Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptation of Enterovirus 71 to Adult Interferon Deficient Mice

Non-polio enteroviruses, including enterovirus 71 (EV71), have caused severe and fatal cases of hand, foot and mouth disease (HFMD) in the Asia-Pacific region. The development of a vaccine or antiviral against these pathogens has been hampered by the lack of a reliable small animal model. In this study, a mouse adapted EV71 strain was produced by conducting serial passages through A129 (α/β interferon (IFN) receptor deficient) and AG129 (α/β, γ IFN receptor deficient) mice. A B2 sub genotype of EV71 was inoculated intraperitoneally (i.p.) into neonatal AG129 mice and brain-harvested virus was subsequently passaged through 12 and 15 day-old A129 mice. When tested in 10 week-old AG129 mice, this adapted strain produced 100% lethality with clinical signs including limb paralysis, eye irritation, loss of balance, and death. This virus caused only 17% mortality in same age A129 mice, confirming that in the absence of a functional IFN response, adult AG129 mice are susceptible to infection by adapted EV71 isolates. Subsequent studies in adult AG129 and young A129 mice with the adapted EV71 virus examined the efficacy of an inactivated EV71 candidate vaccine and determined the role of humoral immunity in protection. Passive transfer of rabbit immune sera raised against the EV71 vaccine provided protection in a dose dependent manner in 15 day-old A129 mice. Intramuscular injections (i.m.) in five week-old AG129 mice with the alum adjuvanted vaccine also provided protection against the mouse adapted homologous strain. No clinical signs of disease or mortality were observed in vaccinated animals, which received a prime-and-boost, whereas 71% of control animals were euthanized after exhibiting systemic clinical signs (P<0.05). The development of this animal model will facilitate studies on EV71 pathogenesis, antiviral testing, the evaluation of immunogenicity and efficacy of vaccine candidates, and has the potential to establish correlates of protection studies.
A real-time experimental prototype for enhancement of vision rehabilitation using auditory substitution

The rehabilitation of blindness, using noninvasive methods, requires sensory substitution. A theoretical frame for sensory substitution has been proposed (C. Veraart, 1989) which consists of a model of the deprived sensory system connected to an inverse model of the substitutive sensory system. This paper addresses the feasibility of this conceptual model in the case of auditory substitution, and its implementation as a rough model of the retina connected to an inverse linear model of the cochlea. The authors have developed an experimental prototype. It aims at allowing optimization of the sensory substitution process. This prototype is based on a personal computer which is connected to a miniature head-fixed video camera and to headphones. A visual scene is captured. Image processing achieves edge detection and graded resolution. Each picture element (pixel) of the processed image is assigned a sinusoidal tone; weighted summation of these sinewaves builds up a complex auditory signal which is transduced by the headphones. On-line selection of various parameters and real-time functioning of the device allow optimization of parameters during psychophysical experimentations. Assessment of this implementation has been initiated, and has so far demonstrated prototype usefulness for pattern recognition. An integrated circuit of this system is to be developed.
Use of Commercial Freezers to Control Cowpea Weevil, Callosobruchus maculatus (Coleoptera: Bruchidae), in Organic Garbanzo Beans

Abstract One California processor of organic garbanzo beans (Cicer arietinum L.), unable to use chemical fumigants, relies on 30-d storage at −18°C to disinfest product of the cowpea weevil, Callosobruchus maculatus (F). To determine whether the storage period may be shortened, the most cold-tolerant life stage of the cowpea weevil was identified. Laboratory studies showed that the egg stage was most tolerant to −18°C and that adults were most susceptible. To examine the efficacy of cold storage disinfestation, bags of black-eyed peas, Vigna unguiculata (L.) Walp. , infested with cowpea weevil eggs were buried within garbanzo bean bins placed in a commercial cold storage facility kept at approximately −18°C and removed after 7, 14, and 21 d. Survival was highest in eggs located at the center of the bins and coincided with the slowest cooling rate. Although temperatures within the bins did not reach −18°C until after 14–19 d, egg mortality was estimated to be >98% after just 7 d of exposure. Complete mortality of eggs occurred after 14 d of cold storage. A 2-wk treatment regimen may be sufficient for control of cowpea weevil in organic legumes.
Event Extraction from Trimmed Dependency Graphs

We describe the approach to event extraction which the JulieLab Team from FSU Jena (Germany) pursued to solve Task 1 in the "BioNLP'09 Shared Task on Event Extraction". We incorporate manually curated dictionaries and machine learning methodologies to sort out associated event triggers and arguments on trimmed dependency graph structures. Trimming combines pruning irrelevant lexical material from a dependency graph and decorating particularly relevant lexical material from that graph with more abstract conceptual class information. Given that methodological framework, the JulieLab Team scored on 2nd rank among 24 competing teams, with 45.8% precision, 47.5% recall and 46.7% F1-score on all 3,182 events.
Large-Scale Variability-Aware Type Checking and Dataflow Analysis

