bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pan-PCR, a Computational Method for Designing Bacterium-Typing Assays Based on Whole-Genome Sequence Data
Authors: Yang Joy Y. , Brooks Shelise , Meyer Jennifer A. , Blakesley Robert R. , Zelazny Adrian M. , Segre Julia A. , Snitkin Evan S. 
Published: December 2012

ABSTRACT

With increasing rates of antibiotic resistance, bacterial infections have become more difficult to treat, elevating the importance of surveillance and prevention. Effective surveillance relies on the availability of rapid, cost-effective, and informative typing methods to monitor bacterial isolates. PCR-based typing assays are fast and inexpensive, but their utility is limited by the lack of targets which are capable of distinguishing between strains within a species. To identify highly informative PCR targets from the growing base of publicly available bacterial genome sequences, we developed pan-PCR. This computer algorithm uses existing genome sequences for isolates of a species of interest and identifies a set of genes whose patterns of presence or absence provide the best discrimination between strains in this species. A set of PCR primers targeting the identified genes is then designed, with each PCR product being of a different size to allow multiplexing. These target DNA regions and PCR primers can then be utilized to type bacterial isolates. To evaluate pan-PCR, we designed an assay for the emerging pathogen
Acinetobacter baumannii
. Taking as input a set of 29 previously sequenced genomes, pan-PCR identified 6 genetic loci whose presence or absence was capable of distinguishing all the input strains. This assay was applied to a set of patient isolates, and its discriminatory power was compared to that of multilocus sequence typing (MLST) and whole-genome optical maps. We found that the pan-PCR assay was capable of making clinically relevant distinctions between strains with identical MLST profiles and showed a discriminatory power similar to that of optical maps. Pan-PCR represents a tool capable of exploiting available genome sequence data to design highly discriminatory PCR assays. The ease of design and implementation makes this approach feasible for diagnostic facilities of all sizes.
Viral Proteinase Requirements for the Nucleocytoplasmic Relocalization of Cellular Splicing Factor SRp20 during Picornavirus Infections
Authors: Fitzgerald Kerry D. , Chase Amanda J. , Cathcart Andrea L. , Tran Genevieve P. , Semler Bert L. 
Published: December 2012

ABSTRACT

Infection of mammalian cells by picornaviruses results in the nucleocytoplasmic redistribution of certain host cell proteins. These viruses interfere with import-export pathways, allowing for the cytoplasmic accumulation of nuclear proteins that are then available to function in viral processes. We recently described the cytoplasmic relocalization of cellular splicing factor SRp20 during poliovirus infection. SRp20 is an important internal ribosome entry site (IRES)
trans
-acting factor (ITAF) for poliovirus IRES-mediated translation; however, it is not known whether other picornaviruses utilize SRp20 as an ITAF and direct its cytoplasmic relocalization. Also, the mechanism by which poliovirus directs the accumulation of SRp20 in the cytoplasm of the infected cell is currently unknown. Work described in this report demonstrated that infection by another picornavirus (coxsackievirus B3) causes SRp20 to relocalize from the nucleus to the cytoplasm of HeLa cells, similar to poliovirus infection; however, SRp20 is relocalized to a somewhat lesser extent in the cytoplasm of HeLa cells during infection by yet another picornavirus (human rhinovirus 16). We show that expression of poliovirus 2A proteinase is sufficient to cause the nucleocytoplasmic redistribution of SRp20. Following expression of poliovirus 2A proteinase in HeLa cells, we detect cleavage of specific nuclear pore proteins known to be cleaved during poliovirus infection. We also find that expression of human rhinovirus 16 2A proteinase alone can cause efficient cytoplasmic relocalization of SRp20, despite the lower levels of SRp20 relocalization observed during rhinovirus infection compared to poliovirus. Taken together, these results further define the mechanism of SRp20 cellular redistribution during picornavirus infections, and they provide additional insight into some of the differences observed between human rhinovirus and other enterovirus infections.
Tra2-Mediated Recognition of HIV-1 5′ Splice Site D3 as a Key Factor in the Processing of
vpr
mRNA
Authors: Erkelenz Steffen , Poschmann Gereon , Theiss Stephan , Stefanski Anja , Hillebrand Frank , Otte Marianne , Stühler Kai , Schaal Heiner 
Published: December 2012

