bluuebunny/crossref_metadata_2025 huggingface dataset:
Museum specimens reveal loss of pollen host plants as key factor driving wild bee decline in The Netherlands
Authors: Scheper Jeroen , Reemer Menno , van Kats Ruud , Ozinga Wim A. , van der Linden Giel T. J. , Schaminée Joop H. J. , Siepel Henk , Kleijn David
Published: November 2014

Significance

Growing concern about bee declines and associated loss of pollination services has increased the urgency to identify the underlying causes. So far, the identification of the key drivers of decline of bee populations has largely been based on speculation. We assessed the relative importance of a range of proposed factors responsible for wild bee decline and show that loss of preferred host plant species is one of the main factors associated with the decline of bee populations in The Netherlands. Interestingly, species foraging on crop plant families have stable or increasing populations. These results indicate that mitigation strategies for loss of wild bees will only be effective if they target the specific host plants of declining bee species.
Structural basis of collagen fiber degradation by cathepsin K
Authors: Aguda Adeleke H. , Panwar Preety , Du Xin , Nguyen Nham T. , Brayer Gary D. , Brömme Dieter
Published: November 2014

Significance

Fibrillar collagens constitute 90% of the organic bone matrix and are subjected either to physiological remodeling or excessive degradation during diseases such as osteoporosis. Cathepsin K is the critical collagenase in bone and represents a major antiresorptive drug target. Despite its critical role in bone remodeling, its mechanism of collagen degradation remained elusive. Here, we demonstrate that the degradation of fibrillar collagen requires the presence of a cathepsin K dimer bound at the surface of collagen fibers via glycosaminoglycans. Structural modifications of the protease dimerization site or the removal of collagen fiber-associated glycosaminoglycans specifically block fibrillar collagen degradation. The provided structure allows the development of a strategy to inhibit this highly relevant drug target in a substrate-specific manner.
Functional differences between neurotransmitter binding sites of muscle acetylcholine receptors
Authors: Nayak Tapan K. , Bruhova Iva , Chakraborty Srirupa , Gupta Shaweta , Zheng Wenjun , Auerbach Anthony
Published: November 2014

Significance

We present here energy measurements for agonist binding to adult and fetal neuromuscular junction acetylcholine receptors. We identify the chemical groups at the three functionally different types of transmitter binding site (αγ, αδ, and αε) that generate energy from the agonist for channel gating. We also predict the structural correlates of the energy differences from experiments and molecular dynamics simulations. This article is of general interest because it is the first time to our knowledge that single ligand-binding-site energies have been measured in any receptor. In addition, the results provide a rationale for understanding the required receptor subunit swap in synapse maturation (a long-standing and unsolved problem), as well as the structural basis for agonist efficacy.
Phylogenetic reconstruction of Bantu kinship challenges Main Sequence Theory of human social evolution
Authors: Opie Christopher , Shultz Susanne , Atkinson Quentin D. , Currie Thomas , Mace Ruth
Published: November 2014

Significance

The agricultural revolution had a dramatic effect on all aspects of human society, but piecing together how humans lived as they spread farming practices worldwide remains difficult. In particular, the fundamental structures of human society, namely the way that property is inherited and the rules governing postmarriage residence, do not leave a clear trace in the archaeological record and, therefore, have been largely intractable. However, the recent availability of phylogenetic language trees coupled with new Bayesian statistical techniques makes it possible to reconstruct the ancestral state of Bantu kinship and reveals that inheritance and residence rules coevolved as farming spread throughout sub-Saharan Africa. Our results question current theory suggesting that residence rules are the primary driver of all other human social structures.
Timing the impact of literacy on visual processing
Authors: Pegado Felipe , Comerlato Enio , Ventura Fabricio , Jobert Antoinette , Nakamura Kimihiro , Buiatti Marco , Ventura Paulo , Dehaene-Lambertz Ghislaine , Kolinsky Régine , Morais José , Braga Lucia W. , Cohen Laurent , Dehaene Stanislas
Published: November 2014

Significance

How does learning to read affect visual processing? We addressed this issue by scanning adults who could not attend school during childhood and either remained illiterate or acquired partial literacy during adulthood (ex-illiterates). By recording event-related brain responses, we obtained a high-temporal resolution description of how illiterate and literate adults differ in terms of early visual responses. The results show that learning to read dramatically enhances the magnitude, precision, and invariance of early visual coding, within 200 ms of stimulus onset, and also enhances later neural activity. Literacy effects were found not only for the expected category of expertise (letter strings), but also extended to other visual stimuli, confirming the benefits of literacy on early visual processing.
Global emissions of refrigerants HCFC-22 and HFC-134a: Unforeseen seasonal contributions
Authors: Xiang Bin , Patra Prabir K. , Montzka Stephen A. , Miller Scot M. , Elkins James W. , Moore Fred L. , Atlas Elliot L. , Miller Ben R. , Weiss Ray F. , Prinn Ronald G. , Wofsy Steven C.
Published: November 2014

