bluuebunny/crossref_metadata_2025_split huggingface dataset:
Goldmann Applanation Tonometry Versus Dynamic Contour Tonometry After Vitrectomy
Authors: Mamas Nikolaos , Fuest Matthias , Koutsonas Antonios , Roessler Gernot , Mazinani Babac E. , Walter Peter , Plange Niklas 
Published: March 2016

Purpose:
The aim of the study was to investigate the agreement of intraocular pressure (IOP) measurement using dynamic contour tonometry (DCT) and Goldmann applanation tonometry (GAT) in eyes after vitrectomy with intraocular gas endotamponade, in eyes after vitrectomy with no tamponade, and in controls.

Methods:
In this prospective comparative study IOP was measured with GAT and DCT in 41 eyes with gas endotamponade (sulfur hexafluoride 20%) 1 to 3 days after vitrectomy, in 32 postvitrectomy eyes with intraocular water, and in 46 control eyes with no history of glaucoma or intraocular surgery. Corneal pachymetry and axial length measurements were additionally performed.

Results:
The mean difference between GAT and DCT (GAT-DCT) in gas-filled eyes was 3.1 mm Hg [SD=6.2 mm Hg], that in eyes after vitrectomy with no tamponade was 0.4 mm Hg (SD=4.8 mm Hg), and in control eyes was 0.4 mm Hg (SD=3.8 mm Hg). No significant correlation was found between the differences of GAT and DCT (GAT-DCT) and the mean IOP of GAT and DCT in water-filled eyes (r=−0.25, P=0.18) and control eyes (r=0.23, P=0.13), but a significant correlation was found in the gas-filled eyes (r=0.71, P<0.0001). A significant correlation between central corneal thickness and the mean difference of both methods was seen only in the control group (r=0.36, P=0.03).

Conclusions:
IOP as determined by DCT underestimates IOP in gas-filled eyes compared with GAT, as GAT values were on average 3.1 mm Hg higher compared with those of DCT. The extent of IOP underestimation using DCT increases with higher IOP values. In the group of eyes after vitrectomy and in normal eyes we found a generally good agreement between the 2 methods, although high interindividual discrepancies were present. Our findings suggest that the 2 devices should not be used interchangeably in IOP evaluation after vitrectomy with gas endotamponade, which remains a difficult challenge.
The Economic Burden of Childhood Glaucoma
Authors: Liu Dan , Huang Linda , Mukkamala Lekha , Khouri Albert S. 
Published: March 2016

Purpose:
To date, there are limited data on the economic burden of childhood glaucoma, a relatively rare but visually debilitating disease. The purpose of this study is to evaluate the immediate costs of illness associated with childhood glaucoma during the first 4 years after presentation.

Methods:
Data on age, sex, surgical interventions, visits, examinations under anesthesia, and medications were collected yearly following presentation in patients with childhood glaucoma. Inclusion criteria included diagnosis of primary or secondary childhood glaucoma, age less than 21 years, and follow-up of 4 years. A total of 23 patients (39 eyes) were included. Cost analysis used 2013 hospital-specific charges and US average hourly wage to calculate outcomes of total, direct, and indirect costs (significance level P<0.05).

Results:
The annual cost of care of childhood glaucoma averaged $21,441.61 per patient, representing 1100% of annual costs in adult glaucoma and an increase of 800% in annual costs of health care per pediatric patient. The average total 4-year cost of care was $85,074.96 per patient. Surgical interventions and examinations under anesthesia were the greatest contributors to costs, representing 69.0% and 23.2% of total 4-year costs, respectively. The annual costs of care for childhood glaucoma were highest in the first year compared with subsequent years, averaging $46,293.62 per patient (P<0.05).

Conclusions:
Childhood glaucoma carries a substantial economic burden with the highest costs occurring in the first year after presentation. The greatest contributors to cost of illness are surgical interventions and examinations and anesthesia.
Phylogeny-aware Identification and Correction of Taxonomically Mislabeled Sequences
Authors: Kozlov Alexey M. , Zhang Jiajie , Yilmaz Pelin , Glöckner Frank Oliver , Stamatakis Alexandros 
Published: March 2016

