bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of tropical forest logging and oil palm agriculture on the soil microbiome
Authors: Tripathi Binu M. , Edwards David P. , Mendes Lucas William , Kim Mincheol , Dong Ke , Kim Hyoki , Adams Jonathan M.
Published: March 2016

Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land‐use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once‐logged and twice‐logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell–cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land‐use changes on the interaction of soil microbes.
Vital and dispensable roles of Plasmodium multidrug resistance transporters during blood‐ and mosquito‐stage development
Authors: Rijpma Sanna R. , van der Velden Maarten , Annoura Takeshi , Matz Joachim M. , Kenthirapalan Sanketha , Kooij Taco W. A. , Matuschewski Kai , van Gemert Geert‐Jan , van de Vegte‐Bolmer Marga , Siebelink‐Stoter Rianne , Graumans Wouter , Ramesar Jai , Klop Onny , Russel Frans G. M. , Sauerwein Robert W. , Janse Chris J. , Franke‐Fayard Blandine M. , Koenderink Jan B.
Published: March 2016

Multidrug resistance (MDR) proteins belong to the B subfamily of the ATP Binding Cassette (ABC) transporters, which export a wide range of compounds including pharmaceuticals. In this study, we used reverse genetics to study the role of all seven Plasmodium MDR proteins during the life cycle of malaria parasites. Four P. berghei genes (encoding MDR1, 4, 6 and 7) were refractory to deletion, indicating a vital role during blood stage multiplication and validating them as potential targets for antimalarial drugs. Mutants lacking expression of MDR2, MDR3 and MDR5 were generated in both P. berghei and P. falciparum, indicating a dispensable role for blood stage development. Whereas P. berghei mutants lacking MDR3 and MDR5 had a reduced blood stage multiplication in vivo, blood stage growth of P. falciparum mutants in vitro was not significantly different. Oocyst maturation and sporozoite formation in Plasmodium mutants lacking MDR2 or MDR5 was reduced. Sporozoites of these P. berghei mutants were capable of infecting mice and life cycle completion, indicating the absence of vital roles during liver stage development. Our results demonstrate vital and dispensable roles of MDR proteins during blood stages and an important function in sporogony for MDR2 and MDR5 in both Plasmodium species.
Conditional gene deletion with DiCre demonstrates an essential role for CRK3 in Leishmania mexicana cell cycle regulation
Authors: Duncan Samuel M. , Myburgh Elmarie , Philipon Cintia , Brown Elaine , Meissner Markus , Brewer James , Mottram Jeremy C.
Published: March 2016

Leishmania mexicana has a large family of cyclin‐dependent kinases (CDKs) that reflect the complex interplay between cell cycle and life cycle progression. Evidence from previous studies indicated that Cdc2‐related kinase 3 (CRK3) in complex with the cyclin CYC6 is a functional homologue of the major cell cycle regulator CDK1, yet definitive genetic evidence for an essential role in parasite proliferation is lacking. To address this, we have implemented an inducible gene deletion system based on a dimerised Cre recombinase (diCre) to target CRK3 and elucidate its role in the cell cycle of L. mexicana. Induction of diCre activity in promastigotes with rapamycin resulted in efficient deletion of floxed CRK3, resulting in G2/M growth arrest. Co‐expression of a CRK3 transgene during rapamycin‐induced deletion of CRK3 resulted in complementation of growth, whereas expression of an active site CRK3T178E mutant did not, showing that protein kinase activity is crucial for CRK3 function. Inducible deletion of CRK3 in stationary phase promastigotes resulted in attenuated growth in mice, thereby confirming CRK3 as a useful therapeutic target and diCre as a valuable new tool for analyzing essential genes in Leishmania.
Genetic alteration of UDP‐rhamnose metabolism in Botrytis cinerea leads to the accumulation of UDP‐KDG that adversely affects development and pathogenicity
Authors: Ma Liang , Salas Omar , Bowler Kyle , Oren‐Young Liat , Bar‐Peled Maor , Sharon Amir
Published: March 2016

Botrytis cinerea is a model plant‐pathogenic fungus that causes grey mould and rot diseases in a wide range of agriculturally important crops. A previous study has identified two enzymes and corresponding genes (bcdh, bcer) that are involved in the biochemical transformation of uridine diphosphate (UDP)‐glucose, the major fungal wall nucleotide sugar precursor, to UDP‐rhamnose. We report here that deletion of bcdh, the first biosynthetic gene in the metabolic pathway, or of bcer, the second gene in the pathway, abolishes the production of rhamnose‐containing glycans in these mutant strains. Deletion of bcdh or double deletion of both bcdh and bcer has no apparent effect on fungal development or pathogenicity. Interestingly, deletion of the bcer gene alone adversely affects fungal development, giving rise to altered hyphal growth and morphology, as well as reduced sporulation, sclerotia production and virulence. Treatments with wall stressors suggest the alteration of cell wall integrity. Analysis of nucleotide sugars reveals the accumulation of the UDP‐rhamnose pathway intermediate UDP‐4‐keto‐6‐deoxy‐glucose (UDP‐KDG) in hyphae of the Δbcer strain. UDP‐KDG could not be detected in hyphae of the wild‐type strain, indicating fast conversion to UDP‐rhamnose by the BcEr enzyme. The correlation between high UDP‐KDG and modified cell wall and developmental defects raises the possibility that high levels of UDP‐KDG result in deleterious effects on cell wall composition, and hence on virulence. This is the first report demonstrating that the accumulation of a minor nucleotide sugar intermediate has such a profound and adverse effect on a fungus. The ability to identify molecules that inhibit Er (also known as NRS/ER) enzymes or mimic UDP‐KDG may lead to the development of new antifungal drugs.
Effects of the spatial repellent metofluthrin on landing rates of outdoor biting anophelines in Cambodia, Southeast Asia
Authors: CHARLWOOD J. D. , NENHEP S. , PROTOPOPOFF N. , SOVANNAROTH S. , MORGAN J. C. , HEMINGWAY J.
Published: March 2016

