A multi‐data ensemble approach for predicting woodland type distribution: Oak woodland in Britain

Interactions between soil, topography, and climatic site factors can exacerbate and/or alleviate the vulnerability of oak woodland to climate change. Reducing climate‐related impacts on oak woodland habitats and ecosystems through adaptation management requires knowledge of different site interactions in relation to species tolerance. In Britain, the required thematic detail of woodland type is unavailable from digital maps. A species distribution model (SDM) ensemble, using biomod2 algorithms, was used to predict oak woodland. The model was cross‐validated (50%:50% ‐ training:testing) 30 times, with each of 15 random sets of absence data, matching the size of presence data, to maximize environmental variation while maintaining data prevalence. Four biomod2 algorithms provided stable and consistent TSS‐weighted ensemble mean results predicting oak woodland as a probability raster. Biophysical data from the Ecological Site Classification (forest site classification) for Britain were used to characterize oak woodland sites. Several forest datasets were used, each with merits and weaknesses: public forest estate subcompartment database map (PFE map) for oak‐stand locations as a training dataset; the national forest inventory (NFI) “published regional reports” of oak woodland area; and an “NFI map” of indicative forest type broad habitat. Broadleaved woodland polygons of the NFI map were filled with the biomod2 oak woodland probability raster. Ranked pixels were selected up to the published NFI regional area estimate of oak woodland and matched to the elevation distribution of oak woodland stands, from “NFI survey” sample squares. Validation using separate oak woodland data showed that the elevation filter significantly improved the accuracy of predictions from 55% (p = .53) to 83% coincidence success rate (p < .0001). The biomod2 ensemble, with masking and filtering, produced a predicted oak woodland map, from which site characteristics will be used in climate change interaction studies, supporting adaptation management recommendations for forest policy and practice.     

On the validation of crystallographic symmetry and the quality of structures

In 2008, Zwart and colleagues observed that the fraction of the structures deposited in the PDB alleged to have “pseudosymmetry” or “special noncrystallographic symmetry” (NCS) was about 6%, and that this percentage was rising annually. A few years later, Poon and colleagues found that 2% of all the crystal structures in the PDB belonged to higher symmetry space groups than those assigned to them. Here, I report an analysis of the X-ray diffraction data deposited for this class of structures, which shows that most of the “pseudosymmetry” and “special NCS” that has been reported is in fact true crystallographic symmetry (CS). This distinction is important because the credibility of crystal structures depends heavily on quality control statistics such as R_free that are unreliable when they are computed incorrectly, which they often are when CS is misidentified as “special NCS” or “pseudosymmetry”. When mistakes of this kind are made, artificially low values of R_free can give unjustified confidence in the accuracy of the reported structures.     

Comparison of optical methods for estimating the opening of the canopy and leaf area in leafy forests

Based on inversion of gap fraction data (Poisson model of foliage distribution), three optical methods using the Demon, the Plant Canopy Analyzer LAI-2000 (PCA) and hemispherical photographs, have been compared to estimate canopy openness (CO) and leaf area index (LAI) in a mature, neutrophil, oak-beech-hornbeam forest on mull in eastern France. Mean CO over the whole hemisphere was similar for PCA (7.9%) and hemispherical photographs (8.0%). The needle method, a vertical point quadrat method, applied to the litter after leaf fall has served as a reference to LAI (4.7). The Demon provided the estimate (4.9) closest to the reference value. The PCA and hemispherical photographs underestimate mean LAI by 30% (3.3) and 19% (3.8), respectively, if used without correction. Based on fish-eye sensors, LAI estimates can be improved if 3 annuli (4.2) or 2 annuli (4.5) are used in place of 5 with the PCA, or by means of logarithmic averaging of gap fractions over azimuth at an appropriate angular resolution (180 degrees: 4.6, or 120 degrees: 5.2) with hemispherical photographs. Not taking into account azimuthal variation in gap fraction distribution generates a more important error than the error induced by light scattering near horizon. In order to improve LAI estimates, an original iterative procedure is presented, which allows the simultaneous calculation of LAI over a broad range of angular azimuthal resolutions.     

