Miracle-dz/UniFAR-FTUs huggingface dataset:
BLACK BOX VARIATIONAL INFERENCE FOR STATE SPACE MODELS

Latent variable time-series models are among the most heavily used tools from machine learning and applied statistics. These models have the advantage of learning latent structure both from noisy observations and from the temporal ordering in the data, where it is assumed that meaningful correlation structure exists across time. A few highly-structured models, such as the linear dynamical system with linear-Gaussian observations, have closed-form inference procedures (e.g. the Kalman Filter), but this case is an exception to the general rule that exact posterior inference in more complex generative models is intractable. Consequently, much work in time-series modeling focuses on approximate inference procedures for one particular class of models. Here, we extend recent developments in stochastic variational inference to develop a `black-box' approximate inference technique for latent variable models with latent dynamical structure. We propose a structured Gaussian variational approximate posterior that carries the same intuition as the standard Kalman filter-smoother but, importantly, permits us to use the same inference approach to approximate the posterior of much more general, nonlinear latent variable generative models. We show that our approach recovers accurate estimates in the case of basic models with closed-form posteriors, and more interestingly performs well in comparison to variational approaches that were designed in a bespoke fashion for specific non-conjugate models.
Note on measurement of woody plant diameter distributions

Introduction Forest ecologists use the frequency distribution of d.b. h. (diameter at breast height, 1.35 m above ground) of the stems of woody species to describe age/size structures and draw inferences about regeneration strategies, synchrony of climatic events, mortality patterns and the effects of animal browsing (e.g. recent New Zealand studies by Allen, Payton and Knowlton, 1984; Mark, 1963; Mark and Sanderson, 1962; Stewart and Veblen, 1982; Veblen and Stewart, 1980; P. Wardle, 1978; J. Wardle, 1970; 1984). Even if it is assumed that diameter distributions are equivalent to age distributions (but see Harper, 1977; Ogden, 1978; Veblen and Stewart 1980), the d.b. h. convention is not particularly appropriate for demographic analysis. Most obviously, it cannot be applied to stems less than 1.35 m tall. One contemporary solution to the problem partitions woody forest plants into four groups and applies different protocols to each of them (Allen and McLennan, 1983): trees, defined as those > 3 cm d.b. h. and >2 m tall, are measured at breast height; saplings, < 3 cm d.b. h. and > 1.35 m, are counted; 'understorey' plants which exceed 15 cm tall are counted in sub-plots by 16-45 cm, 46-75 cm, 76-105 cm, 106-135 cm and > 135 cm height classes; plants less than 15 cm are recorded in subplots as present or absent. Although such measurements can be spliced into a statement of apparent demographic pattern (e.g. Allen, Payton and Knowlton, 1984), the procedure is complex and the criteria of size are not constant throughout the life cycle of plants. Accordingly, Batcheler and Craib (1985) suggested the use of a simple extension of the d.b. h. protocol by which stems ≥ 2.6 m are measured at breast height, whereas those < 2.6 m tall are measured at half their height. The measurement, d.b. h.h. (diameter at breast height or half height), yields a continuous range of size of all plants in a population. Second, in dealing with shrubby species, Batcheler and Craib recognized that recording each stem as a plant results in high estimates of density and low estimates of mean plant basal area. They therefore adopted a procedure by which where more than one stem occurs at the d.b. h.h. measurement point, each stem is measured and the size of the plant is represented by the diameter equivalent to the combined cross sections of the stems.
Maturation of molybdoenzymes and its influence on the pathogenesis of non-typeable Haemophilus influenzae

Mononuclear molybdenum enzymes of the dimethylsulfoxide (DMSO) reductase family occur exclusively in prokaryotes, and a loss of some these enzymes has been linked to a loss of bacterial virulence in several cases. The MobA protein catalyzes the final step in the synthesis of the molybdenum guanine dinucleotide (MGD) cofactor that is exclusive to enzymes of the DMSO reductase family. MobA has been proposed as a potential target for control of virulence since its inhibition would affect the activities of all molybdoenzymes dependent upon MGD. Here, we have studied the phenotype of a mobA mutant of the host-adapted human pathogen Haemophilus influenzae. H. influenzae causes and contributes to a variety of acute and chronic diseases of the respiratory tract, and several enzymes of the DMSO reductase family are conserved and highly expressed in this bacterium. The mobA mutation caused a significant decrease in the activities of all Mo-enzymes present, and also resulted in a small defect in anaerobic growth. However, we did not detect a defect in in vitro biofilm formation nor in invasion and adherence to human epithelial cells in tissue culture compared to the wild-type. In a murine in vivo model, the mobA mutant showed only a mild attenuation compared to the wild-type. In summary, our data show that MobA is essential for the activities of molybdenum enzymes, but does not appear to affect the fitness of H. influenzae. These results suggest that MobA is unlikely to be a useful target for antimicrobials, at least for the purpose of treating H. influenzae infections.
STUDIES ON THE ETIOLOGY OF HEARTWATER