AbstractMolecular sequences in public databases are mostly annotated by the submitting authors without further validation. This procedure can generate erroneous taxonomic sequence labels. Mislabeled sequences are hard to identify, and they can induce downstream errors because new sequences are typically annotated using existing ones. Furthermore, taxonomic mislabelings in reference sequence databases can bias metagenetic studies which rely on the taxonomy. Despite significant efforts to improve the quality of taxonomic annotations, the curation rate is low because of the labour-intensive manual curation process.Here, we present SATIVA, a phylogeny-aware method to automatically identify taxonomically mislabeled sequences (“mislabels”) using statistical models of evolution. We use the Evolutionary Placement Algorithm (EPA) to detect and score sequences whose taxonomic annotation is not supported by the underlying phylogenetic signal, and automatically propose a corrected taxonomic classification for those. Using simulated data, we show that our method attains high accuracy for identification (96.9% sensitivity / 91.7% precision) as well as correction (94.9% sensitivity / 89.9% precision) of mislabels. Furthermore, an analysis of four widely used microbial 16S reference databases (Greengenes, LTP, RDP and SILVA) indicates that they currently contain between 0.2% and 2.5% mislabels. Finally, we use SATIVA to perform an in-depth evaluation of alternative taxonomies for Cyanobacteria.SATIVA is freely available athttps://github.com/amkozlov/sativa.
Oomycetes during 120,000 years of temperate rainforest ecosystem development
Authors: Dickie Ian A. , Wakelin Angela M. , Martinez-Garcia Laura , Richardson Sarah J. , Makiola Andreas , Tylianakis Jason M. 
Published: March 2016

AbstractThe occurrence of plant-associated oomycetes in natural ecosystems and particularly during long-term ecosystem development is largely unknown, despite the importance of many oomycetes as plant pathogens. Using DNA sequencing from roots, we investigated the frequency and host relationships of plant-associated oomycete communities along a 120 000 year glacial chronosequence, comprising site ages with rapid compositional change (“early succession”; 5, 15, and 70 years old soil); relatively stable higher-diversity sites (“mature”, 280, 500, 1000, 5000, 12000 years); and ancient, nutrient-limited soils with declining plant diversity and stature (“retrogression”, 60 000, 120 000 years). Plant-associated oomycetes were frequent in all three early successional sites, occurring in 38 – 65% of plant roots, but rare (average 3%) in all older ecosystems. Oomycetes were highly host specific, and more frequent on those plant species that declined most strongly in abundance between ecosystem ages. The results support the particular importance of plant-associated oomycetes in early succession (up to 70 years). High host specificity and correlations of abundance of oomycete inside roots with declining plant species are consistent with oomycete-driven successional change.
Have coral snake mimics diversified more than non-mimics?
Authors: Caetano Daniel S. , Alencar Laura R. V. , Passos Paulo , Grazziotin Felipe G. , Zaher Hussam , Martins Marcio 
Published: March 2016

AbstractDipsadidae is the most diversified family of snakes, composed of species showing an impressive variety of color patterns. Some species are cryptic whereas others have contrasting patterns comprised by bright colors alternated with darker shades, including particular combinations of vivid colors characteristic of coral snakes (Elapidae). Species with such patterns are thought to be mimics of coral snakes based on their color pattern similarity, predator avoidance of such patterns in field experiments, and the geographical concordance between models and mimics. Here we test whether color patterns associated with coral snake mimicry and contrasting color patterns in general influenced the diversification dynamics of the group. We compile the largest database of color patterns among reptiles to date, with color descriptions for the majority (594 species) of dipsadids. We used trait-dependent diversification models along with extensive simulations to deal with the recently described statistical bias associated with such methods. Despite the apparent survival advantage associated with coral snake mimicry, we show that there is no detectable influence of color types in the dynamics of diversification in Dipsadidae. We discuss insights into the function of color patterns and argue that non-mimic contrasting patterns might serve as pre-adaptations to mimicry of coral snakes.Data archival locationBEAST XML file and BiSSE MCMC results:http://dx.doi.org/10.6084/m9.figshare.831493R code for analyses and simulations:https://github.com/Caetanods/Dipsadidae_color_evolution
Diurnal variation of circulating interleukin-6 in humans: a meta-analysis
Authors: Nilsonne Gustav , Lekander Mats , Åkerstedt Torbjörn , Axelsson John , Ingre Michael 
Published: March 2016

