bluuebunny/crossref_metadata_2025 huggingface dataset:
Veterans with post-traumatic stress disorder exhibit altered emotional processing and attentional control during an emotional Stroop task
Authors: Khanna M. M. , Badura-Brack A. S. , McDermott T. J. , Embury C. M. , Wiesman A. I. , Shepherd A. , Ryan T. J. , Heinrichs-Graham E. , Wilson T. W.
Published: May 2017

Background

Post-traumatic stress disorder (PTSD) is often associated with attention allocation and emotional regulation difficulties, but the brain dynamics underlying these deficits are unknown. The emotional Stroop task (EST) is an ideal means to monitor these difficulties, because participants are asked to attend to non-emotional aspects of the stimuli. In this study, we used magnetoencephalography (MEG) and the EST to monitor attention allocation and emotional regulation during the processing of emotionally charged stimuli in combat veterans with and without PTSD.

Method

A total of 31 veterans with PTSD and 20 without PTSD performed the EST during MEG. Three categories of stimuli were used, including combat-related, generally threatening and neutral words. MEG data were imaged in the time-frequency domain and the network dynamics were probed for differences in processing threatening and non-threatening words.

Results

Behaviorally, veterans with PTSD were significantly slower in responding to combat-related relative to neutral and generally threatening words. Veterans without PTSD exhibited no significant differences in responding to the three different word types. Neurophysiologically, we found a significant three-way interaction between group, word type and time period across multiple brain regions. Follow-up testing indicated stronger theta-frequency (4–8 Hz) responses in the right ventral prefrontal (0.4–0.8 s) and superior temporal cortices (0.6–0.8 s) of veterans without PTSD compared with those with PTSD during the processing of combat-related words.

Conclusions

Our data indicated that veterans with PTSD exhibited deficits in attention allocation and emotional regulation when processing trauma cues, while those without PTSD were able to regulate emotion by directing attention away from threat.
Long-term outcome after percutaneous closure of persistent left superior caval vein draining into the left atrium: a contrast-enhanced CT study
Authors: Marini Davide , Castagno Matteo , Millesimo Michele , Ferroni Francesca , Ferraro Gaetana , Pace Napoleone Carlo , Agnoletti Gabriella
Published: May 2017

Background

Data regarding long-term outcome after percutaneous closure of left superior caval vein draining into the left atrium are lacking. The aim of the present study was to report the long-term follow-up by using contrast-enhanced CT.

Methods

In all, three patients underwent percutaneous closure of left superior caval vein draining into the left atrium between 2005 and 2015. All of them were evaluated clinically and underwent contrast-enhanced CT.

Results

In one patient, the Amplatzer® Septal Occluder was used. In two patients, the Amplatzer® Vascular Plug type-1 was preferred: the device size/LSVC diameter ratio was 1.7 in the child and 1.2 in the adult. There were no early-onset or long-term onset complications. CT was performed 1, 2, and 10 years after the procedure, respectively. Complete occlusion of the vessel was documented in all. After 10 years since the procedure, CT revealed a persistent trivial residual shunt through the accessory hemiazygos vein in one patient, in whom the device was implanted above its drainage into the left superior caval vein. When an Amplatzer® Vascular Plug type-1 is oversized compared with the venous vessel diameter, it immediately assumes a dog-bone shape that disappears early to regain its shape memory and nominal size.

Conclusions

Percutaneous occlusion of left superior caval vein draining into the left atrium has excellent early and long-term outcomes. The optimal implantation of the device is below the drainage of the accessory hemiazygos vein, when present. The device might be oversized compared with the left superior caval vein diameter according to the age of the patient.
Do Symptoms of Irritable Bowel Syndrome Improve when Patients Receive Cognitive Behavioural Therapy for Co-morbid Anxiety Disorders in a Primary Care Psychological Therapy (IAPT) Service?
Authors: Kenwright Mark , McDonald Jason , Talbot Jo , Janjua Kinza
Published: May 2017

Background: Irritable bowel syndrome (IBS) is a common co-morbid condition with anxiety disorders, and patients often report a fear of incontinence in public places. This type of bowel control anxiety (BCA) can be conceptualized as a phobic syndrome. Yet little evidence exists on the prevalence or outcomes of these co-morbidities in routine primary care psychological therapy (Improving Access to Psychological Therapies, IAPT) services. Aims: To examine the prevalence and outcomes of IBS and BCA patients treated with cognitive behavioural therapy (CBT) for anxiety disorders within a routine IAPT service. Method: An observational cohort study screened 2322 referrals to an IAPT service over 12 months for the presence of IBS. Patients with co-morbid anxiety disorders and IBS were grouped into those with, and without BCA. Patients completed the IBS symptom severity scale and the IAPT minimum data set. Diagnoses and outcomes were examined for all groups up to 6 months follow-up. Results: A greater proportion of BCA patients had a primary diagnosis of phobic disorder. After receiving CBT, patients made clinically significant improvement in both anxiety and IBS symptoms at 6 months follow-up. Patients with BCA made greater improvement in phobia scales and IBS symptoms than non-BCA patients. Conclusions: Anxiety disorders with co-morbid IBS improved significantly in a routine IAPT service. A significant proportion of co-morbid IBS sufferers had a fear of incontinence in public places (BCA). Directly addressing and modifying these fears with CBT appeared to enhance improvement in both phobic anxiety and IBS symptoms.
Comparing measured calcium and vitamin D intakes with perceptions of intake in Canadian young adults: insights for designing osteoporosis prevention education
Authors: Holland Alyson , Moffat Tina
Published: May 2017

Objective

To identify the relationship between perceptions of Ca and vitamin D consumption and actual intakes to inform the design of osteoporosis prevention education.

