bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vitro Developmental Competence of Adult Sheep Oocytes Treated with Roscovitine
Authors: Crocomo LF , Ariu F , Bogliolo L , Bebbere D , Ledda S , Bicudo SD 
Published: February 2016

ContentsThe efficiency of in vitro sheep embryo production is still low compared to that observed in vivo and in other species. In this context, meiotic inhibition strategies emerged as a promising alternative to improve this biotechnology. So, this study aimed to evaluate, for the first time, the effects of roscovitine on in vitro maturation of sheep oocytes and their subsequent embryo development. For this, cumulus–oocyte complexes (COCs) were cultured for 6 h in the presence (Rosco) or absence (Control) of 75 μm roscovitine and, subsequently, in vitro matured (IVM) for 18 h with gonadotropins. At 0 (Immature), 6 and 24 h of culture, the nuclear status of oocytes was evaluated by Hoechst staining. Embryo cleavage and blastocyst formation were recorded 30 h after in vitro fertilization and on day 7 of culture, respectively. Blastocyst quality was evaluated by differential staining. At 6 h, the GV rate in the Rosco treatment (93.8%) was similar to that observed in the Immature oocytes (94.9%) and significantly higher compared to Control (41.3%). After IVM for 18 h, a high and similar proportion of oocytes from Rosco (93.6%) and Control (88.4%) reached the MII stage. In both treatments, approximately 70% of oocytes cleaved and 50% of them developed up to blastocyst. The mean percentage of blastocyst cells, embryoblast, trophoblast and pyknosis did also not differ between Control and Rosco. In conclusion, roscovitine, at the studied experimental conditions, was efficient to reversibly inhibit the meiosis of adult sheep oocytes without detrimental effect on development and quality of the in vitro produced embryos.
Assessment of the H‐reflex at two contraction levels before and after fatigue
Authors: Stutzig N. , Siebert T. 
Published: February 2016

The aim of the present study was to compare the H‐reflex evoked at rest and at 20% maximal voluntary contraction (MVC) prior to and after fatiguing the lateral gastrocnemius (LG). The maximal H‐reflex and M‐wave were recorded in the LG, and soleus (SOL). Electrical evoked potentials were delivered to the posterior tibial nerve when muscles were inactivated and at 20% MVC. After fatigue, the Hmax/Mmax ratio of the fatigued LG was increased for both contraction levels (rest and 20% MVC) and remained unaltered for non‐fatigued SOL. Before fatigue, the Hmax/Mmax ratio of SOL was enhanced at rest compared with the Hmax/Mmax ratio at 20% MVC. No differences were observed for LG. Fatigue of a single muscle leads to increased spinal reflex activity of the homonymous muscle. Contrary to previous recommendations in the literature, there appears to be no benefit with regard to the H‐reflex amplitude in evoking electrical potentials during constant voluntary contractions at 20% MVC compared with inactivated muscles. The observed difference in SOL prior to fatigue was most likely due to hyperpolarization of the muscle fiber membrane.
Do UK crops and grassland require greater inputs of sulphur fertilizer in response to recent and forecast reductions in sulphur emissions and deposition?
Authors: Webb J. , Jephcote C. , Fraser A. , Wiltshire J. , Aston S. , Rose R. , Vincent K. , Roth B. 
Published: February 2016

AbstractUK emissions of sulphur dioxide decreased by 94% between 1970 and 2010 and are projected to decrease by another 50% by 2020 as coal fired power stations are decommissioned. We used the Community Multiscale Air Quality model to create maps of sulphur (S) deposition to assess the impact of these forecast decreases in S emissions on net S deposition to crops in England and Wales. Currently, average S deposition, net of S leaching, varies little between the UK regions, being greatest in Yorkshire and Humberside (Y&H), at ca. 5–6 kg/ha S, and least in Wales, at ca. 3–4 kg/ha S. However, even in Y&H S deposition is no more than 25% of S uptake by cereals and only ca. 10% of S uptake by oilseed rape (OSR). By 2020, net S deposition is predicted to decrease by between 30 and 60% and will be no more than 15% of S uptake by cereal crops and <10% of S uptake by OSR. We conclude that, with the exception of a few localities, net S deposition is currently making only a minor contribution to crop S requirements and this small contribution will continue to decline. We recommend S be applied at the rates currently advised, as either mineral fertilizer or livestock manures (or a combination of both), to all crops and grass grown on sandy soils or in areas of >375‐mm overwinter rainfall. The need for S fertilizer appears to be greatest for grass swards cut more than once.
Determining the longer term decline in plant‐available soil phosphorus from short‐term measured values
Authors: Johnston A. E. , Poulton P. R. , White R. P. , Macdonald A. J. 
Published: February 2016

