bluuebunny/crossref_metadata_2025 huggingface dataset:
Discovery of endogenous opioid systems: what it has meant for the clinician's understanding of pain and its treatment
Authors: Ballantyne Jane C. , Sullivan Mark D.
Published: August 2017

Before the discovery of the endogenous opioid system in the 1970s, opioids were understood only through the lens of opioid drug effects. Opium produced sleep, pain relief, and addiction. Once a variety of opioids had been extracted from opium, and still others synthesized chemically, it became clear that there must be endogenous receptors to explain differential drug effects. So, the search was on to identify the receptors, and subsequently their endogenous ligands. Even then, the consequential ways in which the endogenous opioid system influences the way we respond to the environment and survive took time to unravel. Today's understanding extends far beyond simply accepting pain relief and addiction as separate processes, to the realization that the endogenous opioid system achieves constant adjustments between punishment (pain) and reward in communicating areas of the brain previously thought to subserve separate functions. The system also plays a crucial role in socialization. Taken together, these 2 lines of research have led to new insights into why the endogenous opioid system is so important in terms of evolution, individual survival and day-to-day function, and how important it is to consider opioid medications within the context of these critical natural functions.
Occupational Therapy for Prosthetic Rehabilitation in Adults with Acquired Upper-Limb Loss: Body-Powered and Myoelectric Control Systems
Authors: Hermansson Liselotte N. , Turner Kristi
Published: August 2017

There is uncertainty as to whether occupational therapy differs between patients fitted with upper-limb prostheses using different control systems. The aim was to describe occupational therapy in upper-limb prosthetic rehabilitation and discuss potential differences in therapy between patients fitted with body-powered or myoelectric control systems. An overview and description of occupational therapy methods for upper-limb prosthetic rehabilitation is provided based on literature and clinical experience from two independent occupational therapists. Ultimately, the same phased approach to occupational therapy is used for both control systems for upper-limb rehabilitation, inclusive of the evaluation, the pre- and postsurgery phase; preprosthetic therapy; prosthetic training including both controls and functional use training; and discharge planning. The one thing that differed between control systems was the methods for evaluation and training of controls, based on the underlying nature of the systems. The time required to acquire functional use skills differed between control systems—users of myoelectric devices, especially at transhumeral level or higher, and patients with bilateral limb loss often need more time in therapy in order to learn to operate the terminal device and perform bilateral activities. Occupational therapy for prosthetic rehabilitation in adults with acquired upper-limb loss follows a basic structure that is common to several types of prosthetic control systems. Increased time is required for functional use training with myoelectric systems. The shortage of validated outcome measures restricts the ability to cover all aspects of upper-limb prosthesis use. Further studies to provide evidence in support of different training methods for upper-limb prosthesis users are warranted.
Sexual functioning in patients with chronic hepatitis C: a systematic review
Authors: Karaivazoglou Katerina , Tsermpini Evangelia-Eirini , Assimakopoulos Konstantinos , Triantos Christos
Published: August 2017

Chronic hepatitis C virus (HCV) infection is a systematic disease that affects several aspects of patients’ well-being, including physical, mental, social, and sexual quality of life. In recent years, there has been a growing body of literature focusing on HCV patients’ sexual health, providing evidence of clinically significant and enduring disturbances that disrupt everyday living, but commonly evade clinicians’ attention. Relevant studies are characterized by considerable methodological heterogeneity and their findings should be interpreted using a systematic and integrative approach. In this context, we performed a systematic literature review on the topic of HCV patients’ sexual functioning aiming at identifying high-quality investigations reporting scientifically sound and clinically useful data. We performed a thorough search of PudMed, ScienceDirect, and GoogleScholar according to the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) protocol. Twenty-five articles were included to the review, reporting data from over 5300 chronic HCV patients. Sexual dysfunction, predominantly in the domains of sexual desire, drive, and satisfaction, is commonly reported by HCV patients at rates ranging between 19 and 88%. The current review yielded three distinct patterns of sexual impairment, namely, precirrhotic sexual impairment, cirrhosis-induced sexual decline, and interferon-associated sexual difficulties. Our search yielded significant findings on the prevalence, the characteristics, and the determinants of HCV-associated sexual dysfunction. In addition, we detected several areas of scientific controversy and inadequate information, thus highlighting novel directions for future research.
In Their Own Words
Authors: Lewis Stephen P. , Bryant Lindsay A. , Schaefer Brittany M. , Grunberg Paul H.
Published: August 2017

Nonsuicidal self-injury (NSSI) is included in the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) as a condition warranting further study. Although potential advantages and disadvantages regarding this prospect have been documented, no study has examined the perspectives of those who self-injure. The goal of the current study was to give voice to these views. Seventy-six participants with an NSSI history completed quantitative and qualitative measures assessing perspectives about NSSI being included as a DSM disorder. Findings revealed mixed views overall. Thematic analysis of open-ended responses highlighted several unique advantages (i.e., enhanced understanding of NSSI, validation of the NSSI experience, facilitation of NSSI treatment, encouragement of NSSI help-seeking, reduction of NSSI stigma) and disadvantages (i.e., exacerbation of NSSI stigma, diminishment of underlying concerns). These findings speak to the need to consider the perceptions of those with lived NSSI experience; future directions and implications are discussed.
Implementing Quality and Safety Education for Nurses in Postclinical Conferences
Authors: Mohn-Brown Elaine
Published: August 2017

