bluuebunny/crossref_metadata_2025 huggingface dataset:
Carrion consumption and its importance in a freshwater trophic generalist: the invasive apple snail Pomacea canaliculata
Authors: Saveanu Lucía , Manara Enzo , Martín Pablo R.
Published: June 2016

Trophic flexibility is a relevant trait in the potential for organisms to establish widely, maintain high abundances and spread after invasion. Pomacea canaliculata is an apple snail that feeds primarily on aquatic macrophytes, although it also consumes other trophic resources that likely play an important role in its persistence and contribute to its effects in invaded wetlands. In the present study we determined the ingestion rates in P. canaliculata for carrion and subsequent effects on growth, and performed field and laboratory experiments to investigate the mechanism of carrion detection. We observed P. canaliculata snails of all sizes feeding on carrion. The specific ingestion rates of carrion decreased with snail size and were 20 times lower than when feeding on lettuce. The growth rates of snails feeding only on carrion were 15–30% higher than those of fasting snails and 30% of those snails feeding on lettuce or lettuce and carrion. We found no evidence of distant chemoreception of carrion. The importance of carrion for P. canaliculata is mostly as an alternative resource when its preferred food is absent, and not as a complementary resource that could enhance growth. Nevertheless, the ability of P. canaliculata to profit from carrion may help explain its potential to establish widely and to have effects on aquatic vegetation.
A comparison of temperature regimes in dry-season waterholes in the Flinders and Gilbert catchments in northern Australia
Authors: Wallace Jim , Waltham Nathan , Burrows Damien
Published: June 2016

Dry-season waterholes in ephemeral rivers provide vital habitat for aquatic biota, whose survival is dependent on the waterholes lasting throughout the dry season with temperatures that are not lethal. To examine this in the Flinders and Gilbert Rivers, 20-min temperature measurements were taken during the 2012–2013 dry season in 10 waterholes in each catchment. These data were used to derive thermal-frequency curves that quantify how often waterhole temperature exceeds thresholds for (1) the optimum growth of tropical fish and (2) their lethal temperature. Waterholes that remained deeper than ~0.5m throughout the dry season provided thermally suitable fish refugia, especially if they were turbid, because this decreased the risk of exposure to undesirable temperatures at the bottom of the waterhole. However, surface temperatures in these waterholes often exceeded optimal and even potentially lethal temperatures, so fish may have had to move to cooler water at the bottom of these waterholes. The risk to aquatic species in waterhole refugia is, therefore, primarily determined by depth, with shallow waterholes presenting the greatest risk because they become thermally unsuitable well before (1–2 months) they fully dry out.
A morphometric analysis of the Banksia spinulosa complex (Proteaceae) and its complex taxonomic implications
Authors: Stimpson Margaret L. , Weston Peter H. , Whalley Ralph (Wal) D. B. , Bruhl Jeremy J.
Published: June 2016

Specimens of all known taxa and putative entities belonging to the Banksia spinulosa complex were collected from Kuranda in northern Queensland, western to central Queensland and down the eastern coast of Australia to Wilsons Promontory in southern Victoria. These specimens were used to investigate morphological variation in habit, stems, leaves, inflorescences, fruits and seeds in the complex. Phenetic analysis (unweighted pair-group method with arithmetic mean, UPGMA, clustering and semi-strong hybrid multi-dimensional scaling, SSH–MDS, ordination) was performed on the full dataset of 233 entities using 33 characters (18 quantitative, two binary and 13 multistate). To facilitate visualisation of patterns in both clustering and ordination, we also analysed subgroups based on the results of the phenogram from the full dataset. The results showed that the five known and described taxa are phenetically distinct, viz. B. collina sens. str., B. cunninghamii sens. str., B. neoanglica, B. spinulosa and B. vincentia, and provided support for a further 12 morphometrically diagnosable entities, four of which could not be diagnosed with simple combinations of character states and require further investigation. The present study has highlighted that there is much more hidden morphological diversity in the B. spinulosa complex than has previously been recognised in any of the current competing taxonomies.
Dynamic X-ray diffraction observation of shocked solid iron up to 170 GPa
Authors: Denoeud Adrien , Ozaki Norimasa , Benuzzi-Mounaix Alessandra , Uranishi Hiroyuki , Kondo Yoshihiko , Kodama Ryosuke , Brambrink Erik , Ravasio Alessandra , Bocoum Maimouna , Boudenne Jean-Michel , Harmand Marion , Guyot François , Mazevet Stephane , Riley David , Makita Mikako , Sano Takayoshi , Sakawa Youichi , Inubushi Yuichi , Gregori Gianluca , Koenig Michel , Morard Guillaume
Published: June 2016

