Miracle-dz/UniFAR-FTUs huggingface dataset:
Training energy-based models for time-series imputation

Imputing missing values in high dimensional time-series is a difficult problem. This paper presents a strategy for training energy-based graphical models for imputation directly, bypassing difficulties probabilistic approaches would face. The training strategy is inspired by recent work on optimization-based learning (Domke, 2012) and allows complex neural models with convolutional and recurrent structures to be trained for imputation tasks. In this work, we use this training strategy to derive learning rules for three substantially different neural architectures. Inference in these models is done by either truncated gradient descent or variational mean-field iterations. In our experiments, we found that the training methods outperform the Contrastive Divergence learning algorithm. Moreover, the training methods can easily handle missing values in the training data itself during learning. We demonstrate the performance of this learning scheme and the three models we introduce on one artificial and two real-world data sets.
Texture-based Transfer Functions for Direct Volume Rendering

Visualization of volumetric data faces the difficult task of finding effective parameters for the transfer functions. Those parameters can determine the effectiveness and accuracy of the visualization. Frequently, volumetric data includes multiple structures and features that need to be differentiated. However, if those features have the same intensity and gradient values, existing transfer functions are limited at effectively illustrating those similar features with different rendering properties. We introduce texture-based transfer functions for direct volume rendering. In our approach, the voxelpsilas resulting opacity and color are based on local textural properties rather than individual intensity values. For example, if the intensity values of the vessels are similar to those on the boundary of the lungs, our texture-based transfer function will analyze the textural properties in those regions and color them differently even though they have the same intensity values in the volume. The use of texture-based transfer functions has several benefits. First, structures and features with the same intensity and gradient values can be automatically visualized with different rendering properties. Second, segmentation or prior knowledge of the specific features within the volume is not required for classifying these features differently. Third, textural metrics can be combined and/or maximized to capture and better differentiate similar structures. We demonstrate our texture-based transfer function for direct volume rendering with synthetic and real-world medical data to show the strength of our technique.
Impact of Edge Traffic Aggregation on the Performance of FDL-Assisted Optical Core Switching Nodes

In this paper we consider optical burst/packet switching networks with core nodes in which contentions are resolved by means of a hybrid scheme incorporating FDL buffering and wavelength conversion. For such a network we investigate the influence of traffic shaping at the edge nodes, as introduced by optical burst generation algorithms, on the packet drop rate at the core nodes. In particular we focus our attention on the impact of the algorithms that generate fixed-size optical bursts, i.e., volume-based burst assembly. The simulative investigation reveals that the total number of burst flows multiplexed at the core node under consideration as well as the assembly threshold are the two most influential factors, and that the influence of these factors on the drop rate could be as high as several orders of magnitude. Additionally, it is discussed that the assembly process can negatively influence the performance of the so-called void-filling channel scheduling algorithms.
Forest Monitoring Using Landsat Time Series Data: A Review

Abstract Unique among Earth observation programs, the Landsat program has provided continuous earth observation data for the past 41 years. Landsat data are systematically collected and archived following a global acquisition strategy. The provision of free, robust data products since 2008 has spurred a renaissance of interest in Landsat and resulted in an increasingly widespread use of Landsat time series (LTS) for multitemporal characterizations. The science and applications capacity has developed steadily since 1972, with the increase in sophistication offered over time incorporated into Landsat processing and analysis practices. With the successful launch of Landsat-8, the continuity of measures at scales of particular relevance to management and scientific activities is ensured in the short term. In particular, forest monitoring benefits from LTS, whereby a baseline of conditions can be interrogated for both abrupt and gradual changes and attributed to different drivers. Such benefits are enabled by data availability, analysis-ready image products, increased computing power and storage, as well as sophisticated image processing approaches. In this review, we present the status of remote sensing of forests and forest dynamics using LTS, including issues related to the sensors, data availability, data preprocessing, variables used in LTS, analysis approaches, and validation issues.
Persistent Infections by Nontyphoidal Salmonella in Humans: Epidemiology and Genetics.

