bluuebunny/crossref_metadata_2025 huggingface dataset:
Incorporating natural variability in biological reference points and population dynamics into management of Atlantic salmon (Salmo salar L.) stocks returning to home waters
Authors: White Jonathan , Ó Maoiléidigh Niall , Gargan Paddy , de Eyto Elvira , Chaput Gerald , Roche Willie , McGinnity Phil , Crozier Walter W. , Boylan Paddy , Doherty Dennis , O'Higgins Kealan , Kennedy Brian , Lawler Ian , Lyons David , Marnell Ferdia
Published: March 2016

Following advice from the International Council for the Exploration of the Seas and North Atlantic Salmon Conservation Organization, Irish salmon stocks have been managed on a river-by-river basis since 2007 with biological reference points (BRPs) based on maximum sustainable yield (MSY). A method for estimating BRPs at the river scale and the associated variability arising from observed variability in population structures and fecundities is presented here. Calculations of BRPs (referred to as conservation limits, CLs) were updated and their natural variability was included. Angling logbooks provided new river-specific weight data to give sea age and fecundity ranges, and improved estimates of river-wetted areas, to account for available nursery habitat for juveniles and river-specific carrying capacities, were introduced. To transport BRPs, Bayesian stock–recruitment analysis was re-run with an updated list of monitored rivers and smolt ages. Results were converted to salmon numbers per river in Monte Carlo simulations incorporating the variability in sea ages and fecundities. Minimum sample size rules were implemented to reduce sampling error effects. Results showed that average total CL increased by 7%, average one sea-winter (1SW) CL decreased by 5% and average multi-sea-winter (MSW) CL increased by 157%. Differences were attributed to increases in wetted areas, MSW proportions, and changes in both 1SW and MSW fecundities. While some changes were large, we believe that these updated CLs provide more accurate estimates and with associated confidence limits they are more robust, river-specific, and readily incorporated into stock assessments. As a significant improvement on their predecessors, they represent a major development for the conservation and management of salmon stocks. Additionally, the approach described is portable across stocks and has the potential to be implemented in other jurisdictions to improve the management of Atlantic salmon. Finally, this method of incorporating variation has application for the development of BRPs and management of other species.
The Barents Sea euphausiids: methodological aspects of monitoring and estimation of abundance and biomass
Authors: Eriksen Elena , Skjoldal Hein Rune , Dolgov Andrey V. , Dalpadado Padmini , Orlova Emma L. , Prozorkevich Dmitry V.
Published: March 2016

Sampling of euphausiids is difficult because of their intermediate size between macrozooplankton and micronekton. The Barents Sea is one of the few marine areas where there have been long-term studies of euphausiids. We have examined three monitoring datasets on euphausiids and consider likely sources of errors associated with the sampling. Results indicated a high degree of patchiness in the distribution of euphausiids, even at the largest scale of sampling with a pelagic trawl. This indicates that euphausiids may occur in large, but infrequent, swarms that have a low probability of being sampled by small nets. The mean biomass of euphausiids sampled with MOCNESS was 2 g wet weight m−2 integrated over the water column, which is an underestimate due to avoidance of large individuals. The mean biomass obtained with pelagic trawl in the upper 60 m of water at night during an autumn survey was 10 g wet weight m−2. The plankton net on bottom trawl collected mean and median density of euphausiids (0.1–0.2 g wet weight m−3) near bottom during a winter survey similar to the values found with pelagic trawl in the upper layer during autumn. The mean density for the autumn survey showed an increase from 2000 to 2011, while the winter survey showed generally a decrease from 2000–2007 to 2011. The increase in the autumn series coincided with a general warming trend presumably with a larger influx of euphausiids with Atlantic water, notably of Meganyctiphanes norvegica. In contrast, the decline during winter may reflect a decrease, particularly of Thysanoessa raschii in the southeastern Barents Sea in the most recent years. Improvements in sampling gears combined with more and better use of acoustical and optical technologies offer great promise for improved monitoring and quantification of the roles of euphausiids in the Barents Sea ecosystem.
Data-driven health management: reasoning about personally generated data in diabetes with information technologies
Authors: Mamykina Lena , Levine Matthew E , Davidson Patricia G , Smaldone Arlene M , Elhadad Noemie , Albers David J
Published: March 2016

Objective To investigate how individuals with diabetes and diabetes educators reason about data collected through self-monitoring and to draw implications for the design of data-driven self-management technologies.

Materials and Methods Ten individuals with diabetes (six type 1 and four type 2) and 2 experienced diabetes educators were presented with a set of self-monitoring data captured by an individual with type 2 diabetes. The set included digital images of meals and their textual descriptions, and blood glucose (BG) readings captured before and after these meals. The participants were asked to review a set of meals and associated BG readings, explain differences in postprandial BG levels for these meals, and predict postprandial BG levels for the same individual for a different set of meals. Researchers compared conclusions and predictions reached by the participants with those arrived at by quantitative analysis of the collected data.

