Miracle-dz/UniFAR-FTUs huggingface dataset:
The concepts of bias, precision and accuracy, and their use in testing the performance of species richness estimators, with a literature review of estimator performance

The purpose of this review is to clarify the concepts of bias, precision and accuracy as they are commonly defined in the biostatistical literature, with our focus on the use of these concepts in quantitatively testing the performance of point estimators (specifically species richness estimators). We first describe the general concepts underlying bias, precision and accuracy, and then describe a number of commonly used unscaled and scaled performance measures of bias, precision and accuracy (e.g. mean error, variance, standard deviation, mean square error, root mean square error, mean absolute error, and all their scaled counterparts) which may be used to evaluate estimator performance. We also provide mathematical formulas and a worked example for most performance measures. Since every measure of estimator performance should be viewed as suggestive, not prescriptive, we also mention several other performance measures that have been used by biostatisticians or ecologists. We then outline several guidelines of how to test the performance of species richness estimators: the detailed description of data simulation models and resampling schemes, the use of real and simulated data sets on as many different estimators as possible, mathematical expressions for all estimators and performance measures, and the presentation of results for each scaled performance measure in numerical tables with increasing levels of sampling effort. We finish with a literature review of promising new research related to species richness estimation, and summarize the results of 14 studies that compared estimator performance, which confirm that with most data sets, non-parametric estimators (mostly the Chao and jackknife estimators) perform better than other estimators, e.g. curve models or fitting species-abundance distributions.
Robust and Sparse RGBD Data Registration of Scene Views

This paper proposes a complete strategy to optimally filter, enhance and register 3D point clouds captured by commodity RGBD cameras. Starting from the raw data grabbed from multiple viewpoints, we build the scene that gathers all the clouds in one consistent view. The process begins with the innovative adaptation of Kalman filter to Kinect's output. The resulting point cloud is subject to an outlier removal technique and a pre-alignment based on 3D features is performed. Finally, the alignment is refined using Iterative Closest Point (ICP) algorithm. The output of this research work is a consistent 3D model which can be directly used in virtual reality applications, or any 3D rendering process. Test results on real data are presented to validate our approach, and to justify the choice of its different modules.
Phage biocontrol of enteropathogenic and shiga toxin-producing Escherichia coli in meat products

Ten bacteriophages were isolated from faeces and their lytic effects assayed on 103 pathogenic and non-pathogenic Enterobacteriaceae. Two phages (DT1 and DT6) were selected based on their host ranges, and their lytic effects on pathogenic E. coli strains inoculated on pieces of beef were determined. We evaluated the reductions of viable cells of Escherichia coli O157:H7 and non-O157 Shiga toxigenic E. coli strains on meat after exposure to DT6 at 5 and 24°C for 3, 6, and 24 h and the effect of both phages against an enteropathogenic E. coli strain. Significant viable cell reductions, compared to controls without phages, at both temperatures were observed, with the greatest decrease taking place within the first hours of the assays. Reductions were also influenced by phage concentration, being the highest concentrations, 1.7 × 1010 plaque forming units per milliliter (PFU/mL) for DT1 and 1.4 × 1010 PFU/mL for DT6, the most effective. When enteropathogenic E. coli and Shiga toxigenic E. coli (O157:H7) strains were tested, we obtained viable cell reductions of 0.67 log (p = 0.01) and 0.77 log (p = 0.01) after 3 h incubation and 0.80 log (p = 0.01) and 1.15 log (p = 0.001) after 6 h. In contrast, all nonpathogenic E. coli strains as well as other enterobacteria tested were resistant. In addition, phage cocktail was evaluated on two strains and further reductions were observed. However, E. coli bacteriophage insensitive mutants (BIMs) emerged in meat assays. BIMs isolated from meat along with those isolated by using the secondary culture method were tested to evaluate resistance phenotype stability and reversion. They presented low emergence frequencies (6.5 × 10−7–1.8 × 10−6) and variable stability and reversion. Results indicate that isolated phages were stable on storage, negative for all the virulence factors assayed, presented lytic activity for different E. coli virotypes and could be useful in reducing Shiga toxigenic E. coli and enteropathogenic E. coli viable cells in meat products.
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons

