Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying isocenter measurements to establish clinically meaningful thresholds

A dataset range of isocenter congruency verification tests have been examined from a statistical perspective for the purpose of establishing tolerance levels that are meaningful, based on the fundamental limitation of linear accelerator isocentricity and the demands of a high‐precision stereotactic radiosurgery program. Using a laser‐defined isocenter, a total of 149 individual isocenter congruency tests were examined with recorded values for ideal spatial corrections to the isocenter test tool. These spatial corrections were determined from radiation exposures recorded on an electronic portal imaging device (EPID) at various gantry, collimator, and treatment couch combinations. The limitations of establishing an ideal isocenter were quantified from each variable which contributed to uncertainty in isocenter definition. Individual contributors to uncertainty, specifically, daily positioning setup errors, gantry sag, multileaf collimator (MLC) offset, and couch walkout, were isolated from isocenter congruency measurements to determine a clinically meaningful isocenter measurement. Variations in positioning of the test tool constituted, on average, 0.38 mm magnitude of correction. Gantry sag and MLC offset contributed 0.4 and 0.16 mm, respectively. Couch walkout had an average degrading effect to isocenter of 0.72 mm. Considering the magnitude of uncertainty contributed by each uncertainty variable and the nature of their combination, an appropriate schedule action and immediate action level were determined for use in analyzing daily isocenter congruency test results in a stereotactic radiosurgery (SRS) program. The recommendations of this study for this linear accelerator include a schedule action level of 1.25 mm and an immediate action level of 1.50 mm, requiring prompt correction response from clinical medical physicists before SRS or stereotactic body radiosurgery (SBRT) is administered. These absolute values were derived from considering relative data from a specific linear accelerator and, therefore, represent a means by which a numerical quantity can be used as a test threshold with relative specificity to a particular linear accelerator. PACS number: 87.53Ly, 29.20. Ej, 87.56. Fc
Variant at position 10,055 in mitochondrial tRNAGly gene has a negative association with aplastic anemia

Abstract Recently, a growing number of reports had shown the association between mitochondrial DNA (mtDNA) sequence variants and aplastic anemia (AA). Owing to its high mutation rate, mtDNA variant had become biomarker for clinical and molecular diagnosis for AA. However, the relationship between mtDNA variant and AA was largely unknown. In this study, we reanalyzed the possible association between a “pathogenic” mutation A10055G in mt-tRNAGly gene and AA, through the application of bioinformatics tool, we found that this mutation did not alter the secondary structure of tRNAGly, the pathogenicity scoring system indicated that the score of this mutation was only two points and belonged to a “neutral polymorphism”, suggested that the role of A10055G mutation in clinical expression in AA needed to be further experimentally addressed.
Determination of cohesive laws in wood bonded joints under mode I loading using the DCB test

Abstract The cohesive laws (CLs) have been investigated by means of direct and inverse methods concerning wood bonded joints under pure mode I. The experimental results were obtained by tests with double cantilever beam. The direct method is based on the differentiation of the relation between strain energy release rate and crack opening displacement at the crack tip. An equivalent crack method was used to evaluate the strain energy release rate in the course of the test without monitoring the crack length, which is difficult to observe exactly. The crack opening displacement was determined by postprocessing local displacements measured by digital image correlation. The inverse method requires a previous assumption of the CL shape, and as such, a trilinear law with bilinear softening relationship was selected. The cohesive parameters were identified by an optimization procedure involving a developed genetic algorithm. The idea is to minimize an objective function that quantifies the difference between the experimental and the numerical load-displacement curves resulting from the application of a given law. A validation procedure was performed based on a numerical analysis with finite elements. Both methods in focus provided good agreement with the experimental data. It was observed that CLs adopted by the inverse method are consistent with the ones obtained with the direct method.
A survey of Canadian medical physicists: software quality assurance of in‐house software

