Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial Dynamics of Human-Origin H1 Influenza A Virus in North American Swine

The emergence and rapid global spread of the swine-origin H1N1/09 pandemic influenza A virus in humans underscores the importance of swine populations as reservoirs for genetically diverse influenza viruses with the potential to infect humans. However, despite their significance for animal and human health, relatively little is known about the phylogeography of swine influenza viruses in the United States. This study utilizes an expansive data set of hemagglutinin (HA1) sequences (n = 1516) from swine influenza viruses collected in North America during the period 2003-2010. With these data we investigate the spatial dissemination of a novel influenza virus of the H1 subtype that was introduced into the North American swine population via two separate human-to-swine transmission events around 2003. Bayesian phylogeographic analysis reveals that the spatial dissemination of this influenza virus in the US swine population follows long-distance swine movements from the Southern US to the Midwest, a corn-rich commercial center that imports millions of swine annually. Hence, multiple genetically diverse influenza viruses are introduced and co-circulate in the Midwest, providing the opportunity for genomic reassortment. Overall, the Midwest serves primarily as an ecological sink for swine influenza in the US, with sources of virus genetic diversity instead located in the Southeast (mainly North Carolina) and South-central (mainly Oklahoma) regions. Understanding the importance of long-distance pig transportation in the evolution and spatial dissemination of the influenza virus in swine may inform future strategies for the surveillance and control of influenza, and perhaps other swine pathogens.
CoCo (Context vs. Content): Behavior-Inspired Social Media Recommendation for Mobile Apps

Exponential growth of media generated in online social networks demands effective recommendation to improve the efficiency of media access especially for mobile users. In particular, content, objective quality or general popularity are less decisive for the prediction of user-click behavior than friendship-conditioned patterns. Existing recommender systems however, rarely consider user behavior in real-life. By means of a large-scale data-driven analysis over real-life mobile Twitter traces from 15,144 users over a period of one year, we reveal the importance of social closeness related behavior features. This paper proposes CoCo, the first-ever behavior-inspired mobile social media recommender system to improve the media access experience. CoCo exploits representative behavior features via a latent bias based machine learning approach. Our comprehensive evaluation through trace-driven emulations on the Android app exposes a superior accuracy of 72.3%, with a small additional daily energy consumption of 1.3% and a monthly data overhead of 9.1MB.
Direct and Indirect Laser Sintering of Metals

Manufacturing functional prototypes and tools using conventional methods usually is a time consuming procedure with multiple steps. The pressure to get products to market faster has resulted in the creation of several Rapid Prototyping (RP) techniques. However, potentially one of the most important areas of Rapid Manufacturing (RM) technology lies in the field of Rapid Tooling (RT). Layer manufacture technologies are gaining increasing attention in the manufacturing sector for the production of polymer mould tooling. Layer manufacture techniques can be used in this potential manufacturing area to produce tooling either indirectly or directly, and powder metal based layer manufacture systems are considered an effective way of producing rapid tooling. Selective Laser Sintering (SLS) is one of available layer manufacture technologies. SLS is a sintering process in which shaped parts are built up layer by layer from bottom to top of powder material. A laser beam scans the powder layer, filling in the outline of each layers CAD-image, and heats the selected powder to fuse it. This work reports the results of an experimental study examining the potential of layer manufacturing processes to deliver production metal tooling for manufacture of polymer components. Characterisation of indirect selective laser sintering and direct selective laser sintering to provide the metal tooling is reported. Three main areas were addressed during the study: mechanical strength, accuracy, and build rate. Overviews of the results from the studies are presented. Two materials (RapidSteel 2.0 and special grade of highspeed steel) and also two generations of SLS machines Sinterstation 2000 and sinterstation research machine, which was constructed in Leeds) were used during this work.
Second-Generation Hand-Held Force Magnifier for Surgical Instruments