MOTIVATION An increasing number of protein structures are being determined for which no biochemical characterization is available. The analysis of protein structure and function assignment is becoming an unexpected challenge and a major bottleneck towards the goal of well-annotated genomes. As shape plays a crucial role in biomolecular recognition and function, the examination and development of shape description and comparison techniques is likely to be of prime importance for understanding protein structure-function relationships. RESULTS A novel technique is presented for the comparison of protein binding pockets. The method uses the coefficients of a real spherical harmonics expansion to describe the shape of a protein's binding pocket. Shape similarity is computed as the L2 distance in coefficient space. Such comparisons in several thousands per second can be carried out on a standard linux PC. Other properties such as the electrostatic potential fit seamlessly into the same framework. The method can also be used directly for describing the shape of proteins and other molecules. AVAILABILITY A limited version of the software for the real spherical harmonics expansion of a set of points in PDB format is freely available upon request from the authors. Binding pocket comparisons and ligand prediction will be made available through the protein structure annotation pipeline Profunc (written by Roman Laskowski) which will be accessible from the EBI website shortly.
Reply to "Comments on 'New method of performance analysis for diversity reception with correlated Rayleigh-fading signals'"

Fang et al. (2000) attempted to simplify the procedures of performance analysis for maximal ratio combining (MRC), selection combining (SC), and equal gain combining (EGC) diversity systems of two correlated Rayleigh-fading channels by using a known transformation technique. It was then found by Loyka et al. (for comment see ibid., vol. 52, no. 3, p. 725-726 (2003)) that this transformation technique is correct for MRC, but leads to some performance-prediction deviations for SC and EGC diversity systems compared to the results produced by other reported approaches. Because the transformation process redistributes the signal energy among different antennas, the bit error ratio (BER) achieved after the transformation may be different from that without transformation. For SC and EGC, the transformation technique can provide the same BER as that achieved without the transformation technique when the correlation is not strong and the signal-to-noise ratio (SNR) is large (p/sup 2/ 8 dB, for example). In the case of small SNR and strong correlation, desirable performance gain in BER can be achieved by the transformation technique for the SC diversity system. However, the transformation technique produces an undesirable performance loss in terms of the BER for the EGC diversity system. It is not sufficient to use one example, as in Loyka et al. (fig. 2), to assess when the transform technique for SC predicts performance that deviates from reported approaches.
Multi-Granulation Entropy and Its Applications

In the view of granular computing, some general uncertainty measures are proposed through single-granulation by generalizing Shannon’s entropy. However, in the practical environment we need to describe concurrently a target concept through multiple binary relations. In this paper, we extend the classical information entropy model to a multi-granulation entropy model (MGE) by using a series of general binary relations. Two types of MGE are discussed. Moreover, a number of theorems are obtained. It can be concluded that the single-granulation entropy is the special instance of MGE. We employ the proposed model to evaluate the significance of the attributes for classification. A forward greedy search algorithm for feature selection is constructed. The experimental results show that the proposed method presents an effective solution for feature analysis.
Thermal Signatures of Emotional Arousal: A Functional Infrared Imaging Study

Functional infrared imaging was used to study the facial thermal signatures of three fundamental emotional conditions: stress, fear and pleasure arousal. Facial cutaneous temperature and its topographic distribution exhibited specific features clearly correlated to emotional arousal and concomitant measures of standard physiological signals of the sympathetic activity. The results of this study indicate functional infrared imaging as an alternative, touch less, non invasive method for assessing individual's emotional arousal in psychophysiology.
Vesicle properties and health benefits of milk phospholipids: a review

Phospholipids are important ingredients in milk. They serve as bioactive components with processing functionalities, despite representing only a small proportion of total milk lipids. There has been increasing interest in vesicle properties and health effects of milk phospholipids. However, there are limited reports on industry-scale manufacturing of related commercial products. This contribution aims to elucidate the industrial processes of manufacturing milk phospholipid products including phospholipid extraction and fraction as well as summarizing determination assays of milk phospholipids. In addition to industrial production, this review elaborates on application aspects, such as the biological properties of milk phospholipids and their technical importance as delivery vesicles of liposomes and phytosomes. In addition, new insights on large-scale production of milk phospholipids and new applications such as phytosomes and antioxidant properties are discussed.
Multipath direction finding with frequency allocation subspace smoothing for an OFDM wireless communication system

In smart antenna systems, the DOA (direction of arrival) based beamforming algorithms use the information of users DOAs to detect the desired user's signals and suppress other interference. However, in the real wireless environment, the subspace based high resolution DOA estimation algorithms will fail to estimate the correct DOA because of the loss of rank caused by the correlation between the received signals. This paper proposes a new smoothing algorithm associated with OFDM technique to solve the problem of loss of rank. In the simulation, the proposed algorithm with TLS ESPRIT is used to estimate the DOAs. The simulation results showed that this algorithm can really solve the problem of loss of rank in the multipath channel and accurately estimate DOAs of the signals
Simplified polynomial network classifier for handwritten character recognition

