bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detailed Experimental Study of Ion Acceleration by Interaction of an Ultra-Short Intense Laser with an Underdense Plasma
Authors: Kahaly S. , Sylla F. , Lifschitz A. , Flacco A. , Veltcheva M. , Malka V. 
Published: August 2016

AbstractIon acceleration from intense (Iλ2 > 1018 Wcm−2 μm2) laser-plasma interaction is experimentally studied within a wide range of He gas densities. Focusing an ultrashort pulse (duration "Equation missing" ion plasma period) on a newly designed submillimetric gas jet system, enabled us to inhibit total evacuation of electrons from the central propagation channel reducing the radial ion acceleration associated with ponderomotive Coulomb explosion, a mechanism predominant in the long pulse scenario. New ion acceleration mechanism have been unveiled in this regime leading to non-Maxwellian quasi monoenergetic features in the ion energy spectra. The emitted nonthermal ion bunches show a new scaling of the ion peak energy with plasma density. The scaling identified in this new regime differs from previously reported studies.
Cell fusion as the formation mechanism of unreduced gametes in the gynogenetic diploid hybrid fish
Authors: Wang Jing , Liu Qingfeng , Luo Kaikun , Chen Xuan , Xiao Jun , Zhang Chun , Tao Min , Zhao Rurong , Liu Shaojun 
Published: August 2016

AbstractThe gynogenetic diploid hybrid clone line (GDH) derived from red crucian carp (♀ RCC) × common carp (♂ CC) possesses the unusual reproductive trait of producing unreduced diploid eggs. To identify the mechanism underlying this phenomenon, we examined the structure, in vivo developmental process and in vitro dynamic development of the GDH gonad. In summary, compared with RCC and CC, GDH showed certain special straits. First, a high frequency (84.7%) of germ cell fusion occurred in gonadal tissue culture in vitro as observed by time-lapse microscopy. Second, microstructural and ultrastructural observation showed numerous binucleated and multinucleated germ cells in the gonad, providing evidence of germ cell fusion in vivo. By contrast, in the diploid RCC and CC ovaries, neither cell fusion nor multinucleated cells were observed during the development of gonads. Third, the ovary of GDH remained at stage I for 10 months, whereas those of RCC and CC remained at that stage for 2 months, indicating that the GDH germ cells underwent abnormal development before meiosis. This report is the first to demonstrate that cell fusion facilitates the formation of unreduced gametes in vertebrates, which is a valuable finding for both evolutionary biology and reproductive biology.
CRISPR/Cas9 mediated genome editing in ES cells and its application for chimeric analysis in mice
Authors: Oji Asami , Noda Taichi , Fujihara Yoshitaka , Miyata Haruhiko , Kim Yeon Joo , Muto Masanaga , Nozawa Kaori , Matsumura Takafumi , Isotani Ayako , Ikawa Masahito 
Published: August 2016

AbstractTargeted gene disrupted mice can be efficiently generated by expressing a single guide RNA (sgRNA)/CAS9 complex in the zygote. However, the limited success of complicated genome editing, such as large deletions, point mutations, and knockins, remains to be improved. Further, the mosaicism in founder generations complicates the genotypic and phenotypic analyses in these animals. Here we show that large deletions with two sgRNAs as well as dsDNA-mediated point mutations are efficient in mouse embryonic stem cells (ESCs). The dsDNA-mediated gene knockins are also feasible in ESCs. Finally, we generated chimeric mice with biallelic mutant ESCs for a lethal gene, Dnajb13, and analyzed their phenotypes. Not only was the lethal phenotype of hydrocephalus suppressed, but we also found that Dnajb13 is required for sperm cilia formation. The combination of biallelic genome editing in ESCs and subsequent chimeric analysis provides a useful tool for rapid gene function analysis in the whole organism.
Vitality of Neural Networks under Reoccurring Catastrophic Failures
Authors: Sardi Shira , Goldental Amir , Amir Hamutal , Vardi Roni , Kanter Ido 
Published: August 2016