We have developed a novel and relatively simple method for magnifying forces perceived by an operator using a surgical tool. A sensor measures force between the tip of a tool and its handle, and a proportionally greater force is created by an actuator between the handle and a brace attached to the operator’s hand, providing an enhanced perception of forces at the tip of the tool. Magnifying forces in this manner may provide an improved ability to perform delicate surgical procedures. The device is completely hand-held and can thus be easily manipulated to a wide variety of locations and orientations. We have previously developed a prototype capable of amplifying forces only in the push direction, and which had a number of other limiting factors. We now present a second-generation device, capable of both push and pull, and describe some of the engineering concerns in its design and our future directions.
A novel pool of protein phosphatase 2A is associated with microtubules and is regulated during the cell cycle

Immunofluorescence microscopy revealed the presence of protein phosphatase 2A (PP2A) on microtubules in neuronal and nonneuronal cells. Interphase and mitotic spindle microtubules, as well as centrosomes, were all labeled with antibodies against individual PP2A subunits, showing that the AB alpha C holoenzyme is associated with microtubules. Biochemical analysis showed that PP2A could be reversibly bound to microtubules in vitro and that approximately 75% of the PP2A in cytosolic extracts could interact with microtubules. The activity of microtubule-associated PP2A was differentially regulated during the cell cycle. Enzymatic activity was high during S phase and intermediate during G1, while the activity in G2 and M was 20-fold lower than during S phase. The amount of microtubule-bound PP2A remained constant throughout the cell cycle, implying that cell cycle regulation of its enzymatic activity involves factors other than microtubules. These results raise the possibility that PP2A regulates cell cycle-dependent microtubule functions, such as karyokinesis and membrane transport.
Reentry Thermal Analysis of a Generic Crew Exploration Vehicle Structure

Comparative studies were performed on the heat-shielding characteristics of honeycomb-core sandwich panels fabricated with different materials for possible use as wall panels for the proposed crew exploration vehicle. Graphite/epoxy sandwich panel was found to outperform aluminum sandwich panel under the same geometry due to superior heat-shielding qualities and lower material density. Also, representative reentry heat-transfer analysis was performed on the windward wall structures of a generic crew exploration vehicle. The Apollo low Earth orbit reentry trajectory was used to calculate the reentry heating rates. The generic crew exploration vehicle has a graphite/epoxy composite honeycomb sandwich exterior wall and an aluminum honeycomb sandwich interior wall, and is protected with the Apollo thermal protection system ablative material. In the thermal analysis computer program used, the TPS ablation effect was not yet included; however, the results from the nonablation heat-transfer analyses were used to develop a "virtual ablation" method to estimate the ablation heat loads and the thermal protection system recession thicknesses. Depending on the severity of the heating-rate time history, the virtual ablation period was found to last for 87 to 107 seconds and the ablation heat load was estimated to be in the range of 86 to 88 percent of the total heat load for the ablation time period. The thermal protection system recession thickness was estimated to be in the range of 0.08 to 0.11 inches. For the crew exploration vehicle zero-tilt and 18-degree-tilt stagnation points, thermal protection system thicknesses of h = {0.717, 0.733} inches were found to be adequate to keep the substructural composite sandwich temperature below the limit of 300 F.
Modelling and filtering almost periodic signals by time-varying Fourier series with application to near-infrared spectroscopy

We propose a new approach to modelling almost periodic signals and to model-based estimation of such signals from noisy observations. The signal model is based on Fourier series where both the coefficients and the fundamental frequency can continuously change over time. This signal model can be represented by a factor graph which we use to derive message passing algorithms to estimate the time-dependent model parameters from the observed samples. Our motivating application is near-infrared spectroscopy. In this application the observed signal is a superposition of several physiological signals of clinical interest (including, in particular, the arterial pulsation), and we wish to decompose the observed signal into these components. Most of these component signals are almost periodic. We show that the proposed algorithm can be used to extract the arterial pulsation from the measured signal.
Functional conservation despite structural divergence in ligand-responsive RNA switches

