bluuebunny/crossref_metadata_2025 huggingface dataset:
Cytokine Patterns in Healthy Adolescent Girls: Heterogeneity Captured by Variable and Person-Centered Statistical Strategies
Authors: Dorn Lorah D. , Gayles Jochebed G. , Engeland Christopher G. , Houts Renate , Cizza Giovanni , Denson Lee A.
Published: May 2016

Background

Little is known about variation in individual cytokines/cytokine profiles for a large healthy, pediatric population. When cytokines in a healthy group are not abnormally high as in a disease state, it is challenging to determine appropriate statistical strategies. The aims of the study were (1) to describe variation among cytokine concentrations and profiles in healthy adolescent girls, (2) to illustrate utility of data reduction approaches novel to cytokine research, (variable-centered [principal factor analysis, PFA], person-centered [latent profile analysis, LPA]), and (3) to demonstrate utility of such methods in linking cytokine profiles to health outcomes (e.g., depressive, anxiety symptoms).

Method

Serum was analyzed for 13 cytokines representing adaptive and innate immune responses in 262 girls (age = 11, 13, 15, and 17 years).

Results

There was great variation in cytokine concentrations. PFA revealed a four-factor solution explaining 73.13% of the shared variance among 13 cytokines (e.g., factor 1 included interleukin [IL]-4, IL-13, IL-5, interferon gamma; 26.65% of the shared variance). The LPA supported classifying girls into subgroups characterized by “high overall” (7.3% of sample), “high adaptive” (26.7%), “high innate” (21%), or “low overall” (45%) cytokine levels. Factors and profiles were useful in describing individual differences in depressive/anxiety symptoms (e.g., factor 1 positively associated with depressive symptoms but negatively with trait anxiety; increased depressive symptoms or trait anxiety was associated with greater likelihood of being in the “high adaptive” group).

Conclusions

Healthy girls showed differences in cytokine levels and patterns of variation and important associations with psychological variables. PFA and LPA offer novel approaches useful for examining cytokine panels in healthy populations.
Macrophage Superoxide Anion Production in Essential Hypertension: Associations With Biological and Psychological Cardiovascular Risk Factors
Authors: Zuccarella-Hackl Claudia , von Känel Roland , Thomas Livia , Hauser Mark , Kuebler Ulrike , Widmer Hans Rudolf , Wirtz Petra H.
Published: May 2016

Objective

Essential hypertension is an important risk factor for coronary artery disease and its underlying process atherosclerosis, but involved mechanisms are not fully understood. Both macrophages and superoxide anions have been proposed to play a major role in the pathogenesis of atherosclerosis. In the present study, we investigated whether macrophages of individuals with hypertension show higher nicotinamide adenine dinucleotide phosphate oxidase–derived superoxide anion production compared with normotensive individuals. Furthermore, we examined associations between macrophage superoxide anion production and the psychological factors depression and chronic stress independent from hypertension status.

Methods

We studied 30 hypertensive (mean [standard deviation] = 48.7 [2.4] years) and 30 age-matched normotensive men (mean [standard deviation] = 48.6 [2.4] years). We assessed macrophage superoxide anion production using the WST-1 assay. The assay is based on the chemical reduction of the cell-impermeative tetrazolium salt WST-1 by superoxide anions that are produced by activated human ex vivo isolated monocyte-derived macrophages. We further evaluated whether chronic stress or depressive symptom severity was associated with macrophage superoxide anion production. All analyses were adjusted for potential confounders.

Results

Individuals with hypertension showed higher superoxide anion production compared with normotensive individuals (F(1,58) = 11.56, p = .001). Complementary analyses using mean arterial blood pressure as a continuous measure revealed that higher mean arterial pressure correlated significantly with higher WST-1 reduction (ß = .38, p = .003, ΔR
2 = .145). These results remained significant when controlling for potential confounding influences. Chronic stress was related to higher WST-1 reduction scores, but this association was not statistically significant (ß = .24, p = .067, ΔR
2 = .053); depression levels were not significantly associated with WST-1 reduction scores (p = .24).

Conclusions

Our results indicate higher macrophage superoxide anion production in individuals with hypertension compared with normotensive individuals. This may suggest a mechanism underlying cardiovascular risk with hypertension.
A Stepwise Psychotherapy Intervention for Reducing Risk in Coronary Artery Disease (SPIRR-CAD): Results of an Observer-Blinded, Multicenter, Randomized Trial in Depressed Patients With Coronary Artery Disease
Authors: Herrmann-Lingen Christoph , Beutel Manfred E. , Bosbach Alexandra , Deter Hans-Christian , Fritzsche Kurt , Hellmich Martin , Jordan Jochen , Jünger Jana , Ladwig Karl-Heinz , Michal Matthias , Petrowski Katja , Pieske Burkert , Ronel Joram , Söllner Wolfgang , Stöhr Andreas , Weber Cora , de Zwaan Martina , Albus Christian
Published: May 2016

Background

Depression predicts adverse prognosis in patients with coronary artery disease (CAD), but previous treatment trials yielded mixed results. We tested the hypothesis that stepwise psychotherapy improves depressive symptoms more than simple information.

