrial use.
miR-93 regulates Msk2-mediated chromatin remodelling in diabetic nephropathy
Authors: Badal Shawn S. , Wang Yin , Long Jianyin , Corcoran David L. , Chang Benny H. , Truong Luan D. , Kanwar Yashpal S. , Overbeek Paul A. , Danesh Farhad R. 
Published: June 2016

AbstractHow the kidney responds to the metabolic cues from the environment remains a central question in kidney research. This question is particularly relevant to the pathogenesis of diabetic nephropathy (DN) in which evidence suggests that metabolic events in podocytes regulate chromatin structure. Here, we show that miR-93 is a critical metabolic/epigenetic switch in the diabetic milieu linking the metabolic state to chromatin remodelling. Mice with inducible overexpression of a miR-93 transgene exclusively in podocytes exhibit significant improvements in key features of DN. We identify miR-93 as a regulator of nucleosomal dynamics in podocytes. miR-93 has a critical role in chromatin reorganization and progression of DN by modulating its target Msk2, a histone kinase, and its substrate H3S10. These findings implicate a central role for miR-93 in high glucose-induced chromatin remodelling in the kidney, and provide evidence for a previously unrecognized role for Msk2 as a target for DN therapy.
Social inheritance can explain the structure of animal social networks
Authors: Ilany Amiyaal , Akçay Erol 
Published: June 2016

AbstractThe social network structure of animal populations has major implications for survival, reproductive success, sexual selection and pathogen transmission of individuals. But as of yet, no general theory of social network structure exists that can explain the diversity of social networks observed in nature, and serve as a null model for detecting species and population-specific factors. Here we propose a simple and generally applicable model of social network structure. We consider the emergence of network structure as a result of social inheritance, in which newborns are likely to bond with maternal contacts, and via forming bonds randomly. We compare model output with data from several species, showing that it can generate networks with properties such as those observed in real social systems. Our model demonstrates that important observed properties of social networks, including heritability of network position or assortative associations, can be understood as consequences of social inheritance.
Mummified precocial bird wings in mid-Cretaceous Burmese amber
Authors: Xing Lida , McKellar Ryan C. , Wang Min , Bai Ming , O’Connor Jingmai K. , Benton Michael J. , Zhang Jianping , Wang Yan , Tseng Kuowei , Lockley Martin G. , Li Gang , Zhang Weiwei , Xu Xing 
Published: June 2016

AbstractOur knowledge of Cretaceous plumage is limited by the fossil record itself: compression fossils surrounding skeletons lack the finest morphological details and seldom preserve visible traces of colour, while discoveries in amber have been disassociated from their source animals. Here we report the osteology, plumage and pterylosis of two exceptionally preserved theropod wings from Burmese amber, with vestiges of soft tissues. The extremely small size and osteological development of the wings, combined with their digit proportions, strongly suggests that the remains represent precocial hatchlings of enantiornithine birds. These specimens demonstrate that the plumage types associated with modern birds were present within single individuals of Enantiornithes by the Cenomanian (99 million years ago), providing insights into plumage arrangement and microstructure alongside immature skeletal remains. This finding brings new detail to our understanding of infrequently preserved juveniles, including the first concrete examples of follicles, feather tracts and apteria in Cretaceous avialans.
Comprehensive stabilization mechanism of electron-beam irradiated polyacrylonitrile fibers to shorten the conventional thermal treatment
Authors: Park Sejoon , Yoo Seung Hwa , Kang Ha Ri , Jo Seong Mu , Joh Han-Ik , Lee Sungho 
Published: June 2016

AbstractAn electron beam was irradiated on polyacrylonitrile (PAN) fibers prior to thermal stabilization. The electron-beam irradiation effectively shortened the thermal stabilization process by one fourth compared with the conventional thermal stabilization process. A comprehensive mechanistic study was conducted regarding this shortening of the thermal stabilization by electron-beam irradiation. Various species of chain radicals were produced in PAN fibers by electron-beam irradiation and existed for a relatively long duration, as observed by electron spin resonance spectroscopy. Subsequently, these radicals were gradually oxidized to peroxy radicals in the presence of oxygen under storage or heating. We found that these peroxy radicals (CO"Equation missing") enabled such an effective shortcut of thermal stabilization by acting as intermolecular cross-linking and partial aromatization points in the low temperature range (100–130 °C) and as earlier initiation seeds of successive cyclization reactions in the next temperature range (>130–140 °C) of thermal stabilization. Finally, even at a low irradiation dose (200 kGy), followed by a short heat treatment (230 °C for 30 min), the PAN fibers were sufficiently stabilized to produce carbon fibers with tensile strength and modulus of 2.3 and 216 GPa, respectively, after carbonization.
Plasma proteomic analysis of stable coronary artery disease indicates impairment of reverse cholesterol pathway
Authors: Basak Trayambak , Tanwar Vinay Singh , Bhardwaj Gourav , Bhardwaj Nitin , Ahmad Shadab , Garg Gaurav , V Sreenivas , Karthikeyan Ganesan , Seth Sandeep , Sengupta Shantanu 
Published: June 2016

