bluuebunny/crossref_metadata_2025_split huggingface dataset:
A sequencer coming of age: De novo genome assembly using MinION reads
Authors: de Lannoy Carlos , de Ridder Dick , Risse Judith 
Published: July 2017

Nanopore technology provides a novel approach to DNA sequencing that yields long, label-free reads of constant quality. The first commercial implementation of this approach, the MinION, has shown promise in various sequencing applications. This review gives an up-to-date overview of the MinION's utility as a de novo sequencing device. It is argued that the MinION may allow for portable and affordable de novo sequencing of even complex genomes in the near future, despite the currently error-prone nature of its reads. Through continuous updates to the MinION hardware and the development of new assembly pipelines, both sequencing accuracy and assembly quality have already risen rapidly. However, this fast pace of development has also lead to a lack of oversight in the expanding landscape of analysis tools, as performance evaluations are outdated quickly. Now that the MinION is approaching a state of maturity, a thorough comparative benchmarking effort of de novo assembly pipelines may be at place. An earlier version of this article can be found on BioRxiv.
Reporting deaths to the coroner
Authors: Griffith Richard 
Published: July 2017

The Chief Coroner has issued new guidance in relation to death where the person is subject to a deprivation of liberty safeguards standard authorisation ( Chief Coroner, 2017 ). In this article, Richard Griffith discusses the impact of the Police and Crime Act 2017, section 178 on the need to report deaths of patients' subject to a deprivation of liberty safeguards standard authorisation to the coroner.
Hydatid cysts in trapezius muscles: A narrative review
Authors: Okhovatian Farshad , Zamani Sahar , Azimi Hadi 
Published: July 2017

Aims: A hydatid cyst is an endemic parasitic disease that can be formed anywhere in the body, including muscles (3–5% of cases). The cyst can be misdiagnosed in early stages with muscular trigger points. Needling is the popular physical therapy approach in trigger point treatments. Misuse in needling can cause punctures in hydatid cysts and lead to death. The aim of this study was to summarise the available evidence on the manifestation of hydatid cysts in the trapezius muscle. Methods: A search was conducted for any reports of differential diagnosis or misdiagnosis of hydatid cysts and trigger points. Computerised literature searches were performed among publications between 1950 and December 2015 using the following databases: PubMed, Science Direct, SCOPUS, Ovid MEDLINE, CINAHL, Cochrane, and AMED. Results: Only three studies met the inclusion criteria. All three patients were females under 30 and all three had undergone surgery; two received medical treatment. No misdiagnosis with trigger points was reported and consequently there was no case of needling misuse in hydatid cysts either. However, it does not imply the absence of any clinical case. Conclusions: The current study intends to remind the importance of an accurate diagnosis before using needling as a trigger point treatment.
Focus group methodology. Part 1: Design considerations
Authors: Plummer Prudence 
Published: July 2017

Background/Aims: There is a strong tradition of quantitative research in the health sciences, but qualitative research designs are now being used more frequently to investigate certain areas of rehabilitation, such as patients' views of health care services, and how clinicians make decisions during evaluations and treatment. Many qualitative approaches are available for conducting these types of inquiries, such as interviews, participant observation, and focus groups. Methods: This article will review these components of focus group research design, as well as highlight other important considerations for planning and conducting focus groups. Issues specific to analysis and trustworthiness of focus group data will be addressed in the second part of the series. Conclusions: Focus groups are an extremely useful method for exploring people's thoughts, ideas, attitudes, and experiences in relation to a particular topic. The interaction that occurs between participants in focus groups is a powerful stimulus for discussion and can encourage people to elaborate or justify a particular idea. Thus, focus groups have the potential to reveal more about clinicians' knowledge and reasons for particular patterns of thinking than could be obtained in one-to-one interviewing.
The subtalar joint
Authors: Krähenbühl Nicola , Horn-Lang Tamara , Hintermann Beat , Knupp Markus 
Published: July 2017

