bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation
Authors: Wang Xi , Haberer Georg , Mayer Klaus FX 
Published: June 2009

AbstractBackgroundThe spatiotemporal regulation of gene expression largely depends on the presence and absence ofcis-regulatory sites in the promoter. In the economically highly important grass family, our knowledge of transcription factor binding sites and transcriptional networks is still very limited. With the completion of the sorghum genome and the available rice genome sequence, comparative promoter analyses now allow genome-scale detection of conservedcis-elements.ResultsIn this study, we identified thousands of phylogenetic footprints conserved between orthologous rice and sorghum upstream regions that are supported by co-expression information derived from three different rice expression data sets. In a complementary approach,cis-motifs were discovered by their highly conserved co-occurrence in syntenic promoter pairs. Sequence conservation and matches to known plant motifs support our findings. Expression similarities of gene pairs positively correlate with the number of motifs that are shared by gene pairs and corroborate the importance of similar promoter architectures for concerted regulation. This strongly suggests that these motifs function in the regulation of transcript levels in rice and, presumably also in sorghum.ConclusionOur work provides the first large-scale collection ofcis-elements for rice and sorghum and can serve as a paradigm forcis-element analysis through comparative genomics in grasses in general.
249 TP53 mutation has high prevalence and is correlated with larger and poorly differentiated HCC in Brazilian patients
Authors: Nogueira Jeronimo A , Ono-Nita Suzane K , Nita Marcelo E , de Souza Marcelo MT , do Carmo Eliane P , Mello Evandro S , Scapulatempo Cristovan , Paranaguá-Vezozzo Denise C , Carrilho Flair J , Alves Venancio AF 
Published: June 2009

Abstract

Background
Ser-249 TP53 mutation (249Ser) is a molecular evidence for aflatoxin-related carcinogenesis in Hepatocellular Carcinoma (HCC) and it is frequent in some African and Asian regions, but it is unusual in Western countries. HBV has been claimed to add a synergic effect on genesis of this particular mutation with aflatoxin. The aim of this study was to investigate the frequency of 249Ser mutation in HCC from patients in Brazil.

Methods
We studied 74 HCC formalin fixed paraffin blocks samples of patients whom underwent surgical resection in Brazil. 249Ser mutation was analyzed by RFLP and DNA sequencing. HBV DNA presence was determined by Real-Time PCR.

Results
249Ser mutation was found in 21/74 (28%) samples while HBV DNA was detected in 13/74 (16%). 249Ser mutation was detected in 21/74 samples by RFLP assay, of which 14 were confirmed by 249Ser mutant-specific PCR, and 12 by nucleic acid sequencing. All HCC cases with p53-249ser mutation displayed also wild-type p53 sequences. Poorly differentiated HCC was more likely to have 249Ser mutation (OR = 2.415, 95% CI = 1.001 – 5.824, p = 0.05). The mean size of 249Ser HCC tumor was 9.4 cm versus 5.5 cm on wild type HCC (p = 0.012). HBV DNA detection was not related to 249Ser mutation.

Conclusion
Our results indicate that 249Ser mutation is a HCC important factor of carcinogenesis in Brazil and it is associated to large and poorly differentiated tumors.
Are immigrant populations aware about their oral health status? A study among immigrants from Ethiopia
Authors: Zini Avi , Vered Yuval , Sgan-Cohen Harold D 
Published: June 2009

Abstract

Background
Evidence from Western countries indicates that there are fundamental discrepancies between self-perceived illness of immigrants and the provision of health care, according to the Western bio-medical health service model. These need to be understood in the planning and implementation stages of public health care programs for new immigrants. The objectives of the present study were to investigate self-perceived versus clinically diagnosed dental and periodontal health status among immigrants from Ethiopia.

Methods
During 2004–2005, dental and periodontal health status was recorded among 340 Ethiopian immigrants, utilizing the DMFT and CPI indices. Additionally, participants were interviewed using a questionnaire which included perceived dental and periodontal health status. Sensitivity and specificity levels of this perception were calculated and compared with the published scientific literature.

