bluuebunny/crossref_metadata_2025_split huggingface dataset:
A three‐plane architectonic atlas of the rat hippocampal region
Authors: Boccara Charlotte N. , Kjonigsen Lisa J. , Hammer Ingvild M. , Bjaalie Jan G. , Leergaard Trygve B. , Witter Menno P. 
Published: December 2014

ABSTRACTThe hippocampal region, comprising the hippocampal formation and the parahippocampal region, has been one of the most intensively studied parts of the brain for decades. Better understanding of its functional diversity and complexity has led to an increased demand for specificity in experimental procedures and manipulations. In view of the complex 3D structure of the hippocampal region, precisely positioned experimental approaches require a fine‐grained architectural description that is available and readable to experimentalists lacking detailed anatomical experience. In this paper, we provide the first cyto‐ and chemoarchitectural description of the hippocampal formation and parahippocampal region in the rat at high resolution and in the three standard sectional planes: coronal, horizontal and sagittal. The atlas uses a series of adjacent sections stained for neurons and for a number of chemical marker substances, particularly parvalbumin and calbindin. All the borders defined in one plane have been cross‐checked against their counterparts in the other two planes. The entire dataset will be made available as a web‐based interactive application through the Rodent Brain WorkBench (http://www.rbwb.org) which, together with this paper, provides a unique atlas resource. © 2014 Wiley Periodicals, Inc.
Adiponectin Prevents Reduction of Lipid‐Induced Mitochondrial Biogenesis via AMPK/ACC2 Pathway in Chicken Adipocyte
Authors: Gan Lu , Yan Jun , Liu Zhenjiang , Feng Min , Sun Chao 
Published: December 2014

ABSTRACTAdiponectin (APN) stimulates mitochondrial biogenesis and reduces lipid content in human and animal adipocytes. However, the mechanism of adiponectin in regulating mitochondrial biogenesis in chicken adipocytes has never been reported. The objective of this study is to examine the mechanism that adiponectin plays in lipid‐induced mitochondrial biogenesis and mitochondrial function in chicken adipocytes. We found that the overexpression of adiponectin reduced the membrane DAG content and elevated the membrane translocation of PKCθ. In contrast to control groups, the overexpression of adiponectin increased mitochondrial density and mitochondrial DNA contents and peroxisome proliferator‐activated receptor αcoactivator 1α (PGC1‐α) expression. Mitochondrial membrane potential and cytochrome C (Cyt C) content were detected by JC‐1 fluorescent staining and immunofluorescence which indicated that overexpression of adiponectin enhanced mitochondrial ATP synthesis. Moreover, AMPK/ACC2 signaling pathway was activated along with the elevation of PGC1‐α and TFAM by the overexpression of adiponectin, meanwhile the lipid transcription marker genes were down‐regulated. This effect was alleviated by reducing adiponectin and a specific inhibitor of AMPK pathway. We concluded that adiponectin could prevent reduction of lipid‐induced mitochondrial biogenesis via AMPK/ACC2 pathway in chicken adipocytes. J. Cell. Biochem. 116: 1090–1100, 2015. © 2014 Wiley Periodicals, Inc.
Isolation, Characterization and Cardiac Differentiation of Human Thymus Tissue Derived Mesenchymal Stromal Cells
Authors: Lin Ze Bang , Qian Bo , Yang Yu Zhong , Zhou Kai , Sun Jian , Mo Xu Ming , Wu Kai Hong 
Published: December 2014

ABSTRACTMesenchymal stromal cells (MSCs) are promising candidate donor cells for replacement of cardiomyocyte loss during ischemia and in vitro generation of myocardial tissue. We have successfully isolated MSCs from the discarded neonatal thymus gland during cardiac surgery. The thymus MSCs were characterized by cell‐surface antigen expression. These cells have high ability for proliferation and are able to differentiate into osteoblasts and adipocytes in vitro. For cardiac differentiation, the cells were divided into 3 groups: untreated control; 5‐azacytidine group and sequential exposure to 5‐azacytidine, bone morphogenetic protein 4, and basic fibroblast growth factor. Thymus MSCs showed a fibrolast‐like morphology and some differentiated cells increased in size, formed a ball‐like appearance over time and spontaneously contracting cells were observed in sequential exposure group. Immunostaining studies, cardiac specific genes/protein expression confirmed the cardiomyocyte phenotype of the differentiated cells. These results demonstrate that thymus MSCs can be a promising cellular source for cardiac cell therapy and tissue engineering. J. Cell. Biochem. 116: 1205–1212, 2015. © 2014 Wiley Periodicals, Inc.
A Note on Circular Chromatic Number of Graphs with Large Girth and Similar Problems
Authors: Nešetřil Jaroslav , Ossona de Mendez Patrice 
Published: December 2014

