Miracle-dz/UniFAR-FTUs huggingface dataset:
Relationship between Tumor Heterogeneity Measured on FDG-PET/CT and Pathological Prognostic Factors in Invasive Breast Cancer

Background There is currently little support to understand which pathological factors led to differences in tumor texture as measured from FDG PET/CT images. We studied whether tumor heterogeneity measured using texture analysis in FDG-PET/CT images is correlated with pathological prognostic factors in invasive breast cancer. Methods Fifty-four patients with locally advanced breast cancer who had an initial FDG-PET/CT were retrospectively included. In addition to SUVmax, three robust textural indices extracted from 3D matrices: High-Gray-level Run Emphasis (HGRE), Entropy and Homogeneity were studied. Univariate and multivariate logistic regression was used to identify PET parameters associated with poor prognosis pathological factors: hormone receptor negativity, presence of HER-2 and triple negative phenotype. Receiver operating characteristic (ROC) curves and the (AUC) analysis, and reclassification measures, were performed in order to evaluate the performance of combining texture analysis and SUVmax for characterizing breast tumors. Results Tumor heterogeneity, measured with HGRE, was higher in negative estrogen receptor (p = 0.039) and negative progesterone receptor tumors (p = 0.036), and in Scarff-Bloom-Richardson grade 3 tumors (p = 0.047). None of the PET indices could identify HER-2 positive tumors. Only SUVmax was positively correlated with Ki-67 (p<0.0004). Triple negative breast cancer (TNBC) exhibited higher SUVmax (Odd Ratio = 1.22, 95%CI [1.06–1.39],p = 0.004), lower Homogeneity (OR = 3.57[0.98–12.5],p = 0.05) and higher HGRE (OR = 8.06[1.88–34.51],p = 0.005) than non-TNBC. Multivariate analysis showed that HGRE remained associated with TNBC (OR = 5.27[1.12–1.38],p = 0.03) after adjustment for SUVmax. Combining SUVmax and HGRE yielded in higher area under the ROC curves (AUC) than SUVmax for identifying TNBC: AUC = 0.83 and 0.77, respectively. Probability of correct classification also increased in 77% (10/13) of TNBC and 71% (29/41) of non-TNBC (p = 0.003), when combining SUVmax and HGRE. Conclusions Tumor heterogeneity measured on FDG-PET/CT was higher in invasive breast cancer with poor prognosis pathological factors. Texture analysis might be used, in addition to SUVmax, as a new tool to assess invasive breast cancer aggressiveness.
Cross-Checking Multiple Data Sources Using Multiway Join in MapReduce

As data sources accumulate information and data size escalates it becomes more and more difficult to maintain the correctness and validity of these datasets. Therefore, tools must emerge to facilitate this daunting task. Fact checking usually involves a large number of data sources that talk about the same thing but we are not sure which holds the correct information or which has any information at all about the query we care for. A join among all or some data sources can guide us through a fact-checking process. However, when we want to perform this join on a distributed computational environment such as MapReduce, it is not obvious how to distribute efficiently the records in the data sources to the reduce tasks in order to join any subset of them in a single MapReduce job. To this end, we propose an efficient approach using the multiway join to cross-check these data sources in a single round.
Streaming Virtual Reality Content

The recent rise of interest in Virtual Reality (VR) came with the availability of commodity commercial VR prod- ucts, such as the Head Mounted Displays (HMD) created by Oculus and other vendors. To accelerate the user adoption of VR headsets, content providers should focus on producing high quality immersive content for these devices. Similarly, multimedia streaming service providers should enable the means to stream 360 VR content on their platforms. In this study, we try to cover different aspects related to VR content representation, streaming, and quality assessment that will help establishing the basic knowledge of how to build a VR streaming system.
The ubiquitin-conjugating enzyme Rad6 (Ubc2) is required for silencing in Saccharomyces cerevisiae

