bluuebunny/crossref_metadata_2025 huggingface dataset:
Changing trends in diagnosis, staging, treatment and survival in lung cancer: comparison of three consecutive cohorts in an Australian lung cancer centre
Authors: Denton E. J. , Hart D. , Wainer Z. , Wright G. , Russell P. A. , Conron M.
Published: May 2016

Background

Lung cancer accounts for significant morbidity and mortality worldwide. The effect of recent changes in demographics and management on outcomes in Australia has not been clearly defined.

Aims

To compare three consecutive lung cancer cohorts to evaluate emergent differences in diagnosis, management and mortality.

Methods

For comparative analysis, 2119 lung cancer patients were divided into three successive cohorts. Current death data were sought from the Victorian Cancer Registry.

Results

Age at diagnosis, mode of presentation and pathology did not significantly differ between the groups. Significantly more females were diagnosed with lung cancer in the most recent cohort (P = 0.04). Amongst non‐small‐cell lung cancer patients, there were more adenocarcinomas and less large cell carcinomas in the latest cohort (P = <0.01). More patients from the most recent cohort were staged pathologically and via positron emission tomography and fewer were clinically staged (P = <0.01). The most recent cohort had a greater proportion of Stage IV disease (P = <0.01) and more curative surgical or combined modality radiotherapy and chemotherapy versus palliative radiotherapy or supportive care (P = <0.01). Overall 5‐year survival improved significantly in the most recent cohort, even after adjustment for age, gender and stage (P = <0.01).

Conclusion

Comparison of three lung cancer patient cohorts diagnosed between 2001 and 2013 highlights emergent changes in lung cancer demographics, management and outcomes. These include recent increases in proportion of females, pathological and positron emission tomography staging, and Stage IV disease, as well as improved survival despite later stage disease.
LL37:DNA complexes provide antimicrobial activity against intracellular bacteria in human macrophages
Authors: Stephan Alexander , Batinica Marina , Steiger Julia , Hartmann Pia , Zaucke Frank , Bloch Wilhelm , Fabri Mario
Published: May 2016

As part of the innate host response neutrophils release neutrophil extracellular traps (NETs), protein:DNA complexes that contain a number of antimicrobial peptides (AMPs), such as cathelicidin. Human cathelicidin in its active form, LL37, has potent antimicrobial activity against bacteria. However, whether LL37 derived from NETs contributes to antimicrobial activity against intracellular pathogens remains unclear. Here, we report that NETs induced by mycobacteria contain cathelicidin. Human macrophages internalized NET‐bound cathelicidin, which is transported to lysosomal compartments. Furthermore, using a model of in vitro‐generated LL37:DNA complexes we found that LL37 derived from such complexes attacks mycobacteria in macrophage phagolysosomes resulting in antimicrobial activity. Taken together, our results suggest a mechanism by which LL37 in complex with DNA contributes to host defence against intracellular bacteria in human macrophages.
Reduced immunogenicity of Plasmodium falciparum gamete surface antigen (Pfs48/45) in mice after disruption of disulphide bonds – evaluating effect of interferon‐γ‐inducible lysosomal thiol reductase
Authors: Merino Kristen M. , Bansal Geetha P. , Kumar Nirbhay
Published: May 2016

Sexual stages of Plasmodium are critical for malaria transmission and stage‐specific antigens are important targets for development of malaria transmission‐blocking vaccines. Plasmodium falciparum gamete surface antigen (Pfs48/45) is important for male gamete fertility and is being pursued as a candidate vaccine antigen. Vaccine‐induced transmission‐blocking antibodies recognize reduction‐sensitive conformational epitopes in Pfs48/45. Processing and presentation of such disulphide‐bond‐constrained epitopes is critical for eliciting the desired immune responses. Mice lacking interferon‐γ‐inducible lysosomal thiol reductase (GILT), an enzyme that mediates reduction of S‐S bonds during antigen processing, were employed to investigate immunogenicity of Pfs48/45. It has been well established that the ability to reduce S‐S bonds in antigens guides effective T‐cell immune responses; however, involvement of GILT in the induction of subsequent B‐cell responses has not been explored. We hypothesized that the ability to reduce S‐S bonds in Pfs48/45 will impact the generation of T‐cell epitopes, and so influence helper T‐cell responses required for specific B‐cell responses. Non‐reduced and reduced and alkylated forms of Pfs48/45 were employed to evaluate immune responses in wild‐type and GILT knockout mice and studies revealed important differences in several immune response parameters, including differences in putative T‐cell epitope recognition, faster kinetics of waning of Pfs48/45‐specific IgG1 antibodies in knockout mice, differential patterns of interferon‐γ and interleukin‐4 secretions by splenocytes, and possible effects of GILT on induction of long‐lived plasma cells and memory B cells responsible for antigen‐recall responses. These studies emphasize the importance of antigen structural features that significantly influence the development of effective immune responses.
Improved Performance of YIG (Y3Fe5O12) Films Grown on Pt‐Buffered Si Substrates by Chemical Solution Deposition Technique
Authors: Guo Xin , Chen Ying , Wang Genshui , Ge Jun , Zhang Yuanyuan , Tang Xiaodong , Ponchel Freddy , Remiens Denis , Dong Xianlin
Published: May 2016

