bluuebunny/crossref_metadata_2025 huggingface dataset:
Public archaeology in Canada
Authors: Lea Joanne , Smardz Karolyn E.
Published: January 2017

The term ‘public archaeology’ can mean many things. It can be as simple as a photocopied brochure left outside a fenced-off archaeological excavation or as complex as an elaborate series of educational programmes. For the purposes of this paper, the term ‘public archaeology’ is used to describe those projects and programmes designed to enhance popular knowledge of and appreciation for archaeology.
Towards a national training scheme for England and the United Kingdom
Authors: Collis John
Published: January 2017

Archaeology in Britain is going through one of its periodic ‘crises’, but for once it is not a crisis of funding, but one rather brought on by success, with more money, more posts and more archaeology. Much of the new money emanates from Developer Funding; PPG-16 (DoE 1990), brought out by the Department of the Environment in the wake of a European Directive on the need to conserve the historic environment, requires developers, where possible, to preserve archaeological sites, and where not, to preserve by record, i.e. to excavate. Roles were split with, on the one side, local government having ‘curatorial responsibility’ to maintain Sites and Monuments Records (SMRs) and to advise on planning and development; and on the other, independent ‘archaeological units’ to carry out the work.
Multi-disciplinary approaches to the Islamic period in Egypt and the Red Sea Coast
Authors: Kawatoko Mutsuo
Published: January 2017

We are privileged to offer a summary of the massive campaign of excavation and survey conducted by the author and his team from Japan in northern Egypt and the neighbouring coast of Sinai. Over the last few years they have excavated a large sector of al-Fustat (the early Islamic settlement on the outskirts of modern Cairo), mapped the early Christian monastery at Wadi al-Tur (sixth–twelfth century AD), recorded early Islamic rock inscriptions on Mt Naqus eighth–twentieth century AD), mapped the port and mosque at Raya (originating in the sixth–twelfth or thirteenth century AD) and investigated on a large scale the fourteenth–twentieth-century sequence at al-Kilani (al-Tur). Among the objects unearthed at al-Kilani were 4000 fragments of manuscripts. The work is throwing new light on early Islam, its development of social and commercial networks, and its relation with Christian, Coptic and Byzantine cultures.
Politics and narratives: Islamic archaeology in Israel
Authors: Petersen Andrew
Published: January 2017

The author considers the prospects of Islamic archaeology in one of the most politically sensitive places in the world.
Megaliths and post-modernism: the case of Wales
Authors: Fleming Andrew
Published: January 2017

Andrew Fleming takes phenomenology by the horns.
The diagnosis, clinical findings and treatment options for Parkinson's disease patients attending a tertiary referral voice clinic
Authors: Gibbins N , Awad R , Harris S , Aymat A
Published: January 2017

Background:

Parkinson's disease is a degenerative disorder of the central nervous system, mainly affecting motor functions including the voice. The aetiology of dysphonia changes throughout the course of disease progression.

Objectives:

This study aimed to determine the laryngeal changes seen in early-, mid- and late-stage Parkinson's disease. Thirteen patients with Parkinson's disease are presented, representing the largest series of voice patients with Parkinson's disease seen in a voice clinic in the literature.

Method:

Age, gender, severity of handicap caused by voice disorder and possible associated reflux symptoms were examined.

Results:

Laryngeal function appeared to change gradually with progression of the disease, and may have been affected by the presence of pre-existing laryngeal pathology.

Conclusion:

Laryngeal function in Parkinson's disease appears to go through a series of changes that may be helped by both therapeutic and surgical interventions. These patients should be treated within the confines of a voice clinic multidisciplinary model.
Temporal variation in oxidative stress indicators in liver of totoaba (Totoaba macdonaldi) Perciformes: Sciaenidae
Authors: Hernández-Aguilar Sandra Berenice , Zenteno-Savin Tania , De-Anda-Montañez Juan Antonio , Méndez-Rodríguez Lia Celina
Published: January 2017

Several characteristics ofTotoaba macdonaldiPerciformes: Sciaenidae, including migratory movements along temperature gradients make it vulnerable to oxidative stress. Oxidative stress can also be associated with reproduction. The objectives of the present study were to examine oxidative stress indicators in liver of totoaba throughout the seasons (spring, autumn and winter), and the associated fluctuations in superficial sea temperature (SST, °C), as well as to evaluate possible variations between sexes and reproductive maturity stages. A total of 173 liver samples from totoaba captured in the Gulf of California, Mexico, were obtained from April 2010 to February 2013. Superoxide radical production (O2•−), lipid peroxidation (TBARS) levels, and activity of antioxidant enzymes; superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), glutathione reductase (GR) and glutathione S-transferase (GST) were quantified spectrophotometrically. Generalized linear models (GLM) were used to determine which factors contribute to explain O2•−production and TBARS levels. The significant predictive variables were the seasons, which were significant in all applied models, as well as SOD and CAT activities. In general, enzyme activity was higher in immature totoaba; this was not seasonally modified. Low temperatures in winter were associated with high O2•−production and TBARS levels, particularly in totoaba that are not yet reproductively mature. Seasonal changes in sea surface temperature did not affect the oxidative stress indicators in mature totoaba (both males and females); this suggests that mature totoaba are less sensitive to temperature changes from an oxidative stress perspective.
‘BEAMED DIRECTLY TO THE CHILDREN’: SCHOOL BROADCASTING AND SEX EDUCATION IN BRITAIN IN THE 1960s AND 1970s
Authors: Gregory Mara
Published: January 2017

