Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Proteins Associated with Murine Cytomegalovirus Virions

ABSTRACT Proteins associated with the murine cytomegalovirus (MCMV) viral particle were identified by a combined approach of proteomic and genomic methods. Purified MCMV virions were dissociated by complete denaturation and subjected to either separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and in-gel digestion or treated directly by in-solution tryptic digestion. Peptides were separated by nanoflow liquid chromatography and analyzed by tandem mass spectrometry (LC-MS/MS). The MS/MS spectra obtained were searched against a database of MCMV open reading frames (ORFs) predicted to be protein coding by an MCMV-specific version of the gene prediction algorithm GeneMarkS. We identified 38 proteins from the capsid, tegument, glycoprotein, replication, and immunomodulatory protein families, as well as 20 genes of unknown function. Observed irregularities in coding potential suggested possible sequence errors in the 3′-proximal ends of m20 and M31. These errors were experimentally confirmed by sequencing analysis. The MS data further indicated the presence of peptides derived from the unannotated ORFs ORFc225441-226898 (m166.5) and ORF105932-106072. Immunoblot experiments confirmed expression of m166.5 during viral infection.
Isolation and characterization of broad spectrum bacteriophages lytic to Vibrio harveyi from shrimp farms of Kerala, India

Of 33 phages isolated from various shrimp farms in Kerala, India, six were segregated to have broad spectrum lytic efficiency towards 87 isolates of Vibrio harveyi with cross‐infecting potential to a few other important aquaculture pathogens. They were further tested on beneficial aquaculture micro‐organisms such as probiotics and nitrifying bacterial consortia and proved to be noninfective. Morphological characterization by transmission electron microscopy (TEM) and molecular characterization by RAPD and SDS‐PAGE proved them distinct and positioned under Caudovirales belonging to Myoviridae and Siphoviridae.
Area-Efficient Implementation of a Pulse-Mode Neuron Model

In this paper the digital implementation of a pulse-mode neuron based on the voting circuit is presented. As a result of the revision and analysis on the literature, an enhanced area-saving silicon implementation of the voting circuit is presented. The optimized neuron model is hardware efficient when mapped to field programmable gate array (FPGA) technology without compromising the desirable characteristics of a sigmoid-like activation function. The FPGA implementation of the neuron model shows that the hardware utilization is lower than previous implementations especially for wide neuron receptive fields in large neural networks favoring embeddable neural processing.
Buffer Management in a Packet Switch

Consider a single packet switch with a finite number of packet buffers shared between several output queues. An arriving packet is lost if no free buffer is available, as in the CIGALE network. It has been observed by simulation that if load increases too much, congestion may occur, i.e., throughput declines; it appears that the busiest link's queue tends to hog the buffers. Therefore, we will limit the queue length and when the queue is full the packet will be dropped. We expect that this restricted buffer sharing policy will avoid congestion under conditions of heavy load. A queueing model of a packet switch is defied and solved by local balance. Loss probability is evaluated, and values of queue limit to minimize loss are found; they depend on load. A Square-Root rule is introduced to make the choice of queue limit independent of load. For a sample switch, with three output links, a comparison is made between performance under different buffer sharing policies; it is shown that restricted sharing prevents congestion by making throughput an increasing function of load.
A Case of Acute Myopericarditis Associated With Mycoplasma Pneumoniae Infection in a Child

Mycoplasma pneumoniae (M. pneumoniae) primarily causes respiratory tract infections in persons aged 5-20 years. Tracheobronchitis and bronchopneumonia are the most commonly recognized clinical symptoms associated with M. pneumoniae infection. Complications of this infection are unusual; in particular, cardiac involvement is very rare and is generally accompanied by pneumonia. Nonrespiratory illness can therefore involve direct invasion by M. pneumoniae or autoimmune mechanisms, as suggested by the frequency of cross reaction between human antigens and M. pneumoniae. Herein, we report a case of severe acute myopericarditis with pneumonia caused by M. pneumoniae in a healthy young child who presented with fever, lethargy, oliguria and dyspnea. She survived with aggressive therapy including clarithromycin, intravenous immunoglobulin, inotropics, and diuretics. The patient was discharged on the 19th day after admission and followed up 1 month thereafter at the outpatient clinic without sequelae.
Effect of Exercise Program on the Rehabilitation of Patients with Cervical Spondylotic Myelopathy

