Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect and stability of MVCT images on adaptive TomoTherapy

Use of helical TomoTherapy‐based MVCT imaging for adaptive planning is becoming increasingly popular. Treatment planning and dose calculations based on MVCT require an image value to electron density calibration to remain stable over the course of treatment time. In this work, we have studied the dosimetric impact on TomoTherapy treatment plans due to variation in image value to density table (IVDT) curve as a function of target degradation. We also have investigated the reproducibility and stability of the TomoTherapy MVCT image quality over time. Multiple scans of the TomoTherapy “Cheese” phantom were performed over a period of five months. Over this period, a difference of 4.7% in the HU values was observed in high‐density regions while there was no significant variation in the image values for the low densities of the IVDT curve. Changes in the IVDT curves before and after target replacement were measured. Two clinical treatment sites, pelvis and prostate, were selected to study the dosimetric impact of this variation. Dose was recalculated on the MVCTs with the planned fluence using IVDT curves acquired before and after target change. For the cases studied, target replacement resulted in an overall difference of less than 5%, which can be significant for hypo‐fractionated cases. Hence, it is recommended to measure the IVDT curves on a monthly basis and after any major repairs/replacements. PACS numbers: 87.55. Qr, 87.56. bd, 87.57. C, 87.57. Q
Using Active Learning for Speeding up Calibration in Simulation Models

Background. Most cancer simulation models include unobservable parameters that determine disease onset and tumor growth. These parameters play an important role in matching key outcomes such as cancer incidence and mortality, and their values are typically estimated via a lengthy calibration procedure, which involves evaluating a large number of combinations of parameter values via simulation. The objective of this study is to demonstrate how machine learning approaches can be used to accelerate the calibration process by reducing the number of parameter combinations that are actually evaluated. Methods. Active learning is a popular machine learning method that enables a learning algorithm such as artificial neural networks to interactively choose which parameter combinations to evaluate. We developed an active learning algorithm to expedite the calibration process. Our algorithm determines the parameter combinations that are more likely to produce desired outputs and therefore reduces the number of simulation runs performed during calibration. We demonstrate our method using the previously developed University of Wisconsin breast cancer simulation model (UWBCS). Results. In a recent study, calibration of the UWBCS required the evaluation of 378 000 input parameter combinations to build a race-specific model, and only 69 of these combinations produced results that closely matched observed data. By using the active learning algorithm in conjunction with standard calibration methods, we identify all 69 parameter combinations by evaluating only 5620 of the 378 000 combinations. Conclusion. Machine learning methods hold potential in guiding model developers in the selection of more promising parameter combinations and hence speeding up the calibration process. Applying our machine learning algorithm to one model shows that evaluating only 1.49% of all parameter combinations would be sufficient for the calibration.
A light field‐based method to adjust rounded leaf end MLC position for split shape dose calculation correction in a radiation therapy treatment planning system

We present an analytical and experimental study of split shape dose calculation correction by adjusting the position of the round leaf end position in an intensity‐modulated radiation therapy treatment planning system. The precise light field edge position (Xtang.p) was derived from 50% of the central axis dose created by nominal light field using geometry and mathematical methods. Leaf position (Xmlc.p), defined in the treatment planning system for monitor unit calculation, could be derived from Xtang.p. Offset (correction) could be obtained by the position corresponding to 50% of the central axis dose minus the Xmlc.p position. For SSD from 90 cm to 120 cm at 6 MV and 10 MV, the 50% dose position was located outside of Xmlc,p in the MLC leaf position range of +8 cm to ‐8 cm, where the offset correction positively increased, whereas the offset correction negatively increased when the MLC leaf position was in the range of ‐12 cm to ‐8 cm and +20 cm to +8 cm when the 50% position was located inside Xmlc,p. The monitor unit calculation could provide underdosage or overdosage of 7.5% per mm without offset correction. Calibration could be performed at a certain SSD to fit all SSD offset corrections. With careful measurement and an accurate offset correction, it is possible to achieve the dose calculation with 0.5% error for the adjusted MLC leaf edge location in the treatment planning system. PACS number: 87.53. Tf, 87.55. x, 87.55. D, 87.55. dk
Time to implement a national referral pathway for suspected cauda equina syndrome: review and outcome of 250 referrals

