Miracle-dz/UniFAR-FTUs huggingface dataset:
Hyperhomocysteinemia in women with advanced breast cancer

Patients with malignancy have an increased risk of venous thromboembolic disease but the pathophysiology of this association has not been precisely defined. Hyperhomocysteinemia has become established as one of the commonest conditions associated with venous and arterial thrombosis. We examined the prevalence of hyperhomocysteinemia in women with early (group A, n = 31), metastatic breast cancer (group B, n = 41) and in a group of healthy females (group C, n = 29). Blood samples were collected at diagnosis or prior to treatment. We measured both total plasma homocysteine (tHcy) and red cell folate (RCF). The Mean (SD) tHcy were group A – 9.43 μmol/l (5.6), group B – 11.34 μmol/l (5.1) and group C – 7.9 μmol/l (1.5). A total of 39% of patients with metastatic and 22.6% with early breast cancer had tHcy concentrations above the upper limit of normal. Women with metastatic disease had significantly higher tHcy compared with controls (P < 0.01) but not when compared with women with early breast cancer. Also, no difference was observed when women with early disease were compared with controls. We found no correlation between age and tHcy. Lower RCF levels were identified in group B compared with group A, but this does not fully explain the increased tHcy levels seen within the same group. We conclude that hyperhomocysteinemia is common in women with advanced breast cancer. This observation could explain the high rate of venous thrombosis in women with metastatic breast malignancy.
Reduction in lipopolysaccharide-induced thrombocytopenia by triflavin in a rat model of septicemia.

BACKGROUND Thrombocytopenia frequently occurs early in the course of Gram-negative bacterial infections. Triflavin, an Arg-Gly-Asp-containing disintegrin, has been suggested to interfere with the interaction of fibrinogen with the glycoprotein IIb/IIIa complex. The present study was undertaken to determine whether triflavin could prevent thrombocytopenia in lipopolysaccharide (LPS)-treated rats. METHODS AND RESULTS In this study, 51Cr-labeled platelets were used to assess blood and tissue platelet accumulation after LPS challenge. The administration of LPS (4 mg/kg IV bolus) for 4 hours induced a reduction in radiolabeled platelets in blood and an obvious accumulation of platelets in liver. Triflavin (500 microg/kg) but not GRGDS (20 mg/kg) significantly prevented the alteration of radiolabeled platelet distribution in blood and liver when induced by LPS. Furthermore, triflavin but not GRGDS markedly suppressed the elevation in plasma thromboxane B2 concentration within the 4-hour period of LPS administration. In LPS-treated rats, the 5-hydroxytryptamine level was lower in the blood and higher in the liver compared with levels in normal saline-treated rats. Pretreatment with triflavin (500 microg/kg) significantly reversed the 5-hydroxytryptamine concentration in blood and liver of LPS-treated rats. In histological examinations and platelet adhesion assay, triflavin markedly inhibited the adhesion of platelets to subendothelial matrixes in vivo and in vitro. CONCLUSIONS The results indicate that triflavin effectively prevents thrombocytopenia, possibly through the following 2 mechanisms: (1) Triflavin markedly inhibits platelet aggregation, resulting in decreased thromboxane A2 formation. (2) It inhibits the adhesion of platelets to subendothelial matrixes, thereby leading to a reversal in the distribution of platelets in blood and liver in LPS-treated rats.
A small ‘lick’ will sink a great ship: fulminant septicaemia after dog saliva wound treatment in an asplenic patient

Capnocytophaga canimorsus is a bacterium transmitted through the saliva of dogs. An infection can cause severe sepsis with acral necrosis and is potentially fatal. Here, we report the case of a 41‐year‐old man who was infected through a wound that was licked by his dog. He went into septic shock with disseminated intravascular coagulation and subsequently lost both lower legs, his nose and all the fingers on both hands.
Multi-UAV Cooperative Surveillance with Spatio-Temporal Specifications

