bluuebunny/crossref_metadata_2025 huggingface dataset:
The ‘Adapted ADAPTE’: an approach to improve utilization of the ADAPTE guideline adaptation resource toolkit in the Alexandria Center for Evidence‐Based Clinical Practice Guidelines
Authors: Amer Yasser Sami , Elzalabany Mahmoud Munir , Omar Tarek Ismael , Ibrahim Afaf Gaber , Dowidar Nabil Lotfy
Published: December 2015

Rationale, aims and objectives

The ADAPTE methodology for adaptation of guidelines has been used by many organizations to develop high‐quality clinical practice guidelines. Although it is a valid alternative for de novo development of guidelines, it might demand more time and resources in some institutions. The present study demonstrates the proposed ‘adapted ADAPTE’ methodology to support more clarity, simplicity and practicality. It also aims at avoiding duplication within the process and reducing the resources and time allocated to the CPG adaptation projects.

Methods

Clinical guidelines' adaptation in the Center for Evidence‐Based Clinical Practice Guidelines at the Alexandria Faculty of Medicine and University Hospitals involves two stages: (1) cross‐sectional or retrospective study to reveal the current practice and prescribing patterns concerning the selected health topic; (2) the ‘adapted ADAPTE’ methodology for CPGs adaptation that was based on the original ADAPTE Process.

Results

The ‘adapted ADAPTE’ included three modified tools, three new tools based on the original ADAPTE framework and alternatives for four ADAPTE steps to enhance utilization. The finalized adapted CPGs included nine high priority topics for paediatrics and two topics for emergency medicine.

Conclusions

The ADAPTE methodology for guideline adaptation can be customized or ‘adapted’ to the local health care setting and resources. This proposal facilitates supports and improves the utilization and update of the ADAPTE process by CPG programmes or activities in health care organizations. This is of particular importance in health care systems in developing countries with limited resources in the Eastern Mediterranean region like Egypt.
Small but Manifold – Hidden Diversity in “Spumella‐like Flagellates”
Authors: Grossmann Lars , Bock Christina , Schweikert Michael , Boenigk Jens
Published: December 2015

Colourless, nonscaled chrysophytes comprise morphologically similar or even indistinguishable flagellates which are important bacterivors in water and soil crucial for ecosystem functioning. However, phylogenetic analyses indicate a multiple origin of such colourless, nonscaled flagellate lineages. These flagellates are often referred to as “Spumella‐like flagellates” in ecological and biogeographic studies. Although this denomination reflects an assumed polyphyly, it obscures the phylogenetic and taxonomic diversity of this important flagellate group and, thus, hinders progress in lineage‐ and taxon‐specific ecological surveys. The smallest representatives of colourless chrysophytes have been addressed in very few taxonomic studies although they are among the dominant flagellates in field communities. To overcome the blurred picture and set the field for further investigation in biogeography and ecology of the organisms in question, we studied a set of strains of specifically small, colourless, nonscaled chrysomonad flagellates by means of electron microscopy and molecular analyses. They were isolated by a filtration‐acclimatisation approach focusing on flagellates of around 5 μm. We present the phylogenetic position of eight different lineages on both the ordinal and the generic level. Accordingly, we describe the new genera Apoikiospumella, Chromulinospumella, Segregatospumella, Cornospumella and Acrispumella Boenigk et Grossmann n. g. and different species within them.
Pathophysiology of sinusitis of odontogenic origin
Authors: Taschieri Silvio , Torretta Sara , Corbella Stefano , Del Fabbro Massimo , Francetti Luca , Lolato Alessandra , Capaccio Pasquale
Published: December 2015

Sinusitis of odontogenic origin, which is frequently encountered in routine otolaryngological and dental clinical practice, has been described as a reactive maxillary inflammation secondary to maxillary tooth infection or trauma to an odontogenic disease of maxillary bone, dental extractions, implant placement, or endodontic treatment impairing the integrity of the Schneiderian membrane. The aim of the present review was to investigate and discuss the most recent pathophysiological findings, predisposing odontogenic factors, microbiology, and the possible involvement of bacterial biofilms (BB) in the development of sinusitis. The narrative literature review showed that there might be a correlation between the bacteria present in pathological teeth in communication with the sinus and those found in infected sinus. The formation of a BB might be also involved in the etiopathogenesis of sinusitis of odontogenic origin. In conclusion, the true origin of odontogenic sinusitis is still unresolved. In clinical terms, the choice of suitable therapy depends on the characteristics of the biofilm. Further microbiological studies are required to better investigate the role of BB.
“Red‐flag” symptom clusters in transthyretin familial amyloid polyneuropathy
Authors: Conceição Isabel , González‐Duarte Alejandra , Obici Laura , Schmidt Hartmut H.‐J. , Simoneau Damien , Ong Moh‐Lim , Amass Leslie
Published: December 2015

