bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatiotemporal variations in life-history traits and statolith trace elements of Sepioteuthis lessoniana populations around northern Taiwan
Authors: Ching Tzu-Yun , Chen Chih-Shin , Wang Chia-Hui
Published: November 2017

The bigfin reef squid Sepioteuthis lessoniana is a neritic species widely distributed in coastal waters of the Indo-Pacific region and is of interest to fisheries for its high commercial value. Squid samples were collected from Keelung (KL) and Penghu (PH), around northern Taiwan from October 2012 to September 2013. A total of 949 squid were examined, and 620 squid were aged using statoliths. The age range of the squid in KL (55–183 days) was similar to that in PH (77–186 days). The squid hatched almost year-round, except in January and December in KL. Two seasonal cohorts were identified: a spring cohort (hatched in March to May) and an autumn cohort (July to October). Concentrations of nine trace elements in statoliths were analysed using solution-based inductively coupled plasma mass spectrometry (ICP-MS). Significant differences in Fe/Ca, Cu/Ca and Sr/Ca were found between the two locations, while significant differences in concentration ratios of Sr/Ca and Ba/Ca were noted between the two seasonal cohorts. Results of a principal component analysis and cluster analysis varied in life-history traits between the two geographic stocks and in elemental concentrations between the two seasonal cohorts. Squid in KL and PH might undertake different migration routes, while seasonal variability in oceanographic conditions was apparent in the two locations.
Grey matter volume and thickness abnormalities in young people with a history of childhood abuse
Authors: Lim L. , Hart H. , Mehta M. , Worker A. , Simmons A. , Mirza K. , Rubia K.
Published: November 2017

Background

Childhood abuse is associated with abnormalities in brain structure and function. Few studies have investigated abuse-related brain abnormalities in medication-naïve, drug-free youth that also controlled for psychiatric comorbidities by inclusion of a psychiatric control group, which is crucial to disentangle the effects of abuse from those associated with the psychiatric conditions.

Methods

Cortical volume (CV), cortical thickness (CT) and surface area (SA) were measured in 22 age- and gender-matched medication-naïve youth (aged 13–20) exposed to childhood abuse, 19 psychiatric controls matched for psychiatric diagnoses and 27 healthy controls. Both region-of-interest (ROI) and whole-brain analyses were conducted.

Results

For the ROI analysis, the childhood abuse group compared with healthy controls only, had significantly reduced CV in bilateral cerebellum and reduced CT in left insula and right lateral orbitofrontal cortex (OFC). At the whole-brain level, relative to healthy controls, the childhood abuse group showed significantly reduced CV in left lingual, pericalcarine, precuneus and superior parietal gyri, and reduced CT in left pre-/postcentral and paracentral regions, which furthermore correlated with greater abuse severity. They also had increased CV in left inferior and middle temporal gyri relative to healthy controls. Abnormalities in the precuneus, temporal and precentral regions were abuse-specific relative to psychiatric controls, albeit at a more lenient level. Groups did not differ in SA.

Conclusions

Childhood abuse is associated with widespread structural abnormalities in OFC–insular, cerebellar, occipital, parietal and temporal regions, which likely underlie the abnormal affective, motivational and cognitive functions typically observed in this population.
THE TOPOGRAPHY OF THE LUPERCALIA
Authors: Vuković Krešimir
Published: November 2017

The Lupercalia is one of the most important and most controversial of Roman festivals. This paper addresses the issue of its topography, which has received renewed attention in recent years. It is divided into two main sections, the first discussing the hotly debated location of the Lupercal cave, and the second the course of the runningLuperci. The former section reviews the literary and archaeological evidence for the location of the cave, discusses its significance as a unique religious site, and calls for further investigation in the area of the southwest Palatine. The second section seeks to challenge the most influential theories on the course of theLuperciby carefully examining the ancient evidence and the terminology it uses. A contextualization of the sources and the topographic elements they describe shows that many modern theories contain serious flaws when it comes to this subject. Most modern interpretations rely on a passage of Augustine which is very problematic because of his biasedinterpretatio Christiana. The conclusion is that the festival’s typology as a ritual of lustration is key to understanding the course of theLuperci.
Plato Laws 3.680B–C: Antisthenes, The Cyclopes and Homeric Exegesis
Authors: Prauscello Lucia
Published: November 2017

In Laws 3.680b–c the Athenian Stranger's positive evaluation of the Cyclopean ‘way of life’ (Od. 9.112–15) is deeply indebted to Antisthenes’ interpretatio Homerica of the Cyclopes as ‘just’ insofar they do not have the need of written law. Antisthenes’ equation of ‘need of law’ with ‘need of written law’ is then contextualized within the unresolved tension, in the legislative project of the Laws, between oral dissemination (‘proems’ to the laws) and the potentially coercive power of the written text. Finally, Megillus’ inept reply to the Homeric quotation by the Athenian Stranger allows us to gain a more nuanced view of the ‘readerly’ dynamics enacted by the internal audience of the Laws.
Modelling the temperature in joint friction of industrial manipulators
Authors: Simoni Luca , Beschi Manuel , Legnani Giovanni , Visioli Antonio
Published: November 2017

