Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution of the Symmetric Difference Metric on Phylogenetic Trees

The symmetric difference metric has been useful in comparing phylogenetic trees derived from DNA sequence data. The main result shown here is that the frequency of pairs of binary trees a given distance apart is described by a limiting Poisson distribution, with $e^{ -1 / 8} \approx 88$ percent of all pairs maximally distant. Asymptotic bounds on the distribution are derived, and the asymptotic mean and variance of the normalized metric on the class of all phylogenetic trees is also calculated. The results rely on simple combinatorial constructions and analytic properties of appropriate generating functions.
Efficacy of Risk‐Reducing Salpingo‐Oophorectomy in Women with BRCA‐1 and BRCA‐2 Mutations

Abstract: Recognizing the emerging role of genetics in clinical care, in 1996 the American Society of Clinical Oncology established a Task Force on Cancer Genetics Education to develop educational opportunities and resources for its members. These efforts, and recent advances in the understanding of genetic predisposition to breast and ovarian cancers, have resulted in growing numbers of women participating in genetic testing protocols. The first prospective clinical trial involving women with known BRCA‐1 and BRCA‐2 mutations was recently published. In a prospective study involving 170 BRCA‐1 and BRCA‐2 mutation carriers and a mean follow‐up of 2 years, the estimated 5‐year cancer‐free estimates were 96% for the 98 women choosing prophylactic bilateral salpingo‐oophorectomy and 69% for the 72 women choosing intensive surveillance (p = 0.006). Three cases of stage I ovarian cancers were diagnosed at the time of prophylactic surgery. These results are consistent with published literature and data from the Prevention and Observation of Surgical Endpoints (PROSE) study group, which reported a 96% reduction in ovarian cancer risk and a 53% reduction in breast cancer risk among BRCA‐1 and BRCA‐2 mutation carriers who had prophylactic bilateral oophorectomy compared to matched controls. Thus prophylactic bilateral salpingo‐oophorectomy can be regarded as an effective risk‐reducing procedure that permits early diagnosis of ovarian cancer at the time of surgery and significantly reduces the risk of breast and ovarian cancer in women with germ‐line mutations in the BRCA‐1 and BRCA‐2 genes.
Conversion of 5-Hydroxytryptophan into Serotonin by Tryptophan Decarboxylase in Plants, Escherichia coli, and Yeast

The L-tryptophan decarboxylase (TDC) gene of rice was heterologously expressed in various organisms. Transgenic rice overexpressing TDC showed accumulation of serotonin upon 5-hydroxytryptophan treatment, which was consistent with the in vitro 5-hydroxytryptophan decarboxylase enzyme activity of purified recombinant rice TDC in a pyridoxal phosphate-dependent manner. Recombinant yeast harboring TDC produced serotonin at the expense of the endogenous 5-hydroxytryptophan levels.
Die Creol Taal: 250 Years of Negerhollands Texts

Negerhollands is the original creole language, lexically closely related to Dutch, of the Virgin Islands. It emerged as a separate language around 1700 and died out completely only a few years ago, having gradually been replaced by English in the course of the nineteenth century. Apart from giving information about the history and the features of this language, this book is an attempt to document the various phases of Negerhollands and make texts accessible to a wider public.
Induction of Immune‐related Gene Expression in Ctenopharyngodon idella Kidney Cells by Secondary Metabolites from Immunostimulatory Alcaligenes faecalis FY‐3