Study Design: A clinical trial of 30 consecutive patients with cervical spondylotic myelopathy (CSM). Objectives: To evaluate the effect of directed physical exercise in patients with CSM and to measure severity of myelopathy before and after an exercise program. Setting: Christian Medical College and Hospital, India. Participants: Thirty patients with CSM (mean age-54.1 years) with Nuricks Grade 2 and 3. Background: Myelopathy of the spinal cord can be caused by degenerative process of the cervical vertebrae and it is the most common type of dysfunction of the spinal cord in adult population. CSM usually develops insidiously and the natural history is not well understood, there is debate over the indication for operative Vs non operative management. Method: Patients participated in a 6-week exercise program, consisting of active exercises to upper and lower extremities, scapulothoracic muscles, and gentle stretches, sub maximal isometric exercises of the deep neck flexors, relaxation and immobilization with a cervical collar. Main Outcome Measures: The mJOA (modified Japanese orthopaedic association score) and ASIA motor and sensory scoring. The results were processed by using Wilcoxon sign rank test. Results: After comparing the values at the beginning and end of the program a satisfactory neurological result (sensorimotor/motor and sensory) was obtained in all thirty patients. Conclusion: The exercise program had a positive impact for most of the variables of the study. Exercise intervention with neck immobilization may be a treatment of choice in early stages of CSM. Future randomized controlled studies would provide insight into the effectiveness and clinical relevance of this intervention.
GPUswap: Enabling Oversubscription of GPU Memory through Transparent Swapping

Over the last few years, GPUs have been finding their way into cloud computing platforms, allowing users to benefit from the performance of GPUs at low cost. However, a large portion of the cloud's cost advantage traditionally stems from oversubscription: Cloud providers rent out more resources to their customers than are actually available, expecting that the customers will not actually use all of the promised resources. For GPU memory, this oversubscription is difficult due to the lack of support for demand paging in current GPUs. Therefore, recent approaches to enabling oversubscription of GPU memory resort to software scheduling of GPU kernels -- which has been shown to induce significant runtime overhead in applications even if sufficient GPU memory is available -- to ensure that data is present on the GPU when referenced. In this paper, we present GPUswap, a novel approach to enabling oversubscription of GPU memory that does not rely on software scheduling of GPU kernels. GPUswap uses the GPU's ability to access system RAM directly to extend the GPU's own memory. To that end, GPUswap transparently relocates data from the GPU to system RAM in response to memory pressure. GPUswap ensures that all data is permanently accessible to the GPU and thus allows applications to submit commands to the GPU directly at any time, without the need for software scheduling. Experiments with our prototype implementation show that GPU applications can still execute even with only 20 MB of GPU memory available. In addition, while software scheduling suffers from permanent overhead even with sufficient GPU memory available, our approach executes GPU applications with native performance.
An Ink-Jet Printed Eddy Current Position Sensor

An eddy current sensor with an ink-jet printed flexible inductor has been designed and fabricated. The inductor has been designed by means of software developed in-house. It has been fabricated by ink-jet printing with silver ink on a flexible substrate. The inductor is a part of the oscillator circuit whose oscillating frequency is measured by a microcontroller. The sensor characteristics have been analyzed for two types of application. The first considered application is the displacement of a large conductive target in a direction perpendicular to the inductor plane. The second considered application is the displacement of a small steel ball parallel to the inductor plane. Inductance and oscillating frequency have been measured in order to completely characterize the sensor. The obtained results validate the use of the sensor for both considered applications, and are in good agreement with the simulations. The advantages of this type of sensor are low cost, the possibility for the inductor to match any curved surface and flexibility and precision of the inductor design.
Three-Dimensional Genome Organization and Function in Drosophila

