bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Characterization of Extended-Spectrum Cephalosporinase-ProducingSalmonella entericaSerovar Choleraesuis Isolates from Patients in Thailand and Denmark
Authors: Sirichote Pantip , Hasman Henrik , Pulsrikarn Chaiwat , Schønheyder Henrik Carl , Samulioniené Jurgita , Pornruangmong Srirat , Bangtrakulnonth Aroon , Aarestrup Frank M. , Hendriksen Rene S. 
Published: December 2009

ABSTRACTThe objective of this study was to characterize extended-spectrum cephalosporinase (ESC)-producing isolates ofSalmonella entericaserovar Choleraesuis recovered from patients in Thailand and Denmark. Twenty-four blood culture isolates from 22 patients were included in the study, of which 23 isolates were recovered from 21 Thai patients during 2003, 2007, or 2008 and one isolate was recovered from a Danish traveler to Thailand. ESC production was confirmed in 13 out of the 24 isolates by MIC testing. Microarray and plasmid profiling (replicon typing and restriction fragment length polymorphism [RFLP]) were used to characterize the genetic mechanisms of antimicrobial resistance in the 13 ESC-producing isolates. Pulsed-field gel electrophoresis (PFGE) and MIC testing were used to compare the clonality between the 13 ESC-producing isolates and the 11 non-ESC-producing isolates. Based on susceptibility patterns, the ESC-producing isolates were more closely related than non-ESC-producing isolates. Microarray, PCR, plasmid profiling, and replicon typing revealed that the 13 ESC-producing isolates harbored eitherblaCMY-2containingincA/CorblaCTX-M-14containingincFIIA,incFrepB, and an unknown replicon located on plasmids ranging in size from 75 to 200 kb. The RFLP and replicon typing clustered the isolates into four distinct groups. PFGE revealed 16 unique patterns and five clusters; each cluster contained two or three of the 24 isolates. The isolate from the Danish patient was indistinguishable from two Thai clinical isolates by PFGE. This study revealed the emergence of theblaCTX-M-14gene among several clones ofSalmonellaserovar Choleraesuis. Numerous plasmids were identified containing up to two different ESC genes and four distinct replicons. A “travel-associated” spread was confirmed. Overall, a high degree of clonal diversity between isolates resistant and susceptible to cephalosporins was observed. The findings represent a serious threat to public health for the Thai people and tourists.
The Latency-Associated Nuclear Antigen Interacts with MeCP2 and Nucleosomes through Separate Domains
Authors: Matsumura Satoko , Persson Linda M. , Wong LaiYee , Wilson Angus C. 
Published: December 2009

ABSTRACT
Kaposi's sarcoma-associated herpesvirus (KSHV)-infected cells express the latency-associated nuclear antigen (LANA) involved in the regulation of host and viral gene expression and maintenance of the KSHV latent episome. Performance of these diverse functions involves a 7-amino-acid chromatin-binding motif (CBM) situated at the amino terminus of LANA that is capable of binding directly to nucleosomes. LANA interacts with additional chromatin components, including methyl-CpG-binding protein 2 (MeCP2). Here, we show that the carboxy-terminal DNA-binding/dimerization domain of LANA provides the principal interaction with MeCP2 but that this association is modulated by the CBM. Both domains are required for LANA to colocalize with MeCP2 at chromocenters, regions of extensive pericentric heterochromatin that can be imaged by fluorescence microscopy. Within MeCP2, the methyl-CpG-binding domain (MBD) is the primary determinant for chromatin localization and acts together with the adjacent repression domains (the transcription repression domain [TRD] and the corepressor-interacting domain [CRID]) to redirect LANA to chromocenters. MeCP2 facilitates repression by LANA bound to the KSHV terminal repeats, a function that requires the MeCP2 C terminus in addition to the MBD and CRID/TRD. LANA and MeCP2 can also cooperate to stimulate transcription of the human E2F1 promoter, which lacks a LANA DNA-binding sequence, but this function requires both the N and C termini of LANA. The ability of LANA to establish multivalent interactions with histones and chromatin-binding proteins such as MeCP2 would enable LANA to direct regulatory complexes to specific chromosomal sites and thereby achieve stable reprogramming of cellular gene expression in latently infected cells.
Temporal patterns of target catch and sea turtle bycatch in the US Atlantic pelagic longline fishing fleet
Authors: Kot Connie Y. , Boustany Andre M. , Halpin Patrick N. 
Published: December 2009