This paper presents findings from a larger research project that addresses the production, content and reception of sex education broadcasts produced by the British Broadcasting Corporation and Independent Television in the 1960s and 1970s. More than educational aids, these programmes were vehicles of communication with explicit and implicit messages regarding sexual morality and the nature of childhood. With a focus on the broadcast media and their modes of address to children, this paper connects sex education content with classroom practice and broadly questions how broadcasts portrayed and authorised certain images, types of knowledge and methods for teaching children about sex.
GANEing on emotion and emotion regulation
Authors: Hull Thomas D.
Published: January 2017

The function of emotion and its underlying neural mechanisms are often left underspecified. I extend the GANE (glutamate amplifies noradrenergic effects) model by examining its success in accounting for findings in emotion regulation. I also identify points of alignment with construction models of emotion and with the hypothesis that emotion states function to push neural activity toward rapid and efficient action.
Once more with feeling: On the explanatory limits of the GANE model and the missing role of subjective experience
Authors: Huntsinger Jeffrey R. , Storbeck Justin
Published: January 2017

We applaud Mather and colleagues' model, which emphasizes the neurobiological pathways by which affective arousal tunes attention and memory. This commentary offers a friendly discussion of several potential limitations of the theory. We suggest the model is strong when predicting task-driven demands but is limited when predicting the impact of individual biases, interpretations, and experiential feelings.
What BANE can offer GANE: Individual differences in function of hotspot mechanisms
Authors: Todd Rebecca M. , Ehlers Mana R. , Anderson Adam K.
Published: January 2017

In this commentary we focus on individual differences in proposed mechanisms underlying arousal-based enhancement of prioritized stimuli. We discuss the potential of genotyping studies for examining effects of noradrenergic processes on stimulus prioritization in humans and stress the importance of potential individual differences in the activity of specific receptor subtypes in hotspot processes proposed by the GANE model.
Studies on cognitively driven attention suggest that late vision is cognitively penetrated, whereas early vision is not
Authors: Raftopoulos Athanassios
Published: January 2017

Firestone & Scholl (F&S) examine, among other possible cognitive influences on perception, the effects of peripheral attention and conclude that these effects do not entail cognition directly affecting perception. Studies in neuroscience with other forms of attention, however, suggest that a stage of vision, namely late vision, is cognitively penetrated mainly through the effects of cognitively driven spatial and object-centered attention.
The myth of pure perception
Authors: Clore Gerald L. , Proffitt Dennis R.
Published: January 2017

Firestone & Scholl (F&S) assume that pure perception is unaffected by cognition. This assumption is untenable for definitional, anatomical, and empirical reasons. They discount research showing nonoptical influences on visual perception, pointing out possible methodological “pitfalls.” Results generated in multiple labs are immune to these “pitfalls,” suggesting that perceptions of physical layout do indeed reflect bioenergetic resources.
An action-specific effect on perception that avoids all pitfalls
Authors: Witt Jessica K. , Sugovic Mila , Tenhundfeld Nathan L. , King Zachary R.
Published: January 2017

The visual system is influenced by action. Objects that are easier to reach or catch look closer and slower, respectively. Here, we describe evidence for one action-specific effect, and show that none of the six pitfalls can account for the results. Vision is not an isolate module, as shown by this top-down effect of action on perception.
What draws the line between perception and cognition?
Authors: Rolfs Martin , Dambacher Michael
Published: January 2017

The investigation of top-down effects on perception requires a rigorous definition of what qualifies as perceptual to begin with. Whereas Firestone & Scholl's (F&S's) phenomenological demarcation of perception from cognition appeals to intuition, we argue that the dividing line is best attained at the functional level. We exemplify how this approach facilitates scrutinizing putative interactions between judging and perceiving.
Cognition can affect perception: Restating the evidence of a top-down effect
Authors: Levin Daniel T. , Baker Lewis J. , Banaji Mahzarin R.
Published: January 2017

We argue that Firestone & Scholl (F&S) provide worthwhile recommendations but that their critique of research by Levin and Banaji (2006) is unfounded. In addition, we argue that F&S apply unjustified level of skepticism about top-down effects relative to other broad hypotheses about the sources of perceptual intelligence.
The El Greco fallacy and pupillometry: Pupillary evidence for top-down effects on perception
Authors: Xie Weizhen , Zhang Weiwei
Published: January 2017

In this commentary, we address the El Greco fallacy by reviewing some recent pupillary evidence supporting top-down modulation of perception. Furthermore, we give justification for including perceptual effects of attention in tests of cognitive penetrability. Together, these exhibits suggest that cognition can affect perception (i.e., they support cognitive penetrability).
Representation of affect in sensory cortex
Authors: Miskovic Vladimir , Kuntzelman Karl , Chikazoe Junichi , Anderson Adam K.
Published: January 2017