The emergence of artemisinin‐resistant malaria in Southeast Asia is a major problem. The fact that many people become infected with malaria when they are outside has prompted the development of ‘spatial’ rather than topical repellents. The respective effects of one or four slow‐release emanators of metofluthrin, a pyrethroid, were tested in Pailin, Pursat and Koh Kong, Cambodia. Numbers of mosquitoes counted in outdoor landing catches when one or four emanators were suspended close to the collector were compared with control collections. In Pailin, the effects of emanators on catches in Furvela tent traps and Centers for Disease Control (CDC) light traps suspended underneath houses were also investigated. Rate ratios were used to determine differences. A total of 29 255 mosquitoes were collected over 2934 h of landing collections, 87 nights of tent trapping and 81 nights of light trap capture. In Pailin, landing rates were reduced by 48% by a single emanator and by 67% by four emanators (P < 0.001). Similar reductions were observed in the number of mosquitoes collected in tent traps and the number of anophelines only collected in light traps. Results were similar in Pursat, but, for unknown reasons, those in Koh Kong showed no difference between control and metofluthrin collections (P > 0.05). These findings suggest that although the product can produce a significant effect, it requires further improvement.
Development of a high‐resolution melting analysis assay for rapid and high‐throughput identification of clinically important dermatophyte species
Authors: Didehdar M. , Khansarinejad B. , Amirrajab N. , Shokohi T.
Published: March 2016

Accurate identification of dermatophyte species is important both for epidemiological studies and for implementing antifungal treatment strategies. Although nucleic acid amplification‐based assays have several advantages over conventional mycological methods, a major disadvantage is their high cost. The aim of this study was to develop a rapid and accurate real‐time PCR‐based high‐resolution melting (HRM) assay for differentiation of the most common dermatophyte species. The oligonucleotide primers were designed to amplify highly conserved regions of the dermatophyte ribosomal DNA. Analysis of a panel containing potentially interfering fungi demonstrated no cross reactivity with the assay. To evaluate the performance characteristics of the method, a total of 250 clinical isolates were tested in comparison with the long‐established PCR‐RFLP method and the results were reassessed using DNA sequencing, as the reference standard method. The assay is able to type dermatophytes using normalised melting peak, difference plot analysis or electrophoresis on agarose gel methods. The results showed that, in comparison to PCR‐RFLP, the developed HRM assay was able to differentiate at least 10 common dermatophytes species with a higher speed, throughput and accuracy. These results indicate that the HRM assay will be a useful sensitive, high throughput and cost‐effective method for differentiating the most common dermatophyte species
Body mass index, fat free mass, uric acid, and renal function as blood pressure levels determinants in young adults
Authors: Sidoti Antonino , Nigrelli Santi , Rosati Alberto , Bigazzi Roberto , Caprioli Raffaele , Fanelli Roberto , Acconcia Pasqualina , Borracelli Donella , Biagioli Marina , Angelini Daniela , Parrini Manuela , Tonelli Luigi , Tosi Pierluigi , Manzoni Diego
Published: March 2016

Aim

We assessed some major determinants of blood pressure (BP) in young adulthood to plan a lifestyle changes policy

Methods

A cross sectional survey was held, involving 2373 high school people (age 18–21), measuring BP, body mass index (BMI), waist circumference (WCirc), fat free mass (FFM); alcohol and smoking habits were evaluated by a questionnaire. In a subset of this population (n = 60) uric acid (UA), estimated glomerular filtration rate (eGFR) were also evaluated.

Results

Smoking and not alcohol was correlated to systolic blood pressure (SBP) through quartiles (31.7%, 39.1%, 46.5%, 45.5%).

Systolic BP was significantly correlated with FFM in the whole population (r = 0.51) as well as in SBP quartiles (r = 0.243, 0.138, 0.118, 0.204). FFM‐SBP cluster analysis gave two centroids corresponding to sexes; females n = 998; coordinates (116.4 mmHg, 38.9 kg) and males n = 1068; coordinates (131.3 mmHg, 56.7 kg).

In the n = 60 substudy a multiple linear regression model (multiple R = 0.741) with SBP as dependent variable and UA, FFM, BMI, eGFR as explicative ones, only UA (β coefficent = 0.363, partial r = 0.240, P < 0.01) was the determinant of BP particularly in men. Moreover in the same group we found an inverse relationship between eGFR (albeit always in the normal range) and UA, as well as for women (r = −0.54, P < 0.01) and men (r = −0.43, P < 0.01) analyzed separately.