Significance

Iron is the main constituent of the core of rocky planets; therefore, understanding its phase diagram under extreme conditions is fundamental to model the planets’ evolution. Using dynamic compression by laser-driven shocks, pressure and temperature conditions close to what is found in these cores can be reached. However, it remains unclear whether phase boundaries determined at nanosecond timescales agree with static compression. Here we observed the presence of solid hexagonal close-packed iron at 170 GPa and 4,150 K, in a part of the iron phase diagram, where either a different solid structure or liquid iron has been proposed. This X-ray diffraction experiment confirms that laser compression is suitable for studying iron at conditions of deep planetary interiors difficult to achieve with static compression techniques.
Structural model of the dimeric Parkinson’s protein LRRK2 reveals a compact architecture involving distant interdomain contacts
Authors: Guaitoli Giambattista , Raimondi Francesco , Gilsbach Bernd K. , Gómez-Llorente Yacob , Deyaert Egon , Renzi Fabiana , Li Xianting , Schaffner Adam , Jagtap Pravin Kumar Ankush , Boldt Karsten , von Zweydorf Felix , Gotthardt Katja , Lorimer Donald D. , Yue Zhenyu , Burgin Alex , Janjic Nebojsa , Sattler Michael , Versées Wim , Ueffing Marius , Ubarretxena-Belandia Iban , Kortholt Arjan , Gloeckner Christian Johannes
Published: June 2016

Significance

Leucine-rich repeat kinase 2 (LRRK2) represents a promising drug target for treatment and prevention of Parkinson’s disease (PD), because mutations in LRRK2 are the most common cause of Mendelian forms of the disease. PD-associated LRRK2 variants show decreased GTPase and increased kinase activity. By integrating multiple experimental inputs provided by chemical cross-linking, small-angle X-ray scattering, and a negative-stain EM map, we present, to our knowledge, the first structural model of the full-length LRRK2 dimer. The model reveals a compact folding of the LRRK2 dimer with multiple domain–domain interactions that might be involved in the regulation of LRRK2 enzymatic properties.
Borrowed alleles and convergence in serpentine adaptation
Authors: Arnold Brian J. , Lahner Brett , DaCosta Jeffrey M. , Weisman Caroline M. , Hollister Jesse D. , Salt David E. , Bomblies Kirsten , Yant Levi
Published: June 2016

Significance

Serpentine barrens are enormously hostile to plant life. Understanding how plants survive such a perfect storm of low mineral nutrient, drought prone, and toxic metal rich conditions offers a powerful model of adaptation and may help design resilient crops. Advances in genomics enable population-wide views of selection and deep insight into demographic histories. These approaches are agnostic to phenotype and can indicate which traits were most important in complex adaptations and, at the same time, provide novel candidate genes. Here, we identified candidate genes for serpentine adaptation and provide evidence that some selected alleles were borrowed from a related species, whereas others were independently involved in separate adaptation events in different species.
Mapping out spin and particle conductances in a quantum point contact
Authors: Krinner Sebastian , Lebrat Martin , Husmann Dominik , Grenier Charles , Brantut Jean-Philippe , Esslinger Tilman
Published: June 2016

Significance

Predicting the transport properties of interacting particles in the quantum regime is challenging. A conceptually simple situation is realized by connecting two reservoirs through a quantum point contact. For noninteracting fermions, the conductance is quantized in units of the inverse of Planck’s constant, reflecting the contribution to transport of an individual quantum state. We use a cold atomic Fermi gas to map out the spin and particle conductance in a quantum point contact for increasing attractive interactions and observe remarkable effects of interactions on both spin and particle transport. Our work provides maps of conductance over a wide range of parameters and in the presence of many-body correlations, yielding new insights into the nature of strongly attractive Fermi gases.
Properties of Mg laser alloyed with Al or AlSi20
Authors: Mola Renata , Dziadoń Andrzej , Jagielska-Wiaderek Karina
Published: June 2016

The alloyed surface layers were produced using thin Al or AlSi20 plates, which were first diffusion bonded and then melted into the Mg substrate. The microscopic analysis showed that alloying with Al led to the formation of an Al-enriched surface layer containing a high volume fraction of an Mg17Al12 phase. Applying AlSi20, on the other hand, resulted in the formation of an Al/Si-enriched layer containing Mg2Si, Mg2Al3 and Mg17Al12 phases. The experimental results indicate that surface alloying of Mg with Al or AlSi20 using the presented method improved the properties of the material. The microhardness of the Al- and Al/Si-enriched layers was much higher than that of the substrate. Higher wear resistance was observed for the Al/Si-enriched layer. The alloyed layers provided a certain level of protection of Mg against corrosion. The specimens alloyed with Al showed better anticorrosive properties than those alloyed with AlSi20.
Microstructural and abrasion wear characteristics of laser-clad tool steel coatings
Authors: Tuominen J. , Näkki J. , Pajukoski H. , Hyvärinen L. , Vuoristo P.
Published: June 2016