Contemporary neuroscience suggests that perception is perhaps best understood as a dynamically iterative process that does not honor cleanly segregated “bottom-up” or “top-down” streams. We argue that there is substantial empirical support for the idea that affective influences infiltrate the earliest reaches of sensory processing and even that primitive internal affective dimensions (e.g., goodness-to-badness) are represented alongside physical dimensions of the external world.
On the neural implausibility of the modular mind: Evidence for distributed construction dissolves boundaries between perception, cognition, and emotion
Authors: Hackel Leor M. , Larson Grace M. , Bowen Jeffrey D. , Ehrlich Gaven A. , Mann Thomas C. , Middlewood Brianna , Roberts Ian D. , Eyink Julie , Fetterolf Janell C. , Gonzalez Fausto , Garrido Carlos O. , Kim Jinhyung , O'Brien Thomas C. , O'Malley Ellen E. , Mesquita Batja , Barrett Lisa Feldman
Published: January 2017

Firestone & Scholl (F&S) rely on three problematic assumptions about the mind (modularity, reflexiveness, and context-insensitivity) to argue cognition does not fundamentally influence perception. We highlight evidence indicating that perception, cognition, and emotion are constructed through overlapping, distributed brain networks characterized by top-down activity and context-sensitivity. This evidence undermines F&S's ability to generalize from case studies to the nature of perception.
Buried ice in Kennar Valley: a late Pleistocene remnant of Taylor Glacier
Authors: Swanger Kate M.
Published: January 2017

Buried glacier ice is common in the McMurdo Dry Valleys and under ideal climatic and geomorphological conditions may be preserved for multimillion-year timescales. This study focuses on the analysis of ~300 m2 of buried glacier ice in lower Kennar Valley, Quartermain Range. The mapped ice is clean,<10 m thick and covered by a~25 cm sandy drift. The mouth of Kennar Valley is occupied by a lobe of Taylor Glacier, an outlet glacier from Taylor Dome. Based on ice–sediment characteristics, air bubble concentrations and stable isotopic analyses from three ice cores, the lower Kennar Valley ice is glacial in origin. These data coupled with a previously reported exposure age chronology indicate that the buried ice was deposited by a late Pleistocene advance of Taylor Glacier, probably during an interglacial interval. The surface of the buried glacier ice exhibits a patterned ground morphology characterized by small, dome-shaped polygons with deep troughs. This shape possibly reflects the final stages of ice loss, as stagnant, isolated ice pinnacles sublimate in place. This study highlights how polygon morphology can be used to infer the thickness of clean buried ice and its geomorphological stability throughout Antarctica, as well as other in cold, arid landscapes.
La liaison à Orléans, corpus et changement linguistique: une première étude exploratoire
Authors: DUGUA CÉLINE , BAUDE OLIVIER
Published: January 2017

Le corpus des Enquêtes sociolinguistiques à Orléans (ESLO), composé de deux périodes de recueils (1968–1974 et depuis 2006) et comprenant une grande diversité de situations (entretiens, paroles publiques, conversations lors de repas, réunions de travail) nous offre des données uniques pour étudier le changement linguistique sur la base des usages de la liaison en français parlé. A partir d'un sous-corpus comprenant 7 locuteurs enregistrés à 40 ans d'intervalle, nous proposons une méthode de repérage et codage des liaisons et nous ouvrons différentes pistes d'analyse qui reposent nécessairement sur une exploration fine du corpus, dans le respect d'une démarche résolument variationniste.
La liaison en français contemporain: normes, usages, acquisitions
Authors: EYCHENNE JULIEN , LAKS BERNARD
Published: January 2017

La phonologie du français présente un phénomène bien connu de sandhi externe à la jointure de mot appeléliaison: devant une unité lexicale à initiale vocalique, un mot se terminant apparemment par une voyelle s'enchaîne syllabiquement en prenant appui sur une consonne:un petit/ café[pətikafe]vs un petitenfant[pətitãfã]. Cette consonne de liaison (CL), ici le /t/, qui n'apparaît que lorsque le mot de droite commence par voyelle, a été analysée comme latente, épenthétique ou supplétive, appartenant au mot de gauche (mot 1, M1 ci-après), de droite (mot 2, M2 ci-après) ou à aucun selon les auteurs, nous y reviendrons.
Evaluating the Potential Benefits of Advanced Automatic Crash Notification
Authors: Plevin Rebecca E. , Kaufman Robert , Fraade-Blanar Laura , Bulger Eileen M.
Published: January 2017

Objective

Advanced Automatic Collision Notification (AACN) services in passenger vehicles capture crash data during collisions that could be transferred to Emergency Medical Services (EMS) providers. This study explored how EMS response times and other crash factors impacted the odds of fatality. The goal was to determine if information transmitted by AACN could help decrease mortality by allowing EMS providers to be better prepared upon arrival at the scene of a collision.

Methods

The Crash Injury Research and Engineering Network (CIREN) database of the US Department of Transportation/National Highway Traffic Safety Administration (USDOT/NHTSA; Washington DC, USA) was searched for all fatal crashes between 1996 and 2012. The CIREN database also was searched for illustrative cases. The NHTSA’s Fatal Analysis Reporting System (FARS) and National Automotive Sampling System Crashworthiness Data System (NASS CDS) databases were queried for all fatal crashes between 2000 and 2011 that involved a passenger vehicle. Detailed EMS time data were divided into prehospital time segments and analyzed descriptively as well as via multiple logistic regression models.