A software product line is a family of similar software products that share a common set of assets. The advent of proper variability management and generator technology enables end-users to derive individual products solely based on a selection of desired features. This gives rise to a huge configuration space of possible products. But the high degree of variability comes at a cost: classic analysis methods do not scale any more; there are simply too many potential products to analyze. Hence, researchers have begun to develop variabilityaware analyses, which exploit the similarities of the products of a product line to reduce analysis effort. However, while being promising, variability-aware analyses have not been applied to real-world product lines so far. We close this gap by developing and applying two full-fledged analyses to two real-world, largescale systems: the Busybox tool suite and the Linux kernel. We report on our experience with making variability-aware analysis ready for the real world, and with applying it to large-scale product lines. A key result is that variability-aware analysis can outperform even very limited sampling heuristics with respect to analysis time.
Peroxynitrite and Nitric Oxide Donors Induce Neuronal Apoptosis by Eliciting Autocrine Excitotoxicity

Endogenous generation of nitric oxide and its congeners, including peroxynitrite (ONOO‐), has been implicated in the mechanism of neuron loss in neurodegenerative diseases. Accordingly, nitric oxide donors and ONOO‐can elicit both apoptosis and necrosis in neuron cultures. Here we show that nitric oxide donors and ONOO‐ are each able to trigger apoptosis of mouse cerebellar granule cells by an excitotoxic mechanism requiring exocytosis and NMDA receptor‐mediated intracellular Ca2+ overload. This conclusion is supported by the following findings. Apoptosis was induced by various nitric oxide donors or by direct addition of ONOO‐ to differentiated cerebellar granule cell cultures that were sensitive to NMDA toxicity, but not in cerebellar granule cells that did not display NMDA‐induced cell death (i.e. early days in culture) or in various glial cell populations. Donors of ONOO‐ or nitric oxide stimulated a sustained increase in intracellular Ca2+, which was prevented by inhibitors of NMDA receptors, such as MK‐801 and 5‐phospho‐aminovaleric acid, or by dampening neuronal electrical activity with high concentrations of extracellular Mg2+. Moreover, these treatments and the exposure of cerebellar granule cells in nominally Ca2+‐free media prevented apoptotic cell death. Both the intracellular Ca2+ increase and apoptosis elicited by ONOO‐ or the nitric oxide donors were prevented by blocking exocytosis with tetanus toxin or botulinum neurotoxin C.
Rational points on curves

This is an extended version of an invited lecture I gave at the Journees Arithmetiques in St. Etienne in July 2009. We discuss the state of the art regarding the problem of finding the set of rational points on a (smooth projective) geometrically integral curve C over Q. The focus is on practical aspects of this problem in the case that the genus of C is at least 2, and therefore the set of rational points is finite.
Up, down and around the stack: ISP characterization from network intensive applications

Broadband characterization has recently attracted much attention from the research community and the general public. Given this interest and the important business and policy implications of residential Internet service characterization, recent years have brought a variety of approaches to profiling Internet services, ranging from Web-based platforms to dedicated infrastructure inside home networks. We have previously argued that network-intensive applications provide an almost ideal vantage point for broadband service characterization at sufficient scale, nearly continuously and from end users. While we have shown that the approach is indeed effective at characterization and can enable performance comparisons between service providers and geographic regions, a key unanswered question is how well the performance characteristics captured by these network-intensive applications can predict the overall user experience with other applications. In this paper, using BitTorrent as an example network-intensive application, we present initial results that demonstrate how to obtain estimates of bandwidth and latency of a network connection by leveraging passive monitoring and limited active measurements from network intensive applications. We then analyze user experienced web performance under a variety of network conditions and show how estimated metrics from this network intensive application can serve as good web performance predictors.
The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web

Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google. com/p/semanticchemistry/ (license: CC-BY-SA).
Coronary pressure-flow relation in left ventricular hypertrophy. Importance of changes in back pressure versus changes in minimum resistance.

