bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Microfluidic-Enabled Mechanical Microcompressor for the Immobilization of Live Single- and Multi-Cellular Specimens
Authors: Yan Yingjun , Jiang Liwei , Aufderheide Karl J. , Wright Gus A. , Terekhov Alexander , Costa Lino , Qin Kevin , McCleery W. Tyler , Fellenstein John J. , Ustione Alessandro , Robertson J. Brian , Johnson Carl Hirschie , Piston David W. , Hutson M. Shane , Wikswo John P. , Hofmeister William , Janetopoulos Chris 
Published: January 2014

AbstractA microcompressor is a precision mechanical device that flattens and immobilizes living cells and small organisms for optical microscopy, allowing enhanced visualization of sub-cellular structures and organelles. We have developed an easily fabricated device, which can be equipped with microfluidics, permitting the addition of media or chemicals during observation. This device can be used on both upright and inverted microscopes. The apparatus permits micrometer precision flattening for nondestructive immobilization of specimens as small as a bacterium, while also accommodating larger specimens, such as Caenorhabditis elegans, for long-term observations. The compressor mount is removable and allows easy specimen addition and recovery for later observation. Several customized specimen beds can be incorporated into the base. To demonstrate the capabilities of the device, we have imaged numerous cellular events in several protozoan species, in yeast cells, and in Drosophila melanogaster embryos. We have been able to document previously unreported events, and also perform photobleaching experiments, in conjugating Tetrahymena thermophila.
Erratum: Sympatric inhibition and niche differentiation suggest alternative coevolutionary trajectories among Streptomycetes
Authors: Kinkel Linda L , Schlatter Daniel C , Xiao Kun , Baines Anita D 
Published: January 2014

Abstract
Correction to: The ISME Journal (2014) 8, 249–256; doi:10.1038/ismej.2013.175; published online 24 October 2013 Since the online publication of this article, the authors have identified an error concerning Figure 2, namely that the incorrect figure was displayed. The correct figure is shown here. This error has now been rectified, and the corrected article appears in this issue.
High-temperature antiferromagnetism in molecular semiconductor thin films and nanostructures
Authors: Serri Michele , Wu Wei , Fleet Luke R. , Harrison Nicholas M. , Hirjibehedin Cyrus F. , Kay Christopher W.M. , Fisher Andrew J. , Aeppli Gabriel , Heutz Sandrine 
Published: January 2014

AbstractThe viability of dilute magnetic semiconductors in applications is linked to the strength of the magnetic couplings, and room temperature operation is still elusive in standard inorganic systems. Molecular semiconductors are emerging as an alternative due to their long spin-relaxation times and ease of processing, but, with the notable exception of vanadium-tetracyanoethylene, magnetic transition temperatures remain well below the boiling point of liquid nitrogen. Here we show that thin films and powders of the molecular semiconductor cobalt phthalocyanine exhibit strong antiferromagnetic coupling, with an exchange energy reaching 100 K. This interaction is up to two orders of magnitude larger than in related phthalocyanines and can be obtained on flexible plastic substrates, under conditions compatible with routine organic electronic device fabrication. Ab initio calculations show that coupling is achieved via superexchange between the singly occupied a1g ("Equation missing") orbitals. By reaching the key milestone of magnetic coupling above 77 K, these results establish quantum spin chains as a potentially useable feature of molecular films.
Combinatorial gene editing in mammalian cells using ssODNs and TALENs
Authors: Strouse Bryan , Bialk Pawel , Niamat Rohina A. , Rivera-Torres Natalia , Kmiec Eric B. 
Published: January 2014

AbstractThe regulation of gene editing is being elucidated in mammalian cells and its potential as well as its limitations are becoming evident. ssODNs carry out gene editing by annealing to their complimentary sequence at the target site and acting as primers for replication fork extension. To effect a genetic change, a large amount of ssODN molecules must be introduced into cells and as such induce a Reduced Proliferation Phenotype (RPP), a phenomenon in which corrected cells do not proliferate. To overcome this limitation, we have used TAL-Effector Nucleases (TALENs) to increase the frequency, while reducing the amount of ssODN required to direct gene correction. This strategy resolves the problem and averts the serious effects of RPP. The efficiency of gene editing can be increased significantly if cells are targeted while they progress through S phase. Our studies define new reaction parameters that will help guide experimental strategies of gene editing.
Identification of interferon-γ as a new molecular target of liver X receptor
Authors: Wang Qixue , Ma Xingzhe , Chen Yuanli , Zhang Ling , Jiang Meixiu , Li Xiaoju , Xiang Rong , Miao Robert , Hajjar David P. , Duan Yajun , Han Jihong 
Published: January 2014