This study was undertaken to isolate active secondary metabolites from immunostimulatory Alcaligenes faecalis FY‐3 and evaluate their activities using grass carp Ctenopharyngodon idella kidney (CIK) cells. By applying chromatography techniques and successive recrystallization, three purified metabolites were obtained and identified by spectral data (mass spectrometry and nuclear magnetic resonance) as: (1) phenylacetic acid, (2) p‐hydroxyphenylacetylamide and (3) cyclo‐(Gly‐L‐Pro). CIK cells were stimulated by different concentrations (1, 10 and 100 μg/ml) of the isolated compounds, and expression of MyD88, IL‐1β, TNF‐α, type I‐IFN and IL‐8 genes at different time points (2, 8 and 24 h) post‐stimulation was quantified by real‐time PCR. The known immunostimulatory agent lipopolysaccharide (LPS) was used as a positive control. To analyse whether these compounds are toxic to the cells, the methyl tetrazolium assay was employed to measure changes in cell viability. The obtained results revealed that transcribing level of MyD88, an important adaptor molecule in toll‐like receptor signalling pathway, was augmented remarkably by all the three isolated compounds and LPS as early as 2‐h exposure. These compounds also induced gene expression of cytokines such as IL‐1β, TNF‐α and type I‐IFN. Under the experimental conditions, none of the test compounds is toxic to the CIK cells. These findings demonstrate that the immunostimulatory properties of the three metabolites [phenylacetic acid, p‐hydroxyphenylacetylamide and cyclo‐(Gly‐L‐Pro)] from A. faecalis FY‐3 in CIK cells and highlight the potential of using these metabolites as immunostimulants in fish aquaculture.
Saturated control of flexible-joint manipulators using a Hammerstein strictly positive real compensator

SUMMARY In this paper the control of flexible-joint manipulators while explicitly avoiding actuator saturation is considered. The controllers investigated are composed of a bounded proportional control term and a Hammerstein strictly positive real angular rate control term. This control structure ensures that the total torque demanded of each actuator is bounded by a value that is less than the maximum torque that each actuator is able to provide, thereby disallowing actuator saturation. The proposed controllers are shown to render the closed-loop system asymptotically stable, even in the presence of modeling uncertainties. The performance of the controllers is demonstrated experimentally and in simulation.
Immunological and viral features in patients with overactive bladder associated with human T‐cell lymphotropic virus type 1 infection

The majority of patients infected with human T‐cell lymphotropic virus‐type 1 (HTLV‐1) are considered carriers, but a high frequency of urinary symptoms of overactive bladder, common in HTLV‐1 associated myelopathy/tropical spastic paraparesis (HAM/TSP) have been documented in these patients. The aim of this study was to determine if immunological and viral factors that are seen in HAM/TSP are also observed in these patients. Participants were classified as HTLV‐1 carriers (n = 45), HTLV‐1 patients suffering from overactive bladder (n = 45) and HAM/TSP (n = 45). Cells from HTLV‐1 overactive bladder patients produced spontaneously more proinflammatory cytokines than carriers. TNF‐α and IL‐17 levels were similar in HAM/TSP and HTLV‐1 overactive bladder patients. High proviral load was found in patients with overactive bladder and HAM/TSP and correlated with proinflammatory cytokines. In contrast with findings in patients with HAM/TSP, serum levels of Th1 chemokines were similar in HTLV‐1 overactive bladder and carriers. Exogenous addition of regulatory cytokines decreased spontaneous IFN‐γ production in cell cultures from HTLV‐1 overactive bladder patients. The results show that HTLV‐1 overactive bladder and HAM/TSP patients have in common some immunological features as well as similar proviral load profile. The data show that HTLV‐1 overactive bladder patients are still able to down regulate their inflammatory immune response. In addition, these patients express levels of chemokines similar to carriers, which may explain why they have yet to develop the same degree of spinal cord damage as seen in patients with HAM/TSP. These patients present symptoms of overactive bladder, which may be an early sign of HAM/TSP. J. Med. Virol. 84:1809–1817, 2012. © 2012 Wiley Periodicals, Inc.
Hamiltonian Monte Carlo with explicit, reversible, and volume-preserving adaptive step size control

Hamiltonian Monte Carlo is a Markov chain Monte Carlo method that uses Hamiltonian dynamics to efficiently produce distant samples. It employs geometric numerical integration to simulate Hamiltonian dynamics, which is a key of its high performance. We present a Hamiltonian Monte Carlo method with adaptive step size control to further enhance the efficiency. We propose a new explicit, reversible, and volume-preserving integration method to adaptively set the step sizes, which does not violate the detailed balance condition or require a large increase in computational time.
The Last Sherlock Holmes Story

