bluuebunny/crossref_metadata_2025 huggingface dataset:
Root morphological traits that determine phosphorus-acquisition efficiency and critical external phosphorus requirement in pasture species
Authors: Haling Rebecca E. , Yang Zongjian , Shadwell Natalie , Culvenor Richard A. , Stefanski Adam , Ryan Megan H. , Sandral Graeme A. , Kidd Daniel R. , Lambers Hans , Simpson Richard J.
Published: June 2016

Annual pasture legume species can vary more than 3-fold in their critical external phosphorus (P) requirement (i.e. P required for 90% of maximum yield). In this work we investigated the link between root morphology, P acquisition and critical external P requirement among pasture species. The root morphology acclimation of five annual pasture legumes and one grass species to low soil P availability was assessed in a controlled-environment study. The critical external P requirement of the species was low (Dactylis glomerata L., Ornithopus compressus L., Ornithopus sativus Brot.), intermediate (Biserrula pelecinus L., Trifolium hirtum All.) or high (Trifolium subterraneum L.). Root hair cylinder volumes (a function of root length, root hair length and average root diameter) were estimated in order to assess soil exploration and its impact on P uptake. Most species increased soil exploration in response to rates of P supply near or below their critical external P requirement. The legumes differed in how they achieved their maximum root hair cylinder volume. The main variables were high root length density, long root hairs and/or high specific root length. However, total P uptake per unit surface area of the root hair cylinder was similar for all species at rates of P supply below critical P. Species that maximised soil exploration by root morphology acclimation were able to prolong access to P in moderately P-deficient soil. However, among the species studied, it was those with an intrinsic capacity for a high root-hair-cylinder surface area (i.e. long roots and long root hairs) that achieved the lowest critical P requirement.
Musashi-2 (MSI2) supports TGF-β signaling and inhibits claudins to promote non-small cell lung cancer (NSCLC) metastasis
Authors: Kudinov Alexander E. , Deneka Alexander , Nikonova Anna S. , Beck Tim N. , Ahn Young-Ho , Liu Xin , Martinez Cathleen F. , Schultz Fred A. , Reynolds Samuel , Yang Dong-Hua , Cai Kathy Q. , Yaghmour Khaled M. , Baker Karmel A. , Egleston Brian L. , Nicolas Emmanuelle , Chikwem Adaeze , Andrianov Gregory , Singh Shelly , Borghaei Hossein , Serebriiskii Ilya G. , Gibbons Don L. , Kurie Jonathan M. , Golemis Erica A. , Boumber Yanis
Published: June 2016

Significance

The evolutionarily conserved RNA-binding protein Musashi-2 (MSI2) regulates mRNA translation and influences multiple biological processes, including maintenance of stem cell identity. This work for the first time, to our knowledge, identifies that more aggressive patient tumors have higher MSI2 levels. We define a critical role for MSI2 in supporting non-small cell lung cancer (NSCLC) invasiveness and further define claudins 3, 5, and 7 (CLDN3, CLDN5, and CLDN7), TGF-β receptor 1 (TGFβR1), and the small mothers against decapentaplegic homolog 3 (SMAD3) as targets through which MSI2 regulates this process. The observation that MSI2 expression is progressively elevated from an early stage in human NSCLC tumors suggests that this protein may play an essential role in the reprogramming of TGF-β signaling from growth-inhibiting to invasion-promoting during oncogenesis.
Outer membrane vesicles displaying engineered glycotopes elicit protective antibodies
Authors: Chen Linxiao , Valentine Jenny L. , Huang Chung-Jr , Endicott Christine E. , Moeller Tyler D. , Rasmussen Jed A. , Fletcher Joshua R. , Boll Joseph M. , Rosenthal Joseph A. , Dobruchowska Justyna , Wang Zhirui , Heiss Christian , Azadi Parastoo , Putnam David , Trent M. Stephen , Jones Bradley D. , DeLisa Matthew P.
Published: June 2016

Significance

Conjugate vaccines have proven to be an effective and safe strategy for reducing the incidence of disease caused by bacterial pathogens. However, the manufacture of these vaccines is technically demanding, inefficient, and expensive, thereby limiting their widespread use. Here, we describe an alternative methodology for generating glycoconjugate vaccines whereby recombinant polysaccharide biosynthesis is coordinated with vesicle formation in nonpathogenic
Escherichia coli
, resulting in glycosylated outer membrane vesicles (glycOMVs) that can effectively deliver pathogen-mimetic glycotopes to the immune system. An attractive feature of our approach is the fact that different plasmid-encoded polysaccharide biosynthetic pathways can be readily transformed into
E. coli
, enabling a “plug-and-play” platform for the on-demand creation of glycOMV vaccine candidates that carry heterologous glycotopes from numerous pathogenic bacteria.
Neogene biomarker record of vegetation change in eastern Africa
Authors: Uno Kevin T. , Polissar Pratigya J. , Jackson Kevin E. , deMenocal Peter B.
Published: June 2016

