bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chlorine content and crystal chemistry of dellaite from the Birkhin gabbro massif, Eastern Siberia, Russia
Authors: Armbruster T. , Lazic B. , Gfeller F. , Galuskin E. V. , Galuskina I. O. , Savelyeva V. B. , Zadov A. E. , Pertsev N. N. , Dzierżanowski P. 
Published: June 2011

AbstractDellaite crystals of close to end-member composition, Ca6(Si2O7)(SiO4)(OH)2, and with ∼1.5 wt.% Cl. yielding Ca6(Si2O7)(SiO4)(OH)1.75Cl0.25 have been found in skarns within the gabbroid rocks of the Birkhin complex (Eastern Siberia, Russia). The greatest Cl content analysed in a dellaite domain in this skarn is 5.2 wt.% Cl corresponding to 0.8 Cl p.f.u. Dellaite occurs in altered merwmite-larnite-bredigite-gehlenite skarns and also in calcio-olivine skarns with residual larnite. The crystal structures of Cl-free and Cl-bearing (∼1.5 wt.% Cl) dellaite have been refined, including hydrogen positions, from single-crystal X-ray data to R1 = 3.7 and 3.8%, respectively. In addition, both dellaite varieties were studied by Raman spectroscopy indicating stronger hydrogen bonds for the Cl-bearing sample, which agrees with the structural data. Cl is strongly selective and enriches at one (O6) of the two OH positions allowing for the formation of a stronger hydrogen bond O8—H8…C16 compared to O8—H8…O6. Raman spectra of the domain with ∼0.8 Cl p.f.u. confirm the general enhancement of a low-frequency band in the OH range suggesting the dominance of the O—H…Cl hydrogen bond systems.Dellaite and killalaite, Ca3.2(H0.6Si2O7)(OH), have related modular structures, differentiated only by the Si2O7 units in killalaite and alternating Si2O7 and SiO4 units in dellaite. The similarity in cell dimensions and chemical composition suggests that trabzonite, Ca4Si3Oi0-2H2O, with Si3Oi0 trimers also belongs to the same family of structures.
Protein alignment algorithms with an efficient backtracking routine on multiple GPUs
Authors: Blazewicz Jacek , Frohmberg Wojciech , Kierzynka Michal , Pesch Erwin , Wojciechowski Pawel 
Published: June 2011

Abstract

Background
Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for sequence alignment methods in the nearest future. To overcome this challenge several GPU (Graphics Processing Unit) computing approaches have been proposed lately. These solutions show a great potential of a GPU platform but in most cases address the problem of sequence database scanning and computing only the alignment score whereas the alignment itself is omitted. Thus, the need arose to implement the global and semiglobal Needleman-Wunsch, and Smith-Waterman algorithms with a backtracking procedure which is needed to construct the alignment.

Results
In this paper we present the solution that performs the alignment of every given sequence pair, which is a required step for progressive multiple sequence alignment methods, as well as for DNA recognition at the DNA assembly stage. Performed tests show that the implementation, with performance up to 6.3 GCUPS on a single GPU for affine gap penalties, is very efficient in comparison to other CPU and GPU-based solutions. Moreover, multiple GPUs support with load balancing makes the application very scalable.

Conclusions
The article shows that the backtracking procedure of the sequence alignment algorithms may be designed to fit in with the GPU architecture. Therefore, our algorithm, apart from scores, is able to compute pairwise alignments. This opens a wide range of new possibilities, allowing other methods from the area of molecular biology to take advantage of the new computational architecture. Performed tests show that the efficiency of the implementation is excellent. Moreover, the speed of our GPU-based algorithms can be almost linearly increased when using more than one graphics card.
A multiplex real-time PCR assay targeting virulence and resistance genes in Salmonella entericaserotype Typhimurium
Authors: Bugarel Marie , Granier Sophie A , Weill François-Xavier , Fach Patrick , Brisabois Anne 
Published: June 2011

Abstract

Background
Typhimurium is the main serotype of Salmonella enterica subsp. enterica implicated in food-borne diseases worldwide. This study aimed to detect the prevalence of ten markers combined in a macro-array based on multiplex real-time PCR. We targeted characteristic determinants located on pathogenicity islands (SPI-2 to -5, virulence plasmid pSLT and Salmonella genomic island 1 (SGI1)) as well as a specific 16S-23S rRNA intergenic spacer sequence of definitive type 104 (DT104). To investigate antimicrobial resistance, the study also targeted the presence of genes involved in sulfonamide (sul1) and beta-lactam (bla
TEM) resistance. Finally, the intI1 determinant encoding integrase from class 1 integron was also investigated.

