bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cues from a specialist herbivore increase tolerance to defoliation in tomato
Authors: Korpita Timothy , Gómez Sara , Orians Colin M. 
Published: October 2013

Summary

Recent studies have shown that herbivore cues trigger rapid shifts in primary metabolism and resource allocation within a plant. This has been suggested to be an induced mechanism of tolerance to defoliation but there is little evidence supporting this. Here, we investigated, using a cultivar of tomato (Solanum lycopersicum), whether prior herbivore damage confers plants an advantage in terms of increased growth and initial flower production following defoliation.

Plants were mechanically wounded and treated with either regurgitant of the specialist Manduca sexta, deionized water or received no damage for five consecutive days. Chlorophyll content, plant growth and biomass allocation were measured during the 5‐day damage period. After the damage treatments, all leaves were removed to simulate defoliation in the three treatment groups, and regrowth capacity was followed until flowering. The number of regrown leaves, the initial number of flowers and biomass production and allocation were quantified at harvest.

During the 5‐day damage period, plants treated with M. sexta regurgitant grew less in height than undamaged plants (but had thicker stems). Chlorophyll content also decreased sharply in these plants. However, regurgitant‐treated plants recovered more quickly from the defoliation treatment, producing more new leaves compared with undamaged and mechanically damaged treatments.

Our results support the hypothesis that induced changes in resource allocation in response to specialist herbivores results in increased regrowth ability and may be adaptive in the event of severe defoliation. Future studies on wild plants could help inform the evolutionary significance of this response.
Living in risky landscapes: delineating management units in multithreat environments for effective species conservation
Authors: Olea Pedro P. , Mateo‐Tomás Patricia 
Published: October 2013

Summary

Managing threatened species to reduce their extinction risk is a widely used, yet challenging, means of halting biodiversity loss. Species show complex spatial patterns of extinction risk, due to spatial variation in both threats and vulnerability across their ranges. Conservation practitioners, however, rarely consider this spatial variation and routinely apply uniform conservation schemes, either throughout the species’ ranges, or following administrative borders that do not match ecological boundaries. Most of these schemes are experience‐based (e.g. expert opinion) and thus difficult to replicate.

We accounted for spatial variation in species’ threats by using multivariate techniques [i.e. cluster analyses and multidimensional scaling (MDS)] to delineate management units for more effective conservation. We grouped breeding territories of the endangered Egyptian vulture, according to interterritory similarity in presence and intensity of their threats.

The first three MDS axes explained 62% of the data variation. The first axis separated territories in protected areas, with low human presence, but high risk of illegal poisoning from areas highly dominated by humans. The second axis classified territories regarding the density of sheep/goats and griffon vultures and the presence of wind farms. The third axis confronted territories in protected areas with those in unprotected areas with wind farms.

We obtained 18 statistically supported groups (i.e. management units) including 86% of the territories. Territories within the same group were geographically close, agreeing with the underlying spatial autocorrelation of threats. However, six groups (33%) were distributed over more than one administrative region, which will require inter‐regional coordination for cost‐effective conservation.

Synthesis and applications. Our results show wide spatial variation for species’ threats and suggest incorporation of this heterogeneity into conservation schemes. We demonstrate how multivariate statistics, coupled with uncertainty analysis, can be employed in a systematic and repeatable way to deal with the heterogeneous landscapes of risk that species face across their ranges. Our approach allows researchers and managers to delineate management units according to similarity in species’ threats for any targeted organization level (e.g. individuals, territories, populations). The results can be visualized in Euclidean and geographical spaces for better interpretation, allowing managers to design more effective conservation actions.
Gastric microbiota is altered in oesophagitis and Barrett's oesophagus and further modified by proton pump inhibitors
Authors: Amir Itay , Konikoff Fred M. , Oppenheim Michal , Gophna Uri , Half Elizabeth E. 
Published: October 2013