Design

An FFQ was used to approximate usual monthly Ca and vitamin D intakes among a group of young Canadians. Qualitative interviews and a food card pile sort activity explored individuals’ perceptions of nutrient intakes. The FFQ was used to assess nutrient adequacy for individual participants and the qualitative interviews and pile sort were analysed using thematic content analysis.

Setting

Hamilton, Canada.

Subjects

Sixty participants aged 17–30 years, representing varying levels of educational attainment.

Results

Seventy-eight per cent of young adults who consumed inadequate vitamin D perceived their intake as adequate, compared with 57 % for Ca. Thematic analysis revealed three major themes that contributed to young adults’ understandings of intake: belief their diet was correct, absence of symptoms and confusion over nutrient sources.

Conclusions

The majority of participants perceived themselves as consuming adequate amounts of Ca and vitamin D, when they were actually consuming inadequate amounts according to FFQ findings. These perceptions were related to low engagement in prevention activities. Prevention education must motivate young adults to question the adequacy of their micronutrient intakes and design tailored programmes that are geared to a young adult audience.
Implementation of ultrasound bladder volume scanning for patients receiving intensity-modulated radiotherapy to the cervix or endometrium: clinical experiences from a United Kingdom radiotherapy department
Authors: Claxton K. , Appleyard R.
Published: May 2017

Background and purpose

Achieving daily consistent bladder volume is acknowledged as challenging for patients undergoing radiotherapy to the cervix or endometrium. We investigated if use of an ultrasound bladder volume scanner (BioCon-700) improves bladder reproducibility when used during an active volume correction protocol.

Materials and methods

During our method-comparison study, prospectively recruited patients (n=20) followed a fluid-loading protocol to achieve acceptable bladder volume. Bladder ultrasound was performed daily to verify planned volume, with patients actively correcting volumes outside a planned range up to a maximum of three times. Using the Bland–Altman method, we compared mean ultrasound readings (USMean) with mean cone-beam computed tomography (CBCT) volumes (CBCTMean). We also conducted staff focus groups exploring issues encountered during implementation of bladder scanning.

Results

Comparing USMean with CBCTMean produced a mean of the differences −10±49·92 mL (1 SD), demonstrating that bladder volume scanning is equivalent to our standard measure for the stated confidence levels. The cohort mean bladder volume decrease from week 1 to 5 was only 8·4%. Mean USMean was 323 mL, mean CBCTMean was 313 mL. Staff experience with the scanner overall was positive.

Conclusions

The BioCon-700 is suitable for the purpose of daily pre-treatment volume verification, facilitating daily assessment and modification of bladder volume, resulting in reproducible treatment volumes.
Do open online projects create social norms?
Authors: DANG NGUYEN GODEFROY , DEJEAN SYLVAIN , JULLIEN NICOLAS
Published: May 2017

While most scholars emphasize the role of prosocial motivations of contributors in building open online communities, we show that mere users also adhere to their norms of behaviour to some extent. To this end we designed an original experimentation protocol. With the help of the French Wikimédia Foundation, we questioned a large sample (n = 13,000) of Wikipedia users (whether contributors or not). They were invited, after having expressing their feelings about Wikipédia, to play a Dictator Game. A large proportion of respondents, including those who were merely users, chose an equal split (66% of the sample). This surprising result suggests that they have adhered to a social norm of sharing. Investigating the determinants of this result, we prove that an involvement measured by usage (intensity and variety), as well as by attachment to, and time spent, on Wikipedia, is correlated with the choice of the 50/50 split in the dictator game (DG). Furthermore, the method of instrumental variables gives an indication that adherence to the social norm of sharing may be endogenously determined by involvement in the open online community. Our result highlights the importance of interactions with the institutional and technical frameworks of the community.
Bedeutung prognostischer Faktoren bei unspezifischen, lumbalen Rückenschmerzen
Authors: Wertli Maria M. , Steurer Johann
Published: May 2017

Zusammenfassung. Lumbale Rückenschmerzen sind sehr häufig und in rund 90 % der Fälle unspezifisch. Ein einseitiger Fokus auf biomechanische Schmerzursachen führt zu unnötigen Abklärungen und Behandlungen, während die Relevanz des individuellen Umgangs mit Schmerzen unterschätzt wird. Liegt ein maladaptives Coping mit Angst und Vermeideverhalten vor, resultiert dies in Fehlbelastung, Dekonditionierung und einem Circulus vitiosus, der ein negatives Schmerzverhalten unterstützt. Konzepte, die psychische Faktoren wie Angst und Stress suchten und gezielt behandelten, waren effektiv. Es ist wichtig, dies in der hausärztlichen Praxis und auf Notfallstationen bei Patienten mit Rückenschmerzen ohne klare Radikulopathie oder andere Alarmzeichen zu berücksichtigen.
Direct evaluation of influence of electron damage on the subcell performance in triple-junction solar cells using photoluminescence decays
Authors: Tex David M. , Nakamura Tetsuya , Imaizumi Mitsuru , Ohshima Takeshi , Kanemitsu Yoshihiko
Published: May 2017