Colorimetric and Longitudinal Analysis of Leukocoria in Recreational Photographs of Children with Retinoblastoma

Retinoblastoma is the most common primary intraocular tumor in children. The first sign that is often reported by parents is the appearance of recurrent leukocoria (i.e., “white eye”) in recreational photographs. A quantitative definition or scale of leukocoria – as it appears during recreational photography – has not been established, and the amount of clinical information contained in a leukocoric image (collected by a parent) remains unknown. Moreover, the hypothesis that photographic leukocoria can be a sign of early stage retinoblastoma has not been tested for even a single patient. This study used commercially available software (Adobe Photoshop®) and standard color space conversion algorithms (operable in Microsoft Excel®) to quantify leukocoria in actual “baby pictures” of 9 children with retinoblastoma (that were collected by parents during recreational activities i.e., in nonclinical settings). One particular patient with bilateral retinoblastoma (“Patient Zero”) was photographed >7, 000 times by his parents (who are authors of this study) over three years: from birth, through diagnosis, treatment, and remission. This large set of photographs allowed us to determine the longitudinal and lateral frequency of leukocoria throughout the patient''s life. This study establishes: (i) that leukocoria can emerge at a low frequency in early-stage retinoblastoma and increase in frequency during disease progression, but decrease upon disease regression, (ii) that Hue, Saturation and Value (i.e., HSV color space) are suitable metrics for quantifying the intensity of retinoblastoma-linked leukocoria; (iii) that different sets of intraocular retinoblastoma tumors can produce distinct leukocoric reflections; and (iv) the Saturation-Value plane of HSV color space represents a convenient scale for quantifying and classifying pupillary reflections as they appear during recreational photography.     

Molecular Diagnostics of Fine Needle Aspiration for the Presurgical Screening of Thyroid Nodules

“The incidence of thyroid cancer, the most common endocrine malignancy, is rising. The two most common types of thyroid cancer are papillary and follicular” thyroid carcinomas. “Fine-needle aspiration (FNA) of thyroid nodules” can permit to detect many genetic mutations and other molecular alterations, including RAS and BRAF point mutations, PAX8/peroxisome proliferator-activated receptor (PPAR)γ and “RET/PTC rearrangements, occurring in thyroid papillary and follicular carcinomas” (more than 70% of cases), which can be used successfully to improve the diagnosis “and the management of patients with thyroid nodules”. The most extensive experience has been accumulated with “the diagnostic use of BRAF mutation”, which is highly specific for malignancy. “Testing FNA samples for a panel of mutations” that typically includes RAS, BRAF, PAX8/PPARγ and RET/PTC could permit to achieve the biggest diagnostic impact. “The accuracy of cancer diagnosis in thyroid nodules could be improved significantly using these and other emerging molecular markers”.     

Systematic Review and Meta-Analysis of Validation Studies on a Diabetes Case Definition from Health Administrative Records

Objectives

Health administrative data are frequently used for diabetes surveillance. We aimed to determine the sensitivity and specificity of a commonly-used diabetes case definition (two physician claims or one hospital discharge abstract record within a two-year period) and their potential effect on prevalence estimation.

Methods

Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we searched Medline (from 1950) and Embase (from 1980) databases for validation studies through August 2012 (keywords: “diabetes mellitus”; “administrative databases”; “validation studies”). Reviewers abstracted data with standardized forms and assessed quality using Quality Assessment of Diagnostic Accuracy Studies (QUADAS) criteria. A generalized linear model approach to random-effects bivariate regression meta-analysis was used to pool sensitivity and specificity estimates. We applied correction factors derived from pooled sensitivity and specificity estimates to prevalence estimates from national surveillance reports and projected prevalence estimates over 10 years (to 2018).

Results

The search strategy identified 1423 abstracts among which 11 studies were deemed relevant and reviewed; 6 of these reported sensitivity and specificity allowing pooling in a meta-analysis. Compared to surveys or medical records, sensitivity was 82.3% (95%CI 75.8, 87.4) and specificity was 97.9% (95%CI 96.5, 98.8). The diabetes case definition underestimated prevalence when it was ≤10.6% and overestimated prevalence otherwise.