Understanding how the metazoan genome is used during development and cell differentiation is one of the major challenges in the postgenomic era. Early studies in Drosophila suggested that three-dimensional (3D) chromosome organization plays important regulatory roles in this process and recent technological advances started to reveal connections at the molecular level. Here we will consider general features of the architectural organization of the Drosophila genome, providing historical perspective and insights from recent work. We will compare the linear and spatial segmentation of the fly genome and focus on the two key regulators of genome architecture: insulator components and Polycomb group proteins. With its unique set of genetic tools and a compact, well annotated genome, Drosophila is poised to remain a model system of choice for rapid progress in understanding principles of genome organization and to serve as a proving ground for development of 3D genome-engineering techniques.
Networking challenges and principles in diffusion-based molecular communication

Nanotechnology has allowed building nanomachines capable of performing simple tasks, such as sensing, data storage, and actuation. Nanonetworks, networks of nanomachines, will allow cooperation and information sharing among them, thereby greatly expanding the applications of nanotechnology in the biomedical, environmental, and industrial fields. One of the most promising paradigms to implement nanonetworks is diffusion-based molecular communication (DMC). In DMC, nanomachines transmit information by the emission of molecules that diffuse throughout the medium until they reach their destination. Most of the existing literature in DMC has focused on the analysis of its physical channel. In this work, the key differences of the physical channel of DMC with respect to the wireless electromagnetic channel are reviewed with the purpose of learning how they impact the design of networks using DMC. In particular, we find that the uniqueness of the physical channel of DMC will require revisiting most of the protocols and techniques developed for traditional wireless networks in order to adapt them to DMC networks. Furthermore, guidelines for the design of a novel network architecture for DMC networks, including fundamental aspects such as coding, medium access control, addressing, routing and synchronization, are provided.
Third-generation CD28/4-1BB chimeric antigen receptor T cells for chemotherapy relapsed or refractory acute lymphoblastic leukaemia: a non-randomised, open-label phase I trial protocol

Introduction There is no curative treatment available for patients with chemotherapy relapsed or refractory CD19+ B cells-derived acute lymphoblastic leukaemia (r/r B-ALL). Although CD19-targeting second-generation (2nd-G) chimeric antigen receptor (CAR)-modified T cells carrying CD28 or 4-1BB domains have demonstrated potency in patients with advanced B-ALL, these 2 signalling domains endow CAR-T cells with different and complementary functional properties. Preclinical results have shown that third-generation (3rd-G) CAR-T cells combining 4-1BB and CD28 signalling domains have superior activation and proliferation capacity compared with 2nd-G CAR-T cells carrying CD28 domain. The aim of the current study is therefore to investigate the safety and efficacy of 3rd-G CAR-T cells in adults with r/r B-ALL. Methods and analysis This study is a phase I clinical trial for patients with r/r B-ALL to test the safety and preliminary efficacy of 3rd-G CAR-T cells. Before receiving lymphodepleting conditioning regimen, the peripheral blood mononuclear cells from eligible patients will be leukapheresed, and the T cells will be purified, activated, transduced and expanded ex vivo. On day 6 in the protocol, a single dose of 1 million CAR-T cells per kg will be administrated intravenously. The phenotypes of infused CAR-T cells, copy number of CAR transgene and plasma cytokines will be assayed for 2 years after CAR-T infusion using flow cytometry, real-time quantitative PCR and cytometric bead array, respectively. Moreover, several predictive plasma cytokines including interferon-γ, interleukin (IL)-6, IL-8, Soluble Interleukin (sIL)-2R-α, solubleglycoprotein (sgp)130, sIL-6R, Monocyte chemoattractant protein (MCP1), Macrophage inflammatory protein (MIP1)-α, MIP1-β and Granulocyte-macrophage colony-stimulating factor (GM-CSF), which are highly associated with severe cytokine release syndrome (CRS), will be used to forecast CRS to allow doing earlier intervention, and CRS will be managed based on a revised CRS grading system. In addition, patients with grade 3 or 4 neurotoxicities or persistent B-cell aplasia will be treated with dexamethasone (10 mg intravenously every 6 hours) or IgG, respectively. Descriptive and analytical analyses will be performed. Ethics and dissemination Ethical approval for the study was granted on 10 July 2014 (YLJS-2014-7-10). Written informed consent will be taken from all participants. The results of the study will be reported, through peer-reviewed journals, conference presentations and an internal organisational report. Trial registration number NCT02186860.
Experiences with Protocol Description

