bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Genome of
Heliobacterium modesticaldum
, a Phototrophic Representative of the
Firmicutes
Containing the Simplest Photosynthetic Apparatus
Authors: Sattley W. Matthew , Madigan Michael T. , Swingley Wesley D. , Cheung Patricia C. , Clocksin Kate M. , Conrad Amber L. , Dejesa Liza C. , Honchak Barbara M. , Jung Deborah O. , Karbach Lauren E. , Kurdoglu Ahmet , Lahiri Surobhi , Mastrian Stephen D. , Page Lawrence E. , Taylor Heather L. , Wang Zi T. , Raymond Jason , Chen Min , Blankenship Robert E. , Touchman Jeffrey W. 
Published: April 2008

ABSTRACT

Despite the fact that heliobacteria are the only phototrophic representatives of the bacterial phylum
Firmicutes
, genomic analyses of these organisms have yet to be reported. Here we describe the complete sequence and analysis of the genome of
Heliobacterium modesticaldum
, a thermophilic species belonging to this unique group of phototrophs. The genome is a single 3.1-Mb circular chromosome containing 3,138 open reading frames. As suspected from physiological studies of heliobacteria that have failed to show photoautotrophic growth, genes encoding enzymes for known autotrophic pathways in other phototrophic organisms, including ribulose bisphosphate carboxylase (Calvin cycle), citrate lyase (reverse citric acid cycle), and malyl coenzyme A lyase (3-hydroxypropionate pathway), are not present in the
H. modesticaldum
genome. Thus, heliobacteria appear to be the only known anaerobic anoxygenic phototrophs that are not capable of autotrophy. Although for some cellular activities, such as nitrogen fixation, there is a full complement of genes in
H. modesticaldum
, other processes, including carbon metabolism and endosporulation, are more genetically streamlined than they are in most other low-G+C gram-positive bacteria. Moreover, several genes encoding photosynthetic functions in phototrophic purple bacteria are not present in the heliobacteria. In contrast to the nutritional flexibility of many anoxygenic phototrophs, the complete genome sequence of
H. modesticaldum
reveals an organism with a notable degree of metabolic specialization and genomic reduction.
Chromosomal Toxin-Antitoxin Systems May Act as Antiaddiction Modules
Authors: Saavedra De Bast Manuel , Mine Natacha , Van Melderen Laurence 
Published: April 2008

ABSTRACT

Toxin-antitoxin (TA) systems are widespread among bacterial chromosomes and mobile genetic elements. Although in plasmids TA systems have a clear role in their vertical inheritance by selectively killing plasmid-free daughter cells (postsegregational killing or addiction phenomenon), the physiological role of chromosomally encoded ones remains under debate. The assumption that chromosomally encoded TA systems are part of stress response networks and/or programmed cell death machinery has been called into question recently by the observation that none of the five canonical chromosomally encoded TA systems in the
Escherichia coli
chromosome seem to confer any selective advantage under stressful conditions (V. Tsilibaris, G. Maenhaut-Michel, N. Mine, and L. Van Melderen, J. Bacteriol. 189:6101-6108, 2007). Their prevalence in bacterial chromosomes indicates that they might have been acquired through horizontal gene transfer. Once integrated in chromosomes, they might in turn interfere with their homologues encoded by mobile genetic elements. In this work, we show that the chromosomally encoded
Erwinia chrysanthemi ccd
(
c
ontrol of
c
ell
d
eath) (

ccd
Ech

) system indeed protects the cell against postsegregational killing mediated by its F-plasmid
ccd
(
ccd
F
) homologue. Moreover, competition experiments have shown that this system confers a fitness advantage under postsegregational conditions mediated by the
ccd
F
system. We propose that

ccd
Ech

acts as an antiaddiction module and, more generally, that the integration of TA systems in bacterial chromosomes could drive the evolution of plasmid-encoded ones and select toxins that are no longer recognized by the antiaddiction module.
Glucomannan-Mediated Attachment ofRhizobium leguminosarumto Pea Root Hairs Is Required for Competitive Nodule Infection
Authors: Williams Alan , Wilkinson Adam , Krehenbrink Martin , Russo Daniela M. , Zorreguieta Angeles , Downie J. Allan 
Published: April 2008

