bluuebunny/crossref_metadata_2025 huggingface dataset:
INC-Seq: Accurate single molecule reads using nanopore sequencing
Authors: Li Chenhao , Chng Kern Rei , Hui Boey Esther Jia , Qi Ng Amanda Hui , Wilm Andreas , Nagarajan Niranjan
Published: January 2016

Nanopore sequencing provides a rapid, cheap and portable real-time sequencing platform with the potential to revolutionize genomics. Several applications, including RNA-seq, haplotype sequencing and 16S sequencing, are however limited by its relatively high single read error rate (>10%). We present INC-Seq (Intramolecular-ligated Nanopore Consensus Sequencing) as a strategy for obtaining long and accurate nanopore reads starting with low input DNA. Applying INC-Seq for 16S rRNA based bacterial profiling generated full-length amplicon sequences with median accuracy >97%. INC-Seq reads enable accurate species-level classification, identification of species at 0.1% abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling on the MinION system.
Citizen Science for Mining the Biomedical Literature
Authors: Tsueng Ginger , Nanis Steven M. , Fouquier Jennifer , Good Benjamin M , Su Andrew I
Published: January 2016

I.

Biomedical literature represents one of the largest and fastest growing collections of unstructured biomedical knowledge. Finding critical information buried in the literature can be challenging. In order to extract information from freeflowing text, researchers need to: 1. identify the entities in the text (named entity recognition), 2. apply a standardized vocabulary to these entities (normalization), and 3. identify how entities in the text are related to one another (relationship extraction). Researchers have primarily approached these information extraction tasks through manual expert curation, and computational methods. We have previously demonstrated that named entity recognition (NER) tasks can be crowdsourced to a group of nonexperts via the paid microtask platform, Amazon Mechanical Turk (AMT); and can dramatically reduce the cost and increase the throughput of biocuration efforts. However, given the size of the biomedical literature even information extraction via paid microtask platforms is not scalable. With our web-based application Mark2Cure (http://mark2cure.org), we demonstrate that NER tasks can also be performed by volunteer citizen scientists with high accuracy. We apply metrics from the Zooniverse Matrices of Citizen Science Success and provide the results here to serve as a basis of comparison for other citizen science projects. Further, we discuss design considerations, issues, and the application of analytics for successfully moving a crowdsourcing workflow from a paid microtask platform to a citizen science platform. To our knowledge, this study is the first application of citizen science to a natural language processing task.
Improvement in X-ray stress measurement using Debye–Scherrer rings by in-plane averaging
Authors: Miyazaki Toshiyuki , Fujimoto Yohei , Sasaki Toshihiko
Published: January 2016

A technique to improve X-ray stress measurement using Debye–Scherrer rings is reported. In previous work, a Fourier-series-based generalization of the cosα method was proposed, which can measure the stress from a Debye–Scherrer ring. That technique and the cosα method have difficulties in determining the stress when the grain size of the specimen is relatively large and the Debye–Scherrer ring is grainy. To cope with this problem, in-plane averaging has been used to improve the cosα method when measuring coarse-grained specimens. In this study, Fourier series analysis is incorporated with in-plane averaging and it is explained how in-plane averaging improves the stress measurement. Furthermore, the validity of the new technique is demonstrated by measuring the stress of a carbon steel specimen.
Improving diffraction resolution using a new dehydration method
Authors: Huang Qingqiu , Szebenyi Doletha M. E.
Published: January 2016

The production of high-quality crystals is one of the major obstacles in determining the three-dimensional structure of macromolecules by X-ray crystallography. It is fairly common that a visually well formed crystal diffracts poorly to a resolution that is too low to be suitable for structure determination. Dehydration has proven to be an effective post-crystallization treatment for improving crystal diffraction quality. Several dehydration methods have been developed, but no single one of them is suitable for all crystals. Here, a new convenient and effective dehydration method is reported that makes use of a dehydrating solution that will not dry out in air for several hours. Using this dehydration method, the resolution ofArchaeoglobus fulgidusCas5a crystals has been increased from 3.2 to 1.95 Å and the resolution ofEscherichia coliLptA crystals has been increased from <5 to 3.4 Å.
Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations
Authors: Porebski Przemyslaw Jerzy , Cymborowski Marcin , Pasenkiewicz-Gierula Marta , Minor Wladek
Published: January 2016

Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the programFitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation.Fitmunkwas extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability ofFitmunkto model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions.Fitmunkcan be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density.Fitmunkis available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/.
1-[(4-Methoxyphenyl)sulfonyl]-1H-indole-3-carbaldehyde
Authors: Jithesh Babu E. A. , Vinay Kumar K. S. , Chandra  , Sadashiva M. P. , Mahendra M.
Published: January 2016

In the molecule of the title compound, C16H13NO4S, the mean plane of the indole ring system and that of the methoxyphenyl ring, which are bridged by a sulfonyl group, are inclined at a dihedral angle of 88.98 (9)°. The crystal structure is stabilized by intermolecular C—H...O hydrogen bonds.
Field trial of seismic recording using distributed acoustic sensing with broadside sensitive fibre‐optic cables
Authors: Hornman J.C.
Published: January 2016