Several different tool steel grades were deposited on mild steel by the laser-cladding process with coaxial powder feeding. With bidirectional scanning pattern, most of the grades were deposited crack-free with hardness up to 1000 HV without additional preheating. In a 3-body abrasion wear study, the laser clad Ralloy® WR6 with significant portion of retained austenite exhibited superior abrasive wear resistance compared with the predominantly martensitic tool steel coatings (M2, M4, H13, HS-23, HS-30) and the reference material, Raex® Ar500 wear resistant steel. The abrasion wear resistance of austenitic–martensitic WR6 tool steel was further enhanced by the external addition of 20% volume percentage of relatively large (45–106 µm) vanadium carbides. In single point scratch tests, predominantly martensitic tool steels outperformed austenitic–martensitic tool steels and wear resistant steel. The differences in wear performances were explained by different wear mechanisms and types of contact between the abrasive and the surface.
Final Report. Supplementary comparison of 50/60 Hz energy SIM.EM-S7
Authors: Carranza R , Campos S , Castruita A , Nelson T , Ribeiro A M , So E , Spaggiari A , Slomovitz D , Izquierdo D , Postigo H , Díaz H , Sanchez H , Gonzalez J , Ramos R , Zipaquira A
Published: June 2016

From 2010 to 2012, a key comparison of energy standards at 50/60 Hz was conducted in the SIM region.

The comparison included measurements of active and reactive energy at three frequencies, aiming at providing support to high accuracy measurement needs of reactive energy. This work presents the results of the SIM.EM-S7 supplementary comparison.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCEM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Report on key comparison COOMET.AUV.A-K5: pressure calibration of laboratory standard microphones in the frequency range 2 Hz to 10 kHz
Authors: Dobrowolska D , Kosterov A
Published: June 2016

This is the final report for regional key comparison COOMET.AUV.A-K5 on the pressure calibration of laboratory standard microphones in the frequency range from 2 Hz to 10 kHz. Two laboratories—Central Office of Measures (GUM)—the national metrology institute for Poland and the State Enterprise Scientific-Research Institute for Metrology of Measurement and Control Systems (DP NDI Systema)— the designated institute for acoustics in Ukraine took part in this comparison with the GUM as a pilot. One travelling type LS1P microphone was circulated to the participants and results in the form of regular calibration certificates were collected. The results of the DP NDI Systema obtained in this comparison were linked to the CCAUV.A-K5 key comparison through the joint participation of the GUM. The degrees of equivalence were computed for DP NDI Systema with respect to the CCAUV.A-K5 key comparison reference value.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCAUV, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Availability and quality of routine morbidity data: review of studies in South Africa
Authors: Roomaney Rifqah A , Pillay-van Wyk Victoria , Awotiwon Oluwatoyin F , Nicol Edward , Joubert Jané D , Bradshaw Debbie , Hanmer Lyn A
Published: June 2016

Objectives: Routine health information systems (RHISs) provide data that are vital for planning and monitoring individual health. Data from RHISs could also be used for purposes for which they were not originally intended, provided that the data are of sufficient quality. For example, morbidity data could be used to inform burden of disease estimations, which serve as important evidence to prioritize interventions and promote health. The objective of this study was to identify and assess published quantitative assessments of data quality related to patient morbidity in RHISs in use in South Africa.

Materials and Methods: We conducted a review of literature published between 1994 and 2014 that assessed the quality of data in RHISs in South Africa. World Health Organization (WHO) data quality components were used as the assessment criteria.

Results Of 420 references identified, 11 studies met the inclusion criteria. The studies were limited to tuberculosis and HIV. No study reported more than 3 WHO data quality components or provided a quantitative assessment of quality that could be used for burden of disease estimation.

Discussion: The included studies had limited geographical focus and evaluated different source data at different levels of the information system. All studies reported poor data quality.

Conclusion: This review confirmed concerns about the quality of data in RHISs, and highlighted the need for a comprehensive evaluation of the quality of patient-level morbidity data in RHISs in South Africa.
Acute care patient portals: a qualitative study of stakeholder perspectives on current practices
Authors: Collins Sarah A , Rozenblum Ronen , Leung Wai Yin , Morrison Constance RC , Stade Diana L , McNally Kelly , Bourie Patricia Q , Massaro Anthony , Bokser Seth , Dwyer Cindy , Greysen Ryan S , Agarwal Priyanka , Thornton Kevin , Dalal Anuj K
Published: June 2016

Objective: To describe current practices and stakeholder perspectives of patient portals in the acute care setting. We aimed to: (1) identify key features, (2) recognize challenges, (3) understand current practices for design, configuration, and use, and (4) propose new directions for investigation and innovation.

Materials and Methods: Mixed methods including surveys, interviews, focus groups, and site visits with stakeholders at leading academic medical centers. Thematic analyses to inform development of an explanatory model and recommendations.

Results: Site surveys were administered to 5 institutions. Thirty interviews/focus groups were conducted at 4 site visits that included a total of 84 participants. Ten themes regarding content and functionality, engagement and culture, and access and security were identified, from which an explanatory model of current practices was developed. Key features included clinical data, messaging, glossary, patient education, patient personalization and family engagement tools, and tiered displays. Four actionable recommendations were identified by group consensus.

