bluuebunny/crossref_metadata_2025 huggingface dataset:
Análise fitossociológica e do estoque de carbono no estrato arbóreo de um fragmento de Floresta Estacional Semidecidual
Authors: Gaspar Ricardo de Oliveira , Castro Renato Vinícius Oliveira , Peloso Ricardo Vieira Del , Souza Felippe Coelho de , Martins Sebastião Venâncio
Published: July 2014

http://dx.doi.org/10.5902/1980509814569Os estudos direcionados para quantificação de estoques de carbono fixado por florestas naturais estão em ampla evidência, assim como a discussão sobre a efetividade da recuperação de áreas degradadas como estratégia para reduzir os níveis de CO2 atmosférico. Neste sentido, tiveram-se dois objetivos neste artigo: i) quantificar o estoque de carbono presente na biomassa da parte aérea de um fragmento de Floresta Estacional Semidecidual Montana, pertencente ao Bioma Mata Atlântica no estado de Minas Gerais e ii) incorporar a variável estoque de carbono na estrutura horizontal da análise fitossociológica e comparar os resultados aos obtidos pela metodologia padrão, sem utilizar essa variável no cálculo do valor de importâncias das espécies. Os resultados indicam que o estoque de carbono encontrado equivale a fragmentos em estágio médio de sucessão, e que a utilização da variável carbono influencia sobremaneira o valor de importância das espécies. Esta metodologia serve como suporte para a escolha de espécies arbóreas de maior potencial para sequestrar carbono e pode subsidiar programas de restauração de remanescentes florestais do Bioma de Mata Atlântica.
Dendroecologia de um povoamento de Cryptomeria japonica (L. F.) Don. com 25 anos de idade no sul do Brasil
Authors: Dobner Júnior Mário , Trazzi Paulo André , Higa Antonio Rioyei
Published: July 2014

http://dx.doi.org/10.5902/1980509814579Cryptomeria japonica é originária da região temperada do Japão onde é conhecida como ‘sugi’. No Brasil, o plantio da espécie é recomendado em regiões altas e frias do sul do país, onde possui boa adaptação às condições edafoclimáticas. O objetivo do trabalho foi avaliar as correlações entre variáveis meteorológicas e o crescimento de um povoamento de Cryptomeria japonica com 25 anos de idade. Para tal, foram coletados discos transversais de 30 diferentes árvores, compreendendo toda a amplitude de variação diamétrica. Após secos e lixados, os discos tiveram seus anéis anuais de crescimento medidos e correlacionados com dados meteorológicos, utilizando ferramentas de análise dendrocronológica. As séries de crescimento apresentaram uma intercorrelação de 0,668. O crescimento radial da espécie foi influenciado positivamente pela temperatura mínima do mês de setembro e pela temperatura média do mês de maio. Não houve correlação significativa do crescimento com a precipitação, embora tenham sido verificados picos de crescimento em anos mais chuvosos.
Partição espacial de espécies arbóreas em função da drenagem do solo em um fragmento de Floresta com Araucária no sul do Brasil
Authors: Higuchi Pedro , Silva Ana Carolina da , Aguiar Manoela Drews de , Mafra Álvaro Luiz , Negrini Marcelo , Zech Diego Fernando
Published: July 2014

http://dx.doi.org/10.5902/1980509814580O estudo das relações entre a vegetação e os solos pode auxiliar na compreensão da estrutura de uma comunidade florestal, dando suporte à conservação da biodiversidade. Assim, o presente estudo teve como objetivo avaliar a existência da partição espacial da comunidade de espécies arbóreas em um fragmento de Floresta com Araucária, em função da drenagem do solo. Para este propósito, foi realizada a caracterização ambiental (drenagem do solo, propriedades físicas e químicas do solo, topografia, compactação dos solos, profundidade dos solos e cobertura do dossel) em 25 parcelas de 20x20 m, onde indivíduos de espécies arbóreas, com circunferência a altura do peito (CAP) maior ou igual a 15,7 cm, foram previamente contados, medidos e identificados. Os dados foram analisados por meio do teste de Mann-Withney, análise de variância multivariada não paramétrica (NPMANOVA), análise multivariada (NMDS) e análise de espécies indicadoras. Os locais foram classificados como bem e moderadamente drenados, com diferenças ambientais que determinaram a riqueza, a partição espacial da comunidade e a ocorrência de espécies indicadoras na pequena escala espacial considerada. Desta forma, conclui-se que, no fragmento florestal estudado, as variações espaciais na drenagem do solo foram determinantes na heterogeneidade da composição florística-estrutural observada.
Avaliação de adesivos à base de taninos de Pinus caribaea var. bahamensis e de Acacia mearnsii na fabricação de painéis aglomerados
Authors: Carvalho Amélia Guimarães , Lelis Roberto Carlos Costa , Nascimento Alexandre Miguel do
Published: July 2014

