bluuebunny/crossref_metadata_2025 huggingface dataset:
Modification of electron density in F layer of ionosphere by dust suspension
Authors: Sodha M. S. , Mishra S. K.
Published: April 2017

The effect of the suspension of high/low work function dust in the F layer ionospheric plasma has been investigated. On the basis of kinetics formulation of the F-layer dusty plasma, the local electron density is shown to reduce or enhance by inserting fine dust of appropriate physical/material properties. The formulation includes the number and energy balance of the plasma constituents along with the charging of the dust particles; a novel approach to investigate the effect of diffusion on plasma particles in the F-layer has been outlined. The consequence of the physical parameters of dust, namely, number density, material work function, photo-efficiency, and surface temperature, on the charging of dust and local plasma parameters at different ionospheric altitudes in the F layer has been worked out and presented graphically; the significance of plasma diffusion has been highlighted. The modification in local plasma density in the midday F-layer is seen to be sensitive to the dust parameters and altitude profile of the ionospheric plasma. Such modification in the local electron density is certainly of interest for radio wave propagation through the F layer.
Bright narrowband biphoton generation from a hot rubidium atomic vapor cell
Authors: Zhu Lingbang , Guo Xianxin , Shu Chi , Jeong Heejeong , Du Shengwang
Published: April 2017

We demonstrate the generation of high-quality narrowband biphotons from a Doppler-broadened hot rubidium atomic vapor cell. Choosing a double-Λ atomic energy level scheme for optimizing both spontaneous four-wave mixing nonlinear parametric interaction and electromagnetically induced transparency (EIT), we achieve a biphoton spectral brightness as high as 14 000 s−1 MHz−1. Meanwhile, we apply a spatially tailored optical pumping beam for reduction of the Raman noise and obtain a violation of the Cauchy-Schwarz inequality by a factor of 1023.
Stabilization of collapsing scroll waves in systems with random heterogeneities
Authors: Weingard Daniel , Blanco Wilfredo , Steinbock Oliver , Bertram Richard
Published: April 2017

In three-dimensional reaction-diffusion systems, excitation waves may form and rotate around a one-dimensional phase singularity called the filament. If the filament forms a closed curve, it will shrink over time and eventually collapse. However, filaments may pin to non-reactive objects present in the medium, reducing their rate of collapse or even allowing them to persist indefinitely. We use numerical simulations to study how different arrangements of non-reactive spheres affect the dynamics of circular filaments. As the filament contracts, it gets closer to and eventually touches and pins to objects in its path. This causes two possible behaviors. The filament can detach from the spheres in its path, slowing down the rate of contraction, or it can remain pinned to a collection of spheres. In general, more or larger spheres increase the chance that the filament remains pinned, but there are exceptions. It is possible for a small number of small spheres to support the filament and possible for the filament to pass through a large number of large spheres. Our work yields insights into the pinning of scroll waves in excitable tissue such as cardiac muscle, where scar tissue acts in a way similar to the non-reactive domains.
Particle conservation in numerical models of the tokamak plasma edge
Authors: Kotov Vladislav
Published: April 2017

The test particle Monte-Carlo models for neutral particles are often used in the tokamak edge modelling codes. The drawback of these models is that the self-consistent solution suffers from random error introduced by the statistical method. A particular case where the onset of nonphysical solutions can be clearly identified is the violation of the global particle balance due to non-converged residuals. There are techniques that can reduce the residuals—such as internal iterations in the code B2-EIRENE—but they may pose severe restrictions on the time-step and slow down the computations. Numerical diagnostics described in this paper can be used to unambiguously identify when the too large error in the global particle balance is due to finite-volume residuals, and their reduction is absolutely necessary. Algorithms that reduce the error while allowing large time-step are also discussed.
Optic nerve astrocyte reactivity protects function in experimental glaucoma and other nerve injuries
Authors: Sun Daniel , Moore Sara , Jakobs Tatjana C.
Published: April 2017

Reactive remodeling of optic nerve head astrocytes is consistently observed in glaucoma and other optic nerve injuries. However, it is unknown whether this reactivity is beneficial or harmful for visual function. In this study, we used the Cre recombinase (Cre)–loxP system under regulation of the mouse glial fibrillary acidic protein promoter to knock out the transcription factor signal transducer and activator of transcription 3 (STAT3) from astrocytes and test the effect this has on reactive remodeling, ganglion cell survival, and visual function after experimental glaucoma and nerve crush. After injury, STAT3 knockout mice displayed attenuated astrocyte hypertrophy and reactive remodeling; astrocytes largely maintained their honeycomb organization and glial tubes. These changes were associated with increased loss of ganglion cells and visual function over a 30-day period. Thus, reactive astrocytes play a protective role, preserving visual function. STAT3 signaling is an important mediator of various aspects of the reactive phenotype within optic nerve astrocytes.
AAV-mediated expression of anti-tau scFvs decreases tau accumulation in a mouse model of tauopathy
Authors: Ising Christina , Gallardo Gilbert , Leyns Cheryl E.G. , Wong Connie H. , Jiang Hong , Stewart Floy , Koscal Lauren J. , Roh Joseph , Robinson Grace O. , Remolina Serrano Javier , Holtzman David M.
Published: April 2017