Results
Regarding dental caries, according to the three operational cut-off points, sensitivity ranged from 70% to 81%, and specificity ranged from 56% to 67%. Regarding periodontal status, 75% of the subjects clinically diagnosed with periodontal pockets self-perceived a "bad" health status of gums (sensitivity) and 54% of the subjects diagnosed without periodontal pockets, reported a "good" health status of gums (specificity). These indications of perception levels were higher than a previous study conducted among native born Israelis.

Conclusion
Minority ethnic groups should not be prejudicially regarded as less knowledgeable. This is illustrated by the unexpected high level of oral health status perception in the present population. Oral health promotion initiatives among immigrants should be based upon optimal descriptive data in order to accomplish the inherent social commitment to these diverse populations.
Use of risk stratification to target therapies in patients with recent onset arthritis; design of a prospective randomized multicenter controlled trial
Authors: Claessen Susanne JJ , Hazes Johanna MW , Huisman Margriet AM , van Zeben Derkjen , Luime Jolanda J , Weel Angelique EAM 
Published: June 2009

Abstract

Background
Early and intensive treatment is important to inducing remission and preventing joint damage in patients with rheumatoid arthritis. While intensive combination therapy (Disease Modifying Anti-rheumatic Drugs and/or biologicals) is the most effective, rheumatologists in daily clinical practice prefer to start with monotherapy methotrexate and bridging corticosteroids. Intensive treatment should be started as soon as the first symptoms manifest, but at this early stage, ACR criteria may not be fulfilled, and there is a danger of over-treatment. We will therefore determine which induction therapy is most effective in the very early stage of persistent arthritis. To overcome over-treatment and under-treatment, the intensity of induction therapy will be based on a prediction model that predicts patients' propensity for persistent arthritis.

Methods
A multicenter stratified randomized single-blind controlled trial is currently being performed in patients 18 years or older with recent-onset arthritis. Eight hundred ten patients are being stratified according to the likelihood of their developing persistent arthritis. In patients with a high probability of persistent arthritis, we will study combination Disease Modifying Antirheumatic Drug therapy compared to monotherapy methotrexate. In patients with an intermediate probability of persistent arthritis, we will study Disease Modifying Antirheumatic Drug of various intensities. In patients with a low probability, we will study non-steroidal anti-inflammatory drugs, hydroxychloroquine and a single dose of corticosteroids. If disease activity is not sufficiently reduced, treatment will be adjusted according to a step-up protocol. If remission is achieved for at least six months, medication will be tapered off. Patients will be followed up every three months over two years.

Discussion
This is the first rheumatological study to base treatment in early arthritis on a prediction rule. Treatment will be stratified according to the probability of persistent arthritis, and different combinations of treatment per stratum will be evaluated. Treatment will be started early, and patients will not need to meet the ACR-criteria for rheumatoid arthritis.

Trial registration
This trial has been registered in Current Controlled Trials with the ISRCTN26791028.
Factors affecting plasmid production in Escherichia coli from a resource allocation standpoint
Authors: Cunningham Drew S , Koepsel Richard R , Ataai Mohammad M , Domach Michael M 
Published: June 2009

AbstractBackgroundPlasmids are being reconsidered as viable vector alternatives to viruses for gene therapies and vaccines because they are safer, non-toxic, and simpler to produce. Accordingly, there has been renewed interest in the production of plasmid DNA itself as the therapeutic end-product of a bioprocess. Improvement to the best current yields and productivities of such emerging processes would help ensure economic feasibility on the industrial scale. Our goal, therefore, was to develop a stoichiometric model ofEscherichia colimetabolism in order to (1) determine its maximum theoretical plasmid-producing capacity, and to (2) identify factors that significantly impact plasmid production.ResultsSuch a model was developed for the production of a high copy plasmid under conditions of batch aerobic growth on glucose minimal medium. The objective of the model was to maximize plasmid production. By employing certain constraints and examining the resulting flux distributions, several factors were determined that significantly impact plasmid yield. Acetate production and constitutive expression of the plasmid's antibiotic resistance marker exert negative effects, while low pyruvate kinase (Pyk) flux and the generation of NADPH by transhydrogenase activity offer positive effects. The highest theoretical yield (592 mg/g) resulted under conditions of no marker or acetate production, nil Pyk flux, and the maximum allowable transhydrogenase activity. For comparison, when these four fluxes were constrained to wild-type values, yields on the order of tens of mg/g resulted, which are on par with the best experimental yields reported to date.ConclusionThese results suggest that specific plasmid yields can theoretically reach 12 times their current experimental maximum (51 mg/g). Moreover, they imply that abolishing Pyk activity and/or transhydrogenase up-regulation would be useful strategies to implement when designing host strains for plasmid production; mutations that reduce acetate production would also be advantageous. The results further suggest that using some other means for plasmid selection than antibiotic resistance, or at least weakening the marker's expression, would be beneficial because it would allow more precursor metabolites, energy, and reducing power to be put toward plasmid production. Thus far, the impact of eliminating Pyk activity has been explored experimentally, with significantly higher plasmid yields resulting.
Respiratory viral infections detected by multiplex PCR among pediatric patients with lower respiratory tract infections seen at an urban hospital in Delhi from 2005 to 2007
Authors: Bharaj Preeti , Sullender Wayne M , Kabra Sushil K , Mani Kalaivani , Cherian John , Tyagi Vikas , Chahar Harendra S , Kaushik Samander , Dar Lalit , Broor Shobha 
Published: June 2009

