bluuebunny/crossref_metadata_2025 huggingface dataset:
The contributions of the actin machinery to endocytic membrane bending and vesicle formation
Authors: Picco Andrea , Kukulski Wanda , Manenschijn Hetty E. , Specht Tanja , Briggs John A. G. , Kaksonen Marko
Published: May 2018

Branched and cross-linked actin networks mediate cellular processes that move and shape membranes. To understand how actin contributes during the different stages of endocytic membrane reshaping, we analyzed deletion mutants of yeast actin network components using a hybrid imaging approach that combines live imaging with correlative microscopy. We could thus temporally dissect the effects of different actin network perturbations, revealing distinct stages of actin-based membrane reshaping. Our data show that initiation of membrane bending requires the actin network to be physically linked to the plasma membrane and to be optimally cross-linked. Once initiated, the membrane invagination process is driven by nucleation and polymerization of new actin filaments, independent of the degree of cross-linking and unaffected by a surplus of actin network components. A key transition occurs 2 s before scission, when the filament nucleation rate drops. From that time point on, invagination growth and vesicle scission are driven by an expansion of the actin network without a proportional increase of net actin amounts. The expansion is sensitive to the amount of filamentous actin and its cross-linking. Our results suggest that the mechanism by which actin reshapes the membrane changes during the progress of endocytosis, possibly adapting to varying force requirements.
Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features
Authors: Bao Yu , Marini Simone , Tamura Takeyuki , Kamada Mayumi , Maegawa Shingo , Hosokawa Hiroshi , Song Jiangning , Akutsu Tatsuya
Published: May 2018

As one of the few irreversible protein posttranslational modifications, proteolytic cleavage is involved in nearly all aspects of cellular activities, ranging from gene regulation to cell life-cycle regulation. Among the various protease-specific types of proteolytic cleavage, cleavages by casapses/granzyme B are considered as essential in the initiation and execution of programmed cell death and inflammation processes. Although a number of substrates for both types of proteolytic cleavage have been experimentally identified, the complete repertoire of caspases and granzyme B substrates remains to be fully characterized.

To tackle this issue and complement experimental efforts for substrate identification, systematic bioinformatics studies of known cleavage sites provide important insights into caspase/granzyme B substrate specificity, and facilitate the discovery of novel substrates. In this article, we review and benchmark 12 state-of-the-art sequence-based bioinformatics approaches and tools for caspases/granzyme B cleavage prediction. We evaluate and compare these methods in terms of their input/output, algorithms used, prediction performance, validation methods and software availability and utility. In addition, we construct independent data sets consisting of caspases/granzyme B substrates from different species and accordingly assess the predictive power of these different predictors for the identification of cleavage sites. We find that the prediction results are highly variable among different predictors. Furthermore, we experimentally validate the predictions of a case study by performing caspase cleavage assay. We anticipate that this comprehensive review and survey analysis will provide an insightful resource for biologists and bioinformaticians who are interested in using and/or developing tools for caspase/granzyme B cleavage prediction.
canvasDesigner: a versatile interactive high-resolution scientific multi-panel visualization toolkit
Authors: Zhang Baohong , Zhao Shanrong , Neuhaus Isaac
Published: May 2018

We present a bioinformatics and systems biology visualization toolkit harmonizing real time interactive exploring and analyzing of big data, full-fledged customizing of look-n-feel and producing multi-panel publication-ready figures in PDF format simultaneously.

Availability and implementation

Source code and detailed user guides are available at http://canvasxpress.org, https://baohongz.github.io/canvasDesigner and https://baohongz.github.io/canvasDesigner/demo_video.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading
Authors: Rahn René , Budach Stefan , Costanza Pascal , Ehrhardt Marcel , Hancox Jonny , Reinert Knut
Published: May 2018

Motivation

Pairwise sequence alignment is undoubtedly a central tool in many bioinformatics analyses. In this paper, we present a generically accelerated module for pairwise sequence alignments applicable for a broad range of applications. In our module, we unified the standard dynamic programming kernel used for pairwise sequence alignments and extended it with a generalized inter-sequence vectorization layout, such that many alignments can be computed simultaneously by exploiting SIMD (single instruction multiple data) instructions of modern processors. We then extended the module by adding two layers of thread-level parallelization, where we (a) distribute many independent alignments on multiple threads and (b) inherently parallelize a single alignment computation using a work stealing approach producing a dynamic wavefront progressing along the minor diagonal.

Results

We evaluated our alignment vectorization and parallelization on different processors, including the newest Intel® Xeon® (Skylake) and Intel® Xeon PhiTM (KNL) processors, and use cases. The instruction set AVX512-BW (Byte and Word), available on Skylake processors, can genuinely improve the performance of vectorized alignments. We could run single alignments 1600 times faster on the Xeon PhiTM and 1400 times faster on the Xeon® than executing them with our previous sequential alignment module.

Availability and implementation

The module is programmed in C++ using the SeqAn (Reinert et al., 2017) library and distributed with version 2.4 under the BSD license. We support SSE4, AVX2, AVX512 instructions and included UME: SIMD, a SIMD-instruction wrapper library, to extend our module for further instruction sets. We thoroughly test all alignment components with all major C++ compilers on various platforms.