In this paper, a new model for joint dynamic friction of industrial robot manipulators is presented. In particular, the effects of the temperature in the joints are considered. A polynomial-based model is proposed and the parameter estimation is performed without the need of a joint temperature sensor. The use of an observer is then proposed to compensate for the uncertainty in the initial estimation of the temperature value. A large experimental campaign show that the model, in spite of the simplifying assumptions made, is effective in estimating the joint temperature and therefore the friction torque during the robot operations, even for values of velocities that have not been previously employed.
How children learn to produce appropriate referring expressions in narratives: the role of clarification requests and modeling
Authors: CARMIOL Ana M. , MATTHEWS Danielle , RODRÍGUEZ-VILLAGRA Odir A.
Published: November 2017

Asking children to clarify themselves promotes their ability to uniquely identify objects in referential communication tasks. However, little is known about whether parents ask preschoolers for clarification during interactions and, if so, how. Study 1 explored how mothers clarify their preschoolers’ ambiguous descriptions of the characters in their narratives, and whether clarification requests affect children's repairs of their ambiguous descriptions. Mothers were found to use different strategies, including signaling misunderstanding and modeling appropriate descriptions. Presence of these different strategies predicted children's ability to provide informative repairs. Study 2 tested the effect of children's experience with signaling misunderstanding and modeling on their ability to uniquely identify the characters of a story on a second narration. Experiencing modeling, but not misunderstandings, positively affected children's provision of appropriate descriptions during second narrations. Findings are discussed in terms of the role of imitation in driving referential development.
The US–China Naval Balance in the Asia-Pacific: An Overview
Authors: Goldstein Lyle
Published: November 2017

A truism in strategic studies holds that warfare is highly complex and unpredictable. What appears to be a stable and predictable military balance can be suddenly overthrown by innovative doctrines or cunning strategies. This paper attempts to fill a perceived gap in strategic studies analysis with respect to US–China naval conflict scenarios. The author is concerned that most Western analyses on the subject tend to be simplistic and unduly optimistic. The approach in this paper follows a “Chinese style” in that it examines the Asia-Pacific strategic balance as a series of interacting military campaigns. The results of the analysis yield that the US retains a strong advantage in certain warfare domains, to be sure. Yet, the assumption that the US military has a decisive advantage in the relevant scenarios becomes dubious in light of the potentially devastating blow against US and allied bases that could be made by PLA conventional missile forces. Moreover, a Chinese advantage in the use of offensive mine warfare, when combined with China's ability to prevent US and allied aerial anti-submarine forces from flying, could combine to roll back, or at least significantly limit, Washington's heretofore decisive undersea advantage.
Landscape correlates of bushmeat consumption and hunting in a post-frontier Amazonian region
Authors: CARIGNANO TORRES PATRICIA , MORSELLO CARLA , PARRY LUKE , BARLOW JOS , FERREIRA JOICE , GARDNER TOBY , PARDINI RENATA
Published: November 2017

Identifying the drivers of bushmeat consumption and hunting is important for informing conservation strategies and recognizing challenges to human food security. However, studies often neglect the importance of landscape context, which can influence bushmeat supply and demand. Here, by quantifying bushmeat consumption and hunting in 262 households in a post-frontier region in Amazonia, we tested the hypotheses that bushmeat consumption and hunting are positively associated with two landscape characteristics: (1) forest cover, which has been shown to define game availability; and (2) remoteness, which is related to limited access to marketed meat. Bushmeat consumption was widespread but more likely in remote forested areas. Hunting was more likely in more forested areas, especially nearer to urban centres. Our findings suggest that bushmeat remains an important food source even in heavily altered forest regions and that landscape context is an important determinant of bushmeat consumption and hunting. Although people living in remote, forested areas are likely to be the most dependent on bushmeat, those living in more populous, peri-urban areas are likely the actors contributing most to total hunting effort, due to a higher probability of hunting combined with higher human population densities. This finding undermines the assumption that rural–urban migration in the tropics will deliver a much-needed reprieve for many overhunted species.
Keynes and the dollar in 1933: the gold-buying program and exchange rate gyrations
Authors: Edwards Sebastian
Published: November 2017

In December 1933, John Maynard Keyes published an open letter to President Roosevelt, where he wrote: ‘The recent gyrations of the dollar have looked to me more like a gold standard on the booze than the ideal managed currency of my dreams.’ This was a criticism of the ‘gold-buying program’ launched in October 1933. In this article I use high-frequency data on the dollar–pound and dollar–franc exchange rates to investigate whether the gyrations of the dollar were unusually high in late 1933. My results show that although volatility was pronounced, it was not higher than during some other periods after 1921. Moreover, dollar volatility began to subside towards the end of the period alluded to by Keynes.
Reproducibility of Published Research
Authors: Klumpers Johannes
Published: November 2017

Recent articles have put into question the reproducibility of published research and have allocated some of the blame for un-reproducibility on a lack of integrity. This is a matter of major concern for the European Commission, and especially for its Scientific Advice Mechanism Unit. This article gives the view of the Head of that Unit.
Field-Dependent Measurement of GaAs Composition by Atom Probe Tomography
Authors: Di Russo Enrico , Blum Ivan , Houard Jonathan , Da Costa Gérald , Blavette Didier , Rigutti Lorenzo
Published: November 2017