Discussion: Design, development, and implementation of acute care patient portals should consider: (1) providing a single integrated experience across care settings, (2) humanizing the patient-clinician relationship via personalization tools, (3) providing equitable access, and (4) creating a clear organizational mission and strategy to achieve outcomes of interest.

Conclusion: Portals should provide a single integrated experience across the inpatient and ambulatory settings. Core functionality includes tools that facilitate communication, personalize the patient, and deliver education to advance safe, coordinated, and dignified patient-centered care. Our findings can be used to inform a “road map” for future work related to acute care patient portals.
Administration of Woodrow Wilson
Authors: Yellin Eric S.
Published: June 2016

The presidency of Woodrow Wilson deepened the struggle of African Americans in the age of Jim Crow. The rights that Black Americans earned during the Civil War and Reconstruction Era had been under attack since the mid-1870s, and white supremacy began to find its way into southern state constitutions and federal law in the 1890s. By the time Wilson was inaugurated as the nation’s twenty-eighth president in March 1913, much of the structure of de jure Jim Crow was in place across the South. Yet Wilson was the first Democrat to inhabit the White House since Grover Cleveland left in 1897, and he was the first southern-born president since the Civil War. Wilson entered the White House carrying decades of patronage debts for the Democratic Party and the white South. His disregard for Black rights was apparent earlier in his life, such as in his academic publications and in his actions to keep Princeton University white during his tenure there. His presidential administration nationalized the Jim Crow regime by threading discrimination and segregation into the federal bureaucracy and the nation’s capital. When making presidential appointments, Wilson did not fight to overcome his party’s objections to appointing African Americans, even in minor positions long held by Black politicians in previous administrations. Instead, Black administrators disappeared from Washington, DC, ending not just their federal jobs but a national network of Black politicians and civil servants. Wilson’s white appointees leaned southern, and they quickly ensured that government policies and federal jobs would no longer protect or support Black Americans. Wilson did little of the “dirty work” personally, but he approved of the actions of his administrators. When pressed to defend the growing segregation and limitation of Black federal workers, Wilson deployed progressive reform arguments, declaring that “good government” required white leadership and the separation of white and Black public workers. During World War I, the Wilson administration ensured that Black soldiers were segregated into separate units and were generally denied critical roles in the war. Black soldiers showed great valor nonetheless, but they returned home to violence, discrimination, and no federal protections. Dozens of race riots across the country in 1919, including in the nation’s capital, underscored that prospects for Black Americans had indeed worsened under the Wilson Administration.
HIV/AIDS from an African American Studies Perspective
Authors: Geary Adam M.
Published: June 2016

AIDS (acquired immunodeficiency syndrome, or HIV/AIDS) is a global pandemic, affecting most of the world, especially those suffering poverty, social inequality, and marginalization. In the US epidemic, African Americans suffer disproportionately. Although approximately 13 percent of the US population, African Americans accounted for nearly 42 percent of new HIV infections and 40 percent of people living with HIV as of 2019. Over half of all AIDS-related deaths in the United States have been African Americans. Understanding this racially disproportionate disease suffering depends on how one defines AIDS, which, while seemingly technical, is inherently political and contested. Although a few scholars have questioned it in the past, almost all contemporary scholars agree that, most simply, AIDS is the name for the gradual impairment of a person’s cellular immune system by the action of the Human Immunodeficiency Virus (HIV), leaving the infected person increasingly vulnerable to diseases (“opportunistic infections”), many of which can be fatal if untreated. Pharmaceutical treatments exist for preventing HIV infection, suppressing HIV for those living with it, and for many of the opportunistic infections, although these treatments are neither universally effective nor universally available. But beyond the individual experience of a virus, defining AIDS depends on how to define an epidemic, or population-level disease phenomenon, given that the AIDS epidemic has affected some more than others. Two major schools of thought have addressed AIDS as an epidemic. In the United States, the dominant model for understanding the epidemic has been biomedicine, which treats epidemics and their dispersion as aggregates of individual transmission events, focusing attention on the biological qualities of HIV transmission from individual to individual and on the behavioral qualities of those who are at risk of infection (“risk behaviors” and “risk groups”). Critiques of biomedicine have emerged from social epidemiology, which has a rich history in African American reflections on health and disease. Rather than focusing exclusively upon the biology of HIV and the behavioral mechanisms of its transmission from individual to individual, social epidemiologists have prioritized the structuring of human populations, including the ways that racism, poverty, sexism, homophobia, and transphobia have structured vulnerabilities to exposure to HIV (including control over one’s behavioral environment) and embodied susceptibility to infection. Social, political, and cultural responses to the AIDS epidemic in the United States and among African Americans have been shaped by these competing understandings of epidemic disease.
Forecasting in International Relations
Authors: Metternich Nils W. , Gleditsch Kristian Skrede , Dworschak Christoph
Published: June 2016

