bluuebunny/crossref_metadata_2025_split huggingface dataset:
A simulation-based breeding design that uses whole-genome prediction in tomato
Authors: Yamamoto Eiji , Matsunaga Hiroshi , Onogi Akio , Kajiya-Kanegae Hiromi , Minamikawa Mai , Suzuki Akinori , Shirasawa Kenta , Hirakawa Hideki , Nunome Tsukasa , Yamaguchi Hirotaka , Miyatake Koji , Ohyama Akio , Iwata Hiroyoshi , Fukuoka Hiroyuki 
Published: January 2016

AbstractEfficient plant breeding methods must be developed in order to increase yields and feed a growing world population, as well as to meet the demands of consumers with diverse preferences who require high-quality foods. We propose a strategy that integrates breeding simulations and phenotype prediction models using genomic information. The validity of this strategy was evaluated by the simultaneous genetic improvement of the yield and flavour of the tomato (Solanum lycopersicum), as an example. Reliable phenotype prediction models for the simulation were constructed from actual genotype and phenotype data. Our simulation predicted that selection for both yield and flavour would eventually result in morphological changes that would increase the total plant biomass and decrease the light extinction coefficient, an essential requirement for these improvements. This simulation-based genome-assisted approach to breeding will help to optimise plant breeding, not only in the tomato but also in other important agricultural crops.
Intravital Imaging Reveals Dynamics of Lymphangiogenesis and Valvulogenesis
Authors: Kang Gyeong Jin , Ecoiffier Tatiana , Truong Tan , Yuen Don , Li Guangyu , Lee Narae , Zhang Liwei , Chen Lu 
Published: January 2016

AbstractLymphatic research signifies a field of rapid progression in recent years. Though lymphatic dysfunction has been found in a myriad of disorders, to date, few effective treatments are available for lymphatic diseases. It is therefore urgent to develop new experimental approaches and therapeutic protocols. The cornea offers an ideal site for lymphatic research due to its transparent nature, accessible location and lymphatic-free but –inducible features. Moreover, we have recently discovered that corneal lymphatic vessels develop luminal valves as lymphangiogenesis proceeds. This tissue thus provides an optimal tool to study both lymphangiogenesis and valvulogenesis upon a pathological insult. In this paper, we show that the modified Prox-1-GFP mice carrying wildtype C57BL/6 background provide a valuable tool for intravital imaging of corneal lymphatic vessels and valves and can be used to study pathological lymphangiogenesis induced by various insults. Further, we demonstrate the multifaceted dynamics of lymphangiogenesis and valvulogenesis associated with transplantation, from the initiation to regression phases and report several novel and critical phenomena and mechanisms that cannot be detected by conventional ex vivo approaches. Further investigation holds the great potential for divulging new mechanisms and therapeutic strategies for lymphangiogenesis and lymphangiogenesis-related diseases at various stages and inside or outside the eye.
Canonical Notch signaling plays an instructive role in auditory supporting cell development
Authors: Campbell Dean P. , Chrysostomou Elena , Doetzlhofer Angelika 
Published: January 2016

AbstractThe auditory sensory epithelium, composed of mechano-sensory hair cells (HCs) and highly specialized glial-like supporting cells (SCs), is critical for our ability to detect sound. SCs provide structural and functional support to HCs and play an essential role in cochlear development, homeostasis and repair. Despite their importance, however, surprisingly little is known about the molecular mechanisms guiding SC differentiation. Here, we provide evidence that in addition to its well-characterized inhibitory function, canonical Notch signaling plays a positive, instructive role in the differentiation of SCs. Using γ-secretase inhibitor DAPT to acutely block canonical Notch signaling, we identified a cohort of Notch-regulated SC-specific genes, with diverse functions in cell signaling, cell differentiation, neuronal innervation and synaptogenesis. We validated the newly identified Notch-regulated genes in vivo using genetic gain (Emx2Cre/+; Rosa26N1ICD/+) and loss-of-function approaches (Emx2Cre/+; Rosa26DnMAML1/+). Furthermore, we demonstrate that Notch over-activation in the differentiating murine cochlea (Emx2Cre/+; Rosa26N1ICD/+) actively promotes a SC-specific gene expression program. Finally, we show that outer SCs –so called Deiters’ cells are selectively lost by prolonged reduction (Emx2Cre/+; Rosa26DnMAML1/+/+) or abolishment of canonical Notch signaling (Fgfr3-iCreER; Rbpj−/Δ), indicating a critical role for Notch signaling in Deiters’ cell development.
Acupuncture for neurogenesis in experimental ischemic stroke: a systematic review and meta-analysis
Authors: Lu Lin , Zhang Xiao-guang , Zhong Linda L.D. , Chen Zi-xian , Li Yan , Zheng Guo-qing , Bian Zhao-xiang 
Published: January 2016