Methods

In a multicenter trial, we randomized 570 CAD patients scoring higher than 7 on the Hospital Anxiety and Depression Scale-depression subscale to usual care plus either one information session (UC-IS) or stepwise psychotherapy (UC-PT). UC-PT patients received three individual psychotherapy sessions. Those still depressed were offered group psychotherapy (25 sessions). The primary outcome was changed in the Hospital Anxiety and Depression Scale-depression scores from baseline to 18 months. Preplanned subgroup analyses examined whether treatment responses differed by patients' sex and personality factors (Type D).

Results

The mean (standard deviation) depression scores declined from 10.4 (2.5) to 8.7 (4.1) at 18 months in UC-PT and from 10.4 (2.5) to 8.9 (3.9) in UC-IS (both p < .001). There was no significant group difference in change of depressive symptoms (group-by-time effect, p = .90). Preplanned subgroup analyses revealed no differences in treatment effects between men versus women (p
treatment-by-sex interaction = .799) but a significant treatment-by-Type D interaction on change in depressive symptoms (p = .026) with a trend for stronger improvement with UC-PT than UC-IS in Type D patients (n = 341, p = .057) and no such difference in improvement in patients without Type D (n = 227, p = .54).

Conclusions

Stepwise psychotherapy failed to improve depressive symptoms in CAD patients more than UC-IS. The intervention might be beneficial for depressed CAD patients with Type D personality. However, this finding requires further study.

Trial Registration:
www.clinicaltrials.gov
NCT00705965; www.isrctn.com
ISRCTN76240576.
Hepatitis C following liver transplantation: current approach and future research opportunities
Authors: Cosar Arif M. , Durand Christine M. , Cameron Andrew M. , Gurakar Ahmet
Published: May 2016

Purpose of review

The treatment of hepatitis C virus infection (HCV) in liver transplant recipients was very limited until direct-acting antivirals became widely available. We review the current approach to HCV treatment following liver transplantation and future research opportunities.

Recent findings

Current treatment of HCV infection with all oral new direct-acting antivirals in the postliver transplant setting is easier, shorter, tolerable, and more effective with high-sustained virological response rates. However, some challenges remain, including the optimal timing of therapy, drug–drug interactions, renal insufficiency, and HIV coinfection.

Patients with recurrent HCV following liver transplant will significantly benefit from all oral new direct acting antivirals. Ongoing studies will determine the optimal timing and combination in this unique population.
Treatment of mucormycosis in transplant patients: role of surgery and of old and new antifungal agents
Authors: Chitasombat Maria N. , Kontoyiannis Dimitrios P.
Published: May 2016

Purpose of review

Mucormycosis is an opportunistic mold infection whose management is difficult, as there is a paucity of evidence-based data. We summarize the latest advances in diagnosis and management of mucormycosis in transplant recipients.

Recent findings

There is promise for improvement in nonculture-based diagnostics with new biomarkers of Mucorales DNA that can be used for early diagnosis, and monitoring of response. Antifungal treatment consists of high-dose lipid formulations of amphotericin B or isavuconazole as the first-line therapy and posaconazole as salvage therapy. The new, pharmacokinetically more reliable formulations of posaconazole (intravenous, extended-release tablets) are welcomed improvements. Yet, the role of combination therapy is still uncertain. Surgery had a significant role in selected cases, such as in patients with rhinosinusitis form of mucormycosis, which nowadays can be performed with minimal invasive technique.

Mucormycosis remain a life-threatening opportunistic mold infection among transplant patients. Early diagnosis, prompt treatment with effective antifungals in combination with surgery if feasible is essential. Immune adjunct therapy and improvement of early diagnostics are important areas for future research. There are good prospects of progress in diagnostics and management of mucormycosis in transplant patients.
Three-Dimensional CAIPIRINHA SPACE TSE for 5-Minute High-Resolution MRI of the Knee
Authors: Fritz Jan , Fritz Benjamin , Thawait Gaurav G. , Meyer Heiko , Gilson Wesley D. , Raithel Esther
Published: May 2016

Objective

The aim of this study was to prospectively test the hypothesis that a 2-dimensional (2D) CAIPIRINHA (controlled aliasing in parallel imaging results in higher acceleration) sampling pattern facilitates 5-minute high spatial resolution 3-dimensional (3D) sampling perfection with application optimized contrast using different flip angle evolutions (SPACE) magnetic resonance imaging (MRI) of the knee with image quality similar or better than current 2D turbo spin echo (TSE) and 3D SPACE standards.

Materials and Methods

The study was approved by our institutional review board. Twenty asymptomatic subjects (12 men, 8 women; mean age, 42 years; age range, 24–65 years) underwent 3 T MRI of the knee. A 4-fold accelerated 3D SPACE TSE prototype with 2D CAIPIRINHA sampling pattern and 5-minute acquisition time was compared with commercially available 2-fold and 4-fold accelerated 3D SPACE and 2D TSE pulse sequences with acquisition times of 11 minutes and 15 seconds, 6 minutes and 30 seconds, as well as 9 minutes and 48 seconds, respectively. Outcome variables included image quality, anatomic visibility, signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR). Statistical analysis included Friedman, repeated measures analysis of variances, and Cohen's weighted κ tests. Bonferroni-corrected P values of 0.005 and less were considered statistically significant.