The composition of GaAs measured by laser-assisted atom probe tomography may be inaccurate depending on the experimental conditions. In this work, we assess the role of the DC field and the impinging laser energy on such compositional bias. The DC field is found to have a major influence, while the laser energy has a weaker one within the range of parameters explored. The atomic fraction of Ga may vary from 0.55 at low-field conditions to 0.35 at high field. These results have been interpreted in terms of preferential evaporation of Ga at high field. The deficit of As is most likely explained by the formation of neutral As complexes either by direct ejection from the tip surface or upon the dissociation of large clusters. The study of multiple detection events supports this interpretation.
Historical and contemporary aspects of maternal immunity in swine
Authors: Poonsuk Korakrit , Zimmerman Jeff
Published: November 2017

Maternal immunity plays a pivotal role in swine health and production because piglets are born agammaglobulinemic and with limited cell-mediated immunity, i.e. few peripheral lymphoid cells, immature lymphoid tissues, and no effector and memory T-lymphocytes. Swine do not become fully immunologically competent until about 4 weeks of age, which means that their compromised ability to respond to infectious agents during the first month of life must be supplemented by maternal immune components: (1) circulating antibodies derived from colostrum; (2) mucosal antibodies from colostrum and milk; and (3) immune cells provided in mammary secretions. Because maternal immunity is highly effective at protecting piglets against specific pathogens, strengthening sow herd immunity against certain diseases through exposure or vaccination is a useful management tool for ameliorating clinical effects in piglets and delaying infection until the piglets’ immune system is better prepared to respond. In this review, we discuss the anatomy and physiology of lactation, the immune functions of components provided to neonatal swine in mammary secretion, the importance of maternal immunity in the prevention and control of significant pathogens.
Dimensionality of the Iowa-Netherlands Comparison Orientation Measure and Its Relationship to Reinforcement Sensitivity Theory
Authors: Gerson Jennifer , Plagnol Anke C. , Corr Philip J.
Published: November 2017

Abstract. The aims of this study were, first, to reassess the factor structure of the Iowa-Netherlands Social Comparison Orientation Measure (INCOM) and, second, to explore the associations of its factors with the Reinforcement Sensitivity Theory (RST) of personality. Data from 337 respondents were collected via online questionnaire. Structural equation models were used to assess the factor structure of the INCOM and test for relationships with RST traits. The results confirmed previous findings that the INCOM contains two factors: Ability, which relates to the comparison of performance, and Opinion, which relates to the comparison of thoughts and emotions. The two-factor model was found to be superior to the commonly used one-factor solution. The models further revealed significant relationships with RST factors: positive associations between the Ability factor and the Behavioral Inhibition System (BIS) and Behavioral Approach System (BAS) Reward Reactivity; positive associations between the Opinion factor and BAS Reward Reactivity and Goal-Drive Persistence, and a negative association with BAS Impulsivity. These findings indicate that using the INCOM as a single scale is likely to miss significant unique relationships. Our findings also provide new insight into how individual differences in personality may influence social comparison behavior.
Immune checkpoint inhibition: prospects for prevention and therapy of hepatocellular carcinoma
Authors: Elsegood Caryn L , Tirnitz‐Parker Janina EE , Olynyk John K , Yeoh George CT
Published: November 2017

The global prevalence of liver cancer is rapidly rising, mostly as a result of the amplified incidence rates of viral hepatitis, alcohol abuse and obesity in recent decades. Treatment options for liver cancer are remarkably limited with sorafenib being the gold standard for advanced, unresectable hepatocellular carcinoma but offering extremely limited improvement of survival time. The immune system is now recognised as a key regulator of cancer development through its ability to protect against infection and chronic inflammation, which promote cancer development, and eliminate tumour cells when present. However, the tolerogenic nature of the liver means that the immune response to infection, chronic inflammation and tumour cells within the hepatic environment is usually ineffective. Here we review the roles that immune cells and cytokines have in the development of the most common primary liver cancer, hepatocellular carcinoma (HCC). We then examine how the immune system may be subverted throughout the stages of HCC development, particularly with respect to immune inhibitory molecules, also known as immune checkpoints, such as programmed cell death protein‐1, programmed cell death 1 ligand 1 and cytotoxic T lymphocyte antigen 4, which have become therapeutic targets. Finally, we assess preclinical and clinical studies where immune checkpoint inhibitors have been used to modify disease during the carcinogenic process. In conclusion, inhibitory molecule‐based immunotherapy for HCC is in its infancy and further detailed research in relevant in vivo models is required before its full potential can be realised.
Atomic-level molybdenum oxide nanorings with full-spectrum absorption and photoresponsive properties
Authors: Yang Yong , Yang Yang , Chen Shuangming , Lu Qichen , Song Li , Wei Yen , Wang Xun
Published: November 2017

Superthin nanostructures, particularly with atomic-level thicknesses, typically display unique optical properties because of their exceptional light–matter interactions. Here, we report a facile strategy for the synthesis of sulfur-doped molybdenum oxide nanorings with an atomic-level size (thickness of 0.5 nm) and a tunable ring-in-ring architecture. These atomic-level nanorings displayed strong photo-absorption in both the visible and infrared-light ranges and acted as a photothermal agent. Under irradiation with an 808 nm laser with an intensity of 1 W/cm2, a composite of the nanorings embedded in polydimethylsiloxane showed an ultrafast photothermal effect, delivering a local temperature of up to 400 °C within 20 s, which to the best of our knowledge is the highest temperature by light irradiation reported to date. Meanwhile, the resulting nanorings were also employed as a photoinitiator to remotely induce a visible-light shape memory response, self-healing, reshaping performance and reversible actuation of dynamic three-dimensional structures. This study demonstrates an advancement towards controlling atomic-level-sized nanostructures and achieving greatly enhanced optical performances for optoelectronics.
Autophagy acts through TRAF3 and RELB to regulate gene expression via antagonism of SMAD proteins
Authors: Newman Alice C. , Kemp Alain J. , Drabsch Yvette , Behrends Christian , Wilkinson Simon
Published: November 2017

