Miracle-dz/UniFAR-FTUs huggingface dataset:
Searching for phylogenetic trees under the frequency parsimony criterion: an approximation using generalized parsimony.

lelic frequency change as measured by the Manhattan metric. We provided three pri? mary arguments for choosing our method over other parsimony methods proposed for polymorphic data: (1) it accommodates polymorphism without resorting to coding strategies that permit the existence of im? possible conditions (e.g., ancestral loci for which all allele frequencies are zero); (2) it reduces the impact of sampling error (e.g., the failure to detect rare alleles in some populations or taxa; see also Rannala, 1995); and (3) it makes use of potentially useful frequency information that is lost in presence/absence coding strategies. De? spite its theoretical advantages, our meth? od has not been widely used because of its computational intensity and the inadequa? cy of the tree-searching algorithm used in the only existing implementation (FREQPARS; Swofford and Berlocher, 1987). Here, we propose a modification of the original method that overcomes these lim? itations by using an approximation to the original optimality criterion. In our original paper, we suggested that the MANAD (Manhattan distance, additiv? ity requirement) criterion be used to select optimal trees. Tree length is defined as the sum of the branch lengths (edges), where each branch length is measured by a Man? hattan distance. For a single brandi bound? ed by nodes A and B and a single locus ;, this distance D is defined as where p^nd p^are the frequencies of the /th allele at nodes A and B, respectively (nodes may either be terminal nodes rep? resenting terminal taxa or internal nodes representing hypothetical ancestors), and K is the total number of alleles. Obtaining a most-parsimonious reconstruction (MPR; Swofford and Maddison, 1987) under MANAD for a tree T requires finding the set of ancestral allele frequency arrays for all loci that minimize the length L of the tree. Thus,
Thermocline ventilation and pathways of tropical–subtropical water mass exchange

The mechanism of thermocline ventilation is investigated using a global, high-resolution oceanGCM, with realistic topography and surface wind forcing. Because 2-dimensional representationsof circulation can be misleading, the subsurface flow is examined by visualizing the trajectoriesof particles which subduct in the mid-latitudes and travel within the ventilated thermocline.Three model runs are performed, each with identical surface forcing but with different initialparticle distributions. Results from these runs show that the pathways of water mass exchangebetween the tropics and the subtropics are functions of the surface wind forcing, backgrounddensity structure, and basin geometry. In the Pacific, ventilated waters from the northern andsouthern mid-latitudes reach the tropical thermocline through both the western boundary andthe interior of the basin. In the Atlantic Ocean, the equatorial thermocline is ventilated primarilythrough water mass exchange with the southern hemisphere alone. In the Indian Ocean, thepathways of water mass exchange have patterns similar to those in the Atlantic and Pacificbasins, though the lack of a mid-latitude gyre in the northern basin restricts the deep subductionand ventilation to the southern hemisphere.
Low latency protocol for transmission of measurement data from FPGA to Linux computer via 10 Gbps Ethernet link

This paper presents FADE-10G—an integrated solution for modern multichannel measurement systems. Its main aim is a low latency, reliable transmission of measurement data from FPGA-based front-end electronic boards (FEBs) to a computer-based node in the Data Acquisition System (DAQ), using a standard Ethernet 1 Gbps or 10 Gbps link. In addition to transmission of data, the system allows the user to send reliably simple control commands from DAQ to FEB and to receive responses. The aim of the work is to provide a possible simple base solution, which can be adapted by the end user to his or her particular needs. Therefore, the emphasis is put on the minimal consumption of FPGA resources in FEB and the minimal CPU load in the DAQ computer. The open source implementation of the FPGA IP core and the Linux kernel driver published under permissive license facilitates modifications and reuse of the solution. The system has been successfully tested in real hardware, both with 1 Gbps and 10 Gbps links.
A Stable HeLa Cell Line That Inducibly Expresses Poliovirus 2Apro: Effects on Cellular and Viral Gene Expression

