bluuebunny/crossref_metadata_2025 huggingface dataset:
Spore sensitivity to sunlight and freezing can restrict dispersal in wood‐decay fungi
Authors: Norros Veera , Karhu Elina , Nordén Jenni , Vähätalo Anssi V. , Ovaskainen Otso
Published: July 2015

Assessment of the costs and benefits of dispersal is central to understanding species' life‐history strategies as well as explaining and predicting spatial population dynamics in the changing world. While mortality during active movement has received much attention, few have studied the costs of passive movement such as the airborne transport of fungal spores. Here, we examine the potential of extreme environmental conditions to cause dispersal mortality in wood‐decay fungi. These fungi play a key role as decomposers and habitat creators in forest ecosystems and the populations of many species have declined due to habitat loss and fragmentation. We measured the effect of simulated solar radiation (including ultraviolet A and B) and freezing at −25°C on the spore germinability of 17 species. Both treatments but especially sunlight markedly reduced spore germinability in most species, and species with thin‐walled spores were particularly light sensitive. Extrapolating the species' laboratory responses to natural irradiance conditions, we predict that sunlight is a relevant source of dispersal mortality at least at larger spatial scales. In addition, we found a positive effect of spore size on spore germinability, suggesting a trade‐off between dispersal distance and establishment. We conclude that freezing and particularly sunlight can be important sources of dispersal mortality in wood‐decay fungi which can make it difficult for some species to colonize isolated habitat patches and habitat edges.
Tumour necrosis factor receptor I blockade shows that TNF‐dependent and TNF‐independent mechanisms synergise in TNF receptor associated periodic syndrome
Authors: Fairclough Lucy C. , Stoop A. Allart , Negm Ola H. , Radford Paul M. , Tighe Patrick J. , Todd Ian
Published: July 2015

TNF receptor associated periodic syndrome (TRAPS) is an autoinflammatory disease involving recurrent episodes of fever and inflammation. It is associated with autosomal dominant mutations in TNF receptor superfamily 1A gene localised to exons encoding the ectodomain of the p55 TNF receptor, TNF receptor‐1 (TNFR1). The aim of this study was to investigate the role of cell surface TNFR1 in TRAPS, and the contribution of TNF‐dependent and TNF‐independent mechanisms to the production of cytokines. HEK‐293 and SK‐HEP‐1 cell lines were stably transfected with WT or TRAPS‐associated variants of human TNF receptor superfamily 1A gene. An anti‐TNFR1 single domain antibody (dAb), and an anti‐TNFR1 mAb, bound to cell surface WT and variant TNFR1s. In HEK‐293 cells transfected with death domain‐inactivated (R347A) TNFR1, and in SK‐HEP‐1 cells transfected with normal (full‐length) TNFR1, cytokine production stimulated in the absence of exogenous TNF by the presence of certain TNFR1 variants was not inhibited by the anti‐TNFR1 dAb. In SK‐Hep‐1 cells, specific TRAPS mutations increased the level of cytokine response to TNF, compared to WT, and this augmented cytokine production was suppressed by the anti‐TNFR1 dAb. Thus, TRAPS‐associated variants of TNFR1 enhance cytokine production by a TNF‐independent mechanism and by sensitising cells to a TNF‐dependent stimulation. The TNF‐dependent mechanism requires cell surface expression of TNFR1, as this is blocked by TNFR1‐specific dAb.
Impedimetric Aptasensor Based on Disposable Graphite Electrodes Developed for Thrombin Detection
Authors: Eksin Ece , Erdem Arzum , Kuruc Ayben Pınar , Kayi Hilal , Öğünç Aylin
Published: July 2015

The impedimetric aptasensor for Thrombin (THR) was developed for the first time herein by measuring changes at the charge‐transfer resistance, Rct upon to proteinaptamer complex formation. After covalent activation of pencil graphite electrode (PGE) surface using covalent agents, amino linked aptamer (APT) was immobilized onto activated PGE surface. Then APT‐THR interaction was explored by electrochemical impedance spectroscopy (EIS). After the optimization of experimental conditions (e.g., APT and THR concentration, immobilization and interaction times), the selectivity of impedimetric aptasensor was tested in the presence of other biomolecules: factor Va and bovine serum albumine (BSA) both in buffer media, or in diluted fetal bovine serum (FBS).
Understanding response patterns in dyadic conflict: An interactive approach combining self‐construal and opponent's dominance‐submissiveness
Authors: Au Al K. C. , Lam Shui‐fong
Published: July 2015

Previous works on the effect of self‐construal in interpersonal behaviours tend to adopt a main effect approach. The present research proposes an interactive approach in understanding two response patterns in dyadic conflict by combining self‐construal and the stance of the opponent. Independent self‐construal was hypothesised to be associated with a self‐centred pattern of conflict response, which is characterised by taking contending responses regardless of whether the stance of the opponent is dominant or submissive. Relational self‐construal was hypothesised to be associated with a tuning‐in pattern of conflict response, which is characterised by showing contending responses when the opponent is submissive but yielding responses when the opponent is dominant. With trait self‐construal measured and opponent's stance manipulated, Study 1 provided initial support for the hypotheses. Study 2 showed a three‐way interaction effect between trait self‐construal, manipulated self‐construal and the opponent's stance on actual conflict responses during discussion of a scenario. The effect of self‐construal manipulation was only observed among people who were low in trait independent self‐construal and average in trait relational self‐construal. The results pinpoint the importance of considering personal and opponent factors simultaneously in understanding the dynamics of dyadic conflict processes.
Methyl‐CpG‐Binding Protein (MBD) Family: Epigenomic Read‐Outs Functions and Roles in Tumorigenesis and Psychiatric Diseases
Authors: Gigek Carolina Oliveira , Chen Elizabeth Suchi , Smith Marilia Arruda Cardoso
Published: July 2015

