Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of dose kernel calculation using a simplified Monte Carlo method to treatment plan for scanned proton beams.

Full Monte Carlo (FMC) calculation of dose distribution has been recognized to have superior accuracy, compared with the pencil beam algorithm (PBA). However, since the FMC methods require long calculation time, it is difficult to apply them to routine treatment planning at present. In order to improve the situation, a simplified Monte Carlo (SMC) method has been introduced to the dose kernel calculation applicable to dose optimization procedure for the proton pencil beam scanning. We have evaluated accuracy of the SMC calculation by comparing a result of the dose kernel calculation using the SMC method with that using the FMC method in an inhomogeneous phantom. The dose distribution obtained by the SMC method was in good agreement with that obtained by the FMC method. To assess the usefulness of SMC calculation in clinical situations, we have compared results of the dose calculation using the SMC with those using the PBA method for three clinical cases of tumor treatment. The dose distributions calculated with the PBA dose kernels appear to be homogeneous in the planning target volumes (PTVs). In practice, the dose distributions calculated with the SMC dose kernels with the spot weights optimized with the PBA method show largely inhomogeneous dose distributions in the PTVs, while those with the spot weights optimized with the SMC method have moderately homogeneous distributions in the PTVs. Calculation using the SMC method is faster than that using the GEANT4 by three orders of magnitude. In addition, the graphic processing unit (GPU) boosts the calculation speed by 13 times for the treatment planning using the SMC method. Thence, the SMC method will be applicable to routine clinical treatment planning for reproduction of the complex dose distribution more accurately than the PBA method in a reasonably short time by use of the GPU-based calculation engine. PACS number(s): 87.55. Gh.
Possibility of using Smartphones in Distributed Computing Networks

In this article the possible use of smartphones, as potential resources in a distributed computing system has been examined. First, the performance indexes of smartphones, desktop and notebook computers were compared, considering the six year period of the iPhone product line. In the second part some volunteer computing projects were summarized in a glance, to have a better picture of the necessary performance and donation system. Finally some motivating ideas have been proposed, to gather more donors for a smartphone based distributed computing network. Keywords— Distributed Computing, Performance index, Geekbench, Smartphone, Smartphone performance
Letter to the Editor

We have read with interest the Centers for Disease Control and Prevention (CDC) interim guidelines for pregnant women during the Zika virus outbreak in the updated MMWR recommendations of January 22, 2016 [1], and the MMWR publication by Martines and colleagues of February 10, 2016 [2]. Histopathologic examination of placentas from affected pregnancies resulting in briefly viable infants and products of conception from miscarriages was recommended, as well as saving frozen placenta and cord. Indications for placental examination will be clear-cut in clinically established Zika virus cases at all gestational ages, however placental tissue should also be saved in any suspicious situations including spontaneous and elective terminations of pregnancy and late liveborn and stillborn cases. The importance of placental examination must be emphasized to neonatologists and obstetricians as well as pathologists in both academic centers and in circumstances when the placenta may receive less emphasis, such as in cases from community hospitals. The most recent case report by Mlakar and colleagues [3] is an example of in depth discussion of the central nervous findings in an infant dying of congenital Zika virus, and one in which the placenta was reportedly examined. However, these authors did not include an in depth histopathologic description of the placental findings or discussion of what may have been done with the tissue to enhance their study of this newborn. Of note, there is currently no established pathognomonic histopathologic set of findings in Zika virus infection and, per the above, little literature on the subject, so further study is needed to define the full spectrum of disease. Evaluation of these placentas should preferentially be performed by pathologists with expertise in perinatal/placental pathology and should be done in cases of pregnancy loss as well as live birth. A recent global consensus conference on the placenta was held in Amsterdam, The Netherlands, in September 2014 [4]. The forthcoming reference will provide criteria for uniformity of histologic sampling and diagnostic terminology for further studies of the pathogenesis of vertical transmission of Zika virus. Confirmation and diagnosis of Zika virus infection can be made on placental tissue. Fresh or frozen tissue can be tested and molecular testing can be applied to even formalin fixed tissue. A referring hospital’s state Department of Health can be contacted, and will arrange for testing with the CDC. We need to systematically evaluate these placental cases to better elucidate the mechanism of transplacental transfer, and perhaps develop ways of defending against this tragedy.
Stochastic timing in gene expression for simple regulatory strategies.

