bluuebunny/crossref_metadata_2025 huggingface dataset:
Computational Insights into Excited‐State Proton‐Transfer Reactions in Azo and Azomethine Dyes
Authors: Savarese Marika , Brémond Éric , Antonov Liudmil , Ciofini Ilaria , Adamo Carlo
Published: October 2015

State of the art density functional theory approaches are employed to provide an accurate description of the photophysical properties of azodyes and Schiff bases displaying intramolecular hydrogen‐bonding features. These compounds exist as tautomeric mixtures at the ground state and, in the case of Schiff bases, an excited‐state intramolecular proton transfer (ESIPT) occurs upon excitation. The experimentally observed photophysical properties are discussed here in light of the theoretical findings. To rationalize the different experimentally observed radiative behavior of the azo and azomethine structures, a nonradiative decay pathway that is possibly active in such systems is determined. The characterization of this deactivation path, tested for two related compounds exhibiting different fluorescence quantum yields, enables us to disentangle the different and contrasting effects governing the excited‐state behavior of these molecular systems.
Effects of maturity on physicochemical properties of Gac fruit (Momordica cochinchinensis Spreng.)
Authors: Tran Xuan T. , Parks Sophie E. , Roach Paul D. , Golding John B. , Nguyen Minh H.
Published: October 2015

The aril around the seeds of Gac fruit is rich in fatty acids and carotenoids (lycopene and β‐carotene). Understanding how these qualities are affected by fruit maturity at harvest may identify indices for quality assessment. Some physical and chemical properties of Gac fruit were determined for fruit harvested between 8 and 16 weeks after pollination (WAP). Fruit respiration rates and ethylene production rates were assessed after harvest and up to 20 days in storage at 20°C. Fruit harvested at 14 WAP had the highest oil (0.27 ± 0.02 g/g DW), lycopene content (0.45 ± 0.09 mg/g FW), and β‐carotene content (0.33 ± 0.05 mg/g FW) which declined by 16 WAP. External skin color and aril TSS were indicative of oil and carotenoid contents in aril. Skin color, TSS and potentially firmness were good indices of fruit quality. Harvesting less mature fruit at 12 WAP would be practical as the fruit were firmer and more capable of transport; however, quality during postharvest ripening may be limited. Fruits continued to ripen after they were harvested and an ethylene peak in the least mature fruit may reflect a climacteric behavior but this needs further investigation.
Nutritional composition of raw fresh cashew (Anacardium occidentale L.) kernels from different origin
Authors: Rico Ricard , Bulló Mònica , Salas‐Salvadó Jordi
Published: October 2015

The total dietary fiber, sugar, protein, lipid profile, sodium, and energy contents of 11 raw cashew kernel (Anacardium occidentale L.) samples from India, Brazil, Ivory Coast, Kenya, Mozambique, and Vietnam were determined. Total fat was the major component accounting for 48.3% of the total weight, of which 79.7% were unsaturated FA (fatty acids), 20.1% saturated FA, and 0.2% trans FA. Proteins, with 21.3 g/100 g, were ranked second followed by carbohydrates (20.5 g/100 g). The average sodium content was 144 mg/kg. Fourteen FA were identified among which oleic acid was the most abundant with a contribution of 60.7% to the total fat, followed by linoleic (17.77%), palmitic (10.2%), and stearic (8.93%) acids. The mean energy content was 2525 kJ/100g. Furthermore, the sterol profile and content, amino acids, vitamins, and minerals of four raw cashew kernel samples from Brazil, India, Ivory Coast, and Vietnam were determined. β‐Sitosterol with 2380 ± 4 mg/kg fat was the most occurring sterol. Glutamic acid, with 4.60 g/100 g, was the amino acid with highest presence, whereas tryptophan with 0.32 g/100 g was the one with lower presence. Vitamin E with an average contribution of 5.80 mg/100 g was the most abundant vitamin. Potassium with a mean value of 6225 mg/kg was the mineral with highest amount in cashew samples.
Reduction of Foxp3+ T cell subsets involved in incidence of chronic graft‐versus‐host disease after allogeneic hematopoietic stem cell transplantation
Authors: Hu Yongxian , Cui Qu , Ye Yishan , Luo Yi , Tan Yamin , Shi Jimin , Huang He
Published: October 2015

Foxp3+ T cells (CD4+ Tregs and CD8+ Treg) have been demonstrated to play roles in the maintenance of tolerance after allogeneic hematopoietic stem cell transplantation (Allo‐HSCT). We have found that Foxp3+ γδTCR+ Treg cells (γδTregs) exerted regulatory functions. In the current study, patients were recruited and divided as non‐cGVHD, limited cGVHD and extensive cGVHD groups. Healthy volunteers were recruited as healthy group. Treg cells were evaluated by flow cytometry. Serum cytokine levels of IL‐2, tumour necrosis factor‐α, interferon‐γ and transforming growth factor‐β1 (TGF‐β1) were evaluated by ELISA. The results showed that percentages of CD4+ Tregs, CD8+ Tregs and γδTregs were all significantly increased in non‐cGVHD group compared with those in healthy group, limited cGVHD group and extensive cGVHD group. Moreover, compared with extensive cGVHD group, percentages of these three types of Tregs were significantly increased in limited cGVHD group. The levels of TGF‐β1 increased dramatically in non‐cGVHD group compared with other groups. Spearman's correlation analysis revealed that the increased levels of TGF‐β1 and IL‐2 were positively associated with increased Treg subsets, indicating that TGF‐β1 and IL‐2 participated in the expansion process of Foxp3+ Tregs in vivo. Our findings support that increasing the number of Tregs following allo‐HSCT would be a preferential strategy for controlling cGVHD. Copyright © 2015 John Wiley & Sons, Ltd.
Snow and frost: implications for spatiotemporal infiltration patterns – a review
Authors: Lundberg Angela , Ala‐Aho Pertti , Eklo OleMartin , Klöve Björn , Kværner Jens , Stumpp Christine
Published: October 2015

