Metabolic profiling and classification of propolis samples from Southern Brazil: an NMR-based platform coupled with machine learning

The chemical composition of propolis is affected by environmental factors and harvest season, making it difficult to standardize its extracts for medicinal usage. By detecting a typical chemical profile associated with propolis from a specific production region or season, certain types of propolis may be used to obtain a specific pharmacological activity. In this study, propolis from three agroecological regions (plain, plateau, and highlands) from southern Brazil, collected over the four seasons of 2010, were investigated through a novel NMR-based metabolomics data analysis workflow. Chemometrics and machine learning algorithms (PLS-DA and RF), including methods to estimate variable importance in classification, were used in this study. The machine learning and feature selection methods permitted construction of models for propolis sample classification with high accuracy (>75%, reaching 90% in the best case), better discriminating samples regarding their collection seasons comparatively to the harvest regions. PLS-DA and RF allowed the identification of biomarkers for sample discrimination, expanding the set of discriminating features and adding relevant information for the identification of the class-determining metabolites. The NMR-based metabolomics analytical platform, coupled to bioinformatic tools, allowed characterization and classification of Brazilian propolis samples regarding the metabolite signature of important compounds, i.e., chemical fingerprint, harvest seasons, and production regions.

A behavioral study of alpha-1b adrenergic receptor knockout mice: increased reaction to novelty and selectively reduced learning capacities.

Knockout mice lacking the alpha-1b adrenergic receptor were tested in behavioral experiments. Reaction to novelty was first assessed in a simple test in which the time taken by the knockout mice and their littermate controls to enter a second compartment was compared. Then the mice were tested in an open field to which unknown objects were subsequently added. Special novelty was introduced by moving one of the familiar objects to another location in the open field. Spatial behavior and memory were further studied in a homing board test, and in the water maze. The alpha-1b knockout mice showed an enhanced reactivity to new situations. They were faster to enter the new environment, covered longer paths in the open field, and spent more time exploring the new objects. They reacted like controls to modification inducing spatial novelty. In the homing board test, both the knockout mice and the control mice seemed to use a combination of distant visual and proximal olfactory cues, showing place preference only if the two types of cues were redundant. In the water maze the alpha-1b knockout mice were unable to learn the task, which was confirmed in a probe trial without platform. They were perfectly able, however, to escape in a visible platform procedure. These results confirm previous findings showing that the noradrenergic pathway is important for the modulation of behaviors such as reaction to novelty and exploration, and suggest that this is mediated, at least partly, through the alpha-1b adrenergic receptors. The lack of alpha-1b adrenergic receptors in spatial orientation does not seem important in cue-rich tasks but may interfere with orientation in situations providing distant cues only.

Genome-wide association study of recurrent major depressive disorder in two European case-control cohorts.

Major depressive disorder (MDD) is a highly prevalent disorder with substantial heritability. Heritability has been shown to be substantial and higher in the variant of MDD characterized by recurrent episodes of depression. Genetic studies have thus far failed to identify clear and consistent evidence of genetic risk factors for MDD. We conducted a genome-wide association study (GWAS) in two independent datasets. The first GWAS was performed on 1022 recurrent MDD patients and 1000 controls genotyped on the Illumina 550 platform. The second was conducted on 492 recurrent MDD patients and 1052 controls selected from a population-based collection, genotyped on the Affymetrix 5.0 platform. Neither GWAS identified any SNP that achieved GWAS significance. We obtained imputed genotypes at the Illumina loci for the individuals genotyped on the Affymetrix platform, and performed a meta-analysis of the two GWASs for this common set of approximately half a million SNPs. The meta-analysis did not yield genome-wide significant results either. The results from our study suggest that SNPs with substantial odds ratio are unlikely to exist for MDD, at least in our datasets and among the relatively common SNPs genotyped or tagged by the half-million-loci arrays. Meta-analysis of larger datasets is warranted to identify SNPs with smaller effects or with rarer allele frequencies that contribute to the risk of MDD.

MR spectroscopy of the human brain with enhanced signal intensity at ultrashort echo times on a clinical platform at 3T and 7T.