AbstractOnce phosphorus (P) applications stop, it is important to know how long it will take for plant‐available P in soil to decline to a particular level for soils with a history of intensive management. The rate of decline in the absence of applied P can be expressed as a half‐life, that is the time in years for it to halve relative to the lowest level measured in the soil. This knowledge is essential when planning long‐term policies for managing the P status of soils. It is important to farmers who wish to optimize applications of P fertilizers and make better use of accumulated P residues to ensure that plant‐available P does not fall below the critical level for the soil and crop because of the risk of losing yield and the inefficient use of other inputs, especially N fertilizer. Lower levels of plant‐available P are also desirable for environmental and ecological reasons. Allowing plant‐available P to decline to the critical level from unnecessarily high concentrations will reduce the risk from P on eroded soil causing adverse effects of eutrophication in surface water. Low levels of plant‐available P are usually considered necessary for establishing species‐rich grassland. A method for determining the longer term decline in plant‐available soil P from short‐term measured values is presented.
Factors controlling the vegetation distribution and coal‐forming environments in a strike‐slip basin. The Pennsylvanian Peñarroya‐Belmez‐Espiel Basin, southern Spain
Authors: González Felipe , Moreno Carmen , Lorenzo Erica , Márquez Gonzalo 
Published: February 2016

AbstractCoal‐forming environments require humid to perhumid conditions. Tectonics governs the size, location and availability of coal seams developed in such environments. While large Pennsylvanian paralic basins generated thick and continuous coal seams, many other small coeval basins, which were tectonically active, developed a puzzling succession, with carbonaceous deposits that varied in size, thickness and the nature of the coal‐forming flora. This study, conducted in the Peñarroya‐Belmez‐Espiel coalfield, a Variscan strike‐slip basin in the south of Spain, provides insights into this subject. The coal seams analysed, generated in different depositional environments, have quantitatively different palynological assemblages. Lacustrine coals are dominated by lycopsids; distal alluvial plain/marginal lacustrine coals are dominated by sphenophytes and tree ferns, and middle alluvial fan coals are dominated by sphenophytes, tree ferns and lycopsids. This means that when conditions were favourable for peat accumulation, peat accumulated regardless of the nature of the available flora.
RELIGION AND SCIENCE IN DIALOGUE: AN ASIAN CHRISTIAN VIEW
Authors: Seung Chul Kim 
Published: February 2016

AbstractWe may understand natural science as part of the attempt by human beings to understand themselves and their place in the world in which they find themselves. In this sense, as Karl Rahner has suggested, natural science flows naturally into anthropology. Consciously or unconsciously, science is always part of the drive to self‐understanding. In an age of religious pluralism like ours, Christian faith in Asia is also brought face to face with the living reality of other religions, and that, too, cannot but affect how we understand our shared humanity.
WHY IS CONFUCIANISM NOT A RELIGION? THE IMPACT OF ORIENTALISM
Authors: Na Chen 
Published: February 2016

AbstractThis study attempts to answer the question why Confucianism, the dominant “teaching” among the Three Teachings, is not a religion in contemporary China, unlike the other two “teachings,” Buddhism and Daoism. By examining this phenomenon in the social‐historical context, this study finds its origin in Orientalism. The Orientalist conceptualization of religion became part of the New Culture discourse at the turn of the twentieth century. While China has undergone tremendous social changes over the past century, the old discourse remains.
SCIENCE AND CONFUCIANISM IN RETROSPECT AND PROSPECT
Authors: Kuang‐Tai Hsu 
Published: February 2016

