bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-dimensional direct measurement of cardiomyocyte volume, nuclearity, and ploidy in thick histological sections
Authors: Bensley Jonathan Guy , De Matteo Robert , Harding Richard , Black Mary Jane 
Published: April 2016

AbstractQuantitative assessment of myocardial development and disease requires accurate measurement of cardiomyocyte volume, nuclearity (nuclei per cell), and ploidy (genome copies per cell). Current methods require enzymatically isolating cells, which excludes the use of archived tissue, or serial sectioning. We describe a method of analysis that permits the direct simultaneous measurement of cardiomyocyte volume, nuclearity, and ploidy in thick histological sections. To demonstrate the utility of our technique, heart tissue was obtained from four species (rat, mouse, rabbit, sheep) at up to three life stages: prenatal, weaning and adulthood. Thick (40 μm) paraffin sections were stained with Wheat Germ Agglutinin-Alexa Fluor 488 to visualise cell membranes, and DAPI (4′,6-diamidino-2-phenylindole) to visualise nuclei and measure ploidy. Previous methods have been restricted to thin sections (2–10 μm) and offer an incomplete picture of cardiomyocytes. Using confocal microscopy and three-dimensional image analysis software (Imaris Version 8.2, Bitplane AG, Switzerland), cardiomyocyte volume, nuclearity, and ploidy were measured. This method of staining and analysis of cardiomyocytes enables accurate morphometric measurements in thick histological sections, thus unlocking the potential of archived tissue. Our novel time-efficient method permits the entire cardiomyocyte to be visualised directly in 3D, eliminating the need for precise alignment of serial sections.
A wild Indo-Pacific bottlenose dolphin adopts a socially and genetically distant neonate
Authors: Sakai Mai , Kita Yuki F. , Kogi Kazunobu , Shinohara Masanori , Morisaka Tadamichi , Shiina Takashi , Inoue-Murayama Miho 
Published: April 2016

AbstractAlloparental behaviour and adoption have been reported in many mammals and birds. Such behaviours are energetically costly and their causes and functions remain unclear. We observed the adoption behaviour of a wild Indo-Pacific bottlenose dolphin (Tursiops aduncus) near Mikura Island, Japan. A calf was seen with its mother on six observation days. Following the mother’s death, the calf was observed with a sub-adult female on all 18 observation days from May to September 2012. On three days, the calf was observed swimming with this female in the suckling position and milk was seen leaking from the female’s mammary slit. A five-year dataset revealed no significant social or kin relationships between the biological mother and allomother, indicating that kinship and social relationships did not play an important role in the observed adoption.
Phase transformation and deformation behavior of NiTi-Nb eutectic joined NiTi wires
Authors: Wang Liqiang , Wang Cong , Zhang Lai-Chang , Chen Liangyu , Lu Weijie , Zhang Di 
Published: April 2016

AbstractNiTi wires were brazed together via eutectic reaction between NiTi and Nb powder deposited at the wire contact region. Phase transformation and deformation behavior of the NiTi-Nb eutectic microstructure were investigated using transmission electron microscopy (TEM) and cyclic loading-unloading tests. Results show that R phase and B19′ martensite transformation are induced by plastic deformation. R phase transformation, which significantly contributes to superelasticity, preferentially occurs at the interfaces between NiTi and eutectic region. Round-shaped Nb-rich phase with rod-like and lamellar-type eutectics are observed in eutectic regions. These phases appear to affect the deformation behavior of the brazed NiTi-Nb region via five distinct stages in stress-strain curves: (I) R phase reorientation, (II) R phase transformation from parent phase, (III) elastic deformation of reoriented martensite accompanied by the plastic deformation of Nb-rich phase and lamellar NiTi-Nb eutectic, (IV) B19′ martensitic transformation and (V) plastic deformation of the specimen.
Vancomycin-sensitive bacteria trigger development of colitis-associated colon cancer by attracting neutrophils
Authors: Tanaka Yuriko , Ito Sachiko , Isobe Ken-ichi 
Published: April 2016