Conclusion

The diabetes case definition examined misses up to one fifth of diabetes cases and wrongly identifies diabetes in approximately 2% of the population. This may be sufficiently sensitive and specific for surveillance purposes, in particular monitoring prevalence trends. Applying correction factors to adjust prevalence estimates from this definition may be helpful to increase accuracy of estimates.     

Quantifying Auditory Temporal Stability in a Large Database of Recorded Music

“Moving to the beat” is both one of the most basic and one of the most profound means by which humans (and a few other species) interact with music. Computer algorithms that detect the precise temporal location of beats (i.e., pulses of musical “energy”) in recorded music have important practical applications, such as the creation of playlists with a particular tempo for rehabilitation (e.g., rhythmic gait training), exercise (e.g., jogging), or entertainment (e.g., continuous dance mixes). Although several such algorithms return simple point estimates of an audio file’s temporal structure (e.g., “average tempo”, “time signature”), none has sought to quantify the temporal stability of a series of detected beats. Such a method-a “Balanced Evaluation of Auditory Temporal Stability” (BEATS)–is proposed here, and is illustrated using the Million Song Dataset (a collection of audio features and music metadata for nearly one million audio files). A publically accessible web interface is also presented, which combines the thresholdable statistics of BEATS with queryable metadata terms, fostering potential avenues of research and facilitating the creation of highly personalized music playlists for clinical or recreational applications.     

Quality along the Continuum: A Health Facility Assessment of Intrapartum and Postnatal Care in Ghana

Objective

To evaluate quality of routine and emergency intrapartum and postnatal care using a health facility assessment, and to estimate “effective coverage” of skilled attendance in Brong Ahafo, Ghana.

Methods

We conducted an assessment of all 86 health facilities in seven districts in Brong Ahafo. Using performance of key signal functions and the availability of relevant drugs, equipment and trained health professionals, we created composite quality categories in four dimensions: routine delivery care, emergency obstetric care (EmOC), emergency newborn care (EmNC) and non-medical quality. Linking the health facility assessment to surveillance data we estimated “effective coverage” of skilled attendance as the proportion of births in facilities of high quality.

Findings

Delivery care was offered in 64/86 facilities; only 3-13% fulfilled our requirements for the highest quality category in any dimension. Quality was lowest in the emergency care dimensions, with 63% and 58% of facilities categorized as “low” or “substandard” for EmOC and EmNC, respectively. This implies performing less than four EmOC or three EmNC signal functions, and/or employing less than two skilled health professionals, and/or that no health professionals were present during our visit. Routine delivery care was “low” or “substandard” in 39% of facilities, meaning 25/64 facilities performed less than six routine signal functions and/or had less than two skilled health professionals and/or less than one midwife. While 68% of births were in health facilities, only 18% were in facilities with “high” or “highest” quality in all dimensions.

Conclusion

Our comprehensive facility assessment showed that quality of routine and emergency intrapartum and postnatal care was generally low in the study region. While coverage with facility delivery was 68%, we estimated “effective coverage” of skilled attendance at 18%, thus revealing a large “quality gap.” Effective coverage could be a meaningful indicator of progress towards reducing maternal and newborn mortality.     

Concurrent validity of five prediction equations to evaluate fat percentage in a sports group expected to yield high performance from Medellín,Colombia

IntroductionNo equations to predict the body composition of athletes from Medellín expected to have high performance have been constructed and, thus, decisions regarding their training and nutrition plans lack support.ObjectiveTo calculate the concurrent validity of five prediction equations for fat percentage in a group of athletes from Medellín, Colombia, expected to yield high performance.Materials and methodsWe conducted a cross-sectional analysis to validate diagnostic tests using secondary-source data of athletes under the age of 18 who were part of the “Medellín Team”. The gold standard was dual-energy X-ray densitometry (DEXA). We analyzed the Slaughter, Durnin and Rahaman, Lohman, and Johnston prediction equations, as well as the five-component model. We used the intraclass correlation coefficient to assess the consistency of the methods and the Bland-Altman plot to calculate the average bias and agreement limits of each of the equations.ResultsWe included 101 athletes (50,5% of them women). The median age was 14,8 years (IR: 13,0 - 16,0). The concurrent validity was “good/excellent” for the Johnston and the Durnin and Rahaman equations and the five-components model. The Lohman equation overestimated the fat percentage in 12,7 points. All of the equations showed broad agreement limits.ConclusionsThe Durnin and Rahaman and the Johnston equations, as well as the five- component model, can be used to predict the FP in the study population as they showed a “good/excellent” concurrent validity and a low average bias. The equations analyzed have low accuracy, which hinders their use to diagnose the individual fat percentage within this population.     

