bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mucosal‐associated invariant T cells in autoimmunity, immune‐mediated diseases and airways disease
Authors: Hinks Timothy S. C. 
Published: January 2016

SummaryMucosal‐associated invariant T (MAIT) cells are a novel class of innate‐like T cells, expressing a semi‐invariant T‐cell receptor (TCR) and able to recognize small molecules presented on the non‐polymorphic MHC‐related protein 1. Their intrinsic effector‐memory phenotype, enabling secretion of pro‐inflammatory cytokines, and their relative abundance in humans imply a significant potential to contribute to autoimmune processes. However, as MAIT cells were unknown until recently and specific immunological tools were unavailable, little is known of their roles in disease. Here I review observations from clinical studies and animal models of autoimmune and immune‐mediated diseases including the roles of MAIT cells in systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease and airways diseases. MAIT cell deficiencies are frequently observed in peripheral blood, and at sites of disease such as the airways in asthma. However, MAIT cells have a specific sensitivity to suppression by therapeutic corticosteroids that may confound many of these observations, as may the tendency of the surface marker CD161 to activation‐induced down‐regulation. Nonetheless, the dependence on bacteria for the development of MAIT cells suggests a potentially important protective role linking the influences of early life microbial exposures and subsequent development of autoimmunity. Conversely, MAIT cells could contribute to chronic inflammation either through TCR‐independent activation, or potentially by TCR recognition of as yet undiscovered ligands. Future research will be greatly facilitated by the immunological tools that are now available, including murine genetic models and human and murine specific tetramers.
Treating substance abuse and mental health issues as ‘mutually‐exclusive’ entities: Best practice or an outmoded approach to intervention?
Authors: Webber Adrian , Clark Jane , Kelly David 
Published: January 2016

AbstractAddressing the psychological distress of individuals experiencing substance use disorders has too often been relegated to the ‘too hard basket’, leaving those affected with little choice but to receive treatments aimed solely at addressing their drug and alcohol issues. Conversely, individuals receiving support for psychological issues are often underdiagnosed with regards to any comorbid substance misuse problems. In fact, to date, no definitive treatment model exists that gives equal focus to the treatment of both psychological well‐being and substance‐related addictions. This is not to suggest, however, that existing treatment programmes for substance misuse are not impacting positively on clients’ mental health, rather that further research is needed in order to determine what it is that is supporting such improvements. The aim of this study, therefore, was to address this imbalance by examining the correlation between substance dependence and psychological well‐being. Using a descriptive correlation design, the Severity of Dependence and Kessler 10 scales were administered to 37 inpatient and outpatient clients at a rural drug and alcohol rehabilitation service, at intake and 2 months into treatment. Data were analysed using descriptive statistics and paired‐samples t‐tests. Positive correlative factors of improvement between substance dependence and psychological well‐being were found for both groups. In light of these findings, the authors recommend that future research be undertaken to investigate the causal factors for this correlation.
The other side of ranking schemes: generating weights for specified outcomes
Authors: Bougnol Marie‐Laure , Dulá Jose H. 
Published: January 2016

AbstractThis paper treats the problem of how to determine weights in a ranking, which will cause a selected entity to attain the highest possible position. We establish that there are two types of entities in a ranking scheme: those which can be ranked as number one and those which cannot. These two types of entities can be identified using the “ranking hull” of the data; a polyhedral set that envelops the data. Only entities with data points on the boundary of this hull can attain the number one position. There are no weights that will make an entity whose data point is in the interior of the hull to ever attain the number one position. We deal with these two types of entities separately. In the first case, we propose an approach for finding a set of weights that, under special conditions, will result in a selected entity achieving the top of the ranking without ties and without ignoring any of the attributes. For the second category of entities, we devise a procedure to guarantee that these entities will attain their highest possible position in the ranking. The first case will require using interior point methods to solve a linear program (LP). The second case involves a binary mixed integer formulation. These two mathematical programs were tested on data from a well‐known university ranking.
Super SBI Dynamic Network DEA approach to measuring efficiency in the provision of public services
Authors: Moreno Plácido , Lozano Sebastián 
Published: January 2016