For fifty years after Dr Watson's death, a packet of papers, written by the doctor himself, lay hidden in a locked box. The papers contained an extraordinary report of the case of Jack the Ripper and the horrible murders in the East End of London in 1888. The detective, of course, was the great Sherlock Holmes - but why was the report kept hidden for so long? This is the story that Sir Arthur Conan Doyle never wrote. It is a strange and frightening tale .
Academics' responses to encountered information: Context matters

An increasing number of tools are being developed to help academics interact with information, but little is known about the benefits of those tools for their users. This study evaluated academics' receptiveness to information proposed by a mobile app, the SerenA Notebook: information that is based in their inferred interests but does not relate directly to a prior recognized need. The evaluated app aimed at creating the experience of serendipitous encounters: generating ideas and inspiring thoughts, and potentially triggering follow‐up actions, by providing users with suggestions related to their work and leisure interests. We studied how 20 academics interacted with messages sent by the mobile app (3 per day over 10 consecutive days). Collected data sets were analyzed using thematic analysis. We found that contextual factors (location, activity, and focus) strongly influenced their responses to messages. Academics described some unsolicited information as interesting but irrelevant when they could not make immediate use of it. They highlighted filtering information as their major struggle rather than finding information. Some messages that were positively received acted as reminders of activities participants were meant to be doing but were postponing, or were relevant to ongoing activities at the time the information was received.
International Conference on Emerging Ubiquitous Systems and Pervasive Networks ( EUSPN-2014 ) Feature Selection for Place Classification through Environmental Sounds

In this work, an environmental audio classification scheme is proposed using a Chi squared filter as a feature selection strategy. Using feature selection (FS), the original 62 features characteristic vector can be optimized, and it can be used for environmental sound classification. These features are obtained using statistical analysis and frequency domain analysis. As a result, we obtain a reduced feature vector composed of 15 features: 11 statistical and 4 of the frequency domain. Using this reduced vector, a 10 class classification was done, using Support Vector machines (SVM) as classification method, the accuracy is higher than 90%. c © 2014 The Authors. Published by Elsevier B.V. Selection and peer-review under responsibility of Elhadi M. Shakshuki.
Micro-particle impact phenomena on contact surface under different applied voltages in vacuum interrupters

According to the vacuum breakdown model based on Cranberg “clump” hypothesis, micro-particles on contact surface can be detached from the contact surface and accelerated across the vacuum gap towards to the opposite contact under an applied voltage in vacuum interrupters (VIs). Finally they can impact on the target contact surface with high velocities, which probably triggers a breakdown in the vacuum gap. Thus, the mechanism of the impact phenomena may be the key to understanding the mechanism of the vacuum breakdown initiated by the micro-particles. Moreover, the detailed nature of the dynamic impact process is a subject of the hydro-dynamical theories on the projectile impact. The objective of this paper is to study the micro-particles impact phenomena in VIs by introducing a mesh-free numerical calculation method Smoothed Particle Hydrodynamics (SPH) method which is an efficient method of the projectile impact studies. In this paper, the materials of the micro-particle and the target contact were assumed to be copper and stainless-steel, respectively. The radius of the micro-particle was assumed to be 0.1 µm. The characteristics of the deformations occurring during the high-velocity impact processes are investigated under the different applied voltages (10 to 60 kV). As a result, it is found that the deformations of the micro-particles and the target contacts are severer with the increase of applied voltages, due to the increase of the impact velocities. With the applied voltages 50 kV and even to 60 kV (the impact velocity 526 and 631 m/s), there can be damages generated on the contact surface accompanying by a large number of high-velocity secondary particles. Furthermore, the influencing factors of the micro-particles impact phenomena in VIs, such as the size of the micro-particles, the microscopic electric field distribution, the contact materials and so on, have also be considered. The result of this paper may provide some useful information to understand the vacuum breakdown initiated by the micro-particles.
Assessment of dietary fish consumption in pregnancy: comparing one-, four- and thirty-six-item questionnaires