A Gram-negative, intracellular, coccus-like microorganism was found in cases of heartwater in the three species which are susceptible to the disease; namely, goats, sheep, and cattle. It was absent in the case of control animals, both normal ones and those dying of some. other diseases. The presence of this microorganism was definitely related to the febrile reaction. It was most easily detected in the renal glomeruli and in the small capillaries of the cerebral cortex but probably occurred throughout the body. The microorganism was a typical endothelial parasite, being restricted in distribution to the endothelial cells of the smaller blood vessels and to portions of such elements which had broken off into the blood stream. It was never observed to cause injury to the cells other than those incident to mechanical distention through accumulation within them of many individuals in large densely packed masses which were characteristically spherical. A typical attribute was the presence of several of these masses within the cytoplasm of a single endothelial cell. In view of the association of this microorganism with heartwater, a disease of ruminants, and thus far the only one in which microorganisms resembling Rickettsiœ have been reported, the designation Rickettsia ruminantium is proposed.
Thermo-Mechanical Behavior of Textile Heating Fabric Based on Silver Coated Polymeric Yarn

This paper presents a study conducted on the thermo-mechanical properties of knitted structures, the methods of manufacture, effect of contact pressure at the structural binding points, on the degree of heating. The test results also present the level of heating produced as a function of the separation between the supply terminals. The study further investigates the rate of heating and cooling of the knitted structures. The work also presents the decay of heating properties of the yarn due to overheating. Thermal images were taken to study the heat distribution over the surface of the knitted fabric. A tensile tester having constant rate of extension was used to stretch the fabric. The behavior of temperature profile of stretched fabric was observed. A comparison of heat generation by plain, rib and interlock structures was studied. It was observed from the series of experiments that there is a minimum threshold force of contact at binding points of a knitted structure is required to pass the electricity. Once this force is achieved, stretching the fabric does not affect the amount of heat produced.
Combining feature selection and DTW for time-varying functional genomics

Given temporal high-throughput data defining a two-class functional genomic process, feature selection algorithms may be applied to extract a panel of discriminating gene time series. We aim to identify the main trends of activity through time. A reconstruction method based on stagewise boosting is endowed with a similarity measure based on the dynamic time warping (DTW) algorithm, defining a ranked set of time-series component contributing most to the reconstruction. The approach is applied on synthetic and public microarray data. On the Cardiogenomics PGA Mouse Model of Myocardial Infarction, the approach allows the identification of a time-varying molecular profile of the ventricular remodeling process.
Classification of Bacterial Contamination Using Image Processing and Distributed Computing

Disease outbreaks due to contaminated food are a major concern not only for the food-processing industry but also for the public at large. Techniques for automated detection and classification of microorganisms can be a great help in preventing outbreaks and maintaining the safety of the nation's food supply. Identification and classification of foodborne pathogens using colony scatter patterns is a promising new label-free technique that utilizes image-analysis and machine-learning tools. However, the feature-extraction tools employed for this approach are computationally complex, and choosing the right combination of scatter-related features requires extensive testing with different feature combinations. In this study, we used computer clusters to speed up the feature-extraction process, which enables us to analyze the contribution of different scatter-based features to the overall classification accuracy. A set of 1000 scatter patterns representing ten different bacterial strains was used. Zernike and Chebyshev moments as well as Haralick texture features were computed from the available light-scatter patterns. The most promising features were first selected using Fisher's discriminant analysis, and subsequently a support-vector-machine classifier with a linear kernel was used. With extensive testing, we were able to identify a small subset of features that produced the desired results in terms of classification accuracy and execution speed. The use of distributed computing for scatter-pattern analysis, feature extraction, and selection provides a feasible mechanism for large-scale deployment of a light scatter-based approach to bacterial classification.
Agreement of a restricted secret key

A secret key agreement problem is proposed with the additional restriction that the key is a function of a given secret source. An inner bound to the achievable rates, error and secrecy exponents is derived. The maximum key rate strongly achievable with positive exponents is characterized. The result leads to class of admissible restrictions on the key functions that does not diminish the strongly achievable key rate.
Satellite glial cells in the nodose ganglion of the rat vagus nerve: Morphologicalalterations of microglial cells.