Abstract Introduction: Cauda equina syndrome (CES) is a condition with significant implications and medico-legal profile. The literature still lacks large primary studies to provide strong evidence for a robust management pathway. Statements from Neurosurgical and Spinal societies support early diagnosis and imaging but this has not resulted in any noticeable shift in referral pattern. We strongly feel the need for a nationally agreed, evidence-based referral pathway in practice. We present our large series and in-depth analysis of the referral pathway to provide strong evidence for more robust referrals and management. Methods: We reviewed 250 referrals of suspected CES (sCES) to the regional neurosurgical unit, evaluating the importance of clinical findings and the imaging pathway. Results: After clinico-radiological evaluation only 32 (13%) had confirmed CES requiring urgent surgery. There was no significant difference in terms of clinical presentation between these true cases of CES (tCES) and false cases (fCES). Imaging was therefore the key rate-limiting step. MRI was the most common investigation used. 73 patients presented without imaging out of hours (OOH). In this group, investigation was delayed to the next day in 60/73 (82%) patients while only 13 (18%) patients underwent OOH MRI. Only 2 (3%) were able to have this at their local hospital. Conclusions: As with previous studies we conclude that signs/symptoms are insufficient to identify tCES. Taking into consideration the improved outcome with early diagnosis, the importance of early scanning in diagnosing tCES, and the poor availability of OOH MRI scanning outside of neurosurgical units, we recommend a national policy of 24/7 MRI availability for cases of sCES at all hospitals with MRI scanners. This would remove the 87% of patients not requiring urgent surgery from an unnecessary and distracting referral process.
Reduced arterial vasodilatation in response to hypoxia impairs cerebral and peripheral oxygen delivery in hypertensive men

Hypoxaemia evokes a repertoire of homeostatic adjustments that maintain oxygen supply to organs and tissues including the brain and skeletal muscles. Because hypertensive patients have impaired endothelial‐dependent vasodilatation and an increased sympathetic response to arterial oxygen desaturation, we investigated whether hypertension impairs isocapnic hypoxia‐induced cerebral and skeletal muscle hyperaemia to an extent that limits oxygen supply. In middle‐aged hypertensive men, vertebral and femoral artery blood flow do not increase in response to isocapnic hypoxia, limiting brain and peripheral hyperaemia and oxygen supply. Increased chemoreflex‐induced sympathetic activation impairs skeletal muscle perfusion and oxygen supply, whereas an attenuation of local vasodilatory signalling in the posterior cerebrovasculature reduced brain hyperperfusion of hypertensive middle‐aged men in response to isocapnic hypoxia.
Is Heller myotomy better than balloon dilation? A meta-analysis.

BACKGROUND AND AIM Endoscopic balloon dilation (EBD) and laparoscopic Heller myotomy (LHM) are the most commonly performed treatment options for achalasia. Decision between these treatment options is difficult. The aim of this meta-analysis was to evaluate the efficacy of EBD compared to LHM. METHODS The electronic databases PubMed, Embase and Cochrane Controlled Trials Registry were systematically searched for the period between January 1, 1976 and December 31, 2015. Meta-analysis was performed using the PICOS (problem, intervention, comparison, outcome, study design) format. Efficacy and safety of EBD were compared to LHM. Forest plot analyses were used to illustrate the success rate, perforation rate and post-procedural gastroesophageal reflux. RESULTS Using the search strategy, eight studies met the selection criteria and were included in the meta-analysis. The total number of patients included was 749 (360 in the EBD group and 389 in the LHM group). The success rate was lower in the EBD group than in the LHM group (OR=0.486; CI: 0.304-0.779; p=0.003). The rate of perforation did not differ significantly between the EBD and LHM group (RR= 0.635, CI: 0.340-1.186, p=0.154). The incidence of post-procedural symptomatic gastroesophageal reflux did not differ between the two treatment groups (RR=0.663, CI: 0.328-1.343, p=0.254). CONCLUSION Our data suggest that the efficacy of LHM is superior to that of EBD, while there is no difference in safety between the two treatment groups.
Structure and Properties of Cotton Sirospun® Yarn