AbstractAcupuncture has been used for patients with stroke and post-stroke rehabilitation for thousands of years. Previous studies reported that acupuncture enhanced stroke recovery through neurogenesis. Hence, we conducted a systematic review and meta-analysis for preclinical studies to assess the current evidence for acupuncture effect on neurogenesis in treating ischaemic stroke. Studies were obtained from six databases, including PubMed, EMBASE, Cochrane Library, Chinese National Knowledge Infrastructure, VIP information database and Chinese Biomedical Literature Database, Ultimately, 34 studies containing 1617 animals were identified. Neurogenesis markers of Brdu, Nestin, PSA-NCAM, NeuN and GFAP were selected as major outcomes. The pooled results of 15 studies marked with Brdu showed significant effects of acupuncture for improving proliferation when compared with control groups (P < 0.01); 13 studies marked with Nestin showed significant effects of acupuncture for increasing proliferation when compared with control groups (P < 0.01); 4 studies marked with PSA-NCAM showed significant effects of acupuncture for enhancing migration when compared with control groups (P < 0.01); 4 studies marked with NeuN showed significant effects of acupuncture for stimulating differentiation when compared with control groups (P < 0.01). The findings suggest that acupuncture is a prospective therapy targeting neurogenesis for ischemic stroke.
In-Situ High-Resolution Transmission Electron Microscopy Investigation of Overheating of Cu Nanoparticles
Authors: Chen Chunlin , Hu Ziyu , Li Yanfen , Liu Limin , Mori Hirotaro , Wang Zhangchang 
Published: January 2016

AbstractSynthesizing and functionalizing metal nanoparticles supported on substrates is currently the subject of intensive study owing to their outstanding catalytic performances for heterogeneous catalysis. Revealing the fundamental effect of the substrates on metal nanoparticles represents a key step in clarifying mechanisms of stability and catalytic properties of these heterogeneous systems. However, direct identification of these effects still poses a significant challenge due to the complicacy of interactions between substrates and nanoparticles and also for the technical difficulty, restraining our understanding of these heterogeneous systems. Here, we combine in situ high-resolution transmission electron microscopy with molecular dynamics simulations to investigate Cu nanoparticles supported on graphite and Cu2O substrates and demonstrate that melting behavior and thermal stability of Cu nanoparticles can be markedly influenced by substrates. The graphite-supported Cu nanoparticles do not melt during annealing at 1073 K until they vanish completely, i.e. only the sublimation occurs, while the Cu2O-supported Cu nanoparticles suffer melting during annealing at 973 K. Such selective superheating of the Cu nanoparticles can be attributed to the adsorption of a thin carbon layer on the surface of the Cu nanoparticles, which helps guide further stability enhancement of functional nanoparticles for realistic applications.
Noninvasive, Targeted and Non-Viral Ultrasound-Mediated GDNF-Plasmid Delivery for Treatment of Parkinson’s Disease
Authors: Fan Ching-Hsiang , Ting Chien-Yu , Lin Chung‐Yin , Chan Hong-Lin , Chang Yuan-Chih , Chen You-Yin , Liu Hao-Li , Yeh Chih-Kuang 
Published: January 2016