Class-specific feature polynomial classifier (CFPC), a variant of a polynomial classifier (PC), yields high classification accuracy especially in high dimensional feature spaces. However, the computational cost for classification in such a high dimensional space is rather expensive. To overcome this difficulty, we propose a simplified polynomial network (SPN) classifier that reduces the complexity of polynomial networks with little deterioration of classification accuracy. In experiments of handwritten digit recognition on USPS, SPN using features of 30.0 dimensions on average achieved higher classification accuracy and a classification speed about 12.8 times faster than CFPC using features of 250 dimensions. In experiments on MNIST, SPN using features of 40.0 dimensions on average achieved a classification speed about 2.0 times faster than CFPC using features of 100 dimensions with nearly the same classification accuracy.
An improved MPPT converter using current compensation method for small scaled PV-applications

An improved MPPT converter with current compensation method for small-scaled PV-applications is presented in this paper. The proposed method implements maximum power point tracking (MPPT) by variable reference current which is continuously changed during one sampling period. Therefore, the proposed MPPT converter with current compensation method increases the power transferred to the load above 9%. As a result, the utilization efficiency of photovoltaic (PV)-module can be increased. In addition, as it doesn't use a digital signal processor (DSP), this MPPT method has the merits of both a cost efficiency and a simple control circuit design. Therefore, it is considered that the proposed MPPT method is proper to low power, low cost PV-applications. The concept and control principles of this improved MPPT method are explained in detail and the validity of the proposed method is verified through several simulated results.
DESIGN OF LOW POWER DIGITAL I / O CELL WITH ESD CIRCUIT PROTECTION

A novel low-power I/O cell is proposed in this work. The new input/output (I/O) cell is found to reduce the I/O power consumption, which has been considered as the major power dissipation of the whole chip. The maximum operating clock is 500 MHz given a 10-pF off chip load. Physical measurements of the proposed I/O cells show that the delays of the transmitter and the receiver are 2.7ns and 1.6 ns, respectively. The largest power/bandwidth of the proposed design is 38.9 W/MHz when transmitting. This work also facilitates ESD circuit that prevents the circuit from high voltage spikes. KeywordsESD protection, i/o cells,trnsmitter, receiver.
CIRCLE MAPS AS A SIMPLE OSCILLATORS FOR COMPLEX BEHAVIOR: II. EXPERIMENTS

The circle map is a general non-linear iterated function that maps the circle onto itself. In its standard form it can be interpreted as a simple sinusoidal oscillator which is perturbed by a non-linear term. By varying the strength of the non-linear contribution a rich array of non-linear responses can be achieved, including waveshaping, pitch-bending, period-doubling and highly irregular patterns. We describe a number of such examples and discuss their subjective auditory perception.
Monochromatic Electron Photoemission from Diamondoid Monolayers

We found monochromatic electron photoemission from large-area self-assembled monolayers of a functionalized diamondoid, [121]tetramantane-6-thiol. Photoelectron spectra of the diamondoid monolayers exhibited a peak at the low–kinetic energy threshold; up to 68% of all emitted electrons were emitted within this single energy peak. The intensity of the emission peak is indicative of diamondoids being negative electron affinity materials. With an energy distribution width of less than 0.5 electron volts, this source of monochromatic electrons may find application in technologies such as electron microscopy, electron beam lithography, and field-emission flat-panel displays.
Geometric representation and algebraic formalization of musical structures

This thesis presents a generalizations of the neo-Riemannian PLR-group, that acts on the set of 24 major and minor triads. The work begins with a reconstruction on the history of the Tonnetz, a graph associated with the three transformations that generate the PLR-group. The thesis presents two generalizations of the PLR-group for seventh chords. The first one acts on the set of dominant, minor, semi-diminished, major and diminished sevenths, the second one also includes minor major, augmented major, augmented, dominant seventh flat five. We considered the most parsimonious operations exchanging two types of sevenths, moving a single note by a semitone or a whole tone. We also classified the most parsimonious transformations among the 4 types of triads (major, minor,augmented and diminished) and studied the group generated by them. Finally, we have introduced a general approach to define parsimonious operations between sevenths and triads, but also the operations already known between triads and those between sevenths.
Comparison of 99mTc-MIBI uptakes on planar images with those in excised rats organs