Significance

HCFC-22 (CHClF2) and HFC-134a (CH2FCF3) are two major gases currently used worldwide in domestic and commercial refrigeration and air conditioning. HCFC-22 contributes to stratospheric ozone depletion, and both species are potent greenhouse gases. We find pronounced seasonal variations of global emissions for these two major refrigerants, with summer emissions two to three times higher than in winter. Thus results suggest that global emissions of these potent greenhouse gases might be mitigated by improved design and engineering of refrigeration systems and/or by reinforcing system service regulations.
Measuring missing heritability: Inferring the contribution of common variants
Authors: Golan David , Lander Eric S. , Rosset Saharon
Published: November 2014

Significance

Studies have identified thousands of common genetic variants associated with hundreds of diseases. Yet, these common variants typically account for a minority of the heritability, a problem known as “missing heritability.” Geneticists recently proposed indirect methods for estimating the total heritability attributable to common variants, including those whose effects are too small to allow identification in current studies. Here, we show that these methods seriously underestimate the true heritability when applied to case–control studies of disease. We describe a method that provides unbiased estimates. Applying it to six diseases, we estimate that common variants explain an average of 60% of the heritability for these diseases. The framework also may be applied to case–control studies, extreme-phenotype studies, and other settings.
Trajectories of the ribosome as a Brownian nanomachine
Authors: Dashti Ali , Schwander Peter , Langlois Robert , Fung Russell , Li Wen , Hosseinizadeh Ahmad , Liao Hstau Y. , Pallesen Jesper , Sharma Gyanesh , Stupina Vera A. , Simon Anne E. , Dinman Jonathan D. , Frank Joachim , Ourmazd Abbas
Published: November 2014

Significance

Many functions in the cell are performed by Brownian machines, macromolecular assemblies that use energy from the thermal environment for many of the conformational changes involved in their work cycles. Here we present a new approach capable of mapping the continuous motions of such nanomachines along their trajectories in the free-energy landscape and demonstrate this capability in the context of experimental cryogenic electron microscope snapshots of the ribosome, the nanomachine responsible for protein synthesis in all living organisms. We believe our approach constitutes a universal platform for the analysis of free-energy landscapes and conformational motions of molecular nanomachines and their dependencies on temperature, buffer conditions, and regulatory factors.
Elucidating severe urban haze formation in China
Authors: Guo Song , Hu Min , Zamora Misti L. , Peng Jianfei , Shang Dongjie , Zheng Jing , Du Zhuofei , Wu Zhijun , Shao Min , Zeng Limin , Molina Mario J. , Zhang Renyi
Published: November 2014

Significance

We illustrate the similarity and difference in particulate matter (PM) formation between Beijing and other world regions. The periodic cycle of PM events in Beijing is regulated by meteorological conditions. While the particle chemical compositions in Beijing are similar to those commonly measured worldwide, efficient nucleation and growth over an extended period in Beijing are distinctive from the aerosol formation typically observed in other global areas. Gaseous emissions of volatile organic compounds and nitrogen oxides from urban transportation and sulfur dioxide from regional industry are responsible for large secondary PM formation, while primary emissions and regional transport of PM are insignificant. Reductions in emissions of the aerosol precursor gases from transportation and industry are essential to mediate severe haze pollution in China.
Actin polymerization as a key innate immune effector mechanism to control
Salmonella
infection
Authors: Man Si Ming , Ekpenyong Andrew , Tourlomousis Panagiotis , Achouri Sarra , Cammarota Eugenia , Hughes Katherine , Rizzo Alessandro , Ng Gilbert , Wright John A. , Cicuta Pietro , Guck Jochen R. , Bryant Clare E.
Published: November 2014

Significance

Infectious diseases are responsible for one-third of all mortality worldwide. Innate immunity is critical for mounting host defenses that eliminate pathogens.
Salmonella
is a global food-borne pathogen that infects and replicates within macrophages. How inflammasomes—multimeric protein complexes that provide innate immune protection—function to restrict bacterial burden in macrophages remains unknown. We show that actin polymerization is critical for NLRC4 inflammasome activation in response to
Salmonella
infection. NLRC4 activation in
Salmonella
-infected cells prevents further uptake of bacteria by inducing cellular stiffness and antimicrobial responses, which prevent bacterial dissemination in the host. These results demonstrate a critical link between innate immunity and the actin cytoskeleton in the cellular defense against
Salmonella
infection.
Brain–machine interface for eye movements
Authors: Graf Arnulf B. A. , Andersen Richard A.
Published: November 2014

Significance

We developed a brain–machine interface (BMI) that records single cell activity from populations of neurons for decoding planned eye movements (i.e., saccades) without the animals executing them. The recordings were made from the lateral intraparietal area, an important cortical node in the primate saccade system. To our knowledge, this is the first BMI using neuronal populations to predict eye movements in a brain control task. Learning occurred during brain control trials, improving prediction performance by changing the response properties of single neurons. An eye movement BMI can assist patients locked-in from stroke or neurodegenerative disease who are unable to make any movements including eye movements.
Impact of ocean phytoplankton diversity on phosphate uptake
Authors: Lomas Michael W. , Bonachela Juan A. , Levin Simon A. , Martiny Adam C.
Published: November 2014

