bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing effects of cholera vaccination in the presence of interference
Authors: Perez‐Heydrich Carolina , Hudgens Michael G. , Halloran M. Elizabeth , Clemens John D. , Ali Mohammad , Emch Michael E. 
Published: May 2014

SummaryInterference occurs when the treatment of one person affects the outcome of another. For example, in infectious diseases, whether one individual is vaccinated may affect whether another individual becomes infected or develops disease. Quantifying such indirect (or spillover) effects of vaccination could have important public health or policy implications. In this article we use recently developed inverse‐probability weighted (IPW) estimators of treatment effects in the presence of interference to analyze an individually‐randomized, placebo‐controlled trial of cholera vaccination that targeted 121,982 individuals in Matlab, Bangladesh. Because these IPW estimators have not been employed previously, a simulation study was also conducted to assess the empirical behavior of the estimators in settings similar to the cholera vaccine trial. Simulation study results demonstrate the IPW estimators can yield unbiased estimates of the direct, indirect, total, and overall effects of vaccination when there is interference provided the untestable no unmeasured confounders assumption holds and the group‐level propensity score model is correctly specified. Application of the IPW estimators to the cholera vaccine trial indicates the presence of interference. For example, the IPW estimates suggest on average 5.29 fewer cases of cholera per 1000 person‐years (95% confidence interval 2.61, 7.96) will occur among unvaccinated individuals within neighborhoods with 60% vaccine coverage compared to neighborhoods with 32% coverage. Our analysis also demonstrates how not accounting for interference can render misleading conclusions about the public health utility of vaccination.
Partial correlation matrix estimation using ridge penalty followed by thresholding and re‐estimation
Authors: Ha Min Jin , Sun Wei 
Published: May 2014

SummaryMotivated by the problem of construction of gene co‐expression network, we propose a statistical framework for estimating high‐dimensional partial correlation matrix by a three‐step approach. We first obtain a penalized estimate of a partial correlation matrix using ridge penalty. Next we select the non‐zero entries of the partial correlation matrix by hypothesis testing. Finally we re‐estimate the partial correlation coefficients at these non‐zero entries. In the second step, the null distribution of the test statistics derived from penalized partial correlation estimates has not been established. We address this challenge by estimating the null distribution from the empirical distribution of the test statistics of all the penalized partial correlation estimates. Extensive simulation studies demonstrate the good performance of our method. Application on a yeast cell cycle gene expression data shows that our method delivers better predictions of the protein–protein interactions than the Graphic Lasso.
The use of ubiquitous sensor technology in evaluating student thought process during practical operations for improving student technical and creative skills
Authors: Jou Min , Wang Jingying 
Published: May 2014

AbstractThis study investigated a Ubiquitous Sensor System (USS) that we developed to assess student thought process during practical lessons on a real‐time basis and to provide students with a reflective learning environment. Behavioral curves and data obtained by the USS would help students understand where they had made mistakes during practical lessons and the exact times when incorrect process parameters were observed. This research was conducted during a course on manufacturing. The results indicated that the proposed USS was effective in improving student analysis and evaluation skills in manufacturing thinking, as well as the three psychomotor skills of guided response, mechanism and complex overt response. Student psychomotor skills also gained an overall improvement. Results also showed that improvements in student thought process also helped in the learning of psychomotor skills and that the USS helped improve the clarity of student thought process during practical operations. The improved clarity of thought allowed students to understand the reasons behind their thought process for them to make the necessary logical deductions. Through repeated reflection and practice, students would then be able to create works with personal creative elements.
The Incredible Years Parent–Toddler Programme and parental language: a randomised controlled trial
Authors: Gridley N. , Hutchings J. , Baker‐Henningham H. 
Published: May 2014

