bluuebunny/crossref_metadata_2025 huggingface dataset:
Crater production by energetic nanoparticle impact on Au nanofoams
Authors: Anders Christian , Bringa Eduardo M. , Urbassek Herbert M.
Published: March 2016

Impact of energetic nanoparticles on solids produces craters on the surface. We use molecular dynamics simulations to compare crater production on a compact Au solid with that in a porous (foam) target. Our results show a complex picture: (i) At low impact velocities, the nanoparticles produce permanent craters in the foam while they cannot penetrate the compact target. (ii) With increasing velocity and/or projectile mass, the crater depth in the foam target increases less strongly than for the compact target. The plasticity-affected zone in the foam target is of similar size as in the compact target. Our results are relevant for the use of porous structures as shields against nanoparticle impact.
A multiplexed immunoaggregation biomarker assay using a two-stage micro resistive pulse sensor
Authors: Han Y. , Wu H. , Liu F. , Cheng G. , Zhe J.
Published: March 2016

We present an immunoaggregation assay chip for multiplexed biomarkers detection. This chip is based on immunoaggregation of antibody functionalized microparticles (Ab-MPs) to quantify concentrations of multiple biomarkers simultaneously. A mixture of multiple types of Ab-MPs probes with different sizes and magnetic properties, which were functionalized by different antibodies, was used for the multiplexed assay. The interactions between biomarkers and their specific Ab-MPs probes caused the immunoaggregation of Ab-MPs. A two-stage micro resistive pulse sensor was used to differentiate and count the Ab-MP aggregates triggered by different biomarkers via size and magnetic property for multiplexed detection. The volume fraction of each type of Ab-MP aggregates indicates the concentration of the corresponding target biomarker. In our study, we demonstrated multiplexed detection of two model biomarkers (human ferritin and mouse anti-rabbit IgG) in 10% fetal bovine serum, using anti-ferritin Ab and anti-mouse IgG Ab functionalized MPs. We found that the volume fraction of Ab-MP aggregates increased with the increased biomarker concentrations. The detection ranges from 5.2 ng/ml to 208 ng/ml and 3.1 ng/ml to 5.12 × 104 ng/ml were achieved for human ferritin and mouse anti-rabbit IgG. This bioassay chip is able to quantitatively detect multiple biomarkers in a single test without fluorescence or enzymatic labeling process and hence is promising to serve as a useful tool for rapid detection of multiple biomarkers in biomedical research and clinical applications.
Optical droplet vaporization of nanoparticle-loaded stimuli-responsive microbubbles
Authors: Si Ting , Li Guangbin , Wu Qiang , Zhu Zhiqiang , Luo Xisheng , Xu Ronald X.
Published: March 2016

A capillary co-flow focusing process is developed to generate stimuli-responsive microbubbles (SRMs) that comprise perfluorocarbon (PFC) suspension of silver nanoparticles (SNPs) in a lipid shell. Upon continuous laser irradiation at around their surface plasmon resonance band, the SNPs effectively absorb electromagnetic energy, induce heat accumulation in SRMs, trigger PFC vaporization, and eventually lead to thermal expansion and fragmentation of the SRMs. This optical droplet vaporization (ODV) process is further simulated by a theoretical model that combines heat generation of SNPs, phase change of PFC, and thermal expansion of SRMs. The model is validated by benchtop experiments, where the ODV process is monitored by microscopic imaging. The effects of primary process parameters on behaviors of ODV are predicted by the theoretical model, indicating the technical feasibility for process control and optimization in future drug delivery applications.
Low-cost, disposable microfluidics device for blood plasma extraction using continuously alternating paramagnetic and diamagnetic capture modes
Authors: Kim Pilkee , Ong Eng Hui , Li King Ho Holden , Yoon Yong-Jin , Ng Sum Huan Gary , Puttachat Khuntontong
Published: March 2016

Blood plasma contains biomarkers and substances that indicate the physiological state of an organism, and it can be used to diagnose various diseases or body condition. To improve the accuracy of diagnostic test, it is required to obtain the high purity of blood plasma. This paper presents a low-cost, disposable microfluidics device for blood plasma extraction using magnetophoretic behaviors of blood cells. This device uses alternating magnetophoretic capture modes to trap and separate paramagnetic and diamagnetic cells away from blood plasma. The device system is composed of two parts, a disposable microfluidics chip and a non-disposable (reusable) magnetic field source. Such modularized device helps the structure of the disposable part dramatically simplified, which is beneficial for low-cost mass production. A series of numerical simulation and parametric study have been performed to describe the mechanism of blood cell separation in the microchannel, and the results are discussed. Furthermore, experimental feasibility test has been carried out in order to demonstrate the blood plasma extraction process of the proposed device. In this experiment, pure blood plasma has been successfully extracted with yield of 21.933% from 75 μl 1:10 dilution of deoxygenated blood.
Spin-lattice coupling, Jahn-Teller effect and the influence of the measurement rate in La0.7Ca0.3−xSrxMnO3 manganites
Authors: Burrola-Gándara L. A. , Sáenz-Hernández R. J. , Santillán-Rodríguez C. R. , Lardizabal-Gutiérrez D. , Pizá-Ruiz P. , Elizalde Galindo J. T. , Matutes-Aquino J. A.
Published: March 2016

