bluuebunny/crossref_metadata_2025_split huggingface dataset:
Building-up Affordable Data Collection System to Provide 3D Scaled Image for Heritage Documentation
Authors: Abood Nadia , Kareem Imzahim Abdul , Sarhan Hameed 
Published: March 2020

Abstract
To solve the problem of insufficient efficiency of 2D display for damaged and erosional parts of important historical heritage and a high cost of a scanning systems used, affordable data collection system to provide 3D scaled image for Heritage Documentation has been proposed to obtain scaled image with lower cost upon user. The main target of Smart Automated System (SAS) to reconstruct 3D image for various structures and terrain. Mechanically, this system was designed to apply rotation function, that a digital camera will be rotated by using a stepper motor with specific horizontal angles. While the SAS rotates; non-metric digital camera which must be ready to capture automatically a sequence of 2D images. These captured 2D images must be processed and subjected to registration process for obtaining 3D scaled image. MATLAB software has been used to perform automation function between hardware parts (explained bellow) as well as processing of images.
GIS-based approach for rainwater harvesting site selection
Authors: Sayl K N , Mohammed A S , Ahmed A D 
Published: March 2020

Abstract
The main obstacle to development in arid areas is the scarce and intermittent rainfall. Water harvesting is considered one of means to grantee the sustainability of water for use in domestic, irrigation and even industry. The current study carried out on Haqlan valley basin in western part of Iraq. The selection of suitable location for rainwater harvesting is based on different key determinates such as environment, hydrology, socio-economic, and topography as well as the estimation of the storage volume and the surface area. This study aims to identify the suitable location for rainwater harvesting using Geographical Information System (GIS) and remote sensing with multi-criteria decision techniques in the study area. Many thematic maps were extracted such as soil map, vegetation cover, land use/land cover, slope, and digital elevation model. The drainage network and the contour line map were used to suggest six sites in the study area. The result shows that the total suitable area for water harvesting was 28% of the study area, while 21% indicated moderate suitability. The proposed method is relatively supportive in analyzing geospatial data to determine and select the optimal site for rainwater harvesting and minimize evaporation losses.
Temporal Analysis of Ramsar Sites via Remote Sensing Techniques – A Case Study of Meke Maar
Authors: Yagmur N , Musaoglu N 
Published: March 2020

Abstract
Wetlands have globally significant social, economic and environmental benefits. Ramsar supports the conservation and conscious use of wetlands. Meke Maar is one of the Ramsar sites which located in Konya Closed Basin. Aim of the study is analysis of Meke Maar from 1984 to 2017, along with the reasons for the change. Remote sensing techniques were used for change detection from 1984 to 2017. Remote sensing has widely used in environmental analysis and change detection. Change analysis was conducted for 2 different month interval as spring (May-June) and autumn (August-September). For detecting water surface area, Normalized Difference Water Index (NDWI) and Classification and Regression Tree (CART) methods were used. These methods were implemented in the Google Earth Engine (GEE) platform. Obtained results evaluate with meteorological data and groundwater level measurements. Gulfet Yayla well is the nearest well to study area. That is why, its observations were used in evaluation of change detection results. In conclusion, water surface area in the Meke Maar has decreased approximately 90%. As a result of the study, it was determined that the factors affecting the water change in Meke Maar were precipitation and groundwater level.
Effect of sulfur on corrosion behavior of Q235 and 16Mn steel in sodium aluminate solutions
Authors: Quan Bian-li , Li Jun-qi , Chen Chao-yi 
Published: March 2020

Abstract
This study investigates the effect of sulfur on Q235 steel and 16Mn steel corrosion in sodium aluminate solution. The corrosion rate of Q235 steel and 16Mn steel reaches the maximum respectively when S2− and S2O3
2− form synergistic corrosion and S2− is contained alone. But, the size of corroded particles is smaller in the solution containing only S2O3
2− for two kinds of steel. The corrosion rate of 16Mn steel is greater than Q235 steel. Surface corrosion of two kinds of steel is both composed of sulfides (FeS and FeS2) and oxides (Fe2O3, Fe3O4, Al2O3 and NaFeO2). The crystal particles of steel surface are mainly iron oxides according to EDS analysis. Nyquist plots of Q235 steel with different forms of sulfur have two capacitance-resistance arcs and no diffusion impedance. Nyquist plots of 16Mn steel with S2O3
2− alone is consistent with Q235 steel. But, Nyquist plots of 16Mn steel presents a typical Warburg diffusion phenomenon with containing S2− alone and forming synergistic corrosion.
Microstructure and microhardness of carbonate apatite particle-reinforced Mg composite consolidated by warm compaction for biodegradable implant application
Authors: Setyadi Iwan , Marsetio Aldo Fransiskus , Kamal Achmad Fauzi , Rahyussalim  , Supriadi Sugeng , Suharno Bambang 
Published: March 2020