Results

The CIREN data showed that longer times from the collision to notification of EMS providers were associated with more frequent invasive interventions within the first three hours of hospital admission and more transfers from a regional hospital to a trauma center. The NASS CDS and FARS data showed that rural collisions with crash-notification times >30 minutes were more likely to be fatal than collisions with similar crash-notification times occurring in urban environments. The majority of a patient’s prehospital time occurred between the arrival of EMS providers on-scene and arrival at a hospital. The need for extrication increased the on-scene time segment as well as total prehospital time.

Conclusion

An AACN may help decrease mortality following a motor vehicle collision (MVC) by alerting EMS providers earlier and helping them discern when specialized equipment will be necessary in order to quickly extricate patients from the collision site and facilitate expeditious transfer to an appropriate hospital or trauma center.

PlevinRE, KaufmanR, Fraade-BlanarL, BulgerEM. Evaluating the potential benefits of advanced automatic crash notification. Prehosp Disaster Med. 2017;32(2):156–164.
The changingfuture: competition, specialization and reorganization in the contemporary English future temporal reference system
Authors: DENIS DEREK , TAGLIAMONTE SALI A.
Published: January 2017

The English future temporal reference system has long been recognized as a variable system undergoing change. The main variants in contemporary English (willandbe going to) have both been argued to have gone through (and to potentially still be undergoing) grammaticalization. At the same time,be going tohas been gradually increasing in frequency relative towillover the last 500 years. However, investigation of the ongoing development of this system has been sparse. This article makes use of a large contemporary sociolinguistic corpus of a mainstream variety of North American English and the apparent-time construct. Several factors that have been implicated in the development of this system (Sentence Type, Clause Type, Proximity, Verb Type, and the Animacy and Grammatical Person of the Subject) are considered and a multiplex series of changes are uncovered. Underlying an overall, albeit slow, change in frequency towardsbe going to, we find evidence for specialization of one or the other variant in different linguistic contexts, neutralization of a constraint consistent with ongoing loss of variant nuances through semantic bleaching, and the persistence of constraints consistent with morphological doublet competition.
CLOSE-KIN MARRIAGE IN ROMAN ANATOLIA
Authors: Thonemann Peter
Published: January 2017

Many societies have a normative preference for close-kin marriage of one or another variety. Whether this was true of any part of the Roman world has been hotly debated in recent decades. Earlier scholarship suggests that marriage between close kin may have been considerably more common in some parts of the Roman world (e.g. Egypt) than in others (e.g. the Latin West). This paper assembles the evidence for close-kin marriage throughout the Asia Minor peninsula during the Roman Imperial period, and concludes that close-kin marriage – particularly in the form of FBD (father's brother's daughter) first-cousin marriage – may have been unusually common and/or normatively desirable in Lykia and neighbouring regions.
Sustainable Food Governance by Governments and Markets
Authors: Oosterveer Peter
Published: January 2017

The environmental consequences of the increasing global seafood production and consumption are substantial and drive a search for providing more adequate governance responses. In recent years, market-based approaches to sustainable seafood governance have gained considerable traction. Born in part out of perceived failures of state-based regulations, a range of civil society-led governance approaches have emerged. Private seafood governance arrangements interact with public seafood regulations and this may lead to competition, collaboration or hybridity. This interaction should however not be assessed in general but more closely related to the different stages in the regulatory cycle: agenda setting/negotiation, implementation and monitoring/enforcement. Collaboration between public and private global seafood governance arrangements occurs primarily in the first phase of the regulatory cycle but gets much less prominent in later phases where competition or even separation prevails. Harmonization between public and private sustainable seafood governance arrangements in the near future is therefore unlikely.
Marketing and Cultivation of GMOs in the EU
Authors: de Sadeleer Nicolas
Published: January 2017

Due to the astounding revolution sparked off by genetic engineering, the artificial modification of the genome through targeted alterations of DNA and RNA is now competing with the traditional phenotype use of living organisms (selective plant and animal breeding, consumption, manufacturing of products, energy production, etc.). Although until recently these were insurmountable obstacles, interspecies barriers to reproduction are fading away, and it is now possible to transfer genes from one species to the genome of another. In short, the artificial genetic engineering is replacing selective breeding. Furthermore, a new age is dawning – that of synthetic biology – in which man will no longer content himself with modifying existing organisms but, thanks to the radical modification of the genome, will be able to create new cells and new organisms.
Evidence for ACTN3 as a genetic modifier of Duchenne muscular dystrophy
Authors: Hogarth Marshall W. , Houweling Peter J. , Thomas Kristen C. , Gordish-Dressman Heather , Bello Luca ,   Cooperative International Neuromuscular Research Group (CINRG), Vishwanathan V. , Chidambaranathan S. , Douglas Biggar W. , McAdam Laura C. , Mah Jean K. , Tulinius Mar , Cnaan Avital , Morgenroth Lauren P. , Leshner Robert , Tesi-Rocha Carolina , Thangarajh Mathula , Duong Tina , Kornberg Andrew , Ryan Monique , Nevo Yoram , Dubrovsky Alberto , Clemens Paula R. , Abdel-Hamid Hoda , Connolly Anne M. , Pestronk Alan , Teasley Jean , Bertorini Tulio E. , Webster Richard , Kolski Hanna , Kuntz Nancy , Driscoll Sherilyn , Bodensteiner John B. , Carlo Jose , Gorni Ksenija , Lotze Timothy , Day John W. , Karachunski Peter , Henricson Erik K. , Abresch Richard T. , McDonald Craig M. , Pegoraro Elena , Hoffman Eric P. , Head Stewart I. , North Kathryn N.
Published: January 2017