ABSTRACT

Small noncoding HIV-1 leader exon 3 is defined by its splice sites A2 and D3. While 3′ splice site (3′ss) A2 needs to be activated for
vpr
mRNA formation, the location of the
vpr
start codon within downstream intron 3 requires silencing of splicing at 5′ss D3. Here we show that the inclusion of both HIV-1 exon 3 and
vpr
mRNA processing is promoted by an exonic splicing enhancer (ESE

vpr

) localized between exonic splicing silencer ESSV and 5′ss D3. The ESE

vpr

sequence was found to be bound by members of the Transformer 2 (Tra2) protein family. Coexpression of these proteins in provirus-transfected cells led to an increase in the levels of exon 3 inclusion, confirming that they act through ESE

vpr

. Further analyses revealed that ESE

vpr

supports the binding of U1 snRNA at 5′ss D3, allowing bridging interactions across the upstream exon with 3′ss A2. In line with this, an increase or decrease in the complementarity of 5′ss D3 to the 5′ end of U1 snRNA was accompanied by a higher or lower
vpr
expression level. Activation of 3′ss A2 through the proposed bridging interactions, however, was not dependent on the splicing competence of 5′ss D3 because rendering it splicing defective but still competent for efficient U1 snRNA binding maintained the enhancing function of D3. Therefore, we propose that splicing at 3′ss A2 occurs temporally between the binding of U1 snRNA and splicing at D3.
Molecular Evolution of Viruses of the Family Filoviridae Based on 97 Whole-Genome Sequences
Authors: Carroll Serena A. , Towner Jonathan S. , Sealy Tara K. , McMullan Laura K. , Khristova Marina L. , Burt Felicity J. , Swanepoel Robert , Rollin Pierre E. , Nichol Stuart T. 
Published: December 2012

ABSTRACT

Viruses in the
Ebolavirus
and
Marburgvirus
genera (family
Filoviridae
) have been associated with large outbreaks of hemorrhagic fever in human and nonhuman primates. The first documented cases occurred in primates over 45 years ago, but the amount of virus genetic diversity detected within bat populations, which have recently been identified as potential reservoir hosts, suggests that the filoviruses are much older. Here, detailed Bayesian coalescent phylogenetic analyses are performed on 97 whole-genome sequences, 55 of which are newly reported, to comprehensively examine molecular evolutionary rates and estimate dates of common ancestry for viruses within the family
Filoviridae
. Molecular evolutionary rates for viruses belonging to different species range from 0.46 × 10
−4
nucleotide substitutions/site/year for
Sudan ebolavirus
to 8.21 × 10
−4
nucleotide substitutions/site/year for
Reston ebolavirus
. Most recent common ancestry can be traced back only within the last 50 years for
Reston ebolavirus
and
Zaire ebolavirus
species and suggests that viruses within these species may have undergone recent genetic bottlenecks. Viruses within
Marburg marburgvirus
and
Sudan ebolavirus
species can be traced back further and share most recent common ancestors approximately 700 and 850 years before the present, respectively. Examination of the whole family suggests that members of the
Filoviridae
, including the recently described Lloviu virus, shared a most recent common ancestor approximately 10,000 years ago. These data will be valuable for understanding the evolution of filoviruses in the context of natural history as new reservoir hosts are identified and, further, for determining mechanisms of emergence, pathogenicity, and the ongoing threat to public health.
Effectiveness of involving the private medical sector in the National TB Control Programme in Bangladesh: evidence from mixed methods
Authors: Zafar Ullah Abu Naser , Huque Rumana , Husain Ashaque , Akter Salma , Islam Akramul , Newell James Nicholas 
Published: December 2012