Vast regions of the northern hemisphere are exposed to snowfall and seasonal frost. This has large effects on spatiotemporal distribution of infiltration and groundwater recharge processes as well as on the fate of pollutants. Therefore, snow and frost need to be central inherent elements of risk assessment and management schemes. However, snow and frost are often neglected or treated summarily or in a simplistic way by groundwater modellers. Snow deposition is uneven, and the snow is likely to sublimate, be redistributed and partly melt during the winter influencing the mass and spatial distribution of snow storage available for infiltration, the presence of ice layers within and under the snowpack and, therefore, also the spatial distribution of depths and permeability of the soil frost. In steep terrain, snowmelt may travel downhill tens of metres in hours along snow layers. The permeability of frozen soil is mainly influenced by soil type, its water and organic matter content, and the timing of the first snow in relation to the timing of sub‐zero temperatures. The aim with this paper is to review the literature on snow and frost processes, modelling approaches with the purpose to visualize and emphasize the need to include these processes when modelling, managing and predicting groundwater recharge for areas exposed to seasonal snow and frost. Copyright © 2015 John Wiley & Sons, Ltd.
Lipoteichoic acid modulates inflammatory response in macrophages after phagocytosis of titanium particles through Toll‐like receptor 2 cascade and inflammasomes
Authors: Naganuma Yasushi , Takakubo Yuya , Hirayama Tomoyuki , Tamaki Yasunobu , Pajarinen Jukka , Sasaki Kan , Goodman Stuart B. , Takagi Michiaki
Published: October 2015

Toll‐like receptor 2 (TLR2) and nucleotide‐binding and oligomerization domain‐like receptors with a pyrin domain 3 (NLRP3) inflammasomes have been presumed to participate in the pathogenesis of aseptic implant loosening. The aim of this study is to analyze the cellular localization of TLR2 and NLRP3 inflammasomes in the periprosthetic tissue from aseptically loose hip implants as well as the expression of these molecules in macrophages stimulatedin vitrowith titanium particles (Ti) coated with lipoteichoic acid (LTA). Using immunohistochemistry, immunoreactivity of TLR2 and NLRP3 inflammasomes was found in macrophages within the foreign body granulomatosis. Using RAW264.7 cells, stimulation with Ti increased the messenger RNA (mRNA) levels of TLR2 and TNF‐α. Stimulation with LTA‐coated Ti enhanced mRNA levels of NLRP3 and IL‐1β, whereas reinforced secretion of IL‐1β was not detected in spite of marked release of TNF‐α. Finally, the same cells with silenced Irak2, an adaptor protein in the TLR2 cascade, suppressed this NLRP3 upregulation. This study suggests that TLR2 and NLRP3 inflammasomes are factors involved in cross‐talk mediating the foreign body type response to wear particles. In addition, discrepant behavior in the release between TNF‐α and IL‐1β release may explain the variable pathomechanisms of aseptic implant loosening without acute inflammatory reactions. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 435–444, 2016.
Pharmacokinetic Characteristics and Clinical Outcomes of Vancomycin in Young Children With Various Degrees of Renal Function
Authors: Zhang Huanian , Wang Yang , Gao Ping , Hu Jiasheng , Chen Yujun , Zhang Long , Shen Xiantao , Xu Hua , Xu Qiong
Published: October 2015

Although vancomycin pharmacokinetics are affected by age and renal function in adults and older children, its pharmacokinetics in children aged 1 month to 2 years remained unclear. We investigated clinical outcome and nephrotoxicity in younger children with renal insufficiency who were treated with vancomycin. One hundred and ten children aged 1 month to 2 years were enrolled, and they were divided into 3 groups: normal renal function (group A), mild renal insufficiency (group B), and moderate renal insufficiency (group C). A population pharmacokinetic model was established. Significant differences were observed for trough concentration, AUC0–24 h, CL, and t1/2 in the 3 groups. When given at 40 mg/kg per day, 36.4%, 62.5%, and 85.0% of children achieved the target of AUC/MIC ≥ 400, and 47.0%, 70.8%, and 95% of children obtained early good clinical outcomes in groups A, B, and C (P < .05), respectively. One child in group A and 4 children in group C suffered from acute kidney injury. These results indicated that children with renal insufficiency readily achieved the target AUC/MIC but were at increased risk of nephrotoxicity. Vancomycin clearance and creatinine clearance were not correlated with each other in children with renal insufficiency, indicating that both renal function and serum concentration should be monitored during vancomycin therapy.
Porcine 2′, 5′‐oligoadenylate synthetases inhibit Japanese encephalitis virus replication in vitro
Authors: Zheng Sheng , Zhu Dan , Lian Xue , Liu Weiting , Cao Ruibing , Chen Puyan
Published: October 2015