Abstract

Background
Acute lower respiratory tract infections (ALRI) are the major cause of morbidity and mortality in young children worldwide. Information on viral etiology in ALRI from India is limited. The aim of the present study was to develop a simple, sensitive, specific and cost effective multiplex PCR (mPCR) assay without post PCR hybridization or nested PCR steps for the detection of respiratory syncytial virus (RSV), influenza viruses, parainfluenza viruses (PIV1–3) and human metapneumovirus (hMPV). Nasopharyngeal aspirates (NPAs) were collected from children with ALRI ≤ 5 years of age. The sensitivity and specificity of mPCR was compared to virus isolation by centrifugation enhanced culture (CEC) followed by indirect immunofluorescence (IIF).

Results
From April 2005–March 2007, 301 NPAs were collected from children attending the outpatient department or admitted to the ward of All India Institute of Medical Sciences hospital at New Delhi, India. Multiplex PCR detected respiratory viruses in 106 (35.2%) of 301 samples with 130 viruses of which RSV was detected in 61, PIV3 in 22, PIV2 in 17, hMPV in 11, PIV1 in 10 and influenza A in 9 children. CEC-IIF detected 79 viruses only. The sensitivity of mPCR was 0.1TCID50 for RSV and influenza A and 1TCID50 for hMPV, PIV1, PIV2, PIV3 and Influenza B. Mixed infections were detected in 18.8% of the children with viral infections, none detected by CEC-IIF. Bronchiolitis was significantly associated with both total viral infections and RSV infection (p < 0.05). History of ARI in family predisposed children to acquire viral infection (p > 0.05).

Conclusion
Multiplex PCR offers a rapid, sensitive and reasonably priced diagnostic method for common respiratory viruses.
Modeling AIDS survival after initiation of antiretroviral treatment by Weibull models with changepoints
Authors: Yiannoutsos Constantin T 
Published: June 2009

BackgroundMortality of HIV‐infected patients initiating antiretroviral therapy in the developing world is very high immediately after the start of ART therapy and drops sharply thereafter. It is necessary to use models of survival time that reflect this change.MethodsIn this endeavor, parametric models with changepoints such as Weibull models can be useful in order to explicitly model the underlying failure process, even in the case where abrupt changes in the mortality rate are present. Estimation of the temporal location of possible mortality changepoints has important implications on the effective management of these patients. We briefly describe these models and apply them to the case of estimating survival among HIV‐infected patients who are initiating antiretroviral therapy in a care and treatment programme in sub‐Saharan Africa.ResultsAs a first reported data‐driven estimate of the existence and location of early mortality changepoints after antiretroviral therapy initiation, we show that there is an early change in risk of death at three months, followed by an intermediate risk period lasting up to 10 months after therapy.ConclusionBy explicitly modelling the underlying abrupt changes in mortality risk after initiation of antiretroviral therapy we are able to estimate their number and location in a rigorous, data‐driven manner. The existence of a high early risk of death after initiation of antiretroviral therapy and the determination of its duration has direct implications for the optimal management of patients initiating therapy in this setting.
Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea
Authors: Zivanovic Yvan , Armengaud Jean , Lagorce Arnaud , Leplat Christophe , Guérin Philippe , Dutertre Murielle , Anthouard Véronique , Forterre Patrick , Wincker Patrick , Confalonieri Fabrice 
Published: June 2009

Abstract
Background
Thermococcus gammatolerans was isolated from samples collected from hydrothermal chimneys. It is one of the most radioresistant organisms known amongst the Archaea. We report the determination and annotation of its complete genome sequence, its comparison with other Thermococcales genomes, and a proteomic analysis.