ABSTRACTTheRhizobium leguminosarumbiovar viciae genome contains several genes predicted to determine surface polysaccharides. Mutants predicted to affect the initial steps of polysaccharide synthesis were identified and characterized. In addition to the known cellulose (cel) and acidic exopolysaccharide (EPS) (pss) genes, we mutated three other loci; one of these loci (gmsA) determines glucomannan synthesis and one (gelA) determines a gel-forming polysaccharide, but the role of the other locus (anexoY-like gene) was not identified. Mutants were tested for attachment and biofilm formation in vitro and on root hairs; the mutant lacking the EPS was defective for both of these characteristics, but mutation ofgelAor theexoY-like gene had no effect on either type of attachment. The cellulose (celA) mutant attached and formed normal biofilms in vitro, but it did not form a biofilm on root hairs, although attachment did occur. The cellulose-dependent biofilm on root hairs appears not to be critical for nodulation, because thecelAmutant competed with the wild-type for nodule infection. The glucomannan (gmsA) mutant attached and formed normal biofilms in vitro, but it was defective for attachment and biofilm formation on root hairs. Although this mutant formed nodules on peas, it was very strongly outcompeted by the wild type in mixed inoculations, showing that glucomannan is critical for competitive nodulation. The polysaccharide synthesis genes aroundgmsAare highly conserved among other rhizobia and agrobacteria but are absent from closely related bacteria (such asBrucellaspp.) that are not normally plant associated, suggesting that these genes may play a wide role in bacterium-plant interactions.
Variants within theCOL5A1gene are associated with Achilles tendinopathy in two populations
Authors: September A V , Cook J , Handley C J , van der Merwe L , Schwellnus M P , Collins M 
Published: April 2008

Objectives:ACOL5A1gene variant was shown to be associated with chronic Achilles tendinopathy in a South African population. The aim of this case–control genetic association study was to investigate theBstUI andDpnII restriction fragment length polymorphisms (RFLP) in a second population from Australia and to identify a predisposing haplotype for Achilles tendinopathy in both populations.Methods:85 Australian and 93 South African patients with tendinopathy, as well as 210 Australian and 132 white South African control subjects were genotyped for theBstUI (rs12722) andDpnII (rs13946) RFLP, as well as markersrs10858286,rs3196378,rs11103544,rs4504708 andrs3128575.Results:TheBstUI RFLP (p<0.001) and markerrs3196378 (p = 0.016) were associated with chronic Achilles tendinopathy in Australian subjects. Individuals within both populations with a CC genotype for theBstUI RFLP had a significantly decreased risk of developing tendinopathy versus any other genotypes (Australian odds ratio 0.42, 95% CI 0.20 to 0.86, p = 0.017). The TC inferred haplotype (rs12722,rs3196378) was found to be overrepresented (global p = 0.008) in the South African tendinopathy group compared with all other haplotypes.Conclusion:TheBstUI RFLP is associated with chronic Achilles tendinopathy in a second population and a region within theCOL5A13′ untranslated region may predispose individuals to an increased risk of developing chronic Achilles tendinopathy.
Evaluation of strength and set behavior of mortar containing shotcrete set accelerators
Authors: Kim Jincheol , Ryu Jonghyun , Hooton R. D. 
Published: April 2008

The influence of rapid-set accelerating admixtures on the setting behavior and early-age strength of a cement matrix was investigated to evaluate the appropriateness of the specification and test methods for shotcrete set accelerators. The results verified two different rapid setting behaviors according to the types of accelerator. The aluminate-base and the calcium aluminate cement-base accelerators facilitate hydration by formation of a calcium aluminate solid solution, whereas the alkali-free set accelerating agents present rapid setting time by the formation of ettringite. It was also found that the Vicat test was more desirable than the Gillmore test as the standard for setting time evaluation. Additionally, the cement mortar mixed with the aluminate-base and the calcium aluminate cement-base accelerators exhibited very fast development of early-age compressive strength. However, most of the set accelerators, except for alkali-free accelerators, failed to satisfy the specification because of greater than 40% compressive strength loss at 28 d.
What makes the competitive contribution of ERP strategic
Authors: Ragowsky Arik , Gefen David 
Published: April 2008