The 2′, 5′‐oligoadenylate synthetases (OAS) are antiviral proteins and several isoforms have been identified as flavivirus‐resistance biomarkers in human and mouse. The expression kinetics and antiviral functions of porcine OAS family (OAS1, OAS2, and OASL) in PK‐15 cells following infection by Japanese encephalitis virus (JEV) were evaluated in the present study. The endogenous expression of the three OAS genes was efficiently induced by IFN‐α treatment in PK‐15 cells. However, expression of pOAS1 and pOAS2 responded more quickly than pOASL. Infection by JEV also induced the expression of the pOAS isoforms, but at a significantly lower level than that observed following IFN‐α stimulation. Transient overexpression of pOASL and pOAS1 inhibited JEV replication more efficiently than OAS2 overexpression. Interestingly, knockdown of pOAS2 expression by siRNA treatment led to the highest increase in JEV multiplication. Co‐silencing of RNase L and each pOAS revealed that the anti‐JEV function of pOAS1 and pOAS2 were RNase L dependent, while the antiviral activity of pOASL was not. In conclusion, all pOAS isoforms play a significant role in the response to JEV infection, and are differentially induced by different stimuli. The alternative pathways of antiviral activity stimulated by OASL require further study. J. Med. Virol. 88:760–768, 2016. © 2015 Wiley Periodicals, Inc.
Epidemiological, clinical, virological features of hepatitis B newly diagnosed in 2011 in Marseille University hospitals, southeastern France
Authors: Moussa Sahada , Brah Souleymane , Parola Philippe , Gerolami René , Gamerre Marc , Boubli Léon , Ruiz Jean‐Marie , Ravaux Isabelle , Mokhtari Saada , Mancini Julien , Romera Marie‐Hélène , Motte Anne , Tamalet Catherine , Colson Philippe
Published: October 2015

Hepatitis B virus (HBV) infection is a public health problem. In France, 0.68% of adults are chronically infected. We aimed to describe the epidemiological, virological and clinical characteristics of HBV infections newly diagnosed in 2011 in University hospitals of Marseille, the second largest French city. HBV serology was performed for 18,130 sera from 15,744 patients. A total of 167 patients were newly‐diagnosed with HBV based upon the detection of hepatitis B surface antigen and anti‐hepatitis B core antibodies. Clinico‐epidemiological features were analyzed for 78 patients. Patients included a majority of men (59%), women being significantly younger with a mean age of 36 ± 17 versus 43.5 ± 16.2 years (P = 0.009). Country of birth was available for 52 patients and 35% of them originated from sub‐Saharan Africa. Levels of the liver biological parameters were significantly lower in women compared to men, in whom mean alanine aminotransferase and gammaglutamyl transferase levels were 24 ± 39 versus 37 ± 36 IU/l (P = 0.0001) and 20 ± 20 versus 51 ± 53 IU/l (P = 0.0001), respectively. Co‐infections with hepatitis C and human immunodeficiency viruses were found in 5% and 6% of the patients, respectively. HBV DNA was detectable in 90% of the HBeAg‐negative patients. In addition, there was a positive correlation between the HBsAg titer and the HBV DNA level (P = 0.001). Genotype D was the most common HBV genotype and was found in 53% of the patients tested, followed by genotype E (21%). HBV remains a major concern with a slightly greater number of new diagnoses than in 2004. HBV genetic diversity was substantial in the present cohort. J. Med. Virol. 88:828–836, 2016. © 2015 Wiley Periodicals, Inc.
Homogenization and analysis of an expanded long‐term monthly rainfall network for the Island of Ireland (1850–2010)
Authors: Noone S. , Murphy C. , Coll J. , Matthews T. , Mullan D. , Wilby R. L. , Walsh S.
Published: October 2015

Long‐term precipitation series are critical for understanding emerging changes to the hydrological cycle. To this end we construct a homogenized Island of Ireland Precipitation (IIP) network comprising 25 stations and a composite series covering the period 1850–2010, providing the second‐longest regional precipitation archive in the British‐Irish Isles. We expand the existing catalogue of long‐term precipitation records for the island by recovering archived data for an additional eight stations. Following bridging and updating of stations HOMogenisation softwarE in R (HOMER) homogenization software is used to detect breaks using pairwise and joint detection. A total of 25 breakpoints are detected across 14 stations, and the majority (20) are corroborated by metadata. Assessment of variability and change in homogenized and extended precipitation records reveal positive (winter) and negative (summer) trends. Trends in records covering the typical period of digitization (1941 onwards) are not always representative of longer records. Furthermore, trends in post‐homogenization series change magnitude and even direction at some stations. While cautionary flags are raised for some series, confidence in the derived network is high given attention paid to metadata, coherence of behaviour across the network and consistency of findings with other long‐term climatic series such as England and Wales precipitation. As far as we are aware, this work represents the first application of HOMER to a long‐term precipitation network and bodes well for use in other regions. It is expected that the homogenized IIP network will find wider utility in benchmarking and supporting climate services across the Island of Ireland, a sentinel location in the North Atlantic.
Hepatocyte growth factor/c‐met promotes proliferation, suppresses apoptosis, and improves matrix metabolism in rabbit nucleus pulposus cells in vitro
Authors: Ishibashi Hidenobu , Tonomura Hitoshi , Ikeda Takumi , Nagae Masateru , Sakata Munehiro , Fujiwara Hiroyoshi , Tanida Takashi , Mastuda Ken‐Ichi , Kawata Mitsuhiro , Kubo Toshikazu
Published: October 2015