We present a path planning algorithm for time-critical cooperative surveillance using a set of unmanned aerial platforms. The unique constraints imposed by maneuver limits and body-fixed cameras make the problem quite challenging. An integer programming(IP)-based strategy for successfully operating within these constraints is developed. IP is applied over a receding planning horizon with terminal cost to reduce the computational effort of the planner and to incorporate feedback. The main contribution of the paper is the incorporation of highly constrained motion and sensor capabilities of the vehicles in the mathematical programming formalism. Simulation and experimental results are presented to demonstrate the efficacy of the proposed approach
A Multivariate Integer Count Hurdle Model: Theory and Application to Exchange Rate Dynamics

In this paper we propose a model for the conditional multivariate density of integer count variables defined on the set Zn. Applying the concept of copula functions, we allow for a general form of dependence between the marginal processes which is able to pick up the complex nonlinear dynamics of multivariate financial time series at high frequencies. We use the model to estimate the conditional bivariate density of the high frequency changes of the EUR/GBP and the EUR/USD exchange rates.
Multiple News Articles Summarization Based on Event Reference Information

In this paper, we describe our method to generate summary from multiple news articles. Since most of news articles report several events and these events are refereed with following articles, we use this event reference information to calculate importance of a sentence in multiple news articles. We also propose a method to delete redundant description by using similarity of events. Finally we discuss its effectiveness based on the evaluation result.
Mesoscale Spectra of Mars’s Atmosphere Derived from MGS TES Infrared Radiances

Wavenumber spectra of the atmospheric potential energy of Mars at mesoscales (wavelengths of 64–957 km) were obtained as a function of latitude, season, and Martian year using infrared radiance data obtained by the Thermal Emission Spectrometer (TES) onboard the Mars Global Surveyor (MGS) spacecraft. Spectral slopes tend to be flatter at smaller scales, and the slopes are usually flatter than 1 near small-scale ends. Near large-scale ends, the spectra sometimes show prominent steepening with slopes from 2t o3. The power peaks in the high latitudes in winter and equinoxes, suggesting that eddies are generated preferentially in baroclinic zones. The seasonal variation at each latitude band, on the other hand, tends to be obscured by large interannual variability. An enhancement in the power was observed around the storm tracks in the Southern Hemisphere. Spectra of the terrestrial stratosphere were also obtained with a similar method from data taken by the Aura satellite and compared to the results for Mars.
Determining the Single Best Axis for Exercise Repetition Recognition and Counting on SmartWatches

Due to the exploding costs of chronic diseasesstemming from physical inactivity, wearable sensor systems toenable remote, continuous monitoring of individuals has increasedin popularity. Many research and commercial systems exist inorder to track the activity levels of users from general dailymotion to detailed movements. This work examines this problemfrom the space of smartwatches, using the Samsung GalaxyGear, a commercial device containing an accelerometer and agyroscope, to be used in recognizing physical activity. This workalso shows the sensors and features necessary to enable suchsmartwatches to accurately count, in real-time, the repetitions offree-weight and body-weight exercises. The goal of this work isto try and select only the best single axis for each activity byextracting only the most informative activity-specific features, inorder to minimize computational load and power consumptionin repetition counting. The five activities are incorporated in aworkout routine, and knowing this information, a random forestclassifier is built with average area under the curve (AUC) of: 974, with average accuracy of 93%, in cross validation to identify eachrepetition of a given exercise using all available sensors and AUCof: 950 with accuracy of 89.9% using the single best axis foreach activity alone. Adding a gyroscope with the accelerometerincreased the average AUC from: 968 to: 974, increasing theaccuracy of specific movements as much as 2%. Results show that, while a combination of accelerometer and gyroscope provide thestrongest classification results, often times features extracted froma single, best axis are enough to accurately identify movementsfor a personal training routine, where that axis is often, but notalways, an accelerometer axis.
Use of Circumsporozoite Protein Enzyme-Linked Immunosorbent Assay Compared with Microscopic Examination of Salivary Glands for Calculation of Malaria Infectivity Rates in Mosquitoes (Diptera: Culicidae) from Cameroon