It has been previously shown that genes transcribed by RNA polymerase II (RNAP II) are subject to position effect variegation when located near yeast telomeres. This telomere position effect requires a number of gene products that are also required for silencing at the HML and HMR loci. Here, we show that a null mutation of the DNA repair gene RAD6 reduces silencing of the HM loci and lowers the mating efficiency of MATa strains. Likewise, rad6-delta reduces silencing of the telomere-located RNAP II-transcribed genes URA3 and ADE2. We also show that the RNAP III-transcribed tyrosyl tRNA gene, SUP4-o, is subject to position effect variegation when located near a telomere and that this silencing requires the RAD6 and SIR genes. Neither of the two known Rad6 binding factors, Rad18 and Ubr1, is required for telomeric silencing. Since Ubrl is the recognition component of the N-end rule-dependent protein degradation pathway, this suggests that N-end rule-dependent protein degradation is not involved in telomeric silencing. Telomeric silencing requires the amino terminus of Rad6. Two rad6 point mutations, rad6(C88A) and rad6(C88S), which are defective in ubiquitin-conjugating activity fail to complement the silencing defect, indicating that the ubiquitin-conjugating activity of RAD6 is essential for full telomeric silencing.
Height of Water Pouring Effects on Infiltration Runs Carried Out in an Initially Wet Sandy-loam Soil

Height of Water Pouring Effects on Infiltration Runs Carried Out in an Initially Wet Sandy-loam Soil Vincenzo Bagarello*, Noemi Cecere, Simone Di Prima, Giuseppe Giordano, Massimo Iovino Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy Dipartimento di Agraria, Università degli Studi di Sassari, Viale Italia, 39, 07100 Sassari, Italy vincenzo.bagarello@unipa.it
Distributed motion control algorithm for fission behavior of flocks

It is important yet challenging to coordinate the motion of a swarm of mobile agents as a cohesive group. In this paper, we focus on the fission problem of splitting the coherent group into multiple sub-groups for the swarm system without identifier and explicit communication. We propose a novel motion control algorithm which integrates a following interaction with the long-range attraction, short-range repulsion, and consensus-based alignment behaviors, where the following strategy is locally applied to one of the proximity neighbors based on the changes of their motion. Through this algorithm, flocks can be split into multiple sub-groups autonomously when multiple agents with distinct preferred directions are introduced. Finally, simulation examples are provided to illustrate the effectiveness of the proposed method in fission maneuvers.
Intra-Step Belt-Speed Variation and Horizontal Power Transfer during Treadmill Running

The motor driven treadmill is often used in research as a convenient tool for simulating overground running. There has been varied opinion in the literature regarding the accuracy of this assumption. The major difference that has been quantified is the variation in treadmill belt speed as a result of the forces applied by a runner. In comparison, the earth does not vary its speed during overground running. The aim of the present study was to more clearly define the causes of treadmill belt-speed variation and to elucidate its effects on running mechanics. An in-lab fabricated tachometer was used to determine accurate treadmill belt speed while the treadmill was challenged by five subjects weighing 55.2 to 99.6 kg running at four speeds of 2.6, 3.1, 3.5 and 4.0 m/s. The actual running velocity was found on average to be 0.62% higher than the treadmill display setting. The intra-step belt-speed variation ranged from 4.2 to 8.6 % of average belt velocity. Linear regression analysis showed that 86 % of the variance in intra-step belt-speed variation was attributed to total body mass and a further 10 % attributed to running speed. The effect that this variation had on running mechanics was determined from the power transfer between the foot and belt, as calculated from the product of the change in belt speed and the horizontal ground reaction force. The horizontal force, as calculated using a segmental acceleration approach, did not show complete agreement with simultaneously recorded forceplate data. It was found that an average of4.49 J flowed to
A bridgeless power factor rectifier with soft-switching