Postclinical conferences are an essential component of clinical nursing education. Numerous constraints including the rapidly changing clinical teaching environment and the struggle to secure clinical placements are affecting the use and purpose of postclinical conferences. This article describes 1 faculty member’s approach in designing and implementing a teaching strategy to integrate Quality and Safety Education for Nurses and concepts from a concept-based curriculum into a unique clinical seminar format.
Quality and Safety Education for Nurses Competencies in Doctor of Nursing Practice Education
Authors: Acton Cindy , Farus-Brown Susan , Alexander Catherine , Morrow Linda , Ossege Julianne , Tovar Elizabeth
Published: August 2017

Graduate level Quality and Safety Education for Nurses (QSEN) competencies were created to facilitate preparation of the Doctor of Nursing Practice (DNP) graduate to have an impact on health care system changes, advance nursing practice, and improve the health of populations. Although there is agreement that QSEN competencies are important to DNP education, little is known about implementation of the competencies. This article describes the importance of QSEN competencies in DNP education and provides exemplars of QSEN competencies in DNP education and practice.
Learning to Overcome Hierarchical Pressures to Achieve Safer Patient Care
Authors: Reeves Susan A. , Denault Deanna , Huntington Jonathan T. , Ogrinc Greg , Southard Douglas R. , Vebell Renee
Published: August 2017

To positively impact patient safety, the Institute of Medicine, as well as the Quality and Safety Education for Nurses initiative, has recommended clinician training in structured communication techniques. Such techniques are particularly useful in overcoming hierarchical barriers in health care settings. This article describes an interprofessional simulation program to teach structured communication techniques to preprofessional nursing, medical, and physician assistant students. The teaching and evaluation plans are described to aid replication.
Local Boards of Health Characteristics Influencing Support for Health Department Accreditation
Authors: Shah Gulzar H. , Sotnikov Sergey , Leep Carolyn J. , Ye Jiali , Corso Liza
Published: August 2017

Background:

Local boards of health (LBoHs) serve as the governance body for 71% of local health departments (LHDs).

Purpose:

To assess the impact of LBoH governance functions and other characteristics on the level of LBoH support of LHD accreditation.

Methods:

Data from 394 LHDs that participated in the 2015 Local Boards of Health Survey were used for computing summative scores for LBoHs for domains of taxonomy and performing logistic regression analyses in 2016.

Results:

Increased odds of an LBoH directing, encouraging, or supporting LHD accreditation activities were significantly associated with (a) a higher overall combined score measuring performance of governance functions and presence of other LBoH characteristics (adjusted odds ratio [AOR] = 1.05; P < .001); (b) a higher combined score for the Governance Functions subscale (AOR = 1.06; P < .01); (c) the “continuous improvement” governance function (AOR = 1.15; P < .001); and (d) characteristics and strengths such as board composition (eg, LBoH size, type of training, elected vs nonelected members), community engagement and input, and the absence of an elected official on the board (AOR = 1.14; P = .02).

Conclusions:

LBoHs are evenly split by thirds in their attention to Public Health Accreditation Board accreditation among the following categories: (a) encouraged or supported, (b) discussed but made no recommendations, and (c) did not discuss. This split might indicate that they are depending on the professional leadership of the LHD to make the decision or that there is a lack of awareness. The study findings have policy implications for both LBoHs and initiatives aimed at strengthening efforts to promote LHD accreditation.
Never Quit Trying: Reengaging Tobacco Users in Statewide Cessation Services
Authors: Vickerman Katrina A. , Keller Paula A. , Deprey Mona , Lachter Randi B. , Jenssen Jacalyn , Dreher Marietta
Published: August 2017

Context:

Tobacco dependence is well established as a chronic condition typically requiring numerous quit attempts. Tobacco users are unlikely to return to the same cessation program on their own.

Objective:

This program evaluation examined the effectiveness of using multiple outreach methods to reengage tobacco users in a statewide cessation program at varying time points after their initial program enrollment.

Design:

Participants were randomized to receive or not receive reengagement outreach. We conducted outreach via phone, e-mail, and/or text (based on methods participants agreed to receive) at 1, 2, or 3 months post–initial engagement. Participants were offered the opportunity to reenroll in QUITPLAN Services.

Setting:

Minnesota's QUITPLAN Services

Participants:

A total of 3020 tobacco users who enrolled in Minnesota's QUITPLAN Services and either received a 2-week starter kit of nicotine replacement therapy or completed 0-1 QUITPLAN Helpline calls.