Results The participants used both macronutrient composition of meals, most notably the inclusion of carbohydrates, and names of dishes and ingredients to reason about changes in postprandial BG levels. Both individuals with diabetes and diabetes educators reported difficulties in generating predictions of postprandial BG; their predictions varied in their correlations with the actual captured readings from r = 0.008 to r = 0.75.

Conclusion Overall, the study showed that identifying trends in the data collected with self-monitoring is a complex process, and that conclusions reached by both individuals with diabetes and diabetes educators are not always reliable. This suggests the need for new ways to facilitate individuals’ reasoning with informatics interventions.
Sociocultural variation in attitudes toward use of genetic information and participation in genetic research by race in the United States: implications for precision medicine
Authors: Dye Timothy , Li Dongmei , Demment Margaret , Groth Susan , Fernandez Diana , Dozier Ann , Chang Jack
Published: March 2016

Background “Precision medicine” (PM) requires researchers to identify actionable genetic risks and for clinicians to interpret genetic testing results to patients. Whether PM will equally benefit all populations or exacerbate existing disparities is uncertain.

Methods We ascertained attitudes toward genetic testing and genetic research by race in the United States using the online Amazon mTurk US workforce (n = 403 White; n = 56 African American (AA)). Generalized linear models were used to test differences in beliefs and preferences by race, adjusting for sociodemographics and prior genetic experience.

Results AA were less likely than White to believe that genetic tests should be promoted or made available. Further, AA were less likely to want genetic testing results or to participate in genetic research.

Conclusions Important dimensions that underlay PM are not universally accepted by all populations. Without clear attention to concerns, AA communities may not equally benefit from the rapidly-emerging trend in PM-centered research and clinical practice.
Two-fraction high-dose-rate brachytherapy within a single day combined with external beam radiotherapy for prostate cancer: single institution experience and outcomes
Authors: Liu Junyang , Kaidu Motoki , Sasamoto Ryuta , Ayukawa Fumio , Yamana Nobuko , Sato Hiraku , Tanaka Kensuke , Kawaguchi Gen , Ohta Atsushi , Maruyama Katsuya , Abe Eisuke , Kasahara Takashi , Nishiyama Tsutomu , Tomita Yoshihiko , Aoyama Hidefumi
Published: March 2016

We investigated the outcomes of treatment for patients with localized prostate cancer (PCa) treated with 3D conformal radiation therapy (3D-CRT) followed by two-fraction high-dose-rate brachytherapy within a single day (2-fr.-HDR-BT/day) at a single institution. A total of 156 consecutive Asian males (median age, 67 years) were enrolled. To compare our findings with those of other studies, we analyzed our results using the D'Amico classification, assigning the patients to low- ( n = 5; 3.2%), intermediate- ( n = 36; 23.1%) and high-risk ( n = 115; 73.7%) groups (Stage T3 PCa patients were classified as high-risk). One patient in the D'Amico low-risk group (20%), 13 intermediate-risk patients (36.1%) and 99 high-risk patients (86.1%) underwent androgen deprivation therapy. We administered a prescription dose of 39 Gy in 13 fractions of 3D-CRT combined with 18 Gy of HDR-BT in two 9-Gy fractions delivered within a single day. We did not distinguish between risk groups in determining the prescription dose. The median follow-up period was 38 months. Of the 156 patients, one died from primary disease and five died from other diseases. The 3-year overall survival (OS) rates were 100%, 100% and 93.7%, and the 3-year ‘biochemical no evidence of disease (bNED)’ rates were 100%, 100% and 96.9% for the D'Amico low-, intermediate- and high-risk groups, respectively. No patient developed ≥ Grade 3 early toxicity. The Grade 3 late genitourinary toxicity rate was 2.6%, and no ≥ Grade 3 late gastrointestinal toxicity occurred. The efficacy and safety of this study were satisfactory, and longer-term follow-up is necessary.
Characteristics of interventional cardiologists and their work practices for the study on radiation-induced lens opacities based on the methodology developed by ELDO—preliminary results
Authors: Domienik Joanna , Gryglak Szymon , Jurewicz Joanna
Published: March 2016