http://dx.doi.org/10.5902/1980509814588Este trabalho teve por objetivo avaliar os métodos para a extração dos taninos da casca do Pinus caribaea var. bahamensis, assim como verificar a viabilidade técnica de utilização dos taninos da casca de Pinus caribaea var. bahamensis, de Acacia mearnsii, de misturas de taninos de acácia negra e pinus e de misturas do adesivo ureia-formaldeído (UF) com taninos de acácia e pinus na produção de adesivos para aglomerados. As cascas de Pinus caribaea var. bahamensis foram fragmentadas em moinho de martelo, peneiradas, extraídas sob refluxo, por 2 horas, utilizada uma relação casca:licor de 1:15 p:v, em nove tratamentos. A melhor forma de extração foi utilizada para obtenção de grandes quantidades de extratos, que foram utilizados na confecção de adesivos tânicos e nas misturas com adesivo UF e com taninos comerciais de acácia negra na fabricação de painéis aglomerados. A adição de sulfito de sódio proporcionou maior extração de taninos, sendo recomendável a extração com adição de 5% de sulfito de sódio. Os resultados mostraram que tanto os taninos de acácia, quanto os de Pinus caribaea var. bahamensis, apresentam boas propriedades de colagem. É possível a adição de solução tânica de pinus à solução tânica de acácia e também substituir parte do adesivo UF pelos taninos de acácia em até 25% sem comprometer a qualidade da colagem. A substituição de 10% de UF por extrato tânico, tanto de pinus quanto de acácia, não alterou os valores de inchamento em espessura (IE) dos painéis. É possível obter boas propriedades mecânicas com adesivos UF modificados com extratos tânicos na proporção de 10%. Os altos valores encontrados para ligação interna (LI) dos painéis fabricados com extratos tânicos evidenciaram o potencial desses taninos para colagem de painéis de madeira.
Avaliação dos resíduos de uma serraria para a produção de celulose kraft
Authors: Barbosa Lucas Cândido , Pedrazzi Cristiane , Ferreira Érika da Silva , Schneid Guinter Neutzling , Wille Vania Karine Dick
Published: July 2014

http://dx.doi.org/10.5902/1980509814589As indústrias de base florestal apresentam baixo rendimento e geram grande quantidade de resíduos, especialmente as indústrias de transformação primária como, por exemplo, as serrarias. No Brasil, estão sendo criadas iniciativas para aliar a utilização desses resíduos à produção de celulose. Dentro deste propósito, o presente trabalho teve como objetivos avaliar o rendimento de uma serraria de médio porte localizada no município de Rio Grande, RS, e promover análises físico-químicas dos resíduos gerados na etapa de desdobro. Foram utilizadas 20 toras de Pinus elliottii, divididas em duas classes diamétricas. Os resíduos, com exceção da serragem, coletados para análises, encontravam-se dispostos no pátio da empresa, na forma de cavacos. As seguintes propriedades físico-químicas dos cavacos foram analisadas: densidade básica, teor de extrativos solúvel em acetona, grupos acetilas, lignina solúvel e insolúvel em ácido (lignina Klason), grupos urônicos e carboidratos. Como principais resultados verificou-se um ligeiro aumento do rendimento em madeira serrada das madeiras de maiores diâmetros em relação às de menores diâmetros. Das análises físico-químicas foram obtidos os seguintes resultados: densidade básica de 0,402 g/cm³, teor de celulose de 37,42% e de 24,37% para hemiceluloses, lignina Klason de 26,75% e teor de extrativos de 3,80%. Concluiu-se, nesse estudo, que o baixo rendimento da serraria foi devido à falta de uma classificação diamétrica e diagramas de cortes apropriados para as toras, o que resulta em maior perda de madeira na forma de resíduos. Em relação às características química e física dos resíduos madeireiros, os resultados mostraram-se dentro dos padrões de qualidade da madeira utilizada para a produção de celulose kraft de fibra longa e, em algumas situações, apresentando vantagens em relação às madeiras mais jovens usualmente utilizadas pela indústria.
Autologous Adipose Stem Cells in Treatment of Female Stress Urinary Incontinence: Results of a Pilot Study
Authors: Kuismanen Kirsi , Sartoneva Reetta , Haimi Suvi , Mannerström Bettina , Tomás Eija , Miettinen Susanna , Nieminen Kari
Published: July 2014

The purpose of our study was to find out whether transurethral injections of autologous adipose stem cells (ASCs) are an effective and a safe treatment for female stress urinary incontinence (SUI). We treated five SUI patients with ASCs combined with bovine collagen gel and saline. Prior to the treatment, the ASCs were isolated from subcutaneous fat and expanded for 3 weeks in a good manufacturing practice-level laboratory. The mixture of ASCs and collagen was injected transurethrally via cystoscope. Additionally, viability, multipotency, and surface marker profile of ASCs were analyzed in vitro. We followed up with patients 3, 6, and 12 months after the injections. The primary endpoint was a cough test to measure objectively the effect of the treatment. Validated questionnaires were used to determine the subjective cure rate. After 6 months, 1 of 5 patients displayed a negative cough test with full bladder filled with 500 ml of saline. At 1 year, the cough test was negative with three patients; two of them were satisfied with the treatment and did not wish further treatment for SUI. Validated questionnaires showed some subjective improvement in all five patients. This is the first study describing the use of autologous ASCs in combination with collagen gel for female SUI treatments. Thus far, the treatment with autologous ASCs has proven safe and well tolerated. However, the feasibility and efficacy of the treatment were not optimal; therefore, additional research is needed to develop SUI injection therapies.
The EU Habitats Directive and wolf conservation and management on the Iberian Peninsula: a legal perspective
Authors: Trouwborst Arie
Published: July 2014

The focus of this legal paper is on the implications of the EU Directive on the Conservation of Natural Habitats and of Wild Fauna and Flora (Habitats Directive) for wolf (Canis lupus) conservation and management in Portugal and Spain. It addresses the (potential) relevance of both the area protection and the generic species protection rules from the Directive. Special attention is paid to legal issues raised by the range expansion of the northwest Iberian wolf population beyond the Duero River (both south and east), the immigration of wolves from France, the looming extinction of the Sierra Morena population, and the need for transboundary cooperation.
HIV prevalence and high‐risk sexual behaviours among MSM repeat and first‐time testers in China: implications for HIV prevention
Authors: Bai Xue , Xu Jie , Yang Jie , Yang Bo , Yu Maohe , Gao Yongjun , Dong Willa M , Wu Zunyou
Published: July 2014

Introduction

Little is known about HIV testing, HIV infection and sexual behaviour among bathhouse patrons in China. This study aims to assess differences in HIV prevalence and high‐risk sexual behaviours between repeat and first‐time testers among men who have sex with men (MSM) attending bathhouse in Tianjin, China.

