bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThis 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

AbstractInteraction 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

AbstractThis 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

AbstractMitochondrial 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

AbstractBased 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

SummaryGrapevines, 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

AbstractThis 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

AbstractHybrid 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 statementDeleterious 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

AbstractIn 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.
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

ObjectiveTo 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 SettingData 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 DesignWe 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 MethodsWe extracted Medicare claims for the 24 months before through 24 months after assessment via REGARDS for 5,884 participants.Principal FindingsSemi‐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.ConclusionsIn‐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

AbstractCurrent 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

AbstractThis 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.