Duchenne muscular dystrophy (DMD) is characterized by muscle degeneration and progressive weakness. There is considerable inter-patient variability in disease onset and progression, which can confound the results of clinical trials. Here we show that a common null polymorphism (R577X) in ACTN3 results in significantly reduced muscle strength and a longer 10 m walk test time in young, ambulant patients with DMD; both of which are primary outcome measures in clinical trials. We have developed a double knockout mouse model, which also shows reduced muscle strength, but is protected from stretch-induced eccentric damage with age. This suggests that α-actinin-3 deficiency reduces muscle performance at baseline, but ameliorates the progression of dystrophic pathology. Mechanistically, we show that α-actinin-3 deficiency triggers an increase in oxidative muscle metabolism through activation of calcineurin, which likely confers the protective effect. Our studies suggest that ACTN3 R577X genotype is a modifier of clinical phenotype in DMD patients.
Synthesis of ketones from biomass-derived feedstock
Authors: Meng Qinglei , Hou Minqiang , Liu Huizhen , Song Jinliang , Han Buxing
Published: January 2017

Cyclohexanone and its derivatives are very important chemicals, which are currently produced mainly by oxidation of cyclohexane or alkylcyclohexane, hydrogenation of phenols, and alkylation of cyclohexanone. Here we report that bromide salt-modified Pd/C in H2O/CH2Cl2 can efficiently catalyse the transformation of aromatic ethers, which can be derived from biomass, to cyclohexanone and its derivatives via hydrogenation and hydrolysis processes. The yield of cyclohexanone from anisole can reach 96%, and the yields of cyclohexanone derivatives produced from the aromatic ethers, which can be extracted from plants or derived from lignin, are also satisfactory. Detailed study shows that the Pd, bromide salt and H2O/CH2Cl2 work cooperatively to promote the desired reaction and inhibit the side reaction. Thus high yields of desired products can be obtained. This work opens the way for production of ketones from aromatic ethers that can be derived from biomass.
Direct observation of spin-layer locking by local Rashba effect in monolayer semiconducting PtSe2 film
Authors: Yao Wei , Wang Eryin , Huang Huaqing , Deng Ke , Yan Mingzhe , Zhang Kenan , Miyamoto Koji , Okuda Taichi , Li Linfei , Wang Yeliang , Gao Hongjun , Liu Chaoxing , Duan Wenhui , Zhou Shuyun
Published: January 2017

The generally accepted view that spin polarization in non-magnetic solids is induced by the asymmetry of the global crystal space group has limited the search for spintronics materials mainly to non-centrosymmetric materials. In recent times it has been suggested that spin polarization originates fundamentally from local atomic site asymmetries and therefore centrosymmetric materials may exhibit previously overlooked spin polarizations. Here, by using spin- and angle-resolved photoemission spectroscopy, we report the observation of helical spin texture in monolayer, centrosymmetric and semiconducting PtSe2 film without the characteristic spin splitting in conventional Rashba effect (R-1). First-principles calculations and effective analytical model analysis suggest local dipole induced Rashba effect (R-2) with spin-layer locking: opposite spins are degenerate in energy, while spatially separated in the top and bottom Se layers. These results not only enrich our understanding of the spin polarization physics but also may find applications in electrically tunable spintronics.
Biomimetically inspired asymmetric total synthesis of (+)-19-dehydroxyl arisandilactone A
Authors: Han Yi-Xin , Jiang Yan-Long , Li Yong , Yu Hai-Xin , Tong Bing-Qi , Niu Zhe , Zhou Shi-Jie , Liu Song , Lan Yu , Chen Jia-Hua , Yang Zhen
Published: January 2017

Complex natural products are a proven and rich source of disease-modulating drugs and of efficient tools for the study of chemical biology and drug discovery. The architectures of complex natural products are generally considered to represent significant barriers to efficient chemical synthesis. Here we describe a concise and efficient asymmetric synthesis of 19-dehydroxyl arisandilactone A—which belongs to a family of architecturally unique, highly oxygenated nortriterpenoids isolated from the medicinal plant Schisandra arisanensis. This synthesis takes place by means of a homo-Michael reaction, a tandem retro-Michael/Michael reaction, and Cu-catalysed intramolecular cyclopropanation as key steps. The proposed mechanisms for the homo-Michael and tandem retro-Michael/Michael reactions are supported by density functional theory (DFT) calculation. The developed chemistry may find application for the synthesis of its other family members of Schisandraceae nortriterpenoids.
Elevated-temperature-induced acceleration of PACT clearing process of mouse brain tissue
Authors: Yu Tingting , Qi Yisong , Zhu Jingtan , Xu Jianyi , Gong Hui , Luo Qingming , Zhu Dan
Published: January 2017