Significance RNA viruses, including the human pathogenic hepatitis C virus (HCV), use a structured untranslated region of their genome to hijack host cell ribosomes for the synthesis of viral proteins. These genome regions are termed internal ribosome entry site (IRES) elements and are encoded by distinct sequences in different viruses but share common functional RNA motifs. This study shows that viral IRES elements contain conformationally flexible RNA switches, whose state can be captured by the binding of a common ligand. Conformational switching plays a role in the function of the IRES elements. These new RNA switches are smaller than previously discovered “riboswitches” and may be the simplest form of ligand-responsive mechanical modules in nucleic acids. An internal ribosome entry site (IRES) initiates protein synthesis in RNA viruses, including the hepatitis C virus (HCV). We have discovered ligand-responsive conformational switches in viral IRES elements. Modular RNA motifs of greatly distinct sequence and local secondary structure have been found to serve as functionally conserved switches involved in viral IRES-driven translation and may be captured by identical cognate ligands. The RNA motifs described here constitute a new paradigm for ligand-captured switches that differ from metabolite-sensing riboswitches with regard to their small size, as well as the intrinsic stability and structural definition of the constitutive conformational states. These viral RNA modules represent the simplest form of ligand-responsive mechanical switches in nucleic acids.
A microstructure for in situ determination of residual strain

This work presents a new strain sensor with a compact structure. The strain sensor comprises of a pair of cantilever beams with different lengths connected by a short tip. The residual strain causes two beams to deflect each other, thereby magnifying the deflection, which is measured by the tip. The displacement is independent of both Young's modulus and the film's thickness. An analytical model is derived to relate the measured displacement to residual strain. Finite-element modeling is also used to analyze the model. This work also thoroughly considers other factors that influence the designs and the implicit limitations of the strain sensors. Experimental results with an SiO/sub 2/ film as well as undoped LPCVD polysilicon films are used to demonstrate the effectiveness of the proposed structure.
Generation of Anergic and Potentially Immunoregulatory CD25+CD4 T Cells In Vivo After Induction of Peripheral Tolerance with Intravenous or Oral Antigen1

Immunoregulatory CD25+CD4 T cells are thought to arise from the thymus as a distinct lineage of CD4 T cells specific for self Ags. We used the DO11.10 TCR transgenic adoptive transfer system to show that cells of similar phenotype may also arise in the course of peripheral tolerance induction. Such cells emerged within 1 wk following Ag exposure and correlated negatively with the number of initial cell divisions. Limiting i.v. Ag dose or using an oral tolerance protocol yielded the greatest numbers of Ag-specific CD25+CD4 T cells. In contrast, immunogenic Ag exposure in the presence of an adjuvant did not lead to emergence of CD25+CD4 T cells. The profound anergic phenotype of these cells and their potential immunoregulatory properties make them an especially desirable population to induce in the course of immunotherapy in numerous clinical settings. This experimental system may be useful in future studies designed to optimize immunologic tolerance induction.
Comparative Quality Estimation: Automatic Sentence-Level Ranking of Multiple Machine Translation Outputs

A machine learning mechanism is learned from human annotations in order to perform preference ranking. The mechanism operates on a sentence level and ranks the alternative machine translations of each source sentence. Rankings are decomposed into pairwise comparisons so that binary classifiers can be trained using black-box features of automatic linguistic analysis. In order to re-compose the pairwise decisions of the classifier, this work introduces weighing the decisions with their classification probabilities, which eliminates ranking ties and increases the coefficient of the correlation with the human rankings up to 80%. The authors also demonstrate several configurations of successful automatic ranking models; the best configuration achieves acceptable correlation with human judgments (tau=0.30), which is higher than that of state-of-the-art reference-aware automatic MT evaluation metrics such as METEOR and Levenshtein distance.
The Thy-1-bearing cell of murine epidermis. A distinctive leukocyte perhaps related to natural killer cells

