bluuebunny/crossref_metadata_2025 huggingface dataset:
Community-Based Home Health Programs and Chronic Disease
Authors: Vandiver Tonya , Anderson Tracy , Boston Brittani , Bowers Cynthia , Hall Norma
Published: November 2017

Purpose of Study:

This article reviewed and evaluated literature on the various community-based home health programs and their effectiveness at preventing hospital admissions in adults. The research question addressed is as follows: Do community-based home health programs decrease hospital admissions in adult patients with chronic disease?

Primary Practice Setting:

The primary practice setting evaluated in this review of the literature was community-based home health programs.

Methodology and Sample:

In this literature review, a seven-step review method was utilized to assess the evidence. Three electronic databases were used to conduct the initial search inquiry: CINAHL (Cumulative Index to Nursing and Allied Health Literature) Plus with Full Text, Medline, and PsycINFO. The search parameters include research from 2006 through 2016, English-language studies, and research published in peer-reviewed journals. The following search terms were used in multiple combinations: community-based health programs, chronic disease, and home. The primary sample population assessed was older adults with chronic disease.

Results:

The research identified three common themes that influenced quality-of-life outcomes and health care utilization in participants of a community-based home health program. These themes were encouragement and emotional support, home visits, and multidisciplinary coordination of care. Additional concepts of depression and educational reinforcement were also noted.

Implications for Case Management Practice:

This literature review indicates that community-based home health programs are a viable solution to providing cost-effective health care to the adult population with chronic diseases. Community-based home health programs have been shown to have a positive impact on the quality of life and a decrease in health care utilization, including emergency department and primary care practitioner visits and hospital admissions, for adults with chronic disease.
Patient and Nurse Experiences in a Rural Chronic Disease Management Program
Authors: Davisson Erica A. , Swanson Elizabeth A.
Published: November 2017

Purpose:

Rural status confounds chronic disease self-management. The purpose of this qualitative, descriptive study was to evaluate the nurse-led “Living Well” chronic disease management program reporting patient recruitment and retention issues since program initiation in 2013. The Chronic Care Model (CCM) was the guiding framework used to reinforce that interdisciplinary teams must have productive patient interactions for their program(s) to be sustainable.

Primary Practice Setting:

A rural, Midwest county clinic's chronic disease management program.

Methodology and Sample:

Observations, interviews, and within- and across-case coding were used. Patients' responses were analyzed to identify (1) reasons for recruitment and retention problems and (2) program elements that were viewed as successful or needing improvement. A convenience sample of 6 rural, English-speaking adults (65 years or older, with no severe cognitive impairment) with at least one chronic condition was recruited and interviewed.

Results:

Themes emerged related to nurse knowledge, availability, and value; peer support; overcoming barriers; adherence enhancement; and family/friends' involvement. Patients reported engagement in self-management activities because of program elements such as support groups and productive nurse–patient interactions. Interdisciplinary communication, commitment, and patient referral processes were identified as reasons for recruitment and retention issues.

Implications for Case Management Practice:

Findings substantiated that certain elements must be present and improved upon for future rural programs to be successful. Interdisciplinary communication may need to be improved to address recruitment and retention problems. It was clear from patient interviews that the nurse coordinators played a major role in patients' self-management adherence and overall satisfaction with the program. This is important to case management because results revealed the need for programs of this nature that incorporate the vital role of nurse coordinators and align with the CCM value of providing a supportive community health care resource for patients with chronic disease.
Working With Transgender Individuals in Case Management Practice
Authors: Garrett Michael B.
Published: November 2017

Purpose and Objectives:

To understand key concepts, effective communication strategies, and a broad range of health and human services for transgender persons in order to enhance the effectiveness of case management services.

Primary Practice Settings:

Individuals who identify as transgender or gender variant.

Findings/Conclusions:

Transgender persons have faced historic challenges in accessing health care services that are respectful, sensitive, and affirming. Case managers have the opportunity to serve as an advocate for these individuals by understanding effective communication strategies as well as medical, behavioral, and social services to support transgender persons through the transition process.

Implications for Case Management Practice:

To be effective with transgender persons, case managers need to know key terms and communications strategies, medical treatment options, behavioral health issues that need to be evaluated and addressed, and social services available to transgender persons.
Case Managers on the Front Lines of Ethical Dilemmas
Authors: Sortedahl Charlotte , Mottern Nina , Campagna Vivian
Published: November 2017

Purpose:

The purpose of this article is to examine how case managers are routinely confronted by ethical dilemmas within a fragmented health care system and given the reality of financial pressures that influence life-changing decisions. The Code of Professional Conduct for Case Managers (Code), published by the Commission for Case Manager Certification, acknowledges “case managers may often confront ethical dilemmas” (Code 1996, Rev. 2015).

Primary Practice Settings:

The Code and expectations that professional case managers, particularly those who are board certified, will uphold ethical and legal practice apply to case managers in every practice setting across the full continuum of health care.

