bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prokaryotic genes in eukaryotic genome sequences: when to infer horizontal gene transfer and when to suspect an actual microbe
Authors: Artamonova Irena I. , Lappi Tanya , Zudina Liudmila , Mushegian Arcady R. 
Published: April 2015

SummaryAssessment of phylogenetic positions of predicted gene and protein sequences is a routine step in any genome project, useful for validating the species' taxonomic position and for evaluating hypotheses about genome evolution and function. Several recent eukaryotic genome projects have reported multiple gene sequences that were much more similar to homologues in bacteria than to any eukaryotic sequence. In the spirit of the times, horizontal gene transfer from bacteria to eukaryotes has been invoked in some of these cases. Here, we show, using comparative sequence analysis, that some of those bacteria‐like genes indeed appear likely to have been horizontally transferred from bacteria to eukaryotes. In other cases, however, the evidence strongly indicates that the eukaryotic DNA sequenced in the genome project contains a sample of non‐integrated DNA from the actual bacteria, possibly providing a window into the host microbiome. Recent literature suggests also that common reagents, kits and laboratory equipment may be systematically contaminated with bacterial DNA, which appears to be sampled by metagenome projects non‐specifically. We review several bioinformatic criteria that help to distinguish putative horizontal gene transfers from the admixture of genes from autonomously replicating bacteria in their hosts' genome databases or from the reagent contamination.
Characterization of the Supermolecular Structure of Polydatin/6‐O‐α‐Maltosyl‐β‐cyclodextrin Inclusion Complex
Authors: Liu Benguo , Li Yun , Xiao Huizhi , Liu Yonglan , Mo Haizhen , Ma Hanjun , Liang Guizhao 
Published: April 2015

AbstractPolydatin is the main bioactive ingredient in many medicinal plants, such as Hu‐zhang (Polygonum cuspidatum), with many bioactivities. However, its poor aqueous solubility restricts its application in functional food. In this work, 6‐O‐α‐Maltosyl‐β‐cyclodextrin (Malt‐β‐CD), a new kind of β‐CD derivative was used to enhance the aqueous solubility and stability of polydatin by forming the inclusion complex. The phase solubility study showed that polydatin and Malt‐β‐CD could form the complex with the stoichiometric ratio of 1:1. The supermolecular structure of the polydatin/Malt‐β‐CD complex was characterized by ultraviolet–visible spectroscopy (UV), Fourier transform infrared spectroscopy (FT‐IR), X‐ray diffractometry (XRD), thermogravimetric/differential scanning calorimetry (TG/DSC), and proton nuclear magnetic resonance (1H‐NMR) spectroscopy. The changes of the characteristic spectral and thermal properties of polydatin suggested that polydatin could entrap inside the cavity of Malt‐β‐CD. Furthermore, to reasonably understand the complexation mode, the supermolecular structure of polydatin/Malt‐β‐CD inclusion complex was postulated by a molecular docking method based on Autodock 4.2.3. It was clearly observed that the ring B of polydatin oriented toward the narrow rim of Malt‐β‐CD with ring A and glucosyl group practically exposed to the wide rim by hydrogen bonding, which was in a good agreement with the spectral data.
Effect of Infrared Blanching on Enzyme Activity and Retention of β‐Carotene and Vitamin C in Dried Mango
Authors: Guiamba Isabel R.F. , Svanberg Ulf , Ahrné Lilia 
Published: April 2015

AbstractThe objectives of this work were to evaluate infrared (IR) dry blanching in comparison with conventional water blanching prior to hot air drying of mango to inactivate polyphenol oxidase (PPO) and ascorbic acid oxidase (AAO) enzymes, and to study its effect on color change and retention of vitamin C and β‐carotene. Mango cylinders were blanched under similar temperature–time conditions either by IR heating or by immersion in a water bath during 2 min at 90 °C (high‐temperature‐short‐time—HTST) or for 10 min at 65 °C (low‐temperature‐long‐time—LTLT). After blanching mango was hot air dried at 70 °C. PPO was completely inactivated during the blanching treatments, but AAO had a moderate remaining activity after LTLT treatment (∼30%) and a low remaining activity after HTST treatment (9% to 15%). A higher retention of vitamin C was observed in mango subjected to IR dry blanching, 88.3 ± 1.0% (HTST) and 69.2 ± 2.9% (LTLT), compared with water blanching, 61.4 ± 5.3% (HTST) and 50.7 ± 9.6% (LTLT). All‐trans‐β‐carotene retention was significantly higher in water blanched dried mango, 93.2 ± 5.2% (LTLT) and 91.4 ± 5.1% (HTST), compared with IR dry blanched, 73.6 ± 3.6% (LTLT) and 76.9 ± 2.9% (HTST). Increased levels of 13‐cis‐β‐carotene isomer were detected only in IR dry blanched mango, and the corresponding dried mango also had a slightly darker color. IR blanching of mango prior to drying can improve the retention of vitamin C, but not the retention of carotenoids, which showed to be more dependent on the temperature than the blanching process. A reduction of drying time was observed in LTLT IR‐blanching mango.
Macronutrients, Phytochemicals, and Antioxidant Activity of Soybean Sprout Germinated with or without Light Exposure
Authors: Chen Yeming , Chang Sam K.C. 
Published: April 2015

