bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of microstructures and macrotextures for different apple cultivars based on parenchyma morphology
Authors: Hou Jumin , Sun Yonghai , Chen Fangyuan , Yu Libo , Mao Qian , Wang Lu , Guo Xiaolei , Liu Chao 
Published: February 2016

ABSTRACTFuji, Golden Delicious, and Jonagold parenchyma were imaged by confocal laser scanning microscopy to be extracted morphology characteristics, which were used to analyze the relationship with macrotexture of apples tested by penetration and compression. Before analyzing the relationship, the significantly different morphology parameters were reduced in dimensions by principal component analysis and were proved to be availably used for distinguishing the different apple cultivars. For compression results, cell did not absolutely determine the hardness in different apple cultivars, and the pore should also be taken into consideration. With the same size in cell feret diameter, the bigger the pore feret diameter was, the softer the apple became. If no difference existed in pore feret diameter size, the cultivar became harder with a narrower distribution in cell feret diameter. The texture parameters were compared with the roundness parameters in the same or inverse changing trends to explore the relationship. High correlations were found between the texture parameters (energy required in whole penetration (Wt), fracture force (Fp), crispness) and pore solidity (R2 > 0.924, P < 0.001). Compactness of parenchyma played an important role in fruit texture. This research could provide the comprehension about relationship between microstructure and macrotexture of apple cultivars and morphological values for modeling apple parenchyma, contributing to numerical simulation for constitutive relation of fruit. Microsc. Res. Tech. 79:304–312, 2016. © 2016 Wiley Periodicals, Inc.
Development of the synganglion and morphology of the adult nervous system in the mite Archegozetes longisetosus Aoki (Chelicerata, Actinotrichida, Oribatida)
Authors: Hartmann Konstantin , Laumann Michael , Bergmann Paavo , Heethoff Michael , Schmelzle Sebastian 
Published: February 2016

ABSTRACTSmall arthropods show a highly condensed central nervous system, which is accompanied by the loss of the ancestral metameric organization. This results in the formation of one solid mass, a synganglion. Although numerous studies investigated the morphology of Archegozetes longisetosus, the organization of the nervous system is to date unknown. Using synchrotron X‐ray microtomography, we investigated the organization of the nervous system in the adult stage and the development of the synganglion over all five free‐living life stages (larva, proto‐, deuto‐, tritonymph and adult). The general morphology of the synganglion resembles that of other studied mites (in the classic sense) and ticks, being subdivided into a sub‐ and supraesophageal region, and consisting of cortex and neuropil. All nerves entering the walking legs except the first consist of two rami. This split is not based on a functional division into a motor and a sensory ramus, but both rami contain motor and sensory neurites. Within the synganglion, we found structures that resemble the ancestral metameric organization of the nervous system of arthropods. The development of the synganglion of A. longisetosus shows a more or less linear increase in volume, but cortex and neuropil grow at different rates over the five life stages. Between the second and third nymphal stage, the volume of the neuropil increases at a faster rate than the cortex. J. Morphol. 277:537–548, 2016. © 2016 Wiley Periodicals, Inc.
Locally interpolated alkalinity regression for global alkalinity estimation
Authors: Carter B. R. , Williams N. L. , Gray A. R. , Feely R. A. 
Published: February 2016

AbstractWe introduce methods and software for estimating total seawater alkalinity from salinity and any combination of up to four other parameters (potential temperature, apparent oxygen utilization, total dissolved nitrate, and total silicate). The methods return estimates anywhere in the global ocean with comparable accuracy to other published alkalinity estimation techniques. The software interpolates between a predetermined grid of coefficients for linear regressions onto arbitrary latitude, longitude, and depth coordinates, and thereby avoids the estimate discontinuities many similar methods return when transitioning from one regression constant set to another. The software can also return uncertainty estimates scaled by user‐provided input parameter uncertainties. The methods have been optimized for the open ocean, for which we estimate globally averaged errors of 5.8–10.4 μmol kg−1 depending on which combination of regression parameters is used. We expect these methods to be especially useful for better constraining the carbonate system from measurement platforms—such as biogeochemical Argo floats—that are only capable of measuring one carbonate system parameter (e.g., pH). It may also provide a useful way of simulating alkalinity for Earth system models that do not resolve the tracer prognostically.
Lean‐seafood intake decreases urinary markers of mitochondrial lipid and energy metabolism in healthy subjects: Metabolomics results from a randomized crossover intervention study
Authors: Schmedes Mette , Aadland Eli Kristin , Sundekilde Ulrik Kræmer , Jacques Hélène , Lavigne Charles , Graff Ingvild Eide , Eng Øyvin , Holthe Asle , Mellgren Gunnar , Young Jette Feveile , Bertram Hanne Christine , Liaset Bjørn , Clausen Morten Rahr 
Published: February 2016

