bluuebunny/crossref_metadata_2025 huggingface dataset:
Ictal Bigeminy
Authors: Widdess-Walsh P. , Nair D.
Published: February 2012

Seizures can influence cardiac autonomic function and cause abnormalities in the electrocardiogram (EKG). 1 A case of stereotypical bigeminy during left temporal lobe seizures recorded in the epilepsy monitoring unit is presented. The mechanism is likely due to spread of the ictal discharge to primary visceromotor regions in the left insula (Island of Reil). This case illustrates the potential influence of ictal brain activity on cardiac electrophysiology.
Dental Hardware Complicating Diagnosis in Refractory Gelastic Epilepsy Secondary to Hypothalamic Hamartoma
Authors: Bateman Lisa M. , Latchaw Richard , Seyal Masud
Published: February 2012

Hypothalamic hamartomas (HH) are developmental malformations of the hypothalamus associated with a potentially treatable epileptic encephalopathy, characterized by early onset gelastic seizures, the later development of multiple seizure types and progressive cognitive and behavioral decline. Surgical treatment of HH can lead to seizure control and improvement in the cognitive-behavioral syndrome. Video-EEG telemetry (VET) is often necessary to characterize the semiology of the seizures, but there are no specific interictal or ictal EEG patterns that will confirm the diagnosis. Magnetic resonance imaging (MRI) can identify HH and define their anatomy, but the imaging findings may be subtle and susceptible to artifactual contamination. We present a patient with intractable gelastic epilepsy in whom the diagnosis of HH was initially missed due to failure to recognize the clinical syndrome and contamination of the MRI images with dental hardware artifact. VET confirmed the clinical diagnosis and the HH was identified on MRI after the dental hardware was removed. VET should be performed to confirm seizure semiology in patients with suspected gelastic epilepsy. Establishing this diagnosis can subsequently direct the appropriate neuroradiological evaluation for HH and surgical treatment of these lesions.
ERP Generator Patterns in Schizophrenia during Tonal and Phonetic Oddball Tasks: Effects of Response Hand and Silent Count
Authors: Kayser Jürgen , Tenke Craig E. , Gil Roberto , Bruder Gerard E.
Published: February 2012

Greater left than right reductions of P3 amplitude in schizophrenia during auditory oddball tasks have been interpreted as evidence of left-lateralized dysfunction. However, the contributions of methodological factors (response mode, stimulus properties, recording reference), which affect event-related potential (ERP) topographies, remain unclear. We recorded 31-channel ERPs from 23 schizophrenic patients and 23 age- and gender-matched healthy controls (all right-handed) during tonal and phonetic oddball tasks, varying response mode (left press, right press, silent count) within subjects. Performance accuracy was high in both groups but patients were slower. ERP generator patterns were summarized by temporal Principal Components Analysis (PCA; unrestricted Varimax) from reference-free current source density (CSD; spherical spline Laplacians) waveforms, which sharpen scalp topographies. CSD represents the magnitude of the radial current flow entering (source) and leaving (sink) the scalp. Both patients and controls showed asymmetric frontolateral and parietotemporal N2 sinks peaking at 240 ms and asymmetric parietal P3 sources (355 ms) for targets (tonal R < L, phonetic L > R), but frontocentral N2 sinks and parietal P3 sources were bilaterally reduced in patients. A response-related midfrontal sink and accompanying centroparietal source (560 ms) were highly comparable across groups. However, a superimposed left temporal source was larger for silent count compared to button press, and this difference was smaller in patients. In both groups, left or right press produced opposite, region-specific asymmetries originating from central sites, modulating the N2/P3 complex. The results suggest bilaterally reduced neural generators of N2 and P3 in schizophrenia during auditory oddball tasks, but both groups showed comparable topographic effects of task and response mode. However, additional working memory demands during silent count may partially overlap in time the generation of the N2/P3 complex and differentially affect the asymmetry of P3 subcomponents, particularly when employing conventional ERP measures.
EEG Hemispheric Asymmetries during Cognitive Tasks in Depressed Patients with High versus Low Trait Anxiety
Authors: Manna Carlye B.G. , Tenke Craig E. , Gates Nathan A. , Kayser Jürgen , Borod Joan C. , Stewart Jonathan W. , McGrath Patrick J. , Bruder Gerard E.
Published: February 2012

Studies of regional hemispheric asymmetries point to relatively less activity in left frontal and right posterior regions in depression. Anxiety was associated with increased right posterior activity, which may be related to arousal and, in anxious-depressed individuals, offset the posterior asymmetry typically seen in depression. These asymmetries have been indexed by resting EEG or inferred through the use of lateralized auditory and visual tasks (e.g., dichotic listening and chimeric faces). However, associations between regional EEG activity and neurocognitive function in depression or anxiety remain unclear. The present study used matched verbal (Word Finding) and spatial (Dot Localization) tasks to compare task-related alpha asymmetries in depressed patients grouped according to level of trait anxiety. EEG and behavioral performance were recorded from depressed patients with high anxiety (n=14) or low anxiety (n=14) and 21 age- and education-matched healthy adults during the two tasks, and alpha power was averaged within each task. As predicted, the two patient groups exhibited opposite patterns of regional hemispheric alpha asymmetry. Greater right than left central-parietal activation was seen in the high-anxiety depressed group during the spatial task, whereas greater left than right frontal-central activation was found in the low-anxiety depressed group during the verbal task. Group differences in task performance were in the expected direction but did not reach statistical significance. These results are consistent with Heller's two-dimensional model of depression and anxiety and highlight the sensitivity of task-related EEG alpha in discriminating among subgroups of depressed patients differing in trait anxiety.
EEG Topography and Tomography (LORETA) in Diagnosis and Pharmacotherapy of Depression
Authors: Saletu B. , Anderer P. , Saletu-Zyhlarz G.M.
Published: February 2012