Preliminary results of the Polish epidemiology study on eye lens opacities among interventional cardiologists (ICs), based on the methodology proposed by ELDO (epidemiological studies of radio-induced cataracts in interventional cardiologists and radiologists: methodology implementation), are presented. The aim of the study is to test the hypothesis concerning the excess risk of cataract in the group of ICs. The first results concern the study population characteristics, including the most important confounding factors for cataract, as well as a detailed description of the work practices in interventional cardiology needed in order to reconstruct the cumulative eye lens dose. The data from 69 ICs and 23 controls collected based on the general medical questionnaire and the occupational questionnaire (for ICs only) were analyzed. The mean age of ICs and of the control group was 41 and 44, respectively, while the mean duration of work for exposed physicians was 9 years. The analysis of the data from the occupational questionnaire concerning the procedures performed, the use of various access routes, as well as radiation protection tools (eye lens glasses, ceiling suspended transparent shield, etc.) are also presented. On the basis of this information and additional assumptions about the doses per procedure (as well as reduction factors for various types of radiation measures), the cumulative doses to the eye lens of ICs were evaluated. They ranged up to 1.55 Sv and 0.4 Sv for left and right eye, respectively; however, the dose to only 3% of ICs exceeded the new threshold for development of eye lens opacities (0.5 Gy) proposed by the ICRP.
Effects of stand characteristics on tree species richness in and around a conservation area of northeast Bangladesh
Authors: Pavel Muha Abdullah Al , Mukul Sharif A. , Uddin Mohammad Belal , Harada Kazuhiro , Arfin Khan Mohammed A. S.
Published: March 2016

We investigated the effect of tree cover, forest patch and disturbances on tree species richness in a highly diverse conservation area of northeast Bangladesh. A systematic sampling protocol was adopted and 80 sub-plots from twenty five 1 ha plots were used for the vegetation survey. Linear regression analysis was performed to understand the effect of patch area, disturbances and tree cover on tree species richness. Ordination using Redundancy analysis (RDA) and Non-metric Multi Dimensional Scaling (NMDS) were also performed to explore the tree species compositional similarities along the stand characteristics gradient and locations of the sample plots. Our study revealed that, forest patch size has greater influence on species richness. Areas with medium level of disturbances have shown greater species richness. In constrained ordination the selected explanatory variables regulated the richness of common species. Our findings can be useful for better forest management and restoration of landscapes of conservation needs using ecologically important species.
The Deceptively Simple N170 Reflects Network Information Processing Mechanisms Involving Visual Feature Coding and Transfer Across Hemispheres
Authors: Ince Robin A. A. , Jaworska Kasia , Gross Joachim , Panzeri Stefano , van Rijsbergen Nicola J. , Rousselet Guillaume A. , Schyns Philippe G.
Published: March 2016

A key to understanding visual cognition is to determinewhere,whenandhowbrain responses reflect the processing of the specific visual features that modulate categorization behavior—thewhat.The N170 is the earliest Event-Related Potential (ERP) that preferentially responds to faces. Here, we demonstrate that a paradigmatic shift is necessary to interpret the N170 as the product of an information processing network that dynamically codes and transfers face features across hemispheres, rather than as a local stimulus-driven event. Reverse-correlation methods coupled with information-theoretic analyses revealed that visibility of the eyes influences face detection behavior. The N170 initially reflects coding of the behaviorally relevant eye contralateral to the sensor, followed by a causal communication of the other eye from the other hemisphere. These findings demonstrate that the deceptively simple N170 ERP hides a complex network information processing mechanism involving initial coding and subsequent cross-hemispheric transfer of visual features.
Correlation/causation in ecology: towards mechanistic explanations for the Species-Area Relationship
Authors: Prestes Andersonn
Published: March 2016

There is a common intuition in biology that strict laws are very difficult to be found. Still, there are recurrent patterns in nature, suggesting broad generalizations and understanding of phenomena. The problem is that many generalizations in biology, especially in the form of correlations, might be decoupled from causality, weakening their power of explanation. Here, I bring an example on the Species-Area Relationship (SAR). The SAR is a well-known generalization in biology. The recurrent pattern states a positive relationship between area size and species richness. Understanding the mechanisms why there is a correlation between area and diversity remains a major challenge. I suggest an explicitly focus on mechanistic explanations for the SAR. I propose to use the integration, comparison and interpretation of other (associated or secondary) natural patterns in the searching for causal explanations. Areaper semight not account for causality in species diversification or absolute species richness in larger regions. Biotic and abiotic factors of a given area might be studied in order to discover the causal underpinnings of the SAR.
Contour junctions underlie neural representations of scene categories in high-level human visual cortex
Authors: Choo Heeyoung , Walther Dirk. B.
Published: March 2016

Humans efficiently grasp complex visual environments, making highly consistent judgments of entry-level category despite their high variability in visual appearance. How does the human brain arrive at the invariant neural representations underlying categorization of real-world environments? We here show that the neural representation of visual environments in scenes-selective human visual cortex relies on statistics of contour junctions, which provide cues for the three-dimensional arrangement of surfaces in a scene. We manipulated line drawings of real-world environments such that statistics of contour orientations or junctions were disrupted. Manipulated and intact line drawings were presented to participants in an fMRI experiment. Scene categories were decoded from neural activity patterns in the parahippocampal place area (PPA), the occipital place area (OPA) and other visual brain regions. Disruption of junctions but not orientations led to a drastic decrease in decoding accuracy in the PPA and OPA, indicating the reliance of these areas on intact junction statistics. Accuracy of decoding from early visual cortex, on the other hand, was unaffected by either image manipulation. We further show that the correlation of error patterns between decoding from the scene-selective brain areas and behavioral experiments is contingent on intact contour junctions. Finally, a searchlight analysis exposes the reliance of visually active brain regions on different sets of contour properties. Statistics of contour length and curvature dominate neural representations of scene categories in early visual areas and contour junctions in high-level scene-selective brain regions.
mixMC: a multivariate statistical framework to gain insight into Microbial Communities
Authors: Lê Cao Kim-Anh , Costello Mary-Ellen , Lakis Vanessa Anne , Bartolo François , Chua Xin-Yi , Brazeilles Rémi , Rondeau Pascale
Published: March 2016

