Qualitative analysis by online nuclear magnetic resonance using Carr-Purcell-Meiboom-Gill sequence with low refocusing flip angles

The Carr-Purcell-Meiboom-Gill (CPMG) pulse sequence has been used in many applications of magnetic resonance imaging (MRI) and low-resolution NMR (LRNMR) spectroscopy. Recently. CPMG was used in online LRNMR measurements that use long RF pulse trains, causing an increase in probe temperature and, therefore, tuning and matching maladjustments. To minimize this problem, the use of a low-power CPMG sequence based on low refocusing pulse flip angles (LRFA) was studied experimentally and theoretically. This approach has been used in several MRI protocols to reduce incident RF power and meet the specific absorption rate. The results for CPMG with LRFA of 3 pi/4 (CPMG(135)), pi/2 (CPMG(90)) and pi/4 (CPMG(45)) were compared with conventional CPMG with refocusing pi pulses. For a homogeneous field, with linewidth equal to Delta nu = 15 Hz, the refocusing flip angles can be as low as pi/4 to obtain the transverse relaxation time (T(2)) value with errors below 5%. For a less homogeneous magnetic field. Delta nu = 100 Hz, the choice of the LRFA has to take into account the reduction in the intensity of the CPMG signal and the increase in the time constant of the CPMG decay that also becomes dependent on longitudinal relaxation time (T(1)). We have compared the T(2) values measured by conventional CPMG and CPMG(90) for 30 oilseed species, and a good correlation coefficient, r = 0.98, was obtained. Therefore, for oilseeds, the T(2) measurements performed with pi/2 refocusing pulses (CPMG(90)), with the same pulse width of conventional CPMG, use only 25% of the RF power. This reduces the heating problem in the probe and reduces the power deposition in the samples. (C) 2011 Elsevier B.V. All rights reserved.

Microfacies and sequence stratigraphy of the Amapa Formation, Late Paleocene to Early Eocene, Foz do Amazonas Basin, Brazil

On the basis of thin-section studies of cuttings and a core from two wells in the Amapa Formation of the Foz do Amazonas Basin, five main microfacies have been recognized within three stratigraphic sequences deposited during the Late Paleocene to Early Eocene. The facies are: 1) Ranikothalia grainstone to packstone facies; 2) ooidal grainstone to packstone facies; 3) larger foraminiferal and red algal grainstone to packstone facies; 4) Amphistegina and Helicostegina packstone facies; and 5) green algal and small benthic foraminiferal grainstone to packstone facies, divisible locally into a green algal and the miliolid foraminiferal subfacies and a green algal and small rotaliine foraminiferal subfacies. The lowermost sequence (Si) was deposited in the Late Paleocene-Early Eocene (biozone LF1, equivalent to P3-P6?) and includes rudaceous grainstones and packstones with large specimens of Ranikothalia bermudezi representative of the mid- and inner ramp. The intermediate and uppermost sequences (S2 and S3) display well-developed lowstand deposits formed at the end of the Late Paleocene (upper biozone LF1) and beginning of the Early Eocene (biozone LF2) on the inner ramp (larger foraminiferal and red algal grainstone to packstone facies), in lagoons (green algal and small benthic foraminiferal facies) and as shoals (ooidal facies) or banks (Amphistegina and Helicostegina facies). Depth and oceanic influence were the main controls on the distribution of these microfacies. Stratal stacking patterns evident within these sequences may well have been related to sea level changes postulated for the Late Paleocene and Early Eocene. During this time, the Amapa Formation was dominated by cyclic sedimentation on a gently sloping ramp. Environmental and ecological stress brought about by sea level change at the end of the biozone LF1 led to the extinction of the larger foraminifera (Ranikothalia bermudezi). (c) 2009 Elsevier B.V. All rights reserved.

Plasmodium vivax Duffy binding protein: baseline antibody responses and parasite polymorphisms in a well-consolidated settlement of the Amazon Region

Objective To investigate risk factors associated with the acquisition of antibodies against Plasmodium vivax Duffy binding protein (PvDBP) a leading malaria vaccine candidate in a well-consolidated agricultural settlement of the Brazilian Amazon Region and to determine the sequence diversity of the PvDBP ligand domain (DBPII) within the local malaria parasite population. Methods Demographic, epidemiological and clinical data were collected from 541 volunteers using a structured questionnaire. Malaria parasites were detected by conventional microscopy and PCR, and blood collection was used for antibody assays and molecular characterisation of DBPII. Results The frequency of malaria infection was 7% (6% for P. vivax and 1% for P. falciparum), with malaria cases clustered near mosquito breeding sites. Nearly 50% of settlers had anti-PvDBP IgG antibodies, as detected by enzyme-linked immunosorbent assay (ELISA) with subjects age being the only strong predictor of seropositivity to PvDBP. Unexpectedly, low levels of DBPII diversity were found within the local malaria parasites, suggesting the existence of low gene flow between P. vivax populations, probably due to the relative isolation of the studied settlement. Conclusion The recognition of PvDBP by a significant proportion of the community, associated with low levels of DBPII diversity among local P. vivax, reinforces the variety of malaria transmission patterns in communities from frontier settlements. Such studies should provide baseline information for antimalarial vaccines now in development.