Epigenetics is the study of the heritable changes on gene expression that are responsible for the regulation of development and that have an impact on several diseases. However, it is of equal importance to understand how epigenetic machinery works. DNA methylation is the most studied epigenetic mark and is generally associated with the regulation of gene expression through the repression of promoter activity and by affecting genome stability. Therefore, the ability of the cell to interpret correct methylation marks and/or the correct interpretation of methylation plays a role in many diseases. The major family of proteins that bind methylated DNA is the methyl‐CpG binding domain proteins, or the MBDs. Here, we discuss the structure that makes these proteins a family, the main functions and interactions of all protein family members and their role in human disease such as psychiatric disorders and cancer. J. Cell. Biochem. 117: 29–38, 2016. © 2015 Wiley Periodicals, Inc.
IL‐6 Activates PI3K and PKCζ Signaling and Determines Cardiac Differentiation in Rat Embryonic H9c2 Cells
Authors: D'amico Maria Angela , Ghinassi Barbara , Izzicupo Pascal , Di Ruscio Annalisa , Di Baldassarre Angela
Published: July 2015

Introduction: IL‐6 influences several biological processes, including cardiac stem cell and cardiomyocyte physiology. Although JAK‐STAT3 activation is the defining feature of IL‐6 signaling, signaling molecules such as PI3K, PKCs, and ERK1/2 are also activated and elicit different responses. Moreover, most studies on the specific role of these signaling molecules focus on the adult heart, and few studies are available on the biological effects evoked by IL‐6 in embryonic cardiomyocytes. Aim: The aim of this study was to clarify the biological response of embryonic heart derived cells to IL‐6 by analyzing the morphological modifications and the signaling cascades evoked by the cytokine in H9c2 cells. Results: IL‐6 stimulation determined the terminal differentiation of H9c2 cells, as evidenced by the increased expression of cardiac transcription factors (NKX2.5 and GATA4), structural proteins (α‐myosin heavy chain and cardiac Troponin T) and the gap junction protein Connexin 43. This process was mediated by the rapid modulation of PI3K, Akt, PTEN, and PKCζ phosphorylation levels. PI3K recruitment was an upstream event in the signaling cascade and when PI3K was inhibited, IL‐6 failed to modify PKCζ, PTEN, and Akt phosphorylation. Blocking PKCζ activity affected only PTEN and Akt. Finally, the overexpression of a constitutively active form of PKCζ in H9c2 cells largely mimicked the morphological and molecular effects evoked by IL‐6. Conclusions: This study demonstrated that IL‐6 induces the cardiac differentiation of H9c2 embryonic cells though a signaling cascade that involves PI3K, PTEN, and PKCζ activities. J. Cell. Physiol. 231: 576–586, 2016. © 2015 Wiley Periodicals, Inc.
Reciprocal Control of Osteogenic and Adipogenic Differentiation by ERK/MAP Kinase Phosphorylation of Runx2 and PPARγ Transcription Factors
Authors: Ge Chunxi , Cawthorn William P. , Li Yan , Zhao Guisheng , MacDougald Ormond A. , Franceschi Renny T.
Published: July 2015

In many skeletal diseases, including osteoporosis and disuse osteopenia, defective osteoblast differentiation is associated with increased marrow adipogenesis. The relative activity of two transcription factors, RUNX2 and PPARγ, controls whether a mesenchymal cell will differentiate into an osteoblast or adipocyte. Herein we show that the ERK/MAP kinase pathway, an important mediator of mechanical and hormonal signals in bone, stimulates osteoblastogenesis and inhibits adipogenesis via phosphorylation of RUNX2 and PPARγ. Induction of osteoblastogenesis in ST2 mesenchymal cells was associated with increased MAPK activity and RUNX2 phosphorylation. Under these conditions PPARγ phosphorylation also increased, but adipogenesis was inhibited. In contrast, during adipogenesis MAPK activity and phosphorylation of both transcription factors was reduced. RUNX2 phosphorylation and transcriptional activity were directly stimulated by MAPK, a response requiring phosphorylation at S301 and S319. MAPK also inhibited PPARγ‐dependent transcription via S112 phosphorylation. Stimulation of MAPK increased osteoblastogenesis and inhibited adipogenesis, while dominant‐negative suppression of activity had the opposite effect. In rescue experiments using Runx2−/− mouse embryo fibroblasts (MEFs), wild type or, to a greater extent, phosphomimetic mutant RUNX2 (S301E,S319E) stimulated osteoblastogenesis while suppressing adipogenesis. In contrast, a phosphorylation‐deficient RUNX2 mutant (S301A,S319A) had reduced activity. Conversely, wild type or, to a greater extent, phosphorylation‐resistant S112A mutant PPARγ strongly stimulated adipogenesis and inhibited osteoblastogenesis in Pparg−/− MEFs, while S112E mutant PPARγ was less active. Competition between RUNX2 and PPARγ was also observed at the transcriptional level. Together, these studies highlight the importance of MAP kinase signaling and RUNX2/PPARγ phosphorylation in the control of osteoblast and adipocyte lineages. J. Cell. Physiol. 231: 587–596, 2016. © 2015 Wiley Periodicals, Inc.
The PPARβ/δ Agonist GW0742 Induces Early Neuronal Maturation of Cortical Post‐Mitotic Neurons: Role of PPARβ/δ in Neuronal Maturation
Authors: Benedetti Elisabetta , Di Loreto Silvia , D'Angelo Barbara , Cristiano Loredana , d'angelo Michele , Antonosante Andrea , Fidoamore Alessia , Golini Raffaella , Cinque Benedetta , Cifone Maria Grazia , Ippoliti Rodolfo , Giordano Antonio , Cimini Annamaria
Published: July 2015

