bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution with depth from detrital to authigenic smectites in sediments from AND-2A drill core (McMurdo Sound, Antarctica)
Authors: Iacoviello F. , Giorgetti G. , Nieto F. , Memmi I. T. 
Published: December 2012

AbstractWe have examined the nature and origin of smectites in glaciomarine sediments of the AND-2A drill core (McMurdo Sound, Antarctica) by means of X-ray diffraction (XRD) analyses on the clay fraction, field emission scanning electron microscopy (FESEM), scanning electron microscopy (SEM) observations and SEM-EDS microanalyses on smectite particles. Relying on the smectite variation throughout the drill core it was possible to split the sequence into three units. Smectites throughout the core are either detrital or authigenic. Detrital smectites are close to montmorillonite-beidellite in composition while newly-formed smectites frequently have higher Fe-Mg contents and intermediate compositions between the saponite and nontronite field, with lower amounts in the montmorillonite-beidellite field. In the upper sedimentary sections (Unit I, and Unit II, 36-440 mbsf, 0.7-16.5 Ma) smectites are interpreted to be predominantly detrital, whereas in the lower portion of the core (Unit III, 440-1123.20 mbsf, 16.5-20.2 Ma) authigenic smectites are the most common feature. The predominance of mica, the abundance of chlorite, and the nature of smectites in the upper units indicate physical weathering under cold and dry climate, and a dominant provenance for the clay minerals from the Transantarctic Mountains. Smectites in the lower unit are considered mostly authigenic and they are most likely to be the result of early diagenetic processes, being formed from the alteration of volcanic material (glass, pyroxenes and feldspars) and/or through precipitation from fluids of a possible hydrothermal origin. Our survey attests to the importance of discriminating between a detrital and authigenic nature of smectites as the occurrence of authigenic clay minerals in ancient sedimentary successions might lead to incorrect palaeoclimatic interpretations, since they can be affected by diagenetic processes, thus obliterating the climatic signal.
Mineralogical and physico-chemical characterizations of clay from Keur Saër (Senegal)
Authors: Mbaye A. , Diop C. A. K. , Rhouta B. , Brendle J. M. , Senocq F. , Maury F. , Diallo D. P. 
Published: December 2012

AbstractThere is interest in exploiting and developing natural resources, particularly deposits of natural clays. Senegal has several clay mineral deposits for which chemical and mineralogical compositions have been little studied. Some of these natural materials are nowadays used in pottery and ceramics. To extend applications, a better basic knowledge is required and, for this objective, the raw clay and separated <2 μm clay fraction from Keur Saër (Senegal) were subjected to chemical and mineralogical studies. Several techniques including X-ray diffraction (XRD), thermal analysis (TG-DTA), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), N2 adsorption-desorption isotherms, cation exchange capacity (CEC) measurements and solid state nuclear magnetic resonance (NMR) have been used to characterize the material. It was found that the raw clay and the separated clay fraction consist of a mineral mixture in which kaolinite is the main component.29Si and27Al MAS-NMR spectra show the presence of silicon atoms linked to three other silicon atoms via an oxygen atom and six coordinated Al atoms. Significant increases in the specific surface area and cation exchange capacity were observed on purification, reaching a maximum of about 73.2 m2g–1and 9.5 meq/100 g for the separated fine clay fraction while the values for the raw material were around 28.9 m2g–1and 7.3 meq/100 g.
Influence of particle size on the paramagnetic components of kaolins from different origins
Authors: Worasith N. , Goodman B. A. 
Published: December 2012