High‐quality Yttrium iron garnet (YIG) films with crack‐free surface and improved magnetic performance were grown on platinum (Pt)‐buffered Si substrates by chemical solution deposition technique. The saturation magnetization of obtained YIG films can reach 124 emu/cm3, which was the 88% theoretical value of YIG single crystal. The effects of annealing condition were also discussed. When annealed at 750°C for 1 h, YIG films showed a very small coercive field of 12 Oe and the peak‐to‐peak ferromagnetic resonance linewidth can be as low as 95 Oe at 9.10 GHz. The results demonstrated that YIG films prepared on Pt‐buffered Si substrates can be beneficial to the application of YIG films to integrated devices.
High‐Temperature Strength of Boron Suboxide Ceramic Consolidated by Spark Plasma Sintering
Authors: Demirskyi Dmytro , Solodkyi Ievgen , Sakka Yoshio , Vasylkiv Oleg
Published: May 2016

The spark plasma sintering (SPS) of B6O ceramics using a highly crystalline boron suboxide powder with a low oxygen deficiency level is reported. The monolithic boron suboxide ceramic exhibited a room‐temperature strength of 300 ± 20 MPa, which is comparable to the strength of monolithic boron carbide. With increasing flexural test temperature, the strength of the boron suboxide ceramics increased to 450 MPa at 1400°C. The increase in strength with the temperature is associated with the unique microstructure of boron suboxide grains, which allows intergranular “brittle” fracture along subgrains even at 1400°C. This suggests that even higher strengths can be achieved.
Temperature‐dependent phenology and growth potential of the Andean potato tuber moth, Symmetrischema tangolias (Gyen) (Lep., Gelechiidae)
Authors: Sporleder M. , Schaub B. , Aldana G. , Kroschel J.
Published: May 2016

The Andean potato tuber moth, Symmetrischema tangolias (Gyen) [Lepidoptera, Gelechiidae], is an economically important pest of potato (Solanum tuberosum L.) in the mid‐elevated Andean region and an invasive pest of partially global importance. Determination of the pest's population life table parameters is essential for understanding population development and growth under a variety of climates and as part of a pest risk analysis. The development, mortality and reproduction were studied in two pest populations (from Peru and Ecuador) in which cohorts of each life stage were exposed to different constant temperatures ranging from 10°C to 28°C. Using the Insect Life Cycle Modeling software, nonlinear equations were fitted to the data and an overall phenology model established to simulate life table parameters based on temperature. The temperature‐dependent development curve was statistically well described for eggs by Ratkowsky's model and for larvae and pupae by Taylor's model. Variability in development time among individuals independent of temperature was significantly described by a log‐logistic model. Temperature effects on immature mortality were described using different nonlinear models. Optimal temperature for survival was between 14° and 17°C. Temperature effects on adult senescence and oviposition time were described by simple exponential models; within‐group variability was described by a Weibull distribution function. Fecundity per female due to temperature followed a nonlinear model indicating maximum reproduction at ~17°C. The established model revealed good convergence with historical life tables established at fluctuating temperatures. The results confirm that S. tangolias is more adapted to cooler temperature than the common potato tuber moth, Phthorimaea operculella (Zeller). S. tangolias develops at temperatures within the range of 8–28.8°C with a maximum finite rate of population increase (=1.053) at 21°C. The established process‐based physiological model can be used globally to simulate life table parameters for S. tangolias based on temperature and should prove helpful for evaluating the potential establishment risk and in adjusting pest management programmes.
Population genetic diversity and structure of a dominant tropical seagrass, Cymodocea rotundata, in the Western Pacific region
Authors: Arriesgado Dan M. , Kurokochi Hiroyuki , Nakajima Yuichi , Matsuki Yu , Uy Wilfredo H. , Fortes Miguel D. , Campos Wilfredo L. , Nadaoka Kazuo , Lian Chunlan
Published: May 2016

Cymodocea rotundata is an ecologically important tropical pioneer seagrass species distributed in the Indo‐Pacific region. The population genetic diversity and structure of this species were analysed at 46 sites spanning the Philippines, Ryukyu Islands (northern limit) and Hainan Island, by using microsatellite simple sequence repeat (SSR) markers. Analyses revealed the persistence of C. rotundata likely relies on local population dynamics and fitness influenced by environmental gradients, with sexual reproduction prevalent in the Philippines while the Ryukyu and Hainan populations were predominantly established by clonal spread. Analysis of molecular variance showed significant genetic differentiation (P < 0.001) among three geographic regions: the Philippines, Ryukyu and Hainan. Furthermore, the mean fixation index value was very high (FST = 0.36), indicating poor dispersal potential or limited gene flow. Allelic richness and heterozygosity of C. rotundata was comparable in the Philippines and Ryukyu Islands populations. More private alleles were found in the Philippines and excess heterozygotes in the Ryukyu Islands. STRUCTURE analysis revealed that the Ryukyu and Hainan populations were mosaics of admixed alleles of individuals from the Philippines. An assignment test suggested that recruitment occurs from the Northeast Philippines to Ryukyu Islands. These results suggest that the Philippine populations are tropical seagrass hotspots and perhaps the origin of the populations in the Ryukyu and Hainan Islands. This scenario is most likely driven by the Kuroshio Current and island integration events during plate tectonic activities. The Philippine Archipelago is considered of high importance for conservation objectives and management plan of seagrasses. Likewise, the Ryukyu Islands are also important in terms of conserving regional diversity because locally adapted genotypes have important evolutionary potential in the face of environmental change.
Colour polymorphism is likely to be disadvantageous to some populations and species due to genetic architecture and morph interactions
Authors: Bolton Peri E. , Rollins Lee A. , Griffith Simon C.
Published: May 2016

