Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapidly Progressive Dementia Due to Mycobacterium neoaurum Meningoencephalitis

Dementia developed in a patient with widespread neurologic manifestations; she died within 5 months. Pathologic findings showed granulomatous inflammation with caseation necrosis, foreign body–type giant cells, and proliferative endarteritis with vascular occlusions. Broad-range polymerase chain reaction identified Mycobacterium neoaurum as the possible pathogen. Central nervous system infection by M. neoaurum may result in rapidly progressive dementia.
Infection-Associated Nuclear Degeneration in the Rice Blast Fungus Magnaporthe oryzae Requires Non-Selective Macro-Autophagy

Background The rice blast fungus Magnaporthe oryzae elaborates a specialized infection structure called an appressorium to breach the rice leaf surface and gain access to plant tissue. Appressorium development is controlled by cell cycle progression, and a single round of nuclear division occurs prior to appressorium formation. Mitosis is always followed by programmed cell death of the spore from which the appressorium develops. Nuclear degeneration in the spore is known to be essential for plant infection, but the precise mechanism by which it occurs is not known. Methodology/Principal Findings In yeast, nuclear breakdown requires a specific form of autophagy, known as piecemeal microautophagy of the nucleus (PMN), and we therefore investigated whether this process occurs in the rice blast fungus. Here, we report that M. oryzae possesses two conserved components of a putative PMN pathway, MoVac8 and MoTsc13, but that both are dispensable for nuclear breakdown during plant infection. MoVAC8 encodes a vacuolar membrane protein and MoTSC13 a peri-nuclear and peripheral ER protein. Conclusions/Significance We show that MoVAC8 is necessary for caffeine resistance, but dispensable for pathogenicity of M. oryzae, while MoTSC13 is involved in cell wall stress responses and is an important virulence determinant. By functional analysis of ΔMoatg1 and ΔMoatg4 mutants, we demonstrate that infection-associated nuclear degeneration in M. oryzae instead occurs by non-selective macroautophagy, which is necessary for rice blast disease.
Template constructors for reusable object initialization

Reuse of and abstraction over object initialization logic is not properly supported in mainstream object-oriented languages. This may result in significant amount of boilerplate code and proliferation of constructors in subclasses. It also makes it impossible for mixins to extend the initialization interface of classes they are applied to. We propose template constructors, which employ template parameters and pattern matching of them against signatures of superclass constructors to enable a one-to-many binding of super-calls. We demonstrate how template constructors solve the aforementioned problems. We present a formalization of the concept, a Java-based implementation, and use cases which exercise its strengths.
Genetic Evidence for O-Specific Antigen as Receptor of Pseudomonas aeruginosa Phage K8 and Its Genomic Analysis

Phage therapy requires the comprehensive understanding of the mechanisms underlying the host-phage interactions. In this work, to identify the genes related to Pseudomonas aeruginosa phage K8 receptor synthesis, 16 phage-resistant mutants were selected from a Tn5G transposon mutant library of strain PAK. The disrupted genetic loci were identified and they were related to O-specific antigen (OSA) synthesis, including gene wbpR, ssg, wbpV, wbpO, and Y880_RS05480, which encoded a putative O-antigen polymerase Wzy. The Lipopolysaccharide profile of the Y880_RS05480 mutant was analyzed and shown to lack the O-antigen. Therefore, the data from characterization of Y880_RS05480 by TMHMM and SDS-PAGE silver staining analysis suggest that this locus might encode Wzy. The complete phage K8 genome was characterized as 93879 bp in length and contained identical 1188-bp terminal direct repeats. Comparative genomic analysis showed that phage K8 was highly homologous to members of the genus PaP1-like phages. On the basis of our genetic findings, OSA of P. aeruginosa PAK is proven to be the receptor of phage K8. The highly conserved structural proteins among the genetic closely related phages suggest that they may recognize the same receptor.
Development of a Job Task Analysis Tool for Assessing the Work of Physicians in the Intensive Care Unit

This paper describes the development of a job task analysis tool for observing and recording physician tasks in the ICU. Real-time direct observations were conducted by outside observers using a computerized data collection tool developed to document the tasks performed by ICU physicians. The aim of the analysis was to quantify the tasks of the physicians, including measures of frequency, duration, and sequence for tasks. In this paper, we report on the development process, as well as the validity and reliability of the job task analysis tool. Initial results from our analyses provide support for the validity and reliability of the taxonomy developed for assessing work of ICU physicians.
Detecting Human-to-Human Transmission of Avian Influenza A (H5N1)