AbstractBackgroundParental language is associated with children's later language development. Parenting programmes, based on social learning theory, enhance a range of parenting behaviours, yet there is limited evidence for their effect on parental language.AimTo assess the benefits of a behavioural‐based parenting programme, which features components of language and communication, to enhance parental language.MethodParents of toddlers, aged 12 to 36 months, were recruited from eight Flying Start early intervention centres across Wales. Participants were randomised 2:1 either to a parenting programme (n = 60) or to a wait‐list control group (n = 29). Researchers were blind to participant allocation throughout the trial. Fifteen‐minute video‐recorded observations of parents and children interacting during free‐play, both at a pre‐intervention and at 6‐month follow‐up, provided the data for the study. Five observed measures of parental language were assessed; quantity and variety, encouraging, critical, child‐led and parent led interactions.InterventionThe Incredible Years Parent–Toddler Programme (IYPTP) is a 12‐week group‐based behavioural intervention that teaches effective relationship and behavioural management skills including social, emotional and persistence coaching to enable parents to better support their children's development.ResultsOf 89 dyads that completed pre‐intervention assessments 81 (54 intervention and 27 control) met the criteria for the current study. Intention to treat analysis indicated that child‐led language interactions significantly benefited from the intervention [regression coefficient (B) = −1.44, 95% confidence intervals (CI) = −2.59 to −0.29, P = 0.015, effect size (ES) = 0.47] and a positive trend for encouraging language in favour of the intervention sample was evident. Per‐protocol sample analysis replicated these findings with encouraging language reaching statistical significance (B = 1.07, 95% CI = 0.11 to 2.03, P = 0.03, ES = 0.52). No further benefits were evident.ConclusionsThe IYPTP has limited evidence as an effective programme for enhancing some aspects of parental language.
Down-regulated expression of monocyte/macrophage major histocompatibility complex receptors in human and mouse monocytes by expression of their ligands
Authors: Yamana H , Tashiro-Yamaji J , Hayashi M , Maeda S , Shimizu T , Tanigawa N , Uchiyama K , Kubota T , Yoshida R 
Published: May 2014

SummaryMouse monocyte/macrophage major histocompatibility complex (MHC) receptor 1 (MMR1; or MMR2) specific for H-2Dd (or H-2Kd) molecules is expressed on monocytes from non-H-2Dd (or non-H-2Kd), but not those from H-2Dd (or H-2Kd), inbred mice. The MMR1 and/or MMR2 is essential for the rejection of H-2Dd- and/or H-2Kd-transgenic mouse skin onto C57BL/6 (H-2Db Kb) mice. Recently, we found that human leucocyte antigen (HLA)-B44 was the sole ligand of human MMR1 using microbeads that had been conjugated with 80 types of HLA class I molecules covering 94·2% (or 99·4%) and 92·4% (or 96·2%) of HLA-A and B molecules of Native Americans (or Japanese), respectively. In the present study, we also explored the ligand specificity of human MMR2 using microbeads. Microbeads coated with HLA-A32, HLA-B13 or HLA-B62 antigens bound specifically to human embryonic kidney (HEK)293T or EL-4 cells expressing human MMR2 and to the solubilized MMR2-green fluorescent protein (GFP) fusion protein; and MMR2+ monocytes from a volunteer bound HLA-B62 molecules with a Kd of 8·7 × 10−9 M, implying a three times down-regulation of MMR2 expression by the ligand expression. H-2Kd (or H-2Dd) transgene into C57BL/6 mice down-regulated not only MMR2 (or MMR1) but also MMR1 (or MMR2) expression, leading to further down-regulation of MMR expression. In fact, monocytes from two (i.e. MMR1+/MMR2+ and MMR1–/MMR2–) volunteers bound seven to nine types of microbeads among 80, indicating ≤ 10 types of MMR expression on monocytes.The physiological role of constitutive MMRs on monocytes possibly towards allogeneic (e.g. fetal) cells in the blood appears to be distinct from that of inducible MMRs on macrophages toward allografts in tissue.
Evolution of an Innovative Approach to the Delivery of In‐Person Training in the Responsible Conduct of Research
Authors: Schmidt Karen L. , Yasko Laurel , Green Michael , Alexander Jane , Ryan Christopher 
Published: May 2014