AbstractCoronary artery disease (CAD) is one of the largest causes of death worldwide yet the traditional risk factors, although useful in identifying people at high risk, lack the desired predictive accuracy. Techniques like quantitative plasma proteomics holds immense potential to identify newer markers and this study (conducted in three phases) was aimed to identify differentially expressed proteins in stable CAD patients. In the first (discovery) phase, plasma from CAD cases (angiographically proven) and controls were subjected to iTRAQ based proteomic analysis. Proteins found to be differentially expressed were then validated in the second and third (verification and validation) phases in larger number of (n = 546) samples. After multivariate logistic regression adjusting for confounding factors (age, diet, etc.), four proteins involved in the reverse cholesterol pathway (Apo A1, ApoA4, Apo C1 and albumin) along with diabetes and hypertension were found to be significantly associated with CAD and could account for approximately 88% of the cases as revealed by ROC analysis. The maximum odds ratio was found to be 6.70 for albumin (p < 0.0001), followed by Apo AI (5.07, p < 0.0001), Apo CI (4.03, p = 0.001) and Apo AIV (2.63, p = 0.003). Down-regulation of apolipoproteins and albumin implicates the impairment of reverse cholesterol pathway in CAD.
BC1 RNA motifs required for dendritic transport in vivo
Authors: Robeck Thomas , Skryabin Boris V. , Rozhdestvensky Timofey S. , Skryabin Anastasiya B. , Brosius Jürgen 
Published: June 2016

AbstractBC1 RNA is a small brain specific non-protein coding RNA. It is transported from the cell body into dendrites where it is involved in the fine-tuning translational control. Due to its compactness and established secondary structure, BC1 RNA is an ideal model for investigating the motifs necessary for dendritic localization. Previously, microinjection of in vitro transcribed BC1 RNA mutants into the soma of cultured primary neurons suggested the importance of RNA motifs for dendritic targeting. These ex vivo experiments identified a single bulged nucleotide (U22) and a putative K-turn (GA motif) structure required for dendritic localization or distal transport, respectively. We generated six transgenic mouse lines (three founders each) containing neuronally expressing BC1 RNA variants on a BC1 RNA knockout mouse background. In contrast to ex vivo data, we did not find indications of reduction or abolition of dendritic BC1 RNA localization in the mutants devoid of the GA motif or the bulged nucleotide. We confirmed the ex vivo data, which showed that the triloop terminal sequence had no consequence on dendritic transport. Interestingly, changing the triloop supporting structure completely abolished dendritic localization of BC1 RNA. We propose a novel RNA motif important for dendritic transport in vivo.
Central tendency effects in time interval reproduction in autism
Authors: Karaminis Themelis , Cicchini Guido Marco , Neil Louise , Cappagli Giulia , Aagten-Murphy David , Burr David , Pellicano Elizabeth 
Published: June 2016

AbstractCentral tendency, the tendency of judgements of quantities (lengths, durations etc.) to gravitate towards their mean, is one of the most robust perceptual effects. A Bayesian account has recently suggested that central tendency reflects the integration of noisy sensory estimates with prior knowledge representations of a mean stimulus, serving to improve performance. The process is flexible, so prior knowledge is weighted more heavily when sensory estimates are imprecise, requiring more integration to reduce noise. In this study we measure central tendency in autism to evaluate a recent theoretical hypothesis suggesting that autistic perception relies less on prior knowledge representations than typical perception. If true, autistic children should show reduced central tendency than theoretically predicted from their temporal resolution. We tested autistic and age- and ability-matched typical children in two child-friendly tasks: (1) a time interval reproduction task, measuring central tendency in the temporal domain; and (2) a time discrimination task, assessing temporal resolution. Central tendency reduced with age in typical development, while temporal resolution improved. Autistic children performed far worse in temporal discrimination than the matched controls. Computational simulations suggested that central tendency was much less in autistic children than predicted by theoretical modelling, given their poor temporal resolution.
Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens
Authors: Deschamps Stéphane , Mudge Joann , Cameron Connor , Ramaraj Thiruvarangan , Anand Ajith , Fengler Kevin , Hayes Kevin , Llaca Victor , Jones Todd J. , May Gregory 
Published: June 2016

AbstractThe MinION is a portable single-molecule DNA sequencing instrument that was released by Oxford Nanopore Technologies in 2014, producing long sequencing reads by measuring changes in ionic flow when single-stranded DNA molecules translocate through the pores. While MinION long reads have an error rate substantially higher than the ones produced by short-read sequencing technologies, they can generate de novo assemblies of microbial genomes, after an initial correction step that includes alignment of Illumina sequencing data or detection of overlaps between Oxford Nanopore reads to improve accuracy. In this study, MinION reads were generated from the multi-chromosome genome of Agrobacterium tumefaciens strain LBA4404. Errors in the consensus two-directional (sense and antisense) “2D” sequences were first characterized by way of comparison with an internal reference assembly. Both Illumina-based correction and self-correction were performed and the resulting corrected reads assembled into high-quality hybrid and non-hybrid assemblies. Corrected read datasets and assemblies were subsequently compared. The results shown here indicate that both hybrid and non-hybrid methods can be used to assemble Oxford Nanopore reads into informative multi-chromosome assemblies, each with slightly different outcomes in terms of contiguity and accuracy.