bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular analysis of the mating type (MAT1) locus in strains of the heterothallic ascomycete Botrytis cinerea
Authors: De Miccolis Angelini R. M. , Rotolo C. , Pollastro S. , Faretra F.
Published: January 2016

Botrytis cinerea shows a heterothallic bipolar mating‐type system; homothallism has been occasionally observed. MAT1 genes and flanking regions in the reference strains SAS56 (MAT1‐1) and SAS405 (MAT1‐2) and their monoascosporic progeny were analysed. The two mating types confirmed different sequences of 2513 bp (MAT1‐1) and 2776 bp (MAT1‐2), flanked by near identical regions. In all isolates, each idiomorph included two mating‐type specific genes: MAT1‐1‐1 (1161 bp), encoding an alpha‐domain containing protein, and MAT1‐1‐5 (1301 bp); or MAT1‐2‐1 (1236 bp), encoding a HMG‐domain protein, and MAT1‐2‐4 (712 bp); the latter genes encode putative proteins of unknown function. Truncated MAT1‐1‐1 (670 bp) and MAT1‐2‐1 (92 bp) sequences of the opposite mating‐type were found in the flanking regions. Idiomorph‐specific PCR primer pairs were used to explore the structure of the MAT1 locus in ascospore progeny and field isolates showing homothallic behaviour, and the locus organization in all of them did not differ from that of heterothallic strains. Constitutive expression of all the four mating‐type genes was ascertained by RT‐PCR at four different developmental stages (mycelium, sclerotia at two different stages and apothecia). Antisense transcription of the MAT1‐2‐1 gene with isoforms from alternative splicing was detected. Comparative analysis of MAT1 loci in B. cinerea and in the closely related homothallic Sclerotinia sclerotiorum led to the identification of short nearly identical sequences.
Effect of Temporary Meiotic Attenuation of Oocytes with Butyrolactone I and Roscovitine in Resistance to Bovine Embryos on Vitrification
Authors: Maziero RRD , Guaitolini CRF , Paschoal DM , Kievitsbosch T , Guastali MD , Moraes CN , Landim‐Alvarenga FC
Published: January 2016

Contents

This study aimed to produce in vitro bovine embryos by the addition of two drugs, which is responsible for oocyte meiosis inhibition: roscovitine (ROS) and butyrolactone I (BL‐I). Oocytes were recovered from slaughtered cows and matured in a commercial medium and maintained in a 5% CO2 atmosphere. Oocytes were maintained for 6 h in an in vitro maturation (IVM) medium containing ROS (12.5 μm), BL‐I (50 μm) and association of drugs (ROS 6.25 μm and BL‐I 25 μm). Oocytes were cultured for 18 h in an agent‐free medium for the resumption of meiosis. After 24 h of maturation, oocytes were inseminated in the commercial in vitro fertilization (IVF) medium. Presumptive zygotes were cultured in SOFaa medium in a 5% CO2 atmosphere. On day 3, rate of cleavage was evaluated and on days 6 and 7, rate of blastocyst formation. BL‐I and its association with the ROS increased the rates of cleavage and blastocyst formation (p < 0.05). The ROS alone was inefficient, impairing embryonic development, with low rates of blastocyst formation when compared to the control group and other treatments (p < 0.05). The embryos from BL‐I and ROS+BL‐I groups presented higher number of cells and lower rates of cellular apoptosis compared to other groups, either for the fresh or for post‐thawing embryos. Embryos from ROS+BL‐I group showed to be more resistant to the vitrification process, presenting a higher rate of embryonic re‐expansion (p < 0.05). In conclusion, block of meiosis using BL‐I or its association with ROS increased the rate of blastocyst formation, and the association of ROS+BL‐I resulted in a better resistance to the embryo cryopreservation process.
COPD and the microbiome
Authors: Mammen Manoj J. , Sethi Sanjay
Published: January 2016

Traditional culture techniques confirm that bacteria have an important role in Chronic Obstructive Pulmonary Disease (COPD). In individuals with COPD, acquisition of novel bacterial strains is associated with onset of acute exacerbation of COPD, which leads to further lung dysfunction and enormous health‐care costs. Recent study of the human microbiome, the total composite of the bacteria on the human body, posited the microbiome as the last human organ studied, as the microbiome performs a multitude of metabolic functions absent in the human genome. The largest project to study the human microbiome was the National Institutes of Health (NIH) human microbiome project (HMP) started in 2007 to understand the ‘normal’ microbiome. However due to the presumption that the healthy human lung was sterile, the respiratory tract was not included in that study. The advent of next‐generation sequencing technologies has allowed the investigation of the human respiratory microbiome, which revealed that the healthy lung does have a robust microbiome. Subsequent studies in individuals with COPD revealed that the microbiome composition fluctuates with severity of COPD, composition of the individual aero‐digestive tract microbiomes, age, during an acute exacerbation of COPD and with the use of steroids and/or antibiotics. Understanding the impact of the microbiome on COPD progression and risk of exacerbation will lead to directed therapies for prevention of COPD progression and exacerbation.
‘In the tomb of Ser Piero’: death and burial in the family of Leonardo da Vinci
Authors: Leader Anne
Published: January 2016