Recently, the spin-echo full-intensity acquired localized (SPECIAL) spectroscopy technique was proposed to unite the advantages of short TEs on the order of milliseconds (ms) with full sensitivity and applied to in vivo rat brain. In the present study, SPECIAL was adapted and optimized for use on a clinical platform at 3T and 7T by combining interleaved water suppression (WS) and outer volume saturation (OVS), optimized sequence timing, and improved shimming using FASTMAP. High-quality single voxel spectra of human brain were acquired at TEs below or equal to 6 ms on a clinical 3T and 7T system for six volunteers. Narrow linewidths (6.6 +/- 0.6 Hz at 3T and 12.1 +/- 1.0 Hz at 7T for water) and the high signal-to-noise ratio (SNR) of the artifact-free spectra enabled the quantification of a neurochemical profile consisting of 18 metabolites with Cramér-Rao lower bounds (CRLBs) below 20% at both field strengths. The enhanced sensitivity and increased spectral resolution at 7T compared to 3T allowed a two-fold reduction in scan time, an increased precision of quantification for 12 metabolites, and the additional quantification of lactate with CRLB below 20%. Improved sensitivity at 7T was also demonstrated by a 1.7-fold increase in average SNR (= peak height/root mean square [RMS]-of-noise) per unit-time.

EORTC Radiation Oncology Group quality assurance platform: establishment of a digital central review facility.

OBJECTIVE: Quality assurance (QA) in clinical trials is essential to ensure treatment is safely and effectively delivered. As QA requirements have increased in complexity in parallel with evolution of radiation therapy (RT) delivery, a need to facilitate digital data exchange emerged. Our objective is to present the platform developed for the integration and standardization of QART activities across all EORTC trials involving RT. METHODS: The following essential requirements were identified: secure and easy access without on-site software installation; integration within the existing EORTC clinical remote data capture system; and the ability to both customize the platform to specific studies and adapt to future needs. After retrospective testing within several clinical trials, the platform was introduced in phases to participating sites and QART study reviewers. RESULTS: The resulting QA platform, integrating RT analysis software installed at EORTC Headquarters, permits timely, secure, and fully digital central DICOM-RT based data review. Participating sites submit data through a standard secure upload webpage. Supplemental information is submitted in parallel through web-based forms. An internal quality check by the QART office verifies data consistency, formatting, and anonymization. QART reviewers have remote access through a terminal server. Reviewers evaluate submissions for protocol compliance through an online evaluation matrix. Comments are collected by the coordinating centre and institutions are informed of the results. CONCLUSIONS: This web-based central review platform facilitates rapid, extensive, and prospective QART review. This reduces the risk that trial outcomes are compromised through inadequate radiotherapy and facilitates correlation of results with clinical outcomes.

The oldest Triassic platform margin reef from the Alpine - Carpathian region (Aggtelek, NE Hungary): platform evolution, reefal biota and biostratigraphic framework

The 1:10,000 scale mapping of the southern part of the Aggtelek Plateau (Western Carpathians, Silica Nappe, NE Hungary) and the study of five sections revealed two Middle Triassic reef bodies. In the late Pelsonian the uniform Steinalm Platform was drowned and dissected due to the Reifling Event. A connection with the open sea was established, indicated by the appearance of gladigondolellid conodonts from the early Illyrian. Basins and highs were formed. In the NW part of the studied area lower - middle? Illyrian basinal carbonates were followed by a platform margin reef (early? - middle Illyrian; reef stage 1) developed on a morphological high. This is the oldest known Triassic platform margin reef within the Alpine-Carpathian region. The reef association is dominated by sphinctozoans and microproblematics. The fossils are characteristic of the Wetterstein - type reef communities. Differently from this in the SE part of the studied region a basin existed from the late Pelsonian until the early Ladinian. During the late Illyrian - early Ladinian, the reef prograded to the SE, and reef stage 2 was established. Meanwhile, on the NW part of the platform a lagoon was formed behind the reef. Based on our palaeontological study the stratigraphic range of Colospongia catenulata, Follicatena cautica, Solenolmia manon manon, Vesicocaulis oenipontanus must be extended down to the middle Illyrian. Synsedimentary tectonics were detected in the 1. Binodosus Subzone, 2. Trinodosus Zone - the most part of the Reitzi Zone, 3. Avisianum Subzone.

Genome-wide linkage and association analyses to identify genes influencing adiponectin levels: the GEMS Study.

