bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical Pathway Effectiveness
Authors: Murray Ashlee Lynn , Alpern Elizabeth , Lavelle Jane , Mollen Cynthia
Published: January 2017

Objective

Young infants are often treated in emergency departments (EDs) for febrile illnesses. Any delay in care or ineffective management could lead to increased patient morbidity and mortality. A standardized ED clinical pathway may improve care for these patients. The objective of this study is to evaluate the impact of a febrile young infant clinical pathway implemented in a large, urban children's hospital ED on the timeliness and consistency of care.

Methods

This study used a before-and-after retrospective observational study design comparing 2 separate periods: prepathway from September 2007 through August 2008 and postpathway from September 2009 through August 2010. Subjects were infants aged 56 days or younger presenting with a rectal temperature of 38.0°C or higher. Patients were excluded if they were transferred from another hospital or if they developed a fever after initial presentation.

Results

Five hundred twenty infants were enrolled. The mean time to urine collection and time to the first antibiotic administration were reduced after pathway implementation (23-minute reduction to urine collection vs 36-minute reduction to the first antibiotic administration). There was improvement in the proportion of infants who received the pathway-specific antibiotics based on age (odds ratio, 7.2; 95% confidence interval, 4.4, 11.9) and the proportion of infants who were administered acyclovir based on pathway guidelines (odds ratio, 8.8; 95% confidence interval, 2.9–30.0).

Conclusions

An ED-based febrile young infant clinical pathway improved the timeliness of initiation of work-up as measured by urine collection and of therapy by an earlier administration of the first antibiotic, as well as decreased variability of care.
Outcomes From Referrals and Unscheduled Visits From Community Emergency Departments to a Regional Pediatric Emergency Department in Canada
Authors: Reiner Ethan , Ahmadi Ardalan , Grafstein Eric , Doan Quynh
Published: January 2017

Objectives

Existing pediatric literature describing repeat visits to the emergency department (ED) for the same medical complaint has yet to report on patient flow patterns from general EDs (GEDs) to a pediatric ED (PED). We sought to characterize the population of patients who are treated in a GED and subsequently present to a PED for further care.

Methods

We conducted a retrospective cohort study reviewing all pediatric visits (age < 17 y) at 5 GEDs in Vancouver. Our primary outcome measure was the proportion of visits with a subsequent visit to a PED (<7 days) during the 2012 to 2013 fiscal year. Secondary outcomes included reasons for PED consultation, the clinical services accessed, and disposition at the PED.

Results

During the study period, 581 (3.3%) of the 17,824 children seen at GEDs subsequently presented to the PED within 7 days. The top 3 diagnoses among these were fracture, viral infection, and musculoskeletal complaints. Of the 581 children with a visit to the PED, 180 (31.0%) were referred to the PED for a consultation, whereas the rest were family initiated. Referred visits were more frequently associated with pediatric subspecialist consultation than family-initiated visits (45.0% vs 19.5%, P < 0.01). The referred group more frequently resulted in a surgical procedure (13.9% vs 2.5%, P < 0.01) or hospital admission (51.7% vs 8.7%, P < 0.01).

Conclusions

Knowing the proportion, management, and outcomes of children who are treated in a GED and subsequently at a PED may provide an important quality measure and opportunities to improve the management of common pediatric emergencies in the community.
Evaluation of the Association of Early Elevated Lactate With Outcomes in Children With Severe Sepsis or Septic Shock
Authors: Gorgis Noelle , Asselin Jeannette M. , Fontana Cynthia , Heidersbach R. Scott , Flori Heidi R. , Ward Shan L.
Published: January 2017

Objective

The aim of the study was to assess the association of initial lactate (L0) with mortality in children with severe sepsis.

Methods

This prospective cohort study included 74 patients younger than 18 years with severe sepsis admitted to the pediatric intensive care unit (PICU) of a tertiary, academic children's hospital with lactate measured within 3 hours of meeting severe sepsis or septic shock. The primary outcome was in-hospital mortality. The secondary outcomes included PICU and hospital length of stay.

Results

Although overall mortality was 10.5% (n = 18), patients with L0 measured (n = 72) had a higher mortality (16% vs 6%, P = 0.03) and higher median PRISM-III risk of mortality scores (P = 0.02) than those who did not. Median L0 was no different between nonsurvivors and survivors (3.6 mmol/L [interquartile range, 2.0–9.0] in nonsurvivors vs 2.3 mmol/L [interquartile range, 1.4–3.5] in survivors, P = 0.11). However, L0 was independently associated with PRISM-III score (coefficient, 1.12; 95% confidence interval, 0.4–1.8; P = 0.003) with an increase in mean PRISM-III score of 1.12 U for every 1 mmol/L increase in L0, with L0 accounting for 12% of the variability in PRISM-III scores between patients. There was no association between L0 and PICU or hospital length of stay.

Conclusions

Although our single center study did not demonstrate that an elevated early lactate is associated with mortality in pediatric severe sepsis, L0 did correlate strongly with PRISM-III, the most robust measure of mortality risk in pediatrics. Therefore, early lactate measurement may be important as an early biomarker of disease severity. These data should be validated in a larger, multicenter, prospective study.
Ex Vivo Assessment of Coronary Atherosclerotic Plaque by Grating-Based Phase-Contrast Computed Tomography
Authors: Habbel Christopher , Hetterich Holger , Willner Marian , Herzen Julia , Steigerwald Kristin , Auweter Sigrid , Schüller Ulrich , Hausleiter Jörg , Massberg Steffen , Reiser Maximilian , Pfeiffer Franz , Saam Tobias , Bamberg Fabian
Published: January 2017

Objectives

The aim of this study was to determine the diagnostic accuracy of grating-based phase-contrast computed tomography (gb-PCCT) to classify and quantify coronary vessel characteristics in comparison with optical coherence tomography (OCT) and histopathology in an ex vivo setting.