Supplementary information

Supplementary data are available at Bioinformatics online.
MACARON: a python framework to identify and re-annotate multi-base affected codons in whole genome/exome sequence data
Authors: Khan Waqasuddin , Varma Saripella Ganapathi , Ludwig Thomas , Cuppens Tania , Thibord Florian , Génin Emmanuelle , Deleuze Jean-Francois , Trégouët David-Alexandre
Published: May 2018

Predicted deleteriousness of coding variants is a frequently used criterion to filter out variants detected in next-generation sequencing projects and to select candidates impacting on the risk of human diseases. Most available dedicated tools implement a base-to-base annotation approach that could be biased in presence of several variants in the same genetic codon. We here proposed the MACARON program that, from a standard VCF file, identifies, re-annotates and predicts the amino acid change resulting from multiple single nucleotide variants (SNVs) within the same genetic codon. Applied to the whole exome dataset of 573 individuals, MACARON identifies 114 situations where multiple SNVs within a genetic codon induce an amino acid change that is different from those predicted by standard single SNV annotation tool. Such events are not uncommon and deserve to be studied in sequencing projects with inconclusive findings.

Availability and implementation

MACARON is written in python with codes available on the GENMED website (www.genmed.fr).

Supplementary information

Supplementary data are available at Bioinformatics online.
Learning through participation: towards defining adult learning in an African rural village context
Authors: Hlela Zamokwakho
Published: May 2018

This article analyses the studies of adult learning in Africa, where they exist, often draw uncritically on Western theoretical and methodological frameworks such as andragogy, experiential learning, and transformative learning. These frameworks are informed by individualistic conceptions of learners and learning, shaped by industrial and postindustrial political economy, liberal democratic politics and consumerist culture. Such structures are then imposed on African ‘territories’ of learning, much like a colonial template for carving up the continent, for and under Western eyes. This article, based on a study conducted in a rural village in South Africa, challenges the appropriateness of these frameworks. It adopts an Afrocentric research paradigm which understands research as a collective and collaborative humanizing project which is contextually sensitive and culturally informed. The article presents four community learning places, defines the nature of learning in each place, and concludes that learning in the village is still informed by values of interdependence, interconnectedness, and spiritual values.
Can power-sharing foster peace? Evidence from Northern Ireland*
Authors: Mueller Hannes , Rohner Dominic
Published: May 2018

In the absence of power-sharing, minority groups in opposition have powerful incentives to substitute the ballot with the bullet. In contrast, when power is shared among all major groups in society, the relative gains of sticking to electoral politics are larger for minority groups. After making the theoretical argument, we provide in the current paper an empirical analysis of the impact of power-sharing at the local level, making use of fine-grained data from Northern Ireland’s 26 local district councils over the 1973–2001 period. We find that power-sharing has a sizable and robust conflict-reducing impact.
Alignment and political will: upscaling an Australian respectful relationships program
Authors: Joyce Andrew , Green Celia , Kearney Sarah , Leung Loksee , Ollis Debbie
Published: May 2018

Many small scale efficacious programs and interventions need to be ‘scaled-up’ in order to reach a larger population. Although it has been argued that interventions deemed suitable for upscaling need to have demonstrated effectiveness, be able to be implemented cost-effectively and be accepted by intended recipients, these factors alone are insufficient in explaining which programs are adopted more broadly. Upscaling research often identifies political will as a key factor in explaining whether programs are supported and up-scaled, but this research lacks any depth into how political will is formed and has not applied policy theories to understanding the upscaling process. This article uses a political science lens to examine the key factors in the upscaling process of a Respectful Relationships in Schools Program. Focus groups and interviews were conducted with project staff, managers and community organizations involved in the program. The results reveal how a key focusing event related to a highly profiled personal tragedy propelled family violence into the national spotlight. At the same time, the organization leading the respectful relationships program leveraged their networks to position the program within the education department which enabled the government to quickly respond to the issue. The study highlights that political will is not a stand-alone factor as depicted by up-scaling models, but rather is the end point of a complex process that involves many elements including the establishment of networks and aligned programs that can capitalize when opportunities arise.
Question-Order Effects in the Evaluation of Political Institutions in Decentralized Polities
Authors: Tormos Raül
Published: May 2018

This research studies question-order effects in the evaluation of political institutions in socially heterogeneous regions within decentralized countries. Split-ballot experiments were embedded in 3 representative surveys fielded in the Spanish region of Catalonia. Significant consistency effects were spotted in all samples. Respondents who first evaluated the relatively less valued institutions of one governmental level assessed less favorably the relatively better rated institutions of the other level. Clear evidence of the reverse effect was present only in 1 of the experiments. In addition, heterogeneous question-order effects emerged among the 2 distinct national communities coexisting in Catalonia. The article suggests a mechanism beneath this sort of question-order effects and further proposes and empirically tests a remedial solution.
A Pair of Rigid Surfaces with pg= q = 2 and K2= 8 Whose Universal Cover is Not the Bidisk
Authors: Polizzi Francesco , Rito Carlos , Roulleau Xavier
Published: May 2018

