bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nurse Trees as a Forest Restoration Tool for Mixed Plantations: Effects on Competing Vegetation and Performance in Target Tree Species
Authors: Löf Magnus , Bolte Andreas , Jacobs Douglass F. , Jensen Anna M. 
Published: July 2014

AbstractMulti‐species mixed plantations can be designed to meet social, economic, and environmental objectives during forest restoration. This paper reports results from an experiment in southern Sweden concerning the influence of three different fast growing nurse tree species on the cover of herbaceous vegetation and on the performance of several target tree species. After 10 years, the nurse trees had reduced the competing herbaceous vegetation but the effect was weak and it may take more than a decade to achieve effective vegetation control. The nurse tree species Betula pendula and Larix x eurolepis did improve stem form in some target tree species, but had a minor effect on survival and growth. The open conditions before crown closure of nurse trees strongly influence seedling performance and so delayed planting of target tree species may provide a means to avoid those conditions. Survival and growth differed greatly among the tree species. Besides the two nurse tree species mentioned above, high survival was found in Picea abies and Quercus robur and intermediate survival in Fagus sylvatica, Tilia cordata, and in the N‐fixing nurse tree Alnus glutinosa. Survival was low in the target tree species Fraxinus excelsior L. and Prunus avium. For restoration practitioners, our results illustrate the potential of using nurse trees for rapidly building a new forest structure and simultaneously increase productivity, which might be a cost‐effective strategy for forest restoration.
HLA similarities indicate shared genetic risk in 21‐hydroxylase autoantibody positive South African and United States Addison's disease
Authors: Ross I. L. , Babu S. , Armstrong T. , Zhang L. , Schatz D. , Pugliese A. , Eisenbarth G. , Baker II P. 
Published: July 2014

AbstractGenetic similarities between patients from the United States and South African (SA) Addison's Disease (AD) strengthen evidence for genetic association. SA‐AD (n = 73), SA healthy controls (N = 78), and US‐AD patients (N = 83) were genotyped for DQA1, DQB1, DRB1, and HLA‐B alleles. Serum was tested for the quantity of 21OH‐AA and IFNα‐AA at the Barbara Davis Center. Although not as profound as in US‐AD, in SA‐AD 21OH‐AA + subjects the predominantly associated risk haplotypes were DRB1*0301‐DQB1*0201 (DR3), DRB1*04xx‐DQB1*0302 (DR4), and the combined DR3/4 genotype. DQB1*0302 associated DRB1*04xx haplotypes conferred higher risk than those DRB1*04xx haplotypes associated with other DQB1 alleles. We found negative association in 21OH‐AA + SA‐AD for DQA1*0201‐DQB1*0202 and DQA1*0101‐DQB1*0501 vs SA controls, and positive association for DQA1*0401‐DQB1*0402 vs US‐AD. Apart from the class II DR3 haplotype, HLA‐B8 did not have an independent effect; however together DR3 and HLA‐B8 conferred the highest risk vs 21OH‐AA negative SA‐AD and SA‐controls. HLA‐B7 (often with DR4) conferred novel risk in 21OH‐AA + SA‐AD vs controls. This study represents the first comparison between South African and United States AD populations utilizing genotyping and serology performed at the same center. SA‐AD and US‐AD 21OH‐AA + patients share common HLA risk haplotypes including DR4 (with HLA‐B7) and DR3 (with HLA‐B8), strengthening previously described HLA associations and implicating similar genetic etiology.
Diarrhoea in slum children: observation from a large diarrhoeal disease hospital in Dhaka, Bangladesh
Authors: Ferdous Farzana , Das Sumon Kumar , Ahmed Shahnawaz , Farzana Fahmida Dil , Malek Mohammad Abdul , Das Jui , Latham Jonathan Ross , Faruque Abu Syed Golam , Chisti Mohammod Jobayer 
Published: July 2014