Increasing evidences support that signaling lipids participate in synaptic plasticity and cell survival, and that the lipid signaling is closely associated with neuronal differentiation, learning, and memory and with pathologic events, such as epilepsy and Alzheimer's disease. The Peroxisome Proliferator‐Activated Receptors (PPAR) are strongly involved in the fatty acid cell signaling, as many of the natural lypophylic compounds are PPAR ligands. We have previously shown that PPARβ/δ is the main isotype present in cortical neuron primary cultures and that during neuronal maturation, PPARβ/δ is gradually increased and activated. To get more insight into the molecular mechanism by which PPARβ/δ may be involved in neuronal maturation processes, in this work a specific PPARβ/δ agonist, GW0742 was used administered alone or in association with a specific PPARβ/δ antagonist, the GSK0660, and the parameters involved in neuronal differentiation and maturation were assayed. The data obtained demonstrated the strong involvement of PPARβ/δ in neuronal maturation, triggering the agonist an anticipation of neuronal differentiation, and the antagonist abolishing the observed effects. These effects appear to be mediated by the activation of BDNF pathway. J. Cell. Physiol. 231: 597–606, 2016. © 2015 Wiley Periodicals, Inc.
Surface‐engineered Saccharomyces cerevisiae cells displaying redesigned CadR for enhancement of adsorption of cadmium (II)
Authors: Tao Hu‐Chun , Li Peng‐Song , Liu Qi‐Song , Su Jie , Qiu Guo‐Yu , Li Zi‐Gang
Published: July 2015

BACKGROUND

The use of cell‐surface display technology to express recombinant proteins on a microbial cell surface can enhance metal adsorption to microbial cells. The transcription factor CadR of Pseudomonas putida shows highly selective affinity with Cd2+.

RESULTS

CadR was genetically engineered by truncating 47 N‐terminal amino acids and 21 C‐terminal amino acids in order to maximize its expression efficiency while maintaining its metal‐binding domain. The redesigned CadR (named T68CadR) was then displayed with Saccharomyces cerevisiae a‐agglutinin cell‐surface display system. This engineering approach enhanced the H+/OH− buffering capacity and the Cd2+ adsorption capacity of yeast cells. The surface‐engineered cells also performed well at mesophilic and higher temperatures (30–50 °C) under neutral or alkalescent conditions. With an initial concentration of 1.0 mg L−1, the Cd2+ removal efficiency remained 85% when the concentration of Na+ changed from 0 to 400 mmol L−1 (pH 7.8). The surface‐engineered cells also showed highly selective adsorption to Cd2+ in the presence of Zn2+ and Pb2+.

CONCLUSIONS

T68CadR displayed yeast cells constructed in this study provide an option to selectively remove Cd in water. It also might be promising as a tool to determine CadR's Cd‐binding mechanism and to improve its selectivity and affinity to Cd2+. © 2015 Society of Chemical Industry
Combination of column adsorption and supercritical fluid extraction for recovery of dissolved essential oil from distillation waste water of Yulania liliiflora
Authors: Lei Gaoming , Mao Peizhi , He Minqing , Wang Longhu , Liu Xuesong , Zhang Anyun
Published: July 2015

BACKGROUND

Aromatic waste water is the main by‐product of industrial essential oil distillation. To recover the dissolved essential oil from this distillation waste water, an approach combining column adsorption (CA) and supercritical fluid extraction (SFE) was proposed. Yulania liliiflora was selected as a case study. Activated carbon of mixed porosity was employed and quantitative desorption of the adsorbed oil was achieved using supercritical carbon dioxide (SC–CO2).

RESULTS

The optimized condition of CA‐SFE was 18 MPa, 308 K, dynamic extraction for 60 min and CO2 flow rate of 3.6 g min−1. A recovery of 0.668 ± 0.050 g kg−1 (n = 3) was achieved for the dissolved oil from distillation waste water, significantly higher (P < 0.05) than that obtained by liquid–liquid extraction (LLE) (0.405 ± 0.032 g kg−1, n = 3). Yulania liliiflora recovered oil was rich in eucalyptol (52.6–55.2%), α‐terpineol (15.2–18.1%) and terpinen‐4‐ol (8.1–8.7%).

