bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapidly Progressive Dementia: Prevalence and Causes in a Neurologic Unit of a Tertiary Hospital in Brazil
Authors: Studart Neto Adalberto , Soares Neto Herval R. , Simabukuro Mateus M. , Solla Davi J.F. , Gonçalves Márcia R.R. , Fortini Ida , Castro Luiz H.M. , Nitrini Ricardo 
Published: November 2016

Background:
Rapidly progressive dementia (RPD) is usually associated with Creutzfeldt-Jakob disease, a fatal condition. Current advances in the understanding of immune-mediated diseases allow the diagnosis of previously unrecognized treatable RPDs.

Objective of the Study:
The objective of the study was to describe the prevalence and causes of RPD in a neurology service, identifying potentially reversible causes.

Methods:
We carried out a cross-sectional evaluation of all patients admitted to the neurology unit of a tertiary hospital in Brazil between March 2012 and February 2015. We included patients who had progressed to moderate or severe dementia within a few months or up to 2 years at the time of hospitalization, and used multivariable logistic regression analysis to identify factors associated with a favorable outcome.

Results:
We identified 61 RPD (3.7%) cases among 1648 inpatients. Mean RPD patients’ age was 48 years, and median time to progression was 6.4 months. Immune-mediated diseases represented the most commonly observed disease group in this series (45.9% of cases). Creutzfeldt-Jakob disease (11.5%) and nonprion neurodegenerative diseases (8.2%) were less common in this series. Outcome was favorable in 36/61 (59.0%) RPD cases and in 28/31 (89.3%) of immune-mediated cases. Favorable outcome was associated with shorter time from symptom onset to diagnosis and abnormal cerebrospinal fluid findings.

Conclusions:
Immune-mediated diseases were the most common cause of RPD in this series. Timely evaluation and diagnosis along with institution of appropriate therapy are required in RPD, especially in view of potentially reversible causes.
MARS: Motif Assessment and Ranking Suite for transcription factor binding motifs
Authors: Kibet Caleb Kipkurui , Machanick Philip 
Published: November 2016

AbstractWe describe MARS (Motif Assessment and Ranking Suite), a web-based suite of tools used to evaluate and rank PWM-based motifs. The increased number of learned motif models that are spread across databases and in different PWM formats, leading to a choice dilemma among the users, is our motivation. This increase has been driven by the difficulty of modelling transcription factor binding sites and the advance in high-throughput sequencing technologies at a continually reducing cost. Therefore, several experimental techniques have been developed resulting in diverse motif-finding algorithms and databases. We collate a wide variety of available motifs into a benchmark database, including the corresponding experimental ChIP-seq and PBM data obtained from ENCODE and UniPROBE databases, respectively. The implemented tools include: a data-independent consistency-based motif assessment and ranking (CB-MAR), which is based on the idea that ‘correct motifs’ are more similar to each other while incorrect motifs will differ from each other; and a scoring and classification-based algorithms, which rank binding models by their ability to discriminate sequences known to contain binding sites from those without. The CB-MAR and scoring techniques have a 0.86 and 0.73 median rank correlation using ChIP-seq and PBM respectively. Best motifs selected by CB-MAR achieve a mean AUC of 0.75, comparable to those ranked by held out data at 0.76 – this is based on ChIP-seq motif discovery using five algorithms on 110 transcription factors. We have demonstrated the benefit of this web server in motif choice and ranking, as well as in motif discovery. It can be accessed athttp://www.bioinf.ict.ru.ac.za/.
Trace metal imaging of sulfate-reducing bacteria and methanogenic archaea at single-cell resolution by synchrotron X-ray fluorescence imaging
Authors: Glass Jennifer B. , Chen Si , Dawson Katherine S. , Horton Damian R. , Vogt Stefan , Ingall Ellery D. , Twining Benjamin S. , Orphan Victoria J. 
Published: November 2016