Tauopathies are characterized by the progressive accumulation of hyperphosphorylated, aggregated forms of tau. Our laboratory has previously demonstrated that passive immunization with an anti-tau antibody, HJ8.5, decreased accumulation of pathological tau in a human P301S tau-expressing transgenic (P301S-tg) mouse model of frontotemporal dementia/tauopathy. To investigate whether the Fc domain of HJ8.5 is required for the therapeutic effect, we engineered single-chain variable fragments (scFvs) derived from HJ8.5 with variable linker lengths, all specific to human tau. Based on different binding properties, we selected two anti-tau scFvs and tested their efficacy in vivo by adeno-associated virus–mediated gene transfer to the brain of P301S-tg mice. The scFvs significantly reduced levels of hyperphosphorylated, aggregated tau in brain tissue of P301S-tg mice, associated with a decrease in detergent-soluble tau species. Interestingly, these mice showed substantial levels of scFvs in the cerebrospinal fluid without significant effects on total extracellular tau levels. Therefore, our study provides a novel strategy for anti-tau immunotherapeutics that potentially limits a detrimental proinflammatory response.
Explicit solutions and multiplicity results for some equations with the 𝑝-Laplacian
Authors: Korman Philip
Published: April 2017

We derive explicit ground state solutions for several equations with the

p
p

-Laplacian in

R
n

R^n

, including (here

φ
(
z
)
=
z

|

z

|

p
−
2

\varphi (z)=z|z|^{p-2}

, with

p
>
1

p>1

)
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="phi left-parenthesis u prime left-parenthesis r right-parenthesis right-parenthesis Superscript prime Baseline plus StartFraction n minus 1 Over r EndFraction phi left-parenthesis u prime left-parenthesis r right-parenthesis right-parenthesis plus u Superscript upper M Baseline plus u Superscript upper Q Baseline equals 0 period">

φ

(

u
′

(
r
)
)

′

+

n
−
1

r

φ

(

u
′

(
r
)
)

+

u
M

+

u
Q

=
0

.

\varphi \left (u’(r)\right )’ +\frac {n-1}{r} \varphi \left (u’(r)\right )+u^M+u^Q=0 \,.

\]
The constant

M
>
0

M>0

is assumed to be below the critical power, while

Q
=

M
p
−
p
+
1

p
−
1

Q=\frac {M p-p+1}{p-1}

is above the critical power. This explicit solution is used to give a multiplicity result, similarly to C. S. Lin and W.-M. Ni (1998). We also give the

p
p

-Laplace version of G. Bratu’s solution, connected to combustion theory.

In another direction, we present a change of variables which removes the non-autonomous term

r

α

r^{\alpha }

in
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="phi left-parenthesis u prime left-parenthesis r right-parenthesis right-parenthesis Superscript prime Baseline plus StartFraction n minus 1 Over r EndFraction phi left-parenthesis u prime left-parenthesis r right-parenthesis right-parenthesis plus r Superscript alpha Baseline f left-parenthesis u right-parenthesis equals 0 comma">

φ

(

u
′

(
r
)
)

′

+

n
−
1

r

φ

(

u
′

(
r
)
)

+

r

α

f
(
u
)
=
0

,

\varphi \left (u’(r)\right )’ +\frac {n-1}{r} \varphi \left (u’(r)\right )+r^{\alpha } f(u)=0 \,,

\]
while preserving the form of this equation. In particular, we study singular equations, when

α
>
0

\alpha >0

, that occur often in applications. The Coulomb case

α
=
−
1

\alpha =-1

turned out to give the critical power.
Seascapes are landscapes after all; Comment on Manderson (2016): Seascapes are not landscapes: an analysis performed using Bernhard Riemann's rules. ICES Journal of Marine Science, 73:1831–1838
Authors: Bell Susan S. , Furman Bradley T.
Published: April 2017

Recently, Manderson (2016, Seascapes are not landscapes: an analysis performed using Bernhard Riemann's rules: ICES Journal of Marine Science, 73: 1831-1838) argued that landscape ecology approaches developed in terrestrial habitats have little practical application for the study of marine “seascapes”. Here, we offer a contrasting perspective to this over-generalization. We first focus on historical uses of the term “seascape” to delineate the wide range of habitats that have been designated as such. After providing a brief overview of the study of seascape ecology, we argue that concepts and methodology originating from terrestrial disciplines have, in fact, provided an important cornerstone for investigating the dynamics of nearshore marine ecosystems. We present examples of coastal seascape research that have successfully applied terrestrial landscape theory and revisit points raised by Manderson regarding the application of landscape approaches to the marine environment. Overall, we contend that Manderson’s thesis may apply to some, but not most, use of landscape constructs for investigating aquatic environments. Moreover, we suggest that the study of coastal landscapes will continue to yield valuable insight into the spatiotemporal workings of aquatic ecosystems, and that this particular avenue of ecological investigation will only increase in its relevance as human impacts intensify.
Finding forming globular clusters at high redshifts
Authors: Renzini Alvio
Published: April 2017