Implementations for Case Management Practice:

This discussion acknowledges the ethical dilemmas that case managers routinely confront, which empowers them to seek support, guidance, and resources to support ethical practice. In addition, the article seeks to raise awareness of the effects of burnout and moral distress on case managers and others with whom they work closely on interdisciplinary teams.
Ethical Resources
Authors: Powell Suzanne K.
Published: November 2017

There is no way to underestimate the importance of the countless ways that ethics impacts case managers and the patients we serve. In fact, solid ethical decisions are such an integral part of case management practice that the Commission for Case Manager Certification has increased its number of continuing education units required for recertification. Discussion and resources are outlined in the Editorial.
Potential of Noncontrast Magnetic Resonance Imaging With Diffusion-Weighted Imaging in Characterization of Breast Lesions
Authors: Baltzer Pascal A.T. , Bickel Hubert , Spick Claudio , Wengert Georg , Woitek Ramona , Kapetas Panagiotis , Clauser Paola , Helbich Thomas H. , Pinker Katja
Published: November 2017

Objectives

The aim of this study was to assess the potential of noncontrast magnetic resonance imaging (NC-MRI) with diffusion-weighted imaging (DWI) in characterization of breast lesions in comparison to dynamic contrast-enhanced MRI (DCE-MRI) at 3 T.

Materials and Methods

Consecutive patients with conventional imaging (mammography, ultrasound) BI-RADS 4/5 findings were included in this institutional review board–approved single-center study. All underwent 3 T breast MRI including readout-segmented DWI, DCE, and T2-weighted sequences. Final diagnosis was defined by histopathology or follow-up (>24 months). Two experienced radiologists (R1, R2) independently assigned lesion conspicuity (0 = minimal to 3 = excellent) and BI-RADS scores to NC-MRI (readout-segmented DWI including apparent diffusion coefficient maps) and DCE-MRI (DCE and T2-weighted). Receiver operating characteristics, κ statistics, and visual grading characteristics analysis were applied.

Results

Sixty-seven malignant and 56 benign lesions were identified in 113 patients (mean age, 54 ± 14 years). Areas under the receiver operating characteristics curves were similar: DCE-MRI: 0.901 (R1), 0.905 (R2); NC-MRI: 0.882 (R1), 0.854 (R2); P > 0.05, respectively. The κ agreement was 0.968 (DCE-MRI) and 0.893 (NC-MRI). Visual grading characteristics analysis revealed superior lesion conspicuity by DCE-MRI (0.661, P < 0.001).

Conclusions

Diagnostic performance and interreader agreement of both NC-MRI and DCE-MRI is high, indicating a potential use of NC-MRI as an alternative to DCE-MRI. However, inferior lesion conspicuity and lower interreader agreement of NC-MRI need to be considered.
Predictability of bee community composition after floral removals differs by floral trait group
Authors: Urban-Mead Katherine R.
Published: November 2017

Plant–bee visitor communities are complex networks. While studies show that deleting nodes alters network topology, predicting these changes in the field remains difficult. Here, a simple trait-based approach is tested for predicting bee community composition following disturbance. I selected six fields with mixed cover of flower species with shallow (open) and deep (tube) nectar access, and removed all flowers or flower heads of species of each trait in different plots paired with controls, then observed bee foraging and composition. I compared the bee community in each manipulated plot with bees on the same flower species in control plots. The bee morphospecies composition in manipulations with only tube flowers remaining was the same as that in the control plots, while the bee morphospecies on only open flowers were dissimilar from those in control plots. However, the proportion of short- and long-tongued bees on focal flowers did not differ between control and manipulated plots for either manipulation. So, bees within some functional groups are more strongly linked to their floral trait partners than others. And, it may be more fruitful to describe expected bee community compositions in terms of relative proportions of relevant ecological traits than species, particularly in species-diverse communities.
Structural biomechanics determine spectral purity of bush-cricket calls
Authors: Chivers Benedict D. , Jonsson Thorin , Soulsbury Carl D. , Montealegre-Z Fernando
Published: November 2017

Bush-crickets (Orthoptera: Tettigoniidae) generate sound using tegminal stridulation. Signalling effectiveness is affected by the widely varying acoustic parameters of temporal pattern, frequency and spectral purity (tonality). During stridulation, frequency multiplication occurs as a scraper on one wing scrapes across a file of sclerotized teeth on the other. The frequency with which these tooth–scraper interactions occur, along with radiating wing cell resonant properties, dictates both frequency and tonality in the call. Bush-cricket species produce calls ranging from resonant, tonal calls through to non-resonant, broadband signals. The differences are believed to result from differences in file tooth arrangement and wing radiators, but a systematic test of the structural causes of broadband or tonal calls is lacking. Using phylogenetically controlled structural equation models, we show that parameters of file tooth density and file length are the best-fitting predictors of tonality across 40 bush-cricket species. Features of file morphology constrain the production of spectrally pure signals, but systematic distribution of teeth alone does not explain pure-tone sound production in this family.
Studying placebo effects in model organisms will help us understand them in humans
Authors: Harvey Simon C. , Beedie Chris J.
Published: November 2017