ObjectivesIn Bangladesh, private healthcare is common and popular, regardless of income or area of residence, making the private sector an important player in health service provision. Although the private sector offers a good range of health services, tuberculosis (TB) care in the private sector is poor. We conducted research in Dhaka, between 2004 and 2008, to develop and evaluate a public–private partnership (PPP) model to involve private medical practitioners (PMPs) within the National TB Control Programme (NTP)'s activities. Since 2008, this PPP model has been scaled up in two other big cities, Chittagong and Sylhet. This paper reports the results of this development, evaluation and scale-up.DesignMixed method, observational study design. We used NTP service statistics to compare the TB control outcomes between intervention and control areas. To capture detailed insights of PMPs and TB managers about the process and outcomes of the study, we conducted in-depth interviews, focus group discussions and workshops.SettingUrban setting, piloted in four areas in Dhaka city; later scaled up in other areas of Dhaka and in two major cities.FindingsThe partnership with PMPs yielded significantly increased case finding of sputum smear-positive TB cases. Between 2004 and 2010, 703 participating PMPs referred 3959 sputum smear-positive TB cases to the designated Directly Observed Treatment, Short-course (DOTS) centres, contributing about 36% of all TB cases in the project areas. There was a steady increase in case notification rates in the project areas following implementation of the partnership.ConclusionsThe PPP model was highly effective in improving access and quality of TB care in urban settings.
A Novel Criterion for Conduction Block After Catheter Ablation of Right Atrial Tachycardia After Mitral Valve Surgery
Authors: Kanagasundram Arvindh N. , Baduashvili Amiran , Liu Christopher F. , Cheung Jim W. , Thomas George , Ip James E. , Young Shane D. , Lerman Bruce B. , Markowitz Steven M. 
Published: December 2012

Background—
One operative approach to the mitral valve, the superior transseptal incision, is proarrhythmic because of extensive atriotomies. The objective of this study is to describe complex atrial tachycardias (ATs) that occur after this approach and propose methods to verify lines of block as an end point for catheter ablation.

Methods and Results—
Of the 69 patients who had electrophysiological studies for AT after mitral valve surgery, 20 patients had prior superior transseptal incisions. Of these, 14 had complex ATs involving the lateral right atrium (RA). There were 9 dual-loop, 4 single-loop, and 1 focal tachycardias. Lateral wall ablation was performed either by creating a linear lesion from the lateral atriotomy to the inferior vena cava, superior vena cava, or tricuspid annulus or by ablating focally in the lateral RA. After a single ablation procedure, conduction block in the lateral wall was verified in 10 of 14 patients using 1 of 2 distinct patterns of block. One pattern consisted of late activation in an anterolateral corridor of the RA, and a second pattern consisted of wide-spaced double potentials. Recurrent conduction through the lateral wall lesions was associated with intraprocedural and late recurrences of ATs.

Conclusions—
The optimal end point for ablating ATs after mitral valve surgery with the superior transseptal approach is to establish lines of block that can be recognized by characteristic patterns of activation in the lateral RA. A novel criterion for lateral conduction block after catheter ablation is identification of a late-activated corridor in the anterolateral RA.
Dynamics of the Stratiform Sector of a Tropical Cyclone Rainband
Authors: Didlake Anthony C. , Houze Robert A. 
Published: December 2012

Abstract
Airborne Doppler radar documented the stratiform sector of a rainband within the stationary rainband complex of Hurricane Rita. The stratiform rainband sector is a mesoscale feature consisting of nearly uniform precipitation and weak vertical velocities from collapsing convective cells. Upward transport and associated latent heating occur within the stratiform cloud layer in the form of rising radial outflow. Beneath, downward transport is organized into descending radial inflow in response to two regions of latent cooling. In the outer, upper regions of the rainband, sublimational cooling introduces horizontal buoyancy gradients, which produce horizontal vorticity and descending inflow similar to that of the trailing-stratiform region of a mesoscale convective system. Within the zone of heavier stratiform precipitation, melting cooling along the outer rainband edge creates a midlevel horizontal buoyancy gradient across the rainband that drives air farther inward beneath the brightband. The organization of this transport initially is robust but fades downwind as the convection dissipates.
The stratiform-induced secondary circulation results in convergence of angular momentum above the boundary layer and broadening of the storm's rotational wind field. At the radial location where inflow suddenly converges, a midlevel tangential jet develops and extends into the downwind end of the rainband complex. This circulation may contribute to ventilation of the eyewall as inflow of low-entropy air continues past the rainband in both the boundary layer and midlevels. Given the expanse of the stratiform rainband region, its thermodynamic and kinematic impacts likely help to modify the structure and intensity of the total vortex.
Dynamical Control of the Mesosphere by Orographic and Nonorographic Gravity Wave Drag during the Extended Northern Winters of 2006 and 2009
Authors: McLandress Charles , Scinocca John F. , Shepherd Theodore G. , Reader M. Catherine , Manney Gloria L. 
Published: December 2012