AbstractCatastrophic failures are complete and sudden collapses in the activity of large networks such as economics, electrical power grids and computer networks, which typically require a manual recovery process. Here we experimentally show that excitatory neural networks are governed by a non-Poissonian reoccurrence of catastrophic failures, where their repetition time follows a multimodal distribution characterized by a few tenths of a second and tens of seconds timescales. The mechanism underlying the termination and reappearance of network activity is quantitatively shown here to be associated with nodal time-dependent features, neuronal plasticity, where hyperactive nodes damage the response capability of their neighbors. It presents a complementary mechanism for the emergence of Poissonian catastrophic failures from damage conductivity. The effect that hyperactive nodes degenerate their neighbors represents a type of local competition which is a common feature in the dynamics of real-world complex networks, whereas their spontaneous recoveries represent a vitality which enhances reliable functionality.
New evidence for grain specific C4 photosynthesis in wheat
Authors: Rangan Parimalan , Furtado Agnelo , Henry Robert J 
Published: August 2016

AbstractThe C4 photosynthetic pathway evolved to allow efficient CO2 capture by plants where effective carbon supply may be limiting as in hot or dry environments, explaining the high growth rates of C4 plants such as maize. Important crops such as wheat and rice are C3 plants resulting in efforts to engineer them to use the C4 pathway. Here we show the presence of a C4 photosynthetic pathway in the developing wheat grain that is absent in the leaves. Genes specific for C4 photosynthesis were identified in the wheat genome and found to be preferentially expressed in the photosynthetic pericarp tissue (cross- and tube-cell layers) of the wheat caryopsis. The chloroplasts exhibit dimorphism that corresponds to chloroplasts of mesophyll- and bundle sheath-cells in leaves of classical C4 plants. Breeding to optimize the relative contributions of C3 and C4 photosynthesis may adapt wheat to climate change, contributing to wheat food security.
Serum pharmacodynamic biomarkers for chronic corticosteroid treatment of children
Authors: Hathout Yetrib , Conklin Laurie S. , Seol Haeri , Gordish-Dressman Heather , Brown Kristy J. , Morgenroth Lauren P. , Nagaraju Kanneboyina , Heier Christopher R. , Damsker Jesse M. , van den Anker John N. , Henricson Erik , Clemens Paula R. , Mah Jean K. , McDonald Craig , Hoffman Eric P. 
Published: August 2016

AbstractCorticosteroids are extensively used in pediatrics, yet the burden of side effects is significant. Availability of a simple, fast and reliable biochemical read out of steroidal drug pharmacodynamics could enable a rapid and objective assessment of safety and efficacy of corticosteroids and aid development of corticosteroid replacement drugs. To identify potential corticosteroid responsive biomarkers we performed proteome profiling of serum samples from DMD and IBD patients with and without corticosteroid treatment using SOMAscan aptamer panel testing 1,129 proteins in <0.1 cc of sera. Ten pro-inflammatory proteins were elevated in untreated patients and suppressed by corticosteroids (MMP12, IL22RA2, CCL22, IGFBP2, FCER2, LY9, ITGa1/b1, LTa1/b2, ANGPT2 and FGG). These are candidate biomarkers for anti-inflammatory efficacy of corticosteroids. Known safety concerns were validated, including elevated non-fasting insulin (insulin resistance) and elevated angiotensinogen (salt retention). These were extended by new candidates for metabolism disturbances (leptin, afamin), stunting of growth (growth hormone binding protein) and connective tissue remodeling (MMP3). Significant suppression of multiple adrenal steroid hormones was also seen in treated children (reductions of 17-hydroxyprogesterone, corticosterone, 11-deoxycortisol and testosterone). A panel of new pharmacodynamic biomarkers for corticosteroids in children was defined. Future studies will need to bridge specific biomarkers to mechanism of drug action and specific clinical outcomes.
Isozygous and selectable marker-free MSTN knockout cloned pigs generated by the combined use of CRISPR/Cas9 and Cre/LoxP
Authors: Bi Yanzhen , Hua Zaidong , Liu Ximei , Hua Wenjun , Ren Hongyan , Xiao Hongwei , Zhang Liping , Li Li , Wang Zhirui , Laible Götz , Wang Yan , Dong Faming , Zheng Xinmin 
Published: August 2016