The etiology of intervertebral disc (IVD) degeneration is closely related to apoptosis and extracellular matrix degradation in nucleus pulposus (NP) cells. These defects in NP cells are induced by excessive external stressors such as reactive oxygen species (ROS) and inflammatory cytokines. Recently, hepatocyte growth factor (HGF) has been shown to repair damage in various diseases through anti‐apoptotic and anti‐inflammatory activity. In this study, we investigated the effects of HGF on NP cell abnormality caused by ROS and inflammatory cytokines by using primary NP cells isolated from rabbit IVD. HGF significantly enhanced the proliferation of NP cells. Apoptosis of NP cells induced by H2O2 or TNF‐α was significantly inhibited by HGF. Induction of mRNA expression of the inflammation mediators cyclooxygenase‐2 and matrix metalloproteinase‐3 and ‐9 by TNF‐α was significantly suppressed by HGF treatment. Expression of c‐Met, a specific receptor for HGF, was confirmed in NP cells and was increased by TNF‐α, suggesting that inflammatory cytokines increase sensitivity to HGF. These findings demonstrate that activation of HGF/c‐Met signaling suppresses damage caused by ROS and inflammation in NP cells through multiple pathways. We further suggest the clinical potential of HGF for counteracting IVD degradation involved in NP cell abnormalities. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:709–716, 2016.
Modification of gelatin–DNA interaction for optimised DNA extraction from gelatin and gelatin capsule
Authors: Mohamad Nurhidayatul Asma , Mustafa Shuhaimi , El Sheikha Aly Farag , Khairil Mokhtar Nur Fadhilah , Ismail Amin , Ali Md Eaqub
Published: October 2015

BACKGROUND

Poor quality and quantity of DNA extracted from gelatin and gelatin capsules often causes failure in the determination of animal species using PCR. Gelatin, which is mainly derived from porcine and bovine, has been a matter of concern among customers in order to fulfill religious obligation and safety precaution against several transmissible infectious diseases associated with bovine species. Thus, optimised DNA extraction from gelatin is very important for successful real‐time PCR detection of gelatin species. In this work, the DNA extraction method was optimised in terms of lysis incubation period and inclusion of pre‐treatment pH modification of samples.

RESULTS

The yield of DNA extracted from porcine gelatin was significantly increased when the pH of the samples was adjusted to pH 8.5 prior to DNA precipitation with isopropanol. The optimal pH for DNA precipitation from bovine gelatin solution was then determined at the original pH range of solution: pH 7.6 to 8. A DNA fragment of approximately 300 base pairs was available for PCR amplification.

CONCLUSION

DNA extracted from gelatin and commercially available capsules has been successfully utilised for species detection using real‐time PCR assay. However, significant adulterations of porcine and bovine in pure gelatin and capsules have been detected, which require further analytical techniques for validation. © 2015 Society of Chemical Industry
Determining the arsenic, cadmium, lead, copper and chromium contents by atomic absorption spectrometry inPangasiusfillets from Vietnam
Authors: Molognoni Luciano , Vitali Luciano , Ploêncio Leandro AS , Santos Jacson N , Daguer Heitor
Published: October 2015

BACKGROUND

Pangasiusis a fish produced on a large scale in Vietnam and exported to many countries. Since river contamination from human activities can affect the safety of this food, fish consumption can cause exposure to potentially toxic elements for humans. The aim of this study, therefore, was to assess arsenic, cadmium, lead, copper and chromium contents by atomic absorption spectrometry inPangasiusfillet produced in the provinces of Dong Thap and Can Tho (Vietnam) and exported to Brazil.

RESULTS

The limits of detection were: arsenic 0.5443 µg kg−1, cadmium 0.0040 mg kg−1, chromium 0.0004 mg kg−1, copper 0.0037 mg kg−1and lead 0.0284 mg kg−1. Analysis of 20 samples showed results below the limit of detection for arsenic, chromium and lead, while copper average concentration was 0.0234 mg kg−1. Cadmium average concentration was 0.0547 mg kg−1, with no significant difference between the two regions studied.

CONCLUSION

The samples ofPangasiushad no detectable concentrations of arsenic, chromium, copper and lead, and do not represent a hazard to public health. However, cadmium analysis revealed non‐compliant samples, demonstrating the importance of monitoring the quality of imported Pangasius fish. © 2015 Society of Chemical Industry
Ginzburg–Landau turbulence in quasi‐CW Raman fiber lasers
Authors: Sugavanam Srikanth , Tarasov Nikita , Wabnitz Stefan , Churkin Dmitry V.
Published: October 2015

Fiber lasers operating via Raman gain or based on rare‐earth‐doped active fibers are widely used as sources of CW radiation. However, these lasers are only quasi‐CW: their intensity fluctuates strongly on short time scales. Here the framework of the complex Ginzburg–Landau equations, which are well known as an efficient model of mode‐locked fiber lasers, is applied for the description of quasi‐CW fiber lasers. The vector Ginzburg–Landau model of a Raman fiber laser describes the experimentally observed turbulent‐like intensity dynamics, as well as polarization rogue waves. Our results open debates about the common underlying physics of operation of very different laser types – quasi‐CW lasers and passively mode‐locked lasers.

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Treatment of keloid scars with a 1210‐nm diode laser in an animal model
Authors: Philandrianos Cécile , Bertrand Baptiste , Andrac‐Meyer Lucile , Magalon Guy , Casanova Dominique , Kerfant Nathalie , Mordon Serge
Published: October 2015

Background and Objective

A temperature increase can improve wound healing by activation of heat shock protein 70 and stimulation of fibroblasts. Since keloids are a dysfunction of collagen fiber synthesis and organization, this study aimed to evaluate if a 1,210 nm diode laser could have effects in a new animal model of keloid scars.

Study Design/Materials and Methods

A total of 39 nude mice were used for this study. Phototypes IV and V human keloids were grafted into their backs and after 1 month of healing, the mice were divided into four groups: Control, Laser, Resection, Resection/Laser. In the Laser group, the keloids were treated with a 1,210‐nm diode‐laser with the following parameters: 4 W; 10 seconds; fluence: 51 J/cm2; spot: 18.9 × 3.7 mm2. In the Resection group, surgical intra‐lesional excision was performed. In the Resection/Laser group, keloids were treated with the 1,210‐nm laser‐diode after surgical intra‐lesional excision. Temperature measurements were made during the laser treatment. Clinical examination and histological study were performed on the day of treatment and 1 month, 2 months, and 3 months later.