This paper reports on a survey of medical physicists who write and use in‐house written software as part of their professional work. The goal of the survey was to assess the extent of in‐house software usage and the desire or need for related software quality guidelines. The survey contained eight multiple‐choice questions, a ranking question, and seven free text questions. The survey was sent to medical physicists associated with cancer centers across Canada. The respondents to the survey expressed interest in having guidelines to help them in their software‐related work, but also demonstrated extensive skills in the area of testing, safety, and communication. These existing skills form a basis for medical physicists to establish a set of software quality guidelines. PACS number: 87.55. Qr
Conditional End-to-End Audio Transforms

We present an end-to-end method for transforming audio from one style to another. For the case of speech, by conditioning on speaker identities, we can train a single model to transform words spoken by multiple people into multiple target voices. For the case of music, we can specify musical instruments and achieve the same result. Architecturally, our method is a fully-differentiable sequence-to-sequence model based on convolutional and hierarchical recurrent neural networks. It is designed to capture long-term acoustic dependencies, requires minimal post-processing, and produces realistic audio transforms. Ablation studies confirm that our model can separate speaker and instrument properties from acoustic content at different receptive fields. Empirically, our method achieves competitive performance on community-standard datasets.
Synthesis of High‐Purity Ti3SiC2 by Microwave Sintering

High-purity ternary laminated compound Ti3SiC2 was successfully synthesized by a microwave heating method in the flowing argon for the first time. The mixtures of titanium, silicon, and graphitic carbon (Cgc) or activated carbon (Cac) with different molar ratios were used to investigate the reaction mechanisms. It was confirmed that Ti3SiC2 with high purity of 98 vol.% was achieved without the aids of Al. The optimum experimental parameters were determined as Ti/Si/Cgc having the molar ratio of 3/2.2/2, first holding at 1480°C for 30 min, and subsequent dwelling at 1300°C for 60 min.
PIM Kinases Are a Potential Prognostic Biomarker and Therapeutic Target in Neuroblastoma

The majority of high-risk neuroblastoma patients are refractory to, or relapse on, current treatment regimens, resulting in 5-year survival rates of less than 50%. This emphasizes the urgent need to identify novel therapeutic targets. Here, we report that high PIM kinase expression is correlated with poor overall survival. Treatment of neuroblastoma cell lines with the pan-PIM inhibitors AZD1208 or PIM-447 suppressed proliferation through inhibition of mTOR signaling. In a panel of neuroblastoma cell lines, we observed a marked binary response to PIM inhibition, suggesting that specific genetic lesions control responses to PIM inhibition. Using a genome-wide CRISPR-Cas9 genetic screen, we identified NF1 loss as the major resistance mechanism to PIM kinase inhibitors. Treatment with AZD1208 impaired the growth of NF1 wild-type xenografts, while NF1 knockout cells were insensitive. Thus, our data indicate that PIM inhibition may be a novel targeted therapy in NF1 wild-type neuroblastoma. Mol Cancer Ther; 17(4); 849–57. ©2018 AACR.
Crystal structure of secretory abundant heat soluble protein 4 from one of the toughest “water bears” micro‐animals Ramazzottius Varieornatus

Though anhydrobiotic tardigrades (micro‐animals also known as water bears) possess many genes of secretory abundant heat soluble (SAHS) proteins unique to Tardigrada, their functions are unknown. A previous crystallographic study revealed that a SAHS protein (RvSAHS1) from one of the toughest tardigrades, Ramazzottius varieornatus, has a β‐barrel architecture similar to fatty acid binding proteins (FABPs) and two putative ligand binding sites (LBS1 and LBS2) where fatty acids can bind. However, some SAHS proteins such as RvSAHS4 have different sets of amino acid residues at LBS1 and LBS2, implying that they prefer other ligands and have different functions. Here RvSAHS4 was crystallized and analyzed under a condition similar to that for RvSAHS1. There was no electron density corresponding to a fatty acid at LBS1 of RvSAHS4, where a putative fatty acid was observed in RvSAHS1. Instead, LBS2 of RvSAHS4, which was composed of uncharged residues, captured a putative polyethylene glycol molecule. These results suggest that RvSAHS4 mainly uses LBS2 for the binding of uncharged molecules.
Proposal for A Structural Integration Test Coverage Metric for Object-Oriented Programs

