bluuebunny/crossref_metadata_2025 huggingface dataset:
Differences in activation and tissue homing markers of natural killer cell subsets during acute dengue infection
Authors: Keawvichit Rassamon , Khowawisetsut Ladawan , Lertjuthaporn Sakaorat , Tangnararatchakit Kanchana , Apiwattanakul Nopporn , Yoksan Sutee , Chuansumrit Ampaiwan , Chokephaibulkit Kulkanya , Ansari Aftab A. , Onlamoon Nattawat , Pattanapanyasat Kovit
Published: November 2017

Dengue virus (DENV) infection is considered one of the most important mosquito‐borne diseases. It causes a spectrum of illness that could be due to qualitative and/or quantitative difference(s) of the natural killer (NK) cell responses during acute DENV infection. This view prompted us to perform a detailed phenotypic comparative characterization of NK cell subsets from DENV‐infected patients with dengue fever (DF), patients with dengue haemorrhagic fever (DHF) and healthy controls. The activation/differentiation molecules, CD69 and CD57 and a variety of tissue homing molecules were analysed on the CD56hi CD16− and CD56lo CD16+ NK cells. Although there was no increase in the frequency of the total NK cells during DENV infection compared with the healthy individuals, there was a significant increase in the frequency of the CD56hi CD16− subset and the frequency of CD69 expression by both NK cell subsets during the febrile phase of infection. We also found an increase in the frequencies of cells expressing CD69 and CD57 in the CD56lo CD16+ subset compared with those in the CD56hi CD16− subset. Moreover, although the CD56lo CD16+ subset contained a high frequency of cells expressing skin‐homing markers, the CD56hi CD16− subset contained a high frequency of cells expressing bone marrow and lymph node trafficking markers. Interestingly, no differences of these NK cell subsets were noted in samples from patients with DF versus those with DHF. These findings suggest that activation and differentiation and the patterns of tissue homing molecules of the two major NK cell subsets are different and that these might play a critical role in the immune response against acute DENV infection.
A critical comparison of 3D experiments and simulations of tricalcium silicate hydration
Authors: Bullard Jeffrey W. , Hagedorn John , Ley M. Tyler , Hu Qinang , Griffin Wesley , Terrill Judith E.
Published: November 2017

Advances in nano‐computed X‐ray tomography (nCT), nano X‐ray fluorescence spectrometry (nXRF), and high‐performance computing have enabled the first direct comparison between observations of three‐dimensional nanoscale microstructure evolution during cement hydration and computer simulations of the same microstructure, using HydratiCA. nCT observations of a collection of triclinic tricalcium silicate () particles reacting in a calcium hydroxide solution are reported and compared to simulations that duplicate, as nearly as possible, the thermal and chemical conditions of those experiments. Particular points of comparison are the time dependence of the solid phase volume fractions, spatial distributions, and morphologies. Comparisons made at 7 hours of reaction indicate that the simulated and observed volumes of consumed by hydration agree to within the measurement uncertainty. The location of simulated hydration product is qualitatively consistent with the observations, but the outer envelope of hydration product observed by nCT encloses more than twice the volume of hydration product in the simulations at the same time. Simultaneous nXRF measurements of the same observation volume imply calcium and silicon concentrations within the observed hydration product envelope that are consistent with Ca(OH)2 embedded in a sparse network of calcium silicate hydrate (C–S–H) that contains about 70% occluded porosity in addition to the amount usually accounted as gel porosity. An anomalously large volume of Ca(OH)2 near the particles is observed both in the experiments and in the simulations, and can be explained as originating from the hydration of additional particles outside the field of view. Possible origins of the unusually large amount of observed occluded porosity are discussed.
Mean family age of angiosperm tree communities and its climatic correlates along elevational and latitudinal gradients in eastern North America
Authors: Qian Hong , Zhang Jian , Hawkins Bradford A.
Published: November 2017

Aim

The species comprising local communities are assembled from the species pool of the region where they are located, and environmental filtering influences which species occupy local communities based on their traits. Latitude and elevation generate two major thermal gradients, and temperature minimum and seasonality can drive community assembly, but few studies have tested if community assembly along both latitudinal and elevational gradients within the same region generates similar patterns of assembly. Here, we test hypotheses on the relations of mean family age (MFA) of angiosperm trees in local communities with environmental temperature and compare the relations between latitudinal and elevational gradients in eastern North America.

Location

USA.

Method

We used correlation and regression analyses and structure equation modelling approach to assess the relation of MFA to elevation, latitude and climatic variables, which included minimum temperature, temperature seasonality, annual precipitation and precipitation seasonality.

Results

The MFA of a local forest community decreased with increasing latitude and elevation for all gradients examined. For each gradient, the slope of the relationship between MFA and latitude or elevation was steeper for forest communities with larger values of MFA than for those with smaller values of MFA, and the standard deviation of MFA decreased with increasing latitude and elevation. MFA decreased significantly with decreasing minimum temperature for both latitudinal and elevational gradients, but the slope of the relationship between MFA and minimum temperature was steeper for elevational gradients than for latitudinal gradients. Minimum temperature had a much stronger relationship with MFA than temperature seasonality for both latitudinal and elevational gradients.