Abstract A survey in Cameroon compared the usefulness of the circumsporozoite protein enzyme-linked immunosorbent assay (CSP ELISA) to dissection and microscopic examination of anopheline salivary glands for measuring infectivity rates in anopheline mosquitoes. The salivary glands of 375 females, belonging to four species were examined for sporozoites. After microscopic examination, the glands as well as all the remaining heads and thoraces were tested by ELISA. The sensitivity of ELISA was 100% (18/18), confidence interval (CI) (78.1–100) and the specificity was 99.7% (357/358), CI (98.2–100). The Kappa value, agreement between examination of the glands and salivary gland ELISA, was 0.97. The head–thorax CSP ELISA overestimated the true salivary gland infection rate by 12.0%. The results obtained in Central Africa in a village with perennial transmission highly justified the use of the ELISA for measuring the entomological inoculation rate.
Unsupervised Modeling of Dialog Acts in Asynchronous Conversations

We present unsupervised approaches to the problem of modeling dialog acts in asynchronous conversations; i.e., conversations where participants collaborate with each other at different times. In particular, we investigate a graph-theoretic deterministic framework and two probabilistic conversation models (i.e., HMM and HMM+Mix) for modeling dialog acts in emails and forums. We train and test our conversation models on (a) temporal order and (b) graph-structural order of the datasets. Empirical evaluation suggests (i) the graph-theoretic framework that relies on lexical and structural similarity metrics is not the right model for this task, (ii) conversation models perform better on the graph-structural order than the temporal order of the datasets and (iii) HMM+Mix is a better conversation model than the simple HMM model.
Poster: In silico microarray algorithm: Accurate and fast taxonomic profiling from short read sequences

We here propose a novel algorithm that can accurately estimate taxonomic composition of microbial communities from massive amount of short read sequences (60-120 bp). Our accuracy evaluation based on simulated datasets demonstrated that our method achieves much higher accuracies than previously proposed methods including Taxy, Qin's method and RDPClassifier. The source code is freely available under GNU Public Licence (GPL) from http://ism.dna. bio.keio. ac.jp.
Studying functional magnetic resonance imaging with artificial imaging objects

OF DOCTORAL DISSERTATION AALTO UNIVERSITY SCHOOL OF SCIENCE AND TECHNOLOGY P.O. BOX 11000, FI-00076 AALTO http://www.aalto. fi Author Ville Renvall Name of the dissertation Studying functional magnetic resonance imaging with artificial imaging objects Manuscript submitted 19.1. 2010 Manuscript revised 9.3. 2010 Date of the defence 24.3. 2010 Monograph Article dissertation (summary + original articles) Faculty Faculty of Information and Natural Sciences Department Department of Biomedical Engineering and Computational Science Field of research engineering physics, biomedical engineering Opponent(s) Professor Bruce R. Rosen Supervisor Professor Risto Ilmoniemi Instructor Academy Professor Riitta Hari Abstract Blood oxygenation level dependent (BOLD) functional magnetic resonance imaging (fMRI) is an indirect method for measuring information processing in the brain. The method has enabled mapping human brain function in an unprecedented variety of tasks and conditions, and with a spatial resolution of the order of 1 mm. In this dissertation, artificial imaging objects, or phantoms, with adjustable signal intensity were used to simulate and investigate the generation of fMRI signals. The objective was to characterise, and devise means to characterise, fMRI signal components that arise from methodological reasons, impeding the correct physiological interpretation of the signals. The first study involved building an fMRI phantom, where an electric current was applied to introduce magnetic field inhomogeneity within a magnetic resonance signal source. It was shown that the changes of field homogeneity and thus fMRI signal, largely corresponded to the human BOLD changes, even though the physical mechanisms were different. The mechanical properties of phantoms and brain however differ. Thus it was important to look into the attributes of phantoms that would make the fMRI signal from the phantom similar to brain scanning data. The second study examined geometric distortions in the echo-planar imaging method—commonly employed in both fMRI and diffusion tensor imaging —using a purpose-built structural phantom. In the third study, another fMRI activation phantom was built. There the induction wires were located outside the source of the fMRI signal, and thus the partial volume effect limiting the usability of the first fMRI phantom was abated. The phantom was applied to induce artificial activations that could be utilized to deduce periods when simultaneously measured brain activations would yield deviant activation levels due to unphysiological causes. In the last study, an fMRI phantom was used to show that transient fMRI signal components, often witnessed in brain activation data, could occur in the absence of corresponding physiological signal, resulting from the sole signal change.
Compressed sensing-based pooling experiments using next generation sequencing

