Analyses Of Raw Data Research Articles

Pediatric AIDS-Therapeutic Successes Built on a Foundation of Pediatric Clinical Pharmacology with Pharmacokinetic-Pharmacodynamic Modeling.

Pediatric AIDS-Therapeutic Successes Built on a Foundation of Pediatric Clinical Pharmacology with Pharmacokinetic-Pharmacodynamic Modeling.

A hierarchical N-mixture model to estimate behavioral variation and a case study of Neotropical birds.

Understanding how and why animals use the environments where they occur is both foundational to behavioral ecology and essential to identify critical habitats for species conservation. However, some behaviors are more difficult to observe than others, which can bias analyses of raw observational data. To our knowledge, no method currently exists to model how animals use different environments while accounting for imperfect behavior-specific detection probability. We developed an extension of a binomial N-mixture model (hereafter the behavior N-mixture model) to estimate the probability of a given behavior occurring in a particular environment while accounting for imperfect detection. We then conducted a simulation to validate the model's ability to estimate the effects of environmental covariates on the probabilities of individuals performing different behaviors. We compared our model to a naïve model that does not account for imperfect detection, as well as a traditional N-mixture model. Finally, we applied the model to a bird observation data set in northwest Costa Rica to quantify how three species behave in forests and farms. Simulations and sensitivity analyses demonstrated that the behavior N-mixture model produced unbiased estimates of behaviors and their relationships with predictor variables (e.g., forest cover, habitat type). Importantly, the behavior N-mixture model accurately characterized uncertainty, unlike the naïve model, which often suggested erroneous effects of covariates on behaviors. When applied to field data, the behavior N-mixture model suggested that Hoffmann's woodpecker (Melanerpes hoffmanii) and Inca dove (Columbina inca) behaved differently in forested versus agricultural habitats, while turquoise-browed motmot (Eumomota superciliosa) did not. Thus, the behavior N-mixture model can help identify habitats that are essential to a species' life cycle (e.g., where individuals nest, forage) that nonbehavioral models would miss. Our model can greatly improve the appropriate use of behavioral survey data and conclusions drawn from them. In doing so, it provides a valuable path forward for assessing the conservation value of alternative habitat types.

Data Availability of Open T-Cell Receptor Repertoire Data, a Systematic Assessment

Modern data-driven research has the power to promote novel biomedical discoveries through secondary analyses of raw data. Therefore, it is important to ensure data-driven research with great reproducibility and robustness for promoting a precise and accurate secondary analysis of the immunogenomics data. In scientific research, rigorous conduct in designing and conducting experiments is needed, specifically in scientific writing and reporting results. It is also crucial to make raw data available, discoverable, and well described or annotated in order to promote future re-analysis of the data. In order to assess the data availability of published T cell receptor (TCR) repertoire data, we examined 11,918 TCR-Seq samples corresponding to 134 TCR-Seq studies ranging from 2006 to 2022. Among the 134 studies, only 38.1% had publicly available raw TCR-Seq data shared in public repositories. We also found a statistically significant association between the presence of data availability statements and the increase in raw data availability (p = 0.014). Yet, 46.8% of studies with data availability statements failed to share the raw TCR-Seq data. There is a pressing need for the biomedical community to increase awareness of the importance of promoting raw data availability in scientific research and take immediate action to improve its raw data availability enabling cost-effective secondary analysis of existing immunogenomics data by the larger scientific community.

Tools and applications for integrative analysis of DNA methylation in social insects.

DNA methylation is a common epigenetic signalling tool and an important biological process which is widely studied in a large array of species. The presence, level and function of DNA methylation vary greatly across species. In some insects, DNA methylation systems are minimal, and overall methylation rates tend to be low in all studied insect species. Low methylation levels probed by whole-genome bisulphite sequencing require great care with respect to data quality control and interpretation. Here, we introduce BWASP/R, a complete workflow that allows efficient, scalable and entirely reproducible analyses of raw DNA methylation sequencing data. Consistent application of quality control filters and analysis parameters provides fair comparisons among different studies and an integrated view of all experiments on one species. We describe the capabilities of the BWASP/R workflow by re-analysing several publicly available social insect WGBS data sets, comprising 70samples and cumulatively 147 replicates from four different species. We show that the CpG methylome comprises only about 1.5% of CpG sites in the honeybee genome and that the cumulative data are consistent with genetic signatures of site accessibility and physiological control of methylation levels.