In 1984, McFarlan suggested in his HBR article that a company might be able to use Information Technology (IT) to achieve strategic advantage in the marketplace. Although widely cited and recently elaborated on (Nolan & McFarlan, 2005), there is little empirical evidence to support it in the specific context of ERP (Enterprise Resource Planning) systems where IT is especially posed to have such a major impact. The objective of this study is to fill this gap, applying a contingency approach. The results, supporting Nolan and McFarlan (2005), show that while some ERP systems provide strategic advantage to some companies, ERP systems may not necessarily provide similar advantage to other companies due to the specific operational characteristics of each company and the way the ERP is used.
The data collected from senior managers in different manufacturing companies who were closely involved in the implementation of ERP systems in their respective companies, show that McFarlan's (1984) and Nolan and McFarlan's (2005) propositions about IT in general apply also to ERP. Both competitive strategies enabled by the ERP and specific operational characteristics can place the organization in a strategic position, and when this happens, the IT unit is more likely to be under the authority of senior management. These findings seem to contradict Carr (2003) who clamed that IT cannot provide a company with competitive advantage.
Helicobacter pylori Eradication Prevents Progression of Gastric Cancer in Hypergastrinemic INS-GAS Mice
Authors: Lee Chung-Wei , Rickman Barry , Rogers Arlin B. , Ge Zhongming , Wang Timothy C. , Fox James G. 
Published: April 2008

Abstract
Helicobacter pylori infection results in chronic gastritis, which may progress to gastric cancer. In this study, we investigated the efficacy of H. pylori eradication in preventing the progression of gastritis to gastric cancer in H. pylori–infected transgenic INS-GAS mice. H. pylori infection induced severe dysplasia and gastric cancer classified as high-grade and low-grade gastrointestinal intraepithelial neoplasia (GIN) in INS-GAS mice at 28 weeks postinfection (WPI). H. pylori eradication therapy using omeprazole, metronidazole, and clarithromycin was administered p.o. at 8, 12, or 22 WPI. Compared with untreated infected mice, H. pylori eradication at 8, 12, and 22 WPI significantly reduced the severity of dysplasia (P &lt; 0.01). Moreover, H. pylori eradication at 8 WPI completely prevented the development of GIN (P &lt; 0.001). Although not as effective as early antimicrobial treatment, prevention of progression to high-grade GIN was achieved by H. pylori eradication at 12 and 22 WPI (P &lt; 0.05). Consistent with reduced gastric pathology, H. pylori eradication at all time points significantly down-regulated gastric Interferon-γ, tumor necrosis factor-α, inducible nitric oxide synthase, and Reg 1 mRNA levels (P &lt; 0.05) and reduced epithelial proliferation in the corpus (P &lt; 0.01) compared with untreated infected mice. We concluded that H. pylori eradication prevented gastric cancer to the greatest extent when antibiotics are given at an early point of infection, but that eradication therapy given at a later time point delayed the development of severe dysplastic lesions. [Cancer Res 2008;68(9):3540–8]
Democracy and Ontology
Authors: Flynn Bernard 
Published: April 2008

AbstractThis paper elaborates a conception of the relationship between Philosophy and the Political which would not be one of exteriority but one of an intertwining between them. An analogy with Rémi Brague, who presents the conditions whereby the concept of 'the world' became a thematic object of reflection (The Wisdom of the World), is proposed to show the emergence of the concept of 'the political.' Following Lefort's philosophy, we trace the emergence of modern democracy with that of the political by claiming that there is an ontological dimension of the political. As the concept of the world could not emerge within a conception of the universe that united man and world in an organic whole, so too the concept of the political cannot emerge when the discourse on power is determined theologically (premodern societies). It is argued that there is an ontological dimension to the revolutions that introduced our political modernity. Modern revolutions are not simply a change in a form of governance; they effect a mutation in the symbolic order of a society by which the political, as such, can become visible. The indetermination of modern democracy corresponds to "the disappearance of the markers of certainty" that characterize the modern experience of the world, an experience that reveals a transformed ontological dimension. This dimension of uncertainty, the experience of the place of power as an "empty place," is contrasted with the totalitarian impulse to fill this empty place with a determinate image, e.g., the Party, the Fürher.
Assessment of Cloud Cover Characteristics in Satellite Datasets and Reanalysis Products for Greenland
Authors: Griggs J. A. , Bamber J. L. 
Published: April 2008