Forecasting has always been a central aspiration in the study of international relations. Early efforts to develop a “science of politics” typically emphasized the ability to anticipate future events as a key advantage. The behavioral revolution likewise gave strong prominence to the positivist equivalence between explaining phenomena and the ability to predict. However, despite many programmatic statements, predictions have largely remained aspirations until relatively recently. In this bibliography, we will provide an overview of the existing literature on forecasting, and on applications to conflict in particular. This overview will be organized around differences in specific approaches to forecasting, largely categorized by methodology. However, forecasts can differ along a number of dimensions that cut across specific methods. First, there are differences in the scope of forecasts. Some predictions are highly case-specific and predict outcomes for a single unit and particular issue area. Other models have global scope and seek to assess the risks of some general phenomenon across a wide range of units. Between these two extremes there are various more delineations, focusing on a confined sets such as regions or specific groups of actors. Second, forecasts differ considerably in their time horizons, ranging from daily to periods as long as 100 years. Third, forecasts differ in the scope of what analysts try to predict. Many forecasts are limited to predicting the value of the main response variable of interest, based entirely on what is known about predictors ex ante. Other forecasts entail more ambitious efforts to predict larger systems of variables, including the relevant predictors. Finally, one can distinguish between model- and data-driven approaches to forecasting. Purely model-driven forecasts are based on simplified theoretical or mathematical models and a priori assumptions, sometimes devoid of any empirical inputs at all. At the other extreme, there are purely data-driven models, possibly without any assumptions about the structure or functional form of the relationships at work. In between these two extremes, there is a wide range of forecasting approaches, combining a priori modeling assumptions with parameters that are calibrated by empirical data. This article concludes with an overview of the interests in forecasts among policy and applied communities, including some of the barriers that have prevented effective communication of research results, pointing to future directions of forecasting conflict. Nils W. Metternich acknowledges support from the Economic and Social Research Council (ES/L011506/1). Kristian Skrede Gleditsch acknowledges support from the European Research Council (313373).
Political Scandals
Authors: Hartung Uwe
Published: June 2016

Political scandals are a special field of study within mass communication and social sciences. The field is seldom recognized as such, while empirical studies in areas such as news selection, role of journalists, news framing, and media are sometimes conducted using issues that fulfill the criteria to be considered scandals. This article, however, is primarily concerned with literature focusing on scandal as a type of issue in public communication that evolves under special conditions, knows specific roles for participants, offers them certain options for reacting, and follows a typical trajectory. In everyday language, “scandal” refers to violations of social norms or transgressions and to a particular type of public communication that sometimes ensues from the violation. From the perspective of communication, it is imperative to separate the two meanings as not all publicly known transgressions generate scandals, nor are scandals necessarily based on de facto transgressions. Basic questions for the study of scandals in communication research emerge: Which transgressions (social problems, malfunction, misbehavior) does a society select for scandal, and which of them does it ignore or tolerate? Who makes the choices in scandal selection? For what motives? What are the chances to create a scandal? Which devices are promising in creating a scandal? How can a scandal can be contained or terminated? We can formally define scandal as the intense public communication about a real or imagined normative transgression that is by consensus disapproved by the public. In this entry, scandal goes along with the qualifier “political,” referring to the function of politics to codify the norms of a society. Any discussion of the validity and applicability of social norms is therefore political. In that sense, a political scandal is any one in which the validity and applicability of norms is addressed. Many of the texts listed in the various chapters of this bibliography could easily be sorted in other chapters. That is especially true in Macro-Level Theories about Scandals, Edited Books and Components and Parties of a Scandal. Almost all the publications under “macro” also contain chapters you want to read when you are interested in a “micro” or phenomenological approach to scandal. That goes vice versa. And many of the edited volumes contain chapters that would fit in one or both of the theory sections. Aside from this, there are comparative studies of many kinds, and of course single-case studies can also be instructive. Selection criteria were originality and a relationship with the theoretical considerations in the introductory remarks to the chapters.
A Case of Meningococcal Pyomyositis in an Otherwise Healthy Adult
Authors: Barakat Monique T. , Gajurel Kiran , Fischer Katrina , Stevens Kathryn , Ozdalga Errol , Montoya José G.
Published: June 2016

The clinical spectrum of Neisseria meningitidis can range from nasopharyngeal colonization to life-threatening invasive diseases such as meningitis. However, its etiologic role in invasive pyomyositis (PM) has never been reported before in the English language. In this study, we report the first case of PM in the English language and the second case in the literature caused by N meningitidis.
Comparison of norovirus genogroup I, II and IV seroprevalence among children in the Netherlands, 1963, 1983 and 2006
Authors: van Beek Janko , de Graaf Miranda , Xia Ming , Jiang Xi , Vinjé Jan , Beersma Mathias , de Bruin Erwin , van de Vijver David , Holwerda Melle , van Houten Marlies , Buisman Annemarie M. , van Binnendijk Rob , Osterhaus Albert D. M. E. , van der Klis Fiona , Vennema Harry , Koopmans Marion P. G.
Published: June 2016