Earlier investigations suggested an involvement of the right hemisphere and the left prefrontal cortex (PFC) in the pathogenesis of depression. This paper presents our own electroencephalographic (EEG) topography and low-resolution brain electromagnetic tomography (LORETA) data obtained in unmedicated depressed patients, and the effects of two representative drugs of non-sedative and sedative antidepressants, i.e., citalopram (CIT) and imipramine (IMI), as compared with placebo in normal subjects.

Sixty female menopausal syndrome patients with the diagnosis of a depressive episode without psychotic symptoms as well as 30 healthy controls were investigated. Concerning the effects of antidepressants, normal healthy subjects received single oral doses of 20 mg CIT, 75 mg IMI and placebo p.o. A 3-min vigilance-controlled EEG and a 4-min resting EEG was recorded pre- and post-drug administration and analyzed by means of EEG mapping and LORETA.

In the EEG mapping, depressed patients demonstrated a decrease in absolute power in all frequency bands, an augmentation of relative delta/theta and beta and a decrease in alpha activity as well as a slowing of the delta/theta centroid and an acceleration of the alpha and beta centroid, which suggests vigilance decrements. In the alpha asymmetry index, they showed right frontal hyper- and left frontal hypoactivation correlated with the Hamilton Depression Score (HAMD). LORETA predominantly revealed decreased power in the theta and alpha-1 frequency band. Negative correlations between theta power and the HAMD were observed in the ventro-medial PFC, the bilateral rostral anterior cingulate cortex (ACC) and the left insular cortex; between alpha-1 power and the HAMD in the right PFC. In the EEG mapping of antidepressants, 20 mg CIT showed mainly activating, 75 mg IMI partly sedative properties. LORETA revealed that CIT increased alpha-2, beta-1, beta-2 and beta-3 power more over the right than over the left hemisphere. However, also a left temporal and frontal delta increase was observed.

In conclusion, EEG topography and tomography of depressed menopausal patients demonstrated a right frontal hyper- and left frontal hypoactivation in the alpha asymmetry index as well as a vigilance decrease, with a right-hemispheric preponderance. Within antidepressants at least 2 subtypes may be distinguished from the electrophysiological point of view, a non-sedative and a sedative. LORETA identifies cerebral generators responsible for the pathogenesis of depression as well as for the mode of action of antidepressants.
Some Evidence of Bilateral Speech Representation in Sinistrals
Authors: Taylor David C. , Falconer Murray A. , Flor-Henry Pierre
Published: February 2012

The information provided by pre and post-operative surface EEG, cortical EEG, cortical stimulation, intracarotid barbiturization, psychometric testing and ictal semiology are integrated in order to define the speech regions. The three patients described are predominantly left handed and left cerebral hemisphere dominant, all with right hemisphere epilepsy. All are considered to have bi-lateral speech representation to account for dysphasia during cortical stimulation in all three and ictal or post ictal dysphasia in the first two and post-operative dysphasia in the first and third. Some of the evidence that supports the possibility of bi-lateral speech representation is discussed.
The Use of Permutation Entropy to Characterize Sleep Electroencephalograms
Authors: Nicolaou N. , Georgiou J.
Published: February 2012

This work proposes the use of Permutation Entropy (PE), a measure of time-series complexity, to characterize electroencephalogram (EEG) signals recorded during sleep. Such a measure could provide information concerning the different sleep stages and, thus, be utilized as an additional aid to obtain sleep staging information. PE has been estimated for artifact-free 30s segments from more than 80 hours of EEG records obtained from 16 subjects during all-night recordings, from which the mean PE for each sleep stage was obtained. It was found that different sleep stages are characterized by significantly different PE values, which track the physiological changes in the complexity of the EEG signals observed at the different sleep stages. This finding encourages the use of PE as an additional aide to either visual or automated sleep staging.
Low-Frequency Repetitive Transcranial Magnetic Stimulation for the Treatment of Refractory Partial Epilepsy
Authors: Sun Wei , Fu Wei , Mao Wei , Wang Dequan , Wang Yuping
Published: February 2012

Seventeen refractory partial epilepsy patients were enrolled in an open-label study to evaluate the antiepileptic effect of low-frequency repetitive transcranial magnetic stimulation (rTMS). Seven of the patients had not obtained seizure-free status after epileptogenic focus resection surgery before they were enrolled in the study. All patients were treated with low-frequency rTMS which included 3 sessions per day (0.5 Hz, 90% RMT and 500 pulses each session) and lasted for 2 weeks. Seizure frequency, seizure days and epileptic discharges in the EEG obtained before, during and after stimulation were compared. The psychological conditions of all individual patients were evaluated with Symptom Checklist-90 (SCL-90) before and after rTMS treatment.

