bluuebunny/crossref_metadata_2025_split huggingface dataset:
PyRAD: assembly ofde novoRADseq loci for phylogenetic analyses
Authors: Eaton Deren A. R. 
Published: December 2013

AbstractRestriction-site associated genomic markers are a powerful tool for investigating evolutionary questions at the population level, but are limited in their utility at deeper phylogenetic scales where fewer orthologous loci are typically recovered across disparate taxa. While this limitation stems in part from mutations to restriction recognition sites that disrupt data generation, an alternative source of data loss comes from the failure to identify homology during bioinformatic analyses. Clustering methods that allow for lower similarity thresholds and the inclusion of indel variation will perform better at assembling RADseq loci at the phylogenetic scale.PyRADis a pipeline to assemblede novoRADseq loci with the aim of optimizing coverage across phylogenetic data sets. It utilizes a wrapper around an alignment-clustering algorithm which allows for indel variation within and between samples, as well as for incomplete overlap among reads (e.g., paired-end). Here I comparePyRADwith the programStacksin their performance analyzing a simulated RADseq data set that includes indel variation. Indels disrupt clustering of homologous loci inStacksbut not inPyRAD, such that the latter recovers more shared loci across disparate taxa. I show through re-analysis of an empirical RADseq data set that indels are a common feature of such data, even at shallow phylogenetic scales.PyRADutilizes parallel processing as well as an optional hierarchical clustering method which allow it to rapidly assemble phylogenetic data sets with hundreds of sampled individuals.AvailabilitySoftware is written in Python and freely available athttp://www.dereneaton.com/software/SupplementScripts to completely reproduce all simulated and empirical analyses are available in the Supplementary Materials.
OTX2 Dosage Sensitivity is Implicated in Hemifacial Microsomia
Authors: Zielinski Dina , Markus Barak , Sheikh Mona , Gymrek Melissa , Chu Clement , Zaks Marta , Srinivasan Balaji , Hoffman Jodi D. , Aizenbud Dror , Erlich Yaniv 
Published: December 2013

ABSTRACTHemifacial microsomia (HFM) is the second most common facial anomaly after cleft lip and palate. The phenotype is highly variable and most cases are sporadic. Here, we investigated the disorder in a large pedigree with five affected individuals spanning eight meioses. We performed whole-exome sequencing and a genome-wide survey of segmental variations. Analysis of the exome sequencing results indicated the absence of a pathogenic coding point mutation. Inspection of segmental variations identified a 1.3Mb duplication of chromosome 14q22.3 in all affected individuals that was absent in more than 1000 chromosomes of ethnically matched controls. The duplication was absent in seven additional sporadic HFM cases, which is concordant with the known heterogeneity of the disorder. To find the critical gene in the duplicated region, we analyzed signatures of human craniofacial disease networks, mouse expression data, and predictions of dosage sensitivity. All of these approaches implicated OTX2 as the most likely causal gene. Moreover, OTX2 is a known oncogenic driver in medulloblastoma, a condition that was diagnosed in the proband during the course of our study. Our findings highlight dosage sensitivity of OTX2 in human craniofacial development and suggest a possible shared etiology between a subtype of hemifacial microsomia and medulloblastoma.
Double Knockout Mutants of Arabidopsis Grown under Normal Conditions Reveal that the Plastidial Phosphorylase Isozyme Participates in Transitory Starch Metabolism
Authors: Malinova Irina , Mahlow Sebastian , Alseekh Saleh , Orawetz Tom , Fernie Alisdair R. , Baumann Otto , Steup Martin , Fettke Joerg 
Published: December 2013