The placebo effect is widely recognized but important questions remain, for example whether the capacity to respond to a placebo is an evolved, and potentially ubiquitous trait, or an unpredictable side effect of another evolved process. Understanding this will determine the degree to which the physiology underlying placebo effects might be manipulated or harnessed to optimize medical treatments. We argue that placebo effects are cases of phenotypic plasticity where once predictable cues are now unpredictable. Importantly, this explains why placebo-like effects are observed in less complex organisms such as worms and flies. Further, this indicates that such species present significant opportunities to test hypotheses that would be ethically or pragmatically impossible in humans. This paradigm also suggests that data informative of human placebo effects pre-exist in studies of model organisms.
Associations between imprinted gene expression in the placenta, human fetal growth and preeclampsia
Authors: Christians Julian K. , Leavey Katherine , Cox Brian J.
Published: November 2017

Genomic imprinting is essential for normal placental and fetal growth. One theory to explain the evolution of imprinting is the kinship theory (KT), which predicts that genes that are paternally expressed will promote fetal growth, whereas maternally expressed genes will suppress growth. We investigated the expression of imprinted genes using microarray measurements of expression in term placentae. Correlations between birthweight and the expression levels of imprinted genes were more significant than for non-imprinted genes, but did not tend to be positive for paternally expressed genes and negative for maternally expressed genes. Imprinted genes were more dysregulated in preeclampsia (a disorder associated with placental insufficiency) than randomly selected genes, and we observed an excess of patterns of dysregulation in preeclampsia that would be expected to reduce nutrient allocation to the fetus, given the predictions of the KT. However, we found no evidence of coordinated regulation among these imprinted genes. A few imprinted genes have previously been shown to be associated with fetal growth and preeclampsia, and our results indicate that this is true for a broader set of imprinted genes.
Structural similarities in the CPC clip motif explain peptide-binding promiscuity between glycosaminoglycans and lipopolysaccharides
Authors: Pulido David , Rebollido-Rios Rocío , Valle Javier , Andreu David , Boix Ester , Torrent Marc
Published: November 2017

Lipopolysaccharides (LPSs) and glycosaminoglycans (GAGs) are polymeric structures containing negatively charged disaccharide units that bind to specialized proteins and peptides in the human body and control fundamental processes such as inflammation and coagulation. Surprisingly, some proteins can bind both LPSs and GAGs with high affinity, suggesting that a cross-communication between these two pathways can occur. Here, we explore whether GAGs and LPSs can share common binding sites in proteins and what are the structural determinants of this binding. We found that the LPS-binding peptide YI12WF, derived from protein FhuA, can bind both heparin andE. coliLPS with high affinity. Most interestingly, mutations decreasing heparin binding in the peptide also reduce LPS affinity. We show that such mutations involve the CPC clip motif in the peptide, a small three-dimensional signature required for heparin binding. Overall, we conclude that negatively charged polysaccharide-containing polymers such as GAGs and LPSs can compete for similar binding sites in proteins, and that the CPC clip motif is essential to bind both ligands. Our results provide a structural framework to explain why these polymers can cross-interact with the same proteins and peptides and thus contribute to the regulation of apparently unrelated processes in the body.
Non-thermal-plasma-activated de-NO
x
catalysis
Authors: Gholami Rahman , Stere Cristina E. , Goguet Alexandre , Hardacre Christopher
Published: November 2017

The combination of non-thermal plasma (NTP) with catalyst systems as an alternative technology to remove NO
x
emissions in the exhaust of lean-burn stationary and mobile sources is reviewed. Several factors, such as low exhaust gas temperatures (below 300°C), low selectivity to N
2
and the presence of impurities, make current thermally activated technologies inefficient. Various hybrid plasma–catalyst systems have been examined and shown to have a synergistic effect on de-NO
x
efficiency when compared with NTP or catalyst-alone systems. The NTP is believed to form oxygenated species, such as aldehydes and nitrogen-containing organic species, and to convert NO to NO
2
, which improves the reduction efficiency of N
2
during hydrocarbon-selective catalytic reduction reactions. The NTP has been used as a pretreatment to convert NO to its higher oxidation states such as NO
2
to improve NO
x
reduction efficiency in the subsequent processes, e.g. NH
3
-selective catalytic reduction. It has been applied to the lean phase of the NO
x
storage to improve the adsorption capacity of the catalyst by conversion of NO to NO
2
. Alternatively, a catalyst with high adsorption capacity is chosen and the NTP is applied to the rich phase to improve the reduction activity of the catalyst at low temperature.