Abstract Objective Fish consumption influences a number of health outcomes. Few studies have directly compared dietary assessment methods to determine the best approach to estimating intakes of fish and its component nutrients, including DHA, and toxicants, including methylmercury. Our objective was to compare three methods of assessing fish intake. Design We assessed 30 d fish intake using three approaches: (i) a single question on total fish consumption; (ii) a brief comprehensive FFQ that included four questions about fish; and (iii) a focused FFQ with thirty-six questions about different finfish and shellfish. Setting Obstetrics practices in Boston, MA, USA. Subjects Fifty-nine pregnant women who consumed ≤2 monthly fish servings. Results Estimated intakes of fish, DHA and Hg were lowest with the one-question screener and highest with the thirty-six-item fish questionnaire. Estimated intake of DHA with the thirty-six-item questionnaire was 4·4-fold higher (97 v. 22 mg/d), and intake of Hg was 3·8-fold higher (1·6 v. 0·42 μg/d), compared with the one-question screener. Plasma DHA concentration was correlated with fish intake assessed with the one-question screener (Spearman r = 0·27, P = 0·04), but not with the four-item FFQ (r = 0·08, P = 0·54) or the thirty-six-item fish questionnaire (r = 0·01, P = 0·93). In contrast, blood and hair Hg concentrations were similarly correlated with fish and Hg intakes regardless of the assessment method (r = 0·35 to 0·52). Conclusions A longer questionnaire provides no advantage over shorter questionnaires in ranking intakes of fish, DHA and Hg compared with biomarkers, but estimates of absolute intakes can vary by as much as fourfold across methods.
Time to take CT screening to the next level?

The paper by Pompe et al. [1] in this edition of the European Respiratory Journal investigated subjects from the National Lung Cancer Screening Trial (NLST), whose cause of death was recorded as being a respiratory illness other than lung cancer. The patients’ computed tomography (CT) scans were retrospectively reviewed and compared with the NLST participants of the CT arm who were still alive. Not surprisingly, significantly more lung diseases were detected in those who died from respiratory disease than in the matched control group. Transforming lung cancer screening into a comprehensive programme to detect and treat smoking-related disease early http://ow.ly/b8L5309hUri
Hybrid three-dimensional camera pose estimation using particle filter sensor fusion

To properly align objects in the real and virtual worlds in an augmented reality (AR) space it is essential to keep tracking the camera's exact three-dimensional position and orientation (camera pose). State-of-the-art analysis shows that traditional vision-based or inertial sensor-based solutions are not adequate when used individually. Sensor fusion for hybrid tracking has become an active research direction during the past few years, although how to do it in a robust and principled way is still an open problem. In this paper, we develop a hybrid camera pose-tracking system that combines vision and inertial sensor technologies. We propose to use the particle filter framework for the sensor fusion system. Particle filters are sequential Monte-Carlo methods based upon a point mass (or 'particle') representation of probability densities, which can be applied to any state space model and which generalize the traditional Kalman filtering methods. We have tested our algorithm to evaluate its performance and have compared the results obtained by the particle filter with those given by a classical extended Kalman filter. Experimental results are presented
A Test of the Spatial-Frequency Explanation of the Müller-Lyer Illusion

Previous investigations have shown that the response of spatial-frequency-specific channels in the human visual system is differentially affected by adaptation to gratings of distinct spatial frequencies and/or orientations. A study is reported of the effects of adaptation to vertical or horizontal gratings of a high or a low spatial frequency on the extent of the Brentano form of the Müller-Lyer illusion in human observers. It is shown that the illusion decreases after adaptation to vertical gratings of low spatial frequency, but seems unaffected otherwise. These results are consistent with the notion of visual channels that are spatial-frequency and orientation specific, and support the argument that the Müller-Lyer illusion may be due primarily to lower-spatial-frequency components in the Fourier spectra of the image.
CISPR limits for the conducted disturbances of DC ports of PV-GCPCs

This paper reports standardization activities in CISPR and introduces newly developed limits and measurement method of conducted disturbances at the DC ports of Grid Connected Power Converters (GCPCs) applied to solar-photovoltaic power (PV) generating systems. First, background of standardization activities on the development of the limits and measurement method is described. Second, the two proposals on the measurement method and the two approaches for the derivation of the limits are reported. Third, the derivation of the limits based on the two approaches is shown in detail. Finally, the process of reaching an agreement in respect of the limits is reported, and the derived limits are shown.
Air cargo transport by multi-agent based planning