Abstract
In leaves of two starch-related single-knockout lines lacking either the cytosolic transglucosidase (also designated as disproportionating enzyme 2, DPE2) or the maltose transporter (MEX1), the activity of the plastidial phosphorylase isozyme (PHS1) is increased. In both mutants, metabolism of starch-derived maltose is impaired but inhibition is effective at different subcellular sites. Two constitutive double knockout mutants were generated (designated as dpe2-1 × phs1a and mex1 × phs1b) both lacking functional PHS1. They reveal that in normally grown plants, the plastidial phosphorylase isozyme participates in transitory starch degradation and that the central carbon metabolism is closely integrated into the entire cell biology. All plants were grown either under continuous illumination or in a light-dark regime. Both double mutants were compromised in growth and, compared with the single knockout plants, possess less average leaf starch when grown in a light-dark regime. Starch and chlorophyll contents decline with leaf age. As revealed by transmission electron microscopy, mesophyll cells degrade chloroplasts, but degradation is not observed in plants grown under continuous illumination. The two double mutants possess similar but not identical phenotypes. When grown in a light-dark regime, mesophyll chloroplasts of dpe2-1 × phs1a contain a single starch granule but under continuous illumination more granules per chloroplast are formed. The other double mutant synthesizes more granules under either growth condition. In continuous light, growth of both double mutants is similar to that of the parental single knockout lines. Metabolite profiles and oligoglucan patterns differ largely in the two double mutants.
Effect of monochromatic excimer light on palmoplantar pustulosis: A clinical study performed in a private clinic by a dermatological specialist
Authors: Fumimori Takeaki , Tsuruta Daisuke , Kawakami Tamihiro , Ohata Chika , Furumura Minao , Hashimoto Takashi 
Published: December 2013

AbstractPalmoplantar pustulosis (PPP) is currently treated with various modalities, including excimer light, a form of ultraviolet lamp. This study reports effect of excimer light treatment in 34 Japanese PPP patients treated at a private clinic by one doctor, who was certified as a dermatological specialist by the Japanese Dermatological Association. The statistical analyses were performed upon a collaborative basis with faculties in universities. Disease response scores were determined by response to excimer light treatment. Scores of 1, 2, 3 or 4 were assigned to patients whose palmoplantar pustular psoriasis area and severity index (PPPASI) decreased to 25% or less, 25.1–50%, 50.1–75% or more than 75.1% of pretreatment PPPASI, respectively. In this study, 44.1% PPP cases had scores of 1 or 2, and considered good responders to excimer light treatment. There were no statistical differences between males and females, and between older (≥40 years) and younger groups (≤39 years) in terms of disease response score. Disease duration did not show any significant difference among these scores. Treatment times, total amount of ultraviolet and total treatment duration showed significant differences between score 1 and score 4 groups (P = 0.0164, =0.0137 and =0.0267, respectively). Particular interest was paid to smoking habits. Smoking in male patients was significantly higher than that in female patients (P = 0.0169). There was no statistical difference between smokers and non‐smokers in terms of response to excimer light. In conclusion, this study suggested that excimer light is useful for both initial regimen and suppression of exacerbation in treatments of PPP.
Upregulation of S100P, receptor for advanced glycation end products and ezrin in malignant melanoma
Authors: Zhu Li , Ito Takamichi , Nakahara Takeshi , Nagae Konosuke , Fuyuno Yoko , Nakao Masayoshi , Akahoshi Maki , Nakagawa Rieko , Tu Yating , Uchi Hiroshi , Furue Masutaka 
Published: December 2013

AbstractS100P is a member of the S100 family. Increased levels of S100P have been documented in various malignancies. Binding of extracellular S100P to receptor for advanced glycation end products (RAGE) or coupling of intracellular S100P with a cytoskeletal protein, ezrin, play a crucial role in tumor growth, invasion and metastasis. However, little is known about the expression of S100P, RAGE and ezrin in malignant melanoma. We immunostained these three molecules in 20 primary and 20 metastatic melanomas. Samples of 20 benign nevus pigmentosus and 10 of normal skin were tested as controls. The expression levels (percentage of positively stained cells) of S100P, RAGE and ezrin were significantly higher in melanomas than in nevus pigmentosus. Moreover, slightly but significantly higher expression levels were observed in metastatic than in primary melanomas. Significant positive correlations were evident between the expression levels of S100P and RAGE, S100P and ezrin, and RAGE and ezrin, respectively. In conclusion, the coordinate upregulation of S100P, RAGE and ezrin may possibly facilitate malignant transformation of melanoma.
Clinical utility of loop‐mediated isothermal amplification assay for the diagnosis of common alpha herpesvirus skin infections
Authors: Kobayashi Tsukane , Yagami Akiko , Suzuki Kayoko , Ihira Masaru , Yoshikawa Tetsushi , Matsunaga Kayoko 
Published: December 2013

