bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cyclotron radiation emission spectroscopy signal classification with machine learning in project 8
Authors: Esfahani A Ashtari , Böser S , Buzinsky N , Cervantes R , Claessens C , Viveiros L de , Fertl M , Formaggio J A , Gladstone L , Guigue M , Heeger K M , Johnston J , Jones A M , Kazkaz K , LaRoque B H , Lindman A , Machado E , Monreal B , Morrison E C , Nikkel J A , Novitski E , Oblath N S , Pettus W , Robertson R G H , Rybka G , Saldaña L , Sibille V , Schram M , Slocum P L , Sun Y-H , Thümmler T , VanDevender B A , Weiss T E , Wendler T , Zayas E 
Published: March 2020

Abstract
The cyclotron radiation emission spectroscopy (CRES) technique pioneered by Project 8 measures electromagnetic radiation from individual electrons gyrating in a background magnetic field to construct a highly precise energy spectrum for beta decay studies and other applications. The detector, magnetic trap geometry and electron dynamics give rise to a multitude of complex electron signal structures which carry information about distinguishing physical traits. With machine learning models, we develop a scheme based on these traits to analyze and classify CRES signals. Proper understanding and use of these traits will be instrumental to improve cyclotron frequency reconstruction and boost the potential of Project 8 to achieve world-leading sensitivity on the tritium endpoint measurement in the future.
Experimental investigation of the effect of processing parameters on densification, microstructure and hardness of selective laser melted 7075 aluminium alloy
Authors: O E Oko , C Mbakaan , E Barki 
Published: March 2020

Abstract
The 7075 aluminum alloy of the 7xxx series largely used for structures in modern aircraft has been successfully fabricated using selective laser melting (SLM) technology. The morphology of the initial 7075 aluminum alloy powders was characterized by a Zeiss Evo 50 Scanning electron microscope (SEM). Energy Dispersive x-ray (EDX) spectrometer attached to SEM was used as a tool to obtain the chemical composition of the powders. Processing parameters including scan speed, hatch distance and constant laser power (100 and 150 W) effect on densification, microstructure and hardness were investigated. The initial powder particles were found to be elongated and non-spherical and composed of Al, Zn, Mg, Cu, and Ag without Si. The result of the influence of processing parameters on properties of the as-built samples by SLM technology indicates that higher densification of parts can be gained using higher laser power and lower laser scan speed and hatch distance due to significant reduction in the number of pores. Two major types of pores including metallurgical and keyhole pores have been identified with the keyhole pores dominating the samples processed by low laser power of 100 W. The keyhole pores increase in size at a high scan speed and hatch distances. By using higher laser power of 150 W, the keyhole pores reduced significantly while metallurgical pores appear. The result of the hardness test conducted on the samples shows that high values of hardness can be achieved with low scan speed.
Functional composition and diversity of leaf traits in subalpine versus alpine vegetation in the Apennines
Authors: Stanisci Angela , Bricca Alessandro , Calabrese Valentina , Cutini Maurizio , Pauli Harald , Steinbauer Klaus , Carranza Maria Laura 
Published: March 2020

Abstract
Mediterranean high mountain grasslands are shaped by climatic stress and understanding their functional adaptations can contribute to better understanding ecosystems’ response to global change. The present work analyses the plant functional traits of high-elevation grasslands growing in Mediterranean limestone mountains to explore, at the community level, the presence of different plant strategies for resource use (conservative vs. acquisitive) and functional diversity syndromes (convergent or divergent). Thus, we compared the functional composition and diversity of the above-ground traits related to resource acquisition strategies of subalpine and alpine calcareous grasslands in the central Apennines, a mountain region characterized by a dry-summer Mediterranean climate. We used georeferenced vegetation plots and field-measured plant functional traits (plant maximum height, specific leaf area and leaf dry matter content) for the dominant species of two characteristic vegetation types: the subalpine Sesleria juncifolia community and the alpine Silene acaulis community. Both communities are of particular conservation concern and are rich in endemic species for which plant functional traits are measured here for the first time. We analysed the functional composition and diversity using the community-weighted mean trait index and the functional diversity using Rao’s function, and we assessed how much the observed pattern deviated from a random distribution by calculating the respective standardized effect sizes. The results highlighted that an acquisitive resource use strategy and relatively higher functional diversity of leaf traits prevail in the alpine S. acaulis community, optimizing a rapid carbon gain, which would help overcome the constraints exerted by the short growing season. The divergent functional strategy underlines the co-occurrence of different leaf traits in the alpine grasslands, which shows good adaptation to a microhabitat-rich environment. Conversely, in the subalpine S. juncifolia grassland, a conservative resource use strategy and relatively lower functional diversity of the leaf traits are likely related to a high level resistance to aridity over a longer growing season. Our outcomes indicate the preadaptation strategy of the subalpine S. juncifolia grassland to shift upwards to the alpine zone that will become warmer and drier as a result of anthropogenic climate change.
nanoTRON: a Picasso module for MLP-based classification of super-resolution data
Authors: Auer Alexander , Strauss Maximilian T , Strauss Sebastian , Jungmann Ralf 
Published: March 2020