The evolution of C4grassland ecosystems in eastern Africa has been intensely studied because of the potential influence of vegetation on mammalian evolution, including that of our own lineage, hominins. Although a handful of sparse vegetation records exists from middle and early Miocene terrestrial fossil sites, there is no comprehensive record of vegetation through the Neogene. Here we present a vegetation record spanning the Neogene and Quaternary Periods that documents the appearance and subsequent expansion of C4grasslands in eastern Africa. Carbon isotope ratios from terrestrial plant wax biomarkers deposited in marine sediments indicate constant C3vegetation from ∼24 Ma to 10 Ma, when C4grasses first appeared. From this time forward, C4vegetation increases monotonically to present, with a coherent signal between marine core sites located in the Somali Basin and the Red Sea. The response of mammalian herbivores to the appearance of C4grasses at 10 Ma is immediate, as evidenced from existing records of mammalian diets from isotopic analyses of tooth enamel. The expansion of C4vegetation in eastern Africa is broadly mirrored by increasing proportions of C4-based foods in hominin diets, beginning at 3.8 Ma inAustralopithecusand, slightly later,Kenyanthropus. This continues into the late Pleistocene inParanthropus, whereasHomomaintains a flexible diet. The biomarker vegetation record suggests the increase in open, C4grassland ecosystems over the last 10 Ma may have operated as a selection pressure for traits and behaviors inHomosuch as bipedalism, flexible diets, and complex social structure.
Neandertals revised
Authors: Roebroeks Wil , Soressi Marie
Published: June 2016

The last decade has seen a significant growth of our knowledge of the Neandertals, a population of Pleistocene hunter-gatherers who lived in (western) Eurasia between ∼400,000 and 40,000 y ago. Starting from a source population deep in the Middle Pleistocene, the hundreds of thousands of years of relative separation between African and Eurasian groups led to the emergence of different phenotypes in Late Pleistocene Europe and Africa. Both recently obtained genetic evidence and archeological data show that the biological and cultural gaps between these populations were probably smaller than previously thought. These data, reviewed here, falsify inferences to the effect that, compared with their near-modern contemporaries in Africa, Neandertals were outliers in terms of behavioral complexity. It is only around 40,000 y ago, tens of thousands of years after anatomically modern humans first left Africa and thousands of years after documented interbreeding between modern humans, Neandertals and Denisovans, that we see major changes in the archeological record, from western Eurasia to Southeast Asia, e.g., the emergence of representational imagery and the colonization of arctic areas and of greater Australia (Sahul).
Overexpression of a pH-sensitive nitrate transporter in rice increases crop yields
Authors: Fan Xiaorong , Tang Zhong , Tan Yawen , Zhang Yong , Luo Bingbing , Yang Meng , Lian Xingming , Shen Qirong , Miller Anthony John , Xu Guohua
Published: June 2016

Significance

Significant progress has been made in our understanding of plant adaptive responses to maintain cellular pH under varied N supply forms. Rice is a plant adapted to grow in waterlogged or dryland environments, in contrast to other crops, such as wheat, soybean, and maize. The nitrate transporter OsNRT2.3b provides a molecular mechanism explaining plant adaptation to the ammonium-nitrate supply shift between the waterlogged and drained soil environments. The sensing of cytosolic pH by OsNRT2.3b can function to improve rice nitrogen use efficiency and pH balance, providing an explanation for plant adaptation to changes in the form of N supply.
IGF-1 degradation by mouse mast cell protease 4 promotes cell death and adverse cardiac remodeling days after a myocardial infarction
Authors: Tejada Thor , Tan Lin , Torres Rebecca A. , Calvert John W. , Lambert Jonathan P. , Zaidi Madiha , Husain Murtaza , Berce Maria D. , Naib Hussain , Pejler Gunnar , Abrink Magnus , Graham Robert M. , Lefer David J. , Naqvi Nawazish , Husain Ahsan
Published: June 2016

Significance

Coronary heart disease is a leading cause of death worldwide. After acute myocardial infarction, early reperfusion limits infarct progression and improves clinical outcomes. However, despite reperfusion, the incidence of heart failure and cardiovascular deaths remains unacceptably high. Here, we report that a few days after ischemia, the reperfused heart transiently elaborates the cardioprotective polypeptide, insulin-like growth factor-1 (IGF-1). However, tissue IGF-1 levels increase only transiently because it is rapidly degraded by the chymase, mouse mast cell protease 4. Mouse mast cell protease 4 deletion promotes cardiac cell survival by reducing IGF-1 degradation, which ameliorates cardiac dysfunction caused by ischemic injury. Our findings suggest that chymase inhibition may be a viable therapeutic approach to enhance late cardioprotection in postischemic heart disease.
Coherent two-dimensional terahertz-terahertz-Raman spectroscopy
Authors: Finneran Ian A. , Welsch Ralph , Allodi Marco A. , Miller Thomas F. , Blake Geoffrey A.
Published: June 2016