AbstractPredictable, clean genetic modification (GM) in livestock is important for reliable phenotyping and biosafety. Here we reported the generation of isozygous, functional myostatin (MSTN) knockout cloned pigs free of selectable marker gene (SMG) by CRISPR/Cas9 and Cre/LoxP. CRISPR/Cas9-mediated homologous recombination (HR) was exploited to knock out (KO) one allele of MSTN in pig primary cells. Cre recombinase was then used to excise the SMG with an efficiency of 82.7%. The SMG-free non-EGFP cells were isolated by flow cytometery and immediately used as donor nuclei for nuclear transfer. A total of 685 reconstructed embryos were transferred into three surrogates with one delivering two male live piglets. Molecular testing verified the mono-allelic MSTN KO and SMG deletion in these cloned pigs. Western blots showed approximately 50% decrease in MSTN and concurrent increased expression of myogenic genes in muscle. Histological examination revealed the enhanced myofiber quantity but myofiber size remained unaltered. Ultrasonic detection showed the increased longissimus muscle size and decreased backfat thickness. Precision editing of pig MSTN gene has generated isozygous, SMG-free MSTN KO cloned founders, which guaranteed a reliable route for elite livestock production and a strategy to minimize potential biological risks.
Beta-hemolytic Streptococcus dysgalactiae strains isolated from horses are a genetically distinct population within the Streptococcus dysgalactiae taxon
Authors: Pinho Marcos D. , Erol Erdal , Ribeiro-Gonçalves Bruno , Mendes Catarina I. , Carriço João A. , Matos Sandra C. , Preziuso Silvia , Luebke-Becker Antina , Wieler Lothar H. , Melo-Cristino Jose , Ramirez Mario 
Published: August 2016

AbstractThe pathogenic role of beta-hemolytic Streptococcus dysgalactiae in the equine host is increasingly recognized. A collection of 108 Lancefield group C (n = 96) or L (n = 12) horse isolates recovered in the United States and in three European countries presented multilocus sequence typing (MLST) alleles, sequence types and emm types (only 56% of the isolates could be emm typed) that were, with few exceptions, distinct from those previously found in human Streptococcus dysgalactiae subsp. equisimilis. Characterization of a subset of horse isolates by multilocus sequence analysis (MLSA) and 16S rRNA gene sequence showed that most equine isolates could also be differentiated from S. dysgalactiae strains from other animal species, supporting the existence of a horse specific genomovar. Draft genome information confirms the distinctiveness of the horse genomovar and indicates the presence of potentially horse-specific virulence factors. While this genomovar represents most of the isolates recovered from horses, a smaller MLST and MLSA defined sub-population seems to be able to cause infections in horses, other animals and humans, indicating that transmission between hosts of strains belonging to this group may occur.
Limited phosphorus availability is the Achilles heel of tropical reef corals in a warming ocean
Authors: Ezzat Leïla , Maguer Jean-François , Grover Renaud , Ferrier-Pagès Christine 
Published: August 2016

AbstractDuring the 20th century, seawater temperatures have significantly increased, leading to profound alterations in biogeochemical cycles and ecosystem processes. Elevated temperatures have also caused massive bleaching (symbiont/pigment loss) of autotrophic symbioses, such as in coral-dinoflagellate association. As symbionts provide most nutrients to the host, their expulsion during bleaching induces host starvation. However, with the exception of carbon, the nutritional impact of bleaching on corals is still unknown, due to the poorly understood requirements in inorganic nutrients during stress. We therefore assessed the uptake rates of nitrogen and phosphate by five coral species maintained under normal and thermal stress conditions. Our results showed that nitrogen acquisition rates were significantly reduced during thermal stress, while phosphorus uptake rates were significantly increased in most species, suggesting a key role of this nutrient. Additional experiments showed that during thermal stress, phosphorus was required to maintain symbiont density and photosynthetic rates, as well as to enhance the translocation and retention of carbon within the host tissue. These findings shed new light on the interactions existing between corals and inorganic nutrients during thermal stress and highlight the importance of phosphorus for symbiont health.
In-depth phylogenetic analysis of hepatitis C virus subtype 1a and occurrence of 80K and associated polymorphisms in the NS3 protease
Authors: Santos André F. , Bello Gonzalo , Vidal Luãnna L. , Souza Suiane L. , Mir Daiana , Soares Marcelo A. 
Published: August 2016