This work presents a study of how the magnetic and temperature variables, as well as the measurement rate, affect magnetic and structural phase transitions for La0.7Ca0.3−xSrxMnO3 (x=0.15, 0.08, 0.07 and 0.06) manganites. A single phase rhombohedral crystal structure for Sr0.15 compound and a single phase orthorhombic crystal structure for Sr0.08, Sr0.07, and Sr0.06 compounds were identified by X ray diffraction. The Curie temperature adjustment to room temperature was reached for Sr0.07 sample, in which a Jahn-Teller transition was observed. This Jahn-Teller transition showed a susceptible response to 0.5, 1, 2, 3, 5 and 7 K/min measurement rates, and was revealed without measurement sequence at 234, 257, 196, 233, 245 and 238 K respectively in thermomagnetic curves (10mT). Also, Curie temperature increases sequentially around 2 K for the same measurement rates. To avoid magnetic field effect, a differential scanning calorimetry for Sr0.07 sample was obtained in the same temperature region, for 2, 3, 5, 7 K/min showing the Jahn-Teller phase transition at 225 K and a vibrational like behavior in the heat flux below 225 K, for all the temperature rates. The latter, is related to the static to dynamic Jahn-Teller transition. Furthermore, Curie temperature appears around 284 K.
Seasonal feeding on giant cuttlefish (Sepia apama) by Indo-Pacific bottlenose dolphins (Tursiops aduncus) in south-western Australia
Authors: Smith H. C. , Sprogis K. R.
Published: March 2016

We report on observations of Indo-Pacific bottlenose dolphins (Tursiops aduncus) feeding on giant cuttlefish (Sepia apama) from March 2007 to April 2013 in the temperate waters off Bunbury, south-western Australia. Seventeen feeding events were observed during the cooler months between July and September in relatively shallow coastal waters, with 12 dolphins identified as adult females. We observed behavioural sequences of complex prey-handling of cuttlefish where dolphins’ used multiple steps to remove the cuttlefish head, ink and cuttlebone before consuming the flesh of the cuttlefish mantle. Our study provides valuable information to the limited knowledge on the complex prey-handling by T. aduncus on cuttlefish in Australia, and is complementary to other known specialised foraging behaviours of bottlenose dolphins. This study also details a different behavioural sequence of cuttlefish prey-handling to that of the bottlenose dolphins in the Sado estuary, Portugal, where only the head is consumed, and to the Spencer Gulf, Australia, in that the dolphins in Bunbury carry the cuttlefish mantle over their rostrum before removing the cuttlebone. Information on S. apama in Bunbury is scarce, therefore studies on abundance, distribution and egg-laying sites are recommended in order to enable informed decision making and to understand the importance of S. apama to the diet of T. aduncus.
Breaking temporal symmetries for emission and absorption
Authors: Hadad Yakir , Soric Jason C. , Alu Andrea
Published: March 2016

Significance

Antennas, from radiofrequencies to optics, are forced to transmit and receive with the same efficiency to/from the same direction. The same constraint applies to thermophotovoltaic systems, which are forced to emit as well as they can absorb, limiting their efficiency. In this paper, we show that it is possible to efficiently overcome these bounds using temporally modulated traveling-wave circuits. Beyond the basic physics interest of our theoretical and experimental findings, we also prove that the proposed temporally modulated antenna can be efficiently used to transmit without being forced to listen to echoes and reflections, with important implications for radio-wave communications. Similar concepts may be extended to infrared frequencies, with relevant implications for energy harvesting.
Counter-hegemony in today's Belarus: dissident symbols and the mythological figure of Miron Vitebskii
Authors: Astapova Anastasiya
Published: March 2016

Tackling the role of state symbols in negotiating national identity and political development, this research focuses on Belarus where the alternative white-red-white flag became instrumental in protests against the dominant political discourse. Since 1995, oppositional mass media have been reporting about cases of this tricolor being erected in hard-to-reach and/or politically sensitive places. These actions were mainly attributed to some “Miron,” whose identity remained concealed and served as a simulacrum of a national superhero in non-conformist discourse. The image of Miron immediately acquired multiple functions: condemning the Soviet colonial past, struggling for the European future, and creating a nation-state rather than the Russian-speaking civil-state of Belarus. Yet, first and foremost, Miron became a means for contesting the authority of the president who has been in power since 1994. Concentrating on the methods employed for the construction of the counter-hegemonic fakelore project of Miron and its aims, this article explores the vernacular response to its creation.
A Comparison of the HCR-20V3 Among Male and Female Insanity Acquittees: A Retrospective File Study
Authors: Green Debbie , Schneider Melanie , Griswold Hali , Belfi Brian , Herrera Michelle , DeBlasi Ashley
Published: March 2016