We construct two complex-conjugated rigid minimal surfaces with $p_g\!=q=2$ and $K^2\!=8$ whose universal cover is not biholomorphic to the bidisk $\mathbb{H} \times \mathbb{H}$. We show that these are the unique surfaces with these invariants and Albanese map of degree 2, apart from the family of product-quotient surfaces given in [33]. This completes the classification of surfaces with $p_g=q=2, K^2=8$, and Albanese map of degree 2.
Primordial mass and density segregation in a young molecular cloud
Authors: Alfaro Emilio J , Román-Zúñiga Carlos G
Published: May 2018

We analyse the geometry of the Pipe Nebula, drawn by the distribution (Q spatial parameter) and hierarchy (Λ spatial segregation) of column density peaks previously detected and catalogued. By analysing the mass and volume density of the cores, we determine that both variables show spatial segregation with a high degree of substructure. In view of the early evolutionary state of the Pipe Nebula, our results suggest that segregation both by mass and by volume density may be primordial, in the sense of appearing early in the chain of physical processes that lead to cluster formation. We propose that volume density, and not mass, is the parameter that most clearly determines the initial spatial distribution of pre-stellar cores.
A reevaluation of the proposed spin-down of the white dwarf pulsar in AR Scorpii
Authors: Potter Stephen B , Buckley David A H
Published: May 2018

We present high-speed optical photometric observations, spanning ∼2 yr, of the recently discovered white dwarf pulsar AR Scorpii. The amplitudes of the orbital, spin, and beat modulations appear to be remarkably stable and repeatable over the time span of our observations. It has been suggested that the polarized and non-polarized emission from AR Scorpii is powered by the spin-down of the white dwarf. However, we find that our new data are inconsistent with the published spin-down ephemeris. Whilst our data are consistent with a constant spin period, further observations over an extended time-base are required in order to ascertain the true spin-evolution of the white dwarf. This may have implications for the various models put forward to explain the energetics and evolution of AR Scorpii.
Rate of Return to Military Active Duty After Single and 2-Level Anterior Cervical Discectomy and Fusion: A 4-Year Retrospective Review
Authors: Tumialán Luis M , Ponton Ryan P , Cooper Angelina N , Gluf Wayne M , Tomlin Jeffrey M
Published: May 2018

BACKGROUND

Over the years of rigorous of military service, military personnel may experience cervical spondylosis and radiculopathy. Given the frequency of this occurrence, the capacity to return to unrestricted full duty in the military after anterior cervical discectomy and fusion (ACDF) is worthy of analysis.

OBJECTIVE

To identify the rate of return to full, unrestricted active duty after single and 2-level anterior cervical discectomy, and fusion surgery in military personnel.

METHODS

A retrospective chart review was performed at a tertiary care military treatment facility for all active duty personnel who underwent a single or 2-level ACDF over a 4-yr period. Patient and procedural data were collected to include single or 2-level fusion, indication for surgery, fusion level, tobacco use, age, and military rank. Fischer's Exact and Wilcoxon Rank Sum tests were used to identify statistically significant differences in the rate of return to active duty.

RESULTS

A total of 132 anterior cervical discectomy and fusions were analyzed. One hundred sixteen patients (88%) were able to return to unrestricted full active duty, while the remaining 16 required separation from the military for continued pain or disability. The return to active duty rate was significantly higher in service members with a rank of E7 or above (99%) than those E6 and below (73%). There was a strong association between the presence of a pseudoarthrosis and the capacity to return to full duty (P = .013).

CONCLUSION

Both single and 2-level ACDFs have high overall success with an 88% rate of return to full duty.
Leveraging Antimicrobial Stewardship in the Emergency Department to Improve the Quality of Urinary Tract Infection Management and Outcomes
Authors: Jorgensen Sarah C J , Yeung Samantha L , Zurayk Mira , Terry Jill , Dunn Maureen , Nieberg Paul , Pallares Jean , Wong-Beringer Annie
Published: May 2018

Background

The complex and fast-paced emergency department (ED) practice setting presents unique challenges that demand a tailored approach to antimicrobial stewardship. In this article, we describe the strategies applied by 1 institution’s antimicrobial stewardship program (ASP) that were successful in improving prescribing practices and outcomes for urinary tract infection (UTI) in the ED.

Methods

Core strategies included pre-implementation research characterizing the patient population, antimicrobial resistance patterns, prescribing behavior, and morbidity related to infection; collaboration across multiple disciplines; development and implementation of a UTI treatment algorithm; education to increase awareness of the algorithm and the background and rationale supporting it; audit and feedback; and early evaluation of post-implementation outcomes.

Results

We observed a rapid change in prescribing post-implementation with increased empiric nitrofurantoin use and reduced cephalosporin use (P < .05). Our elevation of nitrofurantoin to firstline status was supported by our post-implementation analysis showing that its use was independently associated with reduced 30-day return visits (adjusted odds ratio, 0.547; 95% confidence interval, 0.312–0.960). Furthermore, despite a shift to a higher risk population and a corresponding decrease in antimicrobial susceptibility rates post-implementation, the preferential use of nitrofurantoin did not result in higher bug-drug mismatches while 30-day return visits to the ED remained stable.