Materials and Methods

After excision from 5 heart specimens, 15 human coronary arteries underwent gb-PCCT examination using an experimental imaging setup consisting of a rotating molybdenum anode x-ray tube, a Talbot-Lau grating interferometer, and a single photon counting detector. Subsequently, all vessels were imaged by OCT and histopathologically processed. Optical coherence tomography, gb-PCCT, and histopathology images were manually matched using anatomical landmarks. Optical coherence tomography and gb-PCCT were reviewed by 2 independent observers blinded to histopathology. Vessel, lumen, and plaque area were measured, and plaque characteristics (lipid rich, calcified, and fibrous) were determined for each section. Measures of diagnostic accuracy were derived, applying histopathology as the standard of reference.

Results

Of a total of 286 assessed cross sections, 241 corresponding sections were included in the statistical analysis. Quantitative measures derived from gb-PCCT were significantly higher than from OCT (P < 0.001) and were strongly correlated with histopathology (Pearson r ≥0.85 for gb-PCCT and ≥0.61 for OCT, respectively). Results of Bland-Altman analysis demonstrated smaller mean differences between OCT and histopathology than for gb-PCCT and histopathology. Limits of agreement were narrower for gb-PCCT with regard to lumen area, for OCT with regard to plaque area, and were comparable with regard to vessel area. Based on histopathology, 228/241 (94.6%) sections were classified as fibrous, calcified, or lipid rich. The diagnostic accuracy of gb-PCCT was excellent for the detection of all plaque components (sensitivity, ≥0.95; specificity, ≥0.94), whereas the results for OCT showed sensitivities of ≥0.73 and specificities of ≥0.66.

Conclusions

In this ex vivo setting, gb-PCCT provides excellent results in the assessment of coronary atherosclerotic plaque characteristics and vessel dimensions in comparison to OCT and histopathology. Thus, the technique may serve as adjunct nondestructive modality for advanced plaque characterization in an experimental setting.
Radiomic Analysis Reveals Prognostic Information in T1-Weighted Baseline Magnetic Resonance Imaging in Patients With Glioblastoma
Authors: Ingrisch Michael , Schneider Moritz Jörg , Nörenberg Dominik , Negrao de Figueiredo Giovanna , Maier-Hein Klaus , Suchorska Bogdana , Schüller Ulrich , Albert Nathalie , Brückmann Hartmut , Reiser Maximilian , Tonn Jörg-Christian , Ertl-Wagner Birgit
Published: January 2017

Objectives

The aim of this study was to investigate whether radiomic analysis with random survival forests (RSFs) can predict overall survival from T1-weighted contrast-enhanced baseline magnetic resonance imaging (MRI) scans in a cohort of glioblastoma multiforme (GBM) patients with uniform treatment.

Materials and Methods

This retrospective study was approved by the institutional review board and informed consent was waived. The MRI scans from 66 patients with newly diagnosed GBM from a previous prospective study were analyzed. Tumors were segmented manually on contrast-enhanced 3-dimensional T1-weighted images. Using these segmentations, P = 208 quantitative image features characterizing tumor shape, signal intensity, and texture were calculated in an automated fashion. On this data set, an RSF was trained using 10-fold cross validation to establish a link between image features and overall survival, and the individual risk for each patient was predicted. The mean concordance index was assessed as a measure of prediction accuracy. Association of individual risk with overall survival was assessed using Kaplan-Meier analysis and a univariate proportional hazards model.

Results

Mean overall survival was 14 months (range, 0.8–85 months). Mean concordance index of the 10-fold cross-validated RSF was 0.67. Kaplan-Meier analysis clearly distinguished 2 patient groups with high and low predicted individual risk (P = 5.5 × 10−5). Low predicted individual mortality was found to be a favorable prognostic factor for overall survival in a univariate Cox proportional hazards model (hazards ratio, 1.038; 95% confidence interval, 1.015–1.062; P = 0.0059).

Conclusions

This study demonstrates that baseline MRI in GBM patients contains prognostic information, which can be accessed by radiomic analysis using RSFs.
Metal Artifact Reduction Magnetic Resonance Imaging Around Arthroplasty Implants
Authors: Kumar Neil M. , de Cesar Netto Cesar , Schon Lew C. , Fritz Jan
Published: January 2017

Objectives

Long echo train length (ETL) is an often recommended but unproven technique to decrease metal artifacts on magnetic resonance imaging (MRI) scans. Therefore, we quantitatively and qualitatively assessed the effects of ETL on metal artifact on MRI scans using a cobalt-chromium–containing arthroplasty implant system.