Conclusions

A significant correlation exists between BP and FFM; UA has proven to be the most important SBP determinant. At variance with paediatric age UA was negatively correlated with renal function. Dietary intervention on UA and alcohol habits in young adults seems advisable to prevent hypertension.
Optimal allocation of leaf epidermal area for gas exchange
Authors: de Boer Hugo J. , Price Charles A. , Wagner‐Cremer Friederike , Dekker Stefan C. , Franks Peter J. , Veneklaas Erik J.
Published: March 2016

A long‐standing research focus in phytology has been to understand how plants allocate leaf epidermal space to stomata in order to achieve an economic balance between the plant's carbon needs and water use. Here, we present a quantitative theoretical framework to predict allometric relationships between morphological stomatal traits in relation to leaf gas exchange and the required allocation of epidermal area to stomata.

Our theoretical framework was derived from first principles of diffusion and geometry based on the hypothesis that selection for higher anatomical maximum stomatal conductance (gsmax) involves a trade‐off to minimize the fraction of the epidermis that is allocated to stomata. Predicted allometric relationships between stomatal traits were tested with a comprehensive compilation of published and unpublished data on 1057 species from all major clades.

In support of our theoretical framework, stomatal traits of this phylogenetically diverse sample reflect spatially optimal allometry that minimizes investment in the allocation of epidermal area when plants evolve towards higher gsmax.

Our results specifically highlight that the stomatal morphology of angiosperms evolved along spatially optimal allometric relationships. We propose that the resulting wide range of viable stomatal trait combinations equips angiosperms with developmental and evolutionary flexibility in leaf gas exchange unrivalled by gymnosperms and pteridophytes.
Tasting cheesescapes in Canterbury (New Zealand)
Authors: Fusté‐Forné Francesc
Published: March 2016

Food tourism is a means to connect agriculture produce and tourism activity. Food tourism allows destinations to convey the authenticity that comes from their food heritage, which is closely linked to natural and cultural landscapes. Food and landscapes in New Zealand are strongly related to dairy production, cheese production being one of the main features. This study showcases cheesescapes in Canterbury, the largest region in the South Island of New Zealand in terms of milk production. On one hand, thanks to food tourism, the producers can explore ways to diversify their production. On the other hand, visitors are able to identify with the inhabitants of a country and ‘taste’ a portion of its landscape through gastronomy.
Secondary school student perspectives on community resilience in Grey District
Authors: Pomeroy Ann , Holland Peter
Published: March 2016

For a national competition supported by the New Zealand Board of Geography Teachers, secondary school students in years 10–13 were asked to identify and investigate factors that were building community resilience in their home areas, and the entries provided young people's perspectives on how well individuals, families and communities ‘bounce back’, adapt, change and become stronger following an adverse event. This article concerns the findings of students at Greymouth High School. Their entries showed that community resilience in Grey District depended on individual and collective capacity for action. The greater their involvement in community affairs and projects, the more likely individuals and families were to form networks and participate in communal activities. In Greymouth, as elsewhere in New Zealand, membership of voluntary organisations and participation in planning for, and responding to, catastrophic events has helped residents respond effectively in times of adversity and has enhanced community resilience.
A systematic review and meta‐analysis of screen time behaviour among North American indigenous populations
Authors: Foulds H. J. A. , Rodgers C. D. , Duncan V. , Ferguson L. J.
Published: March 2016

Screen time (computer, television, video game and smartphone/tablet activity) is associated with increased obesity and other health risks. This systematic review evaluates screen time among North American Indigenous populations and compares it with that of North American Europeans. Electronic databases (e.g. MEDLINE and EMBASE) were searched, and citations cross‐referenced. Included articles reported screen time among First Nations/American Indians, Métis, Inuit/Alaskan Natives or Native Hawaiians. From 788 citations evaluated, 40 identified articles report television, video game, computer and/or overall screen time. Overall screen time was 3.65 ± 1.26 h day−1 (n = 2,242, 8 articles) among Indigenous children/youth and 3.61 ± 2.95 h day−1 (n = 155, 1 article) among adults. Among children/youth, 66.0% (n = 11 256, 9 articles) reported less than 2 h day−1 of television screen time, while only 52.8% (n = 2,458, 1 article) of adults reported this volume. Screen time was generally greater among male population, youth, First Nations/American Indians and overweight/obese individuals. Indigenous children/youth reported greater overall screen time than North American Europeans (4.81 ± 2.84 h day−1, n = 1,182 vs. 3.40 ± 2.81 h day−1, n = 2,785; 3 articles; p < 0.0001). Screen time is common among North American Indigenous populations. Further research evaluating interventions to reduce screen time and chronic disease risks is required. © 2016 World Obesity
HPV prevalence and p16INKa overexpression in non‐smoking non‐drinking oral cavity cancer patients
Authors: Dediol E , Sabol I , Virag M , Grce M , Muller D , Manojlović S
Published: March 2016

Objective

Our aim was to compare HPV and p16INK4a (p16) expression and their influence on survival and prognosis in oral cavity squamous cell cancer (OCSCC), between non‐smokers and non‐drinkers (NSND) and smokers and drinkers (SD).

Subjects and Methods

Patients with OCSCC treated with surgery from 2000 to 2010 were included in the study. Patients who did not smoke at all or smoked less than 10 pack per years and did not drink alcohol on a daily basis were considered the NSND group. An equal number of SD were the control group. HPV presence was determined from paraffin‐embedded blocks investigated by PCR analysis. p16 expression was evaluated with immunohistochemistry.

Results

The NSND group were mostly younger or older female patients with tongue or gingival cancers. p16 expression was significantly more frequent in NSND patients (27% vs 10%). Patients with stronger p16 expression had significantly worse survival, especially for tongue cancers (P = 0.026). In Cox multivariate analysis, both HPV and p16 expression carried a negative prognosis for NSND patients (P = 0.0351 and P = 0.0260).

