bluuebunny/crossref_metadata_2025_split huggingface dataset:
Psychological flexibility mediates the effect of an online-based acceptance and commitment therapy for chronic pain: an investigation of change processes
Authors: Lin Jiaxi , Klatt Laura-Isabelle , McCracken Lance M. , Baumeister Harald 
Published: December 2017

Abstract
One way to improve treatment effects of chronic pain is to identify and improve control over mechanisms of therapeutic change. One treatment approach that includes a specific proposed mechanism is acceptance and commitment therapy (ACT) with its focus on increasing psychological flexibility (PF). The aim of the present study was to examine the role of PF as a mechanism of change in ACT. This is based on mediation analyses of data from a previously reported randomized controlled trial, evaluating the effectiveness of an ACT-based online intervention for chronic pain (ACTonPain). We performed secondary analyses on pretreatment, posttreatment, and follow-up data from 302 adults, receiving a guided (n = 100) or unguided (n = 101) version of ACTonPain, or allocated to the waitlist control group (n = 101). Structural equation modelling and a bias-corrected bootstrap approach were applied to examine the indirect effects of the treatment through pretreatment and posttreatment changes in the latent construct reflecting PF. The latent construct consisted of data from the Chronic Pain Acceptance Questionnaire and the Acceptance and Action Questionnaire. The outcomes were pretreatment to follow-up changes in pain interference, anxiety, depression, pain, and mental and physical health. Structural equation modelling analyses revealed that changes in PF significantly mediated pretreatment to follow-up changes in all outcomes in the intervention groups compared with waitlist (standardized estimates ranged from I0.16I to I0.69I). Global model fit yielded modest but acceptable results. Findings are consistent with the theoretical framework behind ACT and contribute to growing evidence, supporting a focus on PF to optimize treatment effects.
Rehabilitation of Visual Loss: Where We Are and Where We Need to Be
Authors: Mansouri Behzad , Roznik Marinya , Rizzo Joseph F. , Prasad Sashank 
Published: December 2017

Background:
Spontaneous recovery of visual loss resulting from injury to the brain is variable. A variety of traditional rehabilitative strategies, including the use of prisms or compensatory saccadic eye movements, have been used successfully to improve visual function and quality-of-life for patients with homonymous hemianopia. More recently, repetitive visual stimulation of the blind area has been reported to be of benefit in expanding the field of vision.

Evidence Acquisition:
We performed a literature review with main focus on clinical studies spanning from 1963 to 2016, including 52 peer-reviewed articles, relevant cross-referenced citations, editorials, and reviews.

Results:
Repetitive visual stimulation is reported to expand the visual field, although the interpretation of results is confounded by a variety of methodological factors and conflicting outcomes from different research groups. Many studies used subjective assessments of vision and did not include a sufficient number of subjects or controls.

Conclusions:
The available clinical evidence does not strongly support claims of visual restoration using repetitive visual stimulation beyond the time that spontaneous visual recovery might occur. This lack of firm supportive evidence does not preclude the potential of real benefit demonstrated in laboratories. Additional well-designed clinical studies with adequate controls and methods to record ocular fixation are needed.
Optical Coherence Tomography in Optic Nerve Hypoplasia: Correlation With Optic Disc Diameter, Nerve Fiber Layer Thickness, and Visual Function
Authors: Kelly John P. , Baran Francine , Phillips James O. , Weiss Avery H. 
Published: December 2017

Background:
The correlation between optic disc diameters (DDs) with average retinal nerve fiber layer thickness (RNFLT) and visual function in children with optic nerve hypoplasia (ONH) having nystagmus is unknown.

Methods:
Data were obtained from a retrospective review of 28 children (mean age: 9.4 years; ±5.1). Optic DD was defined as the maximal horizontal opening of Bruch membrane with spectral optical coherence tomography combined with a confocal laser ophthalmoscope. Average RNFLT was obtained from circumpapillary b-scans. RNFLT was also remeasured at eccentricities that were proportionate with DD to rule out potential sampling artifacts. Visual function was assessed by visual acuity at last follow-up and by visual evoked potentials (VEP) in 11 patients. The eye with the larger DD, which had better visual acuity, was analyzed to exclude potential effects of amblyopia.