BACKGROUND Although chronic infections by typhoidal Salmonella are well-known, prolonged human infections by nontyphoidal Salmonella (NTS) are poorly characterized. METHODS We retrospectively analyzed 48 345 culture-confirmed NTS infections that occurred in Israel 1995-2012. A case-control study was performed to identify risk factors associated with persistent infections. Whole-genome-sequencing, pulsed-field gel electrophoresis (PFGE), and a mouse infection model were used to study genetic and phenotypic differences between same-patient persistent, recurring isolates. RESULTS In total, 1047 cases of persistent NTS infections, comprising 2.2% of all reported cases of salmonellosis, were identified. The persistence periods ranged between 30 days to 8.3 years. The majority (93%) of the persistently infected patients were immunocompetent, and 65% were symptomatic with relapsing diarrhea, indicating a distinct clinical manifestation from the asymptomatic carriage of typhoidal Salmonella. Four NTS serovars (Mbandaka, Bredeney, Infantis and Virchow) were found to be significantly more frequently associated with persistence than others. Comparative genomics between early and later isolates obtained from the same patients confirmed clonal infection and showed 0 to 10 SNPs between persistent isolates. A different composition of mobile genetic elements (plasmids and phages) or amino acid substitutions in global regulators was identified in multiple cases. These changes resulted in differences in phenotype and virulence between early and later same-patient isolates. CONCLUSIONS These results illuminate the overlooked clinical manifestation of persistent salmonellosis that can serve as a human reservoir for NTS infections. Additionally, we demonstrate mechanisms of in-host microevolution and exhibit their potential to shape Salmonella pathogenicity, antimicrobial resistance and host-pathogen interactions.
Accelerated remyelination during inflammatory demyelination prevents axonal loss and improves functional recovery

Demyelination in MS disrupts nerve signals and contributes to axon degeneration. While remyelination promises to restore lost function, it remains unclear whether remyelination will prevent axonal loss. Inflammatory demyelination is accompanied by significant neuronal loss in the experimental autoimmune encephalomyelitis (EAE) mouse model and evidence for remyelination in this model is complicated by ongoing inflammation, degeneration and possible remyelination. Demonstrating the functional significance of remyelination necessitates selectively altering the timing of remyelination relative to inflammation and degeneration. We demonstrate accelerated remyelination after EAE induction by direct lineage analysis and hypothesize that newly formed myelin remains stable at the height of inflammation due in part to the absence of MOG expression in immature myelin. Oligodendroglial-specific genetic ablation of the M1 muscarinic receptor, a potent negative regulator of oligodendrocyte differentiation and myelination, results in accelerated remyelination, preventing axonal loss and improving functional recovery. Together our findings demonstrate that accelerated remyelination supports axonal integrity and neuronal function after inflammatory demyelination. DOI: http://dx.doi. org/10.7554/eLife.18246. 001
Adaptive Global Fast Sliding Mode Control for Steer-by-Wire System Road Vehicles

A steer-by-wire (SbW) system, also known as a next-generation steering system, is one of the core elements of autonomous driving technology. Navigating a SbW system road vehicle in varying driving conditions requires an adaptive and robust control scheme to effectively compensate for the uncertain parameter variations and external disturbances. Therefore, this article proposed an adaptive global fast sliding mode control (AGFSMC) for SbW system vehicles with unknown steering parameters. First, the cooperative adaptive sliding mode observer (ASMO) and Kalman filter (KF) are established to simultaneously estimate the vehicle states and cornering stiffness coefficients. Second, based on the best set of estimated dynamics, the AGFSMC is designed to stabilize the impact of nonlinear tire-road disturbance forces and at the same time to estimate the uncertain SbW system parameters. Due to the robust nature of the proposed scheme, it can not only handle the tire–road variation, but also intelligently adapts to the different driving conditions and ensures that the tracking error and the sliding surface converge asymptotically to zero in a finite time. Finally, simulation results and comparative study with other control techniques validate the excellent performance of the proposed scheme.
Just type polyana and press Enter: a post-processing application designed with simplicity of use in mind

ABSTRACT We present a new version of POLYANA, an application that computes radial distribution functions for centres of mass of whole molecules or subunits thereof, based on DL_POLY trajectories. User friendliness and ease of future extensions were fundamental design principles of POLYANA development. Thus, the new version adds, among others, a flexible syntax to define groups of atoms; calculation of radial distribution functions beyond half the simulation cell size; OpenMP parallelism and other features on top of existing functionality. The impatient user can compile and execute it immediately to obtain molecular radial distribution functions; on the other hand, easy to learn directives offer more advanced capabilities. POLYANA is a self-contained Fortran code, built in a modular fashion that makes it easy to add new functions. It is free and open-source and it is distributed under the MIT license.
High-Efficiency Envelope-Tracking W-CDMA Base-Station Amplifier Using GaN HFETs

A high-efficiency wideband code-division multiple-access (W-CDMA) base-station amplifier is presented using high-performance GaN heterostructure field-effect transistors to achieve high gain and efficiency with good linearity. For high efficiency, class J/E operation was employed, which can attain up to 80% efficiency over a wide range of input powers and power supply voltages. For nonconstant envelope input, the average efficiency is further increased by employing the envelope-tracking architecture using a wide-bandwidth high-efficiency envelope amplifier. The linearity of overall system is enhanced by digital pre-distortion. The measured average power-added efficiency of the amplifier is as high as 50.7% for a W-CDMA modulated signal with peak-to-average power ratio of 7.67 dB at an average output power of 37.2 W and gain of 10.0 dB. We believe that this corresponds to the best efficiency performance among reported base-station power amplifiers for W-CDMA. The measured error vector magnitude is as low as 1.74% with adjacent channel leakage ratio of -51.0 dBc at an offset frequency of 5 MHz
Pattern Recognition Approach to Quantitative Description of the Microstructure of Disordered Composites for Estimation of Thermal Conductivity