AbstractInflammatory bowel disease confers an increased risk of developing colitis-associated colon cancer (CAC). During the active colitis or developing tumor stage, commensal bacteria show dynamic translocation. However, whether alteration of the bacterial composition in the gut causes CAC is still unclear. To clarify the effect of commensal bacteria on CAC development, we employed an azoxymethane (AOM) and dextran sodium sulfate (DSS)-induced murine CAC model treated with or without antibiotics. In addition, we analyzed the effects of antibiotics on infiltration of myeloid cells, colonic inflammatory responses and colorectal cancer formation. We found that vancomycin treatment dramatically suppressed tumor development. In addition, AOM/DSS treatment greatly induced the infiltration of Gr-1high/CD11bhigh neutrophils to the colon, which led to the production of tumor necrosis factor α and inducible nitric oxide synthase. Vancomycin treatment suppressed the infiltration of neutrophils induced by AOM/DSS. Moreover, vancomycin treatment greatly reduced the colon injury and DNA damage caused by AOM/DSS-induced NO radicals. Our results indicate that vancomycin-sensitive bacteria induced colon inflammation and DNA damage by attracting neutrophils into damaged colon tissue, thus promoting tumor formation.
Targeted mutagenesis in chicken using CRISPR/Cas9 system
Authors: Oishi Isao , Yoshii Kyoko , Miyahara Daichi , Kagami Hiroshi , Tagami Takahiro 
Published: April 2016

AbstractThe CRISPR/Cas9 system is a simple and powerful tool for genome editing in various organisms including livestock animals. However, the system has not been applied to poultry because of the difficulty in accessing their zygotes. Here we report the implementation of CRISPR/Cas9-mediated gene targeting in chickens. Two egg white genes, ovalbumin and ovomucoid, were efficiently (>90%) mutagenized in cultured chicken primordial germ cells (PGCs) by transfection of circular plasmids encoding Cas9, a single guide RNA and a gene encoding drug resistance, followed by transient antibiotic selection. We transplanted CRISPR-induced mutant-ovomucoid PGCs into recipient chicken embryos and established three germline chimeric roosters (G0). All of the roosters had donor-derived mutant-ovomucoid spermatozoa and the two with a high transmission rate of donor-derived gametes produced heterozygous mutant ovomucoid chickens as about half of their donor-derived offspring in the next generation (G1). Furthermore, we generated ovomucoid homozygous mutant offspring (G2) by crossing the G1 mutant chickens. Taken together, these results demonstrate that the CRISPR/Cas9 system is a simple and effective gene-targeting method in chickens.
Ndfip2 is a potential regulator of the iron transporter DMT1 in the liver
Authors: Foot Natalie J. , Gembus Kelly M. , Mackenzie Kimberly , Kumar Sharad 
Published: April 2016

AbstractThe regulation of divalent metal ion transporter DMT1, the primary non-heme iron importer in mammals, is critical for maintaining iron homeostasis. Previously we identified ubiquitin-dependent regulation of DMT1 involving the Nedd4 family of ubiquitin ligases and the Ndfip1 and Ndfip2 adaptors. We also established the in vivo function of Ndfip1 in the regulation of DMT1 in the duodenum of mice. Here we have studied the function of Ndfip2 using Ndfip2-deficient mice. The DMT1 protein levels in the duodenum were comparable in wild type and Ndfip2−/− mice, as was the transport activity of isolated enterocytes. A complete blood examination showed no significant differences between wild type and Ndfip2−/− mice in any of the hematological parameters measured. However, when fed a low iron diet, female Ndfip2−/− mice showed a decrease in liver iron content, although they maintained normal serum iron levels and transferrin saturation, compared to wild type female mice that showed a reduction in serum iron and transferrin saturation. Ndfip2−/− female mice also showed an increase in DMT1 expression in the liver, with no change in male mice. We suggest that Ndfip2 controls DMT1 in the liver with female mice showing a greater response to altered dietary iron than the male mice.
SHEsisPlus, a toolset for genetic studies on polyploid species
Authors: Shen Jiawei , Li Zhiqiang , Chen Jianhua , Song Zhijian , Zhou Zhaowei , Shi Yongyong 
Published: April 2016