The origins of Leonardo da Vinci (1452–1519) have fascinated scholars for well over a century. Archival research has revealed much about Leonardo's origins and his complex family that included four stepmothers and twenty‐three half‐brothers and half‐sisters and their offspring. One source, however, has been overlooked by scholars – a Libro dei defunti, or necrology, kept by the Benedictine monks of the Badia Fiorentina, where Leonardo's father installed a family tomb in the late fifteenth century. This book of the dead, which lists burials from 1499 through the late eighteenth century, not only offers precious information about which of Leonardo's relatives found their final rest in Florence at the Badia but also provides invaluable help in reconstructing the disposition of the church interior. This article traces the history of the Da Vinci tomb from its first burial in 1474 to its last in 1614 and provides a transcription and analysis of relevant notices found in the Badia's Libro dei defunti.
Contractual Hazard, Political Hazard andFDIOwnership Structure in Joint‐venture Enterprises in China
Authors: Zhang Yuxiao , Fang Mingyue , Jiang Ting , Nie Huihua
Published: January 2016

This paper investigates how institutional environments, especially the contractual hazard and the political hazard, affect foreign investors’ share ratios in joint‐venture enterprises in China. We build a model combining Transaction Cost Economics and Property Rights Theory to describe the tradeoff that foreign investors face between choosing a larger share ratio and a smaller one. We argue that when the contractual hazard increases, foreign investors request larger shares to avoid being held up by their domestic partners, and when the political hazard increases, they hold smaller shares to circumvent the local government's grabbing hand. Moreover, the effect of the contractual hazard is channeled through enterprises’ asset specificity. These theoretical predictions are verified by studying the relationship between the ownership structure of Chinese manufacturing joint‐venture enterprises and the provincial‐level institutions they are embedded in.
Does Trade Integration Contribute to Peace?
Authors: Lee Jong‐Wha , Pyun Ju Hyun
Published: January 2016

We investigate the effect of trade integration on interstate military conflict. Our empirical analysis, based on a large panel data set of 243,225 country‐pair observations from 1950 to 2000, confirms that an increase in bilateral trade interdependence significantly promotes peace. It also suggests that the peace‐promotion effect of bilateral trade integration is significantly higher for contiguous countries that are likely to experience more conflict. More importantly, we find that not only bilateral trade but global trade openness also significantly promotes peace. It shows, however, that an increase in global trade openness reduces the probability of interstate conflict more for countries far apart from each other than it does for countries sharing borders. The main finding of the peace‐promotion effect of bilateral and global trade integration holds robust when controlling for the simultaneous determination of trade and peace.
The Stability of Ethnic Identity in England and Wales 2001–2011
Authors: Simpson Ludi , Jivraj Stephen , Warren James
Published: January 2016

The instability of ethnicity measured in the national census is found to have doubled from the period 1991–2001 to the period 2001–2011, using the Longitudinal Study that links a sample of individuals’ census records across time. From internal evidence and comparison with results from the Census Quality Survey and the Labour Force Survey, estimates are made of instability due to changing question wording, imputation of missing answers, proxy reporting, recording errors and changes in the allocation of write-in answers. Of the remaining instability, durable changes of ethnicity by individuals are thought to be considerably less common than changes due to a person's sense of identity not closely fitting the categories offered in the census question. The instability creates a net change in size of some ethnic groups that is usually small compared with the change in population between censuses from births, deaths and migration. Consequences for analysis of census aggregate and microdata are explored.
A Space–Time Multivariate Bayesian Model to Analyse Road Traffic Accidents by Severity
Authors: Boulieri Areti , Liverani Silvia , Hoogh Kees , Blangiardo Marta
Published: January 2016

The paper investigates the dependences between levels of severity of road traffic accidents, accounting at the same time for spatial and temporal correlations. The study analyses road traffic accidents data at ward level in England over the period 2005–2013. We include in our model multivariate spatially structured and unstructured effects to capture the dependences between severities, within a Bayesian hierarchical formulation. We also include a temporal component to capture the time effects and we carry out an extensive model comparison. The results show important associations in both spatially structured and unstructured effects between severities, and a downward temporal trend is observed for low and high levels of severity. Maps of posterior accident rates indicate elevated risk within big cities for accidents of low severity and in suburban areas in the north and on the southern coast of England for accidents of high severity. The posterior probability of extreme rates is used to suggest the presence of hot spots in a public health perspective.
Respondent-Driven Sampling Bias Induced by Community Structure and Response Rates in Social Networks
Authors: Rocha Luis E. C. , Thorson Anna E. , Lambiotte Renaud , Liljeros Fredrik
Published: January 2016

Sampling hidden populations is particularly challenging by using standard sampling methods mainly because of the lack of a sampling frame. Respondent-driven sampling is an alternative methodology that exploits the social contacts between peers to reach and weight individuals in these hard-to-reach populations. It is a snowball sampling procedure where the weight of the respondents is adjusted for the likelihood of being sampled due to differences in the number of contacts. The structure of the social contacts thus regulates the process by constraining the sampling within subregions of the network. We study the bias induced by network communities, which are groups of individuals more connected between themselves than with individuals in other groups, in the respondent-driven sampling estimator. We simulate different structures and response rates to reproduce real settings. We find that the prevalence of the estimated variable is associated with the size of the network community to which the individual belongs and observe that low degree nodes may be undersampled if the sample and the network are of similar size. We also find that respondent-driven sampling estimators perform well if response rates are relatively large and the community structure is weak, whereas low response rates typically generate strong biases irrespectively of the community structure.
Work Activation Regimes and Well‐being of Unemployed People: Rhetoric, Risk and Reality of Quasi‐Marketization in the UK Work Programme
Authors: Carter Eleanor , Whitworth Adam
Published: January 2016