Results

Mean temperature measurement was of 44.8°C (42–48°) in the Laser groups. No healing complications or keloid proliferation was observed in any group. Keloid histologic characters were confirmed in all grafts. No histologic particularity was observed in the laser groups in comparison with the Control and Resection groups.

Conclusion

First, this keloid animal model appears to be adapted for laser study. Secondly, the 1,210‐nm diode laser does not induce keloid thermal damage in vivo. Further studies with different 1,210‐nm laser diode parameters should be performed in order to observe significant effects on keloids. Lasers Surg. Med. 47:798–806, 2015. © 2015 Wiley Periodicals, Inc.
Tailored Fringed Platforms Produced by Laser Interference for Aligned Neural Cell Growth
Authors: Peláez Ramón J. , González‐Mayorga Ankor , Gutiérrez María C. , García‐Rama Concepción , Afonso Carmen N. , Serrano María C.
Published: October 2015

Ordering neural cells is of interest for the development of neural interfaces. The aim of this work is to demonstrate an easy‐to‐use, versatile, and cost/time effective laser‐based approach for producing platforms that promote oriented neural growth. We use laser interferometry to generate fringed channels with topography on partially reduced graphene oxide layers as a proof‐of‐concept substrate. We study cell adhesion, morphology, viability, and differentiation in cultures of embryonic neural progenitor cells on platforms with a 9.4 μm period. Results evidence that fringed platforms significantly promote neurite alignment (≈50% at 6 d), while preserving viability and neural differentiation.
Stiffness of Hydrogels Regulates Cellular Reprogramming Efficiency Through Mesenchymal‐to‐Epithelial Transition and Stemness Markers
Authors: Choi Bogyu , Park Kwang‐Sook , Kim Ji‐Ho , Ko Kyoung‐Won , Kim Jin‐Su , Han Dong Keun , Lee Soo‐Hong
Published: October 2015

The stiffness of hydrogels has been reported to direct cell fate. Here, we found that the stiffness of hydrogels promotes the reprogramming of mouse embryonic fibroblasts into induced pluripotent stem cells (iPSCs). We prepared cell culture substrates of various stiffnesses (0.1, 1, 4, 10, and 20 kPa) using a polyacrylamide hydrogel. We found that culture on a soft hydrogel plays an important role in inducing cellular reprogramming into iPSCs via activation of mesenchymal‐to‐epithelial transition and enhancement of stemness marker expression. These results suggest that physical signals at the interface between cell and substrate can be used as a potent regulator to promote cell fate changes associated with reprogramming into iPSCs, which may lead to effective and reproducible iPSC‐production.
On the adaptive finite element analysis of the Kohn–Sham equations: methods, algorithms, and implementation
Authors: Davydov Denis , Young Toby D. , Steinmann Paul
Published: October 2015

In this paper, details of an implementation of a numerical code for computing the Kohn–Sham equations are presented and discussed. A fully self‐consistent method of solving the quantum many‐body problem within the context of density functional theory using a real‐space method based on finite element discretisation of realspace is considered. Various numerical issues are explored such as (i) initial mesh motion aimed at co‐aligning ions and vertices; (ii) a priori and a posteriori optimization of the mesh based on Kelly's error estimate; (iii) the influence of the quadrature rule and variation of the polynomial degree of interpolation in the finite element discretisation on the resulting total energy. Additionally, (iv) explicit, implicit and Gaussian approaches to treat the ionic potential are compared. A quadrupole expansion is employed to provide boundary conditions for the Poisson problem. To exemplify the soundness of our method, accurate computations are performed for hydrogen, helium, lithium, carbon, oxygen, neon, the hydrogen molecule ion and the carbon‐monoxide molecule. Our methods, algorithms and implementation are shown to be stable with respect to convergence of the total energy in a parallel computational environment. Copyright © 2015 John Wiley & Sons, Ltd.
Synthesis and vibrational response of graphite oxide platelets from bamboo for electronic applications
Authors: Prías‐Barragán J. J. , Gross K. , Ariza‐Calderón H. , Prieto P.
Published: October 2015

Graphite oxide is an interesting candidate for electronic applications; therefore, important efforts are dedicated to both large‐scaled and low‐cost graphite oxide production as an intermediate in graphene production. At the same time, research efforts are aimed at identifying the role of defects in the magneto‐electrical properties of platelets for electronic applications. In this paper, we present a new low‐cost fabrication process to obtain graphite oxide platelets of high crystal and thermoelectrical quality. The graphite oxide platelet samples were first obtained from bamboo pyroligneous acid (GO‐BPA) by thermal decomposition method using a pyrolysis system for different carbonization temperatures from 673 to 973 K. The GO‐BPA samples were characterized by using Raman, FTIR, XRD, and TEM techniques, whose results suggest that increased carbonization temperature increases graphite conversion, boundary defects, desorption of some organic compounds and phonon response, respectively. Finally, we discuss potential applications of the GO‐BPA samples involving phonon response that would benefit from a fully scaled technology, advanced electronic sensors, and devices.
The Nyquist stability criterion in the Nichols chart
Authors: Garcia‐Sanz Mario
Published: October 2015

