Miracle-dz/UniFAR-FTUs huggingface dataset:
Gantry and isocenter displacements of a linear accelerator caused by an add-on micromultileaf collimator.

PURPOSE The delivery of high quality stereotactic radiosurgery (SRS) and stereotactic radiotherapy (SRT) treatments to the patient requires knowledge of the position of the isocenter to submillimeter accuracy. To meet the requirements the deviation between the radiation and mechanical isocenters must be less than 1 mm. The use of add-on micromultileaf collimators (μMLCs) in SRS and SRT is an additional challenge to the anticipated high-level geometric and dosimetric accuracy of the treatment. The aim of this work was to quantify the gantry excursions during rotation with and without an add-on μMLC attached to the gantry head. In addition, the shift in the position of the isocenter and its correlation to the kV beam center of the cone-beam CT system was included in the study. METHODS The quantification of the gantry rotational performance was done using a pointer supported by an in-house made rigid holder attached to the gantry head of the accelerator. The pointer positions were measured using a digital theodolite. To quantify the effect of an μMLC of 50 kg, the measurements were repeated with the μMLC attached to the gantry head. The displacement of the isocenter due to an add-on μMLC of 50 kg was also investigated. In case of the pointer measurement the μMLC was simulated by weights attached to the gantry head. A method of least squares was applied to determine the position and displacement of the mechanical isocenter. Additionally, the displacement of the radiation isocenter was measured using a ball-bearing phantom and the electronic portal image device system. These measurements were based on 8 MV photon beams irradiated onto the ball from the four cardinal angles and two opposed collimator angles. The measurements and analysis of the data were carried out automatically using software delivered by the manufacturer. RESULTS The displacement of the mechanical isocenter caused by a 50 kg heavy μMLC was found to be (-0.01 ± 0.05, -0.10 ± 0.03, -0.26 ± 0.05) mm in lateral, longitudinal, and vertical direction, respectively. Similarly, the displacement of the radiation isocenter was found to be (0.00 ± 0.03, -0.08 ± 0.06, -0.32 ± 0.02) mm. Good agreement was found between the displacement of the two isocenters. A displacement of the kV cone-beam CT beam center due to the attached weight of 50 kg could not be detected. CONCLUSIONS General characteristics of the gantry arm excursions and displacements caused by an add-on μMLC have been reported. A 50 kg heavy add-on μMLC results in a isocenter displacement downward of 0.26-0.32 mm. The authors recommend that the beam center of the kV cone-beam CT image system should be matched to the isocenter related to the weight of the μMLC. Consequently, the imperfections in isocenter localizations are transferred to the conventional radiotherapy where the clinical consequences of uncertainties in the submillimeter regime are negligible.
Authentic Replication and Recombination of Tomato Bushy Stunt Virus RNA in a Cell-Free Extract from Yeast

ABSTRACT To study the replication of Tomato bushy stunt virus (TBSV), a small tombusvirus of plants, we have developed a cell-free system based on a Saccharomyces cerevisiae extract. The cell-free system was capable of performing a complete replication cycle on added plus-stranded TBSV replicon RNA (repRNA) that led to the production of ∼30-fold-more plus-stranded progeny RNAs than the minus-stranded replication intermediate. The cell-free system also replicated the full-length TBSV genomic RNA, which resulted in production of subgenomic RNAs as well. The cell-free system showed high template specificity, since a mutated repRNA, minus-stranded repRNA, or a heterologous viral RNA could not be used as templates by the tombusvirus replicase. Similar to the in vivo situation, replication of the TBSV replicon RNA took place in a membraneous fraction, in which the viral replicase-RNA complex was RNase and protease resistant but sensitive to detergents. In addition to faithfully replicating the TBSV replicon RNA, the cell-free system was also capable of generating TBSV RNA recombinants with high efficiency. Altogether, tombusvirus replicase in the cell-free system showed features remarkably similar to those of the in vivo replicase, including carrying out a complete cycle of replication, high template specificity, and the ability to recombine efficiently.
Cytoskeletal Changes in Hypoxic Pulmonary Endothelial Cells Are Dependent on MAPK-activated Protein Kinase MK2*