Well‐being and employment activation have become central and intertwined policy priorities across advanced economies, with the mandation of unemployed claimants towards employability interventions (e.g. curriculum vitae preparation and interview skills). Compelled job search and job transitions are in part justified by the well‐being gains that resulting employment is said to deliver. However, this dominant focus within the activation field on outcome well‐being – the well‐being improvement triggered by a transition to paid work – neglects how participation in activation schemes can itself affect well‐being levels for unemployed people – what we term ‘process well‐being’ effects. Combining theoretical literature with empirical work on the UK's large‐scale quasi‐marketized Work Programme activation scheme, we develop the limited existing academic discussion of process well‐being effects, considering whether and how activation participation mediates the negative well‐being effects of unemployment, irrespective of any employment outcomes. We further relate variation in such process well‐being effects to the literature on activation typologies, in which ‘thinner’ work‐first activation interventions are linked to weaker process well‐being effects for participants compared to ‘thicker’ human capital development interventions. Confirming these expectations, our empirical work shows that Work Programme participants have, to date, experienced a largely ‘thin’ activation regime in which participants are both expected to, and empirically demonstrate, similar if not lower levels of process well‐being than those who are openly unemployed. These concerning findings speak to all nations seeking to promote the well‐being of unemployed people and particularly those perusing ‘black box’ activation schemes based around quasi‐marketization, devolution and New Public Management.
Agreement at PF: An Argument from Partial Control
Authors: Landau Idan
Published: January 2016

Controlled null subjects (PRO) are semantically bound variables that bear morphological features. In certain environments of partial control, the morphological ϕ‐features (specifically, [person]) and the semantic value of PRO diverge. A natural explanation of the fact that the [person] feature of PRO is uninterpreted is that it is assigned at Phonological Form (PF). Given that this feature participates in agreement relations, we conclude that agreement must be (optionally or exclusively) a PF phenomenon.
Structural insights and membrane binding properties of MGD1, the major galactolipid synthase in plants
Authors: Rocha Joana , Sarkis Joe , Thomas Aline , Pitou Laurence , Radzimanowski Jens , Audry Magali , Chazalet Valérie , de Sanctis Daniele , Palcic Monica M. , Block Maryse A. , Girard‐Egrot Agnès , Maréchal Eric , Breton Christelle
Published: January 2016

Monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) are the major lipid components of photosynthetic membranes, and hence the most abundant lipids in the biosphere. They are essential for assembly and function of the photosynthetic apparatus. In Arabidopsis, the first step of galactolipid synthesis is catalyzed by MGDG synthase 1 (MGD1), which transfers a galactosyl residue from UDP‐galactose to diacylglycerol (DAG). MGD1 is a monotopic protein that is embedded in the inner envelope membrane of chloroplasts. Once produced, MGDG is transferred to the outer envelope membrane, where DGDG synthesis occurs, and to thylakoids. Here we present two crystal structures of MGD1: one unliganded and one complexed with UDP. MGD1 has a long and flexible region (approximately 50 amino acids) that is required for DAG binding. The structures reveal critical features of the MGD1 catalytic mechanism and its membrane binding mode, tested on biomimetic Langmuir monolayers, giving insights into chloroplast membrane biogenesis. The structural plasticity of MGD1, ensuring very rapid capture and utilization of DAG, and its interaction with anionic lipids, possibly driving the construction of lipoproteic clusters, are consistent with the role of this enzyme, not only in expansion of the inner envelope membrane, but also in supplying MGDG to the outer envelope and nascent thylakoid membranes.
A randomized, blinded, placebo‐controlled trial of education and iron supplementation for mitigation of iron deficiency in regular blood donors
Authors: Mast Alan E. , Bialkowski Walter , Bryant Barbara J. , Wright David J. , Birch Rebecca , Kiss Joseph E. , D'Andrea Pam , Cable Ritchard G. , Spencer Bryan R.
Published: January 2016

BACKGROUND

The historical approach of offering dietary advice to donors with low hemoglobin (Hb) is ineffective for preventing iron deficiency in frequent donors. Alternative approaches to maintaining donor iron status were explored.

STUDY DESIGN AND METHODS

Frequent blood donors were randomly assigned into five arms for 2 years of follow‐up. Three double‐blinded arms provided 60 once‐daily pills after each donation (38, 19, or 0 mg of iron). Two single‐blinded arms provided iron status (ferritin) or no information letters after each donation. Ferritin, soluble transferrin receptor, and complete blood count were measured at each donation.

RESULTS

There were 692 subjects enrolled and 393 completed the study. Subjects in pill groups deenrolled more than those in letter groups (39% vs. 7%). Adverse events occurred equally in subjects receiving iron or placebo pills. Of those completing the study, the prevalence of ferritin of less than 12 or less than 26 ng/mL declined by more than 50% and was statistically indistinguishable in the three intervention groups (19 or 38 mg of iron; iron status letter). Longitudinal analyses of all subjects showed improved iron status in iron pill groups and worsening iron status in control groups (placebo; no information letter). The iron pill groups experienced a net increase of approximately 0.6 g/dL Hb compared to control groups. The iron status letter group had little change in Hb.