Bone marrow-derived leukocytes of murine epidermis can express two phenotypes: typical Langerhans cells, which are Ia+ and Thy-1-, and a recently discovered second population that is Thy-1+ and Ia-. To verify that these phenotypes are expressed by two different cell types, and to help understand their lineage and function, we have studied morphology and reactivity with a large panel of antibodies. Dual antibody immunofluorescence combined with electron microscopy showed that Thy-1+ and Ia+ cells were each distributed in a regular fashion and formed adjacent dendritic systems in or close to the basal layer. Double- labeling studies with anti-Ia and a second monoclonal antibody revealed that all Langerhans cells expressed F4/80 (macrophage), Mac-1 (C3bi receptor), and 2.4G2 (Fc receptor), as well as the thymus leukemia (TL) and heat-stable (M1.69/16) antigens. A large fraction expressed S100 and all exhibited membrane ATPase and nonspecific esterase. In contrast, Thy-1+ cells lacked all these features of Langerhans cells, except that a minority were strongly reactive with 2.4G2. Thy-1+ cells also lacked differentiation antigens of most other types of leukocytes, except they were rich in asialo GM1. By electron microscopy, Thy-1+ cells had cytoplasmic granules that were similar in structure and in their aryl sulfatase content to those previously described in natural killer cells. The granules were enlarged in beige mice, suggesting a lysosomal origin, and were present in mast cell-deficient W/Wv mice, indicating no relation to mast cells. We conclude that Thy-1+ epidermal cells are thoroughly distinct from Langerhans cells. On the basis of morphology and phenotype, they may represent a type of tissue natural killer cell. Thy-1+ natural killer cells are now being identified in several nonlymphoid sites, such as gut epithelium and the livers of mice given adjuvants. If Thy-1+ epidermal cells prove to be natural killer cells, it is noteworthy that they represent a resident population regularly distributed in the basal layer of all mouse strains. The notion that Thy-1+ epidermal cells are immature natural killer cells is intriguing in light of recent evidence that Ia+ Langerhans cells are also immature with respect to accessory cell function. The epidermis may not have the functional capacities of a lymphoid organ, but it could contribute immature cells important for both natural and acquired resistance.
Characterization of Diverse Gate Oxides on 4H-SiC 3D Trench-MOS Structures

This study focuses on the characterization of silicon dioxide (SiO2) layers, either thermally grown or deposited on trenched 100 mm 4H-silicon carbide (SiC) wafers. We evaluate the electrical properties of silicon dioxide as a gate oxide (GOX) for 3D metal oxide semiconductor (MOS) devices, such as Trench-MOSFETs. Interface state densities (DIT) of 1*1011 cm-2 eV-1 under flat band conditions were determined using the hi-lo CV-method [1]. Furthermore, current-electric field strength (IE) measurements have been performed and are discussed. Trench-MOS structures exhibited dielectric breakdown field strengths up to 10 MV/cm.
The MULI Project: Annotation and Analysis of Information Structure in German and English

The goal of the MULI (MUltiLingual Information structure) project is to empirically analyse information structure in German and English newspaper texts. In contrast to other projects in which information structure is annotated and investigated (e.g. in the Prague Dependency Treebank, which mirrors the basic information about the topic-focus articulation of the sentence), we do not annotate theory-biased categories like topic-focus or theme-rheme. Trying to be as theory-independent as possible, we annotate those features which are relevant to information structure and on the basis of which typical patterns, co-occurrences or correlations can be determined. We distinguish between three annotation levels: syntax, discourse and prosody. The data is based on the TIGER Corpus for German and the Penn Treebank for English, since the existing information on part-of-speech and syntactic structure can be re-used for our purposes. The actual annotation of an English example sequence illustrates our choice of categories on each level. Their combination offers the possibility to investigate how information structure is realised and can be interpreted.
Surface finish and lubrication at low cutting speeds