AbstractGlial cell line-derived neurotrophic factor (GDNF) supports the growth and survival of dopaminergic neurons. CNS gene delivery currently relies on invasive intracerebral injection to transit the blood-brain barrier. Non-viral gene delivery via systematic transvascular route is an attractive alternative because it is non-invasive, but a high-yield and targeted gene-expressed method is still lacking. In this study, we propose a novel non-viral gene delivery approach to achieve targeted gene transfection. Cationic microbubbles as gene carriers were developed to allow the stable formation of a bubble-GDNF gene complex and transcranial focused ultrasound (FUS) exposure concurrently interacting with the bubble-gene complex allowed transient gene permeation and induced local GDNF expression. We demonstrate that the focused ultrasound-triggered GDNFp-loaded cationic microbubbles platform can achieve non-viral targeted gene delivery via a noninvasive administration route, outperform intracerebral injection in terms of targeted GDNF delivery of high-titer GDNF genes and has a neuroprotection effect in Parkinson’s disease (PD) animal models to successfully block PD syndrome progression and to restore behavioral function. This study explores the potential of using FUS and bubble-gene complexes to achieve noninvasive and targeted gene delivery for the treatment of neurodegenerative disease.
Analysis of bacterial diversity in two oil blocks from two low-permeability reservoirs with high salinities
Authors: Xiao Meng , Sun Shan-Shan , Zhang Zhong-Zhi , Wang Jun-Ming , Qiu Long-Wei , Sun Hua-Yang , Song Zhao-Zheng , Zhang Bei-Yu , Gao De-Li , Zhang Guang-Qing , Wu Wei-Min 
Published: January 2016

AbstractThe community diversities of two oil reservoirs with low permeability of 1.81 × 10−3 and 2.29 × 10−3 μm2 in Changqing, China, were investigated using a high throughput sequencing technique to analyze the influence of biostimulation with a nutrient activator on the bacterial communities. These two blocks differed significantly in salinity (average 17,500 vs 40,900 mg/L). A core simulation test was used to evaluate the effectiveness of indigenous microbial-enhanced oil recovery (MEOR). The results indicated that in the two high salinity oil reservoirs, one reservoir having relatively lower salinity level and a narrow salinity range had higher bacterial and phylogenetic diversity. The addition of the nutrient activator increased the diversity of the bacterial community structure and the diversity differences between the two blocks. The results of the core simulation test showed that the bacterial community in the reservoir with a salinity level of 17,500 mg/L did not show significant higher MEOR efficiency compared with the reservoir with 40,900 mg/L i.e. MEOR efficiency of 8.12% vs 6.56% (test p = 0.291 > 0.05). Therefore, salinity levels affected the bacterial diversities in the two low permeability oil blocks remarkably. But the influence of salinity for the MEOR recovery was slightly.
Non-Markovianity hinders Quantum Darwinism
Authors: Galve Fernando , Zambrini Roberta , Maniscalco Sabrina 
Published: January 2016

AbstractWe investigate Quantum Darwinism and the emergence of a classical world from the quantum one in connection with the spectral properties of the environment. We use a microscopic model of quantum environment in which, by changing a simple system parameter, we can modify the information back flow from environment into the system and therefore its non-Markovian character. We show that the presence of memory effects hinders the emergence of classical objective reality, linking these two apparently unrelated concepts via a unique dynamical feature related to decoherence factors.
Epitaxial stabilization and phase instability of VO2 polymorphs
Authors: Lee Shinbuhm , Ivanov Ilia N. , Keum Jong K. , Lee Ho Nyung 
Published: January 2016

AbstractThe VO2 polymorphs, i.e., VO2(A), VO2(B), VO2(M1) and VO2(R), have a wide spectrum of functionalities useful for many potential applications in information and energy technologies. However, synthesis of phase pure materials, especially in thin film forms, has been a challenging task due to the fact that the VO2 polymorphs are closely related to each other in a thermodynamic framework. Here, we report epitaxial stabilization of the VO2 polymorphs to synthesize high quality single crystalline thin films and study the phase stability of these metastable materials. We selectively deposit all the phases on various perovskite substrates with different crystallographic orientations. By investigating the phase instability, phonon modes and transport behaviours, not only do we find distinctively contrasting physical properties of the VO2 polymorphs, but that the polymorphs can be on the verge of phase transitions when heated as low as ~400 °C. Our successful epitaxy of both VO2(A) and VO2(B) phases, which are rarely studied due to the lack of phase pure materials, will open the door to the fundamental studies of VO2 polymorphs for potential applications in advanced electronic and energy devices.
Somatic Copy Number Alterations at Oncogenic Loci Show Diverse Correlations with Gene Expression
Authors: Roszik Jason , Wu Chang-Jiun , Siroy Alan E. , Lazar Alexander J. , Davies Michael A , Woodman Scott E , Kwong Lawrence N 
Published: January 2016