Significance

Nutrient uptake is a central property of ocean biogeochemistry, but our understanding of this process is based on laboratory cultures or bulk environmental studies. Thus, mathematical descriptions of nutrient uptake, at the heart of most biogeochemical models, must rely on this limited information. Hence, we have little knowledge of how natural phytoplankton populations vary in their abilities to take up key nutrients. Using advanced analytical techniques, this study provides the first comprehensive in situ quantification of nutrient uptake capabilities among dominant phytoplankton groups. Supported by a model that considers plastic ecological responses in an evolutionary context, this work further provides a fundamentally new framework for the integration of microbial diversity to describe and understand the controls of ocean nutrient assimilation.
Socio-syntax and variation in acquisition
Authors: Cornips Leonie M.E.A.
Published: November 2014

This paper has two aims:* first, to emphasize how the linguistic input to which children are exposed is inherently variable and complex. To this end, we will discuss two particular phenomena in Dutch, namely Aux+Inf and gender marking in DP’s. These phenomena lend themselves to a comparison in terms of the nature of the individual, social and regional variation in the input. Second, regarding the question of whether bidialectal acquisition is the same as bilingual acquisition, it seems that there are, in fact, significant differences between the two. Bidialectal children score significantly higher on vocabulary tests than bilingual speakers, they use the Aux+Inf structure in a different way and they also acquire the neuter gender of the Dutch definite determiner significantly faster than bilingual children. Importantly, this paper also explores whether we can maintain a distinction between monolingual and bidialectal children in so-called bidialectal areas.
Linguistic variation and micro-cues in first language acquisition
Authors: Westergaard Marit
Published: November 2014

Children are often exposed to considerable variation in the input. Nevertheless, there is very little overgeneralization in child language data and children are typically found to make errors of omission, not errors of commission, a fact which is often referred to as conservative learning. In this paper, these findings are accounted for by a model of micro-cues, a generative approach to language acquisition arguing that children are sensitive to fine syntactic distinctions from early on. The micro-cues are small pieces of abstract syntactic structure resulting from parsing the input. This means that UG provides children with principles, features, and the ability to parse, but not the micro-cues themselves, which are considered to be part of the knowledge of a specific language. The model also considers children’s errors to generally be due to economy and the language acquisition process to be development in small steps, from specific to more general knowledge. Keywords: Conservative learning; economy; English; grammar competition; Norwegian; (over- and under)generalization; parameter; rule “size”; word order
Edge-tone effects and prosodic domain effects on final lengthening
Authors: Themistocleous Charalambos
Published: November 2014

This study reports two experiments that investigate the edge-tones and domain-specific effects on final lengthening. The study shows that in Cypriot Greek the following occur: (a) lengthening applies primarily on the syllable nucleus not the syllable onset, which suggests variety specific effects of lengthening; (b) lengthening depends on the edge-tones, namely, polar questions trigger more lengthening than statements and wh-questions; (c) lengthening provides support for at least two distinct prosodic domains over the phonological word, the intonational phrase and the intermediate phrase; greater lengthening associates with the first and shorter lengthening with the latter; (d) finally, syllable duration depends on the syllable distance from the boundary, i.e. lengthening locally applies on penultimates and ultimates whereas antepenultimates are affected the least. Additionally, by pointing to the distinct lengthening effects of edge-tones and domain-boundaries, the aforementioned findings highlight the application of different lengthening devices. Keywords: Prosodic structure; preboundary lengthening; edge-tone lengthening; Cypriot Greek
Evaluation of Precision and Sample Sizes Using Standardized Sampling in Kansas Reservoirs
Authors: Koch Jeff D. , Neely Ben C. , Colvin Michael E.
Published: November 2014

We evaluated the precision of samples and the number of stock-length fish collected by means of standard methods used for sampling North American freshwater fishes from 2010 to 2013 in Kansas. Additionally, we used resampling procedures to determine the number of gear deployments needed to achieve a relative standard error (RSE) of 25% for the CPUE and collect 100 stock-length individuals. Median RSE of electrofishing samples was generally less than 25% for Largemouth Bass Micropterus salmoides in all sizes of reservoirs and for Channel Catfish Ictalurus punctatus in medium (251–1,000 acres) and large reservoirs (greater than 1,000 acres). The RSE estimates were generally >25% for Bluegill Lepomis macrochirus and crappies Pomoxis spp. collected in trap nets and palmetto bass (female Striped Bass Morone saxatilis × male White Bass M. chrysops) and Walleye Sander vitreus sampled in gill nets. With few exceptions, 100 stock-length individuals of all target species (e.g., Largemouth Bass, Bluegill, crappies, palmetto bass, Channel Catfish, Walleye) were not sampled at current levels of effort. Resampling procedures indicated that fewer than 20 deployments were usually needed to obtain an RSE ≤ 25% and 100 stock-length fish for Largemouth Bass in smaller impoundments (i.e., <250 acres); however, more than 20 deployments were needed in larger impoundments. The median effort needed to achieve an RSE ≤ 25% for Bluegills and crappies in trap nets varied and may exceed what some biologists find practical. Fewer gill-net deployments were needed to reach an RSE ≤ 25% for palmetto bass and Walleyes than to collect 100 stock-length fish. Our results indicate that more samples than are currently prescribed are generally needed to precisely sample sport fishes by means of standardized protocols in Kansas reservoirs. In some instances, obtaining precise samples may not be logistically feasible. In these situations, biologists should be aware of the potential shortcomings of sampling protocols and set objectives accordingly.