Materials and Methods

Using a total ankle arthroplasty system implanted into a human cadaver ankle and a clinical 1.5 T MRI system, turbo spin echo (TSE) pulse sequences were acquired with ETL ranging from 3 to 23 and receiver bandwidth (BW) from 100 to 750 Hz/pixel, whereas effective echo time and spatial resolution were controlled. A compressed sensing slice encoding for metal artifact correction TSE prototype pulse sequence was used as reference standard. End points included the total implant-related artifact area and implant-related signal void areas. Two raters evaluated the overall image quality and preference across varying BW and ETL. Two-factor analysis of variance, Friedman test, Kruskal-Wallis test, and Pearson correlation were used. P values of less than 0.05 were considered statistically significant.

Results

The total implant-related artifact area ranged from 0.119 for compressed sensing slice encoding for metal artifact correction (BW, 600 Hz/pixel; ETL, 3) to 0.265 for TSE (BW, 100 Hz/pixel; ETL, 23). Longer ETL significantly increases the total implant-related artifact area (P = 0.0004), whereas it decreased with increasing BW (P < 0.0001). Implant-related signal void areas were not significantly affected by larger echo train length, but reduced with higher BW (P < 0.0001). Readers had a significant preference for images with high BW and short ETL (P < 0.0001).

Conclusions

High receiver BW is the most effective parameter for reduction of arthroplasty implant-induced metal artifact on MRI scans, whereas in contradiction to prevalent notions, long echo trains fail to reduce implant-related metal artifacts, but in fact cause degradation of image quality around the implant with resultant larger appearing total metal artifacts.
A Case Study of Hemochromatosis and Conflicting Point Shear Wave Measurements in the Assessment of Liver Fibrosis
Authors: Cohen Tal , Barr Richard G.
Published: January 2017

There are multiple factors that affect the shear wave speed in the assessment of liver stiffness. In this case report, we present a case of hemochromatosis that has elevated liver stiffness suggestive of significant fibrosis or cirrhosis; however on liver biopsy, no fibrosis was identified. This article will discuss the possibility that liver iron deposition may affect SWE measurements of the liver, leading to inaccurate assessment of liver fibrosis. In these cases, a liver biopsy may be required for accurate liver assessment.
Cerebrospinal Fluid Biomarkers for the Diagnosis of Alzheimer Disease in South Korea
Authors: Park Sun Ah , Chae Won Seok , Kim Hyeong Jun , Shin Ho Sik , Kim Saeromi , Im Ji Young , Ahn Sang Il , Min Kyoung Dae , Yim Soo Jae , Ye Byoung Seok , Seo Sang Won , Jeong Jee Hyang , Park Kyung Won , Choi Seong Hye , Na Duk L.
Published: January 2017

Laboratory-specific reference values for cerebrospinal fluid (CSF) Alzheimer disease (AD) biomarkers are necessary. Our objective was to apply well-known CSF biomarkers and redetermine their diagnostic cutoff values for AD in South Korea. CSF samples from matched control subjects (n=71), patients with AD dementia (ADD, n=76), and other neurological disorders with cognitive decline (OND, n=47) were obtained from 6 Korean dementia clinics according to a standardized protocol. CSF biomarker concentrations were measured using enzyme-linked immunosorbent assay. CSF biomarkers differed significantly between the ADD and control groups (P<0.001 for all), and between the ADD and OND groups (P<0.001 for all). The areas under the curve in differentiation of ADD from control subjects were 0.97 for Aβ42, 0.93 for total tau (tTau), 0.86 for pTau, and 0.99 for both tTau/Aβ42 and pTau/Aβ42 ratios. Our revised cutoff value for Aβ42 was higher than our previous one, whereas the values for the Tau proteins were similar. The tTau/Aβ42 ratio had the highest accuracy, 97%. Our findings highlight the usefulness of CSF AD biomarkers in South Korea, and the necessity of continually testing the reliability of cutoff values.
Two Versus One High-Frequency Repetitive Transcranial Magnetic Stimulation Session per Day for Treatment-Resistant Depression
Authors: Theleritis Christos , Sakkas Pavlos , Paparrigopoulos Thomas , Vitoratou Silia , Tzavara Chara , Bonaccorso Stefania , Politis Antonios , Soldatos Constantin R. , Psarros Costantin
Published: January 2017

Objectives

High-frequency repetitive transcranial magnetic stimulation (HF-rTMS) has proven antidepressant effects, but the optimal frequency of sessions remains unclear.

Methods

We conducted a 3-week, sham-controlled trial to assess the antidepressant efficacy of 1 active HF-rTMS session per day (A1 group) compared with 2 per day (A2 group) and equivalent sham sessions (once a day, S1 group; twice a day, S2 group) in patients with treatment-resistant major depression with a subsequent 2-week follow-up period. One hundred seventy-seven patients were screened, of whom 105 met eligibility criteria and 98 consented and were randomized. The HF-rTMS (20 Hz) was targeted to the left prefrontal cortex in sessions of approximately 40 trains (2 seconds each) at 100% resting motor threshold with an intertrain interval of 1 minute. Treatment response was defined as a 50% or greater decrease in the Hamilton Depression Rating Scale (HDRS) score and/or Clinician Global Impressions-Severity of Illness (CGI-S) score of 3 or less. Remission was defined as HDRS score less than 8 and/or CGI-S score of 2 or less.

Results

Practically none of the subjects in either sham groups achieved remission. Increased odds of remission were present for CGI-S by stimulating twice rather than once per day (odds ratio [OR] = 1.5, P = 0.018), whereas there was a marginal result for HDRS (OR = 3.9, P = 0.066). Patients who had lower baseline HDRS (OR = 0.75, P = 0.014) and CGI-S scores (OR = 0.18, P = 0.001) were more likely to achieve remission.