Polymorphism describes two or more distinct, genetically determined, phenotypes that co‐occur in the same population, where the rarest morph is maintained at a frequency above the mutation rate (Ford 1945; Huxley 1955). In a recent opinion piece, we explored a new idea regarding the role of genetic architectures and morph interactions in colour polymorphisms and how this can negatively affect population performance (Boltonet al. 2015). In this issue of Molecular Ecology, Forsman (2016) thoroughly discusses the current evidence for polymorphisms enhancing population performance and critiques the validity of the definitions of polymorphism we use in our original paper. We respond by clarifying that the negative consequences of polymorphisms that we discussed are likely to be most pertinent in species that have a particular set of characteristics, such as strong sexual or social interactions between morphs and discrete genetic architectures. Although it was not our intention to redefine polymorphism, we do believe that there should be further discussion about refining or characterizing balanced polymorphisms with respect to the degree of morph sympatry, discreteness of traits and their underlying genetic architecture, and the types of selection that drive and maintain the variation. The latter describes whether polymorphism is primarily maintained by external factors such as predation pressure or internal factors such as interactions with members of the same species. The contribution of Forsman (2016) is useful to this discussion, and we hope that our exchange of opinions will inspire new empirical and theoretical ideas on the origin and maintenance of colour polymorphisms.
Towards understanding the genetic basis of mouth asymmetry in the scale‐eating cichlidPerissodus microlepis
Authors: Raffini Francesca , Fruciano Carmelo , Franchini Paolo , Meyer Axel
Published: May 2016

How polymorphisms consisting in left–right asymmetries are produced and maintained in natural populations is a tantalizing question, which remains largely unanswered. The scale‐eating cichlid fishPerissodus microlepisis a remarkable example of extreme ecological specialization achieved by morphological and behavioural laterality. Its asymmetric mouth is accompanied by a pronounced lateralized foraging behaviour, where a left‐bending morph preferentially feeds on the scales of the right side of its prey, while the opposite is true for the right morph. This striking asymmetry made this fish a textbook example of the astounding degree of ecological specialization and negative frequency‐dependent selection. Yet, the genetic basis underlying this spectacular laterality remains unknown. We addressed this question through analyses of wild‐caught fish using high‐throughputDNAsequencing data. A novel array ofSNPmarkers was developed by ddRADsequencing (ddRADseq) and the use of pooledDNAsamples (PoolSeq). We obtained more than 155 000SNPs using ddRADseq and 3 900 000SNPs with PoolSeq. Among these, we identified one (ddRAD)SNP, and 38 or 378 (PoolSeq) windows that are differentiated between the left and right morphs accounting for spurious associations due to geographic structuring. This allowed us to uncover candidate genomic regions that potentially contain genes for this trait. Then, this interesting trait has a genetic basis that is likely to be influenced by multiple loci. This result contributes to a greater understanding of the genetic bases of left–right asymmetry and, ultimately, the evolutionary processes governing the maintenance of this striking case of laterality.
Monocytes of patients with amyotrophic lateral sclerosis linked to gene mutations display altered TDP‐43 subcellular distribution
Authors: De Marco G. , Lomartire A. , Calvo A. , Risso A. , De Luca E. , Mostert M. , Mandrioli J. , Caponnetto C. , Borghero G. , Manera U. , Canosa A. , Moglia C. , Restagno G. , Fini N. , Tarella C. , Giordana M. T. , Rinaudo M. T. , Chiò A.
Published: May 2016

Aims

Cytoplasmic accumulation of the nuclear protein transactive response DNA‐binding protein 43 (TDP‐43) is an early determinant of motor neuron degeneration in most amyotrophic lateral sclerosis (ALS) cases. We previously disclosed this accumulation in circulating lymphomonocytes (CLM) of ALS patients with mutant TARDBP, the TDP‐43‐coding gene, as well as of a healthy individual carrying the parental TARDBP mutation. Here, we investigate TDP‐43 subcellular localization in CLM and in the constituent cells, lymphocytes and monocytes, of patients with various ALS‐linked mutant genes.

Methods

TDP‐43 subcellular localization was analysed with western immunoblotting and immunocytofluorescence in CLM of healthy controls (n = 10), patients with mutant TARDBP (n = 4, 1 homozygous), valosin‐containing protein (VCP; n = 2), fused in sarcoma/translocated in liposarcoma (FUS; n = 2), Cu/Zn superoxide dismutase 1 (SOD1; n = 6), chromosome 9 open reading frame 72 (C9ORF72; n = 4), without mutations (n = 5) and neurologically unaffected subjects with mutant TARDBP (n = 2).

Results

TDP‐43 cytoplasmic accumulation was found (P < 0.05 vs. controls) in CLM of patients with mutant TARDBP or VCP, but not FUS, in line with TDP‐43 subcellular localization described for motor neurons of corresponding groups. Accumulation also characterized CLM of the healthy individuals with mutant TARDBP and of some patients with mutant SOD1 or C9ORF72. In 5 patients, belonging to categories described to carry TDP‐43 mislocalization in motor neurons (3 C9ORF72, 1 TARDBP and 1 without mutations), TDP‐43 cytoplasmic accumulation was not detected in CLM or in lymphocytes but was in monocytes.

Conclusions

In ALS forms characterized by TDP‐43 mislocalization in motor neurons, monocytes display this alteration, even when not manifest in CLM. Monocytes may be used to support diagnosis, as well as to identify subjects at risk, of ALS and to develop/monitor targeted treatments.
Effectiveness of cognitive behavioral therapy in treating bipolar disorder: An updated meta‐analysis with randomized controlled trials
Authors: Ye Bi‐Yu , Jiang Ze‐Yu , Li Xuan , Cao Bo , Cao Li‐Ping , Lin Yin , Xu Gui‐Yun , Miao Guo‐Dong
Published: May 2016

Aim

The aim of this updated meta‐analysis was to further assess the effectiveness of cognitive behavioral therapy (CBT) in treating bipolar disorder (BD).