Culture independent techniques, such as shotgun metagenomics and 16S rRNA amplicon sequencing have dramatically changed the way we can examine microbial communities. Recently, changes in microbial community structure and dynamics have been associated with a growing list of human diseases. The identification and comparison of bacteria driving those changes requires the development of sound statistical tools, especially if microbial biomarkers are to be used in a clinical setting.

We presentmixMC, a novel multivariate data analysis framework for metagenomic biomarker discovery.mixMCaccounts for the compositional nature of 16S data and enables detection of subtle differences when high inter-subject variability is present due to microbial sampling performed repeatedly on the same subjects but in multiple habitats. Through data dimension reduction the multivariate methods provide insightful graphical visualisations to characterise each type of environment in a detailed manner.

We appliedmixMCto 16S microbiome studies focusing on multiple body sites in healthy individuals, compared our results with existing statistical tools and illustrated added value of using multivariate methodologies to fully characterise and compare microbial communities.
Silent screams and muffled cries
Authors: Walton Grant W
Published: March 2016

Purpose

– The purpose of this paper is to examine the key causes of and solutions to corruption in Papua New Guinea (PNG) and suggest ways for improving anti-corruption efforts.

Design/methodology/approach

– This paper comprises a desk-based review of academic literature, policy documents and media.

Findings

– Fighting corruption in PNG requires an understanding of and response to local political, historic, cultural and economic issues. In particular, anti-corruption actors need to pay attention to: first, the opportunities and threats associated with state politics; second, the structural conditions that cause citizens to support corruption; third, the role of non-state actors in causing corruption; and fourth, ensuring stronger legal responses to corruption that result in prosecutions.

Originality/value

– This paper highlights key issues which anti-corruption organisations in PNG should address, examines state and non-state causes of corruption, and provides an updated analysis of key drives and solutions to corruption in PNG.
Combatting corruption in Brunei Darussalam
Authors: Jones David Seth
Published: March 2016

Purpose

– The purpose of this paper is to examine the government of Brunei’s anti-corruption programme.

Design/methodology/approach

– A range of sources are used including online materials from Brunei government websites, reports of international organisations, press articles, conference papers, a thesis case study, journal articles, a book, chapters in books, and interviews with an officer working with the Anti-Corruption Bureau (ACB) of Brunei.

Findings

– The paper considers the factors that contribute to government corruption, and the measures to combat it. These include various laws to combat corruption and the work of the ACB in enforcing these laws and in undertaking major initiatives of prevention and education. The effectiveness of these measures are assessed and a number of recommendations are made of direct and indirect measures improve the programme to combat corruption. The paper points to the moderately favourable rankings and ratings that Brunei has earned in combating corruption, which is well above neighbouring countries where corruption is still widespread, but noticeably below the rankings and ratings of the least corrupt countries. However, it argues that further progress to combat corruption may be difficult, as a result of the lack accountability and limited transparency, which are essential features of Brunei’s system of government based on absolute monarchy. Also hindering further progress is the inbuilt protection of the privileges of the Malay community within the country, which protects their role in the civil service and the business sector.

Originality/value

– The paper is the first scholarly examination of the anti-corruption programme in Brunei.
Explaining market shares of organic food: evidence from Swiss household data
Authors: Götze Franziska , Mann Stefan , Ferjani Ali , Kohler Andreas , Heckelei Thomas
Published: March 2016

Purpose

– The purpose of this paper is to identify those product characteristics that are of importance to consumers of organic food in Switzerland.

Design/methodology/approach

– In order to identify important organic product characteristics, this study applies a Generalized Linear Model using a six-year sample of Swiss household data distinguishing between organic and conventional products at the product level.

Findings

– The analysis reveals three product-related dimensions of importance. First, Swiss consumers prefer unprocessed organic products over highly processed ones suggesting that communicating potential benefits of organic food is more promising for unprocessed products. Second, organic consumers are reluctant to buy products with high price premiums. Third, Swiss consumers prefer domestically produced organic products over imported ones.

Practical implications

– The results imply that supporting organic agriculture in Switzerland is still promising from a policy and a marketing perspective as long as the organic price premium is not too high.

