Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5.

Chromosome 7q22 has been the focus of many cytogenetic and molecular studies aimed at delineating regions commonly deleted in myeloid leukemias and myelodysplastic syndromes. We have compared a gene-dense, GC-rich sub-region of 7q22 with the orthologous region on mouse chromosome 5. A physical map of 640 kb of genomic DNA from mouse chromosome 5 was derived from a series of overlapping bacterial artificial chromosomes. A 296 kb segment from the physical map, spanning ACHE: to Tfr2, was compared with 267 kb of human sequence. We identified a conserved linkage of 12 genes including an open reading frame flanked by ACHE: and Asr2, a novel cation-chloride cotransporter interacting protein Cip1, Ephb4, Zan and Perq1. While some of these genes have been previously described, in each case we present new data derived from our comparative sequence analysis. Adjacent unfinished sequence data from the mouse contains an orthologous block of 10 additional genes including three novel cDNA sequences that we subsequently mapped to human 7q22. Methods for displaying comparative genomic information, including unfinished sequence data, are becoming increasingly important. We supplement our printed comparative analysis with a new, Web-based program called Laj (local alignments with java). Laj provides interactive access to archived pairwise sequence alignments via the WWW. It displays synchronized views of a dot-plot, a percent identity plot, a nucleotide-level local alignment and a variety of relevant annotations. Our mouse-human comparison can be viewed at http://web.uvic. ca/~bioweb/laj.html. Laj is available at http://bio.cse. psu.edu/, along with online documentation and additional examples of annotated genomic regions.
Constructing, conducting and interpreting animal social network analysis

Summary Animal social networks are descriptions of social structure which, aside from their intrinsic interest for understanding sociality, can have significant bearing across many fields of biology. Network analysis provides a flexible toolbox for testing a broad range of hypotheses, and for describing the social system of species or populations in a quantitative and comparable manner. However, it requires careful consideration of underlying assumptions, in particular differentiating real from observed networks and controlling for inherent biases that are common in social data. We provide a practical guide for using this framework to analyse animal social systems and test hypotheses. First, we discuss key considerations when defining nodes and edges, and when designing methods for collecting data. We discuss different approaches for inferring social networks from these data and displaying them. We then provide an overview of methods for quantifying properties of nodes and networks, as well as for testing hypotheses concerning network structure and network processes. Finally, we provide information about assessing the power and accuracy of an observed network. Alongside this manuscript, we provide appendices containing background information on common programming routines and worked examples of how to perform network analysis using the r programming language. We conclude by discussing some of the major current challenges in social network analysis and interesting future directions. In particular, we highlight the under‐exploited potential of experimental manipulations on social networks to address research questions.
Robust versions of the Tukey boxplot with their application to detection of outliers

The need for fast on-line algorithms to analyze high data-rate measurements is a vital element in production settings. Given the ever-increasing number of data sources coupled with increasing complexity of applications, and workload patterns, anomaly detection methods should be light-weight and must operate in real-time. In many modern applications, data arrive in a streaming fashion. Therefore, the underlying assumption of classical methods that the data is a sample from a stable distribution is not valid, and Gaussian and non-parametric based methods such as the control chart and boxplot are inadequate. Streaming data is an ever-changing superposition of distributions. Detection of such changes in real-time is one of the fundamental challenges. We propose low-complexity robust modifications to the conventional Tukey boxplot based on fast highly efficient robust estimates of scale. Results using synthetic as well as real-world data show that our methods outperform the Tukey boxplot and methods based on Gaussian limits.
Your Picture Says it All: A Study of Personality by Images

: Multimedia enabled devices and an abundant use of internet has made interaction with images through social media a widespread. By posting images daily, the users of social media tend to present their daily activities, temptation, and preferences. In this study, we show how the profile picture of a social media user relates to his personality, as measured by the standard Big-Five model. A profile picture refers to self-representations of the user which reflects their personality on the social media platforms.
Medstract : Creating Large-scale Information Servers for biomedical libraries

The automatic extraction of information from Medline articles and abstracts (commonly referred to now as the biobibliome) promises to play an increasingly critical role in aiding research while speeding up the discovery process. We have been developing robust natural language tools for the automated extraction of structured information from biomedical texts as part of a project we call Medstract.1 Here we will describe an architecture for developing databases for domain specific information servers for research and support in the biomedical community. These are currently comprised of the following: a Bio-Relation Server, and the Bio-Acronym server, Acromed, which will include also aliases. Each information server is derived automatically from an integration of diverse components which employ robust natural language processing of Medline text and IE techniques. The frontend consists of conventional search and navigation capabilities, as well as visualization tools that help to navigate the databases and explore the results of a search. It is hoped that this set of applications will allow for quick, structured access to relevant information on individual genes by biologists over the web. http://www.medstract. org.
Data Integration : state of the art , new issues and research plan