Methods

Between March 2011 and September 2012, a HIV voluntary counselling and testing station was established in a gay bathhouse, which provided HIV testing and conducted a survey among participants recruited through snowball sampling. Differences in demographic and high‐risk sexual behaviours between repeat and first‐time testers were assessed using the chi‐square test. Univariate and multivariate logistic regression analyses were conducted to identify predictors for HIV infection.

Results

Of the 1642 respondents, 699 (42.6%) were repeat testers and 943 (57.4%) were first‐time testers. Among repeat testers, a higher proportion were men aged 18 to 25, single, better educated, had a history of STIs and worked as male sex workers or “money boys” (MBs). Repeat testers were less likely to report having unprotected anal intercourse in the past six months. The overall HIV prevalence was 12.4% (203/1642). There was no difference in HIV prevalence between repeat (11.2%, 78/699) and first‐time (13.3%, 125/943) testers. The HIV prevalence increased with age among first‐time testers (, p=0.002). First‐time MB testers had the highest HIV prevalence of 34.5%.

Conclusions

MSM attending bathhouse had an alarmingly high HIV infection rate, particularly in MB. Targeted interventions are urgently needed especially focusing on older MSM and MBs.
A Quantitative LQ-based Model for Lung Injury in Radiotherapy
Authors: Wang Li , Li Wenhui , Bai Han , Cui Jianguo , Qin Jiyong , Chang Li
Published: July 2014

Establishing a new bio-mathematical model, named quantitative LQ-based (qLQB) model, that can evaluate the radio-toxicity of lung. We assume that each Function Subunit (FSU) of lung is equal and representative in functional status. Based on the Linear-Quadratic model (LQ model), we had derived a model to calculate the ratio/percent (R/P) between damaged cell/FSU and entire cell/FSU of lung for radiation dose response. We can analyse radiation pneumonia probability (RPP) based on the R/P. Forty-five 3D plans from forty-five randomly selected lung cancer patients were generated using the ELEKTA precise 2.12 treatment planning system. The qLQB was tested against the widely used Lyman-Kutcher-Burman model (LKB model). There was no distinct statistical difference in analyzing RPP between using the qLQB model and the LKB model ( p = 0.412). The proposed qLQB model was found to be efficient and reliable for analyzing RPP.
Management of Liver Cancer Argon-helium Knife Therapy with Functional Computer Tomography Perfusion Imaging
Authors: Wang Hongbo , Shu Shengjie , Li Jinping , Jiang Huijie
Published: July 2014

The objective of this study was to observe the change in blood perfusion of liver cancer following argon-helium knife treatment with functional computer tomography perfusion imaging. Twenty-seven patients with primary liver cancer treated with argon-helium knife and were included in this study. Plain computer tomography (CT) and computer tomography perfusion (CTP) imaging were conducted in all patients before and after treatment. Perfusion parameters including blood flows, blood volume, hepatic artery perfusion fraction, hepatic artery perfusion, and hepatic portal venous perfusion were used for evaluating therapeutic effect. All parameters in liver cancer were significantly decreased after argon-helium knife treatment ( p < 0.05 to all). Significant decrease in hepatic artery perfusion was also observed in pericancerous liver tissue, but other parameters kept constant. CT perfusion imaging is able to detect decrease in blood perfusion of liver cancer post-argon-helium knife therapy. Therefore, CTP imaging would play an important role for liver cancer management followed argon-helium knife therapy.
Proton Therapy Facility Planning From a Clinical and Operational Model
Authors: Das Indra J. , Moskvin Vadim P. , Zhao Qingya , Cheng Chee-Wai , Johnstone Peter A.
Published: July 2014

This paper provides a model for planning a new proton therapy center based on clinical data, referral pattern, beam utilization and technical considerations. The patient-specific data for the depth of targets from skin in each beam angle were reviewed at our center providing megavoltage photon external beam and proton beam therapy respectively. Further, data on insurance providers, disease sites, treatment depths, snout size and the beam angle utilization from the patients treated at our proton facility were collected and analyzed for their utilization and their impact on the facility cost. The most common disease sites treated at our center are head and neck, brain, sarcoma and pediatric malignancies. From this analysis, it is shown that the tumor depth from skin surface has a bimodal distribution (peak at 12 and 26 cm) that has significant impact on the maximum proton energy, requiring the energy in the range of 130-230 MeV. The choice of beam angles also showed a distinct pattern: mainly at 90° and 270°; this indicates that the number of gantries may be minimized. Snout usage data showed that 70% of the patients are treated with 10 cm snouts. The cost of proton beam therapy depends largely on the type of machine, maximum beam energy and the choice of gantry versus fixed beam line. Our study indicates that for a 4-room center, only two gantry rooms could be needed at the present pattern of the patient cohorts, thus significantly reducing the initial capital cost. In the USA, 95% and 100% of patients can be treated with 200 and 230 MeV proton beam respectively. Use of multi-leaf collimators and pencil beam scanning may further reduce the operational cost of the facility.
TNF-related Apoptosis-inducing Ligand Delivered by rNDV is a Novel Agent for Cancer Gene Therapy
Authors: Bai Fu-Liang , Tian Hui , Yu Yin-Hang , Yin Jie-Chao , Ren Gui-Ping , Zhou Bing , Li De-Shan
Published: July 2014