Originality/value

– This paper presents results regarding the determinants of the organic market share in Switzerland. They give a first understanding of which product characteristics determine organic market shares. From a policy as well as from a marketing perspective a further investigation at the household level is promising in order to understand and respond to the needs and expectations of Swiss consumers.
Strategies for leading IT-enabled change: lessons from a global transformation case
Authors: Iveroth Einar
Published: March 2016

Purpose

– The aim of this article is to provide strategic insights of how multinational organizations lead IT-enabled change on a global scale. The article summarizes the findings from a three-year case study of the international telecom company Ericsson. This company managed to successfully transform their finance and accounting (F
&
A) unit from a highly decentralized structure into a so-called shared service center (SSC) structure and the whole change was enabled by enterprise resource planning (ERP) system.

Design/methodology/approach

– The case study data consists of in-depth interviews, archival data, and observations collected during three years.

Findings

– The article provides rich description of how the transformation was executed together with three key strategic lessons.

Originality/value

– The article offers unique and novel insights of how strategist drives IT-enabled change on a global scale.
Trends in the identification of children with learning disabilities within state schools in England
Authors: Hatton Chris , Emerson Eric
Published: March 2016

Purpose

– The purpose of this paper is to present data drawn from the Department for Education (DfE)concerning trends in the number of children identified as having a learning disability within state schools in England.

Design/methodology/approach

– Data based on the school census conducted by the DfE was examined annually for 2009/2010 to 2014/2015, to determine the number of children identified as having moderate learning difficulty (MLD), severe learning difficulty (SLD) or profound multiple learning difficulty (PMLD) within state schools in England, at two levels: having a Statement of Educational Needs/Education Health Care Plan, or at School Action Plus.

Findings

– The number of children identified as MLD reduced substantially over time, for both statemented children and children identified at the School Action Plus level. In contrast, the smaller number of statemented children with SLD or PMLD increased over time, in line with increasing school rolls and epidemiological trends.

Research limitations/implications

– Further work is needed to understand the sharp reduction in the number of children being identified as having MLD within schools, and the educational support being offered to this group of children. Better information is also needed on children with learning disabilities not being educated in the state school sector.

Originality/value

– This paper highlights important trends in the identification of children with learning disabilities in state schools in England, with consequences for how large groups of children are being supported.
Can active support improve job satisfaction?
Authors: Rhodes Jennifer A , Toogood Sandy
Published: March 2016

Purpose

– Active support (AS) influences the way staff support people with intellectual disabilities to take part in everyday activities. Changes in work practices may affect job satisfaction. The impact of AS on job satisfaction has not, however, been widely studied. Job satisfaction is linked with levels of staff turnover and the overall quality of services provided to people with intellectual disabilities (Coomber
&
Barriball, 2007; Hatton et al., 2001). The purpose of this paper is to describe an evaluation of job satisfaction amongst 38 direct care staff working in intellectual disability services before and after AS was implemented.

Design/methodology/approach

– A single group, repeated-measures design was used. In total, 38 members of direct care staff received AS training. Data on job satisfaction were collected before, and after, AS was implemented. In total, 19 members of staff took part in a follow-up 12 weeks later.

Findings

– There was a significant increase in reported job satisfaction following the implementation of AS. Subscale analysis revealed that the most significant increases in job satisfaction were related to areas directly targeted by AS, including satisfaction with skill level and satisfaction with amount of time spent with service users.

Originality/value

– Implementing AS may provide an added benefit for direct care staff, who feel more satisfied at work. While a significant number of papers have been published focusing on the benefits of AS, no papers have specifically looked at the impact that the intervention can have on job satisfaction.
Ethical Decision Making in International Business: A Study of Challenge in Teaching to Future Global Talents
Authors: Kim Rebecca Chunghee
Published: March 2016

The importance of ethical decision-making in international business has never been more apparent than in recent years. However, discussion concerning its teaching to future global talents who will be at this stage soon is scant and under-developed. Adapting Rest’s (1986) four-component model, the study attempts to sketch a broad outline of ethical decision-making by university students when they face an ethical dilemma. The imaginary story, which the author intentionally designs to analyze ethical decision-making through covering real-world ethical issues in an international market, is used as the main methodological tool. Participants acknowledge ‘ideal’ ethical decisions according to their own discretion, but their ‘actual’ decision is different due to the intention (motivation) of individuals as to whether they make ethical decisions. This study demonstrates significant gaps in teaching business ethics and suggests a shift of the teaching focus from enlightenment of moral awareness/judgment to stimulating and motivating to initiate ethical decisions and actions.
Experimental Analysis of Sudden Pressure Increase Phenomenon by Real-Time Internal Observation of Diesel Particulate Filter
Authors: Fukui Rui , Okamoto Yuki , Nakao Masayuki
Published: March 2016

