bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of dose calculation algorithms model: Convolution, superposition, and fast superposition in 3-D Conformal Radiotherapy (3D-CRT) treatment plan
Authors: Murat H , Karim M K A , Harun H H , Kayun Z
Published: June 2019

The important task of radiotherapy is to make sure that the radiation dose to the target tumour is accurate as prescribed and the dose to the organ at risk is minimized. Therefore, the aim of this study is to compare and evaluate the efficiency of the dose calculation algorithms: namely convolution, superposition, and fast superposition which installed in Treatment Planning System (TPS) (CMS XiO, USA). In this study, we modified protocols described in IAEATecdoc-1583, where four typical treatment techniques such as single field, multiple field, wedge field, and multi-leaf collimated (MLC) field were analysed from the system. The measurement data for calculated dose and measured dose were taken from thorax CIRS anthropomorphic phantom. The assessment of algorithms was done by comparing the point dose calculated with the measured dose. The study shows that the superposition algorithm produced relative error less than ± 3% which passed 100% of all reference points, whilst the convolution algorithm and fast superposition presented relative error more than ± 3% which passed 82% and 91% of reference points, respectively. In conclusion, the evaluation of radiotherapy treatment plan shall take into account the type of dose calculation algorithm model in order to optimize radiotherapy treatment and ensure the radiation safety to the patient.
Translation and rotational target motion effect in NSCLC case with 3D-CRT, IMRT, and VMAT techniques using in-house dynamic thorax phantom
Authors: Putranto A M Y , Sudarmaji A , Fadli M , Nainggolan A , Liura S , Pawiro S A
Published: June 2019

This study aimed to make in-house dynamic thorax phantom that simulate translational and rotational direction mimicking NSCLC target movement. In addition,this study also investigate dosimetric effect of target movement for several translational amplitude. This work used in-house dynamic thorax phantom based on CIRS Dynamic Thorax Phantom model 008A. This phantom simulated translation in superior-inferior direction, rotational in the anterior-posterior and left-right lateral plane to mimic human respiratory motion. It was designed and controlled by linear actuator motor, servo motor, Adafruit motor shield L293D and Arduino UNO R3. It was implemented to evaluate point dose of 3D-CRT, IMRT, VMAT technique and for 5 mm; 10 mm; 15 mm translational motion amplitude 90° rotational target motion amplitude. The GafChromic EBT 3 film was used as a dosimeter for point dose measurement. This in-house dynamic thorax phantom can mimicking NSCLC target movement for translational amplitude 5 ± 1 mm; 10 ± 1 mm; 15 ± 1 mm and rotational amplitude 90° ± 3°. The average dose deviation of target dose (centre and peripheral) of TPS dose planning and target motion measurement on 3DCRT with 5 mm, 10 mm and 15 mm were 3.2%, 3.1%, and 1.8% respectively, and dose deviation on IMRT were 3.9%, 2.5%, and 2.8%, while dose deviation on VMAT treatment were 4.2%, 4.6%, and 6.1% respectively. The preliminary result supported the previous work by Mukhlisin. Furthermore, rotational movement of phantom contributed in average of 1.5% compare to translational movement only.
Establishment of institutional diagnostic reference level for CT imaging associated with multiple anatomical regions
Authors: Razali M A S M , Ahmad M Z , Roslee M A A M , Osman N D
Published: June 2019

Advancement of CT technology has increased the frequency of CT scanning in diagnosis. However, the concern on dose increment that related to radiation-associated health risk from CT also improved. The aim of this study was to establish an institutional diagnostic reference level (DRL) for computed tomography (CT) imaging associated with multiple or combined anatomical regions and compared with other international DRLs. CT dose data of 705 subjects were collected retrospectively from January 2015 until December 2017 at AMDI, USM, Malaysia. The most common CT examination of combined anatomical regions were neck-thorax-abdomen-pelvis (NTAP), thorax-abdomen (TA), thorax-abdomen-pelvis (TAP), and abdomen-pelvis (AP). CT dose data such as CTDIvol, CTDIw and dose-length product (DLP) were collected including contrast, non-contrast, single-phasic, and multiphasic examinations. The 50th and 75th percentile of dose distribution were calculated and compared with other established DRLs. TAP CT was the most frequently performed examination at AMDI (73%). The local dose values of multiphasic and non-contrast examinations were higher compared to single phasic and contrast study. The results show a weak correlation between different CT sequences and DRLs for AP examination. Local dose values reported for all CT examinations were below any international DRLs except for CT TAP (multiphasic) study. The institutional DRL for combined anatomical regions was established using the third quartile values of dose distribution and is categorized based on CT sequences.
Radiation dose intensity and local tumour control of non-small cell lung cancer: A radiobiological modelling perspective
Authors: Alaswad M , Kleefeld C , Foley M
Published: June 2019