SummaryGastro‐oesophageal reflux can cause inflammation, metaplasia, dysplasia and cancer of the oesophagus. Despite the increased use of proton pump inhibitors (PPIs) to treat reflux, the incidence of oesophageal adenocarcinoma has increased rapidly in Europe and in the United States in the last 25 years. The reasons for this increase remain unclear. In this study, we aimed to determine whether the microbiota of the gastric refluxate and oesophageal biopsies differs between patients with heartburn and normal‐appearing oesophageal mucosa versus patients with abnormal oesophageal mucosa [oesophagitis or Barrett's oesophagus (BE)] and to elucidate the effect of PPIs on the bacterial communities using 16S rRNA gene pyrosequencing. Significant differences in the composition of gastric fluid bacteria were found between patients with heartburn and normal oesophageal tissue versus patients with oesophagitis or BE, but in the oesophagus‐associated microbiota differences were relatively modest. Notably, increased levels of Enterobacteriaceae were observed in the gastric fluid of oesophagitis and BE patients. In addition, treatment with PPIs had dramatic effects on microbial communities both in the gastric fluids and the oesophageal tissue. In conclusion, gastric fluid microbiota is modified in patients with oesophagitis and BE compared with heartburn patients with normal biopsies. Furthermore, PPI treatment markedly alters gastric and oesophageal microbial populations. Determining whether the changes in bacterial composition caused by PPIs are beneficial or harmful will require further investigation.
Use of a dietary exposure system for screening of insecticidal compounds for their toxicity to the planthopper Laodelphax striatellus
Authors: Wang Zeng‐Xia , Lin Ke‐Jian , Romeis Jörg , Liu Yong‐Lei , Liu Ze‐Wen , Li Yun‐He , Peng Yu‐Fa 
Published: October 2013

AbstractWe developed a dietary exposure assay for screening insecticidal compounds for their toxicity and for assessing the side effects of insecticidal proteins produced by genetically engineered (GE) plants on the planthopper Laodelphax striatellus Fallén. The fitness bioassay confirmed that the diet fulfills the requirements to be used in the dietary exposure system. To validate the efficacy of the dietary exposure system, nymphs of L. striatellus were fed diets treated with different concentrations of an inorganic stomach poison, potassium arsenate (PA), or a cysteine protease inhibitor, E‐64. The results showed that with increasing concentrations of E‐64, the larval development time was prolonged, the adult weight was reduced and the survival rate of L. striatellus was decreased. Similarly the survival rates of L. striatellus consistently decreased with increasing PA content in the diet. The data indicate that the dietary exposure assay is able to detect the effects of insecticidal compounds on L. striatellus. Subsequently, this assay was successfully used for assessing the potential toxicity of Cry2Aa. The results showed that L. striatellus larvae were not negatively affected when fed the artificial diet containing purified Cry2Aa at 300 μg/g diet. In the assay, the stability and bioactivity of crystal (Cry) proteins in the food sources were confirmed by enzyme‐linked immunosorbent assay and sensitive‐insect bioassays. These results show that L. striatellus is not sensitive to Cry2Aa. We conclude that the dietary exposure system is valid and useful for assessing the toxicity of insecticidal compounds produced by GE plants on planthoppers.
Development and Application of a Method for the Analysis of 9 Mycotoxins in Maize by HPLC‐MS/MS
Authors: Wang Yutang , Xiao Chunxia , Guo Jing , Yuan Yahong , Wang Jianguo , Liu Laping , Yue Tianli 
Published: October 2013

AbstractA reliable and sensitive liquid chromatography/tandem mass spectrometry (LC‐MS/MS) method was developed for the simultaneous determination of aflatoxins (AFB1, AFB2, AFG1, and AFG2), ochratoxin A (OTA), deoxynivalenol (DON), zearalenone (ZEA), fumonisin B1 (FB1), and T2‐toxin in maize. The samples were first extracted using acetonitrile: water: acetic acid (79 : 20 : 1), and then further cleaned‐up using OASIS HLB cartridge. Optimum conditions for the extraction and chromatographic separation were investigated. The mean recoveries of mycotoxins in spiked maize ranged from 68.3% to 94.3%. Limits of detection and quantification ranged from 0.01 to 0.64 μg/kg and from 0.03 to 2.12 μg/kg, respectively. The LC‐MS/MS method has also been successfully applied to 60 maize samples, which were collected from Shaanxi Province of China. Twenty‐four of the total 60 samples (40%) were contaminated with at least 1 of these 9 mycotoxins. Occurrence of mycotoxins were 6.7%, 1.7%, 3.3%, 6.7%, 1.7%, 23.3%, and 3.3% for AFB1, AFB2, OTA, ZEA, DON, FB1, and T2‐toxin, respectively. The results demonstrated that the procedure was suitable for the simultaneous determination of these mycotoxins in maize matrix.
A novel cyanide‐inducible gene cluster helps protect Pseudomonas aeruginosa from cyanide
Authors: Frangipani Emanuela , Pérez‐Martínez Isabel , Williams Huw D. , Cherbuin Gaëtan , Haas Dieter 
Published: October 2013