The current retrospective risk assessment study evaluated the use of the Historical-Clinical-Risk Management-20 Version 3 (HCR-20V3) in a sample of 100 male and 24 female insanity acquittees, comparing the presence of risk factors and its validity in assessing violence in a state forensic hospital across males and females. Over an average of 15.5 months, 44.4% of the total sample engaged in any act of violence within the institution, highlighting the need for effective risk assessment and management tools. An equivalent proportion of males and females engaged in violence (42.0% of males and 54.2% of females). Results indicated higher interrater reliability on scoring risk factors among males as compared to females, calling for future research into the role of item indicators across genders and possible differences in interpretations of scoring guidelines. Results indicated that females exhibited similar numerical ratings of presence risk factors as males, although they were rated higher on Past Problems in Relationships and Traumatic Experiences. The relationships between scale scores and violence were higher among males than females. However, gender was not a significant moderator in logistic regression analyses predicting likelihood of violence. Additional research is necessary to evaluate how ratings of risk factors are translated into summary risk estimates, opinions about dangerousness, and treatment interventions, with a particular focus on how such decision-making is influenced by the gender of examinees.
The Precondition Model as a Method for Developing Understanding of Female Contact and Non-Contact Sex Offending: A Single Case Study
Authors: Collins Sophia , Duff Simon
Published: March 2016

This research evaluates the use of an established model, typically used for understanding male sex offenders, to understand the behavior of a female sex offender. The Finkelhor ( 1984 ) Precondition Model of offending is used to provide a rare opportunity to explore the process of offending for a female contact and non-contact offender, whose offenses were against children. It reviews the efficacy of utilizing this model in the rehabilitation and collaborative risk management of a female sex offender. The results suggest that this approach can be applied to Internet and contact sex offenses to develop understanding of the progression of offending, including issues such as sexual arousal and the impact of a male co-perpetrator. In this case, the results indicate a post-intervention improvement in areas such as affect control, ability to maintain positive relationships, self-support, and reduced dissociation and dysfunctional sexual behavior. This project provides support for the development of a treatment approach that explores the individual nuances of female sex offending.
Survival of Hatchery Raised Red Drum Exposed to Abrupt Salinity Increases—Simulating Bay Stockings
Authors: McDonald Dusty L , Cason Paul D , Bumguardner Britt W , Tomasso Joseph R
Published: March 2016

As part of a stock enhancement program in Texas, Red Drum Sciaenops ocellatus are subject to a standard salinity acclimation protocol between the hauling trailer and stock site of 1 h per 10‰ salinity difference. In certain circumstances (hypersaline sites or drought) salinity differences can exceed 20‰ between hauling trailer and stock site. Information is needed on whether the current protocol is sufficient to investigate whether extending the acclimation time can improve survival. We conducted nine trials, each exposing pond-cultured Red Drum fingerlings to salinity increases of 10‰ (over 1, 2, and 3 h), 20‰ (over 2, 4, and 6 h), and no salinity change (control). Survival at 96 h following a change in salinity of either 10‰ or 20‰ was independent of the rate of increase in salinity. However, survival was lower among Red Drum subjected to an increase of 20‰ (survival, 61%) than to 10‰ (82%). Fish condition, length and weight of fish examined here had no significant effect on survival, across trials. Results suggest that hatchery personnel should select stocking sites within 10‰ salinity of the production pond and hauling trailer.
Planning sentences while doing other things at the same time: effects of concurrent verbal and visuospatial working memory load
Authors: Klaus Jana , Mädebach Andreas , Oppermann Frank , Jescheniak Jörg D.
Published: March 2016

This study investigated to what extent advance planning during sentence production is affected by a concurrent cognitive load. In two picture–word interference experiments in which participants produced subject–verb–object sentences while ignoring auditory distractor words, we assessed advance planning at a phonological (lexeme) and at an abstract–lexical (lemma) level under visuospatial or verbal working memory (WM) load. At the phonological level, subject and object nouns were found to be activated before speech onset with concurrent visuospatial WM load, but only subject nouns were found to be activated with concurrent verbal WM load, indicating a reduced planning scope as a function of type of WM load (Experiment 1). By contrast, at the abstract–lexical level, subject and object nouns were found to be activated regardless of type of concurrent load (Experiment 2). In both experiments, sentence planning had a more detrimental effect on concurrent verbal WM task performance than on concurrent visuospatial WM task performance. Overall, our results suggest that advance planning at the phonological level is more affected by a concurrently performed verbal WM task than advance planning at the abstract–lexical level. Also, they indicate an overlap of resources allocated to phonological planning in speech production and verbal WM.
Quantifying the Trophic Importance of Gulf Menhaden within the Northern Gulf of Mexico Ecosystem
Authors: Sagarese Skyler R. , Nuttall Matthew A. , Geers Tess M. , Lauretta Matthew V. , Walter John F. , Serafy Joseph E.
Published: March 2016