Several clinical situations call for the use of radiobiological principles as powerful clinical tools. The aim of this project is to examine the effect of radiotherapy dose intensity on local tumour control for non-small cell lung cancer (NSCLC) using the biological effective dose (BED) concept. A two-year tumour control probability (TCP) model was developed based on the linear-quadratic cell concept combined with Poisson statistics. The two-year local control outcome was analysed for the radiotherapy dose using the BEDs. The BED calculations and the TCP model were fitted to a series of NSCLC patients drawn from the literature. The investigation is based on the two-year local tumour control rate for stage I-II NSCLC for a dose fractionation size that varied from 1.5-20 Gy per fraction delivered via three radiotherapy treatments: 3D-conformal radiation therapy (3D-CRT), continuous hyperfractionated accelerated radiotherapy (CHART) and stereotactic ablative body radiotherapy (SABR). The BED values of 2,280 patients were computed and analysed as a function of local tumour control. To quantitatively assess the correlation between the BED and local tumour control, a residuals analysis and linear regression were performed. Higher radiotherapy doses were associated with improved local tumour control and survival rates for NSCLC, as suggested by the coefficient of the correlation R2 statistical test: 0.83 for the 3D-CRT and 0.91 for the SABR treatment.
Fingernail dosimetry using electron spin resonance for radiation disaster response
Authors: Gonzales CAB , Yasuda H , Hirota S , Miki K , Saito A , Taño JE , Nagata Y
Published: June 2019

This study investigates the use of electron spin resonance (ESR) signals from human fingernails for retrospective dosimetry as part of radiation disaster response, focusing on the variabilities of individual responses to radiation. Samples of fingernails were collected from 7 adult donors (Asian type) and irradiated to 35 Gy and 70 Gy of gamma-rays from a Cs-137 source at a dose rate of 0.857 Gy/min. All irradiated fingernails were measured for 39 days with an X-band ESR spectrometer and stored in darkness inside the vacuum desiccator (30% humidity, 20°C) in between measurements at all times. All samples were harvested using one specific nail cutter and given no other special treatments. It was observed that the measured radiation-induced signals faded on about 10-12% after 1 day of exposure. Though the signal intensities showed a significant difference among the donors, stronger linearities in the dose responses were observed in the samples of younger donors. From the results obtained in this study, it is expected that fingernails would be a useful tool for retrospective dosimetry in case of an unexpected radiological accident or medical treatment error associated with exposure in therapeutic dose range, as far as the individual-based calibration curves were available. Further investigations will be made to clarify the reason for the different responses by using the fingernail samples taken from a greater number of donors of different ages and lifestyles.
Challenges and opportunities for a CAMPEP-accredited Medical Physics Graduate Program in Galway, Ireland
Authors: Kleefeld C , Alaswad M , Foley M
Published: June 2019

Established in 2002, this long running MSc in Medical Physics program was awarded CAMPEP accreditation in 2015, thus being one out of only two CAMPEP approved graduate programs outside North America. The program is a full-time, one-year taught master course delivered by a close university–hospital collaboration. This paper will give an outline of the current program structure and will identify challenges likely affecting the areas of teaching, research and course administration. Strategies to address these challenges will be discussed. Since the accreditation, the number of students enrolled in the program increased from 8 in 2015/16 and 16 in 2016/17 to 21 in 2017/18 and 25 in 2018/19. The number of non-EU students in these cohorts was 2, 5, 4, and 9 respectively. Non-EU students predominantly originate from North America and Saudi-Arabia. The total number of applicants averages at approximately 55 per year. A further increase in student intake has been advocated but might impact negatively on the quality of the clinical training which forms a vital part of the program. Students are given access to clinical systems for laboratory exercises as well as for pursuing research projects, thus gaining some clinical experience which will increase their employability. However, local clinical access has to be limited. In order to mitigate the situation, the program cooperates with medical physics departments nationwide and internationally. Curricular challenges arising from clinical implementations of ever-evolving technologies and from a rapidly changing medical physics landscape in general will be expanded on.
Thermoluminescence characteristic of CaSO4:Dy on β and γ radiation
Authors: Nuraeni N , Kartikasari D , Yani S , Hiswara E , Haryanto F , Iskandar F , Waris A
Published: June 2019

The research on the developments of thermoluminescence (TL) material in nano- and microstructure are increasing in recent years. There are many new techniques developed for preparing TL material that aim to improve and investigate the structure, morphology, and TL characteristics. In this study, the TL characteristics of CaSO4 doped with Dysprosium (Dy) were being observed. CaSO4:Dy was performed by co-precipitation method with 0.1 mol% Dy concentration. The obtained sample was irradiated with Cs-137 for gamma source and Sr-90 for beta source with doses of 5, 10, 15, 20 and 25 mGy. After irradiation, the structure, morphology, and TL response were observed by using XRD, SEM, and TLD Reader Harshaw 3500. XRD results showed that the average crystallite size for CaSO4:Dy were 58 nm. But, the presence of dysprosium could not be clearly observed from XRD results. The characterization results from SEM for CaSO4:Dy had shape resembling needle-like crystal. The TL response of CaSO4:Dy was compared from beta and gamma radiation source. TL responses for Cs-137 source were 26.56, 34.09, 51.85, 75.97, and 86.29 nC for 5, 10, 15, 20, and 25 mGy, respectively. Sr-90 source with the same dose obtained TL responses as follows: 35.67, 68.60, 100.87, 121.69, and 179.85 nC. The shapes of the glow curves were almost identical, but these curves had different intensities. The TL response from β-ray source obtained a higher intensity than from γ-ray source because the beta source is a particle with mass so that it will have more interaction than gamma source in TLD material.
Bioinspired calcium phosphate mineralization on Net-Shape-Nonwoven chitosan scaffolds stimulates human bone marrow stromal cell differentiation
Authors: Heinemann C , Brünler R , Kreschel C , Kruppke B , Bernhardt R , Aibibu D , Cherif C , Wiesmann H-P , Hanke T
Published: June 2019