Recombinant Newcastle disease virus (rNDV) as antitumor agent has been shown to be effective for cancer therapy. And TNF-related apoptosis-inducing ligand (TRAIL) also has been demonstrated potentially cancer-therapeutic effects. In this study, we constructed TRAIL delivered by rNDV (rNDV-TRAIL) and investigated whether TRAIL would generate the potential synergistic therapeutic effects with rNDV for cancer therapy. In vitro experiments indicated that TRAIL expressed by rNDV demonstrated good biological activity. TRAIL significantly enhanced inducing apoptosis of rNDV in death receptor expression cancer cell lines. Experiments in malignant melanoma-bearing mice demonstrated that expression of TRAIL delivered by rNDV significantly inhibited the tumor growth and prolonged the survival of treated animals compared to control. In conclusion, oncolytic capacity of rNDV was augmented by TRAIL and the inherent anti-neoplastic properties of NDV were enhanced by the introduction of therapeutic TRAIL gene.
Trends in urodynamics in U.S. female medicare beneficiaries, 2000–2010
Authors: Reynolds W. Stuart , Ni Shenghua , Kaufman Melissa R. , Penson David F. , Dmochowski Roger R.
Published: June 2014

Aims

To document variations and temporal trends in the use of urodynamics (UDS) in female U.S. Medicare beneficiaries.

Methods

Using a 5% sample of U.S. Medicare utilization records, we identified female beneficiaries who had undergone UDS studies between 2000 and 2010 by the presence of Common Procedural Terminology codes for cystometrogram in claims from the Carrier file. We abstracted data for each patient on age, race, residence, ICD9 diagnoses, dates of service, and provider specialty. We calculated rates per 100,000 beneficiaries with data available from the enrollment files (i.e., Denominator files) and reported the numbers and rates per 100,000 by year.

Results

During this period, 1.4 million female U.S. Medicare beneficiaries underwent UDS, of which 6% were videourodynamics. Seventy four percent of UDS were associated with a diagnosis of any urinary incontinence, with 50% specific for stress incontinence. The annual rates of UDS increased by 29%, from 422 in 2000 to 543 in 2010 per 100,000. Similar increases were seen across age groups, geographic regions and racial/ethnic groups. The rate of UDS performed by gynecologists increased by 144% over the study period, while that of urologists decreased by 3%. In 2010, gynecologists performed 35% and urologists 58% of all UDS.

Conclusions

The use of UDS in the female Medicare program increased substantially between 2000 and 2010, with some variation across demographics and marked variation across provider specialty. Neurourol. Urodynam. 34:420–423, 2015. © 2014 Wiley Periodicals, Inc.
Treatment‐refractory multi‐lineage autoimmune cytopenia after unrelated cord blood transplantation: Remission after combined bortezomib and vincristine treatment
Authors: Waespe Nicolas , Zeilhofer Ulrike , Güngör Tayfun
Published: June 2014

Autoimmune cytopenias (AC) after allogeneic hematopoietic stem cell transplantation (HSCT) are associated with a dismal prognosis. We describe a 1‐year‐old female with multi‐lineage AC occurring on day +43 after HSCT. Multi‐agent treatment with high‐dose prednisolone, intravenous immunoglobulins, cyclosporine A, mycophenolate mofetil, sirolimus, and rituximab was unsuccessful. Combined treatment with bortezomib and vincristine in addition to ongoing immunosuppressive therapy was started on day +414 with transfusion‐independence after day +444. Immunosuppressants were tapered until day +638. On day +1,121 the patient remained in remission. Bortezomib with vincristine may be a promising treatment modality for refractory AC after HSCT that requires further study. Pediatr Blood Cancer 2014;61:2112–2114. © 2014 Wiley Periodicals, Inc.
Incidence of platinum‐induced ototoxicity in pediatric patients in Quebec
Authors: Peleva Emilia , Emami Nader , Alzahrani Mohammad , Bezdjian Aren , Gurberg Joshua , Carret Anne‐Sophie , Daniel Sam J.
Published: June 2014

Background

The antineoplastic agents cisplatin and carboplatin are widely‐used and highly‐effective against a variety of pediatric cancers. Unfortunately, ototoxicity is a frequently encountered side effect of platinum‐based chemotherapy. There is currently no treatment or prevention for platinum‐induced ototoxicity and development of hearing loss may lead to devastating consequences on the quality of life of pediatric cancer survivors. The objective of this study is to determine the incidence of platinum‐induced ototoxicity in a large series of pediatric patients and to evaluate the incidence of progression of ototoxicity after completion of treatment.

Procedures

A retrospective chart review of pediatric patients treated with cisplatin or carboplatin between 2000 and 2012 was conducted. The incidence of ototoxicity was determined based on the American‐Speech‐Language‐Hearing Association (ASHA) criteria and severity was based on the Chang classification.