To the Editor: This letter is in response to a recently published article about statistical modeling to assess human-to-human transmission of avian influenza A (H5N1) viruses in 2 case clusters (1). Sporadic cases and clusters of human infection with highly pathogenic avian influenza A (H5N1) viruses have occurred after direct contact with diseased or dead poultry (2,3). Limited, nonsustained human-to-human transmission of avian influenza (H5N1) viruses is believed to have occurred in some clusters (4). Every human infection with a novel influenza A virus should be investigated, and suspected clusters should be investigated immediately to assess exposures and transmission patterns. Yang et al. applied a statistical model to evaluate publicly available data from 2 case clusters of human infection with avian influenza A (H5N1) viruses (1). These clusters were investigated in detail during 2006 by field epidemiologic investigation teams. Yang et al. suggest that statistical methods can prove or confirm human-to-human transmission, but this suggestion is misleading. Modeling approaches can suggest transmission modalities to account for case patterns, but determination of human-to-human transmission requires detailed field epidemiologic investigations in which human, animal, and environmental exposures as well as clinical and laboratory data are assessed and interpreted. Indication that a novel influenza A virus has acquired the ability to spread among humans could be reflected by a change in the epidemiology of clusters, such as increases in 1) size and frequency of clusters, 2) cases among nonrelated persons, and 3) clinically mild cases. This ability could also be reflected in accompanying changes in viruses isolated from case-patients. When facing emerging infectious disease threats such as those posed by highly pathogenic avian influenza A (H5N1) viruses, surveillance should rapidly detect human cases and case clusters and facilitate accurate identification of the agent. Field epidemiologic investigations, initiation of evidence-based clinical management of case-patients, and epidemiologic disease-control methods (including appropriate infection control measures) should be implemented immediately. Statistical modeling can provide useful and supportive insights but should not be viewed as an alternative to a detailed field epidemiologic investigation combined with laboratory data. Timely and comprehensive field investigations remain most critical to guiding decisions about containment efforts for pandemic influenza and other emerging infectious diseases (5).
Indirect Tag Search Mechanism for Instruction Window Energy Reduction

Instruction window is a key component which extracts instruction level parallelism (ILP) in modern out-of-order microprocessors. In order to exploit ILP for improving processor performance, instruction window size should be increased. However, it is difficult to increase the size, since instruction window is implemented by CAM whose power and delay are much large. This paper introduces a low power and scalable instruction window that replaces CAM with RAM. In this window, instructions are explicitly woken up. Evaluation results show that the proposed instruction window decreases performance by only 1.9% on average. Furthermore, dynamic energy is reduced by 67% on average and static power is reduced by 14%.
Motion planning for humanoid walking in a layered environment

Motion planning is one of the key capabilities for autonomous humanoid robots. Previous researches have focused on weight balancing, collision detection, and gait generation. Most planners either assume that the environment can be simplified to a 2D workspace or assume that the path is given. In this paper, we propose a motion planning system capable of generating both global and local motions for a humanoid robot in a layered or two and half dimensional environment. The planner can generate a gross motion that moves the humanoid vertically as well as horizontally to avoid obstacles in the environments. The gross motion is further realized by a local planner that determines the most efficient footsteps and locomotion over uneven terrain. If the local planner fails, the failure is feedback to the global planner to consider other alternative paths. The implemented humanoid planning system is an interactive tool that can compute collision-free motions for a humanoid robot in an online manner.
Fusion of spectrograph and LPC analysis for word recognition: A new fuzzy approach

Word Recognition is generally difficult and imprecise if we use just one method. In this article, data fusion is applied to word recognition by integration of two features extracted form human speech: speech spectrograph and time domain features (spectral coefficients). Four different methods are applied to fusion of these features, including weighted averaging, k-means clustering, fuzzy k-means and fuzzy vector quantization. Simulation results show that fusion of time domain and spectrograph features yields more precise and satisfactory results compared to other methods of word recognition that use just one speech feature for word recognition, like FVQ/MLP (fuzzy vector quantization combined with multi-layered perceptron neural network). The importance of this result is prominent if the signal to noise ratio is low.
A novel tag number estimation method for RFID systems

If the number of tags was gotten in a RFID system, the tags collisions and throughput could be greatly improved. In order to allocate slot number optimally and maximize the efficiency, a novel tag number estimation method is proposed. Utilizing the slot information of the current frame gets the likelihood function of the tag quantity estimation; the proposed algorithm adopted the optimal tag quantity in order to make the average risk minimum. The simulation results show that the estimation error of the proposed method is quite low and the total slots of identifying all tags are less, which proves the effectiveness of the proposed algorithm.
Proportional-Integral Observers for Discrete Time Systems

This paper applies the proportional-integral (PI) observer in connection with LQG and LQG/LTR design for discrete time systems. Both the prediction and the filtering versions of the PI observer are considered. We show that a PI observer makes it possible to obtain time recovery, i.e., exact recovery for t → ∞, under mild conditions. It is shown that LQG/LTR design is a special case of the cheap estimation problem. An analysis of the cheap estimation problem is derived. Based on these results, a systematic LTR design method for PI-observers, based on an extension of the LQG/LTR method for full-order, proportional (P) observers, is derived. Explicit expressions for the recovery error, when exact recovery is not achievable for all frequencies, are also given.
Mechanisms Underlying Dopaminergic Modulation of Striatal Firing and Learning