Subtalar joint anatomy is complex and can vary significantly between individuals. Movement is affected by several adjacent joints, ligaments and periarticular tendons. The subtalar joint has gained interest from foot and ankle surgeons in recent years, but its importance in hindfoot disorders is still under debate. The purpose of this article is to give a general overview of the anatomy, biomechanics and radiographic assessment of the subtalar joint. The influence of the subtalar joint on the evolution of ankle joint osteoarthritis is additionally discussed. Cite this article: EFORT Open Rev 2017;2:309-316. DOI: 10.1302/2058-5241.2.160050
United States and European Multicenter Prospective Study for the Analytical Performance and Clinical Validation of a Novel Sensitive Fully Automated Immunoassay for Calcitonin
Authors: Kahaly George J , Algeciras-Schimnich Alicia , Davis Thomas E , Diana Tanja , Feldkamp Joachim , Karger Stefan , König Jochem , Lupo Mark A , Raue Friedhelm , Ringel Matthew D , Sipos Jennifer A , Kratzsch Juergen 
Published: July 2017

Abstract

BACKGROUND
The objective of this study is the validation and proof of clinical relevance of a novel electrochemiluminescence immunoassay (ECLIA) for the determination of serum calcitonin (CT) in patients with medullary thyroid carcinoma (MTC) and in different diseases of the thyroid and of calcium homeostasis.

METHODS
This was a multicenter prospective study on basal serum CT concentrations performed in 9 US and European referral institutions. In addition, stimulated CT concentrations were measured in 50 healthy volunteers after intravenous calcium administration (2.5 mg/kg bodyweight).

RESULTS
In total, 1929 patients and healthy controls were included. Limits of blank, detection, and quantification for the ECLIA were 0.3, 0.5, and 1 ng/L, respectively. Highest intra- and interassay coefficients of variation were 7.4% (CT concentration, 0.8 ng/L) and 7.0% (1.1 ng/L), respectively. Medians (interval) of serum CT concentrations in 783 healthy controls were 0.8 ng/L (&lt;0.5–12.7) and 3 ng/L (&lt;0.5–18) for females and males, respectively (97.5th percentile, 6.8 and 11.6 ng/L, respectively). Diagnostic sensitivity and specificity were 100%/97.1% and 96.2%/96.4%, for female/males, respectively. Patients (male/female) with primary hyperparathyroidism, renal failure, and neuroendocrine tumors showed CT concentrations &gt;97.5th percentile in 33%/4.7%, 18.5%/10%, and 8.3%/12%, females/males, respectively. Peak serum CT concentrations were reached 2 min after calcium administration (161.7 and 111.8 ng/L in males and females, respectively; P &lt; 0.001).

CONCLUSIONS
Excellent analytical performance, low interindividual variability, and low impact of confounders for increased CT concentrations in non-MTC patients indicate that the investigated assay has appropriate clinical utility. Calcium-stimulated CT results suggest good test applicability owing to low interindividual variability.
PHYTOPLANKTON SPECIES COMPOSITION IN SEAWATER AND TISSUE OF GREEN MUSSELS (PERNA VIRIDIS), AT KALI BARU-CILINCING, NORTH JAKARTA
Authors: Widiarti Riani , Yasman - , Mulyani - , Kurnia Nita , Razi Fachrul 
Published: July 2017

Species composition and abundances of phytoplankton in the shellfish farming area in Jakarta Bay, Kali Baru-Cilincing, were examined in order to identify harmful algae species. Phytoplankton contained in the shellfish was also observed to detect the presence of toxic species, as well as the phycotoxin contained inÂ visceral of green mussel (Perna viridis) collected from the farming area using brine shrimp lethality test (BSLT). We detected the presence ofÂ Alexandrium spp. (PSP causing species), Dinophysis caudata, D. miles and D. rotundata (DSP causing species), and Pseudo-nitzschia spp. (ASP causing species). The last mentioned species was also detected in thestomach content of green mussel. The toxicity of green mussels tested was recorded LC 50 â‰¤ 1,000 ppm and indicatedthe presence of an active compound in the green mussel viscera. Meanwhile, preliminary PSP test of shellfish did not showed any toxin.
Three-dimensional structural model of the Qaidam basin: Implications for crustal shortening and growth of the northeast Tibet
Authors: Guo Jianming , Wei Xuebing , Long Guohui , Wang Bo , Fan Hailong , Xu Shiyang 
Published: July 2017

