bluuebunny/crossref_metadata_2025 huggingface dataset:
Resting heart rate variability is associated with inhibition of conditioned fear
Authors: Wendt Julia , Neubert Jörg , Koenig Julian , Thayer Julian F. , Hamm Alfons O.
Published: June 2015

Startle blink as well as skin conductance responses (SCR) are widely used indices of learning processes associated with fear conditioning and extinction. During safety learning, the amygdala is under top‐down inhibitory control by the prefrontal cortex (PFC). The capacity of the PFC to exert inhibitory control over subcortical brain structures may be indexed by resting state vagally mediated heart rate variability (HRV). The present study investigated the association of resting HRV with startle blink and SCR during conditioned fear inhibition and extinction. Participants first learned to discriminate a threat cue (A) signaling an aversive unconditioned stimulus from a safety signal (B), which were each presented together with a third stimulus X (AX+/BX−). Then, both the threat and safety signal were presented together (AB) to test whether the presence of the learned safety signal inhibits the fear response to the danger signal. Finally, AX was presented without reinforcement (AX−) to investigate fear extinction. Higher HRV was associated with pronounced fear inhibition and fear extinction. Resting HRV levels were associated with fear extinction as indexed by startle blink potentiation but not SCR, which presumably reflect more cognitive aspects of learning. Resting HRV may reflect the capacity of the prefrontal cortex to inhibit subcortical fear responses in the presence of safety or when former threat cues are presented in the absence of threat.
The Mutable Nature of Risk and Acceptability: A Hybrid Risk Governance Framework
Authors: Wong Catherine Mei Ling
Published: June 2015

This article focuses on the fluid nature of risk problems and the challenges it presents to establishing acceptability in risk governance. It introduces an actor‐network theory (ANT) perspective as a way to deal with the mutable nature of risk controversies and the configuration of stakeholders. To translate this into a practicable framework, the article proposes a hybrid risk governance framework that combines ANT with integrative risk governance, deliberative democracy, and responsive regulation. This addresses a number of the limitations in existing risk governance models, including: (1) the lack of more substantive public participation throughout the lifecycle of a project; (2) hijacking of deliberative forums by particular groups; and (3) the treatment of risk problems and their associated stakeholders as immutable entities. The framework constitutes a five‐stage process of co‐selection, co‐design, co‐planning, and co‐regulation to facilitate the co‐production of collective interests and knowledge, build capacities, and strengthen accountability in the process. The aims of this article are twofold: conceptually, it introduces a framework of risk governance that accounts for the mutable nature of risk problems and configuration of stakeholders. In practice, this article offers risk managers and practitioners of risk governance a set of procedures with which to operationalize this conceptual approach to risk and stakeholder engagement.
A learning theory account of depression
Authors: Ramnerö Jonas , Folke Fredrik , Kanter Jonathan W.
Published: June 2015

Learning theory provides a foundation for understanding and deriving treatment principles for impacting a spectrum of functional processes relevant to the construct of depression. While behavioral interventions have been commonplace in the cognitive behavioral tradition, most often conceptualized within a cognitive theoretical framework, recent years have seen renewed interest in more purely behavioral models. These modern learning theory accounts of depression focus on the interchange between behavior and the environment, mainly in terms of lack of reinforcement, extinction of instrumental behavior, and excesses of aversive control, and include a conceptualization of relevant cognitive and emotional variables. These positions, drawn from extensive basic and applied research, cohere with biological theories on reduced reward learning and reward responsiveness and views of depression as a heterogeneous, complex set of disorders. Treatment techniques based on learning theory, often labeled Behavioral Activation (BA) focus on activating the individual in directions that increase contact with potential reinforcers, as defined ideographically with the client. BA is considered an empirically well‐established treatment that generalizes well across diverse contexts and populations. The learning theory account is discussed in terms of being a parsimonious model and ground for treatments highly suitable for large scale dissemination.
Effect of commercial cleansers on skin barrier permeability
Authors: Hornby S. , Walters R. , Tierney N. , Appa Y. , Dorfman G. , Kamath Y.
Published: June 2015

Background

Addition of hydrophobically modified polymers (HMPs) to cleansers can reduce the negative impact of surfactant‐based cleansers. In this study, the effects of a cleanser containing HMPs, a gentle lotion cleanser (GLC), water, and 1% sodium lauryl sulfate (SLS) on barrier permeability, were evaluated in vitro in pig skin and in vivo in humans.

Methods

Skin stratum corneum (SC) barrier function was quantitated by imaging fluorescence intensity of the sulforhodamine B (SRB) in a pig skin model system using 2‐photon and conventional fluorescence confocal microscopy. Solutions containing SRB were applied to pig skin in Franz diffusion cells over a period of 2 h. Penetration of SRB into the skin was monitored from 2 μm to 38 μm. In vivo surfactant/cleanser penetration in human skin was determined using tape stripping.

Results

After 2 h, water, 1% SLS, and GLC, significantly increased SRB intensity at all depths measured. SRB intensity was reduced in the HMP‐cleanser group compared with other groups at each depth. In vivo, the presence of HMP reduced SLS penetration as measured by tape stripping.