CONCLUSION

Providing 19 or 38 mg of daily iron or iron status information were effective and mostly equivalent interventions for mitigating iron deficiency in regular donors when compared at the end of the 2‐year longitudinal phase of the study. Donors without intervention had worsened iron deficiency with continued donation.
Maternal obesity associated with increase in natural killer T cells and CD8+ regulatory T cells in cord blood units
Authors: Gonzalez‐Espinosa Luis Octavio , Montiel‐Cervantes Laura Arcelia , Guerra‐Márquez Angel , Peñaflor‐Juárez Karina , Reyes‐Maldonado Elba , Vela‐Ojeda Jorge
Published: January 2016

BACKGROUND

One of the major limitations of umbilical cord blood (UCB) as hematopoietic stem cell source is its restricted cell number. In mothers who are candidates for stem cell donation, there are variables that affect the quantity and quality of UCB units. The aim of this study was to determine if obstetric, maternal, and fetal factors modify the number of lymphocyte subsets in UCB units.

STUDY DESIGN AND METHODS

This was a prospective, observational study. In UCB units, the numbers of CD34, NK, NKT, iNKT, Type 1 dendritic cells (DCs), Type 2 DCs, T γδ, T CD4+, T CD8+ lymphocytes, CD4+CD25+FoxP3+, and CD8+CD25+FoxP3+ T regulatory (Treg) cells were quantified by flow cytometry.

RESULTS

Fifty‐four UCB units were included; the donors’ mean weight was 75 kg (range, 52 to 102 kg) and they had a mean body mass index (BMI) of 30 kg/m2 (range 22 to 40 kg/m2), of which 12 (22%) had a normal BMI, 14 (26%) were overweight, and 28 (52%) were obese. The mean number of CD34+ cells was 4.45 × 106 (range, 0.7 × 106 to 20.5 × 106). The number of NKT, CD3+, CD4+, CD8+, and CD8+CD25+FoxP3+ Treg cells was significantly higher in overweight or obese mothers; CD34+ cells were decreased in the same group. The number of iNKT and CD34+ cells was decreased in newborns weighing above the average.

CONCLUSIONS

Maternal factors such as BMI, and fetal factors such as weight at birth, should be added to the selection criteria of UCB donors.
Electrochemical detection of Pseudomonas in wound exudate samples from patients with chronic wounds
Authors: Sismaet Hunter J. , Banerjee Anirban , McNish Sean , Choi Yongwook , Torralba Manolito , Lucas Sarah , Chan Agnes , Shanmugam Victoria K. , Goluch Edgar D.
Published: January 2016

In clinical practice, point‐of‐care diagnostic testing has progressed rapidly in the last decade. For the field of wound care, there is a compelling need to develop rapid alternatives for bacterial identification in the clinical setting, where it generally takes over 24 hours to receive a positive identification. Even new molecular and biochemical identification methods require an initial incubation period of several hours to obtain a sufficient number of cells prior to performing the analysis. Here we report the use of an inexpensive, disposable electrochemical sensor to detect pyocyanin, a unique, redox‐active quorum sensing molecule released by Pseudomonas aeruginosa, in wound fluid from patients with chronic wounds enrolled in the WE‐HEAL Study. By measuring the metabolite excreted by the cells, this electrochemical detection strategy eliminates sample preparation, takes less than a minute to complete, and requires only 7.5 μL of sample to complete the analysis. The electrochemical results were compared against 16S rRNA profiling using 454 pyrosequencing. Blind identification yielded 9 correct matches, 2 false negatives, and 3 false positives giving a sensitivity of 71% and specificity of 57% for detection of Pseudomonas. Ongoing enhancement and development of this approach with a view to develop a rapid point‐of‐care diagnostic tool is planned.
The pathobiology of pig‐to‐primate xenotransplantation: a historical review
Authors: Cooper David K.C. , Ezzelarab Mohamed B. , Hara Hidetaka , Iwase Hayato , Lee Whayoung , Wijkstrom Martin , Bottino Rita
Published: January 2016

The immunologic barriers to successful xenotransplantation are related to the presence of natural anti‐pig antibodies in humans and non‐human primates that bind to antigens expressed on the transplanted pig organ (the most important of which is galactose‐α1,3‐galactose [Gal]), and activate the complement cascade, which results in rapid destruction of the graft, a process known as hyperacute rejection. High levels of elicited anti‐pig IgG may develop if the adaptive immune response is not prevented by adequate immunosuppressive therapy, resulting in activation and injury of the vascular endothelium. The transplantation of organs and cells from pigs that do not express the important Gal antigen (α1,3‐galactosyltransferase gene‐knockout [GTKO] pigs) and express one or more human complement‐regulatory proteins (hCRP, e.g., CD46, CD55), when combined with an effective costimulation blockade‐based immunosuppressive regimen, prevents early antibody‐mediated and cellular rejection. However, low levels of anti‐non‐Gal antibody and innate immune cells and/or platelets may initiate the development of a thrombotic microangiopathy in the graft that may be associated with a consumptive coagulopathy in the recipient. This pathogenic process is accentuated by the dysregulation of the coagulation‐anticoagulation systems between pigs and primates. The expression in GTKO/hCRP pigs of a human coagulation‐regulatory protein, for example, thrombomodulin, is increasingly being associated with prolonged pig graft survival in non‐human primates. Initial clinical trials of islet and corneal xenotransplantation are already underway, and trials of pig kidney or heart transplantation are anticipated within the next few years.
A multiple‐gene phylogeny reveals polyphyly among eastern North American Aphaenogaster species (Hymenoptera: Formicidae)
Authors: DeMarco Bernice B. , Cognato Anthony I.
Published: January 2016

