bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular and morphological characterisation of Paurodontella persica n. sp. (Hexatylina: Sphaerulariidae) from soil in Iran
Authors: Esmaeili Mehrab , Heydari Ramin , Ye Weimin 
Published: October 2016

A new species ofPaurodontella,P. persican. sp., collected from the Alborz rangelands of Iran, is described and illustrated. The new species is characterised by its body length of 506 (416-599) μm and 424 (388-461) μm in female and male, respectively, four incisures in lateral field, lip region annulated and continuous with body contour, total stylet 6.2 (5.5-7.0) μm long. Basal pharyngeal bulb with small posterior extension projecting reaching to the intestine. Excretory pore situated at the level of basal pharyngeal bulb region. Post-uterine sac short, 4.5 (3.0-6.0) μm long and uterus with an offset diverticulum. Tail of both sexes similar, conoid pointed, terminus tapering into a long pointed mucron. Male with adanal bursa and spicules 16.5 (16.0-17.0) μm long. The new species comes close in morphology and morphometrics to four known species of the genus, namelyP. auriculata,P. myceliophaga,P. minutaandP. niger. Molecular analyses of the partial small subunit rDNA gene (SSU), D2-D3 expansion segments of the large subunit rDNA gene (LSU) and internal transcribed spacer (ITS) revealed this to be a new species.
Wind-Driven Atlantic Water Flow as a Direct Mode for Reduced Barents Sea Ice Cover
Authors: Lien Vidar S. , Schlichtholz Pawel , Skagseth Øystein , Vikebø Frode B. 
Published: October 2016

AbstractVariability in the Barents Sea ice cover on interannual and longer time scales has previously been shown to be governed by oceanic heat transport. Based on analysis of observations and results from an ocean circulation model during an event of reduced sea ice cover in the northeastern Barents Sea in winter 1993, it is shown that the ocean also plays a direct role within seasons. Positive wind stress curl and associated Ekman divergence causes a coherent increase in the Atlantic water transport along the negative thermal gradient through the Barents Sea. The immediate response connected to the associated local winds in the northeastern Barents Sea is a decrease in the sea ice cover due to advection. Despite a subsequent anomalous ocean-to-air heat loss on the order of 100 W m−2 due to the open water, the increase in the ocean heat content caused by the circulation anomaly reduced refreezing on a time scale of order one month. Furthermore, it is found that coherent ocean heat transport anomalies occurred more frequently in the latter part of the last five decades during periods of positive North Atlantic Oscillation index, coinciding with the Barents Sea winter sea ice cover decline from the 1990s and onward.
Long-term course of patients with primary ocular adnexal MALT lymphoma: a large single-institution cohort study
Authors: Desai Amrita , Joag Madhura G. , Lekakis Lazaros , Chapman Jennifer R. , Vega Francisco , Tibshirani Robert , Tse David , Markoe Arnold , Lossos Izidore S. 
Published: October 2016

Key PointsPOAML (specifically Ann Arbor stage I disease) has an excellent clinical outcome, with only a few patients succumbing to lymphoma. POAML patients face a continuous risk of distant relapse, including in the central nervous system, and transformation to aggressive lymphoma.
Basophil tryptase mMCP-11 plays a crucial role in IgE-mediated, delayed-onset allergic inflammation in mice
Authors: Iki Misako , Tanaka Kensei , Deki Hayato , Fujimaki Mio , Sato Shingo , Yoshikawa Soichiro , Yamanishi Yoshinori , Karasuyama Hajime 
Published: October 2016

Key PointsMice deficient for basophil tryptase mMCP-11 showed ameliorated IgE-mediated allergic inflammation with reduced leukocyte infiltration. This is the first demonstration that the basophil-derived protease plays a crucial role in allergic inflammation.
BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly
Authors: Lam Ka-Kit , Hall Richard , Clum Alicia , Rao Satish 
Published: October 2016

Abstract
Background
The problem of de-novo assembly for metagenomes using only long reads is gaining attention. We study whether post-processing metagenomic assemblies with the original input long reads can result in quality improvement. Previous approaches have focused on pre-processing reads and optimizing assemblers. BIGMAC takes an alternative perspective to focus on the post-processing step.