Tissue optical clearing technique shows a great potential for neural imaging with high resolution, especially for connectomics in brain. The passive clarity technique (PACT) is a relative simple clearing method based on incubation, which has a great advantage on tissue transparency, fluorescence preservation and immunostaining compatibility for imaging tissue blocks. However, this method suffers from long processing time. Previous studies indicated that increasing temperature can speed up the clearing. In this work, we aim to systematacially and quantitatively study this influence based on PACT with graded increase of temperatures. We investigated the process of optical clearing of brain tissue block at different temperatures, and found that elevated temperature could accelerate the clearing process and also had influence on the fluorescence intensity. By balancing the advantages with drawbacks, we conclude that 42–47 °C is an alternative temperature range for PACT, which can not only produce faster clearing process, but also retain the original advantages of PACT by preserving endogenous fluorescence well, achieving fine morphology maintenance and immunostaining compatibility.
QuickProbs 2: Towards rapid construction of high-quality alignments of large protein families
Authors: Gudyś Adam , Deorowicz Sebastian
Published: January 2017

The ever-increasing size of sequence databases caused by the development of high throughput sequencing, poses to multiple alignment algorithms one of the greatest challenges yet. As we show, well-established techniques employed for increasing alignment quality, i.e., refinement and consistency, are ineffective when large protein families are investigated. We present QuickProbs 2, an algorithm for multiple sequence alignment. Based on probabilistic models, equipped with novel column-oriented refinement and selective consistency, it offers outstanding accuracy. When analysing hundreds of sequences, Quick-Probs 2 is noticeably better than ClustalΩ and MAFFT, the previous leaders for processing numerous protein families. In the case of smaller sets, for which consistency-based methods are the best performing, QuickProbs 2 is also superior to the competitors. Due to low computational requirements of selective consistency and utilization of massively parallel architectures, presented algorithm has similar execution times to ClustalΩ, and is orders of magnitude faster than full consistency approaches, like MSAProbs or PicXAA. All these make QuickProbs 2 an excellent tool for aligning families ranging from few, to hundreds of proteins.
Joint genome-wide association and transcriptome sequencing reveals a complex polygenic network underlying hypocotyl elongation in rapeseed (Brassica napus L.)
Authors: Luo Xiang , Xue Zhifei , Ma Chaozhi , Hu Kaining , Zeng Ziru , Dou Shengwei , Tu Jinxing , Shen Jinxiong , Yi Bin , Fu Tingdong
Published: January 2017

Hypocotyl elongation is considered an important typical seedling trait contributing directly to an increase in and stabilization of the yield in Brassica napus, but its molecular genetic mechanism is poorly understood. In the present study, hypocotyl lengths of 210 lines were measured in an illuminated culture room. A genome-wide association study (GWAS) was performed with 23,435 single nucleotide polymorphisms (SNPs) for hypocotyl length. Three lines with long hypocotyl length and three lines with short hypocotyl length from one doubled haploid line (DH) population were used for transcriptome sequencing. A GWAS followed by transcriptome analysis identified 29 differentially expressed genes associated with significant SNPs in B. napus. These genes regulate hypocotyl elongation by mediating flowering morphogenesis, circadian clock, hormone biosynthesis, or important metabolic signaling pathways. Among these genes, BnaC07g46770D negatively regulates hypocotyl elongation directly, as well as flowering time. Our results indicate that a joint GWAS and transcriptome analysis has significant potential for identifying the genes responsible for hypocotyl elongation; The extension of hypocotyl is a complex biological process regulated by a polygenic network.
Identifying the Metabolic Differences of a Fast-Growth Phenotype in Synechococcus UTEX 2973
Authors: Mueller Thomas J. , Ungerer Justin L. , Pakrasi Himadri B. , Maranas Costas D.
Published: January 2017

The photosynthetic capabilities of cyanobacteria make them interesting candidates for industrial bioproduction. One obstacle to large-scale implementation of cyanobacteria is their limited growth rates as compared to industrial mainstays. Synechococcus UTEX 2973, a strain closely related to Synechococcus PCC 7942, was recently identified as having the fastest measured growth rate among cyanobacteria. To facilitate the development of 2973 as a model organism we developed in this study the genome-scale metabolic model iSyu683. Experimental data were used to define CO2 uptake rates as well as the biomass compositions for each strain. The inclusion of constraints based on experimental measurements of CO2 uptake resulted in a ratio of the growth rates of Synechococcus 2973 to Synechococcus 7942 of 2.03, which nearly recapitulates the in vivo growth rate ratio of 2.13. This identified the difference in carbon uptake rate as the main factor contributing to the divergent growth rates. Additionally four SNPs were identified as possible contributors to modified kinetic parameters of metabolic enzymes and candidates for further study. Comparisons against more established cyanobacterial strains identified a number of differences between the strains along with a correlation between the number of cytochrome c oxidase operons and heterotrophic or diazotrophic capabilities.
A new model of sperm nuclear architecture following assessment of the organization of centromeres and telomeres in three-dimensions
Authors: Ioannou Dimitrios , Millan Nicole M. , Jordan Elizabeth , Tempest Helen G.
Published: January 2017