Chitosan fibers were processed using the Net-Shape-Nonwoven (NSN) technique in order to create porous scaffolds which were functionalized in two bioinspired ways: collagen type I coating and unique mineralization with organically modified hydroxyapatite (ormoHAP). While collagen is common to enhance cell attachment on surfaces, the electric-field assisted migration and deposition of ormoHAP on the surface of the NSN-scaffolds is a novel technique which enables sub-micrometer sized mineralization while maintaining the original pore structure. Microscopy revealed fast attachment and morphological adaptation of the cells on both, the pure and the functionalized NSN-scaffolds. Remarkably, the cell number of osteogenically induced hBMSC on ormoHAP-modified NSN-scaffolds increased 3.5–5 fold compared to pure NSN-scaffolds. Osteogenic differentiation of hBMSC/osteoblasts was highest on collagen-functionalized NSN-scaffolds. RT-PCR studies revealed gene expression of ALP, BSP II, and osteocalcin to be high for all NSN-scaffolds. Overall, the NSN-scaffold functionalization with collagen and ormoHAP improved attachment, proliferation, and differentiation of hBMSC and therefore revealed the remarkable potential of their application for the tissue engineering of bone.
Improving Risk Assessment of Noctuid Pests at North American Ports and Farms by Differentiating Egg Morphology
Authors: Blanco Carlos A , Rosario-Lebron Armando , O’Donnell Cheryle A , Portilla Maribel , Gullbronson Connor , Mowery Joseph , Smith-Pardo Allan H , Stocks Ian , Nadel Hannah , Trozzo Lara R , Haslem Patrick S , Young James D , Downes Sharon , Parker Tracey , Walsh Tom , Tay Wee Tek , Oppenheim Sara
Published: June 2019

Heliothine eggs are commonly found on agricultural commodities and ornamental plants transported through domestic and international commerce. Tobacco budworm [Chloridea (Heliothis) virescens (F.)], Chloridea subflexa (Guenée), and the corn earworm [Helicoverpa zea (Boddie)] are indigenous pests of the American continent. Interceptions of the Old World bollworm [Helicoverpa armigera (Hübner)] at various ports of entry into the United States have been detected due to the invasion of this pest in South America, adding to the complexity and importance of decision making at plant inspection stations. The ability to distinguish the eggs of C. virescens from C. subflexa and Helicoverpa species is a critical component for conducting risk assessments by quarantine authorities, taxonomists, and crop consultants. We developed a simple, rapid (~60 min), inexpensive ($0.06 per sample), and accurate (100% reliability) technique to distinguish C. virescens eggs from the possibility of being H. armigera based on the presence, number, and/or size of aeropyle holes on the primary ribs of eggs, near the micropylar rosette. In this location, aeropyles were easily visible at 40× magnification in 213 fresh and ethanol-preserved C. virescens eggs once treated with Hoyer’s solution. A small number of C. subflexa had one or two aeropyles on a few of the primary ribs, whereas no aeropyles were found on 411 H. zea and 269 H. armigera eggs analyzed using optical, electron, and confocal microscopy. We conclude that in most cases multiple aeropyle holes positively identify H. virescens eggs from H. zea or H. armigera, and C. subflexa. This technique potentially will reduce the number of specimens that need to be sent for molecular identification thereby saving program time and resources.
Prostate Biopsy Processing: An Innovative Model for Reducing Cost, Decreasing Test Time, and Improving Diagnostic Material
Authors: Murugan Paari , Shukla Dip , Morocho Jennifer , Smith Deanne , Sciacca Drew , Pickard Meghan , Wahlsten Michelle , Gunderson Ashley , Konety Badrinath , Khalifa Mahmoud A , Warlick Christopher
Published: June 2019

Objectives

Current protocols for processing multiple prostate biopsy cores per case are uneconomical and cumbersome. Tissue fragmentation and loss compromise cancer diagnosis. We sought to study an alternate method to improve processing and diagnosis of prostate cancer.

Methods

Two sets of sextant biopsy specimens from near-identical locations were obtained ex vivo from 48 prostate specimens. One set was processed in the standard fashion while the other was processed using the BxChip, a proprietary biomimetic matrix that accommodates six cores on a single chip. Parameters including grossing, embedding, sectioning and reading time, length of tissue, and degree of fragmentation were compared.

Results

A significant reduction (more than threefold) in preanalytical and analytical time was observed using the multiplex method. Nonlinear fragmentation was absent, in contrast to standard processing.

Conclusions

The BxChip reduced tissue fragmentation and increased efficiency of prostate biopsy diagnosis. It also resulted in overall cost savings and significantly increased tissue length.
DASH Diet and Blood Pressure Among Black Americans With and Without CKD: The Jackson Heart Study
Authors: Tyson Crystal C , Davenport Clemontina A , Lin Pao-Hwa , Scialla Julia J , Hall Rasheeda , Diamantidis Clarissa J , Lunyera Joseph , Bhavsar Nrupen , Rebholz Casey M , Pendergast Jane , Boulware L Ebony , Svetkey Laura P
Published: June 2019

BACKGROUND

The Dietary Approaches to Stop Hypertension (DASH) diet lowers blood pressure (BP) more effectively in blacks compared to other US racial subgroups. Considering chronic kidney disease (CKD) raises BP through complex mechanisms, DASH may affect BP differently among blacks with and without CKD. We compared the association of DASH accordance to BP and prevalent hypertension among blacks with and without CKD.