Significance

The thermally populated motions of liquids, including hydrogen bonds, low-energy bending vibrations, conformational torsions, and hindered rotations, are resonant in the terahertz region of the spectrum. These motions regulate solvation, macromolecular structure, and vibrational energy flow in liquid-phase chemistry. By exciting terahertz motions nonlinearly with multiple pulses of terahertz light, we can measure their anharmonic coupling and distribution of chemical environments. We can also begin to control their quantum coherence and population, a critical step forward in the control of liquid-phase chemistry with light.
How to do things with glosses
Authors: Schiegg Markus
Published: June 2016

This paper provides a novel view on marginalia from the perspective of linguistic pragmatics. It is based on the observation that existing studies often exclude entries in medieval manuscripts that do not comment on the text directly. Many of them, however, are crucial for understanding what medieval monks did when they studied manuscripts. Searle’s (1969) Speech Act Theory, his typology of illocutionary forces, offers a suitable framework for the systematic analysis of the different kinds of manuscript entries and to reconstruct the intellectual contexts of medieval glossing. We can see that in addition to assertives (i.e., glosses that provide further information on a specific text passage) expressives, directives, commissives and declaratives can also be identified in the margins of medieval manuscripts. Sometimes, even the perlocution of marginalia, their effect on medieval readers, can be traced today.
Accessing Morphosyntax in L1 and L2 Word Recognition
Authors: Bosch Sina , Clahsen Harald
Published: June 2016

In fusional languages, inflectional affixes may encode multiple morphosyntactic features such as case, number, and gender. To determine how these features are accessed during both native (L1) and non-native (L2) word recognition, the present study compares the results from a masked visual priming experiment testing inflected adjectives of German to those of a previous overt (cross-modal) priming experiment on the same phenomenon. While for the L1 group both experiments produced converging results, a group of highly-proficient Russian L2 learners of German showed native-like modulations of repetition priming effects under overt, but not under masked priming conditions. These results indicate that not only affixes but also their morphosyntactic features are accessible during initial form-based lexical access, albeit only for L1 and not for L2 processing. We argue that this contrast is in line with other findings suggesting that non-native language processing is less influenced by structural information than the L1.
Transitivity in similarity judgments on German verbs
Authors: Richter Michael , van Hout Roeland
Published: June 2016

This paper investigates set-theoretical transitive and intransitive similarity relationships in triplets of verbs that can be deduced from raters’ similarity judgments on the pairs of verbs involved. We collected similarity judgments on pairs made up of 35 German verbs and found that the concept of transitivity adds to the information obtained from collecting pair-wise semantic similarity judgments. The concept of transitive similarity enables more complex relations to be revealed in triplets of verbs. To evaluate the outcomes that we obtained by analyzing transitive similarities we used two previously developed verb classifications of the same set of 35 verbs based on the analysis of large corpora (Richter & van Hout, 2016). We applied a modified form of weak stochastic transitivity (Block & Marschak, 1960; Luce & Suppes, 1965; Tversky, 1969) and found that (1), in contrast to Rips’ claim (2011), similarity relations in raters’ judgments systematically turn out to be transitive, and (2) transitivity discloses lexical and aspectual properties of verbs relevant in distinguishing verb classes.
Group III-nitride nanowires
Authors: Bao A.
Published: June 2016

Group III-nitride nanowires have attracted a lot of research interest in the past decade. They contain both the intrinsic properties of III-nitride materials and some unique properties induced by the nanowire structures. This article reviews the growth methods to obtain III-nitride nanowires, and discusses the pros and cons of both top-down and bottom-up approaches, with detailed discussions on different epitaxy methods. The most widely used catalyst-induced epitaxy and extrinsic particle free epitaxy to grow III-nitride nanowires are compared. The properties of those nanowires make them promising candidates for a broad range of applications, including optoelectronic, electronic and electromechanical devices, which are also presented, with a focus on the current challenges and recent progresses.

This review was submitted as part of the 2016 Materials Literature Review Prize of the Institute of Materials, Minerals and Mining run by the Editorial Board of MST. Sponsorship of the prize by TWI Ltd is gratefully acknowledged.
Involvement of MAK-1 and MAK-2 MAP kinases in cell wall integrity in Neurospora crassa
Authors: Kamei Masayuki , Yamashita Kazuhiro , Takahashi Masakazu , Fukumori Fumiyasu , Ichiishi Akihiko , Fujimura Makoto
Published: June 2016

Among three MAPK disruptants of Neurospora crassa, Δmak-1 was sensitive and Δmak-2 was hypersensitive to micafungin, a beta-1,3-glucan synthase inhibitor, than the wild-type or Δos-2 strains. We identified six micafungin-inducible genes that are involved in cell wall integrity (CWI) and found that MAK-1 regulated the transcription of non-anchored cell wall protein gene, ncw-1, and the beta-1,3-endoglucanase gene, bgt-2, whereas MAK-2 controlled the expression of the glycosylhydrolase-like protein gene, gh76-5, and the C4-dicarboxylate transporter gene, tdt-1. Western blotting analysis revealed that, in the wild-type strain, MAK-1 was constitutively phosphorylated from conidial germination to hyphal development. In contrast, the phosphorylation of MAK-2 was growth phase-dependent, and micafungin induced the phosphorylation of unphosphorylated MAK-2. It should be noted that the phosphorylation of MAK-1 was virtually abolished in the Δmak-2 strain, but was significantly induced by micafungin, suggesting functional cross talk between MAK-1 and MAK-2 signalling pathway in CWI.
Temperature dependence on the pesticide sampling rate of polar organic chemical integrative samplers (POCIS)
Authors: Yabuki Yoshinori , Nagai Takashi , Inao Keiya , Ono Junko , Aiko Nobuyuki , Ohtsuka Nobutoshi , Tanaka Hitoshi , Tanimori Shinji
Published: June 2016