This article is part of a discussion meeting issue ‘Providing sustainable catalytic solutions for a rapidly changing world’.
Partial oxidation of alkanes by dioxiranes formed
in situ
at low temperature
Authors: Yacob Sara , Caulfield Michael J. , Barckholtz Timothy A.
Published: November 2017

Partial oxidation catalysts capable of efficiently operating at low temperatures may limit the over-oxidation of alkane substrates and thereby improve selectivity. This work focuses on examining alkane oxidation using completely metal-free organocatalysts, dioxiranes. The dioxiranes employed here are synthesized by oxidation of a ketone using a terminal oxidant, such as hydrogen peroxide. Our work generates the dioxirane
in situ
, so that the process can be catalytic with respect to the ketone. To date, we have demonstrated selective partial oxidation of adamantane using ketone catalysts resulting in yields upwards of 60% towards 1-adamantanol with greater than 99% selectivity. Furthermore, we have demonstrated that changing the electrophilic character of the ketone R groups to contain more electron-donating ligands facilitates the dioxirane ring formation and improves overall oxidation yields. Isotopic labelling studies using H
2
18
O
2
show the preferential incorporation of an
18
O label into the parent ketone, providing evidence for a dioxirane intermediate formed
in situ
. The isotopic labelling studies, along with solvent effect studies, suggest the formation of peracetic acid as a reactive intermediate.

This article is part of a discussion meeting issue ‘Providing sustainable catalytic solutions for a rapidly changing world’.
TiO
2
and ZrO
2
in biomass conversion: why catalyst reduction helps
Authors: Tosoni Sergio , Chen Hsin-Yi Tiffany , Ruiz Puigdollers Antonio , Pacchioni Gianfranco
Published: November 2017

Biomass refers to plant-based materials that are not used for food or feed. As an energy source, lignocellulosic biomass (lignin, cellulose and hemicellulose) can be converted into various forms of biofuel using thermal, chemical and biochemical methods. Chemical conversion implies the use of solid catalysts, usually oxide materials. In this context, reducible oxides are considered to be more active than non-reducible oxides. But why? Using density functional theory DFT + U calculations with the inclusion of dispersion forces, we describe the properties of anatase TiO
2
, a reducible oxide, and tetragonal ZrO
2
, a non-reducible oxide, the (101) surfaces in this context. In particular, we focus on the role of surface reduction, either by direct creation of oxygen vacancies via O
2
desorption, or by treatment in hydrogen. We show that the presence of reduced centres on the surface of titania or zirconia (either Ti
3+
or Zr
3+
ions, or oxygen vacancies) results in lower barriers and more stable intermediates in two key reactions in biomass catalytic conversion: ketonization of acetic acid (studied on ZrO
2
) and deoxygenation of phenol (studied on TiO
2
). We discuss the role of Ru nanoparticles in these processes, and in particular in favouring H
2
dissociation and hydrogen spillover, which results in hydroxylated surfaces. We suggest that H
2
O desorption from the hydroxylated surfaces may be a relevant mechanism for the regeneration of oxygen vacancies, in particular on low-coordinated sites of oxide nanoparticles. Finally, we discuss the role of nanostructuring in favouring oxide reduction, by discussing the properties of ZrO
2
nanoparticles of diameter of about 2 nm.

This article is part of a discussion meeting issue ‘Providing sustainable catalytic solutions for a rapidly changing world’.
Silver–palladium catalysts for the direct synthesis of hydrogen peroxide
Authors: Khan Zainab , Dummer Nicholas F. , Edwards Jennifer K.
Published: November 2017

A series of bimetallic silver–palladium catalysts supported on titania were prepared by wet impregnation and assessed for the direct synthesis of hydrogen peroxide, and its subsequent side reactions. The addition of silver to a palladium catalyst was found to significantly decrease hydrogen peroxide productivity and hydrogenation, but crucially increase the rate of decomposition. The decomposition product, which is predominantly hydroxyl radicals, can be used to decrease bacterial colonies. The interaction between silver and palladium was characterized using scanning electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy (XPS) and temperature programmed reduction (TPR). The results of the TPR and XPS indicated the formation of a silver–palladium alloy. The optimal 1% Ag–4% Pd/TiO
2
bimetallic catalyst was able to produce approximately 200 ppm of H
2
O
2
in 30 min. The findings demonstrate that AgPd/TiO
2
catalysts are active for the synthesis of hydrogen peroxide and its subsequent decomposition to reactive oxygen species. The catalysts are promising for use in wastewater treatment as they combine the disinfectant properties of silver, hydrogen peroxide production and subsequent decomposition.

This article is part of a discussion meeting issue ‘Providing sustainable catalytic solutions for a rapidly changing world’.
Metal-promoted titania photocatalysis for destruction of nitrates and organics from aqueous environments
Authors: Anderson James A.
Published: November 2017

This review article provides an overview of activities in the rapidly developing field of water purification via photocatalytic methods and focuses on the removal of nitrate ions with simultaneous removal of the hole scavenger. Many of the issues associated with provision of potable water in the developing world may be resolved by the use of simple physical methodologies such as filtration. However, many of the issues associated with water purity in the developed world involve complex, stable molecules present at low concentrations that are nonetheless capable of producing toxic effects in plants and animals and that require more demanding removal technologies. Photocatalytic methods can be operated remotely and often show minimal production of undesired side products. Titania alone shows limitations, not only in terms of the slow rate of photoreduction of nitrate but also in terms of selectivity and the need to employ radiation in the UV region due to the magnitude of the band gap. Key challenges may be defined as: reducing the band gap/increasing absorption in the visible region, enhancing the adsorption capacity/access to the surface sites and reducing the rate of hole/electron recombination. The present article will focus on the use of titania-based materials that involve metal co-catalysts for nitrate reduction.