Exposure to hypoxia causes structural changes in the endothelial cell layer that alter its permeability and its interaction with leukocytes and platelets. One of the well characterized cytoskeletal changes in response to stress involves the reorganization of the actin cytoskeleton and the formation of stress fibers. This report describes cytoskeletal changes in pulmonary microvascular endothelial cells in response to hypoxia and potential mechanisms involved in this process. The hypoxia-induced actin redistribution appears to be mediated by components downstream of MAPK p38, which is activated in pulmonary endothelial cells in response to hypoxia. Our results indicate that kinase MK2, which is a substrate of p38, becomes activated by hypoxia, leading to the phosphorylation of one of its substrates, HSP27. Because HSP27 phosphorylation is known to alter actin distribution in response to other stimuli, we postulate that it also causes the actin redistribution observed in hypoxia. This notion is supported by the observations that similar actin redistribution occurs in cells overexpressing constitutively active MK2 or phosphomimicking HSP27 mutant. Overexpressing dominant negative MK2 blocks the effects of hypoxia on the actin cytoskeleton. Taken together these results indicate that hypoxia stimulates the p38-MK2-HSP27 pathway leading to significant alteration in the actin cytoskeleton.
Polyphonic music transcription through dynamic networks and spectral pattern identification ∗

The automatic extraction of the notes that were played in a digital musical signal (automatic music transcription) is an open problem. A number of techniques have been applied to solve it without concluding results. This work tries to pose it through the identification of the spectral pattern of a given instrument in the signal spectrogram using time-delay neural networks. We will work in the monotimbrical polyphonic version of the problem: more than one note can sound at the same time but always played by just one instrument. Our purpose is to discover wether a neural network fed only with an spectrogram can detect the notes of a polyphonic music score. In this paper our preliminary but promising results using synthetic instruments are presented.
Improving results of rational non-linear observation functions using a Kalman filter correction

This article deals with the divergence of the Kalman filter when used on non-linear observation functions. The Kalman filter allows to update some parameters according to observations and their uncertainties. The observation model which links the parameters to the observations is often non-linear and has to be linearized. An improper linearization leads to a divergence effect that could be contained by increasing the observation noise. When the observation model can be written as a quotient of two linear functions, the presented method allows to reduce the divergence effect without modifying the observation noise. This method is similar to a proportional correction in the Kalman update step and is more efficient than the unscented Kalman filter or particle filter.
Video segmentation and summarization based on Genetic Algorithm

This paper presents a Binary Genetic Algorithms (BGA) based video summarization system. The similarity functions are first defined to evaluate segmentation, which are extremely expensive to be optimized with traditional methods. Then the system employs binary crossover and mutation operators to get the meaningful summary in a video search space. In order to test performance of the BGA method, we first compare the BGA method with Decimal Genetic Algorithms (DGA) method. The obtained results show that it is more quickly to find the best results for BGA than DGA. Second, the BGA method and the uniform approach have been compared. Experimental results show that the BGA method can capture more information than the uniform method and reduce redundancy.
Cryptanalysis of A PAACP: A Portable Privacy- Preserving Authentication and Access Control Protocol in Vehicular Ad Hoc Networks

Vehicular ad hoc networks (VANETs) are emerging to improve road safety and traffic management. Privacy and security are very important in VANETs. Existing authentication protocols to secure VANETs raise challenges such as certificate distribution and reduction of the strong reliance on tamper-proof devices. Recently, Yeh et al. proposed a portable privacy-preserving authentication and access control protocol in vehicular ad hoc networks (PAACP). However, PAACP in the authorization phase is breakable and cannot keep privacy in VANETs. In this paper, we present a cryptanalysis of an attachable blind signature and show that the PAACP"s Authorized Credential (AC) is not secure and private even the AC secretly stored in a tamper-proof device. Our analysis showed that in PAACP, an eavesdropper can construct the AC from an intercepted blind document. As a result, PAACP in the authorization phase is breakable, and as any outsider can know who has which access privileges to access which service, the user"s privacy in VANETs is jeopardized.
Isolation and phenotypic characterization of virulence-deficient mutants of Vibrio cholerae