Transthyretin familial amyloid polyneuropathy (TTR‐FAP) is a rare, progressive, life‐threatening, hereditary disorder caused by mutations in the transthyretin gene and characterized by extracellular deposition of transthyretin‐derived amyloid fibrils in peripheral and autonomic nerves, heart, and other organs. TTR‐FAP is frequently diagnosed late because the disease is difficult to recognize due to phenotypic heterogeneity. Based on published literature and expert opinion, symptom clusters suggesting TTR‐FAP are reviewed, and practical guidance to facilitate earlier diagnosis is provided. TTR‐FAP should be suspected if progressive peripheral sensory‐motor neuropathy is observed in combination with one or more of the following: family history of a neuropathy, autonomic dysfunction, cardiac hypertrophy, gastrointestinal problems, inexplicable weight loss, carpal tunnel syndrome, renal impairment, or ocular involvement. If TTR‐FAP is suspected, transthyretin genotyping, confirmation of amyloid in tissue biopsy, large‐ and small‐fiber assessment by nerve conduction studies and autonomic system evaluations, and cardiac testing should be performed.
CD1a+ and CD83+ Langerhans cells are reduced in lower lip squamous cell carcinoma
Authors: Gomes Juliane Oliveira , de Vasconcelos Carvalho Marianne , Fonseca Felipe Paiva , Gondak Rogério Oliveira , Lopes Márcio Ajudarte , Vargas Pablo Agustin
Published: December 2015

Background

Actinic cheilitis (AC) is a potentially malignant lesion diagnosed in the lip of patients chronically exposed to the sun that may give rise to a fully invasive lower lip squamous cell carcinoma (LLSCC). It is known that ultraviolet radiation causes dendritic cells (DCs) depletion in the epidermis, but the role of this cellular population in lip cancer progression remains uncertain. Therefore, this study investigated the distribution of DCs in normal, dysplastic and neoplastic tissues of the lower lip.

Methods

Thirteen cases of lower lip mucocele, 42 of ACs and 21 of LLSCC were retrieved and original diagnoses confirmed by two oral pathologists, who further classified ACs as low‐ and high‐risk lesions. Immunoreactions against CD1a and CD83 identified immature and mature DCs, respectively.

Results

Immature CD1a+ Langerhans cells (LCs) were significantly decreased in LLSCC when compared to morphologically normal (P < 0.009) and dysplastic epitheliums (P < 0.003), whereas mature CD83+ LCs were significantly decreased in LLSCC when compared to normal epithelium (P = 0.038). There was no significant difference between low‐ and high‐risk ACs regarding CD1a+ and CD83+ LCs (P > 0.05), but ACs demonstrated a lower concentration of CD1a+ LCs than normal epithelium (P < 0.009). There was no significant difference in the distribution of CD1a+ and CD83+ interstitial dendritic cells (IDCs) in the connective tissue among the studied groups (P > 0.05).

Conclusion

These results suggest that depletion of epithelial LCs, but not IDCs in the connective tissue, would represent an important step for lip cancer development.
mTOR pathway protein immunoexpression as a prognostic factor for survival in head and neck cancer patients: a systematic review and meta‐analysis
Authors: Marques Ana Elizia Mascarenhas , Elias Silvia Taveira , Porporatti André Luís , Castilho Rogerio Moraes , Squarize Cristiane Helena , De Luca Canto Graziela , Guerra Eliete Neves Silva
Published: December 2015

Background

Several mTOR pathway proteins are involved in the regulation of cellular anabolism, growth, proliferation, and survival. Activated proteins in the mTOR pathway are deregulated in multiple types of cancers and could influence prognosis. However, it is unclear whether deregulation of mTOR pathway proteins serves a prognostic role in patients with head and neck cancer (HNC). Furthermore, proteins in the mTOR pathway may be important targets for anticancer therapy. The aim of this study was to summarize existing cohort studies to determine whether immunoexpression of mTOR pathway proteins are important prognostic factors for survival in patients with HNC.

Materials and methods

A systematic review was performed using the Cochrane, Lilacs, PubMed, ScienceDirect, Scopus, and Web of Science databases (up to 23 January 2015). A meta‐analysis was conducted to measure the frequency of protein expression in head and neck cancer patient samples and the prognostic value of mTOR pathway proteins for overall survival (OS) and disease‐free survival (DFS).

Results

Twelve studies were included in our final analysis. The meta‐analysis revealed that the frequency of overall expression of mTOR pathway proteins was 74.42% (CI: 63.3 to 84.0, P < 0.001, n = 2016 samples). The survival meta‐analysis showed a pooled hazard ratio for OS and DFS of 1.44 (95% confidence interval [95% CI] 1.14–1.73) and 1.18 (95% CI 0.71–1.64), respectively.

Conclusion

This systematic review and meta‐analysis support evidence that mTOR pathway proteins can be used as predictive markers for survival in patients with HNC because their expression was significantly associated with poor OS and short DFS.
A Comparative Analysis on Two Types of Oral Implants, Bone‐Level and Tissue‐Level, with Different Cantilever Lengths of Fixed Prosthesis
Authors: Mosavar Alireza , Nili Monireh , Hashemi Sayed Raouf , Kadkhodaei Mahmoud
Published: December 2015

Purpose

Depending on esthetic, anatomical, and functional aspects, in implant‐prosthetic restoration of a completely edentulous jaw, the selection of implant type is highly important; however, bone‐ and tissue‐level implants and their stress distribution in bone have not yet been comparatively investigated. Hence, finite element analysis was used to study the influence of cantilever length in a fixed prosthesis on stress distribution in peri‐implant bone around these two types of oral implants.

Materials and Methods

A 3D edentulous mandible was modeled. In simulations, a framework with four posterior cantilever lengths and two types of implants, bone‐level and tissue‐level, was considered. A compressive load was applied to the distal regions of the cantilevers, and the von‐Mises stress of peri‐implant bone was investigated. The independent t‐test and the Pearson correlation coefficient analyzed the results (α = 0.05).