Mean seizure frequencies per week significantly decreased in the following 4-week rTMS treatment period compared with the pretreatment period (14.09 vs. 5.63, p < 0.05, mean reduction of 60.02% in seizure frequency). Mean seizure days per week during the treatment period and the post-treatment period were lower than that of the pretreatment period (5.18 vs. 2.99 p < 0.05, mean reduction of 42.5% in seizure days). Mean epileptic discharges in the EEG decreased significantly during the treatment period compared to that of the pre-treatment period (78.60 vs. 66.09, p < 0.05, mean reduction of 15.9% in epileptic spikes discharges) in all 17 patients. Fourteen patients completed the test of Symptom Checklist-90 effectively. The scales of Global Severity Index, Depression, Anxiety, Phobic anxiety, Paranoid ideation, Psychoticism, Somatization, Obsession-compulsion, Interpersonal sensitivity, Hostility in patients decreased respectively at the post-treatment periods compared with those of the pre-treatment periods (P < 0.05). Low-frequency rTMS may have a significant antiepileptic effect in patients with refractory partial epilepsy. Additionally, our results indicate rTMS treatment can improve the psychological condition of these patients.
Individualized Alpha Activity and Frontal Asymmetry in Major Depression
Authors: Segrave R.A. , Cooper N.R. , Thomson R.H. , Croft R.J. , Sheppard D.M. , Fitzgerald P.B.
Published: February 2012

Lateralized differences in frontal alpha power in individuals with major depressive disorder (MDD) are thought to reflect an aberrant affective processing style. However research into anterior alpha asymmetry and MDD has often produced conflicting results. The current study aimed to investigate whether individualized alpha bandwidths provide a more sensitive measure of anterior alpha asymmetry in MDD than the traditional fixed 8–13 Hz alpha band. Resting EEG was recorded from 34 right-handed female participants (18 controls, 16 MDD). Each participant's Individual Alpha Frequency was used to delineate a broad individualized alpha band and three individualized narrow alpha sub-bands: lower alpha1, lower alpha 2 and upper alpha. Activity within the broad and narrow individualized bandwidths and within the traditional fixed alpha band were used to compare a) controls and acutely depressed individuals and b) medicated and unmedicated MDD participants. Individualizing and subdividing the alpha bandwidth did not add appreciably to the sensitivity of anterior alpha asymmetry in MDD as no significant differences in lateralized alpha power between controls and MDD participants were observed in any alpha bandwidth. This finding was consistent under two reference schemes and across multiple scalp locations. Within the MDD group, antidepressant use was associated with significantly greater right than left hemispheric power in the lower alpha 1 band. The relevance of this finding is discussed in relation to the electrophysiological correlates of antidepressant medication use, lateralized differences in affective processing and treatment resistant MDD.
Decreased Delta Event-Related Synchronization in Patients with Early Vascular Dementia
Authors: Xu Jin , Zhao Songzhen , Zhang Haoshi , Zheng Chongxun
Published: February 2012

Electroencephalogram (EEG) activity, recorded while performing an “odd ball” detection task, was compared between patients with early vascular dementia (VD), healthy young controls and healthy elderly controls performing the same task. The data were analyzed using the event-related synchronization/desynchronization (ERS/ERD) method. VD patients, compared with controls, showed decreased ERS effects in the delta frequency band (0.5–3.5Hz) of EEG after the target stimulus appeared in frontal, central and parietal regions. Similarly, elderly controls also showed a decreased ERS compared with young controls only in central and parietal regions. As part of this analysis, we introduce a novel quantitative index, the Event-related Energy Change Progression (EECP), which provides a reliable measure that distinguishes these groups and thereby provides a promising marker for early diagnosis of VD.
Bihemispheric Cerebral FDG PET Correlates of Cognitive Dysfunction as Assessed by the CERAD in Alzheimer's Disease
Authors: Schönknecht Oskar Dieter Peter , Hunt Aoife , Toro Pablo , Guenther Thomas , Henze Marcus , Haberkorn Uwe , Schröder Johannes
Published: February 2012

Alzheimer's disease (AD) is characterized by a variety of cognitive deficits which can be reliably assessed by the neuropsychological test battery of the Consortium to Establish a Registry for Alzheimer's Disease (CERAD), but the cerebral changes underlying the respective cognitive deficits are only partly understood. Measures of severity of dementia in AD as well as delayed episodic memory performance in mild cognitive impairment significantly correlated with bihemispheric cerebral glucose hypometabolism. We therefore hypothesized that the CERAD cognitive battery may represent cerebral dysfunction of both hemispheres in patients with AD.

In 32 patients with AD, cerebral glucose metabolism was investigated using positron-emission-tomography with 18 Fluorodeoxyglucose (FDG PET) and associated with the test scores of the CERAD cognitive battery by statistical parametric mapping.