Tandem solar cells are suited for space applications due to their high performance, but also have to be designed in such a way to minimize influence of degradation by the high energy particle flux in space. The analysis of the subcell performance is crucial to understand the device physics and achieve optimized designs of tandem solar cells. Here, the radiation-induced damage of inverted grown InGaP/GaAs/InGaAs triple-junction solar cells for various electron fluences are characterized using conventional current-voltage (I–V) measurements and time-resolved photoluminescence (PL). The conversion efficiencies of the entire device before and after damage are measured with I–V curves and compared with the efficiencies predicted from the time-resolved method. Using the time-resolved data the change in the carrier dynamics in the subcells can be discussed. Our optical method allows to predict the absolute electrical conversion efficiency of the device with an accuracy of better than 5%. While both InGaP and GaAs subcells suffered from significant material degradation, the performance loss of the total device can be completely ascribed to the damage in the GaAs subcell. This points out the importance of high internal electric fields at the operating point.
Bicyclo[2.2.2]octane-1,4-dicarboxylic acid: towards transparent metal–organic frameworks
Authors: Llabres-Campaner P. J. , Pitarch-Jarque J. , Ballesteros-Garrido R. , Abarca B. , Ballesteros R. , García-España E.
Published: May 2017

The preparation of transparent porous materials can offer a different access towards the study of molecules under solid confined space.
Step by step learning using the I diagram in the systematic qualitative analyses of cations within a guided inquiry learning approach
Authors: Akkuzu Nalan , Uyulgan Melis Arzu
Published: May 2017

The current study examines the performance and achievement of students in the Systematic Qualitative Analyses of Cations (SQACs). We sought answers to questions such as, ‘What are the students’ levels of performance?’ and ‘What is the relation between the average scores for performance and achievement?’. This was done by using the I diagram as a tool within a Guided Inquiry Learning Approach (GILA), which is based on the constructivist theory. The sample consisted of sophomore students (N = 31) taking the Analytical Chemistry Laboratory-I course and attending the Chemistry Teaching Program of the Faculty of Education of a state university in the Aegean region of Turkey. During the analyses, the students attempted to solve specific problems and find the results of their qualitative analyses as they followed the sections of I diagram step by step under the guidance of researchers. They also tried to find solutions to problems through logical reasoning and discussions with each other. A positive correlation was found between the achievement and performance of the students. During the experimental process based on the GILA, the students were able to structure their knowledge more clearly by carrying out cation analysis in a systematic manner, inquiring and suggesting scientific explanations. Although they had difficulties in some sections of the I diagram, including logical argument, data transformation and variable definition, they were able to establish a link between theory and practice by using their cognitive and meta-cognitive skills.
Differences in microhabitat selection patterns between a remnant and constructed landscape following management intervention
Authors: Valdez Jose W. , Klop-Toker Kaya , Stockwell Michelle P. , Fardell Loren , Clulow Simon , Clulow John , Mahony Michael J.
Published: May 2017

Context Achieving successful conservation outcomes in habitat creation and reintroductions requires an understanding of how species use their habitat and respond to these interventions. However, few initiatives directly compare microhabitat selection between remnant and managed habitats to measure effectiveness and evaluate outcomes. Probability of detection is also rarely included in studies on microhabitat use, which may lead to erroneous conclusions if detectability varies between variables. Methods In this study, we used the endangered green and golden bell frog (Litoria aurea) to compare differences in microhabitat-use patterns in both a remnant and a constructed habitat. A detectability study was also conducted to determine detection probabilities among microhabitats. Key results Aquatic vegetation was used more than expected in both the remnant and constructed habitats, and rock piles were utilised less than expected in the constructed habitat, despite their recommendation in most habitat templates. We found that detection probabilities altered the outcomes of abundance estimates for nearly all the measured microhabitat variables. Conclusions Future management for this species should focus on providing high proportions of aquatic vegetation. Furthermore, although rock piles have been utilised greatly in past L. aurea habitat creation, placing large rocks on a managed site is expensive and time consuming. Future management initiatives may need to focus on providing smaller proportion of rocks, which would be a more appropriate use of resources. Implications With conservation management projects increasing over the next few decades, understanding habitat use before implementing strategies should be a priority as it will provide important insights and inform decision-making for optimum habitat creation and restoration. Furthermore, accounting for detectability in microhabitat use studies is essential to avoid wrong conclusions that may negatively affect the success of ecological management strategies.
Characterization of cellulolytic enzyme system of Schizophyllum commune mutant and evaluation of its efficiency on biomass hydrolysis
Authors: Sornlake Warasirin , Rattanaphanjak Phatcharamon , Champreda Verawat , Eurwilaichitr Lily , Kittisenachai Suthathip , Roytrakul Sittiruk , Fujii Tatsuya , Inoue Hiroyuki
Published: May 2017

