Miracle-dz/UniFAR-FTUs huggingface dataset:
Real-time motion-adaptive delivery (MAD) using binary MLC: II. Rotational beam (tomotherapy) delivery

TomoTherapy delivery is controlled by a planned, projection-wised leaf sequence (sinogram) that is optimized during treatment planning. In this paper, we developed a software solution for real-time motion compensation that delivers helical TomoTherapy plans without modifying the hardware and workflow of the TomoTherapy delivery system. Unlike the dynamic MLC-based method, our technique only requires instantaneous tumor positions, which greatly simplifies its implementation. This technique re-uses the planned sinogram by shuffling its projections and leaf sequences. In order to compensate for longitudinal tumor motion in real-time, instead of sequential execution of the planned sinogram, the projections are executed out of order. That is, we may choose a past or future projection of the planned sinogram rather than the current projection depending on tumor motion, so that the planned radiation source position of the chosen projection is the same as the radiation source position at the current delivery time in the tumor reference frame. The transverse tumor motion is further compensated for by shifting and scaling the leaf open time of the chosen projection. We tested different planned sinograms that were optimized using various synthetic tumor/OAR configurations, as well as planned sinogram of a lung cancer patient, all with zero motion margins. Various TomoTherapy machine parameters and both regular and irregular respiratory traces were used in calculations. By applying the motion-adaptive delivery (MAD) technique, the delivered dose matched the planned dose very well in both DVH and dose profiles. As for the regular and minor irregular respiration, the dose errors were well below 3 mm and 3% criteria. No hot and cold spots were noticeable. For irregular respiration with some missing breathing cycles, this method demonstrates the capability for motion margin reduction.
Alternative Splicing, Internal Promoter, Nonsense-Mediated Decay, or All Three

Background—Truncating mutations in the giant sarcomeric gene Titin are the most common type of genetic alteration in dilated cardiomyopathy. Detailed studies have amassed a wealth of information about truncating variant position in cases and controls. Nonetheless, considerable confusion exists as to how to interpret the pathogenicity of these variants, hindering our ability to make useful recommendations to patients. Methods and Results—Building on our recent discovery of a conserved internal promoter within the Titin gene, we sought to develop an integrative statistical model to explain the observed pattern of Titin truncation variants in patients with dilated cardiomyopathy and population controls. We amassed Titin truncation mutation information from 1714 human dilated cardiomyopathy cases and >69 000 controls and found 3 factors explaining the distribution of Titin mutations: (1) alternative splicing, (2) whether the internal promoter Cronos isoform was disrupted, and (3) whether the distal C terminus was targeted (in keeping with the observation that truncation variants in this region escape nonsense-mediated decay and continue to be incorporated in the sarcomere). A model using these 3 factors had strong predictive performance with an area under the receiver operating characteristic curve of 0.81. Accordingly, individuals with either the most severe form of dilated cardiomyopathy or whose mutations demonstrated clear family segregation experienced the highest risk profile across all 3 components. Conclusions—We conclude that quantitative models derived from large-scale human genetic and phenotypic data can be applied to help overcome the ever-growing challenges of genetic data interpretation. Results of our approach can be found at http://cvri.ucsf. edu/~deo/TTNtruncationvariant.html.
Recovering shape from contour for constant cross section generalized cylinders

The authors analyze the properties of constant cross section generalized cylinders (CGCs), and derive the types of symmetries that the limb boundaries and cross sections of these objects produce on the image plane. The constraints on the 3-D shape of the objects are formulated based on the symmetries and from the geometry of the projection models. The methods that recover the 3-D shape from the image of their contours are discussed and recovered surfaces are shown for sample objects. <<ETX>>
ALK rearrangements in EBUS‐derived transbronchial needle aspiration cytology in lung cancer

Patients with non‐small cell lung cancer (NSCLC) positive for anaplastic lymphoma kinase (ALK) gene rearrangements may be treated successfully with the ALK inhibitor crizotinib. ALK copy‐number abnormalities have also been described. In this study, we evaluated the suitability of fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) to determine ALK status in endobronchial ultrasound (EBUS)‐derived cytology samples.
Real-world Interaction Networks Buffer Impact of Small Evolutionary Shifts On Biodiversity