Sea turtle bycatch in pelagic longline fishing gear is an ongoing threat to the conservation of sea turtle populations. However, these bycatch events do not occur uniformly in space or time. Leatherback ( Dermochelys coriacea ) and loggerhead ( Caretta caretta ) bycatch rates reported in large fishing regions exhibited different degrees of interannual variability. Target catch and sea turtle bycatch in most regions displayed strong periodicity that corresponded to seasons (~365 days) and/or moon phase (~29 days). When trends in catch and bycatch rates were examined by month and moon phase, the significant periods of higher and lower catch and bycatch related to swordfish ( Xiphias gladius ), yellowfin tuna ( Thunnus albacares ), and sea turtle temporal distributions in foraging and spawning/nesting, oceanographic and prey conditions, and foraging behavior. Catch and bycatch rates tended to depend more on a seasonal rather than a lunar time scale, although there is likely an interaction between the two. These findings provide insights to the susceptibility of target catch and bycatch, regional and temporal patterns of fishing effort, and potential guidance for resource management and conservation.
Effect of temperature and current manipulation on smolting in Chinook salmon (Oncorhynchus tshawytscha): the relationship between migratory behaviour and physiological development
Authors: Sykes Gregory E. , Shrimpton J. Mark 
Published: December 2009

We investigated the role of temperature and current on migration pattern and physiological change in Chinook salmon ( Oncorhynchus tshawytscha ) smolts. Chinook parr were implanted with passive integrated transponder tags and placed in circular tanks with directional current. Paired antennas in each tank allowed for the monitoring of movements with or against the current. Two temperature regimes, naturally increasing (warm) and constant (cool), were combined with high current (>0.5 m·s–1) and low current (<0.1 m·s–1) to create four experimental treatments. At 2-week intervals, fish were sampled for gill Na+,K+-ATPase activity and plasma cortisol concentration. Increasing temperature resulted in an earlier peak in movement than colder groups and showed a distinct peak in gill Na+,K+-ATPase activity. Current did not influence physiological parameters associated with smolting and was not found to initiate movement; movement was related to accumulated thermal units (ATU). The presence of a strong, directional current, however, resulted in a period of more defined movement, suggesting a possible influence of current once migration is underway. A combination of either photoperiod or ATU with gill Na+,K+-ATPase was most strongly linked to movement. ATU was also found to be more strongly correlated with the smolting process than daily mean temperature.
Quantifying thermal effects on contemporary growth variability to predict responses to climate change in northern rock sole (Lepidopsetta polyxystra)
Authors: Hurst Thomas P. , Abookire Alisa A. , Knoth Brian 
Published: December 2009

Understanding the causes of contemporary variation in growth rates can offer insights into the likely consequences of climate change for growth and recruitment of coastal marine fishes. We examined the growth dynamics of age-0 northern rock sole ( Lepidopsetta polyxystra ) over four years in three nurseries at Kodiak Island, Alaska, USA. Following the settlement period, fish were sampled monthly (July–October) with a 3 m beam trawl at fixed-position transects. Postsettlement sizes were positively related to temperatures during the spawning and larval periods, suggesting environmental control of spawning or settlement timing. Summer growth on the nursery grounds varied significantly among sites and years (mean size 32.8–63.1 mm in mid-September), with the Holiday Beach site consistently supporting the fastest growth rates. Contrary to expectations of density dependence and thermal regulation, nursery ground growth rates were not significantly correlated with fish density or water temperatures. The minor contribution of thermal variation to growth rates appears related to the conservative growth strategy and low thermal sensitivity of northern rock sole. These results suggest that climate changes influencing spawning time and larval growth may have larger impacts on first-year growth and recruitment of this species than temperature effects on the growth of nursery-resident juveniles.
Observation of the 557.7 nm to 297.2 nm brightness ratio in the auroral spectrum with OSIRIS on Odin
Authors: Gattinger R. L. , Lloyd N. D. , Bourassa A. E. , Degenstein D. A. , McDade I. C. , Llewellyn E. J. 
Published: December 2009

