bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Xanthomonas fragariae, Xanthomonas axonopodis pv. phaseoli, and Xanthomonas fuscans subsp. fuscans with Novel Markers and Using a Dot Blot Platform Coupled with Automatic Data Analysis
Authors: Albuquerque Pedro , Caridade Cristina M. R. , Marcal Andre R. S. , Cruz Joana , Cruz Leonor , Santos Catarina L. , Mendes Marta V. , Tavares Fernando 
Published: June 2011

ABSTRACT

Phytosanitary regulations and the provision of plant health certificates still rely mainly on long and laborious culture-based methods of diagnosis, which are frequently inconclusive. DNA-based methods of detection can circumvent many of the limitations of currently used screening methods, allowing a fast and accurate monitoring of samples. The genus
Xanthomonas
includes 13 phytopathogenic quarantine organisms for which improved methods of diagnosis are needed. In this work, we propose 21 new
Xanthomonas
-specific molecular markers, within loci coding for
Xanthomonas
-specific protein domains, useful for DNA-based methods of identification of xanthomonads. The specificity of these markers was assessed by a dot blot hybridization array using 23 non-
Xanthomonas
species, mostly soil dwelling and/or phytopathogens for the same host plants. In addition, the validation of these markers on 15
Xanthomonas
spp. suggested species-specific hybridization patterns, which allowed discrimination among the different
Xanthomonas
species. Having in mind that DNA-based methods of diagnosis are particularly hampered for unsequenced species, namely,
Xanthomonas fragariae
,
Xanthomonas axonopodis
pv. phaseoli, and
Xanthomonas fuscans
subsp.
fuscans
, for which comparative genomics tools to search for DNA signatures are not yet applicable, emphasis was given to the selection of informative markers able to identify
X. fragariae
,
X. axonopodis
pv. phaseoli, and
X. fuscans
subsp.
fuscans
strains. In order to avoid inconsistencies due to operator-dependent interpretation of dot blot data, an image-processing algorithm was developed to analyze automatically the dot blot patterns. Ultimately, the proposed markers and the dot blot platform, coupled with automatic data analyses, have the potential to foster a thorough monitoring of phytopathogenic xanthomonads.
Cofermentation of Cellobiose and Galactose by an Engineered Saccharomyces cerevisiae Strain
Authors: Ha Suk-Jin , Wei Qiaosi , Kim Soo Rin , Galazka Jonathan M. , Cate Jamie , Jin Yong-Su 
Published: June 2011

ABSTRACT

We demonstrate improved ethanol yield and productivity through cofermentation of cellobiose and galactose by an engineered
Saccharomyces cerevisiae
strain expressing genes coding for cellodextrin transporter (
cdt-1
) and intracellular β-glucosidase (
gh1
-
1
) from
Neurospora crassa
. Simultaneous fermentation of cellobiose and galactose can be applied to producing biofuels from hydrolysates of marine plant biomass.
Genome Sequences of the Biotechnologically Important Bacillus megaterium Strains QM B1551 and DSM319
Authors: Eppinger Mark , Bunk Boyke , Johns Mitrick A. , Edirisinghe Janaka N. , Kutumbaka Kirthi K. , Koenig Sara S. K. , Huot Creasy Heather , Rosovitz M. J. , Riley David R. , Daugherty Sean , Martin Madeleine , Elbourne Liam D. H. , Paulsen Ian , Biedendieck Rebekka , Braun Christopher , Grayburn Scott , Dhingra Sourabh , Lukyanchuk Vitaliy , Ball Barbara , Ul-Qamar Riaz , Seibel Jürgen , Bremer Erhard , Jahn Dieter , Ravel Jacques , Vary Patricia S. 
Published: June 2011