ABSTRACT A HeLa cell clone (2A7d) that inducibly expresses the gene for poliovirus protease 2A (2Apro) under the control of tetracycline has been obtained. Synthesis of 2Apro induces severe morphological changes in 2A7d cells. One day after tetracycline removal, cells round up and a few hours later die. Poliovirus 2Apro cleaves both forms of initiation factor eIF4G, causing extensive inhibition of capped-mRNA translation a few hours after protease induction. Methoxysuccinyl-Ala-Ala-Pro-Val-chloromethylketone, a selective inhibitor of 2Apro, prevents both eIF4G cleavage and inhibition of translation but not cellular death. Expression of 2Apro still allows both the replication of poliovirus and the translation of mRNAs containing a picornavirus leader sequence, while vaccinia virus replication is drastically inhibited. Translation of transfected capped mRNA is blocked in 2A7d-On cells, while luciferase synthesis from a mRNA bearing a picornavirus internal ribosome entry site (IRES) sequence is enhanced by the presence of 2Apro. Moreover, synthesis of 2Apro in 2A7d cells complements the translational defect of a poliovirus 2Apro-defective variant. These results show that poliovirus 2Apro expression mimics some phenotypical characteristics of poliovirus-infected cells, such as cell rounding, inhibition of protein synthesis and enhancement of IRES-driven translation. This cell line constitutes a useful tool to further analyze 2Aprofunctions, to complement poliovirus 2Apro mutants, and to test antiviral compounds.
Autonomous line follower robot controlled by cell culture

Neuro-electronic hybrid promises to bring up a model architecture for computing. Such computing architecture could help to bring the power of biological connection and electronic circuits together for better computing paradigm. Such paradigms for solving real world tasks with higher accuracy is on demand now. A robot as a autonomous system is modeled here to navigate following a particular line. Sensory inputs from robot is directed as input to the cell culture in response to which motor commands are generated from the culture.
Cohort profile: Norwegian Epidemiologic Osteoporosis Studies (NOREPOS)*

Aims: This paper describes the history, purpose, data collection and contributions in the research collaboration Norwegian Osteoporosis Epidemiologic Studies (NOREPOS). Methods: NOREPOS encompasses almost 85,000 bone mineral density measurements within Cohort of Norway and data on almost 140,000 hip fractures in Norway 1994–2008. Included are anthropometric measurements, blood pressure, lipids and glucose, and 50 standard questions on sociodemographic factors, diseases and risk factors. Blood samples/DNA are stored. The main research question posed in NOREPOS is why hip fracture rates in Norway are the highest in the world. Data on hip fractures 2009–2013 will be added in 2014. Results: Main findings include: Every hour a Norwegian suffers a hip fracture; hip fracture incidence rates declined after 1999; only 16% of patients used anti-osteoporosis drugs 1 year after hip fracture; 25% of patients died within 1 year after the fracture; 12% suffered a new hip fracture within 10 years; rural dwellers had lower hip and forearm fracture incidence than city dwellers; magnesium in tap water may be protective whereas bacterial contamination, cadmium and lead may be harmful to bone health; low serum vitamin D and E levels were associated with higher hip fracture risk; vitamin A was not associated with fracture risk; and abdominal obesity increased the risk of hip fracture when BMI was accounted for. Conclusions: NOREPOS encompasses a unique source of information for aetiological research, genetic studies as well as for biomarkers of osteoporosis and fractures. Because of the increasing number of elderly people in Europe, hip fractures will continue to pose an international public health and health care challenge.
Randomized Controlled Trial Examining the Effects of Fish Oil and Multivitamin Supplementation on the Incorporation of n-3 and n-6 Fatty Acids into Red Blood Cells