Results

Four hundred and sixty‐six patients received platinum‐based chemotherapy. Patients were excluded due to congenital hearing loss (n = 1) and insufficient data for calculating the platinum dose (n = 24) or for assessing ototoxicity (n = 135). Three hundred and six patients were included in the analysis. Post‐chemotherapy ototoxicity was detected in 148 (48%) patients, and clinically‐significant ototoxicity was present in 91 (30%). In addition, based on the ASHA criteria, 48% of patients (97/204) with long‐term follow‐up had further deterioration of their hearing after completion of treatment.

Conclusions

Ototoxicity following chemotherapy with cisplatin or carboplatin is common and can frequently progress after the completion of treatment. Long‐term follow‐up is strongly recommended. Pediatr Blood Cancer 2014;61:2012–2017. © 2014 Wiley Periodicals, Inc.
Prosogynopora riseri, gen. et sp. nov., a phylogenetically problematic lithophoran proseriate (Platyhelminthes : Rhabditophora) with inverted genital pores from the New England coast
Authors: Laumer Christopher E. , Giribet Gonzalo , Curini-Galletti Marco
Published: June 2014

A new lithophoran proseriate flatworm, Prosogynopora riseri, gen. et sp. nov. (Platyhelminthes: Rhabditophora: Proseriata), is described from the New England coast (USA). The species shares characters with members of the families Calviriidae and Coelogynoporidae, e.g. the presence of paracnida, the short common female duct, a septum and diaphragm at the base of the pharynx. However, the inverted topology of the genital system, presenting an anterior female pore shortly behind the mouth and a male pore opening nearly on the caudal terminus, is unique within the Proseriata, and permits inclusion into neither family on morphological grounds. We investigated the phylogenetic position of the new species within the available diversity of proseriate 18S and 28S rRNA sequences. However, an exploration of diverse homology schemes, alignment conditions and optimality criteria proved the position of P. riseri, gen. et sp. nov. to be remarkably unstable, particularly with respect to the method of alignment, variously suggesting sister-group relationships with (or within) Coelogynoporidae, with Calviriidae, or with a clade composed of all other Lithophora. Despite its unique morphology and the absence of molecular phylogenetic evidence for its inclusion within any family as currently defined, we refrain from assigning a higher taxonomic rank to the new lineage, pending critical re-assessment of homology in several character systems and the availability of further taxon- and gene-rich enquiries into the phylogeny of Proseriata. Apingospermata, new taxon and Dolichogynoducta, new taxon are proposed as two rankless taxonomic names of Lithophora, corresponding to well-supported clades in our molecular phylogenetic hypothesis.
Phylogeny of the holly grevilleas (Proteaceae) based on nuclear ribosomal and chloroplast DNA
Authors: Holmes Gareth D. , Downing Trisha L. , James Elizabeth A. , Blacket Mark J. , Hoffmann Ary A. , Bayly Michael J.
Published: June 2014

The holly grevilleas are an informal grouping of 15 species (19 taxa) of woody shrubs from south-eastern Australia, with a centre of distribution in central to western Victoria. Many of the species are narrowly endemic. The present study is the first molecular-phylogenetic analysis of the group, with the aim of providing an evolutionary framework for assessing species-level taxonomy and conservation priorities. Analyses using the nrDNA internal transcribed spacer (ITS) regions were complicated by the presence of divergent paralogues, including inferred pseudogenes; analyses restricted to presumed orthologous, functional ITS sequences were uninformative. Combined analyses of three chloroplast intergenic spacers (trnQ–5′rps16, trnL–trnF and rpoB–trnC) strongly support the monophyly of a core group of 16 taxa (the ‘southern holly grevilleas’) from Victoria and South Australia. However, nodes outside this group are poorly resolved and poorly supported, and the relationships of taxa from New South Wales and eastern Victoria (the ‘northern holly grevilleas’) are unclear. Among the southern holly grevilleas, the following four distinct and partly sympatric cpDNA clades are identified: the ‘Grevillea ilicifolia’, ‘G. aquifolium’, ‘G. dryophylla’ and ‘G. repens’ clades, among which the earliest and most strongly supported divergence is that of the western-most ‘G. ilicifolia’ clade. Variation in cpDNA is incongruent with current species-level taxonomy, especially for G. aquifolium (polyphyletic), G. montis-cole (polyphyletic, but the two subspecies each monophyletic) and G. microstegia (nested in G. aquifolium). The effects of incomplete chloroplast lineage sorting, gene flow through hybridisation or introgression, and inappropriate taxonomy are possible explanations for this incongruence. The formal conservation listing for some species within the holly grevillea group requires re-evaluation.
An expanded phylogenetic analysis of Sannantha (Myrtaceae) and description of a new species
Authors: Wilson Peter G. , Heslewood Margaret M.
Published: June 2014

Sannantha is a genus of shrubs widely distributed in eastern Australia and New Caledonia. We added five taxa to a previously published molecular dataset, four from Australia and the fifth from New Caledonia, a total of 11 of the 16 species in the genus. One of the Australian taxa added is a new species apparently restricted to the Goonoowigall State Conservation Area near Inverell, New South Wales. The results of the molecular analysis are discussed in light of morphology and geographic distribution. The new species, Sannantha whitei Peter G.Wilson, is described.
Estimating the Impact of Minimum Wages on Employment, Wages, and Non‐Wage Benefits: The Case of Agriculture in South Africa
Authors: Bhorat Haroon , Kanbur Ravi , Stanwix Benjamin
Published: June 2014