The Gulf Menhaden Brevoortia patronus is frequently cited as playing a predominant role in the trophic structure and function of the northern Gulf of Mexico (GOM) marine ecosystem, yet much work remains in quantifying its ecological importance. We performed a meta-analysis of diet studies to quantify the trophic role of Gulf Menhaden within this ecosystem. Of the 568 references consulted, 136 identified predator–prey interactions involving Gulf Menhaden, menhaden Brevoortia spp., or unidentified clupeid prey items. Overall, 79 species were reported to consume menhaden, and no significant difference was detected between the Atlantic Ocean and the GOM in the mean occurrence of Brevoortia spp. in predator stomachs. We employed a probabilistic approach using maximum likelihood estimation to quantify trophic interactions within the northern GOM, with a focus on the trophic role of Gulf Menhaden. The estimated contribution of identifiable menhaden to the diets of all predators generally ranged between 2% and 3%; the largest dietary contribution was identified for Blacktip Sharks Carcharhinus limbatus (8%), and lower estimates (<2%) were obtained for oceanic species, including sharks, billfishes, and tunas. When diet compositions were adjusted for unidentified prey by using the proportion of fish species biomass in the ecosystem, five predator groups showed a relatively large dependence on menhaden prey: juvenile King Mackerel Scomberomorus cavalla, juvenile Spanish Mackerel Scomberomorus maculatus, adult Spanish Mackerel, Red Drum Sciaenops ocellatus, and Blacktip Sharks. The quantification of trophic linkages and key predators identified herein will be fundamental to future modeling efforts focused on the northern GOM ecosystem.

Received March 24, 2015; accepted September 3, 2015
Trophic Ecology of a Predatory Community in a Shallow-Water, High-Salinity Estuary Assessed by Stable Isotope Analysis
Authors: Shaw Ashley L. , Frazier Bryan S. , Kucklick John R. , Sancho Gorka
Published: March 2016

Estuaries serve as habitats and nurseries for many recreationally and commercially important fishes, often contributing recruits to adult populations that remain in close proximity to estuarine environments. Upper-level predatory fish species are among the most sought after by fisheries; thus, an understanding of the trophic dynamics of the community can assist ecological fisheries management of these highly productive ecosystems. Dietary niche overlap within the predatory fish community of Bulls Bay, a subtropical estuary in South Carolina, was assessed by using stable isotope analyses (δ13C and δ15N) to compare seven elasmobranch species and three teleost species. Cownose Rays Rhinoptera bonasus and Finetooth Sharks Carcharhinus isodon had no isotopic overlap with other species and therefore exhibited unique isotopic niche spaces that were indicative of potential resource partitioning. The teleosts and remaining elasmobranchs had varying degrees of overlap, implying shared resources; a high degree of dietary niche overlap was observed among Spotted Seatrout Cynoscion nebulosus, Sandbar Sharks Carcharhinus plumbeus, and Atlantic Sharpnose Sharks Rhizoprionodon terraenovae. Although most pairs of species showed some isotopic overlap, there were also interspecific differences in niche overlap, signifying that this predatory fish community has a widely varied prey base overall. Bulls Bay is an important nursery habitat with a balanced predator community, as illustrated by a combination of unique dietary niches and varying degrees of dietary niche overlap.

Received August 31, 2015; accepted November 9, 2015
Impact of an invasive nitrogen-fixing tree on arbuscular mycorrhizal fungi and the development of native species
Authors: Guisande-Collazo Alejandra , González Luís , Souza-Alonso Pablo
Published: March 2016

Arbuscular mycorrhizal fungi (AMF) are obligate soil biotrophs that establish intimate relationships with 80 % of terrestrial plant families. Arbuscular mycorrhizal fungi obtain carbon from host plants and contribute to the acquisition of mineral nutrients, mainly phosphorus. The presence of invasive plants has been identified as a soil disturbance factor, often conditioning the structure and function of soil microorganisms. Despite the investigation of many aspects related to the invasion of Acacia dealbata , the effect produced on the structure of AMF communities has never been assessed. We hypothesize that A. dealbata modifies the structure of AMF community, influencing the establishment and growth of plants that are dependent on these mutualisms. To validate our hypothesis, we carried out denaturing gradient gel electrophoresis (DGGE) analysis and also grew plants of Plantago lanceolata in pots using roots of native shrublands or from A. dealbata , as inoculum of AMF. Cluster analyses from DGGE indicated an alteration in the structure of AMF communities in invaded soils. After 15 weeks, we found that plants grown in pots containing native roots presented higher stem and root growth and also produced higher biomass in comparison with plants grown with A. dealbata inoculum. Furthermore, plants that presented the highest biomass and growth exhibited the maximum mycorrhizal colonization and phosphorus content. Moreover, fluorescence measurements indicated that plants grown with A. dealbata inoculum even presented higher photosynthetic damage. Our results indicate that the presence of the invader A. dealbata modify the composition of the arbuscular fungal community, conditioning the establishment of native plants.
Integrating fishers’ knowledge research in science and management
Authors: Stephenson Robert L. , Paul Stacey , Pastoors Martin A. , Kraan Marloes , Holm Petter , Wiber Melanie , Mackinson Steven , Dankel Dorothy J. , Brooks Kate , Benson Ashleen
Published: March 2016