The present randomized, placebo-controlled, double-blind, parallel-groups clinical trial examined the effects of fish oil and multivitamin supplementation on the incorporation of n-3 and n-6 fatty acids into red blood cells. Healthy adult humans (n = 160) were randomized to receive 6 g of fish oil, 6 g of fish oil plus a multivitamin, 3 g of fish oil plus a multivitamin or a placebo daily for 16 weeks. Treatment with 6 g of fish oil, with or without a daily multivitamin, led to higher eicosapentaenoic acid (EPA) composition at endpoint. Docosahexaenoic acid (DHA) composition was unchanged following treatment. The long chain LC n-3 PUFA index was only higher, compared to placebo, in the group receiving the combination of 6 g of fish oil and the multivitamin. Analysis by gender revealed that all treatments increased EPA incorporation in females while, in males, EPA was only significantly increased by the 6 g fish oil multivitamin combination. There was considerable individual variability in the red blood cell incorporation of EPA and DHA at endpoint. Gender contributed to a large proportion of this variability with females generally showing higher LC n-3 PUFA composition at endpoint. In conclusion, the incorporation of LC n-3 PUFA into red blood cells was influenced by dosage, the concurrent intake of vitamin/minerals and gender.
The color of plant reproduction: macroecological trade-offs between biotic signaling and abiotic tolerance

Flowers and fruits are often vividly coloured. An obvious explanation for fruit and flower pigmentation is that it serves to attract animal mutualists. However, decades of research has produced surprising little support for this hypothesis. Exciting new research into geographic variation in flower colours suggests an alternative explanation - flower pigments protect gametes against the damaging effects of solar radiation. Here, I present several new analyses suggesting that a similar explanation might apply to Rubus spectabilis, a much studied but poorly understood bird-dispersed fruit species. These and other recent results provide a new perspective on the colour of plant reproduction. In addition to signalling to animals, fruit and flower colours might often play vital roles in protecting plants against the harmful effects of solar radiation.
Evaluation of a speech recognition system

Speech recognition is the process of translating an audio signal into text using a computer program. The technique is today widely used in a large variety of areas. Pocketsphinx which is an open source speech recognition system is one of the more promising systems on the market today. It is designed to be effective and to be able to translate speech in real-time on low performance platforms. In this thesis Pocketsphinx is measured with respect to word error rate and translation time using data recorded by two Swedish speakers. A proof of concept was made using Pocketsphinx to control a robot by voice. The system was compared to the similar speech recognition system Google speech with respect to word error rate and translation time. The resulting data from measurements suggests that Google speech has a considerably better accuracy on long grammatically correct sentences, while Pocketsphinx is a less demanding and faster system. The word error rate and translation time of Pocketsphinx is more affected by noise than that of Google speech. The accuracy and recognition speed of Pocketsphinx showed huge improvements when stripping down the dictionary, thus it is more suited for controlling a robot with a limited number of commands in real-time.
Towards explanation of the X-ray–radio correlation in the Vela pulsar

Recent observations of the Vela pulsar have revealed a peculiar connection of its emission in the soft X-ray and radio ranges. We suggest the model of the radio pulse formation in the Vela pulsar, develop the theory of the radio photon reprocessing to high energies, and on this basis interpret the observed X-ray-radio connection. The processes of spontaneous and induced scattering of radio waves off the spiralling particles and their observational consequences are examined. The particles are assumed to acquire relativistic gyration energies due to resonant absorption of the radio emission in the outer magnetosphere of a pulsar. The spectral and angular distributions of the spontaneously scattered power are analysed and compared with the characteristics of the particle synchrotron emission. The consequences of intensity transfer from the radio beam to the background in the course of induced scattering are studied as well. It is demonstrated that the induced scattering can account for the basic features of the Vela's radio profile and its pulse-to-pulse fluctuations. In particular, it can explain a greater role of the leading component and its earlier arrival in stronger pulses. The studies of the radio photon reprocessing to high energies in application to the Vela pulsar show that the scattered and synchrotron spectra peak at ∼0.8 and 0.2 keV, respectively, with the corresponding luminosities of 10 29 and 10 31 erg s -1 . The reprocessing inside the light cylinder results in the profile component, which stretches from the radio pulse position to ∼30° earlier in pulse phase. The synchrotron emission beyond the light cylinder presumably contributes to the component that lags the radio pulse by ∼90°. Within the framework of our model, the observed X-ray-radio connection is explained in terms of the interplay between the processes of induced and spontaneous scattering of the radio pulse.
SELF-STIGMA, ATTITUDES, AND PREFERENCES WHEN SEEKING MENTAL HEALTH AND SPORT PSYCHOLOGY SERVICES: A STUDENT-ATHLETE POINT OF VIEW