ABSTRACT

Bacillus megaterium
is deep-rooted in the
Bacillus
phylogeny, making it an evolutionarily key species and of particular importance in understanding genome evolution, dynamics, and plasticity in the bacilli.
B. megaterium
is a commercially available, nonpathogenic host for the biotechnological production of several substances, including vitamin B
12
, penicillin acylase, and amylases. Here, we report the analysis of the first complete genome sequences of two important
B. megaterium
strains, the plasmidless strain DSM319 and QM B1551, which harbors seven indigenous plasmids. The 5.1-Mbp chromosome carries approximately 5,300 genes, while QM B1551 plasmids represent a combined 417 kb and 523 genes, one of the largest plasmid arrays sequenced in a single bacterial strain. We have documented extensive gene transfer between the plasmids and the chromosome. Each strain carries roughly 300 strain-specific chromosomal genes that account for differences in their experimentally confirmed phenotypes.
B. megaterium
is able to synthesize vitamin B
12
through an oxygen-independent adenosylcobalamin pathway, which together with other key energetic and metabolic pathways has now been fully reconstructed. Other novel genes include a second
ftsZ
gene, which may be responsible for the large cell size of members of this species, as well as genes for gas vesicles, a second β-galactosidase gene, and most but not all of the genes needed for genetic competence. Comprehensive analyses of the global
Bacillus
gene pool showed that only an asymmetric region around the origin of replication was syntenic across the genus. This appears to be a characteristic feature of the
Bacillus
spp. genome architecture and may be key to their sporulating lifestyle.
Bacteriophage Infection in Rod-Shaped Gram-Positive Bacteria: Evidence for a Preferential Polar Route for Phage SPP1 Entry in Bacillus subtilis
Authors: Jakutytė Lina , Baptista Catarina , São-José Carlos , Daugelavičius Rimantas , Carballido-López Rut , Tavares Paulo 
Published: June 2011

ABSTRACT

Entry into the host bacterial cell is one of the least understood steps in the life cycle of bacteriophages. The different envelopes of Gram-negative and Gram-positive bacteria, with a fluid outer membrane and exposing a thick peptidoglycan wall to the environment respectively, impose distinct challenges for bacteriophage binding and (re)distribution on the bacterial surface. Here, infection of the Gram-positive rod-shaped bacterium
Bacillus subtilis
by bacteriophage SPP1 was monitored in space and time. We found that SPP1 reversible adsorption occurs preferentially at the cell poles. This initial binding facilitates irreversible adsorption to the SPP1 phage receptor protein YueB, which is encoded by a putative type VII secretion system gene cluster. YueB was found to concentrate at the cell poles and to display a punctate peripheral distribution along the sidewalls of
B. subtilis
cells. The kinetics of SPP1 DNA entry and replication were visualized during infection. Most of the infecting phages DNA entered and initiated replication near the cell poles. Altogether, our results reveal that the preferentially polar topology of SPP1 receptors on the surface of the host cell determines the site of phage DNA entry and subsequent replication, which occurs in discrete foci.
Complete Genome Sequence of the Crohn's Disease-Associated Adherent-Invasive Escherichia coliStrain HM605
Authors: Clarke David J. , Chaudhuri Roy R. , Martin Helen M. , Campbell Barry J. , Rhodes Jonathan M. , Constantinidou Chrystala , Pallen Mark J. , Loman Nicholas J. , Cunningham Adam F. , Browning Douglas F. , Henderson Ian R. 
Published: June 2011

ABSTRACT

Adherent-invasive
Escherichia coli
strains are increasingly being associated with intestinal pathologies. Here we present the genome sequence of
E. coli
HM605, a strain isolated from colonic biopsy specimens of a patient with Crohn's disease.
Complete Genome Sequences of Four Mammalian Isolates of Chlamydophila psittaci
Authors: Schöfl Gerhard , Voigt Anja , Litsche Katrin , Sachse Konrad , Saluz Hans Peter 
Published: June 2011

ABSTRACT

Chlamydia psittaci
is an obligate intracellular zoonotic pathogen primarily of birds, but it is also known to infect a variety of mammalian species. Here we report the genomes of four strains isolated from sheep (C19/98), pigs (01DC11), cattle (02DC15), and humans (08DC60).
Genome Sequence of Leuconostoc pseudomesenteroides KCTC 3652
Authors: Kim Dong-Wook , Choi Sang-Haeng , Kang Aram , Nam Seong-Hyeuk , Kim Ryong Nam , Kim Aeri , Kim Dae-Soo , Park Hong-Seog 
Published: June 2011

ABSTRACT

We announce the genome sequence of one of the most prevalent lactic acid bacteria present during the manufacturing process of cane juice, the type strain
Leuconostoc pseudomesenteroides
KCTC 3652 (3,244,985 bp, with a G+C content of 38.3%), which consists of 1,160 large contigs (>100 bp in size). All of the contigs were assembled by the Newbler Assembler 2.3 software program (454 Life Sciences).
Emergency department coding of bicycle and pedestrian injuries during the transition from ICD-9 to ICD-10
Authors: Karkhaneh M , Hagel B E , Couperthwaite A , Saunders L D , Voaklander D C , Rowe B H 
Published: June 2011