AbstractMetal cofactors are required for many enzymes in anaerobic microbial respiration. This study examined iron, cobalt, nickel, copper, and zinc in cellular and abiotic phases at the single-cell scale for a sulfate-reducing bacterium (Desulfococcus multivorans) and a methanogenic archaeon (Methanosarcina acetivorans) using synchrotron x-ray fluorescence microscopy. Relative abundances of cellular metals were also measured by inductively coupled plasma mass spectrometry. For both species, zinc and iron were consistently the most abundant cellular metals.M. acetivoranscontained higher nickel and cobalt content thanD. multivorans, likely due to elevated metal requirements for methylotrophic methanogenesis. Cocultures contained spheroid zinc sulfides and cobalt/copper-sulfides.
One‐year safety and efficacy study of bilastine treatment in Japanese patients with chronic spontaneous urticaria or pruritus associated with skin diseases
Authors: Yagami Akiko , Furue Masutaka , Togawa Michinori , Saito Akihiro , Hide Michihiro 
Published: November 2016

AbstractA number of second‐generation non‐sedating antihistamines are used in clinical practices over the world. However, long‐term safety and efficacy have not been proved high level evidence based medicine. We have performed an open‐label, multicenter, phase III study to evaluate the long‐term safety and efficacy of bilastine, a novel non‐sedating H1‐antihistamine for patients with chronic spontaneous urticaria (CSU) or pruritus associated with skin diseases (trial registration no. JapicCTI‐142528). Patients aged 18–74 years were treated with bilastine 20 mg once daily for up to 52 weeks. Safety and tolerability were assessed on the basis of adverse events (AE), bilastine‐related AE, laboratory tests and vital signs. Efficacy was assessed based on rash score, itch score, overall improvement and quality of life. One hundred and ninety‐eight patients enrolled, 122 of whom (61.6%) completed the 52‐week treatment period. AE were reported in 64.5% and bilastine‐related AE in 2.5% of patients throughout the 52‐week treatment period. All AE were mild to moderate in severity. AE associated with the nervous system occurred in 10 patients (5.1%) including seven patients (3.6%) with headache. Somnolence reported in two of these patients (1.0%) was related to bilastine. All efficacy variables improved during treatment with bilastine. In conclusion, long‐term treatment with bilastine 20 mg once daily for 52 weeks is safe and well tolerated in Japanese patients with CSU or pruritus associated with skin diseases. Bilastine improved disease symptoms of both conditions early in treatment, and the efficacy was maintained throughout the treatment.
Lizards paid a greater opportunity cost to thermoregulate in a less heterogeneous environment
Authors: Basson Christine H. , Levy Ofir , Angilletta Michael J. , Clusella‐Trullas Susana 
Published: November 2016

Summary

The theory of thermoregulation has developed slowly, hampering efforts to predict how individuals can buffer climate change through behaviour. Mixed results of field and laboratory experiments underscore the need to test hypotheses about thermoregulation explicitly, while measuring costs and benefits in different thermal landscapes.

We simulated body temperature and energy expenditure of a virtual lizard that either thermoregulates optimally or thermoconforms in a landscape of either low or high quality (one or four basking sites, respectively). We then compare the predicted values in each landscape with the observed values for real lizards in experimental arenas.

Lizards thermoregulated more accurately in the high‐quality landscape than they did on the low‐quality landscape, albeit only slightly so, but spent similar amounts of energy in these landscapes. Basking, rather than shuttling between heat sources, accounted for the majority of the energy consumed in both landscapes.

These results did not support the predictions of our model. In the low‐quality landscape, real lizards thermoregulated intensely despite the potential to save energy by thermoconforming. In the high‐quality landscape, lizards moved more than expected, suggesting that lizards explored their surroundings despite being able to thermoregulate without doing so.

Our results suggest that non‐energetic benefits drive thermoregulatory behaviour in costly environments, despite the missed opportunities arising from thermoregulation. We propose that energetic costs associated with thermoregulatory movement will become substantial in homogeneous environments such as flat plains and dense forests. The theory of thermoregulation should incorporate these aspects if biologists wish to predict responses of ectotherms to changing climates and habitats.