Abstract

Motivation
Classification of images is an essential task in higher-level analysis of biological data. By bypassing the diffraction limit of light, super-resolution microscopy opened up a new way to look at molecular details using light microscopy, producing large amounts of data with exquisite spatial detail. Statistical exploration of data usually needs initial classification, which is up to now often performed manually.

Results
We introduce nanoTRON, an interactive open-source tool, which allows super-resolution data classification based on image recognition. It extends the software package Picasso with the first deep learning tool with a graphic user interface.

Availability and implementation
nanoTRON is written in Python and freely available under the MIT license as a part of the software collection Picasso on GitHub (http://www.github.com/jungmannlab/picasso). All raw data can be obtained from the authors upon reasonable request.

Contact
jungmann@biochem.mpg.de

Supplementary information
Supplementary data are available at Bioinformatics online.
A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks
Authors: Zhang Zi-Chao , Zhang Xiao-Fei , Wu Min , Ou-Yang Le , Zhao Xing-Ming , Li Xiao-Li 
Published: March 2020

Abstract

Motivation
Predicting potential links in biomedical bipartite networks can provide useful insights into the diagnosis and treatment of complex diseases and the discovery of novel drug targets. Computational methods have been proposed recently to predict potential links for various biomedical bipartite networks. However, existing methods are usually rely on the coverage of known links, which may encounter difficulties when dealing with new nodes without any known link information.

Results
In this study, we propose a new link prediction method, named graph regularized generalized matrix factorization (GRGMF), to identify potential links in biomedical bipartite networks. First, we formulate a generalized matrix factorization model to exploit the latent patterns behind observed links. In particular, it can take into account the neighborhood information of each node when learning the latent representation for each node, and the neighborhood information of each node can be learned adaptively. Second, we introduce two graph regularization terms to draw support from affinity information of each node derived from external databases to enhance the learning of latent representations. We conduct extensive experiments on six real datasets. Experiment results show that GRGMF can achieve competitive performance on all these datasets, which demonstrate the effectiveness of GRGMF in prediction potential links in biomedical bipartite networks.

Availability and implementation
The package is available at https://github.com/happyalfred2016/GRGMF.

Contact
leouyang@szu.edu.cn

Supplementary information
Supplementary data are available at Bioinformatics online.
‘How can the governance of communities that care interventions be enhanced by understandings of community development?’: a case study in rural Australia
Authors: Downey Heather , Threlkeld Guinever 
Published: March 2020

AbstractCommunities That Care (CTC) is an evidence-based social development strategy that uses a structured process of intervention based on the evidence about risk and protective factors in communities. CTC uses particular governance groups as central instruments in a process that aims to build the capacity of communities to enhance the lives of young people. This article reports findings from a formal evaluation which used a collaborative governance lens to examine governance of the application of CTC in a small rural Australian community. Specifically, the evaluation focussed on the perspectives of members of the governance structures concerning CTC’s operation and value at the interstice of youth and rural disadvantage. Findings suggest the potential within CTC to achieve sustainable community change may be enhanced through an endogenous governance approach that recognizes and develops community residents’ potential for leadership. The CTC strategy is now utilized internationally. This article offers important insights for practitioners, organizations and communities considering implementing this approach.
Chromatographic Fingerprint Analysis of Radix Hedysari Using Supercritical Fluid Chromatography Coupled with Diode Array Detector
Authors: Wang Bo , Liu Xiaohua , Xue Zhiyuan , Yang Xiuyan , Fang Yaoyao , Zhao Lianggong , Feng Shilan 
Published: March 2020