Episodic memory scores significantly correlated with temporoparietal glucose metabolism of both hemispheres while delayed episodic memory significantly was correlated with the right frontotemporal cortices. Verbal fluency and naming scores significantly correlated with glucose metabolism in left temporoparietal and right frontal cortices, whereas constructional praxis predominantly correlated significantly with the bilateral precuneus.

In conclusion, the results of our study demonstrate that not only memory function but also functions of language and constructional praxis in AD are associated with glucose metabolism as revealed by FDG PET in subsets of uni- and bilateral brain areas. The findings of our study for the first time demonstrate that in AD neuropsychological deficits as assessed by the CERAD refer to different cerebral sites of both hemispheres.
Simultaneous EEG/fMRI Analysis of the Resonance Phenomena in Steady-State Visual Evoked Responses
Authors: Bayram Ali , Bayraktaroglu Zubeyir , Karahan Esin , Erdogan Basri , Bilgic Basar , Özker Muge , Kasikci Itir , Duru Adil D. , Ademoglu Ahmet , Öztürk Cengizhan , Arikan Kemal , Tarhan Nevzat , Demiralp Tamer
Published: February 2012

The stability of the steady-state visual evoked potentials (SSVEPs) across trials and subjects makes them a suitable tool for the investigation of the visual system. The reproducible pattern of the frequency characteristics of SSVEPs shows a global amplitude maximum around 10 Hz and additional local maxima around 20 and 40 Hz, which have been argued to represent resonant behavior of damped neuronal oscillators.

Simultaneous electroencephalogram/functional magnetic resonance imaging (EEG/fMRI) measurement allows testing of the resonance hypothesis about the frequency-selective increases in SSVEP amplitudes in human subjects, because the total synaptic activity that is represented in the fMRI-Blood Oxygen Level Dependent (fMRI-BOLD) response would not increase but get synchronized at the resonance frequency. For this purpose, 40 healthy volunteers were visually stimulated with flickering light at systematically varying frequencies between 6 and 46 Hz, and the correlations between SSVEP amplitudes and the BOLD responses were computed.

The SSVEP frequency characteristics of all subjects showed 3 frequency ranges with an amplitude maximum in each of them, which roughly correspond to alpha, beta and gamma bands of the EEG. The correlation maps between BOLD responses and SSVEP amplitude changes across the different stimulation frequencies within each frequency band showed no significant correlation in the alpha range, while significant correlations were obtained in the primary visual area for the beta and gamma bands.

This non-linear relationship between the surface recorded SSVEP amplitudes and the BOLD responses of the visual cortex at stimulation frequencies around the alpha band supports the view that a resonance at the tuning frequency of the thalamo-cortical alpha oscillator in the visual system is responsible for the global amplitude maximum of the SSVEP around 10 Hz.

Information gained from the SSVEP/fMRI analyses in the present study might be extrapolated to the EEG/fMRI analysis of the transient event-related potentials (ERPs) in terms of expecting more reliable and consistent correlations between EEG and fMRI responses, when the analyses are carried out on evoked or induced oscillations (spectral perturbations) in separate frequency bands instead of the time-domain ERP peaks.
Multimodal Quantitative Neuroimaging Databases and Methods: The Cuban Human Brain Mapping Project
Authors: Hernandez-Gonzalez Gertrudis , Bringas-Vega Maria L. , Galán-Garcia Lidice , Bosch-Bayard Jorge , Lorenzo-Ceballos Yenisleidy , Melie-Garcia Lester , Valdes-Urrutia Lourdes , Cobas-Ruiz Marcia , Valdes-Sosa Pedro A. ,   Cuban Human Brain Mapping Project (CHBMP)
Published: February 2012

This article reviews the contributions of the Cuban Neuroscience Center to the evolution of the statistical parametric mapping (SPM) of quantitative Multimodal Neuroimages (qMN), from its inception to more recent work. Attention is limited to methods that compare individual qMN to normative databases (n/qMN). This evolution is described in three successive stages: (a) the development of one variant of normative topographical quantitative EEG (n/qEEG-top) which carries out statistical comparison of individual EEG spectral topographies with regard to a normative database — as part of the now popular SPM of brain descriptive parameters; (b) the development of n/qEEG tomography (n/qEEG-TOM), which employs brain electrical tomography (BET) to calculate voxelwise SPM maps of source spectral features with respect to a norm; (c) the development of a more general n/qMN by substituting EEG parameters with other neuroimaging descriptive parameters to obtain SPM maps.

The study also describes the creation of Cuban normative databases, starting with the Cuban EEG database obtained in the early 90s, and more recently, the Cuban Human Brain Mapping Project (CHBMP). This project has created a 240 subject database of the normal Cuban population, obtained from a population-based random sample, comprising clinical, neuropsychological, EEG, MRI and SPECT data for the same subjects. Examples of clinical studies using qMN are given and, more importantly, receiver operator characteristics (ROC) analyses of the different developments document a sustained effort to assess the clinical usefulness of the techniques.
A Comparison among Several P300 Brain-Computer Interface Speller Paradigms
Authors: Fazel-Rezai Reza , Gavett Scott , Ahmad Waqas , Rabbi Ahmed , Schneider Eric
Published: February 2012