AbstractLoop‐mediated isothermal amplification (LAMP) is a nucleic acid amplification method with a high specificity, efficiency and speed. No reports exist regarding the usefulness of LAMP for clinically suspected skin infections caused by herpes simplex virus (HSV) or varicella zoster virus (VZV). The aim of this study was to evaluate the clinical usefulness of LAMP in the diagnosis of common cutaneous alpha herpesvirus (HSV type 1 and 2, and VZV) infections. LAMP and real‐time polymerase chain reaction (PCR) were performed using swab samples collected from 106 patients with clinically suspected alpha herpesvirus skin infections. The results of LAMP performed with DNA extraction did not differ from those performed without DNA extraction. The sensitivity of LAMP tested against real‐time PCR was 96% in herpes simplex, 78% in eczema herpeticum, 93% in herpes zoster and 100% in varicella. No viral DNA was detected by LAMP in all negative real‐time PCR samples. Viral DNA load was significantly lower in samples with false‐negative LAMP results than in the LAMP‐positive samples. LAMP enables confirmation of clinically suspected cutaneous HSV and VZV infections. However, the sensitivity of LAMP is lower than real‐time PCR. The accuracy of LAMP may increase if sufficient viral DNA is obtained from lesions. LAMP performed without DNA extraction remains sensitive; thus, LAMP represents a quick and economical method for the diagnosis of common alpha herpesvirus skin infections.
Ultraviolet B irradiation increases the expression of inflammatory cytokines in cultured sebocytes
Authors: Lee Weon Ju , Park Kyung Hea , Sohn Mi Yeung , Lee Won Chae , Lee Seok‐Jong , Kim Do Won 
Published: December 2013

AbstractSebaceous gland hyperplasia and increased sebum secretion after irradiation of ultraviolet (UV)‐B has been widely accepted. This study was performed to clarify expression of inflammatory cytokines after irradiating UV‐B in cultured sebocytes. Reverse transcription polymerase chain reaction was performed to measure gene expression of inflammatory cytokines, including interleukin (IL)‐1β, IL‐6, IL‐8 and tumor necrosis factor‐α, in cultured sebocytes after exposure to 40 and 70 mJ/cm2 UV‐B. Protein expression of inflammatory cytokines and lipid production in cultured sebocytes after exposure to UV‐B were measured using enzyme‐linked immunoassay and lipid analysis kit. The expression of inflammatory cytokines, especially IL‐1β and IL‐8, was significantly increased in cultured sebocytes after treatment with UV‐B. Many more studies on the effect of UV‐B on sebaceous glands should be performed to reveal the pathogenic mechanism of acne.
Simple identification of Trichophyton tonsurans by chlamydospore‐like structures produced in culture media
Authors: Mochizuki Takashi , Anzawa Kazushi , Sakata Yuichi , Fujihiro Machiko 
Published: December 2013

AbstractTrichophyton tonsurans is known to be the causative agent of a worldwide epidemic of dermatophytoses among contact sports practitioners, and is spreading among the general population of Japan. Prompt and simple identification of T. tonsurans in diagnostic laboratories is crucial to control infection. The present study evaluated the availability of observation of chlamydospore‐like structures grown in culture media as a characteristic for identification of T. tonsurans. Twenty‐five strains of T. tonsurans and five strains each of Trichophyton verrucosum, Trichophyton rubrum and Trichophyton mentagrophytes were inoculated on Mycosel agar plates and inoculated Petri dishes were observed by light microscopy from the reverse side. Twenty‐three of 25 T. tonsurans strains showed chlamydospore‐like structures within 5 days, and all strains at day 8. The numbers of chlamydospore‐like structures were very abundant in most strains. The majority of strains of other species showed no chlamydospore‐like structures, or very few when present. Positive for chlamydospore‐like structures among 15 strains other than T. tonsurans was one strain at day 5 and six strains at day 8. As for the identification of T. tonsurans, presence of chlamydospore‐like structures showed 92.0% sensitivity (23/25) and 93.3% specificity (14/15) at day 5, and 100% sensitivity (25/25) and 60.0% specificity (9/15) at day 8. Electron microscopic findings suggest chlamydospore‐like structures are not true chlamydospores but are produced by inflation of actively growing hyphae by developing vacuoles in cells. In conclusion, observation of development of chlamydospore‐like structures in culture media is the simplest method for identification of T. tonsurans.
Clinical analysis of leg ulcers and gangrene in rheumatoid arthritis
Authors: Hasegawa Michiko , Nagai Yayoi , Sogabe Yoko , Hattori Tomoyasu , Inoue Chizuru , Okada Etsuko , Tago Osamu , Ishikawa Osamu 
Published: December 2013

