bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short term ex vivo storage of kidneys cause progressive nuclear ploidy changes of renal tubular epitheliocytes
Authors: Sun Huaibin , Tian Jun , Xian Wanhua , Xie Tingting , Yang Xiangdong 
Published: June 2015

AbstractIn renal transplantation, there has been considerable success, mainly in term of post-transplant graft function. However, upon closer scrutiny, it is known that severe dysfunction, including persistence of renal failure is seen after transplantation. The major condition that potentially cause significant lesion may be hypothesized to be related to the hypothermic approach to storage. To systematically examine these issues, we stored mammalian (sheep) kidneys in UWS at 4 °C for four different time points (0, 1, 3 and 6 hours). We obtained renal histological sections and examined tubular architecture as well as nuclear characteristics of tubular epitheliocytes. The results of our preliminary investigations suggest that there are temporal changes of tubular epitheliocytes, as well as genomic changes. These changes were also seen in tissues stored at room temperature. Our observations suggest the need for additional studies for redesigning of improvised storage solutions. Pilot studies using Celsior also revelaed similar kind of nuclear changes, suggesting that storage conditons are contributory, including perfusion versus static conditions. The results may explain persistence of tubular injury several days after orthotopic transplantation and may potentially be contributory to delayed graft function (DGF).
Residual force depression in single sarcomeres is abolished by MgADP-induced activation
Authors: Trecarten Neal , Minozzo Fabio C. , Leite Felipe S. , Rassier Dilson E. 
Published: June 2015

AbstractThe mechanisms behind the shortening-induced force depression commonly observed in skeletal muscles remain unclear, but have been associated with sarcomere length non-uniformity and/or crossbridge inhibition. The purpose of this study was twofold: (i) to evaluate if force depression is present in isolated single sarcomeres, a preparation that eliminates sarcomere length non-uniformities and (ii) to evaluate if force depression is inhibited when single sarcomeres are activated with MgADP, which biases crossbridges into a strongly-bound state. Single sarcomeres (n = 16) were isolated from rabbit psoas myofibrils using two micro-needles (one compliant, one rigid), piercing the sarcomere externally adjacent to the Z-lines. The sarcomeres were contracted isometrically and subsequently shortened, in both Ca2+- and MgADP-activating solutions. Shortening in Ca2+-activated samples resulted in a 27.44 ± 9.04% force depression when compared to isometric contractions produced at similar final sarcomere lengths (P < 0.001). There was no force depression in MgADP-activated sarcomeres (force depression = −1.79 ± 9.69%, P =  0.435). These results suggest that force depression is a sarcomeric property and that is associated with an inhibition of myosin-actin interactions.
CRISPR/Cas9-mediated reporter knock-in in mouse haploid embryonic stem cells
Authors: Kimura Yasuyoshi , Oda Masaaki , Nakatani Tsunetoshi , Sekita Yoichi , Monfort Asun , Wutz Anton , Mochizuki Hideki , Nakano Toru 
Published: June 2015

AbstractMouse parthenogenetic haploid embryonic stem cells (ESCs) are pluripotent cells generated from chemically activated oocytes. Haploid ESCs provide an opportunity to study the effect of genetic alterations because of their hemizygotic characteristics. However, their further application for the selection of unique phenotypes remains limited since ideal reporters to monitor biological processes such as cell differentiation are missing. Here, we report the application of CRISPR/Cas9-mediated knock-in of a reporter cassette, which does not disrupt endogenous target genes in mouse haploid ESCs. We first validated the system by inserting the P2A-Venus reporter cassette into the housekeeping gene locus. In addition to the conventional strategy using the Cas9 nuclease, we employed the Cas9 nickase and truncated sgRNAs to reduce off-target mutagenesis. These strategies induce targeted insertions with an efficiency that correlated with sgRNA guiding activity. We also engineered the neural marker gene Sox1 locus and verified the precise insertion of the P2A-Venus reporter cassette and its functionality by monitoring neural differentiation. Our data demonstrate the successful application of the CRISPR/Cas9-mediated knock-in system for establishing haploid knock-in ESC lines carrying gene specific reporters. Genetically modified haploid ESCs have potential for applications in forward genetic screening of developmental pathways.
Novel Handheld Magnetometer Probe Based on Magnetic Tunnelling Junction Sensors for Intraoperative Sentinel Lymph Node Identification
Authors: Cousins A. , Balalis G. L. , Thompson S. K. , Forero Morales D. , Mohtar A. , Wedding A. B. , Thierry B. 
Published: June 2015