Since the brain-computer interface (BCI) speller was first proposed by Farwell and Donchin, there have been modifications in the visual aspects of P300 paradigms. Most of the changes are based on the original matrix format such as changes in the number of rows and columns, font size, flash/blank time, and flash order. The improvement in the resulting accuracy and speed of such systems has always been the ultimate goal. In this study, we have compared several different speller paradigms including row-column, single character flashing, and two region-based paradigms which are not based on the matrix format. In the first region-based paradigm, at the first level, characters and symbols are distributed over seven regions alphabetically, while in the second region-based paradigm they are distributed in the most frequently used order. At the second level, each one of the regions is further subdivided into seven subsets. The experimental results showed that the average accuracy and user acceptability for two region-based paradigms were higher than those for traditional paradigms such as row/column and single character.
Accuracy of a P300 Speller for People with Motor Impairments: A Comparison
Authors: Ortner Rupert , Aloise Fabio , Prückl Robert , Schettini Francesca , Putz Veronika , Scharinger Josef , Opisso Eloy , Costa Ursula , Guger Christoph
Published: February 2012

A Brain-Computer Interface (BCI) provides a completely new output pathway that can provide an additional option for a person to express himself/her self if he/she suffers a disorder like amyotrophic lateral sclerosis (ALS), brainstem stroke, brain or spinal cord injury or other diseases which impair the function of the common output pathways which are responsible for the control of muscles. For a P300 based BCI a matrix of randomly flashing characters is presented to the participant. To spell a character the person has to attend to it and to count how many times the character flashes. Although most BCIs are designed to help people with disabilities, they are mainly tested on healthy, young subjects who may achieve better results than people with impairments. In this study we compare measurements, performed on people suffering motor impairments, such as stroke or ALS, to measurements performed on healthy people. The overall accuracy of the persons with motor impairments reached 70.1% in comparison to 91% obtained for the group of healthy subjects. When looking at single subjects, one interesting example shows that under certain circumstances, when it is difficult for a patient to concentrate on one character for a longer period of time, the accuracy is higher when fewer flashes (i.e., stimuli) are presented. Furthermore, the influence of several tuning parameters is discussed as it shows that for some participants adaptations for achieving valuable spelling results are required. Finally, exclusion criteria for people who are not able to use the device are defined.
Graph Theoretical Analysis of Organization of Functional Brain Networks in ADHD
Authors: Ahmadlou Mehran , Adeli Hojjat , Adeli Amir
Published: February 2012

This article presents a new methodology for investigation of the organization of the overall and hemispheric brain network of patients with attention-deficit hyperactivity disorder (ADHD) using theoretical analysis of a weighted graph with the goal of discovering how the brain topology is affected in such patients. The synchronization measure used is the nonlinear fuzzy synchronization likelihood (FSL) developed by the authors recently. Recent evidence indicates a normal neocortex has a small-world (SW) network with a balance between local structure and global structure characteristics. Such a network results in optimal balance between segregation and integration which is essential for high synchronizabilty and fast information transmission in a complex network. The SW network is characterized by the coexistence of dense clustering of connections ( C) and short path lengths ( L) among the network units. The results of investigation of C show the local structure of functional left-hemisphere brain networks of ADHD diverges from that of non-ADHD which is recognizable in the delta electroencephalograph (EEG) sub-band. Also, the results of investigation for L show the global structure of functional left-hemisphere brain networks of ADHD diverges from that of non-ADHD which is observable in the delta EEG sub-band. It is concluded that the changes in left-hemisphere brain's structure of ADHD from that of the non-ADHD are so much that L and C can distinguish the ADHD brain from the non-ADHD brain in the delta EEG sub-band.
Political alienation among migrant youths: Exploring the mechanisms of political alienation and acculturation among migrant youths in Norwegian schools
Authors: Solhaug Trond
Published: February 2012

This article addresses the following question: What characterizes the mechanisms of political alienation among non-Western immigrant students, and how might these mechanisms be related to student’s acculturation attitudes? A theory of political alienation and acculturation is applied. Substantial quantitative data from Norwegian upper secondary school students reveals that non-Western immigrant students particularly see themselves as less politically involved than their Norwegian counterparts. Interviews were carried out with a selection of immigrant students from different background to explore the reasons for their political alienation. A number of mechanisms in political alienation were found and discussed. The interviews reveal a close link between political alienation, and the immigrant identity and their acculturation processes.
Identification of wounding and topping responsive small RNAs in tobacco (Nicotiana tabacum)
Authors: Tang She , Wang Yu , Li Zefeng , Gui Yijie , Xiao Bingguang , Xie Jiahua , Zhu Qian-Hao , Fan Longjiang
Published: February 2012

Background

MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are two major classes of small RNAs. They play important regulatory roles in plants and animals by regulating transcription, stability and/or translation of target genes in a sequence-complementary dependent manner. Over 4,000 miRNAs and several classes of siRNAs have been identified in plants, but in tobacco only computational prediction has been performed and no tobacco-specific miRNA has been experimentally identified. Wounding is believed to induce defensive response in tobacco, but the mechanism responsible for this response is yet to be uncovered.