AbstractThis study examined the macronutrients, phytochemicals, and antioxidant activities of yellow soybean sprout (YSS) and green soybean sprout (GSS) with different germination days. YSS and GSS were obtained by sprouting soybean in darkness or with light exposure at 21 °C. Lipid, protein, carbohydrate, and ash contents were analyzed before and after soybean germination. Phytochemicals (total phenolic compounds, saponin, and isoflavone) were also determined. DPPH, ferric reducing antioxidant power (FRAP), and oxygen radical absorbance capacity (ORAC) were determined to examine the antioxidant activities of soybean sprout. Results showed YSS had a higher yield than GSS. Based on dry mass composition, 7‐d germination of GSS decreased 14% protein, 37% lipid, 22% carbohydrate, and 16% ash, whereas 7‐d germination of YSS decreased 6% protein and 47% lipid. Carbohydrate did not change and ash significantly increased for the 7‐d germinated YSS. Lipid was greatly metabolized in germination, which explained why the protein relative percentage in dried soybean sprout was higher than that in the corresponding soybean. Total phenolic compounds and saponin (mg/g soybean sprout, dry basis) had the same accumulation trend in soybean sprout with the increases in germination days. Aglycone isoflavones (genistein, glycitein, and daidzein) and daidzin showed an increased trend, whereas malonylgenistin and malonylglycitin showed a decreased trend with germination days for both GSS and YSS. The change in other isoflavones did not show definite trends. GSS had 20% more antioxidant activities than YSS (7‐d germinated soybean sprout). The increases in ORAC antioxidant activity suggest eating GSS may be more beneficial than GSS for promoting human health.
Control of Histamine‐Producing Bacteria and Histamine Formation in Fish Muscle by Trisodium Phosphate
Authors: Bjornsdottir‐Butler Kristin , Green David P. , Bolton Greg E. , McClellan‐Green Patricia D. 
Published: April 2015

AbstractScombrotoxin fish poisoning remains the primary cause of seafood poisoning outbreaks despite preventive guidelines. The purpose of this study was to investigate the use of pH for the control of growth and histamine formation by histamine‐producing bacteria in fish muscle. We examined pH effects on growth and histamine formation in tuna fish infusion broth and in inoculated tuna and mahi‐mahi fish muscle. Histamine production was significantly less for all bacterial strains at pH 8.5 compared to pH 5.5 in tuna fish infusion broth with no significant difference in growth. Elevated pH due to phosphate treatment of fish muscle tissues significantly reduced histamine formation with no effect on the growth of histamine‐producing bacteria. This study revealed that phosphate treatment of mahi‐mahi and tuna fish muscle resulted in significantly lower histamine production over 4 d of storage at 10 °C. Phosphate treatment of fish muscle may serve as a secondary barrier in addition to FDA recommended time and temperature controls for reducing public health concerns of scombrotoxin fish poisoning.
Apple Aminoacid Profile and Yeast Strains in the Formation of Fusel Alcohols and Esters in Cider Production
Authors: Eleutério dos Santos Caroline Mongruel , Pietrowski Giovana de Arruda Moura , Braga Cíntia Maia , Rossi Márcio José , Ninow Jorge , Machado dos Santos Tâmisa Pires , Wosiacki Gilvan , Jorge Regina Maria Matos , Nogueira Alessandro 
Published: April 2015