AbstractElectron paramagnetic resonance (EPR) spectra of different particle size fractions of four kaolins from diverse sources in North America, Europe and Asia have been investigated in order to characterize their paramagnetic properties and heterogeneity. There were major differences in the sources of the EPR signals from transition metals; V and Mn were structural, Fe was both structural and as associated oxides, and Cu was in the form of an adsorbed ion. The radiation-induced free radical signals commonly known as the A- and B-centres were observed in three of the deposits; however, in addition to the previously reported27Al hyperfine structure associated with the B-centre, we also observed much smaller27Al hyperfine structure on the g┴ feature of the A-centre. The other kaolin sample produced four free radical signals that have not previously been reported in kaolins. Each had substantial1H hyperfine splitting; three are interpreted as corresponding to defect centres associated with Si-OH groups, and the other to a Si hole surrounded by protonated O atoms. The EPR spectra changed progressively with particle size, and measurements on the Asian specimens after grinding showed major differences in the Fe3+signals from the same particle size fractions separated from the natural samples, thus supporting previous reports that grinding results in major structural changes in the minerals.
Ultrasound assessment of lower limb muscle mass in response to resistance training in COPD
Authors: Menon Manoj K , Houchen Linzy , Harrison Samantha , Singh Sally J , Morgan Michael D , Steiner Michael C 
Published: December 2012

Abstract

Background
Quantifying the improvements in lower limb or quadriceps muscle mass following resistance training (RT), is an important outcome measure in COPD. Ultrasound is a portable, radiation free imaging technique that can measure the size of superficial muscles belonging to the quadriceps group such as the rectus femoris, but has not been previously used in COPD patients following RT. We compared the responsiveness of ultrasound derived measures of quadriceps mass against dual energy x-ray absorptiometry (DEXA), in patients with COPD and healthy controls following a programme of high intensity knee extensor RT.

Methods
Portable ultrasound was used to assess the size of the dominant quadriceps in 45 COPD patients and 19 healthy controls-before, during, and after 8 weeks of bilateral high intensity isokinetic knee extensor RT. Scanning was performed at the mid-thigh region, and 2 indices of quadriceps mass were measured-rectus femoris cross-sectional area (RFcsa) and quadriceps muscle thickness (Qt). Thigh lean mass (Tdexa) was determined by DEXA.

Results
Training resulted in a significant increase in Tdexa, RFcsa and Qt in COPD patients [5.7%, 21.8%, 12.1% respectively] and healthy controls [5.4%, 19.5%, 10.9 respectively]. The effect size for the changes in RFcsa (COPD= 0.77; Healthy=0.83) and Qt (COPD=0.36; Healthy=0.78) were greater than the changes in Tdexa (COPD=0.19; Healthy=0.26) following RT.

Conclusions
Serial ultrasound measurements of the quadriceps can detect changes in muscle mass in response to RT in COPD. The technique has good reproducibility, and may be more sensitive to changes in muscle mass when compared to DEXA.

Trial registration

http://www.controlled-trials.com (Identifier: ISRCTN22764439)
Autophosphorylation of serine 608 in the p85 regulatory subunit of wild type or cancer-associated mutants of phosphoinositide 3-kinase does not affect its lipid kinase activity
Authors: Layton Meredith J , Saad Mirette , Church Nicole L , Pearson Richard B , Mitchell Christina A , Phillips Wayne A 
Published: December 2012

Abstract

Background
The α-isoform of the Type 1A Phosphoinositide 3-kinases (PI3Kα) has protein kinase activity as well as phosphoinositide lipid kinase activity. The best described substrate for its protein kinase activity is its regulatory subunit, p85α, which becomes phosphorylated on Serine 608. Phosphorylation of Serine 608 has been reported to down-regulate its lipid kinase activity.

Results
We have assessed whether oncogenic mutants of PI3Kα, which have up-regulated lipid kinase activity, have altered levels of Serine 608 phosphorylation compared to wild type PI3Kα, and whether differential phosphorylation of Serine 608 contributes to increased activity of oncogenic forms of PI3Kα with point mutations in the helical or the kinase domains. Despite markedly increased lipid kinase activity, protein kinase activity was not altered in oncogenic compared to wild type forms of PI3Kα. By manipulating levels of phosphorylation of Serine 608 in vitro, we found no evidence that the protein kinase activity of PI3Kα affects its phosphoinositide lipid kinase activity in either wild-type or oncogenic mutants of PI3Kα.