AbstractUsing magnetic tunnelling junction sensors, a novel magnetometer probe for the identification of the sentinel lymph node using magnetic tracers was developed. Probe performance was characterised in vitro and validated in a preclinical swine model. Compared to conventional gamma probes, the magnetometer probe showed excellent spatial resolution of 4.0 mm and the potential to detect as few as 5 μg of magnetic tracer. Due to the high sensitivity of the magnetometer, all first-tier nodes were identified in the preclinical experiments and there were no instances of false positive or false negative detection. Furthermore, these preliminary data encourage the application of the magnetometer probe for use in more complex lymphatic environments, such as in gastrointestinal cancers, where the sentinel node is often in close proximity to other non-sentinel nodes and high spatial resolution detection is required.
Trans-generational responses to low pH depend on parental gender in a calcifying tubeworm
Authors: Lane Ackley , Campanati Camilla , Dupont Sam , Thiyagarajan Vengatesen 
Published: June 2015

AbstractThe uptake of anthropogenic CO2 emissions by oceans has started decreasing pH and carbonate ion concentrations of seawater, a process called ocean acidification (OA). Occurring over centuries and many generations, evolutionary adaptation and epigenetic transfer will change species responses to OA over time. Trans-generational responses, via genetic selection or trans-generational phenotypic plasticity, differ depending on species and exposure time as well as differences between individuals such as gender. Males and females differ in reproductive investment and egg producing females may have less energy available for OA stress responses. By crossing eggs and sperm from the calcareous tubeworm Hydroides elegans (Haswell, 1883) raised in ambient (8.1) and low (7.8) pH environments, we observed that paternal and maternal low pH experience had opposite and additive effects on offspring. For example, when compared to offspring with both parents from ambient pH, growth rates of offspring of fathers or mothers raised in low pH were higher or lower respectively, but there was no difference when both parents were from low pH. Gender differences may result in different selection pressures for each gender. This may result in overestimates of species tolerance and missed opportunities of potentially insightful comparisons between individuals of the same species.
Genome-Wide Association Studies of HIV-1 Host Control in Ethnically Diverse Chinese Populations
Authors: Wei Zejun , Liu Yang , Xu Heng , Tang Kun , Wu Hao , Lu Lin , Wang Zhe , Chen Zhengjie , Xu Junjie , Zhu Yufei , Hu Landian , Shang Hong , Zhao Guoping , Kong Xiangyin 
Published: June 2015

AbstractGenome-wide association studies (GWASs) have revealed several genetic loci associated with HIV-1 outcome following infection (e.g., HLA-C at 6p21.33) in multi-ethnic populations with genetic heterogeneity and racial/ethnic differences among Caucasians, African-Americans and Hispanics. To systematically investigate the inherited predisposition to modulate HIV-1 infection in Chinese populations, we performed GWASs in three ethnically diverse HIV-infected patients groups (i.e., HAN, YUN and XIN, N = 538). The reported loci at 6p21.33 was validated in HAN (e.g., rs9264942, P = 0.0018). An independent association signal (rs2442719, P = 7.85 × 10−7, HAN group) in the same region was observed. Imputation results suggest that haplotype HLA-B*13:02/C*06:02, which can partially account for the GWAS signal, is associated with lower viral load in Han Chinese. Moreover, several novel loci were identified using GWAS approach including the top association signals at 6q13 (KCNQ5, rs947612, P = 2.15 × 10−6), 6p24.1 (PHACTR1, rs202072, P = 3.8 × 10−6) and 11q12.3 (SCGB1D4, rs11231017, P = 7.39 × 10−7) in HAN, YUN and XIN groups, respectively. Our findings imply shared or specific mechanisms for host control of HIV-1 in ethnically diverse Chinese populations, which may shed new light on individualized HIV/AIDS therapy in China.
Robustness of plasmon phased array nanoantennas to disorder
Authors: Arango Felipe Bernal , Thijssen Rutger , Brenny Benjamin , Coenen Toon , Koenderink A. Femius 
Published: June 2015