Conclusion

The cleanser containing HMP prevented changes in SC permeability and surfactant penetration, indicating a protective effect on skin barrier properties.
Slow thinking and deep learning: Tversky and Kahneman's taxi cabs
Authors: Bedwell Mike
Published: June 2015

This article is based on classroom application of a problem story constructed by Amos Tversky in the 1970s. His intention was to evaluate human beings' intuitions about statistical inference. The problem was revisited by his colleague, the Nobel Prize winner Daniel Kahneman. The aim of this article is to show how popular science textbooks can serve as a source for rich classroom activity, with a little care in the implementation by teachers. Kahneman describes the problem as ‘standard’ and answers using a fixed point number. I describe how I have encouraged my students to challenge the certainty of this assertion by identifying ambiguities that are left unexplained in the story. This way, I claim to stimulate individuals to indeed move towards Thinking, Fast and Slow, the title of Kahneman's book.
Interfacing Mind and Environment: The Central Role of Search in Cognition
Authors: Fu Wai‐Tat , Hills Thomas , Todd Peter M.
Published: June 2015

Search can be found in almost every cognitive activity, ranging across vision, memory retrieval, problem solving, decision making, foraging, and social interaction. Because of its ubiquity, research on search has a tendency to fragment into multiple areas of cognitive science. The proposed topic aims at providing integrative discussion of the central role of search from multiple perspectives. We focus on controlled search processes, which require (a) a goal, (b) uncertainty about the nature, location, or acquisition method of the objects to be searched for, and (c) a method for sampling through the search environment. While this definition of search is general and applicable to different domains, the specific mechanisms in the search process will likely differ. The goal of this issue is to compare and contrast how these search processes are similar and differ in different cognitive activities, with the goal of understanding the general nature of search in terms of the three characteristics stated above. We expect that given its cross‐domain nature, the topic on search will be of broad interest to cognitive scientists, including psychologists, behavioral ecologists, computer scientists, neuroscientists, linguists, and sociologists.
A laser ablation ICP‐MS based method for multiplexed immunoblot analysis: applications to manganese‐dependent protein dynamics of photosystem II in barley (Hordeum vulgare L.)
Authors: de Bang Thomas Christian , Petersen Jørgen , Pedas Pai Rosager , Rogowska‐Wrzesinska Adelina , Jensen Ole Noerregaard , Schjoerring Jan Kofod , Jensen Poul Erik , Thelen Jay J. , Husted Søren
Published: June 2015

Manganese (Mn) constitutes an essential co‐factor in the oxygen‐evolving complex of photosystem II (PSII). Consequently, Mn deficiency reduces photosynthetic efficiency and leads to changes in PSII composition. In order to study these changes, multiplexed protein assays are advantageous. Here, we developed a multiplexed antibody‐based assay and analysed selected PSII subunits in barley (Hordeum vulgare L.). A selection of antibodies were labelled with specific lanthanides and immunoreacted with thylakoids exposed to Mn deficiency after western blotting. Subsequently, western blot membranes were analysed by laser ablation inductively coupled plasma mass spectrometry (LA‐ICP‐MS), which allowed selective and relative quantitative analysis via the different lanthanides. The method was evaluated against established liquid chromatography electrospray ionization tandem mass spectrometry (LC‐ESI‐MS/MS) methods, based on data‐dependent acquisition (DDA) and selected reaction monitoring (SRM). Manganese deficiency resulted in a general decrease in PSII protein abundances, an effect that was shown to be reversible upon Mn re‐supplementation. Specifically, the extrinsic proteins PsbP and PsbQ showed Mn‐dependent changes in abundances. Similar trends in the response to Mn deficiency at the protein level were observed when comparing DDA, SRM and LA‐ICP‐MS results. A biologically important exception to this trend was the loss of PsbO in the SRM analysis, which highlights the necessity of validating protein changes by more than one technique. The developed method enables a higher number of proteins to be multiplexed in comparison to existing immunoassays. Furthermore, multiplexed protein analysis by LA‐ICP‐MS provides an analytical platform with high throughput appropriate for screening large collections of plants.
Epigenetic control of juvenile‐to‐adult phase transition by the Arabidopsis SAGA‐like complex
Authors: Kim Ji‐Yun , Oh Jee Eun , Noh Yoo‐Sun , Noh Bosl
Published: June 2015

During growth and development, plants undergo a series of phase transitions from the juvenile‐to‐adult vegetative phase to the reproductive phase. In Arabidopsis, vegetative phase transitions and flowering are regulated by SQUAMOSA PROMOTER BINDING PROTEIN‐LIKE (SPL) factors. SPL mRNAs are post‐transcriptionally regulated by miR156 in an age‐dependent manner; however, the role of other mechanisms in this process is not known. In this study, we demonstrate that the HAG1/GCN5‐ and PRZ1/ADA2b‐containing SAGA‐like histone acetyltransferase (HAT) complex directly controls the transcription of SPLs and determines the time for juvenile‐to‐adult phase transition. Thus, epigenetic control by the SAGA‐like HAT complex determines the transcriptional output of SPLs, which might be a prerequisite for the subsequent post‐transcriptional regulation by miR156. Importantly, this epigenetic control mechanism is also crucial for miR156‐independent induction of SPLs and acceleration of phase transition by light and photoperiod or during post‐embryonic growth.
Identification of mutations allowing Natural Resistance Associated Macrophage Proteins (NRAMP) to discriminate against cadmium
Authors: Pottier Mathieu , Oomen Ronald , Picco Cristiana , Giraudat Jérôme , Scholz‐Starke Joachim , Richaud Pierre , Carpaneto Armando , Thomine Sébastien
Published: June 2015

Each essential transition metal plays a specific role in metabolic processes and has to be selectively transported. Living organisms need to discriminate between essential and non‐essential metals such as cadmium (Cd2+), which is highly toxic. However, transporters of the natural resistance‐associated macrophage protein (NRAMP) family, which are involved in metal uptake and homeostasis, generally display poor selectivity towards divalent metal cations. In the present study we used a unique combination of yeast‐based selection, electrophysiology on Xenopus oocytes and plant phenotyping to identify and characterize mutations that allow plant and mammalian NRAMP transporters to discriminate between their metal substrates. We took advantage of the increased Cd2+ sensitivity of yeast expressing AtNRAMP4 to select mutations that decrease Cd2+ sensitivity while maintaining the ability of AtNRAMP4 to transport Fe2+ in a population of randomly mutagenized AtNRAMP4 cDNAs. The selection identified mutations in three residues. Among the selected mutations, several affect Zn2+ transport, whereas only one, E401K, impairs Mn2+ transport by AtNRAMP4. Introduction of the mutation F413I, located in a highly conserved domain, into the mammalian DMT1 transporter indicated that the importance of this residue in metal selectivity is conserved among NRAMP transporters from plant and animal kingdoms. Analyses of overexpressing plants showed that AtNRAMP4 affects the accumulation of metals in roots. Interestingly, the mutations selectively modify Cd2+ and Zn2+ accumulation without affecting Fe transport mediated by NRAMP4 in planta. This knowledge may be applicable for limiting Cd2+ transport by other NRAMP transporters from animals or plants.
The role of plasma membrane H+‐ATPase in jasmonate‐induced ion fluxes and stomatal closure in Arabidopsis thaliana
Authors: Yan Suli , McLamore Eric S. , Dong Shanshan , Gao Haibo , Taguchi Masashige , Wang Ningning , Zhang Ting , Su Xiaohua , Shen Yingbai
Published: June 2015