Conclusions
Phosphorylation of p85α S608 is not a significant regulator of wild-type or oncogenic PI3Kα lipid kinase activity.
Whole genome sequencing of the fish pathogen Francisella noatunensis subsp. orientalis Toba04 gives novel insights into Francisella evolution and pathogenecity
Authors: Sridhar Settu , Sharma Animesh , Kongshaug Heidi , Nilsen Frank , Jonassen Inge 
Published: December 2012

Abstract

Background

Francisella is a genus of gram-negative bacterium highly virulent in fishes and human where F. tularensis is causing the serious disease tularaemia in human. Recently Francisella species have been reported to cause mortality in aquaculture species like Atlantic cod and tilapia. We have completed the sequencing and draft assembly of the Francisella noatunensis subsp. orientalisToba04 strain isolated from farmed Tilapia. Compared to other available Francisella genomes, it is most similar to the genome of Francisella philomiragia subsp. philomiragia, a free-living bacterium not virulent to human.

Results
The genome is rearranged compared to the available Francisella genomes even though we found no IS-elements in the genome. Nearly 16% percent of the predicted ORFs are pseudogenes. Computational pathway analysis indicates that a number of the metabolic pathways are disrupted due to pseudogenes. Comparing the novel genome with other available Francisella genomes, we found around 2.5% of unique genes present in Francisella noatunensis subsp. orientalis Toba04 and a list of genes uniquely present in the human-pathogenic Francisella subspecies. Most of these genes might have transferred from bacterial species through horizontal gene transfer. Comparative analysis between human and fish pathogen also provide insights into genes responsible for pathogenecity. Our analysis of pseudogenes indicates that the evolution of Francisella subspecies’s pseudogenes from Tilapia is old with large number of pseudogenes having more than one inactivating mutation.

Conclusions
The fish pathogen has lost non-essential genes some time ago. Evolutionary analysis of the Francisella genomes, strongly suggests that human and fish pathogenic Francisella species have evolved independently from free-living metabolically competent Francisella species. These findings will contribute to understanding the evolution of Francisella species and pathogenesis.
Whole genome HBV deletion profiles and the accumulation of preS deletion mutant during antiviral treatment
Authors: Zhang Dake , Dong Peiling , Zhang Ke , Deng Libin , Bach Christian , Chen Wei , Li Feifei , Protzer Ulrike , Ding Huiguo , Zeng Changqing 
Published: December 2012

AbstractBackgroundHepatitis B virus (HBV), because of its error-prone viral polymerase, has a high mutation rate leading to widespread substitutions, deletions, and insertions in the HBV genome. Deletions may significantly change viral biological features complicating the progression of liver diseases. However, the clinical conditions correlating to the accumulation of deleted mutants remain unclear. In this study, we explored HBV deletion patterns and their association with disease status and antiviral treatment by performing whole genome sequencing on samples from 51 hepatitis B patients and by monitoring changes in deletion variants during treatment. Clone sequencing was used to analyze preS regions in another cohort of 52 patients.ResultsAmong the core, preS, and basic core promoter (BCP) deletion hotspots, we identified preS to have the highest frequency and the most complex deletion pattern using whole genome sequencing. Further clone sequencing analysis on preS identified 70 deletions which were classified into 4 types, the most common being preS2. Also, in contrast to the core and BCP regions, most preS deletions were in-frame. Most deletions interrupted viral surface epitopes, and are possibly involved in evading immuno-surveillance. Among various clinical factors examined, logistic regression showed that antiviral medication affected the accumulation of deletion mutants (OR = 6.81, 95% CI = 1.296 ~ 35.817, P = 0.023). In chronic carriers of the virus, and individuals with chronic hepatitis, the deletion rate was significantly higher in the antiviral treatment group (Fisher exact test, P = 0.007). Particularly, preS2 deletions were associated with the usage of nucleos(t)ide analog therapy (Fisher exact test, P = 0.023). Dynamic increases in preS1 or preS2 deletions were also observed in quasispecies from samples taken from patients before and after three months of ADV therapy. In vitro experiments demonstrated that preS2 deletions alone were not responsible for antiviral resistance, implying the coordination between wild type and mutant strains during viral survival and disease development.ConclusionsWe present the HBV deletion distribution patterns and preS deletion substructures in viral genomes that are prevalent in northern China. The accumulation of preS deletion mutants during nucleos(t)ide analog therapy may be due to viral escape from host immuno-surveillance.
Altered serum microRNAs as biomarkers for the early diagnosis of pulmonary tuberculosis infection
Authors: Qi Yuhua , Cui Lunbiao , Ge Yiyue , Shi Zhiyang , Zhao Kangchen , Guo Xiling , Yang Dandan , Yu Hao , Cui Lan , Shan Yunfeng , Zhou Minghao , Wang Hua , Lu Zuhong 
Published: December 2012