Conclusions

Twice per day active HF-rTMS might be more effective than once per day active HF-rTMS or sham stimulation.
Analogies between optical and quantum mechanical angular momentum
Authors: Nienhuis Gerard
Published: January 2017

The insight that a beam of light can carry orbital angular momentum (AM) in its propagation direction came up in 1992 as a surprise. Nevertheless, the existence of momentum and AM of an electromagnetic field has been well known since the days of Maxwell. We compare the expressions for densities of AM in general three-dimensional modes and in paraxial modes. Despite their classical nature, these expressions have a suggestive quantum mechanical appearance, in terms of linear operators acting on mode functions. In addition, paraxial wave optics has several analogies with real quantum mechanics, both with the wave function of a free quantum particle and with a quantum harmonic oscillator. We discuss how these analogies can be applied.

This article is part of the themed issue ‘Optical orbital angular momentum’.
The Modulation of Pain by Circadian and Sleep-Dependent Processes: A Review of the Experimental Evidence
Authors: Hagenauer Megan Hastings , Crodelle Jennifer A. , Piltz Sofia H. , Toporikova Natalia , Ferguson Paige , Booth Victoria
Published: January 2017

This proceedings paper is the first in a series of three papers developing mathematical models for the complex relationship between pain and the sleep-wake cycle. Here, we briefly review what is known about the relationship between pain and the sleep-wake cycle in humans and laboratory rodents in an effort to identify constraints for the models. While it is well accepted that sleep behavior is regulated by a daily (circadian) timekeeping system and homeostatic sleep drive, the joint modulation of these two primary biological processes on pain sensitivity has not been considered. Under experimental conditions, pain sensitivity varies across the 24 h day, with highest sensitivity occurring during the evening in humans. Pain sensitivity is also modulated by sleep behavior, with pain sensitivity increasing in response to the build up of homeostatic sleep pressure following sleep deprivation or sleep disruption. To explore the interaction between these two biological processes using modeling, we first compare the magnitude of their effects across a variety of experimental pain studies in humans. To do this comparison, we normalize the results from experimental pain studies relative to the range of physiologicallymeaningful stimulation levels. Following this normalization, we find that the estimated impact of the daily rhythm and of sleep deprivation on experimental pain measurements is surprisingly consistent across different pain modalities. We also review evidence documenting the impact of circadian rhythms and sleep deprivation on the neural circuitry in the spinal cord underlying pain sensation. The characterization of sleep-dependent and circadian influences on pain sensitivity in this review paper is used to develop and constrain the mathematical models introduced in the two companion articles.
Familiarity with companions aids recovery from fear in zebrafish
Authors: Mathuru Ajay S. , Schirmer Annett , Yeng Tabitha Ng Phui , Kibat Caroline , Cheng Ruey-Kuang , Jesuthasan Suresh
Published: January 2017

Interaction with social partners during or after a stressful episode aids recovery in humans and other mammals. We asked if a comparable phenomenon exists in zebrafish(Danio rerio)that live in shoals in the wild. In the first experiment, we observed that most quantifiable parameters of swimming behavior were similar when zerbafish swam alone or with companions. However, after exposure to an alarm substance (Schreckstoff), individuals recovering alone continued to display behaviors associated with fear after removal of the stimulus, while those recovering with companions did not. In the next two experiments, we examined the role of familiarity of companions. Subjects spent more time in the vicinity of familiar companions in a two-choice assay. While both familiar and unfamiliar companions reduced behavioral signs of distress, familiar companions additionally modulated cortisol and endogenous isotocin in subjects. Shortly after being united with familiar companions, isotocin spiked followed by a dampening of circulating cortisol levels. These results suggest that zebrafish experience fear attenuation in the presence of others and familiar companions are more effective at buffering the stress associated with escaping predation. Changes in behavior, circulating cortisol and isotocin levels due to social partners are reminiscent of changes due to amelioration of fear in some mammalian species in the presence of companions. The two phenomena may be related.
Multivariate cross-frequency coupling via generalized eigendecomposition
Authors: Cohen Michael X
Published: January 2017

This paper presents a new framework for analyzing cross-frequency coupling in multichannel electrophysiological recordings. The generalized eigendecomposition-based cross-frequency coupling framework (gedCFC) is inspired by source separation algorithms combined with dynamics of mesoscopic neurophysiological processes. It is unaffected by factors that confound traditional CFC methods such as non-stationarities, non-sinusoidality, and non-uniform phase angle distributions—attractive properties considering that brain activity is neither stationary nor perfectly sinusoidal. The gedCFC framework opens new opportunities for conceptualizing CFC as network interactions with diverse spatial/topographical distributions. five specific methods within the gedCFC framework are detailed, with validations in simulated data and applications in several empirical datasets. gedCFC accurately recovers physiologically plausible CFC patterns embedded in noise where traditional CFC methods perform poorly. It is also demonstrated that spike-field coherence in multichannel local field potential data can be analyzed using the gedCFC framework, with significant advantages over traditional spike-field coherence analyses. Null-hypothesis testing is also discussed.
The 2D-structure of theT. bruceipre-edited RPS12 mRNA is not affected by macromolecular crowding
Authors: Leeder W.-Matthias , Voskuhl Stephan , Göringer H. Ulrich
Published: January 2017