SummaryPseudomonas aeruginosa produces the toxic secondary metabolite hydrogen cyanide (HCN) at high cell population densities and low aeration. Here, we investigated the impact of HCN as a signal in cell‐cell communication by comparing the transcriptome of the wild‐type strain PAO1 to that of an HCN‐negative mutant under cyanogenic conditions. HCN repressed four genes and induced 12 genes. While the individual functions of these genes are unknown, with one exception (i.e. a ferredoxin‐dependent reductase), a highly inducible six‐gene cluster (PA4129‐PA4134) was found to be crucial for protection of P. aeruginosa from external HCN intoxication. A double mutant deleted for PA4129‐PA4134 and cioAB (encoding cyanide‐insensitive oxidase) did not grow with 100 μM KCN, whereas the corresponding single mutants were essentially unaffected, suggesting a synergistic action of the PA4129‐PA4134 gene products and cyanide‐insensitive oxidase.
PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences
Authors: Thomas Gavin H. , Hartmann Klaas , Jetz Walter , Joy Jeffrey B. , Mimoto Aki , Mooers Arne O. 
Published: October 2013

Summary

Phylogenetic trees that include all member lineages are necessary for many questions in macroevolution, biogeography and conservation. Currently, producing such trees when genetic data or phenotypic characters for some tips are missing generally involves assigning missing species to the root of their most exclusive clade, essentially grafting them onto existing and static topologies as polytomies.

We describe an R package, ‘PASTIS’, that enables a two‐stage Bayesian method using MrBayes version 3.2 (or higher) to incorporate lineages lacking genetic data at the tree inference stage. The inputs include a consensus topology, a set of taxonomic statements (e.g. placing species in genera and aligning some genera with each other or placing subspecies within species) and user‐defined priors on edge lengths and topologies. PASTIS produces input files for execution in MrBayes that will produce a posterior distribution of complete ultrametric trees that captures uncertainty under a homogeneous birth‐death prior model of diversification and placement constraints. If the age distribution of a focal node is known (e.g. from fossils), the ultrametric tree distribution can be converted to a set of dated trees. We also provide functions to visualize the placement of missing taxa in the posterior distribution.

The PASTIS approach is not limited to the level of species and could equally be applied to higher or lower levels of organization (e.g. accounting for all recognized subspecies or populations within a species) given an appropriate choice of priors on branching times.
Nursing Diagnoses Determined by First Year Students: A Vignette Study
Authors: Hakverdioğlu Yönt Gülendam , Korhan Esra Akın , Erdemir Firdevs , Müller‐Staub Maria 
Published: October 2013

PurposeThe study aimed to determine the ability of first year students in identifying nursing diagnoses.MethodsIn a descriptive evaluation study, an expert‐validated vignette containing 18 nursing diagnoses was used.ResultsThe students determined 15 nursing diagnoses. The highest percentages of diagnoses identified were disturbed sleep pattern and nutrition imbalance. Students also considered medical diagnoses as nursing diagnoses: hypertension and tachycardia.ConclusionsDespite the fact that students were only at the end of their first semester and had limited clinical experience, they successfully identified the majority of nursing diagnoses.Implications for Nursing PracticePatient case study vignettes are recommended for education. To foster students’ knowledge and experience, it is also suggested that evaluating nursing diagnoses in clinical practicals becomes a requirement.AmaçBu çalışmada birinci sınıf öğrencilerinin hemşirelik tanılarını belirleyebilme durumlarının saptanması amaçladı.YöntemUzmanlar tarafından belirlenmiş 18 hemşirelik tanısını içeren bir vaka kullanılarak yapılan tanımlayıcı bir çalışmadır.BulgularÖğrenciler 15 hemşirelik tanısı belirlemiştir. En çok belirlenen hemşirelik tanıları uyku örüntüsünde rahatsızlık ve beslenmede dengesizlik tanısıdır. Öğrenciler ayrıca hipertansiyon ve taşikardi gibi tıbbi tanıları da hemşirelik tanısı olarak düşünmüşlerdir.SonuçlarÖğrenciler sadece birinci dönemin sonunda ve sınırlı klinik deneyimlere sahip olmasına rağmen, hemşirelik tanılarının büyük bir çoğunluğunu tanımlamada başarılı olmuşlardır.Hemşirelik Uygulamalari Için ÖnerilerEğitim için hasta vaka çalışmalarının kullanılması önerilmektedir. Öğrencilerin bilgi ve deneyimlerini geliştirmek için ayrıca klinik uygulamalarda hemşirelik tanılarının değerlendirilmesi gerektiği önerilmektedir.
Market concentration and pricing behavior in the fertilizer industry: a global approach
Authors: Hernandez Manuel A. , Torero Maximo 
Published: October 2013

