bluuebunny/crossref_metadata_2025_split huggingface dataset:
RF shield parallel-plate waveguide for travelling-wave MRI experiments at 3 T
Authors: Marrufo O. , Vazquez F. , Martin R. , Solis-Najera S. E. , Rodriguez A. O. 
Published: June 2019

Abstract
Ultra high field magnetic resonance imaging systems suffer from the standing wave problems produced by conventional radiofrequency coils. This causes inhomogeneous fields degrading the image quality. To overcome this problems, propagation of RF waves by antennas inside a waveguide is suggested. We assessed the feasibility of using the magnet RF shield with aluminium strips to form a parallel-plate waveguide for travelling-wave magnetic resonance imaging at 3 T. Imaging results showed that a number of constraints must be solved before good image quality can be obtained. A brief discussion is presented on the possible sources or error and interference. Despite these limitations, results are really encouraging to continue investigating the implementation of this approach.
Sensitivity of an optical sensor based on capillary microresonator for the measurement the hydrostatic pressure in microfluidics
Authors: Padilla D Avila , Piñeres S Horta , Torres C O 
Published: June 2019

Abstract
In this investigation, we report the study of an optical device for the measurement of hydrostatic pressure in fluids. The device studied is a sensor based on a dielectric optical resonator in the form of a capillary that confines the light in its interior through the phenomenon of total internal reflection. In the analytical study of the sensor, the excitation of the azimuthal modes WGMs inside the resonant cavity is considered, so that their sensitivity to changes in the hydrostatic pressure was analyzed as a function of the displacement of wavelengths of resonances in the cavity.
Implementation of an ultrasonic tomograph for small specimens
Authors: Villarreal A , Huerta F , Solis-Najera S , Medina L 
Published: June 2019

Abstract
The implementation of an open freeware to acquire and reconstruct ultrasonic images from tomographic projections is presented. This proposed tomograph consists of three main modules: the mechanical position system, control system and the ultrasonic pulse emission-reception system. The communication, synchronization among these modules, experimental parameters and image reconstruction are done by an interface based on JAVA. The preliminary results show that the system is able to produce quality images of tested specimens.
The electrical and optical properties of kesterites
Authors: Grossberg Maarja , Krustok Jüri , Hages Charles J , Bishop Douglas M , Gunawan Oki , Scheer Roland , Lyam Samantha M , Hempel Hannes , Levcenco Sergiu , Unold Thomas 
Published: June 2019

AbstractKesterite Cu2ZnSn(SxSe1-x)4(CZTSSe) semiconductor materials have been extensively studied over the past decade, however despite significant efforts, the open circuit voltage remains below 60% of the theoretical maximum. Understanding the optical and electrical properties is critical to explaining and solving the voltage deficit. This review aims to summarize the present knowledge of optical and electrical properties of kesterites and specifically focuses on experimental data of intrinsic defects, charge carrier density and transport, and minority carrier lifetime and related rate-limiting recombination mechanisms. It concludes with suggestions for further investigation of the electrical and optical properties of kesterite materials.
iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures
Authors: Wang Jiyao , Youkharibache Philippe , Zhang Dachuan , Lanczycki Christopher J , Geer Renata C , Madej Thomas , Phan Lon , Ward Minghong , Lu Shennan , Marchler Gabriele H , Wang Yanli , Bryant Stephen H , Geer Lewis Y , Marchler-Bauer Aron 
Published: June 2019

Abstract

Motivation
Build a web-based 3D molecular structure viewer focusing on interactive structural analysis.

Results
iCn3D (I-see-in-3D) can simultaneously show 3D structure, 2D molecular contacts and 1D protein and nucleotide sequences through an integrated sequence/annotation browser. Pre-defined and arbitrary molecular features can be selected in any of the 1D/2D/3D windows as sets of residues and these selections are synchronized dynamically in all displays. Biological annotations such as protein domains, single nucleotide variations, etc. can be shown as tracks in the 1D sequence/annotation browser. These customized displays can be shared with colleagues or publishers via a simple URL. iCn3D can display structure–structure alignments obtained from NCBI’s VAST+ service. It can also display the alignment of a sequence with a structure as identified by BLAST, and thus relate 3D structure to a large fraction of all known proteins. iCn3D can also display electron density maps or electron microscopy (EM) density maps, and export files for 3D printing. The following example URL exemplifies some of the 1D/2D/3D representations: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1TUP&showanno=1&show2d=1&showsets=1.