Assessments of the impact of minimum wages on labor market outcomes in Africa are relatively rare. In part this is because the available data do not permit adequate treatment of econometric issues that arise in such assessments. This paper, however, attempts to estimate the impact of introducing a minimum wage law in the agriculture sector in South Africa, based on 15 waves of the biannual Labor Force Survey conducted between September 2000 and September 2007. The chosen sample includes six waves before the legislation's effective date (March 2003) and nine afterwards. To assess whether the changes experienced by farm workers are unique, we identify a control group that has similar characteristics to the treatment group. Our econometric approach involves using two alternative specifications of a difference‐in‐differences model. We test whether employers reduced employment, and whether they responded at the intensive margin by reducing hours of work. The results suggest a significant employment reduction in agriculture from the minimum wage (and particularly a noticeable move away from employment of part‐time workers), an increase in wages on average, and a rise in non‐wage benefits compliance. Our analysis also indicates that, firstly, overall average of hours worked fell in the post‐law period, suggesting that employers adjusted to some extent on the intensive margin. Secondly, it appears that hours of work increased more in areas where wages were lower in the pre‐law period, driven largely by the fall in part‐time employment.
Drug repositioning by integrating target information through a heterogeneous network model
Authors: Wang Wenhui , Yang Sen , Zhang Xiang , Li Jing
Published: June 2014

Motivation: The emergence of network medicine not only offers more opportunities for better and more complete understanding of the molecular complexities of diseases, but also serves as a promising tool for identifying new drug targets and establishing new relationships among diseases that enable drug repositioning. Computational approaches for drug repositioning by integrating information from multiple sources and multiple levels have the potential to provide great insights to the complex relationships among drugs, targets, disease genes and diseases at a system level.

Results: In this article, we have proposed a computational framework based on a heterogeneous network model and applied the approach on drug repositioning by using existing omics data about diseases, drugs and drug targets. The novelty of the framework lies in the fact that the strength between a disease–drug pair is calculated through an iterative algorithm on the heterogeneous graph that also incorporates drug-target information. Comprehensive experimental results show that the proposed approach significantly outperforms several recent approaches. Case studies further illustrate its practical usefulness .

Availability and implementation:  http://cbc.case.edu

Contact:  jingli@cwru.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Focus Groups for Developing a Peer Mentoring Program to Improve Self‐Management in Pediatric Inflammatory Bowel Disease
Authors: Mackner Laura M. , Ruff Jessica M. , Vannatta Kathryn
Published: June 2014

Objectives:

Inflammatory bowel disease (IBD) presents challenges for self‐management in many areas. A peer mentoring program may offer advantages over other forms of self‐management interventions because youth may be more receptive to learning self‐management skills from a peer than from a parent or professional. The purpose of the present study was to identify themes from focus groups to inform development of a peer mentoring program for improving self‐management in pediatric IBD.

Methods:

Focus groups were conducted for youth ages 12 to 17, stratified by age (3 groups; n = 14), young adults ages 18 to 20 (1 group; n = 5), and parents of the youth (3 groups; n = 17). Broad questions covered program goals, general program characteristics, mentor/mentee characteristics, and family involvement, and transcriptions were analyzed via directed content analysis, with the a priori codes specified as the broad questions above.

Results:

Participants identified the primary goals of a program as support, role model, information/education, and fun. They described a program that would include a year‐long, 1‐on‐1 mentor relationship with a peer who has had IBD for at least a year, educational group activities, fun activities that are not focused on IBD, expectations for in‐person contact 1 to 2 times per month, and mentor‐to‐mentor and parent support.

Conclusions:

Many of the suggestions from the focus groups correspond with research findings associated with successful mentoring programs. Using participants' suggestions and empirically based best practices for mentoring may result in an effective peer mentoring program for improving self‐management in youth with IBD.
Imaging in the Evaluation of the Young Patient With Inflammatory Bowel Disease
Authors: Anupindi Sudha A. , Grossman Andrew B. , Nimkin Katherine , Mamula Petar , Gee Michael S.
Published: June 2014

Imaging plays a pivotal role in the diagnosis and management of children and young adults with inflammatory bowel disease. The clinician is presented with numerous imaging options, and it can be challenging to decide which test is the best option. In this article we review the present imaging techniques available in the evaluation of inflammatory bowel disease, with emphasis on the advantages, disadvantages, and radiation burden of each test. Finally, we highlight a few common clinical scenarios and propose an imaging algorithm to approach these diagnostic challenges.
Multi-locus analysis of genomic time series data from experimental evolution
Authors: Terhorst Jonathan , Song Yun S.
Published: June 2014

Genomic time series data generated by evolve-and-resequence (E&R) experiments offer a powerful window into the mechanisms that drive evolution. However, standard population genetic inference procedures do not account for sampling serially over time, and new methods are needed to make full use of modern experimental evolution data. To address this problem, we develop a Gaussian process approximation to the multi-locus Wright-Fisher process with selection over a time course of tens of generations. The mean and covariance structure of the Gaussian process are obtained by computing the corresponding moments in discrete-time Wright-Fisher models conditioned on the presence of a linked selected site. This enables our method to account for the effects of linkage and selection, both along the genome and across sampled time points, in an approximate but principled manner. Using simulated data, we demonstrate the power of our method to correctly detect, locate and estimate the fitness of a selected allele from among several linked sites. We also study how this power changes for different values of selection strength, initial haplotypic diversity, population size, sampling frequency, experimental duration, number of replicates, and sequencing coverage depth. In addition to providing quantitative estimates of selection parameters from experimental evolution data, our model can be used by practitioners to design E&R experiments with requisite power. Finally, we explore how our likelihood-based approach can be used to infer other model parameters, including effective population size and recombination rate, and discuss extensions to more complex models.
Crystal structures of an ICAM-5 ectodomain fragment show electrostatic-based homophilic adhesions
Authors: Recacha Rosario , Jiménez David , Tian Li , Barredo Román , Gahmberg Carl G. , Casasnovas José M.
Published: June 2014