AbstractSomatic copy number alterations (SCNAs) affecting oncogenic drivers have a firmly established role in promoting cancer. However, no agreed-upon standard exists for calling locus-specific amplifications and deletions in each patient sample. Here, we report the correlative analysis of copy number amplitude and length with gene expression across 6,109 samples from The Cancer Genome Atlas (TCGA) dataset across 16 cancer types. Using specificity, sensitivity and precision-based scores, we assigned optimized amplitude and length cutoffs for nine recurrent SCNAs affecting known oncogenic drivers, using mRNA expression as a functional readout. These cutoffs captured the majority of SCNA-driven, highly-expression-altered samples. The majority of oncogenes required only amplitude cutoffs, as high amplitude samples were almost invariably focal; however, CDKN2A and PTEN uniquely required both amplitude and length cutoffs as primary predictors. For PTEN, these extended to downstream AKT activation. In contrast, SCNA genes located peri-telomerically or in fragile sites showed poor expression-copy number correlations. Overall, our analyses identify optimized amplitude and length cutoffs as efficient predictors of gene expression changes for specific oncogenic SCNAs, yet warn against one-size-fits-all interpretations across all loci. Our results have implications for cancer data analyses and the clinic, where copy number and mutation data are increasingly used to personalize cancer therapy.
Blood metabolite markers of neocortical amyloid-β burden: discovery and enrichment using candidate proteins
Authors: Voyle N , Kim M , Proitsi P , Ashton N J , Baird A L , Bazenet C , Hye A , Westwood S , Chung R , Ward M , Rabinovici G D , Lovestone S , Breen G , Legido-Quigley C , Dobson R J B , Kiddle S J ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: January 2016

AbstractWe believe this is the first study to investigate associations between blood metabolites and neocortical amyloid burden (NAB) in the search for a blood-based biomarker for Alzheimer’s disease (AD). Further, we present the first multi-modal analysis of blood markers in this field. We used blood plasma samples from 91 subjects enrolled in the University of California, San Francisco Alzheimer’s Disease Research Centre. Non-targeted metabolomic analysis was used to look for associations with NAB using both single and multiple metabolic feature models. Five metabolic features identified subjects with high NAB, with 72% accuracy. We were able to putatively identify four metabolites from this panel and improve the model further by adding fibrinogen gamma chain protein measures (accuracy=79%). One of the five metabolic features was studied in the Alzheimer’s Disease Neuroimaging Initiative cohort, but results were inconclusive. If replicated in larger, independent studies, these metabolic features and proteins could form the basis of a blood test with potential for enrichment of amyloid pathology in anti-amyloid trials.
Response to the comment on “Promising blood-derived biomarkers for estimation of the postmortem interval”
Authors: Dinis-Oliveira Ricardo Jorge , Carvalho Félix , Costa Isabel , Silvestre Ricardo , Magalhães Teresa 
Published: January 2016

Abstract
Following Meurs and Szykuła's comment on our published article titled “Promising blood-derived biomarkers for estimation of the postmortem interval”, we recognize the importance of the issues raised, but we would like to emphasize that these contain some misinterpretations and that most of the points were already discussed in depth in our manuscript particularly in the conclusion section. We also aim to highlight further data regarding the difficulties of postmortem interval estimation.
Internal fatigue crack initiation in drawn Ti–6Al–4V wires
Authors: Everaerts J. , Verlinden B. , Wevers M. 
Published: January 2016

Fatigue cracks in titanium alloys are often found to initiate at faceted alpha grains. In the very high cycle fatigue regime, crack initiation tends to shift from the surface towards the interior of the material, and more initiation facets can be found on the fracture surface. In this study, fatigue tests were performed on drawn and heat-treated Ti–6Al–4V wires. Only a few samples fractured due to interior initiation. The facets at the initiation sites of these samples were not flat, but had markings on the nano-scale, and were highly inclined. A possible explanation for these aspects is the crystallographic texture of the wire, and a reflection is made on the suggested mechanisms of facet formation. This paper is part of a Themed Issue on Euromech 570: Interface-dominated materials.
Very high cycle fatigue of bearing steels with artificial defects in vacuum
Authors: Spriestersbach D. , Brodyanski A. , Lösch J. , Kopnarski M. , Kerscher E. 
Published: January 2016