ScopeProteins constitute an important part of the human diet, but understanding of the effects of different dietary protein sources on human metabolism is sparse. We aimed to elucidate diet‐induced metabolic changes through untargeted urinary metabolomics after four weeks of intervention with lean‐seafood or nonseafood diets. It is shown that lean‐seafood intake reduces urinary excretion of metabolites involved in mitochondrial lipid and energy metabolism possibly facilitating a higher lipid catabolism in healthy subjects.MethodsIn a randomized controlled trial with crossover design, 20 healthy subjects consumed two balanced diets that varied in main protein sources for 4 weeks. Morning spot urine samples were collected before and after each intervention period. Untargeted metabolomics based on 1H NMR spectroscopy and LC‐MS analyses were applied to characterize the urinary metabolic response to the interventions.ResultsThe lean‐seafood diet period reduced the urinary level of l‐carnitine, 2,6‐dimethylheptanoylcarnitine, and N‐methyl‐2‐pyridone‐5‐carboxamide, relative to the nonseafood period. The dietary analysis revealed that the higher urinary level of trimethylamine‐N‐oxide after the lean‐seafood diet period and guanidinoacetate and 3‐methylhistidine after the nonseafood diet period was related to the endogenous content of these compounds in the diets.ConclusionsOur data reveal that 4 weeks of lean‐seafood intake reduces urinary excretion of metabolites involved in mitochondrial lipid and energy metabolism possibly facilitating a higher lipid catabolism in healthy subjects after the lean‐seafood intake.
Anti‐inflammatory effects and molecular mechanisms of 8‐prenyl quercetin
Authors: Hisanaga Ayami , Mukai Rie , Sakao Kozue , Terao Junji , Hou De‐Xing 
Published: February 2016

Scope8‐prenyl quercetin (PQ) is a typical prenylflavonoid distributed in plant foods. It shows higher potential bioactivity than its parent quercetin (Q) although the mechanisms are not fully understood. This study aims to clarify the anti‐inflammatory effects and molecular mechanisms of PQ in cell and animal models, compared to Q.Methods and resultsRAW264.7 cells were treated with PQ or Q to investigate the influence on the production of inducible nitric oxide synthase (iNOS), cyclooxygenase‐2 (COX‐2), and protein kinases by Western blotting. Nitric oxide (NO) and prostaglandin E2 (PGE2) were measured by the Griess method and ELISA, respectively. Cytokines were assayed by the multiplex technology. Mouse paw edema was induced by LPS. The results revealed that PQ had stronger inhibition on the production of iNOS, COX‐2, NO, PGE2, and 12 kinds of cytokines, than Q. PQ also showed in vivo anti‐inflammatory effect by attenuating mouse paw edema. Molecular data revealed that PQ had no competitive binding to Toll‐like receptor 4 with LPS, but directly targeted SEK1‐JNK1/2 (where SEK is stress‐activated protein kinase and JNK1/2 is Jun‐N‐terminal kinase 1/2) and MEK1‐ERK1/2 (where ERK is extracellular signal regulated kinase).ConclusionPQ as a potential inhibitor revealed anti‐inflammatory effect in both cell and animal models at least by targeting SEK1‐JNK1/2 and MEK1‐ERK1/2.
Functional ionotropic glutamate receptors on peripheral axons and myelin
Authors: Christensen Pia Crone , Welch Nicole Cheryl , Brideau Craig , Stys Peter K. 
Published: February 2016