Intercellular cell adhesion molecule-5 (ICAM-5) is a member of the ICAM subfamily that is exclusively expressed in the telencephalon region of the brain. The crystal structure of the four most N-terminal glycosylated domains (D1–D4) of ICAM-5 was determined in three different space groups and the D1–D5 fragment was modelled. The structures showed a curved molecule with two pronounced interdomain bends between D2 and D3 and between D3 and D4, as well as some interdomain flexibility. In contrast to ICAM-1, ICAM-5 has patches of positive and negative electrostatic charge at D1–D2 and at D3–D5, respectively. ICAM-5 can mediate homotypic interactions. In the crystals, several charge-based intermolecular interactions between the N-terminal and C-terminal moieties of the ICAM-5 molecules were observed, which defined an interacting surface in the D1–D4 fragment. One of the crystal lattices has a molecular assembly that could represent the homophilic ICAM-5 cell adhesion complex in neurons.
Structural basis of the transactivation deficiency of the human PPARγ F360L mutant associated with familial partial lipodystrophy
Authors: Lori Clorinda , Pasquo Alessandra , Montanari Roberta , Capelli Davide , Consalvi Valerio , Chiaraluce Roberta , Cervoni Laura , Loiodice Fulvio , Laghezza Antonio , Aschi Massimiliano , Giorgi Alessandra , Pochetti Giorgio
Published: June 2014

The peroxisome proliferator-activated receptors (PPARs) are transcription factors that regulate glucose and lipid metabolism. The role of PPARs in several chronic diseases such as type 2 diabetes, obesity and atherosclerosis is well known and, for this reason, they are the targets of antidiabetic and hypolipidaemic drugs. In the last decade, some rare mutations in human PPARγ that might be associated with partial lipodystrophy, dyslipidaemia, insulin resistance and colon cancer have emerged. In particular, the F360L mutant of PPARγ (PPARγ2 residue 388), which is associated with familial partial lipodystrophy, significantly decreases basal transcriptional activity and impairs stimulation by synthetic ligands. To date, the structural reason for this defective behaviour is unclear. Therefore, the crystal structure of PPARγ F360L together with the partial agonist LT175 has been solved and the mutant has been characterized by circular-dichroism spectroscopy (CD) in order to compare its thermal stability with that of the wild-type receptor. The X-ray analysis showed that the mutation induces dramatic conformational changes in the C-terminal part of the receptor ligand-binding domain (LBD) owing to the loss of van der Waals interactions made by the Phe360 residue in the wild type and an important salt bridge made by Arg357, with consequent rearrangement of loop 11/12 and the activation function helix 12 (H12). The increased mobility of H12 makes the binding of co-activators in the hydrophobic cleft less efficient, thereby markedly lowering the transactivation activity. The spectroscopic analysis in solution and molecular-dynamics (MD) simulations provided results which were in agreement and consistent with the mutant conformational changes observed by X-ray analysis. Moreover, to evaluate the importance of the salt bridge made by Arg357, the crystal structure of the PPARγ R357A mutant in complex with the agonist rosiglitazone has been solved.
Protein phasing at non-atomic resolution by combining Patterson andVLDtechniques
Authors: Caliandro Rocco , Carrozzini Benedetta , Cascarano Giovanni Luca , Comunale Giuliana , Giacovazzo Carmelo , Mazzone Annamaria
Published: June 2014

Phasing proteins at non-atomic resolution is still a challenge for anyab initiomethod. A variety of algorithms [Patterson deconvolution, superposition techniques, a cross-correlation function (Cmap), theVLD(vive la difference) approach, the FF function, a nonlinear iterative peak-clipping algorithm (SNIP) for defining the background of a map and thefree lunchextrapolation method] have been combined to overcome the lack of experimental information at non-atomic resolution. The method has been applied to a large number of protein diffraction data sets with resolutions varying from atomic to 2.1 Å, with the condition that S or heavier atoms are present in the protein structure. The applications include the use ofARP/wARPto check the quality of the final electron-density maps in an objective way. The results show that resolution is still the maximum obstacle to protein phasing, but also suggest that the solution of protein structures at 2.1 Å resolution is a feasible, even if still an exceptional, task for the combined set of algorithms implemented in the phasing program. The approach described here is more efficient than the previously described procedures:e.g.the combined use of the algorithms mentioned above is frequently able to provide phases of sufficiently high quality to allow automatic model building. The method is implemented in the current version ofSIR2014.
BuD, a helix–loop–helix DNA-binding domain for genome modification
Authors: Stella Stefano , Molina Rafael , López-Méndez Blanca , Juillerat Alexandre , Bertonati Claudia , Daboussi Fayza , Campos-Olivas Ramon , Duchateau Phillippe , Montoya Guillermo
Published: June 2014