AbstractCurrently, algorithms and softwares for genetic analysis of diploid organisms with bi-allelic markers are well-established, while those for polyploids are limited. Here, we present SHEsisPlus, the online algorithm toolset for both dichotomous and quantitative trait genetic analysis on polyploid species (compatible with haploids and diploids, too). SHEsisPlus is also optimized for handling multiple-allele datasets. It’s free, open source and also designed to perform a range of analyses, including haplotype inference, linkage disequilibrium analysis, epistasis detection, Hardy-Weinberg equilibrium and single locus association tests. Meanwhile, we developed an accurate and efficient haplotype inference algorithm for polyploids and proposed an entropy-based algorithm to detect epistasis in the context of quantitative traits. A study of both simulated and real datasets showed that our haplotype inference algorithm was much faster and more accurate than existing ones. Our epistasis detection algorithm was the first try to apply information theory to characterizing the gene interactions in quantitative trait datasets. Results showed that its statistical power was significantly higher than conventional approaches. SHEsisPlus is freely available on the web at http://shesisplus.bio-x.cn/. Source code is freely available for download at https://github.com/celaoforever/SHEsisPlus.
Spinal cord lesions shrink peripersonal space around the feet, passive mobilization of paraplegic limbs restores it
Authors: Scandola Michele , Aglioti Salvatore Maria , Bonente Claudio , Avesani Renato , Moro Valentina 
Published: April 2016

AbstractPeripersonal space (PPS) is the space surrounding us within which we interact with objects. PPS may be modulated by actions (e.g. when using tools) or sense of ownership (e.g. over a rubber hand). Indeed, intense and/or prolonged use of a tool may induce a sense of ownership over it. Conversely, inducing ownership over a rubber hand may activate brain regions involved in motor control. However, the extent to which PPS is modulated by action-dependent or ownership-dependent mechanisms remains unclear. Here, we explored the PPS around the feet and the sense of ownership over lower limbs in people with Paraplegia following Complete spinal cord Lesions (PCL) and in healthy subjects. PCL people can move their upper body but have lost all sensory-motor functions in their lower body (e.g. lower limbs). We tested whether PPS alterations reflect the topographical representations of various body parts. We found that the PPS around the feet was impaired in PCL who however had a normal representation of the PPS around the hands. Significantly, passive mobilization of paraplegic limbs restored the PPS around the feet suggesting that activating action representations in PCL brings about short-term changes of PPS that may thus be more plastic than previously believed.
Deletion of BMP receptor type IB decreased bone mass in association with compromised osteoblastic differentiation of bone marrow mesenchymal progenitors
Authors: Shi Ce , Iura Ayaka , Terajima Masahiko , Liu Fei , Lyons Karen , Pan Haichun , Zhang Honghao , Yamauchi Mitsuo , Mishina Yuji , Sun Hongchen 
Published: April 2016

AbstractWe previously found that disruption of two type I BMP receptors, Bmpr1a and Acvr1, respectively, in an osteoblast-specific manner, increased bone mass in mice. BMPR1B, another BMP type I receptor, is also capable of binding to BMP ligands and transduce BMP signaling. However, little is known about the function of BMPR1B in bone. In this study, we investigated the bone phenotype in Bmpr1b null mice and the impacts of loss of Bmpr1b on osteoblasts and osteoclasts. We found that deletion of Bmpr1b resulted in osteopenia in 8-week-old male mice and the phenotype was transient and gender specific. The decreased bone mass was neither due to the changes in osteoblastic bone formation activity nor osteoclastic bone resorption activity in vivo. In vitro differentiation of Bmpr1b null osteoclasts was increased but resorption activity was decreased. Calvarial pre-osteoblasts from Bmpr1b mutant showed comparable differentiation capability in vitro, while they showed increased BMP-SMAD signaling in culture. Different from calvarial pre-osteoblasts, Bmpr1b mutant bone marrow mesenchymal progenitors showed compromised differentiation in vitro, which may be a reason for the osteopenic phenotype in the mutant mice. In conclusion, our results suggested that BMPR1B plays distinct roles from BMPR1A and ACVR1 in maintaining bone mass and transducing BMP signaling.
Mindestmengen und Krankenhaussterblichkeit – Beobachtungsstudie mit deutschlandweiten Krankenhausabrechnungsdaten von 2006 bis 2013
Authors: Nimptsch U. , Peschke D. , Mansky T. 
Published: April 2016