LXR (liver X receptor) is a ligand-activated transcription factor and plays an important role in regulation of lipid homoeostasis and inflammation. Several studies indicate that LXR inhibits IFN-γ (interferon γ)-induced biological responses; however, the influence of LXR on IFN-γ expression has not been fully elucidated. In the present study, we investigated the effects of LXR activation on IFN-γ expression at different levels. At the molecular level, we surprisingly observed that LXR ligand (T0901317) induced macrophage and T-cell IFN-γ protein expression which was associated with increased mRNA and secreted protein levels in culture medium. In contrast, selective inhibition of LXRα and/or LXRβ expression by siRNA reduced IFN-γ expression. Promoter analysis defined the multiple LXREs (LXR-responsive elements) in the proximal region of the IFN-γ promoter. EMSAs and ChIP indicated that LXR activation enhanced the binding of LXR protein to these LXREs. In vivo, T0901317 increased wild-type mouse serum IFN-γ levels and IFN-γ expression in the lung and lymph nodes. Functionally, we observed that administration of T0901317 to wild-type mice increased rates of survival and being tumour-free, and inhibited tumour growth when the animals were inoculated with LLC1 carcinoma. In contrast, these protective effects were substantially attenuated in IFN-γ-knockout (IFN-γ−/−) mice, suggesting that the induction of IFN-γ production plays a critical role in T0901317-inhibited tumour growth. Taken together, the results of the present study show that IFN-γ is another molecular target of LXR activation, and it suggests a new mechanism by which LXR inhibits tumour growth.
Differences in the right inferior longitudinal fasciculus but no general disruption of white matter tracts in children with autism spectrum disorder
Authors: Koldewyn Kami , Yendiki Anastasia , Weigelt Sarah , Gweon Hyowon , Julian Joshua , Richardson Hilary , Malloy Caitlin , Saxe Rebecca , Fischl Bruce , Kanwisher Nancy 
Published: January 2014

Significance
One of the most accepted brain “signatures” of autism spectrum disorder (ASD) is a reduction in the integrity of long-range white-matter fiber tracts. Here, we assessed known white matter tracts in children with ASD by using diffusion-weighted imaging. In contrast to most prior studies, we carefully matched for head motion between groups. When data quality was matched, there was no evidence of widespread changes in white-matter tracts in the ASD group. Instead, differences were present in only one tract, the right inferior longitudinal fasciculus. These data challenge the idea that widespread changes in white-matter integrity are a signature of ASD and highlight the importance of matching for data quality in future diffusion studies of ASD and other clinical disorders.
Log-Lipschitz embeddings of homogeneous sets with sharp logarithmic exponents and slicing products of balls
Authors: Robinson James 
Published: January 2014

IfXXis a compact subset of a Banach space withX−XX-Xhomogeneous (equivalently ‘doubling’ or with finite Assouad dimension), thenXXcan be embedded into someRn\mathbb {R}^n(withnnsufficiently large) using a linear mapLLwhose inverse is Lipschitz to within logarithmic corrections. More precisely, there existc,α>0c,\alpha >0such that\[c ‖x−y‖|log⁡‖x−y‖|α≤|Lx−Ly|≤c‖x−y‖for allx,y∈X, ‖x−y‖>δ,c\ \frac {\|x-y\|}{|\,\log \|x-y\|\,|^\alpha }\le |Lx-Ly|\le c\|x-y\|\quad \mbox {for all}\quad x,y\in X,\ \|x-y\|>\delta ,\]for someδ\deltasufficiently small. It is known that one must haveα>1\alpha >1in the case of a general Banach space andα>1/2\alpha >1/2in the case of a Hilbert space. It is shown in this paper that these exponents can be achieved.