Macroautophagy can regulate cell signalling and tumorigenesis via elusive molecular mechanisms. We establish a RAS mutant cancer cell model where the autophagy gene ATG5 is dispensable in A549 cells in vitro, yet promotes tumorigenesis in mice. ATG5 represses transcriptional activation by the TGFβ-SMAD gene regulatory pathway. However, autophagy does not terminate cytosolic signal transduction by TGFβ. Instead, we use proteomics to identify selective degradation of the signalling scaffold TRAF3. TRAF3 autophagy is driven by RAS and results in activation of the NF-κB family member RELB. We show that RELB represses TGFβ target promoters independently of DNA binding at NF-κB recognition sequences, instead binding with SMAD family member(s) at SMAD-response elements. Thus, autophagy antagonises TGFβ gene expression. Finally, autophagy-deficient A549 cells regain tumorigenicity upon SMAD4 knockdown. Thus, at least in this setting, a physiologic function for autophagic regulation of gene expression is tumour growth.
Polymer mimics of biomacromolecular antifreezes
Authors: Biggs Caroline I. , Bailey Trisha L. , Ben Graham  , Stubbs Christopher , Fayter Alice , Gibson Matthew I.
Published: November 2017

Antifreeze proteins from polar fish species are remarkable biomacromolecules which prevent the growth of ice crystals. Ice crystal growth is a major problem in cell/tissue cryopreservation for transplantation, transfusion and basic biomedical research, as well as technological applications such as icing of aircraft wings. This review will introduce the rapidly emerging field of synthetic macromolecular (polymer) mimics of antifreeze proteins. Particular focus is placed on designing polymers which have no structural similarities to antifreeze proteins but reproduce the same macroscopic properties, potentially by different molecular-level mechanisms. The application of these polymers to the cryopreservation of donor cells is also introduced.
The genomic landscape of pediatric myelodysplastic syndromes
Authors: Schwartz Jason R. , Ma Jing , Lamprecht Tamara , Walsh Michael , Wang Shuoguo , Bryant Victoria , Song Guangchun , Wu Gang , Easton John , Kesserwan Chimene , Nichols Kim E. , Mullighan Charles G. , Ribeiro Raul C. , Klco Jeffery M.
Published: November 2017

Myelodysplastic syndromes (MDS) are uncommon in children and have a poor prognosis. In contrast to adult MDS, little is known about the genomic landscape of pediatric MDS. Here, we describe the somatic and germline changes of pediatric MDS using whole exome sequencing, targeted amplicon sequencing, and/or RNA-sequencing of 46 pediatric primary MDS patients. Our data show that, in contrast to adult MDS, Ras/MAPK pathway mutations are common in pediatric MDS (45% of primary cohort), while mutations in RNA splicing genes are rare (2% of primary cohort). Surprisingly, germline variants in SAMD9 or SAMD9L were present in 17% of primary MDS patients, and these variants were routinely lost in the tumor cells by chromosomal deletions (e.g., monosomy 7) or copy number neutral loss of heterozygosity (CN-LOH). Our data confirm that adult and pediatric MDS are separate diseases with disparate mechanisms, and that SAMD9/SAMD9L mutations represent a new class of MDS predisposition.
Human Cyclophilin B forms part of a multi-protein complex during erythrocyte invasion by Plasmodium falciparum
Authors: Prakash Prem , Zeeshan Mohammad , Saini Ekta , Muneer Azhar , Khurana Sachin , Kumar Chourasia Bishwanath , Deshmukh Arunaditya , Kaur Inderjeet , Dabral Surabhi , Singh Niharika , Anam Zille , Chaurasiya Ayushi , Kaushik Shikha , Dahiya Pradeep , Kalamuddin Md. , Kumar Thakur Jitendra , Mohmmed Asif , Ranganathan Anand , Malhotra Pawan
Published: November 2017

Invasion of human erythrocytes by Plasmodium falciparum merozoites involves multiple interactions between host receptors and their merozoite ligands. Here we report human Cyclophilin B as a receptor for PfRhopH3 during merozoite invasion. Localization and binding studies show that Cyclophilin B is present on the erythrocytes and binds strongly to merozoites. We demonstrate that PfRhopH3 binds to the RBCs and their treatment with Cyclosporin A prevents merozoite invasion. We also show a multi-protein complex involving Cyclophilin B and Basigin, as well as PfRhopH3 and PfRh5 that aids the invasion. Furthermore, we report identification of a de novo peptide CDP3 that binds Cyclophilin B and blocks invasion by up to 80%. Collectively, our data provide evidence of compounded interactions between host receptors and merozoite surface proteins and paves the way for developing peptide and small-molecules that inhibit the protein−protein interactions, individually or in toto, leading to abrogation of the invasion process.
A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family
Authors: Carreras-Puigvert Jordi , Zitnik Marinka , Jemth Ann-Sofie , Carter Megan , Unterlass Judith E. , Hallström Björn , Loseva Olga , Karem Zhir , Calderón-Montaño José Manuel , Lindskog Cecilia , Edqvist Per-Henrik , Matuszewski Damian J. , Ait Blal Hammou , Berntsson Ronnie P. A. , Häggblad Maria , Martens Ulf , Studham Matthew , Lundgren Bo , Wählby Carolina , Sonnhammer Erik L. L. , Lundberg Emma , Stenmark Pål , Zupan Blaz , Helleday Thomas
Published: November 2017

