bluuebunny/crossref_metadata_2025_split huggingface dataset:
CONTROLS ON RESERVOIR DIAGENESIS IN THE LOWER GORU SANDSTONE FORMATION, LOWER INDUS BASIN, PAKISTAN
Authors: Baig M. Omer , Harris N. B. , Ahmed H. , Baig M. O. A. 
Published: December 2015

Sandstones in the Lower Cretaceous Lower Goru Formation in the Lower Indus Basin, Pakistan, are important reservoir rocks for oil, gas and gas‐condensates. For this study, nine metres of core from depths of more than 3400m from well X‐1 in the north‐central part of the basin were analysed for major variations in porosity and permeability in two Lower Goru sandstone units referred to as the Basal and Massive Sands. The Lower Goru Basal Sand was deposited in lower shoreface to inner shelf settings at the well location, while the Massive Sand was deposited in a middle to lower shoreface setting. In both units, intervals with moderate to good (> 15%) porosities alternate with intervals with very low porosity (<5%), and similar variations in core permeability were observed. In this paper, the reasons for this reservoir quality variation at well X‐1 are investigated. Specifically, the study addresses the influence of different clay types on reservoir porosity and permeability within the Lower Goru sands and the distribution and impact of hard cements such as calcite and quartz. A range of petrographical data is integrated including thin sections, whole rock and clay XRD results and SEM images, which together provide some insights into the causes of reservoir quality variation and into the paragenetic relationships between the authigenic minerals.Chlorite grain coats are present in the higher‐porosity sandstones and are interpreted to have inhibited the formation of quartz overgrowths. Dissolution of feldspar and volcanic rock fragments in both the Basal and Massive Sands has contributed to an increase in overall porosity at well X‐1. Relatively low porosity intervals in the Massive Sand are associated with the absence of chlorite grain coats and the presence of abundant quartz overgrowths. By contrast, low porosity intervals in the Basal Sand have undergone early poikilotopic calcite cementation.The formation of authigenic illite resulted in a significant decrease in permeability in both the Basal and Massive Sands. Chlorite and kaolinite also reduced the permeability. The chlorite originated mainly from the dissolution of volcanic rock fragments or from precursor depositional berthierine clay. The transformation of K‐feldspar to illite is suggested to be the main reaction responsible for the formation of both authigenic illite and quartz overgrowths in the two reservoir units; the observed pressure solution will also have contributed to development of quartz overgrowths.
ORGANIC GEOCHEMICAL CHARACTERIZATION AND SHALE GAS POTENTIAL OF THE PERMIAN BARREN MEASURES FORMATION, WEST BOKARO SUB‐BASIN, EASTERN INDIA
Authors: Tewari Anuradha , Dutta Suryendu , Sarkar Tanmoy 
Published: December 2015

This study investigates the shale gas characteristics of the Permian Barren Measures Formation (Gondwana Supergroup) in the West Bokaro sub‐basin of the Damodar Valley Basin, eastern India. A total of 23 core shale samples collected from a borehole located in the western part of the sub‐basin were analysed using organic geochemical techniques and scanning electron microscopy. The samples are black carbonaceous shales composed chiefly of quartz, mica and clay minerals.Rock‐Eval pyrolysis data show that the analysed samples contain a mixture of Type II and Type III kerogen with TOC values of 2.7 to 6.2%. Rock‐Eval Tmax values ranging from 443 to 452 °C correspond to calculated vitrinite reflectance of approximately 0.8–0.9%. A cross‐plot of hydrogen index versus Tmax indicates that the samples have reached peak oil to wet gas maturities. A pristane/n‐C17 versus phytane/n‐C18 cross‐plot, together with biomarker parameters such as the dominance of C29 over C27 and C28 steranes and high moretane/hopane ratios (0.22–0.51), demonstrate that the shale samples contain terrigenous organic matter deposited in a suboxic environment.Scanning electron microscopy images of shale samples show the presence of a complex, mostly intergranular pore network. Both micropores (>0.75μm) and nanopores (<0.75μm) were observed. Some pores are elongated and are associated with layer‐spaces in sheet silicate minerals; others are non‐elongated and irregular in shape. The organic geochemical parameters and the observed pore attributes suggest that the Barren Measures Formation has good shale gas potential.
Short‐term effects of povidone iodine and sodium fluoride therapy on plaque levels and microbiome diversity
Authors: Reilly C , Goettl M , Steinmetz M , Nikrad J , Jones RS 
Published: December 2015