Distributed acoustic sensing is an emerging technology using fibre‐optic cables to detect acoustic disturbances such as flow noise and seismic signals. The technology has been applied successfully in hydraulic fracture monitoring and vertical seismic profiling. One of the limitations of distributed acoustic sensing for seismic recording is that the conventional straight fibres do not have broadside sensitivity and therefore cannot be used in configurations where the raypaths are essentially orthogonal to the fibre‐optic cable, such as seismic reflection methods from the surface. The helically wound cable was designed to have broadside sensitivity. In this paper, a field trial is described to validate in a qualitative sense the theoretically predicted angle‐dependent response of a helically wound cable. P‐waves were measured with a helically wound cable as a function of the angle of incidence in a shallow horizontal borehole and compared with measurements with a co‐located streamer. The results show a similar behaviour as a function of the angle of incidence as the theory. This demonstrates the possibility of using distributed acoustic sensing with a helically wound cable as a seismic detection system with a horizontal cable near the surface. The helically wound cable does not have any active parts and can be made as a slim cable with a diameter of a few centimetres. For that reason, distributed acoustic sensing with a helically wound cable is a potential low‐cost option for permanent seismic monitoring on land.
Migratory connectivity and effects of winter temperatures on migratory behaviour of the European robin Erithacus rubecula: a continent‐wide analysis
Authors: Ambrosini Roberto , Cuervo José Javier , du Feu Chris , Fiedler Wolfgang , Musitelli Federica , Rubolini Diego , Sicurella Beatrice , Spina Fernando , Saino Nicola , Møller Anders Pape
Published: January 2016

Many partially migratory species show phenotypically divergent populations in terms of migratory behaviour, with climate hypothesized to be a major driver of such variability through its differential effects on sedentary and migratory individuals.

Based on long‐term (1947–2011) bird ringing data, we analysed phenotypic differentiation of migratory behaviour among populations of the European robin Erithacus rubecula across Europe.

We showed that clusters of populations sharing breeding and wintering ranges varied from partial (British Isles and Western Europe, NW cluster) to completely migratory (Scandinavia and north‐eastern Europe, NE cluster).

Distance migrated by birds of the NE (but not of the NW) cluster decreased through time because of a north‐eastwards shift in the wintering grounds. Moreover, when winter temperatures in the breeding areas were cold, individuals from the NE cluster also migrated longer distances, while those of the NW cluster moved over shorter distances.

Climatic conditions may therefore affect migratory behaviour of robins, although large geographical variation in response to climate seems to exist.
Appraisers and Valuation Bias: An Empirical Analysis
Authors: Tzioumis Konstantinos
Published: January 2016

Using appraisals from a lender across the 2005–2006 period, we find that the association between appraisers’ valuation inflation patterns and work volume varies across states. Moreover, we find a considerable occupational exit for appraisers, and provide evidence that appraisers, as applicants, did not receive better loan pricing compared with the population of applicants. Overall, this article offers novel insights concerning the political economy of financial regulation through the lens of a specific profession.
Estimating the Value of Proximity to Water, When Ceteris Really Is Paribus
Authors: Rouwendal Jan , Levkovich Or , van Marwijk Ramona
Published: January 2016

Proximity to water is appreciated by households. Hedonic analyses that try to measure the value of this amenity are potentially biased by omitted variables because locations close to water may be selected by households with higher incomes who construct more luxury houses. Because it is difficult to observe all the relevant characteristics, the coefficient for proximity to water may be biased upwards. We circumvent this problem by exploiting a specific characteristic of the Dutch system of planned residential development: often a number of exactly similar houses are constructed close to each other. By comparing the values of such identical houses, we can measure the effect of proximity to water under almost ideal circumstances. Introduction of these fixed effects lowers the estimated impact of this amenity, thereby confirming the conjectured presence of an omitted variable bias.
An evaluation of asset impairments by Australian firms and whether they were impacted by AASB 136
Authors: Bond David , Govendir Brett , Wells Peter
Published: January 2016

This study evaluates how managers of Australian firms are implementing the regulation requiring the impairment of assets and whether asset impairments can be categorised as non‐discretionary. We find some evidence that realised asset impairments are reflective of regulatory requirements. However, for the majority of firms exhibiting at least one externally observable indicator of impairment, they are not recognising asset impairments, and recognition is often delayed. Accordingly, while realised asset impairments might be categorised non‐discretionary, the timing of their recognition appears highly discretionary. There is some evidence that the realisation of asset impairments increased subsequent to transition to IFRS; however, the majority of firms with indicators of impairment are still not recognising asset impairments.
The microbiome and atopic eczema: More than skin deep
Authors: Thomas Charlotte L , Fernández‐Peñas Pablo
Published: January 2016