Fishers' knowledge research (FKR) aims to enhance the use of experiential knowledge of fish harvesters in fisheries research, assessment, and management. Fishery participants are able to provide unique knowledge, and that knowledge forms an important part of “best available information” for fisheries science and management. Fishers' knowledge includes, but is much greater than, basic biological fishery information. It includes ecological, economic, social, and institutional knowledge, as well as experience and critical analysis of experiential knowledge. We suggest that FKR, which may in the past have been defined quite narrowly, be defined more broadly to include both fishery observations and fishers “experiential knowledge” provided across a spectrum of arrangements of fisher participation. FKR is part of the new and different information required in evolving “ecosystem-based” and “integrated” management approaches. FKR is a necessary element in the integration of ecological, economic, social, and institutional considerations of future management. Fishers' knowledge may be added to traditional assessment with appropriate analysis and explicit recognition of the intended use of the information, but fishers' knowledge is best implemented in a participatory process designed to receive and use it. Co-generation of knowledge in appropriately designed processes facilitates development and use of fishers' knowledge and facilitates the participation of fishers in assessment and management, and is suggested as best practice in improved fisheries governance.
Actinobacillus hominis osteomyelitis: First reported case in the English language medical literature
Authors: O’Neill Gavin , Ker Andrew , Mohammed Aslam , Karcher Anne Marie
Published: March 2016

Introduction:

Actinobacillus hominis is currently a rarely reported pathogen. It has previously been associated with respiratory tract infections and bacteraemia in debilitated patients. However, under-reporting may occur due to misidentification by commonly used laboratory bacterial identification systems. This case is, to the best of our knowledge, the first reported case of A. hominis osteomyelitis in the English language medical literature.

Case presentation:

A 37-year-old male presented with a painful foot. He had no previous foot problems, history of injury or animal contact. Osteomyelitis was confirmed by magnetic resonance imaging (MRI), and blood cultures were positive for Gram-variable bacilli. The organism was identified initially as Pasteurella pneumotropica by the local routine diagnostic laboratory and as a Pasteurella species by the UK National Reference Laboratory (Colindale, London, UK), using standard operating procedures at the time. It was finally identified as an A. hominis using 16S rRNA gene sequence analysis. Difficulties in the accurate identification of this organism remain current, as other biochemical identification systems have also resulted in misidentifications. The patient refused admission and intravenous antibiotics. He was successfully treated using an 8-week course of oral ciprofloxacin and amoxicillin based on antibiotic disc susceptibility testing resulting in clinical, serological and radiological resolution.

Conclusion:

Laboratories should maintain a high index of suspicion for A. hominis as several commonly used bacterial identification systems may not accurately identify the organism. Colonial morphology and absence of animal contact should prompt consideration of this organism in appropriate clinical situations. Oral ciprofloxacin and amoxicillin treatment was successful in this case.
A statistical framework for neuroimaging data analysis based on mutual information estimated via a Gaussian copula
Authors: Ince Robin A. A. , Giordano Bruno L. , Kayser Christoph , Rousselet Guillaume A. , Gross Joachim , Schyns Philippe G.
Published: March 2016

We begin by reviewing the statistical framework of information theory as applicable to neuroimaging data analysis. A major factor hindering wider adoption of this framework in neuroimaging is the difficulty of estimating information theoretic quantities in practice. We present a novel estimation technique that combines the statistical theory of copulas with the closed form solution for the entropy of Gaussian variables. This results in a general, computationally efficient, flexible, and robust multivariate statistical framework that provides effect sizes on a common meaningful scale, allows for unified treatment of discrete, continuous, uni-and multi-dimensional variables, and enables direct comparisons of representations from behavioral and brain responses across any recording modality. We validate the use of this estimate as a statistical test within a neuroimaging context, considering both discrete stimulus classes and continuous stimulus features. We also present examples of analyses facilitated by these developments, including application of multivariate analyses to MEG planar magnetic field gradients, and pairwise temporal interactions in evoked EEG responses. We show the benefit of considering the instantaneous temporal derivative together with the raw values of M/EEG signals as a multivariate response, how we can separately quantify modulations of amplitude and direction for vector quantities, and how we can measure the emergence of novel information over time in evoked responses. Open-source Matlab and Python code implementing the new methods accompanies this article.

Highlights

Novel estimator for mutual information and other information theoretic quantities

Provides general, efficient, flexible and robust multivariate statistical framework

Validated statistical performance on EEG and MEG data

Applications to spectral power and phase, 2D magnetic field gradients, temporal derivatives

Interaction information relates information content in different responses
Strawberry: fast and accurate genome-guided transcript reconstruction and quantification from RNA-seq
Authors: Liu Ruolin , Dickerson Julie A.
Published: March 2016

We propose a novel method and computational tool, Strawberry, for transcript reconstruction and quantification from paired-end RNA-seq data under the guidance of genome alignment and independent of gene annotation. Strawberry achieves this through disentangling assembly and quantification in a sequential manner. The application of a fast flow network algorithm for assembly speeds up the construction of a parsimonious set of transcripts. The resulting reduced data representation improves the efficiency of expression-level quantification. Strawberry leverages the speed and accuracy of transcript assembly and quantification in such a way that processing 10 million simulated reads (after alignment) requires only 90 seconds using a single thread while achieving over 92% correlation with the ground truth, making it the state-of-the-art method. Strawberry outperforms Cufflinks and StringTie, the two other leading methods, in many aspects, including the number of corrected assembled transcripts and the correlation with the ground truth of simulated RNA-seq data.