Schizophyllum commune is a basidiomycete equipped with an efficient cellulolytic enzyme system capable of growth on decaying woods. In this study, production of lignocellulose-degrading enzymes from S. commune mutant G-135 (SC-Cel) on various cellulosic substrates was examined. The highest cellulase activities including CMCase, FPase, and β-glucosidase were obtained on Avicel-PH101 while a wider range of enzymes attacking non-cellulosic polysaccharides and lignin were found when grown on alkaline-pretreated biomass. Proteomic analysis of SC-Cel also revealed a complex enzyme system comprising seven glycosyl hydrolase families with an accessory carbohydrate esterase, polysaccharide lyase, and auxiliary redox enzymes. SC-Cel obtained on Avicel-PH101 effectively hydrolyzed all agricultural residues with the maximum glucan conversion of 98.0% using corn cobs with an enzyme dosage of 5 FPU/g-biomass. The work showed potential of SC-Cel on hydrolysis of various herbaceous biomass with enhanced efficiency by addition external β-xylosidase.
Calibration of surface roughness standards
Authors: Salgado  , Duta Alexandru , Lewis Andrew , Gunn Dave , Picotto Gian Bartolo , Borovsky Jiri , Nanits Mats-Maidu , Mudronja Vedran , Castellanos Carlos Colin , Kornbilt Fernando , Renegar Brian , Souza Marcos Motta de
Published: May 2017

The key comparison EURAMET.L-K8.2009 on roughness was carried out in the framework of a EURAMET project starting in 2009 and ending in 2011. It involved the participation of 14 National Metrology Institutes from Europe, North America, Central America, South America and Africa representing three regional metrology organisations. Four surface texture standards of different type were circulated and on each of the standards several roughness parameters according to the standard ISO 4287 had to be determined. 27 out of 171 individual results were not consistent with the reference value. After some corrective actions the number of inconsistent results could be reduced to 24, which correspond to about 14% of the total. In addition to the material standards, two soft-gauges were circulated, which allow to test the software of the instruments used in the comparison. The comparison results help to support the calibraton and measurement capabilities (CMCs) of the laboratories involved in the CIPM MRA.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCL, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
A review of the impacts of fisheries on open-ocean ecosystems
Authors: Ortuño Crespo Guillermo , Dunn Daniel C
Published: May 2017

Open‐ocean fisheries expanded rapidly from the 1960s through the 1980s, when global fish catches peaked, plateaued and possibly began to decline. While catches remain at best stagnant, fishing effort globally continues to increase. The likelihood of ecosystem impacts occurring due to fishing is related to fishing effort and is thus also expected to be increasing. Despite this rapid growth, ecological research into the impacts of fisheries on open‐ocean environments has lagged behind coastal and deep-sea environments. This review addresses this knowledge gap by considering the roles fisheries play in controlling the open-ocean at three ecological scales: (i) species (population or stock); (ii) biological community; and (iii) ecosystem. We find significant evidence for top-down control at the species and community scales. While evidence of ecosystem-level impacts in the open-ocean were not explicit in the literature, we provide examples of these impacts in several marine pelagic systems and encourage further research at this ecological scale. At the species level, fishing can reduce abundance, and alter physiology and life history traits, which, in turn, affect the functional role of the species within the biological community. Fishing may also induce changes to open-ocean community trophodynamics, and reduce biodiversity and resilience in open-ocean ecosystems. Our ability to manage open-ocean ecosystems has significant implications for provisioning of ecosystem services and food security. However, we posit that the monitoring required to assure the sustainability of open-ocean ecosystems is not being undertaken, and will require coordination with the Global Ocean Observing System, industry, and academia.
Dark matter distribution in X-ray luminous galaxy clusters with Emergent Gravity
Authors: Ettori S. , Ghirardini V. , Eckert D. , Dubath F. , Pointecouteau E.
Published: May 2017

We present the radial distribution of the dark matter in two massive, X-ray luminous galaxy clusters, Abell 2142 and Abell 2319, and compare it with the quantity predicted as apparent manifestation of the baryonic mass in the context of the ‘Emergent Gravity’ scenario, recently suggested from Verlinde. Thanks to the observational strategy of the XMM–Newton Cluster Outskirt Programme (X-COP), using the X-ray emission mapped with XMM–Newton and the Sunyaev–Zel'dovich signal in the Planck survey, we recover the gas density, temperature and thermal pressure profiles up to ∼R200, allowing us to constrain at an unprecedented level the total mass through the hydrostatic equilibrium equation. We show that, also including systematic uncertainties related to the X-ray-based mass modelling, the apparent ‘dark’ matter shows a radial profile that has a shape different from the traditional dark matter distribution, with larger discrepancies (by a factor of 2–3) in the inner (r < 200 kpc) cluster's regions and a remarkable agreement only across R500.
Social Support, Unstable Angina, and Stroke as Predictors of Depression in Patients With Coronary Heart Disease
Authors: Su Shu-Fen , Chang Mei-Yu , He Chung-Ping
Published: May 2017

Background:

Depression is known to adversely affect coronary heart disease patients in western countries; however, no study of social support and depression has been conducted in the Chinese population.

Objective:

The aim of this study was to investigate the predictors of depression in patients with coronary heart disease.