Results
Using both the assembled contigs and original long reads as input, BIGMAC first breaks the contigs at potentially mis-assembled locations and subsequently scaffolds contigs. Our experiments on metagenomes assembled from long reads show that BIGMAC can improve assembly quality by reducing the number of mis-assemblies while maintaining or increasing N50 and N75. Moreover, BIGMAC shows the largest N75 to number of mis-assemblies ratio on all tested datasets when compared to other post-processing tools.

Conclusions
BIGMAC demonstrates the effectiveness of the post-processing approach in improving the quality of metagenomic assemblies.
MEvoLib v1.0: the first molecular evolution library for Python
Authors: Álvarez-Jarreta Jorge , Ruiz-Pesini Eduardo 
Published: October 2016

Abstract
Background
Molecular evolution studies involve many different hard computational problems solved, in most cases, with heuristic algorithms that provide a nearly optimal solution. Hence, diverse software tools exist for the different stages involved in a molecular evolution workflow.

Results
We present MEvoLib, the first molecular evolution library for Python, providing a framework to work with different tools and methods involved in the common tasks of molecular evolution workflows. In contrast with already existing bioinformatics libraries, MEvoLib is focused on the stages involved in molecular evolution studies, enclosing the set of tools with a common purpose in a single high-level interface with fast access to their frequent parameterizations. The gene clustering from partial or complete sequences has been improved with a new method that integrates accessible external information (e.g. GenBank’s features data). Moreover, MEvoLib adjusts the fetching process from NCBI databases to optimize the download bandwidth usage. In addition, it has been implemented using parallelization techniques to cope with even large-case scenarios.

Conclusions
MEvoLib is the first library for Python designed to facilitate molecular evolution researches both for expert and novel users. Its unique interface for each common task comprises several tools with their most used parameterizations. It has also included a method to take advantage of biological knowledge to improve the gene partition of sequence datasets. Additionally, its implementation incorporates parallelization techniques to enhance computational costs when handling very large input datasets.
Comparison of dementia recorded in routinely collected hospital admission data in England with dementia recorded in primary care
Authors: Brown Anna , Kirichek Oksana , Balkwill Angela , Reeves Gillian , Beral Valerie , Sudlow Cathie , Gallacher John , Green Jane 
Published: October 2016

Abstract
Background
Electronic linkage of UK cohorts to routinely collected National Health Service (NHS) records provides virtually complete follow-up for cause-specific hospital admissions and deaths. The reliability of dementia diagnoses recorded in NHS hospital data is not well documented.

Methods
For a sample of Million Women Study participants in England we compared dementia recorded in routinely collected NHS hospital data (Hospital Episode Statistics: HES) with dementia recorded in two separate sources of primary care information: a primary care database [Clinical Practice Research Datalink (CPRD), n = 340] and a survey of study participants’ General Practitioners (GPs, n = 244).

Results
Dementia recorded in HES fully agreed both with CPRD and with GP survey data for 85% of women; it did not agree for 1 and 4%, respectively. Agreement was uncertain for the remaining 14 and 11%, respectively; and among those classified as having uncertain agreement in CPRD, non-specific terms compatible with dementia, such as ‘memory loss’, were recorded in the CPRD database for 79% of the women. Agreement was significantly better (p < 0.05 for all comparisons) for women with HES diagnoses for Alzheimer’s disease (95 and 94% agreement with any dementia for CPRD and GP survey, respectively) and for vascular dementia (88 and 88%, respectively) than for women with a record only of dementia not otherwise specified (70 and 72%, respectively). Dementia in the same woman was first mentioned an average 1.6 (SD 2.6) years earlier in primary care (CPRD) than in hospital (HES) data. Age-specific rates for dementia based on the hospital admission data were lower than the rates based on the primary care data, but were similar if the delay in recording in HES was taken into account.