Abstract
Magnesium-based composites with carbonate apatite reinforcement are attractive biodegradable implant materials. In this study, we observed the effect of carbonate apatite content (5, 10, and 15% wt.) and milling time (3, 5, and 7 h) on the microstructure and microhardness of magnesium-carbonate apatite composites fabricated by powder metallurgy. The consolidation process involved warm compaction without sintering. Characterization was achieved through density testing, x-ray diffraction (XRD), optical microscopy, SEM-energy dispersive x-ray spectroscopy (EDS), and microhardness testing. The powder milling time affects the distribution of apatite carbonate; adding carbonate apatite can increase the hardness of magnesium-based composites. In the XRD spectrum, we identify the dominant magnesium peak but not the magnesium oxide peak. Carbonate apatite powder is distributed at the grain boundaries. The hardness range is 40.26–44.82 Hv or increase by 8.21%–20.23% compared to the hardness of consolidated pure magnesium. The relative density is around 95.92%–98.71%, whereas the relative density of pure magnesium is 99.58%. The obtained optimal conditions for fabricating magnesium composites are the following: content of 10 wt% carbonate apatite (milled for 5 h) with a hardness of 43.58 Hv.
Machine learning at the (sub)atomic scale: next generation scanning probe microscopy
Authors: Gordon Oliver M , Moriarty Philip J 
Published: March 2020

Abstract
We discuss the exciting prospects for a step change in our ability to map and modify matter at the atomic/molecular level by embedding machine learning algorithms in scanning probe microscopy (with a particular focus on scanning tunnelling microscopy, STM). This nano-AI hybrid approach has the far-reaching potential to realise a technology capable of the automated analysis, actuation, and assembly of matter with a precision down to the single chemical bond limit.
Are older patients with diabetes still being overtreated in French long-term care homes?
Authors: Quilot Emilienne , Petit Jean-Michel , Vergès Bruno , Bouillet Benjamin 
Published: March 2020

Abstract

Background
Diabetes management has not been evaluated in French nursing homes (NHs) for 10 years.

Objectives
The present study aimed to compare the management of diabetes with guidelines in older patients living in NHs.

Design
Observational, retrospective and multicentre study carried out in 13 NH in the Cote d’Or region of France.

Settings and subjects
Between January and June 2018, all NH residents older than 65 years and known to have diabetes (n = 148) were included.

Methods
Epidemiological, clinical and biological data and diabetes characteristics were collected from the medical records.

Results
The average glycated haemoglobin (HbA1C) was 7.2 ± 1.2%. In total, 51% of patients had HbA1C &lt; 7% (n = 70), of which 39 took one or more antidiabetic drugs. In total, 28 of those patients (40%) were at risk of developing hypoglycaemia as a result of their treatment. In all, 44.6% of patients were treated with insulin. Glinides were the most commonly prescribed oral antidiabetic drug (OAD) (27%). Capillary blood glucose monitoring (CBGM) was not carried out daily for 75% of patients taking a potentially hypoglycaemia-inducing OAD.