Main Outcome Measures:

We explored group differences in the odds of reengagement (defined as enrolling in a phone cessation program or selecting 2 or more of nicotine replacement therapy starter kit, text messaging, e-mail program, or print materials), contributors to reengagement, and costs.

Results:

14.7% in the Reengagement Outreach (RO) group and 3.4% in the Comparison (no outreach) group reengaged. The majority (71%) reengaged during phone outreach. There were no significant differences in reengagement rates by follow-up time period (1, 2, or 3 months). Cost per reengagement was $546, mostly due to one-time setup costs; scaling to 10 000 tobacco users would cost approximately $101 per reengagement.

Conclusions:

Conducting proactive outreach through state-funded quitlines is an effective approach to reengaging tobacco users, yielding a 5-fold greater odds of reengagement compared with no outreach. Since most costs were for initial setup, the cost per reengagement would decrease as the outreach population size increases. Such outreach has the potential to foster treatment utilization and quit attempts.
Use of Acellular Allogenic Dermal Matrix (MegaDerm) in Orbital Wall Reconstruction: A Comparison With Absorbable Mesh Plate and Porous Polyethylene
Authors: Kim Jiye , Lew Dae Hyun , Roh Tai Suk , Lee Won Jai
Published: August 2017

The selection of materials for orbital wall reconstruction has been a matter of debate. This study aimed to evaluate the effectiveness of an acellular allogenic dermal matrix (ADM) as an orbital wall reconstruction material and to compare the results of orbital wall reconstruction with the ADM to those of reconstruction with the more widely used absorbable mesh plate and porous polyethylene. We retrospectively reviewed the clinical charts and computed tomography images of 73 patients who underwent orbital reconstruction at 1 institution between March 2013 and February 2014. In the ADM group, the mean defect size of 29 patients was 2.89 cm2. After orbital wall reconstruction with ADM, patients with preoperative enophthalmos (7 patients), limited range of eyeball movement (6 patients), and diplopia (12 patients) showed improvements. In the comparative study, the 3 groups showed no significant differences with respect to age distribution (P = 0.522), defect size (P = 0.455), and preoperative findings such as enophthalmos (P = 0.811), diplopia (P = 0.357), and limited range of eyeball movement (P = 0.795). All the preoperative symptoms improved in every group, and in the ADM group, no complication was observed during the postoperative follow-up. ADM is a biocompatible material that combines the flexibility and rigidity required to support the orbital soft tissue. Therefore, it could be an excellent alternative material for orbital wall reconstruction.
Gorham–Stout Disease Presenting as Acute Unilateral Proptosis
Authors: Stroh Inna G. , Ediriwickrema Lilangi S. , Miller Neil R.
Published: August 2017

Gorham–Stout disease (GSD) is a rare angiomatous disorder characterized by osteolysis. We report the case of a 66-year-old woman who developed sudden left eye proptosis and facial pain. Neuroimaging demonstrated a destructive mass involving the roof and lateral wall of the left orbit with adjacent abnormal orbital soft tissue. An initial biopsy of the soft tissue was nondiagnostic; however, transcranial biopsy of the orbital roof revealed an intraosseous cavernous angioma, with infiltration of orbital fat by angiomatous tissue. Despite resection of the orbital roof and lateral wall, the orbital lesion continued to expand, leading to signs of a compressive optic neuropathy. The patient then reported severe back pain, prompting imaging that demonstrated disseminated bony involvement of the axial skeleton, eventually leading to the diagnosis of GSD. The patient was treated with a bisphosphonate and a vascular endothelial growth factor inhibitor with stabilization of disease.
Land cover and forest connectivity alter the interactions among host, pathogen and skin microbiome
Authors: Becker C. G. , Longo A. V. , Haddad C. F. B. , Zamudio K. R.
Published: August 2017

Deforestation has detrimental consequences on biodiversity, affecting species interactions at multiple scales. The associations among vertebrates, pathogens and their commensal/symbiotic microbial communities (i.e. microbiomes) have important downstream effects for biodiversity conservation, yet we know little about how deforestation contributes to changes in host microbial diversity and pathogen abundance. Here, we tested the effects of landcover, forest connectivity and infection by the chytrid fungus
Batrachochytrium dendrobatidis
(
Bd
) on amphibian skin bacterial diversity along deforestation gradients in Brazilian landscapes. If disturbance to natural habitat alters skin microbiomes as it does in vertebrate host communities, then we would expect higher host bacterial diversity in natural forest habitats.
Bd
infection loads are also often higher in these closed-canopy forests, which may in turn impact skin-associated bacterial communities. We found that forest corridors shaped composition of host skin microbiomes; high forest connectivity predicted greater similarity of skin bacterial communities among host populations. In addition, we found that host skin bacterial diversity and
Bd
loads increased towards natural vegetation. Because symbiotic bacteria can potentially buffer hosts from
Bd
infection, we also evaluated the bi-directional microbiome-
Bd
link but failed to find a significant effect of skin bacterial diversity reducing
Bd
infections. Although weak, we found support for
Bd
increasing bacterial diversity and/or for core bacteria dominance reducing
Bd
loads. Our research incorporates a critical element in the study of host microbiomes by linking environmental heterogeneity of landscapes to the host–pathogen–microbiome triangle.
Genetic and linguistic histories in Central Asia inferred using approximate Bayesian computations
Authors: Thouzeau Valentin , Mennecier Philippe , Verdu Paul , Austerlitz Frédéric
Published: August 2017