Methyl jasmonate (MeJA) elicits stomatal closure in many plant species. Stomatal closure is accompanied by large ion fluxes across the plasma membrane (PM). Here, we recorded the transmembrane ion fluxes of H+, Ca2+ and K+ in guard cells of wild‐type (Col‐0) Arabidopsis, the CORONATINE INSENSITIVE1 (COI1) mutant coi1‐1 and the PM H+‐ATPase mutants aha1‐6 and aha1‐7, using a non‐invasive micro‐test technique. We showed that MeJA induced transmembrane H+ efflux, Ca2+ influx and K+ efflux across the PM of Col‐0 guard cells. However, this ion transport was abolished in coi1‐1 guard cells, suggesting that MeJA‐induced transmembrane ion flux requires COI1. Furthermore, the H+ efflux and Ca2+ influx in Col‐0 guard cells was impaired by vanadate pre‐treatment or PM H+‐ATPase mutation, suggesting that the rapid H+ efflux mediated by PM H+‐ATPases could function upstream of the Ca2+ flux. After the rapid H+ efflux, the Col‐0 guard cells had a longer oscillation period than before MeJA treatment, indicating that the activity of the PM H+‐ATPase was reduced. Finally, the elevation of cytosolic Ca2+ concentration and the depolarized PM drive the efflux of K+ from the cell, resulting in loss of turgor and closure of the stomata.
Rising BRIC and Changes in Sub‐Saharan Africa's Business Cycle Patterns
Authors: Diallo Oumar , Tapsoba Sampawende J.‐A.
Published: June 2015

This paper assesses the extent to which Sub‐Saharan Africa (SSA)'s business cycle is synchronized with that of the rest of the world (RoW). SSA's business cycle has not only moved in the same direction as that of the RoW, but has also gradually drifted away from the G7 in favor of the BRIC. Trade with the BRIC has been the strongest driver of this shift. As fiscal policy stances in SSA and the BRIC are not synchronized, they have not caused output correlation. Also, financial openness, which is at an early stage in SSA, has acted as a neutral force.
Pocket technique or pocket technique combined with modified orbital rim anchorage for the replacement of a prolapsed gland of the third eyelid in dogs: 353 dogs
Authors: Multari Domenico , Perazzi Anna , Contiero Barbara , De Mattia Giada , Iacopetti Ilaria
Published: June 2015

The aim of this retrospective study was to evaluate the results obtained in 353 dogs (420 eyes) using two different surgical techniques for correction of a prolapsed gland of the third eyelid: the Morgan's pocket technique and a technique combining Morgan's approach with a slightly modified periosteal anchoring technique of Stanley and Kaswan. The pocket technique was used in 234 eyes and the combined technique in 186 eyes. Successful repositioning was obtained in 95% of all cases, with recurrence occurring in 5%. The recurrence rate in large breed dogs such as the English Bulldog and Boxer was lower with the combined technique than with the pocket technique.
Antigenic Detection of Human Strain of Influenza Virus A (H3N2) in Swine Populations at Three Locations in Nigeria and Ghana during the Dry Early Months of 2014
Authors: Adeola O. A. , Olugasa B. O. , Emikpe B. O.
Published: June 2015

Since the first detection of human H3N2 influenza virus in Taiwanese pigs in 1970, infection of pigs with wholly human viruses has been known to occur in other parts of the world. These viruses, referred to as human‐like H3N2 viruses, have been known to cause clinical and subclinical infections of swine populations. Due to the paucity and complete unavailability of information on transmission of influenza viruses from other species, especially humans, to swine in Nigeria and Ghana, respectively, this study was designed to investigate the presence and prevalence of a human strain of influenza A (H3N2) in swine populations at three locations in two cities within these two West African countries in January and February, 2014. Using stratified random technique, nasal swab specimens were collected from seventy‐five (75) pigs at two locations in Ibadan, Nigeria and from fifty (50) pigs in Kumasi, Ghana. These specimens were tested directly by a sensitive Quantitative Solid Phase Antigen‐detection Sandwich ELISA using anti‐A/Brisbane/10/2007 haemagglutinin monoclonal antibody. Influenza virus A/Brisbane/10/2007 (H3N2) was detected among pigs at the three study locations, with an aggregate prevalence of 4.0% for the two locations in Ibadan, Nigeria and also 4.0% for Kumasi, Ghana. Transmission of influenza viruses from other species to swine portends serious sinister prospects for genetic reassortment and evolvement of novel viruses. We therefore recommend that further studies should be carried out to investigate the presence of other circulating human and avian influenza viruses in swine populations in West Africa and also determine the extent of genetic reassortment of strains circulating among these pigs. This would provide an early warning system for detection of novel influenza viruses, which could have pandemic potentials.
Automatic Measurement of End-Diastolic Arterial Lumen Diameter in ARTSENS
Authors: Sahani Ashish Kumar , Joseph Jayaraj , Radhakrishnan Ravikumar , Sivaprakasam Mohanasankar
Published: June 2015