Mitochondrial transcript maturation in African trypanosomes requires RNA editing to convert nucleotide-deficient pre-mRNAs into translatable mRNAs. The different pre-mRNAs have been shown to adopt highly stable 2D-folds, however, it is not known whether these structures resemble thein vivofolds given the extreme “crowding” conditions within the mitochondrion. Here we analyze the effects of macromolecular crowding on the structure of the mitochondrial RPS12 pre-mRNA. We use polyethylene glycol as a macromolecular cosolute and monitor the structure of the RNA globally and with nucleotide resolution. We demonstrate that crowding has no impact on the 2D-fold and we conclude that the MFE-structure in dilute solvent conditions represents a good proxy for the folding of the pre-mRNA in its mitochondrial solvent context.
An epigenetic change in a moth is generated by temperature and transmitted to many subsequent generations mediated by RNA
Authors: Pavelka Jaroslav , Poláková Simona , Pavelková Věra
Published: January 2017

Based on the presented results, the epigenetic phenomenon (paramutation) found in the short antennae (sa) mutation of the flour moth (Ephestia kuehniella) is probably determined by a small RNA (maybe piRNA) and transmitted in this way to subsequent generations through the male and female gametes. It is triggered by a change in the ambient environment; it persists for many generations (20 so far); during the epigenetic effect the original wild type appeared again. The epigenetic effect of the flour moth is induced by changes in ontogenetic development, such as increased temperature on pupae development, little nutritious food, different salts in food of certain chemicals into eggs. We found this mechanism may explain the intermittent clearance of this effect at some individuals and/or progeny of a pair in the generation chain in which the effect transfers. As the nature of the observed phenomenon could related to sirtuin genes, we hypothesize an association of these genes and non-coding small Piwi-interacting RNAs (piRNAs). The key is that the survival of RNA over many generations carries a number of practical implications. It is evident that the reaction to environmental change can manifest through RNA. It follows that there may be evolutionary significance in the long-term transmission of traits to future generations.
Closed-reference metatranscriptomics enablesin plantaprofiling of putative virulence activities in the grapevine trunk-disease complex
Authors: Morales-Cruz Abraham , Allenbeck Gabrielle , Figueroa-Balderas Rosa , Ashworth Vanessa E. , Lawrence Daniel P. , Travadon Renaud , Smith Rhonda J. , Baumgartner Kendra , Rolshausen Philippe E. , Cantu Dario
Published: January 2017

Grapevines, like other perennial crops, are affected by so-called ‘trunk diseases’, which damage the trunk and other woody tissues. Mature grapevines typically contract more than one trunk disease and often multiple grapevine trunk pathogens (GTPs) are recovered from infected tissues. The co-existence of different GTP species in complex and dynamic microbial communities complicates the study of the molecular mechanisms underlying disease development especially under vineyard conditions. The objective of this study was to develop and optimize a community-level transcriptomics (i.e., metatranscriptomics) approach that can monitor simultaneously the virulence activities of multiple GTPsin planta. The availability of annotated genomes for the most relevant co-infecting GTPs in diseased grapevine wood provided the unprecedented opportunity to generate a multi-species reference for mapping and quantifying DNA and RNA sequencing reads. We first evaluated popular sequence read mappers using permutations of multiple simulated datasets. Alignment parameters of the selected mapper were optimized to increase the specificity and sensitivity for its application to metagenomics and metatranscriptomics analyses. Initial testing on grapevine wood experimentally inoculated with individual GTPs confirmed the validity of the method. Using naturally-infected field samples expressing a variety of trunk disease symptoms, we show that our approach provides quantitative assessments of species composition as well as genome-wide transcriptional profiling of potential virulence factors, namely cell wall degradation, secondary metabolism and nutrient uptake for all co-infecting GTPs.
NAPR: a cloud-based framework for neuroanatomical age prediction
Authors: Pardoe Heath R. , Kuzniecky Ruben
Published: January 2017

This paper describes NAPR, a cloud-based framework for accessing age prediction models created using machine learning-based analysis of neuroimaging data. The NAPR service is provided athttps://www.cloudneuro.org. The NAPR system allows external users to predict the age of individual subjects using their own MRI data. As a demonstration of the NAPR approach, age prediction models were trained using healthy control data from the ABIDE, CoRR, DLBS and NKI Rockland neuroimaging datasets (total N = 2367). MRI scans were processed using Freesurfer v5.3. Age prediction models were trained using relevance vector machines and Gaussian processes machine learning techniques. NAPR will allow for rigorous and transparent out-of-sample assessment of age prediction model performance, and may therefore assist in the translation of neuroimaging-based modelling techniques to the clinic.
Hybrid incompatibility caused by an epiallele
Authors: Blevins Todd , Wang Jing , Pflieger David , Pontvianne Frédéric , Pikaard Craig S.
Published: January 2017

Hybrid incompatibility resulting from deleterious gene combinations is thought to be an important step towards reproductive isolation and speciation. Here we demonstrate involvement of a silent epiallele in hybrid incompatibility. InArabidopsis thalianastrain Col-0, one of the two copies of a duplicated histidine biosynthesis gene,HISN6Bis not expressed, for reasons that have been unclear, making its paralog,HISN6Aessential. By contrast, in strain Cvi-0,HISN6Bis essential becauseHISN6Ais mutated. As a result of these differences, Cvi-0 × Col-0 hybrid progeny that are homozygous for both Col-0HISN6Band Cvi-0HISN6Ado not survive. We show thatHISN6Bis not a defective pseudogene in the Col-0 strain, but a stably silenced epiallele. MutatingHISTONE DEACETYLASE 6 (HDA6)or the cytosine methyltransferase genes,MET1orCMT3erasesHISN6B’ssilent locus identity in Col-0, reanimating the gene such thathisn6alethality and hybrid incompatibility are circumvented. These results show thatHISN6-dependent hybrid lethality is a revertible epigenetic phenomenon and provide additional evidence that epigenetic variation has the potential to limit gene flow between diverging populations of a species.