Methods

We carried out a literature search on PubMed, Embase, and the Cochrane Library up to October 2015. We calculated the pooled relative risk of relapse rate and standard mean difference (SMD) of mean change (data at a follow‐up time‐point – baseline) of the Beck Depression Inventory, Beck Hopelessness Scale, Hamilton Rating Scale for Depression, Young Mania Rating Scale (YMRS) and Mania Rating Scale scores with their 95% confidence interval (95%CI). Subgroup analyses based on follow‐up time were performed.

Results

Nine randomized controlled trials with 520 bipolar I or II disorder patients were reanalyzed. Overall analysis showed that CBT did not significantly reduce the relapse rate of BD or improve the level of depression. However, significant efficacy of CBT in improving severity of mania was proved based on the YMRS (SMD = −0.54, 95%CI, −1.03 to −0.06,
P
 = 0.03) but not based on MRS. Subgroup analyses showed that CBT had short‐term efficacy in reducing relapse rate of BD (at 6 months’ follow‐up: relative risk = 0.49, 95%CI: 0.29–0.81,
P
 = 0.006) and improving severity of mania based on YMRS score (post‐treatment: SMD = −0.30, 95%CI, −0.59 to −0.01,
P
 = 0.04).

Conclusion

Short‐term efficacy of CBT in reducing relapse rate of BD and improving the severity of mania was proved. But these effects could be weakened by time. In addition, there was no effect of CBT on level of depression in BD.
Measuring and Forecasting Quality in English Hospitals
Authors: Papanicolas Irene , McGuire Alistair
Published: May 2016

Hospital performance metrics, often in the form of risk-adjusted hospital mortality rates, are increasingly being made available in the public domain to compare hospitals. Despite the proliferation of these metrics, uncertainty remains regarding their validity and reliability given the noise surrounding their underlying measures. The paper considers a quality measure of hospital performance developed by McClellan and Staiger which smooths within hospitals and over time, while remaining computationally straightforward. The McClellan and Staiger method improves on others by incorporating different measures of outcome, eliminating systematic bias arising from the heterogeneous mix of hospital outputs and the noise that is inherent in other measures of quality. The technique also allows the forecasting of future quality. Using English hospital episode statistics for the years 2000–2005 for acute myocardial infarction and hip replacement, we use this technique to return quality measures based on hospital fixed effects estimated from yearly cross-sectional patient level data, and vector auto-regressions estimated over time, which then combine information from different time periods and across conditions to produce robust hospital quality measures. Our results suggest that this method is well suited to measure and predict provider quality of care in the English setting.
Significance of shallow core transects for reef models and sea‐level curves, Heron Reef, Great Barrier Reef
Authors: Webb Gregory E. , Nothdurft Luke D. , Zhao Jian‐Xin , Opdyke Bradley , Price Gilbert
Published: May 2016

A sequence of shallow reef cores from Heron Reef, Great Barrier Reef, provides new insights into Holocene reef growth models. Isochron analysis of a leeward core transect suggests that the north‐western end of Heron Reef reached current sea‐level by ca 6·5 kyr bp and then prograded leeward at a rate of ca 19·6 m/kyr between 5·1 kyr and 4·1 kyr bp (pre‐1950) to the present reef margin. A single short core on the opposing margin of the reef is consistent with greater and more recent progradation there. Further to the east, one windward core reached modern sea‐level by ca 6·3 kyr bp, suggesting near ‘keep‐up’ behaviour at that location, but the opposing leeward margin behind the lagoon reached sea‐level much more recently. Hence, Heron Reef exhibited significantly different reef growth behaviour on different parts of the same margin. Mean reef accretion rates calculated from within 20 m of one another in the leeward core transect varied between ca 2·9 m and 4·7 m/kyr depending on relative position in the prograding wedge. These cores serve as a warning regarding the use of isolated cores to inform reef growth rates because apparent aggradation at any given location on a reef varies depending on its location relative to a prograding margin. Only transects of closely spaced cores can document reef behaviour adequately so as to inform reef growth models and sea‐level curves. The cores also emphasize potential problems in U‐series dates for corals within a shallow (ca 1·5 m) zone beneath the reef flat. Apparent age inversions restricted to that active diagenetic zone may reflect remobilization and concentration of Th in irregularly distributed microbialites or biofilms that were missed during sample vetting. Importantly, the Th‐containing contaminant causes ages to appear too old, rather than too young, as would be expected from younger cement.
Correlation of Serum Vitamin A Levels with Disease Activity Indices and Colonic IL‐23R and FOXP3 mRNA Expression in Ulcerative Colitis Patients
Authors: Verma P. , Subodh S. , Tiwari V. , Rampal R. , Tuteja A. , Toteja G. S. , Gupta S. D. , Ahuja V.
Published: May 2016

Genome‐wide association studies have identified IL‐23 receptor (IL‐23R) as a susceptibility locus for the pathogenesis of ulcerative colitis (UC), which is characterized by exaggerated Th2/Th17 response. Studies have shown that vitamin A (VA) reduces disease progression by promoting FOXP3⁺ T cells and curbing Th17 cells. In this study, we explored the association of colonic IL‐23R and FOXP3 expression in fifty‐one UC patients (23 in remission and 28 with active disease) with serum VA levels and disease activity. We observed that decreased serum VA levels were associated with increased disease activity. However, there was no significant difference in mucosal IL‐23R and FOXP3 expression in UC patients with moderate–to‐severe disease activity compared to those in remission. Also, no significant correlation was drawn between serum VA levels and mucosal IL‐23R and FOXP3 expression. Our study suggests that even after an established role of VA in inhibiting Th17 responses in mice models and humans, serum VA levels and disease activity do not correlate with FOXP3 and IL‐23R expression in colonic mucosa of UC patients.
Missing the Party: Political Categorization and Reasoning in the Absence of Party Label Cues
Authors: Heit Evan , Nicholson Stephen P.
Published: May 2016