The Nyquist stability criterion is a widely used technique for determining in the complex s‐plane the stability of a dynamical system with feedback. This paper presents a practical and comprehensive method to compute the Nyquist stability criterion directly in the Nichols (magnitude/phase) chart. The proposed method also gives guidelines to design controllers to stabilize unstable plants when dealing with frequency domain techniques like the quantitative feedback theory robust control. Copyright © 2015 John Wiley & Sons, Ltd.
A new test and graphical tool to assess the goodness of fit of logistic regression models
Authors: Nattino Giovanni , Finazzi Stefano , Bertolini Guido
Published: October 2015

A prognostic model is well calibrated when it accurately predicts event rates. This is first determined by testing for goodness of fit with the development dataset. All existing tests and graphic tools designed for the purpose suffer several drawbacks, related mainly to the subgrouping of observations or to heavy dependence on arbitrary parameters. We propose a statistical test and a graphical method to assess the goodness of fit of logistic regression models, obtained through an extension of similar techniques developed for external validation. We analytically computed and numerically verified the distribution of the underlying statistic. Simulations on a set of realistic scenarios show that this test and the well‐known Hosmer–Lemeshow approach have similar type I error rates. The main advantage of this new approach is that the relationship between model predictions and outcome rates across the range of probabilities can be represented in the calibration belt plot, together with its statistical confidence. By readily spotting any deviations from the perfect fit, this new graphical tool is designed to identify, during the process of model development, poorly modeled variables that call for further investigation. This is illustrated through an example based on real data. Copyright © 2015 John Wiley & Sons, Ltd.
Delivery of human mesenchymal adipose-derived stem cells restores multiple urological dysfunctions in a rat model mimicking radical prostatectomy damages through tissue-specific paracrine mechanisms
Authors: Yiou René , Mahrouf-Yorgov Meriem , Trébeau Céline , Zanaty Marc , Lecointe Cécile , Souktani Richard , Zadigue Patricia , Figeac Florence , Rodriguez Anne-Marie
Published: October 2015

Urinary incontinence (UI) and erectile dysfunction (ED) are the most common functional urological disorders and the main sequels of radical prostatectomy (RP) for prostate cancer. Mesenchymal stem cell (MSC) therapy holds promise for repairing tissue damage due to RP. Because animal studies accurately replicating post-RP clinical UI and ED are lacking, little is known about the mechanisms underlying the urological benefits of MSC in this setting. To determine whether and by which mechanisms MSC can repair damages to both striated urethral sphincter (SUS) and penis in the same animal, we delivered human multipotent adipose stem cells, used as MSC model, in an immunocompetent rat model replicating post-RP UI and ED. In this model, we demonstrated by using noninvasive methods in the same animal from day 7 to day 90 post-RP injury that MSC administration into both the SUS and the penis significantly improved urinary continence and erectile function. The regenerative effects of MSC therapy were not due to transdifferentiation and robust engraftment at injection sites. Rather, our results suggest that MSC benefits in both target organs may involve a paracrine process with not only soluble factor release by the MSC but also activation of the recipient's secretome. These two effects of MSC varied across target tissues and damaged-cell types. In conclusion, our work provides new insights into the regenerative properties of MSC and supports the ability of MSC from a single source to repair multiple types of damage, such as those seen after RP, in the same individual.
RNA‐based regulation of transposon expression
Authors: Gebert Daniel , Rosenkranz David
Published: October 2015

Throughout the domains of life, transposon activity represents a serious threat to genome integrity and evolution has realized different molecular mechanisms that aim to inhibit the transposition of mobile DNA. Small noncoding RNAs that function as guides for Argonaute effector proteins represent a key feature of so‐called RNA interference (RNAi) pathways and specialized RNAi pathways exist to repress transposon activity on the transcriptional and posttranscriptional level. Transposon transcription can be diminished by targeted DNA methylation or chromatin remodeling via repressive Histone modifications. Posttranscriptional transposon silencing bases on degradation of transposon transcripts to prevent either reverse transcription followed by genomic reintegration or translation into proteins that mediate the transposition process. In plants, Argonaute‐like proteins guided by short interfering RNAs (siRNAs) are essential for transposon repression on the epigenetic and posttranscriptional level. In the germline of animals, these tasks are often assumed by a second subclass of Argonaute proteins referred to as Piwi‐like proteins, which bind a distinct class of small noncoding RNAs named piwi‐interacting RNAs (piRNAs). Though the principals of RNAi pathways are essentially the same in all eukaryotic organisms, remarkable differences can be observed even in closely related species reflecting the astonishing plasticity and diversity of these pathways. WIREs RNA 2015, 6:687–708. doi: 10.1002/wrna.1310

This article is categorized under:

Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs

Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action

Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
Acculturation and Psychological Adjustment of Vietnamese Refugees: An Ecological Acculturation Framework
Authors: Salo Corrina D. , Birman Dina
Published: October 2015

Acculturation to the culture of the host society as well as to one’s heritage culture have been shown to impact immigrants’ adjustment during the years following resettlement. While acculturation has been identified as an important factor in adjustment of Vietnamese immigrants (Birman and Tran in Am J Orthopsychiatr 78(1):109–120. doi:10.1037/0002‐9432.78.1.109, 2008), no clear pattern of findings has emerged and too few studies have employed an ecological approach. The purpose of this paper is to contextualize the study of acculturation and adjustment by taking an ecological approach to exploring these relationships across several life domains, using a bilinear scale, and examining mediators of these relationships for adult Vietnamese refugees (N = 203) in the United States. We call this approach the Ecological Acculturation Framework (EAF). Results of a structural equation model (SEM) showed that job satisfaction fully mediated the relationship between American acculturation and psychological distress, demonstrating that this relationship was specific to an occupational domain. However, while Vietnamese acculturation predicted co‐ethnic social support satisfaction, it did not predict reduced psychological distress. Implications for a life domains approach, including domain specificity, are discussed.
Generation of Bioactive Oxylipins from Exogenously Added Arachidonic, Eicosapentaenoic and Docosahexaenoic Acid in Primary Human Brain Microvessel Endothelial Cells
Authors: Aukema Harold M. , Winter Tanja , Ravandi Amir , Dalvi Siddhartha , Miller Donald W. , Hatch Grant M.
Published: October 2015

