bluuebunny/crossref_metadata_2025_split huggingface dataset:
Double low-dose computed tomography pulmonary angiography in the diagnosis of pulmonary embolism
Authors: Aldosari S , Al-Mantshari A , AlQahtani T , Almoudi M , Al-Amary A , Sun Z 
Published: June 2019

Abstract
The purpose of this study is to investigate the feasibility of double low-dose (low radiation and low contrast medium doses) computed tomography pulmonary angiography (CTPA) in the diagnosis of pulmonary embolism. This retrospective study involved analysis of 59 patients undergoing 64- and 128-slice CTPA examinations which were scanned with a pitch of 0.9 and 100 and 120 kVp, respectively, while flash mode of CTPA was done with a pitch of 3.2 and 120 kVp. There were no significant differences in image quality assessment between the low kVp and standard kVp or high-pitch CTPA protocols (p=0.181-0.186). The mean effective dose for the 100 kVp protocol was significantly lower than that for the120 kVp and the flash mode protocols (p < 0.001). The contrast medium was between 35-45 ml for the 100 and 120 kVp protocols, and 20-30 ml for the 120 kVp flash mode protocol. Double low-dose CT pulmonary angiography is feasible for detection of pulmonary embolism with acquisition of diagnostic images.
The development of Arduino-based low-cost wireless modular device for brainwave acquisition
Authors: Pratama S H , Rahmadhani A , Bramana A , Oktivasari P , Handayani N , Haryanto F , Suprijadi  , Khotimah S N 
Published: June 2019

Abstract
Brainwave is widely used as an indicator of brain activity and can be detected by electroencephalography (EEG). The development of EEG device has become more advanced along with the invention of low-cost tiny electronic modules and wireless technology. This research aimed to develop a low-cost wireless modular device for brainwave acquisition based on Arduino microcontroller. The system was designed into sensor block for brainwave receiver and conditioning, and mainboard block for data processing. Dry-active electrode was developed as the sensor, followed by preamplifier module which was also installed at the sensor block. Active filter and DRL circuits were developed on the mainboard part. Arduino UNO was used as the main processor of the device. The developed modules were then evaluated using signal generator to examine the module characteristics and consistency. As the result, the preamplifier module was detected to reach 40.34 dB on gain ability. The cutoff frequency on the active filter module was calculated on 31 Hz. Furthermore, Arduino UNO was identified to have a consistency on input and output voltage.
Investigating the aberration found in 4.438 MeV 12C photo peak of the Geant4 simulated prompt gamma spectrum
Authors: Ramanathan V , Peterson S 
Published: June 2019

Abstract
The purpose of this study is to investigate the broad 4.438 MeV 12C photo-peak found in the Geant4 simulated prompt gamma spectrum from proton beam collision on a thin carbon target. The broad 4.438 MeV 12C peak has been reported in previous work using the AFRODITE clover detector performing an absolute comparison of measured and simulated prompt gamma production for a carbon target in the proton therapeutic range. The simulated prompt gamma spectrum was obtained for a 95 MeV proton beam collision on the carbon target by counting the emitted prompt gammas over a 4ˇ solid angle using a Geant4(v10.01.p3) cross-section code with the suggested physics list for inelastic scattering in the proton therapeutic range (binary cascade model). This result was compared to prompt gamma spectra from other Geant4 inelastic scattering physics models. First, the default inelastic cross-section data set (Geisha) was compared to the Tripathi data set, producing basically identical spectra, indicating that the cross-section data set has no bearing on the binary cascade inelastic scatter model. Second, comparisons of the precompound model using an exciton number of 1 and the Geisha cross-section data set provides a 4.438 MeV photo peak that is closer to the experimental result. The precompound model with an exciton number of 1 and the default (Geisha) cross-section data set significantly narrowed the 4.438 MeV photo peak, giving the peak that most closely resembled measured data.
Comprehensive external audit for HDR brachytherapy systems – the national experience
Authors: Koniarova Irena , Horakova Ivana , Zackova Helena 
Published: June 2019