AbstractThe Qaidam basin, bounded by the Altyn Tagh fault in the north, is located in the northeast of the Tibet plateau, and it has important implications for understanding the history and mechanism of Tibetan plateau formation during the Cenozoic Indo-Eurasia collision. In this study, we constructed the main geological structures and surfaces in three dimensions through the interpolation of regularly spaced 2D seismic sections, constrained by wells data and surface geology of the Qaidam basin in northeast Tibet. Meanwhile the Cenozoic tectonic history of the Qaidam basin was reconstructed and the uplift mechanism of the Tibetan plateau was discussed. This study presents the subsurface data in conjunction with observations and analysis of the stratigraphic and sedimentary evolution. The Cenozoic deformation history of the Qaidam basin shows geologic synchroneity with uplifting history of the Tibet Plateau. It is therefore proposed that the deformation and uplifting in the south and north edges of the Tibet Plateau was almost synchronous. The total shortening and shortening rate during Cenozoic reached 25.5 km and 11.2% respectively across the Qaidam basin, indicating that the loss of the left-lateral strike slip rates of the Altyn Tagh fault has been structurally transformed into local crustal thickening across NW-trending folds and thrust faults. Meanwhile there is an about 11° vertical component along the strike-slip Altyn Tagh fault, the block oblique slip shows one more growth mechanism of the northeast Tibet.
Failure Mode of the Water-filled Fractures under Hydraulic Pressure in Karst Tunnels
Authors: Dong Xin , Lu Hao , Huang Houxu , Hao Yiqing , Xia Yuanpu 
Published: July 2017

AbstractWater-filled fractures continue to grow after the excavation of karst tunnels, and the hydraulic pressure in these fractures changes along with such growth. This paper simplifies the fractures in the surrounding rock as flat ellipses and then identifies the critical hydraulic pressure values required for the occurrence of tensile-shear and compression-shear failures in water-filled fractures in the case of plane stress. The occurrence of tensile-shear fracture requires a larger critical hydraulic pressure than compression-shear failure in the same fracture. This paper examines the effects of fracture strike and lateral pressure coefficient on critical hydraulic pressure, and identifies compression-shear failure as the main failure mode of water-filled fractures. This paper also analyses the hydraulic pressure distribution in fractures with different extensions, and reveals that hydraulic pressure decreases along with the continuous growth of fractures and cannot completely fill a newly formed fracture with water. Fracture growth may be interrupted under the effect of hydraulic tensile shear.
Marine sediment cores database for the Mediterranean Basin: a tool for past climatic and environmental studies
Authors: Alberico I. , Giliberti I. , Insinga D.D. , Petrosino P. , Vallefuoco M. , Lirer F. , Bonomo S. , Cascella A. , Anzalone E. , Barra R. , Marsella E. , Ferraro L. 
Published: July 2017

AbstractPaleoclimatic data are essential for fingerprinting the climate of the earth before the advent of modern recording instruments. They enable us to recognize past climatic events and predict future trends. Within this framework, a conceptual and logical model was drawn to physically implement a paleoclimatic database named WDB-Paleo that includes the paleoclimatic proxies data of marine sediment cores of the Mediterranean Basin. Twenty entities were defined to record four main categories of data: a) the features of oceanographic cruises and cores (metadata); b) the presence/absence of paleoclimatic proxies pulled from about 200 scientific papers; c) the quantitative analysis of planktonic and benthonic foraminifera, pollen, calcareous nannoplankton, magnetic susceptibility, stable isotopes, radionuclides values of about 14 cores recovered by Institute for Coastal Marine Environment (IAMC) of Italian National Research Council (CNR) in the framework of several past research projects; d) specific entities recording quantitative data on
Simplified Physical Upgrading of High-Acid Adlay Bran Ethanol Extracts by Supercritical CO2
Authors: Qin Xiaoli , Chen Hourong , Liu Yun , Liu Xiong 
Published: July 2017