This paper presents a bridgeless power factor correction rectifier with soft-switching. The proposed rectifier consists of a traditional rectifier diode bridge and a dc/dc power factor correction circuit, and an auxiliary circuit is used to achieve soft-switching. The auxiliary circuit can provide zero-voltage turn-on and zero-current turn-off for the main switch without any additional voltage or current stresses. The auxiliary switch is turned-off with zero-current switching, thus the switching losses and electromagnetic interference are reduced. Therefore, this circuit can improve the overall system efficiency. Finally, the proposed circuit is verified by computer simulation.
Patient Assessment of Chronic Illness Care, Glycemic Control and the Utilization of Community Health Care among the Patients with Type 2 Diabetes in Shanghai, China

Objectives To evaluate the relationship between Patient Assessment of Chronic Illness Care in community health centers and self-management behaviors and glycemic control and to examine the relationship between Patient Assessment of Chronic Illness Care in community health centers and the utilization of community health centers for monitoring and treating diabetes among the patients with type 2 diabetes. Methods A questionnaire including self-management behaviors, glycemic control, Patient Assessment of Chronic Illness Care in community health centers and the most often utilized medical institutions for monitoring and treating diabetes (community health centers vs. hospitals) was administered to 960 patients with type 2 diabetes in Shanghai, China. The relationships between Patient Assessment of Chronic Illness Care and self-management behaviors, self-management behaviors and glycemic control, Patient Assessment of Chronic Illness Care and glycemic control, Patient Assessment of Chronic Illness Care and the most often utilized medical institutions for monitoring and treating diabetes were examined. Results Wilcoxon rank sum tests showed that the high scores of total Patient Assessment of Chronic Illness Care and five subscales in community health centers were positively related to almost all the proper self-management behaviors and good glycemic control (p<0.05). Almost all of the proper self-management behaviors were positively related to good glycemic control (p<0.01). High summary score of the Patient Assessment of Chronic Illness Care was positively associated with the utilization of community health centers for monitoring and treating diabetes (p<0.001). Conclusions Patient Assessment of Chronic Illness Care (implementation of the Chronic Care Model) in community health centers was associated with patients' self-management behaviors and glycemic control, and finally was associated with the utilization of community health centers for monitoring and treating diabetes.
A three-level self-synchronizing hysteresis current regulator with constant switching frequency

While hysteresis current control offers the benefits of a fast dynamic response and inherent overcurrent protection, its variable switching frequency and inherent two-level switching response make it unsuitable for many applications. This paper presents a new approach for three-level hysteresis control of a single phase grid-connected inverter that overcomes these limitations. The strategy adjusts the hysteresis band magnitude in response to variations in the inverter average output voltage, to achieve constant switching frequency using only one hysteresis comparator and without requiring DC offset compensation or current error zero-crossing measurement. The inverter average voltage is also used to estimate the phase of the incoming grid voltage, to create a current reference for the regulator at any required power factor. The result is a robust sensorless hysteresis current regulator suitable for three-level grid connected applications that operates with a constant switching frequency.
Environmental quality of an urban sub-basin: a study case of Alfenas – MG

The cities expansion conditioned by the urban population increase exerts considerable ecosystems pressure, often leading them to high degradation stages. The use of proceedings and techniques that evaluate current conditions and possible future scenarios are indispensable, seeking sustainability for socioeconomic development and environmental protection. Therefore, a Rapid Assessment Protocol was applied to evaluate parameters of urban environmental and water quality of the Corrego do Pântano 1 Hydrographic Sub-basin, Alfenas - MG, located at the municipality periurban limit, important area for the provision of environmental services and a response indicator to the urban processes on the natural environment. Thus, weights were distributed for the environmental quality indicators and, for each variable, was designated a note, making possible the composition of a scenario of the environmental conditions of the studied sites. It was verified that the application of the Rapid Assessment Protocol is an efficient means for directing public policies aimed at mitigating the impacts caused by cities on the environmental and water quality of sub-basins under urban influence. It is recommended the implementation of a sub-basin management plan with guidelines that embrace the conservation of the area mainly directed to the recovery of native vegetation and inspection of the urban effluents emission.
Towards a Framework for Detecting and Managing Opinion Contradictions