Isolation and identification of lymphocytic and myelogenous leukemia-specific sequences in genomes of gibbon oncornaviruses

Five gibbon ape leukemia virus substrains (two from gibbons with lymphocytic leukemia and three from gibbons with myelogenous leukemia) were examined for unique genomic sequences specific for each form of leukemia. By using sequential adsorption procedures, the genome from each gibbon ape leukemia virus was fractionated into four sets of distinct nucleotide sequences. Based on their hybridization specificities toward DNAs of leukemic tissues, these sequences were designated as follows: (i) “COM,” (ii) “LYM” or “MYE,” (iii) “UNI,” and (iv) “UND.” The COM fraction represented sequences common to all of the viral genomes. The LYM fraction, which was isolated only from gibbon ape leukemia viruses associated with lymphocytic leukemia, represented genomic sequences associated with lymphocytic leukemia since the RNA hybridized at a 4- to 15-fold-higher rate to infected tissue DNA from lymphocytic leukemic gibbons than to infected tissue DNA from myelogenous leukemic gibbons. The MYE fraction, which was isolated only from gibbon ape leukemia viruses associated with myelogenous leukemia, represented genomic sequences associated with myelogenous leukemia since the RNA hybridized at a 5- to 15-fold-higher rate to infected tissue DNA from myelogenous leukemic gibbons than to infected tissue DNA from lymphocytic leukemic gibbons. The UNI fraction contained sequences unique to one virus substrain. The UND fraction contained sequences which varied depending upon the substrains involved in the adsorption procedures. These findings suggest that each gibbon ape leukemia virus examined in this study contains subgenomic sequences that are specifically identifiable only with the form of leukemia from which the virus was isolated.     

Membranes of Saccharomyces cerevisiae

A crude small particle pellet, obtained from postmitochondrial supernatant fractions of Saccharomyces cerevisiae, contains about half the ergosterol and phospholipid of crude cell homogenates. Most of the phospholipid of this pellet is in a “heavy” fraction which, with the aid of electron microscopy, shows membranous elements in addition to discrete particles. The “heavy” fraction, upon treatment with deoxycholate, can be freed of membranes, or, with ribonuclease treatment, ribosomes can be removed, leaving relatively clean membranes. The “heavy” fraction resembles the microsomes of animal cells, but contains considerably less lipids, including phospholipids, thus suggesting a less well-developed intracellular membrane system.     

Diversity of Basidiomycetes in Michigan Agricultural Soils

We analyzed the communities of soil basidiomycetes in agroecosystems that differ in tillage history at the Kellogg Biological Station Long-Term Ecological Research site near Battle Creek, Michigan. The approach combined soil DNA extraction through a bead-beating method modified to increase recovery of fungal DNA, PCR amplification with basidiomycete-specific primers, cloning and restriction fragment length polymorphism screening of mixed PCR products, and sequencing of unique clones. Much greater diversity was detected than was anticipated in this habitat on the basis of culture-based methods or surveys of fruiting bodies. With “species” defined as organisms yielding PCR products with ≥99% identity in the 5′ 650 bases of the nuclear large-subunit ribosomal DNA, 241 “species” were detected among 409 unique basidiomycete sequences recovered. Almost all major clades of basidiomycetes from basidiomycetous yeasts and other heterobasidiomycetes through polypores and euagarics (gilled mushrooms and relatives) were represented, with a majority from the latter clade. Only 24 of 241 “species” had 99% or greater sequence similarity to named reference sequences in GenBank, and several clades with multiple “species” could not be identified at the genus level by phylogenetic comparisons with named sequences. The total estimated “species” richness for this 11.2-ha site was 367 “species” of basidiomycetes. Since >99% of the study area has not been sampled, the accuracy of our diversity estimate is uncertain. Replication in time and space is required to detect additional diversity and the underlying community structure.     