Results

To get insight into the role of small RNAs in damage-induced responses, we sequenced and analysed small RNA populations in roots and leaves from wounding or topping treated tobacco plants. In addition to confirmation of expression of 27 known miRNA families, we identified 59 novel tobacco-specific miRNA members of 38 families and a large number of loci generating phased 21- or 24-nt small RNAs (including ta-siRNAs). A number of miRNAs and phased small RNAs were found to be responsive to wounding or topping treatment. Targets of small RNAs were further surveyed by degradome sequencing.

Conclusions

The expression changes of miRNAs and phased small RNAs responsive to wounding or topping and identification of defense related targets for these small RNAs suggest that the inducible defense response in tobacco might be controlled by pathways involving small RNAs.
The relationship between low back pain and leisure time physical activity in a working population of cleaners - a study with weekly follow-ups for 1 year
Authors: Jespersen Tobias , Jørgensen Marie B , Hansen Jørgen V , Holtermann Andreas , Søgaard Karen
Published: February 2012

Background

Low back pain (LBP) and leisure time physical activity (LTPA) are considered to be closely related, and clinical guidelines for the treatment of acute LBP recommend patients stay physically active. However, the documentation for this recommendation is sparse and based on studies involving patient populations. The purpose of the study was (1) to investigate the correlation between LBP and LTPA on a weekly basis over the course of a year in a high-risk group of cleaners; and (2) to investigate if maintaining LTPA during an episode of acute LBP has a positive effect on LBP intensity in the subsequent 4 weeks.

Methods

188 cleaners consented to participate in a 52-week text message survey about hours of LTPA and intensity of LBP (from 0 to 9) over the previous 7 days. The correlation between LBP and LTPA was calculated by Pearson correlation coefficient. During an episode of acute LBP, a mixed effect logistic regression model was used to investigate whether cleaners who maintain LTPA have a lower pain intensity and higher probability of returning to initial pain intensity within the following four weeks compared with cleaners who decrease LTPA during acute LBP.

Results

The correlation between weekly LTPA and LBP data was negative, but numerically low (r = -0.069) and statistically insignificant (p = 0.08). Among the 82 cleaners experiencing at least one episode of acute LBP, those maintaining LTPA during an episode of acute LBP did not have a lower pain intensity (average LBP intensity difference between groups of 0.06; 95% confidence interval (95% CI) of -0.417 to 0.539) or higher probability of returning to initial pain level (Odds ratio 1,02; 95% CI of 0.50 to 2.09) in the following four weeks compared with cleaners decreasing LTPA during acute LBP.

Conclusions

Hours of LTPA and intensity of LBP measured on a weekly basis throughout a year showed no close correlation. Maintaining LTPA during an episode of acute LBP did not result in a positive effect on LBP in the following 4 weeks. Documentation of LTPA recommendations for acute LBP in working populations is still needed.
Nanoscale anisotropic plastic deformation in single crystal GaN
Authors: Huang Jun , Xu Ke , Fan Ying Min , Niu Mu Tong , Zeng Xiong Hui , Wang Jian Feng , Yang Hui
Published: February 2012

Elasto-plastic mechanical deformation behaviors of c-plane (0001) and nonpolar GaN single crystals are studied using nanoindentation, cathodoluminescence, and transmission electron microscopy. Nanoindentation tests show that c-plane GaN is less susceptible to plastic deformation and has higher hardness and Young's modulus than the nonpolar GaN. Cathodoluminescence and transmission electron microscopy characterizations of indent-induced plastic deformation reveal that there are two primary slip systems for the c-plane GaN, while there is only one most favorable slip system for the nonplane GaN. We suggest that the anisotropic elasto-plastic mechanical properties of GaN are relative to its anisotropic plastic deformation behavior.

PACS: 62.20.fq; 81.05.Ea; 61.72.Lk.
Accelerating large-scale protein structure alignments with graphics processing units
Authors: Pang Bin , Zhao Nan , Becchi Michela , Korkin Dmitry , Shyu Chi-Ren
Published: February 2012

Background

Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons.

Findings

We present ppsAlign, a p arallel p rotein s tructure Align ment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs). As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH.

Conclusions

ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper allows large-scale structure comparisons to be performed using massive parallel computing power of GPU.
Interpretation of genome-wide infinium methylation data from ligated DNA in formalin-fixed, paraffin-embedded paired tumor and normal tissue
Authors: Jasmine Farzana , Rahaman Ronald , Roy Shantanu , Raza Maruf , Paul Rupash , Rakibuz-Zaman Muhammad , Paul-Brutus Rachelle , Dodsworth Charlotte , Kamal Mohammed , Ahsan Habibul , Kibriya Muhammad G
Published: February 2012

Background

Formalin-fixed, paraffin-embedded (FFPE) samples are a highly desirable resource for epigenetic studies, but there is no suitable platform to assay genome-wide methylation in these widely available resources. Recently, Thirlwell et al. (2010) have reported a modified ligation-based DNA repair protocol to prepare FFPE DNA for the Infinium methylation assay. In this study, we have tested the accuracy of methylation data obtained with this modification by comparing paired fresh-frozen (FF) and FFPE colon tissue (normal and tumor) from colorectal cancer patients. We report locus-specific correlation and concordance of tumor-specific differentially methylated loci (DML), both of which were not previously assessed.