The NUDIX enzymes are involved in cellular metabolism and homeostasis, as well as mRNA processing. Although highly conserved throughout all organisms, their biological roles and biochemical redundancies remain largely unclear. To address this, we globally resolve their individual properties and inter-relationships. We purify 18 of the human NUDIX proteins and screen 52 substrates, providing a substrate redundancy map. Using crystal structures, we generate sequence alignment analyses revealing four major structural classes. To a certain extent, their substrate preference redundancies correlate with structural classes, thus linking structure and activity relationships. To elucidate interdependence among the NUDIX hydrolases, we pairwise deplete them generating an epistatic interaction map, evaluate cell cycle perturbations upon knockdown in normal and cancer cells, and analyse their protein and mRNA expression in normal and cancer tissues. Using a novel FUSION algorithm, we integrate all data creating a comprehensive NUDIX enzyme profile map, which will prove fundamental to understanding their biological functionality.
Possible nematic to smectic phase transition in a two-dimensional electron gas at half-filling
Authors: Qian Q. , Nakamura J. , Fallahi S. , Gardner G. C. , Manfra M. J.
Published: November 2017

Liquid crystalline phases of matter permeate nature and technology, with examples ranging from cell membranes to liquid-crystal displays. Remarkably, electronic liquid-crystal phases can exist in two-dimensional electron systems (2DES) at half Landau-level filling in the quantum Hall regime. Theory has predicted the existence of a liquid-crystal smectic phase that breaks both rotational and translational symmetries. However, previous experiments in 2DES are most consistent with an anisotropic nematic phase breaking only rotational symmetry. Here we report three transport phenomena at half-filling in ultra-low disorder 2DES: a non-monotonic temperature dependence of the sample resistance, dramatic onset of large time-dependent resistance fluctuations, and a sharp feature in the differential resistance suggestive of depinning. These data suggest that a sequence of symmetry-breaking phase transitions occurs as temperature is lowered: first a transition from an isotropic liquid to a nematic phase and finally to a liquid-crystal smectic phase.
Graphene balls for lithium rechargeable batteries with fast charging and high volumetric energy densities
Authors: Son In Hyuk , Park Jong Hwan , Park Seongyong , Park Kwangjin , Han Sangil , Shin Jaeho , Doo Seok-Gwang , Hwang Yunil , Chang Hyuk , Choi Jang Wook
Published: November 2017

Improving one property without sacrificing others is challenging for lithium-ion batteries due to the trade-off nature among key parameters. Here we report a chemical vapor deposition process to grow a graphene–silica assembly, called a graphene ball. Its hierarchical three-dimensional structure with the silicon oxide nanoparticle center allows even 1 wt% graphene ball to be uniformly coated onto a nickel-rich layered cathode via scalable Nobilta milling. The graphene-ball coating improves cycle life and fast charging capability by suppressing detrimental side reactions and providing efficient conductive pathways. The graphene ball itself also serves as an anode material with a high specific capacity of 716.2 mAh g−1. A full-cell incorporating graphene balls increases the volumetric energy density by 27.6% compared to a control cell without graphene balls, showing the possibility of achieving 800 Wh L−1 in a commercial cell setting, along with a high cyclability of 78.6% capacity retention after 500 cycles at 5C and 60 °C.
Author Correction: Using a smartphone-based self-management platform to support medication adherence and clinical consultation in Parkinson’s disease
Authors: Lakshminarayana Rashmi , Wang Duolao , Burn David , Chaudhuri K. Ray , Galtrey Clare , Guzman Natalie Valle , Hellman Bruce , James Ben , Pal Suvankar , Stamford Jon , Steiger Malcolm , Stott R. W. , Teo James , Barker Roger A. , Wang Emma , Bloem Bastiaan R. , van der Eijk Martijn , Rochester Lynn , Williams Adrian
Published: November 2017

In the original version of this article the copyright notice was missing from Tables 1 and 3. This has now been added alongside the three relevant references inserted as refs. 21–23. The correction has been published and is appended to both the HTML and PDF versions of this paper. The errors have been fixed in the paper.
QTL mapping and molecular characterization of the classical D locus controlling seed and flower color in Linum usitatissimum (flax)
Authors: Sudarshan Gurudatt Pavagada , Kulkarni Manoj , Akhov Leonid , Ashe Paula , Shaterian Hamid , Cloutier Sylvie , Rowland Gordon , Wei Yangdou , Selvaraj Gopalan
Published: November 2017