A lay summary is available for this article.
The effect of colour‐producing mechanisms on plumage sexual dichromatism in passerines and parrots
Authors: Delhey Kaspar , Peters Anne 
Published: November 2016

Summary

Sexual dichromatism (SD) often reflects intense sexual selection on males. It has been hypothesized that sexual selection should favour the elaboration of those male colours that honestly signal quality and that such colours should therefore show higher SD. Costliness of colours is expected to vary according to their production mechanism (pigment type, feather microstructure and combinations thereof). Carotenoid‐based colours, due to their dietary origin and competing functions of carotenoid pigments, are the best documented costly colours, while endogenous pigments and structural colours are expected to be less costly. However, how SD varies with colour‐producing mechanism has not been systematically addressed.

Here, we test the link between SD and mechanisms of colour production across nearly all Australian passerines (n = 302) and parrots (n = 48), using reflectance spectrometry and visual models. We quantified SD [chromatic (hue and saturation) and achromatic (light to dark)] for individual plumage patches as well as for the whole plumage. We then compared whether these SD estimates vary for plumage produced by different mechanisms of colour production.

Not unexpectedly, individual plumage patches were most sexually dichromatic when males and females have different mechanisms of colour production. In most cases however, both sexes share the same mechanism. Among these, red carotenoid‐based plumage in passerines showed the highest SD, while in passerines as well as in parrots, melanin‐based plumage and white plumage have the lowest levels of SD.

Average SD within species is weakly predicted by the proportion of the plumage produced by different mechanisms. This effect is strongest for red carotenoids, but equally so for males and females. In contrast, effects of structural and pheomelanin‐based colours are different between sexes, highlighting the links between high SD and the evolution of different mechanisms of colour production in males and females.

While our analysis showed that colours based on red carotenoids have higher levels of SD, the differences were small, and most mechanisms of colour production were able to produce a similar range of SD. These results do not support the hypothesis that sexual selection should preferentially lead to the elaboration of some types of colours over others.

A lay summary is available for this article.
Functional traits of marine macrophytes predict primary production
Authors: Jänes Holger , Kotta Jonne , Pärnoja Merli , Crowe Tasman P. , Rindi Fabio , Orav‐Kotta Helen 
Published: November 2016

SummaryThe relationship between community structure and the functioning of ecosystems is the subject of ongoing debate. Biological or functional trait‐based approaches that capture life strategy, morphology and behavioural characteristics have received far less attention than taxonomic diversity in this context, despite their more intuitive link to ecosystem functioning.Macrophyte primary production underpins aquatic food webs, regulates benthic and pelagic ecosystems and is a key aspect of the global carbon cycle. This study spans a range of aquatic biomes across Europe and aims to examine potential for predicting primary production of macrophyte communities based on the functional traits of species and identify the traits that are the most informative indicators of macrophyte production.Macrophyte primary production was assessed based on the oxygen production of the whole community, linked to biomasses of selected biological traits derived of its component species and analysed using the novel boosted regression trees modelling technique.Results showed that functional traits derived from macrophyte community data explained most of the variation in primary production of macrophyte communities without the need to incorporate environmental data on the habitats. Macrophyte primary production was influenced by a combination of tolerance, morphology and life habit traits; however tolerance traits contributed most of variability in macrophyte primary production when all traits were analysed jointly.This study also showed the existence of trait clustering as the studied trait categories were not fully independent; strong interlinkages between and within trait categories emerged.Our study suggests that functional trait analysis captures different aspects of ecosystem functioning and thereby enables assessing primary production of macrophyte communities over geographically distinct areas without extensive taxonomic and environmental data. This could result in a novel framework through which a simplification of the general procedure of production estimations and comparisons across environmental gradients can be achieved.Alay summaryis available for this article.
Climatic conditions cause spatially dynamic polygyny thresholds in a large mammal
Authors: Manning Jeffrey A. , McLoughlin Philip D. 
Published: November 2016

Summary

The polygyny threshold (PT) is a critical transition point in the sexual selection process for many organisms in natural populations, characterizing when females choose to mate with an already mated male over an unmated one to improve fitness. Understanding its causes and consequences is therefore of high interest. While both theoretical and empirical work suggest that the degree of polygyny within a species is plastic and a function of male inequality, the functional relationship between underlying availability of resources occupied by breeding males under variable climatic conditions and the dynamics of PTs across space and time has received less attention.