Methods

We used Illumina's Infinium Methylation 27K chip for 12 pairs of FF and 12 pairs of FFPE tissue from tumor and surrounding healthy tissue from the resected colon of the same individual, after repairing the FFPE DNA using Thirlwell's modified protocol.

Results

For both tumor and normal tissue, overall correlation of β values between all loci in paired FF and FFPE was comparable to previous studies. Tissue storage type (FF or FFPE) was found to be the most significant source of variation rather than tissue type (normal or tumor). We found a large number of DML between FF and FFPE DNA. Using ANOVA, we also identified DML in tumor compared to normal tissue in both FF and FFPE samples, and out of the top 50 loci in both groups only 7 were common, indicating poor concordance. Likewise, while looking at the correlation of individual loci between FFPE and FF across the patients, less than 10% of loci showed strong correlation (r ≥ 0.6). Finally, we checked the effect of the ligation-based modification on the Infinium chemistry for SNP genotyping on an independent set of samples, which also showed poor performance.

Conclusion

Ligation of FFPE DNA prior to the Infinium genome-wide methylation assay may detect a reasonable number of loci, but the numbers of detected loci are much fewer than in FF samples. More importantly, the concordance of DML detected between FF and FFPE DNA is suboptimal, and DML from FFPE tissues should be interpreted with great caution.
New full-wave phase-shift approach to solve the Helmholtz acoustic wave equation for modeling
Authors: Maji Kaushik , Gao Fuchun , Abeykoon Sameera K. , Kouri Donald J.
Published: February 2012

We have developed a method of solving the Helmholtz equation based on a new way to generalize the “one-way” wave equation, impose correct boundary conditions, and eliminate exponentially growing evanescent waves. The full two-way nature of the Helmholtz equation is included, but the equation is converted into a pseudo one-way form in the framework of a generalized phase-shift structure consisting of two coupled first-order partial differential equations for wave propagation with depth. A new algorithm, based on the particular structure of the coupling between [Formula: see text] and [Formula: see text], is introduced to treat this problem by an explicit approach. More precisely, in a depth-marching strategy, the wave operator is decomposed into the sum of two matrices: The first one is a propagator in a reference velocity medium, whereas the second one is a perturbation term which takes into account the vertical and lateral variation of the velocity. The initial conditions are generated by solving the Lippmann-Schwinger integral equation formally, in a noniterative fashion. The approach corresponds essentially to “factoring out” the physical boundary conditions, thereby converting the inhomogeneous Lippmann-Schwinger integral equation of the second kind into a Volterra integral equation of the second kind. This procedure supplies artificial boundary conditions, along with a rigorous method for converting these solutions to those satisfying the correct, Lippmann-Scwinger (physical) boundary conditions. To make the solution numerically stable, the Feshbach projection operator technique is used to remove only the nonphysical exponentially growing evanescent waves, while retaining the exponentially decaying evanescent waves, along with all propagating waves. Suitable absorbing boundary conditions are implemented to deal with reflection or wraparound from boundaries. At the end, the Lippmann-Schwinger solutions are superposed to produce time snapshots of the propagating wave.
Phase I Trial of Anti-CD22 Recombinant Immunotoxin Moxetumomab Pasudotox (CAT-8015 or HA22) in Patients With Hairy Cell Leukemia
Authors: Kreitman Robert J. , Tallman Martin S. , Robak Tadeusz , Coutre Steven , Wilson Wyndham H. , Stetler-Stevenson Maryalice , FitzGerald David J. , Lechleider Robert , Pastan Ira
Published: February 2012

Purpose

To conduct a phase I dose-escalation trial assessing safety and response of recombinant immunotoxin moxetumomab pasudotox (CAT-8015, HA22) in chemotherapy-resistant hairy cell leukemia (HCL).

Patients and Methods

Eligible patients had relapsed/refractory HCL after ≥ two prior therapies and required treatment because of abnormal blood counts. Patients received moxetumomab pasudotox 5 to 50 μg/kg every other day for three doses (QOD ×3), with up to 16 cycles repeating at ≥ 4-week intervals if patients did not experience disease progression or develop neutralizing antibodies.

Results

Twenty-eight patients were enrolled, including three patients each at 5, 10, 20, and 30 μg/kg, four patients at 40 μg/kg, and 12 patients at 50 μg/kg QOD ×3 for one to 16 cycles each (median, four cycles). Dose-limiting toxicity was not observed. Two patients had transient laboratory abnormalities consistent with grade 2 hemolytic uremic syndrome with peak creatinine of 1.53 to 1.66 mg/dL and platelet nadir of 106,000 to 120,000/μL. Drug-related toxicities in 25% to 64% of the 28 patients included (in decreasing frequency) grade 1 to 2 hypoalbuminemia, aminotransferase elevations, edema, headache, hypotension, nausea, and fatigue. Of 26 patients evaluable for immunogenicity, 10 patients (38%) made antibodies neutralizing more than 75% of the cytotoxicity of 1,000 ng/mL of immunotoxin, but this immunogenicity was rare (5%) after cycle 1. The overall response rate was 86%, with responses observed at all dose levels, and 13 patients (46%) achieved complete remission (CR). Only 1 CR lasted less than 1 year, with the median disease-free survival time not yet reached at 26 months.