METHODS

Our study involved 3,135 black Americans enrolled in the Jackson Heart Study (2000–2004) with diet and office BP data. Using linear models adjusted for demographics, health behaviors, and clinical factors, we determined the association of a modified DASH score (excluding sodium intake, ranging from 0 to 8 with increasing DASH accordance) with BP. We performed tests for interaction between DASH score and CKD status.

RESULTS

Among participants (mean age: 55 years; hypertension: 60%; CKD: 19%), the median DASH score was similar among participants with and without CKD (1.0 [interquartile range (IQR): 0.5–2] and 1.0 [IQR: 0.5–1.5]). CKD status modified the association of the DASH score with systolic BP (SBP) and diastolic BP (DBP; P interactions were 0.06 and <0.01). Among participants without CKD, SBP and DBP were not associated with the DASH score (−0.4 [95% confidence interval: −1.0, 0.1] mm Hg and −0.1 [−0.4, 0.2] mm Hg per one unit higher DASH score). Among participants with CKD, one unit higher DASH score was associated with lower SBP by 1.6 (0.5, 2.6) mm Hg and lower DBP by 0.9 (0.3, 1.5) mm Hg.

CONCLUSIONS

Despite low DASH scores overall, better DASH accordance was associated with lower BP among Black Americans with CKD.
VI—Should We Believe Philosophical Claims on Testimony?
Authors: Allen Keith
Published: June 2019

This paper considers whether we should believe philosophical claims on the basis of testimony in light of related debates about aesthetic and moral testimony. It is argued that we should not believe philosophical claims on testimony, and different explanations of why we should not are considered. It is suggested that the reason why we should not believe philosophical claims on testimony might be that philosophy is not truth-directed.
VIII—Propositions and Cognitive Relations
Authors: Jones Nicholas K
Published: June 2019

There are two broad approaches to theorizing about ontological categories. Quineans use first-order quantifiers to generalize over entities of each category, whereas type theorists use quantification on variables of different semantic types to generalize over different categories. Does anything of import turn on the difference between these approaches? If so, are there good reasons to go type-theoretic? I argue for positive answers to both questions concerning the category of propositions. I also discuss two prominent arguments for a Quinean conception of propositions, concerning their role in natural language semantics and apparent quantification over propositions within natural language. It will emerge that even if these arguments are sound, there need be no deep question about Quinean propositions’ true nature, contrary to much recent work on the metaphysics of propositions.
SCANVIS: a tool for SCoring, ANnotating and VISualizing splice junctions
Authors: Agius Phaedra , Geiger Heather , Robine Nicolas
Published: June 2019

Motivation

The association of splicing signatures with disease is a leading area of study for prognosis, diagnosis and therapy. We present a novel fast-performing annotation-dependent tool called SCANVIS for scoring and annotating splice junctions (SJs), with an efficient visualization tool that highlights SJ details such as frame-shifts and annotation support for individual samples or a sample cohort.

Results

Using publicly available samples, we show that the tissue specificity inherent in splicing signatures is maintained with the Relative Read Support scoring method in SCANVIS, and we showcase some visualizations to demonstrate the usefulness of incorporating annotation details into sashimi plots.

Availability and implementation

https://github.com/nygenome/SCANVIS and https://bioconductor.org/packages/SCANVIS.

Supplementary information

Supplementary data are available at Bioinformatics online.
Cloud bursting galaxy: federated identity and access management
Authors: Jalili Vahid , Afgan Enis , Taylor James , Goecks Jeremy
Published: June 2019

Motivation

Large biomedical datasets, such as those from genomics and imaging, are increasingly being stored on commercial and institutional cloud computing platforms. This is because cloud-scale computing resources, from robust backup to high-speed data transfer to scalable compute and storage, are needed to make these large datasets usable. However, one challenge for large-scale biomedical data on the cloud is providing secure access, especially when datasets are distributed across platforms. While there are open Web protocols for secure authentication and authorization, these protocols are not in wide use in bioinformatics and are difficult to use for even technologically sophisticated users.

Results

We have developed a generic and extensible approach for securely accessing biomedical datasets distributed across cloud computing platforms. Our approach combines OpenID Connect and OAuth2, best-practice Web protocols for authentication and authorization, together with Galaxy (https://galaxyproject.org), a web-based computational workbench used by thousands of scientists across the world. With our enhanced version of Galaxy, users can access and analyze data distributed across multiple cloud computing providers without any special knowledge of access/authorization protocols. Our approach does not require users to share permanent credentials (e.g. username, password, API key), instead relying on automatically generated temporary tokens that refresh as needed. Our approach is generalizable to most identity providers and cloud computing platforms. To the best of our knowledge, Galaxy is the only computational workbench where users can access biomedical datasets across multiple cloud computing platforms using best-practice Web security approaches and thereby minimize risks of unauthorized data access and credential use.