Over past few years, we are developing a system for facilitating large scale screening of patients for cardiovascular risk—arterial stiffness evaluation for noninvasive screening (ARTSENS). ARTSENS is an image-free device that uses a single element ultrasound transducer to obtain noninvasive measurements of arterial stiffness (AS) in a fully automated manner. AS is directly proportional to end-diastolic lumen diameter (Dd). Multilayered structure of the arterial walls and indistinct characteristics of intima-lumen interface (ILI) makes it quite difficult to accurately estimate Dd in A-mode radio-frequency (RF) frames obtained from ARTSENS. In this paper, we propose a few methods based on fitting simple mathematical models to the echoes from arterial walls, followed by a novel method to fuse the information from curve fitting error and distension curve to arrive at an accurate measure of Dd. To bring down the curve fitting time and facilitate processing on low-end processors, a novel approach using the autocorrelation of echoes from opposite walls of the artery has been discussed. The methods were analyzed for their comparative accuracy against reference Dd obtained from 85 human volunteers using Hitachi-Aloka eTRACKING system. Dd from all reported methods show strong and statistically significant positive correlation with eTRACKING and mean error of less than 7% could be achieved. As expected, Dd from all methods show significant positive correlation with age.
Design of a New Haptic Interface for Endoscopy Simulation
Authors: Gu Yunjin , Kim Cheongjun , Lee Doo Yong
Published: June 2015

This paper reports a novel haptic interface to provide haptic feedback during endoscopy simulation. The proposed haptic interface combines two independent mechanisms to provide two decoupled degrees-of-freedom in the translational and the rotational directions. Effects of the apparent inertia–mass and apparent friction to the user's hand are measured in the form of resistive force and torque. The forces and torques that can be manifested by the developed haptic interface are compared with the exerted force data during actual endoscopy.
Toward a Methodology for Systematically Generating Energy- and Materials-Efficient Concepts Using Biological Analogies
Authors: O'Rourke Julia M. , Seepersad Carolyn C.
Published: June 2015

Energy- and materials-efficient designs are highly valued in the context of sustainable product design, but realizing products with significant changes in efficiency is a difficult task. One means to address this challenge is to use biological analogies during ideation. The use of biological analogies in the design process has been shown to greatly increase the novelty of concepts generated, and many authors in the bioinspired design (BID) community contend that efficiency-related benefits may be conferred as well. However, there is disagreement in the field as to when, how, and why efficiency-related benefits might arise in BIDs. This work explores these issues in-depth. A review of BID literature and an empirical study of BIDs lead to a better understanding of the types of efficiency advantages conferred by BID and set the stage for the development of tools and methods to systematically generate more energy- and materials-efficient design concepts using biological analogies.
At the Mercy of the Gods: Associations Between Weather, Physical Activity, and Sedentary Time in Children
Authors: Lewis Lucy Kate , Maher Carol , Belanger Kevin , Tremblay Mark , Chaput Jean-Philippe , Olds Tim
Published: June 2015

Objectives:

This study investigated associations between weather conditions, physical activity, and sedentary time in primary school-aged children in Australia and Canada.

Methods:

Cross-sectional data on 9–11-year-old children from the Australian (n = 491) and Canadian (n = 524) sites of the International Study of Childhood Obesity, Lifestyle and the Environment were used. Minutes of daily moderate-to-vigorous-physical-activity (MVPA) and sedentary time were determined from 7-day, 24-h accelerometry (Actigraph GT3X+ triaxial accelerometer). Day-matched weather data (temperature, rainfall, snowfall, relative humidity, wind speed) were obtained from the closest weather station to participants’ schools. Covariates included parental highest education level, day type, sex, and BMI z-scores. Generalized mixed model analyses allowing for clustering of participants within schools were completed. Scatterplots with Loess curves were created for maximum temperature, MVPA, and sedentary time.

Results:

Daily maximum temperature was significantly associated with MVPA and sedentary time in Australia (MVPA p = .05, sedentary p = .01) and Canada (p < .001, p = .001). Rainfall was negatively associated with MVPA in Australia (p < .001) and positively associated with sedentary time in Canada (p = .02).

Conclusions:

MVPA and sedentary time appear to be optimal when the maximum temperature ranges between 20°C and 25°C in both countries. The findings have implications for study design and interpretation for surveillance and intervention studies.
Genome Sequences of Six Paenibacillus larvae
Siphoviridae
Phages
Authors: Carson Susan , Bruff Emily , DeFoor William , Dums Jacob , Groth Adam , Hatfield Taylor , Iyer Aruna , Joshi Kalyani , McAdams Sarah , Miles Devon , Miller Delanie , Oufkir Abdoullah , Raynor Brinkley , Riley Sara , Roland Shelby , Rozier Horace , Talley Sarah , Miller Eric S.
Published: June 2015

Six sequenced and annotated genomes of
Paenibacillus larvae
phages isolated from the combs of American foulbrood-diseased beehives are 37 to 45 kbp and have approximately 42% G+C content and 60 to 74 protein-coding genes. Phage Lily is most divergent from Diva, Rani, Redbud, Shelly, and Sitara.
Draft Genome Sequence of the Pathogenic Oomycete Pythium insidiosum Strain Pi-S, Isolated from a Patient with Pythiosis
Authors: Rujirawat Thidarat , Patumcharoenpol Preecha , Lohnoo Tassanee , Yingyong Wanta , Lerksuthirat Tassanee , Tangphatsornruang Sithichoke , Suriyaphol Prapat , Grenville-Briggs Laura J. , Garg Gagan , Kittichotirat Weerayuth , Krajaejun Theerapong
Published: June 2015