ABSTRACTIntroduction: Neurotransmitter‐dependent signaling is traditionally restricted to axon terminals. However, receptors are present on myelinating glia, suggesting that chemical transmission may also occur along axons. Methods: Confocal microscopy and Ca2+‐imaging using an axonally expressed FRET‐based reporter was used to measure Ca2+ changes and morphological alterations in myelin in response to stimulation of glutamate receptors. Results: Activation of α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionic acid (AMPA) or N‐methyl‐D‐aspartate (NMDA) receptors induced a Ca2+ increase in axon cylinders. However, only the latter caused structural alterations in axons, despite similar Ca2+ increases. Myelin morphology was significantly altered by NMDA receptor activation, but not by AMPA receptors. Cu2+ ions influenced the NMDA receptor‐dependent response, suggesting that this metal modulates axonal receptors. Glutamate increased ribosomal signal in Schwann cell cytoplasm. Conclusions: Axon cylinders and myelin of peripheral nervous system axons respond to glutamate, with a consequence being an increase in Schwann cell ribosomes. This may have implications for nerve pathology and regeneration. Muscle Nerve 54: 451–459, 2016
Structural Preferences in Phosphanylthiolato Platinum(II) Complexes
Authors: Duran Josep , Polo Alfonso , Real Julio , Benet‐Buchholz Jordi , Solà Miquel , Poater Albert 
Published: February 2016

AbstractInvited for this month's cover picture are the groups of Prof. Alfonso Polo and Dr. Albert Poater at the Universitat de Girona, as well as their collaborators from the Universitat Autònoma de Barcelona and the Institute of Chemical Research of Catalonia. The cover picture shows phosphanylthiolate ligand coordination on a platinum(II) center to give only the bischelate cis‐P,P isomer when the ligand/Pt ratio is 2, whereas a trinuclear unexpected complex is achieved with a ligand/Pt ratio of 1. Here, the synthesis and structural determination is combined with density functional theory (DFT) calculations to rationalize the reaction mechanistically and through conceptual DFT. The exciting point of this study is that it opens the door to test new experimental pathways to monitor the preferred cis or trans arrangement of bidentate ligands to platinum. (Legend: H‐white, C‐black, P‐purple, S‐yellow, Cl‐green, Pt‐blue.) For more details, see the Full Paper on p. 51 ff.
Introduction of a polar core into the de novo designed protein Top7
Authors: Basanta Benjamin , Chan Kui K. , Barth Patrick , King Tiffany , Sosnick Tobin R. , Hinshaw James R. , Liu Gaohua , Everett John K. , Xiao Rong , Montelione Gaetano T. , Baker David 
Published: February 2016

AbstractDesign of polar interactions is a current challenge for protein design. The de novo designed protein Top7, like almost all designed proteins, has an entirely nonpolar core. Here we describe the replacing of a sizable fraction (5 residues) of this core with a designed polar hydrogen bond network. The polar core design is expressed at high levels in E. coli, has a folding free energy of 10 kcal/mol, and retains the multiphasic folding kinetics of the original Top7. The NMR structure of the design shows that conformations of three of the five residues, and the designed hydrogen bonds between them, are very close to those in the design model. The remaining two residues, which are more solvent exposed, sample a wide range of conformations in the NMR ensemble. These results show that hydrogen bond networks can be designed in protein cores, but also highlight challenges that need to be overcome when there is competition with solvent.
Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia
Authors: Brandão Andreia , Eng Ken Khong , Rito Teresa , Cavadas Bruno , Bulbeck David , Gandini Francesca , Pala Maria , Mormina Maru , Hudson Bob , White Joyce , Ko Tsang-Ming , Saidin Mokhtar , Zafarina Zainuddin , Oppenheimer Stephen , Richards Martin B. , Pereira Luísa , Soares Pedro 
Published: February 2016

AbstractThere has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question using founder analysis of mitochondrial DNA (mtDNA) control-region sequences to identify major lineage clusters most likely to have dispersed from Taiwan into ISEA, proposing that the dispersal had a relatively minor impact on the extant genetic structure of ISEA, and that the role of agriculture in the expansion of the Austronesian languages was therefore likely to have been correspondingly minor. Here we test these conclusions by sequencing whole mtDNAs from across Taiwan and ISEA, using their higher chronological precision to resolve the overall proportion that participated in the “out-of-Taiwan” mid-Holocene dispersal as opposed to earlier, postglacial expansions in the Early Holocene. We show that, in total, about 20 % of mtDNA lineages in the modern ISEA pool result from the “out-of-Taiwan” dispersal, with most of the remainder signifying earlier processes, mainly due to sea-level rises after the Last Glacial Maximum. Notably, we show that every one of these founder clusters previously entered Taiwan from China, 6–7 ka, where rice-farming originated, and remained distinct from the indigenous Taiwanese population until after the subsequent dispersal into ISEA.
Understanding Spatial Genome Organization: Methods and Insights
Authors: Ramani Vijay , Shendure Jay , Duan Zhijun 
Published: February 2016