Availability and implementation

Freely available for academic and commercial use under the open-source Academic Free License (https://opensource.org/licenses/AFL-3.0) from the following Github repositories: https://github.com/galaxyproject/galaxy and https://github.com/galaxyproject/cloudauthz.
Mycorrhiza: genotype assignment using phylogenetic networks
Authors: Georges-Filteau Jeremy , Hamelin Richard C , Blanchette Mathieu
Published: June 2019

Motivation

The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics, invasive species detection and biodiversity monitoring. Existing approaches perform well under ideal conditions but are sensitive to a variety of common violations of the assumptions they rely on.

Results

In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples. Those features are then used as input to a Random Forests classifier. The classification accuracy was assessed on multiple published empirical SNP, microsatellite or consensus sequence datasets with wide ranges of size, geographical distribution and population structure and on simulated datasets. It compared favorably against widely used assessment tests or mixture analysis methods such as STRUCTURE and Admixture, and against another machine-learning based approach using principal component analysis for dimensionality reduction. Mycorrhiza yields particularly significant gains on datasets with a large average fixation index (FST) or deviation from the Hardy-Weinberg equilibrium. Moreover, the phylogenetic network approach estimates mixture proportions with good accuracy.

Availability and implementation

Mycorrhiza is released as an easy to use open-source python package at github.com/jgeofil/mycorrhiza.

Supplementary information

Supplementary data are available at Bioinformatics online.
Immunologic Alterations Associated With Oral Delivery of Anti-CD3 (OKT3) Monoclonal Antibodies in Patients With Moderate-to-Severe Ulcerative Colitis
Authors: Boden Elisa K , Canavan James B , Moran Christopher J , McCann Katelyn , Dunn William A , Farraye Francis A , Ananthakrishnan Ashwin N , Yajnik Vijay , Gandhi Roopali , Nguyen Deanna D , Bhan Atul K , Weiner Howard L , Korzenik Joshua R , Snapper Scott B
Published: June 2019

Aim

The aim of this study was to determine the immunologic effects and safety of oral anti-CD3 in patients with ulcerative colitis (UC).

Methods

An open-label pilot study of orally delivered anti-CD3 was performed in patients with moderate-to-severe UC. The primary end points were changes in immunologic parameters and evaluation for safety.

Results

Six subjects received oral OKT3. Biologic effects of oral anti-CD3 included significantly increased proliferation in response to anti-CD3 and anti-inflammatory gene expression profile in peripheral blood mononuclear cells. No serious treatment-related adverse events occurred.

Conclusion

Orally delivered anti-CD3 resulted in immunologic changes in patients with UC.
Foraging Economics of the Hunt Bumble Bee, a Viable Pollinator for Commercial Agriculture
Authors: Baur Abby , Strange James P , Koch Jonathan B
Published: June 2019

Globally, there are only five bumble bee (Hymenoptera: Apidae, Bombus) species that have been successfully commercialized for agriculture. The Hunt bumble bee, Bombus huntii Green, 1860, has been recognized as a suitable pollinator of crops and has a broad distribution in western North America, making it a viable candidate for commercialization. In this study, our goal was to characterize the foraging dynamics of B. huntii female workers under open field conditions. To accomplish this goal, we monitored three B. huntii colonies over an 8-wk period in the summer of 2012 in northern Utah. Using marked bees, we studied the relationship between foraging duration/offloading and pollen/nonvisible pollen collection. In total, we observed 921 foraging events across all three colonies. Of our observations, 82% (n = 756) were foraging events that included both a departure and arrival time observation. Average duration of pollen and nonpollen (i.e., nectar) trips across foragers is 41.86 ± 5.65 min (±SE) and 32.18 ± 5.89 min, respectively. Workers spent a significantly longer time offloading pollen in the nest after a foraging trip relative to workers without pollen present on their corbicula. Pollen foraging rate increases over the course of the day, likely due to the time it takes to learn how to forage on a diverse array of flower morphologies. Our study provides data on how long it takes for B. huntii to forage in open field conditions and will be useful when comparing foraging rates in controlled crop systems.
Machine learning in agricultural and applied economics
Authors: Storm Hugo , Baylis Kathy , Heckelei Thomas
Published: June 2019

This review presents machine learning (ML) approaches from an applied economist’s perspective. We first introduce the key ML methods drawing connections to econometric practice. We then identify current limitations of the econometric and simulation model toolbox in applied economics and explore potential solutions afforded by ML. We dive into cases such as inflexible functional forms, unstructured data sources and large numbers of explanatory variables in both prediction and causal analysis, and highlight the challenges of complex simulation models. Finally, we argue that economists have a vital role in addressing the shortcomings of ML when used for quantitative economic analysis.
Productivity and Cost of Processors in Whole-Tree Harvesting Systems in Southern Pine Stands
Authors: Conrad Joseph L , Dahlen Joseph
Published: June 2019