AbstractThe pleiotropic cytokine interleukin-6 (IL-6) has been proposed to contribute to circadian regulation of sleepiness by increasing in the blood at night to signal for sleepiness. Earlier studies have reported diurnal variations of IL-6, but phase estimates are conflicting. We have therefore performed a meta-analysis on the diurnal variation of circulating IL-6. Studies were included if they reported circulating levels of IL-6 recorded at least twice within 24 hours in the same individual. A systematic search resulted in the inclusion of 43 studies with 56 datasets, for a total of 1100 participants. Individual participant data were available from 4 datasets with a total of 56 participants. Mixed-effects meta-regression modelling confirmed that IL-6 varied across the day, the most conspicuous effect being a trough in the morning. These results stand in contrast to earlier findings of a peak in the evening or night, and suggest that diurnal variation should be taken into account in order to avoid confounding in studies of IL-6 in plasma or serum.
Hereditary palmoplantar keratoderma “clinical and genetic differential diagnosis”
Authors: Sakiyama Tomo , Kubo Akiharu 
Published: March 2016

AbstractHereditary palmoplantar keratoderma (PPK) is a heterogeneous group of disorders characterized by hyperkeratosis of the palm and the sole skin. Hereditary PPK are divided into four groups – diffuse, focal, striate and punctate PPK – according to the clinical patterns of the hyperkeratotic lesions. Each group includes simple PPK, without associated features, and PPK with associated features, such as involvement of nails, teeth and other organs. PPK have been classified by a clinically based descriptive system. In recent years, many causative genes of PPK have been identified, which has confirmed and/or rearranged the traditional classifications. It is now important to diagnose PPK by a combination of the traditional morphological classification and genetic testing. In this review, we focus on PPK without associated features and introduce their morphological features, genetic backgrounds and new findings from the last decade.
Erythrokeratodermia variabilis et progressiva
Authors: Ishida‐Yamamoto Akemi 
Published: March 2016

AbstractErythrokeratodermia variabilis et progressiva (EKVP) is a rare inherited skin disease characterized by fixed hyperkeratotic plaques and transient erythematous patches. EKVP is most often transmitted in an autosomal dominant manner. Causal mutations were found in the GJB3, GJB4 and GJA1 genes encoding connexins 31, 30.3 and 43, respectively. Approximately 50% of affected individuals develop palmoplantar keratoderma. Connexins are components of gap junctions, which are intercellular channels that are found in almost all tissues including the skin. Treatment of EKVP usually involves use of topical keratolytics and emollients resulting in some improvement in hyperkeratosis. Low‐dose systemic retinoid may be beneficial. Novel therapies targeting connexin hemichannels and gap junctions may become available in the future.
Inherited ichthyosis: Syndromic forms
Authors: Yoneda Kozo 
Published: March 2016

AbstractAmong diseases that cause ichthyosis as one of the symptoms, there are some diseases that induce abnormalities in organs other than the skin. Of these, diseases with characteristic signs are regarded as syndromes. Although these syndromes are very rare, Netherton syndrome, Sjögren–Larsson syndrome, Conradi–Hünermann–Happle syndrome, Dorfman–Chanarin syndrome, ichthyosis follicularis, atrichia and photophobia (IFAP) syndrome, and Refsum syndrome have been described in texts as representative ones. It is important to know the molecular genetics and pathomechanisms in order to establish an effective therapy and beneficial genetic counseling including a prenatal diagnosis.
Effects of environmental temperature on the gut microbial communities of tadpoles
Authors: Kohl Kevin D. , Yahn Jeremiah 
Published: March 2016

SummaryNumerous studies have investigated the effects of diet, phylogeny and immune status on the gut microbial communities of animals. Most of these studies are conducted on endotherms, especially mammals, which maintain constant body temperature in the face of environmental temperature variability. However, the majority of animals and vertebrates are ectotherms, which often experience fluctuations in body temperature as a result of their environment. While there have been several studies investigating the gut microbial diversity of ectotherms, we lack an understanding of how environmental temperature affects these communities. Here, we used high‐throughput sequencing to inventory the gut microbial communities of tadpoles exposed to cool (18°C) or warm (28°C) temperature treatments. We found that temperature significantly impacted the community structure and membership of the tadpole gut. Specifically, tadpoles in the warm treatment exhibited higher abundances of the phylum Planctomycetes and the genus Mycobacterium. These results may be due to the direct effects of temperature, or mediated through changes in host physiology. Given that environmental temperatures are expected to increase due to global climate change, understanding the effects of temperature on the diversity and function of gut microbial communities is critical.
Nutrient pulses driven by internal solitary waves enhance heterotrophic bacterial growth in the South China Sea
Authors: Chen Tzong‐Yueh , Tai Jen‐Hua , Ko Chia‐Ying , Hsieh Chih‐hao , Chen Chung‐Chi , Jiao Nianzhi , Liu Hong‐Bin , Shiah Fuh‐Kwo 
Published: March 2016