Main conclusions

Our results indicate that minimum temperature, rather than temperature seasonality, is a major driver of the pattern of decreasing MFA with increasing latitude and elevation, and the relationship between temperature and MFA is stronger (steeper) for elevational gradients than for latitudinal gradients.
Standardization of regimens in Narrowband UVB and PUVA in early stage mycosis fungoides: position paper from the Italian Task Force for Cutaneous Lymphomas
Authors: Grandi V. , Fava P. , Rupoli S. , Alberti Violetti S. , Canafoglia L. , Quaglino P. , Berti E. , Pimpinelli N. ,   Cutaneous Lymphoma Task Force (Commissione Linfomi Cutanei) of Lymphoma Italian Foundation (Fondazione Italiana Linfomi, FIL)
Published: November 2017

UV‐based (PUVA and narrowband UVB) phototherapy is broadly and commonly used in the treatment of Cutaneous T‐cell Lymphomas (CTCL), yet unfortunately, the evidence for the efficacy of these treatments is based only on case series or prospective but non‐randomized studies. Therefore, no internationally approved guidelines exist and no standardization of schedules has been proposed. Recently, consensus guidelines have been published by the United States Cutaneous Lymphoma Consortium. The aim of this study was to review the biological and clinical evidences on PUVA and NB‐UVB in CTCL and to critically evaluate acceptability and feasibility of these guidelines in the real‐life setting from the perspective of the Cutaneous Lymphoma Task Force of the Italian Lymphoma Foundation (Fondazione Italiana Linfomi, FIL).
Scales of deformation partitioning during exhumation in a continental subduction channel: A petrofabric study of eclogites and gneisses from NW Spain (Malpica‐Tui Allochthonous Complex)
Authors: Puelles P. , Ábalos B. , Gil Ibarguchi J. I. , Rodríguez J.
Published: November 2017

Deformation partitioning is identified as the fingerprint of late Palaeozoic continental subduction that affected various lithologies whose field relationship, thermobarometric and petrofabric features are closely related. Different modes of deformation partitioning can be identified within medium temperature, high‐P eclogite lenses, between them and the host gneisses, and within the latter. Development of foliations and lineations with a coherent attitude in all these rocks and their related structural petrology demonstrate that eclogite enclosures and their country rocks underwent a common, pervasive deformational event. The published P–T stability fields of the eclogite phases that define the microscopic fabric are used to define the metamorphic conditions prevailing during the deformation event and relate it to the subduction process. The mineral equilibria of the gneisses (ortho‐ and paragneisses) fail to record the full range of those P–T conditions, but the field relationships show that eclogites were originally basic dykes emplaced in acid igneous rocks and demonstrate that the eclogites and gneisses shared a common tectonometamorphic evolution. Deformation partitioning within the latter occurred at variable scales and involved (1) meso macroscale preservation of virtually undeformed metagranite bodies, surrounded by (2) pervasively foliated and lineated gneisses, and (3) the simultaneous microscale operation in the latter of ductile and brittle–ductile mechanisms at conditions above 500°C and below 1.5 GPa. A subduction channel tectonic setting is proposed to explain the subduction of upper to mid‐crustal igneous rocks and exhumation subsequent to high‐P metamorphism. Its currently accessible dimensions, and its organization into several lithotectonic units mapped as nappes support tectonic amalgamation of units several km3 in volume. Maximum burial in the subduction channel likely reached depths shallower than the lithostatic pressure implied by geobarometric calculations, possibly conditioned by a sudden pressure drop during the initial retrogression stages accompanying exhumation.
Reply: proton‐pump inhibitor use and the risk of first‐time ischemic stroke in the general population
Authors: Sehested T. S. G. , Hlatky M. A. , Carlson N. , Gislason G. H.
Published: November 2017

Click here to view the Letter to the Editor by Dr. Dai et al.
Dietary fibre alleviates hepatic fat deposition via inhibiting lipogenic gene expression in meat ducks
Authors: Qin S. , Han H. , Zhang K. , Ding X. , Bai S. , Wang J. , Zeng Q.
Published: November 2017

This study investigated the effect of dietary fibre (DF) supplementation on hepatic fat deposition of Cherry Valley meat ducks. A total of 600 1‐d‐old ducks were randomly allotted to five dietary fibre diets (1.46 (basal diet), 3.09, 4.15, 6.18 and 7.52% (analysed)) for 14 days. Growth performance decreased with increasing DF concentrations, when the DF level more than 6.18% the average daily gain (ADG) and feed conversion ratio (F/G) markedly decreased in meat ducks. Meat ducks supplemented over 4.15% DF had lower percentage of liver reported to live weight, liver lipid contents, hepatic triglyceride and total cholesterol concentrations as well as decreased serum aspartate aminotransferase (AST) and alanine aminotransferase (ALT) concentrations at 14 days. The transcription of fatty acid synthase (FAS), acetyl‐CoA carboxylase (ACC) and sterol‐regulatory element‐binding protein‐1 (SREBP‐1) in liver was significantly reduced by DF, while no any significant difference was found about the effect of DF on hepatic peroxisome proliferator‐activated receptor α (PPARα), adipose triglyceride lipase (ATGL), transcription as well as caecal digesta short‐chain fatty acids (SCFA). Data suggested that dietary fibre supplementation decreased hepatic lipid deposition and improved characteristics of liver health via inhibiting hepatic FAS, ACC and SREBP‐1 expression in meat ducks.
Performance, body fat reserves and plasma metabolites in Brown Swiss dairy cows: Indoor feeding versus pasture‐based feeding
Authors: Frey H.‐J. , Gross J. J. , Petermann R. , Probst S. , Bruckmaier R. M. , Hofstetter P.
Published: November 2017