Conclusions
We found that glycaemic control was too tight in at least 36.5% of the total population and that 40% of patients with HbA1C &lt; 7% were potentially overtreated. The use of dipeptidyl peptidase 4 (DPP-4) inhibitors was still insufficient, as was CBGM. Avoiding hypoglycaemia is one of the priorities in the management of older patients with diabetes. Therefore, NHs should focus on improving the use of glycaemic targets and antidiabetic drugs that do not induce hypoglycaemia, as well as better monitoring of capillary blood glucose.
The Common Wind: A Masterful Study of the Masterless Revolutionary Atlantic
Authors: Lightfoot Natasha 
Published: March 2020

Abstract
The 2018 publication of Julius S. Scott’s The Common Wind: Afro-American Currents in the Age of the Haitian Revolution inspired a renewed focus on the reverberations of the Haitian Revolution. Here, six scholars of the Atlantic World and the Age of Revolutions consider the historiographical implications of The Common Wind and remind us how the Haitian upheaval belongs at the very center of the ripples of modernity that spread across the globe from the revolutionary Atlantic.
Contexts for Critique: Revisiting Representations of Violence in Our Beloved Kin
Authors: Mt. Pleasant Alyssa 
Published: March 2020

Abstract
David Silverman offers a critical appraisal of two prizewinning works in Native American and Indigenous studies (NAIS), Our Beloved Kin: A New History of King Philip’s War, by Lisa Brooks, and Memory Lands: King Philip’s War and the Place of Violence in the Northeast, by Christine M. DeLucia. Silverman’s review treats the methodology associated with NAIS with some skepticism, offering the opportunity for a lively discussion about the merits and perils of community-engaged history scholarship. Four scholars of Native American history, including DeLucia, respond, defending new approaches to Indigenous history represented by these recent works.
Is the Utilization of Helicobacter pylori Stool Antigen Tests Appropriate in an Urban Canadian Population?
Authors: Ma Irene , Guo Maggie , Pillai Dylan R , Church Deirdre L , Naugler Christopher 
Published: March 2020

Abstract

Objectives
Helicobacter pylori stool antigen test (HpSAT) appropriateness was investigated by assessing its testing and positivity rates in Calgary, Canada.

Methods
The laboratory information system was accessed for all patients who received an HpSAT in 2018. Testing volume, test results, age, and sex of patients were collected. Sociodemographic risk factors and geospatial analysis were performed by matching laboratory data to the 2016 census data. Testing appropriateness was defined as a concordance between testing and positivity rates for each sociodemographic variable.

Results
In 2018, 25,518 H pylori stool antigen tests were performed in Calgary, with an overall positivity rate of 14.7%. Geospatial mapping demonstrated significant distribution variations of testing and positivity rates of HpSAT in the city. Certain sociodemographic groups studied (eg, recent immigrants) appeared to be appropriately tested (testing rate relative risk [RR] = 2.26, positivity rate RR = 4.32; P &lt; .0001), while other groups (eg, male) may have been undertested (testing rate RR = 0.85, positivity rate RR = 1.14; P &lt; .0001).

Conclusions
Determining concordance of testing and positivity rate of a laboratory test can be used for assessing testing appropriateness for other diseases in other jurisdictions. This study demonstrated some at-risk patients may be missed for H pylori testing.
The Epidemiologic Toolbox: Identifying, Honing, and Using the Right Tools for the Job
Authors: Lesko Catherine R , Keil Alexander P , Edwards Jessie K 
Published: March 2020

Abstract
There has been much debate about the relative emphasis of the field of epidemiology on causal inference. We believe this debate does short shrift to the breadth of the field. Epidemiologists answer myriad questions that are not causal and hypothesize about and investigate causal relationships without estimating causal effects. Descriptive studies face significant and often overlooked inferential and interpretational challenges; we briefly articulate some of them and argue that a more detailed treatment of biases that affect single-sample estimation problems would benefit all types of epidemiologic studies. Lumping all questions about causality creates ambiguity about the utility of different conceptual models and causal frameworks; 2 distinct types of causal questions include 1) hypothesis generation and theorization about causal structures and 2) hypothesis-driven causal effect estimation. The potential outcomes framework and causal graph theory help efficiently and reliably guide epidemiologic studies designed to estimate a causal effect to best leverage prior data, avoid cognitive fallacies, minimize biases, and understand heterogeneity in treatment effects. Appropriate matching of theoretical frameworks to research questions can increase the rigor of epidemiologic research and increase the utility of such research to improve public health.
Leitmotif: protein motif scanning 2.0
Authors: Biđin Siniša , Vujaklija Ivan , Paradžik Tina , Bielen Ana , Vujaklija Dušica 
Published: March 2020

Abstract

Motivation
Motif-HMM (mHMM) scanning has been shown to possess unique advantages over standardly used sequence-profile search methods (e.g. HMMER, PSI-BLAST) since it is particularly well-suited to discriminate proteins with variations inside conserved motifs (e.g. family subtypes) or motifs lacking essential residues (false positives, e.g. pseudoenzymes).