AbstractThe responsible conduct of research (RCR) Center is an innovative, workshop‐based approach to research ethics education at the University of Pittsburgh. A flexibly scheduled program of workshops combines the benefits of traditional case–based discussion and in‐person instruction with greater accessibility and a broader disciplinary reach. Essential features of the program include a rotating schedule of independent workshops with separate registration, expert speakers, and a dedicated program director position. At an institutional level, this novel response to National Institutes of Health‐mandated training requirements increases access to a wide range of interactive RCR training programs and promotes interdisciplinary conversations on research ethics that involves investigators, trainees, and the research community at large.
A critical review of public health interventions aimed at reducing alcohol consumption and/or increasing knowledge among pregnant women
Authors: Crawford‐Williams Fiona , Fielder Andrea , Mikocka‐Walus Antonina , Esterman Adrian 
Published: May 2014

AbstractIssuesIt is well established that alcohol can cross the placenta to the fetus and can affect both physical and psychological development of the infant; however, many women continue to drink during pregnancy. It is therefore important to determine whether interventions can be successful in reducing alcohol consumption among pregnant women. Past reviews have investigated the effectiveness of clinical interventions in reducing alcohol consumption in pregnancy; however, the aim of the current review was to focus on the effectiveness of public health interventions.ApproachA critical literature review was conducted by searching several electronic databases using key words such as ‘pregnancy’, ‘alcohol’, ‘interventions’ and ‘public health’. Studies were included if they utilised a public health intervention and included alcohol consumption or levels of knowledge as an outcome measure.Key FindingsSeven studies were included in the review. Interventions included multimedia and educational interventions. Improvements in knowledge were reported in six studies, whereas one study found contradictory results. Four studies used alcohol consumption rates as an outcome measure, and although a reduction in consumption was reported, the results were non‐significant.ImplicationsThe effectiveness of public health interventions that aim to increase awareness and reduce alcohol consumption among pregnant women cannot be assessed because of the paucity of studies.ConclusionsThe results of this critical review emphasise a lack of evidence and highlight the need for further evaluation research on this topic.[Crawford‐Williams F, Fielder A, Mikocka‐Walus A, Esterman A. A critical review of public health interventions aimed at reducing alcohol consumption and/or increasing knowledge among pregnant women. Drug Alcohol Rev 2015;34:154–61]
Adopting a spatially explicit perspective to study the mysterious fairy circles of Namibia
Authors: Getzin Stephan , Wiegand Kerstin , Wiegand Thorsten , Yizhaq Hezi , von Hardenberg Jost , Meron Ehud 
Published: May 2014

The mysterious ‘fairy circles’ are vegetation‐free discs that cover vast areas along the pro‐Namib Desert. Despite 30 yr of research their origin remains unknown. Here we adopt a novel approach that focuses on analysis of the spatial patterns of fairy circles obtained from representative 25‐ha aerial images of north‐west Namibia. We use spatial point pattern analysis to quantify different features of their spatial structures and then critically inspect existing hypotheses with respect to their ability to generate the observed circle patterns. Our working hypothesis is that fairy circles are a self‐organized vegetation pattern. Finally, we test if an existing partial‐differential‐equation model, that was designed to describe vegetation pattern formation, is able to reproduce the characteristic features of the observed fairy circle patterns. The model is based on key‐processes in arid areas such as plant competition for water and local resource‐biomass feedbacks.The fairy circles showed at all three study areas the same regular spatial distribution patterns, characterized by Voronoi cells with mostly six corners, negative correlations in their size up to a distance of 13 m, and remarkable homogeneity over large spatial scales. These results cast doubts on abiotic gas‐leakage along geological lines or social insects as causal agents of their origin. However, our mathematical model was able to generate spatial patterns that agreed quantitatively in all of these features with the observed patterns. This supports the hypothesis that fairy circles are self‐organized vegetation patterns that emerge from positive biomass‐water feedbacks involving water transport by extended root systems and soil‐water diffusion. Future research should search for mechanisms that explain how the different hypotheses can generate the patterns observed here and test the ability of self‐organization to match the birth‐ and death dynamics of fairy circles and their regional patterns in the density and size with respect to environmental gradients.
Micro‐geographical scale variation inDrosophila melanogasterlarval olfactory behaviour is associated with host fruit heterogeneity
Authors: Satorre I. , Fanara J.J. , Lavagnino N.J. 
Published: May 2014