Results:
DD was correlated with average RNFLT (r2 = 0.61), visual acuity (r2 = 0.32), and VEPs (r2 = 0.66). The relationship between RNFLT and DD was as follows: average RNFLT (μm) = 0.074 * DD (μm) − 18.8. RNFLT also correlated with the ratio of horizontal optic DD to macula-disc-margin distance (DD:DM; r2 = 0.59). RNFLT measured at eccentricities proportionate with DD showed progressive decrease in thickness only for DDs <1,100 μm. All patients with DD <1,000 μm had subnormal visual acuity, whereas those with DD <1,200 μm had subnormal VEPs.

Conclusions:
DD correlates with average RNFLT and with visual function in children with ONH. Using OCT imaging, DD can be obtained in children with nystagmus and provides objective information.
RNA sequencing of Stentor cell fragments reveals key processes underlying cellular regeneration
Authors: Gustafson Henning Onsbring , Jamy Mahwash , Ettema Thijs J. G. 
Published: December 2017

SummaryWhile ciliates of the genus Stentor are known for their ability to regenerate when their cells are damaged or even fragmented, the physical and molecular mechanisms underlying this process are poorly understood. To identify genes involved in the regenerative capability of Stentor cells, RNA sequencing of individual Stentor polymorphus cell fragments was performed. After splitting a cell over the anterior-posterior axis, the posterior fragment has to regenerate the oral apparatus, while the anterior part needs to regenerate the hold fast. Altogether, differential expression analysis of both posterior and anterior S. polymorphus cell fragments for four different post-split time points revealed over 10,000 up-regulated genes throughout the regeneration process. Among these, genes involved in cell signaling, microtubule-based movement and cell cycle regulation seemed to be particularly important during cellular regeneration. We identified roughly nine times as many up-regulated genes in regenerating S. polymorphus posterior fragments as compared to anterior fragments, indicating that regeneration of the anterior oral apparatus is a complex process that involves many genes. Our analyses identified several expanded groups of genes such as dual-specific tyrosine-(Y)-phosphorylation regulated kinases and MORN domain containing proteins that seemingly act as key-regulators of cellular regeneration. In agreement with earlier morphological and cell biological studies, our differential expression analyses indicate that cellular regeneration and vegetative division share many similarities.
AP-4 mediated ATG9A sorting underlies axonal and autophagosome biogenesis defects in a mouse model of AP-4 deficiency syndrome
Authors: Ivankovic Davor , López-Doménech Guillermo , Drew James , Tooze Sharon A. , Kittler Josef T. 
Published: December 2017

AbstractAdaptor protein (AP) complexes have critical roles in transmembrane protein sorting. AP-4 remains poorly understood in the brain despite its loss of function leading to a hereditary spastic paraplegia termed AP-4 deficiency syndrome. Here we demonstrate that knockout (KO) of AP-4 in a mouse model leads to thinning of the corpus callosum and ventricular enlargement, anatomical defects previously described in patients. At the cellular level, we find that AP-4 KO leads to defects in axonal extension and branching, in addition to aberrant distal swellings. Interestingly, we show that ATG9A, a key protein in autophagosome maturation, is critically dependent on AP-4 for its sorting from the trans-golgi network. Failure of AP-4 mediated ATG9A sorting results in its dramatic retention in the trans-golgi network in vitro and in vivo leading to a specific reduction of the axonal pool of ATG9A. As a result, autophagosome biogenesis is aberrant in the axon of AP-4 deficient neurons. The specific alteration to axonal integrity and axonal autophagosome maturation in AP-4 knockout neurons may underpin the pathology of AP-4 deficiency.
Population genomics of pneumococcal carriage in Massachusetts children following PCV-13 introduction
Authors: Mitchell PK , Azarian T , Croucher NJ , Callendrello A , Thompson CM , Pelton SI , Lipsitch M , Hanage WP 
Published: December 2017