The formation of globular clusters (GCs) with their multiple stellar populations remains a puzzling, unsolved problem in astrophysics. One way to gather critical insight consists in finding sizable numbers of GC progenitors (GCPs) while still near the peak of their star formation phase, at a look-back time corresponding to GC ages (∼12.5 Gyr, or z ≃ 5). This opportunity is quantitatively explored, calculating how many GCPs could be detected by deep imaging in the optical, near-IR and mid-IR bands. For concreteness, for the imaging camera performances those of NIRCam on board of James Webb Space Telescope are adopted. The number of GCPs that could be detected scales linearly with their mass, i.e. on how much more massive GCPs were compared to their GC progeny, and perspectives look promising. Besides providing direct evidence on GC formation, the detection of GCPs, their clustering, with or without a central galaxy already in place, would shed light on the relative timing of GC formation and galaxy growth and assembly. All this may be the result of dedicated observations as well as a side benefit of deep imaging meant to search for the agents of cosmic reionization.
Microsurgical Clipping of an Anterior Communicating Artery Aneurysm Using a Novel Robotic Visualization Tool in Lieu of the Binocular Operating Microscope: Operative Video
Authors: Klinger Daniel R , Reinard Kevin A , Ajayi Olaide O , Delashaw Johnny B
Published: April 2017

INTRODUCTION

The binocular operating microscope has been the visualization instrument of choice for microsurgical clipping of intracranial aneurysms for many decades.

OBJECTIVE

To discuss recent technological advances that have provided novel visualization tools, which may prove to be superior to the binocular operating microscope in many regards.

METHODS

We present an operative video and our operative experience with the BrightMatterTM Servo System (Synaptive Medical, Toronto, Ontario, Canada) during the microsurgical clipping of an anterior communicating artery aneurysm. To the best of our knowledge, the use of this device for the microsurgical clipping of an intracranial aneurysm has never been described in the literature.

RESULTS

The BrightMatterTM Servo System (Synaptive Medical) is a surgical exoscope which avoids many of the ergonomic constraints of the binocular operating microscope, but is associated with a steep learning curve. The BrightMatterTM Servo System (Synaptive Medical) is a maneuverable surgical exoscope that is positioned with a directional aiming device and a surgeon-controlled foot pedal. While utilizing this device comes with a steep learning curve typical of any new technology, the BrightMatterTM Servo System (Synaptive Medical) has several advantages over the conventional surgical microscope, which include a relatively unobstructed surgical field, provision of high-definition images, and visualization of difficult angles/trajectories.

CONCLUSION

This device can easily be utilized as a visualization tool for a variety of cranial and spinal procedures in lieu of the binocular operating microscope. We anticipate that this technology will soon become an integral part of the neurosurgeon's armamentarium.
The Association Between Posttraumatic Stress Disorder and Perceptions of Deployment-Related Injury in Veterans With and Without Mild Traumatic Brain Injury
Authors: Bahraini Nazanin H. , Monteith Lindsey L. , Gerber Holly R. , Forster Jeri E. , Hostetter Trisha A. , Brenner Lisa A.
Published: April 2017

Objectives:

To examine whether the association between posttraumatic stress disorder (PTSD) and injury perceptions (ie, consequences, emotional representations, and coherence) differs for Veterans with mild traumatic brain injury (mTBI) compared with Veterans with non-TBI (ie, orthopedic).

Participants:

Eighty Veterans injured during post-9/11 deployments.

Design:

Observational, 2×2 factorial design.

Main Measures:

Injury histories ascertained using the Ohio State University TBI-Identification Method and Deployment Injury Questionnaire; Injury Perception Questionnaire-Revised (injury perceptions); Structured Clinical Interview for the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (PTSD diagnosis); and PTSD Symptom Checklist-Civilian Version (PTSD symptoms).

Results:

The association between PTSD diagnosis and injury perceptions did not differ between Veterans with mTBI and those with non-TBIs, adjusting for age, subjective pain, and depressive symptoms. PTSD symptom severity was significantly associated with injury consequences (P < .0001) and emotional representations (P < .0001), irrespective of injury type (mTBI vs non-TBI). Only injury coherence was associated with a significant interaction between PTSD symptom severity and mTBI (P = .04).

Conclusion:

PTSD symptom severity influences perceptions about mTBI and non-TBIs sustained during deployment. Altering injury perceptions may be an important treatment target for Veterans with co-occurring PTSD and deployment-related injuries.
A Review of Ocular Graft-Versus-Host Disease
Authors: Munir Saleha Z. , Aylward James
Published: April 2017

Graft-versus-host disease (GVHD) is a major complication that occurs following allogeneic hematopoietic stem cell transplantation, which is a potential curative therapy used in a variety of malignant or benign hematological diseases. Graft-versus-host disease primarily occurs in many organs, but most notably in the skin, lungs, gastrointestinal tract, liver, eyes, mucosa, and musculoskeletal system. Ocular manifestations of GVHD may precede other systemic GVHD findings, and it may be a poor prognosis for mortality. While all parts of the eye may be affected, ocular GVHD occurs primarily in the ocular surface. Dry eye disease or keratoconjunctivitis sicca is the most common presenting manifestation of chronic ocular GVHD. Dry eye disease in ocular GVHD is a multifactorial process, which involves destruction and fibrosis of lacrimal glands and conjunctiva, leading to tear film deficiency and instability. Depending on the severity of ocular involvement and response to treatment, ocular GVHD may cause decreased quality of life. Management of GVHD begins with prevention by understanding risk factors and by implementing prophylactic treatment after allogeneic hematopoietic stem cell transplantation. A multidisciplinary approach to the prevention and treatment of GVHD is important, and there are currently no preventive therapies available for ocular GVHD. Once diagnosed, ocular GVHD treatment strategies target ocular surface lubrication and support, tear film stabilization, inflammation reduction, and surgical intervention. The goal of this review is to define ocular GVHD and its categorical manifestations, as well as to describe the importance of comprehensive assessment, diagnosis, and ophthalmologic treatment and management of ocular GVHD with a multidisciplinary approach.
Fear Generalization as Threat Prediction: Adaptive Changes in Facial Exploration Strategies revealed by Fixation-Pattern Similarity Analysis
Authors: Kampermann Lea , Wilming Niklas , Alink Arjen , Büchel Christian , Onat Selim
Published: April 2017