This article is part of a discussion meeting issue ‘Providing sustainable catalytic solutions for a rapidly changing world’.
The fourth wave of biocatalysis is approaching
Authors: Bornscheuer Uwe T.
Published: November 2017

Biocatalysis has undergone a tremendous development in the past few years. A plethora of methods enable the rather rapid tailored-design of an enzyme for a targeted reaction such as asymmetric synthesis of a chiral building block by the combination of information from sequence and structure databases with modern molecular biology methods and high-throughput screening tools. Moreover, novel non-natural reactions could be implemented into protein scaffolds and new enzyme classes are emerging, both broadening the repertoire of reactions now available for organic synthesis. Furthermore, impressive examples of metabolic engineering—the combination of several newly introduced reaction steps in a microbial host—have been developed, paving the way for large-scale processes for both pharmaceuticals and bulk chemicals. This contribution highlights recent developments in this area and points out future challenges.

This article is part of a discussion meeting issue ‘Providing sustainable catalytic solutions for a rapidly changing world’.
Reactivity of CO
2
on the surfaces of magnetite (Fe
3
O
4
), greigite (Fe
3
S
4
) and mackinawite (FeS)
Authors: Santos-Carballal David , Roldan Alberto , Dzade Nelson Y. , de Leeuw Nora H.
Published: November 2017

The growing environmental, industrial and commercial interests in understanding the processes of carbon dioxide (CO
2
) capture and conversion have led us to simulate, by means of density functional theory calculations, the application of different iron oxide and sulfide minerals to capture, activate and catalytically dissociate this molecule. We have chosen the {001} and {111} surfaces of the spinel-structured magnetite (Fe
3
O
4
) and its isostructural sulfide counterpart greigite (Fe
3
S
4
), which are both materials with the Fe cations in the 2+/3+ mixed valence state, as well as mackinawite (tetragonal FeS), in which all iron ions are in the ferrous oxidation state. This selection of iron-bearing compounds provides us with understanding of the effect of the composition, stoichiometry, structure and oxidation state on the catalytic activation of CO
2
. The largest adsorption energies are released for the interaction with the Fe
3
O
4
surfaces, which also corresponds to the biggest conformational changes of the CO
2
molecule. Our results suggest that the Fe
3
S
4
surfaces are unable to activate the CO
2
molecule, while a major charge transfer takes place on FeS{111}, effectively activating the CO
2
molecule. The thermodynamic and kinetic profiles for the catalytic dissociation of CO
2
into CO and O show that this process is feasible only on the FeS{111} surface. The findings reported here show that these minerals show promise for future CO
2
capture and conversion technologies, ensuring a sustainable future for society.

This article is part of a discussion meeting issue ‘Providing sustainable catalytic solutions for a rapidly changing world’.
‘Switch’ catalysis: from monomer mixtures to sequence-controlled block copolymers
Authors: Stößer T. , Chen T. T. D. , Zhu Y. , Williams C. K.
Published: November 2017

A ‘Switch’ catalysis method is reviewed whereby a single catalyst is switched between ring-opening polymerization and ring-opening copolymerization cycles. It allows the efficient synthesis of block copolymers from mixtures of lactones, epoxides, anhydrides and carbon dioxide. In order to use and further develop such ‘Switch’ catalysis, it is important to understand how to monitor the catalysis and characterize the product block copolymers. Here, a step-by-step guide to both the catalysis and the identification of block copolymers is presented.

This article is part of a discussion meeting issue ‘Providing sustainable catalytic solutions for a rapidly changing world’.
Providing sustainable catalytic solutions for a rapidly changing world: a summary and recommendations for urgent future action
Authors: Thomas John Meurig
Published: November 2017

In addition to summarizing the main thrusts of each paper presented at this Discussion, other urgent issues involving the role (and characterization) of new catalysts for eliminating oxides of nitrogen, for using CO2liberated from steel mills, for fuel cells and the need for rapid decarbonization of fossil fuels are outlined.

This article is part of a discussion meeting issue ‘Providing sustainable catalytic solutions for a rapidly changing world’.
Two-Photon Imaging of Striatum Demonstrates Distinct Functions for Striosomes and Matrix in Reinforcement Learning
Authors: Bloem Bernard , Huda Rafiq , Sur Mriganka , Graybiel Ann M.
Published: November 2017