BackgroundThe 13-valent pneumococcal conjugate vaccine (PCV-13) was introduced in the United States in 2010. Using a large pediatric carriage sample collected from shortly after the introduction of PCV-7 to several years after the introduction of PCV-13, we investigate alterations in the composition of the pneumococcal population following the introduction of PCV-13, evaluating the extent to which the post-vaccination non-vaccine type (NVT) population mirrors that from prior to vaccine introduction and the effect of PCV-13 on vaccine type lineages.Methods and FindingsDraft genome assemblies from 736 newly sequenced and 616 previously published pneumococcal carriages isolates from children in Massachusetts between 2001 and 2014 were analyzed. Isolates were classified into one of 22 sequence clusters (SCs) on the basis of their core genome sequence. We calculated the SC diversity for each sampling period as the probability that any two randomly drawn isolates from that period belong to different SCs. The sampling period immediately after the introduction of PCV-13 (2011) was found to have higher diversity than preceding (2007) or subsequent (2014) sampling periods (Simpson’s D 2007: 0.915 95% CI [0.901, 0.929]; 2011: 0.935 [0.927, 0.942]; 2014: 0.912 [0.901, 0.923]). Amongst NVT isolates, we found the distribution of SCs in 2011 to be significantly different from that in 2007 or 2014 (Fisher’s Exact Test p=0.018, 0.0078), but did not find a difference comparing 2007 to 2014 (Fisher’s Exact Test p=0.24), indicating greater similarity between samples separated by a longer time period than between samples from closer time periods. We also found changes in the accessory gene content of the NVT population between 2007 and 2011 to have been reduced by 2014. Amongst the new serotypes targeted by PCV-13, four were present in our sample. The proportion of our sample composed of PCV-13-only vaccine serotypes 19A, 6C, and 7F decreased between 2007 and 2014, but no such reduction was seen for serotype 3. We did, however, observe differences in the genetic composition of the pre- and post-PCV-13 serotype 3 population. Our isolates were collected during discrete sampling periods from a small geographic area, which may limit the generalizability our findings.ConclusionPneumococcal diversity increased immediately following the introduction of PCV-13, but subsequently returned to pre-vaccination levels. This is reflected in the distribution of NVT lineages, and, to a lesser extent, their accessory gene frequencies. As such, there may be a period during which the population is particularly disrupted by vaccination before returning to a more stable distribution. The persistence and shifting genetic composition of serotype 3 is a concern and warrants further investigation.
Additive and interactive effects of spatial attention and expectation on perceptual decisions
Authors: Zuanazzi Arianna , Noppeney Uta 
Published: December 2017

AbstractSpatial attention and expectation are two critical top-down mechanisms controlling perceptual inference. Based on previous research it remains unclear whether their influence on perceptual decisions is additive or interactive.We developed a novel multisensory approach that orthogonally manipulated spatial attention (i.e. task relevance) and expectation (i.e. signal probability) selectively in audition and evaluated their effects on observers’ responses in vision. Critically, while experiment 1 manipulated expectation directly via the probability of task-relevant auditory targets across hemifields, experiment 2 manipulated it indirectly via task-irrelevant auditory non-targets.Surprisingly, our results demonstrate that spatial attention and signal probability influence perceptual decisions either additively or interactively. These seemingly contradictory results can be explained parsimoniously by a model that combines spatial attention, general and spatially selective response probabilities as predictors with no direct influence of signal probability. Our model provides a novel perspective on how spatial attention and expectations facilitate effective interactions with the environment.
A Comprehensive Evaluation of the Genetic Architecture of Sudden Cardiac Arrest
Authors: Ashar Foram N. , Mitchell Rebecca N. , Albert Christine M. , Newton-Cheh Christopher , Brody Jennifer A. , Muller-Nurasyid Martina , Moes Anna , Meitinger Thomas , Mak Angel , Huikuri Heikki , Junttila M. Juhani , Goyette Philippe , Pulit Sara L. , Pazoki Raha , Tanck Michael W. , Blom Marieke T. , Zhao XiaoQing , Hauvlinna Aki S. , Jabbari Reza , Glinge Charlotte , Tragante Vinicius , Escher Stefan A. , Chakravarti Aravinda , Ehret Georg , Coresh Josef , Li Man , Prineas Ronald J. , Franco Oscar H. , Kwok Pui-Yan , Lumley Thomas , Dumas Florence , McKnight Barbara , Rotter Jerome I. , Lemaitre Rozenn N. , Heckbert Susan R. , O’Donnell Christopher J. , Hwang Shih-Jen , Tardif Jean-Claude , Kortelainen Marja-Leena , VanDenburgh Martin , Uitterlinden Andre G. , Hofman Albert , Stricker Bruno H.C. , de Bakker Paul I.W. , Franks Paul W. , Jansson Jan-Hakan , Asselbergs Folkert W. , Halushka Marc K. , Maleszewski Joseph J. , Tfelt-Hansen Jacob , Engstrom Thomas , Salomaa Veikko , Virmani Renu , Kolodgie Frank , Wilde Arthur A.M. , Tan Hanno L. , Bezzina Connie R. , Eijgelsheim Mark , Rioux John D. , Jouven Xavier , Kaab Stefan , Psaty Bruce M. , Siscovick David S. , Arking Dan , Sotoodehnia Nona ,   for the SCD working group of the CHARGE Consortium
Published: December 2017