Results

Stresses in the cortical bone around the bone‐level implants were greater than those in the tissue‐level implants with the same cantilever length. In addition, by extending the cantilever length, the stress values in peri‐implant bone increased. Therefore, when the cantilever was at its maximum length, the maximum stress was in cortical bone and around the bone‐level distal implants.

Conclusion

The results of the present study indicate that treatment with tissue‐level implants is potentially more advantageous than with bone‐level implants for implant‐supported fixed prostheses.
A Comparison of Growth, Survival, and Fatty Acid Composition of the Lined Seahorse, Hippocampus erectus, Juveniles Fed Enriched Artemia and a Calanoid Copepod, Schmackeria dubia
Authors: Zhang Dong , Lin Tingting , Liu Xin
Published: December 2015

The purpose of this study was to evaluate the effect of varying dietary levels of highly unsaturated fatty acids (HUFAs) in live prey (Artemia nauplii and a calanoid copepod, Schmackeria dubia) on the growth performance, survival, and fatty acid composition of the lined seahorse, Hippocampus erectus, juveniles. Artemia nauplii were enriched with a commercial product (SS™ 50DE‐microcapsule as HUFA source, 2/3 DHA, 1/3 EPA. Shengsuo Fishery Feed Research Center of Shandong Province, Qingdao, China) at four concentrations of 0.0, 14.0, 28.0, and 56.0. Newly hatched juveniles were cultured for 35 days. The content of docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and n‐3 HUFAs in the Artemia nauplii was positively related to the enrichment concentration. At the end of the trials, growth performance of the juveniles was positively related to the enrichment concentration as well. However, the juveniles fed prey enriched with the highest concentration of enrichment (56.0 μL/L) had the significantly lower (P < 0.05) survival rate. The juveniles fed the copepod had the best growth performance and the highest survival rate, suggesting that the copepod, S. dubia, is suitable for feeding the seahorse juveniles. The comparisons between the growth, survival, and fatty acid profiles of the juveniles fed Artemia and copepods indicate that the seahorse juveniles require dietary levels of DHA beyond those achieved by enriching prey with the HUFA enrichment. Surplus EPA resulted from an imbalance between DHA and EPA in the enriched Artemia nauplii probably caused an adverse effect on the seahorse juveniles. This study suggests that DHA and EPA requirement of the lined seahorse juveniles is roughly 32% of total fatty acid, and the optimal DHA/EPA ratio for the species is circa 4:1. To avoid an adverse effect resulting from excessive EPA, maximum proportion of EPA in enriched Artemia nauplii should not exceed 13% of total fatty acid, and a recommended minimum DHA/EPA ratio in the enriched Artemia nauplii is 1.46. Arachidonic acid (20:4n‐6) might not be an essential fatty acid for the seahorse juveniles.
Physiological Capillary Regression is not Dependent on Reducing VEGF Expression
Authors: Olfert I. Mark
Published: December 2015

Investigations into physiologically controlled capillary regression report the provocative finding that microvessel regression occurs in the face of persistent elevation of skeletal muscle VEGF expression. TSP‐1, a negative angiogenic regulator, is increasingly being observed to temporally correlate with capillary regression, suggesting that increased TSP‐1 (and not reduction in VEGF per se) is needed to initiate, and likely regulate, capillary regression. Based on evidence being gleaned from physiologically mediated regression of capillaries, it needs to be recognized that capillary regression (and perhaps capillary rarefaction with disease) is not simply the reversal of factors used to stimulate angiogenesis. Rather, the conceptual understanding that angiogenesis and capillary regression each have specific and unique requirements that are biologically constrained to opposite sides of the balance between positive and negative angioregulatory factors may shed light on why anti‐VEGF therapies have not lived up to the promise in reversing angiogenesis and providing the cure that many had hoped toward fighting cancer. Emerging evidence from physiological controlled angiogenesis suggest that cases involving excessive or uncontrolled capillary expansion may be best treated by therapies designed to increase expression of negative angiogenic regulators, whereas those involving capillary rarefaction may benefit from inhibiting negative regulators (like TSP‐1).
G protein‐coupled estrogen receptor is involved in modulating colonic motor function via nitric oxide release in C57BL/6 female mice
Authors: Li Y. , Xu J. , Jiang F. , Jiang Z. , Liu C. , Li L. , Luo Y. , Lu R. , Mu Y. , Liu Y. , Xue B.
Published: December 2015

Background

Estrogen may regulate gastrointestinal motor functions, but the mechanism(s) is not totally understood. Here, we investigated whether G protein‐coupled estrogen receptor (GPER/GPR30) was involved in regulating colonic motor functions and explored the underlying physiological mechanisms.

Methods

Adult female C57BL/6 mice were used. The expression and localization of GPER were examined by RT‐PCR, western blot, and immuno‐labeling. The role of GPER in modulating colonic motor functions was assessed by the bead propulsion test in vivo and organ bath experiments in vitro.

Key Results

GPER was expressed in colonic myenteric neurons. The colonic transit time (CTT) in proestrus and estrus was significantly longer than that in diestrus. In vivo treatment with the selective GPER blocker G15 significantly shortened CTT in proestrus and estrus. In ovariectomized mice, acute estrogen supplementation increased CTT, which could be abolished by G15 co‐administration. The GPER agonist G‐1 caused a concentration‐dependent inhibition of carbachol ‐induced circular muscle strips contraction, which was abolished by tetrodotoxin and the neuronal nitric oxide synthase (nNOS) inhibitor N‐propyl‐l‐arginine. G‐1 stimulated NO production in isolated longitudinal muscle myenteric plexus and cultured myenteric neurons, which was dependent on nNOS. Immunofluorescence labeling showed co‐localization of GPER with nNOS in the myenteric plexus.