AbstractLeg ulcers are often complicated in patients with rheumatoid arthritis (RA), however, the etiology is multifactorial. We examined the cases of leg ulceration or gangrene in seven RA patients who were hospitalized over the past 3 years. One patient was diagnosed as having pyoderma gangrenosum. Although vasculitis was suspected in three patients, no histological evidence was obtained from the skin specimens. In these patients, angiography revealed the stenosis or occlusion of digital arteries. In the remaining three patients, leg ulcers were considered to be due to venous insufficiency. Treatment should be chosen depending on the causes of leg ulcers.
Extensification versus Intensification in Reducing Greenhouse Gas Emissions in Agriculture: Insights from Norway
Authors: Blandford David , Gaasland Ivar , Vårdal Erling 
Published: December 2013

SummaryNorwegian agriculture makes a disproportionate contribution to the country's emissions of greenhouse gases (GHG) relative to its contribution to gross domestic product (GDP) – a picture that is repeated globally. Using a detailed economic model we examine the implications of imposing a tax on GHG emissions from Norwegian agriculture under a continuation of existing agricultural policies. We find that this would result in a reduction of agricultural production, particularly for GHG‐intensive commodities such as beef and sheepmeat. The use of feed and fertiliser would fall. There would be an extensification of production and emissions per hectare would decline. In contrast, if farmers are rewarded for carbon sequestration through agro‐forestry, this would lead to intensification. More inputs would be applied to land that remained in agriculture and emissions per unit of agricultural land would increase. Although the numerical results are specific to the Norwegian setting, they are illustrative of global issues. If agriculture is to meet the needs of an expanding world population while simultaneously contributing to mitigation of GHG emissions, this will require the intensification of production – higher output per unit of land with higher emissions per unit of land area, but with lower emissions per unit of agricultural production.
Can Nutrition Policy Evaluation be Evidence Based? Examples and Dilemmas
Authors: Bruce Traill W. , Mazzocchi Mario , Shankar Bhavani 
Published: December 2013

SummaryThere is much talk about the need for policies to be evidence‐based; an admirable objective but not easily achievable, as illustrated in this article with reference to policies to improve diets. The evidence base requires estimates of policy effectiveness (the impact of policy on diets), of the impact of dietary change on health, and an estimate of the cost‐effectiveness of the measure. Each is problematic. Randomised Control Trials are not suitable for estimating policy effectiveness in a market environment so alternative statistical approaches have used existing secondary data, but these approaches suffer from a lack of longitudinal data, the need to use data collected for other purposes, and the absence of harmonised data across Europe. Also, there are often insufficient observations to make meaningful assessments for relevant population sub‐groups such as the poor, elderly or ethnic minorities. Converting dietary change into health change requires data on dose‐response functions that are almost entirely absent, as are reliable estimates of the likely lags between poor diets and poor health outcomes. Cost effectiveness approaches differ between economists and public health professionals; each makes different (if implicit) assumptions about the behaviour of consumers that leads to poor diets and about the need to distinguish between private and social costs. Neither approach is unambiguously correct. Despite all the limitations, the need for policy action is urgent; fortunately the mounting evidence suggests most policies cause a small improvement in diets and that these are cost effective. They are also widely accepted by the public at large.
How Effective are New Entrant Schemes for Farmers?
Authors: Davis John , Caskie Paul , Wallace Michael 
Published: December 2013