Abstract
The manner by which eukaryotic genomes are packaged into nuclei while maintaining crucial nuclear functions remains one of the fundamental mysteries in biology. Over the last ten years, we have witnessed rapid advances in both microscopic and nucleic acid-based approaches to map genome architecture, and the application of these approaches to the dissection of higher-order chromosomal structures has yielded much new information. It is becoming increasingly clear, for example, that interphase chromosomes form stable, multilevel hierarchical structures. Among them, self-associating domains like so-called topologically associating domains (TADs) appear to be building blocks for large-scale genomic organization. This review describes features of these broadly-defined hierarchical structures, insights into the mechanisms underlying their formation, our current understanding of how interactions in the nuclear space are linked to gene regulation, and important future directions for the field.
Translational Bioinformatics: Past, Present, and Future
Authors: Tenenbaum Jessica D. 
Published: February 2016

Abstract
Though a relatively young discipline, translational bioinformatics (TBI) has become a key component of biomedical research in the era of precision medicine. Development of high-throughput technologies and electronic health records has caused a paradigm shift in both healthcare and biomedical research. Novel tools and methods are required to convert increasingly voluminous datasets into information and actionable knowledge. This review provides a definition and contextualization of the term TBI, describes the discipline’s brief history and past accomplishments, as well as current foci, and concludes with predictions of future directions in the field.
Mechanisms of Glioma Invasion: Role of Matrix-Metalloproteinases
Authors: Uhm J.H. , Dooley N.P. , Villemure J.-G. , Yong V.W. 
Published: February 2016

ABSTRACT:One of the most lethal properties of high grade gliomas is their ability to invade the surrounding normal brain tissue, as infiltrated cells often escape surgical resection and inevitably lead to tumour recurrence. The consequent poor prognosis and survival rate underscore the need to further understand and target the cellular mechanisms that underly tumour invasiveness. Proteases which degrade the surrounding stromal cells and extracellular matrix proteins have been demonstrated to be critical effectors of invasion for tumours of both central and peripheral origin. Within the nervous system, the role of metalloproteinases as well as other classes of proteases in mediating the invasive phenotype of high grade gliomas has been an intense area of research. We present in this article a review of this literature and address the possibility that these proteases and the biochemical pathways that regulate their expression, such as protein kinase C, may represent potential targets in the therapy of high grade gliomas.
Blood Flow Differences Between Leuko-araiosis with and without Lacunar Infarction
Authors: Oishi Minoru , Mochizuki Yoko , Takasu Toshiaki 
Published: February 2016

ABSTRACT:Background:The present study was designed to find the differences in regional cerebral blood flow and cerebrovascular acetazolamide reactivity between leuko-araiosis with and without lacunar infarction.Methods:Fifteen cases of leuko-araiosis with lacunar infarction, 15 cases of leuko-araiosis without lacunar infarction and 15 age-matched controls in which leuko-araiosis and cerebrovascular diseases are absent (control group) were studied. The regional cerebral blood flow was measured using the stable xenon computed tomography method before and 20 minutes after intravenous injection of 17 mg/kg acetazolamide.Results:The blood flows in the leuko-araiosis area and the lacunar area were significantly lower than the blood flow in the cerebral white matter. The blood flows in the cerebral cortex and the cerebral white matter were significantly lower in the leuko-araiosis with lacunar infarction group than in the leuko-araiosis without lacunar infarction group and the control group. The cerebrovascular acetazolamide reactivity in the leuko-araiosis area and the lacunar area was significantly lower than that in the cerebral white matter. The cerebrovascular acetazolamide reactivity in the cerebral cortex and the cerebral white matter was significantly lower in the leuko-araiosis with lacunar infarction group than in the leuko-araiosis without lacunar infarction group and the control group.Conclusions:The degree of arteriolosclerosis is considered to be more severe and the rate of association of hypertension was higher in leuko-araiosis with lacunar infarction than in leuko-araiosis without lacunar infarction.
The Effect of Anticonvulsant Drugs on GABA-Stimulated Chloride Uptake
Authors: Francis J. , Mihic S.J. , Sneddon W.B. , Burnham W.M. 
Published: February 2016