Mutants of Vibrio cholerae was isolated on the basis of reduced ability to induce diarrhea in orally challenged infant mice. Nitrosoguanidine-treated clones were screened for low fluid accumulation ratios in individual mice, and presumptive mutants were confirmed in additional mouse tests. Mutants were examined for alterations in phage type, motility, toxin production, proteolytic activity, neuraminidase production, amylase production, morphology, growth requirements, carbohydrate fermentations, in vitro growth patterns, and cell surface alterations. The types of mutants found included several with previously recognized virulence-associated markers (rough, nonmotile, toxin deficient, protease deficient); several types with pleiotropic alterations (cell morphology, decreased extracellular products); and several with no previously recognized virulence-deficient phenotype (purine requiring, cell surface altered, rapid death in vitro, no defect found). Dose-response kinetics showed that most mutants could provoke diarrhea if given in 100-fold greater numbers than the dose used for screening. Recovery of viable organisms from the gut late in infection showed reduction of survival and/or multiplication capacity for the mutants, with variation in the degree of reduction for the different classes.
Neural Mechanisms of Resistance to Peer Influence in Early Adolescence

During the shift from a parent-dependent child to a fully autonomous adult, peers take on a significant role in shaping the adolescent's behavior. Peer-derived influences are not always positive, however. Here, we explore neural correlates of interindividual differences in the probability of resisting peer influence in early adolescence. Using functional magnetic resonance imaging, we found striking differences between 10-year-old children with high and low resistance to peer influence in their brain activity during observation of angry hand movements and angry facial expressions: compared with subjects with low resistance to peer influence, individuals with high resistance showed a highly coordinated brain activity in neural systems underlying perception of action and decision making. These findings suggest that the probability of resisting peer influence depends on neural interactions during observation of emotion-laden actions.
Abc‐immunoperoxidase staining of cytologic preparations: Improvement of specificity

Immunoperoxidase (IP) methods perfected on formalin‐fixed, paraffin‐embedded tissues (FFPE) and then applied to aspirate smears may result in high background staining and, a significant number of false‐positive results. This is especially true if polyclonal primary antibodies are used or if aspirates and fluids contain a high interstitial or serum protein content. Because of a recurring problem with antiserum to alpha‐fetoprotein (AFP), AFP was selected as the primary test antibody with which to evaluate our avidin‐biotin complex (ABC)‐IP method. The same method, with diaminobenzidine (DAB) or aminoethylcarbazole (AEC) chromogens, was performed on six types of cytologic preparations of a fresh liver specimen. The liver did not stain for AFP in FFPE and frozen tissue; therefore, it could be used to evaluate potential false‐positive staining of direct touch imprints, washed aspirate smears, and cytospins that were both air‐dried and alcohol‐carbowax‐fixed. Initial chromogen incubation times were standardized to give identical results on AFP‐positive fixed hepatoma and fetal liver controls. Cytologic preparations immunostained with ABC‐IP with AEC chromogen resulted in varying background and hepatocyte staining. In comparison, the ABC‐IP method using DAB chromogen resulted in no false‐positive results and a clean background. The ABC‐IP method with AEC standardized for sensitivity on a fixed tissue control required a markedly shortened chromogen incubation time to preclude significant false‐positive staining of cytology specimens. It appears that use of AEC chromogen for this antibody with incubation time standardized on a FFFE tissue control and then applied to cytologic preparations also amplifies nonspecific and background staining, contributing difficulty in assessing a true‐positive result. In contrast, the ABC‐IP method with DAB chromogen standardized on fixed tissues can be directly translated to various types of cytologic preparations. Knowledge of this pitfall should be especially useful in trouble‐shooting other immunoreactions since it is open difficult to obtain and store cytologic quality‐control materials for immunohistochemistry.
Systematically comparing control approaches in the presence of actuator errors