CONCLUSION

The CA‐SFE approach is highly efficient and especially suitable for large‐scale application. The recovered essential oil is valued for being rich in organoleptically important and biologically active compounds. © 2015 Society of Chemical Industry
An Efficient One‐pot Synthesis of Novel Spiro Cyclic 2‐Oxindole Derivatives of Pyrimido[4,5‐b]Quinoline, Pyrido[2,3‐d:6,5‐d′]Dipyrimidine and Indeno[2′,1′:5,6]Pyrido [2,3‐d]Pyrimidine in Water
Authors: Abdelmoniem Amr Mohamed , Hassaneen Huwaida M. E. , Abdelhamid Ismail Abdelshafy
Published: July 2015

A novel and facile one‐pot synthesis of spiro cyclic 2‐oxindole derivatives of pyrimido[4,5‐b]quinoline‐4,6‐dione, pyrido[2,3‐d:6,5‐d′]dipyrimidine‐2,4,6‐trione, and indeno[2′,1′:5,6]pyrido [2,3‐d]pyrimidine employing 6‐aminothiouracil (or 6‐aminouracil), isatin, and cyclic 1,3‐diketone (e.g. 1,3‐indanedione, dimedone, or barbituric acid) has been developed.
Effect of spinach aqueous extract on wound healing in experimental model diabetic rats with streptozotocin
Authors: Rahati Sara , Eshraghian Mohammadreza , Ebrahimi Abdolali , Pishva Hamideh
Published: July 2015

BACKGROUND

Chronic ulcer is still a serious issue for diabetic patients. Diabetes is a prevalent cause of ulcer regeneration delay and (or) disruption. SinceSpinacia oleraceaextract contains compounds with anti‐oxidative and anti‐inflammatory effects, this may be effective in accelerating the healing process of ulcers, especially diabetic ulcers. Hence, this study examined the effect ofSpinacia oleraceaaqueous extract on ulcer regeneration in an experimental animal model.

RESULTS

Macroscopic examination of the wounds of the control group and spinach aqueous extract group between 7 and 21 days compared with diabetic group, significant changes were observed (P< 0.05). On microscopic examination, epithelial tissue formation, formation of granulation tissue and new blood vessels in the spinach aqueous extract group and non‐diabetic group compared to the diabetic group showed significant improvements (P< 0.05). Also, significant differences in vascular endothelial growth factor were observed between groups on days 3 and 7 (P< 0.05).

CONCLUSION

TheSpinacia oleraceaaqueous extract can be effective in regenerating diabetic ulcers. It affects the speed and structure of the ulcer. © 2015 Society of Chemical Industry
Urolithins, gut microbiota‐derived metabolites of ellagitannins, inhibit LPS‐induced inflammation in RAW 264.7 murine macrophages
Authors: Piwowarski Jakub P. , Kiss Anna K. , Granica Sebastian , Moeslinger Thomas
Published: July 2015

Scope

Ellagitannin‐rich food products and medicinal plant materials were shown to have beneficial effects toward intestinal inflammation. Due to the questionable bioavailability of ellagitannins their gut microbiota metabolites‐urolithins have come to be regarded as potential factors responsible for biological activities observed in vivo. The aim of the study was to determine the influence of the three most abundant bioavailable ellagitannin gut microbiota metabolites‐urolithins A, B, and C on inflammatory responses in RAW 264.7 murine macrophages, which are involved in the pathogenesis of intestine inflammation.

Methods and results

Urolithins A, B, and C decreased NO production via inhibition of the iNOS protein and mRNA expression. They decreased the expression of IL‐1β, TNF‐α, and IL‐6 mRNA in LPS challenged RAW 264.7 murine macrophages. A clear inhibition of NF‐κB p65 nuclear translocation and p50 DNA‐binding activity was associated with the observed anti‐inflammatory activities of urolithins. Among the tested compounds urolithin A had the strongest anti‐inflammatory activity.

Conclusion

The anti‐inflammatory effects of urolithins at concentrations that are physiologically relevant for gut tissues (≥40 μM), as revealed in this study, support the data from in vivo studies showing the beneficial effects of ellagitannin‐rich products toward intestinal inflammation.
Local and non‐local elasto‐viscoplasticity in strain localization analysis of multiphase geomaterials
Authors: Lazari M. , Sanavia L. , Schrefler B.A.
Published: July 2015

In this paper, rate‐dependent plasticity is employed to regularize, for the scope of mesh independency, the numerical solution in strain localization process of multiphase geomaterials. Towards this goal, the viscoplastic Duvaut–Lions and the viscoplastic Perzyna models are implemented in an existing finite element code for multiphase porous media. Perzyna's model is then extended according to the non‐local approach, allowing for handling weakly rate‐sensitive materials for which viscoplasticity is not sufficient to meet numerical requirements. Assuming quasi‐static and isothermal conditions, the models are validated and applied in the numerical simulation of an undrained plane strain biaxial compression test on initially water‐saturated dense sand taken from the existing literature. An overview of the significant factors such as loading velocity and soil permeability in conjunction with viscosity on the formation of localization pattern is presented. The interaction of the two internal lengths introduced by non‐locality and viscosity is also discussed. Finally, the obtained results are analysed and compared emphasizing the capabilities and shortcomings of each regularization technique. Copyright © 2015 John Wiley & Sons, Ltd.
Vitamin D attenuates proteinuria by inhibition of heparanase expression in the podocyte
Authors: Garsen Marjolein , Sonneveld Ramon , Rops Angelique LWMM , Huntink Suzanne , van Kuppevelt Toin H , Rabelink Ton J , Hoenderop Joost GJ , Berden Jo HM , Nijenhuis Tom , van der Vlag Johan
Published: July 2015