Conclusions

We demonstrate that an outcomes-based ASP can impart meaningful change to knowledge and attitudes affecting prescribing practices in the ED. The success of our program may be used by other institutions as support for ASP expansion to the ED.
Assessing the public health impact of cannabis legalization in Canada: core outcome indicators towards an ‘index’ for monitoring and evaluation
Authors: Fischer Benedikt , Russell Cayley , Rehm Jürgen , Leece Pamela
Published: May 2018

The legalization of non-medical cannabis use and supply is impending in Canada. This constitutes a major policy change with the declared objective of improving public health outcomes, which requires rigorous monitoring and evaluation. While numerous different aspects associated with legalization will be examined, a focused perspective is required for effective policy evaluation purposes. To these ends, we have identified a set of 10 core indicators associated with cannabis-related risk/harm outcomes—based on current best evidence—that are expected to measure the primary impacts of legalization on public health outcomes. We briefly review these indicators, and their respective data availability in Canada. As ideally an integrated outcome assessment of cannabis legalization’s impact on public health will be available, we further propose options to merge the individual indicators into an integrated, weighted ‘index’, considering their expected relative impact for public health. One possible approach to undertake this is ‘multi-criteria decision analysis’ as a method to weight the relative indicator impact on public health; alternative approaches are proposed. The integrated ‘public health index’ for cannabis legalization will allow for scientifically comprehensive, while focused, monitoring and evaluation of the effects of legalization in Canada for the benefits of science and evidence-based policy alike.
HrpS Is a Global Regulator on Type III Secretion System (T3SS) and Non-T3SS Genes in Pseudomonas savastanoi pv. phaseolicola
Authors: Wang Jingru , Shao Xiaolong , Zhang Yingchao , Zhu Yanan , Yang Pan , Yuan Jian , Wang Tingting , Yin Chunyan , Wang Wei , Chen Sheng , Liang Haihua , Deng Xin
Published: May 2018

The type III secretion system (T3SS) is the main machinery for Pseudomonas savastanoi and other gram-negative bacteria to invade plant cells. HrpR and HrpS form a hetero-hexamer, which activates the expression of HrpL, which induces all T3SS genes by binding to a ‘hrp box’ in promoters. However, the individual molecular mechanism of HrpR or HrpS has not been fully understood. Through chromatin immunoprecipitation coupled to high-throughput DNA sequencing, we found that HrpR, HrpS, and HrpL had four, 47, and 31 targets on the genome, respectively. HrpS directly bound to the promoter regions of a group of T3SS genes and non-T3SS genes. HrpS independently regulated these genes in a hrpL deletion strain. Additionally, a HrpS-binding motif (GTGCCAAA) was identified, which was verified by electrophoretic mobility shift assay and lux-reporter assay. HrpS also regulated motility and biofilm formation in P. savastanoi. The present study strongly suggests that HrpS alone can work as a global regulator on both T3SS and non-T3SS genes in P. savastanoi.

[Formula: see text] Copyright © 2018 The Author(s). This is an open-access article distributed under the CC BY-NC-ND 4.0 International license .
Occurrence of Foliar Pathogens of Watermelon on Commercial Farms in South Carolina Estimated with Stratified Cluster Sampling
Authors: Rennberger Gabriel , Gerard Patrick , Keinath Anthony P.
Published: May 2018

A survey of foliar pathogens of watermelon based on two-stage cluster sampling was conducted on commercial farms in South Carolina in spring 2015, spring and fall 2016, and fall 2017. In total, 60 fields from 27 different growers in seven counties representing the main watermelon-producing areas in the state were sampled, using a stratified two-stage cluster sampling approach. In the sampling design, counties corresponded to strata, growers to first-stage clusters, and fields to second-stage clusters. In each field, 100 symptomatic leaves were collected at five equidistant sampling points along four transects encompassing a square shape of 2,500 m2. After collection, pathogens were identified based on reproductive structures formed on leaves during >12 h incubation. Estimates were obtained for the statewide probability of pathogen occurrence and associations between pathogen pairs. Six fungal pathogens, Stagonosporopsis spp., Podosphaera xanthii, Cercospora citrullina, Colletotrichum orbiculare, Myrothecium sensu lato (s.l.), and Corynespora cassiicola; the oomycete Pseudoperonospora cubensis; and three viral pathogens were identified on the examined leaves. With the exception of fall 2017, Stagonosporopsis spp. was the most prevalent pathogen in every season, followed by P. xanthii. The highest occurrence of P. cubensis was in spring 2015; it did not occur in 2016. The highest occurrence of C. orbiculare was in spring 2016; it did not occur in spring 2015. Myrothecium s.l. was the most common pathogen in fall 2017 and the second most common pathogen occurring by itself in fall 2016. The third most common pathogen in fall 2017, Corynespora cassiicola, was not observed in any other season. Eight of the 80 isolates of Stagonosporopsis spp. collected were identified as S. caricae, the rest as S. citrulli. All isolates of S. caricae were found in spring 2015 and originated from two fields in different counties. A total of three positive and five negative associations were found between pathogen pairs co-occurring on the same leaf. A positive association between Stagonosporopsis spp. and C. citrullina was the only significant association between pathogens found in two seasons, spring 2015 and spring 2016. Based on estimates of probability of pathogen occurrence across seasons, Stagonosporopsis spp. and P. xanthii are the most common pathogens on watermelons in South Carolina. This is the first report of C. cassiicola, S. caricae, and Myrothecium s.l. on watermelon in South Carolina.
Getting somewhere with the Red Queen: chasing a biologically modern definition of the hypothesis
Authors: Strotz Luke C. , Simões Marianna , Girard Matthew G. , Breitkreuz Laura , Kimmig Julien , Lieberman Bruce S.
Published: May 2018