Conclusions

NSND are a specific population of OCSCC patients. In contrast to oropharyngeal cancer, HPV and p16 expression in OCSCC are negative predictive factors, especially in NSND patients.
Selection mosaics differentiate Rhizobium–host plant interactions across different nitrogen environments
Authors: Cauwenberghe Jannick Van , Visch Wouter , Michiels Jan , Honnay Olivier
Published: March 2016

The nature and direction of coevolutionary interactions between species is expected to differentiate among distinct environments. Consequently, locally coevolved symbiotic traits would be well matched in similar environments, but mismatched elsewhere. In a classic mutualistic tradeoff, rhizobia provide nitrogen (N) to legume host plants in return for photosynthates. Despite earlier predictions, there is little evidence so far that spatial differences in soil N content mediate the coevolutionary outcome of the legume–Rhizobium mutualism. To test the existence of such selection mosaics, different genotypes of Vicia cracca and Rhizobium leguminosarum originating from spatially and environmentally highly differentiated sites were cross inoculated across different soil N regimes. In accordance with theoretical predictions, we found highly significant effects of genotype by genotype by environment (G× G × E) interactions, on both nodulation and plant growth, even when R. leguminosarum genotypes showed high genetic similarity. Our results show that the trajectory of the coevolutionary interactions between rhizobia and legumes is differentiated across different environments, and that selection mosaics may play an important role in shaping differences in the genetic composition of rhizobial populations.
TOP‐DOWN AND BOTTOM‐UP: INSTITUTIONAL EFFECTS ON DEBT AND GRANTS AT THE ENGLISH AND GERMAN LOCAL LEVEL
Authors: DE WIDT DENNIS
Published: March 2016

This article investigates the impact of institutional factors on the relationship between grant funding and local debt in England and Germany. Using a panel dataset covering the period 2005–12, the research identifies a positive relationship between grants and local debt. The positive relationship between grants and debt is reduced due to the impact of political and administrative variables. The findings demonstrate three shortcomings of the current literature. First, in contrast to the dominant portrayal of German local administration as predominantly legalistic, partisan dynamics affect the allocation of grants to the German local level. Second, institutional variables operate differently depending upon grant type, providing a rationale against the scholarly practice of using aggregate grants. Third, grant mechanisms provide a promising key to unlock institutional dynamics in systems of multilevel governance, but only when scholars integrate institutional differences more explicitly in their research design than hitherto accounted for by political economy.
Unveiling biases in soft‐tissue phosphatization: extensive preservation of musculature in the Cretaceous (Cenomanian) polychaete Rollinschaeta myoplena (Annelida: Amphinomidae)
Authors: Wilson Paul , Parry Luke A. , Vinther Jakob , Edgecombe Gregory D.
Published: March 2016

The process of soft‐tissue phosphatization (the replication of labile tissues by calcium phosphate) is responsible for many instances of high‐resolution soft tissue preservation, often revealing anatomical insights into the animals that so preserved. However, while much work has gone into exploring key issues such as biases and micro‐controls, phosphatization remains poorly understood as a taphonomic process. Here, using camera lucida, plain‐light microscopy and SEM imagery, we address this issue by describing the taphonomy and fidelity of the musculature of Rollinschaeta myoplena Parry et al., a phosphatized annelid from the Cretaceous Konservat‐Lagerstätten of Hakel and Hjoula, Lebanon, with an unprecedented quantity of three‐dimensional soft‐tissue preservation. Analysis highlights two strong, previously recognized biases affecting the process of phosphatization: (1) a taxonomic bias restricted to R. myoplena that triggers unusually extensive phosphatization; and (2) a tissue bias whereby longitudinal and parapodial musculature show markedly higher fidelity in comparison to the musculature of the intestine and body wall circular muscles. Potential explanations for these biases include internal phosphate‐enrichment by relative muscle density, the relative rate of decay and the physiology of musculature. Incongruence between experimental decay series for polychaetes and the prevalence of labile tissue preservation over recalcitrant tissues in R. myoplena exposes the limits of decay experiments for understanding exceptional preservation.
Test–retest Reliability in Reporting the Pain Induced by a Pain Provocation Test: Further Validation of a Novel Approach for Pain Drawing Acquisition and Analysis
Authors: Leoni Diego , Falla Deborah , Heitz Carolin , Capra Gianpiero , Clijsen Ron , Egloff Michele , Cescon Corrado , Baeyens Jean‐Pierre , Barbero Marco
Published: March 2016

Background

Pain drawings (PD) are frequently used in research to illustrate the pain response to pain provocation tests. However, there is a lack of data on the reliability in defining the extent and location of pain. We investigated the test–retest reliability in reporting an acute painful sensation induced by a pain provocation test using a novel approach for PD acquisition and analysis in healthy volunteers.

Methods

Forty healthy volunteers participated. Each participant underwent 2 upper limb neurodynamic tests 1 (ULNT1), once to the point of pain onset (PO) and once until the point of submaximal pain (SP). After each ULNT1, participants completed 2 consecutive PD with an interval of 1 minute. Custom software was used to quantify the pain extent and analyze the pain overlap. The test–retest reliability of pain extent was examined using Intraclass Correlation Coefficient (ICC 2,1) and Bland–Altman plots. Pain location reliability was examined using the Jaccard similarity coefficient (JSC).