Results
A total of 538 unrelated S. Typhimurium strains isolated between 1999 and 2009 from various sources, including food animals, food products, human and environmental samples were studied. Based on the combined presence or absence of these markers, we distinguished 34 different genotypes, including three major genotypes encountered in 75% of the studied strains, Although SPI determinants were almost always detected, SGI1, intI1, sul1 and bla
TEM determinants were found 47%, 52%, 54% and 12% of the time respectively, varying according to isolation source. Low-marker patterns were most often detected in poultry sources whereas full-marker patterns were observed in pig, cattle and human sources.

Conclusion
The GeneDisc® assay developed in this study madeit easier to explore variability within serotype Typhimurium by analyzing ten relevant gene determinants in a large collection of strains. This real-time multiplex method constitutes a valuable tool for strains characterization on epidemiological purposes.
Agreement between pedometer and accelerometer in measuring physical activity in overweight and obese pregnant women
Authors: Kinnunen Tarja I , Tennant Peter WG , McParlin Catherine , Poston Lucilla , Robson Stephen C , Bell Ruth 
Published: June 2011

Abstract

Background
Inexpensive, reliable objective methods are needed to measure physical activity (PA) in large scale trials. This study compared the number of pedometer step counts with accelerometer data in pregnant women in free-living conditions to assess agreement between these measures.

Methods
Pregnant women (n = 58) with body mass index ≥25 kg/m2 at median 13 weeks' gestation wore a GT1M Actigraph accelerometer and a Yamax Digi-Walker CW-701 pedometer for four consecutive days. The Spearman rank correlation coefficients were determined between pedometer step counts and various accelerometer measures of PA. Total agreement between accelerometer and pedometer step counts was evaluated by determining the 95% limits of agreement estimated using a regression-based method. Agreement between the monitors in categorising participants as active or inactive was assessed by determining Kappa.

Results
Pedometer step counts correlated moderately (r = 0.36 to 0.54) with most accelerometer measures of PA. Overall step counts recorded by the pedometer and the accelerometer were not significantly different (medians 5961 vs. 5687 steps/day, p = 0.37). However, the 95% limits of agreement ranged from -2690 to 2656 steps/day for the mean step count value (6026 steps/day) and changed substantially over the range of values. Agreement between the monitors in categorising participants to active and inactive varied from moderate to good depending on the criteria adopted.

Conclusions
Despite statistically significant correlations and similar median step counts, the overall agreement between pedometer and accelerometer step counts was poor and varied with activity level. Pedometer and accelerometer steps cannot be used interchangeably in overweight and obese pregnant women.
Involvement of gut microbial fermentation in the metabolic alterations occurring in n-3 polyunsaturated fatty acids-depleted mice
Authors: Pachikian Barbara D , Neyrinck Audrey M , Portois Laurence , De Backer Fabienne C , Sohet Florence M , Hacquebard Myrjam , Carpentier Yvon A , Cani Patrice D , Delzenne Nathalie M 
Published: June 2011

Abstract

Backround
Western diet is characterized by an insufficient n-3 polyunsaturated fatty acid (PUFA) consumption which is known to promote the pathogenesis of several diseases. We have previously observed that mice fed with a diet poor in n-3 PUFA for two generations exhibit hepatic steatosis together with a decrease in body weight. The gut microbiota contributes to the regulation of host energy metabolism, due to symbiotic relationship with fermentable nutrients provided in the diet. In this study, we have tested the hypothesis that perturbations of the gut microbiota contribute to the metabolic alterations occurring in mice fed a diet poor in n-3 PUFA for two generations (n-3/- mice).

Methods
C57Bl/6J mice fed with a control or an n-3 PUFA depleted diet for two generations were supplemented with prebiotic (inulin-type Fructooligosaccharides, FOS, 0.20 g/day/mice) during 24 days.