Results
In order to make mHMM widely accessible to a broader scientific community, we developed Leitmotif, an mHMM web application with many parametrization options easily accessible through intuitive interface. Substantial improvement of performance (ROC scores) was obtained by using two novel parameters. To the best of our knowledge, Leitmotif is the only available mHMM application.

Availability and implementation
Leitmotif is freely available at https://leitmotif.irb.hr.

Contact
sinisa@heuristika.hr or ivan.vujaklija@fer.hr

Supplementary information
Supplementary data are available at Bioinformatics online.
SphereCon—a method for precise estimation of residue relative solvent accessible area from limited structural information
Authors: Gress Alexander , Kalinina Olga V 
Published: March 2020

Abstract

Motivation
In proteins, solvent accessibility of individual residues is a factor contributing to their importance for protein function and stability. Hence one might wish to calculate solvent accessibility in order to predict the impact of mutations, their pathogenicity and for other biomedical applications. A direct computation of solvent accessibility is only possible if all atoms of a protein three-dimensional structure are reliably resolved.

Results
We present SphereCon, a new precise measure that can estimate residue relative solvent accessibility (RSA) from limited data. The measure is based on calculating the volume of intersection of a sphere with a cone cut out in the direction opposite of the residue with surrounding atoms. We propose a method for estimating the position and volume of residue atoms in cases when they are not known from the structure, or when the structural data are unreliable or missing. We show that in cases of reliable input structures, SphereCon correlates almost perfectly with the directly computed RSA, and outperforms other previously suggested indirect methods. Moreover, SphereCon is the only measure that yields accurate results when the identities of amino acids are unknown. A significant novel feature of SphereCon is that it can estimate RSA from inter-residue distance and contact matrices, without any information about the actual atom coordinates.

Availability and implementation
https://github.com/kalininalab/spherecon.

Contact
alexander.gress@helmholtz-hips.de

Supplementary information
Supplementary data are available at Bioinformatics online.
CPS analysis: self-contained validation of biomedical data clustering
Authors: Zhang Lixiang , Lin Lin , Li Jia 
Published: March 2020

Abstract

Motivation
Cluster analysis is widely used to identify interesting subgroups in biomedical data. Since true class labels are unknown in the unsupervised setting, it is challenging to validate any cluster obtained computationally, an important problem barely addressed by the research community.

Results
We have developed a toolkit called covering point set (CPS) analysis to quantify uncertainty at the levels of individual clusters and overall partitions. Functions have been developed to effectively visualize the inherent variation in any cluster for data of high dimension, and provide more comprehensive view on potentially interesting subgroups in the data. Applying to three usage scenarios for biomedical data, we demonstrate that CPS analysis is more effective for evaluating uncertainty of clusters comparing to state-of-the-art measurements. We also showcase how to use CPS analysis to select data generation technologies or visualization methods.

Availability and implementation
The method is implemented in an R package called OTclust, available on CRAN.

Contact
lzz46@psu.edu or jiali@psu.edu

Supplementary information
Supplementary data are available at Bioinformatics online.
grabseqs: simple downloading of reads and metadata from multiple next-generation sequencing data repositories
Authors: Taylor Louis J , Abbas Arwa , Bushman Frederic D 
Published: March 2020

Abstract

Summary
High-throughput sequencing is a powerful technique for addressing biological questions. Grabseqs streamlines access to publicly available metagenomic data by providing a single, easy-to-use interface to download data and metadata from multiple repositories, including the Sequence Read Archive, the Metagenomics Rapid Annotation through Subsystems Technology server and iMicrobe. Users can download data and metadata in a standardized format from any number of samples or projects from a given repository with a single grabseqs command.

Availability and implementation
Grabseqs is an open-source tool implemented in Python and licensed under the MIT license. The source code is freely available at https://github.com/louiejtaylor/grabseqs, the Python Package Index and Anaconda Cloud repository.