Satellite glial cells (SGCs) have been well known to be present in the sensory and autonomic ganglia of the peripheral nerves and play an important role in various brain functions. However, interactions between the ganglion cells and SGCs involved in transcytosis of materials remained as a poorly-solved problem. In the present study, the cellular processes and molecular mechanisms of the SGCs were investigated in the nodose ganglion (NG) of the rat vagus nerve. Immunofluorescent experiments of the SGCs led to expression of GFAP- and Iba-1-immunoreactivity in close vicinity to neuronal cell bodies. However, very weak Iba-1 expression was seen in GFAP- immunoreactive cells. It was of particular interest that Iba-1- immunoreactive cells seem to be extending a part of the glial cell bodies into neuronal cell bodies in the NG. In electron microscopic experiments, injection of wheat germ agglutinin conjugated horseradish peroxidase (WGA-HRP) into the vagus nerve resulted in deep extension of the fine processes of the SGCs into neuronal cell bodies and uptake of HRPreaction product. These findings would indicate that the SGCs respond to environmental changes of neuronal cell bodies are reactive microglial cells in the NG.
Muscle Model for Safe Minimally Invasive Surgery

Minimally invasive surgery that is less safe for human beings cannot spread. We propose a system that avoids damaging the nerves and blood in the surgical approach to safe minimally invasive surgery. The system consists of a model of the operative part and a surgical manipulator. The model shows the pressure on the nerves and bloods in surgical procedure. The model requires precise measurement of the physical properties of soft tissue in the view of the surgical procedure. We propose new and precise model for muscle's heterogeneity properties. In this paper a viscoelasticity test is examined to some muscle samples involved in a rectus femoris muscle. Approximating each result of heterogeneity properties to the three-elements model quantitatively showed the difference in the physical properties of each part. This precise three-elements model is build in a simulation of muscle behavior. Comparison of the indentation examinations between real muscle and the simulation confirmed the effectiveness of the parameters obtained from the viscoelasticity examination. The difference between the maximum forces of the indented simulated heterogeneity and homogeneity models is about 21%. The indented simulation resulted in a need for a heterogeneity model of muscle. In the near future proposed model will be based on the control of a surgical manipulator. Proposed system will provide safe minimally invasive surgery.
Percept-related cortical induced activity during bistable perception

Bistable perception arises when a stimulus under continuous view is perceived as the alternation of two mutually exclusive states. Such a stimulus provides a unique opportunity for understanding the neural basis of visual perception because it dissociates the perception from the visual input. In this paper we focus on extracting the percept-related features of the induced activity from the local field potential (LFP) in monkey visual cortex for decoding its bistable structure-from-motion (SFM) perception. Because of the dissociation between the perception and the stimulus in our experimental paradigm, the stimulus-evoked activity in our data is not related to perception. Our proposed feature extraction approach consists of two stages. First, we estimate the stimulus-evoked activity via a wavelet transform based method and remove it from the single trials of each channel. Second, we use the common spatial patterns (CSP) approach to design spatial filters based on the remaining induced activity of multiple channels to extract the percept-related features. We exploit the linear discriminant analysis (LDA) classifier and the support vector machine (SVM) classifier on the extracted features to decode the reported perception on a single-trial basis. We apply the proposed approach to the multichannel intracortical LFP data collected from the middle temporal (MT) visual cortex in a macaque monkey performing a SFM task. We demonstrate that our approach is effective in extracting the discriminative features of the percept-related induced activity from LFP, which leads to excellent decoding performance. We also discover that the enhanced gamma band synchronization and reduced alpha band desynchronization may be the underpinnings of the induced activity.
Does Frye or Daubert Matter? A Study of Scientific Admissibility Standards

Nearly every treatment of scientific evidence begins with a faithful comparison between the Frye and Daubert standards. Since 1993, jurists and legal scholars have spiritedly debated which standard is preferable and whether particular states should adopt one standard or the other. These efforts beg the question: Does a state's choice of scientific admissibility standard matter? A growing number of scholars suspect that the answer is no. Under this theory, the import of the Supreme Court's Daubert decision was not in its doctrinal standard, but rather in the general consciousness it raised about the problems of unreliable scientific evidence. This Article empirically examines this question. Using data provided by the Federal Judicial Center, the National Center for State Courts, and the New York and Connecticut court systems, we apply a novel approach of using removal from state to federal court to measure litigants' perceptions of scientific admissibility standards in practice. Our analysis strongly supports the theory that a state's choice between Frye and Daubert does not matter in tort cases. The results raise larger questions about the efficacy of tort reform through procedural rules, suggesting that the judiciary in some contexts may be more responsive to educative measures than to doctrinally based procedural reforms.
Calculating Benefits of Infrastructural Measures