Biodiversity maintenance and community evolution depend on the species interaction network. The “diversity-stability debate” has revealed that the complex interaction structure within real-world ecosystems determines how ecological communities respond to environmental changes, but can have opposite effects depending on the community type. Here we quantify the influence of shifts on community diversity and stability at both the species level and the community level. We use interaction networks from 19 real-world mutualistic communities and simulate shifts to antagonism. We demonstrate that both the placement of the shifting species in the community, as well as the structure of the interaction network as a whole contribute to stability and diversity maintenance under shifts. Our results suggest that the interaction structure of natural communities generally enhances community robustness against small ecological and evolutionary changes, but exacerbates the consequences of large changes.
Clonotypes in Rhesus Macaques T Cell + Cytomegalovirus-Specific CD4 Induction and Evolution of

CMV infection induces robust CD4 (cid:1) T cell responses in immunocompetent hosts that orchestrate immune control of viral replication, dissemination, and disease. In this study, we characterized the clonotypic composition of CD4 (cid:1) T cell populations speciﬁc for rhesus CMV (RhCMV) in chronically infected adult rhesus macaques (RM) and in juvenile RM undergoing primary RhCMV infection and subsequent secondary challenge with RhCMV. In adult RM with established chronic infection, RhCMV-speciﬁc CD4 (cid:1) T cell populations exhibited stable, pauciclonal structures with skewed hierarchies dominated by two or three clonotypes. During primary infection, in contrast, the initial RhCMV-speciﬁc CD4 (cid:1) T cell populations were highly polyclonal and progressive evolution to the chronic pattern manifest in adults occurred over the ensuing 2–3 years. Clear patterns of clonal succession were observed during this maturation process, such that clonotypes present in the acute phase were largely replaced over time. However, rechallenge with RhCMV expanded virus-speciﬁc CD4 (cid:1) T cell clonotypes identiﬁed solely during acute infection. These ﬁndings indicate that, during persistent viral infection, substantial selection pressures and ongoing clonotype recruitment shape the speciﬁc CD4 (cid:1) T cell repertoire and that rapidly exhausted or superseded clonotypes often remain within the memory T cell pool. The Journal of Immunology, 2008, 180: 269–280.
Spatial-Temporal pattern analysis and prediction of air quality in Taiwan

This study explores the spatial-temporal patterns of particulate matter (PM) in Taiwan. Probability map of PM and daily patterns are discussed in this study. Data mining provides more detailed spatial-temporal information for PM variations and trends. The proposed model will show that data mining provides a relatively high goodness of fit and sufficient space-time explanatory power, particularly air pollution frequency and affect areas. In the proposed model, a method using Dynamic Time Warping is proposed to analyse temporal similarity between stations. The proposed model can eliminate global effect on a single station through the performance of multiple stations. The proposed model will further be used for prediction of PM2.5. The prediction results will discuss the spatial-temporal relations between stations. This study will investigate the distribution of PM and its cyclicality.
A Volumetric SRP with Refinement Step for Sound Source Localization

This letter proposes an efficient method based on the steered-response power (SRP) technique for sound source localization using microphone arrays: the refined volumetric SRP (RV-SRP). By deploying a sparser volumetric grid, the RV-SRP achieves a significant reduction of the computational complexity without sacrificing the accuracy of location estimates. In addition, a refinement step improves on the compromise between complexity and accuracy. Experiments conducted in both simulated- and real-data scenarios show that the RV-SRP outperforms state-of-the-art methods in accuracy with lower computational cost.
Towards modeling question popularity in community question answering