While the argument in a general Banach space is relatively straightforward, the Hilbert space case relies on the fact that the maximum volume of a hyperplane slice of akk-fold product of unit volumeNN-balls is bounded independent ofkk(this provides a ‘qualitative’ generalisation of a result on slices of the unit cube due to Hensley (Proc. AMS73(1979), 95–100) and Ball (Proc. AMS97(1986), 465–473)).
Cooperation against Theft: A Test of Incentives for Water Management in Tunisia
Authors: Mattoussi Wided , Seabright Paul 
Published: January 2014

AbstractWater theft carried out by manipulating water meters constrains volumetric pricing in semi‐arid regions. Cooperative management can reduce theft and improve incentives for efficient water use by inducing peer monitoring. Using a theoretical model, we show that theft is more likely when prices are high, punishments are weak, and cooperatives are large. We also show how cooperative membership and punishment levels are determined endogenously by constraints on monitoring. We test the model on data from Tunisia for the years 2001–2003, relying on instruments that proxy for unobservable monitoring costs. The results confirm that well‐designed incentives can reduce theft, and that constraints on monitoring costs affect institutional design.
Parameterizing and operationalizing zooplankton population dynamic and trophic interaction models
Authors: Plourde Stéphane , Browman Howard I. 
Published: January 2014

Abstract
Plourde, S., and Browman, H. I. 2014. Parameterizing and operationalizing zooplankton population dynamic and trophic interaction models. – ICES Journal of Marine Science, 71: 234–235. This themed set (TS) of articles was motivated by the need for modellers and biologists–ecologists to work more closely together to produce more realistic simulation models of zooplankton population dynamics and trophic interactions. The TS was intended to cover a broad range of subjects and potential approaches, including identifying crucial gaps in our knowledge and parameterization of biological/physiological processes, experimental/fieldwork aimed at quantifying the response of key physiological and behavioural processes to variations in the environment, identifying novel modelling approaches that would enable the development of simulation models that would minimize the need for species-specific (and stage-specific) model parameterization, etc. Five articles were accepted for inclusion in the TS. They cover the majority of these themes. TSs are intended to be instrumental in focusing attention, triggering opinions, and stimulating ideas, discussion and activity in specific research fields. We hope that this TS has achieved that.
Expression, purification and crystallization of a dye-decolourizing peroxidase from Dictyostelium discoideum
Authors: Rai Amrita , Fedorov Roman , Manstein Dietmar J. 
Published: January 2014

Dye-decolourizing peroxidases are haem-containing peroxidases with broad substrate specificity. Using H2O2 as an electron acceptor, they efficiently decolourize various dyes that are of industrial and environmental relevance, such as anthraquninone- and azo-based dyes. In this study, the dye-decolourizing peroxidase DdDyP from Dictyostelium discoideum was overexpressed in Escherichia coli strain Rosetta(DE3)pLysS, purified and crystallized using the vapour-diffusion method. A native crystal diffracted to 1.65 Å resolution and belonged to space group P41212, with unit-cell parameters a = b = 141.03, c = 95.56 Å, α = β = γ = 90°. The asymmetric unit contains two molecules.
Distribution of essential and non‐essential elements on the surface of roadside leaves and in the bulk of various fruits by atomic absorption spectrophotometry
Authors: Ahmad Fiaz , Munir Arshad , Zafar‐uz‐Zaman  , Zafar Ali Naveed 
Published: January 2014