Pythium insidiosum
is an oomycete that causes a life-threatening infectious disease called pythiosis in humans and animals living in tropical and subtropical countries. Here, we report the first draft genome sequence of
P. insidiosum
. The genome of
P. insidiosum
is 53.2 Mb and contains 14,962 open reading frames.
Draft Genome Sequence of the First Human Isolate of the Ruminant Pathogen Mycoplasma capricolum subsp.
capricolum
Authors: Seersholm Frederik Valeur , Fischer Anne , Heller Martin , Jores Joerg , Sachse Konrad , Mourier Tobias , Hansen Anders Johannes
Published: June 2015

Mycoplasma capricolum
subsp.
capricolum
is a well-known pathogen of small ruminants. A recent human case of septicemia involving this agent raised the question of its potential pathogenicity to humans. We present the first draft genome sequence of a human
Mycoplasma capricolum
subsp.
capricolum
isolate.
Genome Sequences of Mycobacteriophages AlanGrant, Baee, Corofin, OrangeOswald, and Vincenzo, New Members of Cluster B
Authors: Pope Welkin H. , Carbonara Maria E. , Cioffi Hanna M. , Cruz Tyler , Dang Brian Q. , Doyle Alexander N. , Fan Olivia H. , Gallagher Molly , Gentile Gabrielle M. , German Brian A. , Farrell Margaret E. , Gerwig Madeline , Hunter Kelsey L. , Lefever Virginia E. , Marfisi Nicole A. , McDonnell Jill E. , Monga Jappmann K. , Quiroz Kevin G. , Pong Alexandra C. , Rimple Patrick A. , Situ Michelle , Sohnen Peri C. , Stockinger Annmarie N. , Thompson Paige K. , Torchio Nicole M. , Toner Chelsea L. , Ulbrich Megan C. , Vohra Neelam I. , Zakir Aala , Adkins Nancy L. , Brown Bryony R. , Churilla Bryce M. , Kramer Zachary J. , Lapin Jonathan S. , Montgomery Matthew T. , Prout Ashley K. , Grubb Sarah R. , Warner Marcie H. , Bowman Charles A. , Russell Daniel A. , Hatfull Graham F.
Published: June 2015

AlanGrant, Baee, Corofin, OrangeOswald, and Vincenzo are newly isolated phages of
Mycobacterium smegmatis
mc
2
155 discovered in Pittsburgh, Pennsylvania, USA. All five phages share nucleotide similarity with cluster B mycobacteriophages but span considerable diversity with Corofin and OrangeOswald in subcluster B3, AlanGrant and Vincenzo in subcluster B4, and Baee in subcluster B5.
Genome Sequences of Cluster G Mycobacteriophages Cambiare, FlagStaff, and MOOREtheMARYer
Authors: Pope Welkin H. , Augustine David A. , Carroll Daniel C. , Duncan Julia C. , Harwi Kyle M. , Howry Rachel , Jagessar Bhavita , Lum Brandon A. , Meinert Justin W. , Migliozzi Jeffrey S. , Milliken Katherine A. , Mitchell Chandler J. , Nalatwad Akanksha S. , Orlandini Kaila C. , Rhein Michael J. , Saravanan Vishmayaa , Seese Brett A. , Schiebel Johnathon G. , Thomas Kayla B. , Adkins Nancy L. , Cohen Karen L. , Iyengar Varun B. , Kim Hannah , Kramer Zachary J. , Montgomery Matthew T. , Schafer Claire E. , Wilkes Kellyn E. , Grubb Sarah R. , Warner Marcie H. , Bowman Charles A. , Russell Daniel A. , Hatfull Graham F.
Published: June 2015

Mycobacteriophages Cambiare, FlagStaff, and MOOREtheMARYer are newly isolated phages of
Mycobacterium smegmatis
mc
2
155 recovered from soil samples in Pittsburgh, PA. All three genomes are closely related to cluster G mycobacteriophages but differ sufficiently in nucleotide sequence and gene content to warrant division of cluster G into several subclusters.
Genome Sequence of a Newly Isolated Mycobacteriophage, ShedlockHolmes
Authors: Pope Welkin H. , Carter Jordan T. , Dasher Kegan L. , Haynberg Mikaela C. , Reddi Anoop , Shedlock Kathleen A. , Lapin Jonathan S. , Prout Ashley K. , Grubb Sarah R. , Warner Marcie H. , Bowman Charles A. , Russell Daniel A. , Hatfull Graham F.
Published: June 2015

Mycobacteriophage ShedlockHolmes is a newly isolated phage infecting
Mycobacterium smegmatis
mc
2
155. It has a 61,081-bp genome containing 99 predicted protein-coding genes and one tRNA gene. ShedlockHolmes is closely related to mycobacteriophages Pixie, Keshu, and MacnCheese and is a new member of subcluster K3.
Draft Genome Sequence of Bacillus coagulans NL01, a Wonderful
l
-Lactic Acid Producer
Authors: Zheng Zhaojuan , Jiang Ting , Lin Xi , Zhou Jie , Ouyang Jia
Published: June 2015

Here, we report the draft genome sequence of
Bacillus coagulans
NL01, which could produce high optically pure
l
-lactic acid using xylose as a sole carbon source. The draft genome is 3,505,081 bp, with 144 contigs. About 3,903 protein-coding genes and 92 rRNAs are predicted from this assembly.
Genome Sequence of the Alkaline-Tolerant
Cellulomonas
sp. Strain FA1
Authors: Cohen Michael F. , Hu Ping , Nguyen My Vu , Kamennaya Nina , Brown Natasha , Woyke Tanja , Kyrpides Nikos , Holman Hoi-Ying , Torok Tamas
Published: June 2015

We present the genome of the cellulose-degrading
Cellulomonas
sp. strain FA1 isolated from an actively serpentinizing highly alkaline spring. Knowledge of this genome will enable studies into the molecular basis of plant material degradation in alkaline environments and inform the development of lignocellulose bioprocessing procedures for biofuel production.
Genome Sequence of a Klebsiella pneumoniae Sequence Type 258 Isolate with Prophage-Encoded K. pneumoniae Carbapenemase
Authors: Chen Liang , Chavda Kalyan D. , DeLeo Frank R. , Bryant Kendall A. , Jacobs Michael R. , Bonomo Robert A. , Kreiswirth Barry N.
Published: June 2015