The organization of chromosomes in sperm nuclei has been proposed to possess a unique “hairpin-loop” arrangement, which is hypothesized to aid in the ordered exodus of the paternal genome following fertilization. This study simultaneously assessed the 3D and 2D radial and longitudinal organization of telomeres, centromeres, and investigated whether chromosomes formed the same centromere clusters in sperm cells. Reproducible radial and longitudinal non-random organization was observed for all investigated loci using both 3D and 2D approaches in multiple subjects. We report novel findings, with telomeres and centromeres being localized throughout the nucleus but demonstrating roughly a 1:1 distribution in the nuclear periphery and the intermediate regions with <15% occupying the nuclear interior. Telomeres and centromeres were observed to aggregate in sperm nuclei, forming an average of 20 and 7 clusters, respectively. Reproducible longitudinal organization demonstrated preferential localization of telomeres and centromeres in the mid region of the sperm cell. Preliminary evidence is also provided to support the hypothesis that specific chromosomes preferentially form the same centromere clusters. The more segmental distribution of telomeres and centromeres as described in this study could more readily accommodate and facilitate the sequential exodus of paternal chromosomes following fertilization.
Fast Bayesian inference of optical trap stiffness and particle diffusion
Authors: Bera Sudipta , Paul Shuvojit , Singh Rajesh , Ghosh Dipanjan , Kundu Avijit , Banerjee Ayan , Adhikari R.
Published: January 2017

Bayesian inference provides a principled way of estimating the parameters of a stochastic process that is observed discretely in time. The overdamped Brownian motion of a particle confined in an optical trap is generally modelled by the Ornstein-Uhlenbeck process and can be observed directly in experiment. Here we present Bayesian methods for inferring the parameters of this process, the trap stiffness and the particle diffusion coefficient, that use exact likelihoods and sufficient statistics to arrive at simple expressions for the maximum a posteriori estimates. This obviates the need for Monte Carlo sampling and yields methods that are both fast and accurate. We apply these to experimental data and demonstrate their advantage over commonly used non-Bayesian fitting methods.
Myosuppressin is involved in the regulation of pupal diapause in the cabbage army moth Mamestra brassicae
Authors: Yamada Nobuto , Kataoka Hiroshi , Mizoguchi Akira
Published: January 2017

Diapause, a programmed developmental arrest, is common in insects, enabling them to survive adverse seasons. It is well established that pupal diapause is regulated by ecdysteroids secreted by the prothoracic glands (PGs), with cessation of ecdysteroid secretion after pupal ecdysis leading to pupal diapause. A major factor regulating the gland activity is prothoracicotropic hormone (PTTH) secreted from the brain. In our previous study, we demonstrated that the cessation of PTTH release after pupal ecdysis resulted in the inactivation of the PGs, leading to pupal diapause in the cabbage army moth Mamestra brassicae. Here we show that a neuropeptide myosuppressin also contributes to the inactivation of PGs at the initiation of diapause. Myosuppressin suppresses PTTH-stimulated activation of the PGs in vitro. Concentrations of myosuppressin in the hemolymph after pupal ecdysis are higher in diapause pupae than in nondiapause pupae.
A bias-minimising measure of the influence of head orientation on perceived gaze direction
Authors: Balsdon Tarryn , Clifford Colin W. G.
Published: January 2017

The orientation of the head is an important cue for gaze direction, and its role has been explained in a dual route model. The model incorporates both an attractive and a repulsive effect of head orientation, which act to support accurate gaze perception across large changes in natural stimuli. However, in all previous studies of which we are aware, measurements of the influence of head orientation on perceived gaze direction were obtained using a single-interval methodology, which may have been affected by response bias. Here we compare the single-interval methodology with a two-interval (bias-minimising) design. We find that although measures obtained using the two-interval design showed a stronger attractive effect of head orientation than previous studies, the influence of head orientation on perceived gaze direction still represents a genuine perceptual effect. Measurements obtained using the two-interval design were also shown to be more stable across sessions one week apart. These findings suggest the two-interval design should be used in future experiments, especially if comparing groups who may systematically differ in their biases, such as patients with schizophrenia or autism.
No effect of Bt Cry1Ie toxin on bacterial diversity in the midgut of the Chinese honey bees, Apis cerana cerana (Hymenoptera, Apidae)
Authors: Jia Hui-Ru , Dai Ping-Li , Geng Li-Li , Jack Cameron J. , Li Yun-He , Wu Yan-Yan , Diao Qing-Yun , Ellis James D.
Published: January 2017

Cry1Ie protein derived from Bacillus thuringiensis (Bt) has been proposed as a promising candidate for the development of a new Bt-maize variety to control maize pests in China. We studied the response of the midgut bacterial community of Apis cerana cerana to Cry1Ie toxin under laboratory conditions. Newly emerged bees were fed one of the following treatments for 15 and 30 days: three concentrations of Cry1Ie toxin (20 ng/mL, 200 ng/mL, and 20 μg/mL) in sugar syrup, pure sugar syrup as a negative control and 48 ng/mL imidacloprid as a positive control. The relative abundance of 16S rRNA genes was measured by Quantitative Polymerase Chain Reaction and no apparent differences were found among treatments for any of these counts at any time point. Furthermore, the midgut bacterial structure and compositions were determined using high-throughput sequencing targeting the V3-V4 regions of the 16S rDNA. All core honey bee intestinal bacterial genera such as Lactobacillus, Bifidobacterium, Snodgrassella, and Gilliamella were detected, and no significant changes were found in the species diversity and richness for any bacterial taxa among treatments at different time points. These results suggest that Cry1Ie toxin may not affect gut bacterial communities of Chinese honey bees.
Accurate discrimination of the wake-sleep states of mice using non-invasive whole-body plethysmography
Authors: Bastianini Stefano , Alvente Sara , Berteotti Chiara , Lo Martire Viviana , Silvani Alessandro , Swoap Steven J. , Valli Alice , Zoccoli Giovanna , Cohen Gary
Published: January 2017