Abstract
On-site audits in brachytherapy are performed for all HDR units after commissioning in the Czech Republic. Air-kerma strength, source positioning accuracy, dose calculation accuracy by treatment planning system, and reconstruction algorithm in terms of geometry accuracy are verified. Results obtained in 2003 – 2018 for 24 audited HDR brachytherapy sources are described in the paper. Weak points in HDR brachytherapy process are emphasized. The audited centres often failed in good knowledge of applicators, especially of needles with different blind tip lengths.
Evaluation of Delta 4 system in patient specific QA for VMAT technique: Retrospective lung VMAT cases
Authors: Khaophong J , Yongvithisatid P , Pairat K , Dechsupa P , Tangboonduangjit P , Asavaphatiboon S 
Published: June 2019

Abstract
The objective of this study was to evaluate the Delta 4 system for lung VMAT technique. The standard fields and VMAT plans were generated into the homogeneous and heterogeneous phantoms and were evaluated using 2%/2 mm criterion to validate the Delta 4 system. For retrospective study, five lung VMAT plans were evaluated using 2%/2 mm criterion. The point dose was measured to ensure the accuracy of beam delivery. Moreover, the 1.0 mm MLC position error was introduced into the VMAT plan of homogeneous phantom and was evaluated using 2%/2 mm and 1%/1 mm criteria to evaluate the small error detection. The range of percentage gamma passing rate for standard fields and VMAT in both phantoms was 94.6% to 99.8%. For five retrospective lung VMAT plans, the range of percentage gamma passing rate was 96.6% to 99.5%. The point dose differences were within ± 3%. For 1.0 mm MLC position error, the percentage gamma passing rate for 2%/2 mm and 1%/1 mm were 99.1% and 83.6%, respectively. In conclusion, the Delta 4 system can be used in patient specific QA for lung VMAT cases using 2%/2 mm criterion. The error magnitude 1.0 mm can be detected by 1%/1 mm criterion.
The impact of flattening filter free (FFF) photon beams to ion recombination correction factor
Authors: Hentihu F K , Ryangga D , Pawiro S A 
Published: June 2019

Abstract
This study aimed to evaluate ion recombination correction for ionization chamber in flattening filter free (FFF) photon beams and compare it to the flattened (with-flattening-filter) photon beams. The evaluation of ion recombination correction factor was performed for FC65-G, SNC600c, and CC13 ionization chambers. The measurements of three ionization chambers were performed using the water phantom and the Varian Trilogy linac with FFF capability. The ion recombination correction factor values for the three ionization chambers were obtained from the calculation using the simple two-voltage method and Jaffe plot curve fitting. The ion recombination correction factor value obtained from all three ionization chambers were higher for unflattened (FFF) photon beams than the flattened (WFF) photon beams with discrepancy less than 3%. The ion recombination correction value obtained from the linear Jaffe plot curve fitting had the highest discrepancy at about 7.67% when compared to the two-voltage method. On the contrary, the ion recombination correction value obtained from the Jaffe plot with quadratic and exponential quadratic curve fitting had discrepancies less than 2% when compared to the two-voltage method.
Using Google trends data to study public interest in radiation
Authors: Mohamad M , Jee S M 
Published: June 2019

Abstract
This study evaluates the correlation and cycle of public interest in radiation worldwide with radiation-related incidents between countries using Google Trends from 2008 to 2018. Google trends was employed to normalise traffic data on a scale of 0 to 100, and were presented as monthly relative search volume (RSV) using radiation, radioactive, nuclear medicine and x-ray as a search term. A remarkable peak was identified in March 2011 during the Fukushima Daiichi nuclear disaster. In conclusion, public interest towards radiation is correlated with radiation-related incidents or events.
Synthesis of Magnesium-Hydroxyapatite Crystal via microwave irradiation
Authors: Hariowibowo F N , Nurlely  , Sari Y W 
Published: June 2019