AbstractObjectivesTo determine and compare socio‐demographic, nutritional and clinical characteristics of children under five with diarrhoea living in slums with those of children who do not live in slums of Dhaka, Bangladesh.MethodsFrom 1993 to 2012, a total of 28 948 under fives children with diarrhoea attended the Dhaka Hospital of icddr,b. Data were extracted from the hospital‐based Diarrhoea Disease Surveillance System, which comprised 17 548 under fives children from slum and non‐slum areas of the city.ResultsMaternal illiteracy [aOR = 1.57; 95% confidence interval (1.36, 1.81), P‐value <0.001], paternal illiteracy [1.37 (1.21, 1.56) <0.001], mother's employment [1.59 (1.37, 1.85) <0.001], consumption of untreated water [2.73 (2.26, 3.30) <0.001], use of non‐sanitary toilets [3.48 (3.09, 3.93) <0.001], 1st wealth quintile background [3.32 (2.88, 3.84) <0.001], presence of fever [1.14 (1.00, 1.29) 0.047], some or severe dehydration [1.21 (1.06, 1.40) 0.007], stunting [1.14 (1.01, 1.29) 0.030] and infection with Vibrio cholerae [1.21 (1.01, 1.45) 0.039] were significantly associated with slum‐dwelling children after controlling for co‐variates. Measles immunisation [0.52 (0.47, 0.59) P < 0.001] and vitamin A supplementation rates [0.36 (0.31, 0.41) P < 0.001] amongst children 12–59 months were lower for slum dwellers than other children in univarate analysis only.ConclusionsSlum‐dwelling children are more malnourished, have lower immunisation rates (measles vaccination and vitamin A supplementation) and higher rates of measles, are more susceptible to diarrhoeal illness due to V. cholerae and suffer from severe dehydration more often than children from non‐slum areas. Improved health and nutrition strategies should give priority to children living in urban slums.
Supplementation with olive oil, but not fish oil, improves cutaneous wound healing in stressed mice
Authors: Rosa Alice dos Santos , Bandeira Luana Graziella , Monte‐Alto‐Costa Andréa , Romana‐Souza Bruna 
Published: July 2014

AbstractSupplementation with olive and fish oils reverses the effects of stress on behavioral activities and adrenal activation. However, previous studies have not shown whether supplementation with olive and fish oil could inhibit the effects of stress on cutaneous wound healing. Thus, this study investigated the effects of supplementation with fish or olive oil on cutaneous healing in stressed mice. Mice were subjected to rotational stress and treated with olive or fish oil daily until euthanasia. An excisional lesion was created on each mouse, and 14 days later, the lesions were analyzed. In addition, murine skin fibroblasts were exposed to elevated epinephrine levels plus olive oil, and fibroblast activity was evaluated. In the in vivo studies, administration of olive oil, but not fish oil, inhibited stress‐induced reduction in wound contraction, reepithelialization, hydroxyproline levels, and blood vessel density. Stress‐induced increases in vascular endothelial growth factor expression and the numbers of macrophages and neutrophils were reversed only by olive oil. Both oils reversed stress‐induced increase in catecholamine levels and oxidative damage. In in vitro studies, olive oil treatment reversed the reduction in fibroblast migration and collagen deposition and the increase in lipid peroxidation induced by epinephrine. In conclusion, supplementation with olive oil, but not fish oil, improves cutaneous wound healing in chronically stressed mice.
Forecasting longitudinal changes in oropharyngeal tumor morphology throughout the course of head and neck radiation therapy
Authors: Yock Adam D. , Rao Arvind , Dong Lei , Beadle Beth M. , Garden Adam S. , Kudchadker Rajat J. , Court Laurence E. 
Published: July 2014

Purpose:To create models that forecast longitudinal trends in changing tumor morphology and to evaluate and compare their predictive potential throughout the course of radiation therapy.Methods:Two morphology feature vectors were used to describe 35 gross tumor volumes (GTVs) throughout the course of intensity‐modulated radiation therapy for oropharyngeal tumors. The feature vectors comprised the coordinates of the GTV centroids and a description of GTV shape using either interlandmark distances or a spherical harmonic decomposition of these distances. The change in the morphology feature vector observed at 33 time points throughout the course of treatment was described using static, linear, and mean models. Models were adjusted at 0, 1, 2, 3, or 5 different time points (adjustment points) to improve prediction accuracy. The potential of these models to forecast GTV morphology was evaluated using leave‐one‐out cross‐validation, and the accuracy of the models was compared using Wilcoxon signed‐rank tests.Results:Adding a single adjustment point to the static model without any adjustment points decreased the median error in forecasting the position of GTV surface landmarks by the largest amount (1.2 mm). Additional adjustment points further decreased the forecast error by about 0.4 mm each. Selection of the linear model decreased the forecast error for both the distance‐based and spherical harmonic morphology descriptors (0.2 mm), while the mean model decreased the forecast error for the distance‐based descriptor only (0.2 mm). The magnitude and statistical significance of these improvements decreased with each additional adjustment point, and the effect from model selection was not as large as that from adding the initial points.Conclusions:The authors present models that anticipate longitudinal changes in tumor morphology using various models and model adjustment schemes. The accuracy of these models depended on their form, and the utility of these models includes the characterization of patient‐specific response with implications for treatment management and research study design.
Genome Sequence of Borrelia garinii Strain SZ, Isolated in China
Authors: Wu Qiong , Liu Zhijie , Li Youquan , Guan Guiquan , Niu Qingli , Chen Ze , Luo Jianxun , Yin Hong 
Published: July 2014