AbstractIn this short note, we extend the result of Galluccio, Goddyn, and Hell, which states that graphs of large girth excluding a minor are nearly bipartite. We also prove a similar result for the oriented chromatic number, from which follows in particular that graphs of large girth excluding a minor have oriented chromatic number at most 5, and for the pth chromatic number , from which follows in particular that graphs G of large girth excluding a minor have .
How can two soft bodied animals be precisely connected? a miniature quick‐connect system in the slugs, Arion lusitanicus and Arion rufus
Authors: Allgaier Christoph 
Published: December 2014

ABSTRACTAmong stylommatophoran gastropods, many species have simplified or reduced their copulatory organs, for example, within the Arionidae, many species lack penes. In this study, I ask two questions 1) How are soft bodied slugs which do not possess a penis connected during copulation? and 2) Is there a mechanical isolating barrier between related sympatric slug species? Observations on the mating behavior and the functional morphology of the distal genital apparatus were made in a mixed population of Arion lusitanicus and Arion rufus. The investigated Arion species exhibit an elaborate copulation process with a quick genital coupling. Prior to full eversion of the distal genitalia, the genital coupling proceeds inside the atrium cavity of one of the partners. This is in contrast to the symmetrical mutual eversion in penis‐bearing species. The donor–recipient channels are tightly connected to one after another and fit precisely. During copulation, the jelly‐coated spermatophore of the donor is pressed out into the connected channel of the partner, where it is implanted only with its frontal part. In the field, successful interspecific matings in terms of spermatophore transfer were rarely observed. The observations presented indicate a mechanical barrier which may profoundly influence the intraspecific and interspecific mating success. J. Morphol. 276:631–648, 2015. © 2014 Wiley Periodicals, Inc.
Quantification of sperm specific mRNA transcripts (PRM1, PRM2, and TNP2) in teratozoospermia and normozoospermia: New correlations between mRNA content and morphology of sperm
Authors: Savadi‐Shiraz Elham , Edalatkhah Haleh , Talebi Saeed , Heidari‐Vala Hamed , Zandemami Mahdi , Pahlavan Somayeh , Modarressi Mohammad Hossein , Akhondi Mohammad Mehdi , Paradowska‐Dogan Agnieszka , Sadeghi Mohammad Reza 
Published: December 2014

SUMMARYSperm mRNAs could be used as a predictor of fertilization capacity since the transcriptional profile of a gamete is critical for the production of viable human sperm. The aim of this study was to determine if PRM1, PRM2, and TNP2 transcripts in spermatozoa from normozoospermic and teratozoospermic men correlate with sperm morphology and/or assisted‐reproduction outcomes. Human ejaculates were collected from 138 men referred to an infertility clinic, and were separated in two groups, teratozoospermic (n = 72) and normozoospermic (n = 66), based on World Health Organization criteria (2010). Chromomycin A3 and analine blue staining were used to evaluate protamination and chromatin integrity, respectively. Quantitative reverse‐transcriptase PCR was performed for PRM1, PRM2, and TNP2. This analysis revealed significantly higher PRM1 and PRM2 mRNA copy numbers in normozoospermic versus teratozoospermic samples (P < 0.001). In contrast, TNP2 transcript abundance was significantly higher in teratozoospermic versus normozoospermic samples (P < 0.001) and positively correlated with sperm‐head defects (P < 0.05). Sperm‐tail defects negatively correlated (P < 0.05) with both PRM1 and PRM2 transcripts in normozoospermic samples. No significant differences were observed between the two groups when comparing transcript levels to the outcome of intracytoplasmic sperm injection cycles (P > 0.05), and a normal PRM1/PRM2 mRNA ratio (∼1) was observed in more than 70% of successful cycles. Thus, the quantity of PRM1, PRM2, and TNP2 transcripts and the PRM1/PRM2 mRNA ratio affect spermiogenesis, sperm morphology, and the function of mature human sperm. These mRNAs could therefore be used as biomarkers for the diagnosis of male infertility. Mol. Reprod. Dev. 82: 26–35, 2015. © 2014 Wiley Periodicals, Inc.
Selective magnetic resonance imaging of magnetic nanoparticles by acoustically induced rotary saturation
Authors: Zhu Bo , Witzel Thomas , Jiang Shan , Huang Susie Y. , Rosen Bruce R. , Wald Lawrence L. 
Published: December 2014