Feeding dairy cows indoors or on pasture affects not only labour, machinery and housing costs, but also animals’ performance and metabolism. This study investigates the effects of indoor feeding (IF) with a partial‐mixed ration (PMR) versus pasture‐based feeding (PF) on milk production, fertility, backfat thickness (BFT), body weight (BW) loss and energy metabolism of Brown Swiss (BS) dairy cows with similar genetic production potential. The IF herd consisted of 13 cows fed a PMR composed of maize and grass silage plus protein concentrate according to each cow's requirements. The PF herd consisted of 14 cows offered barn‐ventilated hay ad libitum after calving from January until March and grazed on semi‐continuous pastures during the vegetation period. The IF cows produced more energy‐corrected milk (ECM) per standard lactation (9,407 vs. 5,960 kg; p < .01), more milk fat (378 vs. 227 kg; p < .01) and milk protein (326 vs. 215 kg; p < .01). The calving interval (377 vs. 405 days; p < .01) and time empty (86 vs. 118 days; p < .01) were shorter in the PF compared to IF, possibly also due to different selection criteria for maintaining the respective seasonal calving rhythm. The empty body fat loss calculated according to BCS until its nadir was higher in IF cows (IF: 10.4 vs. PF: 4.8 MJ/day; p < .01), but no differences were noted in total body fat loss estimated via BFT (p = .24). However, PF had lower blood glucose concentration at all investigated time points, but no differences occurred in serum non‐esterified fatty acid and β‐hydroxybutyrate concentrations post‐partum. In conclusion, BS cows were equally well suited for the IF with PMR and the PF system investigated here without developing a prominent metabolic load despite differences in nutrient supply. As such, investigated BS dairy cows in our trial seem to have a high capacity for metabolic adaptation to different production systems.
In vitro effects of inulin and soya bean oligosaccharide on skatole production and the intestinal microbiota in broilers
Authors: Liu H. Y. , Hou R. , Yang G. Q. , Zhao F. , Dong W. G.
Published: November 2017

The experiment was conducted to investigate the in vitro effects of inulin and soya bean oligosaccharide (SBO) on the metabolism of L‐tryptophan (L‐try) to skatole production, and the intestinal microbiota in broilers. Treatments were as follows: caecal microbiota control (Cc), Cc + inulin, Cc + SBO, rectal microbiota control (Rc), Rc + inulin and Rc + SBO. Microbial suspensions were anaerobically incubated at 38°C for 24 hr. The results showed that concentrations of skatole and acetic acid were significantly lower in caecal microbiota fermentation broth (MFB) than those in rectal MFB (p < .05). Addition of inulin or SBO significantly decreased the concentrations of indole and skatole and rate of L‐try degradation (p < .05). Inulin groups had lower indole than SBO groups (p < .05). PCR‐DGGE analysis revealed that addition of inulin or SBO decreased the microbiota richness (p < .05), but no significant differences in Shannon index (p > .05). Four distinct bands were detected in inulin and SBO groups, which were related to two of Bacteroides, one of Firmicutes and Bifidobacteria. Six bands were detected only in control groups, which represented uncultured Rikenellaceae, Roseburia, Escherichia/Shigella dysenteriae, Bacteroides uniformis (T), Parabacteroides distasonis and Enterobacter aerogenes. Populations of Lactobacilli, Bifidobacteria and total bacteria in inulin groups were higher than those in control groups (p < .05). For SBO groups, only population of total bacteria increased (p < .05). However, there were no significant differences in Escherichia coli population among treatments (p > .05). These results suggest that reduced concentrations of skatole and indole in the presence of inulin and SBO may be caused by decrease in L‐try degradation rate, which were caused by change in microbial ecosystem and pH value. Uncultured B. uniformis (T) and E. aerogenes may be responsible for degradation of L‐try to skatole.
The present and future disease burden of hepatitis C virus infections with today's treatment paradigm: Volume 4
Authors: Chan H. L. Y. , Chen C. J. , Omede O. , Al Qamish J. , Al Naamani K. , Bane A. , Tan S. S. , Simonova M. , Cardenas I. , Derbala M. , Akin O. , Phillips R. O. , Abdelmageed M. K. , Abdulla M. , Adda D. , Al Baqali A. , Al Dweik N. , Al Ejji K. , Al ghazzawi I. , Al Kaabi S. , Al Sadadi M. , Al Salman J. , AlBadri M. , Al‐Busafi S. A. , Al‐Romaihi H. E. , Ampofo W. , Antonov K. , Anyaike C. , Arome F. , Blach S. , Borodo M. M. , Brandon S. M. , Bright B. , Butt M. T. , Chen D. S. , Chen P. J. , Chien R. N. , Chuang W. L. , Cuellar D. , Elbardiny A. A. , Estes C. , Farag E. , Fung J. , Gamkrelidze I. , Garcia V. , Genov J. , Ghandour Z. , Ghuloom M. , Gomez B. , Gunter J. , Habeeb J. , Hajelssedig O. , Hamoudi W. , Himatt S. M. , Hrstic I. , Hu C. C. , Huang C. F. , Hui Y. T. , Jahis R. , Jelev D. , John A. K. , Kaliaskarova K. S. , Kamel Y. , Kao J. H. , Khamis J. , Khattabi H. , Khoudri I. , Konysbekova A. , Kotzev I. , Lai M. S. , Lao W. C. , Layden J. , Lee M. H. , Lesi O. , Li M. , Lo A. , Loo C. K. , Lukšić B. , Maaroufi A. , Malu A. O. , Mateva L. , Mitova R. , Mohamed R. , Morović M. , Murphy K. , Mustapha B. , Nersesov A. , Ngige E. , Njouom R. , Njoya O. , Nonković D. , Obekpa S. , Oguche S. , Okolo E. E. , Omuemu C. , Ondoa P. , Opare‐Sem O. , Owusu‐Ofori S. , Prokopenko Y. N. , Razavi H. , Razavi‐Shearer D. , Razavi‐Shearer K. , Redae B. , Reic T. , Rinke de Wit T. , Rios C. , Robbins S. , Roberts L. R. , Sanad S. J. , Schmelzer J. D. , Sharma M. , Su T. H. , Sultan K. , Tchernev K. , Tsang O. T. Y. , Tsang S. , Tzeuton C. , Ugoeze S. , Uzochukwu B. , Vi R. , Vince A. , Wani H. U. , Wong V. W. S. , Workneh A. , Yacoub R. , Yesmembetov K. I. , Youbi M. , Yuen M. F. , Nde H.
Published: November 2017