Discoveries in the defective molecular composition of the epidermal barrier, such as the epidermal protein filaggrin, in those with atopic eczema (or atopic dermatitis [AD]) have proved crucial in understanding this disease, but its aetiology remains to be fully elucidated. The epidermal barrier is just one interface between the microbial world and our immune system. Recent advances in molecular technology have demonstrated for the first time the true scale of the normal human microbiome and changes seen in disease states. In this review article we discuss the role of the human microbiome in the aetiology and maintenance of AD. The role of Staphylococcus aureus within the skin microbiome is examined, in addition to the role of other bacteria and fungi, identified using novel culture‐independent methods. The significant contribution of the gut microbiome and its manipulation via probiotic use is also reviewed. We emphasise that the microbiome of separate systems, including the gut, has a significant role to play in the manifestation of this cutaneous disorder. To date, there has been a lack of studies investigating whether changes to the lung microbiome may play a role in AD. An early interaction between the microbiome and immune system via multiple routes (skin–gut–lung) could feasibly affect the risk of a subsequent development of atopic diseases. When making management decisions for AD patients, clinicians must be mindful of the role of the microbiome.
Is there a difference in the behaviour and subsequent management of ectopic pregnancies seen at first scan compared to those ectopic pregnancies which commence as pregnancies of unknown location?
Authors: Lattouf Ihab , Lu Chuan , Pixton Sarah , Reid Shannon , Condous George
Published: January 2016

Aims

The primary aim was to assess whether ectopic pregnancies (EPs) visualised on primary scan behave differently to EPs initially characterised as pregnancies of unknown location (PUL). The secondary aim was to assess whether the EP group is more likely to have surgical management compared to the PUL ectopic pregnancy group.

Materials and Methods

Prospective observational study. Consecutive first trimester women presenting from November 2006 to March 2012 underwent transvaginal ultrasound (TVS). Women diagnosed with an EP on TVS were divided into two groups: visualised EPs noted on the first TVS, and PULs which subsequently developed into EPs. Twenty‐five historical, clinical, biochemical and ultrasonographic variables were collected. Different management strategies (expectant, medical, surgical) once an EP was confirmed on TVS were recorded. Univariate analysis was performed to compare differences between the two groups as well as rates for the three final management strategies.

Results

A total of 3341 consecutive women underwent TVS. On initial scan, 86.2% were classified as intrauterine pregnancy, 8.8% as PUL and 5.0% as EP (145 tubal/23 nontubal EPs). There were 194 tubal EPs in final analysis: 49 of 194 (25.3%) initially classified as PUL and 145 of 194 (74.7%) diagnosed as EP at primary TVS. When comparing the EP to the PUL EP group, the pain scores were 3.34 versus 1.91 (P‐value < 0.001), the mean sac diameters were 35.2 versus 18.5 mm (P‐value = 0.0327), and the volume of the EP masses were 8.21E+04 versus 1.40E+04 (P‐value = 0.0341). Cumulative surgical intervention rate was significantly higher in EP compared to PUL EP group (P‐value = 0.036).

Conclusions

EPs seen at the first ultrasound scan appear to be more symptomatic, larger in diameter and volume compared to EPs which started as PULs. Cumulative surgical intervention rate was noted to be higher in this group with EP seen on ultrasound at the outset.
Helicobacter pylori infection is high in paediatric nonulcer dyspepsia but not associated with specific gastrointestinal symptoms
Authors: Correa Silva RGS , Machado NC , Carvalho MA , Rodrigues MAM
Published: January 2016

Aim

The association between Helicobacter pylori infection and gastrointestinal symptoms is debatable in childhood. We examined the potential relationship between H. pylori infection and gastrointestinal symptoms in Brazilian children with nonulcer dyspepsia.

Methods

This prospective observational study analysed 240 Brazilian children and adolescents (68.7% girls) with chronic nonulcer dyspepsia, who underwent upper gastrointestinal endoscopy and biopsy. Their mean age was 9.8 years (range 4–17). Upper gastrointestinal symptoms, including abdominal pain, nausea, burning, early satiety, belching and weigh loss, were evaluated by a questionnaire and H. pylori infection was determined by histopathology of gastric biopsies.

Results

H. pylori infection was identified in 123/240 patients (52%). There was no significant association between the H. pylori infection and gastrointestinal symptoms and no relationship between the infection and abdominal pain or pain characteristics. However, nausea was significantly associated with the H. pylori infection, with an odds ratio of 1.76 and 95% confidence interval of 1.1–2.94 p < 0.03. Symptoms lasting longer than 12 months were significantly more frequent in children with pangastritis than in those with antral gastritis (p < 0.05).