ABSTRACTBackgroundSudden cardiac arrest (SCA) accounts for 10% of adult mortality in Western populations. While several risk factors are observationally associated with SCA, the genetic architecture of SCA in the general population remains unknown. Furthermore, understanding which risk factors are causal may help target prevention strategies.MethodsWe carried out a large genome-wide association study (GWAS) for SCA (n=3,939 cases, 25,989 non-cases) to examine common variation genome-wide and in candidate arrhythmia genes. We also exploited Mendelian randomization methods using cross-trait multi-variant genetic risk score associations (GRSA) to assess causal relationships of 18 risk factors with SCA.ResultsNo variants were associated with SCA at genome-wide significance, nor were common variants in candidate arrhythmia genes associated with SCA at nominal significance. Using cross-trait GRSA, we established genetic correlation between SCA and (1) coronary artery disease (CAD) and traditional CAD risk factors (blood pressure, lipids, and diabetes), (2) height and BMI, and (3) electrical instability traits (QT and atrial fibrillation), suggesting etiologic roles for these traits in SCA risk.ConclusionsOur findings show that a comprehensive approach to the genetic architecture of SCA can shed light on the determinants of a complex life-threatening condition with multiple influencing factors in the general population. The results of this genetic analysis, both positive and negative findings, have implications for evaluating the genetic architecture of patients with a family history of SCA, and for efforts to prevent SCA in highrisk populations and the general community.
Ultraconserved elements occupy specific arenas of three-dimensional mammalian genome organization
Authors: McCole Ruth B. , Erceg Jelena , Saylor Wren , Wu Chao-ting 
Published: December 2017

ABSTRACTThis study explores the relationships between three-dimensional genome organization and the ultraconserved elements (UCEs), an enigmatic set of DNA elements that show very high DNA sequence conservation between vertebrate reference genomes. Examining both human and mouse genomes, we interrogate the relationship of UCEs to three features of chromosome organization derived from Hi-C studies. Firstly, we report that UCEs are enriched within contact ‘domains’ and, further, that the UCEs that fall into domains shared across diverse cell types are linked to kidney-related and neuronal processes. In ‘boundaries’, UCEs are generally depleted, with those that do overlap boundaries being overrepresented in exonic UCEs. Regarding loop anchors, UCEs are neither over- nor under-represented, with those present in loop anchors being enriched for splice sites compared to all UCEs. Finally, as all of the relationships we observed between UCEs and genomic features are conserved in the mouse genome, our findings suggest that UCEs contribute to interspecies conservation of genome organization and, thus, genome stability.
Global, multiplexed dendritic computations under in vivo-like conditions
Authors: Ujfalussy Balázs B , Lengyel Máté , Branco Tiago 
Published: December 2017

AbstractDendrites integrate inputs in highly non-linear ways, but it is unclear how these non-linearities contribute to the overall input-output transformation of single neurons. Here, we developed statistically principled methods using a hierarchical cascade of linear-nonlinear subunits (hLN) to model the dynamically evolving somatic response of neurons receiving complex spatio-temporal synaptic input patterns. We used the hLN to predict the membrane potential of a detailed biophysical model of a L2/3 pyramidal cell receiving in vivo-like synaptic input and reproducing in vivo dendritic recordings. We found that more than 90% of the somatic response could be captured by linear integration followed a single global non-linearity. Multiplexing inputs into parallel processing channels could improve prediction accuracy by as much as additional layers of local non-linearities. These results provide a data-driven characterisation of a key building block of cortical circuit computations: dendritic integration and the input-output transformation of single neurons during in vivo-like conditions.
Growth and extended survival ofEscherichia coliO157:H7 in soil organic matter
Authors: NandaKafle Gitanjali , Christie Amy A. , Vilain Sébastien , Brözel Volker S. 
Published: December 2017