Factors influencing the morbidity and mortality associated with viremic hepatitis C virus (HCV) infection change over time and place, making it difficult to compare reported estimates. Models were developed for 17 countries (Bahrain, Bulgaria, Cameroon, Colombia, Croatia, Dominican Republic, Ethiopia, Ghana, Hong Kong, Jordan, Kazakhstan, Malaysia, Morocco, Nigeria, Qatar and Taiwan) to quantify and characterize the viremic population as well as forecast the changes in the infected population and the corresponding disease burden from 2015 to 2030. Model inputs were agreed upon through expert consensus, and a standardized methodology was followed to allow for comparison across countries. The viremic prevalence is expected to remain constant or decline in all but four countries (Ethiopia, Ghana, Jordan and Oman); however, HCV‐related morbidity and mortality will increase in all countries except Qatar and Taiwan. In Qatar, the high‐treatment rate will contribute to a reduction in total cases and HCV‐related morbidity by 2030. In the remaining countries, however, the current treatment paradigm will be insufficient to achieve large reductions in HCV‐related morbidity and mortality.
Historical epidemiology of hepatitis C virus in select countries—volume 4
Authors: Maaroufi A. , Vince A. , Himatt S. M. , Mohamed R. , Fung J. , Opare‐Sem O. , Workneh A. , Njouom R. , Al ghazzawi I. , Abdulla M. , Kaliaskarova K. S. , Owusu‐Ofori S. , Abdelmageed M. K. , Adda D. , Akin O. , Al Baqali A. , Al Dweik N. , Al Ejji K. , Al Kaabi S. , Al Naamani K. , Al Qamish J. , Al Sadadi M. , Al Salman J. , AlBadri M. , Al‐Busafi S. A. , Al‐Romaihi H. E. , Ampofo W. , Antonov K. , Anyaike C. , Arome F. , Bane A. , Blach S. , Borodo M. M. , Brandon S. M. , Bright B. , Butt M. T. , Cardenas I. , Chan H. L. Y. , Chen C. J. , Chen D. S. , Chen P. J. , Chien R. N. , Chuang W. L. , Cuellar D. , Derbala M. , Elbardiny A. A. , Estes C. , Farag E. , Gamkrelidze I. , Garcia V. , Genov J. , Ghandour Z. , Ghuloom M. , Gomez B. , Gunter J. , Habeeb J. , Hajelssedig O. , Hamoudi W. , Hrstic I. , Hu C. C. , Huang C. F. , Hui Y. T. , Jahis R. , Jelev D. , John A. K. , Kamel Y. , Kao J. H. , Khamis J. , Khattabi H. , Khoudri I. , Konysbekova A. , Kotzev I. , Lai M. S. , Lao W. C. , Layden J. , Lee M. H. , Lesi O. , Li M. , Lo A. , Loo C. K. , Lukšić B. , Malu A. O. , Mateva L. , Mitova R. , Morović M. , Murphy K. , Mustapha B. , Nde H. , Nersesov A. , Ngige E. , Njoya O. , Nonković D. , Obekpa S. , Oguche S. , Okolo E. E. , Omede O. , Omuemu C. , Ondoa P. , Phillips R. O. , Prokopenko Y. N. , Razavi H. , Razavi‐Shearer D. , Redae B. , Reic T. , Rinke de Wit T. , Rios C. , Robbins S. , Roberts L. R. , Sanad S. J. , Schmelzer J. D. , Sharma M. , Simonova M. , Su T. H. , Sultan K. , Tan S. S. , Tchernev K. , Tsang O. T. Y. , Tsang S. , Tzeuton C. , Ugoeze S. , Uzochukwu B. , Vi R. , Wani H. U. , Wong V. W. S. , Yacoub R. , Yesmembetov K. I. , Youbi M. , Yuen M. F. , Razavi‐Shearer K.
Published: November 2017