AbstractThe amino acid profile in dessert apple must and its effect on the synthesis of fusel alcohols and esters in cider were established by instrumental analysis. The amino acid profile was performed in nine apple musts. Two apple musts with high (>150 mg/L) and low (<75 mg/L) nitrogen content, and four enological yeast strains, were used in cider fermentation. The aspartic acid, asparagine and glutamic acid amino acids were the majority in all the apple juices, representing 57.10% to 81.95%. These three amino acids provided a high consumption (>90%) during fermentation in all the ciders. Principal component analysis (PCA) explained 81.42% of data variability and the separation of three groups for the analyzed samples was verified. The ciders manufactured with low nitrogen content showed sluggish fermentation and around 50% less content of volatile compounds (independent of the yeast strain used), which were mainly 3‐methyl‐1‐butanol (isoamyl alcohol) and esters. However, in the presence of amino acids (asparagine, aspartic acid, glutamic acid and alanine) there was a greater differentiation between the yeasts in the production of fusel alcohols and ethyl esters. High contents of these aminoacids in dessert apple musts are essential for the production of fusel alcohols and most of esters by aromatic yeasts during cider fermentation.
Controlling Listeria monocytogenes in Cold Smoked Salmon with the Antimicrobial Peptide Salmine
Authors: Cheng Christopher , Arritt Fletcher , Stevenson Clinton 
Published: April 2015

AbstractListeria monocytogenes (LM) is a major safety concern for smoked salmon producers, as it can survive both the brining and smoking process in cold smoked salmon production. Salmine is a cationic antimicrobial peptide derived from the milt of salmon that has been shown to inhibit the growth of LM in vitro. Commercialization of this peptide would add value to a waste product produced when raising salmon. The purpose of this study was to determine the anti‐listeria activity of salmine in smoked salmon by measuring the viable counts of LM over time. Cold smoked salmon was treated with a salmine solution or coated with agar or k‐carrageenan films incorporating salmine to maintain a high surface concentration of the antimicrobial. Samples were then inoculated with approximately 1.0 × 103 cells of LM. The viable counts were then enumerated throughout 4 wk at 4 °C storage. It was found that 5 mg/g salmine delayed the growth of LM on smoked salmon. These samples had significantly (P < 0.05) lower LM counts than on the untreated samples on days 13 and 22. Edible films did not significantly (P > 0.05) improve the antimicrobial efficacy of salmine. The peptide combined with biopolymers also had lower antimicrobial activity in vitro when compared to salmine alone. These results suggest there is potential for salmine to be used as a natural hurdle to inhibit growth of LM due to post process contamination; however, future investigations for extending this effect throughout the shelf life of smoked salmon products are warranted.
The impact of herd composition and foraging area on livestock predation by big cats in the Pantanal of Brazil
Authors: Tortato F. R. , Layme V. M. G. , Crawshaw P. G. , Izzo T. J. 
Published: April 2015

AbstractThe conflict caused by large carnivore attacks on livestock constitutes a major threat to the conservation of carnivore species worldwide. The objective of this study was to determine what factors influence jaguar Panthera onca and puma Puma concolor attacks on cattle at a ranch in the Brazilian Pantanal. Cattle herds were monitored for 57 months, and data were collected for each recorded mortality event. The economic impact of predation was calculated. We parameterize a generalized linear model with negative binomial error distribution to model the influence of water levels of the Paraguay River, size of cattle herd and the age structure of the herd on the monthly number of cattle killed by big cats. Over half of all recorded herd mortality events were caused by large cat predation, resulting in a maximum 2.83% of the average annual herd size and representing an annual financial loss of US$22 400.00. A positive relationship was found between the frequency of monthly attacks and the water level of the Paraguay River, whereas a negative relationship was found between monthly attacks and proportion of adult cattle in the herd. Juveniles were taken more frequently than adults. Increased water levels caused the herd to concentrate on higher ground usually near forested areas, suggesting an increase in cattle vulnerability to predation. A greater proportion of adults in the herd may also increase the possibility for defensive behavior, likely resulting in greater protection of younger cattle. Understanding the factors that predispose cattle to predation by big cats contributes to the establishment of management strategies that may reduce losses and, ultimately, conflict.
Serum 25‐hydroxyvitamin D increases with NB‐UVB and UVA/UVB phototherapy in patients with psoriasis and atopic dermatitis in Western Australia
Authors: Le Patricia , Tu Jenny , Gebauer Kurt , Brown Suzanne 
Published: April 2015