Conclusion

Moxetumomab pasudotox at doses up to 50 μg/kg QOD ×3 has activity in relapsed/refractory HCL and has a safety profile that supports further clinical development for treatment of this disease.
Reflex Immunohistochemistry and Microsatellite Instability Testing of Colorectal Tumors for Lynch Syndrome Among US Cancer Programs and Follow-Up of Abnormal Results
Authors: Beamer Laura C. , Grant Marcia L. , Espenschied Carin R. , Blazer Kathleen R. , Hampel Heather L. , Weitzel Jeffrey N. , MacDonald Deborah J.
Published: February 2012

Purpose

Immunohistochemistry (IHC) for MLH1, MSH2, MSH6, and PMS2 protein expression and microsatellite instability (MSI) are well-established tools to screen for Lynch syndrome (LS). Although many cancer centers have adopted these tools as reflex LS screening after a colorectal cancer diagnosis, the standard of care has not been established, and no formal studies have described this practice in the United States. The purpose of this study was to describe prevalent practices regarding IHC/MSI reflex testing for LS in the United States and the subsequent follow-up of abnormal results.

Materials and Methods

A 12-item survey was developed after interdisciplinary expert input. A letter of invitation, survey, and online-survey option were sent to a contact at each cancer program. A modified Dillman strategy was used to maximize the response rate. The sample included 39 National Cancer Institute–designated Comprehensive Cancer Centers (NCI-CCCs), 50 randomly selected American College of Surgeons–accredited Community Hospital Comprehensive Cancer Programs (COMPs), and 50 Community Hospital Cancer Programs (CHCPs).

Results

The overall response rate was 50%. Seventy-one percent of NCI-CCCs, 36% of COMPs, and 15% of CHCPs were conducting reflex IHC/MSI for LS; 48% of the programs used IHC, 14% of the programs used MSI, and 38% of the programs used both IHC and MSI. One program used a presurgical information packet, four programs offered an opt-out option, and none of the programs required written consent.

Conclusion

Although most NCI-CCCs use reflex IHC/MSI to screen for LS, this practice is not well-adopted by community hospitals. These findings may indicate an emerging standard of care and diffusion from NCI-CCC to community cancer programs. Our findings also described an important trend away from requiring written patient consent for screening.
Cellular functions of the DUBs
Authors: Clague Michael J. , Coulson Judy M. , Urbé Sylvie
Published: February 2012

Ubiquitylation is a reversible post-translational modification that has emerged as a key regulator of most complex cellular processes. It may rival phosphorylation in scope and exceed it in complexity. The dynamic nature of ubiquitylation events is important for governing protein stability, maintaining ubiquitin homeostasis and controlling ubiquitin-dependent signalling pathways. The human genome encodes ~80 active deubiquitylating enzymes (DUBs, also referred to as deubiquitinases), which exhibit distinct specificity profiles towards the various ubiquitin chain topologies. As a result of their ability to reverse ubiquitylation, these enzymes control a broad range of key cellular processes. In this Commentary we discuss the cellular functions of DUBs, such as their role in governing membrane traffic and protein quality control. We highlight two key signalling pathways – the Wnt and transforming growth factor β (TGF-β) pathways, for which dynamic ubiquitylation has emerged as a key regulator. We also discuss the roles of DUBs in the nucleus, where they govern transcriptional activity and DNA repair pathways.
Linking patterns and processes across scales: the application of scale-transition theory to algal dynamics on rocky shores
Authors: Benedetti-Cecchi Lisandro , Tamburello Laura , Bulleri Fabio , Maggi Elena , Gennusa Vincenzo , Miller Matthew
Published: February 2012

Understanding how species and environments respond to global anthropogenic disturbances is one of the greatest challenges for contemporary ecology. The ability to integrate modeling, correlative and experimental approaches within individual research programs will be key to address large-scale, long-term environmental problems. Scale-transition theory (STT) enables this level of integration, providing a powerful framework to link ecological patterns and processes across spatial and temporal scales. STT predicts the large-scale (e.g. regional) behavior of a system on the basis of nonlinear population models describing local (e.g. patch-scale) dynamics and the interaction between these nonlinearities and spatial variation in population abundance or environmental conditions. Here we use STT to predict the dynamics of turf-forming algae on rocky shores at Capraia Island, in the northwest Mediterranean. We developed a model of algal turf dynamics based on density-dependent growth that included the effects of local interactions with canopy algae. The model was parameterized with field data and used to scale up the dynamics of algal turfs from the plot scale (20×20 cm) to the island scale (tens of km). The interaction between nonlinear growth and spatial variance in cover of turfing algae emerged as a key term to translate the local dynamics up to the island scale. The model successfully predicted short-term and long-term mean values of turf cover estimated independently from a separate experiment. These results illustrate how STT can be used to identify the relevant mechanisms that drive large-scale changes in ecological communities. We argue that STT can contribute significantly to the connection between biomechanics and ecology, a synthesis that is at the core of the emerging field of ecomechanics.