The flowers of flax (linseed) are blue-hued, ephemeral and self-pollinating, and the seeds are typically brown. A century-old interest in natural yellow seed variants and a historical model point to recessive alleles in B1, D and G loci being responsible, but the functional aspects had remained unknown. Here, we characterized the “D” locus by quantitative trait loci (QTL) mapping and identified a FLAVONOID 3′5′ HYDROXYLASE (F3′5′H) gene therein. It does not belong to the F3′5′H clade, but resembles biochemically characterized F3′Hs (flavonoid 3′ hydroxylase) but without F3′H activity. The genome lacks other F3′H or F3′H-like genes. The apparent neo-functionalization from F3′H is associated with a Thr498 → Ser498 substitution in a substrate recognition site (SRS). The yellow seed and white flower phenotypes of the classical d mutation was found to be due to one nucleotide deletion that would truncate the deduced product and remove three of the six potential SRS, negatively impacting delphinidin synthesis. Delphinidin is sporadic in angiosperms, and flax has no known pollination syndrome(s) with functional pollinator group(s) that are attracted to blue flowers, raising questions on the acquisition of F3′5′H. The appearance of d allele is suggestive of the beginning of the loss of F3′5′H in this species.
Gpufit: An open-source toolkit for GPU-accelerated curve fitting
Authors: Przybylski Adrian , Thiel Björn , Keller-Findeisen Jan , Stock Bernd , Bates Mark
Published: November 2017

We present a general purpose, open-source software library for estimation of non-linear parameters by the Levenberg-Marquardt algorithm. The software, Gpufit, runs on a Graphics Processing Unit (GPU) and executes computations in parallel, resulting in a significant gain in performance. We measured a speed increase of up to 42 times when comparing Gpufit with an identical CPU-based algorithm, with no loss of precision or accuracy. Gpufit is designed such that it is easily incorporated into existing applications or adapted for new ones. Multiple software interfaces, including to C, Python, and Matlab, ensure that Gpufit is accessible from most programming environments. The full source code is published as an open source software repository, making its function transparent to the user and facilitating future improvements and extensions. As a demonstration, we used Gpufit to accelerate an existing scientific image analysis package, yielding significantly improved processing times for super-resolution fluorescence microscopy datasets.
A new method to measure mechanics and dynamic assembly of branched actin networks
Authors: Bauër Pierre , Tavacoli Joseph , Pujol Thomas , Planade Jessica , Heuvingh Julien , du Roure Olivia
Published: November 2017

We measured mechanical properties and dynamic assembly of actin networks with a new method based on magnetic microscopic cylinders. Dense actin networks are grown from the cylinders’ surfaces using the biochemical Arp2/3-machinery at play in the lamellipodium extension and other force-generating processes in the cell. Under a homogenous magnetic field the magnetic cylinders self-assemble into chains in which forces are attractive and depend on the intensity of the magnetic field. We show that these forces, from piconewtons to nanonewtons, are large enough to slow down the assembly of dense actin networks and controlled enough to access to their non linear mechanical responses. Deformations are measured with nanometer-resolution, well below the optical resolution. Self-assembly of the magnetic particles into chains simplifies experiments and allows for parallel measurements. The combination of accuracy and good throughput of measurements results in a method with high potential for cell and cytoskeleton mechanics. Using this method, we observed in particular a strong non linear mechanical behavior of dense branched actin networks at low forces that has not been reported previously.
Plastic deformation behaviour of single-crystalline martensite of Ti-Nb shape memory alloy
Authors: Tahara Masaki , Okano Nao , Inamura Tomonari , Hosoda Hideki
Published: November 2017

β-Ti alloys have attracted considerable attention as new biomedical shape memory alloys. Given the critical importance of the plastic deformation in the martensite phase for the shape memory effect and superelasticity, we investigated here the plastic deformation behaviour of a single crystal of α″ (orthorhombic) martensite of Ti-27 mol%Nb shape memory alloy obtained by the stress-induced martensitic transformation of a single crystal of the parent β phase. Four operative plastic deformation modes were observed, including two dislocation slips and two twinnings. To the best of our knowledge, two of these plastic deformation modes (one dislocation slip and one twinning) were discovered for the first time in this study. The identified slip and twinning systems in the martensite phase have corresponding slip and twinning systems in the parent β phase with which they share many similarities. Therefore, we believe that the plastic deformation of the α″ martensite is inherited from that of the parent β phase.
Usefulness of the delta neutrophil index to predict 30-day mortality in patients with ST segment elevation myocardial infarction
Authors: Kong Taeyoung , Kim Tae Hoon , Park Yoo Seok , Chung Sung Phil , Lee Hye Sun , Hong Jung Hwa , Lee Jong Wook , You Je Sung , Park Incheol
Published: November 2017