A Simple Artificial Life Model Explains Irrational Behavior in Human Decision-Making

Although praised for their rationality, humans often make poor decisions, even in simple situations. In the repeated binary choice experiment, an individual has to choose repeatedly between the same two alternatives, where a reward is assigned to one of them with fixed probability. The optimal strategy is to perseverate with choosing the alternative with the best expected return. Whereas many species perseverate, humans tend to match the frequencies of their choices to the frequencies of the alternatives, a sub-optimal strategy known as probability matching. Our goal was to find the primary cognitive constraints under which a set of simple evolutionary rules can lead to such contrasting behaviors. We simulated the evolution of artificial populations, wherein the fitness of each animat (artificial animal) depended on its ability to predict the next element of a sequence made up of a repeating binary string of varying size. When the string was short relative to the animats' neural capacity, they could learn it and correctly predict the next element of the sequence. When it was long, they could not learn it, turning to the next best option: to perseverate. Animats from the last generation then performed the task of predicting the next element of a non-periodical binary sequence. We found that, whereas animats with smaller neural capacity kept perseverating with the best alternative as before, animats with larger neural capacity, which had previously been able to learn the pattern of repeating strings, adopted probability matching, being outperformed by the perseverating animats. Our results demonstrate how the ability to make predictions in an environment endowed with regular patterns may lead to probability matching under less structured conditions. They point to probability matching as a likely by-product of adaptive cognitive strategies that were crucial in human evolution, but may lead to sub-optimal performances in other environments.

Implementing the Objective Structured Clinical Examination in a Geriatrics Fellowship Program-A 3-Year Experience

The Objective Structured Clinical Examination (OSCE) appears to be an effective alternative for assessing not only medical knowledge, but also clinical skills, including effective communication and physical examination skills. The purpose of the current study was to implement an OSCE model in a geriatrics fellowship program and to compare the instrument with traditional essay examination. Seventy first- and second-year geriatric fellows were initially submitted to a traditional essay examination and scored from 0 to 10 by a faculty member. The same fellows subsequently underwent an OSCE with eight 10-minute stations covering a wide range of essential aspects of geriatric knowledge. Each OSCE station had an examiner responsible for its evaluation according to a predefined checklist. Checklist items were classified for analysis purposes as clinical knowledge items (CKI) and communication skills items (CSI); fellow responses were scored from 0 to 10.Although essay examinations took from 30 to 45 minutes to complete, 180200 minutes were required to evaluate fellows using the proposed OSCE method. Fellows scored an average of 6.2 +/- 1.2 on the traditional essay examination and 6.6 +/- 1.0 on the OSCE (P < .001). Subanalyses of OSCE scores indicated that average performance on CKI was lower than the average on CSI (6.4 +/- 1.1 vs. 8.4 +/- 1.1; P < .001). Fellow performance on the essay examination was similar to their performance on CKI (P = .13). Second-year fellows performed better than first-year fellows on the essay examination (P < .001) and CKI (P = .05), but not on CSI (P = .25).The OSCE was successfully implemented as an educational strategy during a geriatrics fellowship program. Combining different testing modalities may provide the best assessment of competence for various domains of knowledge, skills, and behavior.

Assessing Pathogenicity for Novel Mutation/Sequence Variants: The Value of Healthy Older Individuals

Improvement in DNA technology is increasingly revealing unexpected/unknown mutations in healthy persons and generating anxiety due to their still unknown health consequences. We report a 44-year-old healthy father of a 10-year-old daughter with bilateral coloboma and hearing loss, but without muscle weakness, in whom a whole-genome CGH revealed a deletion of exons 38-44 in the dystrophin gene. This mutation was inherited from her asymptomatic father, who was further clinically and molecularly evaluated for prognosis and genetic counseling (GC). This deletion was never identified by us in 982 Duchenne/Becker patients. To assess whether the present case represents a rare case of non-penetrance, and aiming to obtain more information for prognosis and GC, we suggested that healthy older relatives submit their DNA for analysis, to which several complied. Mutation analysis revealed that his mother, brother, and 56-year-old maternal uncle also carry the 38-44 deletion, suggesting it an unlikely cause of muscle weakness. Genome sequencing will disclose mutations and variants whose health impact are still unknown, raising important problems in interpreting results, defining prognosis, and discussing GC. We suggest that, in addition to family history, keeping the DNA of older relatives could be very informative, in particular for those interested in having their genome sequenced.