Results

Overall, image quality, visibility of anatomic structures, SNR, and CNR of 3D CAIPIRINHA SPACE were statistically similar to 2-fold accelerated 3D SPACE and significantly better than 4-fold accelerated 3D SPACE, which exhibited degrading parallel imaging artifacts. Compared with 2.5-mm 2D TSE images, 0.5-mm 3D CAIPIRINHA SPACE images showed statistically similar good edge sharpness and very good contrast resolution, and significantly less partial volume as well as absent chemical shift and pulsatile flow artifacts. Visibility of menisci, anterior cruciate ligament, posterior cruciate ligament, medial collateral ligament, and lateral collateral ligament was good to very good on 0.5-mm 3D CAIPIRINHA SPACE images as compared with good on 2.5-mm 2D TSE image (P < 0.005). The SNR of fat, fluid, and cartilage as well as CNR between cartilage, fluid, fat, posterior cruciate ligament, and menisci were minimally higher on 2.5-mm 2D TSE image (P < 0.005). Image quality, visibility of anatomic structures, SNR, and CNR of 2.5-mm 3D CAIPIRINHA SPACE and 2.5-mm 2D TSE images were good to very good without significant differences.

Conclusions

Three-dimensional SPACE with 2D CAIPIRINHA sampling pattern enables high-quality 3D TSE MRI of the knee at an acquisition time of 5 minutes and image quality, visibility of anatomic structures, SNR, and CNR similar to conventional 3D SPACE and 2D TSE, both of which require approximately 10-minute acquisition times.
Ultrabrief Electroconvulsive Therapy for Mania
Authors: Elias Alby , Ramalingam Jothi , Abidi Nobia , Thangapandian Sathish , Bhat Ravi
Published: May 2016

Electroconvulsive therapy (ECT) is an effective treatment of mania. Ultrabrief ECT is a novel modality that is associated with fewer cognitive adverse effects than the standard pulse width brief pulse ECT. It has been well studied in depression. However, its use in mania is not yet known. Following a retrospective chart view, we report a small sample of patients who had Right Unilateral Ultrabrief ECT (RUB-ECT) for mania. Eleven RUB-ECTs were identified for 9 patients; 72.8% remission rate was observed with RUB-ECT. Two patients required switch into bitemporal ECT in view of minimal clinical response and 1 patient to right unilateral brief pulse ECT because of poor seizure parameters. All patients achieved remission eventually. The possible mechanisms of ECT in mania and clinical implications of ultrabrief ECT are discussed.
Super-sensing technology: industrial applications and future challenges of electrical tomography
Authors: Wei Kent (Hsin-Yu) , Qiu Chang-Hua , Primrose Ken
Published: May 2016

Electrical tomography is a relatively new imaging technique that can image the distribution of the passive electrical properties of an object. Since electrical tomography technology was proposed in the 1980s, the technique has evolved rapidly because of its low cost, easy scale-up and non-invasive features. The technique itself can be sensitive to all passive electrical properties, such as conductivity, permittivity and permeability. Hence, it has a huge potential to be applied in many applications. Owing to its ill-posed nature and low image resolution, electrical tomography attracts more attention in industrial fields than biomedical fields. In the past decades, there have been many research developments and industrial implementations of electrical tomography; nevertheless, the awareness of this technology in industrial sectors is still one of the biggest limitations for technology implementation. In this paper, the authors have summarized several representative applications that use electrical tomography. Some of the current tomography research activities will also be discussed.

This article is part of the themed issue ‘Supersensing through industrial process tomography’.
Arts of electrical impedance tomographic sensing
Authors: Wang Mi , Wang Qiang , Karki Bishal
Published: May 2016

This paper reviews governing theorems in electrical impedance sensing for analysing the relationships of boundary voltages obtained from different sensing strategies. It reports that both the boundary voltage values and the associated sensitivity matrix of an alternative sensing strategy can be derived from a set of full independent measurements and sensitivity matrix obtained from other sensing strategy. A new sensing method for regional imaging with limited measurements is reported. It also proves that the sensitivity coefficient back-projection algorithm does not always work for all sensing strategies, unless the diagonal elements of the transformed matrix, A
T
A, have significant values and can be approximate to a diagonal matrix. Imaging capabilities of few sensing strategies were verified with static set-ups, which suggest the adjacent electrode pair sensing strategy displays better performance compared with the diametrically opposite protocol, with both the back-projection and multi-step image reconstruction methods. An application of electrical impedance tomography for sensing gas in water two-phase flows is demonstrated.