AbstractWe present cathodoluminescence experiments that quantify the response of plasmonic Yagi-Uda antennas fabricated on one-dimensional silicon nitride waveguides as function of electron beam excitation position and emission wavelength. At the near-infrared antenna design wavelength cathodoluminescence signal robustly is strongest when exciting the antenna at the reflector element. Yet at just slightly shorter wavelengths the signal is highly variable from antenna to antenna and wavelength to wavelength. Hypothesizing that fabrication randomness is at play, we analyze the resilience of plasmon Yagi-Uda antennas to varations in element size of just 5 nm. While in our calculations the appearance of directivity is robust, both the obtained highest directivity and the wavelength at which it occurs vary markedly between realizations. The calculated local density of states is invariably high at the reflector for the design wavelength, but varies dramatically in spatial distribution for shorter wavelengths, consistent with the cathodoluminescence experiments.
Compact planar UWB MIMO antenna with on‐demand WLAN rejection
Authors: Khan M.S. , Capobianco A.D. , Naqvi A. , Shafique M.F. , Ijaz B. , Braaten B.D. 
Published: June 2015

Presented are two different frequency reconfigurable ultra‐wideband multiple‐input multiple‐output (MIMO) antenna array designs capable of rejecting on‐demand all WLAN communications in the 4.8 to 6.2 GHz range. Both arrays consist of two monopole UWB radiators placed orthogonally with respect to each other to introduce polarisation diversity and a quarter‐wave stub connected to the ground plane via pin diodes is used to introduce the on‐demand band rejection feature. One array design has separate ground planes and the other has two ground planes connected with a printed conductor (i.e. shared). For both cases, an isolation better than 20 dB between the elements is achieved in the 2 to 12 GHz frequency range with simulations and a manufactured prototype.
Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy
Authors: Micsonai András , Wien Frank , Kernya Linda , Lee Young-Ho , Goto Yuji , Réfrégiers Matthieu , Kardos József 
Published: June 2015

Significance
Circular dichroism (CD) spectroscopy is widely used for protein secondary structure analysis. However, quantitative estimation for β-sheet–containing proteins is problematic due to the huge morphological and spectral diversity of β-structures. We show that parallel/antiparallel orientation and twisting of β-sheets account for the observed spectral diversity. Taking into account the twist of β-structures, our method accurately estimates the secondary structure for a broad range of protein folds, particularly for β-sheet–rich proteins and amyloid fibrils. Moreover, the method can predict the protein fold down to the topology level following the CATH classification. We provide a general tool for a quick and reliable structure analysis using conventional or synchrotron radiation CD spectroscopy, which is especially useful when X-ray or NMR techniques fail.
HIF-1α-induced microRNA-210 reduces hypoxia-induced osteoblast MG-63 cell apoptosis
Authors: Sun Guanwen , Peng Hao 
Published: June 2015

AbstractTo better understand the ischemic-hypoxia-induced fracture healing impairment, we determined in this study the microRNA-210 expression in broken bone specimens and in osteoblasts under hypoxia and then determined the influence of microRNA-210 overexpression on the osteoblast cell proliferation and apoptosis. Results demonstrated that microRNA-210 expression was upregulated with an association with HIF-1α overexpression in clinical human catagmatic tissues and was upregulated HIF-1α-dependently in response to hypoxia in osteoblast MG-63 cells. CCK-8 assay indicated that microRNA-210 upregulation by microRNA-210 mimics reduced the chemotherapeutic 5-FU-induced osteoblast cell death, and colony formation assay demonstrated that microRNA-210 mimics promoted osteoblast cells growth. Moreover, the microRNA-210 mimics transfection inhibited the hypoxia-induced MG-63 cell apoptosis via inhibiting the activation of caspase 3 and caspase 9. Therefore, our research indicated a protective role of microRNA-210 in response to hypoxia. And microRNA-210 might serve as a protective role in bone fracture healing.
lpNet: a linear programming approach to reconstruct signal transduction networks
Authors: Matos Marta R. A. , Knapp Bettina , Kaderali Lars 
Published: May 2015