Community question answering (QA) has become increasingly popular and received a great variety of questions every day. Among them, some questions are very attractive and popular to many users, while some other questions are very tedious and unattractive. In this paper, we aim to identify popular questions in the community QA through modeling question popularity. Three popularity-related features of questions are defined to build the popularity model: (a) potential hits, which reflect how many users are attracted by a question at their first glance; (b) popular terms, from which users find a question attractive; and (c) tedious unpopular terms. The notable characteristic of the proposed framework is extensibility and more features can be incorporated. A large-scale question dataset from a practical community QA website was used to train and test the model. Meanwhile, two well-known classifiers, k-nearest neighbors and support vector machines, were implemented for comparison. Our approach is well validated by the experimental results with much higher prediction accuracy than the baseline methods.
Synthesis of Naturally Derived Bioactive Compounds of Agricultural Interest

Synthetic studies on bioactive compounds are described, involving phytotoxins (tobacco wildfire disease toxin tabtoxinine-β-lactam and rice blast disease toxin pyricuol) a glutarimide antibiotic (actiketal) black vomit toxin (gizzerosine) and marine products (antifeedant pteroenone and serinol compound didemniserinolipid).
An alternative approach to designing stabilizing compensators for saturating linear time-invariant plants

We present a new methodology for designing low-gain linear time-invariant (LTI) controllers for semi-global stabilization of an LTI plant with actuator saturation, that is based on representation of a proper LTI feedback using a precompensator plus static-output-feedback architecture. We also mesh the new design methodology with time-scale notions to develop lower-order controllers for some plants.
Vulnerability of primary neurons derived from Tg2576 Alzheimer mice to oxygen and glucose deprivation: role of intraneuronal amyloid-β accumulation and astrocytes

ABSTRACT Microvascular dysfunction is considered an integral part of Alzheimer disease (AD) pathogenesis, but the possible relationship between amyloid pathology, microvascular dysfunction and cell death is still unclear. In order to investigate the influence of intraneuronal amyloid-β (Aβ) accumulation on vulnerability to hypoxia, we isolated primary cortical neurons from Tg2576 (carrying the amyloid precursor protein APPSwe mutation) and wild-type fetal mice. We first demonstrated that neurons isolated from Tg2576 newborn mice show an increase in VEGFa mRNA expression and a decrease in the expression of the two VEGF receptors, Flt1 and Kdr, compared with wild-type cells. Moreover, APPSwe primary neurons displayed higher spontaneous and glutamate-induced cell death. We then deprived the cultures of oxygen and glucose (OGD) as an in vitro model of hypoxia. After OGD, APPSwe neurons display higher levels of cell death in terms of percentage of pyknotic/fragmented nuclei and mitochondrial depolarization, accompanied by an increase in the intraneuronal Aβ content. To explore the influence of intraneuronal Aβ peptide accumulation, we used the γ-secretase inhibitor LY450139, which showed that the reduction of the intracellular amyloid fully protects APPSwe neurons from OGD-induced degeneration. Conditioned medium from OGD-exposed APPSwe or wild-type astrocytes protected APPswe neurons but not wild-type neurons, during OGD. In conclusion, the presence of the mutated human APP gene, leading to the intracellular accumulation of APP and Aβ fragments, worsens OGD toxicity. Protection of APPSwe neurons can be obtained either using a γ-secretase inhibitor or astrocyte conditioned medium. Summary: In vitro systems derived from AD mice can be used to investigate the vulnerability of AD neurons to different neurotoxic challenges, including oxygen glucose deprivation.
Fly Ash Properties and Their Applications as a Soil Ameliorant

Fly ash is one of the major global pollutants which is produced in millions of tons every year. The high content of heavy metals in fly ash categorizes them as hazardous materials. The presence of ferrous, alumina, and silica along with numerous macro- and micro-nutrients make them a suitable candidate for applications in agriculture, forestry, wasteland reclamation, soil stabilizer, etc. Fly ash has positive effects on the plant growth and crop yield. A numerous literature has reported the applications of fly ash as pesticides, herbicides, and insecticides. It has both alkaline and acidic pH which helps in maintaining the pH of the infertile soil. All these applications are cited with the previous work carried out by the investigators.
Lung dendritic cells facilitate extrapulmonary bacterial dissemination during pneumococcal pneumonia