AbstractIn contrast to Western science and religion, a topic which has been studied very much since the twentieth century, less research has been done on science and Confucianism. By way of a comparative viewpoint within the history of science, this article will deal with some aspects of science and Confucianism in retrospect, for instance, the Confucian origin of the idea of tian yuan di fang 天圓地方, the natural philosophy of qi, and the wu xing li tian zhi qi 五行沴天之氣 bringing abnormal astrological phenomena and reflecting a negative Confucian relation between politics, ethics, and nature. In the late Ming, Xiong Mingyu found that abnormal astrological phenomena, as atmospheric events, happened in the sublunar region rather than in the stars, and in the present time we can reinterpret the crisis of air pollution or global climate change as reflecting a negative Confucian relation between politics, ethics, and nature and as a warning of collective misbehavior in our use of modern scientific technologies.
Intermittent drivers anchoring to structural heterogeneities as a major pathophysiological mechanism of human persistent atrial fibrillation
Authors: Haissaguerre Michel , Shah Ashok J. , Cochet Hubert , Hocini Meleze , Dubois Remi , Efimov Igor , Vigmond Edward , Bernus Olivier , Trayanova Natalia 
Published: February 2016

AbstractThe mechanisms responsible for perpetuation of human persistent atrial fibrillation (AF) are controversial and probably vary between individuals. A wide spectrum of mechanisms have been described in experimental studies, ranging from a single localized stable (focal/reentrant) source, to multiple sources, up to diffuse bi‐atrial wavelets. We characterized AF drivers in patients with persistent AF (lasting less than 1 year) using novel high resolution mapping, imaging and modelling approaches with the objective of evaluating their relationship to atrial structural heterogeneities. Using panoramic non‐invasive mapping in humans, focal or reentrant sources driving AF waves were identified, originating from multiple distinct regions and exhibiting short lifespans and periodic recurrences in the same locations. The reentrant driver regions harboured long, fractionated electrograms covering most of the fibrillatory cycle lengths with varying beat‐to‐beat sequences suggestive of unstable trajectories attached to slow conducting heterogeneous tissue. MRI atrial imaging demonstrated that such drivers preferentially clustered at the borders of fibrotic atrial regions. In patient‐specific computer simulations, sustained AF was shown to be driven by meandering transitory reentries attached to fibrosis borders expressing specific metrics in density and extent. Finally, random microstructural alterations devoid of cellular electrical changes were modelled, showing that a percolation mechanism could also explain atrial reentries and complex fractionated electrograms. These data from clinical, imaging and computational studies strongly suggest that intermittent and spatially unstable drivers anchoring to structural heterogeneities are a major pathophysiological mechanism in human persistent atrial fibrillation.
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The dynamic AMPA receptor extracellular region: a platform for synaptic protein interactions
Authors: García‐Nafría J. , Herguedas B. , Watson J. F. , Greger I. H. 
Published: February 2016

AbstractAMPA receptors (AMPARs) are glutamate‐gated cation channels that mediate fast excitatory neurotransmission and synaptic plasticity. Structures of GluA2 homotetramers in distinct functional states, together with simulations, emphasise the loose architecture of the AMPAR extracellular region (ECR). The ECR encompasses ∼80% of the receptor, and consists of the membrane‐distal N‐terminal domain (NTD) and ligand‐binding domain (LBD), which is fused to the ion channel domain. Minimal contacts within and between layers, together with flexible peptide linkers connecting these three domains give rise to an organisation capable of dynamic rearrangements. This building plan is uniquely suited to engage interaction partners in the crowded environment of synapses, permitting the formation of new binding sites and the loss of existing ones. ECR motions are thereby expected to impact signalling as well as synaptic anchorage and may thereby influence AMPAR clustering during synaptic plasticity.
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Airway tree reconstruction in expiration chest CT scans facilitated by information transfer from corresponding inspiration scans
Authors: Bauer Christian , Eberlein Michael , Beichel Reinhard R. 
Published: February 2016