Zusammenfassung
Hintergrund: Mit dem Ziel der Verbesserung der Versorgung wurden für die Durchführung planbarer Eingriffe und Behandlungen in deutschen Krankenhäusern Mindestmengen festgelegt. Diese Arbeit untersucht retrospektiv ob die Einhaltung der Mindestmengenvorgabe mit den Behandlungsergebnissen in Zusammenhang steht. Analysiert wurden Unterschiede in der Krankenhaussterblichkeit für komplexe Ösophagus- und Pankreaseingriffe, Leber- und Nierentransplantationen, Stammzellentransplantationen sowie Knie-Totalendoprothesen.
Methode: In den Mikrodaten der deutschlandweiten Fallpauschalenbezogenen Krankenhausstatistik (DRG-Statistik) wurden alle Behandlungsfälle identifiziert, die der Mindestmengenregelung unterliegen und die jährliche Fallzahl des jeweiligen Leistungsbereiches pro Krankenhaus berechnet. Jahresweise wurde bestimmt, ob die Mindestmengenvorgabe erreicht wurde. Auf dieser Grundlage wurden die Behandlungsfälle 2 Untersuchungsgruppen zugeordnet: Fälle in Krankenhäusern mit Fallzahl gleich oder größer der Mindestmenge (≥ MM) und Fälle in Krankenhäusern mit Fallzahl unter der Mindestmenge (< MM). Anhand logistischer Regressionsverfahren wurden adjustierte Sterblichkeiten berechnet.
Ergebnisse: Insgesamt wurden 28 931 Eingriffe am Ösophagus, 78 879 Eingriffe am Pankreas, 7 984 Lebertransplantationen, 21 773 Nierentransplantationen, 51 064 Stammzellentransplantationen und 1 093 296 Knie-Totalendprothesenimplantationen untersucht. Die adjustierte Sterblichkeit in Krankenhäusern mit Fallzahl≥MM war signifikant geringer als in Krankenhäusern mit Fallzahl<MM bei Eingriffen am Ösophagus (9,2% [95% KI 8,8–9,6] vs. 12,1% [11,4–12,9]), Eingriffen am Pankreas (8,6% [8,3–8,8] vs. 11,8% [11,2–12,5]), Nierentransplantationen (1,7% [1,4–1,8] vs. 3,3% [2,1–5,0]) und Knie-Totalendoprothesen (0,13% [0,12–0,14] vs. 0,18% [0,14–0,23]). Bei Lebertransplantationen zeigte die adjustierte Sterblichkeit keinen signifikanten Unterschied (15,5% [14,7–16,5] vs. 15,9% [12,9–19,3]). Bei Stammzellentransplantationen war die Sterblichkeit in Krankenhäusern mit Fallzahl≥MM signifikant höher als in Krankenhäusern mit Fallzahl<MM (6,0% [5,7–6,2] vs. 4,0% [3,2–4,9]).
Schlussfolgerung: Die Ergebnisse zeigen für 4 der 6 untersuchten Leistungsbereiche ein signifikant geringeres Sterberisiko bei Behandlung in einem Krankenhaus, das die Mindestmengenvorgabe erreicht. Daraus lässt sich schließen, dass eine stringente Umsetzung der Mindestmengenregelung die Versorgungsqualität bei diesen Eingriffen verbessern könnte.
Asymmetric arginine dimethylation of RelA provides a repressive mark to modulate TNFα/NF-κB response
Authors: Reintjes Anja , Fuchs Julian E. , Kremser Leopold , Lindner Herbert H. , Liedl Klaus R. , Huber Lukas A. , Valovka Taras 
Published: April 2016

Significance
The transcription factor nuclear factor kappa B (NF-κB) plays a vital role in cellular immune, stress, and proliferative responses by regulating genes. To maintain correct execution of the genetic program and to prevent pathologies (e.g., chronic inflammation), the activation of NF-κB has to be transient and precisely controlled. We describe a unique inhibitory mechanism that mediates NF-κB–dependent regulation of inflammation-associated genes and uses arginine methylation of the RelA subunit of NF-κB by protein arginine methyltransferase 1. This modification reduces the DNA-binding affinity of RelA, altering the recruitment to gene promoters and the transcriptional potency of NF-κB. This may be developed into an approach to inhibit the pathological functions of NF-κB.
Perceptual learning modifies the functional specializations of visual cortical areas
Authors: Chen Nihong , Cai Peng , Zhou Tiangang , Thompson Benjamin , Fang Fang 
Published: April 2016

Significance
Using transcranial magnetic stimulation and functional magnetic resonance imaging techniques, we demonstrate here that the transfer of perceptual learning from a task involving coherent motion to a task involving noisy motion can induce a functional substitution of V3A (one of the visual areas in the extrastriate visual cortex) for MT+ (middle temporal/medial superior temporal cortex) to process noisy motion. This finding suggests that perceptual learning in visually normal adults shapes the functional architecture of the brain in a much more pronounced way than previously believed. The effects of perceptual learning extend far beyond the retuning of specific neural populations that mediate performance of the trained task. Learning could dramatically modify the inherent functional specializations of visual cortical areas and dynamically reweight their contributions to perceptual decisions based on their representational qualities.
Direct imaging of magnetic field-driven transitions of skyrmion cluster states in FeGe nanodisks
Authors: Zhao Xuebing , Jin Chiming , Wang Chao , Du Haifeng , Zang Jiadong , Tian Mingliang , Che Renchao , Zhang Yuheng 
Published: April 2016