Adiponectin has a variety of metabolic effects on obesity, insulin sensitivity, and atherosclerosis. To identify genes influencing variation in plasma adiponectin levels, we performed genome-wide linkage and association scans of adiponectin in two cohorts of subjects recruited in the Genetic Epidemiology of Metabolic Syndrome Study. The genome-wide linkage scan was conducted in families of Turkish and southern European (TSE, n = 789) and Northern and Western European (NWE, N = 2,280) origin. A whole genome association (WGA) analysis (500K Affymetrix platform) was carried out in a set of unrelated NWE subjects consisting of approximately 1,000 subjects with dyslipidemia and 1,000 overweight subjects with normal lipids. Peak evidence for linkage occurred at chromosome 8p23 in NWE subjects (lod = 3.10) and at chromosome 3q28 near ADIPOQ, the adiponectin structural gene, in TSE subjects (lod = 1.70). In the WGA analysis, the single-nucleotide polymorphisms (SNPs) most strongly associated with adiponectin were rs3774261 and rs6773957 (P < 10(-7)). These two SNPs were in high linkage disequilibrium (r(2) = 0.98) and located within ADIPOQ. Interestingly, our fourth strongest region of association (P < 2 x 10(-5)) was to an SNP within CDH13, whose protein product is a newly identified receptor for high-molecular-weight species of adiponectin. Through WGA analysis, we confirmed previous studies showing SNPs within ADIPOQ to be strongly associated with variation in adiponectin levels and further observed these to have the strongest effects on adiponectin levels throughout the genome. We additionally identified a second gene (CDH13) possibly influencing variation in adiponectin levels. The impact of these SNPs on health and disease has yet to be determined.

Ultra high throughput sequencing in human DNA variation detection: a comparative study on the NDUFA3-PRPF31 region.

BACKGROUND: Ultra high throughput sequencing (UHTS) technologies find an important application in targeted resequencing of candidate genes or of genomic intervals from genetic association studies. Despite the extraordinary power of these new methods, they are still rarely used in routine analysis of human genomic variants, in part because of the absence of specific standard procedures. The aim of this work is to provide human molecular geneticists with a tool to evaluate the best UHTS methodology for efficiently detecting DNA changes, from common SNPs to rare mutations. METHODOLOGY/PRINCIPAL FINDINGS: We tested the three most widespread UHTS platforms (Roche/454 GS FLX Titanium, Illumina/Solexa Genome Analyzer II and Applied Biosystems/SOLiD System 3) on a well-studied region of the human genome containing many polymorphisms and a very rare heterozygous mutation located within an intronic repetitive DNA element. We identify the qualities and the limitations of each platform and describe some peculiarities of UHTS in resequencing projects. CONCLUSIONS/SIGNIFICANCE: When appropriate filtering and mapping procedures are applied UHTS technology can be safely and efficiently used as a tool for targeted human DNA variations detection. Unless particular and platform-dependent characteristics are needed for specific projects, the most relevant parameter to consider in mainstream human genome resequencing procedures is the cost per sequenced base-pair associated to each machine.

A molecular platform for the diagnosis of multidrug-resistant and pre-extensively drug-resistant tuberculosis based on single nucleotide polymorphism mutations present in Colombian isolates of Mycobacterium tuberculosis

Developing a fast, inexpensive, and specific test that reflects the mutations present in Mycobacterium tuberculosis isolates according to geographic region is the main challenge for drug-resistant tuberculosis (TB) control. The objective of this study was to develop a molecular platform to make a rapid diagnosis of multidrug-resistant (MDR) and extensively drug-resistant TB based on single nucleotide polymorphism (SNP) mutations present in therpoB, katG, inhA,ahpC, and gyrA genes from Colombian M. tuberculosis isolates. The amplification and sequencing of each target gene was performed. Capture oligonucleotides, which were tested before being used with isolates to assess the performance, were designed for wild type and mutated codons, and the platform was standardised based on the reverse hybridisation principle. This method was tested on DNA samples extracted from clinical isolates from 160 Colombian patients who were previously phenotypically and genotypically characterised as having susceptible or MDR M. tuberculosis. For our method, the kappa index of the sequencing results was 0,966, 0,825, 0,766, 0,740, and 0,625 forrpoB, katG, inhA,ahpC, and gyrA, respectively. Sensitivity and specificity were ranked between 90-100% compared with those of phenotypic drug susceptibility testing. Our assay helps to pave the way for implementation locally and for specifically adapted methods that can simultaneously detect drug resistance mutations to first and second-line drugs within a few hours.