Animals can effortlessly adapt their behavior by generalizing from past experiences, and avoid harm in novel aversive situations. In our current understanding, the perceptual similarity between learning and generalization samples is viewed as one major factor driving aversive generalization. Alternatively, the threat-prediction account proposes that perceptual similarity should lead to generalization to the extent it predicts harmful outcomes. We tested these views using a two-dimensional perceptual continuum of faces. During learning, one face is conditioned to predict a harmful event, whereas the most dissimilar face stays neutral; introducing an adversity gradient defined only along one dimension. Learning changed the way how humans sampled information during viewing of faces. These occurred specifically along the adversity gradient leading to an increased dissimilarity of eye-movement patterns along the threat-related dimension. This provides evidence for the threat-prediction account of generalization, which conceives perceptual factors to be relevant to the extent they predict harmful outcomes.
Decoding the Brain: Neural Representation and the Limits of Multivariate Pattern Analysis in Cognitive Neuroscience
Authors: Ritchie J. Brendan , Kaplan David Michael , Klein Colin
Published: April 2017

Since its introduction, multivariate pattern analysis (MVPA), or “neural decoding”, has transformed the field of cognitive neuroscience. Underlying its influence is a crucial inference, which we call the Decoder’s Dictum: if information can be decoded from patterns of neural activity, then this provides strong evidence about what information those patterns represent. Although the Dictum is a widely held and well-motivated principle in decoding research, it has received scant philosophical attention. We critically evaluate the Dictum, arguing that it is false: decodability is a poor guide for revealing the content of neural representations. However, we also suggest how the Dictum can be improved on, in order to better justify inferences about neural representation using MVPA.
Surgically disconnected temporal pole exhibits resting functional connectivity with remote brain regions
Authors: Warren David E. , Sutterer Matthew J. , Bruss Joel , Abel Taylor J. , Jones Andrew , Kawasaki Hiroto , Voss Michelle , Cassell Martin , Howard Matthew A. , Tranel Daniel
Published: April 2017

Functional connectivity, as measured by resting-state fMRI, has proven a powerful method for studying brain systems in the context of behavior, development, and disease states. However, the relationship of functional connectivity to structural connectivity remains unclear. If functional connectivity relies on structural connectivity, then anatomical isolation of a brain region should eliminate functional connectivity with other brain regions. We tested this by measuring functional connectivity of the surgically disconnected temporal pole in resection patients (N=5; mean age 37; 2F, 3M). Functional connectivity was evaluated based on coactivation of whole-brain fMRI data with the average low-frequency BOLD signal from disconnected tissue in each patient. In sharp contrast to our prediction, we observed significant functional connectivity between the disconnected temporal pole and remote brain regions in each disconnection case. These findings raise important questions about the neural bases of functional connectivity measures derived from the fMRI BOLD signal.
Preexisting antibodies can protect against congenital cytomegalovirus infection in monkeys
Authors: Nelson Cody S. , Cruz Diana Vera , Tran Dollnovan , Bialas Kristy M. , Stamper Lisa , Wu Huali , Gilbert Margaret , Blair Robert , Alvarez Xavier , Itell Hannah , Chen Meng , Deshpande Ashlesha , Chiuppesi Flavia , Wussow Felix , Diamond Don J. , Vandergrift Nathan , Walter Mark R. , Barry Peter A. , Cohen-Wolkowiez Michael , Koelle Katia , Kaur Amitinder , Permar Sallie R.
Published: April 2017

Human cytomegalovirus (HCMV) is the most common congenital infection and a known cause of microcephaly, sensorineural hearing loss, and cognitive impairment among newborns worldwide. Natural maternal HCMV immunity reduces the incidence of congenital infection, but does not prevent the disease altogether. We employed a nonhuman primate model of congenital CMV infection to investigate the ability of preexisting antibodies to protect against placental CMV transmission. Pregnant, CD4+ T cell-depleted, rhesus CMV (RhCMV)-seronegative rhesus monkeys were treated with either standardly-produced hyperimmune globulin (HIG) from RhCMV-seropositive macaques or dose-optimized, potently RhCMV-neutralizing HIG prior to intravenous challenge with an RhCMV swarm. HIG passive infusion provided complete protection against fetal loss in both groups, and the potently-neutralizing HIG additionally inhibited placental transmission of RhCMV. Our findings suggest that antibody alone at the time of primary infection can prevent congenital CMV and therefore could be a primary target of vaccines to eliminate this neonatal infection.
Genomic regression of claw keratin, taste receptor and light-associated genes inform biology and evolutionary origins of snakes
Authors: Emerling Christopher A.
Published: April 2017