PurposeThe goal of this study was to introduce a new method to selectively detect iron oxide contrast agents using an acoustic wave to perturb the spin‐locked water signal in the vicinity of the magnetic particles. The acoustic drive can be modulated externally to turn the effect on and off, allowing sensitive and quantitative statistical comparison and removal of confounding image background variations.MethodsWe demonstrated the effect in spin‐locking experiments using piezoelectric actuators to generate vibrational displacements of iron oxide samples. We observed a resonant behavior of the signal changes with respect to the acoustic frequency where iron oxide is present. We characterized the effect as a function of actuator displacement and contrast agent concentration.ResultsThe resonant effect allowed us to generate block‐design “modulation response maps” indicating the contrast agent's location, as well as positive contrast images with suppressed background signal. We found that the acoustically induced rotary saturation (AIRS) effect stayed approximately constant across acoustic frequency and behaved monotonically over actuator displacement and contrast agent concentration.ConclusionAIRS is a promising method capable of using acoustic vibrations to modulate the contrast from iron oxide nanoparticles and thus perform selective detection of the contrast agents, potentially enabling more accurate visualization of contrast agents in clinical and research settings. Magn Reson Med 75:97–106, 2016. © 2015 Wiley Periodicals, Inc.
A nonlinear parametric model reduction method for efficient gear contact simulations
Authors: Blockmans B. , Tamarozzi T. , Naets F. , Desmet W. 
Published: December 2014

SummaryA novel nonlinear parametric model order reduction technique for the solution of contact problems in flexible multibody dynamics is presented. These problems are characterized by significant variations in the location and size of the contact area and typically require high‐dimensional finite element models having multiple inputs and outputs to be solved. The presented technique draws from the fields of nonlinear and parametric model reduction to construct a reduced‐order model whose dimensions are insensitive to the dimensions of the full‐order model. The solution of interest is approximated in a lower‐dimensional subspace spanned by a constant set of eigenvectors augmented with a parameter‐dependent set of global contact shapes. The latter represent deformation patterns of the interacting bodies obtained from a series of static contact analyses. The set of global contact shapes is parameterized with respect to the system configuration and therefore continuously varies in time. An energy‐consistent formulation is assured by explicitly taking into account the dynamic parameter variability in the derivation of the equations of motion. The performance of the novel technique is demonstrated by simulating a dynamic gear contact problem and comparing results against traditional model reduction techniques as well as commercial nonlinear finite element software. Copyright © 2014 John Wiley & Sons, Ltd.
Effect of Oxidizing Slag on Cleanliness of IF Steel during Ladle Holding Process
Authors: Qin Yiming , Wang Xinhua , Li Linping , Huang Fuxiang 
Published: December 2014

AbstractThe effect of oxidizing slag on cleanliness of IF steel produced by ShouGang during ladle holding process was investigated by comparing the differences of slag composition, steel composition and inclusion morphology between two processes of different slag oxidability(Process‐A < Process‐B). The results showed that, the reoxidation of slag to steel was observed during holding process, and Process‐A with the lower slag oxidability was more helpful to improve the cleanliness of molten steel during holding process by comparing the T.O of the two processes. Due to the slag reoxidation during holding process, the large petal shaped and dendritic Al2O3 inclusions generated for Process‐A, and both the numbers of Al2O3 and Al2O3‐TixO inclusions increased significantly for Process‐B. In order to slow down reoxidation rate and improve the ability of slag to absorb inclusions, (FeO) content should be reduced and (CaO)/(Al2O3) should be increased in the case of liquid slag. In conclusion, whether prolonging ladle holding time should depend on (FeO) content, (CaO)/(Al2O3) etc. parameters of slag and initial T.O of molten steel.
MicroRNA-199b Modulates Vascular Cell Fate During iPS Cell Differentiation by Targeting the Notch Ligand Jagged1 and Enhancing VEGF Signaling
Authors: Chen Ting , Margariti Andriana , Kelaini Sophia , Cochrane Amy , Guha Shaunta T. , Hu Yanhua , Stitt Alan W. , Zhang Li , Xu Qingbo 
Published: December 2014