OF THESIS SELF-STIGMA, ATTITUDES, AND PREFERENCES WHEN SEEKING MENTAL HEALTH AND SPORT PSYCHOLOGY SERVICES: A STUDENT-ATHLETE POINT OF VIEW This study explored student-athletes’ attitudes, stigmas, and preferences toward mental health and sport psychology services. Previous research has identified that student-athletes report similar rates of distress compared to the general student population (Davoren & Hwang, 2014; Frank, Hautzinger & Beckmann, 2013). While studentathletes are in need of mental health services, previous research has also found that student-athletes can benefit from the use of sport psychology services. Previous research has demonstrated the need to support student-athletes as people, students, and athletes (Andersen, Miles, Robinson, & Mahoney, 2004; Bond, 2002; Friesen & Orlick, 2010; Miller & Kerr, 2002). However, not all athletic departments offer mental health and sport psychology services for their student-athletes. Additionally, student-athletes, coaches, and athletic departments, often stigmatize mental health and sport psychology services which results in underutilization. In order to better understand the need and preferences of using these services from a student-athlete’s perspective, this study surveyed 174 NCAA Division 1 athletes. The findings of this study revealed that student-athletes were more likely to seek mental health and sport psychology services if they had a) positive attitudes toward seeking help, b) low levels of self-stigma and c) services accessible within their athletic department.
Computational modeling of mineral unmixing and growth An application of the Cahn – Hilliard equation

A new finite element based simulation technique for mineral growth governed by the classical Cahn–Hilliard equation is presented. The particular format of the underlying Flory–Huggins free energy for non-ideal mixtures is characterized through a double-well potential. It allows for uphill diffusion driven by gradients in the chemical potential and thus provides the appropriate framework to simulate phase separation typically encountered in mineral unmixing and growth. For the finite element discretization, the governing fourth order diffusion equation is reformulated in terms of a system of two coupled second order equations. For the temporal discretization, a heuristic adaptive time stepping scheme is applied in order to simulate not only the early stages of phase separation but also the long term behavior of ageing and grain fusion. The basic features of the Cahn–Hilliard equation are elaborated by means of selected geologically relevant examples. In particular, isotropic and anisotropic mineral growth and symplectite formation are studied and the long term response in the sense of Ostwald ripening is illustrated.
Efficient mobile location from time measurements with unknown variances in dynamic scenarios

This work is focused on the study of the maximum likelihood (ML) mobile position estimator when the quality of the available measurements is not a-priori known. Based on a statistical analysis, a polynomial time-evolution model is used to simplify the ML function, finding a closed-form approximation of the ML estimator. Numerical simulations show that the proposed algorithm, with a low implementation complexity, attains the Cramer Rao lower bound (CRB) for all reasonable observed window lengths and for any arbitrary distribution of the measurement variances. Although the mathematical development of this closed-form position estimator is quite dense, the obtained algorithm has a very low complexity implementation.
Cognitive Behaviour Therapy for Children and Families

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A High-Performance Multiplex Immunoassay for Serodiagnosis of Flavivirus-Associated Neurological Diseases in Horses