This article is part of the themed issue ‘Supersensing through industrial process tomography’.
Reconstruction of velocity fields in electromagnetic flow tomography
Authors: Lehtikangas Ossi , Karhunen Kimmo , Vauhkonen Marko
Published: May 2016

Electromagnetic flow meters (EMFMs) are the gold standard in measuring flow velocity in process industry. The flow meters can measure the mean flow velocity of conductive liquids and slurries. A drawback of this approach is that the velocity field cannot be determined. Asymmetric axial flows, often encountered in multiphase flows, pipe elbows and T-junctions, are problematic and can lead to serious systematic errors. Recently, electromagnetic flow tomography (EMFT) has been proposed for measuring velocity fields using several coils and a set of electrodes attached to the surface of the pipe. In this work, a velocity field reconstruction method for EMFT is proposed. The method uses a previously developed finite-element-based computational forward model for computing boundary voltages and a Bayesian framework for inverse problems. In the approach, thevz-component of the velocity field along the longitudinal axis of the pipe is estimated on the pipe cross section. Different asymmetric velocity fields encountered near pipe elbows, solids-in-water flows in inclined pipes and in stratified or multiphase flows are tested. The results suggest that the proposed reconstruction method could be used to estimate velocity fields in complicated pipe flows in which the conventional EMFMs have limited accuracy.

This article is part of the themed issue ‘Supersensing through industrial process tomography’.
Sensing flame structure by process tomography
Authors: Liu Jing , Liu Shi , Zhou Wanting , Qi Xin , Lei Jing , Mu Huaiping
Published: May 2016

Non-intrusive visualization of the structure of flames can offer us many advantages in studying the reaction mechanisms of combustion and observing special distributions of the parameters required for the development of equipment such as jet engines and gas turbines. Process tomography is a relatively new technique for such a task, but is useful owing to its fast speed and capability of detecting signals related to ionizations caused by chemical reactions and thermal effects. Electric capacitance tomography (ECT) is one of the process tomographic techniques. ECT usually comprises a sensor array of electrodes that detect permittivity variations in the measuring zone, a data-logging device and a computer that controls data acquisition and carries out image reconstruction. There have been studies on ECT imaging of flames; however, ECT has not been exploited sufficiently to reveal the inner structure of the flames. In this study, a sensor with planar electrodes is created, and the associated three-dimensional sensitivity map is generated by the finite-element method to detect flame structure. A series of experiments are carried out covering a range of feed rates of fuel and air. Data are collected by the ECT sensor and hardware. The results of the ECT reconstruction show good agreement with actual features, and the structure of the flame is found. This opens up a new route for the study of flames.

This article is part of the themed issue ‘Supersensing through industrial process tomography’.
Interactions between KSHV ORF57 and the novel human TREX proteins, CHTOP and CIP29
Authors: Schumann Sophie , Baquero-Perez Belinda , Whitehouse Adrian
Published: May 2016

The coupling of mRNA processing steps is essential for precise and efficient gene expression. The human transcription/export (hTREX) complex is a highly conserved multi-protein complex responsible for eukaryotic mRNA stability and nuclear export. We have previously shown that the Kaposi’s sarcoma-associated open reading frame 57 (ORF57) protein orchestrates the recruitment of the hTREX complex onto viral intronless mRNA, forming a stable and export-competent viral ribonucleoprotein particle (vRNP). Recently, additional cellular proteins, namely CHTOP, CIP29 and POLDIP3 have been proposed as novel hTREX components. Herein, we extend our previous research and provide evidence that ORF57 interacts with CHTOP and CIP29, in contrast to POLDIP3. Moreover, depletion studies show both CHTOP and CIP29 effect ORF57-mediated viral mRNA processing. As such, these results suggest both CHTOP and CIP29 are hTREX components and are recruited to an ORF57-mediated vRNP.
Retargeting FX-binding-ablated HAdV-5 to vascular cells by inclusion of the RGD-4C peptide in hexon hypervariable region 7 and the HI loop
Authors: Robertson Stacy , Parker Alan L. , Clarke Carolyn , Duffy Margaret R. , Alba Raul , Nicklin Stuart A. , Baker Andrew H.
Published: May 2016

Recent studies have generated interest in the function of human adenovirus serotype 5 (HAdV-5) hexon:  factor X (FX) binding and subsequent hepatocyte transduction and interaction with the immune system. Here, we retargeted adenovirus serotype 5 vectors, ablated for FX interaction, by replacing amino acids in hexon HVR7 with RGD-4C or inserting the peptide into the fibre HI loop. These genetic modifications in the capsid were compatible with virus assembly, and could efficiently retarget transduction of the vector via the αvβ3/5 integrin-mediated pathway, but did not alter immune recognition by pre-existing human neutralizing anti-HAdV-5 antibodies or by natural antibodies in mouse serum. Thus, FX-binding-ablated HAdV-5 can be retargeted but remain sensitive to immune-mediated attack. These findings further refine HAdV-5-based vectors for human gene therapy and inform future vector development.
Acute induction of anomalous blood clotting by molecular amplification of highly substoichiometric levels of bacterial lipopolysaccharide (LPS)
Authors: Pretorius Etheresia , Mbotwa Sthembile , Bester Janette , Robinson Christopher , Kell Douglas B.
Published: May 2016