The glomerular filtration barrier consists of podocytes, the glomerular basement membrane, and endothelial cells covered with a glycocalyx. Heparan sulphate (HS) in the glomerular filtration barrier is reduced in patients with proteinuria, which is associated with increased expression of the HS‐degrading enzyme heparanase. Previously, we showed that heparanase is essential for the development of proteinuria in experimental diabetic nephropathy. Vitamin D supplementation reduces podocyte loss and proteinuria in vitro and in vivo. Therefore, we hypothesize that vitamin D reduces proteinuria by reducing glomerular heparanase. Adriamycin‐exposed rats developed proteinuria and showed increased heparanase expression, which was reduced by 1,25‐dihydroxyvitamin D3 (1,25‐D3) treatment. In vitro, adriamycin increased heparanase mRNA in the podocyte, which could be corrected by 1,25‐D3 treatment. In addition, 1,25‐D3 treatment reduced transendothelial albumin passage after adriamycin stimulation. In line with these results, we showed direct binding of the vitamin D receptor to the heparanase promoter, and 1,25‐D3 dose‐dependently reduced heparanase promoter activity. Finally, 1,25‐D3‐deficient 25‐hydroxy‐1α‐hydroxylase knockout mice developed proteinuria and showed increased heparanase, which was normalized by 1,25‐D3 treatment. Our data suggest that the protective effect of vitamin D on the development of proteinuria is mediated by inhibiting heparanase expression in the podocyte. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Investigation and Management of a Rhizomucor Outbreak in a Pediatric Cancer Hospital in Egypt
Authors: El‐Mahallawy Hadir A. , Khedr Reham , Taha Hala , Shalaby Lobna , Mostafa Ali
Published: July 2015

We describe an outbreak of mucormycosis in a pediatric oncology hospital during December 2010 and the measures taken to stop it. The outbreak began with two consecutive cases of laboratory‐documented mucormycosis infections within 1 week. Investigations to track the source were conducted immediately. Air plate cultures from machines and ducts supplying patients’ rooms revealed the growth of Rhizomucor. Of five affected patients, all had acute leukemia and three were histopathologically proven. All patients were treated with liposomal amphotericin B after mucormycosis was diagnosed. Posaconazole was used as a secondary prophylaxis in one case. Three patients died. Pediatr Blood Cancer © 2015 Wiley Periodicals, Inc.
Metaproteomics and metabolomics analyses of chronically petroleum‐polluted sites reveal the importance of general anaerobic processes uncoupled with degradation
Authors: Bargiela Rafael , Herbst Florian‐Alexander , Martínez‐Martínez Mónica , Seifert Jana , Rojo David , Cappello Simone , Genovese María , Crisafi Francesca , Denaro Renata , Chernikova Tatyana N. , Barbas Coral , von Bergen Martin , Yakimov Michail M. , Ferrer Manuel , Golyshin Peter N.
Published: July 2015

Crude oil is one of the most important natural assets for humankind, yet it is a major environmental pollutant, notably in marine environments. One of the largest crude oil polluted areas in the word is the semi‐enclosed Mediterranean Sea, in which the metabolic potential of indigenous microbial populations towards the large‐scale chronic pollution is yet to be defined, particularly in anaerobic and micro‐aerophilic sites. Here, we provide an insight into the microbial metabolism in sediments from three chronically polluted marine sites along the coastline of Italy: the Priolo oil terminal/refinery site (near Siracuse, Sicily), harbour of Messina (Sicily) and shipwreck of MT Haven (near Genoa). Using shotgun metaproteomics and community metabolomics approaches, the presence of 651 microbial proteins and 4776 metabolite mass features have been detected in these three environments, revealing a high metabolic heterogeneity between the investigated sites. The proteomes displayed the prevalence of anaerobic metabolisms that were not directly related with petroleum biodegradation, indicating that in the absence of oxygen, biodegradation is significantly suppressed. This suppression was also suggested by examining the metabolome patterns. The proteome analysis further highlighted the metabolic coupling between methylotrophs and sulphate reducers in oxygen‐depleted petroleum‐polluted sediments.
A New Reference Material and Safe Sampling of Terrorists Peroxide Explosives by a Non‐Volatile Matrix
Authors: Lubczyk Daniel , Hahma Arno , Brutschy Malte , Siering Carsten , Waldvogel Siegfried R.
Published: July 2015

Highly sensitive peroxide based explosives can be dissolved in ionic liquids for a safe handling. These solutions are easy to use and may be applied as powerful odor sources for analytical testing and training purposes. Moreover, the stabilizing effect of the ionic liquids can be exploited for a safe sampling of large quantities of these explosives. Such samples of triacetone triperoxide are long‐term stable, safe, and valid for forensic evaluations.
CASP11 refinement experiments with ROSETTA
Authors: Park Hahnbeom , DiMaio Frank , Baker David
Published: July 2015

We report new Rosetta‐based approaches to tackling the major issues that confound protein structure refinement, and the testing of these approaches in the CASP11 experiment. Automated refinement protocols were developed that integrate a range of sampling methods using parallel computation and multiobjective optimization. In CASP11, we used a more aggressive large‐scale structure rebuilding approach for poor starting models, and a less aggressive local rebuilding plus core refinement approach for starting models likely to be closer to the native structure. The more incorrectly modeled a structure was predicted to be, the more it was allowed to vary during refinement. The CASP11 experiment revealed strengths and weaknesses of the approaches: the high‐resolution strategy incorporating local rebuilding with core refinement consistently improved starting structures, while the low‐resolution strategy incorporating the reconstruction of large parts of the structures improved starting models in some cases but often considerably worsened them, largely because of model selection issues. Overall, the results suggest the high‐resolution refinement protocol is a promising method orthogonal to other approaches, while the low‐resolution refinement method clearly requires further development. Proteins 2016; 84(Suppl 1):314–322. © 2015 Wiley Periodicals, Inc.
Accurate contact predictions using covariation techniques and machine learning
Authors: Kosciolek Tomasz , Jones David T.
Published: July 2015