Significance statement

Deleterious mutations in different copies of a duplicated gene pair have the potential to cause hybrid incompatibility between diverging subpopulations, contributing to reproductive isolation and speciation. This study demonstrates a case of epigenetic gene silencing, rather than pseudogene creation by mutation, contributing to a lethal gene combination upon hybridization of two strains ofArabidopsis thaliana. The findings provide direct evidence that naturally occurring epigenetic variation can contribute to incompatible hybrid genotypes, reducing gene flow between strains of the same species.
When a foundation crumbles: forecasting forest community dynamics following the decline of the foundation speciesTsuga canadensis
Authors: Case Bradley S. , Buckley Hannah L. , Barker-Plotkin Audrey A. , Orwig David A. , Ellison Aaron M.
Published: January 2017

Abstract

In the forests of northeastern North America, invasive insects and pathogens are causing major declines in some tree species and a subsequent reorganization of associated forest communities. Using observations and experiments to investigate the consequences of such declines are hampered because trees are long-lived. Simulation models can provide a means to forecast possible futures based on different scenarios of tree species decline, death, and removal. Such modeling is particularly urgent for species such as eastern hemlock (Tsuga canadensis), a foundation species in many northeast forest regions that is declining due to the hemlock woolly adelgid (Adelges tsugae). Here, we used an individual-based forest simulator, SORTIE-ND, to forecast changes in forest communities in central Massachusetts over the next 200 years under a range of scenarios: a no-adelgid, status-quo scenario; partial resistance of hemlock to the adelgid; adelgid irruption and total hemlock decline over 25 years, adelgid irruption and salvage logging of hemlock trees; and two scenarios of preemptive logging of hemlock and hemlock/white pine.We applied the model to six study plots comprising a range of initial species mixtures, abundances, and levels of hemlock dominance. Simulations indicated that eastern white pine, and to a lesser extent black birch and American beech, would gain most in relative abundance and basal area following hemlock decline. The relative dominance of these species depended on initial conditions and the amount of hemlock mortality, and their combined effect on neighborhood-scale community dynamics. Simulated outcomes were little different whether hemlock died out gradually due to the adelgid or disappeared rapidly following logging. However, if eastern hemlock were to become partially resistant to the adelgid, hemlock would be able to retain its dominance despite substantial losses of basal area. Our modeling highlights the complexities associated with secondary forest succession due to ongoing hemlock decline and loss. We emphasize the need both for a precautionary approach in deciding between management intervention or simply doing nothing in these declining hemlock forests, and for clear aims and understanding regarding desired community- and ecosystem-level outcomes.
Crystallometric and projective properties of Kikuchi diffraction patterns
Authors: Nolze Gert , Winkelmann Aimo
Published: January 2017

Kikuchi diffraction patterns can provide fundamental information about the lattice metric of a crystalline phase. In order to improve the possible precision and accuracy of lattice parameter determination from the features observed in Kikuchi patterns, some useful fundamental relationships of geometric crystallography are reviewed, which hold true independently of the actual crystal symmetry. The Kikuchi band positions and intersections and the Kikuchi band widths are highly interrelated, which is illustrated by the fact that all lattice plane trace positions of the crystal are predetermined by the definition of only four traces. If, additionally, the projection centre of the gnomonic projection is known, the lattice parameter ratios and the angles between the basis vectors are fixed. A further definition of one specific Kikuchi band width is sufficient to set the absolute sizes of all lattice parameters and to predict the widths of all Kikuchi bands. The mathematical properties of the gnomonic projection turn out to be central to an improved interpretation of Kikuchi pattern data, emphasizing the importance of the exact knowledge of the projection centre.
Can X-ray constrained Hartree–Fock wavefunctions retrieve electron correlation?
Authors: Genoni Alessandro , Dos Santos Leonardo H. R. , Meyer Benjamin , Macchi Piero
Published: January 2017