SummaryThis study demonstrated the potential effects of internal waves (IWs) on heterotrophic bacterial activities for the first time. Nine anchored studies were conducted from 2009–2012 in the South China Sea areas with different physical conditions, i.e. areas subjected to elevation IWs, to depression IWs, and to weak/no IWs. The latter two areas were treated as the Control sites. Field survey results indicated that within the euphotic zone, the minima of the depth‐averaged bacterial production (IBP; ∼1.0 mgC m−3 d−1) and growth rate (IBμ; ∼0.1 d−1) at all sites were similar. Except for one case, the maxima of IBP (6–12 mgC m−3 d−1) and IBμ (0.55–1.13 d−1) of the elevation IWs areas were ∼fivefolds higher than those of the Control sites (IBP 1.7–2.1 mgC m−3 d−1; IBμ 0.13–0.24 d−1). Replicate surveys conducted at the north‐western area of the Dongsha atoll during spring‐to‐neap (NW1 survey) and neap‐to‐spring (NW2 survey) tide periods showed a great contrast to each other. Low variation and averages of IBμ in NW1 survey were similar to those of the Control sites, while those in NW2 were similar to the other elevation IWs sites with larger variation and higher averages of IBμ. This finding suggests that bacterial activities may be a function of the lunar fortnightly (14‐day) cycle. Enrichment experiments suggested more directly that the limiting inorganic nutrients introduced by the elevation waves (EIWs) may contribute a higher IBμ within the euphotic zone.
Esomeprazole, minocycline, metronidazole and bismuth as first‐line and second‐line regimens for Helicobacter pylori eradication
Authors: Song Zhi Qiang , Zhou Li Ya 
Published: March 2016

ObjectiveWhether minocycline can replace tetracycline in Helicobacter pylori (H. pylori) eradication remains unclear. The aim of this study was to determine the efficacy, safety, patient compliance and risk factors of a combination regimen of esomeprazole, minocycline, metronidazole and bismuth (EMMB) for H. pylori eradication.MethodsIn this prospective single‐center study, 152 patients in the first‐line therapy group and 64 in the second‐line therapy group received EMMB therapy (esomeprazole 20 mg twice daily, minocycline 100 mg twice daily, metronidazole 400 mg four times daily and bismuth potassium citrate 110 mg four times daily) for 14 days. The eradication outcome was assessed by 13C‐urea breath test 6–12 weeks after treatment.ResultsEMMB therapy achieved eradication rates of 85.5% [95% confidence interval (CI) 79.6–91.4%] using intention‐to‐treat (ITT) analysis, 90.3% (95% CI 84.7–95.1%) using modified intention‐to‐treat (mITT) analysis and 92.6% (95% CI 88.1–96.3%) using per‐protocol (PP) analysis as the first‐line therapy; and 82.8% (95% CI 71.9–90.6%), 86.9% (95% CI 77.1–95.1%) and 89.5% (95% CI 80.7–96.5%) as the second‐line therapy, respectively. In the first‐line group, 35.6% of the patients experienced adverse effects, 4.7% discontinued medications because of adverse effects and good compliance was achieved in 91.3%, while the results were 36.5%, 3.2% and 90.5% in the second‐line therapy group. Poor compliance was identified as an independent predictor of treatment failure.ConclusionThe efficacy of EMMB therapy for H. pylori eradication as first‐line and second‐line regimens in a region with high rates of antibiotic resistance is satisfactory with relatively good patient compliance and high safety.
Polyethylene glycol plus ascorbic acid is as effective as sodium picosulfate with magnesium citrate for bowel preparation: A randomized trial
Authors: Choi Hyun‐Seok , Chung Jun‐Won , Lee Ji Won , Lim Min Young , Park Dong Kyun , Kim Yoon Jae , Kwon Kwang Ahn , Kim Jung Ho 
Published: March 2016