Conclusions & Inferences

We suggest that activation of GPER exerts an inhibitory effect on colonic motility by promoting NO release from myenteric nitrergic nerves. These results raise a possibility that GPER may be involved in mediating the inhibitory effect of estrogen on colonic motor functions, via a non‐genomic, neurogenic mechanism.
Not dead yet: the seasonal water relations of two perennial ferns during California's exceptional drought
Authors: Baer Alex , Wheeler James K. , Pittermann Jarmila
Published: December 2015

The understory of the redwood forests of California's coast harbors perennial ferns, including Polystichum munitum and Dryopteris arguta. Unusual for ferns, these species are adapted to the characteristic Mediterranean‐type dry season, but the mechanisms of tolerance have not been studied.

The water relations of P. munitum and D. arguta were surveyed for over a year, including measures of water potential (Ψ), stomatal conductance (gs) and frond stipe hydraulic conductivity (K). A dehydration and re‐watering experiment on potted P. munitum plants corroborated the field data.

The seasonal Ψ varied from 0 to below −3 MPa in both species, with gs and K generally tracking Ψ; the loss of K rarely exceeded 80%. Quantile regression analysis showed that, at the 0.1 quantile, 50% of K was lost at −2.58 and −3.84 MPa in P. munitum and D. arguta, respectively. The hydraulic recovery of re‐watered plants was attributed to capillarity.

The seasonal water relations of P. munitum and D. arguta are variable, but consistent with laboratory‐based estimates of drought tolerance. Hydraulic and Ψ recovery following rain allows perennial ferns to survive severe drought, but prolonged water deficit, coupled with insect damage, may hamper frond survival. The legacy effects of drought on reproductive capacity and community dynamics are unknown.
Long‐term nitrogen deposition linked to reduced water use efficiency in forests with low phosphorus availability
Authors: Huang Zhiqun , Liu Bao , Davis Murray , Sardans Jordi , Peñuelas Josep , Billings Sharon
Published: December 2015

The impact of long‐term nitrogen (N) deposition is under‐studied in phosphorus (P)‐limited subtropical forests. We exploited historically collected herbarium specimens to investigate potential physiological responses of trees in three subtropical forests representing an urban‐to‐rural gradient, across which N deposition has probably varied over the past six decades. We measured foliar [N] and [P] and stable carbon (δ13C), oxygen (δ18O) and nitrogen (δ15N) isotopic compositions in tissue from herbarium specimens of plant species collected from 1947 to 2014.

Foliar [N] and N : P increased, and δ15N and [P] decreased in the two forests close to urban centers. Consistent with recent studies demonstrating that N deposition in the region is 15N‐depleted, these data suggest that the increased foliar [N] and N : P, and decreased [P], may be attributable to atmospheric deposition and associated enhancement of P limitation.

Estimates of intrinsic water use efficiency calculated from foliar δ13C decreased by c. 30% from the 1950s to 2014, contrasting with multiple studies investigating similar parameters in N‐limited forests. This effect may reflect decreased photosynthesis, as suggested by a conceptual model of foliar δ13C and δ18O.

Long‐term N deposition may exacerbate P limitation and mitigate projected increases in carbon stocks driven by elevated CO2 in forests on P‐limited soils.
A subset of AID‐dependent B‐1a cells initiates hypersensitivity and pneumococcal pneumonia resistance
Authors: Askenase Phillip W. , Bryniarski Krzysztof , Paliwal Vipin , Redegeld Frank , Groot Kormelink Thomas , Kerfoot Steven , Hutchinson Andrew T. , van Loveren Henk , Campos Regis , Itakura Atsuko , Majewska‐Szczepanik Monika , Yamamoto Natsuo , Nazimek Katarzyn , Szczepanik Marian , Ptak Wold
Published: December 2015

We propose that there is a special B‐1a B cell subset (“sB‐1a” cells) that mediates linked processes very early after immunization to initiate cutaneous contact sensitivity (CS), delayed‐type hypersensitivity (DTH), and immune resistance to pneumococcal pneumonia. Our published data indicate that in CS and DTH, these initiating processes are required for elicitation of the delayed onset and late‐occurring classical T cell–mediated responses. sB‐1a cells resemble memory B2 cells, as they are stimulated within 1 h of immunization and depend on T helper cytokines—uniquely IL‐4 from hepatic iNKT cells—for activation and rapid migration from the peritoneal cavity to the spleen to secrete IgM antibody (Ab) and Ab‐derived free light chains (FLCs) by only 1 day after immunization. Unlike conventional B‐1a (cB‐1a) cell–produced IgM natural Ab, IgM Ab produced by sB‐1a cells has high Ag affinity owing to immunoglobulin V‐region mutations induced by activation‐induced cytidine deaminase (AID). The dominant cB‐1a cells are increased in immunized AID‐deficient mice but do not mediate initiation, CS, or pneumonia resistance because natural Ab has relatively low Ag affinity because of unmutated germ‐line V regions. In CS and DTH, sB‐1a IgM Ag affinity is sufficiently high to mediate complement activation for generation of C5a that, together with vasoactive mediators such as TNF‐α released by FLC‐sensitized mast cells, activate local endothelium for extravascular recruitment of effector T cells. We conclude by discussing the possibility of functional sB‐1 cells in humans.
Natural variation involving deletion alleles of FRIGIDA modulate temperature‐sensitive flowering responses in Arabidopsis thaliana
Authors: Sanchez‐Bermejo Eduardo , Balasubramanian Sureshkumar
Published: December 2015