The precision with which images reflect tracer uptake in the myocardium has been studied. Additionally, the degree to which 99mTc methoxyisobutylisonitrile (99mTc-MIBI) in the liver gave the effect to a myocardial image has been examined. After administering 99mTc-MIBI to normal male rats, we compared the myocardial uptakes obtained using a gamma camera with the actual uptakes in the excised organs. Twenty-nine rats were used. Following imaging, the anterior view at 5, 10, 15, 30, 45, 60, 90 and 120 min after administration of the tracer, uptakes in the heart, lung, liver and blood were estimated with a well-type scintillation counter (WC) and represented as the percentage of the injected dose per gram of tissue (%ID/g). The regions of interest (ROIs) were placed on planar images (PI) and the uptake in each organ was estimated as the percentage of the injected dose per pixel (%ID/pixel). The ratios of PI-to-WC and heart-to-organ were also evaluated. Cardiac uptake with WC was maximum (1.581%±1.893%) at 10 min post-injection. On the other hand, that with PI was maximum (1.493%±0.598%) at 45 min post-injection, but there were significant differences between both measurements (PI/WC ratio: about 1.0 time). Pulmonary uptake with WC was the maximum at 5 min (0.808%±0.015%) post-injection, and decreased gradually. PI measurement showed the maximum value at 45 min (0.760%±0.012%). Hepatic uptake with WC was the maximum at 30 min (0.594%±0.254%). On the other hand, PI measurement showed the same pattern with WC, but these values were higher value than WC as the whole. PI measurement showed higher uptakes in each organ than WC measurement. It was concluded that uptakes or the heart-to-organ ratio obtained clinically with PI might not represent a value that is always accurate.
Laboratory re-enactment of storage practices of older adults to determine potential implications for growth of listeria monocytogenes

Article published in Food Protection Trends on 29 May 2019, available at: https://www.foodprotection. org/publications/food-protection-trends/archive/2019-05-laboratory-re-enactment-of-storage-practices-of-older-adults-to-determine-potential-implicat/.
Cytoarchitecture and neural afferents of orbitofrontal cortex in the brain of the monkey

The orbitofrontal cortex of the monkey can be subdivided into a caudal agranular sector, a transitional dysgranular sector, and an anterior granular sector. The neural input into these sectors was investigated with the help of large horseradish peroxidase injections that covered the different sectors of orbitofrontal cortex. The distribution of retrograde labeling showed that the majority of the cortical projections to orbitofrontal cortex arises from a restricted set of telencephalic sources, which include prefrontal cortex, lateral, and inferomedial temporal cortex, the temporal pole, cingulate gyrus, insula, entorhinal cortex, hippocampus, amygdala, and claustrum. The posterior portion of the orbitofrontal cortex receives additional input from the piriform cortex and the anterolateral portion from gustatory, somatosensory, and premotor areas.
Online Radio Map Update Based on a Marginalized Particle Gaussian Process

In this paper, a novel scheme is reported to adapt radio maps to environmental dynamics in an online fashion by combining crowdsourcing and gaussian process regression (GPR). Specifically, a Marginalized Particle Gaussian Process (MPGP) is adopted to recursively fuse crowdsourced fingerprints with an existing offline radio map. The advantages of the proposed scheme lie in the efficiency and scalability in comparison with the traditional approaches. Extensive experiments are carried out in a real scenario of nearly 1000 m2 during five months, and a comparison is made with several existing popular solutions. It is shown that the proposed scheme outperforms its counterparts in terms of both robustness and accuracy.
Practical Limits of Multi-Tone Signaling Over High-Speed Backplane Electrical Links

Application of Discrete Multi-tone (DMT) signaling to high-speed backplane interconnects requires major modifications to the well-known analysis methods applied to wireline communication systems. Tight power budgets in backplane links impose severe constraints on DMT block size and use of channel shortening filters in the system. Consequently, maximum throughput is achieved in a DMT system that is (residual) interference limited and water-filling is not applicable in its original form. In this paper, the DMT system is cast as a Second Order Conic (SOQ problem with peak transmit power as the constraint and optimum integer bit-loading and power allocation are achieved through a novel incremental integer bit-loading algorithm. The convex framework is subsequently used to find "practical" upper bounds on the performance of multi-tone signaling over highspeed links. The results indicate that DMT has the potential to achieve 15-23 Gbps over typical backplane channels and system requirements in terms of FFT block size and prefix length are obtained.
circadian rhythm disorders British Association for Psychopharmacology consensus statement on evidence-based treatment of

Sleep disorders are common in the general population and even more so in clinical practice, yet are relatively poorly understood by doctors and other health care practitioners. These British Association for Psychopharmacology guidelines are designed to address this problem by providing an accessible up-to-date and evidence-based outline of the major issues, especially those relating to reliable diagnosis and appropriate treatment. A consensus meeting was held in London in May 2009. Those invited to attend included BAP members, representative clinicians with a strong interest in sleep disorders and recognized experts and advocates in the field, including a representative from mainland Europe and the USA. Presenters were asked to provide a review of the literature and identification of the standard of evidence in their area, with an emphasis on meta-analyses, systematic reviews and randomized controlled trials where available, plus updates on current clinical practice. Each presentation was followed by discussion, aimed to reach consensus where the evidence and/or clinical experience was considered adequate or otherwise to flag the area as a direction for future research. A draft of the proceedings was then circulated to all participants for comment. Key subsequent publications were added by the writer and speakers at draft stage. All comments were incorporated as far as possible in the final document, which represents the views of all participants although the authors take final responsibility for the document.