Results

The ICC values for PO and SP were 0.98 (95% CI: 0.96–0.99) and 0.97 (95% CI: 0.95–0.98), respectively. The mean difference and 95% limits of agreement (± 1.96 SD) in the Bland–Altman plots were 14 pixels (−1080;1110) for PO, and 145 (−1610;1900) for SP. The median JSCs (Q1;Q3) were 0.73 (0.64;0.80) for PO and 0.76 (0.65;0.79) for SP.

Conclusions

Pain drawings is a reliable instrument to investigate pain extent and pain location in healthy individuals experiencing an acute painful sensation induced by a pain provocation test.
Bulked sample analysis in genetics, genomics and crop improvement
Authors: Zou Cheng , Wang Pingxi , Xu Yunbi
Published: March 2016

Biological assay has been based on analysis of all individuals collected from sample populations. Bulked sample analysis (BSA), which works with selected and pooled individuals, has been extensively used in gene mapping through bulked segregant analysis with biparental populations, mapping by sequencing with major gene mutants and pooled genomewide association study using extreme variants. Compared to conventional entire population analysis, BSA significantly reduces the scale and cost by simplifying the procedure. The bulks can be built by selection of extremes or representative samples from any populations and all types of segregants and variants that represent wide ranges of phenotypic variation for the target trait. Methods and procedures for sampling, bulking and multiplexing are described. The samples can be analysed using individual markers, microarrays and high‐throughput sequencing at all levels of DNA, RNA and protein. The power of BSA is affected by population size, selection of extreme individuals, sequencing strategies, genetic architecture of the trait and marker density. BSA will facilitate plant breeding through development of diagnostic and constitutive markers, agronomic genomics, marker‐assisted selection and selective phenotyping. Applications of BSA in genetics, genomics and crop improvement are discussed with their future perspectives.
Shoot tolerance mechanisms to iron toxicity in rice (Oryza sativa L.)
Authors: Wu Lin‐Bo , Ueda Yoshiaki , Lai Shang‐Kun , Frei Michael
Published: March 2016

Iron toxicity frequently affects lowland rice and leads to oxidative stress via the Fenton reaction. Tolerance mechanisms were investigated in contrasting genotypes: the intolerant IR29 and the tolerant recombinant inbred line FL483. Seedlings were exposed to 1000 mg L‐1 ferrous iron, and the regulation of genes involved in three hypothetical tolerance mechanisms was investigated (I) Iron uptake, partitioning and storage. The iron concentration and speciation in different plant tissues did not differ significantly between genotypes. Sub‐cellular iron partitioning genes such as vacuolar iron transporters or ferritin showed no genotypic differences. (II) Antioxidant biosynthesis. Only one gene involved in carotenoid biosynthesis showed genotypic differences, but carotenoids are unlikely to scavenge the reactive oxygen species (ROS) involved in Fe toxicity, i.e. H2O2 and hydroxyl radicals. (III) Enzymatic activities for ROS scavenging and antioxidants turnover. In shoots, glutathione‐S‐transferase and ascorbate oxidase genes showed genotypic differences, and consistently, the tolerant FL483 had lower dehydroascorbate reductase and higher ascorbate oxidase activity, suggesting that high rates ascorbate reduction confer sensitivity. This hypothesis was confirmed by application of exogenous reduced ascorbate or L‐galactono‐1,4‐lactone, which increased lipid peroxidation under iron toxic conditions. Our results demonstrate in planta pro‐oxidant activity of reduced ascorbate in the presence of iron.
Comparison of D1´‐ and D1‐containing PS II reaction centre complexes under different environmental conditions in Synechocystis sp. PCC 6803
Authors: Crawford Tim S. , Hanning Kyrin R. , Chua Jocelyn P.S. , Eaton‐Rye Julian J. , Summerfield Tina C.
Published: March 2016

In oxygenic photosynthesis, the D1 protein of Photosystem II is the primary target of photodamage and environmental stress can accelerate this process. The cyanobacterial response to stress includes transcriptional regulation of genes encoding D1, including low‐oxygen‐induction of psbA1 encoding the D1´ protein in Synechocystis sp. PCC 6803. The psbA1 gene is also transiently up‐regulated in high light, and its deletion has been reported to increase ammonium‐induced photoinhibition. Therefore we investigated the role of D1´‐containing PS II centres under different environmental conditions. A strain containing only D1´‐PS II centres under aerobic conditions exhibited increased sensitivity to ammonium chloride and high light compared to a D1‐containing strain. Additionally a D1´‐PS II strain was outperformed by a D1‐PS II strain under normal conditions; however, a strain containing low‐oxygen‐induced D1´‐PS II centres was more resilient under high light than an equivalent D1 strain. These D1´‐containing centres had chlorophyll a fluorescence characteristics indicative of altered forward electron transport and back charge recombination with the donor side of PS II. Our results indicate D1´‐PS II centres are important in the reconfiguration of thylakoid electron transport in response to high light and low oxygen.
Factors affecting N‐terminal pro‐brain natriuretic peptide elevation in the acute phase of Kawasaki disease
Authors: Yanagisawa Daisuke , Ayusawa Mamoru , Kato Masataka , Watanabe Hirofumi , Komori Akiko , Abe Yuriko , Nakamura Takahiro , Kamiyama Hiroshi , Takahashi Shori
Published: March 2016

Background

The aim of this study was to investigate the clinical significance and factors that affect N‐terminal pro‐brain natriuretic peptide (NT‐proBNP) elevation in the acute phase of Kawasaki disease (KD) despite the absence of apparent cardiac complications.