The inhibitory circuits of the striatum are known to be critical for motor function, yet their contributions to Parkinsonian motor deficits are not clear. Altered firing in the globus pallidus suggests that striatal medium spiny neurons (MSN) of the direct (D1 MSN) and indirect pathway (D2 MSN) are imbalanced during dopamine depletion. Both MSN classes receive inhibitory input from each other and from inhibitory interneurons within the striatum, specifically the fast-spiking interneurons (FSI). To investigate the role of inhibition in maintaining striatal balance, we developed a biologically-realistic striatal network model consisting of multi-compartmental neuron models: 500 D1 MSNs, 500 D2 MSNs and 49 FSIs. The D1 and D2 MSN models are differentiated based on published experiments of individual channel modulations by dopamine, with D2 MSNs being more excitable than D1 MSNs. Despite this difference in response to current injection, in the network D1 and D2 MSNs fire at similar frequencies in response to excitatory synaptic input. Simulations further reveal that inhibition from FSIs connected by gap junctions is critical to produce balanced firing. Though gap junctions produce only a small increase in synchronization between FSIs, removing these connections resulted in significant firing differences between D1 and D2 MSNs, and balanced firing
A Framework for Solving Surface Partial Differential Equations for Computer Graphics Applications

Abstract A novel framework for solving variational problems and partial dif-ferential equations for scalar and vector-valued data deﬁned on sur-faces is introduced in this paper. The key idea is to implicitly rep-resent the surface as the level set of a higher dimensional function,and solve the surface equations in a ﬁx ed Cartesian coordinate sys-tem using this new embedding function. This thereby eliminatesthe needforperformingcomplicatedandnot-accuratecomputationson triangulated surfaces, as it is commonly done in the graphicsand numerical analysis literature. We describe the framework andpresent examples in texture synthesis, ﬂo w ﬁeld visualization, aswell as image and vector ﬁeld regularization for data deﬁned on 3Dsurfaces.CR Categories: I.3. 6 [Computer Graphics]: Methodology andTechniques—; G.1. 8 [Numerical Analysis]: Partial DifferentialEquations—; I.4. 10 [Image Processing and Computer Vision]: Im-age representation—;Keywords: Partial differential equations, implicit surfaces, patternformation, natural phenomena, ﬂo w visualization, image and vectorﬁeld regularization.
Far-field pressure from submerged finite cylindrical shell using structural sensors

On the basis of the cylindrical shell equation of motion and the Kirchhoff-Helmholtz integral equation, the estimation of the far-field pressure radiated from the baffled finite cylindrical shell using structural sensors in different fluid is constructed, and the number of required structural sensors for accurately estimating far-field pressure in air and water are compared. The results show that due to the fluid-structure coupling effect introduced by water, the number of structural sensor along the axial direction in water should be greater than the modal index of the mode found in the structural response, similar to that in air; the number of structural sensor along the circumferential direction in water only should be greater than twice the dominant structure modes, but in air, it should be greater than twice the structure modes presented in the frequency of interest.
A An Infrastructure-Free Automated Guided Vehicle Based on Computer Vision

operating effectively in factories for decades. These vehicles have successfully used strategies of deliberately structuring the environment and adapting the process to the automation. The potential of computer vision technology to increase the intelligence and adaptability of AGVs is largely unexploited in contemporary commercially-available vehicles. We developed a virtually infrastructure-free AGV that uses four distinct vision systems to exploit naturallyoccurring visual cues instead of relying on infrastructure. When coupled with a highly capable trajectory generation algorithm, the system produces four visual servos that guide the vehicle continuously in several contexts. These contexts range from gross motion in the facility, to precision operations for lifting and mating parts racks and removing them from semi-trailers. To our knowledge, this is the first instance of an AGV that has operated successfully in a relevant environment for an extended period of time without relying on any infrastructure.
Remote Network Bottleneck Diagnosis Paper Number 171

Introduction: By their very nature, networks are highly distributed systems. This means that nodes and subnets in any one system may be great distances apart. Managing such a distributed system has many challenges, not the least of which is maintaining acceptable performance over channels owned and/ or managed by third parties. Troubleshooting and preventative maintenance on such highly distributed systems depends upon the cooperation of these independent entities. Unfortunately, cooperation may be spotty or non-existent if these vendors believe the requested information is proprietary or increases their exposure to attack. Vendors may even provide mis-information rather than admit a problem exists. In this environment, system administrators need to be able to independently and remotely acquire or verify data about paths outside of their control. A recently developed technique, Network Spectroscopy [1], appears to provide the means to characterize paths at a level of detail not possible any other way. We apply Network Spectroscopy to the problem of remotely identifying the cause of a network bottleneck. Preliminary results discussed below, and shown in Graph 1, are encouraging.
PON1 and Neurodevelopment in Children from the CHAMACOS Study Exposed to Organophosphate Pesticides in Utero