Availability:

Strawberry is written in C++11, and is available as open source software athttps://github.com/ruolin/Strawberryunder the GPLv3 license.
Transcriptome remodeling contributes to epidemic disease caused by the human pathogenStreptococcus pyogenes
Authors: Beres Stephen B. , Kachroo Priyanka , Nasser Waleed , Olsen Randall J. , Zhu Luchang , Flores Anthony R. , de la Riva Ivan , Paez-Mayorga Jesus , Jimenez Francisco E. , Cantu Concepcion , Vuopio Jaana , Jalava Jari , Kristinsson Karl G. , Gottfredsson Magnus , Corander Jukka , Fittipaldi Nahuel , Di Luca Maria Chiara , Petrelli Dezemona , Vitali Luca A. , Raiford Annessa , Jenkins Leslie , Musser James M.
Published: March 2016

For over a century, a fundamental objective in infection biology research has been to understand the molecular processes contributing to the origin and perpetuation of epidemics. Divergent hypotheses have emerged concerning the extent to which environmental events or pathogen evolution dominates in these processes. Remarkably few studies bear on this important issue. Based on population pathogenomic analysis of 1200Streptococcus pyogenestypeemm89 infection isolates, we report that a series of horizontal gene transfer events produced a new pathogenic genotype with increased ability to cause infection, leading to an epidemic wave of disease on at least two continents. In the aggregate, these and other genetic changes substantially remodeled the transcriptomes of the evolved progeny, causing extensive differential expression of virulence genes and altered pathogen - host interaction, including enhanced immune evasion. Our findings delineate the precise molecular genetic changes that occurred and enhance our understanding of the evolutionary processes that contribute to the emergence and persistence of epidemically successful pathogen clones. The data have significant implications for understanding bacterial epidemics and translational research efforts to blunt their detrimental effects.

Importance

The confluence of studies of molecular events underlying pathogen strain emergence, evolutionary genetic processes mediating altered virulence, and epidemics is in its infancy. Although understanding these events is necessary to develop new or improved strategies to protect health, surprisingly few studies have addressed this issue, in particular at the comprehensive population genomic level. Herein we establish that substantial remodeling of the transcriptome of the human-specific pathogenStreptococcus pyogenesby horizontal gene flow and other evolutionary genetic changes is a central factor in precipitating and perpetuating epidemic disease. The data unambiguously show that the key outcome of these molecular events is evolution of a new, more virulent pathogenic genotype. Our findings provide new understanding of epidemic disease.
Climatic warming strengthens a positive feedback between alpine shrubs and fire
Authors: Camac James S , Williams Richard J , Wahren Carl-Henrik , Hoffmann Ary A , Vesk Peter A
Published: March 2016

Climate change is expected to increase fire activity and woody plant encroachment in arctic and alpine landscapes. However, the extent to which these increases interact to affect the structure, function and composition of alpine ecosystems is largely unknown. Here we use field surveys and experimental manipulations to examine how warming and fire affect recruitment, seedling growth and seedling survival in four dominant Australian alpine shrubs. We found that fire increased establishment of shrub seedlings by as much as 33–fold. Experimental warming also doubled growth rates of tall shrub seedlings and could potentially increase their survival. By contrast, warming had no effect on shrub recruitment, post-fire tussock regeneration, or how tussock grass affected shrub seedling growth and survival. These findings indicate that warming, coupled with more frequent or severe fires, will likely result in an increase in the cover and abundance of evergreen shrubs. Given shrubs are one of the most flammable components in alpine and tundra environments, warming is likely to strengthen an existing feedback between woody species abundance and fire in these ecosystems.
The aptabot: an inducibly affinity-switching, minimally invasivein vivocontrast agent
Authors: Webster Heffern Elleard Felix , Fuller Jason , Hanson Russell W.
Published: March 2016

The ambitions of current neuroscience—understanding neurological disease progression and mapping the connectome—demonstrate a need for safein vivotools for creating intricate maps of brain circuitry. Presentin vivocontrast agents are often limited by their specificity, uptake, resolvability, and/or clearance.

We describe an aptamer-functionalized sensor for high-resolution imaging that can switch imaging targets by an induced multi-stage aptamer reaction. Included are synthetic methods as well as calculations of sensor efficacy based on known kinetics. Calculations show that 10 distinct targets may be imaged in a living brain at the submicron scale within 42 hours.
The role of transposable elements for gene expression inCapsellahybrids and allopolyploids
Authors: Steige Kim A. , Reimegård Johan , Rebernig Carolin A. , Köhler Claudia , Scofield Douglas G. , Slotte Tanja
Published: March 2016