In this report we present a summary of the recent literature in the Data Integration research area, focusing our attention on some new issues that are relevant to this area, mostly from an architectural perspective. In fact, although general architectures for data integration systems assign them a centralized role, it does not seem to be a valid approach in real distributed scenarios: some recent works propose new architectures for data integration, deployed in a peer-to-peer environment. We will also summarize some results produced in the first year of the Ph.D. course and we will set out a research plan for the rest of such course.
Throughput assurance of wireless body area networks coexistence based on stochastic geometry

Wireless body area networks (WBANs) are expected to influence the traditional medical model by assisting caretakers with health telemonitoring. Within WBANs, the transmit power of the nodes should be as small as possible owing to their limited energy capacity but should be sufficiently large to guarantee the quality of the signal at the receiving nodes. When multiple WBANs coexist in a small area, the communication reliability and overall throughput can be seriously affected due to resource competition and interference. We show that the total network throughput largely depends on the WBANs distribution density (λp), transmit power of their nodes (Pt), and their carrier-sensing threshold (γ). Using stochastic geometry, a joint carrier-sensing threshold and power control strategy is proposed to meet the demand of coexisting WBANs based on the IEEE 802.15. 4 standard. Given different network distributions and carrier-sensing thresholds, the proposed strategy derives a minimum transmit power according to varying surrounding environment. We obtain expressions for transmission success probability and throughput adopting this strategy. Using numerical examples, we show that joint carrier-sensing thresholds and transmit power strategy can effectively improve the overall system throughput and reduce interference. Additionally, this paper studies the effects of a guard zone on the throughput using a Matern hard-core point process (HCPP) type II model. Theoretical analysis and simulation results show that the HCPP model can increase the success probability and throughput of networks.
Microlensing toward Crowded Fields: Theory and Applications to M31

We present a comprehensive treatment of the pixel-lensing theory and apply it to lensing experiments and their results toward M31. Using distribution functions for the distances, velocities, masses, and luminosities of stars, we derive lensing event rates as a function of the event observables. In contrast to the microlensing regime, in the pixel-lensing regime (crowded or unresolved sources) the observables are the maximum excess flux of the source above a background and the full width at half-maximum (FWHM) time of the event. To calculate lensing event distribution functions depending on these observables for the specific case of M31, we use data from the literature to construct a model of M31, reproducing consistently photometry, kinematics and stellar population. We predict the halo-and self-lensing event rates for bulge and disk stars in M31 and treat events with and without finite source signatures separately. We use the M31 photon noise profile and obtain the event rates as a function of position, field of view, and S/N threshold at maximum magnification. We calculate the expected rates for WeCAPP and for a potential Advanced Camera for Surveys (ACS) lensing campaign. The detection of two events with a peak signal-to-noise ratio larger than 10 and a timescale larger than 1 day in the WeCAPP 2000/2001 data is in good agreement with our theoretical calculations. We investigate the luminosity function of lensed stars for noise characteristics of WeCAPP and ACS. For the pixel-lensing regime, we derive the probability distribution for the lens masses in M31 as a function of the FWHM timescale, flux excess and color, including the errors of these observables. Subject headings: dark matter — galaxies: halos — galaxies: individual (M31) — gravitational lensing — Local Group 1. INTRODUCTION Searches for compact dark matter toward the Large and Small Magellanic Clouds (LMC and SMC) and the Galactic bulge identified numerous microlensing events in the past decade In parallel to these observations, a lot of effort has been spent on the prediction of the number, the spatial distribution, the amplitude, and the duration of lensing events toward these targets. The underlying models require knowledge of density and velocity distribution, as well as of the luminosity and mass function of lensing and lensed stars. The halo MACHO mass fraction and lens mass are free parameters. From that, the contributions of self-lensing and halo-lensing is obtained. The self-lensing predictions (minimum lensing that has to occur due to star-star …
Preferring Abductive Models and Inspecting Side-Effects for Decision Making