Despite the discovery of striosomes several decades ago, technical difficulties have hampered the study of their functions. Here we used 2-photon calcium imaging in neuronal birthdate-labeled Mash1-CreER mice to image simultaneously the activity of striosomal and matrix neuronsin vivo. We report that with this method we can visually identify circumscribed zones of neuropil that correspond to striosomes as verified in immunostained sections. We find that striosomal neurons, relative to matrix neurons, preferentially encode reward-predicting cues, and that their activity contains more information about expected outcome. These characteristics emerge during training and further strengthen during overtraining. Both striatal compartments are active similarly after reward delivery, firing at neuron-specific times during or after consummatory licking. Finally, we find that immediate reward history strongly modulates neuronal activation in the next trial, especially in matrix neurons. These results suggest that striosomes and matrix have distinct functions in relation to reinforcement learning.
A genome-wide association study for host resistance to Ostreid Herpesvirus in Pacific oysters (Crassostrea gigas)
Authors: Gutierrez Alejandro P. , Bearf Tim P. , Hooped Chantelle , Stentort Craig A. , Sanders Matthew B. , Paley Richard K. , Rastas Pasi , Bryrom Michaela , Matika Oswald , Houston Ross D.
Published: November 2017

Ostreid herpesvirus (OsHV) can cause mass mortality events in Pacific oyster aquaculture. While various factors impact on the severity of outbreaks, it is clear that genetic resistance of the host is an important determinant of mortality levels. This raises the possibility of selective breeding strategies to improve the genetic resistance of farmed oyster stocks, thereby contributing to disease control. Traditional selective breeding can be augmented by use of genetic markers, either via marker-assisted or genomic selection. The aim of the current study was to investigate the genetic architecture of resistance to OsHV in Pacific oyster, to identify genomic regions containing putative resistance genes, and to inform the use of genomics to enhance efforts to breed for resistance. To achieve this, a population of ~1,000 juvenile oysters were experimentally challenged with a virulent form of OsHV, with samples taken from mortalities and survivors for genotyping and qPCR measurement of viral load. The samples were genotyped using a recently-developed SNP array, and the genotype data were used to reconstruct the pedigree. Using these pedigree and genotype data, the first high density linkage map was constructed for Pacific oyster, containing 20,353 SNPs mapped to the ten pairs of chromosomes. Genetic parameters for resistance to OsHV were estimated, indicating a significant but low heritability for the binary trait of survival and also for viral load measures (h2 0.12 – 0.25). A genome-wide association study highlighted a region of linkage group 6 containing a significant QTL affecting host resistance. These results are an important step towards identification of genes underlying resistance to OsHV in oyster, and a step towards applying genomic data to enhance selective breeding for disease resistance in oyster aquaculture.
From image formation to image representation: the human visual system preserves the hierarchy of 2-dimensional pattern regularity
Authors: Kohler Peter J. , Norcia Anthony M.
Published: November 2017

Symmetries are present at many scales in images of natural scenes, due to a complex interplay of physical forces that govern pattern formation in nature. The importance of symmetry for visual perception has been known at least since the gestalt movement of the early 20thcentury. Since then, symmetry has been shown to contribute to the perception of shapes[1, 2] scenes[3] and surface properties[4], as well as the social process of mate selection[5]. In the two spatial dimensions relevant for images, the four fundamental symmetries, reflection, rotation, translation and glide reflection, can be combined in 17 distinct ways, the “wallpaper” groups[6–8]. The 17 wallpaper obey a hierarchy of complexity, determined by mathematical group theory, where simpler groups are subgroups of more complex ones[9]. Here we use Steady-State Visual Evoked Potentials (SSVEPs) to measure responses to the complete set of wallpaper groups, and present a complete description of the neural basis of symmetry. We find that activity in human visual cortex is remarkably consistent with the hierarchical relationships between the wallpaper groups. Specifically, the amplitudes of symmetry-specific responses in individual participants (n=25) preserve these relationships at an above-chance level in 88.3% (53 out of 60) of cases. Visual cortex thus encodes all the fundamental symmetries using a representational structure that closely approximates the subgroup relationships from group theory. Given that most participants had no knowledge of group theory, the ordered structure of visual responses to wallpaper groups is likely learned implicitly from regularities in the visual environment.
Effects of increased N and P availability on biomass allocation and root carbohydrate reserves differ between N-fixing and non-N-fixing savanna tree seedlings
Authors: Varma Varan , Catherin Arockia M , Sankaran Mahesh
Published: November 2017

In mixed tree-grass ecosystems, tree recruitment is limited by demographic bottlenecks to seedling establishment arising from inter- and intra-life form competition, and disturbances such as fire. Enhanced nutrient availability resulting from anthropogenic nitrogen (N) and phosphorus (P) deposition can alter the nature of these bottlenecks by changing seedling growth and biomass allocation patterns, and lead to longer-term shifts in tree community composition if different plant functional groups respond differently to increased nutrient availability. However, the extent to which tree functional types characteristic of savannas differ in their responses to increased N and P availability remains unclear. We quantified differences in above- and belowground biomass, and root carbohydrate contents – parameters known to influence the ability of plants to compete, as well as survive and recover from fires – in seedlings of multiple N-fixing and non-N-fixing tree species characteristic of Indian savanna and dry-forest ecosystems to experimental N and P additions. N-fixers in our study were co-limited by N and P availability, while non-N-fixers were N limited. Although both functional groups increased biomass production following fertilisation, non-N-fixers were more responsive and showed greater relative increases in biomass with fertilisation than N-fixers. N-fixers had greater baseline investment in belowground resources and root carbohydrate stocks, and while fertilisation reduced root:shoot ratios in both functional groups, root carbohydrate content only reduced with fertilisation in non-N-fixers. Our results indicate that, even within a given system, plants belonging to different functional groups can be limited by, and respond differentially to, different nutrients, suggesting that long-term consequences of nutrient deposition are likely to vary across savannas contingent on the relative amounts of N and P being deposited in sites.
Cell-Type Specific Interrogation of CeADrd2Neurons to Identify Targets for Pharmacological Modulation of Fear Extinction
Authors: McCullough Kenneth M. , Daskalakis Nikolaos P. , Gafford Georgette , Morrison Filomene G. , Ressler Kerry J.
Published: November 2017