Due to the introduction of newer, more efficacious treatment options, there is a pressing need for policy makers and public health officials to develop or adapt national hepatitis C virus (HCV) control strategies to the changing epidemiological landscape. To do so, detailed, country‐specific data are needed to characterize the burden of chronic HCV infection. In this study of 17 countries, a literature review of published and unpublished data on HCV prevalence, viraemia, genotype, age and gender distribution, liver transplants and diagnosis and treatment rates was conducted, and inputs were validated by expert consensus in each country. Viraemic prevalence in this study ranged from 0.2% in Hong Kong to 2.4% in Taiwan, while the largest viraemic populations were in Nigeria (2 597 000 cases) and Taiwan (569 000 cases). Diagnosis, treatment and liver transplant rates varied widely across the countries included in this analysis, as did the availability of reliable data. Addressing data gaps will be critical for the development of future strategies to manage and minimize the disease burden of hepatitis C.
Analysing Betula litwinowii encroachment and reforestation in the Kazbegi region, Greater Caucasus, Georgia
Authors: Hansen Wiebke , Magiera Anja , Theissen Tim , Waldhardt Rainer , Otte Annette
Published: November 2017

Aims

The encroachment of tree and shrub species in high mountains is an increasing worldwide phenomenon, which is expected to dramatically alter high‐mountain ecosystems and their functioning. Moreover it indicates in some cases a reforestation process, which will result in important ecological and social benefits, including carbon sequestration and protection against landslides. We therefore examined the spatial extent of forest growth and shrub encroachment mainly of birch (Betula litwinowii) in the sub‐alpine belt of the Central Greater Caucasus between 1987 and 2010 and its relation to topographic site conditions.

Location

Kazbegi district, Central Greater Caucasus, Georgia.

Methods

We analysed 155 vegetation relevés sampled in 2009, 2011 and 2015, mainly derived from the Caucasus Vegetation Database, to obtain information about topographic site conditions and structure of B. litwinowii stands. B. litwinowii forest growth was assessed by digitizing the forest outlines from aerial and space‐borne imagery (1987, 2005 and 2010). To identify areas of B. litwinowii encroachment as an indicator for different encroachment stages, we modelled the tree and shrub cover using the Random Forest algorithm.

Results

We found four types of B. litwinowii stands, characterized by different tree and shrub coverage (initial Bromus variegatus–Betula litwinowii encroachment indicating the first stage of succession, Aconitum nasutum–Betula litwinowii forest, Rubus idaeus–Betula litwinowii forest and Rhododendron caucasicum–Betula litwinowii tree line scrubs). B. litwinowii forest increased 25% compared to 1987 mainly in an uphill direction. Furthermore the modelled tree and shrub cover (R2 = .69) could be related to the four vegetation types.

Conclusions

Our results indicate a recent trend towards shrub encroachment and consequently reforestation in the Kazbegi region.
A re‐analysis that supports our main results: A reply to Levine et al.
Authors: Vrij Aldert , Blank Hartmut , Fisher Ronald P.
Published: November 2017

Levine et al. (2018) criticized our meta‐analysis, but their conclusion was the same as ours: The cognitive approach to lie detection results in a modest improvement. We address and dismiss Levine et al.'s (2018) three criticisms. Regarding the ‘confound’, in our meta‐analysis we averaged the results of two cells on statistical grounds, which does not constitute a confound in statistical terms. Regarding ‘aberrant controls’, that depends entirely on the benchmarks selected and type of statistical test and meta‐analysis used. Regarding ‘unreliable data’, the claim that there is a positive relationship between ‘unreliable’ data and total accuracy in the cognitive lie detection conditions is not even supported by their own data (p = .16). We conclude with a request to Levine et al. to focus on our shared aim: to develop interview protocols that enable lie detection.
Analysis of recombinational switching at the antigenic variation locus of the Lyme spirochete using a novel PacBio sequencing pipeline
Authors: Verhey Theodore B. , Castellanos Mildred , Chaconas George
Published: November 2017

The Lyme disease spirochete evades the host immune system by combinatorial variation of VlsE, a surface antigen. Antigenic variation occurs via segmental gene conversion from contiguous silent cassettes into the vlsE locus. Because of the high degree of similarity between switch variants and the size of vlsE, short‐read NGS technologies have been unsuitable for sequencing vlsE populations. Here we use PacBio sequencing technology coupled with the first fully‐automated software pipeline (VAST) to accurately process NGS data by minimizing error frequency, eliminating heteroduplex errors and accurately aligning switch variants. We extend earlier studies by showing use of almost all of the vlsE SNP repertoire. In different tissues of the same mouse, 99.6% of the variants were unique, suggesting that dissemination of Borrelia burgdorferi is predominantly unidirectional with little tissue‐to‐tissue hematogenous dissemination. We also observed a similar number of variants in SCID and wild‐type mice, a heatmap of location and frequency of amino acid changes on the 3D structure and note differences observed in SCID versus wild type mice that hint at possible amino acid function. Our observed selection against diversification of residues at the dimer interface in wild‐type mice strongly suggests that dimerization is required for in vivo functionality of vlsE.
An acetylatable lysine controls CRP function in E. coli
Authors: Davis Robert , Écija‐Conesa Ana , Gallego‐Jara Julia , de Diego Teresa , Filippova Ekaterina V. , Kuffel Gina , Anderson Wayne F. , Gibson Bradford W. , Schilling Birgit , Canovas Manuel , Wolfe Alan J.
Published: November 2017