AbstractThe global fertilizer industry is a market with high and increasing levels of concentration and trade. Low‐income regions such as sub‐Saharan Africa are highly dependent on imported fertilizer, and the landed price of imports at the port of entry usually represents a large fraction of the fertilizer supply costs in these regions. This article formally examines the relationship between market concentration and prices from a global perspective. We follow a dynamic panel approach using annual data on urea for a panel of countries and observe that prices are generally higher in more concentrated markets using different measures of concentration and model specifications. Based on additional simulations, we find that a 10% increase in competition could increase fertilizer use by 13–19% and rural incomes by 1–2% in regions like sub‐Saharan Africa. Overall, the results highlight the need to further examine the pricing behavior and potential market power exertion of major global producers, which can help to better understand the industry supply chain in developing countries and provide additional insights into the design of policies, including input subsidy programs, intended to promote long‐term fertilizer adoption.
The relative merits of transparency: Investigating situations that support the use of robotics in developing student learning adaptability across virtual and physical computing platforms
Authors: Okita Sandra Y. 
Published: October 2013

AbstractThis study examined whether developing earlier forms of knowledge in specific learning environments prepares students better for future learning when they are placed in an unfamiliar learning environment. Forty‐one students in the fifth and sixth grades learned to program robot movements using abstract concepts of speed, distance and direction. Students in high‐transparency environments learned visual programming to control robots (eg, organizing visual icons), and students in low‐transparency environments learned syntactic programming to control robots (eg, text‐based coding). Both groups received feedback and models of solutions during the learning phase. The assessment midway showed students in both conditions learned equally well when solving problems using familiar materials. However, a difference emerged when students were asked to solve new problems, using unfamiliar materials. The low‐transparency group was more successful in adapting and repurposing their knowledge to solve novel problems that required the use of unfamiliar high‐transparency materials. Students in the high‐transparency group were less successful in adapting their knowledge when solving new problems using unfamiliar low‐transparency materials. Both groups then proceeded to learn in the opposing transparency environments. The posttest revealed the benefits of initial learning in low‐transparency environments as students performed better on repeated and new inferential problems across virtual and physical platforms.
Using patient‐reported outcomes to assess and improve prostate cancer brachytherapy
Authors: Talcott James A. , Manola Judith , Chen Ronald C. , Clark Jack A. , Kaplan Irving , D'Amico Anthony V. , Zietman Anthony L. 
Published: October 2013