Quantifying morphological adaptations using direct measurements: The carnivoran appendicular skeleton as a case study.

Here, I study whether locomotor adaptations can be detected in limb bones using a univariate approach, and whether those results are affected by size and/or shared evolutionary history. Ultimately, it tests whether classical papers on locomotor adaptations should be trusted. To do that, I analyzed the effect of several factors (size, taxonomic group, and locomotor habit) on limb bone morphology using a set of 43 measurements of the scapula, long bones, and calcaneus, of 435 specimens belonging to 143 carnivoran species. Size was the main factor affecting limb morphology. Size-corrected analyses revealed artifactual differences between various locomotion-related categories in the analyses of raw data. Additionally, several between-group differences were new to the size-corrected analyses, suggesting that they were masked by the size-effect. Phylogeny had also an important effect, although it only became apparent after removing the effect of size, probably due to the strong covariation of both factors. Regarding locomotor adaptations, locomotor type was used to represent locomotor specialization, and utilized habitat as an indicator of the capacity to adopt different modes of locomotion (running, swimming, climbing, and digging) and thus maximize resource exploitation by being capable of navigating all the substrates in the habitat they use. Locomotor type produced better results than utilized habitat, suggesting that carnivorans use locomotor specialization to minimize locomotion costs. The characteristic limb bone morphology for each locomotor type studied is described, including several adaptations and trends that are novel to the present study. Finally, the results presented here support the hypothesis of a "viverrid-like", forest-dwelling carnivoran ancestor, either arboreal or terrestrial.

Trend of HIV-1 drug resistance in China: A systematic review and meta-analysis of data accumulated over 17 years (2001–2017)

BackgroundThe emergence and spread of HIV-1 drug resistance may compromise HIV control globally. In response to HIV/AIDS epidemic, China launched national HIV/AIDS treatment program in 2003, and started to accumulate drug resistance data since 2001. In this study we aimed to assess the level, trend and distribution of HIV-1 drug resistance during a period of 17 years from 2001 to 2017, and to characterize crucial drug resistance mutations. MethodsWe systematically reviewed 4737 studies published between January 1, 2001 and March 31, 2019 in PubMed, Embase, China National Knowledge Infrastructure (CNKI), WanFang Database, Web of Science, conference abstracts from the Chinese Medical Association and the Chinese AIDS Academic Conferences, and selected 170 studies that met our study criteria. To assess the prevalence of drug resistance in whole country or a local region, we performed pooled analyses of raw data. The transformed proportions were pooled using the inverse variance fixed effects methods or the DerSimonian-Laired random effects methods. The temporal trend of transmitted drug resistance (TDR) was determined using generalized additive model implemented in the Mgcv version 1.8 package. HIV-1 genotypic resistance was analyzed using the Stanford HIVdb algorithm. FindingsWe assembled 218 datasets from 170 selected studies (129 in Chinese and 41 in English), covering 21,451 ART-naïve and 30,475 ART-treated individuals with HIV-1 infection. The pooled prevalence of TDR was 3.0% (95%CI: 2.8–3.2), including 0.7% (95%CI: 0.4–1.0), 1.4% (95%CI: 1.3–1.6) and 0.5% (95%CI: 0.4–0.6) for nucleoside reverse transcriptase inhibitor (NRTI), non-NRTI (NNRTI) and protease inhibitor (PI) resistance, respectively. The acquired drug resistance (ADR) prevalence was 44.7% (95%CI: 39.3–50.2), including 31.4% (95%CI: 28.2–34.6), 39.5% (95%CI: 35.6–43.5) and 1.0% (95%CI: 0.8–1.2) for NRTI, NNRTI and PI resistance, respectively. TDR and ADR prevalence had characteristic regional patterns. The worst prevalence of drug resistance occurred in Central China, and higher ADR prevalence occurred in South China than North China. TDR in whole country has risen since 2012, and this rise was driven mainly by NNRTI resistance. One NRTI-associated (M184V/I) and three NNRTI-associated (K103N/S, Y181C/I and G190A/S) mutations had high percentages in ART-naïve and ART-treated individuals, and these mutations conferred high-level resistance to 3TC, EFV and/or NVP. InterpretationThese findings suggest that the current available first-line ART regimens containing 3TC and/or EFV or NVP need to be revised. In addition, scale-up of multiple viral load measurements per year and drug resistance testing prior to ART initiation are recommended. Furthermore, implementation of pre-treatment education and counseling to improve patient adherence to ART is encouraged. FundingThis work was supported by grants from the National Natural Science Foundation of China (81672033, U1302224, and 81271888) and Open Research Fund Program of the State Key Laboratory of Virology of China (2019IOV002).