PurposeThe purpose of this paper is to establish some acceptable trends in the contamination of roadside vegetation and to define a safety limit regarding the effects of metal contamination arising from various toxic metals deposited on leaves of the plants and in the bulk of the fruits.Design/methodology/approachDistribution of essential and non‐essential elements on the surface of leaves and in bulk of fruits of specific areas of Multan (Pakistan) was estimated and correlated with World Health Organization (WHO) standards. The metal concentrations are expressed as X ± SD for triplicate sub samples with the SD of ± 1.0‐1.5 per cent. The maximum metal levels in bulk of various fruits were calculated for FE, followed by Cu, Zn and Co.FindingsIn samples from roadside leaves Fe (823 mg/kg) was found to be the dominant metal, whereas the observed threshold level was found for Co (17.25 mg/kg). The non‐essential elements in various fruits, the Cr was found to be the dominate (16 mg/kg) on mean basis as compared with other metals in fruits. The increasing order of non‐essential metals on the surface of roadside leaves was Li < Ni < Sr < Pb < Cr. The results revealed that metal concentration decreases with increase in distance from roadside (10, 30 and 50 m) with negative correlation coefficient.Originality/valueThis paper shows that the metals concentration in case of all fruit samples fall within the permissible safe limit, whereas the metal concentrations on the surface of roadside leaves were found to surpass the safe limits laid down by the WHO. It is consequently suggested that edible portions of vegetation and fruits near highways should be consumed cautiously.
Profiling gene expression to distinguish the likely active diazotrophs from a sea of genetic potential in marine sediments
Authors: Brown S. M. , Jenkins B. D. 
Published: January 2014

SummaryNitrogen (N) cycling microbial communities in marine sediments are extremely diverse, and it is unknown whether this diversity reflects extensive functional redundancy. Sedimentary denitrifiers remove significant amounts of N from the coastal ocean and diazotrophs are typically regarded as inconsequential. Recently, N fixation has been shown to be a potentially important source of N in estuarine and continental shelf sediments. Analysis of expressed genes for nitrite reductase (nirS) and a nitrogenase subunit (nifH) was used to identify the likely active denitrifiers and nitrogen fixers in surface sediments from different seasons in Narragansett Bay (Rhode Island, USA). The overall diversity of diazotrophs expressing nifH decreased along the estuarine gradient from the estuarine head to an offshore continental shelf site. Two groups of sequences related to anaerobic sulphur/iron reducers and sulphate reducers dominated libraries of expressed nifH genes. Quantitative polymerase chain reaction (qPCR) and quantitative reverse transcription polymerase chain reaction (qRT‐PCR) data shows the highest abundance of both groups at a mid bay site, and the highest nifH expression at the head of the estuary, regardless of season. Several potential environmental factors, including water temperature, oxygen concentration and metal contamination, may influence the abundance and nifH expression of these two bacterial groups.
The commodification of patient opinion: the digital patient experience economy in the age of big data
Authors: Lupton Deborah 
Published: January 2014

AbstractAs part of the digital health phenomenon, a plethora of interactive digital media platforms have been established in recent years to elicit lay people's experiences of illness and health care. The overt function of these platforms is to provide forums where patients and caregivers can share their experiences with others, benefit from the support and knowledge of other users and contribute to large aggregated data archives as part of developing better medical treatments and services and conducting medical research. However, what may not always be readily apparent to the users of these platforms are the growing commercial uses by many of the platforms’ owners of the data they contribute. This article examines this phenomenon of what I term ‘the digital patient experience economy’. Such aspects of this economy as prosumption (the combination of content consumption and production that is characteristic of the use of Web 2.0 technologies), the valorising of big data, the discourse and ethic of sharing and the commercialisation of affective labour are discussed. It is argued that via these online platforms patients’ opinions and experiences may be expressed in more diverse and accessible forums than ever before, but simultaneously they have become exploited in novel ways.
Functional dental occlusion: an anthropological perspective and implications for practice
Authors: Kaidonis JA , Ranjitkar S , Lekkas D , Brook AH , Townsend GC 
Published: January 2014