Linguistic and genetic data have been widely compared, but the histories underlying these descriptions are rarely jointly inferred. We developed a unique methodological framework for analysing jointly language diversity and genetic polymorphism data, to infer the past history of separation, exchange and admixture events among human populations. This method relies on approximate Bayesian computations that enable the identification of the most probable historical scenario underlying each type of data, and to infer the parameters of these scenarios. For this purpose, we developed a new computer programPopLingSimthat simulates the evolution of linguistic diversity, which we coupled with an existing coalescent-based genetic simulation program, to simulate both linguistic and genetic data within a set of populations. Applying this new program to a wide linguistic and genetic dataset of Central Asia, we found several differences between linguistic and genetic histories. In particular, we showed how genetic and linguistic exchanges differed in the past in this area: some cultural exchanges were maintained without genetic exchanges. The methodological framework and the linguistic simulation tool developed here can be used in future work for disentangling complex linguistic and genetic evolutions underlying human biological and cultural histories.
Local and regional controls of phylogenetic structure at the high-latitude range limits of corals
Authors: Sommer Brigitte , Sampayo Eugenia M. , Beger Maria , Harrison Peter L. , Babcock Russ C. , Pandolfi John M.
Published: August 2017

Understanding how range-edge populations will respond to climate change is an urgent research priority. Here, we used a phylogenetic community ecology approach to examine how ecological and evolutionary processes shape biodiversity patterns of scleractinian corals at their high-latitude range limits in eastern Australia. We estimated phylogenetic signal in seven ecologically important functional traits and conducted tests of phylogenetic structure at local and regional scales using the net relatedness (NRI) and nearest taxon indices (NTI) for the presence/absence and abundance data. Regional tests showed light phylogenetic clustering, indicating that coral species found in this subtropical-to-temperate transition zone are more closely related to each other than are species on the nearby, more northerly Great Barrier Reef. Local tests revealed variable patterns of phylogenetic clustering and overdispersion and higher than expected phylogenetic turnover among sites. In combination, these results are broadly consistent with the hierarchical filtering model, whereby species pass through a regional climatic filter based on their tolerances for marginal conditions and subsequently segregate into local assemblages according to the relative strength of habitat filtering and species interactions. Conservatism of tested traits suggests that corals will likely track their niches with climate change. Nevertheless, high turnover of lineages among sites indicates that range shifts will probably vary among species and highlights the vulnerability and conservation significance of high-latitude reefs.
Stabilizing selection on individual pattern elements of aposematic signals
Authors: Winters Anne E. , Green Naomi F. , Wilson Nerida G. , How Martin J. , Garson Mary J. , Marshall N. Justin , Cheney Karen L.
Published: August 2017

Warning signal variation is ubiquitous but paradoxical: low variability should aid recognition and learning by predators. However, spatial variability in the direction and strength of selection for individual elements of the warning signal may allow phenotypic variation for some components, but not others. Variation in selection may occur if predators only learn particular colour pattern components rather than the entire signal. Here, we used a nudibranch mollusc,Goniobranchus splendidus, which exhibits a conspicuous red spot/white body/yellow rim colour pattern, to test this hypothesis. We first demonstrated that secondary metabolites stored within the nudibranch were unpalatable to a marine organism. Using pattern analysis, we demonstrated that the yellow rim remained invariable within and between populations; however, red spots varied significantly in both colour and pattern. In behavioural experiments, a potential fish predator,Rhinecanthus aculeatus, used the presence of the yellow rims to recognize and avoid warning signals. Yellow rims remained stable in the presence of high genetic divergence among populations. We therefore suggest that how predators learn warning signals may cause stabilizing selection on individual colour pattern elements, and will thus have important implications on the evolution of warning signals.
Nest prospecting brown-headed cowbirds ‘parasitize’ social information when the value of personal information is lacking
Authors: White David J. , Davies Hayden B. , Agyapong Samuel , Seegmiller Nora
Published: August 2017

Brood parasites face considerable cognitive challenges in locating and selecting host nests for their young. Here, we test whether female brown-headed cowbirds,
Molothrus ater
, could use information acquired from observing the nest prospecting patterns of conspecifics to influence their own patterns of nest selection. In laboratory-based experiments, we created a disparity in the amount of personal information females had about the quality of nests. Females with less personal information about the quality of two nests spent more time investigating the nest that more knowledgeable females investigated. Furthermore, there was a strong negative relationship between individual's ability to track nest quality using personal information and their tendency to copy others. These two contrasting strategies for selecting nests are equally effective, but lead to different patterns of parasitism.
The processing of images of biological threats in visual short-term memory
Authors: Quinlan Philip T. , Yue Yue , Cohen Dale J.
Published: August 2017