Screening for carriers of rare variants by resequencing is important for the identification of individuals carrying disease alleles. Rapid sequencing by new technologies enables low-cost resequencing of target regions, although it is still prohibitive to test more than a few individuals. Pooling designs can enable detection of carriers of rare alleles in groups of individuals in a more economical manner. Previous pooling strategies were shown only for a relatively low number of individuals in a pool, and required the design of pooling schemes for particular cases. We propose a novel pooling design, based on a compressed sensing approach, which is general, simple and efficient. We model the experimental procedure and show via computer simulations our ability to recover rare allele carriers in larger groups than were possible before, especially when high coverage is obtained for each individual.
Italic detection and rectification

In this paper, a novel italic detection and rectification method without the prerequisite of character recognition is proposed. The merit of the proposed method is that it can be operated directly on a single character so that more accurate statistical information can be obtained. The rationale of our proposed method is that the difference of certain features derived from italic style characters after shear transformation will be canceled, whereas the difference will be more obvious for non-italic style (normal style) characters.
Activation-Inactivation Cycling of Rab35 and ARF6 Is Required for Phagocytosis of Zymosan in RAW264 Macrophages

Phagocytosis of zymosan by phagocytes is a widely used model of microbial recognition by the innate immune system. Live-cell imaging showed that fluorescent protein-fused Rab35 accumulated in the membranes of phagocytic cups and then dissociated from the membranes of newly formed phagosomes. By our novel pull-down assay for Rab35 activity, we found that Rab35 is deactivated immediately after zymosan internalization into the cells. Phagosome formation was inhibited in cells expressing the GDP- or GTP-locked Rab35 mutant. Moreover, the simultaneous expression of ACAP2—a Rab35 effector protein—with GTP-locked Rab35 or the expression of plasma membrane-targeted ACAP2 showed a marked inhibitory effect on phagocytosis through ARF6 inactivation by the GAP activity of ACAP2. ARF6, a substrate for ACAP2, was also localized on the phagocytic cups and dissociated from the membranes of internalized phagosomes. In support of the microscopic observations, ARF6-GTP pull-down experiments showed that ARF6 is transiently activated during phagosome formation. Furthermore, the expression of GDP- or GTP-locked ARF6 mutants also suppresses the uptake of zymosan. These data suggest that the activation-inactivation cycles of Rab35 and ARF6 are required for the uptake of zymosan and that ACAP2 is an important component that links Rab35/ARF6 signaling during phagocytosis of zymosan.
On the Minimum Distance of Non Binary LDPC Codes

Minimum distance is an important parameter of a linear error correcting code. For improved performance of binary Low Density Parity Check (LDPC) codes, we need to have the minimum distance grow fast with n, the codelength. However, the best we can hope for is a linear growth in dmin with n. For binary LDPC codes, the necessary and sufficient conditions on the LDPC ensemble parameters, to ensure linear growth of minimum distance is well established. In the case of non-binary LDPC codes, the structure of logarithmic weight codewords is different from that of binary codes. We have carried out a preliminary study on the logarithmic bound on the the minimum distance of non-binary LDPC code ensembles. In particular, we have investigated certain configurations which would lead to low weight codewords. A set of simulations are performed to identify some of these configurations. Finally, we have provided a bound on the logarithmic minimum distance of nonbinary codes, using a strategy similar to the girth bound for binary codes. This bound has the same asymptotic behaviour as that of binary codes.
Long-term effects of deep-seated landslides on transportation infrastructure: a case study from the Swiss Jura Mountains