The Red Queen hypothesis (RQH) is both familiar and murky, with a scope and range that has broadened beyond its original focus. Although originally developed in the palaeontological arena, it now encompasses many evolutionary theories that champion biotic interactions as significant mechanisms for evolutionary change. As such it de-emphasizes the important role of abiotic drivers in evolution, even though such a role is frequently posited to be pivotal. Concomitant with this shift in focus, several studies challenged the validity of the RQH and downplayed its propriety. Herein, we examine in detail the assumptions that underpin the RQH in the hopes of furthering conceptual understanding and promoting appropriate application of the hypothesis. We identify issues and inconsistencies with the assumptions of the RQH, and propose a redefinition where the Red Queen's reign is restricted to certain types of biotic interactions and evolutionary patterns occurring at the population level.
Data-driven dynamical model indicates that the heat shock response in
Chlamydomonas reinhardtii
is tailored to handle natural temperature variation
Authors: Magni Stefano , Succurro Antonella , Skupin Alexander , Ebenhöh Oliver
Published: May 2018

Global warming exposes plants to severe heat stress, with consequent crop yield reduction. Organisms exposed to high temperature stresses typically protect themselves with a heat shock response (HSR), where accumulation of unfolded proteins initiates the synthesis of heat shock proteins through the heat shock transcription factor HSF1. While the molecular mechanisms are qualitatively well characterized, our quantitative understanding of the underlying dynamics is still very limited. Here, we study the dynamics of HSR in the photosynthetic model organism
Chlamydomonas reinhardtii
with a data-driven mathematical model of HSR. We based our dynamical model mostly on mass action kinetics, with a few nonlinear terms. The model was parametrized and validated by several independent datasets obtained from the literature. We demonstrate that HSR quantitatively and significantly differs if an increase in temperature of the same magnitude occurs abruptly, as often applied under laboratory conditions, or gradually, which would rather be expected under natural conditions. In contrast to rapid temperature increases, under gradual changes only negligible amounts of misfolded proteins accumulate, indicating that the HSR of
C. reinhardtii
efficiently avoids the accumulation of misfolded proteins under conditions most likely to prevail in nature. The mathematical model we developed is a flexible tool to simulate the HSR to different conditions and complements the current experimental approaches.
Catalytic methyl esterification of colophony over ZnO/SFCCR with subcritical CO
2
: catalytic performance, reaction pathway and kinetics
Authors: Wang Xubin , Wang Linlin , Chen Xiaopeng , Zhou Dan , Xiao Han , Wei Xiaojie , Liang Jiezhen
Published: May 2018

A heterogeneous catalyst (ZnO/SFCCR) composed of ZnO supported on spent fluid cracking catalyst by wet impregnation was synthesized and applied to the esterification of colophony acids with methanol under subcritical CO
2
conditions. The catalyst was characterized by SEM-EDS, BET, ICP, FTIR, XRD and Py-IR. An experimental set-up involving a new injection technique was designed to promote the heterogeneous methyl esterification, and the subcritical CO
2
played a role in auxiliary acid catalysis (a pH range of 3.54–3.91), increasing the lifespan of ZnO/SFCCR, reducing the viscosity of the system to promote gas–liquid mass transfer. A maximum conversion rate of 97.01% was obtained in a relatively short time of 5 h. Kinetic experiments were performed from 190 to 220°C using a special high-temperature sampling device and analysing aliquots with high-performance liquid chromatography. A new reaction pathway, involving methyl abietate, methyl dehydroabietate, methyl neoabietate and methyl palustrate along with other kinds of colophony acids, was developed. The kinetic parameters were obtained using the Levenberg–Marquardt nonlinear least-squares method, and the activation energies for the isomerizations of neoabietic and palustric acids and for the methyl esterification of neoabietic, abietic, palustric and dehydroabietic acids were found to be 107.09, 113.95, 68.99, 49.85, 75.43 and 59.20 kJ mol
−1
, respectively. The results from the kinetic model were in good agreement with experimental values.
Bare carbon electrodes as simple and efficient sensors for the quantification of caffeine in commercial beverages
Authors: Redivo Luca , Stredanský Miroslav , De Angelis Elisabetta , Navarini Luciano , Resmini Marina , Švorc Ĺubomír
Published: May 2018