This research addressed theoretical approaches in political science arguing that the American electorate is either poorly informed or dependent on party label cues, by assessing performance on political judgment tasks when party label information is missing. The research materials were created from the results of a national opinion survey held during a national election. The experiments themselves were run on nationally representative samples of adults, identified from another national electoral survey. Participants saw profiles of simulated individuals, including information about demographics and issue positions, but omitting party labels. In Experiment 1, participants successfully judged the likelihood of party membership based on the profiles. In Experiment 2, participants successfully voted based on their party interests. The results were mediated by participants' political knowledge. Conclusions are drawn with respect to theories from political science and issues in cognitive science regarding categorization and reasoning.
Exploring Psychology in the Field: Steps and Examples From the Used‐Car Market
Authors: Pope Devin G.
Published: May 2016

The growing availability of large datasets in a variety of domains presents an opportunity for researchers to use field data to better understand psychological concepts. I discuss, from an empirical economics point of view, steps for how to study cognition in large datasets. I use two recent papers that explore psychology in the used‐car market as motivating examples. These examples help illustrate the potential importance of big data as a way to explore human psychology and cognition.
Knowledge, Attitudes and Practices Regarding Risk to Human Infection due to Mycobacterium bovis among Cattle Farming Communities in Western Uganda
Authors: Kazoora H. B. , Majalija S. , Kiwanuka N. , Kaneene J. B.
Published: May 2016

A cross‐sectional study involving multistage cluster sampling was undertaken in Kashari county, Mbarara district, western Uganda, in which quantitative and qualitative approaches were utilized to determine the knowledge, attitudes and practices regarding risk of human infection with zoonotic tuberculosis due to Mycobacterium bovis among cattle farmers. Of 496 respondents, 50% were farm owners and 50% herdsmen. Males were 70.9% of all the study participants. Among these, 37.5% had good knowledge, 41.4% had positive attitudes and 75.2% good practices regarding zoonotic tuberculosis. In the multivariable model, good knowledge was associated with having ever received health education, spending more than 5 years keeping cattle, having heard of cattle condemned at the abattoir due to tuberculosis and marital status. Positive attitudes were associated with having ever received health education, having heard of cattle condemned at the abattoir due to tuberculosis and being a farm owner versus being a herdsman. Good practices were associated with health education and good knowledge of the disease. Overall, knowledge and attitudes towards zoonotic tuberculosis due to M. bovis in humans was found to be low. While the majority of the respondents reported good practices, there were some still consuming raw milk and its products, which may predispose them to infection and indicates the need for greater outreach for zoonotic tuberculosis education.
Toward synthesis of oxide films on graphene with sputtering based processes
Authors: Ahlberg Patrik , Nyberg Tomas , Zhang Shi-Li , Zhang Zhi-Bin , Jansson Ulf
Published: May 2016

The impact of energetic particles associated with a sputter deposition process may introduce damage to single layer graphene films, making it challenging to apply this method when processing graphene. The challenge is even greater when oxygen is incorporated into the sputtering process as graphene can be readily oxidized. This work demonstrates a method of synthesizing ZnSn oxide on graphene without introducing an appreciable amount of defects into the underlying graphene. Moreover, the method is general and applicable to other oxides. The formation of ZnSn oxide is realized by sputter deposition of ZnSn followed by a postoxidation step. In order to prevent the underlying graphene from damage during the initial sputter deposition process, the substrate temperature is kept close to room temperature, and the processing pressure is kept high enough to effectively suppress energetic bombardment. Further, in the subsequent postannealing step, it is important not to exceed temperatures resulting in oxidation of the graphene. The authors conclude that postoxidation of ZnSn is satisfactorily performed at 300 °C in pure oxygen at reduced pressure. This process results in an oxidized ZnSn film while retaining the initial quality of the graphene film.
Impact of errors in recorded compressed breast thickness measurements on volumetric density classification using volpara v1.5.0 software
Authors: Waade Gunvor Gipling , Highnam Ralph , Hauge Ingrid H. R. , McEntee Mark F. , Hofvind Solveig , Denton Erika , Kelly Judith , Sarwar Jasmine J. , Hogg Peter
Published: May 2016

Purpose:

Mammographic density has been demonstrated to predict breast cancer risk. It has been proposed that it could be used for stratifying screening pathways and recommending additional imaging. Volumetric density tools use the recorded compressed breast thickness (CBT) of the breast measured at the x‐ray unit in their calculation; however, the accuracy of the recorded thickness can vary. The aim of this study was to investigate whether inaccuracies in recorded CBT impact upon volumetric density classification and to examine whether the current quality control (QC) standard is sufficient for assessing mammographic density.

Methods:

Raw data from 52 digital screening mammograms were included in the study. For each image, the clinically recorded CBT was artificially increased and decreased in increments of 1 mm to simulate measurement error, until ±15% from the recorded CBT was reached. New images were created for each 1 mm step in thickness resulting in a total of 974 images which then had volpara density grade (VDG) and volumetric density percentage assigned.

Results:

A change in VDG was observed in 38.5% (n = 20) of mammograms when applying ±15% error to the recorded CBT and 11.5% (n = 6) was within the QC standard prescribed error of ±5 mm.