The paper continues the ongoing discussion about the concept of accessibility and its applicability to infrastructural appraisal. David Metz states that travel time savings disappear in a long term perspective and to empirically untested "constant travel time budget" literature. Metz therefore concludes that it is inadequate to measure the benefits of an infrastructural investment by means of travel time savings only. Further it is noted that the inadequacy results from longer term decisions - such as location choice - which arise in the long run. These longer term decisions should therefore be included in the modeling of transport - or better of the comprehensive economic - systems for public infrastructure appraisal respectively. Some authors hint at the possibility to measure consumer surplus applying the concept of the expected maximum utility (EMU). If we accept this argument the question arises to what extent we produce errors with "short term" models. To examine this issue we implement a proof of concept model with the purpose to simulate long term equilibrium with different decision possibilities in a minimal urban system. We use random utility maximisation and discrete choice theory with an agent-based modelling approach to respect the discrete nature, consistency with discrete choice theory and to what seems to many to be the way forward in the field. We simulate equilibrium conditions letting the agents chose their commuting situation allowing for different combinations of decision dimensions. The results show that improving accessibility results in an increasing and expected demand for more peripheral locations. Thus we conclude that profiteers of infrastructural measures are property owners whose properties get higher accessibility. Concerning the utility indicators we find that EMU is more consistent. Further we note substantial differences when applying different decision spaces. The appropriateness of using travel time savings as indicator for utility gains very much depends on considered time horizons because trade-offs between utility out of short- and long-term decisions is likely to occur. In case of assessing long time periods we should operate with models incorporating long-term decisions such as location choice. This is a strong argument in favor of LUTI-models.
A Real-Time Fatigue Monitoring and Analysis System for Lower Extremity Muscles with Cycling Movement

A real-time muscle fatigue monitoring system was developed to quantitatively detect the muscle fatigue of subjects during cycling movement, where a fatigue progression measure (FPM) was built-in. During the cycling movement, the electromyogram (EMG) signals of the vastus lateralis and gastrocnemius muscles in one leg as well as cycling speed are synchronously measured in a real-time fashion. In addition, the heart rate (HR) and the Borg rating of perceived exertion scale value are recorded per minute. Using the EMG signals, the electrical activity and median frequency (MF) are calculated per cycle. Moreover, the updated FPM, based on the percentage of reduced MF counts during cycling movement, is calculated to measure the onset time and the progressive process of muscle fatigue. To demonstrate the performance of our system, five young healthy subjects were recruited. Each subject was asked to maintain a fixed speed of 60 RPM, as best he/she could, under a constant load during the pedaling. When the speed reached 20 RPM or the HR reached the maximal training HR, the experiment was then terminated immediately. The experimental results show that the proposed system may provide an on-line fatigue monitoring and analysis for the lower extremity muscles during cycling movement.
The explanation paradox

This paper examines mathematical models in economics and observes that three mutually inconsistent hypotheses concerning models and explanation are widely held: (1) economic models are false; (2) economic models are nevertheless explanatory; and (3) only true accounts explain. Commentators have typically resolved the paradox by rejecting either one of these hypotheses. I will argue that none of the proposed resolutions work and conclude that therefore the paradox is genuine and likely to stay.
Spatial Covariance between Aesthetic Value & Other Ecosystem Services

Mapping the spatial distribution of ecosystem goods and services represents a burgeoning field of research, although how different services covary with one another remains poorly understood. This is particularly true for the covariation of supporting, provisioning and regulating services with cultural services (the non-material benefits people gain from nature). This is largely because of challenges associated with the spatially specific quantification of cultural ecosystem services. We propose an innovative approach for evaluating a cultural service, the perceived aesthetic value of ecosystems, by quantifying geo-tagged digital photographs uploaded to social media resources. Our analysis proceeds from the premise that images will be captured by greater numbers of people in areas that are more highly valued for their aesthetic attributes. This approach was applied in Cornwall, UK, to carry out a spatial analysis of the covariation between ecosystem services: soil carbon stocks, agricultural production, and aesthetic value. Our findings suggest that online geo-tagged images provide an effective metric for mapping a key component of cultural ecosystem services. They also highlight the non-stationarity in the spatial relationships between patterns of ecosystem services.
SEGEMENTATION-BASED IMAGE COPY-MOVE FORGERY DETECTION METHOD WITH CONSIDERATION OF SPATIAL CORRELATION

In this paper, we improve an existing scheme of detecting the copy-move forgery. The main difference between our method and prior arts is that we seek spatial correlation in the test image. Our method has 4 stages. In the first stage, we segment test image. In second stage, we find the suspicious pairs and group them into suspicious groups by their spatial correlation, and then find a transform matrix between them. In third stage, we refine the transform matrix from step two by an iterated algorithm. In the last step, we use mix DSIFT feature approach and ZNCC feature approach and get a better estimation of copy-move forgery regions.