BackgroundThe international classification of diseases version 10 (ICD-10) uses alphanumeric expanded codes and external cause of injury codes (E-codes).ObjectiveTo examine the reliability and validity of emergency department (ED) coders in applying E-codes in ICD-9 and -10.MethodsBicycle and pedestrian injuries were identified from the ED information system from one period before and two periods after transition from ICD-9 to -10 coding. Overall, 180 randomly selected bicycle and pedestrian injury charts were reviewed as the reference standard (RS). Original E-codes assigned by ED coders (ICD-9 in 2001 and ICD-10 in 2004 and 2007) were compared with charts (validity) and also to ICD-9 and -10 codes assigned from RS chart review, to each case by an independent (IND) coder (reliability). Sensitivity, specificity, simple, and chance-corrected agreements (κ statistics) were calculated.ResultsSensitivity of E-coding bicycle injuries by the IND coder in comparison with the RS ranged from 95.1% (95% CI 86.3 to 99.0) to 100% (95% CI 94.0 to 100.0) for both ICD-9 and -10. Sensitivity of ED coders in E-coding bicycle injuries ranged from 90.2% (95% CI 79.8 to 96.3) to 96.7% (95% CI 88.5 to 99.6). The sensitivity estimates for the IND coder ranged from 25.0% (95% CI 14.7 to 37.9) to 45.0% (95% CI 32.1 to 58.4) for pedestrian injuries for both ICD-9 and -10.ConclusionBicycle injuries are coded in a reliable and valid manner; however, pedestrian injuries are often miscoded as falls. These results have important implications for injury surveillance research.
The Decline in Stroke Mortality
Authors: Kunst Anton E. , Amiri Masoud , Janssen Fanny 
Published: June 2011

Background and Purpose—
This article aims to make projections of future trends in stroke mortality in the Year 2030 based on recent trends in stroke mortality in 7 Western European countries.

Methods—
Mortality data were obtained from national cause of death registries. Annual rates of decline in stroke mortality of 1980 to 2005 were determined for men and women in the United Kingdom, France, the Netherlands, and 4 Nordic countries on the basis of regression analysis. Estimated rates of decline were extrapolated until 2030. Cause-elimination life tables were used to determine the effect of stroke in 2030 in terms of potential gain in life expectancy. The absolute numbers of stroke deaths in 2030 were estimated using national population projections of Eurostat.

Results—
In all countries, stroke mortality rates declined incessantly until 2005 among both men and women. If these trends were to continue, age-adjusted mortality rates would decline by approximately half between 2005 and 2030 with larger declines in France (approximately two thirds) and smaller declines in the Netherlands, Denmark, and Sweden (approximately one fourth). Similar rates of decline would be observed in terms of potential gain in life expectancy. Because of population aging, the absolute number of stroke deaths would decline slowly in the United Kingdom and France and stabilize or even increase in other countries.

Conclusions—
In the near future, stroke may lose much of its effects on life expectancy but remain a frequent cause of death among elderly populations. The prevention of stroke-related disability instead of mortality may become increasingly more important.
Comparison of Plasmin With Recombinant Tissue-Type Plasminogen Activator in Lysis of Cerebral Thromboemboli Retrieved From Patients With Acute Ischemic Stroke
Authors: Marder Victor J. , Blinc Ales , Gruber Theresa , Tratar Gregor , Sabovic Miso , Starkman Sidney , Jahan Reza , Duckwiler Gary , Vinuela Fernando , Tateshima Satoshi , Liebeskind David , Ovbiagele Bruce , Ali Letisha , Kim Doojin , Gonzalez Nestor , Vespa Paul M. , Saver Jeffrey L. 
Published: June 2011

Background and Purpose—
Plasmin is a direct-acting thrombolytic with a better safety profile than recombinant tissue-type plasminogen activator (rtPA) in animal models. With the application of retrieval devices for managing acute ischemic stroke, extracted thromboemboli are available for ex vivo examination. We ask whether such thrombi are amenable to plasmin thrombolysis and whether such activity is different with rtPA.

Methods—

Thromboembolic fragments (total 29) were retrieved from the intracranial carotid artery system of 15 patients with acute ischemic stroke and randomly assigned to ex vivo thrombolysis with plasmin or rtPA. After an initial 2-hour exposure, residual material was exposed to the other agent for an additional 2 hours. Thrombolysis was quantified by change in thrombus area and released
d
-dimer.