Conclusion

The prevalence of H. pylori infection was high in Brazilian children with nonulcer dyspepsia, but was not associated with specific signs and symptoms, except for nausea.
Expression and function of endogenous retroviruses in the placenta
Authors: Denner Joachim
Published: January 2016

Although the expression of endogenous retroviruses in the placenta of numerous species was observed a long time ago, their physiological function during gestation was demonstrated only very recently. Expression of retroviral envelope proteins, also called syncytins, in the placenta allows generation of the multinuclear syncytiotrophoblast as an outer cellular layer of the placenta by fusion of the trophoblast cells. This fusion process is crucial for the development of the placenta and for successful pregnancy. It is still unclear whether the immunosuppressive properties of the transmembrane envelope protein of the endogenous retroviruses expressed in the placenta contribute to immunosuppression to prevent the rejection of the semiallotransplant embryo. The presence of placenta cells expressing retroviral envelope proteins surrounded by immune cells deep in the maternal tissue supports an immunosuppressive function. It is important to emphasize that during evolution different species utilized (‘enslaved’) different endogenous retroviruses and that two or more endogenous retroviruses are involved in placentogenesis in each species.
Human endogenous retroviruses: friend or foe?
Authors: Weiss Robin A.
Published: January 2016

The integration of proviral DNA into host chromosomal DNA as an obligatory step in the replication cycle of retroviruses is a natural event of genetic recombination between virus and host. When integration occurs in cells of the germ line, it results in mendelian inheritance of viral sequences that we call endogenous retroviruses (ERV) and HERV for humans. HERVs and host often establish a symbiotic relationship, especially in the placenta and in pluripotent embryonic stem cells, but HERVs occasionally have deleterious consequences for the host. This special issue of APMIS features the fascinating relationships between HERV and humans in health and disease.
The role of molecular mimicry and other factors in the association of Human Endogenous Retroviruses and autoimmunity
Authors: Trela Malgorzata , Nelson Paul N. , Rylance Paul B.
Published: January 2016

Human Endogenous Retroviruses (HERVs) have been implicated in autoimmune and other diseases. Molecular mimicry has been postulated as a potential mechanism of autoimmunity. Exogenous viruses have also been reported to be associated with the same diseases, as have genetic and environmental factors. If molecular mimicry were to be shown to be an initiating mechanism of some autoimmune diseases, then therapeutic options of blocking antibodies and peptides might be of benefit in halting diseases at the outset. Bioinformatic and molecular modelling techniques have been employed to investigate molecular mimicry and the evidence for the association of HERVs and autoimmunity is reviewed. The most convincing evidence for molecular mimicry is in rheumatoid arthritis, where HERV K‐10 shares amino acid sequences with IgG1Fc, a target for rheumatoid factor. Systemic lupus erythematosus is an example of a condition associated with several autoantibodies, and several endogenous and exogenous viruses have been reported to be associated with the disease. The lack of a clear link between one virus and this condition, and the spectrum of clinical manifestations, suggests that genetic, environmental and the inflammatory response to a virus or viruses might also be major factors in the pathogenesis of lupus and other autoimmune conditions. Where there are strong associations between a virus and an autoimmune condition, such as in hepatitis C and cryoglobulinaemia, the use of bioinformatics and molecular modelling can also be utilized to help to understand the role of molecular mimicry in how HERVs might trigger disease.
Viral symbiosis and the holobiontic nature of the human genome
Authors: Ryan Francis Patrick
Published: January 2016

The human genome is a holobiontic union of the mammalian nuclear genome, the mitochondrial genome and large numbers of endogenized retroviral genomes. This article defines and explores this symbiogenetic pattern of evolution, looking at the implications for human genetics, epigenetics, embryogenesis, physiology and the pathogenesis of inborn errors of metabolism and many other diseases.
How can we Understand the Demise of Kids Company?
Authors: Foster Angela
Published: January 2016

The sudden closure of the charity Kids Company was headline news in the UK on 6 August 2015. In this piece the author shares her feeling of shock, her questions and her concerns arising from the BBC interviews with the charity's founder Camila Batmanghelidjh who had been at the helm for 19 years. While alluding to the vision of charismatic leaders and their extraordinary ability to bring about social transformations, the author refers to Weber and others highlighting that charismatic leadership must be transitional if the enterprise is to survive. However, charisma can lead to idealization which puts the enterprise at risk.
Grass Physiognomic Trait Variation in African Herbaceous Biomes
Authors: Pasturel Marine , Alexandre Anne , Novello Alice , Dièye Amadou M. , Wélé Abdoulaye , Paradis Laure , Cordova Carlos , Hély Christelle
Published: January 2016

African herbaceous biomes will likely face drastic changes in the near future, due to climate change and pressures from increasing human activities. However, these biomes have been simulated only by dynamic global vegetation models and failing to include the diversity of C4 grasses has limited the accuracy of these models. Characterizing the floristic and physiognomic diversity of these herbaceous biomes would enhance the parameterization of C4 grass plant functional types, thereby improving simulations. To this end, we used lowermost and uppermost values of three grass physiognomic traits (culm height, leaf length, and leaf width) available in most floras to identify several grass physiognomic groups that form the grass cover in Senegal. We then checked the capacity of these groups to discriminate herbaceous biomes and mean annual precipitation domains. Specifically, we assessed whether these groups were sufficiently generic and robust to be applied to neighboring (Chad) and distant (South Africa) phytogeographic areas. The proportions of two physiognomic groups, defined by their lowermost limits, delineate steppe from savanna and forest biomes in Senegal, and nama‐karoo, savanna, and grassland biomes in South Africa. Proportions of these two physiognomic groups additionally delineate the mean annual precipitation domains <600 mm and >600 mm in Senegal, Chad, and South Africa, as well as the <250 mm and >1000 mm domains in South Africa. These findings should help to identify and parameterize new C4 grass plant functional types in vegetation models applied to West and South Africa.
Induced Floral and Extrafloral Nectar Production Affect Ant‐pollinator Interactions and Plant Fitness
Authors: Hernandez‐Cumplido Johnattan , Forter Bastien , Moreira Xoaquín , Heil Martin , Benrey Betty
Published: January 2016