Cotton Sirospun® yarn has a circular cross-sectional shape, with the two strands segregated and consolidated into an adjacent array. When it is untwisted, the strand twists in an alternate direction. When compared to single yam with the same linear density and twist multiplier, cotton Sirospun yam is superior in tenacity, evenness, hairiness, and abrasion resistance. Although cotton Sirospun yam is less hairy and more extensible than two-plied yarn, it is inferior to two-plied yam in evenness and imperfections.
Neurofeedback-induced facilitation of the supplementary motor area affects postural stability

Abstract. Near-infrared spectroscopy-mediated neurofeedback (NIRS-NFB) is a promising therapeutic intervention for patients with neurological diseases. Studies have shown that NIRS-NFB can facilitate task-related cortical activation and induce task-specific behavioral changes. These findings indicate that the effect of neuromodulation depends on local cortical function. However, when the target cortical region has multiple functions, our understanding of the effects is less clear. This is true in the supplementary motor area (SMA), which is involved both in postural control and upper-limb movement. To address this issue, we investigated the facilitatory effect of NIRS SMA neurofeedback on cortical activity and behavior, without any specific task. Twenty healthy individuals participated in real and sham neurofeedback. Balance and hand dexterity were assessed before and after each NIRS-NFB session. We found a significant interaction between assessment periods (pre/post) and condition (real/sham) with respect to balance as assessed by the center of the pressure path length but not for hand dexterity as assessed by the 9-hole peg test. SMA activity only increased during real neurofeedback. Our findings indicate that NIRS-NFB itself has the potential to modulate focal cortical activation, and we suggest that it be considered a therapy to facilitate the SMA for patients with postural impairment.
Dynamics of an Infectious Keratoconjunctivitis Outbreak by Mycoplasma conjunctivae on Pyrenean Chamois Rupicapra p. pyrenaica

Between 2006 and 2008, an outbreak of Infectious Keratoconjunctivitis (IKC) affected Pyrenean chamois Rupicapra p. pyrenaica, an endemic subspecies of mountain ungulate that lives in the Pyrenees. The study focused on 14 mountain massifs (180,000 ha) where the species’ population is stable. Cases of IKC were detected in ten of the massifs and, in five of them, mortality was substantial. The outbreak spread quickly from the first location detected, with two peaks in mortality that affected one (2007) and three (2008) massifs. In the latter, the peak was seasonal (spring to autumn) and, in the former, the outbreak persisted through winter. To identify the outbreak’s aetiology, we examined 105 Pyrenean chamois clinically affected with IKC. TaqMan rt-PCR identified Mycoplasma conjunctivae in 93 (88.5%) of the chamois. Another rt-PCR detected Chlamydophila spp. in 14 of chamois, and 12 of those had mixed infections with mycoplasmas. In the period 2000–2007, the chamois population increased slightly (λ 1.026) but decreased significantly during the IKC outbreak (λ 0.8, 2007–2008; λ 0.85, 2008–2009) before increasing significantly after the outbreak (λ 1.1, 2009–2010). Sex-biased mortality shifted the adult sex ratio toward males (from 0.6 to 0.7 males per female) and reduced productivity slightly. Hunting was practically banned in the massifs where chamois experienced significant mortality and allowed again after the outbreak ended. Long-term monitoring of wild populations provides a basis for understanding the impacts of disease outbreaks and improves management decisions, particularly when species are subject to extractive exploitation.
Phlegmonous Gastritis: A Report of Three Cases with Clinical and Imaging Features