AbstractOrganisms utilize environmental cues to deal with heterogeneous environments. In this sense, behaviours that mediate interactions between organisms and their environment are complex traits, especially sensitive to environmental conditions. In animals, olfaction is a critical sensory system that allows them to acquire chemical information from the environment. The genetic basis and physiological mechanisms of the olfactory system ofDrosophila melanogasterMeigen (Diptera:Drosophilidae) are well known, but the effects of ecological factors on the olfactory system have received less attention. In this study, we analysed the effect of environmental heterogeneity (different host fruits) on variation in larval olfactory behaviour in a natural population ofD. melanogaster. We generated half‐sib lines ofD. melanogasterderived from two nearby fruit plantations,Vitis viniferaL. (Vitaceae) (‘grape’) andPrunus persicaL. (Rosaceae) (‘peach’), and measured, using a simple behavioural assay, larval olfactory response to natural olfactory stimuli. Results indicate that patterns of variation for this trait depend on host fruit plantation where lines were collected. In fact, only lines derived from ‘grape’ showed phenotypic plasticity for larval olfaction, whereas a genotype*environment interaction was detected solely in lines derived from ‘peach’. Therefore, our results demonstrate the existence of genetic differences inD. melanogasterlarval olfactory behaviour at a micro‐geographical scale and also reveal that the trait studied presents a dynamic genetic architecture which is strongly influenced by the environment.
Enriched environment impacts trimethylthiazoline‐induced anxiety‐related behavior and immediate early gene expression: critical role of Crhr1
Authors: Sotnikov S. V. , Chekmareva N. Y. , Schmid B. , Harbich D. , Malik V. , Bauer S. , Kuehne C. , Markt P. O. , Deussing J. M. , Schmidt M. V. , Landgraf R. 
Published: May 2014

AbstractIt has been shown previously (Sotnikov et al., ) that mice selectively inbred for high anxiety‐related behavior (HAB) vs. low anxiety‐related behavior in the elevated plus maze differentially respond to trimethylthiazoline (TMT), a synthetic fox fecal odor. However, less is known about whether environmental factors can rescue these extreme phenotypes. Here, we found that an enriched environment (EE) provided during early adolescence induced anxiolytic effects in HAB (HAB‐EE) mice, rescuing their strong avoidance behavior induced by TMT. In a series of experiments, the contribution of maternal, juvenile and adolescent behavior to the anxiolytic effects elicited by EE was investigated. At the molecular level, using c‐fos expression mapping, we found that the activity of the medial and basolateral amygdala was significantly reduced in HAB‐EE mice after TMT exposure. We further analysed the expression of Crhr1, as its amount in the amygdala has been reported to be important for the regulation of anxiety‐related behavior after EE. Indeed, in situ hybridisation indicated significantly decreased Crhr1 expression in the basolateral and central amygdala of HAB‐EE mice. To further test the involvement of Crhr1 in TMT‐induced avoidance, we exposed conditional glutamatergic‐specific Crhr1‐knockout mice to the odor. The behavioral response of Crhr1‐knockout mice mimicked that of HAB‐EE mice, and c‐fos expression in the amygdala after TMT exposure was significantly lower compared with controls, thereby further supporting a critical involvement of Crhr1 in environmentally‐induced anxiolysis. Altogether, our results indicate that EE can rescue strong avoidance of TMT by HAB mice with Crhr1 expression in the amygdala being critically involved.
Our view of islands: Joining the values of science and society
Authors: Sides Alexandra , Davis Lloyd , Rock Jenny 
Published: May 2014

SummaryBoth the public and the scientific perception of an island's value are important in deciding its future, with regard to the levels of access, protection and funding for research. There is a popular belief that the preservation of islands equates to the slightly idiosyncratic conservation of unique remote habitats, where the value of any island is its isolation. However, by understanding how scientists use islands, a different picture emerges; islands may be seen also as integrated, or representative fragments of the world that contribute to biodiversity and scientific theory far beyond their narrow geographical boundaries. Here, we broadly review the full scope of values science places on islands. We resolve four central perspectives by which scientists view islands, based on how islands are incorporated into their research: (i) species‐level studies; (ii) island‐level studies; (iii) islands as model systems; and (iv) islands as part of a global network. Recognising this diverse value system helps enlarge our understanding of islands and reforges their importance to the public and policy makers.
The Lure of the Brand: Evidence from the European Mutual Fund Industry
Authors: Hazenberg Jan Jaap , Irek Fabian , van der Scheer Willem , Stefanova Mariela 
Published: May 2014