Results—

Plasmin induced significant ex vivo thrombolysis of cerebral arterial thromboemboli, decreasing area by 45.9%±29.4% and 69.2%±52.5% and inducing median
d
-dimer release of 108 180 μg/L (range, 16 780 to 668 050 μg/L) and 16 905 μg/L (range, 240 to 403 085 μg/L) during the first and second 2-hour incubation periods, respectively. These changes were not different from those obtained with rtPA, which decreased area by 34.7%±57.8% (
P
=0.63) and by 68.4%±26.9% (
P
=0.97) and induced median
d
-dimer release of 151 990 μg/L (range, 9870 to 338 350 μg/L;
P
=0.51) and 34 520 μg/L (range 3794 to 325 400 μg/L;
P
=0.19) during the first and second 2-hour incubations.

Conclusions—
Retrieved human cerebral thromboemboli were amenable to ex vivo lysis by plasmin, the rate and degree of which was not different than that achieved with rtPA.
Limited Ability to Activate Protein C Confers Left Atrial Endocardium A Thrombogenic Phenotype
Authors: Cerveró Jorge , Montes Ramón , España Francisco , Esmon Charles T. , Hermida José 
Published: June 2011

Background and Purpose—
Atrial fibrillation is the most important risk factor for cardioembolic stroke. Thrombi form in the left atrial appendage rather than in the right. The causes of this different thrombogenicity are not well-understood. The goal herein was to compare the activation of the anticoagulant protein C and the thrombomodulin and endothelial protein C receptor/activated protein C receptor expression on the endocardium between right and left atria.

Methods—

We harvested the atria of 6 monkeys (
Macaca fascicularis
) and quantified their ability to activate protein C ex vivo and we measured the thrombomodulin and endothelial protein C receptor expression by immunofluorescence.

Results—

We found the ability to activate protein C decreased by half (
P
=0.028) and there was lower expression of thrombomodulin in the left atrial endocardium than the right (52.5±19.9 and 72.1±18.8 arbitrary intensity units, mean±standard deviation;
P
=0.028). No differences were detected in endothelial protein C receptor expression.

Conclusions—
Impaired protein C activation on the left atrial endocardium attributable to low thrombomodulin expression may explain its higher thrombogenicity and play a role in cardioembolic stroke.
The Validity and Interrater Reliability of Video-Based Posture Observation During Asymmetric Lifting Tasks
Authors: Xu Xu , Chang Chien-chi , Faber Gert S. , Kingma Idsart , Dennerlein Jack T. 
Published: June 2011

Objective: The objective was to evaluate the validity and interrater reliability of a video-based posture observation method for the major body segment angles during asymmetric lifting tasks. Background: Observational methods have been widely used as an awkward-posture assessment tool for ergonomics studies. Previous research proposed a video-based posture observation method with estimation of major segment angles during lifting tasks. However, it was limited to symmetric lifting tasks. The current study extended this method to asymmetric lifting tasks and investigated the validity and the interrater reliability. Method: Various asymmetric lifting tasks were performed in a laboratory while a side-view video camera recorded the lift, and the body segment angles were measured directly by a motion tracking system. For this study, 10 raters estimated seven major segment angles using a customized program that played back the video recording, thus allowing users to enter segment angles. The validity of estimated segment angles was evaluated in relation to measured segment angles. Interrater reliability was assessed among the raters. Results: For all the segment angles except trunk lateral bending, the estimated segment angles were strongly correlated with the measured segment angles (r > .8), and the intraclass correlation coefficient was greater than 0.75. Conclusion: The proposed observational method was able to provide a robust estimation of major segment angles for asymmetric lifting tasks based on side-view video clips. The estimated segment angles were consistent among raters. Application: This method can be used for assessing posture during asymmetric lifting tasks. It also supports developing a video-based rapid joint loading estimation method.
Are Meniscus and Cartilage Injuries Related to Time to Anterior Cruciate Ligament Reconstruction?
Authors: Chhadia Ankur M. , Inacio Maria C. S. , Maletis Gregory B. , Csintalan Rick P. , Davis Brent R. , Funahashi Tadashi T. 
Published: June 2011