SummaryThe two main policy approaches to promoting structural adjustment in EU agriculture are Farmer Early Retirement Schemes and New Entrant Schemes for Farmers. The evidence suggests that the former do not represent value for money. We report the results of a farm business modelling exercise using a sample of Northern Irish farm businesses from the Farm Accountancy Data Network to compare and contrast ex ante the effectiveness of two alternative approaches to a New Entrant Scheme, a working capital installation grant and an interest subsidy on a farm development loan. The interest rate subsidy on a farm development loan appeared to provide much better value for money in that it resulted in consistently superior performance across all of the farm performance indicators used. These outcomes were achieved despite the assumption of a very modest return of 3 per cent on the investment in the farm business. We postulate that the benefits of the interest rate subsidy are associated with the potential dynamic impacts of the farm investments, linked to the long‐term effects of differences in age related lifecycle goals. The reform proposals for the post‐2013 CAP to assist the setting up of young farmers could potentially capture these farm business dynamic effects.
Cross‐trade in Biofuels: How Uncoordinated Environmental Legislation Fuels Resource Use and GHG Emissions
Authors: Meyer Seth , Schmidhuber Josef , Barreiro‐Hurlé Jesús 
Published: December 2013

SummaryThe uncoordinated and distinct biofuel policies in Brazil and the US have induced cross‐trade of physically identical, but legislatively differentiated, ethanol between the two countries. US biofuel policy distinguishes between biofuels based primarily on feedstocks and estimated greenhouse gas reduction scores. In doing so, the US treats ethanol produced from maize starch differently than that produced from sugarcane, giving preference to sugarcane ethanol. Alternatively, Brazil makes no distinction between feedstocks, instead setting a minimum ethanol inclusion rate for retail gasoline blends, giving rise to arbitrage opportunities through biofuel exchange between the two countries. Under the US Energy Independence and Security Act of 2007, future cross‐trade between the two countries could be multiples of what has been seen to date and recent actions by the EU commission concerning the Renewable Energy Directive could draw it into the trilateral trade of biofuels. The proposed ‘book and claim’ system could allow countries to maintain individual policy objectives and mitigate the negative externalities – additional transport costs and greenhouse gas emissions – of biofuel cross‐trade due to uncoordinated biofuel policies.
Vitamin D levels and bone metabolism in Chinese adult patients with inflammatory bowel disease
Authors: Tan Bei , Li Pan , Lv Hong , Li Yue , Wang Ou , Xing Xiao Ping , Qian Jia Ming 
Published: December 2013

ObjectiveWe aimed to investigate the serum 25‐hydroxyvitamin D3 (25[OH]D3) levels and bone metabolism in adult Chinese patients with inflammatory bowel disease (IBD) and to evaluate the correlation between vitamin D levels and the disease activity as well as the potential risk factors.MethodsAge‐ and gender‐matched cohort of IBD patients (124 with ulcerative colitis [UC] and 107 with Crohn's disease [CD]) and 122 healthy controls were enrolled in this study. Serum levels of 25(OH)D3 and bone mineral density (BMD) were measured, and the correlation between the two parameters and the severity of the disease as well as the clinical risk factors were analyzed.ResultsSerum 25(OH)D3 levels were lower in UC (10.32 ± 4.46 ng/mL, P < 0.001) and CD patients (11.57 ± 5.02 ng/mL, P = 0.029) than that in healthy controls (12.87 ± 4.40 ng/mL). 25(OH)D3 levels were negatively correlated with the disease severity of both UC (r = −0.371, P < 0.001) and CD (r = −0.285, P = 0.030). The incidences of osteopenia and osteoporosis were high in the IBD patients (37.9% and 3.2% in UC and 30.8% and 4.7% in CD, respectively). Cumulative quantity of glucocorticoids use was significantly associated with osteopenia and osteoporosis in both UC (odds ratio [OR] 1.219, 95% confidence interval [CI] 1.054−1.410, P = 0.008) and CD patients (OR 1.288, 95% CI 1.033−1.606, P = 0.025).ConclusionsVitamin D deficiency is likely to occur in Chinese patients with IBD and is closely associated with the severity of the disease. Glucocorticoids accumulation is a risk factor for osteopenia and osteoporosis.