As a way of reducing the amount of particulate matter (PM) contained in the exhaust gas, diesel particulate filter (DPF) is widely used. To keep the condition of DPF normal and effective, estimation of the amount of PM deposits in the DPF is important. The estimation is mainly conducted based on the value of pressure drop across the DPF. Occasionally, the value of the pressure drop rises suddenly and it leads to overestimation of the amount of PM deposits. In order to elucidate the cause of the sudden pressure drop increase phenomenon, this paper first reveals the engine operating conditions which invoke this phenomenon. The authors also have developed a visualization method to realize the wide-perspective internal observation of the DPF. The observation experiment has been conducted with a commercial engine and DPF under the revealed conditions. Experimental results make clear that the phenomenon is caused by PM deposit layer collapse and channel plugging.
Field emission properties of p-type black silicon on pillar structures
Authors: Langer Christoph , Prommesberger Christian , Ławrowski Robert , Schreiner Rupert , Serbun Pavel , Müller Günter , Düsberg Felix , Hofmann Martin , Bachmann Michael , Pahlke Andreas
Published: March 2016

Arrays of black silicon field emission pillar structures were fabricated on p-type silicon substrates. Two types of samples with the same number of pillars (arrays of 10 × 10) but different pillar heights (8 and 20 μm) were prepared as well as a black silicon reference sample without pillars. The field emission properties of these cathodes were investigated both by means of integral current-voltage measurements and by field emission scanning microscopy. Samples with a pillar height of 20 μm revealed onset fields as low as 6.4 V/μm, field enhancement factors up to 800, and emission currents up to 8 μA at an applied field of 20 V/μm. Due to the p-type material, a saturation of the emission current for fields above 11 V/μm was observed. This saturation leads to a stable operation with a current fluctuation of less than ±8%. It was found that samples with a pillar height of 20 μm showed improved emission characteristics compared to samples with a pillar height of 8 μm or without pillars. The voltage maps revealed an increased emission homogeneity after a “burn-in” sequence of the sample. The current map showed that a few of the pillars dominate the emission. Integral current stability measurements were performed under different vacuum pressures, in order to investigate altered emission behavior and a potential degradation of the emitters. At pressures above 10−6 mbar, the sample starts to degrade irreversibly. Nevertheless, even after a harsh treatment over 30 min at 5 × 10−5 mbar and at an applied field of 23 V/μm, the cathode was still operating, and did not fail during further operation over 20 h at 5 × 10−8 mbar and at an applied field of 28 V/μm.
Beam profile measurement of volcano-structured double-gate Spindt-type field emitter arrays
Authors: Nagao Masayoshi , Gotoh Yasuhito , Neo Yoichiro , Mimura Hidenori
Published: March 2016

Double-gated Spindt-type field emitter arrays with volcano structures were fabricated using a double-layered photoresist as a lift-off layer for image sensor application. The gate aperture height and emitter tip angle were varied to optimize the device structure, wherein the gate aperture height was changed by controlling the etch-back time during the gate opening process and the emitter tip angle was changed by selecting the emitter material. The Ni emitter had a narrow tip angle while the Mo emitter had wider tip angle. For the formation of the Mo emitter, a thick Ni buffer layer was necessary to prevent delamination. Electron beam focusing characteristics were evaluated using the scanning slit method, and it was found that both a higher gate aperture and a wider tip angle facilitated better beam focusing. A wider tip angle, however, increased the operating voltage of the field emitter arrays. Additionally, a higher gate aperture did not affect the operational voltage. Therefore, a narrow tip angle with a higher gate aperture produced the best result among our tested samples.
Sound field reconstruction using a spherical microphone array
Authors: Fernandez-Grande Efren
Published: March 2016

A method is presented that makes it possible to reconstruct an arbitrary sound field based on measurements with a spherical microphone array. The proposed method (spherical equivalent source method) makes use of a point source expansion to describe the sound field on the rigid spherical array, from which it is possible to reconstruct the sound field over a three-dimensional domain, inferring all acoustic quantities: sound pressure, particle velocity, and sound intensity. The problem is formulated using a Neumann Green's function that accounts for the presence of the rigid sphere in the medium. One can reconstruct the total sound field, or only the incident part, i.e., the scattering introduced by the sphere can be removed, making the array virtually transparent. The method makes it possible to use sequential measurements: different measurement positions can be combined, providing an extended measurement area consisting of an array of spheres, and the sound field at any point of the source-free domain can be estimated, not being restricted to spherical surfaces. Because it is formulated as an elementary wave model, it allows for diverse solution strategies (least squares, ℓ1-norm minimization, etc.), revealing an interesting perspective for further work.
A Bacterial Glycoengineered Antigen for Improved Serodiagnosis of Porcine Brucellosis
Authors: Cortina María E. , Balzano Rodrigo E. , Rey Serantes Diego A. , Caillava Ana J. , Elena Sebastián , Ferreira A. C. , Nicola Ana M. , Ugalde Juan E. , Comerci Diego J. , Ciocchini Andrés E.
Published: March 2016