Availability and implementation
iCn3D is freely available to the public. Its source code is available at https://github.com/ncbi/icn3d.

Supplementary information
Supplementary data are available at Bioinformatics online.
Deep representation learning for domain adaptable classification of infrared spectral imaging data
Authors: Raulf Arne P , Butke Joshua , Küpper Claus , Großerueschkamp Frederik , Gerwert Klaus , Mosig Axel 
Published: June 2019

Abstract

Motivation
Applying infrared microscopy in the context of tissue diagnostics heavily relies on computationally preprocessing the infrared pixel spectra that constitute an infrared microscopic image. Existing approaches involve physical models, which are non-linear in nature and lead to classifiers that do not generalize well, e.g. across different types of tissue preparation. Furthermore, existing preprocessing approaches involve iterative procedures that are computationally demanding, so that computation time required for preprocessing does not keep pace with recent progress in infrared microscopes which can capture whole-slide images within minutes.

Results
We investigate the application of stacked contractive autoencoders as an unsupervised approach to preprocess infrared microscopic pixel spectra, followed by supervised fine-tuning to obtain neural networks that can reliably resolve tissue structure. To validate the robustness of the resulting classifier, we demonstrate that a network trained on embedded tissue can be transferred to classify fresh frozen tissue. The features obtained from unsupervised pretraining thus generalize across the large spectral differences between embedded and fresh frozen tissue, where under previous approaches separate classifiers had to be trained from scratch.

Availability and implementation
Our implementation can be downloaded from https://github.com/arnrau/SCAE_IR_Spectral_Imaging.

Supplementary information
Supplementary data are available at Bioinformatics online.
sefOri: selecting the best-engineered sequence features to predict DNA replication origins
Authors: Lou Chenwei , Zhao Jian , Shi Ruoyao , Wang Qian , Zhou Wenyang , Wang Yubo , Wang Guoqing , Huang Lan , Feng Xin , Zhou Fengfeng 
Published: June 2019

Abstract

Motivation
Cell divisions start from replicating the double-stranded DNA, and the DNA replication process needs to be precisely regulated both spatially and temporally. The DNA is replicated starting from the DNA replication origins. A few successful prediction models were generated based on the assumption that the DNA replication origin regions have sequence level features like physicochemical properties significantly different from the other DNA regions.

Results
This study proposed a feature selection procedure to further refine the classification model of the DNA replication origins. The experimental data demonstrated that as large as 26% improvement in the prediction accuracy may be achieved on the yeast Saccharomyces cerevisiae. Moreover, the prediction accuracies of the DNA replication origins were improved for all the four yeast genomes investigated in this study.

Availability and implementation
The software sefOri version 1.0 was available at http://www.healthinformaticslab.org/supp/resources.php. An online server was also provided for the convenience of the users, and its web link may be found in the above-mentioned web page.

Supplementary information
Supplementary data are available at Bioinformatics online.
Perinatal health of refugee and asylum-seeking women in Sweden 2014–17: a register-based cohort study
Authors: Liu Can , Ahlberg Mia , Hjern Anders , Stephansson Olof 
Published: June 2019

Abstract

Background
An increasing number of migrants have fled armed conflict, persecution and deteriorating living conditions, many of whom have also endured risky migration journeys to reach Europe. Despite this, little is known about the perinatal health of migrant women who are particularly vulnerable, such as refugees, asylum-seekers, and undocumented migrants, and their access to perinatal care in the host country.

Methods
Using the Swedish Pregnancy Register, we analyzed indicators of perinatal health and health care usage in 31 897 migrant women from the top five refugee countries of origin between 2014 and 2017. We also compared them to native-born Swedish women.

Results
Compared to Swedish-born women, migrant women from Syria, Iraq, Somali, Eritrea and Afghanistan had higher risks of poor self-rated health, gestational diabetes, stillbirth and infants with low birthweight. Within the migrant population, asylum-seekers and undocumented migrants had a higher risk of poor maternal self-rated health than refugee women with residency, with an adjusted risk ratio (RR) of 1.84 and 95% confidence interval (95% CI) of 1.72–1.97. They also had a higher risk of preterm birth (RR 1.47, 95% CI 1.21–1.79), inadequate antenatal care (RR 2.56, 95% CI 2.27–2.89) and missed postpartum care visits (RR 1.15, 95% CI 1.10–1.22).