Results
n-3/-mice exhibited a marked drop in caecum weight, a decrease in lactobacilli and an increase in bifidobacteria in the caecal content as compared to control mice (n-3/+ mice). Dietary supplementation with FOS for 24 days was sufficient to increase caecal weight and bifidobacteria count in both n-3/+ and n-3/-mice. Moreover, FOS increased lactobacilli content in n-3/-mice, whereas it decreased their level in n-3/+ mice. Interestingly, FOS treatment promoted body weight gain in n-3/-mice by increasing energy efficiency. In addition, FOS treatment decreased fasting glycemia and lowered the higher expression of key factors involved in the fatty acid catabolism observed in the liver of n-3/-mice, without lessening steatosis.

Conclusions
the changes in the gut microbiota composition induced by FOS are different depending on the type of diet. We show that FOS may promote lactobacilli and counteract the catabolic status induced by n-3 PUFA depletion in mice, thereby contributing to restore efficient fat storage.
Survey on medicinal plants and spices used in Beni-Sueif, Upper Egypt
Authors: AbouZid Sameh F , Mohamed Abdelhalim A 
Published: June 2011

Abstract
Background
This study was conducted to identify medicinal plants and spices used for medicine by the community of Beni-Sueif, Upper Egypt.

Methods
Ethnobotanical data from local people was collected using direct interviews and a semi-structured questionnaire.

Results
Forty-eight plant species belonging to twenty-seven families and forty-seven genera were encountered during the study. Their botanical and vernacular names, plant parts used and medicinal uses are given. Results of the study were analyzed using two quantitative tools. The factor informant consensus indicated the agreement in the use of plants and the fidelity level indicated the ratio between the number of informants who independently suggested the use of a species for the same major purpose and the total number of informants who mentioned the plant for any use. The results of the factor informant consensus showed that the cardiovascular category has the greatest agreement, followed by the immunological, gastrointestinal and respiratory categories. The most important species according to their fidelity are: Hibiscus sabdariffa L. for the cardiovascular category; Trigonella foenum-graecum L. for the immunological category; Mentha piperita L. for the gastrointestinal category and Pimpinella anisum L. for the respiratory category.

Conclusions
Medicinal plants are still used for treatment in Beni-Sueif community despite the availability of prescribed medications. Documentation of this ethnomedicinal knowledge is important. Evaluation of pharmacological activity for the promising medicinal plants is suggested.
Reconsidering low-dose aspirin therapy for cardiovascular disease: a study protocol for physician and patient behavioral change
Authors: Folks Brittany , LeBlanc William G , Staton Elizabeth W , Pace Wilson D 
Published: June 2011

Abstract

Background
There are often disparities between current evidence and current practice. Decreasing the gap between desired practice outcomes and observed practice outcomes in the healthcare system is not always easy. Stopping previously recommended or variably recommended interventions may be even harder to achieve than increasing the use of a desired but under-performed activity. For over a decade, aspirin has been prescribed for primary prevention of cardiovascular disease and for patients with the coronary artery disease risk equivalents; yet, there is no substantial evidence of an appropriate risk-benefit ratio to support this practice. This paper describes the protocol of a randomized trial being conducted in six primary care practices in the Denver metropolitan area to examine the effectiveness of three interventional strategies to change physician behavior regarding prescription of low-dose aspirin.

Methods
All practices received academic detailing, one arm received clinician reminders to reconsider aspirin, a second arm received both clinician and patient messages to reconsider aspirin. The intervention will run for 15 to 18 months. Data collected at baseline and for outcomes from an electronic health record will be used to assess pre- and post-interventional prescribing, as well as to explore any inappropriate decrease in aspirin use by patients with known cardiovascular disease.

Discussion
This study was designed to investigate effective methods of changing physician behavior to decrease the use of aspirin for primary cardiovascular disease prevention. The results of this study will contribute to the small pool of knowledge currently available on the topic of ceasing previously supported practices.