Hippocampal subfield CA2+3 exhibits accelerated aging in Alcohol Use Disorder: A preliminary study.

The profile of brain structural dysmorphology of individuals with Alcohol Use Disorders (AUD) involves disruption of the limbic system. In vivo imaging studies report hippocampal volume loss in AUD relative to controls, but only recently has it been possible to articulate different regions of this complex structure. Volumetric analysis of hippocampal regions rather than total hippocampal volume may augment differentiation of disease processes. For example, damage to hippocampal subfield cornu ammonis 1 (CA1) is often reported in Alzheimer's disease (AD), whereas deficits in CA4/dentate gyrus are described in response to stress and trauma. Two previous studies explored the effects of chronic alcohol use on hippocampal subfields: one reported smaller volume of the CA2+3 in alcohol-dependent subjects relative to controls, associated with years of alcohol consumption; the other, smaller volumes of presubiculum, subiculum, and fimbria in alcohol-dependent relative to control men.The current study, conducted in 24 adults with DSM5-diagnosed AUD (7 women, 53.7 ± 8.8) and 20 controls (7 women, 54.1 ± 9.3), is the first to use FreeSurfer 6.0, which provides state-of-the art hippocampal parcellation, to explore the sensitivity of hippocampal sufields to alcoholism. T1- and T2- images were collected on a GE MR750 system with a 32-channel Nova head coil. FreeSurfer 6.0 hippocampal subfield analysis produced 12 subfields: parasubiculum; presubiculum; subiculum; CA1; CA2+3; CA4; GC-ML-DG (Granule Cell (GC) and Molecular Layer (ML) of the Dentate Gyrus (DG)); molecular layer; hippocampus-amygdala-transition-area (HATA); fimbria; hippocampal tail; hippocampal fissure; and whole volume for left and right hippocampi. A comprehensive battery of neuropsychological tests comprising attention, memory and learning, visuospatial abilities, and executive functions was administered.Multiple regression analyses of raw volumetric data for each subfields by group, age, sex, hemisphere, and supratentorial volume (svol) showed significant effects of svol (p < .04) on nearly all structures (excluding tail and fissure). Volumes corrected for svol showed effects of age (fimbria, fissure) and group (subiculum, CA1, CA4, GC-ML-DG, HATA, fimbria); CA2+3 showed a diagnosis-by-age interaction indicating older AUD individuals had a smaller volume than would be expected for their age. There were no selective relations between hippocampal subfields and performance on neuropsychological tests, likely due to lack of statistical power.The current results concur with the previous study identifying CA2+3 as sensitive to alcoholism, extend them by identifying an alcoholism-age interaction, and suggest an imaging phenotype distinguishing AUD from AD and stress/trauma.

Comparison of efficiency of techniques for delineating uni-element anomalies from stream sediment geochemical landscapes

This paper compares analyses of raw geochemical data and processed stream sediment geochemical data (i.e., background-corrected and dilution-corrected via the sample catchment basin approach (SCBA)). Both sets of analyses, based on multifractal approach, aimed to identify geochemical anomalies in three study regions in Iran with different geological characteristics and mineralization styles. The results of both analyses were validated for robustness by using the concept of normalized density (ND), which simultaneously considers both mineralized locations and area of anomalous zones. The comparison of the results emphasizes the efficiency of background and dilution correction procedures, which deal with stream sediment geochemical landscapes in the search for mineral deposits. This paper also presents results of discrete (catchment-based) and continuous (interpolation-based) field modelling of stream sediment geochemical dataset per region study. Although interpolation-based field modelling is rapid, time efficient and simple for delineation of geochemical anomalies, the results of discrete-based field modelling of geochemical anomalies are more superior. Therefore, regardless of the mineralization styles and geological settings, the SCBA to identify geochemical anomalies for mineral exploration is efficient.