The human blood–brain barrier (BBB) is the restrictive barrier between the brain parenchyma and the circulating blood and is formed in part by microvessel endothelial cells. The brain contains significant amounts of arachidonic acid (ARA), and docosahexaenoic acid (DHA), which potentially give rise to the generation of bioactive oxylipins. Oxylipins are oxygenated fatty acid metabolites that are involved in an assortment of biological functions regulating neurological health and disease. Since it is not known which oxylipins are generated by human brain microvessel endothelial cells (HBMECs), they were incubated for up to 30 min in the absence or presence of 0.1‐mM ARA, eicosapentaenoic acid (EPA) or DHA bound to albumin (1:1 molar ratio), and the oxylipins generated were examined using high performance liquid chromatography‐tandem mass spectrometry (HPLC/MS/MS). Of 135 oxylipins screened in the media, 63 were present at >0.1 ng/mL at baseline, and 95 were present after incubation with fatty acid. Oxylipins were rapidly generated and reached maximum levels by 2–5 min. While ARA, EPA and DHA each stimulated the production of oxylipins derived from these fatty acids themselves, ARA also stimulated the production of oxylipins from endogenous 18‐ and 20‐carbon fatty acids, including α‐linolenic acid. Oxylipins generated by the lipoxygenase pathway predominated both in resting and stimulated states. Oxylipins formed via the cytochrome P450 pathway were formed primarily from DHA and EPA, but not ARA. These data indicate that HBMECs are capable of generating a plethora of bioactive lipids that have the potential to modulate BBB endothelial cell function.
Almost everywhere convergence of ergodic series
Authors: FAN AIHUA
Published: October 2015

We consider ergodic series of the form $\sum _{n=0}^{\infty }a_{n}f(T^{n}x)$, where $f$ is an integrable function with zero mean value with respect to a $T$-invariant measure $\unicode[STIX]{x1D707}$. Under certain conditions on the dynamical system $T$, the invariant measure $\unicode[STIX]{x1D707}$ and the function $f$, we prove that the series converges $\unicode[STIX]{x1D707}$-almost everywhere if and only if $\sum _{n=0}^{\infty }|a_{n}|^{2}<\infty$, and that in this case the sum of the convergent series is exponentially integrable and satisfies a Khintchine-type inequality. We also prove that the system $\{f\circ T^{n}\}$ is a Riesz system if and only if the spectral measure of $f$ is absolutely continuous with respect to the Lebesgue measure and the Radon–Nikodym derivative is bounded from above as well as from below by a constant. We check the conditions for Gibbs measures $\unicode[STIX]{x1D707}$ relative to hyperbolic dynamics $T$ and for Hölder functions $f$. An application is given to the study of differentiability of the Weierstrass-type functions $\sum _{n=0}^{\infty }a_{n}f(3^{n}x)$.
Wave field and zonal flow of a librating disk
Authors: Le Dizès Stéphane
Published: October 2015

In this work, we provide a viscous solution of the wave field generated by librating a disk (harmonic oscillation of the rotation rate) in a stably stratified rotating fluid. The zonal flow (mean flow correction) generated by the nonlinear interaction of the wave field is also calculated in the weakly nonlinear framework. We focus on the low dissipative limit relevant for geophysical applications and for which the wave field and the zonal flow exhibit generic features (Ekman scaling, universal structures, etc.). General expressions are obtained which depend on the disk radius $a^{\ast }$, the libration frequency ${\it\omega}^{\ast }$, the rotation rate ${\it\Omega}^{\ast }$ of the frame, the buoyancy frequency $N^{\ast }$ of the fluid, its kinematic diffusion ${\it\nu}^{\ast }$ and its thermal diffusivity ${\it\kappa}^{\ast }$. When the libration frequency is in the inertia-gravity frequency interval ($\min ({\it\Omega}^{\ast },N^{\ast })<{\it\omega}^{\ast }<\max ({\it\Omega}^{\ast },N^{\ast })$), the presence of conical internal shear layers is observed in which the spatial structures of the harmonic response and of the mean flow correction are provided. At the point of focus of these internal shear layers on the rotation axis, the largest amplitudes are obtained: the angular velocity of the harmonic response and the mean flow correction are found to be $O({\it\varepsilon}E^{-1/3})$ and $({\it\varepsilon}^{2}E^{-2/3})$ respectively, where ${\it\varepsilon}$ is the libration amplitude and $E={\it\nu}^{\ast }/({\it\Omega}^{\ast }a^{\ast 2})$ is the Ekman number. We show that the solution in the internal shear layers and in the focus region is at leading order the same as that generated by an oscillating source of axial flow localized at the edge of the disk (oscillating Dirac ring source).
Viscous fingering and deformation of a miscible circular blob in a rectilinear displacement in porous media
Authors: Pramanik Satyajit , De Wit A. , Mishra Manoranjan
Published: October 2015