Regressive evolution of anatomical traits corresponds with the regression of genomic loci underlying such characters. As such, studying patterns of gene loss can be instrumental in addressing questions of gene function, resolving conflicting results from anatomical studies, and understanding the evolutionary history of clades. The origin of snakes coincided with the regression of a number of anatomical traits, including limbs, taste buds and the visual system. By studying the genomes of snakes, I was able to test three hypotheses associated with the regression of these features. The first concerns two keratins that are putatively specific to claws. Both genes that encode these keratins were pseudogenized/deleted in snake genomes, providing additional evidence of claw- specificity. The second hypothesis is whether snakes lack taste buds, an issue complicated by unequivocal, conflicting results in the literature. I found evidence that different snakes have lost one or more taste receptors, but all snakes examined retained at least some capacity for taste. The final hypothesis I addressed is that the earliest snakes were adapted to a dim light niche. I found evidence of deleted and pseudogenized genes with light- associated functions in snakes, demonstrating a pattern of gene loss similar to other historically nocturnal clades. Together these data also provide some bearing on the ecological origins of snakes, including molecular dating estimates that suggest dim light adaptation preceded the loss of limbs.
GlnK facilitates the dynamic regulation of bacterial nitrogen assimilation
Authors: Gosztolai Adam , Schumacher Jörg , Behrends Volker , Bundy Jacob G , Heydenreich Franziska , Bennett Mark H , Buck Martin , Barahona Mauricio
Published: April 2017

Ammonium assimilation inE. coliis regulated by two paralogous proteins (GlnB and GlnK), which orchestrate interactions with regulators of gene expression, transport proteins and metabolic pathways. Yet how they conjointly modulate the activity of glutamine synthetase (GS), the key enzyme for nitrogen assimilation, is poorly understood. We combine experiments and theory to study the dynamic roles of GlnB and GlnK during nitrogen starvation and upshift. We measure time-resolvedin vivoconcentrations of metabolites, total and post-translationally modified proteins, and develop a concise biochemical model of GlnB and GlnK that incorporates competition for active and allosteric sites, as well as functional sequestration of GlnK. The model predicts the responses of GS, GlnB and GlnK under time-varying external ammonium level in the wild type and two genetic knock-outs. Our results show that GlnK is tightly regulated under nitrogen-rich conditions, yet it is expressed during ammonium run-out and starvation. This suggests a role for GlnK as a buffer of nitrogen shock after starvation, and provides a further functional link between nitrogen and carbon metabolisms.
Genomics-enabled analysis of the emergent disease cotton bacterial blight
Authors: Phillips Anne Z. , Berry Jeffrey C. , Wilson Mark C. , Vijayaraghavan Anupama , Burke Jillian , Bunn J. Imani , Allen Tom W. , Wheeler Terry , Bart Rebecca
Published: April 2017

Cotton bacterial blight (CBB), an important disease of (Gossypium hirsutum) in the early 20th century, had been controlled by resistant germplasm for over half a century. Recently, CBB re-emerged as an agronomic problem in the United States. Here, we report analysis of cotton variety planting statistics that indicate a steady increase in the percentage of susceptible cotton varieties grown each year since 2009. Phylogenetic analysis revealed that strains from the current outbreak cluster with race 18 Xanthomonas citri pv. malvacearum (Xcm) strains.

Illumina based draft genomes were generated for thirteen Xcm isolates and analyzed along with 4 previously published Xcm genomes. These genomes encode 24 conserved and nine variable type three effectors. Strains in the race 18 clade contain 3 to 5 more effectors than other Xcm strains. SMRT sequencing of two geographically and temporally diverse strains of Xcm yielded circular chromosomes and accompanying plasmids. These genomes encode eight and thirteen distinct transcription activator-like effector genes. RNA-sequencing revealed 52 genes induced within two cotton cultivars by both tested Xcm strains. This gene list includes a homeologous pair of genes, with homology to the known susceptibility gene, MLO. In contrast, the two strains of Xcm induce different clade III SWEET sugar transporters. Subsequent genome wide analysis revealed patterns in the overall expression of homeologous gene pairs in cotton after inoculation by Xcm. These data reveal host-pathogen specificity at the genetic level and strategies for future development of resistant cultivars.

Author Summary

Cotton bacterial blight (CBB), caused by Xanthomonas citri pv. malvacearum (Xcm), significantly limited cotton yields in the early 20th century but has been controlled by classical resistance genes for more than 50 years. In 2011, the pathogen re-emerged with a vengeance. In this study, we compare diverse pathogen isolates and cotton varieties to further understand the virulence mechanisms employed by Xcm and to identify promising resistance strategies. We generate fully contiguous genome assemblies for two diverse Xcm strains and identify pathogen proteins used to modulate host transcription and promote susceptibility. RNA-Sequencing of infected cotton reveals novel putative gene targets for the development of durable Xcm resistance. Together, the data presented reveal contributing factors for CBB re-emergence in the U.S. and highlight several promising routes towards the development of durable resistance including classical resistance genes and potential manipulation of susceptibility targets.
StateHub-StatePaintR: rapid and reproducible chromatin state evaluation for custom genome annotation
Authors: Coetzee Simon G. , Ramjan Zachary , Dinh Huy Q. , Berman Benjamin P. , Hazelett Dennis J.
Published: April 2017