Timing is essential for many cellular processes, from cellular responses to external stimuli to the cell cycle and circadian clocks. Many of these processes are based on gene expression. For example, an activated gene may be required to reach in a precise time a threshold level of expression that triggers a specific downstream process. However, gene expression is subject to stochastic fluctuations, naturally inducing an uncertainty in this threshold-crossing time with potential consequences on biological functions and phenotypes. Here, we consider such 'timing fluctuations' and we ask how they can be controlled. Our analytical estimates and simulations show that, for an induced gene, timing variability is minimal if the threshold level of expression is approximately half of the steady-state level. Timing fluctuations can be reduced by increasing the transcription rate, while they are insensitive to the translation rate. In presence of self-regulatory strategies, we show that self-repression reduces timing noise for threshold levels that have to be reached quickly, while self-activation is optimal at long times. These results lay a framework for understanding stochasticity of endogenous systems such as the cell cycle, as well as for the design of synthetic trigger circuits.
Sodium pumps mediate activity-dependent changes in mammalian motor networks.

Ubiquitously expressed sodium pumps are best known for maintaining the ionic gradients and resting membrane potential required for generating action potentials. However, activity- and state-dependent changes in pump activity can also influence neuronal firing and regulate rhythmic network output. Here we demonstrate that changes in sodium pump activity regulate locomotor networks in the spinal cord of neonatal mice. The sodium pump inhibitor, ouabain, increased the frequency and decreased the amplitude of drug-induced locomotor bursting, effects which were dependent on the presence of the neuromodulator dopamine. Conversely, activating the pump with the sodium ionophore monensin decreased burst frequency. When more "natural" locomotor output was evoked using dorsal-root stimulation, ouabain increased burst frequency and extended locomotor episode duration, whilst monensin slowed and shortened episodes. Decreasing the time between dorsal-root stimulation, and therefore inter-episode interval, also shortened and slowed activity, suggesting that pump activity encodes information about past network output and contributes to feedforward control of subsequent locomotor bouts. Using whole-cell patch-clamp recordings from spinal motoneurons and interneurons, we describe a long duration (∼60s), activity-dependent, TTX- and ouabain-sensitive, hyperpolarisation (∼5mV), which is mediated by spike-dependent increases in pump activity. The duration of this dynamic pump potential is enhanced by dopamine. Our results therefore reveal sodium pumps as dynamic regulators of mammalian spinal motor networks that can also be affected by neuromodulatory systems. Given the involvement of sodium pumps in movement disorders such as Amyotrophic Lateral Sclerosis and Rapid-onset Dystonia Parkinsonism, knowledge of their contribution to motor network regulation also has considerable clinical importance. SIGNIFICANCE STATEMENT The sodium pump is ubiquitously expressed and responsible for at least half of total brain energy consumption. The pumps maintain ionic gradients and the resting membrane potential of neurons, but increasing evidence suggests that activity- and state-dependent changes in pump activity also influence neuronal firing. Here we demonstrate that changes in sodium pump activity regulate locomotor output in the spinal cord of neonatal mice. We describe a sodium pump-mediated afterhyperpolarisation in spinal neurons, mediated by spike-dependent increases in pump activity, which is affected by dopamine. Understanding how sodium pumps contribute to network regulation and are targeted by neuromodulators, including dopamine, has clinical relevance due to the role of the sodium pump in diseases including ALS, parkinsonism, epilepsy and hemiplegic migraine.
Assessment of statistical classification rules: implications for computational intelligence

The problem of binary classification is of great interest across many fields, including data mining, satellite imaging, and medical diagnostics. The performance of a classifier is, mostly, measured in terms of the error rate, i.e., the total probability of misclassification. A more general approach is to use the Receiver Operating Characteristic (ROC). The ROC is a plot of all the possible values of one type of errors versus the other one. Very practical and easy-to-interpret summary measures can be derived from such a curve, e.g., the Area Under the Curve (AUC), and the Partial Area Under the Curve (PAUC). This dissertation studies the assessment of classification rules using the entire ROC space with no parametric assumptions. That is, the present approach requires having no knowledge about the distribution of the data. In addition, when data are scarce the classification rule should be designed and assessed from the single available data set. In the present regulatory setting for public-policy making, e.g., in the area of medical diagnostics, the available data set is required to be split into two disjoint sets, one for design and the other for assessment. In this dissertation, both strategies are studied. Moreover, the techniques developed in this dissertation assume no particular form for the classification rule to be assessed: the methodology is general across classical as well as novel modern architectures. The linear and quadratic discriminants used in the dissertation were selected, simply, for demonstration purposes. The contemporary use of the expression Computational Intelligence refers to a number of rapidly maturing branches of the general field of artificial intelligence, including neural networks, fuzzy logic, evolutionary algorithms,. etc. Algorithms developed in these subfields to solve classification problems are, from a statistical point of view, nonparametric classification rules. This dissertation may, therefore, provide critical assessment tools for such algorithms when they must be developed within a setting in which data are scarce.
[Corrigendum] Functional analysis of Zyxin in cell migration and invasive potential of oral squamous cell carcinoma cells.