Laboratory experiments were performed to determine the sampling rates of pesticides for the polar organic chemical integrative samplers (POCIS) used in Japan. The concentrations of pesticides in aquatic environments were estimated from the accumulated amounts of pesticide on POCIS, and the effect of water temperature on the pesticide sampling rates was evaluated. The sampling rates of 48 pesticides at 18, 24, and 30 °C were obtained, and this study confirmed that increasing trend of sampling rates was resulted with increasing water temperature for many pesticides.
Metal-catalyzed oxidation of 2-alkenals generates genotoxic 4-oxo-2-alkenals during lipid peroxidation
Authors: Nuka Erika , Tomono Susumu , Ishisaka Akari , Kato Yoji , Miyoshi Noriyuki , Kawai Yoshichika
Published: June 2016

Lipid peroxidation products react with cellular molecules, such as DNA bases, to form covalent adducts, which are associated with aging and disease processes. Since lipid peroxidation is a complex process and occurs in multiple stages, there might be yet unknown reaction pathways. Here, we analyzed comprehensively 2′-deoxyguanosine (dG) adducts with oxidized arachidonic acid using liquid chromatography–tandem mass spectrometry and found the formation of 7-(2-oxo-hexyl)-etheno-dG as one of the major unidentified adducts. The formation of this adduct was reproduced in the reaction of dG with 2-octenal and predominantly with 4-oxo-2-octenal (OOE). We also found that other 2-alkenals (with five or more carbons) generate corresponding 4-oxo-2-alkenal-type adducts. Importantly, it was found that transition metals enhanced the oxidation of C4-position of 2-octenal, leading to the formation of OOE-dG adduct. These findings demonstrated a new pathway for the formation of 4-oxo-2-alkenals during lipid peroxidation and might provide a mechanism for metal-catalyzed genotoxicity.
Peptidoglycan-associated outer membrane protein Mep45 of rumen anaerobeSelenomonas ruminantiumforms a non-specific diffusion pore via its C-terminal transmembrane domain
Authors: Kojima Seiji , Hayashi Kanako , Tochigi Saeko , Kusano Tomonobu , Kaneko Jun , Kamio Yoshiyuki
Published: June 2016

The major outer membrane protein Mep45 of Selenomonas ruminantium, an anaerobic Gram-negative bacterium, comprises two distinct domains: the N-terminal S-layer homologous (SLH) domain that protrudes into the periplasm and binds to peptidoglycan, and the remaining C-terminal transmembrane domain, whose function has been unknown. Here, we solubilized and purified Mep45 and characterized its function using proteoliposomes reconstituted with Mep45. We found that Mep45 forms a nonspecific diffusion channel via its C-terminal region. The channel was permeable to solutes smaller than a molecular weight of roughly 600, and the estimated pore radius was 0.58 nm. Truncation of the SLH domain did not affect the channel property. On the basis of the fact that Mep45 is the most abundant outer membrane protein in S. ruminantium, we conclude that Mep45 serves as a main pathway through which small solutes diffuse across the outer membrane of this bacterium.
Learning temporal rules to forecast instability in continuously monitored patients
Authors: Guillame-Bert Mathieu , Dubrawski Artur , Wang Donghan , Hravnak Marilyn , Clermont Gilles , Pinsky Michael R
Published: June 2016

Inductive machine learning, and in particular extraction of association rules from data, has been successfully used in multiple application domains, such as market basket analysis, disease prognosis, fraud detection, and protein sequencing. The appeal of rule extraction techniques stems from their ability to handle intricate problems yet produce models based on rules that can be comprehended by humans, and are therefore more transparent. Human comprehension is a factor that may improve adoption and use of data-driven decision support systems clinically via face validity. In this work, we explore whether we can reliably and informatively forecast cardiorespiratory instability (CRI) in step-down unit (SDU) patients utilizing data from continuous monitoring of physiologic vital sign (VS) measurements. We use a temporal association rule extraction technique in conjunction with a rule fusion protocol to learn how to forecast CRI in continuously monitored patients. We detail our approach and present and discuss encouraging empirical results obtained using continuous multivariate VS data from the bedside monitors of 297 SDU patients spanning 29 346 hours (3.35 patient-years) of observation. We present example rules that have been learned from data to illustrate potential benefits of comprehensibility of the extracted models, and we analyze the empirical utility of each VS as a potential leading indicator of an impending CRI event.
Improving the quality of EHR recording in primary care: a data quality feedback tool
Authors: van der Bij Sjoukje , Khan Nasra , ten Veen Petra , de Bakker Dinny H , Verheij Robert A
Published: June 2016

Objective: Electronic health record (EHR) data are used to exchange information among health care providers. For this purpose, the quality of the data is essential. We developed a data quality feedback tool that evaluates differences in EHR data quality among practices and software packages as part of a larger intervention.