Results
T. gammatolerans has a circular chromosome of 2.045 Mbp without any extra-chromosomal elements, coding for 2,157 proteins. A thorough comparative genomics analysis revealed important but unsuspected genome plasticity differences between sequenced Thermococcus and Pyrococcus species that could not be attributed to the presence of specific mobile elements. Two virus-related regions, tgv1 and tgv2, are the only mobile elements identified in this genome. A proteogenome analysis was performed by a shotgun liquid chromatography-tandem mass spectrometry approach, allowing the identification of 10,931 unique peptides corresponding to 951 proteins. This information concurrently validates the accuracy of the genome annotation. Semi-quantification of proteins by spectral count was done on exponential- and stationary-phase cells. Insights into general catabolism, hydrogenase complexes, detoxification systems, and the DNA repair toolbox of this archaeon are revealed through this genome and proteome analysis.

Conclusions
This work is the first archaeal proteome investigation done at the stage of primary genome annotation. This archaeon is shown to use a large variety of metabolic pathways even under a rich medium growth condition. This proteogenomic study also indicates that the high radiotolerance of T. gammatolerans is probably due to proteins that remain to be characterized rather than a larger arsenal of known DNA repair enzymes.
Inhibition of Nuclear Factor-κB or Bax Prevents Endoplasmic Reticulum Stress- But Not Nitric Oxide-Mediated Apoptosis in INS-1E Cells
Authors: Tonnesen Morten F. , Grunnet Lars G. , Friberg Josefine , Cardozo Alessandra K. , Billestrup Nils , Eizirik Décio L. , Størling Joachim , Mandrup-Poulsen Thomas 
Published: June 2009

AbstractAccumulating evidence suggests that endoplasmic reticulum (ER) stress by mechanisms that include ER Ca2+ depletion via NO-dependent down-regulation of sarcoendoplasmic reticulum Ca2+ ATPase 2b (SERCA2b) contributes to β-cell death in type 1 diabetes. To clarify whether the molecular pathways elicited by NO and ER Ca2+ depletion differ, we here compare the direct effects of NO, in the form of the NO donor S-nitroso-N-acetyl-d,l-penicillamine (SNAP), with the effects of SERCA2 inhibitor thapsigargin (TG) on MAPK, nuclear factor κB (NFκB), Bcl-2 proteins, ER stress, and apoptosis. Exposure of INS-1E cells to TG or SNAP caused caspase-3 cleavage and apoptosis. Both TG and SNAP induced activation of the proapoptotic transcription factor CCAAT/enhancer-binding protein homologous protein (CHOP). However, other classical ER stress-induced markers such as up-regulation of ER chaperone Bip and alternative splicing of the transcription factor Xbp-1 were exclusively activated by TG. TG exposure caused NFκB activation, as assessed by IκB degradation and NFκB DNA binding. Inhibition of NFκB or the Bcl-2 family member Bax pathways protected β-cells against TG- but not SNAP-induced β-cell death. These data suggest that NO generation and direct SERCA2 inhibition cause two quantitative and qualitative different forms of ER stress. In contrast to NO, direct ER stress induced by SERCA inhibition causes activation of ER stress signaling pathways and elicit proapoptotic signaling via NFκB and Bax.
Activation of Liver X Receptor Regulates Substrate Oxidation in White Adipocytes
Authors: Stenson Britta M. , Rydén Mikael , Steffensen Knut R. , Wåhlén Kerstin , Pettersson Amanda T. , Jocken Johan W. , Arner Peter , Laurencikiene Jurga 
Published: June 2009