At high-strength steels very high cycle fatigue (VHCF) failure always occurs at subsurface inclusions. As a result, the failure shows large scatter and is not observable or predictable prior to failure. In order to understand the mechanisms leading to crack initiation in VHCF, it is necessary to make the failure observable. Within our work, a new testing procedure is introduced that enables the simulation of subsurface conditions at the surface and thereby the localisation of the failure. Therefore, specimens with artificial surface defects were tested in vacuum atmosphere. In our work, we will show the testing procedure and the validation of the results. Further, the transferability of our results on the failure at subsurface inclusions is discussed. This paper is part of a Themed Issue on Recent developments in bearing steels.
Metapopulation viability of swamp rabbits in southern Illinois: potential impacts of habitat change
Authors: Robinson Christopher D. , Crawford Joanne C. , Corcoran Lyann , Schauber Eric M. , Nielsen Clayton K. 
Published: January 2016

Abstract
Swamp rabbits ( Sylvilagus aquaticus ) in southern Illinois exist as a metapopulation due to fragmentation of the bottomland hardwood forests in which they live. This fragmentation makes their persistence in Illinois uncertain. We used population viability analysis (PVA) to estimate the probability of persistence of the swamp rabbit metapopulation in Illinois, using a habitat suitability map we created and life history parameters drawn from the literature. We varied the parameters used in our PVA from 50% to 150% of the initial value to compare their effects on extinction risk and to direct future management and research. We tested the effects of potential habitat loss and fragmentation by 1) removing patches individually and in groups from the analysis and by 2) adding 60, 120, and 180 m to the edge of all patches. We also tested the potential effect of dispersal corridors by increasing dispersal between connected patches. Under baseline conditions, the model suggests a 0% chance of quasi-extinction (90% metapopulation decline) of swamp rabbits within 25 (or even 50) years. Changes in fecundity values and the effects of catastrophic flooding had the greatest effect on extinction risk, and changes in no other parameter yielded any appreciable impact. Removing the largest patches from the population increased the 25-year risk of extinction to 4%, whereas any other modifications to the habitat did not change the extinction risk. We suggest that managers focus on sustaining habitat quality, particularly upland habitats adjacent to occupied bottomland hardwood forests to improve the likelihood of swamp rabbit persistence in Illinois.
The complete mitochondrial genomes of nine white-tailed deer subspecies and their genomic differences
Authors: Ambriz-Morales Pascuala , De La Rosa-Reyna Xochitl F. , Sifuentes-Rincon Ana Maria , Parra-Bracamonte G. Manuel , Villa-Melchor Abraham , Chassin-Noria Omar , Arellano-Vera Williams 
Published: January 2016

Abstract
The white-tailed deer ( Odocoileus virginianus ) is an important, sustainable-use species in Mexico; 14 subspecies are widely distributed throughout the Mexican territory. The criteria for classifying subspecies is based on morphological features throughout their geographical range; however, the complete genetic characterization of Mexican subspecies has not been established. The objective of the present work is to report the mitogenomes of 9 of the 14 white-tailed deer subspecies from Mexico and identify their unique variations. Typical vertebrate mitogenomes structures (i.e., 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes) were observed in the studied subspecies. The greatest numbers of polymorphisms were identified in the D-loop, ND4, ND5, CYTB/COI, ATP6, and COIII genes. Phylogenetic analyses showed that the southern and southeastern subspecies were distinct from the central and northern subspecies; the greatest genetic distances were also observed between these 2 groups. These subspecies-specific variations could be useful for designing a strategy to genetically characterize the studied subspecies.
El venado cola blanca es una de las especies de mayor importancia dentro del aprovechamiento de la fauna silvestre de México, donde se distribuyen de manera natural 14 subespecies. Actualmente, estas subespecies se han clasificado de acuerdo a sus variaciones fenotípicas que presentan a lo largo de su rango de distribución, sin embargo no se ha establecido la caracterización genética completa de las mismas. Es por esto que el objetivo del presente estudio es reportar los mitogenomas de 9 de las 14 subespecies de venado cola blanca, así como identificar las variaciones únicas de cada subespecie. En las 9 subespecies se observó la estructura típica de los mitogenomas de vertebrados (13 genes que codifican para proteínas, 22 ARNt, 2 ARNr). Los genes con mayor polimorfismo fueron D-loop, ND4, ND5, CYTB/COI, ATP6 y COIII. El análisis filogenético mostró la separación de las subespecies del sur y sureste de las subespecies del centro y norte del país, a su vez las distancias genéticas entre estos dos grupos fueron las más altas. Estas variaciones subespecie-específicas podrían ser útiles para diseñar una estrategia para caracterizar genéticamente las subespecies estudiadas.