ObjectivesThe objective of this study is to evaluate the effect of short‐term changes in the oral microbial ecology of dental plaque and plaque levels after topical treatment of a combination of 10% povidone iodine (PI) and 5% sodium fluoride varnish (FV).Materials and MethodsA single group design intervention study on 12 pediatric patients, who underwent two baseline plaques samplings before the intervention, were enrolled in the study. A modified mixed dentition Silness‐Löe plaque index score was used to assess plaque accumulation and microbial composition was assessed by amplicon sequencing analysis of the 16S rRNA V4 region.ResultsDental plaque accumulation (P = 0.0424) was reduced after 1 week using PI/FV application. This reduction was not observed between the two double‐baseline visits. 16S rRNA analysis showed that the single PI/FV therapy did not have dramatic shifts in the plaque microbiome community depicted by hierarchical cluster and principle component analysis. More subtle changes were found when analyzing the Shannon diversity index after the application of PI/FV vs two baselines prior to combination therapy.ConclusionsThe bacteria within the dental biofilms showed resilience in maintaining the overall community diversity but reduced biofilm accumulation following PI/FV therapy. Repeated uses of PI/FV may augment plaque control during dental rehabilitation in children.
Analysis on the development and current situation of rainbow trout (Oncorhynchus mykiss) farming in Mexico
Authors: Ortega César , Valladares Benjamín 
Published: December 2015

AbstractThe rainbow trout (Oncorhynchus mykiss), originally from North America, was introduced to Mexico in 1888 and gradually distributed to various areas of the country. Currently, rainbow trout are cultivated in Mexico under a number of production systems, but this sector has grown less than 1% annually for the last 10 years. The present review analysed the production status of rainbow trout in Mexico, describing the key situations and actors that have influenced the establishment and current level of aquaculture development. Since its beginnings, rainbow trout cultivation in Mexico has depended on egg import due to insufficient egg and fry production by national hatcheries. Moreover, the industry is deficient in regard to a number of aspects in the production and management processes, with a notable necessity for specialists in the areas of production, health and sanitary diagnosis to rapidly and efficiently respond to situations such as low productivity or the presence of diseases. With such specialists, appropriate control and prevention decisions could be taken and acted upon. Likewise, the Mexican rainbow trout industry has high development potential and market expectations, but sector growth will require the active participation and commitment of competent authorities, in compliance with established Mexican regulations and laws, which are oriented towards advancing and protecting the fish farming industry.
Authority and Incentives in Organizations
Authors: Kräkel Matthias 
Published: December 2015

AbstractI consider a corporation that consists of an owner, a manager, and two divisions. There exist externalities between the divisions: if a division behaves cooperatively, its success will increase the performance of the other division. The owner creates monetary effort incentives and allocates decision authority over the divisions. I characterize how externalities and benefits of control determine the corporation's optimal organization. The introduction of endogenous incentives changes the major findings of the existing literature, because then concentrated delegation of authority over both divisions to one of the division heads will be optimal if cooperation is important and divisions are difficult to incentivize.
Electoral Thresholds as Coordination Devices
Authors: Núñez Matías , Xefteris Dimitrios 
Published: December 2015