A major limitation in the study of sleep breathing disorders in mouse models of pathology is the need to combine whole-body plethysmography (WBP) to measure respiration with electroencephalography/electromyography (EEG/EMG) to discriminate wake-sleep states. However, murine wake-sleep states may be discriminated from breathing and body movements registered by the WBP signal alone. Our goal was to compare the EEG/EMG-based and the WBP-based scoring of wake-sleep states of mice, and provide formal guidelines for the latter. EEG, EMG, blood pressure and WBP signals were simultaneously recorded from 20 mice. Wake-sleep states were scored based either on EEG/EMG or on WBP signals and sleep-dependent respiratory and cardiovascular estimates were calculated. We found that the overall agreement between the 2 methods was 90%, with a high Cohen’s Kappa index (0.82). The inter-rater agreement between 2 experts and between 1 expert and 1 naïve sleep investigators gave similar results. Sleep-dependent respiratory and cardiovascular estimates did not depend on the scoring method. We show that non-invasive discrimination of the wake-sleep states of mice based on visual inspection of the WBP signal is accurate, reliable and reproducible. This work may set the stage for non-invasive high-throughput experiments evaluating sleep and breathing patterns on mouse models of pathophysiology.
Dynamic evolution of hepatitis C virus resistance-associated substitutions in the absence of antiviral treatment
Authors: Eltahla Auda A. , Leung Preston , Pirozyan Mehdi R. , Rodrigo Chaturaka , Grebely Jason , Applegate Tanya , Maher Lisa , Luciani Fabio , Lloyd Andrew R. , Bull Rowena A.
Published: January 2017

Resistance against new hepatitis C virus (HCV) antivirals is an area of increasing interest. Resistance-associated substitutions (RASs) have been identified in treatment-naïve individuals, but pressures driving treatment-independent RAS emergence are poorly understood. We analysed the longitudinal evolution of RASs in twelve participants with early acute HCV infections. Full-genome deep sequences were analysed for changes in RAS frequency within NS3, NS5A and NS5B-coding regions over the course of the infection. Emergence of RASs relevant only to the polymerase non-nucleoside inhibitors (NNI) was detected, and these lay within CD8+ T-cell epitopes. Conversely, the loss of NNI RASs over time appeared likely to be driven by viral fitness constraints. These results highlight the importance of monitoring CD8+ T cell epitope-associated RASs in populations with dominant HLA types.
Non-AUG start codons responsible for ABO weak blood group alleles on initiation mutant backgrounds
Authors: Cid Emili , Yamamoto Miyako , Yamamoto Fumiichiro
Published: January 2017

Histo-blood group ABO gene polymorphism is crucial in transfusion medicine. We studied the activity and subcellular distribution of ABO gene-encoded A glycosyltransferases with N-terminal truncation. We hypothesized that truncated enzymes starting at internal methionines drove the synthesis of oligosaccharide A antigen in those already described alleles that lack a proper translation initiation codon. Not only we tested the functionality of the mutant transferases by expressing them and assessing their capacity to drive the appearance of A antigen on the cell surface, but we also analyzed their subcellullar localization, which has not been described before. The results highlight the importance of the transmembrane domain because proteins deprived of it are not able to localize properly and deliver substantial amounts of antigen on the cell surface. Truncated proteins with their first amino acid well within the luminal domain are not properly localized and lose their enzymatic activity. Most importantly, we demonstrated that other codons than AUG might be used to start the protein synthesis rather than internal methionines in translation-initiation mutants, explaining the molecular mechanism by which transferases lacking a classical start codon are able to synthesize A/B antigens.
Single α-particle irradiation permits real-time visualization of RNF8 accumulation at DNA damaged sites
Authors: Muggiolu Giovanna , Pomorski Michal , Claverie Gérard , Berthet Guillaume , Mer-Calfati Christine , Saada Samuel , Devès Guillaume , Simon Marina , Seznec Hervé , Barberet Philippe
Published: January 2017

As well as being a significant source of environmental radiation exposure, α-particles are increasingly considered for use in targeted radiation therapy. A better understanding of α-particle induced damage at the DNA scale can be achieved by following their tracks in real-time in targeted living cells. Focused α-particle microbeams can facilitate this but, due to their low energy (up to a few MeV) and limited range, α-particles detection, delivery, and follow-up observations of radiation-induced damage remain difficult. In this study, we developed a thin Boron-doped Nano-Crystalline Diamond membrane that allows reliable single α-particles detection and single cell irradiation with negligible beam scattering. The radiation-induced responses of single 3 MeV α-particles delivered with focused microbeam are visualized in situ over thirty minutes after irradiation by the accumulation of the GFP-tagged RNF8 protein at DNA damaged sites.