Streptococcus pneumoniae is a leading cause of bacterial pneumonia worldwide. Given the critical role of dendritic cells (DCs) in regulating and modulating the immune response to pathogens, we investigated here the role of DCs in S. pneumoniae lung infections. Using a well-established transgenic mouse line which allows the conditional transient depletion of DCs, we showed that ablation of DCs resulted in enhanced resistance to intranasal challenge with S. pneumoniae. DCs-depleted mice exhibited delayed bacterial systemic dissemination, significantly reduced bacterial loads in the infected organs and lower levels of serum inflammatory mediators than non-depleted animals. The increased resistance of DCs-depleted mice to S. pneumoniae was associated with a better capacity to restrict pneumococci extrapulmonary dissemination. Furthermore, we demonstrated that S. pneumoniae disseminated from the lungs into the regional lymph nodes in a cell-independent manner and that this direct way of dissemination was much more efficient in the presence of DCs. We also provide evidence that S. pneumoniae induces expression and activation of matrix metalloproteinase-9 (MMP-9) in cultured bone marrow-derived DCs. MMP-9 is a protease involved in the breakdown of extracellular matrix proteins and is critical for DC trafficking across extracellular matrix and basement membranes during the migration from the periphery to the lymph nodes. MMP-9 was also significantly up-regulated in the lungs of mice after intranasal infection with S. pneumoniae. Notably, the expression levels of MMP-9 in the infected lungs were significantly decreased after depletion of DCs suggesting the involvement of DCs in MMP-9 production during pneumococcal pneumonia. Thus, we propose that S. pneumoniae can exploit the DC-derived proteolysis to open tissue barriers thereby facilitating its own dissemination from the local site of infection.
Generalized syntactic and semantic models of query reformulation

We present a novel approach to query reformulation which combines syntactic and semantic information by means of generalized Levenshtein distance algorithms where the substitution operation costs are based on probabilistic term rewrite functions. We investigate unsupervised, compact and efficient models, and provide empirical evidence of their effectiveness. We further explore a generative model of query reformulation and supervised combination methods providing improved performance at variable computational costs. Among other desirable properties, our similarity measures incorporate information-theoretic interpretations of taxonomic relations such as specification and generalization.
Modern, Preindustrial, and Past (Last 25 ka) Carbon Isotopic (δ13C) Variability in the Surface Waters of the Southwest Pacific

Carbon stable isotopes (δ13C) in modern seawater samples and planktic foraminifera Globigerina bulloides from core top and downcore sediments are used to estimate the distribution of δ13C of dissolved inorganic carbon (DIC) in the surface waters of the southwest Pacific in the modern, preindustrial (PI), and over the last 25 kyr. The predicted δ13C distribution in the modern (δ13CDIC), PI (δ13CPI), and late Holocene (from planktic foraminifera Globigerina bulloides [temperature corrected δ13CG.bulloidesTC] from core tops) displays a broad peak at the subtropical front) and subantarctic surface waters due to the combination of high biological productivity and thermodynamic air‐sea gas exchange of CO2 in this region. The estimated δ13CPI values and measured δ13CG.bulloidesTC values from the core tops are higher than the modern values due to the Suess Effect. However, there is poor agreement between the δ13CPI values and core top δ13CG.bulloidesTC values south of 40°S as the back‐calculation approach using chlorofluorocarbon‐11 (CFC‐11) method for removing the anthropogenic δ13C is not effective at these higher southern latitudes. The δ13CG.bulloidesTC from a latitudinal transect of cores in the southwest Pacific were compiled by region using a Monte Carlo approach to determine the long‐term trends in δ13C over the last 25 kyr. Glacial subantarctic δ13CG.bulloidesTC values are low, while subtropical δ13C G.bulloidesTC are high. The peak in δ13CG.bulloidesTC values shifts south in the early Holocene. These latitudinal variations in δ13C G.bulloidesTC are linked to changes in ocean circulation, biological productivity (associated with the shifts in the subtropical front), and air‐sea CO2 exchange, likely related to the structure and position of the Southern Hemisphere Westerly Wind in the South Pacific region.
Flashlight jigsaw: an exploratory study of an ad-hoc multi-player game on public displays