Thousands of plant species throughout tropical and temperate zones secrete extrafloral nectar to attract ants, whose presence provides an indirect defense against herbivores. Extrafloral nectaries are located close to flowers and may modify competition between ants and pollinators. Here, we used Lima bean (Phaseolus lunatus L.) to study the plants interaction between ants and flower visitors and its consequences for plant fitness. To test these objectives, we carried out two field experiments in which we manipulated the presence of ants and nectar production via induction with jasmonic acid (JA). We then measured floral and extrafloral nectar production, the number of patrolling ants and flower visitors as well as specific plant fitness traits. Lima bean plants under JA induction produced more nectar in both extrafloral nectaries and flowers, attracted more ants and produced more flowers and seeds than non‐induced plants. Despite an increase in floral nectar in JA plants, application of this hormone had no significant effects on flower visitor attraction. Finally, ant presence did not result in a decrease in the number of visits, but our results suggest that ants could negatively affect pollination efficiency. In particular, JA‐induced plants without ants produced a greater number of seeds compared with the JA‐treated plants with ants.
Collagen barrier membranes adsorb growth factors liberated from autogenous bone chips
Authors: Caballé‐Serrano Jordi , Sawada Kosaku , Miron Richard J. , Bosshardt Dieter D. , Buser Daniel , Gruber Reinhard
Published: January 2016

Objective

Collagen membranes serve as barriers to separate bone grafts from soft tissues. Bone grafts harvested with a bone scraper release growth factors activating transforming growth factor‐β (TGF‐β) signaling in mesenchymal cells. The aim of the present pilot study was to determine whether collagen membranes adsorb molecules from bone‐conditioned medium (BCM) with the capacity to provoke the expression of TGF‐β target genes in vitro.

Materials and Methods

Collagen membranes were soaked in aqueous extracts from fresh and demineralized bone chips placed in cell culture medium. Recombinant human TGF‐β1 served as control. Gingival fibroblasts were seeded onto the washed collagen membranes and evaluated for the expression of adrenomedullin, pentraxin 3, interleukin 11, and proteoglycan 4. Cell viability and morphology with phalloidin staining were also determined.

Results

Incubation of collagen membranes with BCM for at least one minute caused fibroblasts to decrease the expression of adrenomedullin and pentraxin 3, and to increase the expression of interleukin 11 and proteoglycan 4. Four different membrane treatments – incubated with recombinant TGF‐β1, pre‐wetted with saline solution, exposed to UV light, and dry out and stored one week at room temperature – also provoked significant changes in gene expression. Likewise, conditioned medium from demineralized bone chips caused gene expression changes. BCM did not alter the viability or morphology of gingival fibroblasts.

Conclusions

These findings demonstrate that collagen membranes rapidly adsorb the TGF‐β activity released from bone chips, a molecular process that might contribute to guided bone regeneration.
Progesterone modulates endothelial progenitor cell (EPC) viability through theCXCL12/CXCR4/PI3K/Akt signalling pathway
Authors: Yu Peng , Zhang Zhifei , Li Shengjie , Wen Xiaolong , Quan Wei , Tian Qilong , Chen Jieli , Zhang Jianning , Jiang Rongcai
Published: January 2016

Objectives

Progesterone treatment can effectively increase levels of circulating endothelial progenitor cells (EPCs) and improve neurological functional outcome in a traumatic brain injury (TBI) rat model. However, the mechanisms of progesterone's effects onEPCviability remain elusive. TheCXCL12/CXCR4 (CXCchemokine ligand 12/CXCchemokine receptor 4) signalling pathway regulates cell proliferation; we hypothesize that it mediates progesterone‐inducedEPCviability.

Materials and methods

EPCs were isolated from bone marrow‐derived mononuclear cells (BM‐MNCs) and treated with progesterone (5, 10 and 100 nm).MTSassay was used to investigateEPCviability. Protein expression was examined by Western blotting,ELISAassay and flow cytometry. Cell membrane and cytoplasm proteins were extracted with membrane and cytoplasm protein extraction kits.CXCR4 antagonist (AMD3100) and phosphatidylinositol 3‐kinases (PI3K) antagonist (LY294002) were used to characterize underlying mechanisms.

Results

Progesterone‐inducedEPCviability was time‐ and dose‐dependent. Administration of progesterone facilitatedEPCviability and increased expression ofCXCL12 and phosphorylated Akt (also known as protein kinase B,pAkt) activity (P< 0.05). Progesterone did not regulateCXCR4 protein expression in culturedEPCmembranes or cytoplasm. However, progesterone‐inducedEPCviability was significantly attenuated byAMD3100 orLY294002. Inhibition of the signalling pathway withAMD3100 andLY294002 subsequently reduced progesterone‐inducedCXCL12/CXCR4/PI3K/pAkt signalling activity.