The idea that there is enhanced memory for negatively, emotionally charged pictures was examined. Performance was measured under rapid, serial visual presentation (RSVP) conditions in which, on every trial, a sequence of six photo-images was presented. Briefly after the offset of the sequence, two alternative images (a target and a foil) were presented and participants attempted to choose which image had occurred in the sequence. Images were of threatening and non-threatening cats and dogs. The target depicted either an animal expressing an emotion distinct from the other images, or the sequences contained only images depicting the same emotional valence. Enhanced memory was found for targets that differed in emotional valence from the other sequence images, compared to targets that expressed the same emotional valence. Further controls in stimulus selection were then introduced and the same emotional distinctiveness effect obtained. In ruling out possible visual and attentional accounts of the data, an informal dual route topic model is discussed. This places emphasis on how visual short-term memory reveals a sensitivity to the emotional content of the input as it unfolds over time. Items that present with a distinctive emotional content stand out in memory.
Rapid functional and evolutionary changes follow gene duplication in yeast
Authors: Naseeb Samina , Ames Ryan M. , Delneri Daniela , Lovell Simon C.
Published: August 2017

Duplication of genes or genomes provides the raw material for evolutionary innovation. After duplication a gene may be lost, recombine with another gene, have its function modified or be retained in an unaltered state. The fate of duplication is usually studied by comparing extant genomes and reconstructing the most likely ancestral states. Valuable as this approach is, it may miss the most rapid evolutionary events. Here, we engineered strains ofSaccharomyces cerevisiaecarrying tandem and non-tandem duplications of the singleton geneIFA38to monitor (i) the fate of the duplicates in different conditions, including time scale and asymmetry of gene loss, and (ii) the changes in fitness and transcriptome of the strains immediately after duplication and after experimental evolution. We found that the duplication brings widespread transcriptional changes, but a fitness advantage is only present in fermentable media. In respiratory conditions, the yeast strains consistently lose the non-tandemIFA38gene copy in a surprisingly short time, within only a few generations. This gene loss appears to be asymmetric and dependent on genome location, since the originalIFA38copy and the tandem duplicate are retained. Overall, this work shows for the first time that gene loss can be extremely rapid and context dependent.
PANINI: Pangenome Neighbor Identification for Bacterial Populations
Authors: Abudahab Khalil , Prada Joaquín M. , Yang Zhirong , Bentley Stephen D. , Croucher Nicholas J. , Corander Jukka , Aanensen David M.
Published: August 2017

The standard workhorse for genomic analysis of the evolution of bacterial populations is phylogenetic modelling of mutations in the core genome. However, in the current era of population genomics, a notable amount of information about evolutionary and transmission processes in diverse populations can be lost unless the accessory genome is also taken into consideration. Here we introduce PANINI, a computationally scalable method for identifying the neighbours for each isolate in a data set using unsupervised machine learning with stochastic neighbour embedding. PANINI is browser-based and integrates with the Microreact platform for rapid online visualisation and exploration of both core and accessory genome evolutionary signals together with relevant epidemiological, geographic, temporal and other metadata. Several case studies with single-and multi-clone pneumococcal populations are presented to demonstrate ability to identify biologically important signals from gene content data. PANINI is available athttp://panini.wgsa.net/and code athttp://gitlab.com/cgps/panini
Multiple tasks viewed from the neural manifold: Stable control of varied behavior
Authors: Gallego Juan A. , Perich Matthew G. , Naufel Stephanie N. , Ethier Christian , Solla Sara A. , Miller Lee E.
Published: August 2017

How do populations of cortical neurons have the flexibility to perform different functions? We investigated this question in primary motor cortex (M1), where populations of neurons are able to generate a rich repertoire of motor behaviors. We recorded neural activity while monkeys performed a variety of wrist and reach-to-grasp motor tasks, each requiring a different pattern of neural activity. We characterized the flexibility of M1 movement control by comparing the “neural modes” that capture covariation across neurons, believed to arise from network connectivity. We found large similarities in the structure of the neural modes across tasks, as well as striking similarities in their temporal activation dynamics. These similarities were only apparent at the population level. Moreover, a subset of these well-preserved modes captured a task-independent mapping onto muscle commands. We hypothesize that this system of flexibly combined, stable neural modes gives M1 the flexibility to generate our wide-ranging behavioral repertoire.
Using Outliers in Freesurfer Segmentation Statistics to Identify Cortical Reconstruction Errors in Structural Scans
Authors: Waters Abigail B. , Mace Ryan A. , Sawyer Kayle S. , Gansler David A.
Published: August 2017

Introduction

Quality assurance (QA) is vital for ensuring the integrity of processed neuroimaging data for use in clinical neurosciences research. Manual QA (visual inspection) of processed brains for cortical surface reconstruction errors is resource-intensive, particularly with large datasets. Several semi-automated QA tools use quantitative detection of subjects for editing based on outlier brain regions. There were two project goals: (1) evaluate the adequacy of a statistical QA method relative to visual inspection, and (2) examine whether error identification and correction significantly impacts estimation of cortical parameters and established brain-behavior relationships.