Significance
The rapid growth of data volume demands faster and denser storage devices. The noncoplanar swirling spin texture, known as magnetic skyrmion, has potential application in future memory devices. To realize such applications, it is essential to understand the properties of individual skyrmion in patterned nanoelements. While quite a number of theoretical efforts have been made in this field, direct experimental demonstration in such a real modeling system is a challenge. Here, we report the direct visualization of skyrmion cluster states in FeGe nanodisks. We determine the common relationship among the temperature, magnetic field, and disk size. These results have an immediate implication for designing future skyrmion-based devices.
Comparison of syncytiotrophoblast generated from human embryonic stem cells and from term placentas
Authors: Yabe Shinichiro , Alexenko Andrei P. , Amita Mitsuyoshi , Yang Ying , Schust Danny J. , Sadovsky Yoel , Ezashi Toshihiko , Roberts R. Michael 
Published: April 2016

Significance
Syncytiotrophoblast (STB) is responsible for nutrient and gas exchange in the human placenta. STB also forms when human embryonic stem cells (ESCs) differentiate to trophoblast. Here we compare ESC-derived STB with cytotrophoblasts isolated from term placentas before and after such cells had fused to form STB. Although both types of STB expressed all common trophoblast marker genes, there were dissimilarities indicative of altered function and ontology. We propose that STB derived from ESCs represents syncytial tissue encountered at the initiation of placental development. These cells may provide the first in vitro model for studying origins of diseases of placentation ranging from implantation failure and early pregnancy loss to intrauterine growth retardation and preeclampsia.
Analysis of fast-ion Dα data from the National Spherical Torus Experiment
Authors: Heidbrink W.W. , Ruskov E. , Liu D. , Stagner L. , Fredrickson E.D. , Podestà M. , Bortolon A. 
Published: April 2016

Abstract
Measured fast-ion

D

α

(FIDA) data from an extensive NSTX database are compared to ‘classical’ predictions that neglect transport by instabilities. Even in the absence of appreciable MHD, in many cases, the profile peaks at smaller major radius and the profile is broader than the predictions. Abrupt large-amplitude MHD events flatten the FIDA profile, as do most toroidal Alfvén eigenmode (TAE) avalanche events. Generally, the onset of a long-lived mode also flattens the FIDA profile.
Unconventional Gas and Oil Development in the United States: Economic Experience and Policy Issues
Authors: Kelsey Timothy W. , Partridge Mark D. , White Nancy E. 
Published: April 2016

AbstractThis paper examines the economic experience of past energy booms and that of current unconventional shale gas and oil development. We focus on key economic characteristics of gas and oil production such as its employment potential, its geography, and its boom‐bust nature. This background is used to discuss important economic policy issues arising with unconventional oil and gas development such as taxation, governmental use of those revenues, preemption, and equity in the distribution of costs and benefits. The paper concludes with economic policy recommendations for states and communities affected by such development including not viewing oil and gas development as an effective long‐run economic development strategy, leveraging short‐run financial gains from the development into permanent advantages, and strengthening the capacity for local governments to understand and manage this activity.
SATORI: A System for Ontology-Guided Visual Exploration of Biomedical Data Repositories
Authors: Lekschas Fritz , Gehlenborg Nils 
Published: April 2016

AbstractThe ever-increasing number of biomedical data sets provides tremendous opportunities for re-use but current data repositories provide limited means of exploration apart from text-based search. Ontological metadata annotations provide context by semantically relating data sets. Visualizing this rich network of relationships can improve the explorability of large data repositories and help researchers find data sets of interest. We developed SATORI—an integrative search and visual exploration interface for the exploration of biomedical data repositories. The design is informed by a requirements analysis through a series of semi-structured interviews. We evaluated the implementation of SATORI in a field study on a real-world data collection.SATORI enables researchers to seamlessly search, browse, and semantically query data repositories via two visualizations that are highly interconnected with a powerful search interface. SATORI is an open-source web application,which is freely available athttp://satori.refinery-platform.organd integrated into the Refinery Platform.