This paper presents three conclusions about the description of protocols, based on extensive experience: (1) Informal methods are inadequate for widely used protocols. (2) Lightweight formal methods are easy and useful. (3) Informal natural language cannot be trusted, but natural-language paraphrases of formal language can be trusted for certain purposes. None of these conclusions will be new or surprising to participants in this workshop. The purpose of this paper is to provide new, specific, and relevant evidence for these conclusions, in the hopes that researchers can use this evidence to justify their methods and influence the thinking of others.
Natural Breeding Conditions and Artificial Increases in Testosterone Have Opposite Effects on the Brains of Adult Male Songbirds: A Meta-analysis

A meta-analysis of the literature shows that in adult male songbirds, brain mass, telencephalon volume and n. rotundus (a thalamic visual nucleus) volume increase from the nonbreeding season (low testosterone) to the breeding season (higher testosterone). These effects can at least partially be mimicked by photoperiod manipulations in captivity. In contrast, an artificial testosterone (T) titer increase by chronic implants yields the opposite results: telencephalon, n. rotundus, and n. pretectalis volumes are lower in T-treated animals than in controls. These results suggest that artificial testosterone manipulations do not necessarily mimic the effects of natural variations in hormone levels and that results from experiments using T implants to mimic natural hormonal effects should be interpreted with caution.
Development of Localization Method of Mobile Robot with RFID Technology and Stereo Vision

Many service robotic systems have been developed in order to improve care costs and the quality of the elderly people in the aging population [L. Nagi et al., 2002; Vogl, M.et al., 2005]. Our HumanAssistance Robotic System Project (HARSP) project has been developing a network distributed Human-Assistance Robotic System since 2000 [S. Jia et al., 2002, 2004, 2005]. We developed a hardware base, key technologies and implemented several Common Object Request Broker Architecture (CORBA) application servers to provide some basic services to aid the aged or disabled. Localization and obstacle recognition in indoor environments for mobile robots are main topics in order to navigate a mobile robot to perform a service task at facilities or at home. Many efforts have been made to solve this problem using sensors such as cameras and laser ranger scanners [A. Davision, 2003; W. Shen et al., 2005; H. Surmann et al., 2003]. In our previously developed system, the indoor Global Positioning System (iGPS) has been developed to localize a mobile robot [Y. Hada et al., 2004]. Recently, some research has used radio frequency identification (RFID) technology for indoor mobile robot localization as the information written in ID tags can be easily read out by an RFID reader. Kulyukin et al. used RFID to localize a mobile robot within a coarse position and decided the next movement based on the information written in ID tags [V. Kulyukin et al., 2004]. Kim et al. developed an RFID system including three orthogonal antenna, which determines the direction and distance of a tag by comparing the signal strength in each direction [M. Kim et al., 2004; W. Lin et al., 2004]. In this paper, a novel method is proposed for indoor environmental obstacle recognition and localization of a mobile robot by using an RFID system with a stereo camera as it is inexpensive, flexible and easy to use in the practical environment. As the information (such as type, colour, shape or size of the obstacles) can be written in ID tags in advance, the proposed method enables easy and quick obstacle recognition. The proposed method is also helpful to improve dynamic obstacle recognition (such as a chair or person) and occlusion problems that are very difficult to solve. This is because the communication between the ID reader and ID tags uses RF, and the information written in ID tags can be simultaneously read by an RFID reader. RF is not so stable, so determining the accurate position of obstacle objects is difficult. In order to localize the ID tags accurately, the Bayes rule was introduced to calculate the probability where the ID tag exists after the tag reader detects a tag. Then the stereo camera O pe n A cc es s D at ab as e w w w . ite ch on lin e. co m
Improved Soundness for QMA with Multiple Provers