Perfusion abnormalities in the pressure-overloaded hypertrophied left ventricle could result from an increase in minimum coronary resistance or an increase in effective back pressure due to increased extravascular compressive forces. Since the pressure-flow relation of the maximally vasodilated coronary bed allows dissociation of minimum resistance (inverse slope [1/alpha PF]) and back pressure (pressure at zero flow [Pf = 0]), the present study was undertaken to examine the coronary pressure-flow relation in left ventricular hypertrophy (LVH). Ascending aortic banding in eight dogs at 6-8 weeks of age (LVH group) increased the left ventricular to body weight ratio to 8.7 +/- 0.6 g/kg as compared with 4.8 +/- 0.2 g/kg in nine normal dogs (p < 0.05). Maximum coronary vasodilation was produced by infusion of adenosine (1 mg/kg per minute i.v.). The slope of the coronary pressure-flow relation (alpha PF) was 5.8 +/- 0.5 10(-2) (ml/min per gram)/mm Hg in the LVH group and 9.3 +/- 0.6 10(-2) (ml/min per gram)/mm Hg in the normal group (p < 0.05). alpha PF was significantly correlated with the left ventricular to body weight ratio but not with coronary pressure, suggesting that the degree of hypertrophy and not exposure to high coronary pressure was responsible for the observed decrease in alpha PF. Pf = 0 was 24.1 +/- 2.6 mm Hg in the LVH group and 11.7 +/- 1.2 mm Hg in the normal group (p < 0.05). (ABSTRACT TRUNCATED AT 250 WORDS)
Towards Scalable Algorithm for Closed Itemset Mining in High-Dimensional Data

Mining frequent itemsets from large dataset has a major drawback in which the explosive number of itemsets requires additional mining process which might filter the interesting ones. Therefore, as the solution, the concept of closed frequent itemset was introduced that is lossless and condensed representation of all the frequent itemsets and their corresponding supports. Unfortunately, many algorithms are not memory-efficient since it requires the storage of closed itemsets in main memory for duplication checks. This paper presents BFF, a scalable algorithm for discovering closed frequent itemsets from high-dimensional data. Unlike many well-known algorithms, BFF traverses the search tree in breadth-first manner resulted to a minimum use of memory and less running time. The tests conducted on a number of microarray datasets show that the performance of this algorithm improved significantly as the support threshold decreases which is crucial in generating more interesting rules.
Design Space Exploration of Z-Axis CMOS-MEMS Accelerometers

The dimensions of a CMOS-MEMS Z-axis accelerometer are varied in a parametric study that pursues to explore the design space of the spring stiffness that can be achieved by this device. The results of the spring stiffness obtained via simulation will be compared to the one obtained via analytical results, to evaluate the accuracy obtained by using the analytical formulas.
Invited review Multicell spheroids as a model for cell kinetic studies

Abstract. Cells growing in tissue culture as three‐dimensional, multicellular aggregates called ‘spheroids’ typically show a decreasing growth fraction and development of quiescent subpopulations as the spheroids enlarge. Kinetic studies in a number of spheroid systems have indicated that the primary reason for the tumour‐like growth is a progressive decrease in growth fraction, with only a modest elongation of cell cycle time in larger spheroids. In this paper, the cellular growth kinetics for spheroids of V79 Chinese hamster lung cells are reviewed, and the regrowth kinetics of cells resuming growth after recovery from quiescent regions of the spheroids are described. Further, the role of regrowth/repopulation in determining the spheroid response to anti‐tumour cytotoxics is explored, with particular emphasis on treatment with cisplatin and etoposide. By separating the effects of cytotoxicity and regrowth in the overall spheroid response to anti‐neoplastic drugs, it is suggested that ‘drug resistance’ in tumours can be a kinetic as well as a genetic problem.
Creating High-quality Paths for Motion Planning

Many algorithms have been proposed that create a path for a robot in an environment with obstacles. Most methods are aimed at finding a solution. However, for many applications, the path must be of a good quality as well. That is, a path should be short and should keep some amount of minimum clearance to the obstacles. Traveling along such a path reduces the chances of collisions due to the difficulty of measuring and controlling the precise position of the robot. This paper reports a new technique, called Partial shortcut, which decreases the path length. While current methods have difficulties in removing all redundant motions, the technique efficiently removes these motions by interpolating one degree of freedom at a time. Two algorithms are also studied that increase the clearance along paths. The first one is fast but can only deal with rigid, translating bodies. The second algorithm is slower but can handle a broader range of robots, including three-dimensional free-flying and articulated robots, which may reside in arbitrary high-dimensional configuration spaces. A big advantage of these algorithms is that clearance along paths can now be increased efficiently without using complex data structures and algorithms. Finally, we combine the two criteria and show that high-quality paths can be obtained for a broad range of robots.
2-[(E)-4-(Diethylamino)styryl]-1-methylpyridinium iodide