Following the publication of this article, an interested reader drew to our attention an anomaly associated with the presentation of Figs. 2 and 3. Essentially, there was a direct duplication of certain of the western blotting data between Fig. 2 (the E-cadherin and Actin data) and Fig. 3C (the Zyxin and Actin data). After having re-examined our original data, we realize that we inadvertently duplicated the data from Fig. 2 in Fig. 3C (the Zyxin and Actin data). A corrected version of Fig. 3C (containing the true Zyxin and Actin data), and, by natural process, also of Fig. 6, are presented below, in which the Zyxin data in Figs. 3C and 6 are now correctly shown. Since the Zyxin data was a control for the siZyxin knockout of HOC313, this error did not affect the results of the Rho family analysis in this study. We sincerely apologize for this mistake, and thank the reader of our article who drew this matter to our attention. Furthermore, we regret any inconvenience this mistake has caused. [the original article was published in the International Journal of Oncology 42: 873-880, 2013; DOI: 10.3892/ijo.2013. 1761].
Congenital heart disease and Down syndrome: various aspects of a confirmed association.

BACKGROUND Congenital heart disease (CHD) is frequently described in patients with Down syndrome (DS) and is the main cause of death in this population during the first two years of life. The spectrum of CHD patterns in DS varies widely worldwide; this variation could be due to sociodemographic, genetic and geographic factors. METHODS A six-year retrospective, descriptive study was carried out from December 2008 to October 2014, based on the Paediatric Unit CHD registry of Ibn Rochd University Hospital. Clinical, echocardiographic and outcomes data were collected and sorted according to confirmation of the syndrome. RESULTS Among 2 156 patients with CHD, 128 were identified with Down syndrome. The genders were equally represented (gender ratio 1) and the median age at diagnosis was 9.5 months (2 days to 16 years). The median age of mothers at delivery was 39 years (16-47). Of the 186 CHD lesions reported, the most common was atrioventricular septal defect (AVSD, 29%), followed by ventricular septal defect (VSD, 21.5%) and atrial septal defect (ASD, 19.9%). The most common associations of CHD were AVSD + ASD (10%) and VSD + ASD (7.8%). Surgery was the most common modality of treatment (54.3%). The overall mortality rate was 14.1%. CONCLUSION Our study confirmed that the profile and type of CHD in DS in the Moroccan setting exhibited slight differences in the distribution of these CHDs compared with European neighbours and other Western countries. Further studies are needed to determine which variables have an impact on these differences.
Continuous Move Optimization for Truckload Pickup and Delivery Problem

We present in this paper a prototype optimization model for generating continuous move plans for the large-scale truckload pickup and delivery problem. Our model matches truckload moves for a given set of origin-destination (OD) pairs, allowing continuous moves of trucks (i.e., multiple and sequential pickups and deliveries) when possible. We present a set partitioning formulation and describe a solution algorithm based on the column generation technique. We test the model on largescale problems with more than one million variables. Computational results show impressive runtimes and significant reduction of empty-haul distances, which translates to major saving in fuel and other operating costs as well as reduction in pollution released to the environment.
AER synthetic generation in hardware for bio-inspired spiking systems

Address Event Representation (AER) is an emergent neuromorphic interchip communication protocol that allows for real-time virtual massive connectivity between huge number neurons located on different chips. By exploiting high speed digital communication circuits (with nano-seconds timings), synaptic neural connections can be time multiplexed, while neural activity signals (with mili-seconds timings) are sampled at low frequencies. Also, neurons generate 'events' according to their activity levels. More active neurons generate more events per unit time, and access the interchip communication channel more frequently, while neurons with low activity consume less communication bandwidth. When building multi-chip muti-layered AER systems it is absolutely necessary to have a computer interface that allows (a) to read AER interchip traffic into the computer and visualize it on screen, and (b) convert conventional frame-based video stream in the computer into AER and inject it at some point of the AER structure. This is necessary for test and debugging of complex AER systems. This paper addresses the problem of converting, in a computer, a conventional frame-based video stream into the spike event based representation AER. There exist several proposed software methods for synthetic generation of AER for bio-inspired systems. This paper presents a hardware implementation for one method, which is based on Linear-Feedback-Shift-Register (LFSR) pseudo-random number generation. The sequence of events generated by this hardware, which follows a Poisson distribution like a biological neuron, has been reconstructed using two AER integrator cells. The error of reconstruction for a set of images that produces different traffic loads of event in the AER bus is used as evaluation criteria. A VHDL description of the method, that includes the Xilinx PCI Core, has been implemented and tested using a general purpose PCI-AER board. This PCI-AER board has been developed by authors, and uses a Spartan II 200 FPGA. This system for AER Synthetic Generation is capable of transforming frames of 64x64 pixels, received through a standard computer PCI bus, at a frame rate of 25 frames per second, producing spike events at a peak rate of 107 events per second.
Carbetocin is a Functional Selective Gq Agonist That Does Not Promote Oxytocin Receptor Recycling After Inducing β‐Arrestin‐Independent Internalisation