Here we present the results of residue–residue contact predictions achieved in CASP11 by the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On a set of 40 target domains with a median family size of around 40 effective sequences, our server achieved an average top‐L/5 long‐range contact precision of 27%. MetaPSICOV method bases on a combination of classical contact prediction features, enhanced with three distinct covariation methods embedded in a two‐stage neural network predictor. Some unique features of our approach are (1) the tuning between the classical and covariation features depending on the depth of the input alignment and (2) a hybrid approach to generate deepest possible multiple‐sequence alignments by combining jackHMMer and HHblits. We discuss the CONSIP2 pipeline, our results and show that where the method underperformed, the major factor was relying on a fixed set of parameters for the initial sequence alignments and not attempting to perform domain splitting as a preprocessing step. Proteins 2016; 84(Suppl 1):145–151. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
Methods and data sources for identifying members of a regulated community
Authors: Pittman William C. , Han Zhe , Harding Brian Z. , Jiang Jiaojun , Rosas Camilo , Pineda Alba , Mannan M. Sam
Published: July 2015

The Ammonium Nitrate explosion that shook West, Texas in April 2013 revealed deficiencies in the current regulatory enforcement system used for chemical safety and security in the United States. This cannot be said to be a failure of existing regulations. Rather, it is a failure in enforcement as federal regulators either had not inspected the site in decades—as with OSHA—or had not been aware of its existence at all, as with Department of Homeland Security (DHS). Regulations cannot be effective if they are not enforced and cannot be enforced unless the regulator knows who the members of the regulated community are. Methods for identifying the regulated community and moving past the voluntary reporting and compliance system currently in place have become topics of acute interest and paramount importance. This article discusses existing data sources at federal, state, and local levels that could be exploited immediately to help DHS and other regulators identify regulated facilities and begin more concerted outreach programs. © 2015 American Institute of Chemical Engineers Process Saf Prog 35: 47–52, 2016
Thin film solar cell of SnS absorber with cubic crystalline structure
Authors: Garcia‐Angelmo A. R. , Romano‐Trujillo R. , Campos‐Álvarez J. , Gomez‐Daza O. , Nair M. T. S. , Nair P. K.
Published: July 2015

In a solar cell: stainless steel/SnS/CdS/ZnO/ZnO:Al, we report conversion efficiency of 1.28%, open‐circuit voltage (Voc) of 0.470 V, and short‐circuit current density (Jsc) of 6.2 mA cm−2, measured on cells of area 1 cm2 under standard conditions. The thin film of SnS absorber of 550 nm in thickness used in this cell was deposited from a chemical bath. Average crystalline diameter of the material is 24 nm, and its X‐ray diffraction pattern fits a cubic unit cell with cube edge of 1.159 nm. The optical band gap of the material is 1.74 eV and its electrical conductivity is 10−6 Ω−1 cm−1. The mobility‐lifetime product of the film was determined as 2 × 10−7 cm2 V−1 from photoconductivity measurement. To build the solar cell, a CdS thin film of 50 nm in thickness was deposited from a chemical bath on the SnS thin film prepared on the stainless steel substrate. Subsequently, a ZnO film of 180 nm and ZnO:Al film of 450 nm in thickness were deposited on this CdS defining a solar cell area of 1 cm2. This solar cell is stable under concentrated sunlight of 2–16 suns, attaining Voc of 0.6 V and Jsc of 35 mA cm−2 under 16 suns.
Innate immune response during herpes simplex virus encephalitis and development of immunomodulatory strategies
Authors: Piret Jocelyne , Boivin Guy
Published: July 2015

Herpes simplex viruses are large double‐stranded DNA viruses. These viruses have the ability to establish a lifelong latency in sensory ganglia and to invade and replicate in the CNS. Apart from relatively benign mucosal infections, HSV is responsible for severe illnesses including HSV encephalitis (HSE). HSE is the most common cause of sporadic, potentially fatal viral encephalitis in Western countries. If left untreated, the mortality rate associated with HSE is approximately 70%. Despite antiviral therapy, the mortality is still higher than 30%, and almost 60% of surviving individuals develop neurological sequelae. It is suggested that direct virus‐related and indirect immune‐mediated mechanisms contribute to the damages occurring in the CNS during HSE. In this manuscript, we describe the innate immune response to HSV, the development of HSE in mice knock‐out for proteins of the innate immune system as well as inherited deficiencies in key components of the signaling pathways involved in the production of type I interferon that could predispose individuals to develop HSE. Finally, we review several immunomodulatory strategies aimed at modulating the innate immune response at a critical time after infection that were evaluated in mouse models and could be combined with antiviral therapy to improve the prognosis of HSE. In conclusion, the cerebral innate immune response that develops during HSE is a “double‐edged sword” as it is critical to control viral replication in the brain early after infection, but, if left uncontrolled, may also result in an exaggerated inflammatory response that could be detrimental to the host. Copyright © 2015 John Wiley & Sons, Ltd.
Fish Assemblage and Ecosystem Metabolism Responses to Reconnection of the Bird's Point‐New Madrid Floodway during the 2011 Mississippi River Flood
Authors: Rantala H. , Glover D. , Garvey J. , Phelps Q. , Tripp S. , Herzog D. , Hrabik R. , Crites J. , Whiles M.
Published: July 2015