Trial Registration
ClinicalTrials.gov: NCT01247454
Integrative network analysis reveals active microRNAs and their functions in gastric cancer
Authors: Tseng Chien-Wei , Lin Chen-Ching , Chen Chiung-Nien , Huang Hsuan-Cheng , Juan Hsueh-Fen 
Published: June 2011

AbstractBackgroundMicroRNAs (miRNAs) are a class of endogenous, small and highly conserved noncoding RNAs that control gene expression either by degradation of target mRNAs or by inhibition of protein translation. They play important roles in cancer progression. A single miRNA can provoke a chain reaction and further affect protein interaction network (PIN). Therefore, we developed a novel integrative approach to identify the functional roles and the regulated PIN of oncomirs.ResultsWe integrated the expression profiles of miRNA and mRNA with the human PIN to reveal miRNA-regulated PIN in specific biological conditions. The potential functions of miRNAs were determined by functional enrichment analysis and the activities of miRNA-regulated PINs were evaluated by the co-expression of protein-protein interactions (PPIs). The function of a specific miRNA, miR-148a, was further examined by clinical data analysis and cell-based experiments. We uncovered several miRNA-regulated networks which were enriched with functions related to cancer progression. One miRNA, miR-148a, was identified and its function is to decrease tumor proliferation and metastasis through its regulated PIN. Furthermore, we found that miR-148a could reduce the invasiveness, migratory and adhesive activities of gastric tumor cells. Most importantly, elevated miR-148a level in gastric cancer tissues was strongly correlated with distant metastasis, organ and peritoneal invasion and reduced survival rate.ConclusionsThis study provides a novel method to identify active oncomirs and their potential functions in gastric cancer progression. The present data suggest that miR-148a could be a potential prognostic biomarker of gastric cancer and function as a tumor suppressor through repressing the activity of its regulated PIN.
Deprivation of Liberty Safeguards in England: implementation
costs
Authors: Shah Ajit , Pennington Mark , Heginbotham Chris , Donaldson Cam 
Published: June 2011

BackgroundThe Deprivation of Liberty Safeguards (DoLS), introduced into the Mental
Capacity Act 2005, were fully implemented on 1 April 2009 in England and
Wales. The government estimated 20 000 assessments for DoLS at a cost of
£600 per assessment.AimsTo estimate the costs likely to be incurred with the implementation of
DoLS in England.MethodThe cost of conducting a single DoLS assessment was estimated using
resource-utilisation data ascertained from 37 professionals, secretarial
staff and independent mental capacity advocates involved with DoLS
assessments in six diverse local DoLS offices.ResultsThe estimated average cost of a single DoLS assessment was £1277.ConclusionsThe estimated average cost of a single DoLS assessment was significantly
higher than the £600 estimated by the government. However, the allocated
budget, based on 20 000 estimated DoLS assessments in the first year of
its implementation, is likely to be adequate because a significantly
lower number of assessments (only 5200) were conducted in the first 9
months after its implementation.
Secondary Somatic Mutations RestoringBRCA1/2Predict Chemotherapy Resistance in Hereditary Ovarian Carcinomas
Authors: Norquist Barbara , Wurz Kaitlyn A. , Pennil Christopher C. , Garcia Rochelle , Gross Jenny , Sakai Wataru , Karlan Beth Y. , Taniguchi Toshiyasu , Swisher Elizabeth M. 
Published: June 2011

PurposeSecondary somatic BRCA1/2 mutations may restore BRCA1/2 protein in hereditary ovarian carcinomas. In cell lines, BRCA2 restoration mediates resistance to platinum chemotherapy and poly (ADP-ribose) polymerase (PARP) inhibitors. We assessed primary and recurrent BRCA1/2-mutated ovarian carcinomas to define the frequency of secondary mutations and correlate these changes with clinical outcomes.MethodsNeoplastic cells were isolated with laser capture microdissection, and DNA was sequenced at the site of the known germline BRCA1/2 mutation. When secondary mutations were found that restored wild-type sequence, haplotyping was performed using single nucleotide polymorphisms in tumor and paired lymphocyte DNA to rule out retention of the wild-type allele.ResultsThere were 64 primary and 46 recurrent ovarian carcinomas assessed. Thirteen (28.3%) of 46 (95% CI, 17.3% to 42.6%) recurrent carcinomas had a secondary mutation compared with two (3.1%) of 64 (95% CI, 1.0% to 10.7%) primary carcinomas (P = .0003, Fisher's exact test). Twelve (46.2%) of 26 (95% CI, 28.7% to 64.7%) platinum-resistant recurrences had secondary mutations restoring BRCA1/2, compared with one (5.3%) of 19 (95% CI, 1.2% to 24.8%) platinum-sensitive recurrences (P = .003, Fisher's exact test). Six (66.7%) of nine (95% CI, 34.8% to 87.8%) women with prior breast carcinoma had a recurrent carcinoma with a secondary mutation, compared with six (17.1%) of 35 (95% CI, 8.2% to 32.8%) with no history of breast carcinoma (P = .007, Fisher's exact test).ConclusionSecondary somatic mutations that restore BRCA1/2 in carcinomas from women with germline BRCA1/2 mutations predict resistance to platinum chemotherapy and may also predict resistance to PARP inhibitors. These mutations were detectable only in ovarian carcinomas of women whom have had previous chemotherapy, either for ovarian or breast carcinoma.
Relapsed or Refractory Anaplastic Large-Cell Lymphoma in Children and Adolescents After Berlin-Frankfurt-Muenster (BFM)–Type First-Line Therapy: A BFM-Group Study
Authors: Woessmann Willi , Zimmermann Martin , Lenhard Meike , Burkhardt Birgit , Rossig Claudia , Kremens Bernhard , Lang Peter , Attarbaschi Andishe , Mann Georg , Oschlies Ilske , Klapper Wolfram , Reiter Alfred 
Published: June 2011