Transcriptional regulation is the key to ensuring that proteins are expressed at the proper time and the proper amount. In Escherichia coli, the transcription factor cAMP receptor protein (CRP) is responsible for much of this regulation. Questions remain, however, regarding the regulation of CRP activity itself. Here, we demonstrate that a lysine (K100) on the surface of CRP has a dual function: to promote CRP activity at Class II promoters, and to ensure proper CRP steady state levels. Both functions require the lysine's positive charge; intriguingly, the positive charge of K100 can be neutralized by acetylation using the central metabolite acetyl phosphate as the acetyl donor. We propose that CRP K100 acetylation could be a mechanism by which the cell downwardly tunes CRP‐dependent Class II promoter activity, whilst elevating CRP steady state levels, thus indirectly increasing Class I promoter activity. This mechanism would operate under conditions that favor acetate fermentation, such as during growth on glucose as the sole carbon source or when carbon flux exceeds the capacity of the central metabolic pathways.
Recent advances in the understanding of Xanthomonas citri ssp. citri pathogenesis and citrus canker disease management
Authors: Ference Christopher M. , Gochez Alberto M. , Behlau Franklin , Wang Nian , Graham James H. , Jones Jeffrey B.
Published: November 2017

Taxonomic status: Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadaceae; Genus Xanthomonas; Species Xanthomonas citri ssp. citri (Xcc).

Host range: Compatible hosts vary in their susceptibility to citrus canker (CC), with grapefruit, lime and lemon being the most susceptible, sweet orange being moderately susceptible, and kumquat and calamondin being amongst the least susceptible.

Microbiological properties: Xcc is a rod‐shaped (1.5–2.0 × 0.5–0.75 µm), Gram‐negative, aerobic bacterium with a single polar flagellum. The bacterium forms yellow colonies on culture media as a result of the production of xanthomonadin.

Distribution: Present in South America, the British Virgin Islands, Africa, the Middle East, India, Asia and the South Pacific islands. Localized incidence in the USA, Argentina, Brazil, Bolivia, Uruguay, Senegal, Mali, Burkina Faso, Tanzania, Iran, Saudi Arabia, Yemen and Bangladesh. Widespread throughout Paraguay, Comoros, China, Japan, Malaysia and Vietnam. Eradicated from South Africa, Australia and New Zealand. Absent from Europe.
Multiplex fusion gene testing in pediatric acute myeloid leukemia
Authors: Iijima‐Yamashita Yuka , Matsuo Hidemasa , Yamada Miho , Deguchi Takao , Kiyokawa Nobutaka , Shimada Akira , Tawa Akio , Takahashi Hiroyuki , Tomizawa Daisuke , Taga Takashi , Kinoshita Akitoshi , Adachi Souichi , Horibe Keizo
Published: November 2017

Background

Gene abnormalities, particularly chromosome rearrangements generating gene fusion, are associated with clinical characteristics and prognosis in pediatric acute myeloid leukemia (AML). Karyotyping is generally performed to enable risk stratification, but the results are not always consistent with those of reverse transcription–polymerase chain reaction (RT‐PCR), and more accurate and rapid methods are required.

Methods

A total of 487 samples from de novo AML patients enrolled in the Japanese Pediatric Leukemia/Lymphoma Study Group (JPLSG) AML‐05 study (n = 448), and from acute promyelocytic leukemia (APL) patients enrolled in the JPLSG AML‐P05 study (n = 39) were available for this investigation. Multiplex quantitative RT‐PCR was performed to detect eight important fusion genes: AML1(RUNX1)‐ETO(RUNX1T1), CBFB‐MYH11, MLL(KMT2A)‐AF9(MLLT3), MLL‐ELL, MLL‐AF6(MLLT4), FUS(TLS)‐ERG, NUP98‐HOXA9, and PML‐RARA.

Results

Fusion genes were detected in 207 (46.2%) of the 448 AML‐05 patient samples. After exclusion of two samples with PML‐RARA, no chromosomal abnormalities were identified on karyotyping in 19 of 205 patients (9.3%) positive for fusion genes on RT‐PCR. Fusion genes were confirmed on fluorescence in situ hybridization (FISH) in 11 of these 19 patients. In contrast, fusion genes were detected in 37 of 39 patients (94.9%) from the AML‐P05 study, and 33 of these results were consistent with the karyotyping. There were discrepancies in four patients (10.8%), three with normal karyotypes and one in whom karyotyping was not possible. All four of these patients were PML‐RARA positive on FISH.

Conclusions

Multiplex quantitative RT‐PCR‐based fusion gene screening may be effective for diagnosis of pediatric AML.
The function of the floral corona in the pollination of a Mediterranean style dimorphic daffodil
Authors: Pérez‐Barrales R. , Abarca C. A. , Santos‐Gally R. , Schiestl F. P. , Arroyo J.
Published: November 2017

Narcissus papyraceus is a style dimorphic species with two floral forms, with anthers at similar height and stigmas above (long‐styled L) and below (short‐styled S) the anther level. The species is self‐incompatible, but intra‐ and inter‐morph compatible. Populations are either dimorphic (including both morphs) in the region of the Strait of Gibraltar, or L‐monomorphic (with only L plants) in the inland of the Iberian Peninsula. This variation correlates with the most common floral visitors, being primarily long‐tongued and short‐tongued pollinators, respectively, a rare condition in Mediterranean plants. The maintenance of S‐flowers relies on long‐tongued insects, as only those deliver pollen to short‐styled stigmas. Narcissus flowers present a long and narrow tube, at the bottom of which nectar accumulates, and a floral corona, which has been proposed as an important trait for the attraction of pollinators. Here we tested the importance of the corona on pollination of L and S flowers.