Food quality control is a mandatory task in the food industry and relies on the availability of simple, cost-effective and stable sensing platforms. In the present work, the applicability of bare glassy carbon electrodes for routine analysis of food samples was evaluated as a valid alternative to chromatographic techniques, using caffeine as test analyte. A number of experimental parameters were optimized and a differential pulse voltammetry was applied for quantification experiments. The detection limit was found to be 2 × 10−5 M (3σ criterion) and repeatability was evaluated by the relative standard deviation of 4.5%. The influence of sugars, and compounds structurally related to caffeine on the current response of caffeine was evaluated and found to have no significant influence on the electrode performance. The suitability of bare carbon electrodes for routine analysis was successfully demonstrated by quantifying caffeine content in seven commercially available drinks and the results were validated using a standard ultra-high performance liquid chromatography method. This work demonstrates that bare glassy carbon electrodes are a simple, reliable and cost-effective platform for rapid analysis of targets such as caffeine in commercial products and they represent therefore a competitive alternative to the existing analytical methodologies for routine food analysis.
Detection of nitrite based on fluorescent carbon dots by the hydrothermal method with folic acid
Authors: Lin Haitao , Ding Liyun , Zhang Bingyu , Huang Jun
Published: May 2018

A fluorescent carbon dots probe for the detection of aqueous nitrite was fabricated by a one-pot hydrothermal method, and the transmission electron microscope, X-ray diffractometer, UV–Vis absorption spectrometer and fluorescence spectrophotometer were used to study the property of carbon dots. The fluorescent property of carbon dots influenced by the concentration of aqueous nitrite was studied. The interaction between the electron-donating functional groups and the electron-accepting nitrous acid could account for the quenching effect on carbon dots by adding aqueous nitrite. The products of the hydrolysis of aqueous nitrite performed a stronger quenching effect at lower pH. The relationship between the relative fluorescence intensity of carbon dots and the concentration of nitrite was described by the Stern–Volmer equation (I0/I − 1 = 0.046[Q]) with a fine linearity (R2 = 0.99). The carbon dots-based probe provides a convenient method for the detection of nitrite concentration.
Competition between sympatric wolf taxa: an example involving African and Ethiopian wolves
Authors: Gutema Tariku Mekonnen , Atickem Anagaw , Bekele Afework , Sillero-Zubiri Claudio , Kasso Mohammed , Tsegaye Diress , Venkataraman Vivek V. , Fashing Peter J. , Zinner Dietmar , Stenseth Nils C.
Published: May 2018

Carnivore populations are declining globally due to range contraction, persecution and prey depletion. One consequence of these patterns is increased range and niche overlap with other carnivores, and thus an elevated potential for competitive exclusion. Here, we document competition between an endangered canid, the Ethiopian wolf (EW), and the newly discovered African wolf (AW) in central Ethiopia. The diet of the ecological specialist EW was dominated by rodents, whereas the AW consumed a more diverse diet also including insects and non-rodent mammals. EWs used predominantly intact habitat, whereas AWs used mostly areas disturbed by humans and their livestock. We observed 82 encounters between the two species, of which 94% were agonistic. The outcomes of agonistic encounters followed a territory-specific dominance pattern, with EWs dominating in intact habitat and AWs in human-disturbed areas. For AWs, the likelihood of winning encounters also increased with group size. Rodent species consumed by EWs were also available in the human-disturbed areas, suggesting that these areas could be suitable habitat for EWs if AWs were not present. Increasing human encroachment not only affects the prey base of EWs, but also may impact their survival by intensifying competition with sympatric AWs.
Emo, love and god: making sense of Urban Dictionary, a crowd-sourced online dictionary
Authors: Nguyen Dong , McGillivray Barbara , Yasseri Taha
Published: May 2018

The Internet facilitates large-scale collaborative projects and the emergence of Web 2.0 platforms, where producers and consumers of content unify, has drastically changed the information market. On the one hand, the promise of the ‘wisdom of the crowd’ has inspired successful projects such as Wikipedia, which has become the primary source of crowd-based information in many languages. On the other hand, the decentralized and often unmonitored environment of such projects may make them susceptible to low-quality content. In this work, we focus on Urban Dictionary, a crowd-sourced online dictionary. We combine computational methods with qualitative annotation and shed light on the overall features of Urban Dictionary in terms of growth, coverage and types of content. We measure a high presence of opinion-focused entries, as opposed to the meaning-focused entries that we expect from traditional dictionaries. Furthermore, Urban Dictionary covers many informal, unfamiliar words as well as proper nouns. Urban Dictionary also contains offensive content, but highly offensive content tends to receive lower scores through the dictionary’s voting system. The low threshold to include new material in Urban Dictionary enables quick recording of new words and new meanings, but the resulting heterogeneous content can pose challenges in using Urban Dictionary as a source to study language innovation.
Collective cell migration without proliferation: density determines cell velocity and wave velocity
Authors: Tlili Sham , Gauquelin Estelle , Li Brigitte , Cardoso Olivier , Ladoux Benoît , Delanoë-Ayari Hélène , Graner François
Published: May 2018