Noroviruses are a major cause of acute gastroenteritis worldwide and are a genetically diverse group of viruses. Since 2002, an increasing number of norovirus outbreaks have been reported globally, but it is not clear whether this increase has been caused by a higher awareness or reflects the emergence of new genogroup II genotype 4 (GII.4) variants. The hypothesis that norovirus prevalence has increased post-2002 and is related to the emergence of GII.4 is tested in this study. Sera collected from children aged <5 years of three Dutch cross-sectional population based cohorts in 1963, 1983 and 2006/2007 (n=143, n=130 and n=376, respectively) were tested for specific serum IgG by protein array using antigens to GII.4 and a range of other antigens representing norovirus GI, GII and GIV genotypes. The protein array was validated by paired sera of norovirus infected patients and supernatants of B-cell cultures with single epitope specificity. Evidence for norovirus infection was found to be common among Dutch children in each cohort, but the prevalence towards different genotypes changed over time. At the genogroup level, GI seroprevalence decreased significantly between 1963 and 2006/2007, while a significant increase of GII and, in particular, specific antibodies of the genotype GII.4 was detected in the 2006/2007 cohort. There were no children with only GII.4 antibodies in the 1963 cohort. This study shows that the high GII.4 norovirus incidence in very young children is a recent phenomenon. These findings are of importance for vaccine development and trials that are currently focusing mostly on GII.4 viruses.
Collective strategy for obstacle navigation during cooperative transport by ants
Authors: McCreery Helen F. , Dix Zachary A. , Breed Michael D. , Nagpal Radhika
Published: June 2016

Group cohesion and consensus have primarily been studied in the context of discrete decisions, but some group tasks require making serial decisions that build on one another. We examine such collective problem solving by studying obstacle navigation during cooperative transport in ants. In cooperative transport, a group of ants works together to move a large object back to their nest. We blocked cooperative transport groups ofParatrechinal longicorniswith obstacles of varying complexity, analyzing groups trajectories to infer what kind of strategy the ants employed. Simple strategies require little information, but more challenging, robust strategies succeed with a wider range of obstacles. We found that transport groups use a stochastic strategy that leads to efficient navigation around simple obstacles, and still succeeds at difficult ones. While groups navigating obstacles preferentially move directly toward the nest, they change their behavior over time; the longer the ants are obstructed, the more likely they are to move away from the nest. This increases the chance of finding a path around the obstacle. Groups rapidly changed directions and rarely stalled during navigation, indicating that these ants maintain consensus even when the nest direction is blocked. While some decisions were aided by the arrival of new ants, at many key points direction changes were initiated within the group, with no apparent external cause. This ant species is highly effective at navigating complex environments, and implements a flexible strategy that works quickly for simple obstacles and still succeeds with complex obstacles.
Characterization of kinase gene expression and splicing profile in prostate cancer with RNA-Seq data
Authors: Feng Huijuan , Li Tingting , Zhang Xuegong
Published: June 2016

Background

Alternative splicing is a ubiquitous post-transcriptional process in most eukaryotic genes. Aberrant splicing isoforms and abnormal isoform ratios can contribute to cancer development. Kinase genes are key regulators of various cellular processes. Many kinases are found to be oncogenic and have been intensively investigated in the study of cancer and drugs. RNA-Seq provides a powerful technology for genome-wide study of alternative splicing in cancer besides the conventional gene expression profiling. But this potential has not been fully demonstrated yet.

Methods

Here we characterized the transcriptome profile of prostate cancer using RNA-Seq data from viewpoints of both differential expression and differential splicing, with an emphasis on kinase genes and their splicing variations. We built up a pipeline to conduct differential expression and differential splicing analysis. Further functional enrichment analysis was performed to explore functional interpretation of the genes. With focus on kinase genes, we performed kinase domain analysis to identify the functionally important candidate kinase gene in prostate cancer. We further calculated the expression level of isoforms to explore the function of isoform switching of kinase genes in prostate cancer.

Results

We identified distinct gene groups from differential expression and splicing analysis, which suggested that alternative splicing adds another level to gene expression regulation. Enriched GO terms of differentially expressed and spliced kinase genes were found to play different roles in regulation of cellular metabolism. Function analysis on differentially spliced kinase genes showed that differentially spliced exons of these genes are significantly enriched in protein kinase domains. Among them, we found that geneCDK5has isoform switching between prostate cancer and benign tissues, which may affect cancer development by changing androgen receptor (AR) phosphorylation. The observation was validated in another RNA-Seq dataset of prostate cancer cell lines.