The formation of an allopolyploid species involves the merger of two genomes with separate evolutionary histories. In allopolyploids, genes derived from one progenitor species are often expressed at higher levels than those from the other progenitor. It has been suggested that this could be due to differences in transposable element (TE) content among progenitors, as silencing of TEs can affect expression of nearby genes. Here, we examine the role of TEs for expression biases in the widespread allotetraploidCapsella bursa-pastorisand in diploid F1 hybrids generated by crossingCapsella orientalisandCapsella rubella, two close relatives of the progenitors ofC. bursa-pastoris. AsC. rubellaharbors more TEs thanC. orientalis, we expectC. orientalisalleles to be expressed at higher levels if TE content is key for expression biases. To test this hypothesis, we quantified expression biases at approximately 5800 genes in flower buds and leaves, while correcting for read mapping biases using genomic data. While three of fourC. bursa-pastorisaccessions exhibited a shift toward higher relative expression ofC. orientalisalleles, the fourthC. bursa-pastorisaccession had the opposite direction of expression bias, as did diploid F1 hybrids. Associations between TE polymorphism and expression bias were weak, and the effect of TEs on expression bias was small. These results suggest that differences in TE content alone cannot fully explain expression biases in these species. Future studies should investigate the role of differences in TE silencing efficacy, as well as a broader set of other factors. Our results are important for a more general understanding of the role of TEs for cis-regulatory evolution in plants.
The Pattern of Bacteria and its Resistance on Adult Sepsis Patient at Dr. Moewardi General Hospital, Indonesia
Authors: Mahendra Andika Dwi , Kuswandi M. , Kusuma Ika Trisharyanti D.
Published: March 2016

Background

Sepsis incidence which related with morbidity and mortality, is globally increasing. Sepsis occurs because of severe infections. Sepsis has life-threatening potential with organ disfungction complication, septic shock, and death. Alteration of resistance pattern always change at certain period. The aim of the study is to investigate the bacteria pattern and its resistance from adult sepsis patient at Dr. Moewardi Regional General Hospital.

Methods

Isolated bacteria from adult sepsis patient’s blood at Dr. Moewardi Regional General Hospital. 7 bacteria isolates were taken from blood of adult sepsis patient (September - October 2014) and 46 bacteria isolates of secondary data (January - March 2014) at Dr. Moewardi Regional General Hospital. Bacteria isolation was performed based on standard Laboratory of Microbiology of Dr. Moewardi Regional General Hospital. 7 bacteria isolates were tested by using disc diffusion antibiotic on Mueller Hinton and coupled by 46 secondary data.

Results

The bacteria pattern from adult sepsis patients wereStaphylococcus haemolyticus(15,09%),Staphylococcus hominis(15,09%),Escherichia coli(13,21%), andAcinetobacter baumannii(11,32%). Resistance pattern of bacteria on adult sepsis with level of resistant more than 50% asStaphylococcus haemolyticus(ciprofloxacin, erythromycin, levofloxacin, moxifloxacin, and gentamicin),Escherichia coli(gentamicin, ciprofloxacin, and levofloxacin), andAcinetobacter baumannii(gentamicin, ciprofloxacin, levofloxacin, and ceftazidime)

Conclutions

Based on this research, revealed that the most common bacteria caused sepsis was Gram negative about 64,64% of all bacteria on sepsis patient. The most frequent cause of sepsis wasStaphylococcus hominis, Staphylococcus haemolyticus, andEscherichia coli.
Membrane insertion of‐ and membrane potential sensing by semiconductor voltage nanosensors: feasibility demonstration
Authors: Park Kyoungwon , Kuo Yung , Shvadchak Volodymyr , Ingargiola Antonino , Dai Xinghong , Hsiung Lawrence , Kim Wookyeom , Zhou Z. Hong , Zou Peng , Levine Alex J. , Li Jack , Weiss Shimon
Published: March 2016

We develop membrane voltage nanosensors that are based on inorganic semiconductor nanoparticles. These voltage nanosensors are designed to self-insert into the cell membrane and optically record the membrane potentialviathe quantum confined Stark effect, with single-particle sensitivity. We present here the approach, design rules, and feasibility proves for this concept. With further improvements, semiconductor nanoparticles could potentially be used to study signals from many neurons in a large field-of-view over a long duration. Moreover, they could potentially report and resolve voltage signals on the nanoscale.
LeafCutter: annotation-free quantification of RNA splicing
Authors: Li Yang I , Knowles David A , Humphrey Jack , Barbeira Alvaro N. , Dickinson Scott P. , Kyung Im Hae , Pritchard Jonathan K
Published: March 2016

The excision of introns from pre-mRNA is an essential step in mRNA processing. We developed LeafCutter to study sample and population variation in intron splicing. LeafCutter identifies variable intron splicing events from short-read RNA-seq data and finds alternative splicing events of high complexity. Our approach obviates the need for transcript annotations and circumvents the challenges in estimating relative isoform or exon usage in complex splicing events. LeafCutter can be used both for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs). Compared to contemporary methods, we find 1.4–2.1 times more sQTLs, many of which help us ascribe molecular effects to disease-associated variants. Strikingly, transcriptome-wide associations between LeafCutter intron quantifications and 40 complex traits increased the number of associated disease genes at 5% FDR by an average of 2.1-fold as compared to using gene expression levels alone. LeafCutter is fast, scalable, easy to use, and available athttps://github.com/davidaknowles/leafcutter.
Divergence of gene regulatory network linkages during specification of ectoderm and mesoderm in early development of sea urchins
Authors: Erkenbrack Eric M. , Davidson Eric H.
Published: March 2016