Whole-rock geochemistry and Sr-Nd isotopic composition of the pre-rift sequence of the Camamu Basin, northeastern Brazil

Whole-rock geochemistry, combined with Sr-Nd isotopic composition of pelitic sedimentary rocks, have been considered to be useful parameters to estimate not only their provenance but also to make inferences about their depositional environment as well as the weathering processes they have been through. The basal sedimentary units of the basins of the northeastern Brazilian continental margin, particularly those of the pre-rift sequence, have been subject of interest of studies based on chemical and isotopic data, since they lack fossil content to establish their age and, therefore, stratigraphic correlations are difficult. The major and trace element contents as well as Sr-Nd isotopic compositions of whole-rock shale samples from five outcrops attributed to the pre-rift supersequence of the Camamu Basin were analyzed with the purpose of characterizing and obtaining further information that would allow a better correlation between the sites studied. The geochemical data suggest that the rocks exposed in the studied outcrops are part of the same sedimentary unit and that they might be correlated to the Capianga Member of the Alianca Formation of the Reconcavo Basin, exposed to the north of the Camamu Basin. The chemical index of alteration (CIA) suggests conditions associated with a humid tropical/subtropical climate at the time of deposition. Nd isotopic compositions indicate provenance from the Paleoproterozoic rocks of the Sao Francisco craton. The results presented here, therefore, show that the combined use of chemical and isotopic analyses may be of great interest to characterize and correlate lithologically homogeneous clastic sedimentary sequences. (C) 2012 Elsevier Ltd. All rights reserved.

Genome Sequence of the Bacterioplanktonic, Mixotrophic Vibrio campbellii Strain PEL22A, Isolated in the Abrolhos Bank

Vibrio campbellii PEL22A was isolated from open ocean water in the Abrolhos Bank. The genome of PEL22A consists of 6,788,038 bp (the GC content is 45%). The number of coding sequences (CDS) is 6,359, as determined according to the Rapid Annotation using Subsystem Technology (RAST) server. The number of ribosomal genes is 80, of which 68 are tRNAs and 12 are rRNAs. V. campbellii PEL22A contains genes related to virulence and fitness, including a complete proteorhodopsin cluster, complete type II and III secretion systems, incomplete type I, IV, and VI secretion systems, a hemolysin, and CTX Phi.

Complete Sequence of Broad-Host-Range Plasmid pRIO-5 Harboring the Extended-Spectrum-beta-Lactamase Gene bla(BES-1)

Broad-host-range plasmid pRIO-5, harboring the extended-spectrum beta-lactamase bla(BES-1) gene in Serratia marcescens, was fully sequenced. Analysis of the 12,957-bp sequence of this IncP6-type plasmid revealed that the bla(BES-1) gene was associated with two copies of the insertion sequence IS26. The promoter responsible for the bla(BES-1) expression was hybrid, made of a - 35 box located inside the inverted repeat of IS26 and a - 10 box inside a remnant of an insertion sequence.

A countably compact free Abelian group of size continuum that admits a non-trivial convergent sequence

We show that it is consistent with ZFC that the free Abelian group of cardinality c admits a topological group topology that makes it countably compact with a non-trivial convergent sequence. (C) 2011 Elsevier B.V. All rights reserved.

Analysis of expressed sequence tags from the agarophyte Gracilaria tenuistipitata (Rhodophyta)

A total of 3,631 expressed sequence tags (ESTs) were established from two size-selected cDNA libraries made from the tetrasporophytic phase of the agarophytic red alga Gracilaria tenuistipitata. The average sizes of the inserts in the two libraries were 1,600 bp and 600 bp, with an average length of the edited sequences of 850 bp. Clustering gave 2,387 assembled sequences with a redundancy of 53%. Of the ESTs, 65% had significant matches to sequences deposited in public databases, 11% to proteins without known function, and 35% were novel. The most represented ESTs were a Na/K-transporting ATPase, a hedgehog-like protein, a glycine dehydrogenase and an actin. Most of the identified genes were involved in primary metabolism and housekeeping. The largest functional group was thus genes involved in metabolism with 14% of the ESTs; other large functional categories included energy, transcription, and protein synthesis and destination. The codon usage was examined using a subset of the data, and the codon bias was found to be limited with all codon combinations used.