AbstractA newly and rapid supercritical fluid chromatography method for the simultaneous determination of 11 active compounds in Radix Hedysari samples has been developed and validated. Optimum separation was achieved on a HSS SB C18 column with a gradient elution at a flow rate of 1.5 mL/min, back pressure of 11.03 Mpa and diode array detector at 260 nm. The results from the quantitative data showed that contents of these 11 active compounds were different from plant regions. Especially the contents of formononetin in the Minxian county are ~6-fold than in wild Radix Hedysari. The chromatographic fingerprint of Radix Hedysari was recorded under the same chromatographic condition. Data analytic procedure was performed to differentiate the 25 batches of Radix Hedysari samples. Data from chromatographic fingerprint were also analyzed using hierarchical cluster analysis. The results showed that 23 batches of Radix Hedysari samples had a high similarity (&gt; 0.90) and overall 25 batches of sample were divided into two clusters. Moreover, according to the comparison contents of active compounds in each Radix Hedysari samples, the cultivated location of Radix Hedysari was successfully distinguished. This method presented good stability, repeatability and precision and would be a useful and reliable approach for the quality control of Radix Hedysari. Moreover, all target compounds were quantified by ultra-high performance liquid chromatography–time-of-flight mass spectrometry.
Multimode multioffset phase analysis of surface waves, a new approach to extend MOPA to higher modes
Authors: Barone I , Strobbia C , Cassiani G 
Published: March 2020

SUMMARY
Multioffset phase analysis (MOPA) is a fairly recent technique for evaluating seismic surface wave dispersion and estimating the presence of lateral variations. The main limitation of MOPA is that it is based on the assumption of one predominant mode, usually the fundamental mode, in the wave propagation. However, MOPA can be extended (at least) to the two-mode case: this new technique will be called multimode MOPA (MMMOPA). The method employs both amplitude and phase spectral information. The analysis is performed for each frequency independently. The presence of two modes causes the amplitude to have an oscillating behaviour as a function of offset (beats): the spatial period of the oscillating amplitude is identified, amplitude maxima and minima are extracted, and the local wavenumber is computed via linear regression. The resulting multimodal dispersion curve is consequently derived. Model uncertainties can be estimated by propagating the experimental phase and amplitude error variances through the different steps of the analysis all the way to the final phase velocities. An algorithm running the process in an automatic way has been implemented and tested on both synthetic and real data, with success. This is the base for future developments that, in the MOPA framework, can take into account rapid lateral velocity variations within the same acquisition window and estimate the modal absorption, for the estimation of the damping ratio, even in the presence of multimode surface wave propagation.
Efficient spatial-spectral computation of local planar gravimetric terrain corrections from high-resolution digital elevation models
Authors: Goyal R , Featherstone W E , Tsoulis D , Dikshit O 
Published: March 2020

SUMMARY
Computation of gravimetric terrain corrections (TCs) is a numerical challenge, especially when using very high-resolution (say, ∼30 m or less) digital elevation models (DEMs). TC computations can use spatial or/and spectral techniques: Spatial domain methods are more exact but can be very time-consuming; the discrete/fast Fourier transform (D/FFT) implementation of a binomial expansion is efficient, but fails to achieve a convergent solution for terrain slopes &gt;45°. We show that this condition must be satisfied for each and every computation-roving point pair in the whole integration domain, not just at or near the computation points. A combination of spatial and spectral methods has been advocated by some through dividing the integration domain into inner and outer zones, where the TC is computed from the superposition of analytical mass-prism integration and the D/FFT. However, there remain two unresolved issues with this combined approach: (1) deciding upon a radius that best separates the inner and outer zones and (2) analytical mass-prism integration in the inner zone remains time-consuming, particularly for high-resolution DEMs. This paper provides a solution by proposing: (1) three methods to define the radius separating the inner and outer zones and (2) a numerical solution for near-zone TC computations based on the trapezoidal and Simpson's rules that is sufficiently accurate w.r.t. the exact analytical solution, but which can reduce the computation time by almost 50 per cent.
Theoretical conceptions of intervention research addressing cancer control issues
Authors: Dupin Cécile-Marie , Estaquio Carla , Nabi Hermann 
Published: March 2020

Abstract
Population health intervention research (PHIR) involves the use of scientific methods to produce knowledge about policy and program interventions that operate within or outside of the health sector and have the potential to impact health at the population level. PHIR is a relatively new research field that has gained momentum internationally. When developing PHIR, it is important to have a program theory with the potential to increase intervention success by identifying underlying mechanisms, areas of failure and unintended outcomes. Since 2010, the French National Cancer Institute (Institut National du Cancer—INCa) has supported a national, competitive, dedicated call for proposals in PHIR to tackle cancer control issues. After 5 years of activity, specific analysis of the proposals submitted for funding and/or funded (n = 63) from descriptive and analytic perspectives was called for. Analysis of the data revealed diversity in terms of targeted populations, partnerships engaged and methodological approaches. Projects were more likely to be funded (n = 15) if presented with a robust methodological approach and diversity in methodology, and/or with research objectives at different levels of action. The analysis also revealed that researchers do not explicitly describe theoretical constructs underpinning their interventions to combat cancer. PHIR still needs improvement to better incorporate social, institutional and policy approaches to cancer control. Researchers should apply a theory-driven approach to distinguish between ‘program failure’ and ‘theory failure’. Following up the funded projects will allow successes and failures to be evaluated with respect to the use (or non-use) of theory-driven approaches.
A Phylogenetic Analysis of Hepatitis C Virus Transmission, Relapse, and Reinfection Among People Who Inject Drugs Receiving Opioid Agonist Therapy
Authors: Akiyama Matthew J , Lipsey Daniel , Ganova-Raeva Lilia , Punkova Lili T , Agyemang Linda , Sue Amanda , Ramachandran Sumathi , Khudyakov Yury , Litwin Alain H 
Published: March 2020

