Miracle-dz/UniFAR-FTUs huggingface dataset:
Dissecting comimetic radiations in Heliconius reveals divergent histories of convergent butterflies

Mimicry among Heliconius butterflies provides a classic example of coevolution but unresolved relationships among mimetic subspecies have prevented examination of codiversification between species. We present amplified fragment length polymorphism and mtDNA datasets for the major comimetic races of Heliconius erato and H. melpomene. The AFLP data reveal unprecedented resolution, clustering samples by geography and race in both species. Our results show that, although H. erato and H. melpomene co-occur, mimic each other, and exhibit parallel shifts in color pattern, they experienced very different modes of diversification and geographic histories. Our results suggest that H. erato originated on the western side of South America whereas H. melpomene originated in the east. H. erato underwent rapid diversification and expansion with continued gene-flow following diversification, resulting in widely dispersed sister taxa. In contrast, H. melpomene underwent a slower pace of diversification with lower levels of gene flow, producing a stepwise directional expansion from west to east. Our results also suggest that each of the three main wing pattern phenotypes originated and/or was lost multiple times in each species. The rayed pattern is likely to be the ancestral phenotype in H. erato whereas postman or red patch is likely to be ancestral in H. melpomene. Finally, H. cydno and H. himera are monophyletic entities clearly nested within H. melpomene and H. erato, rather than being their respective sister species. Estimates of mtDNA divergence suggest a minimum age of 2.8 and 2.1 My for H. erato and H. melpomene, respectively, placing their origins in the late Pliocene.
An affine combination of adaptive filters for sparse impulse response identification

In this paper we present an affine combination strategy for two adaptive filters. One filter is designed to handle sparse impulse responses and the other one performs better if impulse response is dispersive. Filter outputs are combined using an adaptive mixing parameter and the resulting output shows better performance than each of the combining filters separately. We also demonstrate that affine combination results in faster convergence than convex combination of two adaptive filters.
Lifetime Risk of Cardiovascular Disease Among Individuals With and Without Diabetes Stratified by Obesity Status in the Framingham Heart Study

OBJECTIVE—We assessed the lifetime risk of cardiovascular disease (CVD) among individuals with and without obesity and diabetes. RESEARCH DESIGN AND METHODS—Participants were drawn from the original and offspring cohorts of the Framingham Heart Study. Lifetime (30-year) risk of CVD was assessed using a modified Kaplan-Meier approach adjusting for the competing risk of death, beginning from age 50 years. RESULTS—Over 30 years, the lifetime risk of CVD among women with diabetes was 54.8% among normal-weight women and 78.8% among obese women. Among normal-weight men with diabetes, the lifetime risk of CVD was 78.6%, whereas it was 86.9% among obese men. CONCLUSIONS—The lifetime risk of CVD among individuals with diabetes is high, and this relationship is further accentuated with increasing adiposity.
A spoken term detection framework for recovering out-of-vocabulary words using the web

Vocabulary restrictions in large vocabulary continuous speech recognition (LVCSR) systems mean that out-of-vocabulary (OOV) words are lost in the output. However, OOV words tend to be information rich terms (often named entities) and their omission from the transcript negatively affects both usability and downstream NLP technologies, such as machine translation or knowledge distillation. We propose a novel approach to OOV recovery that uses a spoken term detection (STD) framework. Given an identified OOV region in the LVCSR output, we recover the uttered OOVs by utilizing contextual information and the vast and constantly updated vocabulary on the Web. Discovered words are integrated into system output, recovering up to 40% of OOVs and resulting in a reduction in system error.
Two-Photon Algebra Eigenstates: A Unified Approach to Squeezing

Abstract We use the concept of the algebra eigenstates that provides a unified description of the generalized coherent states (belonging to different sets) and of the intelligent states associated with a dynamical symmetry group. The formalism is applied to the two-photon algebra and the corresponding algebra eigenstates are studied by using the Fock–Bargmann analytic representation. This formalism yields a unified analytic approach to various types of single-mode photon states generated by squeezing and displacing transformations.
Constant Communication ORAM without Encryption