Twenty‐three Aphaenogaster species (Hymenoptera: Formicidae) occur in North America. While morphology and ecology define most species, the species limits of a group in the Eastern United States are unclear. In particular, the morphological and behavioural characters of A. carolinensis, A. picea and A. rudis overlap. These observations suggest that these three species are not monophyletic. We therefore tested the monophyly of Aphaenogaster in the context of molecular phylogenetic analyses. We used DNA data from five genes: CO1, CAD, EF1αF2, long‐wavelength rhodopsin and wingless, to reconstruct phylogenies for 44 Aphaenogaster and outgroup species. In the resulting trees, reconstructed using parsimony and Bayesian inference, species boundaries associated with well‐supported monophyletic clades of individuals in most of the 23 North American Aphaenogaster collected from multiple locations. However, some clades were unresolved, and both A. picea and A. rudis were not monophyletic. Although this may indicate that clades of multiple species represent fewer but morphologically varied species, given the short branch lengths, the lack of resolution may reflect the fact that these ants have recently radiated, and a lack of gene lineage sorting explains the non‐monophyly of species. Additional biological information concerning pre‐ and postmating barriers is needed before a complete revision of species boundaries for Aphaenogaster.
Chip Fracture Behavior in the High Speed Machining of Titanium Alloys
Authors: Zhang Xueping , Shivpuri Rajiv , Srivastava Anil K.
Published: January 2016

Machining of titanium alloy is a severe fracture procedure associated with localized adiabatic shearing process. Chip segmentation of titanium alloy is usually characterized with adiabatic shear band (ASB) and localized microfracture evolution process. ASB has been recognized as the precursor of fracture locus due to its sealed high strain intensity. Besides strain intensity, stress triaxiality (pressure-stress states) has also been identified as a significant factor to control fracture process through altering critical loading capacity and critical failure strain. The effect of stress triaxiality on failure strain was traditionally assessed by dynamic split Hopkinson pressure bar (SHPB), quasi-static tests of tension, compression, torsion, and shear for finite element (FE) analysis. However, the stress triaxiality magnitudes introduced by these experiments were much lower than those generated from the high speed machining operation due to the fact that ASBs in chip segmentation are usually involved in much higher strain, high strain rate, high stress, and high temperature associated with phase transformation. However, this aspect of fracture evolution related with stress triaxiality and phase transformation is not well understood in literature. This paper attempts to demonstrate the roles of stress triaxiality and phase transformation in chip segmentation especially in the high speed machining of titanium alloy in FE framework. Johnson–Cook (JC) failure model is calibrated by addressing the characteristics of stress triaxiality and phase transformation associated with high speed machining. This research confirms that the selection of failure criterion parameters incorporated the effects of stress triaxiality and the alpha–beta phase transformation is indispensible to successfully predict fracture behavior during chip segmentation process in the high speed machining of titanium alloys.
Strength of a Container Ship in Extreme Waves Obtained by Nonlinear Hydroelastoplasticity Dynamic Analysis and Finite Element Modeling
Authors: Liu Weiqin , Song Xuemin , Wu Weiguo , Suzuki Katsuyuki
Published: January 2016

Extreme waves have caused a lot of ship accidents and casualties. In this paper, a two-dimensional (2D) hydroelastoplasticity method is proposed to study the nonlinear dynamic responses of a container ship in extreme waves. On the one hand, the traditional ultimate strength evaluation is mainly performed using a quasi-static assumption without considering the dynamic wave effect. On the other hand, the dynamic response of a ship induced by a wave is studied based on hydroelasticity theory, which means the ship structural response to large waves is linear. Therefore, a 2D hydroelastoplasticity method that accounts for the coupling between the time-domain wave and ship beam for nonlinear vertical bending moment (VBM) is proposed. In addition, a nonlinear dynamic finite element method (FEM) is also applied for the nonlinear VBM of ship beam. The computational results of the FEM, including the nonlinear VBM and deformational angle, are compared with the results of the 2D hydroelastoplasticity and hydroelasticity. A number of numerical extreme wave models are selected for computations of hydroelasticity-plasticity, hydroelasticity, and FEM. A difference is observed between the nonlinear VBM calculated by FEM and linear VBM calculated by hydroelasticity, and conclusions are drawn.
Emergence of superconductivity in the canonical heavy-electron metal YbRh
2
Si
2
Authors: Schuberth Erwin , Tippmann Marc , Steinke Lucia , Lausberg Stefan , Steppke Alexander , Brando Manuel , Krellner Cornelius , Geibel Christoph , Yu Rong , Si Qimiao , Steglich Frank
Published: January 2016

Going to extremes to find superconductivity

Quantum phase transitions (QPTs) occur at zero temperature when parameters such as magnetic field or pressure are varied. In heavy fermion compounds, superconductivity often accompanies QPTs, a seeming exception being the material YbRh
2
Si
2
, which undergoes a magnetic QPT. Schuberth
et al.
performed magnetic and calorimetric measurements at extremely low temperatures and magnetic fields and found that it does become superconducting after all. Almost simultaneously with superconductivity, another order appeared that showed signatures of nuclear spin origin.