Abstract

Background
Understanding hepatitis C virus (HCV) transmission among people who inject drugs (PWID) is essential for HCV elimination. We aimed to differentiate reinfections from treatment failures and to identify transmission linkages and associated factors in a cohort of PWID receiving opioid agonist therapy (OAT).

Methods
We analyzed baseline and follow-up specimens from 150 PWID from 3 OAT clinics in the Bronx, New York. Next-generation sequencing data from the hypervariable region 1 of HCV were analyzed using Global Hepatitis Outbreak and Surveillance Technology.

Results
There were 3 transmission linkages between study participants. Sustained virologic response (SVR) was not achieved in 9 participants: 7 had follow-up specimens with similar sequences to baseline, and 2 died. In 4 additional participants, SVR was achieved but the participants were viremic at later follow-up: 2 were reinfected with different strains, 1 had a late treatment failure, and 1 was transiently viremic 17 months after treatment. All transmission linkages were from the same OAT clinic and involved spousal or common-law partnerships.

Conclusion
This study highlights the use of next-generation sequencing as an important tool for identifying viral transmission and to help distinguish relapse and reinfection among PWID. Results reinforce the need for harm reduction interventions among couples and those who report ongoing risk factors after SVR.
T2 Safety of Early Post-operative Range of Motion in Burn Patients with Newly Placed Hand Autografts
Authors: Dewey William S , Cunningham Kyle B , Shingleton Sarah K , Pruskowski Kaitlin A , Welsh Ashley M , Rizzo Julie A 
Published: March 2020

Abstract

Introduction
Patients who suffer hand burns are at a high risk for developing contractures, partly due to the presence of numerous cutaneous functional units, or contracture risk areas, located within the hand.
Patients who undergo split-thickness skin grafting (STSG) are often immobilized post-operatively for graft protection. Restricting mobility following a STSG is thought to protect against subdermal edema and shear forces, despite limited evidence.
Early range of motion (EROM) has been described previously. Recent practice at our burn center includes EROM following hand STSG to limit unnecessary immobilization. The purpose of this retrospective study was to determine if EROM is safe to perform after hand STSG and if there is any clinical benefit.

Methods
In an approved, retrospective, matched case-control study of adult patients who sustained hand burns, patients who received EROM were defined as cases; patients who did not receive EROM were considered controls and received the standard 3–5 days of post-operative immobilization in a resting hand splint. Adult patients admitted over a 3-year period were eligible for inclusion. Patients were evaluated for graft loss and range of motion.

Results
Seventy-two patients were included in this study; 37 EROM patients and 35 matched controls. EROM patients tended to have a larger area excised (170.4 ± 69.8cm2 vs. 132.9 ± 76.2cm2; p=0.034) and grafted (171 ± 70.8 cm2 vs. 132.9 ± 76.2 cm2; p=0.033).
Most patients were male, with an average age of 39 years. Patients had an average of approximately 5% TBSA burns with 1.5% to the hands. On post-op day (POD) 1 and 2, patients received EROM for an average of 30 minutes (29.25 ± 14.9 vs. 31 ± 16.4 minutes).
Six patients experienced minor graft loss. Three patients (8%) experienced graft loss not attributable to EROM. One patient (2.7%) experienced graft loss pre-EROM on POD2 and 3 patients (8%) experienced graft loss post-EROM on either POD1 or POD2. All graft loss was less than 1 cm in greatest dimension and no patient who experienced graft loss required additional surgery as they all closed by their first outpatient follow-up. Significantly more patients who received EROM achieved full digital flexion by the first outpatient visit (25/27=92.6% vs. 15/22=68.2%; p=0.028).

Conclusions
Performing EROM does not cause an increase in graft loss. All areas of graft loss from the EROM group healed without intervention. There appears to be a benefit to EROM since there was a significant improvement in the patients’ ability to make a full fist at initial outpatient follow up. Further prospective analysis is needed to examine the true clinical utility of EROM in the hand and other contracture-prone areas.

Applicability of Research to Practice
Clinical change in post-operative management after hand grafting.