Abstract
Summary: With the widespread availability of high-throughput experimental technologies it has become possible to study hundreds to thousands of cellular factors simultaneously, such as coding- or non-coding mRNA or protein concentrations. Still, extracting information about the underlying regulatory or signaling interactions from these data remains a difficult challenge. We present a flexible approach towards network inference based on linear programming. Our method reconstructs the interactions of factors from a combination of perturbation/non-perturbation and steady-state/time-series data. We show both on simulated and real data that our methods are able to reconstruct the underlying networks fast and efficiently, thus shedding new light on biological processes and, in particular, into disease’s mechanisms of action. We have implemented the approach as an R package available through bioconductor.
Availability and implementation: This R package is freely available under the Gnu Public License (GPL-3) from bioconductor.org (http://bioconductor.org/packages/release/bioc/html/lpNet.html) and is compatible with most operating systems (Windows, Linux, Mac OS) and hardware architectures.
Contact: bettina.knapp@helmholtz-muenchen.de
Supplementary information: Supplementary data are available at Bioinformatics online.
RPdb: a database of experimentally verified cellular reprogramming records
Authors: Shen Yi , Gao Fan , Wang Minghui , Li Ao 
Published: May 2015

Abstract
Summary: Many cell lines can be reprogrammed to other cell lines by forced expression of a few transcription factors or by specifically designed culture methods, which have attracted a great interest in the field of regenerative medicine and stem cell research. Plenty of cell lines have been used to generate induced pluripotent stem cells (IPSCs) by expressing a group of genes and microRNAs. These IPSCs can differentiate into somatic cells to promote tissue regeneration. Similarly, many somatic cells can be directly reprogrammed to other cells without a stem cell state. All these findings are helpful in searching for new reprogramming methods and understanding the biological mechanism inside. However, to the best of our knowledge, there is still no database dedicated to integrating the reprogramming records. We built RPdb (cellular reprogramming database) to collect cellular reprogramming information and make it easy to access. All entries in RPdb are manually extracted from more than 2000 published articles, which is helpful for researchers in regenerative medicine and cell biology.
Availability and Implementation: RPdb is freely available on the web at http://bioinformatics.ustc.edu.cn/rpdb with all major browsers supported.
Contact: aoli@ustc.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes
Authors: van Zundert G.C.P. , Bonvin A.M.J.J. 
Published: May 2015

Abstract
Summary: We present DisVis, a Python package and command line tool to calculate the reduced accessible interaction space of distance-restrained binary protein complexes, allowing for direct visualization and quantification of the information content of the distance restraints. The approach is general and can also be used as a knowledge-based distance energy term in FFT-based docking directly during the sampling stage.
Availability and implementation: The source code with documentation is freely available from https://github.com/haddocking/disvis.
Contact: a.m.j.j.bonvin@uu.nl
Supplementary information: Supplementary data are available at Bioinformatics online.
Smartphone-based diagnostic for preeclampsia: an mHealth solution for administering the Congo Red Dot (CRD) test in settings with limited resources
Authors: Jonas Stephan Michael , Deserno Thomas Martin , Buhimschi Catalin Sorin , Makin Jennifer , Choma Michael Andrew , Buhimschi Irina Alexandra 
Published: May 2015

Abstract
Objective Morbidity and mortality due to preeclampsia in settings with limited resources often results from delayed diagnosis. The Congo Red Dot (CRD) test, a simple modality to assess the presence of misfolded proteins in urine, shows promise as a diagnostic and prognostic tool for preeclampsia. We propose an innovative mobile health (mHealth) solution that enables the quantification of the CRD test as a batch laboratory test, with minimal cost and equipment.
Methods A smartphone application that guides the user through seven easy steps, and that can be used successfully by non-specialized personnel, was developed. After image acquisition, a robust analysis runs on a smartphone, quantifying the CRD test response without the need for an internet connection or additional hardware. In the first stage, the basic image processing algorithms and supporting test standardizations were developed using urine samples from 218 patients. In the second stage, the standardized procedure was evaluated on 328 urine specimens from 273 women. In the third stage, the application was tested for robustness using four different operators and 94 altered samples.
Results In the first stage, the image processing chain was set up with high correlation to manual analysis (z-test P &lt; 0.001). In the second stage, a high agreement between manual and automated processing was calculated (Lin’s concordance coefficient ρ c = 0.968). In the last stage, sources of error were identified and remedies were developed accordingly. Altered samples resulted in an acceptable concordance with the manual gold-standard (Lin’s ρc = 0.914).
Conclusion Combining smartphone-based image analysis with molecular-specific disease features represents a cost-effective application of mHealth that has the potential to fill gaps in access to health care solutions that are critical to reducing adverse events in resource-poor settings.
Voice
Authors: Grover-Friedlander Michal 
Published: June 2015