Genome Sequence of Exiguobacterium antarcticum B7, Isolated from a Biofilm in Ginger Lake, King George Island, Antarctica

Exiguobacterium antarcticum is a psychotropic bacterium isolated for the first time from microbial mats of Lake Fryxell in Antarctica. Many organisms of the genus Exiguobacterium are extremophiles and have properties of biotechnological interest, e. g., the capacity to adapt to cold, which make this genus a target for discovering new enzymes, such as lipases and proteases, in addition to improving our understanding of the mechanisms of adaptation and survival at low temperatures. This study presents the genome of E. antarcticum B7, isolated from a biofilm sample of Ginger Lake on King George Island, Antarctic peninsula.

Trichoderma harzianum expressed sequence tags for identification of genes with putative roles in mycoparasitism against Fusarium solani

The plant pathogen Fusarium solani causes a disease root rot of common bean (Phaseolus vulgaris) resulting in great losses of yield in irrigated areas of the Southeast and Midwest regions of Brazil. Species of the genus Trichoderma have been used in the biological control of this pathogen as an alternative to chemical control. To gain new insights into the biocontrol mechanism used by Trichoderma harzianum against the phytopathogenic fungus, Fusarium solani, we performed a transcriptome analysis using expressed sequence tags (ESTs) and quantitative real-time PCR (RT-qPCR) approaches. A cDNA library from T. harzianum mycelium (isolate ALL42) grown on cell walls of F. solani (CWFS) was constructed and analyzed. A total of 2927 high quality sequences were selected from 3845 and 37.7% were identified as unique genes. The Gene Ontology analysis revealed that the majority of the annotated genes are involved in metabolic processes (80.9%), followed by cellular process (73.7%). We tested twenty genes that encode proteins with potential role in biological control. RT-qPCR analysis showed that none of these genes were expressed when T. harzianum was challenged with itself. These genes showed different patterns of expression during in vitro interaction between T. harzianum and F. solani. (C) 2012 Elsevier Inc. All rights reserved.

SIS: a program to generate draft genome sequence scaffolds for prokaryotes

Background: Decreasing costs of DNA sequencing have made prokaryotic draft genome sequences increasingly common. A contig scaffold is an ordering of contigs in the correct orientation. A scaffold can help genome comparisons and guide gap closure efforts. One popular technique for obtaining contig scaffolds is to map contigs onto a reference genome. However, rearrangements that may exist between the query and reference genomes may result in incorrect scaffolds, if these rearrangements are not taken into account. Large-scale inversions are common rearrangement events in prokaryotic genomes. Even in draft genomes it is possible to detect the presence of inversions given sufficient sequencing coverage and a sufficiently close reference genome. Results: We present a linear-time algorithm that can generate a set of contig scaffolds for a draft genome sequence represented in contigs given a reference genome. The algorithm is aimed at prokaryotic genomes and relies on the presence of matching sequence patterns between the query and reference genomes that can be interpreted as the result of large-scale inversions; we call these patterns inversion signatures. Our algorithm is capable of correctly generating a scaffold if at least one member of every inversion signature pair is present in contigs and no inversion signatures have been overwritten in evolution. The algorithm is also capable of generating scaffolds in the presence of any kind of inversion, even though in this general case there is no guarantee that all scaffolds in the scaffold set will be correct. We compare the performance of SIS, the program that implements the algorithm, to seven other scaffold-generating programs. The results of our tests show that SIS has overall better performance. Conclusions: SIS is a new easy-to-use tool to generate contig scaffolds, available both as stand-alone and as a web server. The good performance of SIS in our tests adds evidence that large-scale inversions are widespread in prokaryotic genomes.

The impact of structured teaching methods on the quality of education in Brazil

This paper estimates the impact of the use of structured methods on the quality of education for students in primary public school in Brazil. Structured methods encompass a range of pedagogical and managerial instruments applied in the educational system. In recent years, several municipalities in the state of Sao Paulo have contracted out private educational providers to implement these structured methods in their schooling systems. Their pedagogical proposal involves structuring of curriculum content, development of teacher and student textbooks, and the training and supervision of teachers anti instructors. Using a difference-in-differences estimation strategy, we find that the 4th- and 8th-grade students in the municipalities with structured methods performed better in Portuguese and mathematics than did students in municipalities not exposed to these methods. We find no differences in passing rates. A robustness test supports the assumption that there is no unobserved municipal characteristics associated with proficiency changes over time that may affect the results. (C) 2012 Elsevier Ltd. All rights reserved.