The two optically forbidden lines of atomic oxygen, O(1S–1D) at 557.7 nm and O(1S–3P) at 297.2 nm, serve as important diagnostics in atmospheric, planetary, and cometary studies. Originating from the same upper state, the emission brightness ratio, B(557.7)/B(297.2), must necessarily be constant. The reported emission ratio of these two lines from both theoretical and experimental investigations varies by approximately a factor of two. These two emissions are observed simultaneously in auroral spectra by the OSIRIS spectrograph on the Odin spacecraft, offering another opportunity to perform the ratio measurement. Because of the considerable wavelength separation between these two atomic lines, precise instrumental relative response calibrations can be problematic. To maintain accurate on-orbit spectral calibrations, an atmospheric radiation model with multiple Rayleigh scatter is employed to constantly track instrumental response. An example of a calibrated single bright auroral spectrum over the full OSIRIS wavelength range of 275 to 815 nm, limb tangent altitude 105 km, is presented. Using a number of individual auroral spectra, the observed OI 557.7 nm brightness is plotted versus the observed OI 297.2 nm brightness to both verify the required linear relationship and to experimentally determine the brightness ratio. Spectral contamination by other auroral emission features is removed. From the linear fit, the observed B(557.7)/B(297.2) ratio is 9.3 ± 0.5. By comparison, a ratio of 9.8 ± 1 was recently reported, determined by combining results from a number of observational databases separated in time and in wavelength coverage.
A Bilateral Perspective on the Digital Divide in South Africa
Authors: Blignaut Pieter 
Published: December 2009

AbstractThere is an awareness of the need for “access to technology,” and there are several initiatives by government, non-governmental organizations and other community development programs to fulfill this demand. The digital divide is, however, not only a matter of access; the challenge is also to empower people to become proficient computer users, even those with general literacy backlogs. People should become actively involved in order to stay computer literate. Demographic aspects such as age, gender, education and socio-economic status affect usage patterns and the gratification gained from Internet usage. The long-term solution to solve the problem of the digital divide is to uplift the socio-economic standard of a community.
Using mechanistic Bayesian networks to identify downstream targets of the Sonic Hedgehog pathway
Authors: Shah Abhik , Tenzen Toyoaki , McMahon Andrew P , Woolf Peter J 
Published: December 2009

Abstract

Background
The topology of a biological pathway provides clues as to how a pathway operates, but rationally using this topology information with observed gene expression data remains a challenge.

Results
We introduce a new general-purpose analytic method called Mechanistic Bayesian Networks (MBNs) that allows for the integration of gene expression data and known constraints within a signal or regulatory pathway to predict new downstream pathway targets. The MBN framework is implemented in an open-source Bayesian network learning package, the Python Environment for Bayesian Learning (PEBL). We demonstrate how MBNs can be used by modeling the early steps of the sonic hedgehog pathway using gene expression data from different developmental stages and genetic backgrounds in mouse. Using the MBN approach we are able to automatically identify many of the known downstream targets of the hedgehog pathway such as Gas1 and Gli1, along with a short list of likely targets such as Mig12.

Conclusions
The MBN approach shown here can easily be extended to other pathways and data types to yield a more mechanistic framework for learning genetic regulatory models.
Clonal dissemination of the multi-drug resistant Salmonella enterica serovar Braenderup, but not the serovar Bareilly, of prevalent serogroup C1 Salmonella from Taiwan
Authors: Chiou Chien-Shun , Lin Jui-Ming , Chiu Cheng-Hsun , Chu Chi-Hong , Chen Shu-Wun , Chang Yung-Fu , Weng Bor-Chun , Tsay Jwu-Guh , Chen Chyi-Liang , Liu Chien-Hsing , Chu Chishih 
Published: December 2009

Abstract

Background
Nontyphoidal Salmonella is the main cause of human salmonellosis. In order to study the prevalent serogroups and serovars of clinical isolates in Taiwan, 8931 Salmonellae isolates were collected from 19 medical centers and district hospitals throughout the country from 2004 to 2007. The pulsed-field eletrophoresis types (PFGE) and antibiotic resistance profiles of Salmonella enterica serovars Bareilly (S. Bareilly) and Braenderup (S. Braenderup) were compared, and multi-drug resistance (MDR) plasmids were characterized.