ABSTRACT

We announce the genome sequence of
Borrelia garinii
strain SZ, isolated from
Dermacentor
ticks collected in northeastern China.
B. garinii
strain SZ carries numerous plasmids, both 10 circular and 9 linear plasmids. The 902,487-bp linear chromosome (28.2% GC content) contains 820 open reading frames, 33 tRNAs, and 4 complete rRNAs. The plasmid cp32-10 contains one clustered regularly interspaced short palindromic repeat (CRISPR) with four repeats.
Draft Genome Sequence of Enterococcus hirae Strain INF E1 Isolated from Cultured Milk
Authors: Porcellato Davide , Østlie Hilde M. , Skeie Siv B. 
Published: July 2014

ABSTRACT

Here, we present the draft genome of
Enterococcus hirae
INF E1, found as a contaminant in cultured milk and studied for its ability to metabolize milk fat globule membrane glycoconjugates.
Genome Sequence of Bacillus thuringiensis subsp.
kurstaki
Strain HD-1
Authors: Day Michael , Ibrahim Mohamed , Dyer David , Bulla Lee 
Published: July 2014

ABSTRACT

We report here the complete genome sequence of
Bacillus thuringiensis
subsp.
kurstaki
strain HD-1, which serves as the primary U.S. reference standard for all commercial insecticidal formulations of
B. thuringiensis
manufactured around the world.
Strain Kaplan of Pseudorabies Virus Genome Sequenced by PacBio Single-Molecule Real-Time Sequencing Technology
Authors: Tombácz Dóra , Sharon Donald , Oláh Péter , Csabai Zsolt , Snyder Michael , Boldogkői Zsolt 
Published: July 2014

ABSTRACT
Pseudorabies virus (PRV) is a neurotropic herpesvirus that causes Aujeszky's disease in pigs. PRV strains are widely used as transsynaptic tracers for mapping neural circuits. We present here the complete and fully annotated genome sequence of strain Kaplan of PRV, determined by Pacific Biosciences RSII long-read sequencing technology.
Prognostic impact of moderate or severe mitral regurgitation (MR) irrespective of concomitant comorbidities: a retrospective matched cohort study
Authors: Prakash Roshan , Horsfall Matthew , Markwick Andrew , Pumar Marsus , Lee Leong , Sinhal Ajay , Joseph Majo X , Chew Derek P 
Published: July 2014

ObjectiveWe sought to objectively quantify the independent impact of significant mitral regurgitation (MR) on prognosis in patients with multiple comorbidities and ascertain the extent to which median survival is affected by increasing comorbidities.MethodsThis was a retrospective matched cohort study using a clinical-echocardiography reporting database linked to a clinical and administrative database in an Australian tertiary hospital. We identified our study cohort (patients with significant MR) and control cohort (without MR) on transthoracic echocardiographies performed between 2005 and 2010. The main outcome measures were mortality and heart failure rehospitalisation. A Cox proportional hazards model was used to adjust for clinical covariates and the ‘win ratio’ methodology was utilised to estimate the impact of MR on main outcomes.ResultsA total of 218 matched patients with and without significant MR were followed-up for 1 year. Significant MR was associated with an adjusted HR for mortality of 1.83 (95% CI 1.28 to 2.62, p<0.001). The win ratio for death and death or heart failure readmission was 0.57 (95% CI 0.40 to 0.78, p=0.0002) and 0.53 (95% CI 0.39 to 0.71, p<0.0001), respectively. Significant MR with left ventricular (LV) systolic dysfunction and age between 75 and 85 years were associated with a substantial reduction in median survival by 2.3 years. Significant MR with LV systolic dysfunction, age beyond 85 and advance comorbidities were associated with a lesser reduction in median survival by 0.2 years.ConclusionsSignificant MR in patients with multiple comorbidities leads to increase in death and heart failure rehospitalisation with reduced estimated median survival. However, its impact diminishes with increasing comorbidities.
A Conversation with Paul Friedrich
Authors: Friedrich Paul , Pesmen Dale 
Published: July 2014