Methods:

Between January and December 2015, a cross-sectional sample of 105 Taiwanese patients from cardiology units completed a demographic and clinical characteristics questionnaire, Enhancing Recovery in Coronary Heart Disease Social Support Inventory, and Patient Health Questionnaire-9.

Results:

Thirty-nine percent of the participants reported low social support, and 61.0% had depression symptoms. Eight factors predicted depression. Social support was significantly and adversely correlated with depression (r = −.481, P < .01). The other 7 factors were positively correlated with depression: age (r = .212, P < .05), reported monthly income of less than US $600 (F = 4.98, P = .001), lack of exercise (F = 3.75, P = .027), history of stroke (t = −2.45, P = .016) and kidney disease (t = −2.41, P = .018), unstable angina (F = 3.56, P = .031), and groin puncture (F = 3.27, P = .042). A hierarchical regression model explained 43.7% of the variance in depression.

Conclusion:

Social support, unstable angina, and stroke may be important predictors of depression in patients with coronary heart disease. These findings help clinical staff to understand physical and mental health problems in cardiovascular patients. Thus, we suggest that early depression prediction and sufficient social support can help patients to face their disease and thus improve depression and health care quality.
Assessment of Nevirapine Prophylactic and Therapeutic Dosing Regimens for Neonates
Authors: Cressey Tim R. , Punyawudho Baralee , Le Coeur Sophie , Jourdain Gonzague , Saenjum Chalermpong , Capparelli Edmund V. , Jittayanun Kanokwan , Phanomcheong Siriluk , Luvira Anita , Borkird Thitiporn , Puangsombat Achara , Aarons Leon , Sukrakanchana Pra-ornsuda , Urien Saik , Lallemant Marc ,   for the PHPT-5 study team
Published: May 2017

Background:

Nevirapine (NVP) is a key component of antiretroviral prophylaxis and treatment for neonates. We evaluated current World Health Organization (WHO) weight-band NVP prophylactic dosing recommendations and investigated optimal therapeutic NVP dosing for neonates.

Methods:

The PHPT-5 study in Thailand assessed the efficacy of “Perinatal Antiretroviral Intensification” to prevent mother-to-child transmission of HIV in women with <8 weeks of antiretroviral treatment before delivery (NCT01511237). Infants received a 2-week course of zidovudine/lamivudine/NVP (NVP syrup/once daily: 2 mg/kg for 7 days; then 4 mg/kg for 7 days). Infant samples were assessed during the first 2 weeks of life. NVP population pharmacokinetics (PK) parameters were estimated using nonlinear mixed-effects models. Simulations were performed to estimate the probability of achieving target NVP trough concentrations for prophylaxis (>0.10 mg/L) and for therapeutic efficacy (>3.0 mg/L) using different infant dosing strategies.

Results:

Sixty infants (55% male) were included. At birth, median (range) weight was 2.9 (2.3–3.6) kg. NVP concentrations were best described by a 1-compartment PK model. Infant weight and postnatal age influenced NVP PK parameters. Based on simulations for a 3-kg infant, ≥92% would have an NVP trough >0.1 mg/L after 48 hours through 2 weeks using the PHPT-5 and WHO-dosing regimens. For NVP-based therapy, a 6-mg/kg twice daily dose produced a trough >3.0 mg/L in 87% of infants at 48 hours and 80% at 2 weeks.

Conclusion:

WHO weight-band prophylactic guidelines achieved target concentrations. Starting NVP 6 mg/kg twice daily from birth is expected to achieve therapeutic concentrations during the first 2 weeks of life.
EyeBallGUI: A Tool for Visual Inspection and Binary Marking of Multi-channel Bio-signals
Authors: Mohr Kieran S. , Nasseroleslami Bahman , Iyer Parameswaran M. , Hardiman Orla , Lalor Edmund C.
Published: May 2017

A wide range of studies in human neuroscience rely on the analysis of electrophysiological bio-signals such as electroencephalogram (EEG) where customized data analysis may require supervised artefact rejection, binary marking through visual inspection, selection of noise and artefact samples for pre-processing algorithms, and selection of clinically-relevant signal segments in neurological conditions. Nevertheless, the existing preprocessing tools do not provide the needed flexibility to handle such tasks efficiently. We therefore developed a free open-source Graphical User Interface (GUI), EyeBallGUI, that allows visualization and flexible, manual marking (binary classification) of multi-channel bio-signal data. EyeBallGUI, developed for MATLAB®, allows the user to interactively and accurately inspect and mark multi-channel digitized data with no restriction on marking periods of data in subsets of channels (a restriction in place in existing tools). The new tool facilitates precise, manual marking of bio-signals by allowing any desired segment of data to be marked in any subset of channels. It is therefore of utility in circumstances where such flexibility is essential. The developed GUI is an auxiliary analysis tool that shall facilitate neural signal (pre-)processing applications where it is desirable to perform accurate supervised artefact rejection, flexible data marking for increased data retention yield, extraction of specific signal segments by expert users from sample data, or labeling of data for clinical and scientific research purposes.
Systemic activation coordinates the heat shock response of the insulin/IGF-1 pathway inCaenorhabditis elegans
Authors: Kopito Ronen B , Watkins Kathie , Levine Erel
Published: May 2017