We present the draft genome sequence of a
Klebsiella pneumoniae
carbapenemase (KPC)-producing sequence type 258 (ST258)
K. pneumoniae
strain, ST258_FL. Uniquely, strain ST258_FL harbors two copies of the
bla
KPC
gene on the chromosome, one of which is integrated into a prophage.
Genome Sequence of Rhizobacterium Serratia marcescens Strain 90-166, Which Triggers Induced Systemic Resistance and Plant Growth Promotion
Authors: Jeong Haeyoung , Kloepper Joseph W. , Ryu Choong-Min
Published: June 2015

The rhizobacterium
Serratia marcescens
strain 90-166 elicits induced systemic resistance against plant pathogens and herbivores and promotes plant growth under greenhouse and field conditions. Strain 90-166 secretes volatile compounds, siderophores, salicylic acid, and quorum-sensing autoinducers as bacterial determinants toward plant health. Herein, we present its draft genome sequence.
Draft Genome Sequence of
Shewanella
sp. ECSMB14102, a Mussel Recruitment-Promoting Bacterium Isolated from the East China Sea
Authors: Yang Jin-Long , Guo Xing-Pan , Chen Yu-Ru , Gao Wei , Ding De-Wen
Published: June 2015

Shewanella
sp. ECSMB14102, which promotes recruitment of the mussel
Mytilus coruscus
, was isolated from natural biofilms formed on glass slides submerged in the East China Sea. Here, we present the draft genome sequence, which comprises 4.41 Mb with a G+C content of 52.2%. The genomic information in this strain will contribute to deepening our understanding of bacteria-animal interaction.
Genome Sequences of Pseudomonas amygdali pv. tabaci Strain ATCC 11528 and pv. lachrymans Strain 98A-744
Authors: Jeong Haeyoung , Kloepper Joseph W. , Ryu Choong-Min
Published: June 2015

Certain pathovars of
Pseudomonas amygdali
, which is newly reclassified from
Pseudomonas syringae
by DNA-DNA hybridization and ribotyping, cause many serious diseases of major crop plants. Herein, we present draft genome sequences of
P. amygdali
pv. tabaci strain ATCC 11528 and
P. amygdali
pv. lachrymans strain 98A-744.
Systematic review of rehabilitation programmes initiated within 90 days of a transient ischaemic attack or ‘minor’ stroke: a protocol
Authors: Heron Neil , Kee Frank , Donnelly Michael , Cupples Margaret E
Published: June 2015

Introduction

Transient ischaemic attacks (TIAs) and strokes are highly prevalent conditions. Stroke killed 5.7 million people worldwide in 2005 and is estimated to cause 6.5 million deaths globally in 2015. Stroke survivors are often left with considerable disability. Many strokes are preceded by a TIA/‘minor’ stroke in the previous 90 days and therefore the immediate period after a TIA/minor’ stroke is a crucial time to intervene to tackle known vascular risk factors. Although rehabilitation following a TIA/minor stroke is widely recommended, there is a paucity of research that offers an evidence base on which the development or optimisation of interventions can be based, particularly for home-based approaches and non-pharmacological interventions in the acute period following the initial TIA/‘minor’ stroke. This systematic review will investigate the effect of rehabilitation programmes initiated within 90 days of the diagnosis of a TIA or ‘minor’ stroke aimed at reducing the subsequent risk of stroke.

Methods/design

This systematic review will be reported in line with the Preferred Reporting Items for Systematic Reviews and Meta-analyses(PRISMA) guidance. Randomised and quasi-randomised controlled trials of rehabilitation programmes initiated within 90 days of a TIA or ‘minor’ stroke will be included. Articles will be identified through a comprehensive search of the following databases, guided by a medical librarian: the Cochrane Library, Web of Science, MEDLINE, Embase, CINAHL and PsycINFO. Two review authors will independently screen articles retrieved from the search for eligibility and extract relevant data on methodological issues. A narrative synthesis will be completed when there is insufficient data to permit a formal meta-analysis.

Discussion

This review will be of value to clinicians and healthcare professionals working in TIA and stroke services as well as to general practitioners/family physicians who care for these patients in the community and to researchers involved in designing and evaluating rehabilitation interventions.

Trial registration number

CRD42015016450.
BET 1: Impact of point-of-care ultrasound on length of stay for paediatric appendicitis
Authors: Lalande Élizabeth , Parent Marc-Charles
Published: June 2015

A short cut review was carried out to establish whether point-of-care abdominal ultrasound could affect the emergency department (ED) length of stay (LOS) of children attending with suspected appendicitis. Using the reported searches, one paper presented the best evidence to answer the clinical question. The author, date and country of publication, patient group studied, study type, relevant outcomes, results and study weaknesses of this best paper are tabulated. It is concluded that point-of-care abdominal ultrasound has sufficient specificity to be used to reduce LOS of paediatric patients in the ED with positive results for appendicitis. It is insufficiently sensitive to be used to rule out appendicitis.
Infundibular dilations of the posterior communicating arteries: pathogenesis, anatomical variants, aneurysm formation, and subarachnoid hemorrhage
Authors: Chen Ching-Jen , Moosa Shayan , Ding Dale , Raper Daniel M , Burke Rebecca M , Lee Cheng-Chia , Chivukula Srinivas , Wang Tony R , Starke Robert M , Crowley R Webster , Liu Kenneth C
Published: June 2015

Background

Cerebrovascular infundibular dilations (IDs) are triangular-shaped widenings less than 3 mm in diameter, which are most commonly found at the posterior communicating artery (PCoA). The aims of this systematic review are to elucidate the natural histories of IDs, determine their risk of progression to significant pathology, and discuss potential management options.