A quantitative comparison of different approaches to control the trajectory of an autonomous vehicle can be achieved by measuring the overall performance of the whole system in closed loop. This work compares two trajectory generation and control approaches for autonomous driving in simulation. One approach is based on a low frequency check of geometric safety distances and a high frequency check of control deviations. The other approach minimizes the probability of colliding with obstacles by explicitly considering actuator uncertainties and solving a chance constraint optimization problem. The comparison is based on systematically applying actuator inaccuracies and searching for event combinations leading to collisions. We demonstrate that the control approach incorporating uncertainties performs better in one class of critical scenarios although its error model is different to the applied inaccuracies.
Moderate diet-induced weight loss is associated with improved insulin sensitivity in middle-aged healthy obese Korean women

BACKGROUND/OBJECTIVE The goal of the present study was to investigate the effects of moderate caloric restriction on β-cell function and insulin sensitivity in middle-aged obese Korean women. SUBJECTS/METHODS Fifty-seven obese pre-menopausal Korean women participated in a 12-week calorie restriction program. Data on total cholesterol (TC), high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C), triglycerides (TG), and fasting serum levels of glucose, insulin, C-peptide, blood pressure, leptin and anthropometrics were collected. A dietary intake assessment was based on three days of food recording. Additionally, β-cell function [homeostasis model assessment of β-cell (HOMA-β), insulinogenic index (ISI), C-peptide:glucose ratio, and area under curve insulin/glucose (AUCins/glu)] and insulin sensitivity [homeostasis model assessment for insulin resistance (HOMA-IR), Quantitative insulin-sensitivity check index (QUICKI) and Matsuda index (MI)] were recorded. RESULTS When calories were reduced by an average of 422 kcal/day for 12 weeks, BMI (-2.7%), body fat mass (-10.2%), and waist circumference (-5%) all decreased significantly (P < 0.05). After calorie restriction, weight, body fat percentage, hip circumference, BP, TC, HDL-C, LDL-C, plasma glucose at fasting, insulin at fasting and 120 min, AUCglu and the insulin area under the curve all decreased significantly (all P < 0.05), while insulin sensitivity (HOMA-IR, QUICKI and Matsuda index) measured by OGTT improved significantly (P < 0.01). CONCLUSIONS Moderate weight loss due to caloric restriction with reduction in insulin resistance improves glucose tolerance and insulin sensitivity in middle-aged obese women and thereby may help prevent the development of type 2 diabetes mellitus.
Kinetics of concentration decay of specific organic matter in UASB reactors operating with and without return of aerobic sludge

This study aimed at assessing the influence of the return of excess aerobic sludge from a trickling filter (TF) upon the anaerobic digestion process in an upflow anaerobic sludge blanket (UASB) reactor, by evaluating its effect on the kinetics of the decay of specific organic matter (carbohydrates, proteins and lipids), as well as on the concentrations of volatile fatty acids in the UASB reactor. A pilot-scale UASB/TF system was used to perform the experiments, operating with (phase 2) and without (phase 1) excess sludge return from the TF to the UASB reactor. Sampling was carried out at different heights of the UASB reactor (0, 25, 125 and 225-cm height), and profile concentrations were determined for the following parameters: carbohydrates, proteins, lipids and volatile fatty acids. First-order kinetics showed the best fit to the decay of concentrations of carbohydrates, proteins, lipids and chemical oxygen demand (COD) in the UASB reactor. The parameters showing the best fit to the first-order kinetics were proteins and COD, during the sludge return phase. The occurrence of higher apparent reaction constants was further observed during the sludge return phase. For an influent COD concentration of 600 mg L −1 and hydraulic retention times of 2.1, 2.6 and 3.0 h in phase 1, the effluent COD concentrations were 125.3, 88.4 and 62.4 mg L −1, respectively, whereas in phase 2, the effluent COD concentrations were 75.5, 47.6 and 30.1 mg L −1, respectively.
Asthma, Eczema, Rhinitis and the Risk for Dementia