Behavioral and molecular characterization of cell-type specific populations governing fear learning and behavior is a promising avenue for the rational identification of potential therapeutics for fear-related disorders. Examining cell-type specific changes in neuronal translation following fear learning allows for targeted pharmacological intervention during fear extinction learning, mirroring possible treatment strategies in humans. Here we identify the central amygdala (CeA)Drd2-expressing population as a novel fear-supporting neuronal population that is molecularly distinct from other, previously identified, fear-supporting CeA populations. Sequencing of actively translating transcripts ofDrd2neurons using translating ribosome affinity purification (TRAP) technology identifies mRNAs that are differentially regulated following fear learning. Differentially expressed transcripts with potentially targetable gene products includeNpy5r, Rxrg, Adora2a, Sst5r, Fgf3, Erbb4, Fkbp14, Dlk1, andSsh3. Direct pharmacological manipulation of NPY5R, RXR, and ADORA2A confirms the importance of this cell population and these cell-type specific receptors in fear behavior. Furthermore, these findings validate the use of functionally identified specific cell populations to predict novel pharmacological targets for the modulation of emotional learning.
A reassessment of DNA immunoprecipitation-based genomic profiling
Authors: Lentini Antonio , Lagerwall Cathrine , Vikingsson Svante , Mjoseng Heidi K. , Douvlataniotis Karolos , Vogt Hartmut , Green Henrik , Meehan Richard R. , Benson Mikael , Nestor Colm E.
Published: November 2017

DNA immunoprecipitation sequencing (DIP-seq) is a common enrichment method for profiling DNA modifications in mammalian genomes. However, DIP-seq profiles often exhibit significant variation between independent studies of the same genome and from profiles obtained by alternative methods. Here we show that these differences are primarily due to intrinsic affinity of IgG for short unmodified DNA repeats. This pervasive experimental error accounts for 50 – 99% of regions identified as ‘enriched’ for DNA modifications in DIP-seq data. Correction of this error profoundly alters DNA modification profiles for numerous cell types, including mouse embryonic stem cells, and subsequently reveals novel associations between DNA modifications, chromatin modifications and biological processes. We propose new methodological guidelines that minimize the impact of these errors on future DIP-seq experiments and allow new insights to be made from the wealth of existing DIP-seq data.
Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye
Authors: Sohn Jang-il , Nam Kyoungwoo , Hong Hyosun , Kim Jun-Mo , Lim Dajeong , Lee Kyung-Tai , Do Yoon Jung , Cho Chang Yeon , Kim Namshin , Chae Han-Ha , Nam Jin-Wu
Published: November 2017

Yeonsan Ogye (YO), an indigenous Korean chicken breed (gallus gallus domesticus), has entirely black external features and internal organs. In this study, the draft genome of YO was assembled using a hybrid de novo assembly method that takes advantage of high-depth Illumina short-reads (232.2X) and low-depth PacBio long-reads (11.5X). Although the contig and scaffold N50s (defined as the shortest contig or scaffold length at 50% of the entire assembly) of the initial de novo assembly were 53.6Kbp and 10.7Mbp, respectively, additional and pseudo-reference-assisted assemblies extended the assembly to 504.8Kbp for contig N50 (pseudo-contig) and 21.2Mbp for scaffold N50, which included 551 structural variations including the Fibromelanosis (FM) locus duplication, compared to galGal4 and 5. The completeness (97.6%) of the draft genome (Ogye_1) was evaluated with single copy orthologous genes using BUSCO, and found to be comparable to the current chicken reference genome (galGal5; 97.4%), which was assembled with a long read-only method, and superior to other avian genomes (92~93%), assembled with short read-only and hybrid methods. To comprehensively reconstruct transcriptome maps, RNA sequencing (RNA-seq) and representation bisulfite sequencing (RRBS) data were analyzed from twenty different tissues, including black tissues. The maps included 15,766 protein-coding and 6,900 long non-coding RNA genes, many of which were expressed in the tissue-specific manner, closely related with the DNA methylation pattern in the promoter regions.
Deep-coverage whole genome sequences and blood lipids among 16,324 individuals
Authors: Natarajan Pradeep , Peloso Gina M. , Zekavat S. Maryam , Montasser May , Ganna Andrea , Chaffin Mark , Khera Amit V. , Zhao Wei , Bloom Jonathan M. , Engreitz Jesse M. , Ernst Jason , O’Connell Jeffrey R. , Ruotsalainen Sanni E. , Alver Maris , Manichaikul Ani , Johnson W. Craig , Perry James A. , Poterba Timothy , Seed Cotton , Surakka Ida L. , Esko Tonu , Ripatti Samuli , Salomaa Veikko , Correa Adolfo , Vasan Ramachandran S. , Kellis Manolis , Neale Benjamin M. , Lander Eric S. , Abecassis Goncalo , Mitchell Braxton , Rich Stephen S. , Wilson James G. , Cupples L. Adrienne , Rotter Jerome I. ,   NHLBI TOPMed Lipids Working Group, Willer Cristen J. , Kathiresan Sekar
Published: November 2017