Here, we use a standardized measure of male mating inequality as the culmination of female mate choices to analyse how spatially dynamic PTs in a naturally regulated feral horse (Equus ferus caballus) population emerge along a geographic gradient in a known, limiting resource (freshwater) each year from variable climatic conditions. Polygyny threshold distance from permanent freshwater increased with increasing precipitation during the breeding season of each year, suggesting a relationship between annual resource availability and female mate choice.

The mechanism by which climatic conditions underpin the spatial dynamics of PTs was likely through precipitation providing ephemeral freshwater sources across the study area that effectively weakened the gradient in availability of permanent freshwater, thereby providing mating males that occupied home ranges far from permanent water with access to this limiting resource and enabling them to attract and retain females. Increased precipitation also coincided with a decreased proportion of males in the population that experienced sexual selection pressure attributed to female mate choice in relation to the acquisition and/or defence of freshwater sources.

Climatic conditions caused spatial shifts in PTs annually along the geographic gradient in resource availability. Our findings reveal that such environmental gradients may either buffer or amplify impacts of climatic variation on selection pressure operating in natural populations, and emphasize the importance of integrating spatially explicit PTs with atmospheric fluctuations when predicting the effect of climatic change on selection processes within populations that occupy environmental gradients.
Genetic erosion and escalating extinction risk in frogs with increasing wildfire frequency
Authors: Potvin Dominique A. , Parris Kirsten M. , Smith Date Katie L. , Keely Claire C. , Bray Rebecca D. , Hale Joshua , Hunjan Sumitha , Austin Jeremy J. , Melville Jane 
Published: November 2016

Summary

Wildfires are increasing in both frequency and intensity in many ecosystems, with climate change models predicting further escalations in fire‐prone environments. Set against this background is the global decline of amphibians, with up to 40% of species facing extinction from multiple additive threats. Despite these disturbing figures, it is currently unclear how increasing fire frequency may impact the long‐term persistence of frog populations.

Following a severe wildfire in south‐eastern Australia in 2009, field surveys indicated healthy tree frog populations. However, the 2009 fire had significant impacts on genetic diversity, including increased levels of inbreeding and declines in effective population size.

Using stochastic population modelling under a range of fire‐frequency scenarios, we demonstrate that amphibian populations in fire‐prone environments may be increasingly vulnerable to extinction, particularly where rates of immigration are low.

Synthesis and applications. This study of amphibian population genetics before and after a major wildfire emphasizes the importance of integrating both ecological and genetic data into population models. This will help managers make more appropriate conservation decisions regarding fire management of natural environments, especially those containing threatened populations. Priorities for agencies involved in planning controlled burns should consider carefully the timing of controlled burns, along with maintaining habitat connectivity.
The influence of spatially structured soil properties on tree community assemblages at a landscape scale in the tropical forests of southern Cameroon
Authors: Vleminckx Jason , Doucet Jean‐Louis , Morin‐Rivat Julie , Biwolé Achille B. , Bauman David , Hardy Olivier J. , Fayolle Adeline , Gillet Jean‐François , Daïnou Kasso , Gorel Anaïs , Drouet Thomas 
Published: November 2016

Summary

Species distribution within plant communities results from both the influence of deterministic processes, related to environmental conditions, and neutral processes related to dispersal limitation and stochastic events, the relative importance of each factor depending on the observation scale.

Assessing the relative contribution of environment necessitates controlling for spatial dependences among data points. Recent methods, combining multiple regression and Moran's eigenvectors maps (MEM), have been proved successful in disentangling the influence of pure spatial processes related to dispersal limitation, pure environmental variables (not spatially structured) and spatially structured environmental properties. However, the latter influence is usually not testable when using advanced spatial models like MEM.

To overcome this issue, we propose an original approach, based on torus‐translations and Moran spectral randomizations, to test the fraction of species abundance variation that is jointly explained by space and seven soil variables, using three environmental and tree species abundance data sets (consisting of 120, 52 and 34 plots of 0·2 ha each, located along 101‐, 66‐ and 35‐km‐long transect‐like inventories, respectively) collected in tropical moist forests in southern Cameroon.