Purpose To evaluate risk factors for outcome in children and adolescents with relapse of anaplastic large-cell lymphoma (ALCL) after comparable first-line therapy. Patients and Methods We analyzed a population-based cohort of 74 children with relapsed ALCL after Berlin-Frankfurt-Muenster–type first-line therapy between April 1990 and December 2003. The recommended salvage strategy was reinduction chemotherapy followed by autologous hematopoietic stem-cell transplantation (SCT). Results With a median follow-up time of 8.4 years (range, 4.5 to 16.4 years), the 5-year overall survival (OS) rate after first relapse was 57% ± 6%. Survival correlated with time of relapse and clinically advanced dissemination. Five-year OS of 16 patients who experienced progression during first-line therapy was 25% ± 11% compared with 66% ± 6% for 58 patients with a later relapse (P = .002). Five-year OS of 11 patients with bone marrow or CNS involvement was 27% ± 13% compared with 62% ± 6% for 63 patients without involvement (P = .001). Five-year event-free survival (EFS) and OS of 39 children who received the recommended autologous SCT were 59% ± 8% and 77% ± 7%, respectively. EFS after autologous SCT was significantly associated with time to relapse (progression: n = 3; EFS, 0; later relapse: n = 36; EFS, 64% ± 8%; P = .014) and CD3 expression (CD3 negative: n = 25; EFS, 72% ± 9%; CD3 positive: n = 11; EFS, 18% ± 12%; P < .001), but not with site of relapse, conditioning regimen, or graft manipulation. No relapses occurred among 10 patients with relapsed CD3-positive ALCL treated with allogeneic SCT. Conclusion Reinduction chemotherapy followed by autologous SCT proved feasible and efficacious for patients with a first relapse of CD3-negative ALCL after first-line therapy. Patients with progression during first-line therapy or relapsed CD3-positive ALCL may benefit from allogeneic SCT.
Phonological similarity in multi-word units
Authors: Gries Stefan Th. 
Published: June 2011

Abstract
In this paper, I investigate the phonological similarity of different elements of the phonological pole of multi-word units. I discuss two case studies on slightly different levels of abstractness. The first case study investigates lexically fully-specified V-NPDirObj idioms such as kick the bucket and lose one's cool; the idioms investigated are taken from the Collins Cobuild Dictionary of Idioms (Harper Collins, 2002). The second case study investigates the lexically less specified way-construction, which is exemplified by He fought his way through the crowd (cf. Goldberg, Constructions: A Construction Grammar approach to argument structure, The University of Chicago Press, 1995: Ch. 9), on the basis of data from the British National Corpus 1.0.
I show that both patterns exhibit a strong phonological within-pole relation, namely a strong preference for having their slots filled with phonologically similar elements, where phonological similarity is manifested in alliteration patterns. These preferences are statistically significant when compared to chance-level expectations derived both from the corpora and from the CELEX database (Baayen et al., The CELEX Lexical Database (CD-ROM), University of Pennsylvania, 1995) and are explained on the basis of Langacker's concept of syntactic and phonological constituents as well as current exemplar-/usage-based approaches.