Ambient temperature is one of the major environmental factors that modulate plant growth and development. There is extensive natural genetic variation in thermal responses of plants exemplified by the variation exhibited by the accessions of Arabidopsis thaliana. In this work we have studied the enhanced temperature response in hypocotyl elongation and flowering shown by the Tsu‐0 accession in long days. Genetic mapping in the Col‐0 × Tsu‐0 recombinant inbred line (RIL) population identified several QTLs for thermal response including three major effect loci encompassing candidate genes FRIGIDA (FRI), FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT). We confirm and validate these QTLs. We show that the Tsu‐0 FRI allele, which is the same as FRI‐Ler is associated with late flowering but only at lower temperatures in long days. Using transgenic lines and accessions, we show that the FRI‐Ler allele confers temperature‐sensitive late flowering confirming a role for FRI in photoperiod‐dependent thermal response. Through quantitative complementation with heterogeneous inbred families, we further show that cis‐regulatory variation at FT contributes to the observed hypersensitivity of Tsu‐0 to ambient temperature. Overall our results suggest that multiple loci that interact epistatically govern photoperiod‐dependent thermal responses of A. thaliana.
Maintenance of meristem activity under stress: is there an interplay of RSS1‐like proteins with the RBR pathway?
Authors: Ebel C. , Hanin M.
Published: December 2015

Plants have acquired rapid responses to a constantly changing environment. These adaptive and protective responses are the result of a complex signalling network regulating different aspects, ranging from ion homeostasis to cell cycle control. It is well established that stress inhibits cell division, which negatively impacts plant growth and development and hence results in biomass decrease and yield loss. Therefore understanding the link between stress perception and cell cycle control would allow development of new crops with increased productivity when subjected to stress. However, studies on cell cycle control under stress have been limited to well‐known regulators of the cell cycle such as cyclins and stress‐related phytohormone integrators. The recent discovery of RSS1, a novel intrinsically unstructured protein of rice, opened up new insights into how stress perception can be connected with cell cycle control in meristematic zones. Whereas RSS1 is well conserved among other plant lineages, eudicots present proteins sharing little sequence homology with RSS1. Here, we discuss how RSS1‐like proteins might also be functional in dicots, and possibly act through the retinoblastoma‐related pathway to regulate both S‐phase transition and cell fate in meristems.
Differentiation in populations of the apple scab fungusVenturia inaequalison cultivars in a mixed orchard remain over time
Authors: Passey T. A. J. , Shaw M. W. , Xu X.‐M.
Published: December 2015

The ascomyceteVenturia inaequaliscauses annual epidemics of apple scab worldwide. Scab development is reduced in mixed cultivar orchards compared with monocultures. In order to use mixtures in commercial production, how the population of scab changes in a mixed orchard needs to be understood, together with how likely a super race, with virulence factors overcoming multiple resistance factors in the mixed orchard, is to emerge and become dominant. This study used simple sequence repeat (SSR) markers to investigate the temporal change of scab populations in two mixed cultivar orchards in theUKto infer the likelihood of emergence of a scab super race. There were no significant differences between the populations at the two sampling times (6 or 7 years apart) in either of the two mixed orchards. In one of the orchards, apple scab populations on different cultivars were significantly different and the differences did not diminish over time. These results suggest that it is not inevitable that a super race ofV. inaequaliswill become dominant during the lifetime of a commercial apple orchard.
PCR‐based identification of cacao black pod causal agents and identification of biological factors possibly contributing to Phytophthora megakarya's field dominance in West Africa
Authors: Ali S. S. , Amoako‐Attah I. , Bailey R. A. , Strem M. D. , Schmidt M. , Akrofi A. Y. , Surujdeo‐Maharaj S. , Kolawole O. O. , Begoude B. A. D. , ten Hoopen G. M. , Goss E. , Phillips‐Mora W. , Meinhardt L. W. , Bailey B. A.
Published: December 2015

Among the Phytophthora species that cause black pod of cacao, P. megakarya is the most virulent, posing a serious threat to cacao production in Africa. Correct identification of the species causing the black pod and understanding the virulence factors involved are important for developing sustainable disease management strategies. A simple PCR‐based species identification method was developed using the species‐specific sequences in the ITS regions of the rRNA gene. A phylogenetic tree generated for 119 Phytophthora isolates, based on the 60S ribosomal protein L10 gene and rDNA sequence, verified the PCR‐based identification assay and showed high interspecific variation among the species causing black pod. Phytophthora megakarya isolates were uniformly virulent in an assay using susceptible cacao pod husks inoculated with zoospores, while the P. palmivora isolates showed greater divergence in virulence. The virulence of P. megakarya was associated with earlier production of sporangia and an accelerated induction of necrosis. While zoospore germ tubes of both species penetrated pods through stomata, only P. megakarya produced significant numbers of appressoria. A hypersensitive‐like response was observed when attached SCA‐6 pods were inoculated with P. palmivora. SCA‐6 pods became vulnerable to P. palmivora when wounded prior to zoospore inoculation. Phytophthora megakarya was more aggressive than P. palmivora on attached SCA‐6 pods, causing expanding necrotic lesions with or without wounding. Phytophthora megakarya is predominant in the Volta region of Ghana and it remains to be seen whether it can displace P. palmivora from cacao plantations of Ghana as it has in Nigeria and Cameroon.
Interleukin (IL)‐25: Pleiotropic roles in asthma
Authors: Yao Xiujuan , Sun Yongchang , Wang Wei , Sun Ying
Published: December 2015