Genome annotation is critical to understand the function of disease variants, especially for clinical applications. To meet this need there are segmentations available from public consortia reflecting varying unsupervised approaches to functional annotation based on epigenetics data, but there remains a need for transparent, reproducible, and easily interpreted genomic maps of the functional biology of chromatin. We introduce a new methodological framework for defining a combinatorial epigenomic model of chromatin state on a web database,StateHub. In addition, we created an annotation tool for bioconductor,StatePaintR, which accesses these models and uses them to rapidly (on the order of seconds) produce chromatin state segmentations in standard genome browser formats. Annotations are fully documented with change history and versioning, authorship information, and original source files.StatePaintRcalculates ranks for each state from next-gen sequencing peak statistics, facilitating variant prioritization, enrichment testing, and other types of quantitative analysis.StateHubhosts annotation tracks for major public consortia as a resource, and allows users to submit their own alternative models.
CRAST Leads to Homologous-ncRNA Search in Genomic Scale
Authors: Tagashira Masaki
Published: April 2017

Motivation

Non-coding RNAs (ncRNAs) play important roles in various biological processes. In past, homologousncRNA search in genomic scale (e.g., search all house mouse ncRNAs for several human ones) is difficult since explicit consideration of secondary structure in alignment leads to impractical complexity on both of time and space.

Results

In this study, building the programCRAST(Context RNA Alignment Search Tool, available at “https://github.com/heartsh/crast” including the used validation/test set), we developed the CRAST algorithm, a“seed-and-extend”alignment one based on adaptive seed and RNA secondary structure context (motif probabilities) as in Fig. 1. The algorithm isO(n:a sum of lengths of target sequences) on time through help of adaptive seed, implicitly considering both of sequence and secondary structure; it provides computation time comparable with other BLAST-like tools, significantly reduced from any variant of the Sankoff algorithm for alignment with the explicit consideration. It detects homologs as many as other BLAST-like tools and the lowest number of non-homologous ncRNAs.
GeoDiver: Differential Gene Expression Analysis & Gene-Set Analysis For GEO Datasets
Authors: Moghul Ismail , Hewapathirana Suresh , Nawaz Nazrath , Rashid Anisatu , Priebe Marian , Vieira Bruno , Smeraldi Fabrizio , Bessant Conrad
Published: April 2017

GeoDiver is an online web application for performing Differential Gene Expression Analysis (DGEA) and Generally Applicable Gene-set Enrichment Analysis (GAGE) on gene expression datasets from the publicly available Gene Expression Omnibus (GEO). The output produced includes numerous high quality interactive graphics, allowing users to easily explore and examine complex datasets instantly. Furthermore, the results produced can be reviewed at a later date and shared with collaborators.

Availability

GeoDiver is freely available online athttp://www.geodiver.co.uk. The source code is available on Github:https://github.com/GeoDiver/GeoDiverand a docker image is available for easy installation.
Challenges and emerging directions in single-cell analysis
Authors: Yuan Guo-Cheng , Cai Long , Elowitz Michael , Enver Tariq , Fan Guoping , Guo Guoji , Irizarry Rafael , Kharchenko Peter , Kim Junhyong , Orkin Stuart , Quackenbush John , Saadatpour Assieh , Schroeder Timm , Shivdasani Ramesh , Tirosh Itay
Published: April 2017

Single-cell analysis is a rapidly evolving approach to characterize genome-scale molecular information at the individual cell level. Development of single-cell technologies and computational methods has enabled systematic investigation of cellular heterogeneity in a wide range of tissues and cell populations, yielding fresh insights into the composition, dynamics, and regulatory mechanisms of cell states in development and disease. Despite substantial advances, significant challenges remain in the analysis, integration, and interpretation of single-cell omics data. Here, we discuss the state of the field and recent advances, and look to future opportunities.
Changes in LXRα phosphorylation promote a novel diet-induced transcriptome that alters the transition from fatty liver to steatohepatitis
Authors: Becares Natalia , Gage Matthew C , Martin-Gutierrez Lucia , Shrestha Elina , Louie Rikah , Pourcet Benoit , Pello Oscar M , Luong Tu Vinh , Goñi Saioa , Liang Ning , Pichardo Cesar , Røberg-Larsen Hanne , Diaz Vanessa , Steffensen Knut R. , Garabedian Michael J. , Rombouts Krista , Treuter Eckardt , Pineda-Torra Inés
Published: April 2017