Conclusions
Dementia recorded in routinely collected NHS hospital admission data for women in England agrees well with primary care records of dementia assessed separately from two different sources, and is sufficiently reliable for epidemiological research.
A novel method of measuring passive quasi‐stiffness in the first metatarsophalangeal joint
Authors: Heng Marabelle L. , Chua Yaohui K. , Pek Hong K. , Krishnasamy Priathashini , Kong Pui W. 
Published: October 2016

AbstractBackgroundFirst metatarsophalangeal joint (MTPJ) mobility is commonly assessed by its angular displacement (joint angle) or subjectively rated as ‘hypermobile’, ‘normal’ or ‘stiff’ by a clinician. Neither of these methods is ideal because displacement alone does not take into account the force required to displace the joint and subjective evaluation is not always reliable. This study presented a novel method to determine the passive quasi‐stiffness of the first MTPJ. The reliability of the proposed method was also assessed. The first MTPJ passive quasi‐stiffness of 13 healthy subjects were measured at two occasions, 7 days apart, by two testers (experienced and inexperienced). A tactile pressure sensing system was used to measure the force applied to dorsiflex the first toe by the testers. The torque (in Nmm) about the first MTPJ was calculated as the applied force (in N) multiplied by a moment arm (in mm), where moment arm was the length of the first proximal phalanx. A video camera recorded the motion of the first MTPJ, simultaneously with force measurements, to determine the joint angular displacement (in degrees) using the Dartfish software. The quasi‐stiffness (in Nmm/degrees) was calculated as the slope of a graph where torque was plotted against first MTPJ angular displacement. Descriptive statistics of the first MTPJ quasi‐stiffness were calculated. Intra‐rater and inter‐rater reliability were assessed using Bland and Altman plot, intraclass correlation coefficients (ICC), and standard error of measurement (SEM).ResultsFirst MTPJ quasi‐stiffness of the subjects ranged widely from 0.66 to 53.4 Nmm/degrees. Intra‐rater reliability for experienced tester was moderate (Session 1: 14.9 ± 14.6 Nmm/degrees, Session 2: 14.2 ± 8.5 Nmm/degrees, ICC = .568, SEM = 7.71 Nmm/degrees). Inter‐rater reliability between experienced (12.6 ± 8.4 Nmm/degrees) and non‐experienced (19.9 ± 9.2 Nmm/degrees) testers was poor (ICC = ‐.447, SEM = 11.29 Nmm/degrees).ConclusionsFirst MTPJ passive quasi‐stiffness can be quantified from torque and angular displacement measurements using simple equipment in a clinical setting. The tester's experience affected the consistency in joint quasi‐stiffness measurements.
Skin appendage-derived stem cells: cell biology and potential for wound repair
Authors: Xie Jiangfan , Yao Bin , Han Yutong , Huang Sha , Fu Xiaobing 
Published: October 2016

AbstractStem cells residing in the epidermis and skin appendages are imperative for skin homeostasis and regeneration. These stem cells also participate in the repair of the epidermis after injuries, inducing restoration of tissue integrity and function of damaged tissue. Unlike epidermis-derived stem cells, comprehensive knowledge about skin appendage-derived stem cells remains limited. In this review, we summarize the current knowledge of skin appendage-derived stem cells, including their fundamental characteristics, their preferentially expressed biomarkers, and their potential contribution involved in wound repair. Finally, we will also discuss current strategies, future applications, and limitations of these stem cells, attempting to provide some perspectives on optimizing the available therapy in cutaneous repair and regeneration.
At the Bench: Chimeric antigen receptor (CAR) T cell therapy for the treatment of B cell malignancies
Authors: Daniyan Anthony F O , Brentjens Renier J 
Published: October 2016

Abstract
The chimeric antigen receptor (CAR) represents the epitome of cellular engineering and is one of the best examples of rational biologic design of a synthetic molecule. The CAR is a single polypeptide with modular domains, consisting of an antibody-derived targeting moiety, fused in line with T cell-derived signaling domains, allowing for T cell activation upon ligand binding. T cells expressing a CAR are able to eradicate selectively antigen-expressing tumor cells in a MHC-independent fashion. CD19, a tumor-associated antigen (TAA) present on normal B cells, as well as most B cell-derived malignancies, was an early target of this technology. Through years of experimental refinement and preclinical optimization, autologously derived CD19-targeting CAR T cells have been successfully, clinically deployed, resulting in dramatic and durable antitumor responses but not without therapy-associated toxicity. As CD19-targeted CAR T cells continue to show clinical success, work at the bench continues to be undertaken to increase further the efficacy of this therapy, while simultaneously minimizing the risk for treatment-related morbidities. In this review, we cover the history and evolution of CAR technology and its adaptation to targeting CD19. Furthermore, we discuss the future of CAR T cell therapy and the need to ask, as well as answer, critical questions as this treatment modality is being translated to the clinic.
A Practical One-Pot Electrochemical Synthesis of Pyrimido[4,5-b]indole Derivatives
Authors: Shabani-Nooshabadi Mehdi , Moradian Mohsen , Dadkhah-Tehrani Samira 
Published: October 2016