The overall abundance of species represented by ≥30 individuals, and 27% of these species taken individually, were significantly explained by fine‐scale (<5 km) and/or broad‐scale (5–100 km) spatially structured variations in soil nutrient concentrations (essentially the concentration of available Mn, Mg and Ca) along the 120‐plots area. The number of significant tests considerably decreased when investigating the two smaller data sets, which mostly resulted from low statistical power rather than weaker floristic and/or edaphic variation captured among plots.

Synthesis. Our results provide evidence that tree species turnovers are partly controlled by spatially structured concentrations in soil nutrients at scales ranging from few hundreds of metres to c. 100 km, a poorly documented subject in Central African forests. We also highlight the usefulness of our testing procedure to correctly interpret the space‐soil fraction of variation partitioning analyses (which always accounted here for the most important part of the soil contribution), as this fraction was sometimes relatively high (R2 values up to c. 0·3) but nearly or not significant.
Decreased percentage of NKG2D+NK cells in patients with incident onset of Type 1 Diabetes
Authors: Zhang Yupan , Wang Haifeng , Lou Xiaoqian , Qu Xiaozhang , Gao Lichao , Liu Xiaolei , Li Man , Guo Hui , Jiang Yanfang 
Published: November 2016

SummaryType 1 diabetes mellitus (T1DM) is characterized by absolute insulin deficiency owing to autoimmune destruction of the pancreatic β cells. A significant decrease in natural killer (NK) cells in peripheral blood has been observed in patients with untreated T1DM. In the present study, we aimed to explore the role of NK cells and their subsets in young T1DM patients. A total of 30 children and adolescents with untreated T1DM and 27 healthy controls (HC) were recruited in this study. Flow cytometry analysis indicated that the percentage of peripheral blood CD3‐CD56+ NK cells and NK cells subsets (CD56bright, CD56dim and CD56neg), were significantly decreased in the T1DM patients compared to healthy controls. In addition, the percentage of inducible CD107a+ and IFN‐γ‐secreting NK cells was significantly decreased compared to HC. Interestingly, the percentage of NKG2D+ NK cells negatively correlated with the level of serum TCHOL and TG in T1DM patients. Our data indicate that decreased number and impaired function of NK cells may have a role in the pathogenesis of T1DM.
Microbial processes of the carbon and sulfur cycles in an ice‐covered, iron‐rich meromictic lake Svetloe (Arkhangelsk region, Russia)
Authors: Savvichev Alexander S. , Kokryatskaya Natalia M. , Zabelina Svetlana A. , Rusanov Igor I. , Zakharova Elena E. , Veslopolova Elena F. , Lunina Olga N. , Patutina Ekaterina O. , Bumazhkin Boris K. , Gruzdev Denis S. , Sigalevich Pavel A. , Pimenov Nikolay V. , Kuznetsov Boris B. , Gorlenko Vladimir M. 
Published: November 2016

SummaryBiogeochemical, isotope geochemical and microbiological investigation of Lake Svetloe (White Sea basin), a meromictic freshwater was carried out in April 2014, when ice thickness was ∼0.5 m, and the ice‐covered water column contained oxygen to 23 m depth. Below, the anoxic water column contained ferrous iron (up to 240 μμM), manganese (60 μM), sulfide (up to 2 μM) and dissolved methane (960 μM). The highest abundance of microbial cells revealed by epifluorescence microscopy was found in the chemocline (redox zone) at 23–24.5 m. Oxygenic photosynthesis exhibited two peaks: the major one (0.43 μmol C L−1 day−1) below the ice and the minor one in the chemocline zone, where cyanobacteria related to Synechococcus rubescens were detected. The maximum of anoxygenic photosynthesis (0.69 μmol C L−1 day−1) at the oxic/anoxic interface, for which green sulfur bacteria Chlorobium phaeoclathratiforme were probably responsible, exceeded the value for oxygenic photosynthesis. Bacterial sulfate reduction peaked (1.5 μmol S L−1 day−1) below the chemocline zone. The rates of methane oxidation were as high as 1.8 μmol CH4 L−1 day−1 at the oxi/anoxic interface and much lower in the oxic zone. Small phycoerythrin‐containing Synechococcus‐related cyanobacteria were probably involved in accumulation of metal oxides in the redox zone.