Abstract
Magnesium-Hydroxyapatite (MgHA) is synthesized by substituting magnesium (Mg) into hydroxyapatite (HA). The study’s aim was to synthesize MgHA nano-powder via microwave irradiation and determine the effects of the microwave irradiation’s power and irradiation time variation on the synthesis of the MgHA crystal. The synthesis of MgHA was done by titrating solutions of diammonium hydrogen phosphate and magnesium hydroxide into a solution of calcium hydroxide. The microwave irradiation was done with variations of irradiation power and time. The phase composition, functional groups, morphology, particle size, and the element composition of the MgHA powder was evaluated using the following characterization method; XRD, FTIR, and SEM-EDX. The XRD patterns show that lattice parameters a and c, crystallinity index, and crystallite size of MgHA decreases as the irradiation time increases. The FTIR results show that a stretching mode is caused by the bonding of Mg2+ and the hydroxyl group. The SEM and EDX results shows that the substitution of Mg2+ causes the particles to agglomerate and the Ca/P value of MgHA was determined to be lesser than 1.67, showing that some Ca2+ was released from the apatite. The results show that higher irradiation power and longer irradiation time is more effective in MgHA synthesis.
Formation and characterization of collagen and hydroxyapatite composite
Authors: Julia S , Sari Y W , Nurlely  , Soejoko D S 
Published: June 2019

Abstract
The formation of composite of collagen and hydroxyapatite (HA) was investigated by ex-situ precipitation method. Synthesis of HA was carried out by precipitation of Ca(OH)2 1 M and (NH4)2.HPO4 0.6 M with the molar ratio of Ca/P 1.67, the mixture was exposed to microwave irradiation (450 W) for 45 min. Subsequently, the result was sintered to produce the powders of HA. Verification of HA powders was performed using X-Ray Diffraction (XRD). Chicken collagen was prepared in our laboratory (Physics Department, Universitas Indonesia). Composite was synthesized by ex-situ precipitation method with a mass fraction of collagen and HA was 2:1. The mixture was stirring continuously for 2 h and aged for 20 h at room temperature. The precipitate was dried by freeze-drying method. The composite result was examined by Scanning Electron Microscopy (SEM). XRD pattern of sintered powder shown as HA crystal. The unit cell of HA crystals was evaluated by High Score Plus Program (a=b=9.425 and c=6.884) with the accuracy 98.175% for a and b lattice and 98.406% for c lattice. The collagen had been verified by SDS PAGE as type 1 collagen and the micrograph illustrated the presence of micropores. Based on SEM examination, the composite revealed that HA had been deposited onto collagen and filled part of void space of collagen. The preliminary study will be beneficial for leading the formation of composites of collagen-HA as biomaterials.
Application of high resolution DLP stereolithography for fabrication of tricalcium phosphate scaffolds for bone regeneration
Authors: Schmidleithner Christina , Malferrari Sara , Palgrave Robert , Bomze Daniel , Schwentenwein Martin , Kalaskar Deepak M 
Published: June 2019

Abstract
Bone regeneration requires porous and mechanically stable scaffolds to support tissue integration and angiogenesis, which is essential for bone tissue regeneration. With the advent of additive manufacturing processes, production of complex porous architectures has become feasible. However, a balance has to be sorted between the porous architecture and mechanical stability, which facilitates bone regeneration for load bearing applications. The current study evaluates the use of high resolution digital light processing (DLP) -based additive manufacturing to produce complex but mechanical stable scaffolds based on β-tricalcium phosphate (β-TCP) for bone regeneration. Four different geometries: a rectilinear Grid, a hexagonal Kagome, a Schwarz primitive, and a hollow Schwarz architecture are designed with 400 μm pores and 75 or 50 vol% porosity. However, after initial screening for design stability and mechanical properties, only the rectilinear Grid structure, and the hexagonal Kagome structure are found to be reproducible and showed higher mechanical properties. Micro computed tomography (μ-CT) analysis shows <2 vol% error in porosity and <6% relative deviation of average pore sizes for the Grid structures. At 50 vol% porosity, this architecture also has the highest compressive strength of 44.7 MPa (Weibull modulus is 5.28), while bulk specimens reach 235 ± 37 MPa. To evaluate suitability of 3D scaffolds produced by DLP methods for bone regeneration, scaffolds were cultured with murine preosteoblastic MC3T3-E1 cells. Short term study showed cell growth over 14 d, with more than two-fold increase of alkaline phosphatase (ALP) activity compared to cells on 2D tissue culture plastic. Collagen deposition was increased by a factor of 1.5–2 when compared to the 2D controls. This confirms retention of biocompatible and osteo-inductive properties of β-TCP following the DLP process. This study has implications for designing of the high resolution porous scaffolds for bone regenerative applications and contributes to understanding of DLP based additive manufacturing process for medical applications.
Immunogenicity and Safety of the Measles Vaccine in HIV-Infected Children: An Updated Systematic Review
Authors: Mehtani Nicky J , Rosman Lori , Moss William J 
Published: June 2019