AbstractHCV genetic diversity is high and impacts disease progression, treatment and drug resistance. HCV subtype 1a is divided in two clades (I and II), and the 80 K natural polymorphism in the viral NS3 protease is prevalent in clade I. Paradoxically, countries dominated by this clade have contrasting frequencies of 80 K. Over 2,000 HCV 1a NS3 sequences were retrieved from public databases representing Europe, Oceania and the Americas. Sequences were aligned with HCV reference sequences and subjected to phylogenetic analysis to investigate the relative presence of different subtype 1a clades and NS3 protease mutations. HCV-1a sequences split into clades I and II. Clade I was further structured into three subclades, IA to C. Sub-clade IA prevailed in the U.S., while subclade IC was major in Brazil. The NS3 80 K polymorphism was associated with subclade IA, but nearly absent in subclades IB and IC, a pattern similarly seen for the 91S/T compensatory mutation. Three HCV-1a-I sub-clades have been identified, with different frequencies in distinct regions. The 80 K and 91A/S mutations were associated with subclade IA, which provide an explanation for the disparities seen in simeprevir resistance profiles of countries dominated by HCV 1a-I, like the U.S. and Brazil.
Spatiotemporal Divergence of the Warming Hiatus over Land Based on Different Definitions of Mean Temperature
Authors: Zhou Chunlüe , Wang Kaicun 
Published: August 2016

AbstractExisting studies of the recent warming hiatus over land are primarily based on the average of daily minimum and maximum temperatures (T2). This study compared regional warming rates of mean temperature based on T2 and T24 calculated from hourly observations available from 1998 to 2013. Both T2 and T24 show that the warming hiatus over land is apparent in the mid-latitudes of North America and Eurasia, especially in cold seasons, which is closely associated with the negative North Atlantic Oscillation (NAO) and Arctic Oscillation (AO) and cold air propagation by the Arctic-original northerly wind anomaly into mid-latitudes. However, the warming rates of T2 and T24 are significantly different at regional and seasonal scales because T2 only samples air temperature twice daily and cannot accurately reflect land-atmosphere and incoming radiation variations in the temperature diurnal cycle. The trend has a standard deviation of 0.43 °C/decade for T2 and 0.41 °C/decade for T24 and 0.38 °C/decade for their trend difference in 5° × 5° grids. The use of T2 amplifies the regional contrasts of the warming rate, i.e., the trend underestimation in the US and overestimation at high latitudes by T2.
Esophageal Atresia: Future Directions for Research on the Digestive Tract
Authors: Rommel Nathalie , Tack Jan , Deprest Jan , Allegaert Karel , Rayyan Maissa 
Published: August 2016

AbstractEsophageal atresia (EA) is a congenital malformation defined by the discontinuity of the esophagus occurring in 2.4 in 10,000 births. As survival rates are high, the significant medical morbidity became more relevant. Short-term and long-term morbidities involve the respiratory and gastrointestinal system in the majority of the patients. The impact of this morbidity seems large enough to inspire researchers to develop experimental animal models that may help understanding the pathogenesis and pathophysiology. These models can also be used to explore potential surgical therapies. We reviewed the clinical and experimental literature focusing on esophageal morbidity in EA. Although the consequences of esophageal motility disorders are very relevant in the clinical setting, research remains largely underexplored. Consequently, we suggest integrating motility function assessment in the existing research models.
DOMINO: development of informative molecular markers for phylogenetic and genome-wide population genetic studies in non-model organisms
Authors: Frías-López Cristina , Sánchez-Herrero José F. , Guirao-Rico Sara , Mora Elisa , Arnedo Miquel A. , Sánchez-Gracia Alejandro , Rozas Julio 
Published: August 2016