Methods

T1 MPRAGE images (N = 530) of healthy adults were obtained from the NKI-Rockland Sample and reconstructed using Freesurfer 5.3. Visual inspection of T1 images was conducted for: (1) participants (n= 110) with outlier values (zscores ± 3SD) for subcortical and cortical segmentation volumes (outlier group), and (2) a random sample of remaining participants (n= 110) with segmentation values that did not meet the outlier criterion (nonoutlier group).

Results

The outlier group had 21% more participants with visual inspection-identified errors than participants in the non-outlier group, with a medium effect size (Φ= 0.22). Nevertheless, a considerable portion of images with errors of cortical extension were found in the non-outlier group (41%). Sex significantly predicted error rate; men were 2.8 times more likely to have errors than women. Although nine brain regions significantly changed size from pre-to postediting (with effect sizes ranging from 0.26 to 0.59), editing did not substantially change the correlations of neurocognitive tasks and brain volumes (ps> 0.05).

Conclusions

Statistically-based QA, although less resource intensive, is not accurate enough to supplant visual inspection. We discuss practical implications of our findings to guide resource allocation decisions for image processing.
Best practices for genome-wide RNA structure analysis: combination of mutational profiles and drop-off information
Authors: Novoa Eva Maria , Beaudoin Jean-Denis , Giraldez Antonio J , Mattick John S , Kellis Manolis
Published: August 2017

Genome-wide RNA structure maps have recently become available through the coupling ofin vivochemical probing reagents with next-generation sequencing. Initial analyses relied on the identification of truncated reverse transcription reads to identify the chemically modified nucleotides, but recent studies have shown that mutational signatures can also be used. While these two methods have been employed interchangeably, here we show that they actually provide complementary information. Consequently, analyses using exclusively one of the two methodologies may disregard a significant portion of the structural information. We also show that the identity and sequence environment of the modified nucleotide greatly affect the odds of introducing a mismatch or causing reverse transcriptase drop-off. Finally, we identify specific mismatch signatures generated by dimethyl sulfate probing that can be exploited to remove false positives typically produced in RNA structurome analyses, and how these signatures vary depending on the reverse transcription enzyme used.
Metagenomic sequencing to replace semi-quantitative urine culture for detection of urinary tract infections: a proof of concept
Authors: Janes Victoria A. , Matamoros Sébastien , Willemse Niels , Visser Caroline E. , Wever Bob de , Jakobs Marja E. , Subramanian Poorani , Hasan Nur A. , Colwell Rita R. , de Jong Menno D. , Schultsz Constance
Published: August 2017

ABSTRACT

Semi-quantitative bacterial culture is the standard method to diagnose urinary tract infections (UTI), but bacterial growth rate limits diagnostic speed and it is unreliable when patients have been pre-treated with antibiotics. Metagenomics could increase diagnostic speed and accuracy by sequencing the microbiome and resistome directly from urine samples, bypassing culture. However, a semi-quantitative approach – as needed for diagnosing UTIs – has not been established.

Metagenomics was deployed to identify and semi-quantify bacterial presence indicative of UTI, predict antimicrobial susceptibility (AMR), and results were compared to semi-quantitative culture. Whole genome sequencing of the corresponding uropathogens was done for comparison. Analysis time and cost were tracked.

Forty-one consecutive urine samples underwent metagenomic analysis. All culture positive samples contained >200ng of DNA, suggestive of a threshold below which UTI could be ruled out solely based on DNA quantity. A semi-quantitative Diagnostic Index (DI) was created by multiplying the total DNA quantity by the relative abundance of uropathogens per urine sample. The DI allowed discrimination of UTI from non-UTI samples in all but 1 case. Metagenomic detection of AMR determinants correctly predicted the phenotype of uropathogens in 20 of 32 cases. The metagenomic work-flow was 31h and cost €116 per sample, but could be reduced to 4.5h and €5 for low-DNA-yield non-UTI samples.