Methods: The tool was applied in 92 practices in the Netherlands using different software packages. Practices received data quality feedback in 2010 and 2012.

Results: We observed large differences in the quality of recording. For example, the percentage of episodes of care that had a meaningful diagnostic code ranged from 30% to 100%. Differences were highly related to the software package. A year after the first measurement, the quality of recording had improved significantly and differences decreased, with 67% of the physicians indicating that they had actively changed their recording habits based on the results of the first measurement. About 80% found the feedback helpful in pinpointing recording problems. One of the software vendors made changes in functionality as a result of the feedback.

Conclusions: Our EHR data quality feedback tool is capable of highlighting differences among practices and software packages. As such, it also stimulates improvements. As substantial variability in recording is related to the software package, our study strengthens the evidence that data quality can be improved substantially by standardizing the functionalities of EHR software packages.
Health informatics and analytics — building a program to integrate business analytics across clinical and administrative disciplines
Authors: Tremblay Monica Chiarini , Deckard Gloria J , Klein Richard
Published: June 2016

Health care organizations must develop integrated health information systems to respond to the numerous government mandates driving the movement toward reimbursement models emphasizing value-based and accountable care. Success in this transition requires integrated data analytics, supported by the combination of health informatics, interoperability, business process design, and advanced decision support tools. This case study presents the development of a master’s level cross- and multidisciplinary informatics program offered through a business school. The program provides students from diverse backgrounds with the knowledge, leadership, and practical application skills of health informatics, information systems, and data analytics that bridge the interests of clinical and nonclinical professionals. This case presents the actions taken and challenges encountered in navigating intra-university politics, specifying curriculum, recruiting the requisite interdisciplinary faculty, innovating the educational format, managing students with diverse educational and professional backgrounds, and balancing multiple accreditation agencies.
Assessment-based health informatics curriculum improvement
Authors: Berner Eta S , Dorsey Amanda D , Garrie Robert L , Qu Haiyan
Published: June 2016

Objective Informatics programs need assurance that their curricula prepare students for intended roles as well as ensuring that students have mastered the appropriate competencies. The objective of this study is to describe a method for using assessment data to identify areas for curriculum, student selection, and assessment improvement.

Materials and Methods A multiple-choice examination covering the content in the Commission for Health Accreditation of Informatics and Information Management Education curricular facets/elements was developed and administered to 2 cohorts of entering students prior to the beginning of the program and to the first cohort after completion of the first year’s courses. The reliability of the examination was assessed using Cronbach’s alpha. Content validity was assessed by having 2 raters assess the match of the items to the Commission for Health Accreditation of Informatics and Information Management Education requirements. Construct validation included comparison of exam performance of instructed vs uninstructed students. Criterion-related validity was assessed by examining the relationship of background characteristics to exam performance and by comparing examination performance to graduate Grade Point Average (GPA).

Results Reliability of the examination was 0.91 and 0.82 (Cohort 1 pre/post-tests) and 0.43 (Cohort 2 pretest). Both raters judged 76% of the test items as appropriate. There were statistically significant differences between the instructed (Cohort 1 post-test) and uninstructed (Cohort 2 pretest) students (t = 2.95 P < .01), as well as between the Cohort 1 pre/post-tests (t = 6.52, P < .001). Neither the background variables nor the graduate GPA were significantly correlated with the examination scores.

Conclusion We found that the examination had generally good psychometric properties and the exceptions could be used to identify areas for curriculum and assessment improvement.
SMART-on-FHIR implemented over i2b2
Authors: Wagholikar Kavishwar B , Mandel Joshua C , Klann Jeffery G , Wattanasin Nich , Mendis Michael , Chute Christopher G , Mandl Kenneth D , Murphy Shawn N
Published: June 2016

We have developed an interface to serve patient data from Informatics for Integrating Biology and the Bedside (i2b2) repositories in the Fast Healthcare Interoperability Resources (FHIR) format, referred to as a SMART-on-FHIR cell. The cell serves FHIR resources on a per-patient basis, and supports the “substitutable” modular third-party applications (SMART) OAuth2 specification for authorization of client applications. It is implemented as an i2b2 server plug-in, consisting of 6 modules: authentication, REST, i2b2-to-FHIR converter, resource enrichment, query engine, and cache. The source code is freely available as open source. We tested the cell by accessing resources from a test i2b2 installation, demonstrating that a SMART app can be launched from the cell that accesses patient data stored in i2b2. We successfully retrieved demographics, medications, labs, and diagnoses for test patients. The SMART-on-FHIR cell will enable i2b2 sites to provide simplified but secure data access in FHIR format, and will spur innovation and interoperability. Further, it transforms i2b2 into an apps platform.
A universal EDF for repeating fast radio bursts?
Authors: Lu Wenbin , Kumar Pawan
Published: June 2016