AbstractThe current financial crisis has had a significant impact on European governments’ finances and has led to a series of government interventions to control the public debt and deficit. Therefore, the aim of this paper is to identify inefficiencies in the management of public finance, such as overspending, unreasonable debt, and excessive taxes, while maintaining the same level of social welfare. Thus, we propose a two‐stage network data envelopment analysis (DEA) structure that accounts for both allocation of the public budget and transformation of government expenditures into services to the people and the economy. Financial assets, debt, and employment have been included as carryover activities over successive periods of time. Finally, a super‐efficiency approach allows discriminating between the efficient European governments. We have applied the proposed approach to the period from fiscal years 2008 to 2012. Results show that not only high‐deficit countries, but also major countries such as Germany and France have performed poorly. The slack‐based measure of inefficiency (SBI) metrics, whose directional vector components are defined as the yearly national GDP, point out the feasible reductions in taxes and debt issuances, along with feasible targets for government expenditure.
Tuning of shortening speed in coleoid cephalopod muscle: no evidence for tissue‐specific muscle myosin heavy chain isoforms
Authors: Shaffer Justin F. , Kier William M. 
Published: January 2016

AbstractThe contractile protein myosin II is ubiquitous in muscle. It is widely accepted that animals express tissue‐specific myosin isoforms that differ in amino acid sequence and ATPase activity in order to tune muscle contractile velocities. Recent studies, however, suggested that the squid Doryteuthis pealeii might be an exception; members of this species do not express muscle‐specific myosin isoforms, but instead alter sarcomeric ultrastructure to adjust contractile velocities. We investigated whether this alternative mechanism of tuning muscle contractile velocity is found in other coleoid cephalopods. We analyzed myosin heavy chain transcript sequences and expression profiles from muscular tissues of a cuttlefish, Sepia officinalis, and an octopus, Octopus bimaculoides, to determine if these cephalopods express tissue‐specific myosin heavy chain isoforms. We identified transcripts of four and six different myosin heavy chain isoforms in S. officinalis and O. bimaculoides muscular tissues, respectively. Transcripts of all isoforms were expressed in all muscular tissues studied, and thus S. officinalis and O. bimaculoides do not appear to express tissue‐specific muscle myosin isoforms. We also examined the sarcomeric ultrastructure in the transverse muscle fibers of the arms of O. bimaculoides and the arms and tentacles of S. officinalis using transmission electron microscopy and found that the fast contracting fibers of the prey capture tentacles of S. officinalis have shorter thick filaments than those found in the slower transverse muscle fibers of the arms of both species. It thus appears that coleoid cephalopods, including the cuttlefish and octopus, may use ultrastructural modifications rather than tissue‐specific myosin isoforms to adjust contractile velocities.
Accuracy of genomic prediction using imputed whole‐genome sequence data in white layers
Authors: Heidaritabar M. , Calus M.P.L. , Megens H‐J. , Vereijken A. , Groenen M.A.M. , Bastiaansen J.W.M. 
Published: January 2016