Though a large number of test coverage metrics have been proposed in the context of unit and system testing of object oriented programs, structural coverage metrics for integration testing have scarcely been reported. In this context, we propose an integration test coverage metric based on the coverage of the data and control dependency edges of the JSysDG (Java System Dependency Graph).
Autophagy is induced by resistance exercise in young men, but unfolded protein response is induced regardless of age

Autophagy and unfolded protein response (UPR) appear to be important for skeletal muscle homoeostasis and may be altered by exercise. Our aim was to investigate the effects of resistance exercise and training on indicators of UPR and autophagy in healthy untrained young men (n = 12, 27 ± 4 years) and older men (n = 8, 61 ± 6 years) as well as in resistance‐trained individuals (n = 15, 25 ± 5 years).
Techniques for Enhancing Durability and Equivalence Ratio Control in a Rich-Lean, Three-Stage, Ground Power Gas Turbine Combustor

This effort summarizes the work performed under Task IV, Sector Rig Tests of the CRT - Critical Research and Support Technology Program, a Department of Energy funded project. The rig tests of a can-type combustor were performed to demonstrate two advanced ground power engine combustor concepts: steam cooled rich-burn combustor primary zones for enhanced durability; and variable combustor geometry for three stage combustion equivalence ratio control. Both concepts proved to be highly successful in achieving their desired objectives. The steam cooling reduced peak liner temperatures to less than 800 K. This offers the potential of both long life and reduced use of strategic materials for liner fabrication. Three degrees of variable geometry were successfully implemented to control airflow distribution within the combustor. One was a variable blade angle axial flow air swirler to control primary airflow while the other two consisted of rotating bands to control secondary and tertiary or dilution air flow.Copyright © 1982 by ASME
LC-MS/MS-based assay for free and deconjugated testosterone and epitestosterone in rat urine and serum

Testosterone and epitestosterone are mainly excreted as glucuronides. The aim of this study was to develop and validate a method using liquid chromatography tandem mass spectrometry (LC-MS/MS) to analyse testosterone and epitestosterone in rat serum and urine to assist in vivo studies on steroid metabolism. The method was developed by spiking charcoal stripped rat plasma and urine with the analytes. The developed method was then applied to serum (n=6) and urine samples (n=6) from young male brown Norway rats to determine testosterone and epitestosterone concentrations. The assay showed linearity within quantification range coefficient (r2) values above 0.991. Optimum conditions were determined for the deconjugation of glucuronidated testosterone and epitestosterone along with the internal standard stanozolol D3. Accuracy, precision and extraction recovery for both compounds was satisfactory in both matrices. The method was capable of quantifying 0.250 ng/mL concentrations of testosterone and epitestosterone in 100 μL of serum and urine. The average concentrations of free and deconjugated testosterone and epitestosterone found in the rat samples were: urine–201.68 ± 90.16 ng/mL and 85.37 ± 21.20 ng/mL; serum– 363.40 ± 11.615 ng/mL and 1.75 ± 0.118 ng/mL, respectively. This method is sensitive, specific and reproducible for the determination of free and deconjugated testosterone and epitestosterone in rat serum and urine. The method can be used for in vivo analysis for further investigations of testosterone and epitestosterone concentrations in studies monitoring endocrine dysfunctions and doping.
Architectures for a quantum random access memory