Abstract
In the present work, electrochemical synthesis of novel pyrimido[4,5-b]indoles was directly carried out via the electrochemical oxidation of catechols in the presence of 2,4-diamino-6-hydroxypyrimidine in an aqueous media. The results suggested that electrogenerated o-benzoquinone moieties participated in the Michael-type addition reaction with 2,4-diamino-6-hydroxypyrimidine via the ECEC mechanism. These new compounds were synthesized in high yields and purity in an aqueous solution without toxic reagents or catalyst and with high atom economy in ambient conditions.
Household air pollution and its effects on health
Authors: Apte Komalkirti , Salvi Sundeep 
Published: October 2016

Household air pollution is a leading cause of disability-adjusted life years in Southeast Asia and the third leading cause of disability-adjusted life years globally. There are at least sixty sources of household air pollution, and these vary from country to country. Indoor tobacco smoking, construction material used in building houses, fuel used for cooking, heating and lighting, use of incense and various forms of mosquito repellents, use of pesticides and chemicals used for cleaning at home, and use of artificial fragrances are some of the various sources that contribute to household air pollution. Household air pollution affects all stages of life with multi-systemic health effects, and its effects are evident right from pre-conception to old age. In utero exposure to household air pollutants has been shown to have health effects which resonate over the entire lifetime. Exposures to indoor air pollutants in early childhood also tend to have repercussions throughout life. The respiratory system bears the maximum brunt, but effects on the cardiovascular system, endocrine system, and nervous system are largely underplayed. Household air pollutants have also been implicated in the development of various types of cancers. Identifying household air pollutants and their health implications helps us prepare for various health-related issues. However, the real challenge is adopting changes to reduce the health effects of household air pollution and designing innovative interventions to minimize the risk of further exposure. This review is an attempt to understand the various sources of household air pollution, the effects on health, and strategies to deal with this emergent risk factor of global mortality and morbidity.
The notion of inclusive education and challenges for the teacher in kindergartens and the first stage of school
Authors: Häidkind Pille , Oras Kaja 
Published: October 2016

Kaasava hariduse eesmärk on suurendada haridussüsteemi võimekust jõuda kõikide õppijateni, põhiliseks sihtgrupiks on enamikus riikides hariduslike erivajadustega õppijad. Siinse uurimuse eesmärk on selgitada välja, kuidas mõistetakse kaasavat haridust Eesti lasteaedades ja koolides (esimene kooliaste) ning millised on õpetajate ees seisvad ülesanded ja asutuste võimalused erivajadustega õppijate kaasamisel tavaharidussüsteemi. Andmeid kogusime küsitluse ja vaatluse teel, lisaks analüüsisime kaasamise edendamise kavasid. Saadud tulemused võimaldavad käsitleda erivajadustega õppija teemat sügavuti ja tõhustada õpetajakoolitust. Hädavajalik on valmistada õpetajaid ette erivajadustega õppija ja ülejäänud laste koosõpetamiseks (grupiprotsessid, -juhtimine), laiendada arusaamu keskkonna kohandamise võimalustest ning suurendada valmisolekut meeskonnatööks.
Summary
Construction of the meaning of giftedness as a special educational need in the context of the changed learning approach in Estonia
Authors: Põlda Halliki , Aava Katrin 
Published: October 2016