Exposure to high temperatures has an adverse effect on cellular processes and results in activation of the cellular heat shock response (HSR), a highly conserved program of inducible genes to maintain protein homeostasis1. The insulin/IGF-1 signaling (IIS) pathway, which has diverse roles from metabolism to stress response and longevity, is activated as part of the HSR2–4. Recent evidence suggest that the IIS pathway is able to affect proteostasis non-autonomously5,6, yet it is not known if it is activated autonomously in stressed cells or systemically as part of an organismic program. InCaenorhabditis elegans, the single forkhead box O (FOXO) homologue DAF-16 functions as the major target of the IIS pathway7and, together with the heat-shock factor HSF-1, induce the expression of small heat shock proteins in response to heat shock8–10,3. Here we use a novel microfluidic device that allows precise control of the spatiotemporal temperature profile to show that cellular activation of DAF-16 integrates local temperature sensation with systemic signals. We demonstrate that DAF-16 activation in head sensory neurons is essential for DAF-16 activation in other tissues, but show that no known thermosensory neuron is individually required. Our findings demonstrate that systemic and cell-autonomous aspects of stress response act together to facilitate a coordinated cellular response at the organismic level.
Heterogeneity among estimates of the core genome and pan-genome in different pneumococcal populations
Authors: van Tonder Andries J , Bray James E , Jolley Keith A , Quirk Sigríður J , Haraldsson Gunnsteinn , Maiden Martin CJ , Bentley Stephen D , Haraldsson Ásgeir , Erlendsdóttir Helga , Kristinsson Karl G , Brueggemann Angela B
Published: May 2017

Background

Understanding the structure of a bacterial population is essential in order to understand bacterial evolution, or which genetic lineages cause disease, or the consequences of perturbations to the bacterial population. Estimating the core genome, the genes common to all or nearly all strains of a species, is an essential component of such analyses. The size and composition of the core genome varies by dataset, but our hypothesis was that variation between different collections of the same bacterial species should be minimal. To test this, the genome sequences of 3,121 pneumococci recovered from healthy individuals in Reykjavik (Iceland), Southampton (United Kingdom), Boston (USA) and Maela (Thailand) were analysed.

Results

The analyses revealed a ‘supercore’ genome (genes shared by all 3,121 pneumococci) of only 303 genes, although 461 additional core genes were shared by pneumococci from Reykjavik, Southampton and Boston. Overall, the size and composition of the core genomes and pan-genomes among pneumococci recovered in Reykjavik, Southampton and Boston were very similar, but pneumococci from Maela were distinctly different. Inspection of the pan-genome of Maela pneumococci revealed several >25 Kb sequence regions that were homologous to genomic regions found in other bacterial species.

Conclusions

Some subsets of the global pneumococcal population are highly heterogeneous and thus our hypothesis was rejected. This is an essential point of consideration before generalising the findings from a single dataset to the wider pneumococcal population.
DeepDeath: Learning to Predict the Underlying Cause of Death with Big Data
Authors: Hassanzadeh Hamid Reza , Sha Ying , Wang May D.
Published: May 2017

Multiple cause-of-death data provides a valuable source of information that can be used to enhance health standards by predicting health related trajectories in societies with large populations. These data are often available in large quantities across U.S. states and require Big Data techniques to uncover complex hidden patterns. We design two different classes of models suitable for large-scale analysis of mortality data, a Hadoop-based ensemble of random forests trained over N-grams, and the DeepDeath, a deep classifier based on the recurrent neural network (RNN). We apply both classes to the mortality data provided by the National Center for Health Statistics and show that while both perform significantly better than the random classifier, the deep model that utilizes long short-term memory networks (LSTMs), surpasses the N-gram based models and is capable of learning the temporal aspect of the data without a need for building ad-hoc, expert-driven features.
A carbon nanotube optical reporter maps endolysosomal lipid flux
Authors: Jena Prakrit V. , Roxbury Daniel , Galassi Thomas V. , Akkari Leila , Horoszko Christopher P. , Iaea David B. , Budhathoki-Uprety Januka , Pipalia Nina H. , Haka Abigail S. , Harvey Jackson D. , Mittal Jeetain , Maxfield Frederick R. , Joyce Johanna A. , Heller Daniel A.
Published: May 2017

Lipid accumulation within the lumen of endolysosomal vesicles is observed in various pathologies including atherosclerosis, liver disease, neurological disorders, lysosomal storage disorders, and cancer. Current methods cannot measure lipid flux specifically within the lysosomal lumen of live cells. We developed an optical reporter, composed of a photoluminescent carbon nanotube of a single chirality, which responds to lipid accumulation via modulation of the nanotube’s optical bandgap. The engineered nanomaterial, composed of short-single stranded DNA and a single nanotube chirality, localizes exclusively to the lumen of endolysosomal organelles without adversely affecting cell viability or proliferation, or organelle morphology, integrity, or function. The emission wavelength of the reporter can be spatially resolved from within the endolysosomal lumen to generate quantitative maps of lipid content in live cells. Endolysosomal lipid accumulation in cell lines, an example of drug-induced phospholipidosis (DIPL), was observed for multiple drugs in macrophages, and measurements of patient-derived Niemann-Pick type C fibroblasts identified lipid accumulation and phenotypic reversal of this lysosomal storage disease. Single-cell measurements using the reporter discerned sub-cellular differences in equilibrium lipid content, illuminating significant intracellular heterogeneity among endolysosomal organelles of differentiating bone marrow-derived monocytes. Single-cell kinetics of lipoprotein-derived cholesterol accumulation within macrophages revealed rates that differed among cells by an order of magnitude. This carbon nanotube optical reporter of endolysosomal lipid content in live cells confers new capabilities for drug development processes and the investigation of lipid-linked diseases.
Homology modeling in a dynamical world
Authors: Monzon Alexander Miguel , Zea Diego Javier , Marino-Buslje Cristina , Parisi Gustavo
Published: May 2017