Purpose:Analysis and comparison of airways imaged in pairs of inspiration and expiration lung CT scans provides important information for quantitative assessment of lung diseases like chronic obstructive pulmonary disease. However, airway tree reconstruction in expiration CT scans is a challenging problem. Typically, only a low number of airway branches are found in expiration scans, compared to inspiration scans. To detect more airways in expiration CT scans, the authors introduce a novel airway reconstruction approach and assess its performance.Methods:The method requires a pair of inspiration and expiration CT scans and utilizes information from the inspiration scan to facilitate reconstructing the airway tree in the expiration lung CT scan. First, an initial airway tree (high confidence) and airway candidates (limited confidence) are reconstructed in the expiration scan by utilizing a 3D graph‐based reconstruction method. Then, the 3D airway tree is reconstructed in the inspiration scan. Second, correspondences between expiration and inspiration tree structures are identified by utilizing a novel hierarchical tree matching algorithm that utilizes a local CT image‐based similarity criterion. Third, the tree information from the inspiration airway tree is used to select expiration candidates, resulting in the final expiration tree structure. The approach was evaluated on a diverse set of 40 scan pairs and compared to the baseline method, which utilizes only the expiration CT scan.Results:The proposed method produced a significant (p < 0.05) increase in airway tree length by 13.35 cm, on average, which represents an 11.21% increase relative to the baseline result using only the expiration CT scan. A detailed analysis of all additionally identified airways resulted in a true and false positive rate of 94.8% and 5.2%, respectively. The true positive rate was found to be significantly higher than the false positive rate (p < 0.05).Conclusions:The proposed method allowed increasing the number of found airways in expiration scans significantly. In addition, the algorithm establishes correspondence between inspiration and expiration airway trees, which can facilitate label transfer between airway trees and quantitative assessment of change in airways. The approach can be adapted to facilitate airway reconstruction in several longitudinal lung CT scans by means of mutual information transfer.
Seeded Amplification of Chronic Wasting Disease Prions in Nasal Brushings and Recto-anal Mucosa-Associated Lymphoid Tissues from Elk by Real-Time Quaking-Induced Conversion
Authors: Haley Nicholas J. , Siepker Chris , Hoon-Hanks Laura L. , Mitchell Gordon , Walter W. David , Manca Matteo , Monello Ryan J. , Powers Jenny G. , Wild Margaret A. , Hoover Edward A. , Caughey Byron , Richt Jürgen A. 
Published: February 2016

ABSTRACT

Chronic wasting disease (CWD), a transmissible spongiform encephalopathy of cervids, was first documented nearly 50 years ago in Colorado and Wyoming and has since been detected across North America and the Republic of Korea. The expansion of this disease makes the development of sensitive diagnostic assays and antemortem sampling techniques crucial for the mitigation of its spread; this is especially true in cases of relocation/reintroduction or prevalence studies of large or protected herds, where depopulation may be contraindicated. This study evaluated the sensitivity of the real-time quaking-induced conversion (RT-QuIC) assay of recto-anal mucosa-associated lymphoid tissue (RAMALT) biopsy specimens and nasal brushings collected antemortem. These findings were compared to results of immunohistochemistry (IHC) analysis of ante- and postmortem samples. RAMALT samples were collected from populations of farmed and free-ranging Rocky Mountain elk (
Cervus elaphus nelsoni
;
n
= 323), and nasal brush samples were collected from a subpopulation of these animals (
n
= 205). We hypothesized that the sensitivity of RT-QuIC would be comparable to that of IHC analysis of RAMALT and would correspond to that of IHC analysis of postmortem tissues. We found RAMALT sensitivity (77.3%) to be highly correlative between RT-QuIC and IHC analysis. Sensitivity was lower when testing nasal brushings (34%), though both RAMALT and nasal brush test sensitivities were dependent on both the
PRNP
genotype and disease progression determined by the obex score. These data suggest that RT-QuIC, like IHC analysis, is a relatively sensitive assay for detection of CWD prions in RAMALT biopsy specimens and, with further investigation, has potential for large-scale and rapid automated testing of antemortem samples for CWD.
Multicenter Assessment of Gram Stain Error Rates
Authors: Samuel Linoj P. , Balada-Llasat Joan-Miquel , Harrington Amanda , Cavagnolo Robert 
Published: February 2016