AbstractSurface finish is one of the most important parameters to be controlled during machining as it affects many functional properties of components. It can be effected by workpiece and cutting tool material, geometry, cutting fluid, and cutting conditions. When machining at low cutting speeds a cutting fluid with good lubricant properties is often recommended to improve surface finish. This improvement is often thought to affect built up edge (BUE) formation, which is a major cause of poor surface finish. This work studies the effect of sulphur, an extreme pressure (EP) additive, in an oil lubricant on the surface finish of an AISI 1040 steel machined with a cemented carbide cutting tool. The application of a lubricant, with and without sulphur, does not prevent the formation of BUE but does affect the surface finish. This work suggests that the BUE is squeezed against the workpiece material close to the tool nose affecting surface finish. This region is where lubricant acts to improve surface quality.
Correction for Meese and Summers, Area summation in human vision at and above detection threshold

Correction for ‘Area summation in human vision at and above detection threshold’ by Tim S. Meese and Robert J. Summers (Proc. R. Soc. B 274, 2891–2900. (doi: 10.1098/rspb.2007.0957)). Several equations, detailed below, were presented incorrectly.
Fiber-Optic Controlled PCSS Triggers For High Voltage Pulsed Power Switches

This paper reports on progress in the development of fiber optically triggered photoconductive semiconductor switches (PCSS) for triggering high voltage pulsed power switches with improved precision. This technology can eliminate the need for large-diameter trigger cables and line-of-sight optics. It also has the potential of significantly reducing the cost of trigger generation systems. It has the potential to improve the performance of prime power switches, diverters, and diagnostics because of the low-jitter sub-nanosecond rise times. Test results will be presented that demonstrate sub-nanosecond jitter from a PCSS, less than 1.2 nanoseconds of jitter from a commercial trigatron switch triggered by PCSS, and the performance analysis of a 200 kV class switch triggered by a PCSS based triggering system. This work is a step toward the creation of a reliable self-contained PCSS-based trigger generator that can be physically located on a high voltage switch, allowing the triggering hardware to float. The only connection to the trigger system will be a low energy optical fiber, thereby eliminating the need for HV cables traversing high potential fields or for line-of-sight-optics
The Periaqueductal Gray Orchestrates Sensory and Motor Circuits at Multiple Levels of the Neuraxis

The periaqueductal gray (PAG) coordinates behaviors essential to survival, including striking changes in movement and posture (e.g., escape behaviors in response to noxious stimuli vs freezing in response to fear-evoking stimuli). However, the neural circuits underlying the expression of these behaviors remain poorly understood. We demonstrate in vivo in rats that activation of the ventrolateral PAG (vlPAG) affects motor systems at multiple levels of the neuraxis through the following: (1) differential control of spinal neurons that forward sensory information to the cerebellum via spino-olivo-cerebellar pathways (nociceptive signals are reduced while proprioceptive signals are enhanced); (2) alterations in cerebellar nuclear output as revealed by changes in expression of Fos-like immunoreactivity; and (3) regulation of spinal reflex circuits, as shown by an increase in α-motoneuron excitability. The capacity to coordinate sensory and motor functions is demonstrated in awake, behaving rats, in which natural activation of the vlPAG in fear-conditioned animals reduced transmission in spino-olivo-cerebellar pathways during periods of freezing that were associated with increased muscle tone and thus motor outflow. The increase in spinal motor reflex excitability and reduction in transmission of ascending sensory signals via spino-olivo-cerebellar pathways occurred simultaneously. We suggest that the interactions revealed in the present study between the vlPAG and sensorimotor circuits could form the neural substrate for survival behaviors associated with vlPAG activation. SIGNIFICANCE STATEMENT Neural circuits that coordinate survival behaviors remain poorly understood. We demonstrate in rats that the periaqueductal gray (PAG) affects motor systems at the following multiple levels of the neuraxis: (1) through altering transmission in spino-olivary pathways that forward sensory signals to the cerebellum, reducing and enhancing transmission of nociceptive and proprioceptive information, respectively; (2) by alterations in cerebellar output; and (3) through enhancement of spinal motor reflex pathways. The sensory and motor effects occurred at the same time and were present in both anesthetized animals and behavioral experiments in which fear conditioning naturally activated the PAG. The results provide insights into the neural circuits that enable an animal to be ready and able to react to danger, thus assisting in survival.