Phlegmonous gastritis is a rare but often fatal acute pyogenic infection of the stomach. We herein report three cases of phlegmonous gastritis with different causes: the long-term placement of a nasogastric feeding tube, bacteremia associated with cellulitis in a diabetic patient, and an adverse reaction to paclitaxel/carboplatin chemotherapy for cancer of unknown primary cause, which were classified as primary, secondary, and idiopathic types, respectively. Coping with the increasing morbidity rate associated with the diverse background of such patients requires a thorough understanding of the clinical features and image findings associated with this entity.
Distributed Cooperative Fault Detection for Multiagent Systems: A Mixed $H_{\infty }/H_2$ Optimization Approach

This paper handles the distributed cooperative fault detection problem for multiagent systems (MASs) with additive type of faults and external disturbances. A distributed cooperative fault detection scheme is proposed through which the strict requirement on single agent's performance can be released. Moreover, a mixed $H_{\infty }/H_2$ optimization approach is presented to guarantee that the cooperative fault detection scheme can get a proper compromise between sensitivity to faults and robustness to disturbances on the network level. In order to be applicable with MASs, a distributed implementation of the proposed scheme is developed by applying an iterative approach. Effectiveness and improvements of the proposed scheme are validated on a multivehicle experimental platform.
Model checking and abstraction

We describe a method for using abstraction to reduce the complexity of temporal logic model checking. The basis of this method is a way of constructing an abstract model of a program without ever examining the corresponding unabstracted model. We show how this abstract model can be used to verify properties of the original program. We have implemented a system based on these techniques, and we demonstrate their practicality using a number of examples, including a pipelined ALU circuit with over 101300 states.
The Autographa californica Multiple Nucleopolyhedrovirus ac83 Gene Contains a cis-Acting Element That Is Essential for Nucleocapsid Assembly

ABSTRACT Baculoviridae is a family of insect-specific viruses that have a circular double-stranded DNA genome packaged within a rod-shaped capsid. The mechanism of baculovirus nucleocapsid assembly remains unclear. Previous studies have shown that deletion of the ac83 gene of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) blocks viral nucleocapsid assembly. Interestingly, the ac83-encoded protein Ac83 is not a component of the nucleocapsid, implying a particular role for ac83 in nucleocapsid assembly that may be independent of its protein product. To examine this possibility, Ac83 synthesis was disrupted by insertion of a chloramphenicol resistance gene into its coding sequence or by deleting its promoter and translation start codon. Both mutants produced progeny viruses normally, indicating that the Ac83 protein is not required for nucleocapsid assembly. Subsequently, complementation assays showed that the production of progeny viruses required the presence of ac83 in the AcMNPV genome instead of its presence in trans. Therefore, we reasoned that ac83 is involved in nucleocapsid assembly via an internal cis-acting element, which we named the nucleocapsid assembly-essential element (NAE). The NAE was identified to lie within nucleotides 1651 to 1850 of ac83 and had 8 conserved A/T-rich regions. Sequences homologous to the NAE were found only in alphabaculoviruses and have a conserved positional relationship with another essential cis-acting element that was recently identified. The identification of the NAE may help to connect the data of viral cis-acting elements and related proteins in the baculovirus nucleocapsid assembly, which is important for elucidating DNA-protein interaction events during this process. IMPORTANCE Virus nucleocapsid assembly usually requires specific cis-acting elements in the viral genome for various processes, such as the selection of the viral genome from the cellular nucleic acids, the cleavage of concatemeric viral genome replication intermediates, and the encapsidation of the viral genome into procapsids. In linear DNA viruses, such elements generally locate at the ends of the viral genome; however, most of these elements remain unidentified in circular DNA viruses (including baculovirus) due to their circular genomic conformation. Here, we identified a nucleocapsid assembly-essential element in the AcMNPV (the archetype of baculovirus) genome. This finding provides an important reference for studies of nucleocapsid assembly-related elements in baculoviruses and other circular DNA viruses. Moreover, as most of the previous studies of baculovirus nucleocapsid assembly have been focused on viral proteins, our study provides a novel entry point to investigate this mechanism via cis-acting elements in the viral genome.
Phytochemical Analysis, Antioxidant and Antibacterial Properties of Spilanthes mauritiana Used Traditionally in Limpopo Province, South Africa