Abstract
A version of the Canadian Middle Atmosphere Model (CMAM) that is nudged toward reanalysis data up to 1 hPa is used to examine the impacts of parameterized orographic and nonorographic gravity wave drag (OGWD and NGWD) on the zonal-mean circulation of the mesosphere during the extended northern winters of 2006 and 2009 when there were two large stratospheric sudden warmings. The simulations are compared to Aura Microwave Limb Sounder (MLS) observations of mesospheric temperature and carbon monoxide (CO) and derived zonal winds. The control simulation, which uses both OGWD and NGWD, is shown to be in good agreement with MLS. The impacts of OGWD and NGWD are assessed using simulations in which those sources of wave drag are removed. In the absence of OGWD the mesospheric zonal winds in the months preceding the warmings are too strong, causing increased mesospheric NGWD, which drives excessive downwelling, resulting in overly large lower-mesospheric values of CO prior to the warming. NGWD is found to be most important following the warmings when the underlying westerlies are too weak to allow much vertical propagation of the orographic gravity waves to the mesosphere. NGWD is primarily responsible for driving the circulation that results in the descent of CO from the thermosphere following the warmings. Zonal-mean mesospheric winds and temperatures in all simulations are shown to be strongly constrained by (i.e., slaved to) the stratosphere. Finally, it is demonstrated that the responses to OGWD and NGWD are nonadditive because of their dependence and influence on the background winds and temperatures.
Autumn Sea Ice Cover, Winter Northern Hemisphere Annular Mode, and Winter Precipitation in Eurasia
Authors: Li Fei , Wang Huijun 
Published: December 2012

Abstract
This paper examines the impacts of the previous autumn sea ice cover (SIC) on the winter Northern Hemisphere annular mode (NAM) and winter precipitation in Eurasia. The coherent variations among the Kara–Laptev autumn SIC, winter NAM, and Eurasian winter precipitation appear after the year 1982, which may prove useful for seasonal prediction of winter precipitation. From a physical point of view, the Kara–Laptev SIC and sea surface temperature (SST) anomalies develop in autumn and remain in winter. Given that winter NAM is characterized by an Arctic–midlatitude seesaw centered over the Barents Sea and Kara–Laptev Seas, it is closely linked to the Arctic forcing that corresponds to the Kara–Laptev sea ice increase (reduction) and the associated surface temperature cooling (warming). Moreover, based on both model simulations and observations, the diminishing Kara–Laptev sea ice does induce positive sea level pressure (SLP) anomalies over high-latitude Eurasia in winter, which is accompanied by a significant surface warming in northern Eurasia and cooling south of the Mediterranean. This surface air temperature (SAT) anomaly pattern facilitates increases of specific humidity in northern Eurasia with a major ridge extending southward along the East Asian coast. As a result, the anomalous Eurasian winter precipitation has a more zonal band structure.
Is the Interannual Variability of the Summer Asian–Pacific Oscillation Predictable?
Authors: Huang Yanyan , Wang Huijun , Zhao Ping 
Published: December 2012