It is well known that a variety of inflammatory diseases are accompanied by hypercoagulability, and a number of more-or-less longer-term signalling pathways have been shown to be involved. In recent work, we have suggested a direct and primary role for bacterial lipopolysaccharide in this hypercoagulability, but it seems never to have been tested directly. Here we show that the addition of tiny concentrations (0.2 ng.L−1) of bacterial lipopolysaccharide (LPS) to both whole blood and platelet-poor plasma of normal, healthy donors leads to marked changes in the nature of the fibrin fibres so formed, as observed by ultrastructural and fluorescence microscopy (the latter implying that the fibrin is actually in an amyloid β-sheet-rich form. They resemble those seen in a number of inflammatory (and also amyloid) diseases, consistent with an involvement of LPS in their aetiology. These changes are mirrored by changes in their viscoelastic properties as measured by thromboelastography. Since the terminal stages of coagulation involve the polymerisation of fibrinogen into fibrin fibres, we tested whether LPS would bind to fibrinogen directly. We demonstrated this using isothermal calorimetry. Finally, we show that these changes in fibre structure are mirrored when the experiment is done simply with purified fibrinogen and thrombin (± 0.2 ng.L−1LPS). This ratio of concentrations of LPS:fibrinogenin vivorepresents a molecular amplification by the LPS of more than 108-fold, a number that is probably unparalleled in biology. The observation of a direct effect of such highly substoichiometric amounts of LPS on both fibrinogen and coagulation can account for the role of very small numbers of dormant bacteria in disease progression, and opens up this process to further mechanistic analysis and possible treatment.

Significance statement

Most chronic diseases (including those classified as cardiovascular, neurodegenerative, or autoimmune) are accompanied by long-term inflammation. Although typically mediated by ‘inflammatory’ cytokines, the origin of this inflammation is unclear. We have suggested that one explanation is a dormant microbiome that can shed the highly inflammatory lipopolysaccharide LPS. Such inflammatory diseases are also accompanied by a hypercoagulable phenotype. We here showdirectly(using 6 different methods) that very low concentrations of LPS can affect the terminal stages of the coagulation properties of blood and plasma significantly, and that this may be mediated via a direct binding of LPS to a small fraction of fibrinogen monomers as assessed biophysically. Such amplification methods may be of more general significance.
Cassava brown streak virushas a rapidly evolving genome: implications for virus speciation, variability, diagnosis and host resistance
Authors: Alicai Titus , Ndunguru Joseph , Sseruwagi Peter , Tairo Fred , Okao-Okuja Geoffrey , Nanvubya Resty , Kiiza Lilliane , Kubatko Laura , Kehoe Monica A. , Boykin Laura M.
Published: May 2016

Cassava is a major staple food for about 800 million people in the tropics and subGtropical regions of the world. Production of cassava is significantly hampered by cassava brown streak disease (CBSD), which is caused byCassava brown streak virus(CBSV) andUgandan cassava brown streak virus(UCBSV). The disease is suppressing cassava yields in eastern Africa at an alarming rate. Previous studies have documented that CBSV is more devastating than UCBSV because it more readily infects both susceptible and tolerant cassava cultivars, resulting in greater yield losses. Using whole genome sequences from NGS data, we produced the first coalescentGbased species tree estimate for CBSV and UCBSV. This species framework led to the finding that CBSV has a faster rate of evolution when compared with UCBSV. Furthermore, we have discovered that in CBSV, nonsynonymous substitutions are more predominant than synonymous substitution and occur across the entire genome. All comparative analyses between CBSV and UCBSV presented here suggest that CBSV may be outsmarting the cassava immune system, thus making it more devastating and harder to control.
Bottom-up and top-down computations in high-level visual cortex
Authors: Kay Kendrick N. , Yeatman Jason D.
Published: May 2016

The ability to read a page of text or recognize a person’s face depends on category-selective visual regions in ventral temporal cortex (VTC). To understand how these regions mediate word and face recognition, it is necessary to characterize how stimuli are represented and how this representation is used in the execution of a cognitive task. Here, we show that the response of a category-selective region in VTC can be computed as the degree to which the low-level properties of the stimulus match a category template. Moreover, we show that during execution of a task, the bottom-up representation is scaled by the intraparietal sulcus (IPS), and that the level of IPS engagement reflects the cognitive demands of the task. These results provide a unifying account of neural processing in VTC in the form of a model that addresses both bottom-up and top-down effects and quantitatively predicts VTC responses.
gmos: Rapid detection of genome mosaicism over short evolutionary distances
Authors: Domazet-Lošo Mirjana , Domazet-Lošo Tomislav
Published: May 2016

Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenicEnterococcus faeciumstrain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos).
An improved reversibly dimerizing mutant of the FK506-binding protein FKBP
Authors: Barrero Juan J. , Papanikou Effrosyni , Casler Jason C. , Day Kasey J. , Glick Benjamin S.
Published: May 2016