Conclusion
Refugee, asylum-seeking and undocumented migrant women were vulnerable during pregnancy and childbirth. Living without residence permits negatively affected self-rated health, pregnancy and birth outcomes in asylum-seekers and undocumented migrants. Pregnant migrant women’s special needs should be addressed by those involved in the asylum reception process and by health care providers.
Sound Stories: A Context-Based Study of Everyday Listening to Augmented Soundscapes
Authors: Droumeva Milena , McGregor Iain 
Published: June 2019

Abstract
With an increasing number of everyday operations and communications becoming both automated and autonomous, ambient intelligent soundscapes are transforming to accommodate additional sonic feedback, and with it, new frameworks of listening. While this type of research and design of audio augmented technology is not new, the impact pre-existing acoustic environments upon listeners’ sense-making activities is rarely considered holistically. Much of the study into the design of effective auditory displays focuses on perceptual acuity and correct source identification, often at the expense of understanding the context of meaning-making. This paper presents a study involving 70 participants who listened to unidentified audio recordings of two archetypal everyday urban sound environments naturally containing artificial signals as well as typical sounds. Using a ThinkAloud protocol we investigated listeners’ approaches to meaning-making in both semantic and temporal dimensions. Through a semantic content analysis, we articulate five aspects of sonic meaning-making: spatial, descriptive, experiential, associational and narrative. We further analyse the use of these perceptual elements on a temporal plane, in order to investigate how listeners construct a narrative of what they hear in real-time, naturally evolving as each subsequent sound event is interpreted. Results suggest that while listeners attend to sound events and spatial characteristics of a sound environment at the beginning of a new listening situation, as the soundscape unfolds they utilize associations and familiarity in order to place individual sounds into increasingly coherent narratives. Finally, we suggest that this approach could provide sound designers and human–computer interaction specialists with a model for investigating the context aspects of a soundscape more holistically, allowing them to evaluate the effect of any new designed sounds prior to introduction into real-world environments.
Methanogenic potential of tropical feeds rich in hydrolyzable tannins1,2
Authors: Rira Moufida , Morgavi Diego P , Genestoux Lucette , Djibiri Sihem , Sekhri Ines , Doreau Michel 
Published: June 2019

Abstract
The present study was carried out to determine the effect of Acacia nilotica, a tropical plant rich in hydrolyzable tannins (HT), on rumen fermentation and methane (CH4) production in vitro. We used leaves and pods from A. nilotica alone and combined. The combination of HT from A. nilotica leaves and pods and condensed tannins (CT) from Calliandra calothyrsus and Leucaena leucocephala were also evaluated to assess potential differences in biological activity between HT and CT. Four series of 24-h incubations were performed using rumen contents of 4 sheep fed a tropical grass (natural grassland based on Dichanthium spp.). A first experiment tested different levels of replacement of this tropical forage (control [CTL] without tannins) by A. nilotica leaves or pods: 0:100, 25:75, 50:50, 75:25 and 100:0. A second experiment tested the mixture of A. nilotica leaves and pods in different proportions: 100:0, 75:25, 50:50, 25:75, and 0:100. A third experiment tested the 50:50 combination of A. nilotica leaves or pods with C. calothyrsus and L. leucocephala. Acacia nilotica pods and leaves had a high content of HT (350 and 178 g/kg DM, respectively), whereas C. calothyrsus and L. leucocephala had a high content of CT (361 and 180 g/kg DM, respectively). The inclusion of HT from A. nilotica leaves and pods decreased CH4 production dose-dependently (P < 0.01). Total replacement of the CTL by A. nilotica decreased CH4 production by 64 and 55% with leaves and pods, respectively. Pods were richer in HT than leaves, but their antimethanogenic effect did not differ (P > 0.05). Although A. nilotica leaves and pods inhibited fermentation, as indicated by the lower gas production and VFA production (P < 0.01), this effect was less pronounced than for CH4. Volatile fatty acid production decreased by 12% in leaves and by 30% in pods when compared with the CTL alone. Positive associative effect was reported for VFA, when HT-rich sources and CT-rich sources were mixed. Combining the 2 sources of HT did not show associative effects on fermentation or CH4 production (P > 0.05). Hydrolyzable tannin-rich sources were more effective in suppressing methanogenesis than CT-rich sources. Our results show that HT-rich A. nilotica leaves and pods have the potential to reduce ruminal CH4 production.
Morphology and star formation in IllustrisTNG: the build-up of spheroids and discs
Authors: Tacchella Sandro , Diemer Benedikt , Hernquist Lars , Genel Shy , Marinacci Federico , Nelson Dylan , Pillepich Annalisa , Rodriguez-Gomez Vicente , Sales Laura V , Springel Volker , Vogelsberger Mark 
Published: June 2019