AbstractBackground/ObjectiveThe benefit of NB‐UVB phototherapy on serum 25‐hydroxyvitamin D [25(OH)D] levels in patients with inflammatory skin conditions has been reported in the northern hemisphere. Vitamin D status is known to differ between geographical latitudes. The objective of this study was to investigate the influence of NB‐UVB and UVA/UVB phototherapy on the 25(OH)D serum levels in patients with psoriasis and atopic dermatitis in Western Australia.MethodsA total of 35 patients with psoriasis or atopic dermatitis requiring phototherapy thrice weekly for a minimum of 4 weeks were enrolled. Of these, 20 patients completed the study. Serum vitamin D levels were measured at baseline and at approximately 6 weeks into phototherapy. Data were adjusted for season, patients' age, sex, skin condition and Fitzpatrick skin phototype.ResultsThere was a statistically significant increase in serum 25(OH)D from pre‐ to post‐NB‐UVB and UVA/UVB phototherapy (P < 0.0001), with a mean raw increase of 34.6 (25) nmol/L; or 45.1 (7.5) nmol/L when adjusted for covariates. This was also true for patients receiving NB‐UVB phototherapy with a baseline vitamin D of <80 nmol/L (P < 0.05) and >80 nmol/L (P < 0.004).ConclusionsNB‐UVB and UVA/UVB phototherapy significantly increased 25(OH)D serum level in patients with psoriasis and atopic dermatitis in Western Australia. Our study cohort had a higher baseline vitamin D level and a lower percentage increase of serum 25(OH)D post‐phototherapy than the increases reported in the literature from cohorts in the northern hemisphere.
Priming with DNA Enhances Considerably the Immunogenicity of hCG β‐LTB Vaccine
Authors: Nand Kripa N. , Gupta Jagdish C. , Panda Amulya K. , Jain Swatantra K. , Talwar Gursaran P. 
Published: April 2015

ProblemNecessity to elicit antibody response above the protective threshold titres by sexually active women immunized to prevent pregnancy.Method of studyRecombinant hCGβ‐LTB vaccine expressed as both DNA and protein. Balb C mice employed for testing immunogenicity.ResultsNecessity to give three primary injections of the vaccine to elicit proper antibody response. Immunization twice with DNA form of the vaccine at fortnightly interval followed by the protein elicits a distinctly higher antibody response than proteinic vaccine alone. Antibodies generated are bio‐effective against hCG.ConclusionImmunization with the DNA form of the recombinant hCGβ‐LTB vaccine twice at fortnightly interval followed by the proteinic form of the vaccine induces distinctly higher antibody response.
A Microcontroller Platform for the Rapid Prototyping of Functional Electrical Stimulation‐Based Gait Neuroprostheses
Authors: Luzio de Melo Paulo , da Silva Miguel Tavares , Martins Jorge , Newman Dava 
Published: April 2015

AbstractFunctional electrical stimulation (FES) has been used over the last decades as a method to rehabilitate lost motor functions of individuals with spinal cord injury, multiple sclerosis, and post‐stroke hemiparesis. Within this field, researchers in need of developing FES‐based control solutions for specific disabilities often have to choose between either the acquisition and integration of high‐performance industry‐level systems, which are rather expensive and hardly portable, or develop custom‐made portable solutions, which despite their lower cost, usually require expert‐level electronic skills. Here, a flexible low‐cost microcontroller‐based platform for rapid prototyping of FES neuroprostheses is presented, designed for reduced execution complexity, development time, and production cost. For this reason, the Arduino open‐source microcontroller platform was used, together with off‐the‐shelf components whenever possible. The developed system enables the rapid deployment of portable FES‐based gait neuroprostheses, being flexible enough to allow simple open‐loop strategies but also more complex closed‐loop solutions. The system is based on a modular architecture that allows the development of optimized solutions depending on the desired FES applications, even though the design and testing of the platform were focused toward drop foot correction. The flexibility of the system was demonstrated using two algorithms targeting drop foot condition within different experimental setups. Successful bench testing of the device in healthy subjects demonstrated these neuroprosthesis platform capabilities to correct drop foot.
Calcitonin gene‐related peptide in the joint: contributions to pain and inflammation
Authors: Walsh David A. , Mapp Paul I. , Kelly Sara 
Published: April 2015