Methods

A comprehensive literature search of PubMed was used to find all case reports and series relating to cerebral IDs. IDs were classified into three types: type I IDs do not exhibit morphological change over a long follow-up period, type II IDs evolve into saccular aneurysms, while type III IDs are those that result in subarachnoid hemorrhage without prior aneurysmal progression. Data were extracted from studies that demonstrated type II or III IDs.

Results

We reviewed 16 cases of type II and seven cases of type III IDs. For type II IDs, 81.3% of patients were female with a median age at diagnosis of 38. All type II IDs were located at the PCoA without a clear predilection for sidedness. Median time to aneurysm progression was 7.5 years. For type III IDs there was no clear gender preponderance and the median age at diagnosis was 51. The PCoA was involved in 85.7% of cases, with 57.1% of IDs occurring on the left. Most patients were treated with clipping. Risk factors for aneurysm formation appear to be female gender, young age, left-sided localization, coexisting aneurysms, and hypertension.

Conclusions

IDs can rarely progress to aneurysms or rupture. Young patients with type II or III IDs with coexisting aneurysms or hypertension may benefit from long-term imaging surveillance.
Screening and incorporation of rust resistance from Allium cepa into bunching onion (Allium fistulosum) via alien chromosome addition
Authors: Wako Tadayuki , Yamashita Ken-ichiro , Tsukazaki Hikaru , Ohara Takayoshi , Kojima Akio , Yaguchi Shigenori , Shimazaki Satoshi , Midorikawa Naoko , Sakai Takako , Yamauchi Naoki , Shigyo Masayoshi
Published: June 2015

Bunching onion (Allium fistulosum L.; 2n = 16), bulb onion (Allium cepa L. Common onion group), and shallot (Allium cepa L. Aggregatum group) cultivars were inoculated with rust fungus, Puccinia allii, isolated from bunching onion. Bulb onions and shallots are highly resistant to rust, suggesting they would serve as useful resources for breeding rust resistant bunching onions. To identify the A. cepa chromosome(s) related to rust resistance, a complete set of eight A. fistulosum – shallot monosomic alien addition lines (MAALs) were inoculated with P. allii. At the seedling stage, FF+1A showed a high level of resistance in controlled-environment experiments, suggesting that the genes related to rust resistance could be located on shallot chromosome 1A. While MAAL, multi-chromosome addition line, and hypoallotriploid adult plants did not exhibit strong resistance to rust. In contrast to the high resistance of shallot, the addition line FF+1A+5A showed reproducibly high levels of rust resistance.
AN ANALYTICAL APPROXIMATION FOR EUROPEAN OPTION PRICES UNDER STOCHASTIC INTEREST RATES
Authors: FUNAHASHI HIDEHARU
Published: June 2015

This paper extends the Wiener–Itô chaos expansion approach proposed by Funahashi & Kijima (2015) to an equity-interest-rate hybrid model for the pricing of European contingent claims with special emphasis on calibration to the option markets. Our model can capture the volatility skew and smile of option markets, as well as the stochastic nature of interest rates. Further, the proposed method is applicable to widely used option pricing models such as local volatility models (LVM), stochastic volatility models (SVM), and their combinations with the stochastic nature of interest rates; hence, it is suitable for practical purposes. Through numerical examples, we show that our approximation is quite accurate even for long-maturity and/or high-volatility cases.
IFN-γ-induced JAK/STAT, but not NF-κB, signaling pathway is insensitive to glucocorticoid in airway epithelial cells
Authors: O'Connell Danielle , Bouazza Belaid , Kokalari Blerina , Amrani Yassine , Khatib Alaa , Ganther John David , Tliba Omar
Published: June 2015

Although the majority of patients with asthma are well controlled by inhaled glucocorticoids (GCs), patients with severe asthma are poorly responsive to GCs. This latter group is responsible for a disproportionate share of health care costs associated with asthma. Recent studies in immune cells have incriminated interferon-γ (IFN-γ) as a possible trigger of GC insensitivity in severe asthma; however, little is known about the role of IFN-γ in modulating GC effects in other clinically relevant nonimmune cells, such as airway epithelial cells. We hypothesized that IFN-γ-induced JAK/STAT-associated signaling pathways in airway epithelial cells are insensitive to GCs and that strategies aimed at inhibiting JAK/STAT pathways can restore steroid responsiveness. Using Western blot analysis we found that all steps of the IFN-γ-induced JAK/STAT signaling pathway were indeed GC insensitive. Transfection of cells with reporter plasmid showed IFN-γ-induced STAT1-dependent gene transcription to be also GC insensitive. Interestingly, real-time PCR analysis showed that IFN-γ-inducible genes (IIGs) were differentially affected by GC, with CXCL10 being GC sensitive and CXCL11 and IFIT2 being GC insensitive. Further investigation showed that the differential sensitivity of IIGs to GC was due to their variable dependency to JAK/STAT vs. NF-κB signaling pathways with GC-sensitive IIGs being more NF-κB dependent and GC-insensitive IIGs being more JAK/STAT dependent. Importantly, transfection of cells with siRNA-STAT1 was able to restore steroid responsiveness of GC-insensitive IIGs. Taken together, our results show the insensitivity of IFN-γ-induced JAK/STAT signaling pathways to GC effects in epithelial cells and also suggest that targeting STAT1 could restore GC responsiveness in patients with severe asthma.
Cerebrovascular and ventilatory responses to acute isocapnic hypoxia in healthy aging and lung disease: effect of vitamin C
Authors: Hartmann Sara E. , Waltz Xavier , Kissel Christine K. , Szabo Lian , Walker Brandie L. , Leigh Richard , Anderson Todd J. , Poulin Marc J.
Published: June 2015