A random access memory, or RAM, is a device that, when interrogated, returns the content of a memory location in a memory array. A quantum RAM, or qRAM, allows one to access superpositions of memory sites, which may contain either quantum or classical information. RAMs and qRAMs with n-bit addresses can access 2^n memory sites. Any design for a RAM or qRAM then requires O(2^n) two-bit logic gates. At first sight this requirement might seem to make large scale quantum versions of such devices impractical, due to the difficulty of constructing and operating coherent devices with large numbers of quantum logic gates. Here we analyze two different RAM architectures (the conventional fanout and the "bucket brigade") and propose some proof-of-principle implementations which show that in principle only O(n) two-qubit physical interactions need take place during each qRAM call. That is, although a qRAM needs O(2^n) quantum logic gates, only O(n) need to be activated during a memory call. The resulting decrease in resources could give rise to the construction of large qRAMs that could operate without the need for extensive quantum error correction.
Prenatal Diagnosis of a Case of Norrie Disease with Late Development of Bilateral Ocular Malformation

ABSTRACT We report a case of Norrie disease, diagnosed by prenatal ultrasound, confirmed by Sanger sequencing of the DNP gene from the aborted fetal cord blood and histologically. Prenatal ultrasound revealed no abnormality in either eye at 22+1 and 31+4 gestational weeks, but at 36+5 gestational weeks both eyes had massive vitreous cavity opacities with complete retinal detachment. Norrie disease was initially suspected because of an older male sibling with the disease. To our knowledge, prenatal ultrasound diagnosis of Norrie disease has been previously described only one case in 1993 in a 34-week-old fetus. The normal eye development until after 31 + 4 gestational weeks provides insight into the first manifestation and then the rapid progression of the eye disease.
Evaluation of metrics for benchmarking antimicrobial use in the UK dairy industry

The issue of antimicrobial resistance is of global concern across human and animal health. In 2016, the UK government committed to new targets for reducing antimicrobial use (AMU) in livestock. Although a number of metrics for quantifying AMU are defined in the literature, all give slightly different interpretations. This paper evaluates a selection of metrics for AMU in the dairy industry: total mg, total mg/kg, daily dose and daily course metrics. Although the focus is on their application to the dairy industry, the metrics and issues discussed are relevant across livestock sectors. In order to be used widely, a metric should be understandable and relevant to the veterinarians and farmers who are prescribing and using antimicrobials. This means that clear methods, assumptions (and possible biases), standardised values and exceptions should be published for all metrics. Particularly relevant are assumptions around the number and weight of cattle at risk of treatment and definitions of dose rates and course lengths; incorrect assumptions can mean metrics over-represent or under-represent AMU. The authors recommend that the UK dairy industry work towards the UK-specific metrics using the UK-specific medicine dose and course regimens as well as cattle weights in order to monitor trends nationally.
Chitosan as a Surface Sizing Agent for Offset Printing Paper

The biopolymer chitosan has been shown to improve the surface properties of paper for offset printing. The quality of the sized paper was investigated after treatment with chitosan of different molecular weights and different concentrations as well as in a blend with oxidised starch. The results were compared with the sizing quality of polyvinyl alcohol and oxidised starch. It was found that the molecular weight and concentration of the chitosan influenced the sizing quality. Blending of oxidised starch with a small quantity of chitosan significantly improved the sizing quality of the former. It was concluded that the chitosansized paper was superior for offset printing compared to paper sized with either oxidised starch or polyvinyl alcohol.
Trap-Neuter-Return Activities in Urban Stray Cat Colonies in Australia