IL‐25, also named IL‐17E, is a distinct member of the IL‐17 cytokine family, which can promote and augment T helper type 2 (Th2) responses locally or systemically. Growing evidence from experimental and clinical studies indicates that the expression of IL‐25 and its cognate receptor, IL‐17RB/RA, is markedly upregulated in asthmatic conditions. It has also been found that IL‐25 induces not only typical eosinophilic inflammation and airway hyperresponsiveness (AHR), but also airway remodelling, manifested by goblet cell hyperplasia, subepithelial collagen deposition and angiogenesis. This review will focus on the discovery, cellular origins and targets of IL‐25, and try to update current animal and human studies elucidating the roles of IL‐25 in asthma. We conclude that although IL‐25 is a pleiotropic cytokine, it may only play its dominant role in a certain specific asthmatic endotype, named ‘IL‐25 high’ phenotype. Thus, targeting IL‐25 or its receptor might selectively benefit some subgroups with asthma. Furthermore, the major IL‐25 producing as well as responsive cells in the changeable milieu of asthma should be assessed in the future.
Secular variations in seawater chemistry controlling dolomitization in shallow reflux systems: insights from reactive transport modelling
Authors: Gabellone Tatyana , Whitaker Fiona
Published: December 2015

Dolomitization often plays a critical role in the pore network development of platform carbonates, with implications for reservoir quality distribution. Understanding both the hydrological system driving dolomitization and the chemistry of the fluids involved is fundamental to constrain predictions of the geometry and the petrophysical properties of dolomite bodies. Here, the role of secular variations in seawater Mg/Ca as a control on dolomitization and early porosity modification was evaluated using one‐dimensional reactive transport models and fluids based on modern (aragonite sea), Mississippian and Aptian (calcite sea) seawaters. The sensitivity of dolomitization to a range of extrinsic controls (brine salinity, temperature, fluid flow rate and pCO2) and to intrinsic reactivity of the sediments (effective reactive surface area) was also explored. Simulations suggest faster calcite replacement by dolomite for seawaters with higher Mg/Ca, indicating that dolomitization potential is determined more by Mg/Ca rather than saturation index. Increasing evaporative concentration enhances reaction rate independent of the effect of enhanced density‐driven fluid flux. In addition to brine composition, effective surface area of precursor sediments and temperature exert a critical control on replacement rate, while secular variations of pH and carbonate alkalinity associated with changes in pCO2 are only secondary controls. Above flow rates of 0·01 m yr−1 replacive dolomitization is reaction‐limited rather than flux limited, favouring alteration of fine‐grained carbonates and suggesting that preferential alteration of grainstone units is rare unless head gradients are low. Post‐replacement dolomite cementation is flux dependent, and thus favoured in areas of high head gradient and high permeability sediments and, contrary to replacement, supersaturation is a more important driver than Mg/Ca. While uncertainties remain regarding low‐temperature dolomitization kinetics, the capability of numerical simulations to decouple individual controls provides new insights which can be used, in conjunction with traditional comparative sedimentology, to generate more rigorous conceptual models for individual reservoir settings.
Pre‐Cenomanian vs. Cenozoic folding in the High Atlas revealed by palaeomagnetic data
Authors: Torres‐López Sara , Casas Antonio M. , Villalaín Juan José , El Ouardi Hamidou , Moussaid Bennacer
Published: December 2015

Palaeomagnetic data, and specifically remagnetizations, are used to constrain the geometric reconstruction at 100 Ma of three anticlines cored by gabbroic intrusions and Triassic shales in the Central High Atlas, Morocco. Previous palaeomagnetic results have revealed that the Mesozoic sediments of this region acquired a pervasive remagnetization at the end of the Early Cretaceous. The restoration of palaeomagnetic vectors to the remagnetization stage (100 Ma) allows us to determine the dip of the beds during this period and, thereby, to reconstruct structures during that time and determine the relative contributions of Mesozoic magmatic/diapiric uplift vs. Cenozoic compression to the present‐day dip. Our results indicate that three major anticlines in the Central High Atlas (Tasraft, Tassent and Tissila) were initiated to different degrees before the Late Cretaceous and were reactivated during Cenozoic compression to acquire their present‐day geometry. We also discuss the origin of these structures.
A versatile Multisite Gateway‐compatible promoter and transgenic line collection for cell type‐specific functional genomics in Arabidopsis
Authors: Marquès‐Bueno Maria Mar , Morao Ana K. , Cayrel Anne , Platre Matthieu P. , Barberon Marie , Caillieux Erwann , Colot Vincent , Jaillais Yvon , Roudier François , Vert Grégory
Published: December 2015