We described UV reflectance patterns of the corona and tepals, and characterised VOCs in intact flowers and flowers with trimmed coronas. We also conducted a field experiment in the dimorphic and monomorphic region to estimate the importance of corona removal on seed production in stands with solitary plants and in groups to control for compatible pollen limitation.

Reflectance was higher in the tepals than the corona, although both traits presented a reflectance peak around 450 nm wavelength. L‐ and S‐flowers produced similar volatiles, regardless of the manipulation of the corona. Across dimorphic and monomorphic regions, S‐flowers with the corona removed suffered a reduction in seed production of ca. 50%, while seed production remained similar in L flowers both with the corona intact and removed. Plants in solitary stands suffered a strong reduction in seed production, which was more pronounced in the monomorphic region.

Our results suggest that the corona in Narcissus is more important for the pollination of S‐flowers, which generally have lower seed production compared to L‐flowers. Taken together, these results suggest that the floral corona indirectly plays an important role for maintenance of the polymorphism.
Silique valves as sails in anemochory of Lunaria (Brassicaceae)
Authors: Leins P. , Fligge K. , Erbar C.
Published: November 2017

The generally held opinion that seeds of Lunaria remain at the replum after detachment of the two valves and then wind causes a shaking or rattling of the replum with its diaphragm, thus launching the seeds, is challenged. In a sparse forest in the Swabian Alb, the first author noticed flying valves of Lunaria rediviva to which the narrow‐winged flat seeds are attached.

Investigations with SEM and histology have shown that the valves secrete a glue only at those sites where the seeds rest on the valves before valve tissues die. Further analysis has shown (using the periodic acid‐Schiff reaction) that the glue consists of polysaccharides. After detachment and dispersal of the valves, the adhesive strength continuously decreases.

This is the first report for a sticky valve exudate in the Brassicaceae. Because of the adhesion of Lunaria seeds to their valves for some time, the 1st order diaspore is a mericarp, in a broad sense, and can be interpreted as an adaptation to long‐distance dispersal by stronger winds. In this context, the ‘flying carpets’ of Lunaria are more effective and transport more than one seed.

Molecular studies assigned Lunaria to the tribe Biscutelleae, which now contains the angustiseptate genera Biscutella and Megadenia as well as the latiseptate genera Lunaria and Ricotia. The valves in Ricotia can easily be detached (studied in herbarium material and a living plant), but, in contrast to Lunaria, the ripe seeds remain at the replum and its diaphragm, respectively.
Early pneumopericardium after heart transplantation
Authors: Duero Posada Juan G. , Moayedi Yasbanoo , Alhussein Mosaad , Bunce Paul E. , Yau Terrence M. , Ross Heather J.
Published: November 2017

A 60‐year‐old woman with a history of dilated cardiomyopathy underwent heart transplantation. One month post discharge, she presented to clinic with low‐grade fever and productive cough. Her chest radiograph showed air‐fluid levels in the pericardial silhouette. Transthoracic echocardiogram showed a large complex pericardial collection with no evidence of cardiac tamponade. The patient was urgently taken to the operating room for exploration. A large “egg‐shaped” mass in the pericardium measuring 10 × 12 cm with gaseous material was aspirated. As the posterior wall of the mass was firmly adhered to the right atrium, the capsule was incompletely excised. We present the case of a potentially life‐threatening complication post transplantation that required surgical debridement and life‐long antibiotic suppressive therapy. To our knowledge, this is the first report of purulent pericardial collection caused by Enterobacter cancerogenous. Further research is required to better understand the biology of this microorganism and the role it may play as a pathogen in immunocompromised patients following solid organ transplantation.
3D Machined Surface Topography Forecasting With Space-Time Multioutput Support Vector Regression Using High Definition Metrology
Authors: Shao Yiping , Du Shichang , Xi Lifeng
Published: November 2017

Satisfied surface topography is important to achieve the function of a part, thereby machined surface prediction is essential. A surface forecasting model called space-time multioutput support vector regression (STMSVR) is developed in this paper. With machined surfaces pervading in manufacturing, high definition metrology (HDM) is adopted to measure the three dimensional machined surface. Millions of data points are generated to represent the entire surface. The STMSVR model captures the spatial-temporal characteristics of the successively machined surface and predicts the future surface. To verify the prediction accuracy of STMSVR, a case study on the engine cylinder block face milling process is applied. The results indicate that the developed model achieves a good agreement between the predicted surface and the real surface using four important indexes.
Motion Tolerancing Based on Skin Model Shapes by Form Deviation Parametrization and Meta-Modelling
Authors: Schleich Benjamin , Wartzack Sandro
Published: November 2017

The inevitable presence of geometrical part deviations and their effects on the product function and quality forces companies to manage these deviations along the product life-cycle. Computer-aided tolerancing and variation simulation tools support these activities by enabling the early prediction and assessment of the effects of such part deviations. However, available approaches for the tolerance analysis and variation simulation imply shortcomings regarding the consideration of form deviations, particularly when analysing mechanism and moving systems. This paper presents an approach for the motion tolerancing, i. e. for the tolerance analysis of mechanism and moving systems, employing discrete geometry representations of parts with geometrical deviations (Skin Model Shapes). In this regard, a novel method for the parametrization of form deviations is proposed and the use of meta-modelling techniques for the reduction of the computational effort is illustrated. Moreover, the presented approach is applied on two case studies. Based on the obtained results, it can be found, that the consideration of form deviations in the tolerance analysis for mechanism and moving systems may lead to more purposeful tolerancing decisions.
Digital Design Method of Dyeing Patterns Based on Kansei
Authors: Ichimura Yohei , Aoyama Hideki
Published: November 2017

Dyeing involves fixing a dye on a cloth, or creating a dyeing pattern. Because dyeing patterns depend on the physical properties of fibers, dyes, and dyeing technique that are employed, predicting a finished dyeing pattern is difficult even for artisans. Because dyeing is an irreversible phenomenon that requires a lot of time, to accurately predict a completed pattern would improve the efficiency of dyeing and reduce its costs.