Cretaceous coastal lagoon facies: Geochemical insights into multi-stage diagenesis and palaeoclimatic signals

Shallow-water Cretaceous, carbonate platform archives have only rarely been explored through their elemental signature. Yet, facies-sensitive geochemical records can shed light onto the specific dynamics of shallow/proximal settings, where changes in depositional conditions are pronounced. Changes stemming from early and later diagenetic processes must be considered, since they may alter the original geochemical signals, but still contribute to a better understanding of the evolution of ancient shallow carbonates.Here, the elemental record of a variety of carbonate materials from two middle Cenomanian coastal lagoon settings is examined. The two selected sections (Lousa and Lampas, W Portugal) provide a varied record of lithofacies, including matrix micrite, corresponding to diverse palaeoenvironments (marine, marine lagoon, restricted lagoon and subaerial exposed intervals), along with dolomitized beds and atypical darkened grey carbonate horizons. Sparry carbonate veinlets that intersect these materials are included for comparison. Based on the characteristic elemental composition of each carbonate material, and by means of a stepwise statistical approach, dolomitization was determined to be a rather early feature occurring exclusively along shallow to frequently exposed intervals. In contrast, carbonate veinlets were identified as the latest diagenetic event. Matrix micrite and darkened beds present the lowest degree of geochemical differentiation, though certain key elemental contrasts allow for their comparison. Accordingly, the atypical case of darkened beds was attributed to an early blackening process in which low contents of organic matter and non-carbonate mineral phases played a decisive role. Matrix micrite samples—presenting a rather narrow range of elemental fluctuations—were linked to previously identified palaeoenvironmental settings by means of stratigraphically constrained cluster analysis. Specific combinations of elemental trends identified for each established cluster reflect variations in palaeoclimatic regimes throughout the studied interval. Furthermore, the degree of connectivity between open waters and coastal lagoons emerged as predictive of the distribution of major and trace elements in ancient shallow carbonates.This study explores the depositional and diagenetic controls forcing elemental distribution across dynamic shallow carbonate settings, as is the case of coastal lagoons. Complex and atypical elemental fingerprints, established by means of statistical analysis, provide arguments to reconstruct the evolution of the examined carbonate materials. Our findings are highly pertinent, as they: (i) provide a rich dataset not only regarding Lusitanian Basin deposits, but also for coeval settings where basin evolution and diagenesis are pivotal; (ii) underline the insight to be gained from time series analyses of raw elemental data collected from carbonate facies; and (iii) place a suite of numerical analyses within a logical hierarchy for stratigraphic facies analysis, fully supported by independent data.

Multivariate EEG analyses support high-resolution tracking of feature-based attentional selection

The primary electrophysiological marker of feature-based selection is the N2pc, a lateralized posterior negativity emerging around 180–200 ms. As it relies on hemispheric differences, its ability to discriminate the locus of focal attention is severely limited. Here we demonstrate that multivariate analyses of raw EEG data provide a much more fine-grained spatial profile of feature-based target selection. When training a pattern classifier to determine target position from EEG, we were able to decode target positions on the vertical midline, which cannot be achieved using standard N2pc methodology. Next, we used a forward encoding model to construct a channel tuning function that describes the continuous relationship between target position and multivariate EEG in an eight-position display. This model can spatially discriminate individual target positions in these displays and is fully invertible, enabling us to construct hypothetical topographic activation maps for target positions that were never used. When tested against the real pattern of neural activity obtained from a different group of subjects, the constructed maps from the forward model turned out statistically indistinguishable, thus providing independent validation of our model. Our findings demonstrate the power of multivariate EEG analysis to track feature-based target selection with high spatial and temporal precision.

ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface

BackgroundNext generation sequencing (NGS) technologies enable studies and analyses of the diversity of both T and B cell receptors (TCR and BCR) in human and animal systems to elucidate immune functions in health and disease. Over the last few years, several algorithms and tools have been developed to support respective analyses of raw sequencing data of the immune repertoire. These tools focus on distinct aspects of the data processing and require a strong bioinformatics background. To facilitate the analysis of T and B cell repertoires by less experienced users, software is needed that combines the most common tools for repertoire analysis.ResultsWe introduce a graphical user interface (GUI) providing a complete analysis pipeline for processing raw NGS data for human and animal TCR and BCR clonotype determination and advanced differential repertoire studies. It provides two applications. ClonoCalc prepares the raw data for downstream analyses. It combines a demultiplexer for barcode splitting and employs MiXCR for paired-end read merging and the extraction of human and animal TCR/BCR sequences. ClonoPlot wraps the R package tcR and further contributes self-developed plots for the descriptive comparative investigation of immune repertoires.ConclusionThis workflow reduces the amount of programming required to perform the respective analyses and supports both communication and training between scientists and technicians, and across scientific disciplines.The Open Source development in Java and R is modular and invites advanced users to extend its functionality. Software and documentation are freely available at https://bitbucket.org/ClonoSuite/clonocalc-plot.