Most major airlines decide to take new strategies for the competition in the air cargo industry. They are concerned with assigning cargo over flights in creative ways. The paper considers the multi-agent solution for cargo assignment. First we present cargo control principles and introduce the pipelining assignment concept, then the difficulties of traditional operations research for solving this assignment are pointed out. After explaining the motivations for an agent solution, we propose a robust solution in which the flights are represented as agents and the cargo assignment is viewed as a coalition formation process among these agents. Finally, future perspectives are summarized. The main solution idea is that the agents communicate and cooperate with each other to form the best coalitions of delivering the planned shipments, and coalitions get along with available information so that the control principles can be fully performed and air capacity can be best managed.
Neurobehaviors and psychotic symptoms in Alzheimer's disease

Psychotic symptoms are common in Alzheimer's disease (AD) and clinicoanatomical and neuropsychological evidence indicate an association between these symptoms and frontal lobe dysfunction. Neurobehaviors associated with frontal dysfunction were assessed in Alzheimer's disease (AD) patients with (n = 20) and without psychotic symptoms (n = 21) matched for mean age, education, gender, and dementia severity. The Frontal Lobe Personality Scale (FLOPs) was completed by patient caregivers to measure behaviors typically associated with frontal dysfunction. Findings indicated that AD patients with psychotic symptoms exhibited significantly greater neurobehavioral dysfunction (FLOPs M = 130.69, SD = 24.70) than AD patients without psychotic symptoms (FLOPs M = 111.10, SD = 25.83). Subscale analyses indicated that psychotic AD patients were more disinhibited (M = 28.28, SD = 7.54) than patients without psychotic symptoms (M = 20.92, SD = 4.9). Findings are consistent with and contribute to previous neuropsychological and clinicoanatomical research suggesting increased frontal dysfunction in AD with psychotic symptoms and lend additional empirical support to subtyping AD based on the presence of psychotic symptoms. Furthermore, findings provide preliminary evidence indicating which specific type of neurobehavioral abnormalities are related to the presence of distressing psychotic symptoms. (JINS, 2000, 6, 815–820.)
GPU Accelerated ACF Detector

The field of pedestrian detection has come a long way in recent decades. In terms of accuracy, the current state-of-the-art is hands down reached by Deep Learning methods. However in terms of running speed this is not always the case, traditional methods are often still faster than their Deep Learning counterparts. This is especially true on embedded hardware, embedded platforms are often used in applications that require realtime performance while at same the time having to make do with a limited amount of resources. In this paper we present a GPU implementation of the ACF pedestrian detector and compare it to current Deep Learning approaches (YOLO) on both a desktop GPU as well as the Jetson TX2 embedded GPU platform.
A 60 GHz CMOS power amplifier with modified pre-distortion linearizer

This paper proposes a new pre-distortion linearizer for CMOS power amplifier (PA) to improve the performance of the output 1-dB compression power and power added efficiency at 1-dB compression power. By adopting the proposed pre-distortion linearizer, a 60 GHz cascode PA with 13.7-dBm 1-dB compression power (P1dB) and 14.3% power added efficiency (PAE) at P1dB is demonstrated. The chip size is 0.55 × 0.45 mm2 including all testing pads.
The right ventricle in congenital heart disease

In patients with congenital heart disease the right ventricle (RV) may support the pulmonary (subpulmonary RV) or the systemic circulation (systemic RV). During the last 50 years evidence is accumulating that RV dysfunction develops in many of these patients and leads to considerable morbidity and mortality. Therefore RV function in certain groups of congenital heart disease patients needs close surveillance and timely and appropriate intervention to optimise outcomes. Despite major progress being made, assessing the RV either in the subpulmonary or the systemic circulation remains challenging, often requiring a multi-imaging approach and expertise (echocardiography, magnetic resonance imaging, nuclear and occasionally invasive assessment with angiography). This review discusses the implications of volume and pressure loading of the RV in the context of congenital heart disease and describes the most relevant imaging modalities for monitoring RV function.