Understanding the ecological function of developed large rivers remains elusive because these systems have long been altered for multiple uses. In particular, floodplains of large rivers, such as the Mississippi River, have been contained behind extensive levees. A historic flood occurred in the lower Mississippi River system during spring of 2011, prompting the US Army Corps of Engineers to activate the Bird's Point‐New Madrid floodway, a 55 000‐ha, agriculturally dominated, leveed area. Water entered the floodway at flows >1 m s−1 through two crevasses created in the upper portion of the levee and exited through a crevasse at the lower end. During the month, the floodway was inundated; we quantified discharge, water chemistry, primary production and fish production in the floodway and the adjacent river. Water entering the floodway was retained <1.3 d, and nutrient concentrations were not elevated in the floodway beyond those in the river, despite expected contributions from a legacy of fertilization. Primary production equaled respiration in the floodway, while the adjacent river was heterotrophic. Gizzard shad and freshwater drum were more abundant in the floodway than the river, while channel catfish were more abundant in the river. Growth rates of young native fishes, normalized for temperature, were the same in the floodway and the river, with the exception of gizzard shad, which grew faster in the floodway. Fish community structure, especially in the lower floodway, was temporally and spatially dynamic. Even though it has been heavily modified for agriculture, the floodway provided benefits, albeit limited, to the Mississippi River. With multifunctional management and strategic planning, systems such as these may provide substantial services such as flood abatement, nutrient transformation and fish production in the Mississippi River basin and potentially reduce nutrient loading downstream in areas such as the Gulf of Mexico. Copyright © 2015 John Wiley & Sons, Ltd.
Structurally Flexible C3‐Symmetric Receptors for Molecular Recognition and Their Self‐Assembly Properties
Authors: Singh Ashutosh S. , Sun Shih‐Sheng
Published: July 2015

The bioinspired design and synthesis of building blocks and their assemblies by the supramolecular approach has ever fascinated scientists to utilize such artificial systems for numerous purposes. Flexibility is a basic feature of natural systems. However, in artificial systems this is difficult to control, especially if there is no preorganization of the component(s) of a system. We have designed and synthesized a series of C3‐symmetric N‐bridged flexible receptors and successfully utilized them to selectively entrap the notorious and toxic nitrate anion in aqueous medium. This was the first report of highest binding affinity for the nitrate anion in aqueous medium. An impressive self‐sorting phenomenon of reversibly formed hydrogen‐bonded capsules, which self‐assembled from flexible tripodal receptors having branches of similar size and bearing the same amide functionality, has been disclosed. Encapsulated nitrate anion has been further utilized for the photochemical [2+2] cycloaddition reaction for the synthesis of strained four‐membered ring structures through dynamic self‐assembly. In this Personal Account, we summarize these results showing the utility of naturally inspired flexibility in artificial systems.

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From Fragmentation to Construction—from Void to Massive: Fascination with Organic Mass Spectrometry and the Synthesis of Novel Three‐Dimensional Polycyclic Aromatic Hydrocarbons
Authors: Kuck Dietmar
Published: July 2015

Detailed insights gained from our research into the gas‐phase chemistry of ionized and protonated diphenylalkanes and their congeners, obtained by extended synthesis of isotopically labeled model compounds and mass spectrometry, are presented and merged with those acquired during our development of a new family of polycyclic hydrocarbons, the centropolyindanes. Aside from a Personal Account that describes “two scientific lives in one”, it is demonstrated, on the one hand, how our understanding of organic chemistry can help to shed light on the details of mass spectrometric fragmentation and to unravel, in a more fundamental way, the unimolecular reactivity of gaseous ions. On the other hand, it is shown how unexpected reactivity of related ions in solution, being subject to the very same fundamentals of organic chemistry, can lead to the construction of novel and, in part, unique three‐dimensional polycyclic structures that may contribute to future research in material science. Two such apparently independent fields of organic chemistry may be seen as joint contributions of the art of science.
Developing and using geomorphic condition assessments for river rehabilitation planning, implementation and monitoring
Authors: Fryirs Kirstie A.
Published: July 2015

Frameworks for assessing geomorphic river condition constitute a core part of the river management process, providing a critical platform for environmental decision‐making and associated actions. The evolution of approaches for assessing the geomorphic (also called physical, morphological, or hydromorphological) condition of rivers has shifted from a design and development phase in the late‐1990s and early 2000s to application and use of approaches for assessment, monitoring, and rehabilitation decision making. In this paper I review the core geomorphic principles that are embedded in more sophisticated, process‐based frameworks, and demonstrate how the information generated through use of these frameworks can be used to guide management choices, change management activities or opt‐out of management activities as part of precautionary river management practice. I propose that a key challenge now faced by geomorphologists and managers is to move beyond the development of more new frameworks, and consolidate efforts to use, test, and adapt existing approaches and datasets to achieve river management visions and objectives framed around improving river condition. WIREs Water 2015, 2:649–667. doi: 10.1002/wat2.1100

This article is categorized under:

Water and Life > Conservation, Management, and Awareness

Engineering Water > Planning Water
Examination of the Causes of Instability of Soy Protein Isolate During Storage Through Probing of the Heat‐Induced Aggregation
Authors: Guo Feng‐Xian , Xiong Youling L. , Qin Fang , Jian Hua‐Jun , Huang Xiao‐Lin , Chen Jie
Published: July 2015