This work proposes the application of preferences over abductive logic programs as an appealing declarative formalism to model choice situations. In particular, both a priori and a posteriori handling of preferences between abductive extensions of a theory are addressed as complementary and essential mechanisms in a broader framework for abductive reasoning. The preference-based decision making process may depend, not only on the available abducibles chosen, but also (and foremost) on specific side-effects of adopting such abducibles. We present the concept of Inspection Point in Abductive Logic Programs, and show how, by means of examples, one can employ it to investigate sideeffects of interest (the inspection points) in order to help evaluate and prefer among abductive solutions. We show how this type of reasoning requires a new mechanism, not provided by others already available. We furthermore show how to implement this new mechanism on top of the XSB-XASP platform in a way that can be adopted by other systems too. Furthermore, all of these preference mechanisms are combined with other formalisms for decision making, like economic decision theory, resulting in theories containing the best advantages from both qualitative and quantitative formalisms. Several examples are presented throughout to illustrate the enounced methodologies. These have been tested in our implementation, which we explain in detail.
Interiors of compact contractible $n$-manifolds are hyperbolic $(n\geq 5)$

The interior of every compact contractible PL n-manifold (n 5) supports a complete geodesic metric of strictly negative curvature. This provides a new family of simple examples illustrating the negative answer to a question of M. Gromov which asks whether metrically convex geodesic spaces which are topological manifolds must be homeomorphic to Euclidean spaces. The rst examples verifying the negative answer to this question were given by M. Davis and T. Januszkiewicz 11]. 0. Introduction One goal of Riemannian geometry is to use local information about a manifold to make conclusions about its global structure. A prime example is the classical Cartan-Hadamard Theorem which guarantees that every complete simply connected Riemannian manifold with non-positive sectional curvature at each point is diieomorphic to Euclidean space. The success of Riemannian geometry has inspired generalizations of its deenitions and methods to wider classes of spaces. One eeort, initiated by A. D. Aleksandrov (see 1], 2] and 3]) in the 1950's, and returned to prominence by M. Gromov in the 1980's, uses properties of triangles to extend the notion of curvature, (X), at a point x, to \geodesic spaces". These are metric spaces in which (as in complete Riemannian manifolds), the distance between two points can always be realized by a geodesic arc between them. A result of this theory which illustrates the extent to which it generalizes Riemannian geometry is the following version of the Cartan-Hadamard Theorem. (See 13] and 14]).
Efficacy and safety of teneligliptin

11 Incretin‐based therapies (IBT) including dipeptidyl peptidase‐4 inhibitors (DPP‐4Is) and glucagon‐like peptide‐1 receptor agonists (GLP‐1RAs) have been the cornerstone of therapy for type 2 diabetes mellitus (T2DM) since the evolution of incretin science. DPP‐4Is are particularly popular in the treatment of T2DM as they are oral drugs, less costlier than GLP‐RAs, with modest to moderate glucose lowering similar to sulfonylureas (SU) depending on the baseline glycemic load. DPP‐4Is carries novel mechanism of action and also have additional potential to protect from hypoglycemia, through unique glucagon dynamics. [1] Indeed, consensus statements from the American College of Endocrinology/American Association of Clinical Endocrinologist and the Latin American Diabetes Association consider DPP‐4I ahead of SU, mainly driven by their lower risk of hypoglycemia as well as weight neutrality. [2,3]
Laryngeal preservation in stage III/IV resectable laryngo-hypopharyngeal squamous cell carcinoma following concurrent chemoradiotherapy with capecitabine/cisplatin

Concurrent chemoradiotherapy has become the standard of care for advanced head and neck cancers in organ preservation strategies. However, the optimal regimen for concurrent chemoradiotherapy to maximise treatment response and minimise toxicity has not been determined. The purpose of the present clinical study was to review our experience with concurrent chemoradiotherapy by using the capecitabine and cisplatin (XP) regimen with the aim of organ preservation in patients with locoregionally advanced laryngo-hypopharyngeal squamous cell carcinoma (LHSCC). Thirty-one patients with stage III/IV resectable LHSCC treated with concurrent chemoradiotherapy using the XP regimen were enrolled in the present study. The patients fulfilled the criteria for total laryngectomy when surgery was selected. The primary endpoint of this study was disease-free survival with a functional larynx, which was indicated by the following conditions: survival, disease-free status at all sites and retention of a functional larynx. Following concurrent chemoradiotherapy, 23 patients (74.2%) exhibited complete response (CR) at the primary site and 18 (69.2%) exhibited CR at the lymph nodes. CR at the primary site and lymph nodes was identified in 19 patients (61.3%). The Kaplan-Meier 2- and 3-year cumulative disease-free survival rates were 71.5 and 59.6%, respectively. Anatomical laryngeal preservation was feasible in 27 patients (87.1%) during the 36-month follow-up period. Permanent gastrostomy was required in 1 disease-free patient with an intact larynx. For the entire cohort, the 2- and 3-year cumulative disease-free survival with a functional larynx was 58.5 and 50.7%, respectively. The most frequent grade 3–4 haematological and non-haematological toxicities of concurrent chemoradiotherapy were leucopenia and mucositis, which developed in 4 (12.9%) and 8 (25.8%) patients, respectively. There was no treatment-related death. Concurrent chemoradiotherapy with the XP regimen resulted in functional laryngeal preservation accompanied by disease-free survival and the toxicities were more tolerable and manageable compared to those reported by previous studies.
Using Galois Theory to Prove Structure from Motion Algorithms are Optimal