Abstract
Aims: Recent ability to derive endothelial cells (ECs) from induced pluripotent stem (iPS) cells holds a great therapeutic potential for personalized medicine and stem cell therapy. We aimed that better understanding of the complex molecular signals that are evoked during iPS cell differentiation toward ECs may allow specific targeting of their activities to enhance cell differentiation and promote tissue regeneration. Methods and Results: In this study, we have generated mouse iPS cells from fibroblasts using established protocol. When iPS cells were cultivated on type IV mouse collagen-coated dishes in differentiation medium, cell differentiation toward vascular lineages were observed. To study the molecular mechanisms of iPS cell differentiation, we found that miR-199b is involved in EC differentiation. A step-wise increase in expression of miR-199 was detected during EC differentiation. Notably, miR-199b targeted the Notch ligand JAG1, resulting in vascular endothelial growth factor (VEGF) transcriptional activation and secretion through the transcription factor STAT3. Upon shRNA-mediated knockdown of the Notch ligand JAG1, the regulatory effect of miR-199b was ablated and there was robust induction of STAT3 and VEGF during EC differentiation. Knockdown of JAG1 also inhibited miR-199b-mediated inhibition of iPS cell differentiation toward smooth muscle markers. Using the in vitro tube formation assay and implanted Matrigel plugs, in vivo, miR-199b also regulated VEGF expression and angiogenesis. Conclusions: This study indicates a novel role for miR-199b as a regulator of the phenotypic switch during vascular cell differentiation derived from iPS cells by regulating critical signaling angiogenic responses. Stem Cells 2015;33:1405–1418
Vitamin C Facilitates Dopamine Neuron Differentiation in Fetal Midbrain Through TET1- and JMJD3-Dependent Epigenetic Control Manner
Authors: He Xi-Biao , Kim Mirang , Kim Seon-Young , Yi Sang-Hoon , Rhee Yong-Hee , Kim Taeho , Lee Eun-Hye , Park Chang-Hwan , Dixit Shilpy , Harrison Fiona E. , Lee Sang-Hun 
Published: December 2014

AbstractIntracellular Vitamin C (VC) is maintained at high levels in the developing brain by the activity of sodium-dependent VC transporter 2 (Svct2), suggesting specific VC functions in brain development. A role of VC as a cofactor for Fe(II)-2-oxoglutarate-dependent dioxygenases has recently been suggested. We show that VC supplementation in neural stem cell cultures derived from embryonic midbrains greatly enhanced differentiation toward midbrain-type dopamine (mDA) neurons, the neuronal subtype associated with Parkinson's disease. VC induced gain of 5-hydroxymethylcytosine (5hmC) and loss of H3K27m3 in DA phenotype gene promoters, which are catalyzed by Tet1 and Jmjd3, respectively. Consequently, VC enhanced DA phenotype gene transcriptions in the progenitors by Nurr1, a transcription factor critical for mDA neuron development, to be more accessible to the gene promoters. Further mechanism studies including Tet1 and Jmjd3 knockdown/inhibition experiments revealed that both the 5hmC and H3K27m3 changes, specifically in the progenitor cells, are indispensible for the VC-mediated mDA neuron differentiation. We finally show that in Svct2 knockout mouse embryos, mDA neuron formation in the developing midbrain decreased along with the 5hmC/H3k27m3 changes. These findings together indicate an epigenetic role of VC in midbrain DA neuron development. Stem Cells 2015;33:1320–1332
Computational challenges, tools, and resources for analyzing co‐ and post‐transcriptional events in high throughput
Authors: Bahrami‐Samani Emad , Vo Dat T. , de Araujo Patricia Rosa , Vogel Christine , Smith Andrew D. , Penalva Luiz O. F. , Uren Philip J. 
Published: December 2014