This study investigated the mechanism of instability of soy protein isolate (SPI) as influenced by thermal aggregation during SPI preparation. Samples with different degrees of aggregation but similar protein solubility were prepared by heating native SPI (5 % w/v) at 80 or 90 °C for different times before spray‐drying. The samples were then stored at 37 °C for up to 12 weeks and analyzed periodically by atomic force microscopy, gel permeation chromatography, and SDS–PAGE. All SPI samples underwent remarkable protein solubility decreases during the first 8 weeks of storage. The rates of solubility loss were positively correlated with the amounts and/or sizes of soluble aggregates contained in the initial samples (time zero), suggesting their nucleation and activation effects. Solubility tests in SDS–urea solutions and disulfide analysis indicated that non‐covalent interactions were the main driving forces for protein storage instability. Conversely, disulfide bonds and protein carbonyls were abundant in soluble aggregates, and their content increased markedly during storage. This effect suggested that covalent linkages acted as blockers for hydrophobic aggregation.
A Unitary Patent for a (Dis)United Europe: The Long Shadow of History
Authors: Plomer Aurora
Published: July 2015

This article retraces the history of patent harmonization in Europe and reviews the European Union “patent package” and its approval by the Grand Chamber of the Court of Justice of the European Union in the light of this history. The article draws on archived and hitherto unused confidential documents to retrace the key institutions and players in the origins and evolution of the European patent unification movement. The study reveals that the EU project was originally led by the Council of Europe and analyzes the reasons why the EU has struggled to develop a coherent model of integration to facilitate realization of the internal market ever since. The historical legacy suggests that a critical turning point was the creation of the European Patent Organization as the leading engine of patent policy in Europe, an autonomous organization which is not subject to judicial oversight by the EU court or meaningful political scrutiny by the European Union and its members. The article concludes with a case study illustrating how the latent difficulties over the relationship between different European institutions and the jurisdiction of European tribunals and courts are manifested today in the unitary patent and the unified patent court.
Stabilization of intracellular trafficking and metabolism of amyloid β‐protein precursor and Alcadein β by apolipoprotein E
Authors: Kimura Ayano , Hata Saori , Suzuki Toshiharu
Published: July 2015

Intracellular metabolism of amyloid β‐protein precursor (APP) is important for the pathogenesis of Alzheimer's disease (AD). Alcadeins (Alcα, Alcβ, and Alcγ) are neural membrane proteins similar to APP in their localization, metabolism, and cellular function. Isoform ε4 of apolipoprotein E (ApoE) is a major risk factor for AD. We found that ApoE expression attenuated intracellular trafficking of APP and Alcβ, resulting in metabolic stabilization of both proteins. By contrast, Alcα intracellular proteolysis was facilitated by ApoE expression, which was not due to an increase in the primary cleavage of Alcα. This difference may result from binding of ApoE to membrane proteins.
Research training, productivity and challenges among trainees of pediatric residency programs across Saudi Arabia
Authors: Alhaider S.A. , Alshehri H.A. , Almedhesh S.A.
Published: July 2015

Background and objectives:

Research provides skills for lifelong learning and pro-motes patient care. In Saudi Arabia, until recently, research training has not been integrated effectively in postgraduate medical education. The aim of this study was to investigate the factors involved in research training, productivity, challenges, and attitude among trainees in pediatric residency programs across Saudi Arabia.

Materials and methods:

This is a cross-sectional, multicenter study using a questionnaire de-signed to assess several aspects of research training among trainees of the national pediatric residency program in Saudi Arabia from September to December 2013.

Results:

Eighty-three residents from seven training centers participated (response rate of 65.5%). Ninety percent of participants agreed that research training must be mandated in each residency program. The majority of participants (85.5-89.2%) agree that research is beneficial because it improves patient care, enhances the pursuit of academic careers, and improves fellowship acceptance rates and success. More than half (51.8%) of participants believe that research training will interfere with their efforts to become a medical expert in their fields. The survey indicated low research involvement by trainees, with 86.7% of participants having never published scientific manuscripts. The majority of participants (73.5%) reported a lack of regular, structured research activity in their training curriculum. The main challenge in research training was the lack of protected time (according to 86.7% of respondents). The ma-jority of participants (85.6%) agreed that training in research methodologies represents their top educational need.

Conclusion:

This study represents a "needs assessment” phase in the development of a research training curriculum for the Saudi pediatric residency program. The majority of participating residents have a positive attitude toward research. Research productivity and training were found to be low. A dedicated research curriculum within the residency program represents an effective and evidence-based solution.
Healing from Intrafamilial Child Sexual Abuse: The Role of Relational Processes between Survivor and Offender
Authors: Paige Janice , Thornton Jennifer
Published: July 2015

The research aim was to discover the circumstances, if any, in which contact with the parent who had abused them, could help survivors of intrafamilial child sexual abuse (ICSA) to recover from the inherent relational trauma. Thirty-five (31 female and 4 male) participants were recruited from across Australia and New Zealand to speak about their experience of post-abuse contact. The research methodology was primarily qualitative, and analysed in a contextual framework. In the Pre-Contact stage, themes such as the need for empowerment versus the fear of the response, linked to motivations for and against contact. Emotional reactions, and issues of acknowledgment and apology were core themes in the Contact stage. Post-contact themes related to evaluation of the overall experience. The majority of participants believed that their contact experience had helped more than hindered their recovery. Participants articulated the need for more public education about the complexity of ICSA, more options for dealing with the crime, and access to non-judgmental professional help for all the family at disclosure. The emergent themes provide a valuable guide for future research, policy and practice and perhaps most importantly, insight into the needs of victims and their recovery processes.