AbstractIn this paper, we study one‐person–one‐vote parliamentary elections where voters care both about the winner of elections and about the composition of the parliament. Parties enter the parliament if and only if their vote share exceeds some predetermined threshold. We show that equilibria generically exist in which all parties obtain a non‐degenerate vote‐share and, perhaps more importantly, we show that the size of the electoral threshold acts as a coordination device, which crucially affects the win prospects of the Condorcet winner party. In particular, we argue that the win prospects of the Condorcet winner party decrease with the size of the entry threshold.
The cytokinin response factors modulate root and shoot growth and promote leaf senescence in Arabidopsis
Authors: Raines Tracy , Shanks Carly , Cheng Chia‐Yi , McPherson Duncan , Argueso Cristiana T. , Kim Hyo J. , Franco‐Zorrilla José M. , López‐Vidriero Irene , Solano Roberto , Vaňková Radomíra , Schaller G. Eric , Kieber Joseph J. 
Published: December 2015

SummaryThe cytokinin response factors (CRFs) are a group of related AP2/ERF transcription factors that are transcriptionally induced by cytokinin. Here we explore the role of the CRFs in Arabidopsis thaliana growth and development by analyzing lines with decreased and increased CRF function. While single crf mutations have no appreciable phenotypes, disruption of multiple CRFs results in larger rosettes, delayed leaf senescence, a smaller root apical meristem (RAM), reduced primary and lateral root growth, and, in etiolated seedlings, shorter hypocotyls. In contrast, overexpression of CRFs generally results in the opposite phenotypes. The crf1,2,5,6 quadruple mutant is embryo lethal, indicating that CRF function is essential for embryo development. Disruption of the CRFs results in partially insensitivity to cytokinin in a root elongation assay and affects the basal expression of a significant number of cytokinin‐regulated genes, including the type‐A ARRs, although it does not impair the cytokinin induction of the type‐A ARRs. Genes encoding homeobox transcription factors are mis‐expressed in the crf1,3,5,6 mutant, including STIMPY/WOX9 that is required for root and shoot apical meristem maintenance roots and which has previously been linked to cytokinin. These results indicate that the CRF transcription factors play important roles in multiple aspects of plant growth and development, in part through a complex interaction with cytokinin signaling.
Improving cardiomyocyte model fidelity and utility via dynamic electrophysiology protocols and optimization algorithms
Authors: Krogh‐Madsen Trine , Sobie Eric A. , Christini David J. 
Published: December 2015

AbstractMathematical models of cardiac electrophysiology are instrumental in determining mechanisms of cardiac arrhythmias. However, the foundation of a realistic multiscale heart model is only as strong as the underlying cell model. While there have been myriad advances in the improvement of cellular‐level models, the identification of model parameters, such as ion channel conductances and rate constants, remains a challenging problem. The primary limitations to this process include: (1) such parameters are usually estimated from data recorded using standard electrophysiology voltage‐clamp protocols that have not been developed with model building in mind, and (2) model parameters are typically tuned manually to subjectively match a desired output. Over the last decade, methods aimed at overcoming these disadvantages have emerged. These approaches include the use of optimization or fitting tools for parameter estimation and incorporating more extensive data for output matching. Here, we review recent advances in parameter estimation for cardiomyocyte models, focusing on the use of more complex electrophysiology protocols and global search heuristics. We also discuss future applications of such parameter identification, including development of cell‐specific and patient‐specific mathematical models to investigate arrhythmia mechanisms and predict therapy strategies.
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SNaPBceBcon
: a Practical Tool for Identification and Genotyping of Burkholderia cepacia and Burkholderia contaminans
Authors: Araujo Ricardo , Caramalho Rita , Coutinho Carla , Sá-Correia Isabel 
Published: December 2015

ABSTRACT

We propose an optimized protocol for an extensive population analysis of
Burkholderia cepacia
and
Burkholderia contaminans
. Seven new polymorphisms were added to the recently proposed
SNaPBcen
assay, and a total of 18 markers ensured the clear identification and distinction of
B. cepacia
and
B. contaminans
isolates and high genotypic discrimination (Simpson index of 0.94) compared to those for multilocus sequence typing.
Evolution of Newcastle Disease Virus Quasispecies Diversity and Enhanced Virulence after Passage through Chicken Air Sacs
Authors: Meng Chunchun , Qiu Xusheng , Yu Shengqing , Li Chuanfeng , Sun Yingjie , Chen Zongyan , Liu Kaichun , Zhang Xiangle , Tan Lei , Song Cuiping , Liu Guangqing , Ding Chan 
Published: December 2015