Abstract
The summer (June–August) Asian–Pacific Oscillation (APO) measures the interannual variability of large-scale atmospheric circulation over the Asian–North Pacific Ocean sector. In this study, the authors assess the predictability of the summer APO index interannual variability and the associated atmospheric circulation anomalies using the 1959–2001 hindcast data from the European Centre for Medium-Range Weather Forecasts (ECMWF), Centre National de Recherches Météorologiques (CNRM), and the Met Office (UKMO) general circulation models from the Development of a European Multimodel Ensemble System for Seasonal-to-Interannual Prediction (DEMETER) project. The results show that these models predict the summer APO index interannual variability well and have higher skill for the North Pacific than for the Asian upper-tropospheric temperature. Meanwhile, the observed APO-related atmospheric circulation anomalies in the South Asian high, the tropical easterly wind jet over the Asian monsoon region in the upper troposphere, the subtropical anticyclone over the North Pacific, and the summer southwest monsoon over Asia in the lower troposphere are reasonably well predicted in their spatial patterns and intensities. Compared with the observations, however, these models display low skill in predicting the long-term varying trends of the upper-tropospheric temperature over the Asian–North Pacific sector or the APO index during 1959–2001.
On the Variability of Wind Power Input to the Oceans with a Focus on the Subpolar North Atlantic
Authors: Zhai Xiaoming , Wunsch Carl 
Published: December 2012

Abstract
Variations in power input to the ocean using a recent global “reanalysis” extending back to 1871 show a strong trend in the net power input since then, a trend dominated by the Southern Ocean region. This trend is interpreted as a spurious result of the changing observational system. Focusing therefore on the North Atlantic Ocean, where the database is somewhat more secure, it is found that the input power in the subpolar North Atlantic varies significantly in time, showing a strong relationship to the North Atlantic Oscillation (NAO). During positive NAO index years, power input is greater owing to enhanced synoptic activity. Furthermore, cumulative power input to the subpolar North Atlantic is found to correlate significantly with both the eddy kinetic energy there and the Atlantic multidecadal oscillation (AMO), although the physical mechanism at work remains unclear. The assumption that the changing ocean can be neglected relative to the changing atmosphere in calculating the power input is found to be a usefully accurate approximation over the two decades for which changing ocean state estimates are available. Strong dependence on synoptic weather systems of monthly-mean stress distributions implies that past and future climate simulations must account properly for changes in weather systems, not just the large-scale variations.
Automatic Monitoring of the Amount of Deposited Precipitation
Authors: Fišák J. , Chum J. , Vojta J. , Bartůňková K. 
Published: December 2012

AbstractAn automatic device for measurement of the amount (weight) of deposited precipitation developed at the Institute of Atmospheric Physics, Academy of Sciences of the Czech Republic, is described. Examples of measurements of various types of deposited precipitation are presented. The paper also discusses the response of the measuring instrument to falling precipitation and the influence of wind on the measurements. The results of first measurements proved that the instrument is suitable for automatic and continuous monitoring of deposited precipitation.
Surface Wind and Upper-Ocean Variability Associated with the Madden–Julian Oscillation Simulated by the Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS)
Authors: Shinoda Toshiaki , Jensen Tommy G. , Flatau Maria , Chen Sue 
Published: December 2012

AbstractSimulation of surface wind and upper-ocean variability associated with the Madden–Julian oscillation (MJO) by a regional coupled model, the Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS), is evaluated by the comparison with in situ and satellite observations. COAMPS is configured for the tropical Indian Ocean domain with the horizontal resolution of 27 km for the atmospheric component and ⅛° for the ocean component. A high-resolution nested grid (9 km) for the atmospheric component is used for the central Indian Ocean. While observational data are assimilated into the atmospheric component, no data are assimilated into the ocean component. The model was integrated during 1 March–30 April 2009 when an active episode of large-scale convection associated with the MJO passed eastward across the Indian Ocean. During this MJO event, strong surface westerly winds (~8 m s−1) were observed in the central equatorial Indian Ocean, and they generated a strong eastward jet (~1 m s−1) on the equator. COAMPS can realistically simulate these surface wind and upper-ocean variations. The sensitivity of upper-ocean variability to the atmospheric model resolution is examined by the COAMPS experiment without the high-resolution nested grid. The equatorial jet generated in this experiment is about 20% weaker than that in the first experiment, which significantly influences upper-ocean salinity and temperature. The large diurnal warming of SST during the suppressed phase of the MJO is also adequately simulated by the model. Weak winds during this period are mostly responsible for the large SST diurnal variation based on the comparison with the spatial variation of surface forcing fields.