A key concept in template-based modeling is the high correlation between sequence and structural divergence, with the practical consequence that homologous proteins that are similar at the sequence level will also be similar at the structural level. However, conformational diversity of the native state will reduce the correlation between structural and sequence divergence, because structural variation can appear without sequence diversity.

In this work, we explore the impact that conformational diversity has on the relationship between structural and sequence divergence. We find that the extent of conformational diversity can be as high as the maximum structural divergence among families. Also, as expected, conformational diversity impairs the well-established correlation between sequence and structural divergence, which is nosier than previously suggested. However, we found that this noise can be resolved usinga prioriinformation coming from the structure-function relationship. We show that protein families with low conformational diversity show a well-correlated relationship between sequence and structural divergence, which is severely reduced in proteins with larger conformational diversity. This lack of correlation could impair Template-based modelling (TMB) results in highly dynamical proteins. Finally, we also find that the presence of order/disorder can provide useful beforehand information for better TBM performance.

Author summary

Template-based modelling (TBM) is the most reliable and fastest approach to obtain protein structural models. TBM relies in the high correlation between sequence and structural divergence, with the practical consequence that proteins that are similar at the sequence level will also be similar at the structural level, allowing in this way the selection of the better template to obtain the 3D model of the target sequence. However, protein native state could be described by a collection of conformers in equilibrium where their structural differences are called conformational diversity.

In this work, we explore the impact that conformational diversity has on the relationship between structural and sequence divergence. We firstly found that the extent of conformational diversity can be as high as the maximum structural differences reached by families differing in their sequences. In these proteins with higher conformational diversity levels, the well-established correlation between sequence and structural divergence is nosier than previously suggested due to the presence of structural change without sequence variation. This lack of correlation could impair TBM results due to the uncertainty in the correct template selection. Finally, we also found that the presence of order/disorder can provide useful beforehand information for better TBM performance.
Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration
Authors: Shukron O. , Hauer MH. , Holcman D.
Published: May 2017

Stochastic single particle trajectories are used to explore the local chromatin organization. We present here a statistical analysis of the first contact time distributions between two tagged loci recorded experimentally. First, we extract the association and dissociation times from data for various genomic distances between loci and we show that the looping time occurs in confined nanometer regions. Second, we characterize the looping time distribution for two loci in the presence of multiple DNA damages. Finally, we construct a polymer model that accounts for the local chromatin organization before and after a double-stranded DNA break (DSB) to estimate the level of chromatin decompaction. This novel passage time statistics method allows extracting transient dynamic at scales from one to few hundreds of nanometers, predicts the local changes in the number of binding molecules following DSB and can be used to better characterize the local dynamic of the chromatin.
Single-cell sequencing deciphers a convergent evolution of copy number alterations from primary to circulating tumor cells
Authors: Gao Yan , Ni Xiaohui , Guo Hua , Su Zhe , Ba Yi , Tong Zhongsheng , Guo Zhi , Yao Xin , Chen Xixi , Yin Jian , Yan Zhao , Guo Lin , Liu Ying , Bai Fan , Xie X. Sunney , Zhang Ning
Published: May 2017

Copy number alteration (CNA) is a major contributor to genome instability, a hallmark of cancer. Here, we studied genomic alterations in single primary tumor cells and circulating tumor cells (CTCs) from the same patient. Single-nucleotide variants (SNVs) in single cells from both samples occurred sporadically, whereas CNAs among primary tumor cells emerged accumulatively rather than abruptly, converging toward the CNA in CTCs. Focal CNAs affecting the MYC gene and the PTEN gene were observed only in a minor portion of primary tumor cells but were present in all CTCs, suggesting a strong selection toward metastasis. Single-cell structural variant (SV) analyses revealed a two-step mechanism, a complex rearrangement followed by gene amplification, for the simultaneous formation of anomalous CNAs in multiple chromosome regions. Integrative CNA analyses of 97 CTCs from 23 patients confirmed the convergence of CNAs and revealed single, concurrent, and mutually exclusive CNAs that could be the driving events in cancer metastasis.
Developing a comprehensive performance measurement system forwaqfinstitutions
Authors: Noordin Nazrul Hazizi , Haron Siti Nurah , Kassim Salina
Published: May 2017

Purpose

The purpose of this paper is to contribute to the literature on management ofwaqfinstitutions by developing a contingency framework and outlining approaches that can be followed to instigate a comprehensive performance measurement system (PMS).