Logging businesses in the US South have not adopted cut-to-length harvesting systems. Adding dangle head processors on the landing of whole-tree harvesting systems may allow southern loggers to achieve some of the advantages of cut-to-length systems (i.e., precise length and diameter measurements) while maintaining high productivity and low costs per ton characteristic of current whole-tree systems. We conducted a designed study of conventional (i.e., feller-buncher, grapple skidder, loader) and processor (i.e., feller-buncher, grapple skidder, processor, loader) systems. Four harvest sites were split, with half of each site harvested by a conventional system and the other half by a processor system. Harvesting productivity was estimated using time-and-motion studies, and costs were estimated using the machine rate method. Cut-and-load costs averaged US$13.57 and US$14.67 ton–1 on the processor and conventional harvests, respectively (P > .10). Cost per ton was elevated on several conventional harvest tracts because of long skidding distances, indicating harvest planning is more important than harvesting system in determining harvesting costs. Processing and loading costs were US$1.70 ton–1 higher on processor harvests, which, combined with restrictive mill quotas being more problematic for processor crews, suggests loggers will require a logging rate premium in order to invest in processors.
The Effects of Neighborhood Built Environment on Walking for Leisure and for Purpose Among Older People
Authors: Christman Zachary J , Wilson-Genderson Maureen , Heid Allison , Pruchno Rachel
Published: June 2019

Background and Objectives

Characteristics of a neighborhood’s built environment affect the walking behavior of older people, yet studies typically rely on small nonrepresentative samples that use either subjective reports or aggregate indicators from administrative sources to represent neighborhood characteristics. Our analyses examine the usefulness of a novel method for observing neighborhoods—virtual observations—and assess the extent to which virtual-based observations predict walking among older adults.

Research Design and Methods

Using Google Street View, we observed the neighborhoods of 2,224 older people and examined how characteristics of the neighborhood built environments are associated with the amount of time older people spend walking for leisure and purpose.

Results

Multilevel model analyses revealed that sidewalk characteristics had significant associations with both walking for purpose and leisure. Land use, including the presence of multifamily dwellings, commercial businesses, and parking lots were positively associated with walking for purpose and single-family detached homes were negatively associated with walking for purpose, but none of these characteristics were associated with leisure walking. Gardens/flowers were associated with walking for leisure but not purpose. Garbage/litter was not associated with either type of walking behavior.

Discussion and Implications

Virtual observations are a useful method that provides meaningful information about neighborhoods. Findings demonstrate how neighborhood characteristics assessed virtually differentially impact walking for leisure and purpose among older adults and are interpreted within a social-ecological model.
Damage-Fitness Model: Evaluation and synthesis
Authors: Wada Haruka , Heidinger Britt
Published: June 2019

Decades of research into stress responses have highlighted large variation among individuals, populations, and species, and the sources of this variation have been a center of research across disciplines. The most common measure of the vertebrate stress response is glucocorticoids. However, the predictive power of glucocorticoid responses to fitness is surprisingly low. This is partly because the hormone levels rapidly change in response to stressor exposure and elevated levels at one time point can indicate either that glucocorticoids are helping the organism cope with the stressor or that dysregulation of hormone release is harming the organism. Meaning, the fitness consequences of the stressor depends on how efficient the stress responses are at negating the harmful impacts of stressors to cells and tissues. To encompass the idea of the efficiency of stress responses and to integrate cellular and organismal stress responses, a new theoretical model called the Damage-Fitness Model was developed. The model focuses on the downstream effects of stress responses and predicts that the accumulation of damage in cells and tissues (e.g., persistent damage to proteins, lipids, and DNA) negatively impacts fitness components. In this mini-review, we examine evidence supporting the Damage-Fitness Model and explore new directions forward.
The Structure of the Grothendieck Rings of Wreath Product Deligne Categories and their Generalisations
Authors: Ryba Christopher
Published: June 2019

Given a tensor category $\mathcal{C}$ over an algebraically closed field of characteristic zero, we may form the wreath product category $\mathcal{W}_n(\mathcal{C})$. It was shown in [10] that the Grothendieck rings of these wreath product categories stabilise in some sense as $n \to \infty $. The resulting “limit” ring, $\mathcal{G}_\infty ^{\mathbb{Z}}(\mathcal{C})$, is isomorphic to the Grothendieck ring of the wreath product Deligne category $S_t(\mathcal{C})$ as defined by [9] (although it is also related to $FI_G$-modules). This ring only depends on the Grothendieck ring $\mathcal{G}(\mathcal{C})$. Given a ring $R$ that is free as a $\mathbb{Z}$-module, we construct a ring $\mathcal{G}_\infty ^{\mathbb{Z}}(R)$ that specialises to $\mathcal{G}_\infty ^{\mathbb{Z}}(\mathcal{C})$ when $R = \mathcal{G}(\mathcal{C})$. We give a description of $\mathcal{G}_\infty ^{\mathbb{Z}}(R)$ using generators very similar to the basic hooks of [5]. We also show that $\mathcal{G}_\infty ^{\mathbb{Z}}(R)$ is a $\lambda $-ring wherever $R$ is and that $\mathcal{G}_\infty ^{\mathbb{Z}}(R)$ is (unconditionally) a Hopf algebra. Finally, we show that $\mathcal{G}_\infty ^{\mathbb{Z}}(R)$ is isomorphic to the Hopf algebra of distributions on the formal neighbourhood of the identity in $(W\otimes _{\mathbb{Z}} R)^\times $, where $W$ is the ring of Big Witt Vectors.
Production and characterization of monoclonal antibodies against the DNA binding domain of the RE1-silencing transcription factor
Authors: Cortés-Sarabia Karen , Medina-Flores Yolanda , Alarcón-Romero Luz Del Carmen , Mata-Ruíz Olga , Vences-Velázquez Amalia , Rodríguez-Ruíz Hugo Alberto , Valdés Jesús , Ortuño-Pineda Carlos
Published: June 2019