Abstract
Deacidification is one of the key steps in oil-refining processes. This study reported a simple approach for upgrading high-acid adlay bran oil by supercritical carbon dioxide (SC-CO2) extraction. The high-acid adlay bran oil was obtained by three-stage countercurrent ethanol extraction of adlay bran, with high free fatty acids (34 % FFAs). The FFA content in adlay bran oil reduced to 10.6 % by SC-CO2 extraction under optimized conditions. Interestingly, the SC-CO2 deacidification process also markedly reduced oil color value from 11.5 (Red) to 0.3 (Red) and acetone-insoluble matters in the oil from 1.56 % to 0.17 %. The results indicated solvent extraction combined with SC-CO2 deacidification method could be a feasible approach to significantly upgrade high-acid adlay bran oil and simplify refining process of adlay bran oil.
The Political Economy of EU-funds: Evidence from Poland
Authors: Banaszewska Monika , Bischoff Ivo 
Published: July 2017

Abstract
We provide an empirical study analysing the distribution of EU funds among 2478 Polish municipalities in the period 2007–2011. EU funds are found to be concentrated in smaller municipalities and economically weak sub-regions, and do not increase in the municipalities’ fiscal capacity. Our primary focus rests on the question whether regional governments follow their own political self-interest when allocating EU funds even though national parties only play a minor role in Polish local politics and thus the conventional logic of supporting aligned governments does not apply. Difference-in-difference estimations show that the answer is affirmative: Municipalities whose voters are aligned with the regional government receive more EU funds per capita than non-aligned municipalities. Furthermore, we find support for the swing-district hypothesis: EU funds per capita decrease in the vote-share differential between the two leading parties.
Expression of Hepcidin and Neogenin in colorectal cancer
Authors: Xiang-tao Pan 
Published: July 2017

Abstract

Objective
To investigate the expression of Hepcidin and Neogenin in tissue from patients with colorectal cancer, to evaluate the relationship between Hepcidin and Neogenin with clinical features, and to study their relationship with anemia.

Methods
Immuno- histochemical method was used to detect the expression of Hepcidin and Neogenin in 62 cases of colorectal cancer. At the same time, the relationship between them and their relationship with clinical characteristics and anemia were analyzed.

Results
The expression of Hepcidin was related to T stage (P<0.05), but not with age, gender, lymph node metastasis and distant metastasis. The expression of Neogenin was not correlated with T stage and lymph node metastasis, age, gender, and distant metastasis (P>0.05). There was no significant difference in the expression of Hepcidin and Neogenin between anemia group and non-anemia group. There was no correlation between Hepcidin and Neogenin (r =-0.04, P>0.05).

Conclusion
The expression of Hepcidin in colorectal cancer was related to the T stage, and had no correlation with Neogenin. The expression of Neogenin could not be used as an objective index to reflect the biological behavior of colorectal cancer.
Self-identified Linguistic Microaggressions among Monolingual Pre-service Teachers: Why They Matter for English Language Learners
Authors: Shim Jenna 
Published: July 2017

Abstract
Using the concept of racial microaggressions as an analytical tool, this study reports on white monolingual pre-service teachers’ self-identified linguistic microaggressions by exploring their attitudinal and affective responses to those who speak languages other than English. The assumption is that teachers’ pedagogical practices and their relationship with students are not contained within classrooms but are rather intertwined with their lives outside the classroom and their thinking in everyday context. The themes identified by analyzing the self-identified linguistic microaggressions of the participating pre-service teachers are (1) Self-consciousness/discomfort, worry, fear, anxiety, and frustration; (2) Judgments: (un)intelligence, (dis)likability, and (un)trustworthiness; (3) (In)appropriateness and English dominance; and (4) Stereotypes. This study also reports the findings pertaining to the participants’ reflections on the factors that contribute to difficulties they face when attempting to engage in self-identifying linguistic microaggressions. The common challenges among these monolingual pre-service teachers are: (1) Identification and commitment are not enough; (2) Am I a bad person? and (3) Unconscious dispositions. The significance of this study stems from its exploration of the white pre-service teachers’ self-identification of microaggressions as opposed to those identified by the victims of microaggressions. By using the concept of microaggressions as the main analytical tool, the study reveals that the dominant members who are microaggressive toward language subordinate group members must understand, recognize, and acknowledge their microaggressions if they are to more productively support English language learners (ELLs) succeed socially and academically. The study offers implications for educators working with ELLs as well as for the field of teacher education.
Positioning Theory: Kinesiology Students’ Experiences Teaching in an Adapted Aquatics Practicum
Authors: Sato Takahiro , Haegele Justin 
Published: July 2017