Methods

The laboratory and echocardiography results of 44 KD patients in the acute and subacute phases were reviewed.

Results

With preserved cardiac function, median NT‐proBNP was significantly elevated in the acute phase compared with the subacute phase (343 pg/mL, IQR, 162–1182 pg/mL vs 98 pg/mL, IQR, 61–205 pg/mL, respectively; P < 0.0001). The respective levels of tumor necrosis factor (TNF)‐α, soluble TNF receptor (sTNFR)1, and sTNFR2 were also significantly elevated in the acute phase compared with the subacute phase: TNF‐α, 3.3 pg/mL (IQR, 2.6–4.8 pg/mL) versus 2.4 pg/mL (IQR 1.9–4.0 pg/mL; P < 0.01), sTNFR1, 2741 pg/mL (IQR, 2080–3183 pg/mL) versus 976 pg/mL (IQR, 814–1247 pg/mL; P < 0.0001), sTNFR2, 5644 pg/mL (IQR, 4693–7520 pg/mL) versus 3169 pg/mL (IQR, 2132–3878 pg/mL; P < 0.0001). Log‐transformed NT‐proBNP was correlated with TNF‐α (r = 0.29, P = 0.056), sTNFR1 (r = 0.60, P < 0.0001), and sTNFR2 (r = 0.65, P < 0.0001). TNF‐α was correlated with sTNFR1 (r = 0.35, P = 0.02) and sTNFR2 (r = 0.51, P < 0.001).

Conclusion

Tumor necrosis factor‐α may cause NT‐proBNP elevation in the acute phase of KD, and NT‐proBNP level may be an indicator of TNF‐α activity.
Autoimmune hepatitis in a child presenting with hepatopulmonary syndrome (HPS)
Authors: Grabinski Zoe , Beg Mirza , Wali Prateek
Published: March 2016

HPS has been described in 9–20% of children with end‐stage liver disease. We present a case of a previously, asymptomatic nine‐yr‐old incidentally found to have low oxygen saturation. Physical exam was remarkable for digital clubbing, splenomegaly and orthodeoxia. Laboratory evaluation revealed a low platelet count, hyperammonemia, and prolonged coagulation studies. Sonography showed evidence of splenomegaly and portal venous hypertension. High resolution CT thorax and CTA were normal. HPS was confirmed by agitated saline contrast enhanced echocardiography and Tc‐99m MAA scan with evidence of intrapulmonary vascular dilatations. Liver biopsy was performed and consistent with autoimmune hepatitis. A high clinical index of suspicion should be maintained for HPS in pediatric patients who have unexplained hypoxemia as typical signs and symptoms of severe liver disease are often absent. In this report, we discuss a case of HPS complicated AIH in a pediatric patient and review the relevant literature.
Physiological, biochemical and molecular characterization of an induced mutation conferring imidazolinone resistance in wheat
Authors: Jimenez Francisco , Rojano‐Delgado Antonia M. , Fernández Pablo Tomas , Rodríguez‐Suárez Cristina , Atienza Sergio G. , De Prado Rafael
Published: March 2016

The Clearfield® wheat cultivars possessing imidazolinone (IMI)‐resistant traits provide an efficient option for controlling weeds. The imazamox‐resistant cultivar Pantera (Clearfield®) was compared with a susceptible cultivar (Gazul). Target and non‐target mechanisms of resistance were studied to characterize the resistance of Pantera and to identify the importance of each mechanism involved in this resistance. Pantera is resistant to imazamox as was determined in previous experiments. The molecular study confirmed that it carries a mutation Ser‐Asn627 conferring resistance to imazamox in two out of three acetolactate synthase (ALS) genes (imi1 and imi2), located in wheat on chromosomes 6B and 6D, respectively. However, the last gene (imi3) located on chromosome 6A does not carry any mutation conferring resistance. As a result, photosynthetic activity and chlorophyll content were reduced after imazamox treatment. Detoxification was higher in the resistant biotype as shown by metabolomic study while imazamox translocation was higher in the susceptible cultivar. Interestingly, imazamox metabolism was higher at higher doses of herbicide, which suggests that the detoxification process is an inducible mechanism in which the upregulation of key gene coding for detoxification enzymes could play an important role. Thus, the identification of cultivars with a higher detoxification potential would allow the development of more resistant varieties.
Ultrasound assessment of diaphragmatic function in patients with amyotrophic lateral sclerosis
Authors: Fantini Riccardo , Mandrioli Jessica , Zona Stefano , Antenora Federico , Iattoni Andrea , Monelli Marco , Fini Nicola , Tonelli Roberto , Clini Enrico , Marchioni Alessandro
Published: March 2016

Background and objective

Evaluation of diaphragm function in Amyotrophic Lateral Sclerosis (ALS) is critical in determining when to commence non‐invasive mechanical ventilation (NIV).

Currently, forced vital capacity (FVC) and sniff nasal inspiratory pressure (SNIP) are volitional measures for this evaluation, but require collaboration and are poorly specific. The primary aim of this study was to assess whether diaphragmatic thickness measured by ultrasound (US) correlates with lung function impairment in ALS patients. The secondary aim was then to compare US diaphragm thickness index (ΔTdi) with a new parameter (ΔTmax index).