Eesti uus haridusstrateegia rõhutab muutunud õpikäsituse raames vajadust toetada õppija individuaalset ja sotsiaalset arengut, tuues samas kitsaskohana välja, et õppijate erivajadusi, sh eri tüüpi andekust, ei märgata ega väärtustata. Samuti on PISA uuringutes Eesti probleemina nimetatud vähest tööd andekatega. Siinse uurimuse eesmärk on kirjeldada, milliste keeleliste valikutega konstrueerivad hariduslikke erivajadusi, eriti andekust, haridusvaldkonna sidusrühmad. Fookusgrupi intervjuudega kogutud materjali analüüsist kriitilise diskursuseanalüüsi meetodil selgub, et hariduslikke erivajadusi seostatakse eelkõige eri- ja erakoolidega, mitte muutunud õpikäsitusega ehk individuaalse lähenemisega õppijale. Andekust nähakse pigem kaasasündinud isikuomadusena kui arengulise protsessina. Andekad paigutatakse sotsiaalse hierarhia tippu (geeniused) või kõige madalamale positsioonile (nohikud, tõrjutud). Neid käsitletakse teistest õppijatest eraldatud rühmana, kelle jaoks pole ressursse, kes saadetakse olümpiaadile, klassiruumist välja.
Summary
The impact of an educational game on participants’ acculturation attitudes
Authors: Männamaa Ivar , Komsaare Aurika , Leijen Äli 
Published: October 2016

Euroopa põgenikekriis nõuab Eesti koolisüsteemilt valmisolekut sisserändajatest õpilaste vastuvõtmiseks. Elanikkonna hoiakud mõnest muust religioossest või kultuurilisest grupist pärinevate sisserändajate suhtes pole alati pooldavad (Beilmann, 2016; Laineste, Raus, Timmi, Vetik, & Vihalemm, 2011), ent sisserändajate peredest pärit õpilaste kohanemist kooliga mõjutab ka kaasõpilaste suhtumine. Koolikaaslaste suhtumise ja hoiakute kujundamisel on mitmes valdkonnas edukalt rakendatud mänge, ent pole teada, kuivõrd mõjutavad nende käigus omandatud kogemused õpilase hoiakuid väljaspool mängu (Chin, Dukes, & Gamson, 2009; Wouters, van Nimwegen, van Oostendorp, & van der Spek, 2013). Praegune uuring võimaldab hinnata mängu mõju põlisrahvusest osalejate akulturatsioonihoiakute muutumisele. Uuringus kasutati sekkumisvahendina mudeldusmängu „Allikad” (Männamaa, 2015; Männamaa, Vetik, & Liiv, 2011), akulturatsioonihoiakuid hinnati 12 väitest koosneva küsimustiku abil. Analüüs näitas erinevust mängus osalenud õpilaste eel- ja järeltesti tulemustes (p < 0,05). Tulemused osutavad sellele, et eesmärgipäraselt loodud mäng võib aidata kaasa õpilaste akulturatsioonihoiakute muutumisele.
Summary
Variability analyses, site characterization, and regional [OH] estimates using trace gas measurements from the NOAA Global Greenhouse Gas Reference Network
Authors: Pollmann Jan , Helmig Detlev , Liptzin Daniel , Thompson Chelsea R. , Hueber Jacques , Tans Pieter P. , Lelieveld Jos 
Published: October 2016

Abstract
Trace gas measurements from whole air samples collected weekly into glass flasks at background monitoring sites within the NOAA Global Greenhouse Gas Reference Network program (with most of the sites also being World Meteorological Organization (WMO) Global Atmospheric Watch (GAW) stations) were used to investigate the variability-lifetime relationship for site characterization and to estimate regional and seasonal OH concentrations. Chemical species considered include the atmospheric trace gases CO, H2, and CH4, as well as the non-methane hydrocarbons (NMHC) ethane (C2H6), propane (C3H8), i-butane (i-C4H10), and n-butane (n-C4H10). The correlation between atmospheric variability and lifetime was applied on a global scale spanning 42 sites with observations covering a period of 5 years. More than 50,000 individual flask measurement results were included in this analysis, making this the most extensive study of the variability-lifetime relationship to date. Regression variables calculated from the variability-lifetime relationship were used to assess the “remoteness” of sampling sites and to estimate the effect of local pollution on the measured distribution of atmospheric trace gases. It was found that this relationship yields reasonable results for description of the site remoteness and local pollution influences. Comparisons of seasonal calculated OH concentrations ([OH]) from the variability-lifetime relationships with six direct station measurements yielded variable agreement, with deviations ranging from ∼20% to a factor of ∼2–3 for locations where [OH] monitoring results had been reported. [OH] calculated from the variability-lifetime relationships was also compared to outputs from a global atmospheric model. Resutls were highly variable, with approximately half of the sites yielding agreement to within a factor of 2–3, while others showed deviations of up to an order of magnitude, especially during winter.