The genomic determinants of AMR and their distribution across uropathogens need to be better understood for prediction of AMR phenotypes by metagenomics. The introduction of the DI demonstrates the potential of semi-quantitative metagenomics to replace culture as rapid diagnostic method for UTI.
Single-cell RNA-seq reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress
Authors: Gasch Audrey P. , Yu Feiqiao Brian , Hose James , Escalante Leah E. , Place Mike , Bacher Rhonda , Kanbar Jad , Ciobanu Doina , Sandor Laura , Grigoriev Igor V. , Kendziorski Christina , Quake Stephen R. , McClean Megan N.
Published: August 2017

From bacteria to humans, individual cells within isogenic populations can show significant variation in stress tolerance, but the nature of this heterogeneity is not clear. To investigate this, we used single-cell RNA sequencing to quantify transcript heterogeneity in singleS. cerevisiaecells treated with and without salt stress, to explore population variation and identify cellular covariates that influence the stress-responsive transcriptome. Leveraging the extensive knowledge of yeast transcriptional regulation, we uncovered significant regulatory variation in individual yeast cells, both before and after stress. We also discovered that a subset of cells decouple expression of ribosomal protein genes from the environmental stress response, in a manner partly correlated with the cell cycle but unrelated to the yeast ultradian metabolic cycle. Live-cell imaging of cells expressing pairs of fluorescent regulators, including the transcription factor Msn2 with Dot6, Sfp1, or MAP kinase Hog1, revealed both coordinated and decoupled nucleocytoplasmic shuttling. Together with transcriptomic analysis, our results reveal that cells maintain a cellular filter against decoupled bursts of transcription-factor activation but mount a stress response upon coordinated regulation, even in a subset of unstressed cells.
A genome-scale study of metabolic complementation in endosymbiotic consortia: the case of the cedar aphid
Authors: Ponce-de-Leon Miguel , Tamarit Daniel , Calle-Espinosa Jorge , Mori Matteo , Latorre Amparo , Montero Francisco , Pereto Juli
Published: August 2017

Bacterial endosymbionts and their insect hosts establish an intimate metabolic relationship. Bacteria offer a variety of essential nutrients to their hosts, whereas insect cells provide the necessary sources of matter and energy to their tiny metabolic allies. These nutritional complementations sustain themselves on a diversity of metabolite exchanges between the cell host and the reduced yet highly specialized bacterial metabolism –which, for instance, overproduces a small set of essential amino acids and vitamins. A well-known case of metabolic complementation is provided by the cedar aphidCinara cedrithat harbors two co-primary endosymbionts,Buchnera aphidicolaBCc andCa.Serratia symbiotica SCc, and in which some metabolic pathways are partitioned between different partners. Here we present a genome scale metabolic network (GEM) for the bacterial consortium from the cedar aphidiBSCc. The analysis of this GEM allows us the confirmation of cases of metabolic complementation previously described by genome analysis (i.e. tryptophan and biotin biosynthesis) and the proposal of a hitherto unnoticed event of metabolic pathway sharing between the two endosymbionts, namely the biosynthesis of tetrahydrofolate.In silicoknock-out experiments withiBSCc showed that the consortium metabolism is a highly integrated yet fragile network. We also have explored the evolutionary pathways leading to the emergence of metabolic complementation between reduced metabolisms starting from individual, complete networks. Our results suggest that, during the establishment of metabolic complementation in endosymbionts, adaptive evolution is more significant than previously thought.
Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach
Authors: Jacobs A. , De Noia M. , Praebel K. , Kanstad-Hanssen Ø , Paterno M. , Jackson D. , McGinnity P. , Sturm A. , Elmer KR , Llewellyn MS
Published: August 2017

Caligid sea lice represent a significant threat to salmonid aquaculture worldwide.Lepeophtheirus salmonisis the predominant species that occurs in the Northern Hemisphere. Dispersal of sea lice between marine aquaculture sites and geographic regions is thought to occur rapidly via planktonic transport of larvae. Population genetic analyses have consistently shown minimal population genetic structure in North AtlanticL. salmonis, frustrating efforts to track louse populations, improve targeted control measures and understand local adaption to environmental conditions. The aim of this study was to test the power of reduced representation library sequencing (IIb-RAD sequencing) coupled with random forest machine learning algorithms to define markers for fine-scale discrimination of louse populations. We identified 1286 robustly supported SNPs among fourL. salmonispopulations from Ireland (N=2, 27 individuals), Scotland (N=1, 11 individuals) and North Norway (N=1, 12 individuals). Weak global structure (FSC= 0.018, p<0.0001) and only one significant pairwise FSTcomparison was observed (Scotland vs Kenmare Bay, (FST= 0.018, p<0.0001)) using all 1286 SNPs. The application of a random forest machine-learning algorithm identified 98 discriminatory SNPs that dramatically improved population assignment (DAPC assignment probability = 1), increased global Fsc= 0.098, (p<0.0001) and resulted in pairwise comparisons that all showed highly significant Fst-values (range = 0.081 – 0.096, p<0.0001). Out of 19 SNPs found to be under directional selection between populations, 12 corresponded to the discriminatory SNPs identified using random forest. Taken together our data suggest thatL. salmonisSNP diversity exists with which it is possible to discriminate differences between nearby populations given suitable marker selection approaches, and that such differences might have an adaptive basis. We discuss these data in light of sea lice adaption to anthropogenic and environmental pressures as well as novel approaches to track and predict sea louse dispersal.
Effect of ligands on stability of H-Ras GTPase
Authors: Kovrigina Elizaveta A , O’Connor Casey , Kovrigin Evgenii L
Published: August 2017