A multi-level modeling approach examining PTSD symptom reduction during prolonged exposure therapy: moderating effects of number of trauma types experienced, having an HIV-related index trauma, and years since HIV diagnosis among HIV-positive adults

ABSTRACTPeople living with HIV (PLWH) have extensive interpersonal trauma histories and higher rates of posttraumatic stress disorder (PTSD) than the general population. Prolonged exposure (PE) therapy is efficacious in reducing PTSD across a variety of trauma samples; however, research has not examined factors that influence how PTSD symptoms change during PE for PLWH. Using multi-level modeling, we examined the potential moderating effect of number of previous trauma types experienced, whether the index trauma was HIV-related or not, and years since HIV diagnosis on PTSD symptom reduction during a 10-session PE protocol in a sample of 51 PLWH. In general, PTSD symptoms decreased linearly throughout the PE sessions. Experiencing more previous types of traumatic events was associated with a slower rate of PTSD symptom change. In addition, LOCF analyses found that participants with a non-HIV-related versus HIV-related index trauma had a slower rate of change for PTSD symptoms over the course of PE. However, analyses of raw data decreased this finding to marginal. Years since HIV diagnosis did not impact PTSD symptom change. These results provide a better understanding of how to tailor PE to individual clients and aid clinicians in approximating the rate of symptom alleviation. Specifically, these findings underscore the importance of accounting for trauma history and index trauma type when implementing a treatment plan for PTSD in PLWH.

Cerebral Reorganization after Hemispherectomy: A DTI Study.

Hemispherectomy is a neurosurgical procedure to treat children with intractable seizures. Postsurgical improvement of cognitive and behavioral functions is observed in children after hemispherectomy suggesting plastic reorganization of the brain. Our aim was to characterize changes in DTI scalars in WM tracts of the remaining hemisphere in children after hemispherectomy, assess the associations between WM DTI scalars and age at the operation and time since the operation, and evaluate the changes in GM fractional anisotropy values in patients compared with controls. Patients with congenital or acquired neurologic diseases who required hemispherectomy and had high-quality postsurgical DTI data available were included in this study. Atlas- and voxel-based analyses of DTI raw data of the remaining hemisphere were performed. Fractional anisotropy and mean, axial, and radial diffusivity values were calculated for WM and GM regions. A linear regression model was used for correlation between DTI scalars and age at and time since the operation. Nineteen patients after hemispherectomy and 21 controls were included. In patients, a decrease in fractional anisotropy and axial diffusivity values and an increase in mean diffusivity and radial diffusivity values of WM regions were observed compared with controls (P < .05, corrected for multiple comparisons). In patients with acquired pathologies, time since the operation had a significant positive correlation with white matter fractional anisotropy values. In all patients, an increase in cortical GM fractional anisotropy values was found compared with controls (P < .05). Changes in DTI metrics likely reflect Wallerian and/or transneuronal degeneration of the WM tracts within the remaining hemisphere. In patients with acquired pathologies, postsurgical fractional anisotropy values correlated positively with elapsed time since the operation, suggesting a higher ability to recover compared with patients with congenital pathologies leading to hemispherectomy.

Sustained Mesozoic–Cenozoic diversification of marine Metazoa: A consistent signal from the fossil record