Received May 12, 2014; accepted August 23, 2014
Abandoned Agave sisalana fiber crop plantation in the Negev Desert, Israel as source of firewood for local Bedouins
Authors: Lev-Yadun Simcha
Published: November 2014

Firewood is a vital energy source for cooking and heating in traditional societies worldwide. During the past century, increasing human populations have depleted many previously available resources, resulting in severe shortages of firewood in many regions, especially in arid zones. Here, I describe the use as a source of firewood for a local semi-nomadic Bedouin village of several dozen families and the fate of a 0.3 km2abandoned fiber-crop plantation ofAgave sisalanaPerr. which is more than 50 years old in the Negev Desert, Israel. The amount of firewood extracted in the last decade equals several thousand local wild shrubs, which, in the current vegetation density, grow in a radius of several square kilometers. Harvesting the plantation for about 20 years almost fully exploited the plantation. Because the Bedouins do not replant plants used only for firewood, this source is not sustainable despite its biological potential to be so. However, becauseAgaveare CAM (Crassulacean acid metabolism) plants, they can grow under very arid conditions, and because they are well defended from grazing by thorns and poisons, they may be planted as a source of firewood in various arid regions where other plants will not sustain.
Functional characterization of a member of alanine or glycine: cation symporter family in halotolerant cyanobacterium Aphanothece halophytica
Authors: Bualuang Aporn , Kageyama Hakuto , Tanaka Yoshito , Incharoensakdi Aran , Takabe Teruhiro
Published: November 2014

Membrane proteins of amino acid–polyamine–organocation (APC) superfamily transport amino acids and amines across membranes and play important roles in the regulation of cellular processes. The alanine or glycine: cation symporter (AGCS) family belongs to APC superfamily and is found in prokaryotes, but its substrate specificity remains to be clarified. In this study, we found that a halotolerant cyanobacterium, Aphanothece halophytica has two putative ApagcS genes. The deduced amino acid sequence of one of genes, ApagcS1, exhibited high homology to Pseudomonas AgcS. The ApagcS1 gene was expressed in Escherichia coli JW4166 which is deficient in glycine uptake. Kinetics studies in JW4166 revealed that ApAgcS1 is a sodium-dependent glycine transporter. Competition experiments showed the significant inhibition by glutamine, asparagine, and glycine. The level of mRNA for ApagcS1 was induced by NaCl and nitrogen-deficient stresses. Uptake of glutamine by ApAgcS1 was also observed. Based on these data, the physiological role of ApAgcS1 was discussed.
Control of lymphocyte egress from lymph nodes through β2-adrenergic receptors
Authors: Nakai Akiko , Hayano Yuki , Furuta Fumika , Noda Masaki , Suzuki Kazuhiro
Published: November 2014

Lymphocyte recirculation through secondary lymphoid organs is essential for immunosurveillance and lymphocyte effector functions. Here, we show that signals through β2-adrenergic receptors (β2ARs) expressed on lymphocytes are involved in the control of lymphocyte dynamics by altering the responsiveness of chemoattractant receptors. Agonist stimulation of lymphocyte β2ARs inhibited egress of lymphocytes from lymph nodes (LNs) and rapidly produced lymphopenia in mice. Physiological inputs from adrenergic nerves contributed to retention of lymphocytes within LNs and homeostasis of their distribution among lymphoid tissues. β2ARs physically interacted with CCR7 and CXCR4, chemokine receptors promoting lymphocyte retention in LNs. Activation of β2ARs enhanced retention-promoting signals through CCR7 and CXCR4, and consequently inhibited lymphocyte egress from LNs. In models of T cell–mediated inflammatory diseases, β2AR-mediated signals inhibited LN egress of antigen-primed T cells and reduced their recruitment into peripheral tissues. Thus, this study reveals a novel mechanism for controlling lymphocyte trafficking and provides additional insights into immune regulation by the nervous system.
DOCK8 regulates lymphocyte shape integrity for skin antiviral immunity
Authors: Zhang Qian , Dove Christopher G. , Hor Jyh Liang , Murdock Heardley M. , Strauss-Albee Dara M. , Garcia Jordan A. , Mandl Judith N. , Grodick Rachael A. , Jing Huie , Chandler-Brown Devon B. , Lenardo Timothy E. , Crawford Greg , Matthews Helen F. , Freeman Alexandra F. , Cornall Richard J. , Germain Ronald N. , Mueller Scott N. , Su Helen C.
Published: November 2014

DOCK8 mutations result in an inherited combined immunodeficiency characterized by increased susceptibility to skin and other infections. We show that when DOCK8-deficient T and NK cells migrate through confined spaces, they develop cell shape and nuclear deformation abnormalities that do not impair chemotaxis but contribute to a distinct form of catastrophic cell death we term cytothripsis. Such defects arise during lymphocyte migration in collagen-dense tissues when DOCK8, through CDC42 and p21-activated kinase (PAK), is unavailable to coordinate cytoskeletal structures. Cytothripsis of DOCK8-deficient cells prevents the generation of long-lived skin-resident memory CD8 T cells, which in turn impairs control of herpesvirus skin infections. Our results establish that DOCK8-regulated shape integrity of lymphocytes prevents cytothripsis and promotes antiviral immunity in the skin.
Species, Historicity, and Path Dependency
Authors: Ereshefsky Marc
Published: November 2014