AbstractEnterohaemorrhagicEscherichia colisuch as serotype O157:H7 are a leading cause of food-associated outbreaks. While the primary reservoir is associated with cattle, plant foods have been associated as sources of human infection.E. coliis able to grow in the tissue of food plants such as spinach. While fecal contamination is the primary suspect, soil has been underestimated as a potential reservoir. Persistence of bacterial populations in open systems is the product of growth, death, predation, and competition. Here we report thatE. coliO157:H7 can grow using the soluble compounds in soil, and characterize the effect of soil growth in the stationary phase proteome.E. coli933D (stxII-) was cultured in Soil Extracted Soluble Organic Matter (SESOM) and the culturable count determined for 24 d. The proteomes of exponential and stationary phase populations were characterized by 2D gel electrophoresis and protein spots were identified by MALDI-TOF mass spectrometry. While LB controls displayed a death phase, SESOM grown population remained culturable for 24 d, indicating an altered physiological state with superior longevity. This was not due to decreased cell density on entry to stationary phase as 24h SESOM populations concentrated 10-fold retained their longevity. Principal component analysis showed that stationary phase proteomes from SESOM and LB were different. Differences included proteins involved in stress response, motility, membrane and wall composition, nutrient uptake, translation and protein turnover, and anabolic and catabolic pathways, indicating an altered physiological state of soil-grown cells entering stationary phase. The results suggest thatE. colimay be a soil commensal that in absence of predation and competition maintains stable populations in soil.
A cortical pathway modulates sensory input into the olfactory striatum
Authors: White Kate A. , Zhang Yun-Feng , Zhang Zhijian , Bhattarai Janardhan P. , Moberly Andrew H. , in ‘t Zandt Estelle , Mi Huijie , Jia Xianglian , Fuccillo Marc V. , Xu Fuqiang , Ma Minghong , Wesson Daniel W. 
Published: December 2017

SummarySensory cortices process stimuli in manners essential for perception. The piriform ‘primary’ olfactory cortex (PCX) extends dense association fibers into the ventral striatum’s olfactory tubercle (OT), yet the function of this cortico-striatal pathway is unknown. We optically stimulated channelrhodopsin-transduced PCX glutamatergic neurons or their association fibers while recording OT neural activity in mice performing an olfactory task. Activation of PCX neurons or their association fibers within the OT controlled the firing of some OT neurons and bidirectionally modulated odor coding dependent upon the neuron’s intrinsic odor responsivity. Further, patch clamp recordings and retroviral tracing from D1 and D2 dopamine receptor-expressing OT medium spiny neurons revealed this input can be monosynaptic and that both cell types receive most of their input from a specific spatial zone localized within the ventro-caudal PCX. These results demonstrate that the PCX functionally accesses the direct and indirect pathways of the basal ganglia within the OT.
Modulation of formin processivity by profilin and mechanical tension
Authors: Kerleau Mikael , Cao Luyan , Suzuki Emiko , Wioland Hugo , Jouet Sandy , Guichard Bérengère , Lenz Martin , Romet-Lemonne Guillaume , Jégou Antoine 
Published: December 2017

ABSTRACTFormins are major regulators of actin networks. They enhance actin filament dynamics by remaining processively bound to filament barbed ends. How biochemical and mechanical factors affect formin processivity are open questions. Monitoring individual actin filaments in a microfluidic flow, we report that formin mDia1 dissociates faster under higher ionic strength and when actin concentration is increased. Profilin, known to increase the elongation rate of formin-associated filaments, surprisingly decreases the formin dissociation rate, by bringing formin FH1 domains in transient contact with the barbed end. In contrast, piconewton tensile forces applied to actin filaments accelerate formin dissociation by orders of magnitude, largely overcoming profilin-mediated stabilization. We developed a model of formin conformations and its confrontation to our data indicates the existence of two different dissociation pathways, with force favoring one over the other. How cells limit formin dissociation under tension is now a key question for future studies.