SummaryThere is an increasing interest in using whole‐genome sequence data in genomic selection breeding programmes. Prediction of breeding values is expected to be more accurate when whole‐genome sequence is used, because the causal mutations are assumed to be in the data. We performed genomic prediction for the number of eggs in white layers using imputed whole‐genome resequence data including ~4.6 million SNPs. The prediction accuracies based on sequence data were compared with the accuracies from the 60 K SNP panel. Predictions were based on genomic best linear unbiased prediction (GBLUP) as well as a Bayesian variable selection model (BayesC). Moreover, the prediction accuracy from using different types of variants (synonymous, non‐synonymous and non‐coding SNPs) was evaluated. Genomic prediction using the 60 K SNP panel resulted in a prediction accuracy of 0.74 when GBLUP was applied. With sequence data, there was a small increase (~1%) in prediction accuracy over the 60 K genotypes. With both 60 K SNP panel and sequence data, GBLUP slightly outperformed BayesC in predicting the breeding values. Selection of SNPs more likely to affect the phenotype (i.e. non‐synonymous SNPs) did not improve the accuracy of genomic prediction. The fact that sequence data were based on imputation from a small number of sequenced animals may have limited the potential to improve the prediction accuracy. A small reference population (n = 1004) and possible exclusion of many causal SNPs during quality control can be other possible reasons for limited benefit of sequence data. We expect, however, that the limited improvement is because the 60 K SNP panel was already sufficiently dense to accurately determine the relationships between animals in our data.
Not all Treaties are Created Equal: The Effects of Treaty Changes on Legislative Efficiency in the EU
Authors: Bølstad Jørgen , Cross James P. 
Published: January 2016

AbstractOne of the key motives behind recent reforms of the EU's legislative process has been to increase efficiency. This study examines whether the Amsterdam, Nice and Lisbon treaties have successfully increased the speed with which the EU creates new laws. An interrupted time series approach is utilized to detect the total effects of treaty change on the decision‐making process. This study thus complements existing research on the effects of decision‐making rules, by employing a design more robust to the challenge of endogeneity. The findings suggest that the Amsterdam treaty was very successful at increasing legislative efficiency. In contrast, the Nice treaty does not appear to have had a notable impact, and, more interestingly, neither does the Lisbon treaty.
Evolutionary history of the little fire ant Wasmannia auropunctata before global invasion: inferring dispersal patterns, niche requirements and past and present distribution within its native range
Authors: Chifflet L. , Rodriguero M. S. , Calcaterra L. A. , Rey O. , Dinghi P. A. , Baccaro F. B. , Souza J. L. P. , Follett P. , Confalonieri V. A. 
Published: January 2016

AbstractThe evolutionary history of invasive species within their native range may involve key processes that allow them to colonize new habitats. Therefore, phylogeographic studies of invasive species within their native ranges are useful to understand invasion biology in an evolutionary context. Here we integrated classical and Bayesian phylogeographic methods using mitochondrial and nuclear DNA markers with a palaeodistribution modelling approach, to infer the phylogeographic history of the invasive ant Wasmannia auropunctata across its native distribution in South America. We discuss our results in the context of the recent establishment of this mostly tropical species in the Mediterranean region. Our Bayesian phylogeographic analysis suggests that the common ancestor of the two main clades of W. auropunctata occurred in central Brazil during the Pliocene. Clade A would have differentiated northward and clade B southward, followed by a secondary contact beginning about 380 000 years ago in central South America. There were differences in the most suitable habitats among clades when considering three distinct climatic periods, suggesting that genetic differentiation was accompanied by changes in niche requirements, clade A being a tropical lineage and clade B a subtropical and temperate lineage. Only clade B reached more southern latitudes, with a colder climate than that of northern South America. This is concordant with the adaptation of this originally tropical ant species to temperate climates prior to its successful establishment in the Mediterranean region. This study highlights the usefulness of exploring the evolutionary history of invasive species within their native ranges to better understand biological invasions.
The role of selection and historical factors in driving population differentiation along an elevational gradient in an island bird
Authors: Bertrand J. A. M. , Delahaie B. , Bourgeois Y. X. C. , Duval T. , García‐Jiménez R. , Cornuault J. , Pujol B. , Thébaud C. , Milá B. 
Published: January 2016