Collective cell migration contributes to embryogenesis, wound healing and tumour metastasis. Cell monolayer migration experiments help in understanding what determines the movement of cells far from the leading edge. Inhibiting cell proliferation limits cell density increase and prevents jamming; we observe long-duration migration and quantify space–time characteristics of the velocity profile over large length scales and time scales. Velocity waves propagate backwards and their frequency depends only on cell density at the moving front. Both cell average velocity and wave velocity increase linearly with the cell effective radius regardless of the distance to the front. Inhibiting lamellipodia decreases cell velocity while waves either disappear or have a lower frequency. Our model combines conservation laws, monolayer mechanical properties and a phenomenological coupling between strain and polarity: advancing cells pull on their followers, which then become polarized. With reasonable values of parameters, this model agrees with several of our experimental observations. Together, our experiments and model disantangle the respective contributions of active velocity and of proliferation in monolayer migration, explain how cells maintain their polarity far from the moving front, and highlight the importance of strain–polarity coupling and density in long-range information propagation.
Effects of thermal treatment on the properties of defatted soya bean flour and its adhesion to plywood
Authors: Zhang Bing-Han , Fan Bo , Li Ming , Zhang Yue-Hong , Gao Zhen-Hua
Published: May 2018

With an attempt to economically and efficiently improve the water resistance of defatted soya bean flour (DSF)-based wood adhesives, DSF was subjected to thermal treatment at various temperatures (65°C, 80°C, 95°C, 110°C and 125°C) for 30 min. The effects of thermal treatment temperature onto the chemical structure, crystalline degree, water-insoluble content and acetaldehyde value of the thermally treated DSF (T-DSF) were investigated. The thermal stabilities and bonding properties of soya bean adhesives prepared from T-DSF and cross-linker epichlorohydrin-modified polyamide (EMPA) were also investigated. Test results indicated that both the water-insoluble content and the acetaldehyde value of T-DSF increased after thermal treatment, reaching the highest values of 27.28% and 26.81 mg g
−1
, respectively. All plywood bonded with the T-DSF-based adhesive withstood a 28 h boiling–dry–boiling accelerated ageing treatment, while plywood bonded with the DSF-based adhesive delaminated after 4 h of water boiling, demonstrating the significantly improved water resistance of the T-DSF-based adhesives. Related analyses also confirmed that this improvement was due to: (i) the formation of insoluble cross-linked structures of T-DSF resulting from protein–protein self-cross-linking reactions and the protein–carbohydrate Maillard reaction and (ii) increased cross-linking efficiency between T-DSF and cross-linker EMPA owing to more T-DSF-reactive groups being released after thermal treatment.
Investigation on the hydrolytic mechanism of cucurbit[6]uril in alkaline solution
Authors: Zhu Chao , Meng Zihui , Liu Wenjin , Ma Hongwei , Li Jiarong , Yang Tongtong , Liu Yang , Liu Ni , Xu Zhibin
Published: May 2018

The structure of cucurbit[6]uril (CB[6]), as a fascinating supramolecular receptor, is regarded as ‘indestructible’. Herein, we investigated the hydrolysis of CB[6] catalysed by alkali. Our results showed that CB[6] was easily hydrolysed in 30% NaOH at 160°C within 3 h. Separation and purification of hydrolytic products demonstrated the presence of NH
3
, CO
2
, HCOONa, glycine and hydantoic acid. Based on the studies of the hydrolysis of substances similar to CB[6] including 4,5-dihydroxyethyleneurea, glycoluril and glycoluril dimer, we proposed that a plausible reaction mechanism involved a Cannizzaro reaction, which is supported by HPLC, mass spectrometry data and previous reports. Further studies are dedicated towards a controlled hydrolysis of CB[6], which will provide a new route for direct functionalization of CB[6].
Individual-based modelling and control of bovine brucellosis
Authors: Nepomuceno Erivelton G. , Barbosa Alípio M. , Silva Marcos X. , Perc Matjaž
Published: May 2018

We present a theoretical approach to control bovine brucellosis. We have used individual-based modelling, which is a network-type alternative to compartmental models. Our model thus considers heterogeneous populations, and spatial aspects such as migration among herds and control actions described as pulse interventions are also easily implemented. We show that individual-based modelling reproduces the mean field behaviour of an equivalent compartmental model. Details of this process, as well as flowcharts, are provided to facilitate the reproduction of the presented results. We further investigate three numerical examples using real parameters of herds in the São Paulo state of Brazil, in scenarios which explore eradication, continuous and pulsed vaccination and meta-population effects. The obtained results are in good agreement with the expected behaviour of this disease, which ultimately showcases the effectiveness of our theory.
Time periodic solutions of one-dimensional forced Kirchhoff equations with
x
-dependent coefficients
Authors: Ma Mu , Ji Shuguan
Published: May 2018

In this paper, we consider the one-dimensional Kirchhoff equation with
x
-dependent coefficients under Dirichlet boundary conditions, which models the forced vibrations of a clamped inhomogeneous string in the presence of a time periodic external forcing with period 2
π
/
ω
and amplitude
ϵ
. By using the Nash–Moser iteration technique, we obtain the existence, regularity and local uniqueness of time periodic solutions with period 2
π
/
ω
and order
ϵ
. Such results hold for parameters (
ω
,
ϵ
) in a positive measure Cantor set that has asymptotically full measure as the amplitude
ϵ
goes to zero.
Behavioural changes controlled by catecholaminergic systems explain recurrent loss of pigmentation in cavefish
Authors: Bilandžija Helena , Abraham Lindsey , Ma Li , Renner Kenneth J. , Jeffery William R.
Published: May 2018