AbstractWe investigate the effect of the fund family's brand on mutual fund flows by using a unique data set that represents a direct assessment of the brand image of European fund providers. A superior brand image increases the sensitivity of flows to good past performance, while it protects against outflows when there is underperformance. Flows of funds of independent providers have a higher sensitivity to past performance and brand image than flows of funds of providers owned by banks or insurers. These findings highlight the importance of marketing and brand in generating growth for the fund families.
Crystal structure of calpain‐3 penta‐EF‐hand (PEF) domain – a homodimerized PEF family member with calcium bound at the fifth EF‐hand
Authors: Partha Sarathy K. , Ravulapalli Ravikiran , Allingham John S. , Campbell Robert L. , Davies Peter L. 
Published: May 2014

Calpains are Ca2+dependent intracellular cysteine proteases that cleave a wide range of protein substrates to help implement Ca2+ signaling in the cell. The major isoforms of this enzyme family, calpain‐1 and calpain‐2, are heterodimers of a large and a small subunit, with the main dimer interface being formed through their C‐terminal penta‐EF hand (PEF) domains. Calpain‐3, or p94, is a skeletal muscle‐specific isoform that is genetically linked to limb‐girdle muscular dystrophy. Biophysical and modeling studies with the PEF domain of calpain‐3 support the suggestion that full‐length calpain‐3 exists as a homodimer. Here, we report the crystallization of calpain‐3′s PEF domain and its crystal structure in the presence of Ca2+, which provides evidence for the homodimer architecture of calpain‐3 and supports the molecular model that places a protease core at either end of the elongated dimer. Unlike other calpain PEF domain structures, the calpain‐3 PEF domain contains a Ca2+ bound at the EF5‐hand used for homodimer association. Three of the four Ca2+‐binding EF‐hands of the PEF domains are concentrated near the protease core, and have the potential to radically change the local charge within the dimer during Ca2+ signaling. Examination of the homodimer interface shows that there would be steric clashes if the calpain‐3 large subunit were to try to pair with a calpain small subunit.DatabaseStructural data are available in the Protein Data Bank database under accession number 4OKH.Structured digital abstractCalpain-3 and Calpain-3 bind by x-ray crystallography (View interaction)
A novel geranylgeranyl reductase from the methanogenic archaeon Methanosarcina acetivorans displays unique regiospecificity
Authors: Ogawa Takuya , Isobe Keisuke , Mori Takeshi , Asakawa Susumu , Yoshimura Tohru , Hemmi Hisashi 
Published: May 2014

Saturation of a prenyl group to various levels is a frequently observed modification of isoprenoids. The members of the geranylgeranyl reductase family, however, are the only known enzymes responsible for such reductive modifications in archaea. A methanogenic archaeon, Methanosarcina acetivorans, has proteins homologous to phytoene desaturase CrtI, which is the carotenogenic enzyme that catalyzes oxidation/isomerization of phytoene to lycopene, but their function in carotenogenesis is unlikely in a methanogen that does not produce carotenoids. In the present study, we identified one of the homologues, MA1492, as a new type of archaeal geranylgeranyl reductase that is not homologous to known geranylgeranyl reductases. The expression of MA1492 in Escherichia coli cells, which were genetically modified to produce unsaturated archaeal‐type lipids, led to the production of partially saturated lipid derivatives. Furthermore, we analyzed the substrate specificity of recombinant MA1492 via in vitro assays. The LC‐MS, or radio‐TLC, analysis of the reaction products showed that the enzyme was definitely specific to compounds containing C20 geranylgeranyl groups and reduced only one of four double bonds in a geranylgeranyl chain. The GC‐MS analysis of the product from geranylgeraniol confirmed that the reduction selectively occurred on the ω‐terminal double bond. The available crystallographic structure of an orthologue enzyme may explain the reaction mechanism that achieves the substrate specificity and regiospecificity.DatabaseMicrobial Genome Database (http://mbgd.genome.ad.jp/), EMBOSS Needle (https://www.ebi.ac.uk/Tools/psa/emboss_needle)