Brucellosis is a highly zoonotic disease that affects animals and human beings.
Brucella suis
is the etiological agent of porcine brucellosis and one of the major human brucellosis pathogens. Laboratory diagnosis of porcine brucellosis mainly relies on serological tests, and it has been widely demonstrated that serological assays based on the detection of anti O-polysaccharide antibodies are the most sensitive tests. Here, we validate a recombinant glycoprotein antigen, an
N
-formylperosamine O-polysaccharide–protein conjugate (OAg-AcrA), for diagnosis of porcine brucellosis. An indirect immunoassay based on the detection of anti-O-polysaccharide IgG antibodies was developed coupling OAg-AcrA to enzyme-linked immunosorbent assay plates (glyco-iELISA). To validate the assay, 563 serum samples obtained from experimentally infected and immunized pigs, as well as animals naturally infected with
B. suis
biovar 1 or 2, were tested. A receiver operating characteristic (ROC) analysis was performed, and based on this analysis, the optimum cutoff value was 0.56 (relative reactivity), which resulted in a diagnostic sensitivity and specificity of 100% and 99.7%, respectively. A cutoff value of 0.78 resulted in a test sensitivity of 98.4% and a test specificity of 100%. Overall, our results demonstrate that the glyco-iELISA is highly accurate for diagnosis of porcine brucellosis, improving the diagnostic performance of current serological tests. The recombinant glycoprotein OAg-AcrA can be produced in large homogeneous batches in a standardized way, making it an ideal candidate for further validation as a universal antigen for diagnosis of “smooth” brucellosis in animals and humans.
A Universal Culture Medium for Screening Polymyxin-Resistant Gram-Negative Isolates
Authors: Nordmann Patrice , Jayol Aurélie , Poirel Laurent
Published: March 2016

The colistin-containing SuperPolymyxin medium was developed for screening polymyxin-resistant Gram-negative bacteria. It was evaluated with 88 polymyxin-susceptible or polymyxin-resistant cultured Gram-negative isolates. Its sensitivity and specificity of detection were ca. 100%. The SuperPolymyxin medium is the first screening medium that is able to detect intrinsic and acquired polymyxin-resistant bacteria.
Laboratory Diagnosis of Mycobacterium tuberculosis Infection and Disease in Children
Authors: Dunn James J. , Starke Jeffrey R. , Revell Paula A.
Published: March 2016

Diagnosis of tuberculosis in children is challenging; even with advanced technologies, the diagnosis is often difficult to confirm microbiologically in part due to the paucibacillary nature of the disease. Clinical diagnosis lacks standardization, and traditional and molecular microbiologic methods lack sensitivity, particularly in children. Immunodiagnostic tests may improve sensitivity, but these tests cannot distinguish tuberculosis disease from latent infection and some lack specificity. While molecular tools like Xpert MTB/RIF have advanced our ability to detect
Mycobacterium tuberculosis
and to determine antimicrobial resistance, decades old technologies remain the standard in most locales. Today, the battle against this ancient disease still poses one of the primary diagnostic challenges in pediatric laboratory medicine.
Evaluation of Molecular Methods for Serotyping Shigella flexneri
Authors: Gentle Amy , Ashton Philip M. , Dallman Timothy J. , Jenkins Claire
Published: March 2016

Shigella flexneri
can be phenotypically serotyped using antisera raised to type-specific somatic antigens and group factor antigens and genotypically serotyped using PCR targeting O-antigen synthesis or modification genes. The aim of this study was to evaluate a real-time PCR for serotyping
S. flexneri
and to use whole-genome sequencing (WGS) to investigate the phenotypic and genotypic serotype identifications. Of the 244 cultures tested retrospectively, 226 (92.6%) had concordant results between phenotypic serotyping and PCR. Seventy of the 244 isolates (including 15 of the 18 isolates where a serotype-PCR mismatch was identified) were whole-genome sequenced, and the serotype was derived from the genome. Discrepant results between the phenotypic and genotypic tests were attributed to insertions/deletions or point mutations identified in O-antigen synthesis or modification genes, rendering them dysfunctional; inconclusive serotyping results due to nonspecific cross-reactions; or novel genotypes. Phylogenetic analysis of the WGS data indicated that the serotype, regardless of whether it was phenotypically or genotypically determined, was a weak predictor of phylogenetic relationships between strains of
S. flexneri
. WGS data provided both genome-derived serotyping, thus supporting backward compatibility with historical data and facilitating data exchange in the community, and more robust and discriminatory typing at the single-nucleotide-polymorphism level.
Symbiosis in the Soil: Citizen Microbiology in Middle and High School Classrooms
Authors: McKenney Erin , Flythe Taylar , Millis Courtney , Stalls Jennifer , Urban Julie M. , Dunn Robert R. , Stevens Julia L.
Published: March 2016

Microorganisms are vital to environmental health, yet their association with disease often overshadows these benefits. Building citizen-science activities around the positive role of microorganisms and an understanding of their ubiquity can begin to dispel misconceptions while simultaneously engaging the public in research. Here, we describe a citizen-science microbiology project geared toward implementation in middle and high school classrooms. Students culture environmental microorganisms and document microbial diversity of plant root systems compared with adjacent bulk soil. Results contribute data toward research on microbiome recruitment of weeds and other successful plants while addressing core topics in science education.
Building Research Integrity and Capacity (BRIC): An Educational Initiative to Increase Research Literacy among Community Health Workers and Promotores
Authors: Nebeker Camille , López-Arenas Araceli
Published: March 2016