Science
, this issue p.
485
An unprecedented mechanism of nucleotide methylation in organisms containing
thyX
Authors: Mishanina Tatiana V. , Yu Liping , Karunaratne Kalani , Mondal Dibyendu , Corcoran John M. , Choi Michael A. , Kohen Amnon
Published: January 2016

A special way to make T

The genomes of all cell-based life consist of DNA. Blocking DNA synthesis is thus lethal, and if targeted selectively, its inhibition can provide cancer and antibiotic treatments. For example, the drug methotrexate interferes with the synthesis of thymidine, the base T in DNA. Mishanina
et al.
found that the enzyme that carries out the last step of thymidine synthesis in several human pathogens, which cause tuberculosis, anthrax, and typhus, uses a previously undescribed mechanism. Knowing the mechanism may allow the development of specific inhibitors for this enzyme.

Science
, this issue p.
507
Comment on “Worldwide evidence of a unimodal relationship between productivity and plant species richness”
Authors: Tredennick Andrew T. , Adler Peter B. , Grace James B. , Harpole W. Stanley , Borer Elizabeth T. , Seabloom Eric W. , Anderson T. Michael , Bakker Jonathan D. , Biederman Lori A. , Brown Cynthia S. , Buckley Yvonne M. , Chu Chengjin , Collins Scott L. , Crawley Michael J. , Fay Philip A. , Firn Jennifer , Gruner Daniel S. , Hagenah Nicole , Hautier Yann , Hector Andy , Hillebrand Helmut , Kirkman Kevin , Knops Johannes M. H. , Laungani Ramesh , Lind Eric M. , MacDougall Andrew S. , McCulley Rebecca L. , Mitchell Charles E. , Moore Joslin L , Morgan John W. , Orrock John L. , Peri Pablo L. , Prober Suzanne M. , Risch Anita C. , Schütz Martin , Speziale Karina L. , Standish Rachel J. , Sullivan Lauren L. , Wardle Glenda M. , Williams Ryan J. , Yang Louie H.
Published: January 2016

Fraser
et al
. (Reports, 17 July 2015, p. 302) report a unimodal relationship between productivity and species richness at regional and global scales, which they contrast with the results of Adler
et al
. (Reports, 23 September 2011, p. 1750). However, both data sets, when analyzed correctly, show clearly and consistently that productivity is a poor predictor of local species richness.
Ancient Babylonian astronomers calculated Jupiter’s position from the area under a time-velocity graph
Authors: Ossendrijver Mathieu
Published: January 2016

Babylonian astronomers tracked Jupiter

Ancient Babylonian astronomers developed many important concepts that are still in use, including the division of the sky into 360 degrees. They could also predict the positions of the planets using arithmetic. Ossendrijver translated several Babylonian cuneiform tablets from 350 to 50 BCE and found that they contain a sophisticated calculation of the position of Jupiter. The method relies on determining the area of a trapezium under a graph. This technique was previously thought to have been invented at least 1400 years later in 14th-century Oxford. This surprising discovery changes our ideas about how Babylonian astronomers worked and may have influenced Western science.

Science
, this issue p.
482
The intersection of nonalcoholic fatty liver disease and obesity
Authors: Woo Baidal Jennifer A. , Lavine Joel E.
Published: January 2016

New insights into the overlap and differences between obesity and nonalcoholic fatty liver disease (NAFLD) are contributing to advances in diagnosis and treatment of NAFLD.
No lung cancer left behind
Authors: Thomas Anish
Published: January 2016

Molecular profiling of lung cancer is feasible at the population scale.
Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel
Authors: Graf Erin H. , Simmon Keith E. , Tardif Keith D. , Hymas Weston , Flygare Steven , Eilbeck Karen , Yandell Mark , Schlaberg Robert
Published: January 2016

Current infectious disease molecular tests are largely pathogen specific, requiring test selection based on the patient's symptoms. For many syndromes caused by a large number of viral, bacterial, or fungal pathogens, such as respiratory tract infections, this necessitates large panels of tests and has limited yield. In contrast, next-generation sequencing-based metagenomics can be used for unbiased detection of any expected or unexpected pathogen. However, barriers for its diagnostic implementation include incomplete understanding of analytical performance and complexity of sequence data analysis. We compared detection of known respiratory virus-positive (
n
= 42) and unselected (
n
= 67) pediatric nasopharyngeal swabs using an RNA sequencing (RNA-seq)-based metagenomics approach and Taxonomer, an ultrarapid, interactive, web-based metagenomics data analysis tool, with an FDA-cleared respiratory virus panel (RVP; GenMark eSensor). Untargeted metagenomics detected 86% of known respiratory virus infections, and additional PCR testing confirmed RVP results for only 2 (33%) of the discordant samples. In unselected samples, untargeted metagenomics had excellent agreement with the RVP (93%). In addition, untargeted metagenomics detected an additional 12 viruses that were either not targeted by the RVP or missed due to highly divergent genome sequences. Normalized viral read counts for untargeted metagenomics correlated with viral burden determined by quantitative PCR and showed high intrarun and interrun reproducibility. Partial or full-length viral genome sequences were generated in 86% of RNA-seq-positive samples, allowing assessment of antiviral resistance, strain-level typing, and phylogenetic relatedness. Overall, untargeted metagenomics had high agreement with a sensitive RVP, detected viruses not targeted by the RVP, and yielded epidemiologically and clinically valuable sequence information.
The L, M, and S Segments of Rift Valley Fever Virus MP-12 Vaccine Independently Contribute to a Temperature-Sensitive Phenotype
Authors: Nishiyama Shoko , Lokugamage Nandadeva , Ikegami Tetsuro
Published: January 2016