Acute hypoxia increases cerebral blood flow (CBF) and ventilation (V̇e). It is unknown if these responses are impacted with normal aging, or in patients with enhanced oxidative stress, such as (COPD). The purpose of the study was to 1) investigate the effects of aging and COPD on the cerebrovascular and ventilatory responses to acute hypoxia, and 2) to assess the effect of vitamin C on these responses during hypoxia. In 12 Younger, 14 Older, and 12 COPD, we measured peak cerebral blood flow velocity (V̄p; index of CBF), and V̇e during two 5-min periods of acute isocapnic hypoxia, under conditions of 1) saline-sham; and 2) intravenous vitamin C. Antioxidants [vitamin C, superoxide dismutase (SOD), glutathione peroxidase, and catalase], oxidative stress [malondialdehyde (MDA) and advanced protein oxidation product], and nitric oxide metabolism end products (NOx) were measured in plasma. Following the administration of vitamin C, vitamin C, SOD, catalase, and MDA increased, while NOx decreased. V̄p and V̇e sensitivity to hypoxia was reduced in Older by ∼60% ( P < 0.02). COPD patients exhibited similar V̄p and V̇e responses to Older ( P > 0.05). Vitamin C did not have an effect on the hypoxic V̇e response but selectively decreased the V̄p sensitivity in Younger only. These findings suggest a reduced integrative reflex (i.e., cerebrovascular and ventilatory) during acute hypoxemia in healthy older adults. Vitamin C does not appear to have a large influence on the cerebrovascular or ventilatory responses during acute hypoxia.
Identification and Functional Validation of Reciprocal microRNA–mRNA Pairings in African American Prostate Cancer Disparities
Authors: Wang Bi-Dar , Ceniccola Kristin , Yang Qi , Andrawis Ramez , Patel Vyomesh , Ji Youngmi , Rhim Johng , Olender Jacqueline , Popratiloff Anastas , Latham Patricia , Lai Yinglei , Patierno Steven R. , Lee Norman H.
Published: June 2015

Purpose: African Americans (AA) exhibit higher rates of prostate cancer incidence and mortality compared with European American (EA) men. In addition to socioeconomic influences, biologic factors are believed to play a critical role in prostate cancer disparities. We investigated whether population-specific and -enriched miRNA–mRNA interactions might contribute to prostate cancer disparities.

Experimental Design: Integrative genomics was used, combining miRNA and mRNA profiling, miRNA target prediction, pathway analysis, and functional validation, to map miRNA–mRNA interactions associated with prostate cancer disparities.

Results: We identified 22 AA-specific and 18 EA-specific miRNAs in prostate cancer versus patient-matched normal prostate, and 10 “AA-enriched/-depleted” miRNAs in AA prostate cancer versus EA prostate cancer comparisons. Many of these population-specific/-enriched miRNAs could be paired with target mRNAs that exhibited an inverse pattern of differential expression. Pathway analysis revealed EGFR (or ERBB) signaling as a critical pathway significantly regulated by AA-specific/-enriched mRNAs and miRNA–mRNA pairings. Novel miRNA–mRNA pairings were validated by qRT-PCR, Western blot, and/or IHC analyses in prostate cancer specimens. Loss/gain of function assays performed in population-specific prostate cancer cell lines confirmed miR-133a/MCL1, miR-513c/STAT1, miR-96/FOXO3A, miR-145/ITPR2, and miR-34a/PPP2R2A as critical miRNA–mRNA pairings driving oncogenesis. Manipulating the balance of these pairings resulted in decreased proliferation and invasion, and enhanced sensitization to docetaxel-induced cytotoxicity in AA prostate cancer cells.

Conclusions: Our data suggest that AA-specific/-enriched miRNA–mRNA pairings may play a critical role in the activation of oncogenic pathways in AA prostate cancer. Our findings also suggest that miR-133a/MCL1, miR-513c/STAT1, and miR-96/FOXO3A may have clinical significance in the development of novel strategies for treating aggressive prostate cancer. Clin Cancer Res; 21(21); 4970–84. ©2015 AACR.
Treatment with Ibrutinib Inhibits BTK- and VLA-4–Dependent Adhesion of Chronic Lymphocytic Leukemia Cells In Vivo
Authors: Herman Sarah E.M. , Mustafa Rashida Z. , Jones Jade , Wong Deanna H. , Farooqui Mohammed , Wiestner Adrian
Published: June 2015

Purpose: Ibrutinib leads to a transient lymphocytosis in patients with chronic lymphocytic leukemia (CLL) that develops within hours of starting drug and is due to the efflux of cells from lymphoid tissues into the blood. We therefore sought to investigate the in vivo effect of ibrutinib on migration and adhesion of CLL cells.

Experimental Design: Patients received single-agent ibrutinib (420 mg daily) on an investigator-initiated phase II trial. Serial blood samples were collected pretreatment and during treatment for ex vivo functional assays.

Results: Adhesion of CLL cells to fibronectin was rapidly (within hours) and almost completely inhibited (median reduction 98% on day 28, P < 0.001), while the effect on migration to chemokines was more moderate (median reduction 64%, P = 0.008) and less uniform. Although cell surface expression of key adhesion molecules such as CD49d, CD29, and CD44 were modestly reduced, this was only apparent after weeks of treatment. Stimulation of CLL cells from patients on ibrutinib with PMA, which activates PKC independent of BTK, restored the ability of the cells to adhere to fibronectin in a VLA-4–dependent manner. Finally, the addition of ibrutinib to CLL cells adhered to fibronectin in vitro caused the detachment of 17% of the cells, on average; consisten t with in vivo observations of an increasing lymphocytosis within 4 hours of starting ibrutinib.

Conclusions: Inhibition of BTK and VLA-4–dependent adhesion of CLL cells to stroma and stromal components provides a mechanistic explanation for the treatment-induced lymphocytosis and may reduce CD49d-dependent prosurvival signals in the tissue microenvironment. Clin Cancer Res; 21(20); 4642–51. ©2015 AACR.