Research Article| November 01, 2015 Sustained Mesozoic–Cenozoic diversification of marine Metazoa: A consistent signal from the fossil record Andrew M. Bush; Andrew M. Bush 1Department of Ecology and Evolutionary Biology and Center for Integrative Geosciences, University of Connecticut, 75 North Eagleville Road, Storrs, Connecticut 06269-3043, USA Search for other works by this author on: GSW Google Scholar Richard K. Bambach Richard K. Bambach 2Department of Paleobiology, MRC-121, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, D.C. 20013-7012, USA Search for other works by this author on: GSW Google Scholar Author and Article Information Andrew M. Bush 1Department of Ecology and Evolutionary Biology and Center for Integrative Geosciences, University of Connecticut, 75 North Eagleville Road, Storrs, Connecticut 06269-3043, USA Richard K. Bambach 2Department of Paleobiology, MRC-121, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, D.C. 20013-7012, USA Publisher: Geological Society of America Received: 16 Jul 2015 Revision Received: 02 Sep 2015 Accepted: 07 Sep 2015 First Online: 09 Mar 2017 Online Issn: 1943-2682 Print Issn: 0091-7613 © 2015 Geological Society of America Geology (2015) 43 (11): 979–982. https://doi.org/10.1130/G37162.1 Article history Received: 16 Jul 2015 Revision Received: 02 Sep 2015 Accepted: 07 Sep 2015 First Online: 09 Mar 2017 Cite View This Citation Add to Citation Manager Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Get Permissions Search Site Citation Andrew M. Bush, Richard K. Bambach; Sustained Mesozoic–Cenozoic diversification of marine Metazoa: A consistent signal from the fossil record. Geology 2015;; 43 (11): 979–982. doi: https://doi.org/10.1130/G37162.1 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietyGeology Search Advanced Search Abstract Paleobiological data provide a key historical record of global biodiversity dynamics, but their interpretation is controversial due to geological and sampling biases. Raw data suggest that marine metazoans diversified dramatically during the late Mesozoic and Cenozoic, whereas bias-corrected analyses based on occurrence-level data in the Paleobiology Database (PBDB) have indicated much less Cenozoic diversification. These standardized analyses are cited as evidence that biases strongly conceal underlying patterns in the global fossil record. However, we show that marine diversity did increase substantially and continuously from the Jurassic to the Neogene, even after correcting for biases in PBDB data. Previous standardized analyses did not capture this diversification in full because they were based on incomplete data. In the Cenozoic, observed richness rose to twice the Paleozoic average, which is within the range of values seen in analyses of raw data, suggesting that even the raw global marine fossil record preserves first-order signals of diversity history. You do not have access to this content, please speak to your institutional administrator if you feel you should have access.

Low copy target detection by Droplet Digital PCR through application of a novel open access bioinformatic pipeline, ‘definetherain’

Droplet Digital PCR (ddPCR) represents a new and alternative platform to conventional quantitative-PCR (qPCR) for the quantitation of DNA templates. However, the proposed improvement in sensitivity and reproducibility offered by ddPCR is not yet fully proven, partly because the delineation between positive and negative responses is not always clear.Data are presented demonstrating the sensitivity of the ddPCR system to both reagent concentrations and choice of cut-off for defining positive and negative results. By implementing k-nearest clustering, cut-offs are produced that improve the accuracy of ddPCR where target DNA is present at low copy numbers, a key application of ddPCR. This approach is applied to human albumin and HIV-1 proviral DNA ddPCR quantitative protocols. This tool is coded in JavaScript and has been made available for free in a web browser at http://www.definetherain.org.uk. Optimisation of the analyses of raw ddPCR data using ‘definetherain’ indicates that low target number detection can be improved by its implementation. Further application to patient samples will help define the clinical utility of this approach.

Experimental determination of a representative texture and insight into the range of significant neighboring grain interactions via orientation and misorientation statistics

Abstract The mechanical response of polycrystalline metallic materials is heavily influenced by the orientations of their grains. To predict polycrystalline behavior more accurately, crystal plasticity models account for grain orientations and also, sometimes, for interactions between neighboring grains. However, these models often lack sound experimental input or validation. Furthermore, experimental studies themselves rarely tackle simply the concept of representativity in terms of texture; neither do they try to analyze up to what range neighbor interactions appear to be significant. In this article, we address both aforementioned issues in a single and easily implementable framework by performing extensive statistical analyses of discrete raw orientation and misorientation data respectively, obtained by means of electron back-scattered diffraction on thousand-grain microstructures. First, we show that the analysis of orientation statistics helps determine whether an experimental dataset can be considered as a microstructurally representative volume element in terms of texture. Second, we explain how the statistical processing of misorientations can shed some light on the range of neighbors that have a significant weight in the misorientation distributions and possibly on the grain interactions.