ABSTRACT
Using the IllustrisTNG simulations, we investigate the connection between galaxy morphology and star formation in central galaxies with stellar masses in the range 109–1011.5 M⊙. We quantify galaxy morphology by a kinematical decomposition of the stellar component into a spheroidal and a disc component (spheroid-to-total ratio, S/T) and by the concentration of the stellar mass density profile (C82). S/T is correlated with stellar mass and star formation activity, while C82 correlates only with stellar mass. Overall, we find good agreement with observational estimates for both S/T and C82. Low- and high-mass galaxies are dominated by random stellar motion, while only intermediate-mass galaxies (M⋆ ≈ 1010–1010.5 M⊙) are dominated by ordered rotation. Whereas higher mass galaxies are typical spheroids with high concentrations, lower mass galaxies have low concentration, pointing to different formation channels. Although we find a correlation between S/T and star formation activity, in the TNG model galaxies do not necessarily change their morphology when they transition through the green valley or when they cease their star formation, this depending on galaxy stellar mass and morphological estimator. Instead, the morphology (S/T and C82) is generally set during the star-forming phase of galaxies. The apparent correlation between S/T and star formation arises because earlier forming galaxies had, on average, a higher S/T at a given stellar mass. Furthermore, we show that mergers drive in situ bulge formation in intermediate-mass galaxies and are responsible for the recent spheroidal mass assembly in the massive galaxies with M⋆ &gt; 1011 M⊙. In particular, these massive galaxies assemble about half of the spheroidal mass while star-forming and the other half through mergers while quiescent.
Determining mass limits around HD 163296 through SPHERE direct imaging data
Authors: Mesa D , Langlois M , Garufi A , Gratton R , Desidera S , D’Orazi V , Flasseur O , Barbieri M , Benisty M , Henning T , Ligi R , Sissa E , Vigan A , Zurlo A , Boccaletti A , Bonnefoy M , Cantalloube F , Chauvin G , Cheetham A , De Caprio V , Delorme P , Feldt M , Fusco T , Gluck L , Hagelberg J , Lagrange A-M , Lazzoni C , Madec F , Maire A-L , Menard F , Meyer M , Ramos J , Rickman E L , Rouan D , Schmidt T , Van der Plas G 
Published: June 2019

ABSTRACT
HD 163296 is a Herbig Ae/Be star known to host a protoplanetary disc with a ringed structure. To explain the disc features, previous works proposed the presence of planets embedded into the disc. We have observed HD 163296 with the near-infrared (NIR) branch of SPHERE composed by IRDIS (InfraRed Dual-band Imager and Spectrograph) and IFS (integral field spectrograph) with the aim to put tight constraints on the presence of substellar companions around this star. Despite the low rotation of the field of view during our observation we were able to put upper mass limits of few MJup around this object. These limits do not allow to give any definitive conclusion about the planets proposed through the disc characteristics. On the other hand, our results seem to exclude the presence of the only candidate proposed until now using direct imaging in the NIR even if some caution has to be taken considered the different wavelength bands of the two observations.
Economic Burden Attributed to Children Presenting to Hospitals With Hand, Foot, and Mouth Disease in Vietnam
Authors: Nhan Le Nguyen Thanh , Turner Hugo C , Khanh Truong Huu , Hung Nguyen Thanh , Lien Le Bich , Hong Nguyen Thi Thu , Nhu Le Nguyen Truc , Ny Nguyen Thi Han , Nguyet Lam Anh , Thanh Tran Tan , Van Hoang Minh Tu , Viet Ho Lu , Tung Trinh Huu , Phuong Tran Thi Lan , Devine Angela , Thwaites Guy , Chau Nguyen Van Vinh , Thwaites Louise , van Doorn H Rogier , Tan Le Van 
Published: June 2019

Abstract

Background
Hand, foot, and mouth disease (HFMD) has become a major public health concern in the Asia-Pacific region. Knowledge of its economic burden is essential for policy makers in prioritizing the development and implementation of interventions.