Paul Friedrich has played a distinctive and multifaceted role within and well beyond anthropology over the past 50 years. He is currently Professor Emeritus in the Departments of Anthropology and Linguistics and on the Committee on Social Thought at the University of Chicago. Friedrich's research sites have ranged from southwestern Mexico to south India, as well as with Russians. He has also written extensively in historical linguistics, classics, and anthropological theory. Much of Friedrich's writing has focused on the interplay of the practice of poetry and poetically focused analyses of language and interaction. He has published extensively, producing numerous volumes of poetry as well as path-breaking scholarship. On May 13, 2013, at the University of Chicago, Professor Friedrich was interviewed by Dr. Dale Pesmen, an anthropologist, Russian scholar, artist, and translator who received her PhD in Anthropology at the University of Chicago and worked closely with Professor Friedrich. She is the author of Russia and Soul: An Exploration (Cornell University Press, 2000). Their conversation explored the remarkably heterogeneous and imaginative range of Friedrich's work and career, as well as highlighting ongoing core underlying concerns and themes. What follows is an edited transcript of that conversation.
The Increasing Urgency for Standards in Basic Biologic Research
Authors: Freedman Leonard P. , Inglese James 
Published: July 2014

Abstract
Research advances build upon the validity and reproducibility of previously published data and findings. Yet irreproducibility in basic biologic and preclinical research is pervasive in both academic and commercial settings. Lack of reproducibility has led to invalidated research breakthroughs, retracted articles, and aborted clinical trials. Concerns and requirements for transparent, reproducible, and translatable research are accelerated by the rapid growth of “post-publication peer review,” open access publishing, and data sharing that facilitate the identification of irreproducible data/studies; they are magnified by the explosion of high-throughput technologies, genomics, and other data-intensive disciplines. Collectively, these changes and challenges are decreasing the effectiveness of traditional research quality mechanisms and are contributing to unacceptable—and unsustainable—levels of irreproducibility. The global oncology and basic biologic research communities can no longer tolerate or afford widespread irreproducible research. This article discusses (i) how irreproducibility in preclinical research can ultimately be traced to an absence of a unifying life science standards framework, and (ii) makes an urgent case for the expanded development and use of consensus-based standards to both enhance reproducibility and drive innovations in cancer research. Cancer Res; 74(15); 4024–9. ©2014 AACR.
Epigenetic Targeting of Ovarian Cancer Stem Cells
Authors: Wang Yinu , Cardenas Horacio , Fang Fang , Condello Salvatore , Taverna Pietro , Segar Matthew , Liu Yunlong , Nephew Kenneth P. , Matei Daniela 
Published: July 2014

AbstractEmerging results indicate that cancer stem–like cells contribute to chemoresistance and poor clinical outcomes in many cancers, including ovarian cancer. As epigenetic regulators play a major role in the control of normal stem cell differentiation, epigenetics may offer a useful arena to develop strategies to target cancer stem–like cells. Epigenetic aberrations, especially DNA methylation, silence tumor-suppressor and differentiation-associated genes that regulate the survival of ovarian cancer stem–like cells (OCSC). In this study, we tested the hypothesis that DNA-hypomethylating agents may be able to reset OCSC toward a differentiated phenotype by evaluating the effects of the new DNA methytransferase inhibitor SGI-110 on OCSC phenotype, as defined by expression of the cancer stem–like marker aldehyde dehydrogenase (ALDH). We demonstrated that ALDH+ ovarian cancer cells possess multiple stem cell characteristics, were highly chemoresistant, and were enriched in xenografts residual after platinum therapy. Low-dose SGI-110 reduced the stem-like properties of ALDH+ cells, including their tumor-initiating capacity, resensitized these OCSCs to platinum, and induced reexpression of differentiation-associated genes. Maintenance treatment with SGI-110 after carboplatin inhibited OCSC growth, causing global tumor hypomethylation and decreased tumor progression. Our work offers preclinical evidence that epigenome-targeting strategies have the potential to delay tumor progression by reprogramming residual cancer stem–like cells. Furthermore, the results suggest that SGI-110 might be administered in combination with platinum to prevent the development of recurrent and chemoresistant ovarian cancer. Cancer Res; 74(17); 4922–36. ©2014 AACR.
Oral Human Papillomavirus Infection and Its Risk Factors among 5,410 Healthy Adults in China, 2009–2011
Authors: Hang Dong , Liu Fangfang , Liu Mengfei , He Zhonghu , Sun Min , Liu Ying , Li Jingjing , Pan Yaqi , Ning Tao , Guo Chuanhai , Liang Yongmei , Xu Ruiping , Zhang Lixin , Cai Hong , Ke Yang 
Published: July 2014