ObjectiveThis study was aimed to evaluate the efficacy and safety of two low‐volume agents, polyethylene glycol (PEG)‐3350 plus ascorbic acid (PEG + Asc) and sodium picosulfate with magnesium citrate (SPMC), for bowel preparation.MethodsWe performed a prospective, endoscopist‐blinded, single‐center, randomized controlled trial comparing PEG + Asc with SPMC to evaluate the bowel cleansing efficacy of the two regimens using the modified Ottawa bowel preparation scale (OBPS) and the Aronchick scale. Patients’ taste and overall tolerance were assessed with a questionnaire.ResultsIn total, 200 patients were randomized to receive either PEG + Asc (n = 98) or SPMC (n = 102). Both treatments were similarly efficacious in bowel cleansing, based on the modified OBSP (PEG + Asc 4.01 ± 2.29 vs SPMC 3.86 ± 2.47, P = 0.62) and Aronchick scale (PEG + Asc 1.96 ± 0.70 vs SPMC 1.89 ± 0.70, P = 0.42). Patient‐reported taste and tolerance of each regimen, as reported by the questionnaire, were significantly greater in the PEG + Asc group than in the SPMC group (P = 0.01). In terms of adverse events, dizziness was more frequently observed in the PEG + Asc group (P = 0.03), whereas nausea was more common in the SPMC group (P = 0.02).ConclusionsPEG + Asc and SPMC show similar efficacy for bowel preparation. However, patient's overall tolerance is higher in the PEG + Asc group.
Finding the right coverage: the impact of coverage and sequence quality on single nucleotide polymorphism genotyping error rates
Authors: Fountain Emily D. , Pauli Jonathan N. , Reid Brendan N. , Palsbøll Per J. , Peery M. Zachariah 
Published: March 2016

AbstractRestriction‐enzyme‐based sequencing methods enable the genotyping of thousands of single nucleotide polymorphism (SNP) loci in nonmodel organisms. However, in contrast to traditional genetic markers, genotyping error rates in SNPs derived from restriction‐enzyme‐based methods remain largely unknown. Here, we estimated genotyping error rates in SNPs genotyped with double digest RAD sequencing from Mendelian incompatibilities in known mother–offspring dyads of Hoffman's two‐toed sloth (Choloepus hoffmanni) across a range of coverage and sequence quality criteria, for both reference‐aligned and de novo‐assembled data sets. Genotyping error rates were more sensitive to coverage than sequence quality and low coverage yielded high error rates, particularly in de novo‐assembled data sets. For example, coverage ≥5 yielded median genotyping error rates of ≥0.03 and ≥0.11 in reference‐aligned and de novo‐assembled data sets, respectively. Genotyping error rates declined to ≤0.01 in reference‐aligned data sets with a coverage ≥30, but remained ≥0.04 in the de novo‐assembled data sets. We observed approximately 10‐ and 13‐fold declines in the number of loci sampled in the reference‐aligned and de novo‐assembled data sets when coverage was increased from ≥5 to ≥30 at quality score ≥30, respectively. Finally, we assessed the effects of genotyping coverage on a common population genetic application, parentage assignments, and showed that the proportion of incorrectly assigned maternities was relatively high at low coverage. Overall, our results suggest that the trade‐off between sample size and genotyping error rates be considered prior to building sequencing libraries, reporting genotyping error rates become standard practice, and that effects of genotyping errors on inference be evaluated in restriction‐enzyme‐based SNP studies.
Estimating fish abundance and biomass from eDNA concentrations: variability among capture methods and environmental conditions
Authors: Lacoursière‐Roussel Anaïs , Rosabal Maikel , Bernatchez Louis 
Published: March 2016

AbstractEnvironmental DNA (eDNA) promises to ease noninvasive quantification of fish biomass or abundance, but its integration within conservation and fisheries management is currently limited by a lack of understanding of the influence of eDNA collection method and environmental conditions on eDNA concentrations in water samples. Water temperature is known to influence the metabolism of fish and consequently could strongly affect eDNA release rate. As water temperature varies in temperate regions (both seasonally and geographically), the unknown effect of water temperature on eDNA concentrations poses practical limitations on quantifying fish populations using eDNA from water samples. This study aimed to clarify how water temperature and the eDNA capture method alter the relationships between eDNA concentration and fish abundance/biomass. Water samples (1 L) were collected from 30 aquaria including triplicate of 0, 5, 10, 15 and 20 Brook Charr specimens at two different temperatures (7 °C and 14 °C). Water samples were filtered with five different types of filters. The eDNA concentration obtained by quantitative PCR (qPCR) varied significantly with fish abundance and biomass and types of filters (mixed‐design ANOVA, P < 0.001). Results also show that fish released more eDNA in warm water than in cold water and that eDNA concentration better reflects fish abundance/biomass at high temperature. From a technical standpoint, higher levels of eDNA were captured with glass fibre (GF) filters than with mixed cellulose ester (MCE) filters and support the importance of adequate filters to quantify fish abundance based on the eDNA method. This study supports the importance of including water temperature in fish abundance/biomass prediction models based on eDNA.