Abstract
Liver X receptors (LXRs) are nuclear receptors with established roles in cholesterol, lipid, and carbohydrate metabolism, although their function in adipocytes is not well characterized. Increased adipose tissue mass in obesity is associated with increased adipocyte lipolysis. Fatty acids (FA) generated by lipolysis can be oxidized by mitochondrial β-oxidation, reesterified, or released from the adipocyte. The latter results in higher circulating levels of free FAs, in turn causing obesity-related metabolic complications. However, mitochondrial β-oxidation can at least in part counteract an increased output of FA into circulation. In this study, we provide evidence that activation of LXRs up-regulates mitochondrial β-oxidation in both human and murine white adipocytes. We also show that the expression of a kinase regulating the cellular fuel switch, pyruvate dehydrogenase kinase 4 (PDK4), is up-regulated by the LXR agonist GW3965 in both in vitro differentiated human primary adipocytes and differentiated murine 3T3-L1 cells. Moreover, activation of LXR causes PDK4-dependent phosphorylation of the pyruvate dehydrogenase complex, thereby decreasing its activity and attenuating glucose oxidation. The specificity of the GW3965 effect on oxidation was confirmed by RNA interference targeting LXRs. We propose that LXR has an important role in the regulation of substrate oxidation and the switch between lipids and carbohydrates as cellular fuel in both human and murine white adipocytes.
Cleaner gobies evolve advertising stripes of higher contrast
Authors: Lettieri L. , Cheney K. L. , Mazel C. H. , Boothe D. , Marshall N. J. , Streelman J. T. 
Published: June 2009

SUMMARYElacatinus gobies of the Caribbean have undergone rapid speciation along ecological axes, and particular species from this genus act as`cleaners' that remove ectoparasites from larger coral reef fish, termed`clients'. Evolutionary shifts in habitat use, behavior and lateral body stripe colors differentiate cleaners from ancestral sponge-dwelling lineages. High-contrast stripe colors associated with cleaning behavior on coral reefs may have evolved as a signal of cleaning status. We asked whether cleaner gobies with blue stripes are more conspicuous than ancestral yellow- and green-stripe phenotypes to a diverse set of potential client visual systems in the tropical reef environment where cleaning stations are commonly observed. Using spectrophotometric measurements of cleaners with blue and yellow stripes and their F1 hybrid, we tested the contrast of each color stripe to both potential dichromatic and trichromatic reef fish visual systems, against typical coral and sponge microhabitat background colors. Blue stripes provide the highest average chromatic contrast across a range of possible microhabitat colors to the majority of fish visual systems tested. The contrast provided by yellow and hybrid green stripes are comparable across habitats to dichromatic visual systems. The green stripe is less contrasting than both blue and yellow to many potential trichromatic visual systems. We suggest that the evolution of blue stripes in Elacatinus gobies could be a result of natural selection for signals of high color contrast, driven by the sensory biases and visual systems of diverse reef fish clients.
Mudskipper pectoral fin kinematics in aquatic and terrestrial environments
Authors: Pace C. M. , Gibb A. C. 
Published: June 2009

SUMMARY
Mudskippers use pectoral fins for their primary mode of locomotion on land and pectoral fins in conjunction with the axial musculature and caudal fin to move in water. We hypothesized that distinct pectoral fin movements enable effective locomotion in each environment. Additionally, we made three functional predictions about fin movements during locomotion on land versus water: the pectoral fin is depressed more on land than in water; the pectoral fin will have greater changes in fin area between propulsive and recovery phases in water versus land; anterior and posterior excursions will be greater on land than in water. Locomotion was recorded in each environment using a high-speed digital-imaging system and kinematic variables were calculated from digitized landmark points. Variables were analyzed using principal components analysis and matched pairs t-tests. Mudskippers produce distinct kinematic patterns across environments (P&lt;0.003), although only some of our predictions were supported. The magnitude of fin depression is the same across habitats. However, depression occurs during the propulsive phase on land (by –0.60 cm), whereas during the propulsive phase in water the fin is elevated (by+0.13 cm). We were unable to support the hypothesis that fin orientation differs between environments. Lastly, anterior extension of the fin is greater on land (1.8 cm, versus 1.3 cm in water), creating a larger stride length in this environment. We posit that the mudskipper pectoral fin may facilitate stability in water and thrust production on land, and suggest that the robust fin morphology of the goby lineage may predispose species within this group to terrestrial locomotion.