Background Paraoxonase 1 (PON1) detoxifies oxon derivatives of some organophosphate (OP) pesticides, and its genetic polymorphisms influence enzyme activity and quantity. We previously reported that maternal urinary concentrations of dialkyl phosphate (DAP) metabolites, a marker of OP pesticide exposure, were related to poorer mental development and maternally reported symptoms consistent with pervasive developmental disorder (PDD) in 2-year-olds participating in the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS) study. Objective We determined whether PON1 genotypes and enzyme measurements were associated with child neurobehavioral development and whether PON1 modified the association of in utero exposure to OPs (as assessed by maternal DAPs) and neurobehavior. Methods We measured DAP concentrations in maternal urine during pregnancy, PON1192 and PON1−108 genotypes in mothers and children, and arylesterase (ARYase) and paraoxonase (POase) in maternal, cord, and 2-year-olds’ blood. We assessed 353 2-year-olds on the Mental Development Index (MDI) and Psychomotor Development Index (PDI) of the Bayley Scales of Infant Development and queried their mothers on the Child Behavior Checklist to obtain a score for PDD. Results Children with the PON1−108T allele had poorer MDI scores and somewhat poorer PDI scores. Children were less likely to display PDD when they or their mothers had higher ARYase activity and when their mothers had higher POase activity. The association between DAPs and MDI scores was strongest in children with PON1−108T allele, but this and other interactions between DAPs and PON1 polymorphisms or enzymes were not significant. Conclusion PON1 was associated with child neurobehavioral development, but additional research is needed to confirm whether it modifies the relation with in utero OP exposure.
Research article ANTIOXIDANT POTENTIAL OF VARIOUS EXTRACTS OF STEM OF THUJA ORIENTALIS: IN VITRO STUDY

The antioxidant activity of different extracts of Thuja orientalis was evaluated by employing three in vitro experiments namely (1, 1-Diphenyl-2-picrylhydrazyl) (DPPH), reducing power and chelating power assays. The stem powder of the plant was extracted with different solvents by maceration method in order of decreasing polarity and then partitioned (Flow Chart 1). The differential activities of the different extracts could be correlated with their respective phenolic and flavanoid contents and compared with standards L-ascorbic acid and butylated hydroxytoluene (BHT). All the extracts exhibit a remarkable concentration dependant scavenging activity. Moreover, among the different extract, methanol extract exhibited good scavenging response of 74.3%, 59.51% and 0.997% in DPPH, chelating power and reducing power assay in decreasing order of solvent polarity at maximum concentration, respectively. Studies are in progress to isolate and identify the active principle components responsible for this activity.
Modeling visual attention on scenes

La modelisation computationelle de l'attention visuelle connait actuellement un essor considerable. Les premieres modeles, purement bases sur l'attention dite exogene, permettent de calculer une carte de saillance indiquant les zones d'interet visuel d'une image. Cependant, afin d'ameliorer cette prediction, il s'avere necessaire de prendre en compte des informations de plus haut niveaux relatives a l'attention endogene, c'est a dire des informations liees aux processus cognitifs. Afin de rendre compte de cette problematique, le present article decrit un certain nombre de modeles exogenes ainsi que des modeles integrant de la connaissance a priori. Les methodes d'evaluation des performances sont egalement decrites. Afin d'aller plus loin dans la modelisation et dans la comprehension des processus cognitifs, de nouvelles perspectives et direction d'etudes sont exposees.
Spatial metaphors and disorientation in hypertext browsing

Abstract The spatial metaphor can be used as a framework for explaining and designing tools that alleviate disorientation problems in hypertext systems. The approach based on this metaphor would involve developing tools analogous to navigational aids in physical environments and applying analogous concepts from research on human spatial processing and navigation in physical spaces. Research on hypertext browsing with respect to the spatial metaphor is reviewed and contrasted with the larger task context where users are trying to explore, learn, analyse, and summarize the contents of the hypertext space.
The study on dynamic population size improvements for classical particle swarm optimization

In this work we presented two dynamic population size improvements for the classical PSO. EP-PSO started with a small number of particles and increased the number of particles dynamically by iteratively duplicating the updated particles. DP-PSO started with a large number of particles then reduced the number by dropping the worst performing half iteratively. Both EP-PSO and DP-PSO reduced the execution time by 60% on average compared to the classical PSO. EP-PSO fared quite badly when convergence rate and convergence ability to the global optimum was considered. On the other hand, DP-PSO performed reasonably well compared to the classical PSO but at a much faster convergence and execution speed.