Design/methodology/approach

It conducts a thorough and critical review of the literature on relevant performance measurement literature of third sector organizations andwaqfinstitutions.

Findings

The findings suggest that an effective PMS is undoubtedly significant in promoting good governance and ethical management ofwaqfinstitutions. However, the current practice of performance measurement inwaqfinstitutions is less standardized and does not cover its entire aspects of performance as a religious as well as a voluntary organization. It is also found that mostwaqfinstitutions’ management and researchers primarily rely on financial reporting and economic indicators to report to the stakeholders about the performance ofwaqfinstitutions.

Practical implications

The contributions of this paper are twofold. First, the authors develop a contingency framework for assessing performance ofwaqfinstitutions. Second, the authors outline eight necessary steps that can serve as guidelines forwaqfinstitutions in designing their own comprehensive PMS.

Originality/value

The novelty of this paper lies in highlighting the feasibility of adopting qualitative approaches bywaqfinstitutions. This study hopes to shed light on a standard measurement system that can be adopted by thewaqfinstitutions to ensure efficiency and sustainability of thewaqfinstitutions, not just in Malaysia but in the Muslim world.
Methods of evaluation of intangible assets and intellectual capital
Authors: Osinski Marilei , Selig Paulo Mauricio , Matos Florinda , Roman Darlan José
Published: May 2017

Purpose

The competitive model has changed. In this context, society entered into an era in which intangible assets are the greatest assets of a company. However, some gaps and uncertainties are presented in the literature as to understand the value of a company based on knowledge intensive activities. The purpose of this paper is to analyze the methods of evaluation of intangible assets in the context of business, economic and strategic management.

Design/methodology/approach

This is a qualitative research. This research is characterized as descriptive, bibliographic, inductive.

Findings

The main results of this research can highlight the existence of valuation methods of intangible assets intended for specific industries, as public and/or private, that can be better aligned to the context of business; economic and/or strategic management.

Originality/value

It was found that intangible assets are a current topic and increasingly addressed in the literature.
Switching of biologics in psoriasis: Reasons and results
Authors: Honda Hiromi , Umezawa Yoshinori , Kikuchi Sota , Yanaba Koichi , Fukuchi Osamu , Ito Toshihiro , Nobeyama Yoshimasa , Asahina Akihiko , Nakagawa Hidemi
Published: May 2017

Efficacy and safety profiles of biologics have been established for moderate to severe psoriasis. However, inefficacy or adverse events sometimes require changing the treatment to other biologics. Here, we examine the effectiveness of this strategy. We retrospectively investigated cases requiring switching biologics. We enrolled 275 psoriatic patients treated with biologics between January 2010 and December 2014 in our hospital. Of these, 51 required a switch to another biologic. First‐line therapies were infliximab (IFX, n = 26), adalimumab (ADA, n = 18) and ustekinumab (UST, n = 7), and second‐line therapies were IFX (n = 5), ADA (n = 21) and UST (n = 25). Reasons for switching were inefficacy (n = 38), adverse events (n = 11) and others (n = 2). The details were primary failure (n = 15), secondary failure (n = 23) and infusion reactions (n = 8). In 49 patients who switched biologics due to inefficacy and adverse events, the mean Psoriasis Area and Severity Index (PASI) score at week 16 was 4.3 for first‐line therapies and 2.9 for second‐line therapies (P < 0.05). Switching to a second biologic therapy to address the first's inefficacy or adverse events often results in significant improvement in moderate to severe psoriasis.
Experimental verification of effective anisotropic crack theories in variable crack aspect ratio medium
Authors: Henriques Jessica P. , de Figueiredo Jose J. S. , Santos Leo K. , Macedo Daniel L. , Coutinho Icaro , da Silva Carolina B. , Melo Alberto L. , Sousa Mykel , Azevedo Felipe L.
Published: May 2017

Physical modelling of cracked/fractured media using downscaled laboratory experiments has been used with great success as a useful alternative for understanding the effect of anisotropy in the hydrocarbon reservoir characterization and in the crustal and mantle seismology. The main goal of this work was to experimentally verify the predictions of effective elastic parameters in anisotropic cracked media by Hudson and Eshelby–Cheng's effective medium models. For this purpose, we carried out ultrasonic measurements on synthetic anisotropic samples with low crack densities and different aspect ratios. Twelve samples were prepared with two different crack densities, 5% and 8%. Three samples for each crack density presented cracks with only one crack aspect ratio, whereas other three samples for each crack density presented cracks with three different aspect ratios in their composition. It results in samples with aspect ratio values varying from 0.13 to 0.26. All the cracked samples were simulated by penny‐shaped rubber inclusions in a homogeneous isotropic matrix made with epoxy resin. Moreover, an isotropic sample for reference was constructed with epoxy resin only. Regarding velocity predictions performed by the theoretical models, Eshelby–Cheng shows a better fit when compared with the experimental results for samples with single and mix crack aspect ratio (for both crack densities). From velocity values, our comparisons were also performed in terms of the ε, γ, and δ parameters (Thomsen parameters). The results show that Eshelby–Cheng effective medium model fits better with the measurements of ε and γ parameters for crack samples with only one type of crack aspect ratio.