Background: Inflammation is associated with Alzheimer’s disease (AD) and dementia. In light of the chronic inflammatory properties of the atopic disorders asthma, eczema and rhinitis, we hypothesized an association with dementia. Methods: Self-reported asthma, eczema or rhinitis was assessed (prior to dementia follow-up) through questionnaires in the 1960s or 1970s in twins from the population-based Swedish Twin Registry. Dementia was assessed both longitudinally (n = 22,188), through linkages to two population-based registers, and cross-sectionally (n = 7,800), through telephone cognitive screening followed by a clinical evaluation of suspects of dementia. Risk ratios were estimated with Cox and logistic regression models controlling for vascular disease and genetic confounding. Results: In the longitudinal study, a history of atopy was positively associated with dementia (HR = 1.16; 1.01–1.33). In the cross-sectional study we found overall lower risks, none of which was statistically significant. Asthma was associated with a shorter survival time following AD onset. Conclusions: Atopy is associated with a modestly increased risk of AD and dementia that is not mediated by vascular disease or due to genetic confounding. A history of asthma is associated with shorter life expectancy after AD diagnosis.
A Facile and Sensitive Method for Quantification of Cyclic Nucleotide Monophosphates in Mammalian Organs: Basal Levels of Eight cNMPs and Identification of 2',3'-cIMP

A sensitive, versatile and economical method to extract and quantify cyclic nucleotide monophosphates (cNMPs) using LC-MS/MS, including both 3',5'-cNMPs and 2',3'-cNMPs, in mammalian tissues and cellular systems has been developed. Problems, such as matrix effects from complex biological samples, are addressed and have been optimized. This protocol allows for comparison of multiple cNMPs in the same system and was used to examine the relationship between tissue levels of cNMPs in a panel of rat organs. In addition, the study reports the first identification and quantification of 2',3'-cIMP. The developed method will allow for quantification of cNMPs levels in cells and tissues with varying disease states, which will provide insight into the role(s) and interplay of cNMP signalling pathways.
The cyprinodont fish Rivulus ( Aplocheiloidei : Rivulidae ) in Trinidad and Tobago : molecular evidence for marine dispersal , genetic isolation and local differentiation

Mitochondrial DNA sequences (756 bp) were obtained from the cytochrome b gene of 36 Rivulus individuals collected from 10 sites in Trinidad and one site in Tobago. Eight haplotypes were identified. Low genetic divergence (0.5%) between one western Trinidad (Blue Basin) haplotype and Rivulus hartii from north-western Venezuela (Paria peninsula) and high genetic divergence (c. 11%) between these and the remaining other Trinidad and Tobago haplotypes suggests that the islands were colonized by two lineages. The commoner haplotype is distributed throughout lowland Trinidad, possibly a reflection of flooding of the Orinoco River leading to high dispersal between watersheds. Rivulus from higher altitude (Northern Range) localities that would not have been affected by such flooding show high genetic divergence between sites. The genetic differentiation between northern and southern watersheds suggests isolation between some of these drainages.
A Mobile Anchor Assisted Localization Algorithm Based on Regular Hexagon in Wireless Sensor Networks

Localization is one of the key technologies in wireless sensor networks (WSNs), since it provides fundamental support for many location-aware protocols and applications. Constraints of cost and power consumption make it infeasible to equip each sensor node in the network with a global position system (GPS) unit, especially for large-scale WSNs. A promising method to localize unknown nodes is to use several mobile anchors which are equipped with GPS units moving among unknown nodes and periodically broadcasting their current locations to help nearby unknown nodes with localization. This paper proposes a mobile anchor assisted localization algorithm based on regular hexagon (MAALRH) in two-dimensional WSNs, which can cover the whole monitoring area with a boundary compensation method. Unknown nodes calculate their positions by using trilateration. We compare the MAALRH with HILBERT, CIRCLES, and S-CURVES algorithms in terms of localization ratio, localization accuracy, and path length. Simulations show that the MAALRH can achieve high localization ratio and localization accuracy when the communication range is not smaller than the trajectory resolution.