Abstract
Background: Despite the established link between oral human papillomavirus (HPV) infection and a subset of oropharyngeal squamous cell carcinoma (OSCC), little is known about the epidemiology of oral HPV infection among healthy adults in China.
Methods: Oral swab specimens and questionnaires were collected from 5,410 individuals (ages 25–65 years). HPV DNA in oral exfoliated cells was tested by general primer-mediated (SPF1/GP6+) PCR and sequencing. Univariate and multivariate analyses were performed to assess the associations between exposure factors and oral infection.
Results: Alpha mucosal HPV types were detected in 0.67% [95% confidence interval (CI), 0.47%–0.93%] of 5,351 β-globin–positive specimens, and cutaneous HPV in 5.46% (95% CI, 4.86%–6.10%). HPV 16 and 3 were the most prevalent types of α mucosal (0.43%; 95% CI, 0.27%–0.64%) and cutaneous HPV (4.17%; 95% CI, 3.65%–4.74%), respectively. The prevalence of α mucosal HPV decreased with increasing age (25–65 years) from 0.93% to 0.36% (Ptrend = 0.033), and was associated with self-reported history of oral disease [adjusted odds ratio (OR), 4.78; 95% CI, 1.07–21.41]. In 1,614 heterosexual couples, cutaneous HPV in one partner was found to increase the other partner's risk of cutaneous HPV infection (adjusted OR, 2.33; 95% CI, 1.22–4.48).
Conclusions: Oral HPV infection, particularly with α mucosal types, is rare among healthy adults in China. A younger age and a history of oral disease imply higher risk of α mucosal HPV infection.
Impact: This study addresses the paucity of epidemiological data on oral HPV infection among healthy population in China. Cancer Epidemiol Biomarkers Prev; 23(10); 2101–10. ©2014 AACR.
Extrinsic Apoptosis Is Impeded by Direct Binding of the APL Fusion Protein NPM-RAR to TRADD
Authors: Chattopadhyay Anuja , Hood Brian L. , Conrads Thomas P. , Redner Robert L. 
Published: July 2014

Abstract
A subset of acute promyelocytic leukemia (APL) cases has been characterized by the t(5;17)(q35;q21) translocation variant, which fuses nucleophosmin (NPM) to retinoic acid receptor α (RARA). The resultant NPM-RAR fusion protein blocks myeloid differentiation and leads to a leukemic phenotype similar to that caused by the t(15;17)(q22;q21) PML-RAR fusion. The contribution of the N-terminal 117 amino acids of NPM contained within NPM-RAR has not been well studied. As a molecular chaperone, NPM interacts with a variety of proteins implicated in leukemogenesis. Therefore, a proteomic analysis was conducted to identify novel NPM-RAR–associated proteins. TNF receptor type I–associated DEATH domain protein (TRADD) was identified as a relevant binding partner for NPM-RAR. This interaction was validated by coprecipitation and colocalization analysis. Biologic assessment found that NPM-RAR expression impaired TNF-induced signaling through TRADD, blunting TNF-mediated activation of caspase-3 (CASP3) and caspase-8 (CASP8), to ultimately block apoptosis.
Implications: This study identifies a novel mechanism through which NPM-RAR affects leukemogenesis. Mol Cancer Res; 12(9); 1283–91. ©2014 AACR.
Targeting Cancer-Derived Adenosine:New Therapeutic Approaches
Authors: Young Arabella , Mittal Deepak , Stagg John , Smyth Mark J. 
Published: July 2014

Abstract
CD73 generation of immunosuppressive adenosine within the hypoxic tumor microenvironment causes dysregulation of immune cell infiltrates, resulting in tumor progression, metastases, and poor disease outcomes. Therapies targeted toward the adenosinergic pathway, such as antibodies targeting CD73 and CD39, have proven efficacy in mouse tumor models; however, humanized versions are only in preliminary development. In contrast, A2A adenosine receptor antagonists have progressed to late-stage clinical trials in Parkinson disease, yet evidence of their role in oncology is limited. This review will compare the merits and challenges of these therapeutic approaches, identifying tumor indications and combinations that may be fruitful as they progress to the clinic.
Significance: High concentrations of immunosuppressive adenosine have been reported in cancers, and adenosine is implicated in the growth of tumors. This brief review delineates the current treatment strategies and tumor subtypes that will benefit from targeting adenosinergic pathways, alone or in combination with contemporary approaches to cancer treatment. Cancer Discov; 4(8); 879–88. ©2014 AACR.
Alfabetização no Brasil
Authors: Oliveira João Batista Araujo de 
Published: July 2014

O presente artigo aborda o conceito de alfabetização a partir da perspectiva da ciência cognitiva de leitura. Usando dados empíricos e documentais, ilustra como as políticas e as práticas de alfabetização prevalentes no país, ao ignorarem os avanços científicos na área, vêm contribuindo, de forma deliberada, para os baixos níveis que caracterizam o desempenho dos alunos.