West Nile virus (WNV), Japanese encephalitis virus (JEV), and tick-borne encephalitis virus (TBEV) are flaviviruses responsible for severe neuroinvasive infections in humans and horses. The confirmation of flavivirus infections is mostly based on rapid serological tests such as enzyme-linked immunosorbent assays (ELISAs). These tests suffer from poor specificity, mainly due to antigenic cross-reactivity among flavivirus members. Robust diagnosis therefore needs to be validated through virus neutralisation tests (VNTs) which are time-consuming and require BSL3 facilities. The flavivirus envelope (E) glycoprotein ectodomain is composed of three domains (D) named DI, DII, and DIII, with EDIII containing virus-specific epitopes. In order to improve the serological differentiation of flavivirus infections, the recombinant soluble ectodomain of WNV E (WNV.sE) and EDIIIs (rEDIIIs) of WNV, JEV, and TBEV were synthesised using the Drosophila S2 expression system. Purified antigens were covalently bonded to fluorescent beads. The microspheres coupled to WNV.sE or rEDIIIs were assayed with about 300 equine immune sera from natural and experimental flavivirus infections and 172 nonimmune equine sera as negative controls. rEDIII-coupled microspheres captured specific antibodies against WNV, TBEV, or JEV in positive horse sera. This innovative multiplex immunoassay is a powerful alternative to ELISAs and VNTs for veterinary diagnosis of flavivirus-related diseases.
Research on Theory and Method for Facial Expression Recognition SystemBased on Dynamic Image Sequence

We studied the tracking theory based on Candide3 facial model and according to the research we further developed the tracking process. Based on the research of facial tracking, we put forward a dynamic feature extraction method based on six parameters of facial model. We introduced the active appearance model algorithm to locate and track feature points of facial expression, then studied the tracking theory. Based on Candide3 facial model and according to the research we further developed the tracking process. We use the Dynamic Time Warping (DTW) technique to align the image sequence, and then extract the feature vector. The results show that the method based on the model parameters has a good classification results when extract dynamic characteristics.
Antenna Calibration Method with Rectangular Weighting for High-Resolution DOA Estimation Using SAGE Algorithm

あらまし 移動通信や室内無線通信(無線 LAN)において,周囲の状況や環境に応じて電波伝搬構造を詳細 に把握するには,アレーアンテナを用いた到来波の高分解能到来方向 (DOA)推定が重要な技術となる. しかし, アレーアンテナには素子間相互結合や素子位置誤差などのアレー誤差が存在するため,DOA 推定に誤差が生じ てしまう. したがって,推定誤差の低減のために,アレーアンテナの校正が必要不可欠となる. 本研究では,最 ゆう推定法に基づく SAGE アルゴリズムに着目し,このアルゴリズムによる高分解能 DOA 推定の校正のため に,方形重み付き校正法を提案した. 本校正法は,参照信号を用いる校正法に,重み付けを導入したものである. この校正付き SAGE アルゴリズムを用いれば,SAGE 内の個々の到来波推定に適切なアレー校正を施すことが でき,良好な DOA 推定が可能となる. 本論文では,計算機シミュレーションにより,いくつかの電波環境にお ける本アルゴリズムの特性について検討した. その結果,適切な方形重み付けを施せば,アレー誤差を十分低減 でき,良好な DOA 推定ができることが分かり,本アルゴリズムの有効性が確認できた. キーワード 到来方向推定,SAGE,アレーアンテナ,校正法,高分解能
A hybrid algorithm based on Artificial Potential Field and BUG for path planning of mobile robot

A hybrid algorithm based on the Artificial Potential Field and Bug algorithm (APF-B) is developed in this paper. It is applied to the path-planning problem of mobile robot. The potential field function is modified to deal with the GNRON (Goal Non Reachable with Obstacle Nearby) problem. A BUG algorithm is introduced into the Artificial Potential Field to escape from the local minima. The convergence of this hybrid algorithm is verified. Finally, the simulated experiments show the validity of this approach.
Approximate Linear Programming for Network Control : Column Generation and Subproblems

Approximate linear programming (ALP) has been shown to provide useful bounds on optimal average cost for multiclass queueing network control problems. Approximation architectures can be chosen so that a manageable number of variables gives moderate accuracy; however, the number of constraints grows exponentially in the number of queues. We use column generation to more efficiently solve the dual of this LP. Approximation architectures that are additive across part types are shown to simplify the column selection step of the algorithm. Efficient methods are developed for quadratic approximation architectures. A very efficient algorithm is given when the quadratic approximation architecture is also required to be additive across sets of servers. Examples with up to 40 queues are approximated.