DNA editing offers new possibilities in synthetic biology and biomedicine for modulation or modification of cellular functions to organisms. However, inaccuracy in this process may lead to genome damage. To address this important problem, a strategy allowing specific gene modification has been achieved through the addition, removal or exchange of DNA sequences using customized proteins and the endogenous DNA-repair machinery. Therefore, the engineering of specific protein–DNA interactions in protein scaffolds is key to providing `toolkits' for precise genome modification or regulation of gene expression. In a search for putative DNA-binding domains, BurrH, a protein that recognizes a 19 bp DNA target, was identified. Here, its apo and DNA-bound crystal structures are reported, revealing a central region containing 19 repeats of a helix–loop–helix modular domain (BurrH domain; BuD), which identifies the DNA target by a single residue-to-nucleotide code, thus facilitating its redesign for gene targeting. New DNA-binding specificities have been engineered in this template, showing that BuD-derived nucleases (BuDNs) induce high levels of gene targeting in a locus of the human haemoglobin β (HBB) gene close to mutations responsible for sickle-cell anaemia. Hence, the unique combination of high efficiency and specificity of the BuD arrays can push forward diverse genome-modification approaches for cell or organism redesign, opening new avenues for gene editing.
Neural Networks Solving Free and Fixed Final Time Optimal Control Problems
Authors: Kmet Tibor
Published: June 2014

In this paper, the neural network based optimal control synthesis is presented for solving free and fixed final time optimal control problems with the control and state constraints. The optimal control problem is transcribed into a nonlinear programming problem, which is implemented with the adaptive critic neural network. The proposed simulation methods are illustrated by the optimal control problem of photosynthetic production and the nitrogen transformation cycle model. The results show that the adaptive critic based systematic approach is promising in obtaining free and fixed final time optimal control with the control and state constraints.
Task Balanced Workflow Scheduling Technique considering Task Processing Rate in Spot Market
Authors: Jung Daeyong , Lim JongBeom , Gil JoonMin , Lee Eunyoung , Yu Heonchang
Published: June 2014

Recently, the cloud computing is a computing paradigm that constitutes an advanced computing environment that evolved from the distributed computing. And the cloud computing provides acquired computing resources in a pay-as-you-go manner. For example, Amazon EC2 offers the Infrastructure-as-a-Service (IaaS) instances in three different ways with different price, reliability, and various performances of instances. Our study is based on the environment using spot instances. Spot instances can significantly decrease costs compared to reserved and on-demand instances. However, spot instances give a more unreliable environment than other instances. In this paper, we propose the workflow scheduling scheme that reduces the out-of-bid situation. Consequently, the total task completion time is decreased. The simulation results reveal that, compared to various instance types, our scheme achieves performance improvements in terms of an average combined metric of 12.76% over workflow scheme without considering the processing rate. However, the cost in our scheme is higher than an instance with low performance and is lower than an instance with high performance.
New Kinetic Spectrophotometric Method for Determination of Fexofenadine Hydrochloride in Pharmaceutical Formulations
Authors: Ashour Safwan , Khateeb Mouhammed
Published: June 2014

A simple and sensitive kinetic spectrophotometric method was developed for the determination of fexofenadine hydrochloride in bulk and pharmaceutical preparations. The method is based on a kinetic investigation of the oxidation reaction of fexofenadine using alkaline potassium permanganate as an oxidizing agent at room temperature. The reaction is followed spectrophotometrically by measuring the increase of absorbance owing to the formation of manganate ion at 610 nm. The initial rate and fixed time (at 15 min) methods are utilized for construction of calibration graphs. All the reaction conditions for the proposed method have been studied. The linearity range was found to be 2.5–50.0 μg mL−1 with detection limit of 0.055 μg mL−1 for both initial rate and fixed time methods. The proposed method was applied successfully for the determination of fexofenadine in pharmaceutical formulations; the percentage recoveries were 99.98–101.96%. The results obtained were compared statistically with those obtained by the official method and showed no significant differences regarding accuracy and precision.
Fresh-Cut Pineapple as a New Carrier of Probiotic Lactic Acid Bacteria
Authors: Russo Pasquale , de Chiara Maria Lucia Valeria , Vernile Anna , Amodio Maria Luisa , Arena Mattia Pia , Capozzi Vittorio , Massa Salvatore , Spano Giuseppe
Published: June 2014

Due to the increasing interest for healthy foods, the feasibility of using fresh-cut fruits to vehicle probiotic microorganisms is arising scientific interest. With this aim, the survival of probiotic lactic acid bacteria, belonging toLactobacillus plantarumandLactobacillus fermentumspecies, was monitored on artificially inoculated pineapple pieces throughout storage. The main nutritional, physicochemical, and sensorial parameters of minimally processed pineapples were monitored. Finally, probioticLactobacilluswere further investigated for their antagonistic effect againstListeria monocytogenesandEscherichia coliO157:H7 on pineapple plugs. Our results show that at eight days of storage, the concentration ofL. plantarumandL. fermentumon pineapples pieces ranged between 7.3 and 6.3 log cfu g−1, respectively, without affecting the final quality of the fresh-cut pineapple. The antagonistic assays indicated thatL. plantarumwas able to inhibit the growth of both pathogens, whileL. fermentumwas effective only againstL. monocytogenes. This study suggests that bothL. plantarumandL. fermentumcould be successfully applied during processing of fresh-cut pineapples, contributing at the same time to inducing a protective effect against relevant foodborne pathogens.