Spilanthes mauritiana belonging to the family Asteraceae, was screened for biological activity against bacterial pathogen. Antibacterial activity of the plant was investigated using microbroth dilution assay and bioautography. Total phenols and tannins of the extract were 52.47 ± 2.29 and 23.9 ± 1.18 as mg of gallic acid equivalents, respectively. Total flavonoid content was 25.1 ± 0.79 as mg of quercetin equivalents. Free radical scavenging activity of constituents in all the extract, against 2,2-diphenyl-1-picrylhydrazyl showed minimal activity. All extracts contained compounds with antibacterial activity against tested pathogens. Hexane extract had an average minimum inhibitory concentration value of 2.50 mg/mL, followed by methanol extract (1.72 mg/mL), acetone and dichloromethane extracts (1.96 mg/mL). The present study revealed the presence of compounds in S mauritiana with potent antibacterial activity against tested pathogens that are exhibiting the observed activity independent of other constituents contained in the extracts.
Thinking in Pharmacy Practice: A Study of Community Pharmacists’ Clinical Reasoning in Medication Supply Using the Think-Aloud Method

Medication review and supply by pharmacists involves both cognitive and technical skills related to the safety and appropriateness of prescribed medicines. The cognitive ability of pharmacists to recall, synthesise and memorise information is a critical aspect of safe and optimal medicines use, yet few studies have investigated the clinical reasoning and decision-making processes pharmacists use when supplying prescribed medicines. The objective of this study was to examine the patterns and processes of pharmacists’ clinical reasoning and to identify the information sources used, when making decisions about the safety and appropriateness of prescribed medicines. Ten community pharmacists participated in a simulation in which they were required to review a prescription and make decisions about the safety and appropriateness of supplying the prescribed medicines to the patient, whilst at the same time thinking aloud about the tasks required. Following the simulation each pharmacist was asked a series of questions to prompt retrospective thinking aloud using video-stimulated recall. The simulated consultation and retrospective interview were recorded and transcribed for thematic analysis. All of the pharmacists made a safe and appropriate supply of two prescribed medicines to the simulated patient. Qualitative analysis identified seven core thinking processes used during the supply process: considering prescription in context, retrieving information, identifying medication-related issues, processing information, collaborative planning, decision making and reflection; and align closely with other health professionals. The insights from this study have implications for enhancing awareness of decision making processes in pharmacy practice and informing teaching and assessment approaches in medication supply.
Lignin from Micro- to Nanosize: Production Methods

Lignin is the second most abundant biopolymer after cellulose. It has long been obtained as a by-product of cellulose production in pulp and paper production, but had rather low added-value applications. A changing paper market and the emergence of biorefinery projects should generate vast amounts of lignin with the potential of value addition. Nanomaterials offer unique properties and the preparation of lignin nanoparticles and other nanostructures has therefore gained interest as a promising technique to obtain value-added lignin products. Due to lignin’s high structural and chemical heterogeneity, methods must be adapted to these different types. This review focuses on the ability of different formation methods to cope with the huge variety of lignin types and points out which particle characteristics can be achieved by which method. The current research’s main focus is on pH and solvent-shifting methods where the latter can yield solid and hollow particles. Solvent shifting also showed the capability to cope with different lignin types and solvents and antisolvents, respectively. However, process conditions have to be adapted to every type of lignin and reduction of solvent demand or the integration in a biorefinery process chain must be focused.
Impact of Arbitrary Co-Channel MIMO Modes on Alamouti Coding under Path-Loss and Rayleigh Fading

In this paper, we evaluate the impact of a mix of co-channel MIMO interferers on the performance of Alamouti Coding in the downlink of a cellular-like system. In particular, taking into account the effects of both path-loss and Rayleigh fading, we derive closed-form expressions for the probability density functions of the resulting signal-to-interference ratios. Simulation results verify the validity of the analyses.