This paper clarifies the historical nature of species by showing that species are path-dependent entities. A species’ identity is not determined by its intrinsic properties or its origin, but by its unique evolutionary path. Seeing that species are path-dependent entities has three implications: it shows that origin essentialism is mistaken, it rebuts two challenges to the species-are-historical-entities thesis, and it demonstrates that the identity of a species during speciation depends on future events.
How the Concept of Population Resolves Concepts of Environment
Authors: Millstein Roberta L.
Published: November 2014

Elsewhere, I defend the “causal interactionist population concept” (CIPC). Here I further defend the CIPC by showing how it clarifies another concept that biologists grapple with, namely, environment. Should we understand selection as ranging only over homogeneous environments or, alternatively, as ranging over any habitat area we choose to study? I argue instead that the boundaries of the population dictate the range of the environment, whether homogeneous or heterogeneous, over which selection operates. Thus, understanding the concept of population helps us to understand concepts of selective environment, exemplifying the importance of the CIPC to other concepts and debates.
The Creation and Reuse of Information in Gene Regulatory Networks
Authors: Calcott Brett
Published: November 2014

Recent work on the evolution of signaling systems provides a novel way of thinking about genetic information, where information is passed between genes in a regulatory network. I use examples from evolutionary developmental biology to show how information can be created in these networks and how it can be reused to produce rapid phenotypic change.
A Radical Solution to the Race Problem
Authors: Spencer Quayshawn
Published: November 2014

It has become customary among philosophers and biologists to claim that folk racial classification has no biological basis. This paper attempts to debunk that view. In this paper I show that ‘race’, as used in current US race talk, picks out a biologically real entity. I do this by first showing that ‘race’, in this use, is not a kind term, but a proper name for a set of human population groups. Next, using recent human genetic clustering results, I show that this set of human population groups is a partition of human populations that I call ‘the Blumenbach partition’.
On Space-Time Singularities, Holes, and Extensions
Authors: Manchak John Byron
Published: November 2014

Here, we clarify the relationship among three space-time conditions of interest: geodesic completeness, hole-freeness, and inextendibility. In addition, we introduce a related fourth condition: effective completeness.
On the Fundamentality of Symmetries
Authors: McKenzie Kerry
Published: November 2014

The view that it is symmetries, not particles, that are fundamental to nature is frequently expressed by physicists. But comparatively little has been written either on what this claim means or whether it should be regarded as true. After placing the claim into a general fundamentality framework, I consider whether the priority of symmetries over particles can be defended. The conclusions drawn are largely negative.
Complex Systems and Renormalization Group Explanations
Authors: Morrison Margaret
Published: November 2014

Despite the close connection between the central limit theorem and renormalization group (RG) methods, the latter should be considered fundamentally distinct from the kind of probabilistic framework associated with statistical mechanics, especially the notion of averaging. The mathematics of RG is grounded in dynamical systems theory rather than probability, which raises important issues with respect to the way RG generates explanations of physical phenomena. I explore these differences and show why RG methods should be considered not just calculational tools but the basis for a physical understanding of complex systems in terms of structural properties and relations.
A Novel Exercise for Teaching the Philosophy of Science
Authors: Hardcastle Gary , Slater Matthew H.
Published: November 2014

We describe a simple, flexible exercise that can be implemented in the philosophy of science classroom: students are asked to determine the contents of a closed container without opening it. This exercise has revealed itself as a useful platform from which to examine a wide range of issues in the philosophy of science and may, we suggest, even help us think about improving the public understanding of science.
Neural Signaling of Probabilistic Vectors
Authors: Shea Nicholas
Published: November 2014

Recent work combining cognitive neuroscience with computational modeling suggests that distributed patterns of neural firing may represent probability distributions. This article asks, what makes it the case that distributed patterns of firing, as well as carrying information about (correlating with) probability distributions over worldly parameters, represent such distributions? In examples of probabilistic population coding, it is the way information is used in downstream processing so as to lead to successful behavior. In these cases content depends on factors beyond bare information, contra Brian Skyrms’s view that representational content can be fully characterized in information-theoretic terms.
Hypertension Control and Antihypertensive Therapy in Patients With Chronic Kidney Disease
Authors: Unni Sudhir , White Kellee , Goodman Michael , Ye Xiangyang , Mavros Panagiotis , Bash Lori D. , Brixner Diana
Published: November 2014

BACKGROUND

Hypertension is a major risk factor in the progression of chronic kidney disease (CKD). Although hypertension is more prevalent and treated more often among CKD patients, it is less likely to be controlled. Current guidelines recommend the use of multiple antihypertensive agents to achieve optimal blood pressure (BP) control. However, BP control attained by number and type of antihypertensive therapy according to CKD stage has not been examined thoroughly.

STUDY DESIGN

Cross-sectional analysis of an electronic medical record (EMR) database.

SETTING AND PARTICIPANTS

A total of 115,608 patients with CKD (Stages 1–4) and diagnosed or treated hypertension in General Electric Centricity EMR from 1996 to 2012.

OUTCOME

BP control, based on JNC 7 guidelines, was defined as less than 130/80mm Hg.