We make three assumptions: fast radio bursts (FRBs) are produced by neutron stars at cosmological distances; FRB rate tracks the core-collapse supernova rate; and all FRBs repeat with a universal energy distribution function (EDF) $\mathrm{d}\dot{N}/\mathrm{d}E \propto E^{-\beta }$ with a cutoff at burst energy Emax. We then find that observations so far are consistent with a universal EDF with 1.5 ≲ β ≲ 2.2, high-end cutoff Emax/E0 ≳ 30 and normalization $\dot{N}_0 \lesssim 2\rm \ d^{-1}$; where $\dot{N}_0$ is the integrated rate above the reference energy $E_0 \simeq 1.2\times 10^{39} f_{\rm r}^{-1} \rm \ erg$ (fr is the radio emission efficiency). Implications of such an EDF are discussed.
Why Experimenters Might Not Always Want to Randomize, and What They Could Do Instead
Authors: Kasy Maximilian
Published: June 2016

Suppose that an experimenter has collected a sample as well as baseline information about the units in the sample. How should she allocate treatments to the units in this sample? We argue that the answer does not involve randomization if we think of experimental design as a statistical decision problem. If, for instance, the experimenter is interested in estimating the average treatment effect and evaluates an estimate in terms of the squared error, then she should minimize the expected mean squared error (MSE) through choice of a treatment assignment. We provide explicit expressions for the expected MSE that lead to easily implementable procedures for experimental design.
Disparity processing in primary visual cortex
Authors: Henriksen Sid , Tanabe Seiji , Cumming Bruce
Published: June 2016

The first step in binocular stereopsis is to match features on the left retina with the correct features on the right retina, discarding ‘false’ matches. The physiological processing of these signals starts in the primary visual cortex, where the binocular energy model has been a powerful framework for understanding the underlying computation. For this reason, it is often used when thinking about how binocular matching might be performed beyond striate cortex. But this step depends critically on the accuracy of the model, and real V1 neurons show several properties that suggest they may be less sensitive to false matches than the energy model predicts. Several recent studies provide empirical support for an extended version of the energy model, in which the same principles are used, but the responses of single neurons are described as the sum of several subunits, each of which follows the principles of the energy model. These studies have significantly improved our understanding of the role played by striate cortex in the stereo correspondence problem.

This article is part of the themed issue ‘Vision in our three-dimensional world’.
Depth perception in disparity-defined objects: finding the balance between averaging and segregation
Authors: Cammack P. , Harris J. M.
Published: June 2016

Deciding what constitutes an object, and what background, is an essential task for the visual system. This presents a conundrum: averaging over the visual scene is required to obtain a precise signal for object segregation, but segregation is required to define the region over which averaging should take place. Depth, obtained via binocular disparity (the differences between two eyes’ views), could help with segregation by enabling identification of object and background via differences in depth. Here, we explore depth perception in disparity-defined objects. We show that a simple object segregation rule, followed by averaging over that segregated area, can account for depth estimation errors. To do this, we compared objects with smoothly varying depth edges to those with sharp depth edges, and found that perceived peak depth was reduced for the former. A computational model used a rule based on object shape to segregate and average over a central portion of the object, and was able to emulate the reduction in perceived depth. We also demonstrated that the segregated area is not predefined but is dependent on the object shape. We discuss how this segregation strategy could be employed by animals seeking to deter binocular predators.

This article is part of the themed issue ‘Vision in our three-dimensional world’.
Binocular depth processing in the ventral visual pathway
Authors: Verhoef Bram-Ernst , Vogels Rufin , Janssen Peter
Published: June 2016

One of the most powerful forms of depth perception capitalizes on the small relative displacements, or binocular disparities, in the images projected onto each eye. The brain employs these disparities to facilitate various computations, including sensori-motor transformations (reaching, grasping), scene segmentation and object recognition. In accordance with these different functions, disparity activates a large number of regions in the brain of both humans and monkeys. Here, we review how disparity processing evolves along different regions of the ventral visual pathway of macaques, emphasizing research based on both correlational and causal techniques. We will discuss the progression in the ventral pathway from a basic absolute disparity representation to a more complex three-dimensional shape code. We will show that, in the course of this evolution, the underlying neuronal activity becomes progressively more bound to the global perceptual experience. We argue that these observations most probably extend beyond disparity processing
per se
, and pertain to object processing in the ventral pathway in general. We conclude by posing some important unresolved questions whose answers may significantly advance the field, and broaden its scope.