Multicellular organisms are composed of many cell types that acquire their specific fate through a precisely controlled pattern of gene expression in time and space dictated in part by cell type‐specific promoter activity. Understanding the contribution of highly specialized cell types in the development of a whole organism requires the ability to isolate or analyze different cell types separately. We have characterized and validated a large collection of root cell type‐specific promoters and have generated cell type‐specific marker lines. These benchmarked promoters can be readily used to evaluate cell type‐specific complementation of mutant phenotypes, or to knockdown gene expression using targeted expression of artificial miRNA. We also generated vectors and characterized transgenic lines for cell type‐specific induction of gene expression and cell type‐specific isolation of nuclei for RNA and chromatin profiling. Vectors and seeds from transgenic Arabidopsis plants will be freely available, and will promote rapid progress in cell type‐specific functional genomics. We demonstrate the power of this promoter set for analysis of complex biological processes by investigating the contribution of root cell types in the IRT1‐dependent root iron uptake. Our findings revealed the complex spatial expression pattern of IRT1 in both root epidermis and phloem companion cells and the requirement for IRT1 to be expressed in both cell types for proper iron homeostasis.
Engraftment for CD34 selected stem cell products is not compromised by cryopreservation
Authors: Reich‐Slotky Ronit , Bachegowda Lohith S. , Ancharski Michael , Gergis Usama , van Besien Koen , Cushing Melissa M.
Published: December 2015

BACKGROUND

The coinfusion of haploidentical CD34+ selected peripheral blood stem cell products with umbilical cord blood (UCB) provides early neutrophil recovery, long‐term UCB engraftment, and a lower incidence of graft‐versus‐host disease; however, this complex transplant presents a scheduling challenge for both the cellular therapy laboratory and the clinical team. Cryopreservation of the haploidentical product can facilitate scheduling, but has been previously shown to be associated with infusion reactions and delayed platelet (PLT) engraftment in allogeneic hematopoietic progenitor cell transplant.

STUDY DESIGN AND METHODS

To test whether cryopreservation of the CD34+ selected product compromises the graft, we compared neutrophil and PLT engraftment kinetics for patients receiving freshly infused or cryopreserved products. Seventy‐two products collected from haploidentical related donors were CD34+ selected and infused in a combined transplant with UCB: 32 were cryopreserved before infusion and 40 were infused fresh.

RESULTS

No adverse infusion events were reported in either group and there was no difference in neutrophil and PLT engraftment time between fresh and cryopreserved products.

CONCLUSION

Cryopreservation of a CD34+‐selected product can be safely used in a combined transplant with UCB and does not affect engraftment time.
EMG RECORDING OF WRIST GESTURES UNDER NON-IDEAL ELECTRODE PLACEMENT FOR MACHINE CONTROL IN A MANUFACTURING ENVIRONMENT
Authors: Fu Zinvi , Bani Hashim A. Y. , Jamaludin Z. , Mohamad I. S.
Published: December 2015

The use of electromyography (EMG) for machine control in a manufacturing environment is challenging due to the inherent electrical noise, and also because machine operators lack anatomy knowledge of muscle location for electrode placement. In this research, an electrode placement scheme is proposed for this user group. An EMG preamp was constructed to observe EMG patterns in lower forearm when electrodes placed by untrained operators are in less optimal locations. Crosstalk was found to be a major issue when electrodes are placed in imperfect locations. The EMG preamplifier was deliberately constructed with low cost components to simulate the increased floor noise due to electrical interferences f however from the results, the resulting SNR is acceptable. This study shows that in designing a practical EMG input system, electrode placement is a bigger factor compared to electrical interference.
STUDY ON CORROSION FEATURES ANALYSIS FOR VISUAL INSPECTION & MONITORING SYSTEM: AN NDT TECHNIQUE
Authors: Bin Idris Syahril Anuar , Jafar Fairul Azni , Abdullah Nurhidayu
Published: December 2015

These days, utilization of camera as inspection tools has been expanded. The flexibility functions of camera is good to get different kind of information. This research work is focusing on developing a robust visual inspection system for NDT corrosion detection. An investigation on corrosion types based on appearance features is simulated to identify the profiling of each corrosion types. The result found that each corrosion types has different features that can be used for classifying the corrosion. By identifying the type of corrosion, we can understand the pattern of attack, thus early prevention can be done. It is expected that the output of this research will be a new method of corrosion detection and improve vision inspection as the pioneer in NDT method for corrosion inspection. Furthermore, the system is able to adapt to the unrefined environment, thus, making the proposed system robust and useful for other detection applications.
REDESIGNING EFFECT OF AUTO TAPING MACHINE SYSTEM IN SMALL PRODUCTION SCALE
Authors: Istardi Didi , Simatupang Remon
Published: December 2015

Productivity increase can be achieved by reducing the standard time that is used in a production process, especially due to human movement and by using an automation system. In this paper, changing the design and development of a semi-automation of Brother Hitap BT-61, a taping machine to become full-automation is presented by implementing the PLC and Electro Pneumatic system onto the mechanical system of feeding, taping, and pick up process. This research can contribute higher value added output, such as increase of productivity from 95.66% to 97.09%, reducing defects of sample products chassis RH that is used for revolving lights fabrication from 0.65% to 0.01%. Also, the system can avoid on-site working accident during machine operation. Based on the calculation of cost saving, the return of investment period of this research project is 8.5 months.
OBJECT QUALITY ENHANCEMENT OF MULTI-FRAME LOW-RESOLUTION VIDEO
Authors: Aisyah Siti , Arnia Fitri
Published: December 2015

A good quality image is required in various applications such as object identification and authentication. This research presents the performance of image resolution enhancement method, in which the low-resolution image originated from low-resolution CCTV video. The enhancement method is initialized by averaging video frames and continued by interpolating the resulted images using the existing interpolation techniques, namely bilinear, bi-cubic, nearest neighbor and spleen. Frame rate of 15 and 25 frames per second (fps) has been applied to the testing video. The result shows that the differences of frame rate and number of the averaged frame would affect image quality. Subjective assessment of respondents of MOS above 3 has been obtained by increasing the frame rate and the number of averaging frames.
A CASE STUDY OF THE WEAKNESS OF FRESHMEN CHOSEN PASSWORD FOR ACADEMIC INFORMATION SYSTEM
Authors: Ahmadiar Ahmadiar , Muchallil Sayed
Published: December 2015