Background: Functional instability after anterior cruciate ligament injury can be successfully treated with ligament reconstruction. However, the associated meniscus and cartilage lesions often cannot be repaired and may have long-term detrimental effects on knee function. Purpose: The authors used the large database within the Kaiser Permanente Anterior Cruciate Ligament Reconstruction Registry to evaluate time to surgery, age, and gender as risk factors for meniscus and cartilage injury and associations with meniscus repair rates in patients. Study Design: Cross-sectional study; Level of evidence, 3. Methods: A retrospective review of the Kaiser Permanente Anterior Cruciate Ligament Reconstruction Registry was performed. The associations between time to surgery, age, and gender with meniscus and cartilage lesions and meniscus repair were analyzed using binary logistic regression modeling to calculate odds ratios (ORs) while adjusting for potential confounding variables. Results: A total of 1252 patients met the inclusion criteria. The risk of medial meniscus injury increased only with time to surgery (6–12 months: OR = 1.81, 95% confidence internal [CI] 1.29-2.54, P = .001; and >12 months: OR = 2.19, 95% CI 1.58-3.02, P < .001). The risk of lateral meniscus injury decreased only with female gender (OR = 0.65, 95% CI 0.51-0.83, P = .001). The risk of cartilage injury increased with age (OR = 1.05 per year, 95% CI 1.04-1.07, P < .001) and time to surgery >12 months (OR = 1.57, 95% CI 1.12-2.20, P = .009), but decreased with female gender (OR = 0.71, 95% CI 0.54-0.92, P = .009). Medial meniscus repairs relative to medial meniscus injury decreased with increasing time to surgery (3-6 months: OR = 0.61, 95% CI 0.37-1.00, P = .050; and >12 months: OR = 0.41, 95% CI 0.25-0.67, P < .001) and increasing age (OR = 0.96 per year, 95% CI 0.94-0.98, P < .001). Conclusion: Increased risk of medial meniscus injury and decreased repair rate were strongly associated with increasing time to surgery. Increased risk of cartilage injury was associated with increasing age, increasing time to surgery, and male gender.
Chronic Tears of the Reflected Head of the Rectus Femoris
Authors: Wittstein Jocelyn , Klein Steven , Garrett William E. 
Published: June 2011

Background: While the majority of quadriceps muscle strains can be managed nonoperatively, rare cases remain symptomatic despite nonoperative treatment. Purpose: The purpose of this study is to report on results of surgical treatment of a limited number of cases of persistently symptomatic tears of the reflected head of the rectus femoris. Study Design: Case series; Level of evidence, 4. Methods: The records of 5 patients with chronic tears of the rectus femoris treated with excision of the reflected head were reviewed. A telephone interview regarding return to sport and current limitations was completed if patients were available for further follow-up. Results: A review of 5 cases of surgical treatment of chronic tears of the reflected head of the rectus was completed. Patients included 1 woman and 4 men with an average age of 21 years (range, 18-24 years). Three patients played football (2 kickers) and 2 played soccer at a collegiate level. All 5 reported a significant decrease in pain during sport and activities of daily living and were able to return to collegiate athletics. Two patients had a late recurrence of pain with kicking that resolved with nonoperative treatment, 1 had residual thigh pain with intense play, 1 had no pain but noted decreased kicking accuracy, and 1 patient returned to play without symptoms. Conclusion: Strain injuries to the reflected head of the rectus femoris can benefit from delayed excision in rare cases that fail nonoperative management. High-level kicking athletes are likely to experience significant reduction in pain, but may have some residual or recurrent symptoms that limit competitive level of play postoperatively.
Attentional status of faces for people with autism spectrum disorder
Authors: Remington Anna , Campbell Ruth , Swettenham John 
Published: June 2011

In recent years there has been a growing interest in the role of attention in the processing of social stimuli in individuals with autism spectrum disorders (ASD). Research has demonstrated that, for typical adults, faces have a special status in attention and are processed in an automatic and mandatory fashion even when participants attempt to ignore them. Under conditions of high load in a selective attention task, when irrelevant stimuli are usually not processed, typical adults continue to process distractor faces. Although there is evidence of a lack of attentional bias towards faces in ASD, there has been no direct test of whether faces are processed automatically using the distractor-face paradigm. In the present study 16 typical adults and 16 adults with ASD performed selective attention tasks with face and musical instrument distractors. The results indicated that even when the load of the central task was high, typical adults continued to be distracted by irrelevant face stimuli, whereas individuals with ASD were able to ignore them. In the equivalent non-social task, distractors had no effect at high load for either group. The results suggest that faces are processed in an automatic and mandatory fashion in typical adults but not in adults with ASD.