We present three contributions to the understanding of QMA with multiple provers: 1) We give a tight soundness analysis of the protocol of [Blier and Tapp, ICQNM '09], yielding a soundness gap Omega(1/N^2). Our improvement is achieved without the use of an instance with a constant soundness gap (i.e., without using a PCP). 2) We give a tight soundness analysis of the protocol of [Chen and Drucker, ArXiV '10], thereby improving their result from a monolithic protocol where Theta(sqrt(N)) provers are needed in order to have any soundness gap, to a protocol with a smooth trade-off between the number of provers k and a soundness gap Omega(k^2/N), as long as k>=Omega(log N). (And, when k=Theta(sqrt(N)), we recover the original parameters of Chen and Drucker. ) 3) We make progress towards an open question of [Aaronson et al., ToC '09] about what kinds of NP-complete problems are amenable to sublinear multiple-prover QMA protocols, by observing that a large class of such examples can easily be derived from results already in the PCP literature - namely, at least the languages recognized by a non-deterministic RAMs in quasilinear time.
A new approach for effective malware detection in Android-based devices

Recently Android security has been considered by researchers since it is targeted by malware developers due to its wide usage for mobile phones, tablets, and other devices. Android security mainly relies on user decisions regarding to installing applications (apps) by approving their requested permissions. Therefore, systematic user assistance for making appropriate decisions can significantly improve the security of Android based devices. In this study, a new metric is introduced for effective risk computation of untrusted apps based on their required permissions. The proposed metric leverages both frequency of permission usage in malwares and rarity of them in normal apps. This metric can be directly used by the mobile owner to make better decisions or by Android markets to filter out suspicious apps for further analysis. Empirical evaluations show that the proposed metric has higher detection rates and is more effective than recently proposed risk score measurements.
PHP Aspis: Using Partial Taint Tracking to Protect Against Injection Attacks

Web applications are increasingly popular victims of security attacks. Injection attacks, such as Cross Site Scripting or SQL Injection, are a persistent problem. Even though developers are aware of them, the suggested best practices for protection are error prone: unless all user input is consistently filtered, any application may be vulnerable. When hosting web applications, administrators face a dilemma: they can only deploy applications that are trusted or they risk their system's security. To prevent injection vulnerabilities, we introduce PHP Aspis: a source code transformation tool that applies partial taint tracking at the language level. PHP Aspis augments values with taint meta-data to track their origin in order to detect injection vulnerabilities. To improve performance, PHP Aspis carries out taint propagation only in an application's most vulnerable parts: third-party plugins. We evaluate PHP Aspis with Wordpress, a popular open source weblog platform, and show that it prevents all code injection exploits that were found in Wordpress plugins in 2010.
THE LUPUS TRANSIT SURVEY FOR HOT JUPITERS: RESULTS AND LESSONS

We present the results of a deep, wide-field transit survey targeting “Hot Jupiter” planets in the Lupus region of the Galactic plane conducted over 53 nights concentrated in two epochs separated by a year. Using the Australian National University 40-inch telescope at Siding Spring Observatory (SSO), the survey covered a 0.66 deg2 region close to the Galactic plane (b = 11°) and monitored a total of 110,372 stars (15.0 ⩽ V ⩽ 22.0). Using difference imaging photometry, 16,134 light curves with a photometric precision of σ < 0.025 mag were obtained. These light curves were searched for transits, and four candidates were detected that displayed low-amplitude variability consistent with a transiting giant planet. Further investigations, including spectral typing and radial velocity measurements for some candidates, revealed that of the four, one is a true planetary companion (Lupus-TR-3), two are blended systems (Lupus-TR-1 and 4), and one is a binary (Lupus-TR-2). The results of this successful survey are instructive for optimizing the observational strategy and follow-up procedure for deep searches for transiting planets, including an upcoming survey using the SkyMapper telescope at SSO.