Results
Over 95% of human salmonellosis in Taiwan was caused by five Salmonella serogroups: B, C1, C2-C3, D1, and E1. S. Typhymurium, S. Enteritidis, S. Stanley and S. Newport were the four most prevalent serovars, accounting for about 64% of isolates. While only one or two major serovars from four of the most prevalent serogroups were represented, four predominant serovars were found in serogroup C1 Salmonellae. The prevalence was decreasing for S. Choleraeuis and S. Braenderup, and S. Virchow and increasing for S. Bareilly. S. Braenderup mainly caused gastroenteritis in children; in contrast, S. Bareiley infected children and elderly people. Both serovars differed by Xba I-PFGE patterns. Almost all S. Bareilly isolates were susceptible to antibiotics of interest, while all lacked plasmids and belonged to one clone. Two distinct major clones in S. Braenderup were cluster A, mainly including MDR isolates with large MDR plasmid from North Taiwan, and cluster B, mainly containing susceptible isolates without R plasmid from South Taiwan. In cluster A, there were two types of conjugative R plasmids with sizes ranging from 75 to 130 kb. Type 1 plasmids consisted of replicons F1A/F1B, bla
TEM, IS26, and a class 1 integron with the genes dfrA12-orfF-aadA2-qacE Δ1-sulI. Type 2 plasmids belonged to incompatibility group IncI, contained tnpA-bla
CMY-2-blc-sugE genetic structures and lacked both IS26 and class 1 integrons. Although type 2 plasmids showed higher conjugation capability, type 1 plasmids were the predominant plasmid.

Conclusions
Serogroups B, C1, C2-C3, D1, and E1 of Salmonella caused over 95% of human salmonellosis. Two prevalent serovars within serogroup C1, S. Bareilly and cluster B of S. Braenderup, were clonal and drug-susceptible. However, cluster A of S. Braenderup was MDR and probably derived from susceptible isolates by acquiring one of two distinct conjugative R plasmids.
Quantifying the impact of community quarantine on SARS transmission in Ontario: estimation of secondary case count difference and number needed to quarantine
Authors: Bondy Susan J , Russell Margaret L , Laflèche Julie ML , Rea Elizabeth 
Published: December 2009

AbstractBackgroundCommunity quarantine is controversial, and the decision to use and prepare for it should be informed by specific quantitative evidence of benefit. Case-study reports on 2002-2004 SARS outbreaks have discussed the role of quarantine in the community in transmission. However, this literature has not yielded quantitative estimates of the reduction in secondary cases attributable to quarantine as would be seen in other areas of health policy and cost-effectiveness analysis.MethodsUsing data from the 2003 Ontario, Canada, SARS outbreak, two novel expressions for the impact of quarantine are presented. Secondary Case Count Difference (SCCD) reflects reduction in the average number of transmissions arising from a SARS case in quarantine, relative to not in quarantine, at onset of symptoms. SCCD was estimated using Poisson and negative binomial regression models (with identity link function) comparing the number of secondary cases to each index case for quarantine relative to non-quarantined index cases. The inverse of this statistic is proposed as the number needed to quarantine (NNQ) to prevent one additional secondary transmission.ResultsOur estimated SCCD was 0.133 fewer secondary cases per quarantined versus non-quarantined index case; and a NNQ of 7.5 exposed individuals to be placed in community quarantine to prevent one additional case of transmission in the community. This analysis suggests quarantine can be an effective preventive measure, although these estimates lack statistical precision.ConclusionsRelative to other health policy areas, literature on quarantine tends to lack in quantitative expressions of effectiveness, or agreement on how best to report differences in outcomes attributable to control measure. We hope to further this discussion through presentation of means to calculate and express the impact of population control measures. The study of quarantine effectiveness presents several methodological and statistical challenges. Further research and discussion are needed to understand the costs and benefits of enacting quarantine, and this includes a discussion of how quantitative benefit should be communicated to decision-makers and the public, and evaluated.
Increased hallux angle in children and its association with insufficient length of footwear: A community based cross-sectional study
Authors: Klein Christian , Groll-Knapp Elisabeth , Kundi Michael , Kinz Wieland 
Published: December 2009