Simple Summary Urban stray cats in Australia are poorly regarded because of wildlife predation and nuisance behaviors. However, current methods of population control via low level culling are ineffective. Effective control requires culling 30% to 50% of the population every six months, which is prohibitive for municipalities. Overseas, trap, neuter and return is frequently used to control urban cat numbers, and reduce nuisance behaviors, but is considered illegal in many Australian jurisdictions. An anonymous questionnaire was used to gather data on trap, neuter and return of urban stray cats in Australia. Respondents were mostly middle-aged women, and more participated as individuals than with organizations. Colony size decreased from a median of 11.5 cats to 6.5 cats over 2.2 years, through adoptions and desexing a median of 69% of the colony. Cats were fed once or twice daily, and provided with prophylactic health care. Programs were largely funded by private sources, with some funding by animal welfare organizations. We conclude that trap, neuter and return associated with high desexing rates in colonies, and adoption of kittens and friendly adults substantially reduces colony size, and improves the welfare of cats and kittens. This model is cost-effective for municipalities, and should be legalized in Australia. Abstract Trap, neuter and return (TNR) describes a non-lethal approach to the control of urban stray cat populations. Currently, in Australia, lethal control is common, with over 85% of cats entering some municipal pounds euthanized. No research has been published describing TNR activities in Australia. Adults involved with TNR in Australia were invited to participate. Data from 53 respondents were collected via an anonymous online questionnaire. Most respondents were females 36 to 65 years of age, and slightly more participated in TNR as individuals than as part of an organization. Respondents generally self-funded at least some of their TNR activities. The median number of colonies per respondent was 1.5 (range 1 to over 100). Median colony size declined from 11.5 to 6.5 cats under TNR over a median of 2.2 years, and the median percent reduction was 31%; this was achieved by rehoming cats and kittens and reducing reproduction. A median of 69% of cats in each colony were desexed at the time of reporting. Most respondents fed cats once or twice daily, and at least 28% of respondents microchipped cats. Prophylactic healthcare was provided to adult cats and kittens, commonly for intestinal parasites (at least 49%), and fleas (at least 46%); vaccinations were less common. Time-consuming activities for respondents were feeding (median 4 h/week) and locating resources (median 1.1 h/week). These findings indicate that TNR, when involving high desexing rates within colonies, adoption of kittens and friendly adults, and ongoing oversight by volunteer caretakers, can reduce cat numbers over time, improve health and welfare of cats and kittens, and is largely funded by private individuals and organizations.
Technical Note: A respiratory monitoring and processing system based on computer vision: prototype and proof of principle

Monitoring and controlling respiratory motion is a challenge for the accuracy and safety of therapeutic irradiation of thoracic tumors. Various commercial systems based on the monitoring of internal or external surrogates have been developed but remain costly. In this article we describe and validate Madibreast, an in‐house‐made respiratory monitoring and processing device based on optical tracking of external markers. We designed an optical apparatus to ensure real‐time submillimetric image resolution at 4 m. Using OpenCv libraries, we optically tracked high‐contrast markers set on patients' breasts. Validation of spatial and time accuracy was performed on a mechanical phantom and on human breast. Madibreast was able to track motion of markers up to a 5 cm/s speed, at a frame rate of 30 fps, with submillimetric accuracy on mechanical phantom and human breasts. Latency was below 100 ms. Concomitant monitoring of three different locations on the breast showed discrepancies in axial motion up to 4 mm for deep‐breathing patterns. This low‐cost, computer‐vision system for real‐time motion monitoring of the irradiation of breast cancer patients showed submillimetric accuracy and acceptable latency. It allowed the authors to highlight differences in surface motion that may be correlated to tumor motion. PACS number(s): 87.55. km
Flexural Behavior of Epoxy Matrix Composites Reinforced with Malva Fiber

Polymer composites reinforced with natural fibers have been increasingly investigated and applied as engineering materials owing to their economical, technical, societal and environmental advantages. The malva fiber, particularly an important resource in the Amazon region in Brazil, only recently begin to be investigated as possible composite reinforcement for engineering application. However, the mechanical properties of composites reinforced with malva fiber are still unknown. In this paper, the flexural behavior of epoxy matrix composites reinforced with continuous malva fiber was for the first time investigated. Specimens of continuous malva fibers aligned along an epoxy matrix were press-molded. Three-points bending test were performed and the fractured specimens were analyzed by SEM. The results showed a marked improvement in the composites flexural properties with the increase in the amount of reinforced malva fiber. This improvement was found to match the Rule of Mixtures, which revealed the unique potential of malva composites for engineering applications.