FK506-binding protein (FKBP) is a monomer that binds to FK506, rapamycin, and related ligands. The F36M substitution, in which Phe36 in the ligand-binding pocket is changed to Met, leads to formation of antiparallel FKBP dimers, which can be dissociated into monomers by ligand binding. This FKBP(M) mutant has been employed in the mammalian secretory pathway to generate aggregates that can be dissolved by ligand addition to create cargo waves. However, when testing this approach in yeast, we found that dissolution of FKBP(M) aggregates was inefficient. An improved reversibly dimerizing FKBP formed aggregates that dissolved more readily. This FKBP(L,V) mutant carries the F36L mutation, which increases the affinity of ligand binding, and the I90V mutation, which accelerates ligand-induced dissociation of the dimers. The FKBP(L,V) mutant expands the utility of reversibly dimerizing FKBP.
Crystal structures of 3-fluoro-N-[2-(trifluoromethyl)phenyl]benzamide, 3-bromo-N-[2-(trifluoromethyl)phenyl]benzamide and 3-iodo-N-[2-(trifluoromethyl)phenyl]benzamide
Authors: Suchetan P. A. , Suresha E. , Naveen S. , Lokanath N. K.
Published: May 2016

In the title compounds, C14H9F4NO, (I), C14H9BrF3NO, (II), and C14H9F3INO, (III), the two benzene rings are inclined to one another by 43.94 (8)° in moleculeAand 55.66 (7)° in moleculeBof compound (I), which crystallizes with two independent molecules in the asymmetric unit, but by only 10.40 (12)° in compound (II) and 12.5 (2)° in compound (III). In the crystals of all three compounds, N—H...O hydrogen bonds link the molecules to form chains propagating along thea-axis direction for (I), and along theb-axis direction for (II) and (III). In the crystal of (I), –A–B–A–B– chains are linked by C—H...O hydrogen bonds, forming layers parallel to (010). Within the layers there are weak offset π–π interactions present [intercentroid distances = 3.868 (1) and 3.855 (1) Å]. In the crystals of (II) and (III), the chains are linkedviashort halogen–halogen contacts [Br...Br = 3.6141 (4) Å in (II) and I...I = 3.7797 (5) Å in (III)], resulting in the formation of ribbons propagating along theb-axis direction.
We live in a VUCA World: the importance of responsible leadership
Authors: Sarkar Anita
Published: May 2016

Purpose

This paper aims to describe the role of responsible leadership in a VUCA (volatile, uncertain, complex and ambiguous) world.

Design/methodology/approach

This paper explains how responsible leadership is aligned with the critical success factors necessary to thrive in a VUCA world.

Findings

Critical success factors in the VUCA world are: sound business principles, a firm’s agility to respond speedily, strong collaborative networks, innovation and ethical practices. These are aligned with a responsible leadership style, which is a combination of transformational, servant and authentic leadership.

Socialimplications

This paper argues that responsible leadership embraces the broader societal issues and concerns based on ethical judgment.

Originality/value

This paper provides insights on how responsible leaders can meet the requirements of VUCA world.
Motivating language theory: antecedent variables – critical to both the success of leaders and organizations
Authors: Holmes William T.
Published: May 2016

Purpose

The purpose of this conceptual paper is twofold, i.e. first, to elevate an assumption of Motivating Language Theory (MLT) – walk and talk congruence – to the level of antecedent variable serving as a prerequisite to the implementation of Motivating Language (ML) and second, to explore the components of walk and talk congruence (Behavioral Integrity and Credibility) to understand how they are vital in the establishment of trust at the organizational level which is the key lever for ML to be strategically implemented.

Design/methodology/approach

The approach is cross-disciplinary, as it utilized MLT from the field of business; applied in the field of education with research from educational researchers; and for the purpose of utilization by organizations, leaders, and scholars from all fields.

Findings

The findings are leadership communication matters and is how leadership gets done, ML makes a difference to employees and organizations, trust is a critical factor in organizational success, Credibility is all that stands between a leader’s believability or not, and Behavioral Intergrity is the key determiner in walk and talk alignment.

Researchlimitations/implications

The implications for researchers are new research opportunities in the ML field.

Practicalimplications

The implications for practitioners are clear in terms of how to maximize leader effectiveness and organizational trust/citizenship, increase employee and organizational outcomes and drive leadership development.

Originality/value

The value of this paper is to both the practitioner and scholar in terms of application and deepening of the field.
A comparative study of fractional step method in its quasi-implicit, semi-implicit and fully-explicit forms for incompressible flows
Authors: Bevan Rhodri LT , Boileau Etienne , van Loon Raoul , Lewis R.W. , Nithiarasu P
Published: May 2016

Purpose

– The purpose of this paper is to describe and analyse a class of finite element fractional step methods for solving the incompressible Navier-Stokes equations. The objective is not to reproduce the extensive contributions on the subject, but to report on long-term experience with and provide a unified overview of a particular approach: the characteristic-based split method. Three procedures, the semi-implicit, quasi-implicit and fully explicit, are studied and compared.