Conclusions:

The current QC standard of ±5 mm error in recorded CBT creates the potential for error in mammographic density measurement. This may lead to inaccurate classification of mammographic density. The current QC standard for assessing mammographic density should be reconsidered.
Validation of Varian TrueBeam electron phase–spaces for Monte Carlo simulation of MLC‐shaped fields
Authors: Lloyd Samantha A. M. , Gagne Isabelle M. , Bazalova‐Carter Magdalena , Zavgorodni Sergei
Published: May 2016

Purpose:

This work evaluates Varian's electron phase–space sources for Monte Carlo simulation of the TrueBeam for modulated electron radiation therapy (MERT) and combined, modulated photon and electron radiation therapy (MPERT) where fields are shaped by the photon multileaf collimator (MLC) and delivered at 70 cm SSD.

Methods:

Monte Carlo simulations performed with EGSnrc‐based BEAMnrc/DOSXYZnrc and penelope‐based PRIMO are compared against diode measurements for 5 × 5, 10 × 10, and 20 × 20 cm2 MLC‐shaped fields delivered with 6, 12, and 20 MeV electrons at 70 cm SSD (jaws set to 40 × 40 cm2). Depth dose curves and profiles are examined. In addition, EGSnrc‐based simulations of relative output as a function of MLC‐field size and jaw‐position are compared against ion chamber measurements for MLC‐shaped fields between 3 × 3 and 25 × 25 cm2 and jaw positions that range from the MLC‐field size to 40 × 40 cm2.

Results:

Percent depth dose curves generated by BEAMnrc/DOSXYZnrc and PRIMO agree with measurement within 2%, 2 mm except for PRIMO's 12 MeV, 20 × 20 cm2 field where 90% of dose points agree within 2%, 2 mm. Without the distance to agreement, differences between measurement and simulation are as large as 7.3%. Characterization of simulated dose parameters such as FWHM, penumbra width and depths of 90%, 80%, 50%, and 20% dose agree within 2 mm of measurement for all fields except for the FWHM of the 6 MeV, 20 × 20 cm2 field which falls within 2 mm distance to agreement. Differences between simulation and measurement exist in the profile shoulders and penumbra tails, in particular for 10 × 10 and 20 × 20 cm2 fields of 20 MeV electrons, where both sets of simulated data fall short of measurement by as much as 3.5%. BEAMnrc/DOSXYZnrc simulated outputs agree with measurement within 2.3% except for 6 MeV MLC‐shaped fields. Discrepancies here are as great as 5.5%.

Conclusions:

TrueBeam electron phase–spaces available from Varian have been implemented in two distinct Monte Carlo simulation packages to produce dose distributions and outputs that largely reflect measurement. Differences exist in the profile shoulders and penumbra tails for the 20 MeV phase–space off‐axis and in the outputs for the 6 MeV phase–space.
Broadband and chiral binary dielectric meta-holograms
Authors: Khorasaninejad Mohammadreza , Ambrosio Antonio , Kanhaiya Pritpal , Capasso Federico
Published: May 2016

This is a study of basic holographic principles in designing new nanostructured devices that enable broadband and chiral imaging.
Carbon sequestration potential of second-growth forest regeneration in the Latin American tropics
Authors: Chazdon Robin L. , Broadbent Eben N. , Rozendaal Danaë M. A. , Bongers Frans , Zambrano Angélica María Almeyda , Aide T. Mitchell , Balvanera Patricia , Becknell Justin M. , Boukili Vanessa , Brancalion Pedro H. S. , Craven Dylan , Almeida-Cortez Jarcilene S. , Cabral George A. L. , de Jong Ben , Denslow Julie S. , Dent Daisy H. , DeWalt Saara J. , Dupuy Juan M. , Durán Sandra M. , Espírito-Santo Mario M. , Fandino María C. , César Ricardo G. , Hall Jefferson S. , Hernández-Stefanoni José Luis , Jakovac Catarina C. , Junqueira André B. , Kennard Deborah , Letcher Susan G. , Lohbeck Madelon , Martínez-Ramos Miguel , Massoca Paulo , Meave Jorge A. , Mesquita Rita , Mora Francisco , Muñoz Rodrigo , Muscarella Robert , Nunes Yule R. F. , Ochoa-Gaona Susana , Orihuela-Belmonte Edith , Peña-Claros Marielos , Pérez-García Eduardo A. , Piotto Daniel , Powers Jennifer S. , Rodríguez-Velazquez Jorge , Romero-Pérez Isabel Eunice , Ruíz Jorge , Saldarriaga Juan G. , Sanchez-Azofeifa Arturo , Schwartz Naomi B. , Steininger Marc K. , Swenson Nathan G. , Uriarte Maria , van Breugel Michiel , van der Wal Hans , Veloso Maria D. M. , Vester Hans , Vieira Ima Celia G. , Bentos Tony Vizcarra , Williamson G. Bruce , Poorter Lourens
Published: May 2016

Models reveal the high carbon mitigation potential of tropical forest regeneration.
Chemical vapor deposition synthesis of near-zigzag single-walled carbon nanotubes with stable tube-catalyst interface
Authors: Zhao Qiuchen , Xu Ziwei , Hu Yue , Ding Feng , Zhang Jin
Published: May 2016

Enriching near-zigzag single-walled carbons, which have a small tube-catalyst interface, by a “tandem plate” CVD method.
Measurement of a vacuum-induced geometric phase
Authors: Gasparinetti Simone , Berger Simon , Abdumalikov Abdufarrukh A. , Pechal Marek , Filipp Stefan , Wallraff Andreas J.
Published: May 2016