ABSTRACT
It has been reported that lentogenic Newcastle disease virus (NDV) isolates have the potential to become velogenic after their transmission and circulation in chickens, but the underlying mechanism is unclear. In this study, a highly velogenic NDV variant, JS10-A10, was generated from the duck-origin lentogenic isolate JS10 through 10 consecutive passages in chicken air sacs. The velogenic properties of this selected variant were determined using mean death time (MDT) assays, intracerebral pathogenicity index (ICPI), the intravenous pathogenicity index (IVPI), histopathology, and the analysis of host tissue tropism. In contrast, JS10 remained lentogenic after 20 serial passages in chicken eggs (JS10-E20). The JS10, JS10-A10, and JS10-E20 genomes were sequenced and found to be nearly identical, suggesting that both JS10-A10 and JS10-E20 were directly generated from JS10. To investigate the mechanism for virulence enhancement, the partial genome covering the F0 cleavage site of JS10 and its variants were analyzed using ultradeep pyrosequencing (UDPS) and the proportions of virulence-related genomes in the quasispecies were calculated. Velogenic NDV genomes accumulated as a function of JS10 passaging through chicken air sacs. Our data suggest that lentogenic NDV strains circulating among poultry might be a risk factor to future potential velogenic NDV outbreaks in chickens.

IMPORTANCE
An avirulent isolate, JS10, was passaged through chicken air sacs and embryos, and the pathogenicity of the variants was assessed. A virulent variant, JS10-A10, was generated from consecutive passage in air sacs. We developed a deep-sequencing approach to detect low-frequency viral variants across the NDV genome. We observed that virulence enhancement of JS10 was due to the selective accumulation of velogenic quasispecies and the concomitant disappearance of lentogenic quasispecies. Our results suggest that because it is difficult to avoid contact between natural waterfowl reservoirs and sensitive poultry operations, circulating lentogenic NDV strains may represent a potential reservoir for emergent velogenic NDV strains that could cause outbreaks in chickens.
Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States
Authors: Tan Yi , Hassan Ferdaus , Schuster Jennifer E. , Simenauer Ari , Selvarangan Rangaraj , Halpin Rebecca A. , Lin Xudong , Fedorova Nadia , Stockwell Timothy B. , Lam Tommy Tsan-Yuk , Chappell James D. , Hartert Tina V. , Holmes Edward C. , Das Suman R. 
Published: December 2015

ABSTRACT
In August 2014, an outbreak of enterovirus D68 (EV-D68) occurred in North America, causing severe respiratory disease in children. Due to a lack of complete genome sequence data, there is only a limited understanding of the molecular evolution and epidemiology of EV-D68 during this outbreak, and it is uncertain whether the differing clinical manifestations of EV-D68 infection are associated with specific viral lineages. We developed a high-throughput complete genome sequencing pipeline for EV-D68 that produced a total of 59 complete genomes from respiratory samples with a 95% success rate, including 57 genomes from Kansas City, MO, collected during the 2014 outbreak. With these data in hand, we performed phylogenetic analyses of complete genome and VP1 capsid protein sequences. Notably, we observed considerable genetic diversity among EV-D68 isolates in Kansas City, manifest as phylogenetically distinct lineages, indicative of multiple introductions of this virus into the city. In addition, we identified an intersubclade recombination event within EV-D68, the first recombinant in this virus reported to date. Finally, we found no significant association between EV-D68 genetic variation, either lineages or individual mutations, and a variety of demographic and clinical variables, suggesting that host factors likely play a major role in determining disease severity. Overall, our study revealed the complex pattern of viral evolution within a single geographic locality during a single outbreak, which has implications for the design of effective intervention and prevention strategies.