AbstractAdaptation to local environmental conditions and the range dynamics of populations can influence evolutionary divergence along environmental gradients. Thus, it is important to investigate patterns of both phenotypic and genetic variations among populations to reveal the respective roles of these two types of factors in driving population differentiation. Here, we test for evidence of phenotypic and genetic structure across populations of a passerine bird (Zosterops borbonicus) distributed along a steep elevational gradient on the island of Réunion. Using 11 microsatellite loci screened in 401 individuals from 18 localities distributed along the gradient, we found that genetic differentiation occurred at two spatial levels: (i) between two main population groups corresponding to highland and lowland areas, respectively, and (ii) within each of these two groups. In contrast, several morphological traits varied gradually along the gradient. Comparison of neutral genetic differentiation (FST) and phenotypic differentiation (PST) showed that PST largely exceeds FST at several morphological traits, which is consistent with a role for local adaptation in driving morphological divergence along the gradient. Overall, our results revealed an area of secondary contact midway up the gradient between two major, cryptic, population groups likely diverged in allopatry. Remarkably, local adaptation has shaped phenotypic differentiation irrespective of population history, resulting in different patterns of variation along the elevational gradient. Our findings underscore the importance of understanding both historical and selective factors when trying to explain variation along environmental gradients.
A new species of philometrid parasite (Nematoda, Philometridae) and histopathological lesions in juvenile whitemouth croakers, Micropogonias furnieri (Desmarest)
Authors: Montes M M , Plaul S E , Martorelli S R 
Published: January 2016

AbstractA new species of nematode parasite, Philometroides tahieli sp. nov. is described. The juvenile whitemouth croaker, Micropogonias furnieri Desmarest, was collected during the spring and summer of the years 2008–2010 from estuarial environments of Argentina. During investigations of the parasite fauna a nematode encapsulated in the musculature of the operculum was found. The nematodes were removed from the host's muscle tissue and slide‐mounted in lactophenol solution to clarify the specimens. Opercular muscle with the parasite was processed for histopathological examination. Philometroides tahieli sp. nov. can be identified by the location of gravid females in the host, presence of anterior oesophageal bulb, bosses on the surface of the body, presence of transversal mounds and 14 cephalic papillae in two circular rows. The pathogenicity of the parasite is low in the natural environment, but lesions are consistent with a chronic process. The appearance of caseous necrosis suggests the presence of a locally acting substance. Philometroides tahieli sp. nov. is the second species of this genera described from brackish waters, and since the discovery of Philometroides maplestoni in 1928, is the first species of this genus recorded for South America.
Morphological diversity of Paramoeba perurans trophozoites and their interaction with Atlantic salmon, Salmo salar L., gills
Authors: Wiik‐Nielsen J , Mo T A , Kolstad H , Mohammad S N , Hytterød S , Powell M D 
Published: January 2016

AbstractAmoebic gill disease (AGD) caused by the ectoparasite Paramoeba perurans affects several cultured marine fish species worldwide. In this study, the morphology and ultrastructure of P. perurans in vitro and in vivo was investigated using scanning and transmission electron microscopy (SEM and TEM, respectively). Amoebae cultures contained several different morphologies ranging from a distinct rounded cell structure and polymorphic cells with pseudopodia of different lengths and shapes. SEM studies of the gills of AGD‐affected Atlantic salmon, Salmo salar L., revealed the presence of enlarged swellings in affected gill filaments and fusion of adjacent lamellae. Spherical amoebae appeared to embed within the epithelium, and subsequently leave hemispherical indentations with visible fenestrations in the basolateral surface following their departure. These fenestrated structures corresponded to the presence of pseudopodia which could be seen by TEM to penetrate into the epithelium. The membrane–membrane interface contained an amorphous and slightly fibrous matrix. This suggests the existence of cellular glycocalyces and a role for extracellular products in mediating pathological changes in amoebic gill disease.
Essential oils to control ichthyophthiriasis in pacu, Piaractus mesopotamicus (Holmberg): special emphasis on treatment with Melaleuca alternifolia
Authors: Valladão G M R , Gallani S U , Ikefuti C V , da Cruz C , Levy‐Pereira N , Rodrigues M V N , Pilarski F 
Published: January 2016