MEASUREMENTS

BP and antihypertensive therapy use was obtained from the EMR. The Cockcroft–Gault equation was used to calculate estimated glomerular filtration rate and classify CKD stage.

RESULTS

Overall prevalence of BP control was 24.3%. BP control varied by CKD stage and number of antihypertensive therapy. In multivariable analysis, younger age was less likely to be associated with BP control, regardless of CKD stage. Multiple antihypertensive therapy use and BP control was strongest among CKD Stage 2 (odds ratio (OR): 1.41; 95% confidence interval (CI): 1.05, 1.90). Diuretic use was less likely to be associated with BP control among CKD Stage 1 (OR: 0.71; 95% CI: 0.59, 0.87) and 2 (OR: 0.78; 95% CI: 0.72, 0.85).

LIMITATIONS

Information on antihypertensive prescription fill data and adherence to medication regimens was unavailable.

CONCLUSIONS

This study highlighted the need to pay closer attention to achieving BP treatment goals for younger individuals with CKD. More research is needed to assess the extent to which specific combinations of antihypertensive drugs leads to adequate BP control.
DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent
Authors: Jones Graham , Aydin Zeynep , Oxelman Bengt
Published: November 2014

Motivation: The multispecies coalescent model provides a formal framework for the assignment of individual organisms to species, where the species are modeled as the branches of the sp tree. None of the available approaches so far have simultaneously co-estimated all the relevant parameters in the model, without restricting the parameter space by requiring a guide tree and/or prior assignment of individuals to clusters or species.

Results: We present DISSECT, which explores the full space of possible clusterings of individuals and species tree topologies in a Bayesian framework. It uses an approximation to avoid the need for reversible-jump Markov Chain Monte Carlo, in the form of a prior that is a modification of the birth–death prior for the species tree. It incorporates a spike near zero in the density for node heights. The model has two extra parameters: one controls the degree of approximation and the second controls the prior distribution on the numbers of species. It is implemented as part of BEAST and requires only a few changes from a standard *BEAST analysis. The method is evaluated on simulated data and demonstrated on an empirical dataset. The method is shown to be insensitive to the degree of approximation, but quite sensitive to the second parameter, suggesting that large numbers of sequences are needed to draw firm conclusions.

Availability and implementation: http://tree.bio.ed.ac.uk/software/beast/, http://www.indriid.com/dissectinbeast.html.

Contact: bengt.oxelman@gu.se, www.indriid.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bcl11b prevents the intrathymic development of innate CD8 T cells in a cell intrinsic manner
Authors: Hirose Satoshi , Touma Maki , Go Rieka , Katsuragi Yoshinori , Sakuraba Yoshiyuki , Gondo Yoichi , Abe Manabu , Sakimura Kenji , Mishima Yukio , Kominami Ryo
Published: November 2014

If Bcl11b activity is compromised, CD4+CD8+ double-positive (DP) thymocytes produce a greatly increased fraction of innate CD8+ single-positive (SP) cells highly producing IFN-γ, which are also increased in mice deficient of genes such as Itk, Id3 and NF-κB1 that affect TCR signaling. Of interest, the increase in the former two is due to the bystander effect of IL-4 that is secreted by promyelocytic leukemia zinc finger-expressing NKT and γδT cells whereas the increase in the latter is cell intrinsic. Bcl11b zinc-finger proteins play key roles in T cell development and T cell-mediated immune response likely through TCR signaling. We examined thymocytes at and after the DP stage in Bcl11bF/S826GCD4cre, Bcl11bF/+CD4cre and Bcl11b+/S826G mice, carrying the allele that substituted serine for glycine at the position of 826. Here we show that Bcl11b impairment leads to an increase in the population of TCRαβhighCD44highCD122high innate CD8SP thymocytes, together with two different developmental abnormalities: impaired positive and negative selection accompanying a reduction in the number of CD8SP cells, and developmental arrest of NKT cells at multiple steps. The innate CD8SP thymocytes express Eomes and secrete IFN-γ after stimulation with PMA and ionomycin, and in this case their increase is not due to a bystander effect of IL-4 but cell intrinsic. Those results indicate that Bcl11b regulates development of different thymocyte subsets at multiple stages and prevents an excess of innate CD8SP thymocytes.
First Report of Phakopsora pachyrhizi on Soybean in Costa Rica
Authors: Murillo-Williams A. , Esker P. , Allen T. , Stone C. , Frederick R.
Published: November 2014