Shoulder sensorimotor control assessment by force platform: feasibility and reliability.

Given the important role of the shoulder sensorimotor system in shoulder stability, its assessment appears of interest. Force platform monitoring of centre of pressure (CoP) in upper-limb weight-bearing positions is of interest as it allows integration of all aspects of shoulder sensorimotor control. This study aimed to determine the feasibility and reliability of shoulder sensorimotor control assessment by force platform. Forty-five healthy subjects performed two sessions of CoP measurement using Win-Posturo(®) Medicapteurs force platform in an upper-limb weight-bearing position with the lower limbs resting on a table to either the anterior superior iliac spines (P1) or upper patellar poles (P2). Four different conditions were tested in each position in random order: eyes open or eyes closed with trunk supported by both hands and eyes open with trunk supported on the dominant or non-dominant side. P1 reliability values were globally moderate to high for CoP length, CoP velocity and CoP standard deviation (SD), standard error of measurement ranged from 6·0% to 26·5%, except for CoP area. P2 reliability values were globally low and not clinically acceptable. Our results suggest that shoulder sensorimotor control assessment by force platform is feasible and has good reliability in upper-limb weight-bearing positions when the lower limbs are resting on a table to the anterior superior iliac spines. CoP length, CoP velocity and CoP SD velocity appear to be the most reliable variables.

Anachronistic facies from a drowned Lower Triassic carbonate platform: Lower member of the Alwa Formation (Ba'id Exotic), Oman Mountains

- The lower member of the Alwa Formation (Lower Olenekian), found within the Ba'id Exotic in the Oman Mountains (Sultanate of Oman), consists of ammonoid-bearing, pelagic limestones that were deposited on an isolated, drowned carbonate platform on the Neotethyan Gondwana margin. The strata contain a variety of unusual carbonate textures and features, including thrombolites, Frutexites-bearing microbialites that contain synsedimentary cements, matrix-free breccias surrounded by isopachous calcite cement, and fissures and cavities filled with large botryoidal cements. Thrombolites are found throughout the study interval, and occur as 0.5-1.0 m thick lenses or beds that contain laterally laterally-linked stromatactis cavities. The Frutexites-bearing microbialites occur less frequently, and also form lenses or beds, up to 30 cm thick; the microbialites may be laminated, and often developed on hardgrounds. In addition, the Frutexites-bearing microbialites also contain synsedimentary calcite cement crusts and botryoids (typically <1 cm thick) that harbour layers or pockets of what appear to be bacterial sheaths and coccoids, and are indicative of biologically mediated precipitation of the cement bodies. Slumping following lithification led to fracturing of the limestone and the precipitation of large, botryoidal aragonite cements in fissures that cut across the primary fabric. Environmental conditions, specifically palaeoxygenation and the degree of calcium carbonate supersaturation, likely controlled whether the thrombolites (high level of calcium carbonate supersaturation associated with vertical mixing of water masses and dysoxic conditions) or Frutexites-bearing microbialites (low level of calcium carbonate supersaturation associated with anoxic conditions and deposition below a stable chemocline) formed. The results of this study point to continued environmental stress in the region during the Early Triassic that likely contributed to the uneven recovery from the Permian-Triassic mass extinction.

Is the capture success of orchid bees (Hymenoptera, Apoidea) influenced by different baited trap designs? A case study from southern Brazil

Orchid bees are increasingly applied on Neotropical biomonitoring and bioindication studies due to the relative easiness of sampling and identification when compared to other bee groups. A considerable number of orchid bee community studies have been adopting baited traps as a sampling method, especially for replication purposes. However, the trap attributes are variable, and hitherto no evaluation of different designs was carried out. Here, five attributes of baited traps were tested: trap volume, number of entrance holes, presence of landing platform, kind of landing platform, and fixation content. We use Mann-Whitney tests to access differences in richness and abundance capture rates for each trap design. We found that volume, number of entrance holes, and fixation content do not influence orchid bees capture. However, the design without landing platforms had a significantly higher capture rate for richness when compared with sanded landing platforms. On the other hand, analyzing the kind of landing platform, we detected a significantly higher richness and abundance for the trap with landing platforms glued with sand. Despite the fact that the effects of different designs tested here were very punctual, we consider that results from samples taken with different baited trap designs are comparable. Some adjustments on trap design can be done according to the particularities of future studies.