Multiple cave populations of the teleostAstyanax mexicanushave repeatedly reduced or lost eye and body pigmentation during adaptation to dark caves. Albinism, the complete absence of melanin pigmentation, is controlled by loss-of-function mutations in theoca2gene. The mutation is accompanied by an increase in the melanin synthesis precursorl-tyrosine, which is also a precursor for catecholamine synthesis. In this study, we show a relationship between pigmentation loss, enhanced catecholamine synthesis and responsiveness to anaesthesia, determined as a proxy for catecholamine-related behaviours. We demonstrate that anaesthesia resistance (AR) is enhanced in multiple depigmented and albino cavefish (CF), inversely proportional to the degree of pigmentation loss, controlled by theoca2gene, and can be modulated by experimental manipulations ofl-tyrosine or the catecholamine norepinephrine (NE). Moreover, NE is increased in the brains of multiple albino and depigmented CF relative to surface fish. The results provide new insights into the evolution of pigment modification because NE controls a suite of adaptive behaviours similar to AR that may represent a target of natural selection. Thus, understanding the relationship between loss of pigmentation and AR may provide insight into the role of natural selection in the evolution of albinism via a melanin–catecholamine trade-off.
Isolation by environment in the highly mobile olive ridley turtle (Lepidochelys olivacea) in the eastern Pacific
Authors: Rodríguez-Zárate Clara J. , Sandoval-Castillo Jonathan , van Sebille Erik , Keane Robert G. , Rocha-Olivares Axayácatl , Urteaga Jose , Beheregaray Luciano B.
Published: May 2018

Spatial and temporal scales at which processes modulate genetic diversity over the landscape are usually overlooked, impacting the design of conservation management practices for widely distributed species. We examine processes shaping population divergence in highly mobile species by re-assessing the case of panmixia in the iconic olive ridley turtle from the eastern Pacific. We implemented a biophysical model of connectivity and a seascape genetic analysis based on nuclear DNA variation of 634 samples collected from 27 nesting areas. Two genetically distinct populations largely isolated during reproductive migrations and mating were detected, each composed of multiple nesting sites linked by high connectivity. This pattern was strongly associated with a steep environmental gradient and also influenced by ocean currents. These findings relate to meso-scale features of a dynamic oceanographic interface in the eastern tropical Pacific (ETP) region, a scenario that possibly provides different cost–benefit solutions and selective pressures for sea turtles during both the mating and migration periods. We reject panmixia and propose a new paradigm for olive ridley turtles where reproductive isolation due to assortative mating is linked to its environment. Our study demonstrates the relevance of integrative approaches for assessing the role of environmental gradients and oceanographic currents as drivers of genetic differentiation in widely distributed marine species. This is relevant for the conservation management of species of highly mobile behaviour, and assists the planning and development of large-scale conservation strategies for the threatened olive ridley turtles in the ETP.
Inconspicuous echolocation in hoary bats (
Lasiurus cinereus
)
Authors: Corcoran Aaron J. , Weller Theodore J.
Published: May 2018

Echolocation allows bats to occupy diverse nocturnal niches. Bats almost always use echolocation, even when other sensory stimuli are available to guide navigation. Here, using arrays of calibrated infrared cameras and ultrasonic microphones, we demonstrate that hoary bats (
Lasiurus cinereus
) use previously unknown echolocation behaviours that challenge our current understanding of echolocation. We describe a novel call type (‘micro’ calls) that has three orders of magnitude less sound energy than other bat calls used in open habitats. We also document bats flying close to microphones (less than 3 m) without producing detectable echolocation calls. Acoustic modelling indicates that bats are not producing calls that exceed 70–75 dB at 0.1 m, a level that would have little or no known use for a bat flying in the open at speeds exceeding 7 m s
−1
. This indicates that hoary bats sometimes fly without echolocation. We speculate that bats reduce echolocation output to avoid eavesdropping by conspecifics during the mating season. These findings might partly explain why tens of thousands of hoary bats are killed by wind turbines each year. They also challenge the long-standing assumption that bats—model organisms for sensory specialization—are reliant on sonar for nocturnal navigation.
Coral resistance to ocean acidification linked to increased calcium at the site of calcification
Authors: DeCarlo T. M. , Comeau S. , Cornwall C. E. , McCulloch M. T.
Published: May 2018

Ocean acidification threatens the persistence of biogenic calcium carbonate (CaCO
3
) production on coral reefs. However, some coral genera show resistance to declines in seawater pH, potentially achieved by modulating the chemistry of the fluid where calcification occurs. We use two novel geochemical techniques based on boron systematics and Raman spectroscopy, which together provide the first constraints on the sensitivity of coral calcifying fluid calcium concentrations (

) to changing seawater pH. In response to simulated end-of-century pH conditions,
Pocillopora damicornis
increased

to as much as 25% above that of seawater and maintained constant calcification rates. Conversely,
Acropora youngei
displayed less control over

, and its calcification rates strongly declined at lower seawater pH. Although the role of

in driving calcification has often been neglected, increasing

may be a key mechanism enabling more resistant corals to cope with ocean acidification and continue to build CaCO
3
skeletons in a high-CO
2
world.