Phakopsora meibomiae (Arthur) Arthur has been reported to occur in several legume species in the tropical regions of Central and South America. In Costa Rica, this pathogen was initially reported as P. pachyrhizi Sydow (1); however, to our knowledge, P. pachyrhizi has not been detected in Costa Rica. In routine evaluations of a 0.2-ha field planted with soybean (Glycine max (L.) Merr var. CIGRAS 06) in La Garita, Alajuela, Costa Rica, symptoms similar to Asian soybean rust were observed in December 2012 and January 2013. Soybean plants were at growth stages R4 to R5 when these symptoms were observed, which included yellow spots on leaves with brown spots on the abaxial surface. Further evaluations at growth stage R5 to R6 indicated that the spots had coalesced, turned grayish-brown, and caused substantial defoliation. Microscopic examination of symptomatic leaves showed the presence of uredinia and urediniospores on the lower surface of the leaf. While initial symptoms were on the southern side of the field, a substantial area of the field was infected at the second evaluation. Infected leaves were submitted to the USDA-ARS Foreign Disease-Weed Science Research Unit under the appropriate USDA-Animal Plant Health Inspection Service permit for molecular characterization and identification. Urediniospores were collected by washing infected leaves with sterile water and then pelleted by centrifugation. DNA was extracted from urediniospore pellets and excised leaf pieces using a DNeasy Plant Mini Kit (Qiagen, Germantown, MD), and eight samples were amplified in real-time polymerase chain reaction (PCR) with P. pachyrhizi-specific primers Ppm1 and Ppa2 but not with the P. meibomiae-specific primers Ppm1 and Pme2 (2). Nucleotide sequence alignment of the internal transcribed spacer (ITS) regions 1 and 2 that were amplified by PCR using the primers Ppa1 and Ppa2 further confirmed the identification as P. pachyrhizi. To the best of our knowledge, this is the first known confirmation of soybean rust, caused by P. pachyrhizi in Costa Rica. CIGRAS-06 is the only soybean variety bred in the country as well as one of the very few varieties available for growers. Given that breeding for disease resistance is not a short-term option for P. pachyrhizi, alternative disease management strategies will have to be developed.

References: (1) K. R. Bromfield. Soybean Rust, Monograph No. 11. APS Press, St. Paul, MN, 1984. (2) R. D. Frederick et al. Phytopathology 92:217, 2002.
Potato spindle tuber viroid: Stability on Common Surfaces and Inactivation With Disinfectants
Authors: Mackie A. E. , Coutts B. A. , Barbetti M. J. , Rodoni B. C. , McKirdy S. J. , Jones R. A. C.
Published: November 2014

The length of time Potato spindle tuber viroid (PSTVd) remained infective in extracted tomato leaf sap on common surfaces and the effectiveness of disinfectants against it were investigated. When sap from PSTVd-infected tomato leaves was applied to eight common surfaces (cotton, wood, rubber tire, leather, metal, plastic, human skin, and string) and left for various periods of time (5 min to 24 h) before rehydrating the surface and rubbing onto healthy tomato plants, PSTVd remained infective for 24 h on all surfaces except human skin. It survived best on leather, plastic, and string. It survived less well after 6 h on wood, cotton, and rubber and after 60 min on metal. On human skin, PSTVd remained infective for only 30 min. In general, rubbing surfaces contaminated with dried infective sap directly onto leaves caused less infection than when the sap was rehydrated with distilled water but overall results were similar. The effectiveness of five disinfectant agents at inactivating PSTVd in sap extracts was investigated by adding them to sap from PSTVd-infected leaves before rubbing the treated sap onto leaves of healthy tomato plants. Of the disinfectants tested, 20% nonfat dried skim milk and a 1:4 dilution of household bleach (active ingredient sodium hypochlorite) were the most effective at inactivating PSTVd infectivity in infective sap. When reverse-transcription polymerase chain reaction was used to test the activity of the five disinfectants against PSTVd in infective sap, it detected PSTVd in all instances except in sap treated with 20% nonfat dried skim milk. This study highlights the stability of PSTVd in infective sap and the critical importance of utilizing hygiene practices such as decontamination of clothing, tools, and machinery, along with other control measures, to ensure effective management of PSTVd and, wherever possible, its elimination in solanaceous crops.
Resurgence of Cucurbit Downy Mildew in the United States: A Watershed Event for Research and Extension
Authors: Holmes Gerald J. , Ojiambo Peter S. , Hausbeck Mary K. , Quesada-Ocampo Lina , Keinath Anthony P.
Published: November 2014

In 2004, an outbreak of cucurbit downy mildew (CDM) caused by the oomycete Pseudoperonospora cubensis (Berk. & M. A. Curtis) Rostovzev resulted in an epidemic that stunned the cucumber (Cucumis sativus L.) industry in the eastern United States. The disease affects all major cucurbit crops, including cucumber, muskmelon, squashes, and watermelon. Although the 2004 epidemic began in North Carolina, the cucumber crop from Florida to the northern growing regions in the United States was devastated, resulting in complete crop loss in several areas. Many cucumber fields were abandoned prior to harvest. The rapid spread of the disease coupled with the failure of fungicide control programs surprised growers, crop consultants, and extension specialists. The epidemic raised several fundamental questions about the potential causes for the resurgence of the disease. Some of these questions revolved around whether the epidemic would recur in subsequent years and the possible roles that changes in the host, pathogen, and environment may have played in the epidemic.
Genetic Variability of Grapevine Pinot gris virus and Its Association with Grapevine Leaf Mottling and Deformation
Authors: Saldarelli P. , Giampetruzzi A. , Morelli M. , Malossini U. , Pirolo C. , Bianchedi P. , Gualandri V.
Published: November 2014