Co‐ and post‐transcriptional regulation of gene expression is complex and multifaceted, spanning the complete RNA lifecycle from genesis to decay. High‐throughput profiling of the constituent events and processes is achieved through a range of technologies that continue to expand and evolve. Fully leveraging the resulting data is nontrivial, and requires the use of computational methods and tools carefully crafted for specific data sources and often intended to probe particular biological processes. Drawing upon databases of information pre‐compiled by other researchers can further elevate analyses. Within this review, we describe the major co‐ and post‐transcriptional events in the RNA lifecycle that are amenable to high‐throughput profiling. We place specific emphasis on the analysis of the resulting data, in particular the computational tools and resources available, as well as looking toward future challenges that remain to be addressed. WIREs RNA 2015, 6:291–310. doi: 10.1002/wrna.1274This article is categorized under:

RNA Evolution and Genomics > Computational Analyses of RNA
Distance-dependent switching of anti-predator behavior of frogs from immobility to fleeing
Authors: Nishiumi Nozomi , Mori Akira 
Published: December 2014

AbstractTo avoid predation, many animals are required to appropriately switch between immobility for crypsis and fleeing for escape. We conducted two staged-encounter experiments using a frog and a snake to examine factors that affect the occurrence of immobility and fleeing, and to evaluate the efficiency of them. The first experiment demonstrated that frogs initially exhibit immobility, when snakes are moving at a long distance, and then switch from immobility to fleeing at a shorter distance even when snakes have not detected them. The second experiment demonstrated that snakes at 400–800 mm distance detect only fleeing frogs, whereas snakes at 100 mm or closer detect both immobile and fleeing frogs. Thus, the ability of snakes to detect motionless frogs depends on the distance, and the distance-dependent switching can be considered an adaptive strategy of the frog. However, a previous model predicts that cryptic prey should flee immediately on seeing a predator or not flee until being detected by the predator. To explain this discordance, we propose two factors: engagement of intensive searching mode by predator at short distance and effects of sudden fleeing at close distance. We suggest incorporating them in future theory for better understanding of anti-predator strategy.
Acquisition of the pulmonary venous and left atrial anatomy with non‐contrast‐enhanced MRI for catheter ablation of atrial fibrillation: Usefulness of two‐dimensional balanced steady‐state free precession
Authors: Shigenaga Yutaka , Kiuchi Kunihiko , Okajima Katsunori , Ikeuchi Kazushi , Ikeda Takayuki , Shimane Akira , Yokoi Kiminobu , Teranishi Jin , Aoki Kousuke , Chimura Misato , Masai Hideyuki , Yamada Shinichiro , Taniguchi Yasuyo , Yasaka Yoshinori , Kawai Hiroya 
Published: December 2014

AbstractBackgroundUsually, the pulmonary venous and left atrial (PV–LA) anatomy is assessed with contrast‐enhanced computed tomographic imaging for catheter ablation of atrial fibrillation (AF). A non‐contrast‐enhanced magnetic resonance (MR) imaging method has not been established. Three‐dimensional balanced steady‐state free precession (3D b‐SSFP) sequences cannot visualize the PV–LA anatomy simultaneously because of the signal intensity defect of pulmonary veins. We compared two‐dimensional (2D) b‐SSFP sequences with 3D b‐SSFP sequences in depicting the PV–LA anatomy with non‐contrast‐enhanced MR imaging for AF ablation.MethodsEleven healthy volunteers underwent non‐contrast‐enhanced MR imaging with 3D b‐SSFP and 2D b‐SSFP sequences. The MR images were reconstructed on the 3D PV–LA surface image. Two experienced radiological technicians independently scored the multiplanar reformatted (MPR) images on a scale of 1–4 (from 1, not visualized, to 4, excellent definition). The overall score was a sum of 5 segments (LA and 4 PVs).ResultsIn the 2D b‐SSFP method, MR imaging was successfully performed, and the 3D PV–LA surface image was precisely reconstructed in all healthy volunteers. The image score was significantly higher in the 2D b‐SSFP method compared to the 3D b‐SSFP method (19 [19; 20] vs. 12 [11; 15], p=0.004, for both observers). No PV signal intensity defects occurred in the 2D b‐SSFP method.ConclusionsThe 2D b‐SSFP sequence was more useful than the 3D b‐SSFP sequence in adequately depicting the PV–LA anatomy.