Sentiment Analysis gains in interest due to the large amount of potential applications and the increasing number of opinions expressed in particular in the Web. The focus of this paper is the development of a framework on top of sentiment analysis for detecting contradictions. First, we introduce a statistical model of contradictions based on a mean value and the variance of sentiments among different posts. It can be used to analyze and track sentiment evolution over time, to identify interesting trends and patterns or even to enable argument extraction. Using synthetic datasets, we demonstrate the effectiveness of our method in capturing contradictions on noisy data. Inspired by this model, which has proven to be effective and efficient for numeric sentiments, we are trying to generalize it for arbitrary opinion data and outline a universal framework which can be efficiently used on a large scale. We discuss various problems and challenges of such a formulation and outline the scope of our future work in this direction.
Systematic Structural Analyses of Attachment Organelle in Mycoplasma pneumoniae

Mycoplasma pneumoniae, a human pathogenic bacterium, glides on host cell surfaces by a unique and unknown mechanism. It forms an attachment organelle at a cell pole as a membrane protrusion composed of surface and internal structures, with a highly organized architecture. In the present study, we succeeded in isolating the internal structure of the organelle by sucrose-gradient centrifugation. The negative-staining electron microscopy clarified the details and dimensions of the internal structure, which is composed of terminal button, paired plates, and bowl complex from the end of cell front. Peptide mass fingerprinting of the structure suggested 25 novel components for the organelle, and 3 of them were suggested for their involvement in the structure through their subcellular localization determined by enhanced yellow fluorescent protein (EYFP) tagging. Thirteen component proteins including the previously reported ones were mapped on the organelle systematically for the first time, in nanometer order by EYFP tagging and immunoelectron microscopy. Two, three, and six specific proteins localized specifically to the terminal button, the paired plates, and the bowl, respectively and interestingly, HMW2 molecules were aligned parallel to form the plate. The integration of these results gave the whole image of the organelle and allowed us to discuss possible gliding mechanisms.
Full waveform numerical simulations of seismoelectromagnetic wave conversions in fluid‐saturated stratified porous media

[1] We present a full-waveform modeling technique of the coupled seismoelectromagnetic wave propagation in fluid-saturated stratified porous media. Our simulation code uses the macroscopic governing equations derived by Pride [1994], which couple Biot's theory and Maxwell equations via flux/force transport equations. In this theory the coupling mechanism is explained by electrokinetic effects taking place at the pore level. The synthetic seismoelectrograms and seismomagnetrograms are computed by extending the generalized reflection and transmission matrix method and by using a discrete wave number integration of the global reflectivity obtained in the frequency wave number domain. Synthetic time sections and snapshots of the wave propagation are used to study the seismic, electromagnetic, and seismoelectromagnetic waves properties in fluid-saturated layered porous media. Two wave phenomena are investigated: (1) the electric and magnetic fields induced by the propagation of a seismic perturbation in a homogeneous porous medium and (2) the electromagnetic waves generated at depth when seismic waves propagate through a vertically heterogeneous porous medium. Concentrating on the second effect, we show that the zone which effectively contributes to the generation of EM disturbances along a plane interface coincides with the first Fresnel zone associated with a seismic-to-electromagnetic wave conversion. A numerical sensitivity study shows that the EM waves generated at depth by the passage of seismic waves through an interface are particularly sensitive to contrasts in porosity, permeability, fluid salinity, and fluid viscosity. Our numerical simulations highlight the potential of artificially generated seismoelectromagnetic converted waves for the characterization of the subsurface and its fluid content.
Evolving a Diversity of Creatures through Novelty Search and Local Competition