The G domain of a small monomeric GTPase Ras contains a nucleotide-binding pocket and a magnesium-binding site essential for the Ras function in cellular signaling. The G domain also has another (allosteric) ion-binding site on the rear surface of the G domain, which function is still unknown. In this paper, we detailed the effect of calcium and magnesium ions on stability of Ras bound to GDP, GTP, and GTP-mimic GppNHp. We revealed that the remote allosteric ion-binding site contributes very significantly to stability of Ras in the GDP-bound conformation, but nearly not at all—when Ras is bound to a GTP mimic. These findings highlight that further studies of the remote ion-binding site are warranted to reveal its role in the Ras function.
High Aspect Ratio Nanomaterials Enable Delivery of Functional Genetic Material Without DNA Integration in Mature Plants
Authors: Demirer Gozde S. , Zhang Huan , Matos Juliana L. , Goh Natalie , Cunningham Francis , Sung Younghun , Chang Roger , Aditham Abhishek J. , Chio Linda , Cho Myeong-Je , Staskawicz Brian , Landry Markita P.
Published: August 2017

Genetic engineering of plants is at the core of sustainability efforts, natural product synthesis, and agricultural crop engineering. The plant cell wall is a barrier that limits the ease and throughput with which exogenous biomolecules can be delivered to plants. Current delivery methods either suffer from host range limitations, low transformation efficiencies, tissue damage, or unavoidable DNA integration into the host genome. Here, we demonstrate efficient diffusion-based biomolecule delivery into tissues and organs of intact plants of several species with a suite of pristine and chemically-functionalized high aspect ratio nanomaterials. Efficient DNA delivery and strong protein expression without transgene integration is accomplished in Nicotiana benthamiana (Nb), Eruca sativa (arugula), Triticum aestivum (wheat) and Gossypium hirsutum (cotton) leaves and arugula protoplasts. We also demonstrate a second nanoparticle-based strategy in which small interfering RNA (siRNA) is delivered to Nb leaves and silence a gene with 95% efficiency. We find that nanomaterials not only facilitate biomolecule transport into plant cells but also protect polynucleotides from nuclease degradation. Our work provides a tool for species-independent and passive delivery of genetic material, without transgene integration, into plant cells for diverse biotechnology applications.
Artifact reduction in the CSPAD detectors used for LCLS experiments
Authors: Pietrini Alberto , Nettelblad Carl
Published: August 2017

The existence of noise and column-wise artifacts in the CSPAD-140K detector and in a module of the CSPAD-2.3M large camera, respectively, is reported for the L730 and L867 experiments performed at the CXI Instrument at the Linac Coherent Light Source (LCLS), in low-flux and low signal-to-noise ratio regime. Possible remedies are discussed and an additional step in the preprocessing of data is introduced, which consists of performing a median subtraction along the columns of the detector modules. Thus, we reduce the overall variation in the photon count distribution, lowering the mean false-positive photon detection rate by about 4% (from 5.57 × 10−5 to 5.32 × 10−5 photon counts pixel−1 frame−1 in L867, cxi86715) and 7% (from 1.70 × 10-3 to 1.58 × 10−3 photon counts pixel−1 frame−1 in L730, cxi73013), and the standard deviation in false-positive photon count per shot by 15% and 35%, while not making our average photon detection threshold more stringent. Such improvements in detector noise reduction and artifact removal constitute a step forward in the development of flash X-ray imaging techniques for high-resolution, low-signal and in serial nano-crystallography experiments at X-ray free-electron laser facilities.
Crystal structure and Hirshfeld surface analysis of aquabis(nicotinamide-κN1)bis(2,4,6-trimethylbenzoato-κO)zinc
Authors: Hökelek Tuncer , Aşkın Gülçin Şefiye , Özkaya Safiye , Necefoğlu Hacali
Published: August 2017

The asymmetric unit of the title complex, [Zn(C10H11O2)2(C6H6N2O)2(H2O)], contains one half of the complex molecule, and the ZnIIcation and the water O atom lie on a twofold rotation axis. The ZnIIcation is coordinated by two carboxylate O atoms of the two symmetry-related 2,4,6-trimethylbenzoate (TMB) anions and by the water O atom at distances of 2.0311 (16) and 2.076 (2) Å to form a slightly distorted trigonal–planar arrangement, while the distorted trigonal–bipyramidal coordination sphere is completed by the two pyridine N atoms of the two symmetry-related monodentate nicotinamide (NA) ligands at distances of 2.2066 (19) Å in the axial positions. In the crystal, molecules are linkedviaintermolecular N—H...O and O—H...O hydrogen bonds withR22(12),R33(10) andR33(16) ring motifs, forming a double-column structure running along thec-axis direction. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H...H (58.4%), H...C/C...H (20.3%) and H...O/O...H (18.3%) interactions.