Deep-coverage whole genome sequencing at the population level is now feasible and offers potential advantages for locus discovery, particularly in the analysis rare mutations in non-coding regions. Here, we performed whole genome sequencing in 16,324 participants from four ancestries at mean depth >29X and analyzed correlations of genotypes with four quantitative traits – plasma levels of total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol, and triglycerides. We conducted a discovery analysis including common or rare variants in coding as well as non-coding regions and developed a framework to interpret genome sequence for dyslipidemia risk. Common variant association yielded loci previously described with the exception of a few variants not captured earlier by arrays or imputation. In coding sequence, rare variant association yielded known Mendelian dyslipidemia genes and, in non-coding sequence, we detected no rare variant association signals after application of four approaches to aggregate variants in non-coding regions. We developed a new, genome-wide polygenic score for LDL-C and observed that a high polygenic score conferred similar effect size to a monogenic mutation (~30 mg/dl higher LDL-C for each); however, among those with extremely high LDL-C, a high polygenic score was considerably more prevalent than a monogenic mutation (23% versus 2% of participants, respectively).
Alpha/beta power compresses time in sub-second temporal judgments
Authors: van Viegen Tara , Charest Ian , Jensen Ole , Mazaheri Ali
Published: November 2017

While the perception of time plays a crucial role in our day-to-day functioning, the underlying neural mechanism of time processing on short time scales (~1s) remains to be elucidated. Recently, the power of beta oscillations (~20 Hz) has been suggested to play an important role in temporal processing. However, the paradigms supporting this view have often had confounds of working memory, as well as motor preparation. In the current EEG study, we set out to investigate if power of oscillatory activity would be involved in time perception without an explicit working memory component or confound of a motor response. Participants indicated through a button press whether the time between a tone and a visual stimulus was 1 or 1.5s.Critically, we focused on the differences in oscillatory activity in the alpha (~10 Hz) and beta (~20 Hz) ranges preceding correct versus incorrect temporal judgments. Behaviourally, we found participants made more errors on the long (1.5s) than on the short (1s) interval. In addition, we found that participants were fastest to correctly respond to a long interval. The onset of the tone induced a suppression of alpha and beta activity over occipital and parietal electrodes. In the long estimation intervals, this suppression was greater for correct than incorrect estimations. Interestingly, alpha and beta suppression allowed us to predict whether participants would judge the long interval correctly. For the short interval trials we did not find a significant difference in alpha or beta band activity for the correct and incorrect judgments. Taken together, our behavioural and EEG results suggest a multifaceted role of alpha and beta activity in the temporal estimation of sub- and supra-second intervals, where power increases seem to lead to temporal compression. Higher alpha and beta power resulted in shorter temporal judgments for sub-second intervals.

Highlights

Temporal judgments without motor confounds were studied with EEG.

Alpha/beta activity differences for correct and incorrect temporal judgments.

Sub-second intervals were judged as short when alpha/beta power was higher.
Reassessing the Revolution’s Resolutions
Authors: van Heel Marin , Schatz Michael
Published: November 2017

We are currently facing an avalanche of cryo-EM (cryogenic Electron Microscopy) publications presenting beautiful structures at resolution levels of ~3Å: a true “resolution revolution” [Kühlbrandt, Science 343(2014)1443-1444]. Impressive as these results may be, a fundamental statistical error has persisted in the literature that affects the numerical resolution values for practically all published structures. The error goes back to a misinterpretation of basic statistics and pervades virtually all popular cryo-EM quality metrics. The resolution in cryo-EM is typically assessed by the Fourier Shell Correlation “FSC” [Harauz & van Heel: Optik73(1986)146-156] using a fixed threshold value of 0.143 (“FSC0.143”) [Rosenthal, Henderson, J. Mol. Biol.333(2003)721–745]. Using a simple model experiment we illustrate why this fixed threshold is flawed and we pinpoint the source of the resolution confusion. When two vectors are uncorrelated the expectation value of their inner-product is zero. That, however, does not imply that each individual inner-product of the vectors is zero (the vectors are not orthogonal). This error was introduced to electron microscopy in [Frank & Al-Ali, Nature256(1975)376-379] and has since proliferated into virtually all quality and resolution-related metrics in EM. One criterion not affected by this error is the information-based ½-bit FSC threshold [van Heel & Schatz: J. Struct. Biol.151(2005)250-262].