Conclusions

Our work characterized the expression and splicing profile of kinase genes in prostate cancer and proposed a hypothetical model on isoform switching ofCDK5andARphosphorylation in prostate cancer. These findings bring new understanding to the role of alternatively spliced kinases in prostate cancer and demonstrate the use of RNA-Seq data in studying alternative splicing in cancer.
Evaluating the diagnostic utility of applying a machine learning algorithm to diffusion tensor MRI measures in individuals with major depressive disorder
Authors: Schnyer David M , Clasen Peter C. , Gonzalez Christopher , Beevers Christopher G
Published: June 2016

Using MRI to diagnose mental disorders has been a long-term goal. Despite this, the vast majority of prior neuroimaging work has been descriptive rather than predictive. The current study applies support vector machine (SVM) learning to MRI measures of brain white matter to classify adults with Major Depressive Disorder (MDD) and healthy controls. In a precisely matched group of individuals with MDD (n= 25) and healthy controls (n= 25), SVM learning accurately (70%) classified patients and controls across a brain map of white matter fractional anisotropy values (FA). The study revealed three main findings: 1) SVM applied to DTI derived FA maps can accurately classify MDD vs. healthy controls; 2) prediction is strongest when only right hemisphere white matter is examined; and 3) removing FA values from a region identified by univariate contrast as significantly different between MDD and healthy controls does not change the SVM accuracy. These results indicate that SVM learning applied to neuroimaging data can classify the presence versus absence of MDD and that predictive information is distributed across brain networks rather than being highly localized. Finally, MDD group differences revealed through typical univariate contrasts do not necessarily reveal patterns that provide accurate predictive information.
Compensatory responses by managers, commercial and recreational harvesters to variation in stock abundance of Lake Erie walleye (Sander vitreus vitreus)
Authors: Turgeon Katrine , Reid Kevin B. , Fryxell John M. , Nudds Thomas D.
Published: June 2016

Delayed quota adjustments, and/or lagged fishing effort and catch by harvesters, to changes in stock abundance may induce unstable population dynamics and exacerbate the risk of fishery collapse. We examined a 39-y time series of change to quotas by managers, and to effort and catch by both commercial harvesters and anglers, in response to changes in Lake Erie walleye abundance (Sander vitreus) estimated both contemporaneously and retrospectively. Quotas, commercial effort and catch were entrained by contemporaneous estimates of stock abundance. Recreational effort and harvest were not; they had better tracked abundance, as better estimated today, than did the commercial fishery. During the 1990s, a significant mismatch developed between the quota-driven commercial harvest and stock abundance that persisted until a new assessment process obtained. The quasi-open access recreational fishery, instead, freed anglers to respond better to stock abundance. Further elaboration of adaptive risk governance processes, including multi-model inference for stock assessments, may bode well to further reduce risk to fisheries imposed by lagged adjustments to variation in stock abundance.
A signal detection theoretic demonstration of hiring rate asymmetries in competitive academic job markets
Authors: Miuccio Michael , Liu Ka-yuet , Lau Hakwan , Peters Megan A. K.
Published: June 2016

To get a faculty job, graduating doctoral students have to substantially outperform their peers, given the competitive nature of the academic job market. In an ideal, meritocratic world, factors such as prestige of degree-granting university ought not to play a substantial role. However, it has recently been reported that top-ranked universities produced about 2–6 times more faculty than did universities that were ranked lower (Clauset, Arbesman, and Larremore 2015), necessitating un-meritocratic factors: how could students from top-ranked universities be six times more productive than their peers from lower-ranked universities? Here we present a signal detection model to demonstrate that substantially higher rates of faculty production need not require substantially (and unrealistically) higher levels of student productivity. Instead, it is a high hiring threshold due to keen competition that causes small difference in average student productivity between universities to result in manifold differences in placement rates. Under this framework, the previously reported results are compatible with a purely meritocratic system. As a simple proof of concept, we examined the association between university ranking and the impact factors of students publications from a small selected sample of psychology departments in the U.S. The results are in agreement with our theoretical model. Whereas these results do not necessarily mean that the actual faculty hiring market is purely meritocratic, they highlight the difficulty in empirically demonstrating that it is not so.
The mutation rate in human evolution and demographic inference
Authors: Scally Aylwyn
Published: June 2016

The germline mutation rate has long been a major source of uncertainty in human evolutionary and demographic analyses based on genetic data, but estimates have improved substantially in recent years. I discuss our current knowledge of the mutation rate in humans and the underlying biological factors affecting it, which include generation time, parental age and other developmental and reproductive timescales. There is good evidence for a slowdown in mean mutation rate during great ape evolution, but not for a more recent change within the timescale of human genetic diversity. Hence, pending evidence to the contrary, it is reasonable to use a present-day rate of approximately 0.5 × 10−9bp−1yr−1in all human or hominin demographic analyses.
How to evaluate phase differences between trial groups in ongoing electrophysiological signals
Authors: VanRullen Rufin
Published: June 2016