This study aimed to evaluate the association between the delta neutrophil index (DNI), which reflects immature granulocytes, and the severity of ST-elevation myocardial infarction (STEMI), as well as to determine the significance of the DNI as a prognostic marker for early mortality and other clinical outcomes in patients with STEMI who underwent reperfusion. This retrospective, observational cohort study was conducted using patients prospectively integrated in a critical pathway program for STEMI. We included 842 patients diagnosed with STEMI who underwent primary percutaneous coronary intervention (pPCI). Higher DNI values at time-I (within 2 h of pPCI; hazard ratio [HR], 1.075; 95% confidence interval [CI]: 1.046–1.108; p < 0.001) and time-24 (24 h after admission; HR, 1.066; 95% CI: 1.045–1.086; p < 0.001) were significant independent risk factors for 30-day mortality. Specifically, DNI values >2.5% at time-I (HR, 13.643; 95% CI: 8.13–22.897; p < 0.001) and > 2.9% at time-24 (HR, 12.752; 95% CI: 7.308–22.252; p < 0.001) associated with increased risks of 30-day mortality. In conclusion, an increased DNI value, which reflects the proportion of circulating immature granulocytes in the blood, was found to be an independent predictor of 30-day mortality and poor clinical outcomes in patients with acute STEMI post-pPCI.
Andy’s Algorithms: new automated digital image analysis pipelines for FIJI
Authors: Law Andrew M. K. , Yin Julia X. M. , Castillo Lesley , Young Adelaide I. J. , Piggin Catherine , Rogers Samuel , Caldon Catherine Elizabeth , Burgess Andrew , Millar Ewan K. A. , O’Toole Sandra A. , Gallego-Ortega David , Ormandy Christopher J. , Oakes Samantha R.
Published: November 2017

Quantification of cellular antigens and their interactions via antibody-based detection methods are widely used in scientific research. Accurate high-throughput quantitation of these assays using general image analysis software can be time consuming and challenging, particularly when attempted by users with limited image processing and analysis knowledge. To overcome this, we have designed Andy’s Algorithms, a series of automated image analysis pipelines for FIJI, that permits rapid, accurate and reproducible batch-processing of 3,3′-diaminobenzidine (DAB) immunohistochemistry, proximity ligation assays (PLAs) and other common assays. Andy’s Algorithms incorporates a step-by-step tutorial and optimization pipeline to make batch image analysis simple for the untrained user and adaptable across laboratories. Andy’s algorithms provide a simpler, faster, standardized work flow compared to existing programs, while offering equivalent performance and additional features, in a free to use open-source application of FIJI. Andy’s Algorithms are available at GitHub, publicly accessed at https://github.com/andlaw1841/Andy-s-Algorithm.
Radiographic assessment of the skeletons of Dolly and other clones finds no abnormal osteoarthritis
Authors: Corr S. A. , Gardner D. S. , Langley-Hobbs S. , Ness M. G. , Kitchener A. C. , Sinclair K. D.
Published: November 2017

Our recent report detailing the health status of cloned sheep concluded that the animals had aged normally. This is in stark contrast to reports on Dolly (first animal cloned from adult cells) whose diagnoses of osteoarthritis (OA) at 5½ years of age led to considerable scientific concern and media debate over the possibility of early-onset age-related diseases in cloned animals. Our study included four 8-year old ewes derived from the cell line that gave rise to Dolly, yet none of our aged sheep showed clinical signs of OA, and they had radiographic evidence of only mild or, in one case, moderate OA. Given that the only formal record of OA in Dolly is a brief mention of a single joint in a conference abstract, this led us to question whether the original concerns about Dolly’s OA were justified. As none of the original clinical or radiographic records were preserved, we undertook radiographic examination of the skeletons of Dolly and her contemporary clones. We report a prevalence and distribution of radiographic-OA similar to that observed in naturally conceived sheep, and our healthy aged cloned sheep. We conclude that the original concerns that cloning had caused early-onset OA in Dolly were unfounded.
Association of a variant in the gene encoding for ERV1/ChemR23 with reduced inflammation in visceral adipose tissue from morbidly obese individuals
Authors: López-Vicario Cristina , Rius Bibiana , Alcaraz-Quiles José , González-Périz Ana , Martínez-Puchol Ana Isabel , Casulleras Mireia , Duran-Güell Marta , Ibarzabal Ainitze , Corcelles Ricard , Laguna-Fernández Andrés , Back Magnus , Titos Esther , Clària Joan
Published: November 2017

Obesity comorbidities are closely associated with chronic low-grade adipose tissue inflammation. A number of SNPs associated with inflammation has been identified, underscoring the impact of genetic determinants on this process. Here, we screened SNPs in genes with pro-inflammatory (IL-1β, IL-6, STAT3 and JAK2), anti-inflammatory (IL-10 and SOCS3) and pro-resolving (ERV1/ChemR23) properties in 101 obese and 99 non-obese individuals. Among the SNPs analyzed, we identified that individuals carrying a C allele in the rs1878022 polymorphism of the ERV1/ChemR23 gene, which encodes for the receptor of the pro-resolving mediator RvE1, had increased ERV1/ChemR23 protein expression and reduced levels of the inflammatory cytokine IL-6 in adipose tissue. Moreover, patients carrying the C allele in homozygosity had lower plasma levels of IL-6, IFN-α2, IL-15, IL-1ra, IL-10, GM-CSF, G-CSF and VEGF and enhanced leukocyte responsiveness to RvE1. C-carriers also exhibited decreased TAG to HDL ratio, a surrogate marker of insulin resistance and a predictor of incident fatty liver. Finally, we confirmed in vivo that the ERV1/ChemR23 receptor regulates systemic and tissue inflammation since mice lacking ERV1/ChemR23 expression showed increased IL-6 levels in adipose tissue and peritoneal macrophages. Together, our study identified an ERV1/ChemR23 variant that protects patients with obesity from excessive inflammatory burden.
A novel magnet-actuated droplet manipulation platform using a floating ferrofluid film
Authors: Yang Chao , Li Gang
Published: November 2017