In this paper, we propose a digital method for designing dyeing patterns based on a simulation of the dyeing process. Dyeing experiments was conducted to model dyeing process accurately. From experiments, we defined the dyeing process is combination of two phenomena: capillary phenomenon and diffusion phenomenon. In the proposed method, integrated these two phenomena by using the cellular automaton method and generate dyeing patterns that produce different results depending on the pattern-generating parameters.

The thickness of yarn and spaces between yarns in fabric is not uniform because of the influence of spinning and weaving. Therefore, in the proposed method, we use the fluctuation property, which is inherent in nature, to generate a dyeing pattern that preserves a natural impression.

Based on the simulation of the proposed dyeing process, we developed a system that generates patterns based on KANSEI. Associating KANSEI with pattern generation parameters produces dyeing patterns that exhibit the required impressions (KANSEI) for the generated dyeing patterns. Based on this development method, we constructed a basic system for pattern generation and verified the effectiveness of the method.
Sensible Pathways for Sensorium-Gameness Integration and Embedment in Design Tools for Multi-Phase Iterative Creative Synthesis in Design and Engineering Processes
Authors: Wendrich Robert E.
Published: November 2017

Current and ongoing research and experimentations in the creation, design and build of low-cost, high-value prototypes for novel and unconventional interaction devices (IxD) in combination with cyber-physical system (CPS) (i.e. hybrid design tools (HDT), blended spaces) tangible user interfaces (TUI) and use of sensor technology lead to a variety of novel interaction modalities, experiences and possibilities. In line with this research, we propose a first prototype Human Sensor Selection Tool (HSST) as a preliminary guide and guidelines for design and engineering domains. The HSST is based on and inspired by the ‘five human senses’ [1], a plethora in human body signals (e.g. proprioceptive, vestibular) and gestures (e.g. facial expression, (e-)motions) that could be integrated, translated, transformed, adapted or mimicked to enhance and enrich the interaction modalities with for example computer-aided design (CAD), computer-aided technologies (CAx), and effectively affective CPS.
A Framework for Automated Model Interface Coordination Using SysML
Authors: Bailey William C. , Che Judy , Tsou Poyu , Jennings Mark
Published: November 2017

Integrated vehicle simulation models are being increasingly used to improve engineering efficiency and reduce the number of real-world prototypes needed to understand vehicle attributes and subsystem interactions. Each domain within the vehicle must be represented by its own model developed with the appropriate operating ranges, behaviors, fidelity, and interfaces needed to interact appropriately with other domains in the vehicle. Planning and managing the development of these models across a large, multidisciplinary group of engineers can be a significant effort. In particular, carefully managing each model’s interfaces is crucial to enabling the entire process; missing or inappropriately used signals can cause significant issues when many separate domain models are integrated into a single vehicle model. To help system engineers better manage these interfaces across a broad variety of applications, a SysML-based modeling approach is proposed to describe these models and their interfaces formally and completely. However, even with a consistent modeling approach, creating and managing the interfaces across a large number of domains and applications can be a significant, error-prone task. To reduce the amount of manual modeling work required to maintain and update Simulink model interfaces, an interface management toolset is proposed to help automate the process of importing existing interfaces, routing and visualizing them, and exporting model templates for developers to use when creating new models. By automating this process, it becomes significantly easier to reuse models across vehicle platforms (rather than creating new models from scratch) and frees up resources to create more accurate simulations throughout the system design process.
Design of a Reconfigurable Dynamic Testbed for Co-Design Method Validation
Authors: Deshmukh Anand P. , Lohan Danny J. , Allison James T.
Published: November 2017

Physical testing as a technique for validation of engineering design methods can be a valuable source of insights not available through simulation alone. Physical testing also helps to ensure that design methods are suitable for design problems with a practical level of detail, and can reveal issues related to interactions not captured by physics-based computer models. Construction of physical and testing of physical prototypes, however, is costly and time consuming so it is not often used when investigating new design methods for complex systems. This gap is addressed through an innovative testbed presented here that can be reconfigured to achieve a range of different prototype design properties, including kinematic behavior and different control system architectures. Thus, a single testbed can be used for validation of numerous design geometries and control system architectures. The testbed presented here is a mechanically and electronically reconfigurable quarter-car suspension testbed with nonlinear elements that is capable of testing a wide range of both optimal and sub-optimal design prototypes using a single piece of equipment. Kinematic suspension properties can be changed in an automated way to reflect different suspension linkage designs, spring and damper properties can be adjusted in real time, and control system design can be changed easily through streamlined software modifications. While the specific case study is focused on development of a reconfigurable system for validation of co-design methods, the concept extends to physical validation using reconfigurable systems for other classes of design methods.