Tracking Protests Using Geotagged Flickr Photographs

Recent years have witnessed waves of protests sweeping across countries and continents, in some cases resulting in political and governmental change. Much media attention has been focused on the increasing usage of social media to coordinate and provide instantly available reports on these protests. Here, we investigate whether it is possible to identify protest outbreaks through quantitative analysis of activity on the photo sharing site Flickr. We analyse 25 million photos uploaded to Flickr in 2013 across 244 countries and regions, and determine for each week in each country and region what proportion of the photographs are tagged with the word “protest” in 34 different languages. We find that higher proportions of “protest”-tagged photographs in a given country and region in a given week correspond to greater numbers of reports of protests in that country and region and week in the newspaper The Guardian. Our findings underline the potential value of photographs uploaded to the Internet as a source of global, cheap and rapidly available measurements of human behaviour in the real world.     

Relativity Theory and Time Perception: Single or Multiple Clocks?

Background

Current theories of interval timing assume that humans and other animals time as if using a single, absolute stopwatch that can be stopped or reset on command. Here we evaluate the alternative view that psychological time is represented by multiple clocks, and that these clocks create separate temporal contexts by which duration is judged in a relative manner. Two predictions of the multiple-clock hypothesis were tested. First, that the multiple clocks can be manipulated (stopped and/or reset) independently. Second, that an event of a given physical duration would be perceived as having different durations in different temporal contexts, i.e., would be judged differently by each clock.

Methodology/Principal Findings

Rats were trained to time three durations (e.g., 10, 30, and 90 s). When timing was interrupted by an unexpected gap in the signal, rats reset the clock used to time the “short” duration, stopped the “medium” duration clock, and continued to run the “long” duration clock. When the duration of the gap was manipulated, the rats reset these clocks in a hierarchical order, first the “short”, then the “medium”, and finally the “long” clock. Quantitative modeling assuming re-allocation of cognitive resources in proportion to the relative duration of the gap to the multiple, simultaneously timed event durations was used to account for the results.

Conclusions/Significance

These results indicate that the three event durations were effectively timed by separate clocks operated independently, and that the same gap duration was judged relative to these three temporal contexts. Results suggest that the brain processes the duration of an event in a manner similar to Einstein''s special relativity theory: A given time interval is registered differently by independent clocks dependent upon the context.     

Ensuring the quality and specificity of preregistrations

Researchers face many, often seemingly arbitrary, choices in formulating hypotheses, designing protocols, collecting data, analyzing data, and reporting results. Opportunistic use of “researcher degrees of freedom” aimed at obtaining statistical significance increases the likelihood of obtaining and publishing false-positive results and overestimated effect sizes. Preregistration is a mechanism for reducing such degrees of freedom by specifying designs and analysis plans before observing the research outcomes. The effectiveness of preregistration may depend, in part, on whether the process facilitates sufficiently specific articulation of such plans. In this preregistered study, we compared 2 formats of preregistration available on the OSF: Standard Pre-Data Collection Registration and Prereg Challenge Registration (now called “OSF Preregistration,” http://osf.io/prereg/). The Prereg Challenge format was a “structured” workflow with detailed instructions and an independent review to confirm completeness; the “Standard” format was “unstructured” with minimal direct guidance to give researchers flexibility for what to prespecify. Results of comparing random samples of 53 preregistrations from each format indicate that the “structured” format restricted the opportunistic use of researcher degrees of freedom better (Cliff’s Delta = 0.49) than the “unstructured” format, but neither eliminated all researcher degrees of freedom. We also observed very low concordance among coders about the number of hypotheses (14%), indicating that they are often not clearly stated. We conclude that effective preregistration is challenging, and registration formats that provide effective guidance may improve the quality of research.