The deformation of an initially circular miscible blob in a rectilinear displacement is investigated numerically for porous media when the blob is more viscous than the displacing fluid. We find in the parameter space spanned by the Péclet number and log-mobility ratio the existence of a new lump-shaped instability zone between two distinct regimes of comet and viscous fingering (VF) deformations. The more viscous circular blob is destabilized by VF only over a finite window of log-mobility ratio, contrary to the displacement of a more viscous finite slice with planar interfaces. This difference is attributed to the initial curvature of the miscible blob.
Peroxidised dietary lipids impair intestinal function and morphology of the small intestine villi of nursery pigs in a dose-dependent manner
Authors: Rosero David S. , Odle Jack , Moeser Adam J. , Boyd R. Dean , van Heugten Eric
Published: October 2015

The objective of this study was to investigate the effect of increasing degrees of lipid peroxidation on structure and function of the small intestine of nursery pigs. A total of 216 pigs (mean body weight was 6·5 kg) were randomly allotted within weight blocks and sex and fed one of five experimental diets for 35 d (eleven pens per treatment with three to four pigs per pen). Treatments included a control diet without added lipid, and diets supplemented with 6 % soyabean oil that was exposed to heat (80°C) and constant oxygen flow (1 litre/min) for 0, 6, 9 and 12 d. Increasing lipid peroxidation linearly reduced feed intake (P<0·001) and weight gain (P=0·024). Apparent faecal digestibility of gross energy (P=0·001) and fat (P<0·001) decreased linearly as the degree of peroxidation increased. Absorption of mannitol (linear,P=0·097) andd-xylose (linear,P=0·089), measured in serum 2 h post gavage with a solution containing 0·2 g/ml ofd-xylose and 0·3 g/ml of mannitol, tended to decrease progressively as the peroxidation level increased. Increasing peroxidation also resulted in increased villi height (linear,P<0·001) and crypt depth (quadratic,P=0·005) in the jejunum. Increasing peroxidation increased malondialdehyde concentrations (quadratic,P=0·035) and reduced the total antioxidant capacity (linear,P=0·044) in the jejunal mucosa. In conclusion, lipid peroxidation progressively diminished animal performance and modified the function and morphology of the small intestine of nursery pigs. Detrimental effects were related with the disruption of redox environment of the intestinal mucosa.
Biological parameters of interbreeding subspecies ofMeccus phyllosomus(Hemiptera: Reduviidae: Triatominae) in western Mexico
Authors: Martínez-Ibarra J. A. , Nogueda-Torres B. , Cárdenas-De la Cruz M. Á. , Villagrán M. E. , de Diego-Cabrera J. A. , Bustos-Saldaña R.
Published: October 2015

Understanding the biological parameters of some triatomine subspecies ofMeccus phyllosomus(Burmeister) is a crucial first step in estimating the epidemiological importance of this group. Biological parameters related to egg eclosion, egg-to-adult development time, number of blood meals to moult, percentage of females at the end of the cycle, number of laid eggs, and the accumulative mortality for each instar of threeM. phyllosomussubspecies [Meccus phyllosomus pallidipennis(Stål),Meccus phyllosomus longipennis(Usinger), andMeccus phyllosomus picturatus(Usinger)] as well as their laboratory hybrids were evaluated and compared. No significant differences (P> 0.05) were recorded among the experimental hybrids (M. p. longipennis×M. p. pallidipennis, M. p. longipennis×M. p. picturatus, M. p. pallidipennis×M. p. picturatus) and reciprocal cohorts. In five of the six studied parameters (egg eclosion, egg-to-adult development time, number of blood meals to moult, number of laid eggs and accumulative mortality), with the exception of the non-significant percentage of females obtained among all the studied cohorts, at least one of the parental cohorts in each set of crosses exhibited better fitness results than by those of their hybrid descendants. The lack of hybrid fitness in our study indicates the maintenance of reproductive isolation of parental genotypes. Moreover, the results lead us to propose that an incipient speciation process by distance is currently developing among the three studied subspecies, increasing the differences between them that modify the transmission efficiency ofTrypanosoma cruzito human beings in Mexico.
Detecting association of rare and common variants by adaptive combination of P-values
Authors: ZHOU YAJING , WANG YONG
Published: October 2015

Genome-wide association studies (GWAS) can detect common variants associated with diseases. Next generation sequencing technology has made it possible to detect rare variants. Most of association tests, including burden tests and nonburden tests, mainly target rare variants by upweighting rare variant effects and downweighting common variant effects. But there is increasing evidence that complex diseases are caused by both common and rare variants. In this paper, we extend the ADA method (adaptive combination of P-values; Lin et al., 2014) for rare variants only and propose a RC-ADA method (common and rare variants by adaptive combination of P-values). Our proposed method combines the per-site P-values with the weights based on minor allele frequencies (MAFs). The RC-ADA is robust to directions of effects of causal variants and inclusion of a high proportion of neutral variants. The performance of the RC-ADA method is compared with several other association methods. Extensive simulation studies show that the RC-ADA method is more powerful than other association methods over a wide range of models.
Regulating the Activities of Oil Multinationals in Nigeria: A Case for Self-Regulation?
Authors: Ekhator Eghosa O
Published: October 2015

The activities of oil multinational corporations (MNCs) in Nigeria, especially in the oil and gas sector, have come under focus in recent years. The BP oil spill in the Gulf of Mexico in the USA highlighted the negative or unintended consequences of the activities of MNCs. Also, oil MNCs in Nigeria have been at the centre of scandals about poor labour standards, environmental degradation and human rights violations amongst others. Furthermore, the extant state-oriented or command and control regulatory regime has been ineffective. Thus, self-regulation by oil MNCs has risen to help counter these negative consequences. This article contends that the self-regulatory regime is ineffective and advocates for reforms to remedy it.