Abstract

Background
Pulmonary tuberculosis (TB) is a highly lethal infectious disease and early diagnosis of TB is critical for the control of disease progression. The objective of this study was to profile a panel of serum microRNAs (miRNAs) as potential biomarkers for the early diagnosis of pulmonary TB infection.

Methods
Using TaqMan Low-Density Array (TLDA) analysis followed by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) validation, expression levels of miRNAs in serum samples from 30 patients with active tuberculosis and 60 patients with Bordetella pertussis (BP), varicella-zoster virus (VZV) and enterovirus (EV) were analyzed.

Results
The Low-Density Array data showed that 97 miRNAs were differentially expressed in pulmonary TB patient sera compared with healthy controls (90 up-regulated and 7 down-regulated). Following qRT-PCR confirmation and receiver operational curve (ROC) analysis, three miRNAs (miR-361-5p, miR-889 and miR-576-3p) were shown to distinguish TB infected patients from healthy controls and other microbial infections with moderate sensitivity and specificity (area under curve (AUC) value range, 0.711-0.848). Multiple logistic regression analysis of a combination of these three miRNAs showed an enhanced ability to discriminate between these two groups with an AUC value of 0.863.

Conclusions
Our study suggests that altered levels of serum miRNAs have great potential to serve as non-invasive biomarkers for early detection of pulmonary TB infection.
Prognostic value of stromal and epithelial periostin expression in human prostate cancer: correlation with clinical pathological features and the risk of biochemical relapse or death
Authors: Nuzzo Pier Vitale , Rubagotti Alessandra , Zinoli Linda , Ricci Francesco , Salvi Sandra , Boccardo Simona , Boccardo Francesco 
Published: December 2012

AbstractBackgroundThe purpose of the present study was to evaluate the prognostic value of POSTN expression following prostatectomy.MethodsPeriostin (POSTN) expression in prostate cancer (PCa) and in normal specimens was evaluated in 90 patients by an immuno-reactive score(IRS) based on the intensity of immunostaining and on the quantity of stained cells. The t-test was applied to compare IRS values in cancer specimens to values in normal specimens. Pearson’s test was used to correlate POSTN expression to clinical pathologic features. PSA progression-free and survival curves were constructed by the Kaplan–Meier method and compared using the log-rank test. Multi-parametric models were constructed according to the Cox technique adding all the covariates predicting for either PSA progression or death into the models after univariate analysis.ResultsBoth stromal and epithelial POSTN expression were significantly increased in tumor tissues.In particular, we found stromal expression to be significantly higher than epithelial expression as compared to normal tissues (p<0.000 and p=0.001).A significant correlation between POSTN epithelial expression and extra-prostatic extension was found (p=0.03). While high stromal expression was significantly associated with shorter survival (p=0.008), a low epithelial score significantly correlated with shorter PSA-free survival (p=0.04), suggesting that POSTN plays an apparently opposing biological role depending on its compartmentalization.Regardless of the mechanism that is involved, patients showing both high stromal and low epithelial expression made up a subgroup with a very bleak prognosis.ConclusionsAlthough requiring further validation through larger studies, our findings show that POSTN might represent a novel prognostic marker for PCa.
Outcome at two years of age in a Swiss national cohort of extremely preterm infants born between 2000 and 2008
Authors: Schlapbach Luregn J , Adams Mark , Proietti Elena , Aebischer Maude , Grunt Sebastian , Borradori-Tolsa Cristina , Bickle-Graz Myriam , Bucher Hans Ulrich , Latal Beatrice , Natalucci Giancarlo ,   for the Swiss Neonatal Network & Follow-up Group
Published: December 2012