AbstractBackgroundWearing shoes of insufficient length during childhood has often been cited as leading to deformities of the foot, particularly to the development of hallux valgus disorders. Until now, these assumptions have not been confirmed through scientific research. This study aims to investigate whether this association can be statistically proven, and if children who wear shoes of insufficient length actually do have a higher risk of a more pronounced lateral deviation of the hallux.Methods858 pre-school children were included in the study. The study sample was stratified by sex, urban/rural areas and Austrian province. The hallux angle and the length of the feet were recorded. The inside length of the children's footwear (indoor shoes worn in pre-school and outdoor shoes) were assessed. Personal data and different anthropometric measurements were taken. The risk of hallux valgus deviation was statistically tested by a stepwise logistic regression analysis and the relative risk (odds ratio) for a hallux angle ≥ 4 degrees was calculated.ResultsExact examinations of the hallux angle could be conducted on a total of 1,579 individual feet. Only 23.9% out of 1,579 feet presented a straight position of the great toe. The others were characterized by lateral deviations (valgus position) at different degrees, equalling 10 degrees or greater in 14.2% of the children's feet.88.8% of 808 children examined wore indoor footwear that was of insufficient length, and 69.4% of 812 children wore outdoor shoes that were too short. A significant relationship was observed between the lengthwise fit of the shoes and the hallux angle: the shorter the shoe, the higher the value of the hallux angle. The relative risk (odds ratio) of a lateral hallux deviation of ≥ 4 degrees in children wearing shoes of insufficient length was significantly increased.ConclusionsThere is a significant relationship between the hallux angle in children and footwear that is too short in length. The fact that the majority of the children examined were wearing shoes of insufficient length makes the issue particularly significant. Our results emphasize the importance of ensuring that children's footwear fits properly.
Solution structure of the Equine Infectious Anemia Virus p9 protein: a rationalization of its different ALIX binding requirements compared to the analogous HIV-p6 protein
Authors: Sharma Alok , Bruns Karsten , Röder René , Henklein Peter , Votteler Jörg , Wray Victor , Schubert Ulrich 
Published: December 2009

Abstract

Background
The equine infection anemia virus (EIAV) p9 Gag protein contains the late (L-) domain required for efficient virus release of nascent virions from the cell membrane of infected cell.

Results
In the present study the p9 protein and N- and C-terminal fragments (residues 1-21 and 22-51, respectively) were chemically synthesized and used for structural analyses. Circular dichroism and 1H-NMR spectroscopy provide the first molecular insight into the secondary structure and folding of this 51-amino acid protein under different solution conditions. Qualitative 1H-chemical shift and NOE data indicate that in a pure aqueous environment p9 favors an unstructured state. In its most structured state under hydrophobic conditions, p9 adopts a stable helical structure within the C-terminus. Quantitative NOE data further revealed that this α-helix extends from Ser-27 to Ser-48, while the N-terminal residues remain unstructured. The structural elements identified for p9 differ substantially from that of the functional homologous HIV-1 p6 protein.

Conclusions
These structural differences are discussed in the context of the different types of L-domains regulating distinct cellular pathways in virus budding. EIAV p9 mediates virus release by recruiting the ALG2-interacting protein X (ALIX) via the YPDL-motif to the site of virus budding, the counterpart of the YPXnL-motif found in p6. However, p6 contains an additional PTAP L-domain that promotes HIV-1 release by binding to the tumor susceptibility gene 101 (Tsg101). The notion that structures found in p9 differ form that of p6 further support the idea that different mechanisms regulate binding of ALIX to primary versus secondary L-domains types.