Motivation: The development of molecular markers is one of the most important challenges in phylogenetic and genome wide population genetics studies, especially in studies with non-model organisms. A highly promising approach for obtaining suitable markers is the utilization of genomic partitioning strategies for the simultaneous discovery and genotyping of a large number of markers. Unfortunately, not all markers obtained from these strategies provide enough information for solving multiple evolutionary questions at a reasonable taxonomic resolution.
Results: We have developed Development Of Molecular markers In Non-model Organisms (DOMINO), a bioinformatics tool for informative marker development from both next generation sequencing (NGS) data and pre-computed sequence alignments. The application implements popular NGS tools with new utilities in a highly versatile pipeline specifically designed to discover or select personalized markers at different levels of taxonomic resolution. These markers can be directly used to study the taxa surveyed for their design, utilized for further downstream PCR amplification in a broader set taxonomic scope, or exploited as suitable templates to bait design for target DNA enrichment techniques. We conducted an exhaustive evaluation of the performance of DOMINO via computer simulations and illustrate its utility to find informative markers in an empirical dataset.
Availability and Implementation: DOMINO is freely available from www.ub.edu/softevol/domino.
Contact: elsanchez@ub.edu or jrozas@ub.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
ImmQuant: a user-friendly tool for inferring immune cell-type composition from gene-expression data
Authors: Frishberg Amit , Brodt Avital , Steuerman Yael , Gat-Viks Irit 
Published: August 2016

Summary: The composition of immune-cell subsets is key to the understanding of major diseases and pathologies. Computational deconvolution methods enable researchers to investigate immune cell quantities in complex tissues based on transcriptome data. Here we present ImmQuant, a software tool allowing immunologists to upload transcription profiles of multiple tissue samples, apply deconvolution methodology to predict differences in cell-type quantities between the samples, and then inspect the inferred cell-type alterations using convenient visualization tools. ImmQuant builds on the DCQ deconvolution algorithm and allows a user-friendly utilization of this method by non-bioinformatician researchers. Specifically, it enables investigation of hundreds of immune cell subsets in mouse tissues, as well as a few dozen cell types in human samples.Availability and implementation: ImmQuant is available for download at http://csgi.tau.ac.il/ImmQuant/.Contact: iritgv@post.tau.ac.ilSupplementary information: Supplementary data are available at Bioinformatics online.
Characterization of a Cryopreserved Split-Thickness Human Skin Allograft–TheraSkin
Authors: Landsman Adam , Rosines Eran , Houck Amanda , Murchison Angela , Jones Alyce , Qin Xiaofei , Chen Silvia , Landsman Arnold R. 
Published: August 2016

ABSTRACT

OBJECTIVE:
The purpose of this study was to examine the characteristics of a cryopreserved split-thickness skin allograft produced from donated human skin and compare it with fresh, unprocessed human split-thickness skin.

BACKGROUND:
Cutaneous wound healing is a complex and organized process, where the body re-establishes the integrity of the injured tissue. However, chronic wounds, such as diabetic or venous stasis ulcers, are difficult to manage and often require advanced biologics to facilitate healing. An ideal wound care product is able to directly influence wound healing by introducing biocompatible extracellular matrices, growth factors, and viable cells to the wound bed.

MATERIALS AND METHODS:
TheraSkin (processed by LifeNet Health, Virginia Beach, Virginia, and distributed by Soluble Systems, Newport News, Virginia) is a minimally manipulated, cryopreserved split-thickness human skin allograft, which contains natural extracellular matrices, native growth factors, and viable cells. The authors characterized TheraSkin in terms of the collagen and growth factor composition using ELISA, percentage of apoptotic cells using TUNEL analysis, and cellular viability using alamarBlue assay (Thermo Fisher Scientific, Waltham, Massachusetts), and compared these characteristics with fresh, unprocessed human split-thickness skin.

RESULTS:
It was found that the amount of the type I and type III collagen, as well as the ratio of type I to type III collagen in TheraSkin, is equivalent to fresh unprocessed human split-thickness skin. Similar quantities of vascular endothelial growth factor, insulinlike growth factor 1, fibroblast growth factor 2, and transforming growth factor β1 were detected in TheraSkin and fresh human skin. The average percent of apoptotic cells was 34.3% and 3.1% for TheraSkin and fresh skin, respectively.

CONCLUSIONS:
Cellular viability was demonstrated in both TheraSkin and fresh skin.