Objective
To describe a successful quality improvement process that arose from unexpected differences in control groups' short‐term patient‐reported outcomes (PROs) within a comparative effectiveness study of a prostate brachytherapy technique intended to reduce urinary morbidity.
Patients and Methods
Patients planning prostate brachytherapy at one of three institutions were enrolled in a prospective cohort study.
Patients were surveyed using a validated instrument to assess treatment‐related toxicity before treatment and at pre‐specified intervals.
Unexpectedly, urinary PROs were worse in one of two standard brachytherapy technique control populations (US‐BT1 and US‐BT2). Therefore, we collaboratively reviewed treatment procedures, identified a discrepancy in technique, made a corrective modification, and evaluated the change.
Results
The patient groups were demographically and clinically similar.
In the first preliminary analysis, US‐BT2 patients reported significantly more short‐term post‐treatment urinary symptoms than US‐BT1 patients.
The study's treating physicians reviewed the US‐BT1 and US‐BT2 treatment protocols and found that they differed in whether they used an indwelling urinary catheter.
After adopting the US‐BT1 approach, short‐term urinary morbidity in US‐BT2 patients decreased significantly. Brachytherapy procedures were otherwise unchanged.
Conclusion
Many procedures in cancer treatments are not evaluated, resulting in practice variation and suboptimal outcomes. Patients, the primary medical consumers, provide little direct input in evaluations of their care.
We used PROs, a sensitive and valid measure of treatment‐related toxicity, for quality assessment and quality improvement (QA/QI) of prostate brachytherapy. This serendipitous patient‐centred QA/QI process may be a useful model for empirically evaluating complex cancer treatment procedures and for screening for substandard care.
Higher rates of upgrading and upstaging in older patients undergoing radical prostatectomy and qualifying for active surveillance
Authors: Busch Jonas , Magheli Ahmed , Leva Natalia , Ferrari Michelle , Kramer Juergen , Klopf Christian , Kempkensteffen Carsten , Miller Kurt , Brooks James D. , Gonzalgo Mark L. 
Published: October 2013

Objective
To determine pathological and oncological outcomes of patients diagnosed with low‐risk prostate cancer in two age cohorts who underwent radical prostatectomy (RP) and qualified for active surveillance (AS) according to Prostate Cancer Research International: Active Surveillance (PRIAS) criteria, as AS for low‐risk prostate cancer represents an acceptable management strategy especially for older patients.
Patients and Methods
In all, 320 patients aged ≥65 years who underwent RP and were eligible for AS according to PRIAS criteria were propensity score matched 1:1 to patients aged <65 years.
Patient characteristics were compared with chi‐square, Kruskal–Wallis, and one‐way anova tests. Predictors of RP pathological upgrading or upstaging were analysed using logistic regression.
Recurrence‐free survival (RFS) and overall survival (OS) were calculated using the Kaplan–Meier method. Predictors of RFS were analysed within Cox regression models.
Results
Pathological upgrading and upstaging were significantly higher among older (≥65 years) vs younger (<65 years) patients (53.1% vs 44.1% and 12.2% vs 7.2%, respectively).
Higher prostate‐specific antigen levels and increasing age were independent predictors of upgrading among patients aged <65 years.
There were no differences in RFS or OS between the two age groups.
Positive surgical margin status was the only independent predictor of shorter RFS.
Conclusions
Patients aged ≥65 years who are eligible for AS by PRIAS criteria have a higher risk of being upgraded and upstaged at RP than those aged <65 years.
These findings should be taken into consideration when discussing treatment options for patients diagnosed with prostate cancer.
Toxicological effect of engineered nanomaterials on the liver
Authors: Kermanizadeh A , Gaiser B K , Johnston H , Brown D M , Stone V 
Published: October 2013

The liver has a crucial role in metabolic homeostasis, as it is responsible for the storage, synthesis, metabolism and redistribution of carbohydrates, fats and vitamins, and numerous essential proteins. It is also the principal detoxification centre of the body, removing xenobiotics and waste products by metabolism or biliary excretion. An increasing number of studies have shown that some nanomaterials (NMs) are capable of distributing from the site of exposure (e.g. lungs, gut) to a number of secondary organs, including the liver. As a secondary exposure site the liver has been shown to preferentially accumulate NMs (>90% of translocated NMs compared with other organs), and alongside the kidneys may be responsible for the clearance of NMs from the blood. Research into the toxicity posed by NMs to the liver is expanding due to the realization that NMs accumulate in this organ following exposure via a variety of routes (e.g. ingestion, injection and inhalation). Thus it is critical to consider what advances have been made in the investigation of NM hepatotoxicity, as well as appraising the quality of the information available and gaps in the knowledge that still exist. The overall aim of this review is to outline what data are available in the literature for the toxicity elicited by NMs to the liver in order to establish a weight of evidence approach (for risk assessors) to inform on the potential hazards posed by NMs to the liver.Linked ArticlesThis article is part of a themed section on Nanomedicine. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2014.171.issue‐17