Contact
bushman@pennmedicine.upenn.edu

Supplementary information
Supplementary data are available at Bioinformatics online.
A Metacommunity Approach to Improve Biological Assessments in Highly Dynamic Freshwater Ecosystems
Authors: Cid Núria , Bonada Núria , Heino Jani , Cañedo-Argüelles Miguel , Crabot Julie , Sarremejane Romain , Soininen Janne , Stubbington Rachel , Datry Thibault 
Published: March 2020

AbstractRapid shifts in biotic communities due to environmental variability challenge the detection of anthropogenic impacts by current biomonitoring programs. Metacommunity ecology has the potential to inform such programs, because it combines dispersal processes with niche-based approaches and recognizes variability in community composition. Using intermittent rivers—prevalent and highly dynamic ecosystems that sometimes dry—we develop a conceptual model to illustrate how dispersal limitation and flow intermittence influence the performance of biological indices. We produce a methodological framework integrating physical- and organismal-based dispersal measurements into predictive modeling, to inform development of dynamic ecological quality assessments. Such metacommunity-based approaches could be extended to other ecosystems and are required to underpin our capacity to monitor and protect ecosystems threatened under future environmental changes.
To trust or distrust?: Unpacking ethnic minority immigrants’ trust in police
Authors: Pass Michael D , Madon Natasha S , Murphy Kristina , Sargeant Elise 
Published: March 2020

Abstract
Studies find that immigrants can be less trusting of police than non-immigrants, with immigrants’ views deteriorating as their length of residence in a host country increases. However, existing research has failed to consider different dimensions of trust. This study applies different trust measures (single-item and multi-item measures) to examine whether trust in police varies by immigrant status and length of residence. Using survey data from 1,367 first- and second-generation ethnic minority immigrants in Australia, we find that the effect of immigrant status and length of residence on trust varies depending on how trust in police is measured. The theoretical and policy implications of these findings are discussed.
Cerebellar lesions at a young age predict poorer long-term functional recovery
Authors: Beuriat Pierre-Aurélien , Cristofori Irene , Richard Nathalie , Bardi Lara , Loriette Celia , Szathmari Alexandru , Di Rocco Federico , Leblond Pierre , Frappaz Didier , Faure-Conter Cécile , Claude Line , Mottolese Carmine , Desmurget Michel 
Published: March 2020

Abstract
Early studies on long-term functional recovery after motor and premotor lesions showed better outcomes in younger monkeys than in older monkeys. This finding led to the widespread belief that brain injuries cause less impairment in children than adults. However, this view has limitations and a large body of evidence now indicates that cerebral damages can be more harmful when inflicted at young age, during critical periods of neural development. To date, this issue has been mainly investigated in the context of focal and diffuse cortical lesions. Much less is known about the potential influence of early cerebellar damages. Several studies exist in survivor of posterior fossa tumours. However, in these studies, critical confounders were not always considered and contradictory conclusions were provided. We studied the impact or early cerebellar damage on long-term functional recovery in three groups of 15 posterior fossa survivors, comparable with respect to their tumour characteristics (type, size and location) but operated at different ages: young (≤7 years), middle (&gt;7 and ≤13 years) and older (&gt;13 years). Daily (health-related quality of life scale, performance status scale), motor (International Cooperative Ataxia Rating Scale, Pegboard Purdue Test) and cognitive (full-scale intelligence quotient) functioning were assessed. A general linear model controlling for age at surgery, radiotherapy, preservation of deep cerebellar nuclei, tumour volume and delay between surgery and assessment was used to investigate significant variations in outcome measures. Early age at surgery, lesion of deep cerebellar nuclei and postoperative radiotherapy had a significant, independent negative influence on long-term recovery. Tumour volume and delay between surgery and assessment had no statistically detectable impact. The negative influence of early age at surgery was significant in all domains: daily functioning (health-related quality of life scale, performance status scale), motor functioning (International Cooperative Ataxia Rating Scale, Pegboard Purdue Test) and cognitive functioning (full-scale intelligence quotient). These results support the existence of an early critical period of development during which the cerebellar ‘learning machine’ is of critical importance. Although the extent to which the early deficits here observed can be reversed needs now to be established, our data plead for the implementation of prompt and intense rehabilitation interventions in children operated before 7 years of age.