Abstract
Children infected with human immunodeficiency virus (HIV) are at increased risk of measles morbidity and mortality. We searched abstracts from the PubMed, Embase, and Latin American and Caribbean Center on Health Sciences Information databases for articles published from the earliest date available through September 26, 2017. The primary outcome of interest was serological responses to measles vaccine, stratified by HIV infection status. A total of 2,858 potentially eligible articles were identified, and the final review included 12 studies published between 1992 and 2013, 9 of which reported data on vaccine safety. The studies we included represented 3,573 children, of whom at least 335 were infected with HIV, 788 were HIV-exposed but not infected, and 1,478 were unexposed to HIV. Four of the 12 studies found statistically significant reductions in seropositivity among HIV-infected children compared with HIV-uninfected children within 4 months of vaccination (prevalence ratio range, 0.44–0.70), and forest plots provided visual trends of decreasing immunity over time among HIV-infected children in 2 additional studies. No vaccine-related deaths or serious adverse events were reported. This updated review demonstrated limitations of the existing published literature but supported evidence of reduced immunogenicity of measles vaccine among HIV-infected children, supporting the World Health Organization recommendation to revaccinate HIV-infected children against measles following immune reconstitution with combination antiretroviral therapy.
MOLI: multi-omics late integration with deep neural networks for drug response prediction
Authors: Sharifi-Noghabi Hossein , Zolotareva Olga , Collins Colin C , Ester Martin 
Published: June 2019

Abstract

Motivation
Historically, gene expression has been shown to be the most informative data for drug response prediction. Recent evidence suggests that integrating additional omics can improve the prediction accuracy which raises the question of how to integrate the additional omics. Regardless of the integration strategy, clinical utility and translatability are crucial. Thus, we reasoned a multi-omics approach combined with clinical datasets would improve drug response prediction and clinical relevance.

Results
We propose MOLI, a multi-omics late integration method based on deep neural networks. MOLI takes somatic mutation, copy number aberration and gene expression data as input, and integrates them for drug response prediction. MOLI uses type-specific encoding sub-networks to learn features for each omics type, concatenates them into one representation and optimizes this representation via a combined cost function consisting of a triplet loss and a binary cross-entropy loss. The former makes the representations of responder samples more similar to each other and different from the non-responders, and the latter makes this representation predictive of the response values. We validate MOLI on in vitro and in vivo datasets for five chemotherapy agents and two targeted therapeutics. Compared to state-of-the-art single-omics and early integration multi-omics methods, MOLI achieves higher prediction accuracy in external validations. Moreover, a significant improvement in MOLI’s performance is observed for targeted drugs when training on a pan-drug input, i.e. using all the drugs with the same target compared to training only on drug-specific inputs. MOLI’s high predictive power suggests it may have utility in precision oncology.

Availability and implementation
https://github.com/hosseinshn/MOLI.

Supplementary information
Supplementary data are available at Bioinformatics online.
MetOSite: an integrated resource for the study of methionine residues sulfoxidation
Authors: Valverde Héctor , Cantón Francisco R , Aledo Juan Carlos 
Published: June 2019

Abstract

Motivation
The oxidation of protein-bound methionine to form methionine sulfoxide has traditionally been regarded as an oxidative damage. However, growing evidences support the view of this reversible reaction also as a regulatory post-translational modification. Thus, the oxidation of methionine residues has been reported to have multiple and varied implications for protein function. However, despite the importance of this modification and the abundance of reports, all these data are scattered in the literature. No database/resource on methionine sulfoxidation exists currently. Since this information is useful to gain further insights into the redox regulation of cellular proteins, we have created a primary database of experimentally confirmed sulfoxidation sites.