The X-ray constrained wavefunction (XC-WF) method proposed by Jayatilaka [Jayatilaka & Grimwood (2001),Acta Cryst.A57, 76–86] has attracted much attention because it represents a possible third way of theoretically studying the electronic structure of atoms and molecules, combining features of the more popular wavefunction- and DFT-based approaches. In its original formulation, the XC-WF technique extracts statistically plausible wavefunctions from experimental X-ray diffraction data of molecular crystals. A weight is used to constrain the pure Hartree–Fock solution to the observed X-ray structure factors. Despite the wavefunction being a single Slater determinant, it is generally assumed that its flexibility could guarantee the capture, better than any other experimental model, of electron correlation effects, absent in the Hartree–Fock Hamiltonian but present in the structure factors measured experimentally. However, although the approach has been known for long time, careful testing of this fundamental hypothesis is still missing. Since a formal demonstration is impossible, the validation can only be done heuristically and, to accomplish this task, X-ray constrained Hartree–Fock calculations have been performed using structure factor amplitudes computed at a very high correlation level (coupled cluster) for selected molecules in isolation, in order to avoid the perturbations due to intermolecular interactions. The results show that a single-determinant XC-WF is able to capture the electron correlation effects only partially. The largest amount of electron correlation is extracted when: (i) a large external weight is used (much larger than what has normally been used in XC-WF calculations using experimental data); and (ii) the high-order reflections, which carry less information on the electron correlation, are down-weighted (or even excluded), otherwise they would bias the fitting towards the unconstrained Hartree–Fock wavefunction.
Crystal structure of (E)-N1-[(anthracen-9-yl)methylidene]-N4-phenylbenzene-1,4-diamine
Authors: Faizi Md. Serajul Haque , Haque Ashanul , Ahmad Musheer , Golenya Irina A.
Published: January 2017

The title compound, C27H20N2, a Schiff base synthesizedviaa condensation reaction between anthracene-9-carbaldehyde andN-phenyl-p-phenylenediamine, crystallizes with three independent molecules in the asymmetric unit. The three molecules have slightly varying overall conformations, all havingtransconformations with respect to the C=N bond. In the crystal, the packing features N—H...N hydrogen bonds, which connect molecules into chains extending along thec-axis direction, interlinked by C—H...π interactions (minimum H...Cg= 2.65 Å) into sheets lying parallel to (001).
Crystal structure of (2,2′-bipyridyl)[2,6-bis(1-butyl-1H-benzimidazol-2-yl)pyridine]chloridoiridium(III) trifluoromethanesulfonate
Authors: Smith Victoria I. , Nozari Mohammad , Zeller Matthias , Addison Anthony W.
Published: January 2017

The title complex compound, [Ir(C27H29N5)Cl(C10H8N2)](CF3SO3)2, was synthesized for a study of iridium(III)/periodate redox systems in water. The coordination geometry of the complex can be best described as distorted octahedral, with an r.m.s. deviation of 8.8 (8)% from ideal octahedral rectangular geometry. In the crystal, C—H...O and C—H...F interactions between the complex cation and the trifluoromethanesulfonate anions are observed, as well as a C—H...Cl intermolecular interaction between neighboring complex cations. In addition, the benzimidazole ring systems display parallel-displaced π–π stacking with centroid–centroid distances of 3.585 (3)–3.907 (3) Å. One of the two trifluoromethanesulfonate anions is disordered over two orientations with an occupancy ratio of 0.582 (6):0.418 (6). The title complex was characterized using FT–IR, cyclic voltammetry/rotating disc electrode polarography, fluorescence spectrometry, high resolution mass spectrometry, CHN elemental analysis and1H NMR spectroscopy.
Crystal structures of two mixed-valence copper cyanide complexes withN-methylethylenediamine
Authors: Corfield Peter W. R. , Sabatino Alexander
Published: January 2017

The crystal structures of two mixed-valence copper cyanide compounds involvingN-methylethylenediamine (meen), are described. In compound (I), poly[bis(μ3-cyanido-κ3C:C:N)tris(μ2-cyanido-κ2C:N)bis(N-methylethane-1,2-diamine-κ2N,N′)tricopper(I)copper(II)], [Cu4(CN)5(C3H10N2)2] or Cu4(CN)5meen2, cyanide groups link CuIatoms into a three-dimensional network containing open channels parallel to thebaxis. In the network, two tetrahedrally bound CuIatoms are bonded by the C atoms of two end-on bridging CN groups to form Cu2(CN)6moieties with the Cu atoms in close contact at 2.560 (1) Å. Other trigonally bound CuIatoms link these units together to form the network. The CuIIatoms, coordinated by two meen units, are covalently linked to the networkviaa cyanide bridge, and project into the open network channels. In the molecular compound (II), [(N-methylethylenediamine-κ2N,N′)copper(II)]-μ2-cyanido-κ2C:N-[bis(cyanido-κC)copper(I)] monohydrate, [Cu2(CN)3(C3H10N2)2]·H2O or Cu2(CN)3meen2·H2O, a CN group connects a CuIIatom coordinated by two meen groups with a trigonal–planar CuIatom coordinated by CN groups. The molecules are linked into centrosymmetric dimersviahydrogen bonds to two water molecules. In both compounds, the bridging cyanide between the CuIIand CuIatoms has the N atom bonded to CuIIand the C atom bonded to CuI, and the CuIIatoms are in a square-pyramidal coordination.
Building capabilities for change: the crucial role of resilience
Authors: Hodges Julie
Published: January 2017

Purpose

This paper aims to discuss the importance of building internal capabilities for change. The main elements of building capabilities are highlighted, along with the benefits. In particular, there is focus on building resilience and how it can help people to respond to and cope with changes more effectively and efficiently. The paper concludes by emphasizing that developing resilience takes time but that research shows that it can impact on how individuals engage in organizational change.

Design/methodology/approach

The approach taken is a review of the literature. Data are also used from a group of executive MBA students who were asked what capabilities they thought were necessary to lead and manage change.

Findings

Findings show that resilience is a key capability for leading and managing organizational change. The components of resilience play a vital role in enabling people to cope with change.