In the last decades, some extensive research explored new algorithms and protocols how to secure data or user information using password and username. There are new methods such as biometrics. The drawback of this method is that it needs other hardware or device. On the other hand, the username and password combination to authenticate user identity has been widely used because cheap and user-friendly. The latter method has some weakness such as dictionary attack, brute force or other method. The purpose of this research to find out the weakness of freshmen chosen password to protect their identity in the Academic Information System. The experiment is done in a public university in Indonesia. This research carried on around 12 faculties and 102 departments. The freshmen at this university is around 6499 students. The sampling method is population, so that all the freshmen student account investigated. The first scenario is to find out how many students use the same password as username. The second scenario is a dictionary attack on some freshmen account that cannot be found on the first scenario. The result of this experiment about 60% to 75% of freshmen’s password in each faculty can be guessed because the students used the same username and password. Other method used in this research has been revealed more password from freshmen.
BIOCONVERSION OF SEAWEED WITH WHITE ROT FUNGI FOR PRODUCTION OF PROTEIN ENRICHED FISH FEEDSTOCK
Authors: Jamal Parveen , Kola Saheed Olorunnisola , Jaswir Irwandi , I. D. Ruqayyah Tijani
Published: December 2015

Viable and economical source of fish feed ingredients remained one of most important factors for a successful and profitable fish production for peasant farmers and industries. Solid state bioconversion (SSB) involving Phanerochaete chrysosporium (P. chrysosporium) was conducted to enrich seaweed with protein. Optimization of processing parameters (moisture content, inoculum size and minerals) with response surface methodology (RSM) showed crude protein increased to 120.29 mg/g. Positive interaction existed among all investigated process parameters and the quadratic model describing the process was significant at p˂0.05. The coefficient of determination –R-squared, of the model was close to unity. The optimum value of moisture content was 73.5% (v/w), 8.5% (v/w) for inoculum size and 7% (v/w) of mineral supplement. Validation of the model showed protein production falling within 10% tolerable point.
SPATIAL AND TEMPORAL DISTRIBUTION OF BACTERIAL COMMUNITIES AND HEAVY METALS (CR, CD AND PB) COMPOSITION IN SEDIMENTS ALONG PAHANG RIVER, MALAYSIA
Authors: Mohd Amin Mohd Huzaimi , Chowdhury Ahmed Jalal Khan , Yunus Kamaruzzaman , Nordin Noor Faizul Hadry
Published: December 2015

Bacterial communities show complex and sensitive response towards the environmental stimulation. Pahang River is one of the important inland aquatic biodiversity resources that provide food and excellent habitat for many organisms including microorganisms. Higher bacterial diversity is assumed to increase ecosystem capacity to resist and recover from perturbation. Hence, it is important to assess the impacts of heavy metals composition towards distribution of bacteria in sediments along Pahang River. A study on heavy metals composition such as chromium, cadmium and lead was carried out along the Pahang River using Teflon Bomb digestion processes and were analyzed using ICP-MS. Overall 19 sampling areas along Pahang River with frequency of 20-30 km for each site were chosen as our sampling stations. Sampling was conducted during pre and post of North-East monsoon season. The average dry weight concentration for chromium (Cr) was found between 3.250 and 21.950 µg/g, cadmium (Cd) ranged from 0.019 to 0.403 µg/g and lead (Pb) 8.024 to 20.660 µg/g. The bacterial community in sediments along Pahang River was determined using culture-based method. The bacterial colony-forming unit (CFU) range was found between 1013.33 CFU/g and 28826.67 CFU/g. This study demonstrated that the concentration of heavy metals and bacterial colony number different at each station during pre and post-monsoon. Apart from that, the heavy metals composition can influence the changes of bacterial colony number. However this changes also influence by other factors such as physicochemical parameters, sediments size, nutrient contents in the river and also sediments and water run-off. The condition of Pahang River is still conducive and activities that causing pollution should be stopped.
ILLUMINA®TRUSEQ® VS NEBNEXT® SMALL RNA LIBRARY PREPARATION KIT FOR MIRNA PROFILING IN PERSICARIA MINOR: WHICH BETTER?
Authors: A. Samad Abdul Fatah , Muhammad Ali Nazaruddin , Ismail Ismanizan
Published: December 2015

In plants, a group of non-coding small RNA (sRNA) has been provento be an important player in regulating gene expression that can govern network of genetic systems. The two major classes of sRNA which are very extensively studied through deep sequencing, microRNA (miRNA) and small-interfering RNA (siRNA) classes, are well documented. However, the isolation method of sRNA differs depending on the type of sample. Here, we demonstrate the miRNA library preparation using two different Small RNA Library preparation kit, Illumina®TruSeq® Small RNA Preparation and NEBNext® Multiplex Small RNA Library Preparation kit on a plant rich in secondary metabolite Persicaria minor using recommended protocol. The result show NEBNext® Multiplex Small RNA Library Preparation kit can recover small RNA better than Illumina®TruSeq® Small RNA Preparation kit. Thus, this study recommended NEBNext® Multiplex Small RNA Library Preparation kit for miRNA library preparation on Persicaria minor.