Methods

41 patients with ALS and 30 healthy subjects were enrolled in the study. All subjects underwent spirometry, SNIP and diaphragm US evaluation, while arterial blood gases were measured in some patients only. US assessed diaphragm thickness (Tdi) at tidal volume (Vt) or total lung capacity (TLC), and their ratio (ΔTmax) were recorded. Changes (Δ) in Tdi indices during tidal volume (ΔTdiVt) and maximal inspiration (ΔTdiTLC) were also assessed.

Results

ΔTdiTLC (p <0.001) and ΔTmax (p = 0.007), but not ΔTdiVt, differed between patients and controls. Significant correlation (p < 0.05) was found between ΔTdiTLC, ΔTmax and FVC. The ROC curve analysis for comparison of individual testing showed better accuracy with Δtmax than with ΔtdiTLC for FVC (AUC 0.76 and 0.27) and SNIP (AUC 0.71 and 0.25).

Conclusion

Diaphragm thickness assessed by ultrasound significantly correlates with global respiratory alterations in patients with ALS. ΔTmax represents a new US index of early diaphragmatic dysfunction, better related with the routinely performed lung function tests.
Clinical features of usual interstitial pneumonia with anti‐neutrophil cytoplasmic antibody in comparison with idiopathic pulmonary fibrosis
Authors: Hosoda Chiaki , Baba Tomohisa , Hagiwara Eri , Ito Hiroyuki , Matsuo Norikazu , Kitamura Hideya , Iwasawa Tae , Okudela Koji , Takemura Tamiko , Ogura Takashi
Published: March 2016

Background and objective

Myeloperoxidase anti‐neutrophil cytoplasmic antibody (MPO‐ANCA) is occasionally positive in patients with usual interstitial pneumonia (UIP). However, the differences from idiopathic pulmonary fibrosis (IPF/UIP) have not been well documented. We aimed to clarify the clinical, radiological and pathological features of UIP associated with MPO‐ANCA (ANCA/UIP).

Methods

We retrospectively reviewed the medical records of 12 consecutive ANCA/UIP patients not manifesting microscopic polyangiitis and 108 IPF/UIP patients with no autoantibodies, both diagnosed by surgical lung biopsy.

Results

There was no significant difference in clinical background, laboratory results and pulmonary function tests between ANCA/UIP patients and IPF/UIP patients except for the percentage of bronchoalveolar lavage neutrophils. HRCT showed subpleural reticulation in both groups. Increased attenuation around honeycombing and cysts was significantly observed in ANCA/UIP. Pathologically, ANCA/UIP had more prominent inflammatory cell infiltration, lymphoid follicles with germinal centres and cellular bronchiolitis. During the disease course, three of 12 patients (25%) developed microscopic polyangiitis. Immunosuppressive treatment tended to be more effective in ANCA/UIP patients, and the survival time in ANCA/UIP patients tended to be longer than those with IPF/UIP.

Conclusion

ANCA/UIP may be distinguishable from IPF/UIP with a combination of HRCT findings of increased attenuation around honeycombing and cysts and some of the characteristic pathological findings. In contrast to IPF/UIP, immunosuppressive treatment could be a therapeutic option for ANCA/UIP.
Tumour‐Associated Autoantibodies as Diagnostic Biomarkers for Breast Cancer: A Systematic Review and Meta‐Analysis
Authors: Xia J. , Shi J. , Wang P. , Song C. , Wang K. , Zhang J. , Ye H.
Published: March 2016

Tumour‐associated autoantibodies may be promising biomarkers that could facilitate breast cancer (BC) diagnosis and improve patient outcomes. This review aims to identify the tumour‐associated autoantibodies with the greatest diagnostic potential. Systematic searches were conducted using PubMed and Web of Science. The most studied tumour‐associated autoantibody was included in a meta‐analysis, and its clinical value was determined using Fagan's nomogram. The analysis included 84 studies regarding tumour‐associated autoantibodies with the diagnostic value. Anti‐p53 antibody was the most frequently studied autoantibody, followed by autoantibodies against MUC1, HER2 and cyclin B1. Although individual tumour‐associated autoantibodies showed low diagnostic sensitivity, combinations of autoantibodies offered relatively high sensitivity. Enzyme‐linked immunosorbent assay (ELISA) was the most common detection method, and nucleic acid programmable protein microarrays appeared preferable to common protein microarrays. As the most commonly studied autoantibody, anti‐p53 antibody was included in a meta‐analysis. When it had been detected using ELISA and cut‐off values were defined as the mean +2 or 3 standard deviations, the summary area under the receiver operating characteristic curve for the presence of BC was 0.78. Fagan's nomogram showed post‐test probabilities of 32% and 6% for positive and negative results, respectively. Mammography might be supplemented by the use of tumour‐associated autoantibodies as biomarkers for BC diagnosis in younger women with increased risks of BC. Even though several studies have investigated the diagnostic use of tumour‐associated autoantibodies as biomarkers for BC detection, a high‐quality prospective study is needed to validate their diagnostic value in practice.
Simultaneous Confidence Tubes in Multivariate Linear Regression
Authors: Liu Wei , Han Yang , Wan Fang , Bretz Frank , Hayter Anthony J.
Published: March 2016