AbstractPhysiologic changes occur in dental occlusion throughout life, resulting from the interplay between functional demands and reciprocating adaptive responses. These changes have been reported in the anthropological literature and they reflect evolutionary changes in the human stomatognathic system during the Paleolithic, hunter‐gatherer period. Specific occlusal changes occur in response to different environments, leading to extensive variation within and between extinct and extant human populations. For example, functional demands can cause occlusal and interproximal tooth wear, resulting in shortening of the dental arch, continual tooth eruption and changes in masticatory patterns.Since the advent of farming through to our current industrialized culture, functional demands on the human masticatory system, and its adaptive responses to these demands, have been reduced considerably. Indeed, it is only occasionally that functional demands are severe enough to lead to obvious pathology in the modern human dentition. In contrast to normal masticatory activity, ‘modern‐day conditions’ such as dental caries, periodontal disease and erosion, can lead to significant changes in dental occlusion that are pathological and need to be treated.The masticatory system is a dynamic, functional unit that displays considerable change over a lifetime. In this concept paper, it is proposed that modern human populations living in industrialized environments display dental occlusions that can be considered to be ‘neotenous’; that is, our dentitions tend to reflect an unworn stage of our ancestors that was only seen in infants, juveniles and young adults. Clinicians can draw on both phylogenetic and ontogenetic perspectives of ‘functional dental occlusion’ to differentiate continual physiological changes occurring over time that require ongoing review, from pathological responses that require intervention.
Worldwide frequency distribution of the ‘Gait keeper’ mutation in the DMRT3 gene
Authors: Promerová M. , Andersson L. S. , Juras R. , Penedo M. C. T. , Reissmann M. , Tozaki T. , Bellone R. , Dunner S. , Hořín P. , Imsland F. , Imsland P. , Mikko S. , Modrý D. , Roed K. H. , Schwochow D. , Vega‐Pla J. L. , Mehrabani‐Yeganeh H. , Yousefi‐Mashouf N. , G. Cothran E. , Lindgren G. , Andersson L. 
Published: January 2014

SummaryFor centuries, domestic horses have represented an important means of transport and served as working and companion animals. Although their role in transportation is less important today, many horse breeds are still subject to intense selection based on their pattern of locomotion. A striking example of such a selected trait is the ability of a horse to perform additional gaits other than the common walk, trot and gallop. Those could be four‐beat ambling gaits, which are particularly smooth and comfortable for the rider, or pace, used mainly in racing. Gaited horse breeds occur around the globe, suggesting that gaitedness is an old trait, selected for in many breeds. A recent study discovered that a nonsense mutation in DMRT3 has a major impact on gaitedness in horses and is present at a high frequency in gaited breeds and in horses bred for harness racing. Here, we report a study of the worldwide distribution of this mutation. We genotyped 4396 horses representing 141 horse breeds for the DMRT3 stop mutation. More than half (2749) of these horses also were genotyped for a SNP situated 32 kb upstream of the DMRT3 nonsense mutation because these two SNPs are in very strong linkage disequilibrium. We show that the DMRT3 mutation is present in 68 of the 141 genotyped horse breeds at a frequency ranging from 1% to 100%. We also show that the mutation is not limited to a geographical area, but is found worldwide. The breeds with a high frequency of the stop mutation (>50%) are either classified as gaited or bred for harness racing.
Quantitative trait loci for magnitude of the plasma cortisol response to confinement in rainbow trout
Authors: Quillet E. , Krieg F. , Dechamp N. , Hervet C. , Bérard A. , Le Roy P. , Guyomard R. , Prunet P. , Pottinger T. G. 
Published: January 2014

SummaryBetter understanding of the mechanisms underlying interindividual variation in stress responses and their links with production traits is a key issue for sustainable animal breeding. In this study, we searched for quantitative trait loci (QTL) controlling the magnitude of the plasma cortisol stress response and compared them to body size traits in five F2 full‐sib families issued from two rainbow trout lines divergently selected for high or low post‐confinement plasma cortisol level. Approximately 1000 F2 individuals were individually tagged and exposed to two successive acute confinement challenges (1 month interval). Post‐stress plasma cortisol concentrations were determined for each fish. A medium density genome scan was carried out (268 markers, overall marker spacing less than 10 cM). QTL detection was performed using qtlmap software, based on an interval mapping method (http://www.inra.fr/qtlmap). Overall, QTL of medium individual effects on cortisol responsiveness (<10% of phenotypic variance) were detected on 18 chromosomes, strongly supporting the hypothesis that control of the trait is polygenic. Although a core array of QTL controlled cortisol concentrations at both challenges, several QTL seemed challenge specific, suggesting that responses to the first and to a subsequent exposure to the confinement stressor are distinct traits sharing only part of their genetic control. Chromosomal location of the steroidogenic acute regulatory protein (STAR) makes it a good potential candidate gene for one of the QTL. Finally, comparison of body size traits QTL (weight, length and body conformation) with cortisol‐associated QTL did not support evidence for negative genetic relationships between the two types of traits.