In this paper, we propose a novel but versatile magnet-actuated platform for droplet manipulation, which uses a ferrofluid film floating on a liquid surface as magnetic actuator. In contrast to the traditional magnetic droplet manipulation, this platform can handle droplets without magnetically functionalizing them. Due to the immiscibility of the oil-based ferrofluid and water, the droplets desired to be manipulated can stably rest on the surface of the floating ferrofluid film (FFF) under the action of surface tension, thereby offering possibilities for magnetically-driven droplet manipulations. Such a floating, magnetically responsive liquid film not only offers an open surface for active 2D droplet manipulation, but also enables complex droplet manipulations in 3D space. Using FFF, we demonstrate a “full-space” droplet manipulation, including droplet transport/coalescence above FFF (i.e. in air), droplet transport/coalescence on FFF and droplet encapsulation/release under FFF (i.e. in liquid). Furthermore, we investigated the effects of the magnetic field intensity, the ferrofluid concentration, the droplet volume, and the FFF thickness on droplet kinematics. By finely tuning these operating conditions, the FFF strategy can enjoy more operational latitude than traditional droplet systems, thus allowing more versatile liquid handling.
Binary phase masks for easy system alignment and basic aberration sensing with spatial light modulators in STED microscopy
Authors: Klauss André , Conrad Florian , Hille Carsten
Published: November 2017

The use of binary phase patterns to improve the integration and optimization of spatial light modulators (SLM) in an imaging system, especially a confocal microscope, is proposed and demonstrated. The phase masks were designed to create point spread functions (PSF), which exhibit specific sensitivity to major disturbances in the optical system. This allows direct evaluation of misalignment and fundamental aberration modes by simple visual inspection of the focal intensity distribution or by monitoring the central intensity of the PSF. The use of proposed phase masks is investigated in mathematical modelling and experiment for the use in a stimulated emission depletion (STED) microscope applying wavefront shaping by a SLM. We demonstrate the applicability of these phase masks for modal wavefront sensing of low order aberration modes up to the third order of Zernike polynomials, utilizing the point detector of a confocal microscope in a ‘guide star’ approach. A lateral resolution of ~25 nm is shown in STED imaging of the confocal microscope retrofitted with a SLM and a STED laser and binary phase mask based system optimization.
Preparation and functional evaluation of collagen oligopeptide-rich hydrolysate from fish skin with the serine collagenolytic protease from Pseudoalteromonas sp. SM9913
Authors: Chen Xiu-Lan , Peng Ming , Li Jing , Tang Bai-Lu , Shao Xuan , Zhao Fang , Liu Chang , Zhang Xi-Ying , Li Ping-Yi , Shi Mei , Zhang Yu-Zhong , Song Xiao-Yan
Published: November 2017

Although several serine collagenolytic proteases from bacteria were reported, none has been used to prepare bioactive collagen peptides. MCP-01 is the most abundant extracellular protease of deep-sea Pseudoalteromonas sp. SM9913 and is a serine collagenolytic protease with high efficiency on fish collagen hydrolysis. Here, we set up a pilot scale process to ferment SM9913 for extracellular protease production. With SM9913 extracellular protease as a tool, a process to prepare collagen oligopeptide-rich hydrolysate from codfish skin was set up, which was further scaled up to pilot (100 L) and plant (2000 L) levels with yields >66%. The hydrolysates from laboratory-, pilot- and plant-scales had quite similar quality, containing ~95% peptides with molecular weights lower than 3000 Da and approximately 60% lower than 1000 Da, in which collagen oilgopeptides account for approximately 95%. Bioactivity analyses showed that the hydrolysate had moisture-retention ability, antioxidant activity, and promoting effect on cell viability of human dermal fibroblasts. Safety evaluation showed that the hydrolysate was nontoxic and nonirritating to skin. Therefore, SM9913 extracellular protease is a good enzyme to prepare bioactive oligopeptides from fish skin. The results also suggest that the collagen oligopeptides-rich hydrolysate may have potentials in biomedical, functional food, pharmaceutical and cosmetic industries.
GABA concentrations in the anterior temporal lobe predict human semantic processing
Authors: Jung JeYoung , Williams Stephen R. , Sanaei Nezhad Faezeh , Lambon Ralph Matthew A.
Published: November 2017

There is now considerable convergent evidence from multiple methodologies and clinical studies that the human anterior temporal lobe (ATL) is a semantic representational hub. However, the neurochemical nature of the ATL in the semantic processing remains unclear. The current study investigated the neurochemical mechanism underlying semantic processing in the ATL. We combined functional magnetic resonance imaging (fMRI) with resting-state magnetic resonance spectroscopy (MRS) to measure task-related blood-oxygen level-dependent (BOLD) signal changes during sematic processing and resting-state GABA concentrations in the ATL. Our combined fMRI and MRS investigation showed that the stronger ATL BOLD response induced by the semantic task, the lower GABA concentration in the same region. Moreover, individuals with higher GABA concentration in the ATL showed better semantic performance and stronger BOLD-related fluctuations in the semantic network. Our data demonstrated that the resting-state GABA concentration predicts neural changes in the human ATL and task performance during semantic processing. Our findings indicate that individuals with higher GABA may have a more efficient semantic processing leading to better task performance and imply that GABAergic neurochemical processes are potentially crucial to the neurobiological contribution of the ATL to semantic cognition.