This article is part of the themed issue ‘Vision in our three-dimensional world’.
Lesions to right posterior parietal cortex impair visual depth perception from disparity but not motion cues
Authors: Murphy Aidan P. , Leopold David A. , Humphreys Glyn W. , Welchman Andrew E.
Published: June 2016

The posterior parietal cortex (PPC) is understood to be active when observers perceive three-dimensional (3D) structure. However, it is not clear how central this activity is in the construction of 3D spatial representations. Here, we examine whether PPC is essential for two aspects of visual depth perception by testing patients with lesions affecting this region. First, we measured subjects' ability to discriminate depth structure in various 3D surfaces and objects using binocular disparity. Patients with lesions to right PPC (
N
= 3) exhibited marked perceptual deficits on these tasks, whereas those with left hemisphere lesions (
N
= 2) were able to reliably discriminate depth as accurately as control subjects. Second, we presented an ambiguous 3D stimulus defined by structure from motion to determine whether PPC lesions influence the rate of bistable perceptual alternations. Patients' percept durations for the 3D stimulus were generally within a normal range, although the two patients with bilateral PPC lesions showed the fastest perceptual alternation rates in our sample. Intermittent stimulus presentation reduced the reversal rate similarly across subjects. Together, the results suggest that PPC plays a causal role in both inferring and maintaining the perception of 3D structure with stereopsis supported primarily by the right hemisphere, but do not lend support to the view that PPC is a critical contributor to bistable perceptual alternations.

This article is part of the themed issue ‘Vision in our three-dimensional world’.
Recovering stereo vision by squashing virtual bugs in a virtual reality environment
Authors: Vedamurthy Indu , Knill David C. , Huang Samuel J. , Yung Amanda , Ding Jian , Kwon Oh-Sang , Bavelier Daphne , Levi Dennis M.
Published: June 2016

Stereopsis is the rich impression of three-dimensionality, based on binocular disparity—the differences between the two retinal images of the same world. However, a substantial proportion of the population is stereo-deficient, and relies mostly on monocular cues to judge the relative depth or distance of objects in the environment. Here we trained adults who were stereo blind or stereo-deficient owing to strabismus and/or amblyopia in a natural visuomotor task—a ‘bug squashing’ game—in a virtual reality environment. The subjects' task was to squash a virtual dichoptic bug on a slanted surface, by hitting it with a physical cylinder they held in their hand. The perceived surface slant was determined by monocular texture and stereoscopic cues, with these cues being either consistent or in conflict, allowing us to track the relative weighting of monocular versus stereoscopic cues as training in the task progressed. Following training most participants showed greater reliance on stereoscopic cues, reduced suppression and improved stereoacuity. Importantly, the training-induced changes in relative stereo weights were significant predictors of the improvements in stereoacuity. We conclude that some adults deprived of normal binocular vision and insensitive to the disparity information can, with appropriate experience, recover access to more reliable stereoscopic information.

This article is part of the themed issue ‘Vision in our three-dimensional world’.
A moving observer in a three-dimensional world
Authors: Glennerster Andrew
Published: June 2016

For many tasks such as retrieving a previously viewed object, an observer must form a representation of the world at one location and use it at another. A world-based three-dimensional reconstruction of the scene built up from visual information would fulfil this requirement, something computer vision now achieves with great speed and accuracy. However, I argue that it is neither easy nor necessary for the brain to do this. I discuss biologically plausible alternatives, including the possibility of avoiding three-dimensional coordinate frames such as ego-centric and world-based representations. For example, the distance, slant and local shape of surfaces dictate the propensity of visual features to move in the image with respect to one another as the observer's perspective changes (through movement or binocular viewing). Such propensities can be stored without the need for three-dimensional reference frames. The problem of representing a stable scene in the face of continual head and eye movements is an appropriate starting place for understanding the goal of three-dimensional vision, more so, I argue, than the case of a static binocular observer.

This article is part of the themed issue ‘Vision in our three-dimensional world’.
Effects of generalized pooling on binocular disparity selectivity of neurons in the early visual cortex
Authors: Kato Daisuke , Baba Mika , Sasaki Kota S. , Ohzawa Izumi
Published: June 2016

The key problem of stereoscopic vision is traditionally defined as accurately finding the positional shifts of corresponding object features between left and right images. Here, we demonstrate that the problem must be considered in a four-dimensional parameter space; with respect not only to shifts in space (
X
,
Y
), but also spatial frequency (SF) and orientation (OR). The proposed model sums outputs of binocular energy units linearly over the multi-dimensional V1 parameter space (
X
,
Y
, SF, OR). Theoretical analyses and physiological experiments show that many binocular neurons achieve sharp binocular tuning properties by pooling the output of multiple neurons with relatively broad tuning. Pooling in the space domain sharpens disparity-selective responses in the SF domain so that the responses to combinations of unmatched left–right SFs are attenuated. Conversely, pooling in the SF domain sharpens disparity selectivity in the space domain, reducing the possibility of false matches. Analogous effects are observed for the OR domain in that the spatial pooling sharpens the binocular tuning in the OR domain. Such neurons become selective to relative OR disparity. Therefore, pooling allows the visual system to refine binocular information into a form more desirable for stereopsis.