Abstract
The purpose of this study was to describe and explain undergraduate students’ positions of teaching and assisting students with disabilities during adapted aquatics practicum experiences. The participants were eight kinesiology students who enrolled in an introductory adapted physical education (APE) course at a public university in the Midwest region of the United States. This study used a descriptive qualitative research method and exploratory case study design (Yin, 2003). This case study was situated in the positioning theory. The term positioning means to analyze interpersonal encounters from a discursive viewpoint (Hollway, 1984). This framework allows researchers to explore the capacity of students to position themselves and, in this case, to describe how undergraduate students negotiate and implement aquatics lessons with students with disabilities. The data sources were face-to-face interviews, self-reflective journaling entries, and follow–up e-mail messages. Data were analyzed using constant comparative analysis and we uncovered the following themes: (a) ethical and unethical treatment of students with disabilities, (b) conflicts of parents’ and students’ interests, and (c) medical and gender sensitivity. This study’s results indicate that all the undergraduate students were becoming, albeit novice, reflective practitioners and ascribed their own reflective positions to their sense of advocacy. They were concerned that they had managerial challenges that exacerbated the difficulties in adjusting to the disability, medical, family and gendered backgrounds of students with disabilities. To improve preparation of undergraduate students, APE course instructors are required to use an appropriate adapted aquatic curriculum model such as the curriculum and assessment model. Using the logic of the positioning theory, researchers should study undergraduate students’ self and interactive positioning about assisting and teaching students with various levels of disabilities in adapted aquatic settings.
Slow Booms and Deep Busts: 160 Years of Business Cycles in Spain
Authors: Gries Thomas , Fritz Marlon , Feng Yuanhua 
Published: July 2017

Abstract
This paper introduces an economically important new idea for detrending macroeconomic time series and examines the Spanish business cycle pattern with respect to potential asymmetries. To address difficulties in the trend and cycle decomposition, a nonparametric trend estimation approach is introduced and exemplary applied to the Spanish GDP data for the period 1850 to 2015. The application of an iterative plug-in (IPI) algorithm for endogenous bandwidth selection solves the problem of choosing an adequate smoothing parameter for nonparametric regression. The algorithm identifies continuously Moving Trends (MT) with a time length of 34 years. After we estimate the trend nonparametrically, we fit several time series models to the residuals for further analysis. Although asymmetry during expansion and recession phases is indicated, it is not unambiguous.
The influence of microstructure geometry on the scale effect in mechanical behaviour of heterogeneous materials
Authors: Różański Adrian , Rajczakowska Magdalena , Serwicki Andrzej 
Published: July 2017

AbstractThere are a significant number of factors which have impact on the scale effect in the mechanical behaviour of composite materials. In this paper, the influence of the microstructure on this phenomenon is examined. In particular, how the results of the uniaxial compression test are affected by the microstructure geometry is verified. For the purposes of this study, two different materials are chosen, i.e. pure gypsum and mortar. Firstly, the microstructures of the two considered materials are compared with the use of different microstructure measures, i.e. attenuation profiles, porosity and pore size distributions, calculated based on the images obtained from the X-ray microCT. Then, a series of uniaxial compression tests is performed for a large number of cylindrical specimens made of the two materials under study. Four different sample diameters are assumed in order to investigate the size effect in the considered composites. For both materials, the results of uniaxial compressive strength and the Young modulus are presented. The relationship between the microstructure of the material and the scale effect in mechanical properties is proved. The scale effect is more demonstrable in the case of the material which exhibits a more heterogeneous microstructure.