Understanding the transition from fatty liver (steatosis) to inflammatory and fibrotic steatohepatitis, is key to define strategies that alter its progression. Here we show that, when challenged with a high fat-high cholesterol diet, mice carrying a mutation that abolishes phosphorylation at Ser196 (S196A) in the liver X receptor alpha (LXRα) exhibit reduced hepatic inflammation and fibrosis despite displaying enhanced steatosis. This is associated with a marked protection against cholesterol accumulation. Reduced steatohepatitis in S196A mice involves unique reprogramming of the liver transcriptome in response to the diet. Remarkably, impaired LXRα phosphorylation uncovers novel diet-specific/phosphorylation-sensitive genes, whose regulation does not simply mirror ligand-induced LXR activation. Regulation of these unique, dually responsive genes, is associated with the promotion of LXR and cofactor occupancy under a cholesterol-rich diet. Therefore, Ser196-LXRα phosphorylation acts as a novel nutritional sensor that triggers a unique diet-induced transcriptome, thereby modulating metabolic, inflammatory and fibrotic responses important in the transition to steatohepatitis.
Cell-type specific burst firing interacts with theta and beta activity in prefrontal cortex during attention states
Authors: Voloh B. , Womelsdorf T.
Published: April 2017

Population-level theta and beta band activity in anterior cingulate and prefrontal cortex (ACC/PFC) are prominent signatures of endogenously controlled, adaptive behaviors. But how these rhythmic activities are linked to cell-type specific activity has remained unclear. Here, we suggest such a cell-to-systems level linkage. We found that the rate of burst spiking events is enhanced particularly during attention states and that attention-specific burst spikes have a unique temporal relationship to local theta and beta band population level activities. For the 5-10Hz theta frequency range, bursts coincided with transient increases of local theta power relative to non-bursts, particularly for bursts of putative interneurons. For the 16-30Hz beta frequency, bursts of putative interneurons phase synchronized stronger than nonbursts, and were associated with larger beta power modulation. In contrast, burst of putative pyramidal cells were overall similarly beta-synchronized than nonbursts, but were linked with stronger beta power only when they occurred early in the beta cycle. These findings suggests that in the ACC/PFC during attention states, mechanisms underlying burst firing are intimately linked to narrow band population level activities, providing a cell-type specific window into the emergence, resetting, or termination of oscillatory activities.
InDel assembly: A novel framework for engineering protein loops through length and compositional variation
Authors: Tizei Pedro A. G. , Harris Emma , Renders Marleen , Pinheiro Vitor B.
Published: April 2017

Insertions and deletions (indels) are known to affect function, biophysical properties and substrate specificity of enzymes, and they play a central role in evolution. Despite such clear significance, this class of mutation remains an underexploited tool in protein engineering with no available platforms capable of systematically generating or analysing libraries of varying sequence composition and length. We present a novel DNA assembly platform (InDel assembly), based on cycles of endonuclease restriction and ligation of standardised dsDNA building blocks, that can generate libraries exploring both composition and sequence length variation. In addition, we developed a framework to analyse the output of selection from InDel-generated libraries, combining next generation sequencing and alignment-free strategies for sequence analysis. We demonstrate the approach by engineering the well-characterized TEM-1 β-lactamase Ω-loop, involved in substrate specificity, identifying multiple novel extended spectrum β-lactamases with loops of modified length and composition areas of the sequence space not previously explored. Together, the InDel assembly and analysis platforms provide an efficient route to engineer protein loops or linkers where sequence length and composition are both essential functional parameters.
Debt policy and firm performance of family firms: the impact of economic adversity
Authors: Vieira Elisabete Simões
Published: April 2017

Purpose

The purpose of this paper is to analyse the relationship between debt policy and performance among family firms (FF), providing evidence on whether FF differ from non-family firms (NFF). It also focusses on the possibility of asymmetrical debt policy impact on performance between periods of stability and economic adversity.

Design/methodology/approach

The paper employs panel data regression, considering a sample of Portuguese listed firms for the period between 1999 and 2014.

Findings

Overall, the author find evidence that debt contributes negatively to firms’ performance, which is consistent with the pecking order prediction, and that the relationship between debt and performance do not differ significantly between FF and NFF. After addressing the endogeneity issue, the author conclude that firms’ performance is negatively influenced by both short- and long-term debt. Considering the total debt, the negative relationship between the two variables differs from family and non-family companies. The results show that age and size influences positively, and the independence of the board directors influences negatively the firms’ performance. The empirical findings suggest that under economic adversity, the firms’ performance is negatively affected. Finally, the author conclude that return on assets appear to fit better than return on equity or MB when you want to relate debt and firm performance.

Research limitations/implications

A limitation of this study is the small size of the Euronext Lisbon that results in a small sample.

Originality/value

This paper offers some insights on the relationship between debt policy and firm performance from a country with weak protection of minority shareholders, concentrated ownership and a significant family control. It also gives the opportunity to analyse whether firm performance differs according to market conditions.
Knowledge strategy planning: an integrated approach to manage uncertainty, turbulence, and dynamics
Authors: Bolisani Ettore , Bratianu Constantin
Published: April 2017

Purpose

Knowledge strategy and its planning are affected by uncertainty and environmental turbulence. This paper aims to discuss these issues and present knowledge strategy planning as an integrated approach for facing these conditions.

Design/methodology/approach

Based on an extensive survey and an original re-elaboration of the literature, the paper addresses these research questions: What is the meaning of knowledge strategy, and how can it be related to concepts such as strategic thinking, business strategy and knowledge management (KM) in organizations? What are the limitations of a pure rational approach to knowledge strategy in turbulent environments and under uncertainty? and What approaches can be consequently proposed to formulate knowledge strategies?