The role of Grapevine Pinot gris virus (GPGV) in the etiology of grapevine leaf mottling and deformation was investigated by biological and molecular assays. A survey on different cultivars from the Trentino Region in Italy showed a widespread distribution of GPGV, which was associated with symptomatic (79%) but also with symptomless (21%) vines. Symptomatic and GPGV-infected ‘Pinot gris’ vines induced symptoms on grafted vines of healthy Pinot gris or ‘Traminer’, whereas GPGV-infected but symptomless vines did not. High-throughput sequencing of small RNA (sRNA) populations of two infected Pinot gris accessions confirmed the existence of nearly overlapping viromes in vines with or without symptoms but phylogenetic analyses of the genomes of seven GPGV isolates from Italy and the Czech and Slovak Republics clearly differentiated those infecting symptomatic vines. The involvement of Grapevine rupestris vein feathering virus (GRVFV) in the disease, which was only infecting the symptomatic vine, was ruled out by reverse-transcription polymerase chain reaction studies. Maximum likelihood and Bayesian phylogenetic analysis of two GPGV genomic regions, encompassing part of the movement protein (MP) and coat protein gene sequences and the RNA-dependent RNA polymerase domain of the replicase gene, showed that isolates from symptomatic vines form a lineage distinct from that of symptomless vines. Moreover, the presence or lack of the MP stop codon identified in viral isolates from symptomatic or symptomless vines, respectively, is likely responsible for an MP six amino acids longer in symptomless isolates.
Symmetry breaking and the deconstruction of mass
Authors: Álvarez-Gaumé Luis
Published: November 2014

We briefly review some of the connections between symmetry breaking in condensed matter physics and in particle physics, assisting, in particular, our current understanding of the origin of mass.
Technical challenges of the Large Hadron Collider experiments (ATLAS and CMS)
Authors: Ball Austin
Published: November 2014

This review article introduces the design of the general purpose experiments ATLAS and CMS, which independently discovered the Higgs boson, showing how generic features are motivated by the characteristics needed to explore the physics landscape made accessible by the Large Hadron Collider accelerator, whose high collision rate creates an extremely challenging operating environment for instrumentation. Examples of the very different component designs chosen by the two experiment collaborations are highlighted, as an introduction to briefly describing techniques used in the construction of some of these elements and, subsequently, in the assembly of both detection systems in their respective underground caverns.
Global regime shift dynamics of catastrophic sea urchin overgrazing
Authors: Ling S. D. , Scheibling R. E. , Rassweiler A. , Johnson C. R. , Shears N. , Connell S. D. , Salomon A. K. , Norderhaug K. M. , Pérez-Matus A. , Hernández J. C. , Clemente S. , Blamey L. K. , Hereu B. , Ballesteros E. , Sala E. , Garrabou J. , Cebrian E. , Zabala M. , Fujita D. , Johnson L. E.
Published: November 2014

A pronounced, widespread and persistent regime shift among marine ecosystems is observable on temperate rocky reefs as a result of sea urchin overgrazing. Here, we empirically define regime-shift dynamics for this grazing system which transitions between productive macroalgal beds and impoverished urchin barrens. Catastrophic in nature, urchin overgrazing in a well-studied Australian system demonstrates a discontinuous regime shift, which is of particular management concern as recovery of desirable macroalgal beds requires reducing grazers to well below the initial threshold of overgrazing. Generality of this regime-shift dynamic is explored across 13 rocky reef systems (spanning 11 different regions from both hemispheres) by compiling available survey data (totalling 10 901 quadrats surveyed
in situ
) plus experimental regime-shift responses (observed during a total of 57
in situ
manipulations). The emergent and globally coherent pattern shows urchin grazing to cause a discontinuous ‘catastrophic’ regime shift, with hysteresis effect of approximately one order of magnitude in urchin biomass between critical thresholds of overgrazing and recovery. Different life-history traits appear to create asymmetry in the pace of overgrazing versus recovery. Once shifted, strong feedback mechanisms provide resilience for each alternative state thus defining the catastrophic nature of this regime shift. Importantly, human-derived stressors can act to erode resilience of desirable macroalgal beds while strengthening resilience of urchin barrens, thus exacerbating the risk, spatial extent and irreversibility of an unwanted regime shift for marine ecosystems.
Marine regime shifts: drivers and impacts on ecosystems services
Authors: Rocha J. , Yletyinen J. , Biggs R. , Blenckner T. , Peterson G.
Published: November 2014

Marine ecosystems can experience regime shifts, in which they shift from being organized around one set of mutually reinforcing structures and processes to another. Anthropogenic global change has broadly increased a wide variety of processes that can drive regime shifts. To assess the vulnerability of marine ecosystems to such shifts and their potential consequences, we reviewed the scientific literature for 13 types of marine regime shifts and used networks to conduct an analysis of co-occurrence of drivers and ecosystem service impacts. We found that regime shifts are caused by multiple drivers and have multiple consequences that co-occur in a non-random pattern. Drivers related to food production, climate change and coastal development are the most common co-occurring causes of regime shifts, while cultural services, biodiversity and primary production are the most common cluster of ecosystem services affected. These clusters prioritize sets of drivers for management and highlight the need for coordinated actions across multiple drivers and scales to reduce the risk of marine regime shifts. Managerial strategies are likely to fail if they only address well-understood or data-rich variables, and international cooperation and polycentric institutions will be critical to implement and coordinate action across the scales at which different drivers operate. By better understanding these underlying patterns, we hope to inform the development of managerial strategies to reduce the risk of high-impact marine regime shifts, especially for areas of the world where data are not available or monitoring programmes are not in place.