This paper explores the application of pattern recognition techniques in the characterization of a multiphase realistic disordered composite. Some descriptors based on Voronoi cells are extracted for different fiber distributions. Principal Components Analysis is used to find the best features to estimate effective thermal conductivity with a Multiple Linear Regression model instead of the Finite Element Method.
The implementation of SCADA open protocol PUR 2.4

As the choice of the communications protocol for a given application represents one of the most significant tasks in the development of information technical solutions, this article focuses on the high level open protocol of SCADA systems: PUR 2.4, as well as its implementation and the design of a RTU TESTER and the conception of a RTU.
Cloud, Aerosol, and Boundary Layer Structure across the Northeast Pacific Stratocumulus–Cumulus Transition as Observed during CSET

During the Cloud System Evolution in the Trades (CSET) field study, 14 research flights of the National Science Foundation G-V sampled the stratocumulus–cumulus transition between Northern California and Hawaii and its synoptic variability. The G-V made vertically resolved measurements of turbulence, cloud microphysics, aerosol characteristics, and trace gases. It also carried dropsondes and a vertically pointing W-band radar and lidar. This paper summarizes these observations with the goals of fostering novel comparisons with theory, models and reanalyses, and satellite-derived products. A longitude–height binning and compositing strategy mitigates limitations of sparse sampling and spatiotemporal variability. Typically, a 1-km-deep decoupled stratocumulus-capped boundary layer near California evolved into 2-km-deep precipitating cumulus clusters surrounded by patches of thin stratus that dissipated toward Hawaii. Low cloud cover was correlated with estimated inversion strength more than with cloud droplet number, even though the thickest clouds were generally precipitating and ultraclean layers indicative of aerosol–cloud–precipitation interaction were common west of 140°W. Accumulation-mode aerosol concentration correlated well with collocated cloud droplet number concentration and was typically largest near the surface. Aitken mode aerosol concentration was typically larger in the free troposphere. Wildfire smoke produced spikes of aerosol and trace gases on some flights. CSET data are compared with space–time collocated output from MERRA-2 reanalysis and from the CAM6 climate model run with winds and temperature nudged toward this reanalysis. The reanalysis compares better with the observed relative humidity than does nudged CAM6. Both vertically diffuse the stratocumulus cloud layer versus observations. MERRA-2 slightly underestimates in situ carbon monoxide measurements and underestimates ozone depletion within the boundary layer.
Interactions between Cytosolic Phospholipase A2 Activation and Mitochondrial Reactive Oxygen Species Production in the Development of Ventilator-Induced Diaphragm Dysfunction

Cytosolic phospholipase A2 (cPLA2) has been reported to be critical for infection-induced mitochondrial reactive oxygen species (ROS) production and diaphragm dysfunction (DD). In the present study, we aim to investigate whether cPLA2 was involved in ventilator-induced diaphragm dysfunction (VIDD). Our results showed that mechanical ventilation (MV) induced cPLA2 activation in the diaphragm with excessive mitochondrial ROS generation and muscle weakness. Specific inhibition of cPLA2 with CDIBA resulted in decreased mitochondrial ROS levels and improved diaphragm forces. In addition, mitochondria-targeted antioxidant MitoTEMPO attenuated ventilator-induced mitochondrial oxidative stress and downregulated cPLA2 activation in vivo. Both CDIBA and MitoTEMPO were able to attenuate protein degradation, muscle atrophy, and weakness following prolonged MV. Furthermore, laser Doppler imaging showed that MV decreased diaphragm tissue perfusion and induced subsequent hypoxia. An in vitro study also demonstrated a positive association between cPLA2 activation and mitochondrial ROS generation in C2C12 cells cultured under hypoxic condition. Collectively, our study showed that cPLA2 activation positively interacts with mitochondrial ROS generation in the development of VIDD, and ventilator-induced diaphragm hypoxia serves as a possible contributor to this positive feedback loop.
Phase‐Change‐Material‐Based Low‐Loss Visible‐Frequency Hyperbolic Metamaterials for Ultrasensitive Label‐Free Biosensing