As large displays become prevalent in public spaces, they could be employed to create novel game experiences for the public. We present an exploratory study of an ad-hoc multi-player game played on such public displays. The game, Flashlight Jigsaw, was deployed in a shared lab space and a public atrium for two weeks in total. Through interviews supported by observations and system logs we explored the experiences and behaviors of players and spectators. We also investigated the interrelationship between public display games and the spaces they are deployed in. The research resulted in findings regarding game play, communication, social interaction, spectatorship, and space and location around such a game. We use our findings to develop design implications for future public display games.
Audiovisual asynchrony detection for speech and nonspeech signals

This study investigated the “intersensory temporal synchrony window” [1] for audiovisual (AV) signals. A speede d asynchrony detection task was used to measure each participant’s temporal synchrony window for speech and nonspeech signals over an 800-ms range of AV asynch ro ies. Across three sets of stimuli, the video-leading thr es old for asynchrony detection was larger than the audio-lead ing threshold, replicating previous findings reported i n the literature. Although the audio-leading threshold d id not differ for any of the stimulus sets, the video-lead ing threshold was significantly larger for the point-light displa y (PLD) condition than for either the full-face (FF) or non speech (NS) conditions. In addition, a small but reliable phon otactic effect of visual intelligibility was found for the FF condition. High visual intelligibility words produced larger v ideoleading thresholds than low visual intelligibility words. Relationships with recent neurophysiological data o n multisensory enhancement and convergence are discus sed.
Topographic gray level multiscale analysis and its application to histogram modification

This paper describes a framework for multi-scale gray level analysis of images. It defines scales based on gray levels and organizes the basic “atoms” with a topographic map. The aim of this approach is to separate a large number of pixels concentrating in a narrow range of gray values. The main advantage of the methodology is that it allows manipulating pixels according to gray levels and spatial relations simultaneously. We apply it to histogram modification of Synthetic Aperture Radar (SAR) images. The experiments on displaying and classification prove the superiority of the approach.
Statistical comparison of satellite-retrieved precipitation products with rain gauge observations over Bangladesh

ABSTRACT In this investigation, six satellite-derived precipitation products namely Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks (PERSIANN), Climate Prediction Centre (CPC) Morphing Technique (CMORPH), Integrated Multi-satellite Retrievals for Global Precipitation Measurement (IMERG) final run both non gauge-calibrated (IMERG) and gauge-calibrated (IMERG-GC), and Global Satellite Mapping of Precipitation (GSMaP) for GPM both non gauge-calibrated (GSMaP) and gauge-calibrated (GSMaP-GC) are evaluated over Bangladesh, using ground-based rain gauge observations as reference over a 3 years period from January 2014 to December 2016. Nine widely used categorical and volumetric statistical matrices such as bias, probability of detection, volumetric hit index, false alarm ratio, volumetric false alarm ratio, critical success index, volumetric critical success index, miss index, and volumetric miss index are employed to exploit the performance of the precipitation products in detecting extremes above different quantile thresholds (i.e. 50%, 75%, and 90% quantiles) for various temporal window (i.e. 3 h, 6 h, 12 h, and 24 h). The bias values show that none of the satellite rainfall data sets are ideal for detecting extreme rainfall accumulations. In fact, all products lose their detection skills consistently as the extreme precipitation thresholds (50%, 75%, and 90% quantiles) increase. The results indicate that PERSIANN shows the worst performance over the study region. Overall, GSMaP-GC performs better than the other precipitation products. However, the FAR values of GSMaP are also higher over monsoon and post-monsoon months. The categorical and volumetric scores reveal that the detection skill increases remarkably for all rainfall data sets throughout the year with the increase of extreme quantile thresholds. At higher temporal accumulations, the detection capability of the products also improves considerably, and this improvement is more significant during monsoon period. The performance is relatively poor for all precipitation data sets over the cold months. In general, all six satellite precipitation products are doing well in detecting the occurrence of rainfall but are not so good in estimating the amount of rainfall.