In the title compound, C18H23N2 +·I−, the cation exists in the E configuration with respect to the ethenyl C=C bond. The pyridinium and benzene rings are nearly coplanar, making a dihedral angle of 4.63 (7)°. The two ethyl groups of the diethylamino substituent point in opposite directions with respect to the benzene plane. In the crystal, the cation and the iodide anion are linked by a weak C—H⋯I interaction. The cations are stacked in an anti-parallel manner along the a axis by a π–π interaction with a centroid–centroid distance of 3.5262 (9) Å. The crystal structure is further stabilized by C—H⋯π interactions.
Sky Writer: Sketch-Based Collaboration for UAV Pilots and Mission Specialists

Sky Writer is a collaborative communication medium that augments the traditional display of a UAV pilot and allows other stakeholders to communicate their needs and intentions to the pilot. UAV pilots engaging in time-critical missions, such as urban disaster responses, often must allocate most of their cognitive capacity towards flight tasks, making communication and collaboration with other stakeholders difficult or dangerous. Sky Writer addresses the needs of stakeholders while requiring minimal cognitive effort from the UAV pilot. The application presents stakeholders with an interface that provides contextual flight information and a live video stream of the flight. Stakeholders are able to sketch directly on the video stream or use a spotlight indicator that is mirrored across all displays in the system, including the pilot's display. The application can be used in any modern web browser and works with traditional and touch devices. Concept experimentation performed at Disaster City with two pilots indicated that the spotlight feature was particularly useful while the UAV was in motion, and the sketching features were most useful while the UAV was stationary. The system will be tested with professional responders soon to determine its efficacy in a simulated response, and to inform the ongoing design process.
The LIM-homeobox transcription factor Isl1 plays crucial roles in the development of multiple arcuate nucleus neurons

Neurons in the hypothalamic arcuate nucleus relay and translate important cues from the periphery into the central nervous system. However, the gene regulatory program directing their development remains poorly understood. Here, we report that the LIM-homeodomain transcription factor Isl1 is expressed in several subpopulations of developing arcuate neurons and plays crucial roles in their fate specification. Mice with conditional deletion of the Isl1 gene in developing hypothalamus display severe deficits in both feeding and linear growth. Consistent with these results, their arcuate nucleus fails to express key fate markers of Isl1-expressing neurons that regulate feeding and growth. These include the orexigenic neuropeptides AgRP and NPY for specifying AgRP-neurons, the anorexigenic neuropeptide αMSH for POMC-neurons, and two growth-stimulatory peptides, growth hormone-releasing hormone (GHRH) for GHRH-neurons and somatostatin (Sst) for Sst-neurons. Finally, we show that Isl1 directly enhances the expression of AgRP by cooperating with the key orexigenic transcription factors glucocorticoid receptor and brain-specific homeobox factor. Our results identify Isl1 as a crucial transcription factor that plays essential roles in the gene regulatory program directing development of multiple arcuate neuronal subpopulations. Summary: During hypothalamus development in mice, Isl1 is expressed in several subpopulations of developing arcuate neurons and plays crucial roles in specifying their cell fate.
Development and Validation

and ruptures usually occur in middle-aged men during sporting activity. The incidence of these ruptures has increased during the past few decades. The treatment is still controversial, and the main alternatives are either surgical or nonsurgical. During the past decade, surgical treatment has been regarded as the first choice in many hospitals. In addition, it has become common to add early functional mobilization, such as using an adjustable brace, after surgical treatment. Studies on treatment with only early functional mobilization, using a mobile cast without any preceding surgery, also show promising results. It has been shown that the incidence of rerupture is higher in nonsurgically treated patients, but the risk varies between different studies. Surgically treated patients have, The Achilles Tendon Total Rupture Score (ATRS)
Learning Sampling Functions for Efficient Object Detection

—Object detection is an important task in computer vision and learning systems. Multistage particle windows (MPW), proposed by Gualdi et al . , is an algorithm of fast and accurate object detection. By sampling particle windows from a proposal distribution (PD), MPW avoids exhaustively scanning the image. Despite its success, it is unknown how to determine the number of stages and the number of particle windows in each stage. Moreover, it has to generate too many particle windows in the initialization step and it redraws unnecessary too many particle windows around object-like regions. In this paper, we attempt to solve the problems of MPW. An important fact we used is that there is a large probability for a randomly generated particle window not to contain the object because the object is a sparse event relevant to the huge number of candidate windows. Therefore, we design the proposal distribution so as to efﬁciently reject the huge number of non-object windows. Speciﬁcally, we propose the concepts of rejection, acceptance, and ambiguity windows and regions. This contrasts to MPW which utilizes only on region of support. The PD of MPW is acceptance-oriented whereas the PD of our method (called iPW) is rejection-oriented. Experimental results on human and face detection demonstrate the efﬁciency and effectiveness of the iPW algorithm. The source code is publicly accessible.