Design/methodology/approach

– This work provides a thorough assessment of the accuracy and efficiency of these schemes, both for a first and second order pressure split.

Findings

– In transient problems, the quasi-implicit form significantly outperforms the fully explicit approach. The second order (pressure) fractional step method displays significant convergence and accuracy benefits when the quasi-implicit projection method is employed. The fully explicit method, utilising artificial compressibility and a pseudo time stepping procedure, requires no second order fractional split to achieve second order or higher accuracy. While the fully explicit form is efficient for steady state problems, due to its ability to handle local time stepping, the quasi-implicit is the best choice for transient flow calculations with time independent boundary conditions. The semi-implicit form, with its stability restrictions, is the least favoured of all the three forms for incompressible flow calculations.

Originality/value

– A comprehensive comparison between three versions of the CBS method is provided for the first time.
The effect of an embedded solid block on the onset of convection in a porous cavity
Authors: Rees D.  Andrew S. , Nield Donald A.
Published: May 2016

Purpose

– The purpose of this paper is to determine how the presence of an embedded, centrally placed, solid but heat-conducting block affects the onset and development of Darcy-Bénard convection.

Design/methodology/approach

– Steady solutions are obtained using finite difference methods with SOR as the smoother. A detailed presentation is given of how the interface conditions are modelled, and how a continuity of pressure argument is used to determine the value of the streamfunction on the solid block.

Findings

– The presence of the block affects strongly both the onset of convection and the nonlinear properties such as the mean Nusselt number and the strength of the fluid circulation. The smallest possible critical Darcy-Rayleigh is found to be 22.0152, which is smaller than 4π2, the value when the block is absent.

Research limitations/implications

– The Darcy-Rayleigh number is restricted to values at or below 200, which is five times the critical value without a solid block, but the size and conductivity of the block vary between all admissible values.

Originality/value

– This is the first investigation of the effect of internal obstacles on Darcy-Bénard convection.
On the accuracy of some explicit and implicit methods for the inviscid GRLW equation subject to initial Gaussian conditions
Authors: Ramos J I
Published: May 2016

Purpose

– The purpose of this paper is to both determine the effects of the nonlinearity on the wave dynamics and assess the temporal and spatial accuracy of five finite difference methods for the solution of the inviscid generalized regularized long-wave (GRLW) equation subject to initial Gaussian conditions.

Design/methodology/approach

– Two implicit second- and fourth-order accurate finite difference methods and three Runge-Kutta procedures are introduced. The methods employ a new dependent variable which contains the wave amplitude and its second-order spatial derivative. Numerical experiments are reported for several temporal and spatial step sizes in order to assess their accuracy and the preservation of the first two invariants of the inviscid GRLW equation as functions of the spatial and temporal orders of accuracy, and thus determine the conditions under which grid-independent results are obtained.

Findings

– It has been found that the steepening of the wave increase as the nonlinearity exponent is increased and that the accuracy of the fourth-order Runge-Kutta method is comparable to that of a second-order implicit procedure for time steps smaller than 100th, and that only the fourth-order compact method is almost grid-independent if the time step is on the order of 1,000th and more than 5,000 grid points are used, because of the initial steepening of the initial profile, wave breakup and solitary wave propagation.

Originality/value

– This is the first study where an accuracy assessment of wave breakup of the inviscid GRLW equation subject to initial Gaussian conditions is reported.
Computations of anomalous phase change
Authors: Voller V R
Published: May 2016

Purpose

– The purpose of this paper is to demonstrate how anomalous diffusion behaviors can be manifest in physically realizable phase change systems.

Design/methodology/approach

– In the presence of heterogeneity the exponent in the diffusion time scale can become anomalous, exhibiting values that differ from the expected value of 1/2. Here the author investigates, through directed numerical simulation, the two-dimensional melting of a phase change material (PCM) contained in a pattern of cavities separated by a non-PCM matrix. Under normal circumstances we would expect that the progress of melting F(t) would exhibit the normal diffusion time exponent, i.e., F∼t1/2. The author’s intention is to investigate what features of the PCM cavity pattern might induce anomalous phase change, where the progress of melting has a time exponent different from n=1/2.

Findings

– When the PCM cavity pattern has an internal length scale, i.e., when there is a sub-domain pattern which, when reproduced, gives us the full domain pattern, the direct simulation recovers the normal ∼t1/2 phase change behavior. When, however, there is no internal length scale, e.g., the pattern is a truncated fractal, an anomalous super diffusive behavior results with melting going as t
n; n
>
1/2. By studying a range of related fractal patterns, the author is able to relate the observed sub-diffusive exponent to the cavity pattern’s fractal dimension. The author also shows, how the observed behavior can be modeled with a non-local fractional diffusion treatment and how sub-diffusion phase change behavior (F∼t
n; n
<
1/2) results when the phase change nature of the materials in the cavity and matrix are inverted.

Research limitations/implications

– Although the results clearly demonstrate under what circumstances anomalous phase change behavior can be practically produced, the question of an exact theoretical relationship between the cavity pattern geometry and the observed anomalous time exponent is not known.