Deep-seated landslides (DSLs) involve large-scale deformation and likely affect transportation infrastructure. Movement rates are in general very slow (less than a metre per year) with acceleration periods controlled by external factors such as the seasonal fluctuation of groundwater pressure. Acceleration response may change from season to season depending on hydrogeological conditions, changes in slope geometry and degradation of geological materials. More localized landslide types are associated with and develop within DSLs, such as rock falls, topples and debris slides. Management of hazards related to DSLs requires first the assessment of geological, hydrogeological and geomechanical processes. This is the starting point for developing a management strategy. This paper presents the characterization of a deep-seated landslide located in the Swiss Jura Mountains, Les Buges landslide, where a railway line, a power line and an aqueduct of regional importance cross the slide, as well as a highly frequented hiking trail beneath the landslide toe. Slide kinematics is governed by the geology and hydrogeology of the slope, which can be subdivided into two dominant bodies. A management strategy is subsequently discussed for this DSL. Les Buges is a good example illustrating that hazards related to deep-seated landslides must be tackled first of all by means of the observational method.
How to Use Bitcoin to Play Decentralized Poker

Back and Bentov (arXiv 2014) and Andrychowicz et al. (Security and Privacy 2014) introduced techniques to perform secure multiparty computations on Bitcoin. Among other things, these works constructed lottery protocols that ensure that any party that aborts after learning the outcome pays a monetary penalty to all other parties. Following this, Andrychowicz et al. (Bitcoin Workshop 2014) and concurrently Bentov and Kumaresan (Crypto 2014) extended the solution to arbitrary secure function evaluation while guaranteeing fairness in the following sense: any party that aborts after learning the output pays a monetary penalty to all parties that did not learn the output. Andrychowicz et al. (Bitcoin Workshop 2014) also suggested extending to scenarios where parties receive a payoff according to the output of a secure function evaluation, and outlined a 2-party protocol for the same that in addition satisfies the notion of fairness described above. In this work, we formalize, generalize, and construct multiparty protocols for the primitive suggested by Andrychowicz et al. We call this primitive secure cash distribution with penalties. Our formulation of secure cash distribution with penalties poses it as a multistage reactive functionality (i.e., more general than secure function evaluation) that provides a way to securely implement smart contracts in a decentralized setting, and consequently suffices to capture a wide variety of stateful computations involving data and/or money, such as decentralized auctions, market, and games such as poker, etc. Our protocol realizing secure cash distribution with penalties works in a hybrid model where parties have access to a claim-or-refund transaction functionality FCR}* which can be efficiently realized in (a variant of) Bitcoin, and is otherwise independent of the Bitcoin ecosystem. We emphasize that our protocol is dropout-tolerant in the sense that any party that drops out during the protocol is forced to pay a monetary penalty to all other parties. Our formalization and construction generalize both secure computation with penalties of Bentov and Kumaresan (Crypto 2014), and secure lottery with penalties of Andrychowicz et al. (Security and Privacy 2014).
Dynamic Multichannel Scheduling for 802.15.3 WPANs

We propose a dynamic scheduler for multichannel 802.15. 3 WPANs which exploits both channel reuse and interference control. A maximal-weighted-matching based scheduling scheme is designed to arrange simultaneous transmissions in each single channel and a multichannel assignment scheme is proposed to obtain the ultimate schedule in each superframe. For successful signal decoding, accumulated interference among simultaneous transmissions is taken into account to ensure that signal reception occurs with sufficient SINR. To improve the efficiency of channel reuse, the scheduler fragments each transmission request to multiple requests with the equal duration. An analysis is given of the optimal way to implement such process according to online traffic load and overhead. Simulations are used to evaluate the performance and to compare against existing schemes.