Conclusions

TheCXCL12/CXCR4/PI3K/pAkt signalling pathway increased progesterone‐inducedEPCviability.
German guidelines for the diagnosis and therapy of localized scleroderma
Authors: Kreuter Alexander , Krieg Thomas , Worm Margitta , Wenzel Jörg , Moinzadeh Pia , Kuhn Annegret , Aberer Elisabeth , Scharffetter‐Kochanek Karin , Horneff Gerd , Reil Emma , Weberschock Tobias , Hunzelmann Nicolas
Published: January 2016

Localized scleroderma designates a heterogeneous group of sclerotic skin disorders. Depending on the subtype, severity, and site affected, adjacent structures such as adipose tissue, muscles, joints, and bones may be involved. This is an update of the existing German AWMF (Association of the Scientific Medical Societies in Germany) guidelines (classification: S2k). These guidelines provide an overview of the definition, epidemiology, classification, pathogenesis, laboratory workup, histopathology, clinical scoring systems, as well as imaging and device‐based workup of localized scleroderma. Moreover, consensus‐based recommendations are given on the management of localized scleroderma depending on its clinical subtype. Treatment recommendations are presented in a therapeutic algorithm. No financial support was given by any pharmaceutical company. The guidelines are valid until July 2019.
Misdiagnosis in Hypoplastic Sinus of Valsalva with Localized Aneurysm: A Diagnostic Pitfall in Computed Tomography
Authors: Hu Yu‐Ning , Tsai Wei‐Chuan , Tsai Yi‐Shan , Luo Chwan‐Yau
Published: January 2016

Mini‐Abstract

A 56‐year‐old woman was misdiagnosed, based on a coronary computed tomography, with a left main coronary artery aneurysm the referring hospital. Detailed diagnostic modalities—conventional angiography, transesophageal echocar‐diography, and electrocardiography‐gated cardiac computed tomography—showed the accurate anatomical structure and supported a final diagnosis of a rare case of hypoplastic sinus of Valsalva with a small localized aneurysm.
Effects of Quaternary climatic fluctuations on the distribution of Neotropical savanna tree species
Authors: Bueno Marcelo Leandro , Pennington R. Toby , Dexter Kyle G. , Kamino Luciana H. Yoshino , Pontara Vanessa , Neves Danilo Mesquita , Ratter James Alexander , de Oliveira‐Filho Ary Teixeira
Published: January 2016

In order to develop niche models for tree species characteristic of the cerrado vegetation (woody savannas) of central South America, and to hindcast their distributions during the Last Glacial Maximum and Last Inter‐Glacial, we compiled a dataset of tree species checklists for typical cerrado vegetation (n = 282) and other geographically co‐occurring vegetation types, e.g. seasonally dry tropical forest (n = 355). We then performed an indicator species analysis to select ten species that best characterize typical cerrado vegetation and developed niche models for them using the Maxent algorithm. We used these models to assess the probability of occurrence of each species across South America at the following time slices: Current (0 ka pre‐industrial), Holocene (6 ka BP), Last Glacial Maximum (LGM – 21 ka BP), and Last Interglacial (LIG – 130 ka BP). The niche models were robust for all species and showed the highest probability of occurrence in the core area of the Cerrado Domain. The palaeomodels suggested changes in the distributions of cerrado tree species throughout the Quaternary, with expansion during the LIG into the adjacent Amazonian and Atlantic moist forests, as well as connections with other South American savannas. The LGM models suggested a retraction of cerrado vegetation to inter‐tableland depressions and slopes of the Central Brazilian Highlands. Contrary to previous hypotheses, such as the Pleistocene refuge theory, we found that the widest expansion of cerrado tree species seems to have occurred during the LIG, most probably due to its warmer climate. On the other hand, the postulated retractions during the LGM were likely related to both decreased precipitation and temperature. These results are congruent with palynological and phylogeographic studies in the Cerrado Domain.
White matter alterations in individuals experiencing attenuated positive psychotic symptoms
Authors: Cooper Shanna , Alm Kylie H. , Olson Ingrid R. , Ellman Lauren M.
Published: January 2016

Aim

Diffusion tensor imaging (DTI) studies suggest that reduced fractional anisotropy (FA) in the inferior longitudinal fasciculus (ILF) and superior longitudinal fasciculus (SLF) occurs among schizophrenia patients and those at risk for psychosis. Nevertheless, there is a dearth of knowledge investigating white matter fibre pathways in non‐help‐seeking individuals who endorse attenuated positive psychotic symptoms (APPS) across a range of mental disorders. The aim of the current study was to determine if alterations in ILF and SLF microstructures were specific to distressing APPS related to risk for psychosis or to APPS symptoms occurring in multiple mental disorders, which would suggest a shared phenotype among disorders.