AbstractOpera’s aesthetic foundation is to be sought in the singing voice that is unique and unlike any other. In the writings of Cavell and Abbate, for instance, we find discussions of the voice’s mode of signification and its ways of constructing meaning. Distinctions have been drawn between “realistic” and “operatic” singing, between “singing” and “speaking,” between “voice” and “body,” as well as between phenomenological and psychoanalytical approaches to the voice of opera. The idea of opera that endows voices with unique powers can be traced back to the myth of Orpheus. That myth articulates the phenomenon of the voice as hovering between worlds, as having the power to overturn death. The voice of opera is thereby specifically theorized with respect to the death and the afterlife of the voice. Two case studies are discussed in these terms: Puccini’s Gianni Schicchi and Hindemith’s Hin und Zurück.
Acting
Authors: Williams Simon 
Published: June 2015

AbstractActing and singing have often been considered incompatible activities, but most successful operatic performances depend in part on successful acting. Acting in opera is, however, different from acting in spoken drama. Realistic characterization is often difficult to achieve when acting with music, and often the formal gestures of a more rhetorical representation are more appropriate. A more vivid style of acting was initiated with the bel cantoopera early in the nineteenth century, and later verismoopera required acting that brought out the unconscious motivation of characters. Wagner, Stanislavski, and Felsenstein all developed a style of acting that reflected the psychology of the character and encouraged ensemble. Modern operatic performance incorporates a variety of styles, but a combination of realism and minimalism may be most effective on stage. Callas’s performance in Act 2 of Toscaand Nicholas Lehnhoff’s production of Parsifalare analyzed.
The Orchestra
Authors: Di Profio Alessandro 
Published: June 2015

AbstractThis chapter shows how variable the makeup of the opera orchestra has been throughout the history of opera from the seventeenth century to the present day. This variability cannot be explained only by historical evolution. Rather, the changes in the constitution of the orchestra were influenced by geography (local traditions), repertoire, performance space, and organology. The transmission of works, the movement of conductors from one country to another, and the increasing complexity of instrumental language in opera contributed to the standardization of the orchestra that was achieved only after World War II on a model established in the 1870s. Recent interest in historically informed performance tends to put forward old peculiarities that had been erased with time. Four main cases are discussed: (1) the orchestra at the time of Monteverdi and the heritage of the Renaissance, (2) the Paris Opéra and the French tradition, (3) La Scala and the reforms encouraged by Verdi, and (4) Wagner and the search for an ideal orchestra.
Costumes
Authors: Isaac Veronica 
Published: June 2015

AbstractThis chapter discusses the role of costume in opera. It is intended as an initial introduction to the topic and as such not only outlines key examples of existing scholarship, but also endeavors to illustrate the scope that exists for further research into this area of opera history. The 1881 production of Patienceby W. S. Gilbert and Arthur Sullivan is employed as a case study through which to demonstrate potential modes of analysis, to explore the connections between contemporary fashions and stage costume, and to illustrate the crucial role these garments play in communicating meaning.
Patronage
Authors: De Lucca Valeria 
Published: June 2015

AbstractThe history of opera, one of the most expensive of the performing arts to produce, is inextricably intertwined with the history of its patrons, who not only sustained it financially, but also shaped its form and content in profound and persistent ways. By looking at two case studies from early modern Italy—one from the Medici court of Florence and one from the Venetian commercial theaters—this chapter discusses the double nature of patronage: (1) a process through which composers, poets, and performers helped patrons build a public image that would reflect their social and political agenda; and (2) a form of managerial and financial contribution to the production of opera in the context of public theaters.