Wechsel von einem mechanischen Mikrokeratom auf einen Femtosekunden-Laser zur Korrektur von Astigmatismus mittels LASIK: klinische Ergebnisse einer retrospektiven, konsekutiven Vergleichsstudie Moving from a Mechanical Microkeratome to a Femtosecond Laser for LASIK to Correct Astigmatic Patients: Clinical Outcomes of a Retrospective, Consecutive, Comparative Study.

Background: To evaluate outcomes after optimized laser in situ keratomileusis (LASIK) for astigmatism correction with flap created by a mechanical microkeratome or a femtosecond laser. Patients and Methods: In this retrospective study, a total of 102 eyes of 71 consecutive patients were enrolled undergoing optimized LASIK treatments using the Allegretto laser system (WaveLight Laser Technologie AG, Erlangen, Germany). A mechanical microkeratome for flap creation was used (One Use, Moria®) in 46 eyes (31 patients, spherical equivalent [SE] -4.44 D ± 2.4) and a femtosecond laser was used (LDV, Ziemer®) in 56 eyes (40 patients, spherical equivalent [SE] -3.07 D ± 3.3). The two groups were matched for inclusion criteria and were operated under similar conditions by the same surgeon. Results: Overall, the preoperative spherical equivalent was -9.5 diopters (D) to +3.37 D; the preoperative manifest astigmatism was between -1.5 D and -3.5 D. At 6 months postoperatively, the mean postoperative uncorrected distance visual acuity (UDVA) was 0.93 ± 0.17 (range 0.4 to 1.2) in the Moria group and 1.0 ± 0.21 (range 0.6 to 1.6) in the Femto group, which was statistically significant (p = 0.003). Comparing the cylinder power there was a statistical difference between the two groups (p = 0.0015). Conclusions: This study shows that the method of flap creation has a significant impact on postoperative astigmatism with a significantly better postoperative UDVA in the Femto group. These findings suggest that the femtosecond laser provides a better platform for LASIK treatment of astigmatism than the commonly used microkeratome.

Dermoscopy of acral melanoma: a multicenter study on behalf of the international dermoscopy society.

Background: Most studies on dermoscopy of acral lesions were conducted in Asian populations. In this study, we analyzed these features in a predominantly Caucasian population. Objective: Estimate the prevalence of dermoscopic features in acral lesions, and assess their level of agreement between observers. Methods: In this retrospective multicenter study, 167 acral lesions (66 melanomas) were evaluated for 13 dermoscopic patterns by 26 physicians, via a secured Internet platform. Results: Parallel furrow pattern, bizarre pattern, and diffuse pigmentation with variable shades of brown had the highest prevalence. The agreement for lesion patterns between physicians was variable. Agreement was dependent on the level of diagnostic difficulty. Conclusion: Lesions with a diameter >1 cm were more likely to be melanoma. We found as well that a benign pattern can be seen in parts of melanomas. For this reason one should evaluate an acral lesion for the presence of malignant patterns first. © 2013 S. Karger AG, Basel.

Automated DNA extraction using the QIAsymphony platform: Estimation of DNA recovery from simulated forensic stains

The aim of this study was to evaluate the forensic protocol recently developed by Qiagen for the QIAsymphony automated DNA extraction platform. Samples containing low amounts of DNA were specifically considered, since they represent the majority of samples processed in our laboratory. The analysis of simulated blood and saliva traces showed that the highest DNA yields were obtained with the maximal elution volume available for the forensic protocol, that is 200 ml. Resulting DNA extracts were too diluted for successful DNA profiling and required a concentration. This additional step is time consuming and potentially increases inversion and contamination risks. The 200 ml DNA extracts were concentrated to 25 ml, and the DNA recovery estimated with real-time PCR as well as with the percentage of SGM Plus alleles detected. Results using our manual protocol, based on the QIAamp DNA mini kit, and the automated protocol were comparable. Further tests will be conducted to determine more precisely DNA recovery, contamination risk and PCR inhibitors removal, once a definitive procedure, allowing the concentration of DNA extracts from low yield samples, will be available for the QIAsymphony.