Rift Valley fever (RVF) is endemic to Africa, and the mosquito-borne disease is characterized by “abortion storms” in ruminants and by hemorrhagic fever, encephalitis, and blindness in humans. Rift Valley fever virus (RVFV; family
Bunyaviridae
, genus
Phlebovirus
) has a tripartite negative-stranded RNA genome (L, M, and S segments). A live-attenuated vaccine for RVF, the MP-12 vaccine, is conditionally licensed for veterinary use in the United States. MP-12 is fully attenuated by the combination of the partially attenuated L, M, and S segments. Temperature sensitivity (ts) limits viral replication at a restrictive temperature and may be involved with viral attenuation. In this study, we aimed to characterize the ts mutations for MP-12. The MP-12 vaccine showed restricted replication at 38°C and replication shutoff (100-fold or greater reduction in virus titer compared to that at 37°C) at 39°C in Vero and MRC-5 cells. Using rZH501 reassortants with either the MP-12 L, M, or S segment, we found that all three segments encode a temperature-sensitive phenotype. However, the ts phenotype of the S segment was weaker than that of the M or L segment. We identified Gn-Y259H, Gc-R1182G, L-V172A, and L-M1244I as major ts mutations for MP-12. The ts mutations in the L segment decreased viral RNA synthesis, while those in the M segment delayed progeny production from infected cells. We also found that a lack of NSs and/or 78kD/NSm protein expression minimally affected the ts phenotype. Our study revealed that MP-12 is a unique vaccine carrying ts mutations in the L, M, and S segments.

IMPORTANCE
Rift Valley fever (RVF) is a mosquito-borne viral disease endemic to Africa, characterized by high rates of abortion in ruminants and severe diseases in humans. Vaccination is important to prevent the spread of disease, and a live-attenuated MP-12 vaccine is currently the only vaccine with a conditional license in the United States. This study determined the temperature sensitivity (ts) of MP-12 vaccine to understand virologic characteristics. Our study revealed that MP-12 vaccine contains ts mutations independently in the L, M, and S segments and that MP-12 displays a restrictive replication at 38°C.
Spatiotemporal Analysis of the Genetic Diversity of Seal Influenza A(H10N7) Virus, Northwestern Europe
Authors: Bodewes Rogier , Zohari Siamak , Krog Jesper S. , Hall Matthew D. , Harder Timm C. , Bestebroer Theo M. , van de Bildt Marco W. G. , Spronken Monique I. , Larsen Lars E. , Siebert Ursula , Wohlsein Peter , Puff Christina , Seehusen Frauke , Baumgärtner Wolfgang , Härkönen Tero , Smits Saskia L. , Herfst Sander , Osterhaus Albert D. M. E. , Fouchier Ron A. M. , Koopmans Marion P. , Kuiken Thijs
Published: January 2016

Influenza A viruses are major pathogens for humans, domestic animals, and wildlife, and these viruses occasionally cross the species barrier. In spring 2014, increased mortality of harbor seals (
Phoca vitulina
), associated with infection with an influenza A(H10N7) virus, was reported in Sweden and Denmark. Within a few months, this virus spread to seals of the coastal waters of Germany and the Netherlands, causing the death of thousands of animals. Genetic analysis of the hemagglutinin (HA) and neuraminidase (NA) genes of this seal influenza A(H10N7) virus revealed that it was most closely related to various avian influenza A(H10N7) viruses. The collection of samples from infected seals during the course of the outbreak provided a unique opportunity to follow the adaptation of the avian virus to its new seal host. Sequence data for samples collected from 41 different seals from four different countries between April 2014 and January 2015 were obtained by Sanger sequencing and next-generation sequencing to describe the molecular epidemiology of the seal influenza A(H10N7) virus. The majority of sequence variation occurred in the HA gene, and some mutations corresponded to amino acid changes not found in H10 viruses isolated from Eurasian birds. Also, sequence variation in the HA gene was greater at the beginning than at the end of the epidemic, when a number of the mutations observed earlier had been fixed. These results imply that when an avian influenza virus jumps the species barrier from birds to seals, amino acid changes in HA may occur rapidly and are important for virus adaptation to its new mammalian host.

IMPORTANCE
Influenza A viruses are major pathogens for humans, domestic animals, and wildlife. In addition to the continuous circulation of influenza A viruses among various host species, cross-species transmission of influenza A viruses occurs occasionally. Wild waterfowl and shorebirds are the main reservoir for most influenza A virus subtypes, and spillover of influenza A viruses from birds to humans or other mammalian species may result in major outbreaks. In the present study, various sequencing methods were used to elucidate the genetic changes that occurred after the introduction and subsequent spread of an avian influenza A(H10N7) virus among harbor seals of northwestern Europe by use of various samples collected during the outbreak. Such detailed knowledge of genetic changes necessary for introduction and adaptation of avian influenza A viruses to mammalian hosts is important for a rapid risk assessment of such viruses soon after they cross the species barrier.
Functional Comparison of HBZ and the Related APH-2 Protein Provides Insight into Human T-Cell Leukemia Virus Type 1 Pathogenesis
Authors: Panfil Amanda R. , Dissinger Nathan J. , Howard Cory M. , Murphy Brandon M. , Landes Kristina , Fernandez Soledad A. , Green Patrick L.
Published: January 2016