The use of monoclonal antibodies for the detection of cellular biomarkers during carcinogenesis provides new strategies for cancer diagnosis or prognosis in patients. Loss of the Restrictive Element 1-Silencing Transcription (REST) factor has been observed in previous molecular and immunological approaches in aggressive breast cancer, small cell lung cancer, liver carcinoma, and colo-rectal cancer; however, for clinic diagnosis, monoclonal antibodies for REST recognition are unavailable. The goal of this work was to design, produce and characterize monoclonal antibodies against the REST DNA binding damain (DBD) that would be suitable for immunoassays. We searched for conserved domains, and immunogenic and antigenic sites in the REST structure via in silico analysis. For mice immunization, we used a recombinant REST DBD purified by affinity chromatography, and then Hybridomas were generated by mouse spleen fusion with myeloma cells. Finally, for monoclonal antibody characterization, we performed enzyme-linked immunosorbent (ELISA), western blot, dot blot, immunocytochemistry (ICC) and immunoprecipitation assays. Results showed that the DBD is conserved in REST isoforms and contains immunogenic and antigenic sites. We generated three clones producing monoclonal antibodies against REST DBD, one of them specifically recognized native REST and was suitable for ICC in samples from patients.
Recent Developments in the Case-Law of the ECtHR on the Right to a Fair Trial in Competition Proceedings
Authors: Berghe Pascal
Published: June 2019

Judgment of 23 October 2018, Produkcija Plus Storitveno Podjetje v Slovenia, Application No 47072/15

Judgment of 14 February 2019, SA-Capital v Finland, Application No 5556/10
Dynamics of Apis cerana Sacbrood Virus (AcSBV) Prevalence in Apis cerana (Hymenoptera: Apidae) in Northern Taiwan and Demonstration of its Infection in Apis mellifera (Hymenoptera: Apidae)
Authors: Ko Chong-Yu , Chiang Zong-Lin , Liao Ruo-Jyun , Chang Zih-Ting , Chang Ju-Chun , Kuo Tsun-Yung , Chen Yue-Wen , Nai Yu-Shin
Published: June 2019

Since 2016, Apis cerana sacbrood virus (AcSBV) has been recorded in Taiwan. It is epizootic in Apis cerana (Hymenoptera: Apidae) and causing serious loss of A. cerana. Herein, we performed a long-term survey of AcSBV prevalence in the populations of A. cerana in Northern Taiwan from January 2017 to July 2018. The surveillance of AcSBV prevalence in A. mellifera (Hymenoptera: Apidae) populations was starting and further confirmed by sequencing since April 2017; thus, these data were also included in this survey. In our survey, the average prevalence rates of AcSBV were 72 and 53% in A. cerana and A. mellifera, respectively, in 2017, which decreased to 45 and 27% in 2018. For the spatial analysis of AcSBV in two honey bee populations, Hsinchu showed the highest prevalence, followed by New Taipei, Yilan, Taipei, and Keelung, suggesting that AcSBV might have come from the southern part of Taiwan. Interestingly, the AcSBV prevalence rates from A. cerana and A. mellifera cocultured apiaries gradually synchronized. The result of phylogenetic analysis and comparison of the annual AcSBV prevalence in A. cerana-only, A. mellifera-only, and A. cerana/A. mellifera cocultured sample sites indicate cross-infection between A. cerana and A. mellifera; however, AcSBV may lose the advantage of virulence in A. mellifera. The evidence suggested that the transmission of AcSBV might occur among these two honey bee species in the field. Therefore, A. mellifera may serve as a guard species to monitor AcSBV in A. cerana, but the cross-infection still needs to be surveyed.
Are Non-Target Honey Bees (Hymenoptera: Apidae) Exposed to Dinotefuran From Spotted Lanternfly (Hemiptera: Fulgoridae) Trap Trees?
Authors: Underwood Robyn , Breeman Brian , Benton Joseph , Bielski Jason , Palkendo Julie , Betts Thomas
Published: June 2019

The spotted lanternfly, Lycorma delicatula, is an introduced plant hopper that causes significant damage to host plants in the United States. Because of its affinity for tree of heaven, Ailanthus altissima, control efforts have focused on the use of the systemic insecticide, dinotefuran, in designated trap trees. There is concern about exposure to this pesticide by non-target species, especially honey bees, Apis mellifera, via lanternfly honeydew. Therefore, honey bee colonies were established in areas of high densities of trap trees and samples of honey, bees, and beeswax were collected in May, July, and October of 2017 for analysis. Samples were extracted by the QuEChERS method and analyzed using high-performance liquid chromatography with tandem mass spectrometry to determine the presence and quantity of dinotefuran. Additionally, honeydew from lanternflies was analyzed for dinotefuran and informal observations of trap tree visitors were made. None of the worker bee, wax, or honey samples indicated detectable levels of dinotefuran; however, honeydew samples collected did contain dinotefuran above the detection limit with amounts ranging from 3 to 100 ng per sample. The lack of dinotefuran in honey bee products matches the general absence of honey bees at trap trees in informal observations.
Pediatric Mucormycosis: A 10-Year Systematic Review of Reported Cases and Review of the Literature
Authors: Otto William R , Pahud Barbara A , Yin Dwight E
Published: June 2019