IMPORTANCE
Until recently, EV-D68 was considered to be an uncommon human pathogen, associated with mild respiratory illness. However, in 2014 EV-D68 was responsible for more than 1,000 disease cases in North America, including severe respiratory illness in children and acute flaccid myelitis, raising concerns about its potential impact on public health. Despite the emergence of EV-D68, a lack of full-length genome sequences means that little is known about the molecular evolution of this virus within a single geographic locality during a single outbreak. Here, we doubled the number of publicly available complete genome sequences of EV-D68 by performing high-throughput next-generation sequencing, characterized the evolutionary history of this outbreak in detail, identified a recombination event, and investigated whether there was any correlation between the demographic and clinical characteristics of the patients and the viral variant that infected them. Overall, these results will help inform the design of intervention strategies for EV-D68.
Kaposi's Sarcoma-Associated Herpesvirus Latency Locus Compensates for Interleukin-6 in Initial B Cell Activation
Authors: Sin Sang-Hoon , Kang Sun Ah , Kim Yongbaek , Eason Anthony , Tan Kelly , An Hyowon , Dittmer Dirk P. 
Published: December 2015

ABSTRACTInterleukin 6 (IL-6) is considered a proliferation and survival factor for B cells. To assess the role of IL-6 in Kaposi sarcoma-associated herpesvirus (KSHV) latency, KSHV latency locus-transgenic mice (referred to as latency mice) lacking IL-6 were evaluated. IL-6−/−latency mice had the same phenotypes as the latency mice, i.e., increased frequency of marginal zone B cells, hyperplasia, and hyperglobulinemia, indicating that the KSHV latency locus, which includes all viral microRNAs (miRNAs), can compensate for lack of IL-6 in premalignant B cell activation.
Deletion of a Predicted β-Sheet Domain within the Amino Terminus of Herpes Simplex Virus Glycoprotein K Conserved among Alphaherpesviruses Prevents Virus Entry into Neuronal Axons
Authors: Jambunathan Nithya , Charles Anu-Susan , Subramanian Ramesh , Saied Ahmad A. , Naderi Misagh , Rider Paul , Brylinski Michal , Chouljenko Vladimir N. , Kousoulas Konstantin G. 
Published: December 2015

ABSTRACT
We have shown previously that herpes simplex virus 1 (HSV-1) lacking expression of the entire glycoprotein K (gK) or expressing gK with a 38-amino-acid deletion (gKΔ31–68 mutation) failed to infect ganglionic neurons after ocular infection of mice. We constructed a new model for the predicted three-dimensional structure of gK, revealing that the gKΔ31–68 mutation spans a well-defined β-sheet structure within the amino terminus of gK, which is conserved among alphaherpesviruses. The HSV-1(McKrae) gKΔ31–68 virus was tested for the ability to enter into ganglionic neuronal axons in cell culture of explanted rat ganglia using a novel virus entry proximity ligation assay (VEPLA). In this assay, cell surface-bound virions were detected by the colocalization of gD and its cognate receptor nectin-1 on infected neuronal surfaces. Capsids that have entered into the cytoplasm were detected by the colocalization of the virion tegument protein UL37, with dynein required for loading of virion capsids onto microtubules for retrograde transport to the nucleus. HSV-1(McKrae) gKΔ31–68 attached to cell surfaces of Vero cells and ganglionic axons in cell culture as efficiently as wild-type HSV-1(McKrae). However, unlike the wild-type virus, the mutant virus failed to enter into the axoplasm of ganglionic neurons. This work suggests that the amino terminus of gK is a critical determinant for entry into neuronal axons and may serve similar conserved functions for other alphaherpesviruses.

IMPORTANCE
Alphaherpesviruses, unlike beta- and gammaherpesviruses, have the unique ability to infect and establish latency in neurons. Glycoprotein K (gK) and the membrane protein UL20 are conserved among all alphaherpesviruses. We show here that a predicted β-sheet domain, which is conserved among alphaherpesviruses, functions in HSV-1 entry into neuronal axons, suggesting that it may serve similar functions for other herpesviruses. These results are in agreement with our previous observations that deletion of this gK domain prevents the virus from successfully infecting ganglionic neurons after ocular infection of mice.