Human T-cell leukemia virus type 1 (HTLV-1) and type 2 (HTLV-2) are highly related retroviruses that transform T cells
in vitro
but have distinct pathological outcomes
in vivo
. HTLV-1 encodes a protein from the antisense strand of its proviral genome, the HTLV-1 basic leucine zipper factor (HBZ), which inhibits Tax-1-mediated viral transcription and promotes cell proliferation, a high proviral load, and persistence
in vivo
. In adult T-cell leukemia/lymphoma (ATL) cell lines and patient T cells,
hbz
is often the only viral gene expressed. The antisense strand of the HTLV-2 proviral genome also encodes a protein termed APH-2. Like HBZ, APH-2 is able to inhibit Tax-2-mediated viral transcription and is detectable in most primary lymphocytes from HTLV-2-infected patients. However, unlike HBZ, the loss of APH-2
in vivo
results in increased viral replication and proviral loads, suggesting that HBZ and APH-2 modulate the virus and cellular pathways differently. Herein, we examined the effect of APH-2 on several known HBZ-modulated pathways: NF-κB (p65) transactivation, transforming growth factor β (TGF-β) signaling, and interferon regulatory factor 1 (IRF-1) transactivation. Like HBZ, APH-2 has the ability to inhibit p65 transactivation. Conversely, HBZ and APH-2 have divergent effects on TGF-β signaling and IRF-1 transactivation. Quantitative PCR and protein half-life experiments revealed a substantial disparity between HBZ and APH-2 transcript levels and protein stability, respectively. Taken together, our data further elucidate the functional differences between HBZ and APH-2 and how these differences can have profound effects on the survival of infected cells and, ultimately, pathogenesis.

IMPORTANCE
Human T-cell leukemia virus type 1 (HTLV-1) and type 2 (HTLV-2) are highly related retroviruses that have distinct pathological outcomes in infected hosts. Functional comparisons of HTLV-1 and HTLV-2 proteins provide a better understanding about how HTLV-1 infection is associated with disease and HTLV-2 infection is not. The HTLV genome antisense-strand genes
hbz
and
aph-2
are often the only viral genes expressed in HTLV-infected T cells. Previously, our group found that HTLV-1 HBZ and HTLV-2 APH-2 had distinct effects
in vivo
and hypothesized that the differences in the interactions of HBZ and APH-2 with important cell signaling pathways dictate whether cells undergo proliferation, apoptosis, or senescence. Ultimately, these functional differences may affect how HTLV-1 causes disease but HTLV-2 generally does not. In the current study, we compared the effects of HBZ and APH-2 on several HTLV-relevant cellular pathways, including the TGF-β signaling, NF-κB activation, and IRF-1 transactivation pathways.
High-velocity facial gunshot wounds: multidisciplinary care from prehospital to discharge
Authors: Sinnott J D , Morris G , Medland P J , Porter K
Published: January 2016

A case is presented in which a high velocity rifle (shotgun) was fired into the inferior part of a patient's face in an attempted suicide causing widespread trauma to the inferior and left side of the patient's face. He presented to his general practitioner where an ambulance was called. The patient is followed from prehospital care (air ambulance) to resuscitation in accident and emergency and through the first stages of reconstructive surgery. The article focuses on the multidisciplinary approach to the patient's prehospital care and initial resuscitation at a major trauma centre. CT reconstruction images of the patient's skull allow visualisation of the extent of bone damage at presentation. Medical photography allows visualisation of the extent of the initial damage and shows how reconstructive surgery was undertaken early and in progressive stages. A literature review was performed allowing discussion of the current evidence and best practice in the management of facial gunshot wounds.
Use of butane–isobutane refrigerant spray in the management of a mucocoele in a visually impaired child
Authors: Birapu Uday Chowdary , Puppala Ravindar , Kethineni Balaji , Banavath Sunitha
Published: January 2016

Mucocoeles are commonly observed lesions in children and young adults. Conventional management using a scalpel aims at enucleation, requiring psychological preparation of the parent as well as the child because of inherent fear and apprehension towards surgery. This is still more complex in children with visual impairment. The other management techniques are laser, cryotherapy and micromarsupialisation, management strategies that, being painless and tolerable, reduce the anxiety of the child and are therefore more acceptable. The basic technique of cryotherapy stresses on rapid cooling, gradual thawing and repeated freezing to ensure tissue destruction. We report a case of a 13-year-old boy with visual impairment, presenting with a mucocoele on the lower lip, which was managed using butane–isobutane refrigerant spray, which is otherwise routinely employed for pulp vitality testing. A single, 2 min freeze/thaw cycle was used. The healing was uneventful.
Advanced rectal cancer in a long-term Hartmann's pouch: a forgotten organ revisited
Authors: Al Maksoud Ahmed Mahmoud Abd El Aziz , Ahmed Iftikhar
Published: January 2016

Hartmann's procedure is widely performed as a first-stage operation in cases of left colon emergencies when a one stage management is judged to be unsafe. Forty per cent of patients with Hartmann's procedure never get their stoma reversed, ending with a permanent stoma. The distal excluded Hartmann's pouch is usually forgotten compared to the proximal functioning colon. A 70-year-old man with Hartmann's procedure carried out previously for complicated diverticular disease presented with bleeding per rectum. Invasive adenocarcinoma was confirmed on histology. Subsequent staging revealed a locally advanced rectal cancer. The tumour progressed despite a course of neoadjuvant chemoradiation. The general condition of the patient deteriorated with development of renal failure. The patient died a few weeks later. By reporting this case, we are revisiting the long forgotten Hartmann's pouch to highlight the potential pathologies in the distal stump and to emphasise that a distal stump should not be forgotten even in asymptomatic patients.