Perceptions towards aging among selected Filipino adults

The study aims to explore perceptions of selected Filipino adults towards aging. A total of twelve adults (6 married and 6 single) whose age ranges from 40 to 59 years old were recruited as participants. The study employed a qualitative-narrative research design. Participants were interviewed in accordance with their lived experiences and were analyzed through thematic analysis. The themes emerged from analyses of raw data are as follows: Aging as a responsibility; Aging as a maturation period; Aging as a promising experience; Aging as the process of increasing autonomy; Aging as a phase of increased productivity; Aging as a positive experience; Aging as a stage of physiological; and physical decline and aging as an apprehensive process. Implications of the study are discussed.

Conserving and promoting evenness: organic farming and fire‐based wildland management as case studies

Healthy ecosystems include many species (high richness) with similar abundances (high evenness). Thus, both aspects of biodiversity are worthy of conservation. Simultaneously conserving richness and evenness might be difficult, however, if, for example, the restoration of previously absent species to low densities brings a cost in reduced evenness. Using meta-analysis, we searched for benefits to biodiversity following adoption of two common land-management schemes: the implementation of organic practices by farmers and of controlled burning by natural-land managers. We used rarefaction to eliminate sampling bias in all of our estimates of richness and evenness. Both conservation practices significantly increased evenness and overall abundance across taxonomic classifications (arthropods, birds, non-bird vertebrates, plants, soil organisms). Evenness and richness varied independently, leading to no richness-evenness correlation and no significant overall change in richness. Demonstrating the importance of rarefaction, analyses of raw data that did not receive rarefaction indicated misleadingly strong benefits of organic agriculture and burning for richness while underestimating true gains in evenness. Both organic farming and burning favored species that were not numerically dominant, re-balancing communities as uncommon species gained individuals. Our results support the assertion that richness and evenness capture separate facets of biodiversity, each needing individual attention during conservation.

Inter-observer reliability of forceful exertion analysis based on video-recordings

The objectives were to examine inter-observer reliability of job-level forceful exertion analyses and temporal agreement of detailed time study results. Three observers performed the analyses on 12 different jobs. Continuous duration, frequency and % time of lifting, pushing/pulling, power and pinch gripping exertions and estimated level of the exertions were obtained. Intraclass correlation coefficient and variance components were computed. Temporal agreement analyses of raw time study data were performed. The inter-observer reliability was good for most job-level exposure parameters (continuous duration, frequency and % time of forceful exertions), but only fair to moderate for the estimated level of forceful exertions. The finding that the between-observer variability was less than the between-exertion variability confirmed that the forceful exertion analysis method used in the present study can detect job exertion differences.Using three observers to perform detailed time studies on task activities and getting consensus of the majority can increase the between-observer agreement up to 97%. Statement of Relevance: The results inform researchers that inter-observer reliability for job-level exposure measurement of forceful exertion analysis obtained from detailed time studies is generally good, but the observers' ability in the estimation of forceful exertion level can be poor. It also provides information on the temporal agreement of detailed forceful exertion analysis and guidelines on achieving better agreement for studies where accurate synchronisation of task activities and direct physiological/biomechanical measurements is crucial.

Debate on GMOs Health Risks after Statistical Findings in Regulatory Tests

We summarize the major points of international debate on health risk studies for the main commercialized edible GMOs. These GMOs are soy, maize and oilseed rape designed to contain new pesticide residues since they have been modified to be herbicide-tolerant (mostly to Roundup) or to produce mutated Bt toxins. The debated alimentary chronic risks may come from unpredictable insertional mutagenesis effects, metabolic effects, or from the new pesticide residues. The most detailed regulatory tests on the GMOs are three-month long feeding trials of laboratory rats, which are biochemically assessed. The tests are not compulsory, and are not independently conducted. The test data and the corresponding results are kept in secret by the companies. Our previous analyses of regulatory raw data at these levels, taking the representative examples of three GM maize NK 603, MON 810, and MON 863 led us to conclude that hepatorenal toxicities were possible, and that longer testing was necessary. Our study was criticized by the company developing the GMOs in question and the regulatory bodies, mainly on the divergent biological interpretations of statistically significant biochemical and physiological effects. We present the scientific reasons for the crucially different biological interpretations and also highlight the shortcomings in the experimental protocols designed by the company. The debate implies an enormous responsibility towards public health and is essential due to nonexistent traceability or epidemiological studies in the GMO-producing countries.