While citizen science is gaining attention of late, for those of us involved in community-based public health research, community/citizen involvement in research has steadily increased over the past 50 years. Community Health Workers (CHWs), also known as Promotores de Salud in the Latino community, are critical to reaching underserved populations, where health disparities are more prevalent. CHWs/Promotores provide health education and services and may also assist with the development and implementation of community- and clinic-based research studies. Recognizing that CHWs typically have no formal academic training in research design or methods, and considering that rigor in research is critical to obtaining meaningful results, we designed instruction to fill this gap. We call this educational initiative “Building Research Integrity and Capacity” or BRIC. The BRIC training consists of eight modules that can be administered as a self-paced training or incorporated into in-person, professional development geared to a specific health intervention study. While we initially designed this culturally-grounded, applied ethics training for Latino/Hispanic community research facilitators, BRIC training modules have been adapted for and tested with non-Latino novice research facilitators. This paper describes the BRIC core content and instructional design process.
The Tragedy of the Unexamined Cat: Why K–12 and University Education Are Still in the Dark Ages and How Citizen Science Allows for a Renaissance
Authors: Dunn Robert R. , Urban Julie , Cavelier Darlene , Cooper Caren B.
Published: March 2016

At the end of the dark ages, anatomy was taught as though everything that could be known was known. Scholars learned about what had been discovered rather than how to make discoveries. This was true even though the body (and the rest of biology) was very poorly understood. The renaissance eventually brought a revolution in how scholars (and graduate students) were trained and worked. This revolution never occurred in K–12 or university education such that we now teach young students in much the way that scholars were taught in the dark ages, we teach them what is already known rather than the process of knowing. Citizen science offers a way to change K–12 and university education and, in doing so, complete the renaissance. Here we offer an example of such an approach and call for change in the way students are taught science, change that is more possible than it has ever been and is, nonetheless, five hundred years delayed.
Student-Designed Service-Learning Projects in an Undergraduate Neurobiology Course
Authors: Northcutt Katharine V.
Published: March 2016

One of the challenges in teaching a service-learning course is obtaining student buy-in from all students in the course. To circumvent this problem, I have let students in my undergraduate Neurobiology course design their own service-learning projects at the beginning of the semester. Although this can be chaotic because it requires last-minute planning, I have made it successful through facilitating student communication in the classroom, requiring thorough project proposals, meeting with students regularly, and monitoring group progress through written reflection papers. Most of my students have strong opinions about the types of projects that they want to carry out, and many students have used connections that they have already made with local organizations. Almost all projects that students have designed to this point involve teaching basic concepts of neurobiology to children of various ages while simultaneously sparking their interest in science. Through taking ownership of the project and designing it such that it works well with their strengths, interests, and weekly schedule, students have become more engaged in service learning and view it as a valuable experience. Despite some class time being shifted away from more traditional assignments, students have performed equally well in the course, and they are more eager to talk with others about course concepts. Furthermore, the feedback that I have received from community partners has been excellent, and some students have maintained their work with the organizations.
Games that Enlist Collective Intelligence to Solve Complex Scientific Problems
Authors: Burnett Stephen , Furlong Michelle , Melvin Paul Guy , Singiser Richard
Published: March 2016

There is great value in employing the collective problem-solving power of large groups of people. Technological advances have allowed computer games to be utilized by a diverse population to solve problems. Science games are becoming more popular and cover various areas such as sequence alignments, DNA base-pairing, and protein and RNA folding. While these tools have been developed for the general population, they can also be used effectively in the classroom to teach students about various topics. Many games also employ a social component that entices students to continue playing and thereby to continue learning. The basic functions of game play and the potential of game play as a tool in the classroom are discussed in this article.
Microbes Should Be Central to Ecological Education and Outreach
Authors: Barberán Albert , Hammer Tobin J. , Madden Anne A. , Fierer Noah
Published: March 2016

Our planet is changing rapidly, and responding to the ensuing environmental challenges will require an informed citizenry that can understand the inherent complexity of ecological systems. However, microorganisms are usually neglected in the narratives that we use to understand nature. Here, we advocate for the inclusion of microbial ecology across education levels and delineate the often neglected benefits of incorporating microbes into ecology curricula. We provide examples across education levels, from secondary school (by considering one’s self as a microbial ecosystem), to higher education (by incorporating our knowledge of the global ecological role and medical application of microbes), to the general public (by engagement through citizen-science projects). The greater inclusion of microbes in ecological education and outreach will not only help us appreciate the natural world we are part of, but will ultimately aid in building a citizenry better prepared to make informed decisions on health and environmental policies.