Developmental gene regulatory networks (GRNs) are assemblages of gene regulatory interactions that direct ontogeny of animal body plans. Studies of GRNs operating in early development of euechinoid sea urchins has revealed that little appreciable change has occurred since their divergence approximately 90 million years ago (mya). These observations suggest that strong conservation of GRN architecture has been maintained in early development of the sea urchin lineage. To test whether this is true for all sea urchins, comparative analyses of echinoid taxa that diverged deeper in geological time must be conducted. Recent studies highlighted extensive divergence of skeletogenic mesoderm specification in the sister clade of euechinoids, the cidaroids, suggesting that comparative analyses of cidaroid GRN architecture may confer a greater understanding of the evolutionary dynamics of developmental GRNs. Here, we report spatiotemporal patterning of 55 regulatory genes and perturbation analyses of key regulatory genes involved in euechinoid oral-aboral patterning of non-skeletogenic mesodermal and ectodermal domains in early development of the cidaroidEucidaris tribuloides. Our results indicate that developmental GRNs directing mesodermal and ectodermal specification have undergone marked alterations since the divergence of cidaroids and euechinoids. Notably, statistical and clustering analyses of echinoid temporal gene expression datasets indicate that regulation of mesodermal genes has diverged more markedly than regulation of ectodermal genes. Although research on indirect-developing euechinoid sea urchins suggests strong conservation of GRN circuitry during early embryogenesis, this study indicates that since the divergence of cidaroids and euechinoids developmental GRNs have undergone significant divergence.
nanoCAGE reveals 5′ UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs
Authors: Gandin Valentina , Masvidal Laia , Hulea Laura , Gravel Simon-Pierre , Cargnello Marie , McLaughlan Shannon , Cai Yutian , Balanathan Preetika , Morita Masahiro , Rajakumar Arjuna , Furic Luc , Pollak Michael , Porco John A. , St-Pierre Julie , Pelletier Jerry , Larsson Ola , Topisirovic Ivan
Published: March 2016

The diversity of MTOR-regulated mRNA translation remains unresolved. Whereas ribosome-profiling suggested that MTOR almost exclusively stimulates translation of the TOP (terminal oligopyrimidine motif) and TOP-like mRNAs, polysome-profiling indicated that MTOR also modulates translation of mRNAs without the 5′ TOP motif (non-TOP mRNAs). We demonstrate that in ribosome-profiling studies, detection of MTOR-dependent changes in non-TOP mRNA translation was obscured by low sensitivity and methodology biases. Transcription start site profiling using nano-cap analysis of gene expression (nanoCAGE) revealed that not only do many MTOR-sensitive mRNAs lack the 5′ TOP motif but that 5′ UTR features distinguish two functionally and translationally distinct subsets of MTOR-sensitive mRNAs: (1) mRNAs with short 5′ UTRs enriched for mitochondrial functions, which require EIF4E but are less EIF4A1-sensitive; and (2) long 5′ UTR mRNAs encoding proliferation- and survival-promoting proteins, which are both EIF4E- and EIF4A1-sensitive. Selective inhibition of translation of mRNAs harboring long 5′ UTRs via EIF4A1 suppression leads to sustained expression of proteins involved in respiration but concomitant loss of those protecting mitochondrial structural integrity, resulting in apoptosis. Conversely, simultaneous suppression of translation of both long and short 5′ UTR mRNAs by MTOR inhibitors results in metabolic dormancy and a predominantly cytostatic effect. Thus, 5′ UTR features define different modes of MTOR-sensitive translation of functionally distinct subsets of mRNAs, which may explain the diverse impact of MTOR and EIF4A inhibitors on neoplastic cells.
Combating corruption in Cambodia
Authors: Ear Sophal
Published: March 2016

Purpose

– The purpose of this paper is to provide a critical analysis and survey of Cambodia’s recent efforts to combat corruption. It explores the policy context, perceived extent of corruption, causes of corruption, anti-corruption measures, evaluates those anti-corruption measures, and provides policy recommendations.

Design/methodology/approach

– This paper reviews the literature on corruption and anti-corruption efforts in Cambodia. It relies on available data from the World Bank and Transparency International, and compares these data over time.

Findings

– The paper shows that corruption in Cambodia is pervasive and that anti-corruption efforts are limited because of a lack of political will. Existing anti-corruption measures designed with loopholes must be amended, but implementation remains the primary challenge.

Originality/value

– This paper contributes to the limited literature on combating corruption in Cambodia.
Combating corruption in Vietnam: a commentary
Authors: Gregory Robert
Published: March 2016

Purpose

– The purpose of this paper is to discuss the causes and circumstances of what has become systemic corruption in Vietnam, and the reasons why the moves taken by the regime to combat it have been largely ineffective so far.

Design/methodology/approach

– The paper offers a commentary based on published secondary sources.

Findings

– The paper concludes that the immediate prospects for any substantial reduction in the level of corruption in Vietnam appear to be bleak. Endemic corruption, especially in the form of elite rent-seeking, is likely to remain strong. However, the paper sketches two more possible scenarios on anti-corruption prospects in the country for the intermediate future.

Originality/value

– The paper relies on secondary sources in providing a macro-level discussion of corruption in Vietnam.