Abstract
Clouds have an important controlling influence on the radiation balance, and hence surface melting, over the Greenland ice sheet and need to be classified to derive reliable albedo estimates from visible imagery. Little is known, however, about the true cloud cover characteristics for the largest island on Earth, Greenland. Here, an attempt is made to address this knowledge gap by examining cloud characteristics, as determined by three complementary satellites sensors: the Advanced Very High Resolution Radiometer (AVHRR), the Along Track Scanning Radiometer-2 (ATSR-2), and the Moderate Resolution Imaging Spectroradiometer (MODIS). The first provides a multidecadal time series of clouds, albedo, and surface temperature, and is available, in the form of the extended AVHRR Polar Pathfinder dataset (APP-x), as a homogeneous, consistent dataset from 1982 until 2004. APP-x data, however, are also the most challenging to cloud classify over snow-covered terrain, due to the limited spectral capabilities of the instrument. ATSR-2 permits identification and classification using stereophotogrammetric techniques and MODIS has enhanced spectral sampling in the visible and thermal infrared but over more limited time periods. The spatial cloud fractions from the three sensors are compared and show good agreement in terms of both magnitude and spatial pattern. The cloud fractions, and inferred patterns of accumulation, are then assessed from three commonly used reanalysis datasets: NCEP–NCAR, the second NCEP–Department of Energy (DOE) Atmospheric Model Intercomparison Project (AMIP-II), and the 40-yr ECMWF Re-Analysis (ERA-40). Poor agreement between the reanalysis datasets is found. NCEP–DOE AMIP-II produces a cloud fraction similar to that observed by the satellites. NCEP–NCAR and ERA-40, however, bear little similarity to the cloud fractions derived from the satellite observations. This suggests that they may produce poor accumulation estimates over the ice sheet and poor estimates of radiation balance. Using these reanalysis data to force a mass balance model of the ice sheet, without appropriate downscaling and correction for the substantial biases present, may, therefore, produce substantial errors in surface melt rate estimates.
Prolonged Dry Episodes over the Conterminous United States: New Tendencies Emerging during the Last 40 Years
Authors: Groisman Pavel Ya , Knight Richard W. 
Published: April 2008

AbstractA disproportionate increase in precipitation coming from intense rain events, in the situation of general warming (thus, an extension of the vegetation period with intensive transpiration), and an insignificant change in total precipitation could lead to an increase in the frequency of a potentially serious type of extreme events: prolonged periods without precipitation (even when the mean seasonal rainfall totals increase). This paper investigates whether this development is already occurring during the past several decades over the conterminous United States, for the same period when changes in frequency of intense precipitation events are being observed. Lengthy strings of “dry” days without sizeable (&gt;1.0 mm) precipitation were assessed only during the warm season (defined as a period when mean daily temperature is above the 5°C threshold) when water is intensively used for transpiration and prolonged periods without sizable rainfall represent a hazard for terrestrial ecosystem’s health and agriculture. During the past four decades, the mean duration of prolonged dry episodes (1 month or longer in the eastern United States and 2 months or longer in the southwestern United States) has significantly increased. As a consequence the return period of 1-month-long dry episodes over the eastern United States has reduced more than twofold from 15 to 6–7 yr. The longer average duration of dry episodes has occurred during a relatively wet period across the country but is not observed over the northwestern United States.
Interannual Atmospheric Variability Affects Continental Ice Sheet Simulations on Millennial Time Scales
Authors: Pritchard Michael S. , Bush Andrew B. G. , Marshall Shawn J. 
Published: April 2008