Findings

The study provides a critical reading of the current literature. Also, it proposes an integrated approach that sees planning as a continuous effort of learning and adaptation to needs and opportunities that dynamically emerge from daily practices.

Research limitations/implications

The proposed framework can inspire a new research agenda to detect how knowledge strategies are planned in companies and how they are continuously adapted on the basis of a dialog between rational contributions and perceptions of reality, practical views, intuitions and emotions. This can also inspire a new agenda for company strategists and KM professionals.

Originality/value

In the literature, little attention has been devoted to knowledge strategy planning. The paper contributes to fill this gap and proposes a new way to see knowledge strategy as an integration of rational thinking and dynamic learning.
Managing extracted knowledge from big social media data for business decision making
Authors: He Wu , Wang Feng-Kwei , Akula Vasudeva
Published: April 2017

Purpose

This paper aims to propose a knowledge management (KM) framework for leveraging big social media data to help interested organizations integrate Big Data technology, social media and KM systems to store, share and leverage their social media data. Specifically, this research focuses on extracting valuable knowledge on social media by contextually comparing social media knowledge among competitors.

Design/methodology/approach

A case study was conducted to analyze nearly one million Twitter messages associated with five large companies in the retail industry (Costco, Walmart, Kmart, Kohl’s and The Home Depot) to extract and generate new knowledge and to derive business decisions from big social media data.

Findings

This case study confirms that this proposed framework is sensible and useful in terms of integrating Big Data technology, social media and KM in a cohesive way to design a KM system and its process. Extracted knowledge is presented visually in a variety of ways to discover business intelligence.

Originality/value

Practical guidance for integrating Big Data, social media and KM is scarce. This proposed framework is a pioneering effort in using Big Data technologies to extract valuable knowledge on social media and discover business intelligence by contextually comparing social media knowledge among competitors.
Diffusion of integrated reporting in an emerging South Asian (SAARC) nation
Authors: Gunarathne Nuwan , Senaratne Samanthi
Published: April 2017

Purpose

This paper aims to examine how and why integrated reporting (IR) as a managerial technology is diffused in Sri Lanka, an emerging South Asian (South Asian Association for Regional Cooperation) nation, from an expansion diffusion perspective.

Design/methodology/approach

The study followed two analytical steps. First, the adopter groups of IR of the country’s stock exchange were identified based on their annual reports. Second, the key stakeholders (both internal and external) in the process of IR diffusion in the country were interviewed. Thereafter, a content analysis of these semi-structured interviews was carried out based on the demand-pull and supply-push sides of the diffusion theory of innovation.

Findings

The temporal trend of IR suggests that the country is currently in the diffusion stage with many first time adopters are likely to join the bandwagon of IR. In the primary stage, its early adoption has been driven by the efficient-choice perspective. However, in the diffusion stage, most of the adopters are driven by fashion setting, which is mainly attributable to the active propagators in the supply side of IR diffusion. IR has been mainly a transition evolving through the incremental changes in sustainability reporting. Many firms have not internalized the IR principles with the danger of IR becoming a mere reporting mechanism.

Originality/value

The application of both demand-pull and supply-push sides of the diffusion theory of innovation is still limited, particularly in the case of new reporting mechanisms. The study provides new insights into how these two forces contribute to creating a “practice-reporting portrayal gap” in IR.
Corporate governance and risk reporting: Indian evidence
Authors: Saggar Ridhima , Singh Balwinder
Published: April 2017

Purpose

This study aims to measure the extent of voluntary risk disclosure and examine the relationship between corporate governance firm level quality in the form of board characteristics and ownership concentration’s impact on risk disclosure in the annual reports of Indian listed companies.

Design/methodology/approach

The method adopted in this study is automated content analysis, which is applied to a sample of 100 listed Indian non-financial companies to find out the extent of risk disclosure. Further, multiple linear regressions have been applied to find out the relationship between corporate governance firm level quality in the form of board characteristics, ownership concentration and risk disclosure.

Findings

The findings reveal that the total number of positive risk keywords surpasses negative risk keywords disclosure. The corporate governance mainsprings, namely, board size and gender diversity have a positively significant effect on risk disclosure, whereas ownership concentration in the hands of the largest shareholder insignificantly affects risk disclosure, but identity of the largest shareholder having ownership concentration negatively affects disclosure of risk information in the case of Indian promoter body corporate, foreign promoter body corporate and non-institutions in comparison to family ownership.

Research limitations/implications

This study relied on a set of 39 risk keywords for measuring the extent of risk disclosure. Further, it uses a sample of 100 companies to examine the effect of corporate governance on risk disclosure at one point of time. However, a longitudinal study can help in understanding risk disclosure adopted by Indian listed companies in a better manner.

Practical implications

The findings have implications for regulatory bodies such as the Securities and Exchange Board of India, which needs to strengthen corporate governance norms with respect to board characteristics and keep a check on ownership concentration for improving risk disclosure by companies.

Originality/value

To best of the authors’ knowledge, this study is a preliminary attempt linking two research lines in India, that is, corporate risk disclosure and corporate governance quality in the form of board characteristics and ownership concentration. The study identifies corporate governance firm level qualities which lead to divulgation of risk information by the companies pointing towards strengthening of regulatory regime in the country for improved corporate governance regulations adopted by listed companies.