Practical implications

The practical implications are that organizations need to develop the capabilities for change to ensure that change is sustained in organizations. Managers and HR staff should consider ways of building capabilities for change, especially resilience.

Originality/value

The value of this paper is that it emphasizes the importance of building capabilities for change, especially resilience.
Does Identification of Previously Undiagnosed Conditions Change Care‐Seeking Behavior?
Authors: Myerson Rebecca M. , Colantonio Lisandro D. , Safford Monika M. , Huang Elbert S.
Published: January 2017

Objective

To determine whether identification of previously undiagnosed high cholesterol, hypertension, and/or diabetes during an in‐home assessment impacts care seeking among Medicare beneficiaries.

Data Sources/Study Setting

Data from the REasons for Geographic And Racial Differences in Stroke (REGARDS) study, which recruited African American and white participants across the continental United States from 2003–2007, were linked to Medicare claims.

Study Design

We used panel data models to analyze changes in doctor visits for evaluation and management of conditions after participants were assessed, utilizing the study's rolling recruitment to control for secular trends.

Data Extraction Methods

We extracted Medicare claims for the 24 months before through 24 months after assessment via REGARDS for 5,884 participants.

Principal Findings

Semi‐annual doctor visits for previously undiagnosed conditions increased by 22 percentage points (95 percent confidence interval: 16–28) 2 years following assessment. The effect was similar by gender, race, region, and Medicaid, but it may have been lower among participants who lacked a usual health care provider.

Conclusions

In‐home assessment of cholesterol, blood pressure, and blood glucose can increase doctor visits for individuals with previously undiagnosed conditions. However, biomarker assessment may have more limited impact among individuals with low access to care.
Improving Nonmetric Sex Classification for Hispanic Individuals
Authors: Klales Alexandra R. , Cole Stephanie J.
Published: January 2017

Current techniques used by forensic anthropologists for the identification of unknown human skeletal remains have largely been created using U.S. Black and White samples. When applied to Hispanics, these techniques perform poorly and can lead to misclassifications; consequently, there is an imperative need for population‐specific standards for Hispanics. This research examines the classification accuracies obtained by the original Walker (Am J Phys Anthropol, 136, 2008) and Klales et al. (Am J Phys Anthropol, 149, 2012) methods for nonmetric sex estimation and provides recalibrated regression equations specifically for Hispanics. Ordinal data were collected for five skull and three pelvic traits from a sample of 54 modern Hispanic individuals. Recalibration of the Klales et al. equation improved accuracy (90.3% vs. 94.1%), while recalibration of the Walker method equation decreased accuracy (81.5% vs. 74.1%), but greatly improved sex bias (22.2% vs. −7.4%), thereby making the recalibrated equations more appropriate for use with Hispanics.
Academic work as radical practice: getting in, creating a space, not giving up
Authors: Underhill‐Sem Yvonne Te Ruki‐Rangi‐O‐Tangaroa
Published: January 2017

This paper makes three key points. First, beginning with a personal narrative on the radical practice of getting into the academy, it argues that scholars with non‐traditional academic trajectories must still be able to be competitive in employment rounds. Second, it outlines three particular pedagogies of radical practice: focussing on subjectivities; using local languages; and developing peer learning. Finally, it argues that active scholarly citizens bring intellectual agility that allows for creative, imaginative, and just development thinking and practice.
Urban households' engagement in agriculture: implications for household food security in Ghana's medium sized cities
Authors: Ayerakwa Hayford Mensah
Published: January 2017

Urban and peri‐urban agriculture plays an important role in meeting the food and nutrition needs of those living in the increasingly urbanised cities in Africa. The extent and scope of the practise of urban and peri‐urban agriculture differs from one city to another depending on the economic, environmental, socio‐political, and contextual conditions at play. Using household data drawn from urban Techiman and Tamale in the Brong Ahafo and Northern regions of Ghana respectively, this paper descriptively analyses the contribution of households' engagement in agriculture on urban households' food security. The results show that, nearly half (43%) of urban residents are involved in the production of food either in the urban or rural areas or both, primarily for household consumption and sale of surplus produce. Households who do not engage in agriculture raise their cash incomes through engagement in informal businesses. The picture is however different for households that engage in urban and rural agriculture. For such households, income raised from agriculture (rural and urban combined) is the highest in both cities contributing nearly half (43%) and about a third (33%) of total cash incomes in Techiman and Tamale respectively. The results underscore the need to place the discussion on the contribution of urban agriculture to urban food security in the broader context of the different food production arrangements available to urban households, both in urban and rural areas.
Contested geographies: competing constructions of community and efficiency in small school debates
Authors: Corbett Michael , Helmer Leif
Published: January 2017

The history of rural education in North America can be understood as a history of school closure, amalgamation, and consolidation of schools. Typically, historical and geographical arguments have converged in debates about whether or not to close small community schools, which are positioned as the victims of the march of time and reconfiguration of space. In this paper, we analyse the archetypical positioning of rural parents in the ‘school wars’ as emotional and irrational participants who want to turn back time and who fail or refuse to understand and accept what is alleged to be the inevitable transformation of rural space. We then analyse the political strategy and tactics engaged in by school governance officials and community agents in these struggles over the meaning and future of rural space. We argue that the confrontational politics that ensues do not support strong rural development conversations and that the unilateral search for what we call ‘trump cards’ to settle arguments with data and rational or emotional ‘appeals’ has led to ongoing tension in rural communities.