A Berry phase is induced on an artificial atom coupled to a quantum field in the vacuum state by slowly varying their coupling.
Multiple hot-carrier collection in photo-excited graphene Moiré superlattices
Authors: Wu Sanfeng , Wang Lei , Lai You , Shan Wen-Yu , Aivazian Grant , Zhang Xian , Taniguchi Takashi , Watanabe Kenji , Xiao Di , Dean Cory , Hone James , Li Zhiqiang , Xu Xiaodong
Published: May 2016

Morié-engineered graphene devices can collect multiple electrons per absorbed photon, promising efficient optoelectronics.
Biomimetic gyroid nanostructures exceeding their natural origins
Authors: Gan Zongsong , Turner Mark D. , Gu Min
Published: May 2016

Researchers demonstrate the replication of 3D natural gyroid nanostructures with superior optical performance and properties.
Rapid oxygenation of Earth’s atmosphere 2.33 billion years ago
Authors: Luo Genming , Ono Shuhei , Beukes Nicolas J. , Wang David T. , Xie Shucheng , Summons Roger E.
Published: May 2016

Continuous multiple sulfur isotope profiles from South African rocks pinpoint the Great Oxygenation Event in the geologic record.
Pre-Clovis occupation 14,550 years ago at the Page-Ladson site, Florida, and the peopling of the Americas
Authors: Halligan Jessi J. , Waters Michael R. , Perrotti Angelina , Owens Ivy J. , Feinberg Joshua M. , Bourne Mark D. , Fenerty Brendan , Winsborough Barbara , Carlson David , Fisher Daniel C. , Stafford Thomas W. , Dunbar James S.
Published: May 2016

Page-Ladson, Florida, provides evidence of the oldest human occupation in the North American Gulf Coastal Plain at 14,550 B.P.
Aggressiveness Changes in Populations of Didymella pinodes over Winter and Spring Pea Cropping Seasons
Authors: Laloi G. , Montarry J. , Guibert M. , Andrivon D. , Michot D. , Le May C.
Published: May 2016

Ascochyta blight, caused by the necrotrophic ascomycete
Didymella pinodes
, is responsible for severe losses in winter and spring pea crops. Despite different climatic conditions, epidemics on winter and spring crops are due to a single population of
D. pinodes
, suggesting gene flow either between the two crops or from reservoir sources during the cropping season. This should lead to similar pathogenicity characteristics in isolates sampled from the two crops. However, these hypotheses have never been formally tested. We therefore sampled a total of 520
D. pinodes
strains throughout a growing season from winter and spring pea plots (WP and SP, respectively) and from winter and spring trap plants (TWP and TSP). Amplified fragment length polymorphism (AFLP) markers revealed high genetic diversity within subpopulations, whereas pathogenicity tests showed that mean aggressiveness increases over the course of an epidemic. These results support the idea that alloinoculum contributes to the carryover of epidemics between winter and spring crops and that the most aggressive isolates are selected as an epidemic progresses.

IMPORTANCE
Ascochyta blight, caused by
Didymella pinodes
, is responsible for severe losses in pea crops. While previous studies have shown that ascochyta blight epidemics on winter and spring crops are due to a single population of
D. pinodes
, suggesting that isolates from the two crops present similar pathogenicity characteristics, that hypothesis have never been tested. Genetic analysis of subpopulations sampled throughout a growing season from winter and spring pea plots revealed high genetic diversity within subpopulations, whereas pathogenicity tests showed that mean aggressiveness increases over the course of an epidemic.
A Highly Thermostable Kanamycin Resistance Marker Expands the Tool Kit for Genetic Manipulation of Caldicellulosiruptor bescii
Authors: Lipscomb Gina L. , Conway Jonathan M. , Blumer-Schuette Sara E. , Kelly Robert M. , Adams Michael W. W.
Published: May 2016

Caldicellulosiruptor bescii
, an anaerobic Gram-positive bacterium with an optimal growth temperature of 78°C, is the most thermophilic cellulose degrader known. It is of great biotechnological interest, as it efficiently deconstructs nonpretreated lignocellulosic plant biomass. Currently, its genetic manipulation relies on a mutant uracil auxotrophic background strain that contains a random deletion in the
pyrF
genome region. The
pyrF
gene serves as a genetic marker to select for uracil prototrophy, and it can also be counterselected for loss via resistance to the compound 5-fluoroorotic acid (5-FOA). To expand the
C. bescii
genetic tool kit, kanamycin resistance was developed as a selection for genetic manipulation. A codon-optimized version of the highly thermostable kanamycin resistance gene (named Cb
htk
) allowed the use of kanamycin selection to obtain transformants of either replicating or integrating vector constructs in
C. bescii
. These strains showed resistance to kanamycin at concentrations >50 μg · ml
−1
, whereas wild-type
C. bescii
was sensitive to kanamycin at 10 μg · ml
−1
. In addition, placement of the Cb
htk
marker between homologous recombination regions in an integrating vector allowed direct selection of a chromosomal mutation using both kanamycin and 5-FOA. Furthermore, the use of kanamycin selection enabled the targeted deletion of the
pyrE
gene in wild-type
C. bescii
, generating a uracil auxotrophic genetic background strain resistant to 5-FOA. The
pyrE
gene functioned as a counterselectable marker, like
pyrF
, and was used together with Cb
htk
in the Δ
pyrE
background strain to delete genes encoding lactate dehydrogenase and the CbeI restriction enzyme.