AbstractArthritis is the commonest cause of disabling chronic pain, and both osteoarthritis (OA) and rheumatoid arthritis (RA) remain major burdens on both individuals and society. Peripheral release of calcitonin gene‐related peptide (CGRP) contributes to the vasodilation of acute neurogenic inflammation. Contributions of CGRP to the pain and inflammation of chronic arthritis, however, are only recently being elucidated. Animal models of arthritis are revealing the molecular and pathophysiological events that accompany and lead to progression of both arthritis and pain. Peripheral actions of CGRP in the joint might contribute to both inflammation and joint afferent sensitization. CGRP and its specific receptors are expressed in joint afferents and up‐regulated following arthritis induction. Peripheral CGRP release results in activation of synovial vascular cells, through which acute vasodilatation is followed by endothelial cell proliferation and angiogenesis, key features of chronic inflammation. Local administration of CGRP to the knee also increases mechanosensitivity of joint afferents, mimicking peripheral sensitization seen in arthritic joints. Increased mechanosensitivity in OA knees and pain behaviour can be reduced by peripherally acting CGRP receptor antagonists. Effects of CGRP pathway blockade on arthritic joint afferents, but not in normal joints, suggest contributions to sensitization rather than normal joint nociception. CGRP therefore might make key contributions to the transition from normal to persistent synovitis, and the progression from nociception to sensitization. Targeting CGRP or its receptors within joint tissues to prevent these undesirable transitions during early arthritis, or suppress them in established disease, might prevent persistent inflammation and relieve arthritis pain.
Identity appropriateness and the structure of the theory of planned behaviour
Authors: Case Philippa , Sparks Paul , Pavey Louisa 
Published: April 2015

In contrast to the cost‐benefit, utility‐based approach to decision‐making implicit in models such as the theory of planned behaviour (TPB), the logic of appropriateness (March, 1994. A Primer on Decision Making: How decisions happen. New York, NY: The Free Press) describes decision‐making in terms of heuristic decision rules that involve matching identities to situations. This research is the first to apply the logic of appropriateness in conjunction with the theoretical structure of the TPB and assessed whether a measure of identity appropriateness might independently predict adults' intentions to engage in binge drinking. In Study 1, participants (N = 197) completed questionnaires assessing attitudes, subjective norm, perceived behavioural control, past behaviour, and identity appropriateness in relation to binge drinking. Path analysis revealed an independent predictive effect of identity appropriateness on intentions in addition to an indirect effect via attitudes. In Study 2 (N = 179), a prospective measure of behaviour was included in a similar study: Identity appropriateness again predicted intentions independently of the extended TPB predictors. It was again also found to be a strong predictor of attitudes. We suggest that the notion of identity appropriateness may assist in explaining the capacity of measures of self‐identity to predict people's behavioural intentions.
Tectonic heritage in drainage pattern and dynamics: the case of the French South Alpine Foreland Basin (ca. 45–20 Ma)
Authors: Grosjean Anne‐Sabine , Pittet Bernard , Gardien Véronique , Leloup Philippe‐Hervé , Mahéo Gweltaz , Barraza Garcia Jackeline 
Published: April 2015

AbstractThe spatial and temporal organization of depositional environments in drainage networks of foreland basins reflect the tectonic and erosional dynamics associated with the development of mountain belts. We provide field evidences for the initiation and evolution of a complex drainage system in the French South Alpine Foreland Basin related to Western Alps exhumation. Sedimentological and structural analyses of the Eocene–Early Miocene succession were investigated in the (1) Argens/Peyresq, (2) Barrême/Blieux/Taulanne and (3) Montmaur/St‐Disdier sectors. Combined with the existing structural data set, we propose a new model that integrates the regional tectonic activity, the palaeovalley orientation and their dynamics through time. The Eocene–Miocene deposits clearly show the existence of N–S‐oriented palaeovalleys. The systematic presence of early NE–SW‐ to N–S‐oriented strike‐slip and extensional faults in the palaeovalleys suggests that these tectonic structures were responsible for the formation of the initial N–S‐oriented basin‐floor topographies. The vertical offset of the strike‐slip faults induced sufficient accommodation space for the Cenozoic sedimentation since the Middle Eocene. It implies the creation of N–S‐oriented palaeovalleys during the northward Pyrenean‐Provençal phase, pre‐dating westward Alpine compression. Later, the Oligocene Alpine tectonic phase induced drainage expansion toward the orogenic wedge and the erosion of the exhumed internal massifs by transverse streams. The establishment of new connections between the old topographic lows formed a longitudinal drainage pattern that remains the locus of deposition in a regional sedimentary routing system. In this model, former strike‐slip faults correspond to weakness zones overprinted by the westward Alpine shortening that allowed the formation of the modern piggyback basin structure of the foreland and the long‐time preservation of the palaeovalley geometry.