Method

Twenty‐six non‐help‐seeking young adults were administered the Prodromal Questionnaire. DTI was conducted on participants (n = 13) who endorsed eight or more distressing APPS (D‐APPS, a potentially clinically relevant group) and those who endorsed three or fewer distressing APPS (low‐APPS; n = 13). Semistructured interviews were administered to determine diagnoses, as well as clinical risk for psychosis status.

Results

Results indicated that the D‐APPS group exhibited decreased FA in the left ILF compared with the low‐APPS group, even after removing four D‐APPS participants who were considered at risk for psychosis.

Conclusion

Findings suggest that white matter microstructure is altered in individuals experiencing APPS across a range of disorders, independent of clinical high risk for psychosis status. Reduced FA in the left ILF may not be specific to psychosis risk, but rather for APPS that occur in a number of mental disorders.
N‐Acetyl cysteine does not prevent liver toxicity from chronic low‐dose plus subacute high‐dose paracetamol exposure in young or old mice
Authors: Kane Alice Elizabeth , Huizer‐Pajkos Aniko , Mach John , McKenzie Catriona , Mitchell Sarah Jayne , de Cabo Rafael , Jones Brett , Cogger Victoria , Le Couteur David G , Hilmer Sarah Nicole
Published: January 2016

Paracetamol is an analgesic commonly used by people of all ages, which is well documented to cause severe hepatotoxicity with acute overexposures. The risk of hepatotoxicity from nonacute paracetamol exposures is less extensively studied, and this is the exposure most common in older adults. Evidence on the effectiveness of N‐acetyl cysteine (NAC) for nonacute paracetamol exposures, in any age group, is lacking. This study aimed to examine the effect of long‐term exposure to therapeutic doses of paracetamol and subacute paracetamol overexposure, in young and old mice, and to investigate whether NAC was effective at preventing paracetamol hepatotoxicity induced by these exposures. Young and old male C57BL/6 mice were fed a paracetamol‐containing (1.33 g/kg food) or control diet for 6 weeks. Mice were then dosed orally eight times over 3 days with additional paracetamol (250 mg/kg) or saline, followed by either one or two doses of oral NAC (1200 mg/kg) or saline. Chronic low‐dose paracetamol exposure did not cause hepatotoxicity in young or old mice, measured by serum alanine aminotransferase (ALT) elevation, and confirmed by histology and a DNA fragmentation assay. Subacute paracetamol exposure caused significant hepatotoxicity in young and old mice, measured by biochemistry (ALT) and histology. Neither a single nor double dose of NAC protected against this toxicity from subacute paracetamol in young or old mice. This finding has important clinical implications for treating toxicity due to different paracetamol exposure types in patients of all ages, and implies a need to develop new treatments for subacute paracetamol toxicity.
Seagrass sediments reveal the long‐term deterioration of an estuarine ecosystem
Authors: Serrano Oscar , Lavery Paul , Masque Pere , Inostroza Karina , Bongiovanni James , Duarte Carlos
Published: January 2016

The study of a Posidonia australis sediment archive has provided a record of ecosystem dynamics and processes over the last 600 years in Oyster Harbour (SW Australia). Ecosystem shifts are a widespread phenomenon in coastal areas, and this study identifies baseline conditions and the time‐course of ecological change (cycles, trends, resilience and thresholds of ecosystem change) under environmental stress in seagrass‐dominated ecosystem. The shifts in the concentrations of chemical elements, carbonates, sediments <0.125 mm and stable carbon isotope signatures (δ13C) of the organic matter were detected between 1850s and 1920s, whereas the shift detected in P concentration occurred several decades later (1960s). The first degradation phase (1850s–1950s) follows the onset of European settlement in Australia and was characterized by a strong increase in sediment accumulation rates and fine‐grained particles, driven primarily by enhanced run‐off due to land clearance and agriculture in the catchment. About 80% of total seagrass area at Oyster Harbour was lost during the second phase of environmental degradation (1960s until present). The sharp increase in P concentration and the increasing contribution of algae and terrestrial inputs into the sedimentary organic matter pool around 1960s provides compelling evidence of the documented eutrophication of the estuary and the subsequent loss of seagrass meadows. The results presented demonstrate the power of seagrass sedimentary archives to reconstruct the trajectories of anthropogenic pressures on estuarine ecosystem and the associated regime shifts, which can be used to improve the capacity of scientists and environmental managers to understand, predict and better manage ecological change in these ecosystems.
The effects of nitrogen enrichment on soil CO2 fluxes depending on temperature and soil properties
Authors: Zhong Yangquanwei , Yan Weiming , Shangguan Zhouping
Published: January 2016

Aim

The continuous increase in anthropogenic nitrogen (N) may have a substantial impact on soil carbon (C) fluxes; thus, understanding the dynamics of soil C fluxes under N enrichment is important. Our main goal was to resolve the conflicting results presented to date and to expand our knowledge about the response of soil respiration (Rs) to N enrichment, which may be affected by the physico‐chemical properties of soil and environmental factors.

Methods

We assembled a large dataset for meta‐analysis, including 563 datasets on annual and seasonal Rs with N enrichment from 154 published papers at 163 sites, covering seven types of biomes world‐wide.