Hyperbolic metamaterials (HMMs) have emerged as a burgeoning field of research over the past few years as their dispersion can be easily engineered in different spectral regions using various material combinations. Even though HMMs have comparatively low optical loss due to a single resonance, the noble‐metal‐based HMMs are limited by their strong energy dissipation in metallic layers at visible frequencies. Here, the fabrication of noble‐metal‐free reconfigurable HMMs for visible photonic applications is experimentally demonstrated. The low‐loss and active HMMs are realized by combining titanium nitride (TiN) and stibnite (Sb2S3) as the phase change material. A reconfigurable plasmonic biosensor platform based on active Sb2S3–TiN HMMs is proposed, and it is shown that significant improvement in sensitivity is possible for small molecule detection at low concentrations. In addition, a plasmonic apta‐biosensor based on a hybrid platform of graphene and Sb2S3–TiN HMM is developed and the detection and real‐time binding of thrombin concentration as low as 1 × 10−15 m are demonstrated. A biosensor operating in the visible range has several advantages including the availability of sources and detectors in this region, and ease of operation particularly for point‐of‐care applications.
A Constrained Formulation for Hybrid State Estimation

This paper presents a new hybrid constrained power system state estimator. The conventional and synchrophasor measurements are simultaneously incorporated in the estimation problem without using any transformation of measurements. This constrained formulation makes it possible to take advantage of information from phasor measurement unit (PMU) branch current and voltage measurements, improving the accuracy of the existing estimators. The methodology is applied on the IEEE 14-, 57-, and 118-bus test systems, and its performance is compared with other hybrid estimators.
HCMV glycoprotein B is expressed in primary glioblastomas and enhances growth and invasiveness via PDGFR-alpha activation

Our laboratory first demonstrated that human cytomegalovirus (HCMV) is associated with the most deadly form of primary brain tumor, glioblastoma (GBM). We showed that HCMV glycoprotein B (gB) mediates viral cellular entry via the receptor tyrosine kinase PDGFR-alpha (PDGFRα), resulting in activation of the PI3K/Akt pathway, a critical signaling axis gliomagenesis. Here, we investigated the effects of gB overexpression on glioma progression. We demonstrate that gB is endogenously expressed in primary GBM samples and show that ectopic gB expression in glioma cells induced sustained phosphorylation of PDGFRα, Akt, and Src. Recombinant gB protein and the whole virus enhanced invasion of primary glioblastoma cells into Matrigel and rat brain slices, and this effect was specifically inhibited by neutralizing antibodies to either gB or PDGFRα. Importantly, neutralizing antibodies to gB significantly inhibited the invasiveness of patient-derived HCMV-positive glioblastoma cells, suggesting that functional inhibition of this viral protein could hinder glioblastoma progression. gB overexpression promoted in vivo glioma growth and enhanced phosphor-Akt levels and tumor cell dispersal relative to controls. Taken together, our results demonstrate that HCMV gB promotes key hallmarks of glioblastoma and suggest that targeting gB may have therapeutic benefits for patients with HCMV -positive gliomas.
8. Conclusions 5.2.4 Overhead in Exec() 5.2.5 " System Call " Overhead 6. Evaluation 7. Future Work 5.2.1 Overhead in Fork() 5.2.2 Overhead in Copyin() and Copyout() 5.2.3 Rpc Latency 5.2 Current Performance Problems

15 drafts of the paper. Special thanks to John Ousterhout for providing the modified benchmark and for technical assistance and guidance. Beside additional development, it would be useful to conduct research using the Sprite server. For example, it would be interesting to compare the performance of the Sprite server with the performance of a similar server that uses Mach IPC for remote device access or for process migration [13]. Porting Sprite to Mach was a mixed success. On the one hand, it greatly reduced the amount of machine-dependent code in Sprite, which should make Sprite much easier to port to new hardware. The asynchronous interfaces provided by Mach require some unpleasant complexity in the Sprite server, but this complexity is manageable. On the other hand, the server is almost unusably slow, even after a couple months of tuning, and it appears that much work is still needed to bring performance within striking distance of the native system. At least one third of the performance gap results from the distributed nature of Sprite. However, the slowdown is not primarily due to RPC latency or throughput problems. Rather, it is due to the Sprite server's heavy use of an external pager, plus problems such as Sprite's inability to use mapped files to avoid copy overhead. The lesson here seems to be that there is more to high-performance distributed systems than fast communication, and although Mach shows promise as a general platform for distributed computing, it still has some serious shortcomings. For some problems (e.g., copy-on-write for external pagers) it should be possible to fix Mach, but in other cases (e.g., use of mapped files for performance), it may be necessary to redesign the distributed system instead. If one asks whether it is worth porting an existing system to run on top of Mach, the answer seems to be " it depends. " For a research system like Sprite, with its small development community, increased portability seems attractive enough to warrant a large one-time porting and tuning effort. On the other hand, a large commercial vendor, particularly a hardware vendor that would have to do its own Mach ports, would probably be better off to spend the time redesigning internal interfaces. There are other potential advantages to running on Mach, such as interoperability with different environments, but portability by itself seems inadequate justification to convert existing code to use Mach. The sources for …