Methods
A multi-hospital-based study was prospectively conducted at 3 major hospitals in Ho Chi Minh City, Vietnam, during 2016–2017. Data on direct and productivity costs were collected alongside clinical information and samples and demographic information from study participants.

Results
A total of 466 patients were enrolled. Two hundred three of 466 (43.6%) patients lived in Ho Chi Minh City, and 72/466 (15.5%) had severe HFMD. An enterovirus was identified in 74% of 466 patients, with EV-A71, CV-A6, CV-A10, and CV-A16 being the most common viruses identified (236/466, 50.6%). The mean economic burden per case was estimated at US$400.80 (95% confidence interval [CI], $353.80–$448.90), of which the total direct (medical) costs accounted for 69.7%. There were considerable differences in direct medical costs between groups of patients with different clinical severities and pathogens (ie, EV-A71 vs non-EV-A71). In Vietnam, during 2016–2017, the economic burden posed by HFMD was US$90 761 749 (95% CI, $79 033 973–$103 009 756).

Conclusions
Our findings are of public health significance because for the first time we demonstrate that HFMD causes a substantial economic burden in Vietnam, and although multivalent vaccines are required to control HFMD, effective EV-A71 vaccine could substantially reduce the burden posed by severe HFMD. The results will be helpful for health policy makers in prioritizing resources for the development and implementation of intervention strategies to reduce the burden of HFMD.
Federalism and Foreign Affairs in India
Authors: Asthana Anamika , Jacob Happymoon 
Published: June 2019

Abstract
This chapter locates India’s foreign affairs within the federal structure of the country’s constitution. As a formal matter, India’s constitution strongly favors the central government’s authority, especially in matters of foreign policy and defense. India’s foreign policymaking processes, however, do not strictly correspond either to a unitary or a federal model and often are responsive to contextual dynamics. As the chapter explains, the central government has over time pursued a pragmatic approach in dealing with subnational engagement in the country’s foreign policymaking, without bringing about substantive and formal structural changes either in the constitution or the front-line institutions dedicated to foreign policy decision-making. Such pragmatism has been prominently evident in the area of international trade, especially since the onset of economic liberalization. Moreover, despite the constitutional preeminence of the central government in matters of foreign policy and defense, state entities in the era of coalition politics have successfully deployed extraconstitutional means, mostly through bargaining and pressure tactics, to influence the central government’s foreign policy processes. Federalization of foreign policymaking therefore, though limited, is an ongoing process in India’s vibrant polity.
Foreign Affairs Federalism in the European Union
Authors: Schütze Robert 
Published: June 2019

Abstract
The European Union was born as an international organization. The 1957 Treaty of Rome formed part of international law, although the European Court of Justice was eager to emphasize that the Union constitutes “a new legal order” of international law. With time, this new legal order has indeed evolved into a true “federation of States.” Yet how would the foreign affairs powers of this new supranational entity be divided? Would the European Union gradually replace the member states, or would it preserve their distinct and diverse foreign affairs voices? In the past sixty years, the Union has indeed significantly sharpened its foreign affairs powers. While still based on the idea that it has no plenary power, the Union’s external competences have expanded dramatically, and today it is hard to identify a nucleus of exclusive foreign affairs powers reserved for the member states. And in contrast to a classic international law perspective, the Union’s member states only enjoy limited treaty-making powers under European law. Their foreign affairs powers are limited by the exclusive powers of the Union, and they may be preempted through European legislation. There are, however, moments when both the Union and its states enjoy overlapping foreign affairs powers. For these situations, the Union legal order has devised a number of cooperative mechanisms to safeguard a degree of “unity” in the external actions of the Union. Mixed agreements constitute an international mechanism that brings the Union and the member states to the same negotiating table. The second constitutional device is internal to the Union legal order: the duty of cooperation.