Results
MetOSite currently contains 7242 methionine sulfoxide sites found in 3562 different proteins from 23 species, with Homo sapiens, Arabidopsis thaliana and Bacillus cereus as the main contributors. Each collected site has been classified according to the effect of its sulfoxidation on the biological properties of the modified protein. Thus, MetOSite documents cases where the sulfoxidation of methionine leads to (i) gain of activity, (ii) loss of activity, (iii) increased protein–protein interaction susceptibility, (iv) decreased protein–protein interaction susceptibility, (v) changes in protein stability and (vi) changes in subcellular location.

Availability and implementation
MetOSite is available at https://metosite.uma.es.
iTUPA: an online automated application to perform Topographic-Unit Parsimony Analysis
Authors: Hammoud Muhsen , Santos Charles Morphy D , Gois João Paulo 
Published: June 2019

Abstract

Summary
iTUPA is a free online application for automatizing the Topographic-Unit Parsimony Analysis (TUPA), which identifies areas of endemism based on topography. iTUPA generates species-occurrences matrices based on user-defined topographic units (TUs) and provides a parsimony analysis of the generated matrix. We tested iTUPA after a proposal of regionalization for the Brazilian Atlantic Forest. iTUPA can handle millions of species registers simultaneously and uses Google Earth high-definition maps to visually explore the endemism data. We believe iTUPA is a useful tool for further discussions on biodiversity conservation.

Availability and implementation
iTUPA is hosted on Google cloud and freely available at http://nuvem.ufabc.edu.br/itupa. iTUPA is implemented using R (version 3.5.1), with RStudio 1.1.453 used as the implementation IDE, Shiny 1.1.0 web framework, and Google Maps® API version 3.36.
Foodborne Botulism Outbreak Associated With Commercial Nacho Cheese Sauce From a Gas Station Market
Authors: Rosen Hilary E , Kimura Akiko C , Crandall John , Poe Alyssa , Nash June , Boetzer Jason , Tecle Selam , Mukhopadhyay Rituparna , Mcauley Kate , Kasirye Olivia , Garza Alvaro , Shahkarami Mahtab , Chaturvedi Vishnu , Kiang David , Vidanes Jeff , Mccoy Kelly , Barcellos Mark , Derby Tammy , Jain Seema , Vugia Duc J 
Published: June 2019

Abstract

Background
Botulism is a rare and potentially fatal paralytic disease caused by botulinum neurotoxin (BoNT). In April 2017, 4 California residents from 2 adjacent counties were hospitalized with suspected foodborne botulism, precipitating an investigation by state and local public health departments in California.

Methods
We interviewed suspected botulism patients and their families, inspected the suspect establishment, and collected suspect food. We tested patient sera, stool, and gastric aspirates using mouse bioassay for BoNT and/or culture for Clostridium botulinum. We tested suspect food and environmental samples for BoNT and confirmed presumptive positives using direct mouse bioassay and culture. We performed whole-genome sequencing on food and clinical isolates.

Results
From April 2017 through May 2017, 10 patients in the Sacramento area were hospitalized with laboratory-confirmed botulism; 7 required mechanical ventilation, and 1 died. Of 9 patients with information, all had visited Gas Station X before illness onset, where 8 reported consuming a commercial cheese sauce. BoNT/A and/or BoNT/A-producing C. botulinum were detected from each patient and from leftover cheese sauce. Clostridium botulinum isolates from 4 patients were closely related to cheese sauce isolates by whole-genome high-quality single-nucleotide polymorphism analysis. No other botulism cases associated with this cheese sauce were reported elsewhere in the United States.

Conclusions
This large foodborne botulism outbreak in California was caused by consumption of commercial cheese sauce dispensed at a gas station market. The epidemiologic and laboratory evidence confirmed the cheese sauce as the outbreak source. The cheese sauce was likely locally contaminated, although the mechanism is unclear.