ABSTRACT
Gram stains remain the cornerstone of diagnostic testing in the microbiology laboratory for the guidance of empirical treatment prior to availability of culture results. Incorrectly interpreted Gram stains may adversely impact patient care, and yet there are no comprehensive studies that have evaluated the reliability of the technique and there are no established standards for performance. In this study, clinical microbiology laboratories at four major tertiary medical care centers evaluated Gram stain error rates across all nonblood specimen types by using standardized criteria. The study focused on several factors that primarily contribute to errors in the process, including poor specimen quality, smear preparation, and interpretation of the smears. The number of specimens during the evaluation period ranged from 976 to 1,864 specimens per site, and there were a total of 6,115 specimens. Gram stain results were discrepant from culture for 5% of all specimens. Fifty-eight percent of discrepant results were specimens with no organisms reported on Gram stain but significant growth on culture, while 42% of discrepant results had reported organisms on Gram stain that were not recovered in culture. Upon review of available slides, 24% (63/263) of discrepant results were due to reader error, which varied significantly based on site (9% to 45%). The Gram stain error rate also varied between sites, ranging from 0.4% to 2.7%. The data demonstrate a significant variability between laboratories in Gram stain performance and affirm the need for ongoing quality assessment by laboratories. Standardized monitoring of Gram stains is an essential quality control tool for laboratories and is necessary for the establishment of a quality benchmark across laboratories.
Highly Efficient CRISPR/Cas9-Mediated Cloning and Functional Characterization of Gastric Cancer-Derived Epstein-Barr Virus Strains
Authors: Kanda Teru , Furuse Yuki , Oshitani Hitoshi , Kiyono Tohru 
Published: February 2016

ABSTRACT
The Epstein-Barr virus (EBV) is etiologically linked to approximately 10% of gastric cancers, in which viral genomes are maintained as multicopy episomes. EBV-positive gastric cancer cells are incompetent for progeny virus production, making viral DNA cloning extremely difficult. Here we describe a highly efficient strategy for obtaining bacterial artificial chromosome (BAC) clones of EBV episomes by utilizing a CRISPR/Cas9-mediated strand break of the viral genome and subsequent homology-directed repair. EBV strains maintained in two gastric cancer cell lines (SNU719 and YCCEL1) were cloned, and their complete viral genome sequences were determined. Infectious viruses of gastric cancer cell-derived EBVs were reconstituted, and the viruses established stable latent infections in immortalized keratinocytes. While Ras oncoprotein overexpression caused massive vacuolar degeneration and cell death in control keratinocytes, EBV-infected keratinocytes survived in the presence of Ras expression. These results implicate EBV infection in predisposing epithelial cells to malignant transformation by inducing resistance to oncogene-induced cell death.

IMPORTANCE
Recent progress in DNA-sequencing technology has accelerated EBV whole-genome sequencing, and the repertoire of sequenced EBV genomes is increasing progressively. Accordingly, the presence of EBV variant strains that may be relevant to EBV-associated diseases has begun to attract interest. Clearly, the determination of additional disease-associated viral genome sequences will facilitate the identification of any disease-specific EBV variants. We found that CRISPR/Cas9-mediated cleavage of EBV episomal DNA enabled the cloning of disease-associated viral strains with unprecedented efficiency. As a proof of concept, two gastric cancer cell-derived EBV strains were cloned, and the infection of epithelial cells with reconstituted viruses provided important clues about the mechanism of EBV-mediated epithelial carcinogenesis. This experimental system should contribute to establishing the relationship between viral genome variation and EBV-associated diseases.