A growing number of studies endeavor to reveal periodicities in sensory and cognitive functions, by comparing the distribution of ongoing (pre-stimulus) oscillatory phases between two (or more) trial groups reflecting distinct experimental outcomes. A systematic relation between the phase of spontaneous electrophysiological signals, before a stimulus is even presented, and the eventual result of sensory or cognitive processing for that stimulus, would be indicative of an intrinsic periodicity in the underlying neural process. Prior studies of phase-dependent perception have used a variety of analytical methods to measure and evaluate phase differences, and there is currently no established standard practice in this field. The present report intends to remediate this need, by systematically comparing the statistical power of various measures of “phase opposition” between two trial groups, in a number of real and simulated experimental situations. Seven measures were evaluated: one parametric test (circular Watson-Williams test), and three distinct measures of phase opposition (phase bifurcation index, phase opposition sum and phase opposition product) combined with two procedures for non-parametric statistical testing (permutation, or a combination of z-score and permutation). While these are obviously not the only existing or conceivable measures, they have all been used in recent studies. All tested methods performed adequately on a previously published dataset (Busch, Dubois & VanRullen, 2009). On a variety of artificially constructed datasets, no single measure was found to surpass all others, but instead the suitability of each measure was contingent on several experimental factors: the time, frequency and depth of oscillatory phase modulation; the absolute and relative amplitudes of post-stimulus event-related potentials for the two trial groups; the absolute and relative trial numbers for the two groups; and the number of permutations used for non-parametric testing. The concurrent use of two phase opposition measures, the parametric Watson-Williams test and a non-parametric test based on summing inter-trial coherence values for the two trial groups, appears to provide the most satisfactory outcome in all situations tested. Matlab code is provided to automatically compute these phase opposition measures.
Aberrant prefrontal beta oscillations predict episodic memory encoding deficits in schizophrenia
Authors: Meconi Federica , Anderl-Straub Sarah , Raum Heidelore , Landgrebe Michael , Langguth Berthold , Bäuml Karl-Heinz T. , Hanslmayr Simon
Published: June 2016

Verbal episodic memory is one of the core cognitive functions affected in patients suffering from schizophrenia (SZ). Although this verbal memory impairment in SZ is a well-known finding, our understanding about its underlying neurophysiological mechanisms is rather scarce. Here we address this issue by recording brain oscillations during a memory task in a sample of healthy controls and patients suffering from SZ. Brain oscillations represent spectral fingerprints of specific neurocognitive operations and are therefore a promising tool to identify neurocognitive mechanisms that are affected by SZ. Healthy controls showed a prominent suppression of left prefrontal beta oscillatory activity during successful memory formation, which replicates several previous oscillatory memory studies. In contrast, patients failed to exhibit such left prefrontal beta power suppression. Utilizing a new topographical pattern similarity approach, we further demonstrate that the degree of similarity between a patient's beta power decrease to that of the controls reliably predicted memory performance. This relationship between beta power decreases and memory was such that the patients' memory performance improved as they showed a more similar topographical beta desynchronization pattern compared to that of healthy controls. These findings suggest that left prefrontal beta power suppression (or lack thereof) during memory encoding is a possible biomarker for the observed encoding impairments in SZ in verbal memory. This lack of left prefrontal beta power decreases might indicate a specific semantic processing deficit of verbal material in patients with schizophrenia.
The rhythms of predictive coding: pre-stimulus phase modulates the influence of shape perception on luminance judgments
Authors: Han Biao , VanRullen Rufin
Published: June 2016

Predictive coding is an influential model emphasizing interactions between feedforward and feedback signals. Here, we investigated its temporal dynamics. Two gray disks with different versions of the same stimulus, one enabling predictive feedback (a 3D-shape) and one impeding it (random-lines), were simultaneously presented on the left and right of fixation. Human subjects judged the luminance of the two disks while EEG was recorded. Independently of the spatial response (left/right), we found that the choice of 3D-shape or random-lines as the brighter disk (our measure of post-stimulus predictive coding efficiency on each trial) fluctuated along with the pre-stimulus phase of two spontaneous oscillations: a ~5Hz oscillation in contralateral frontal electrodes and a ~16Hz oscillation in contralateral occipital electrodes. This pattern of results demonstrates that predictive coding is a rhythmic process, and suggests that it could take advantage of faster oscillations in low-level areas and slower oscillations in high-level areas.
When is a bacterial “virulence factor” really virulent?
Authors: Granato Elisa T. , Harrison Freya , Kümmerli Rolf , Ross-Gillespie Adin
Published: June 2016

Bacterial traits that contribute to disease are termed ‘virulence factors’ and there is much interest in therapeutic approaches that disrupt such traits. However, ecological theory predicts disease severity to be multifactorial and context dependent, which might complicate our efforts to identify the most generally important virulence factors. Here, we use meta-analysis to quantify disease outcomes associated with one well-studied virulence factor – pyoverdine, an iron-scavenging compound secreted by the opportunistic pathogenPseudomonas aeruginosa. Consistent with ecological theory, we found that the effect of pyoverdine, albeit frequently contributing to disease, varied considerably across infection models. In many cases its effect was relatively minor, suggesting that pyoverdine is rarely essential for infections. Our work demonstrates the utility of meta-analysis as a tool to quantify variation and overall effects of purported virulence factors across different infection models. This standardised approach will help us to evaluate promising targets for anti-virulence approaches.