This paper presents a general method, based on Galois theory, for establishing that a problem can not be solved by a 'machine' that is capable of the standard arithmetic operations, extraction of radicals (that is, m-th roots for any m), as well as extraction of roots of polynomials of degree smaller than n, but no other numerical operations. The method is applied to two well known structure from motion problems: five point calibrated relative orientation, which can be realized by solving a tenth degree polynomial [6], and L2-optimal two-view triangulation, which can be realized by solving a sixth degree polynomial [3]. It is shown that both these solutions are optimal in the sense that an exact solution intrinsically requires the solution of a polynomial of the given degree (10 or 6 respectively), and cannot be solved by extracting roots of polynomials of any lesser degree.
Analysis and Extension of the Percentile Method, Estimating a Noise Curve from a Single Image

Given a white Gaussian noise signal Non a sampling grid, its variance � 2 can be estimated from a small w × w pixels sample. However, in natural images we observe ˜ U = U + N�, the combination of the geometry of the scene that is photographed and the added noise. In this case, estimating directly the standard deviation of the noise from w × w samples of ˜ U is not reliable since the measured standard deviation is not explained just by the noise but also by the geometry of U. The Percentile method tries to estimate the standard deviationfrom w × w blocks of a high-passed version of ˜ U by a small p-percentile of these standard deviations. The idea behind is that edges and textures in a block of the image increase the observed standard deviation but they never make it decrease. Therefore, a small percentile (0.5%, for example) in the list of standard deviations of the blocks is less likely to be affected by the edges and textures than a higher percentile (50%, for example). The 0.5%-percentile is empirically proven to be adequate for most natural, medical and microscopy images. The Percentile method is adapted to deal with signal-dependent noise, which is realistic with the Poisson noise model obtained by a CCD device in a digital camera.
GMDF/spl alpha/ with adaptive reconstruction filters and zero throughput delay

With reduction of the block size (increasing the number of subfilters) regular generalized multi-delay frequency domain adaptive filter (GMDF/spl alpha/) can achieve low throughput delay at the expense of the system performance. In situations where zero delay is desirable, we propose a new method which is not dependent on the block size. In addition, by using an adaptive reconstruction filter, further performance gains can be achieved with minimal additional computation complexity. Results from experiments performed in a conference room show an increase in the average echo return loss enhancement (ERLE) of >2.5 dB for acoustic echo cancellation over the traditional moving average reconstruction filter.
A passive, origami-inspired, continuously variable transmission

Transmissions play a vital role in machines by transforming the torque and speed of a motor into a desired output. They are often necessary for operating a motor at peak efficiency or power. The majority of variable transmissions are mechanically complex, large, and expensive, which limits scalability and is often cost prohibitive. As an alternative, we propose an origami-wheel design that is capable of varying its own transmission ratio between motor torque and ground reaction force, effectively creating a passive, continuously variable transmission. The wheel responds to an increase in torque by reducing its radius through the spring-like properties of the origami structure, increasing the force applied by the wheel to the ground. We demonstrate that the wheel is able to match the speed of a 55 mm fixed-radius wheel when unloaded, and can also tow loads as high as a 25 mm wheel without stalling. This design could be used to provide smaller, cheaper robots with an effective means to vary their output while maintaining motor efficiency.
Optimal incentive timing strategies for product marketing on social networks

We consider the problem of devising incentive strategies for viral marketing of a product. In particular, we assume that the seller can influence penetration of the product by offering two incentive programs: a) direct incentives to potential buyers (influence) and b) referral rewards for customers who influence potential buyers to make the purchase (exploit connections). The problem is to determine the optimal timing of these programs over a finite time horizon. In contrast to algorithmic perspective popular in the literature, we take a mean-field approach and formulate the problem as a continuous-time deterministic optimal control problem. We show that the optimal strategy for the seller has a simple structure and can take both forms, namely, influence-and-exploit and exploit-and-influence. We also show that in some cases it may optimal for the seller to deploy incentive programs mostly for low degree nodes. We support our theoretical results through numerical studies and provide practical insights by analyzing various scenarios.