bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA sequencing with stacked nanopores and exonuclease: a simulation-based analysis
Authors: Sampath G. 
Published: January 2016

AbstractExperiments (Clarke et al.,Nat. Nanotech., 2009,4, 265-270) have shown that DNA could be sequenced using a nanopore-based electrolytic cell in which an exonuclease enzyme in thecischamber cleaves the leading base of a strand of DNA. The base is identified (with a reported accuracy that exceeds 99%) by the level of the current blockade it causes in the pore; a biological adapter inside slows down the base to lower the detection bandwidth required. This approach, which has been mathematically modeled, analyzed, and simulated (Reiner et al.,J. Chem. Phys.,2012,137, 214903; Brady and Reiner,ibid.,2015,143, 074904), is error-prone because bases may be lost to diffusion or enter the pore out of order. Here a modified cell with three stacked nanopores (UNP, MNP, and DNP) and the enzyme attached to thetransside of UNP is proposed. Translocation of a base is simulated with the random walk of a dimensionless particle; the results show that bases translocate through MNP and DNP in sequence order without loss. If this holds in practice then with a suitably designed adapter and compatible enzyme turnover rates base calling accuracy would be limited only by the accuracy of base discrimination. Potential implementation issues are discussed.
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

AbstractNanopore 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.AbstractBiomedical 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.
Field trial of seismic recording using distributed acoustic sensing with broadside sensitive fibre‐optic cables
Authors: Hornman J.C. 
Published: January 2016

ABSTRACTDistributed 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

Summary

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.
Estimating the Value of Proximity to Water, When Ceteris Really Is Paribus
Authors: Rouwendal Jan , Levkovich Or , van Marwijk Ramona 
Published: January 2016

AbstractProximity 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

AbstractThis 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

AbstractDiscoveries 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

AimsThe 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 MethodsProspective 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.ResultsA 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).ConclusionsEPs 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

AbstractAimThe 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.MethodsThis 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.ResultsH. 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).ConclusionThe 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.
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

AbstractAfrican 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

AbstractThousands 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

AbstractObjectiveCollagen 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 MethodsCollagen 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.ResultsIncubation 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.ConclusionsThese 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

AbstractObjectivesProgesterone 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 methodsEPCs 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.ResultsProgesterone‐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.ConclusionsTheCXCL12/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

SummaryLocalized 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‐AbstractA 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.