An ambitious challenge in artificial life is to craft an evolutionary process that discovers a wide diversity of welladapted virtual creatures within a single run. Unlike in nature, evolving creatures in virtual worlds tend to converge to a single morphology because selection therein greedily rewards the morphology that is easiest to exploit. However, novelty search, a technique that explicitly rewards diverging, can potentially mitigate such convergence. Thus in this paper an existing creature evolution platform is extended with multi-objective search that balances drives for both novelty and performance. However, there are different ways to combine performance-driven search and novelty search. The suggested approach is to provide evolution with both a novelty objective that encourages diverse morphologies and a local competition objective that rewards individuals outperforming those most similar in morphology. The results in an experiment evolving locomoting virtual creatures show that novelty search with local competition discovers more functional morphological diversity within a single run than models with global competition, which are more predisposed to converge. The conclusions are that novelty search with local competition may complement recent advances in evolving virtual creatures and may in general be a principled approach to combining novelty search with pressure to achieve.
An Oscillator-Based Active Bridge Circuit for Interfacing Capacitive Sensors With Microcontroller Compatibility

This paper deals with the development of a signal conditioning circuit, with microcontroller compatibility, for interfacing capacitive sensors suitable for a wide range of applications. The circuit comprises of a capacitive active bridge, along with a relaxation oscillator for converting capacitance changes into frequency directly. The design, analysis, and experimental results of the circuit and its application to a thin-film-based humidity sensor and a capacitive transducer for measurement of the dielectric constant of edible oil are reported. The experimental results confirm the theoretical values predicted. The frequency output of the circuit has been used to determine the response characteristics of the trace moisture sensor and the dielectric constants of the edible oils. Finally, the output frequency has been calibrated in terms of the trace moisture in parts per million (ppm), using commercial dew point meter (SHAW, U.K.). The accuracy of moisture measurement using custom designed capacitive sensor for the full-scale moisture range of 4-100 ppm, compared with the dew point meter (accuracy ±0.1%), is found to be nearly ±1% and the resolution is 1 ppm moisture. The circuit is less complex and is easy to integrate to application-specific integrated circuits in a standard CMOS technology with high sensitivity (selectable). It can be easily reproduced with the cheapest possible components, while achieving fairly good performance in terms of both accuracy and dynamic range.
BALANCING THE LOAD: A VORONOI BASED SCHEME FOR PARALLEL COMPUTATIONS

One of the key issues when running a simulation on multiple CPUs is maintaining a proper load balance throughout the run and minimizing communications between CPUs. We propose a novel method of utilizing a Voronoi diagram to achieve a nearly perfect load balance without the need of any global redistributions of data. As a show case, we implement our method in RICH, a two-dimensional moving mesh hydrodynamical code, but it can be extended trivially to other codes in two or three dimensions. Our tests show that this method is indeed efficient and can be used in a large variety of existing hydrodynamical codes.
GI-SVM: A sensitive method for predicting genomic islands based on unannotated sequence of a single genome

Genomic islands (GIs) are clusters of functionally related genes acquired by lateral genetic transfer (LGT), and they are present in many bacterial genomes. GIs are extremely important for bacterial research, because they not only promote genome evolution but also contain genes that enhance adaption and enable antibiotic resistance. Many methods have been proposed to predict GI. But most of them rely on either annotations or comparisons with other closely related genomes. Hence these methods cannot be easily applied to new genomes. As the number of newly sequenced bacterial genomes rapidly increases, there is a need for methods to detect GI based solely on sequences of a single genome. In this paper, we propose a novel method, GI-SVM, to predict GIs given only the unannotated genome sequence. GI-SVM is based on one-class support vector machine (SVM), utilizing composition bias in terms of k-mer content. From our evaluations on three real genomes, GI-SVM can achieve higher recall compared with current methods, without much loss of precision. Besides, GI-SVM allows flexible parameter tuning to get optimal results for each genome. In short, GI-SVM provides a more sensitive method for researchers interested in a first-pass detection of GI in newly sequenced genomes.