AbstractIn vitro effect of the Melaleuca alternifolia, Lavandula angustifolia and Mentha piperita essential oils (EOs) against Ichthyophthirius multifiliis and in vivo effect of M. alternifolia for treating ichthyophthiriasis in one of the most important South American fish, Piaractus mesopotamicus (Holmberg), were evaluated. The in vitro test consisted of three EOs, each at concentrations of 57 μL L−1, 114 μL L −1, 227 μL L−1 and 455 μL L −1, which were assessed once an hour for 4 h in microtitre plates (96 wells). The in vitro results demonstrated that all tested EOs showed a cytotoxic effect against I. multifiliis compared to control groups (P < 0.05). The in vivo treatment for white spot disease was performed in a bath for 2 h day−1 for 5 days using the M. alternifolia EO (50 μL L −1). In this study, 53.33% of the fish severely infected by I. multifiliis survived after the treatment with M. alternifolia (50 μL L −1) and the parasitological analysis has shown an efficacy of nearly 100% in the skin and gills, while all the fish in the control group died. Furthermore, the potential positive effect of M. alternifolia EO against two emergent opportunistic bacteria in South America Edwardsiella tarda and Citrobacter freundii was discussed.
Development, validation and implementation of a quantitative food frequency questionnaire to assess habitual vitamin D intake
Authors: Kiely M. , Collins A. , Lucey A. J. , Andersen R. , Cashman K. D. , Hennessy Á. 
Published: January 2016

AbstractBackgroundA well‐designed, validated quantitative food frequency questionnaire (FFQ) could offer an efficient and cost‐effective method for assessing habitual vitamin D intake. The present study aimed to describe the development, validation and implementation of a vitamin D FFQ.MethodsNational food consumption survey data obtained from Irish adults (18–64 years) were used to identify foods that contribute 95% of vitamin D intake. A winter‐based validation study was carried out for the resulting FFQ in 120 females, including 98 women [mean (SD) 65.0 (7.3) years] and 22 girls [12.2 (0.8) years], using a 14‐day diet history (DH) as a comparator. Serum 25(OH)D concentrations were analysed. Validity coefficients were calculated using the method of triads. Cross‐classification and Bland–Altman analysis were also performed.ResultsMedian (interquartile range) vitamin D intakes (including the contribution from nutritional supplements) were 5.4 (3.7) and 3.7 (5.9) μg day−1 from the FFQ and DH, respectively and intakes of vitamin D from food sources were 3.6 (3.1) and 2.4 (2.2) μg day−1. The FFQ and DH classified 86% and 87% of individuals into the same and adjacent thirds of wintertime serum 25(OH)D status, respectively. There was a strong association (r = 0.71, P < 0.0001) and no significant systematic or proportional bias observed for the difference between estimates from the FFQ and DH. The validity coefficient for the FFQ was 0.92 (95% confidence interval = 0.80–0.97). Repeatability analysis (n = 56) performed 6–12 months later showed no significant difference in estimates of vitamin D between administrations.ConclusionsThe data obtained in the present study indicate high validity and good reproducibility of a short, interviewer‐administered FFQ for vitamin D.
Medicinal and cosmetics soap production from Jatropha oil
Authors: Shahinuzzaman M. , Yaakob Zahira , Moniruzzaman M. 
Published: January 2016

SummarySoap is the most useful things which we use our everyday life in various cleansing and cosmetics purposes. Jatropha oil is nonedible oil which has more benefits to soap making. It has also cosmetics and medicinal properties. But the presence of toxic Phorbol esters in Jatropha oil is the main constrains to use it. So it is necessary to search a more suitable method for detoxifying the Jatropha oil before the use as the main ingredient of soap production. This review implies a more suitable method for removing phorbol esters from Jatropha oil. Several parameters such as the % yield of pure Jatropha oil soap, TFM value of soap, total alkali content, free caustic alkalinity content, pH, the antimicrobial activity, and CMC value of general soap should be taken into consideration for soap from detoxified Jatropha oil.