Results

(1) N enrichment was not significantly related to global Rs but we found a negative relationship in forests and a positive one in other biomes. (2) Rs showed a negative correlation with the N levels in forests and croplands and a positive correlation with the N levels in deserts; heterotrophic respiration exhibited negative correlations with N levels globally, and its response was correlated with the incubation environment. (3) The response of Rs to N enrichment was also correlated with mean annual temperature and soil properties, with 15 °C being the threshold for switching between increasing and decreasing Rs. (4) The estimated total C flux for global terrestrial lands was 97.01 Pg C year−1, and 1 kg of N enrichment at ha−1 year−1 induced an average efflux of 1.33 kg C ha−1 year−1.

Main conclusions

The response of Rs to future N enrichment should be predicted separately for each biome. The association between changes in Rs and temperature and soil properties under N enrichment makes soil C flux a more complex challenge in the context of future increases in temperature and N deposition.
Sustainable construction and socio‐technical transitions in London's mega‐projects
Authors: Brooks Andrew , Rich Hannah
Published: January 2016

Sustainable construction attempts to mitigate the destructive impacts of building on the global environment. Mega‐projects in London, such as Blackfriars Station and the Shard, symbolise urban renewal and are promoted as engines for sustainable development, principally through their use of sustainably procured materials. Unique buildings which are monumental and often state backed act as niches or incubators for sustainable construction, because they operate as protected spaces where the general rules of construction do not apply. Decision making in sustainable construction is complicated by the multiple state and public stakeholders involved in projects such as large stations and skyscrapers, and the different perspectives of architects, developers, procurement specialists, end users and others. While there are diverse actors involved, there has been some international convergence in the construction sector around how to deliver sustainability, and sustainable procurement has become the primary social and technological change through which more sustainable approaches to construction are delivered. Using interviews and questionnaires undertaken with six leading contractors involved in some of London's mega property and transport infrastructure projects, we analyse how sustainability procurement is deployed in the construction industry. Socio‐technical transition theory provides a way to understand the context‐specific developments led through mega‐projects, which are at the forefront of promoting the use of sustainably procured materials and technologies. Our research demonstrates that moves to deploy a more sustainable approach are based around modifications to current practices rather than fundamental transformation. Cost and risks are frequently cited as barriers to the sustainable procurement of materials, while some contractors are sceptical of the improvements that can be delivered through sustainable procurement.
Prevalence of depression and related social and physical factors amongst the Iranian elderly population in 2012
Authors: Taheri Tanjanai Parisa , Moradinazar Mahdi , Najafi Farid
Published: January 2016

Aim

Depression is the most common psychiatric disorder and the second most common cause of disability among older adults. The objective of the present study was to investigate the prevalence of depression and related social and physical factors in the Iranian elderly population in 2012.

Methods

In this cross‐sectional study, 1350 Iranian older adults aged older than 60 years were selected considering the gender proportion of the population of five out of 31 provinces of Iran. To define depression, the short form (15‐item) of the Geriatric Depression Scale was administered. To analyze the data, logistic regression was carried out using stata software (version 12.0).

Results

From 1350 participants, 642 (47.5%) were men and the rest were women. The mean ± SD age of the sample was 69 ± 7 years. The prevalence of depression was 36.7% (42.5% in women and 30.2% in men). At the bivariate level, sex, educational level, marital status, satisfaction with income, occupation, relationship with the financial provider, leisure time, activities of daily living, and frequency of meeting with friends and relatives were factors determining the odds of depression. However, after multivariate control, marital status and educational level were removed from the final model. In contrast, smoking, which was insignificant at the bivariate level, became significant at the multivariate level.

Conclusions

Depression has a high prevalence among the Iranian elderly population. Therefore, it is important that this vulnerable group is provided with access to supportive environments that involve active participation in occupational and social activities, which in turn help reduce the chance of suffering from depression. Geriatr Gerontol Int 2017; 17: 126–131.
Correlating biostratigraphy and palaeoceanographic changes during late Quaternary at cold seeps with gas hydrate‐free areas of the Japan Sea using foraminifera paleoecology
Authors: Saeidi Ortakand Mahsa , Hasegawa Shiro , Matsumoto Ryo , Matsuda Hiroki
Published: January 2016

Late Quaternary foraminifera assemblages have been examined in two sediment cores (MD179‐3296 and MD179‐3317) from cold seep areas in the eastern margin of the Japan Sea, off Joetsu, Niigata Prefecture. Foraminifera assemblages in core MD179‐3296, which was located at the center of a pockmark on the Umitake Spur, show no evidence of methane flux and, especially in its upper portion, share the same paleo‐environmental history as other free gas hydrate areas of the Japan Sea. In comparison, in the core MD179‐3317 at the center of a pockmark at Joetsu Knoll, foraminiferal distributions were strongly affected by methane activities and, in the main part of the core, were deposited under local conditions. Three horizons were identified in this core, which are characterized by the high abundance value of Thalmannammina parkerae and might be related to methane flux due to sea level fall especially through late marine isotope stage (MIS) 3 and MIS 2.