This article is part of the themed issue ‘Vision in our three-dimensional world’.
A Pd4Br4macrocycle trapped by cocrystallization from a highly dynamic equilibrium of η3-cycloheptatrienide complexes
Authors: Jandl C. , Stegbauer S. , Pöthig A.
Published: June 2016

In the coordination chemistry of palladium, dimers bridgedviahalides are a common motif. Higher oligomers, however, are still rare. We report the structure of an alternating eight-membered [Pd4Br4]4−ring framed by cycloheptatrienide ligands, which was obtained by cocrystallization of dimers and tetramers of the complex salt bromido{η3-[3-(2,6-diisopropylphenyl)imidazolium-1-yl]cycloheptatrienido}palladium(II) tetrafluoroborate, namely bis[di-μ-bromido-bis({η3-[3-(2,6-diisopropylphenyl)imidazolium-1-yl]cycloheptatrienido}palladium(II))]cyclo-tetra-μ-bromido-tetrakis({η3-[3-(2,6-diisopropylphenyl)imidazolium-1-yl]cycloheptatrienido}palladium(II)) octakis(tetrafluoroborate) dichloromethane octasolvate, [Pd4Br4(C22H26N2)4][Pd2Br2(C22H26N2)2]2(BF4)8·8CH2Cl2. These dimers and tetramers form a highly dynamic equilibrium in solution which was studied by low-temperature NMR spectroscopy. In the light of the presented results, tetrameric PdIIspecies can be assumed to co-exist as a second species in many cases where by current knowledge only a dimeric compound would be expected.
Corrosion inhibition studies of cigarette waste on the iron surface in acid medium: electrochemical and surface morphology analysis
Authors: Lucatero Luis Manuel Becerra , Ortega David Turcio , Pandiyan Thangarasu , Singh Narinder , Singh Harpreet , Sarao Tejinder Pal Singh
Published: June 2016

Purpose

The purpose of this paper is to study the corrosion inhibition tendency of cigarette waste (water extracts of cigarette butts, WECB) on an iron surface in an acid medium.

Design/methodology/approach

The electrochemical impedance spectroscopy and polarization techniques were used to analyze the performance of WECB on the iron working electrode. Electrochemical polarization curves were used to determine the intensity of the metal corrosion, specifically to see the effectiveness of the anodic and cathodic reactions in the corrosive medium having WECB. Moreover, the electrochemical impedance of WECB with electrode was analyzed qualitatively. The electrochemical data that relate isotherm adsorption of WECB with iron were analyzed; furthermore, the scanning electron microscope was used to analyze morphology change during the corrosion inhibition.

Findings

After analyzing the impedance data, it is seen that there exists a single capacitive semicircle at the higher frequency range corresponding to a one-time constant in the Bode-phase plot. In the polarization curves studies (Tafel slopes), the current densities of both cathodic and anodic branches are greatly affected in the presence of WECB in the corrosive medium, suggesting that WECB performs as a mixed inhibitor. The free energy data and Temkin adsorption isotherm process show that the adsorption process of WECB on the metal surface follows a physisorption. Furthermore, the WECB-coated metal surface analyzed by scanning electron microscopy confirms the corrosion inhibition of WECB in the acid medium.

Research limitations/implications

An in-depth characterization of the corroded scales is recommended to endorse the results of this study.

Social implications

There may be some people who may challenge that the research may encourage smoking; however, if taken positively, the research offers a very cost-effective and eco-friendly solution to tackle the cigarette waste.

Originality/value

Idea of the present work is to reuse the WECB as corrosion inhibitors for the metal surface, as this waste contains large amount of nicotine, which exhibits corrosion inhibition properties. The present work deals with the study of corrosion inhibition properties of WECB on the iron surface in acid medium. The findings of this study can be very useful from scientific, as well as industrial application point of view. Moreover, the research is important as there is no proper recycling process for this waste so as to maintain a clean environment.
Inhibition effect of Bdellovibrio bacteriovorus on the corrosion of X70 pipeline steel induced by sulfate-reducing bacteria
Authors: Qiu Lina , Mao Yanan , Gong Aijun , Zhang Weiwei , Cao Yanqiu , Tong Lu
Published: June 2016

Purpose

Bdellovibrio bacteriovorus is a gram-negative predatory bacterium which can potentially inhibit microbiologically influenced corrosion by preying on sulfate-reducing bacteria (SRB). However, no researches about the inhibition are reported according to the authors’ knowledge. The purpose of this paper was to investigate the Inhibition effect of B. bacteriovorus on the corrosion of X70 pipeline steel induced by SRB.

Design/methodology/approach

The effect of B. bacteriovorus on the growth of SRB was studied by measuring the optical density at 600 nm (OD600) and sulfate concentration in culture medium. X70 pipeline steel was used as the test material to investigate the anti-corrosion effect of B. bacteriovorus on SRB by conducting electrochemical analysis (including Tafel polarization curves and electrochemical impendence spectroscopy) and weight loss measurement.

Findings

B. bacteriovorus could inhibit the growth of SRB in culture medium by its predation on SRB, which led to decrease of OD600 value and increase of sulfate concentration. The results of electrochemical analysis indicated that B. bacteriovorus had positive inhibition efficiencies on SRB-induced corrosion of X70 pipeline steel. Moreover, corrosion rate of X70 pipeline steel was declined from 19.17 to 3.75 mg·dm-2·day-1 by the presence of B. bacteriovorus.

Originality/value

This is the first report about using B. bacteriovorus to inhibit the corrosion induced by SRB. Compared to other anti-corrosion methods, the microbial inhibition methods exhibit more considerable application value due to its low cost, high efficiency and non-pollution.