Abstract
To inform the ongoing development of earth system models that aim to incorporate interactive ice, the potential impact of interannual variability associated with synoptic variability and El Niño–Southern Oscillation (ENSO) at the Last Glacial Maximum (LGM) on the evolution of a large continental ice sheet is explored through a series of targeted numerical modeling experiments. Global and North American signatures of ENSO at the LGM are described based on a multidecadal paleoclimate simulation using an atmosphere–ocean general circulation model (AOGCM). Experiments in which a thermomechanical North American ice sheet model (ISM) was forced with persistent LGM ENSO composite anomaly maps derived from the AOGCM showed only modest ice sheet thickness sensitivity to ENSO teleconnections. In contrast, very high model sensitivity was found when North American climate variations were incorporated directly in the ISM as a looping interannual time series. Under this configuration, localized transient cold anomalies in the atmospheric record instigated substantial new ice formation through a dynamically mediated feedback at the ice sheet margin, altering the equilibrium geometry and resulting in a bulk 10% growth of the Laurentide ice sheet volume over 5 kyr.
Possible Role of the Indian Ocean in the In-Phase Transition of the Indian-to-Australian Summer Monsoon
Authors: Wu Renguang 
Published: April 2008

Abstract
Analysis of observations shows that in-phase transitions from the Indian summer monsoon (ISM) to the Australian summer monsoon (ASM) have occurred both in El Niño–Southern Oscillation (ENSO) and non-ENSO years. The present study investigates possible roles of the Indian Ocean in the in-phase ISM-to-ASM transitions. It is shown that an anomalous ISM leads to sea surface temperature (SST) anomalies in the tropical Indian Ocean through wind–evaporation effects. The resultant Indian Ocean SST anomalies induce an anomalous ASM of the same sign as the ISM through an anomalous east–west circulation over the eastern Indian Ocean and the Maritime Continent–northern Australia. The results indicate that the in-phase ISM-to-ASM transitions in non-ENSO years can be accomplished through monsoon–Indian Ocean interactions. The results of observational analysis are confirmed with numerical model experiments.
Arthroscopic Rotator Cuff Repair in Overhead-Throwing Athletes
Authors: Liem Dennis , Lichtenberg Sven , Magosch Petra , Habermeyer Peter 
Published: April 2008

Background When overhead-throwing athletes suffer from a rotator cuff tear, their ability to perform sporting activities is significantly impaired. Hypothesis Arthroscopic rotator cuff repair allows amateur overhead-throwing athletes to return to their preoperative level of overhead-throwing sports. Study Design Cohort study; Level of evidence, 3. Methods Twenty-one overhead-throwing athletes (14 male and 7 female; average age, 58.9 years, range, 46-69 years) were reviewed for clinical outcome with the Constant Score and structural integrity of the repair on magnetic resonance imaging. The average follow-up was 25.7 months (24-29 months). Athletes were asked to retrospectively assess their sporting activity for pain, strength, endurance, and range of motion before onset of symptoms, preoperatively and at follow-up. They also were asked to evaluate their overall performance as a percentage of their original performance (0% to 100%). Retear rates and Constant Scores were compared with those of 32 patients who were not overhead-throwing athletes and who were operated on during the same time span. Results Patients significantly improved their Constant Score from 54.9 to 84.2 ( P < .001). Sporting activity was not significantly influenced by repair integrity; the retear rate was 23.8% (5/21). There was no significant difference for retear rate (25%; 8/32) or clinical outcome (Constant Score 84.5, P = .993) compared with patients who were not involved in overhead-throwing sports or any sports. All patients returned to their overhead-throwing sport an average of 6.3 months (3-12 months) after the surgery. Participation (2.1 per week) and duration (2.3 hours) of overhead-throwing activity postoperatively were not significantly lower than before the Patient was injured (2.2 per week, P = .290; and 2.4 hours, P = .285). Patients estimated their overall activity level to be 91.9% of their original, noninjured condition, which was significantly improved from the preoperative condition of 34.8% ( P < .001). Conclusion Arthroscopic rotator cuff repair led to good clinical results in this group of overhead-throwing athletes. Patients were able to return to overhead-throwing sports, most of them at the same preoperative level.