Simultaneous confidence bands have been shown in the statistical literature as powerful inferential tools in univariate linear regression. While the methodology of simultaneous confidence bands for univariate linear regression has been extensively researched and well developed, no published work seems available for multivariate linear regression. This paper fills this gap by studying one particular simultaneous confidence band for multivariate linear regression. Because of the shape of the band, the word ‘tube’ is more pertinent and so will be used to replace the word ‘band’. It is shown that the construction of the tube is related to the distribution of the largest eigenvalue. A simulation‐based method is proposed to compute the 1 − α quantile of this eigenvalue. With the computation power of modern computers, the simultaneous confidence tube can be computed fast and accurately. A real‐data example is used to illustrate the method, and many potential research problems have been pointed out.
Effect of Socioeconomic Status on the Linkage Between Suicidal Ideation and Suicide Attempts
Authors: Kim Jeong Lim , Kim Ji Man , Choi Young , Lee Tae‐Hoon , Park Eun‐Cheol
Published: March 2016

Previous suicide attempts are a leading risk factor for completed suicide. To identify specific characteristics of those at high risk for attempts, we investigated associations with socioeconomic status (SES). Data from the 2013 Korean Community Health Survey (KCHS) included adults who reported suicidal ideation (N = 220,245). Attempts in the past 12 months were assessed. Associations of demographic, socioeconomic, and suicide‐related behavioral factors were analyzed using multiple logistic regression. Among those with suicidal ideation, 862 (3.9%) had attempted suicide. After stratification by age and gender, results showed that low education and unemployed young adult men and women had significantly higher rates of attempts. The lowest income level was associated with significantly higher rates of attempts in only young adult women. Among those with the lowest and highest income, the association between ideation and attempts was attenuated, whereas it was enhanced among other income groups.
Primary and secondary effects of real‐time feedback to reduce vertical loading rate during running
Authors: Baggaley M. , Willy R. W. , Meardon S. A.
Published: March 2016

Gait modifications are often proposed to reduce average loading rate (AVLR) during running. While many modifications may reduce AVLR, little work has investigated secondary gait changes. Thirty‐two rearfoot runners [16M, 16F, 24.7 (3.3) years, 22.72 (3.01) kg/m2, >16 km/week] ran at a self‐selected speed (2.9 ± 0.3 m/s) on an instrumented treadmill, while 3D mechanics were calculated via real‐time data acquisition. Real‐time visual feedback was provided in a randomized order to cue a forefoot strike (FFS), a minimum 7.5% decrease in step length, or a minimum 15% reduction in AVLR. AVLR was reduced by FFS (mean difference = 26.4 BW/s; 95% CI = 20.1, 32.7; P < 0.001), shortened step length (8.4 BW/s; 95% CI = 2.9, 14.0; P = 0.004), and cues to reduce AVLR (14.9 BW/s; 95% CI = 10.2, 19.6; P < 0.001). FFS, shortened step length, and cues to reduce AVLR all reduced eccentric knee joint work per km [(−48.2 J/kg*m; 95% CI = −58.1, −38.3; P < 0.001), (−35.5 J/kg*m; 95% CI = −42.4, 28.6; P < 0.001), (−23.1 J/kg*m; 95% CI = −33.3, −12.9; P < 0.001)]. However, FFS and cues to reduce AVLR also increased eccentric ankle joint work per km [(54.49 J/kg*m; 95% CI = 45.3, 63.7; P < 0.001), (9.20 J/kg*m; 95% CI = 1.7, 16.7; P = 0.035)]. Potentially injurious secondary effects associated with FFS and cues to reduce AVLR may undermine their clinical utility. Alternatively, a shortened step length resulted in small reductions in AVLR, without any potentially injurious secondary effects.
The Protestant Reading Ethic and Variation in Its Effects
Authors: Mosher James S.
Published: March 2016

Max Weber's thesis that a “Protestant ethic” in a subset of Protestant sects created a “spirit of capitalism” is often interpreted as an explanation for the increase in economic growth in the Protestant parts of the West before and during the industrial revolution. One alternative pathway through which Protestantism might have contributed to high economic performance is that it was Protestantism's promotion of literacy that led to higher economic growth and not behavioral changes due to a Protestant ethic as suggested by Weber. To evaluate the “Protestant reading ethic” thesis, this study examines historical events for the period from 1500 up to the 1800s in nine countries. The study also explores available cross‐national quantitative data on economic development and literacy for the same period. The qualitative and quantitative evidence supports the overall thesis that Protestantism promoted literacy and rises in literacy likely contributed to the economic development. The evidence also suggests that the impact of Protestantism on literacy varied depending on what actions were taken by Protestant states and Protestant national churches to promote literacy.
Introducing dolomite seams: hybrid compaction–solution bands in dolomitic limestones
Authors: Tavani Stefano , Vitale Stefano , Grifa Celestino , Iannace Alessandro , Parente Mariano , Mazzoli Stefano
Published: March 2016

Bedding‐parallel dolomite seams occur in a clay‐poor carbonate succession of the Apennines. The seams are composed of a high concentration of dolomite crystals compared to the hosting dolomitic limestone. SEM images document microcracking, and in many cases even crushing and fragmentation, of dolomite crystals and accumulation of non‐carbonate insoluble material both along micro‐stylolites within the seams and around dolomite crystals of the seams. We interpret the seams as hybrid structures between pressure‐solution seams and compaction bands, which formed during burial. The euhedral dolomite crystals scattered in the micritic matrix represent the insoluble residue produced by the progressive dissolution of calcite. As calcite dissolution proceeds, the concentration of dolomite crystals increases, eventually resulting in a dolomite seam in which locally a dolomite crystal‐supported texture is attained. At this stage, the dolomite crystals within the seam start to collide, crush and fragment, so that the dolomite seam behaves like a compaction band.