AbstractBackgroundWhile survival rates of extremely preterm infants have improved over the last decades, the incidence of neurodevelopmental disability (ND) in survivors remains high. Representative current data on the severity of disability and of risk factors associated with poor outcome in this growing population are necessary for clinical guidance and parent counselling.MethodsProspective longitudinal multicentre cohort study of preterm infants born in Switzerland between 240/7and 276/7weeks gestational age during 2000–2008. Mortality, adverse outcome (death or severe ND) at two years, and predictors for poor outcome were analysed using multilevel multivariate logistic regression. Neurodevelopment was assessed using Bayley Scales of Infant Development II. Cerebral palsy was graded after the Gross Motor Function Classification System.ResultsOf 1266 live born infants, 422 (33%) died. Follow-up information was available for 684 (81%) survivors: 440 (64%) showed favourable outcome, 166 (24%) moderate ND, and 78 (11%) severe ND. At birth, lower gestational age, intrauterine growth restriction and absence of antenatal corticosteroids were associated with mortality and adverse outcome (p < 0.001). At 360/7weeks postmenstrual age, bronchopulmonary dysplasia, major brain injury and retinopathy of prematurity were the main predictors for adverse outcome (p < 0.05). Survival without moderate or severe ND increased from 27% to 39% during the observation period (p = 0.02).ConclusionsIn this recent Swiss national cohort study of extremely preterm infants, neonatal mortality was determined by gestational age, birth weight, and antenatal corticosteroids while neurodevelopmental outcome was determined by the major neonatal morbidities. We observed an increase of survival without moderate or severe disability.
Methadone treatments in a Swiss Region, 2001–2008: a registry-based analysis
Authors: Huissoud Thérèse , Rousson Valentin , Dubois-Arber Françoise 
Published: December 2012

Abstract

Background
To determine, in a region of Switzerland, the duration of retention in opioid substitution treatments with methadone (OSTM), duration of treatment interruptions, probability of re-entry to treatment after a treatment interruption, and associated factors.

Methods
A secondary analysis of registry-based data was performed with patients (n = 2880) registered in the methadone treatment register database of the Public Health Service of the canton of Vaud between January 1, 2001 and June 30, 2008. Survival analysis and multivariate analysis was conducted.

Results
The probability of remaining on treatment was 69% at 1 year and 45% at 3 years (n =1666). One-third of patients remained on treatment beyond 5 years. The estimated hazard of leaving treatment was increased by a ratio of 1.31 in the case of a first treatment (P = 0.001), 1.83 for those without a fixed home (P < 0.001), and 1.29 for those younger than 30 years old (P < 0.001). The probability of having begun a new treatment after a first interruption was 21% at one year, 38% at 3 years, and 43% at 5 years (n = 1581). Factors at the interruption of treatment associated with a higher probability of re-entering were: interruption not due to methadone withdrawal, bad physical health, and higher methadone dose.

Conclusions
OSTM are long-term (maintenance) treatments in Switzerland. Younger age, bad living conditions at entry, and first treatment are predictors of lower retention. Approximately one-half of patients who interrupt treatment will re-enter treatment within 5 years.