Researchers face many, often seemingly arbitrary choices in formulating hypotheses, designing protocols, collecting data, analyzing data, and reporting results. A study of two formats of preregistration available on the OSF reveals that the opportunistic use of researcher degrees of freedom aimed at obtaining statistical significance is restricted by using more extensive preregistration guidelines; however, these guidelines should be further improved.     

Characterization of the Denitrification-Associated Phosphorus Uptake Properties of “Candidatus Accumulibacter phosphatis” Clades in Sludge Subjected to Enhanced Biological Phosphorus Removal

To characterize the denitrifying phosphorus (P) uptake properties of “Candidatus Accumulibacter phosphatis,” a sequencing batch reactor (SBR) was operated with acetate. The SBR operation was gradually acclimated from anaerobic-oxic (AO) to anaerobic-anoxic-oxic (A2O) conditions by stepwise increases of nitrate concentration and the anoxic time. The communities of “Ca. Accumulibacter” and associated bacteria at the initial (AO) and final (A2O) stages were compared using 16S rRNA and polyphosphate kinase genes and using fluorescence in situ hybridization (FISH). The acclimation process led to a clear shift in the relative abundances of recognized “Ca. Accumulibacter” subpopulations from clades IIA > IA > IIF to clades IIC > IA > IIF, as well as to increases in the abundance of other associated bacteria (Dechloromonas [from 1.2% to 19.2%] and “Candidatus Competibacter phosphatis” [from 16.4% to 20.0%]), while the overall “Ca. Accumulibacter” abundance decreased (from 55.1% to 29.2%). A series of batch experiments combined with FISH/microautoradiography (MAR) analyses was performed to characterize the denitrifying P uptake properties of the “Ca. Accumulibacter” clades. In FISH/MAR experiments using slightly diluted sludge (∼0.5 g/liter), all “Ca. Accumulibacter” clades successfully took up phosphorus in the presence of nitrate. However, the “Ca. Accumulibacter” clades showed no P uptake in the presence of nitrate when the sludge was highly diluted (∼0.005 g/liter); under these conditions, reduction of nitrate to nitrite did not occur, whereas P uptake by “Ca. Accumulibacter” clades occurred when nitrite was added. These results suggest that the “Ca. Accumulibacter” cells lack nitrate reduction capabilities and that P uptake by “Ca. Accumulibacter” is dependent upon nitrite generated by associated nitrate-reducing bacteria such as Dechloromonas and “Ca. Competibacter.”     

Task Shifting for Non-Communicable Disease Management in Low and Middle Income Countries – A Systematic Review

Background

One potential solution to limited healthcare access in low and middle income countries (LMIC) is task-shifting- the training of non-physician healthcare workers (NPHWs) to perform tasks traditionally undertaken by physicians. The aim of this paper is to conduct a systematic review of studies involving task-shifting for the management of non-communicable disease (NCD) in LMIC.

Methods

A search strategy with the following terms “task-shifting”, “non-physician healthcare workers”, “community healthcare worker”, “hypertension”, “diabetes”, “cardiovascular disease”, “mental health”, “depression”, “chronic obstructive pulmonary disease”, “respiratory disease”, “cancer” was conducted using Medline via Pubmed and the Cochrane library. Two reviewers independently reviewed the databases and extracted the data.

Findings

Our search generated 7176 articles of which 22 were included in the review. Seven studies were randomised controlled trials and 15 were observational studies. Tasks performed by NPHWs included screening for NCDs and providing primary health care. The majority of studies showed improved health outcomes when compared with usual healthcare, including reductions in blood pressure, increased uptake of medications and lower depression scores. Factors such as training of NPHWs, provision of algorithms and protocols for screening, treatment and drug titration were the main enablers of the task-shifting intervention. The main barriers identified were restrictions on prescribing medications and availability of medicines. Only two studies described cost-effective analyses, both of which demonstrated that task-shifting was cost-effective.

Conclusions

Task-shifting from physicians to NPHWs, if accompanied by health system re-structuring is a potentially effective and affordable strategy for improving access to healthcare for NCDs. Since the majority of study designs reviewed were of inadequate quality, future research methods should include robust evaluations of such strategies.