Practical implications

– The clear role of the influence of heterogeneity on heat flow behavior is illustrated. Suggesting that modeling heat and fluid flow in heterogeneous systems requires careful consideration.

Originality/value

– The novel direct simulation of melting in a two-dimensional PCM cavity pattern provides a clear illustration of anomalous behavior in a classic heat and fluid flow system and by extension provides motivation to continue the numerical investigation of anomalous and non-local behaviors and fractional calculus tools.
Analytical characterization of gaseous slip flow and heat transport through a parallel-plate microchannel with a centered porous substrate
Authors: Wang Keyong , Vafai Kambiz , Wang Dazhong
Published: May 2016

Purpose

– The purpose of this paper is to analytically perform gaseous slip flow and heat transfer analysis within a parallel-plate microchannel partially filled with a centered porous medium under local thermal non-equilibrium (LTNE) condition. Heat transfer of gaseous flow in a porous microchannel is analytically studied. Energy communication at the porous-fluid interface is considered by two approaches: the gas rarefaction negatively impacts the heat transfer performance, and the optimum ratio of porous thickness is found to be around 0.8.

Design/methodology/approach

– Both Models A and B are utilized to consider the heat flux splitting for the fluid and solid phases at the porous-fluid interface.

Findings

– Analytical solutions for the fluid and solid phase temperature distributions and the Nusselt number are derived. In the no-slip flow limit, the present analytical solutions are validated by the partially and fully filled cases available in the literature.

Research limitations/implications

– The continuum flow (no-slip flow) is only a special case of the slip flow. Meanwhile, the effects of pertinent parameters on the heat transfer are also discussed.

Practical implications

– A survey of available literature mentioned above indicates a shortage of information for slip flow and heat transfer in partially filled porous systems. The main objective of the present study is to investigate the slip flow and heat transfer characteristics for forced convection through a microchannel partially filled with a porous medium under LTNE condition. The porous substrate is placed at the center of the microchannel. Analytical solutions for the temperature distributions of the fluid and solid phases and the Nusselt number at the microchannel wall are obtained.

Originality/value

– Heat transfer of gaseous flow in a porous microchannel is analytically studied. Energy communication at the porous-fluid interface is considered by two approaches: the gas rarefaction negatively impacts the heat transfer performance, and the optimum ratio of porous thickness is found to be around 0.8. Gaseous slip flow and heat transfer analysis is analytically performed within a parallel-plate microchannel partially filled with a centered porous medium under LTNE condition. Analytical solutions for the fluid and solid phase temperature distributions and the Nusselt number are derived for the first time. The effects of pertinent parameters on the heat transfer are also discussed. Compared with the results obtained for the continuum flow regime, the gas rarefaction negatively impacts the heat transfer efficiency and has little influence on the optimal porous thickness.
A short remark on Chien’s variational principle of maximum power losses for viscous fluids
Authors: Liu H.Y. , Si Na , He Ji-Huan
Published: May 2016

Purpose

– The purpose of this paper is to point out a paradox in variational theory for viscous flows. Chien (1984) claimed that a variational principle of maximum power loses for viscous fluids was established, however, it violated the well-known Helmholtz’s principle.

Design/methodology/approach

– Restricted variables are introduced in the derivation, the first order and the second order of variation of the restricted variables are zero.

Findings

– An approximate variational principle of minimum power loses is established, which agrees with the Helmholtz’s principle, and the paradox is solved.

Research limitations/implications

– This paper focusses on incompressible viscose flows, and the theory can be extended to compressible one and other viscose flows. It is still difficult to obtain a variational formulation for Navier-Stokes equations.

Practical implications

– The variational principle of minimum power loses can be directly used for numerical methods and analytical analysis.

Originality/value

– It is proved that Chien’s variational principle is a minimum principle.
Constrained large-eddy simulation of turbulent flow and heat transfer in a stationary ribbed duct
Authors: Jiang Zhou , Xiao Zuoli , Shi Yipeng , Chen Shiyi
Published: May 2016

Purpose

– The knowledge about the heat transfer and flow field in the ribbed internal passage is particularly important in industrial and engineering applications. The purpose of this paper is to identify and analyze the performance of the constrained large-eddy simulation (CLES) method in predicting the fully developed turbulent flow and heat transfer in a stationary periodic square duct with two-side ribbed walls.

Design/methodology/approach

– The rib height-to-duct hydraulic diameter ratio is 0.1 and the rib pitch-to-height ratio is 9. The bulk Reynolds number is set to 30,000, and the bulk Mach number of the flow is chosen as 0.1 in order to keep the flow almost incompressible. The CLES calculated results are thoroughly assessed in comparison with the detached-eddy simulation (DES) and traditional large-eddy simulation (LES) methods in the light of the experimentally measured data.

Findings

– It is manifested that the CLES approach can predict both aerodynamic and thermodynamic quantities more accurately than the DES and traditional LES methods.

Originality/value

– This is the first time for the CLES method to be applied to simulation of heat and fluid flow in this widely used geometry.