Mucormycosis is a severe infection that affects a variety of patients, including immunocompromised children and neonates. Given improved survival rates from advances in the treatment of malignancies, the population at risk for mucormycosis is increasing. We conducted a systematic review of cases of mucormycosis in children in the English-language literature reported between August 2008 and June 2017 and analyzed the clinical characteristics, diagnosis, management, and outcome of those infections. The most common underlying diagnoses included neutropenia (41%), hematologic malignancy (39%), prematurity (13%), and hematopoietic stem cell transplant (11%). Sinus disease (28%) and disseminated disease (24%) were the most common presentations. Rhizopus spp were the most common organisms isolated (22%). Amphotericin B remains the backbone of treatment and was prescribed in 86% of these cases. The resulting mortality rate remains high (32%). We provide here the results of a literature review of mucormycosis in children, including its epidemiology and clinical manifestations, and describe current advances in its diagnosis and treatment.
Evaluation of a commercially available, point-of-care Coccidioides antibody lateral flow assay to aid in rapid diagnosis of coccidioidomycosis in dogs
Authors: Schlacks Sallianne , Vishkautsan Polina , Butkiewicz Christine , Shubitz Lisa
Published: June 2019

Coccidioidomycosis in dogs can range from mild respiratory disease or vague, chronic malaise to acute, severe life-threatening illness. The diagnosis of coccidioidomycosis in dogs is based on clinical presentation and serology. Spherule identification is not typical because of low numbers of organisms in specimens, and the invasive nature of sampling tissues and lungs. Conventional serological assays require samples to be submitted to a reference laboratory and results take several days to one week. The sōna Coccidioides Antibody Lateral Flow Assay (LFA) (IMMY Diagnostics) is a rapid, bench-side test used for detection of Coccidioides antibodies that is available and FDA-cleared for use in humans but has not been evaluated in dogs. The goal of this study was to compare the LFA to conventional agar gel immunodiffusion (AGID). Paired serum samples were collected for screening by the LFA and submitted to a commercial reference laboratory for AGID screen and titer. Of 56 paired serum samples analyzed, 30 were positive and 26 were negative on the sōna Coccidioides antibody LFA. The overall percentage agreement plus 95% confidence interval (CI) was 87.5% (76.20–93.99). Positive percent agreement was 89.7% (73.38–96.65) and negative percent agreement was 85.2% (67.25–94.36). The kappa coefficient to assess agreement was 0.749 (95% CI, 0.576–0.923), which is interpreted as good agreement between the tests (>70%). The sōna Coccidioides antibody LFA provided rapid, point-of-care results with a high level of agreement to standard AGID serology in dogs clinically suspected to have coccidioidomycosis, and may aid in diagnosis of coccidioidomycosis in dogs.
Dipole distortions in the intergalactic medium
Authors: Inman Derek , Pen Ue-Li , Villaescusa-Navarro Francisco
Published: June 2019

Baryonic feedback can significantly modify the spatial distribution of matter on small scales and create a bulk relative velocity between the dominant cold dark matter and the hot gas. We study the consequences of such bulk motions using two high-resolution hydrodynamic simulations, one with no feedback and one with very strong feedback. We find that relative velocities of order $100\ {\rm km}\, {\rm s}^{-1}$ are produced in the strong feedback simulation, whereas it is much smaller when there is no feedback. Such relative motions induce dipole distortions to the gas, which we quantify by computing the dipole correlation function. We find halo coordinates and velocities are systematically changed in the direction of the relative velocity. Finally, we discuss potential to observe the relative velocity via large-scale structure, Sunyaev–Zel’dovich and line emission measurements. Given the non-linear nature of this effect, it should next be studied in simulations with different feedback implementations/strengths to determine the available model space.
First study of reionization in tilted flat and untilted non-flat dynamical dark energy inflation models
Authors: Mitra Sourav , Park Chan-Gyung , Choudhury Tirthankar Roy , Ratra Bharat
Published: June 2019

We examine the effects of dark energy dynamics and spatial curvature on cosmic reionization by studying reionization in tilted spatially flat and untilted non-flat XCDM and ϕCDM dynamical dark energy inflation models that best fit the Planck 2015 cosmic microwave background (CMB) anisotropy and a large compilation of non-CMB data. We carry out a detailed statistical study, based on a principal component analysis and a Markov chain Monte Carlo analysis of a compilation of lower-redshift reionization data to estimate the uncertainties in the cosmological model reionization histories. We find that, irrespective of the nature of dark energy, there are significant differences between the reionization histories of the spatially flat and non-flat models. Although both the flat and non-flat models can accurately match the low-redshift (z ≲ 6) reionization observations, there is a clear discrepancy between high-redshift (z > 7) Lyman-α emitter data and the predictions from non-flat models. This is solely due to the fact that the non-flat models have a significantly larger electron scattering optical depth, τel, compared to the flat models, which requires an extended and much earlier reionization scenario supported by more high-redshift ionizing sources in the non-flat models. Non-flat models also require strong redshift evolution in the photon escape fraction, which can become unrealistically high (≳1) at some redshifts. However, τel is about 0.9-σ lower in the tilted flat ΛCDM model when the new Planck 2018 data are used and this reduction will partially alleviate the tension between the non-flat model predictions and the data.