Carbetocin, a long‐acting oxytocin analogue, has been reported to elicit interesting and peculiar behavioural effects. The present study investigated the molecular pharmacology of carbetocin, aiming to better understand the molecular basis of its action in the brain. Using bioluminescence resonance energy transfer biosensors, we characterised the effects of carbetocin on the three human oxytocin/vasopressin receptors expressed in the nervous system: the oxytocin receptor (OXTR) and the vasopressin V1a (V1aR) and V1b (V1bR) receptors. Our results indicate that (i) carbetocin activates the OXTR but not the V1aR and V1bR at which it may act as an antagonist; (ii) carbetocin selectively activates only the OXTR/Gq pathway displaying a strong functional selectivity; (iii) carbetocin is a partial agonist at the OXTR/Gq coupling; (iv) carbetocin promotes OXTR internalisation via a previously unreported β‐arrestin‐independent pathway; and (v) carbetocin does not induce OXTR recycling to the plasma membrane. Altogether, these molecular pharmacology features identify carbetocin as a substantially different analogue compared to the endogenous oxytocin and, consequently, carbetocin is not expected to mimic oxytocin in the brain. Whether these unique features of carbetocin could be exploited therapeutically remains to be established.
Dysregulation of Acetylation Enzymes in Animal Models of Psychostimulant use Disorders: Evolving Stories

Substance use disorders are neuropsychiatric illnesses that have substantial negative biopsychosocial impact. These diseases are defined as compulsive abuse of licit or illicit substances despite adverse medicolegal consequences. Although much research has been conducted to elucidate the pathobiological bases of these disorders, much remains to be done to develop an overarching neurobiological understanding that might be translatable to beneficial pharmacological therapies. Recent advances in epigenetics promise to lead to such an elucidation. Here I provide a brief overview of observations obtained using some models of psychostimulant administration in rodents. The review identifies CREB binding protein (CBP), HDAC1, HDAC2, HADC3, HDAC4, and HDAC5 as important players in the acetylation and deacetylation processes that occur after contingent or non-contingent administration of psychostimulants. These observations are discussed within a framework that suggests a need for better animal models of addiction in order to bring these epigenetic advances to bear on the pharmacological treatment of human addicts.
GPU-Based Ray Tracing Algorithm Using Uniform Grid Structure

Ray tracing rendering technique had been widely used in several application including 3D animation, CAD, dan architecture software. The biggest challenge to implement the ray tracing rendering system is a large computation power needed by application. In order to tackle that problem, we use uniform grid data structure to divide the scene into small grid and 3D Digital Differential Analyzer (3D-DDA) to access the structure. Our system are split into two steps, the first step is to construct the uniform grid structure based on scene condition and the second step is ray tracing traversal based on uniform grid structure that processed in previous step. Uniform grid structure is used in our system because it’s GPU friendly data structure and easier to implement in GPU. Our system runs at 6 ms until 200 ms for constructing the uniform grid structure and 2 fps until 30 fps for scene rendering time. Comparing with CPU implementation, our system run 2 until 6 time faster depends on scene condition.
Ontology Revision on the Semantic Web: Integration of belief revision theory

Ontology is used to define terms and relations on the semantic Web to form well-structured semantics of Web resources. Ontology revision refers to the process of updating ontology to ensure changes are made in a consistent manner. Belief revision theory deals with approaches to ensure consistency in the belief sets is maintained when beliefs need to be revised. This paper discusses the integration of belief revision theory to the ontology reengineering method as a means to ensure consistency in ontology revision
Specification and verification of multimedia synchronization scenarios using time‐Estelle

Multimedia synchronization scenario modelling can be classified into four categories: axes‐based model; synchronization point control; event‐based model; and interval‐based model.1 Existing formal languages do not support the specifications and verifications of all these four categories of synchronization scenarios. Estelle,2 an internationally standardised Formal Description Technique (FDT), unfortunately does not have enough expressive power to specify the time‐dependent behaviours of a multimedia system. To address this limitation, we have developed an extended Estelle, called Time‐Estelle3 to express multimedia QoS parameters, to identify various types of media objects, to describe temporal and spatial relationships, and to specify a range of synchronization scenarios. This paper discusses how Time‐Estelle can be used for specifying the four categories of synchronization scenarios, and describes how these scenarios can be verified for correctness, thus enabling any potential temporal inconsistencies to be identified. © 1998 John Wiley & Sons, Ltd.