ABSTRACT:Eight anticonvulsant drugs – including clonazepam, diazepam and phenobarbital – were tested for their effects on GABA-stimulated chloride uptake in rat cerebral cortical microsacs (unfiltered synaptoneurosomes). “Mid” and “high” therapeutic concentrations were screened, and, if significant enhancement was found, full concentration-response tests were done. In the initial screens, enhancement of GABA-stimulated uptake was found only with phenobarbital, clonazepam and diazepam. In subsequent concentration-response tests, the effects of phenobarbital were found to occur throughout the range of normal, anticonvulsant concentrations, whereas the effects of clonazepam and diazepam were observed only above the concentrations normally used for the chronic control of seizures or anxiety. These data suggest that phenobarbital's anticonvulsant effects are mediated via the GABAA receptor complex, but that the low-dose effects of the benzodiazepines may be mediated via some other mechanism.
Inversion of Spin Signal and Spin Filtering in Ferromagnet|Hexagonal Boron Nitride-Graphene van der Waals Heterostructures
Authors: Kamalakar M. Venkata , Dankert André , Kelly Paul J. , Dash Saroj P. 
Published: February 2016

AbstractTwo dimensional atomically thin crystals of graphene and its insulating isomorph hexagonal boron nitride (h-BN) are promising materials for spintronic applications. While graphene is an ideal medium for long distance spin transport, h-BN is an insulating tunnel barrier that has potential for efficient spin polarized tunneling from ferromagnets. Here, we demonstrate the spin filtering effect in cobalt|few layer h-BN|graphene junctions leading to a large negative spin polarization in graphene at room temperature. Through nonlocal pure spin transport and Hanle precession measurements performed on devices with different interface barrier conditions, we associate the negative spin polarization with high resistance few layer h-BN|ferromagnet contacts. Detailed bias and gate dependent measurements reinforce the robustness of the effect in our devices. These spintronic effects in two-dimensional van der Waals heterostructures hold promise for future spin based logic and memory applications.
ZIF-Derived Nitrogen-Doped Porous Carbons for Xe Adsorption and Separation
Authors: Zhong Shan , Wang Qian , Cao Dapeng 
Published: February 2016

AbstractCurrently, finding high capacity adsorbents with large selectivity to capture Xe is still a great challenge. In this work, nitrogen-doped porous carbons were prepared by programmable temperature carbonization of zeolitic imidazolate framework-8 (ZIF-8) and ZIF-8/xylitol composite precursors and the resultant samples are marked as Carbon-Z and Carbon-ZX, respectively. Further adsorption measurements indicate that ZIF-derived nitrogen-doped Carbon-ZX exhibits extremely high Xe capacity of 4.42 mmol g−1 at 298 K and 1 bar, which is higher than almost all other pristine MOFs such as CuBTC, Ni/DOBDC, MOF-5 and Al-MIL-53, and even more than three times of the matrix ZIF-8 at similar conditions. Moreover, Carbon-ZX also shows the highest Xe/N2 selectivity about ~120, which is much larger than all other reported MOFs. These remarkable features illustrate that ZIF-derived nitrogen-doped porous carbon is an excellent adsorbent for Xe adsorption and separation at room temperature.
Transcription-associated processes cause DNA double-strand breaks and translocations in neural stem/progenitor cells
Authors: Schwer Bjoern , Wei Pei-Chi , Chang Amelia N. , Kao Jennifer , Du Zhou , Meyers Robin M. , Alt Frederick W. 
Published: February 2016

Significance
DNA double-strand breaks (DSBs) occur in all cells, including neural stem/progenitor cells (NSPCs) that give rise to the brain. We previously found that developing neural cells lacking a major DSB end-joining pathway are subject to widespread death. Because DSBs may result from gene transcription, we assayed for DSBs near active transcription start sites (TSSs) genome-wide in NSPCs. DSBs occur near TSSs of highly transcribed genes involved in general cellular processes but occur less often near neural-specific TSSs. These TSS-associated DSBs can translocate to other DSBs by both the normal and alternative DSB repair pathways. We report similar findings in B lymphocytes, suggesting that highly transcribed genes involved in general cellular processes are subject to TSS-associated DSBs in divergent cell types.