IMPORTANCE
Caldicellulosiruptor bescii
is a thermophilic anaerobic bacterium with an optimal growth temperature of 78°C, and it has the ability to efficiently deconstruct nonpretreated lignocellulosic plant biomass. It is, therefore, of biotechnological interest for genetic engineering applications geared toward biofuel production. The current genetic system used with
C. bescii
is based upon only a single selection strategy, and this uses the gene involved in a primary biosynthetic pathway. There are many advantages with an additional genetic selection using an antibiotic. This presents a challenge for thermophilic microorganisms, as only a limited number of antibiotics are stable above 50°C, and a thermostable version of the enzyme conferring antibiotic resistance must be obtained. In this work, we have developed a selection system for
C. bescii
using the antibiotic kanamycin and have shown that, in combination with the biosynthetic gene marker, it can be used to efficiently delete genes in this organism.
Evidence of Avian and Possum Fecal Contamination in Rainwater Tanks as Determined by Microbial Source Tracking Approaches
Authors: Ahmed W. , Hamilton K. A. , Gyawali P. , Toze S. , Haas C. N.
Published: May 2016

Avian and possum fecal droppings may negatively impact roof-harvested rainwater (RHRW) water quality due to the presence of zoonotic pathogens. This study was aimed at evaluating the performance characteristics of a possum feces-associated (PSM) marker by screening 210 fecal and wastewater samples from possums (
n
= 20) and a range of nonpossum hosts (
n
= 190) in Southeast Queensland, Australia. The host sensitivity and specificity of the PSM marker were 0.90 and 0.95 (maximum value, 1.00), respectively. The mean concentrations of the GFD marker in possum fecal DNA samples (8.8 × 10
7
gene copies per g of feces) were two orders of magnitude higher than those in the nonpossum fecal DNA samples (5.0 × 10
5
gene copies per g of feces). The host sensitivity, specificity, and concentrations of the avian feces-associated GFD marker were reported in our recent study (W. Ahmed, V. J. Harwood, K. Nguyen, S. Young, K. Hamilton, and S. Toze, Water Res 88:613–622, 2016,
http://dx.doi.org/10.1016/j.watres.2015.10.050
). The utility of the GFD and PSM markers was evaluated by testing a large number of tank water samples (
n
= 134) from the Brisbane and Currumbin areas. GFD and PSM markers were detected in 39 of 134 (29%) and 11 of 134 (8%) tank water samples, respectively. The GFD marker concentrations in PCR-positive samples ranged from 3.7 × 10
2
to 8.5 × 10
5
gene copies per liter, whereas the concentrations of the PSM marker ranged from 2.0 × 10
3
to 6.8 × 10
3
gene copies per liter of water. The results of this study suggest the presence of fecal contamination in tank water samples from avian and possum hosts. This study has established an association between the degradation of microbial tank water quality and avian and possum feces. Based on the results, we recommend disinfection of tank water, especially for tanks designated for potable use.

IMPORTANCE
The use of roof-harvested rainwater (RHRW) for domestic purposes is a globally accepted practice. The presence of pathogens in rainwater tanks has been reported by several studies, supporting the necessity for the management of potential health risks. The sources of fecal pollution in rainwater tanks are unknown. However, the application of microbial source tracking (MST) markers has the potential to identify the sources of fecal contamination in a rainwater tank. In this study, we provide evidence of avian and possum fecal contamination in tank water samples using molecular markers. This study established a potential link between the degradation of the microbial quality of tank water and avian and possum feces.
Different Cellular Origins and Functions of Extracellular Proteins from Escherichia coli O157:H7 and O104:H4 as Determined by Comparative Proteomic Analysis
Authors: Islam Nazrul , Nagy Attila , Garrett Wesley M. , Shelton Dan , Cooper Bret , Nou Xiangwu
Published: May 2016

Extracellular proteins play important roles in bacterial interactions with the environmental matrices. In this study, we examined the extracellular proteins from
Escherichia coli
O157:H7 and O104:H4 by tandem mass spectrometry. We identified 500 and 859 proteins from the growth media of
E. coli
O157:H7 and O104:H4, respectively, including 371 proteins common to both strains. Among proteins that were considered specific to
E. coli
O157:H7 or present at higher relative abundances in O157:H7 medium, most (57 of 65) had secretion signal sequences in their encoding genes. Noticeably, the proteins included locus of enterocyte effacement (LEE) virulence factors, proteins required for peptidyl-lipoprotein accumulation, and proteins involved in iron scavenging. In contrast, a much smaller proportion of proteins (37 of 150) that were considered specific to O104:H4 or presented at higher relative abundances in O104:H4 medium had signals targeting them for secretion. These proteins included Shiga toxin 2 subunit B and O104:H4 signature proteins, including AAF/1 major fimbrial subunit and serine protease autotransporters. Most of the abundant proteins from the growth medium of
E. coli
O104:H4 were annotated as having functions in the cytoplasm. We provide evidence that the extensive presence of cytoplasmic proteins in
E. coli
O104:H4 growth medium was due to biological processes independent of cell lysis, indicating alternative mechanisms for this potent pathogen releasing cytoplasmic contents into the growth milieu, which could play a role in interaction with the environmental matrices, such as pathogenesis and biofilm formation.

IMPORTANCE
In this study, we compared the extracellular proteins from two of the most prominent foodborne pathogenic
E. coli
organisms that have caused severe outbreaks in the United States and in Europe.
E. coli
O157:H7 is a well-studied Shiga toxigenic foodborne pathogen of the enterohemorrhagic pathotype that has caused numerous outbreaks associated with various contaminated foods worldwide.
E. coli
O104:H4 is a newly emerged Shiga toxigenic foodborne pathogen of the enteroaggregative pathotype that gained notoriety for causing one of the most deadly foodborne outbreaks in Europe in 2011. Comparison of proteins in the growth medium revealed significant differences in the compositions of the extracellular proteins for these two pathogens. These differences may provide valuable information regarding the cellular responses of these pathogens to their environment, including cell survival and pathogenesis.