Recent techniques reduce ORAM communication complexity down to constant in the number of blocks N . However, they induce expensive additively homomorphic encryption on both the server and the client. We present two new hybrid ORAM constructions that combine ORAM with Private Information Storage. We store and access individual ORAM buckets with PIS. As a result, our first ORAM features Õ(logN) communication complexity and a small block size of Ω(logN) bit. The second ORAM features optimal O(1) communication complexity and Ω(logN) bit block size. Both ORAMs have constant clientside memory complexity. The highlight of our approach is that neither client nor server are required to perform any encryption. The above properties make our ORAMs extremely lightweight, suitable for deployment even on resource-constrained devices. In addition to a theoretical analysis, we also implement our ORAMs to show their practicality and compare to related work.
Applications of a PET device with 1.5 mm FWHM intrinsic spatial resolution to breast cancer imaging

Operation of a high resolution compact clinical PET Scanner (PEM Flex/spl trade/) device as a breast scanner is described. The device features high spatial resolution (1.5 mm FWHM intrinsic resolution) as a result of small crystals and compact position-sensitive photomultipliers. The compactness of the system allows it to reside within a stereotactic X-ray mammography unit, or as a separate standalone system capable of breast compression. The gamma rays are detected for a volumetric reconstruction by two heads, each of which contains 2,028 2 mm by 2 mm by 10 mm lutetium-containing crystals. The heads travel within X-ray transparent compression paddles. A window is provided in one of the paddles for direct correlation with ultrasound transducers and for interventional access. To enable real-time interventions, images are reconstructed and displayed while the detectors are still acquiring data. The maximum-likelihood reconstruction provides quantitative images with threefold improved contrast as compared to simple back-projections.
Mid-infrared observations of the ultraluminous galaxies IRAS 14348-1447, IRAS 19254-7245, and IRAS 23128-5919

We present a study of the three ultraluminous infrared galaxies IRAS 14348-1447, IRAS 19254-7245, and IRAS 23128-5919, based on mid-infrared (MIR) spectro-imaging (5-18m) observations performed with ISOCAM. We find that the MIR emission from each system, which consists of a pair of interacting late type galaxies, is principally confined to the nuclear regions with diameters of 1-2 kpc and can account for more than 95% of their IRAS 12m flux. In each interacting system, the galaxy hosting an active galactic nucleus (AGN) dominates the total spectrum and shows stronger dust continuum (12-16m) relative to the Unidentified Infrared Band (UIB) emission (6-9m), suggestive of its enhanced radiation field. The MIR dominant galaxy also exhibits elevated 15m/H and 15m/K ratios which trace the high extinction due to the large quantities of molecular gas and dust present in its central regions. Using only diagnostics based on our mid-infrared spectra, we can establish that the Seyfert galaxy IRAS 19254-7245 exhibits MIR spectral features of an AGN while the MIR spectrum of the Seyfert (or LINER) member of IRAS 23128-5919 is characteristic of dust emission principally heated by star forming regions.
Highly accurate phonetic segmentation using boundary correction models and system fusion

Accurate phone-level segmentation of speech remains an important task for many subfields of speech research. We investigate techniques for boosting the accuracy of automatic phonetic segmentation based on HMM acoustic-phonetic models. In prior work [25] we were able to improve on state-of-the-art alignment accuracy by employing special phone boundary HMM models, trained on phonetically segmented training data, in conjunction with a simple boundary-time correction model. Here we present further improved results by using more powerful statistical models for boundary correction that are conditioned on phonetic context and duration features. Furthermore, we find that combining multiple acoustic front-ends gives additional gains in accuracy, and that conditioning the combiner on phonetic context and side information helps. Overall, we reduce segmentation errors on the TIMIT corpus by almost one half, from 93.9% to 96.8% boundary accuracy with a 20-ms tolerance.
Prior-informed Distant Supervision for Temporal Evidence Classification

Temporal evidence classification, i.e., finding associations between temporal expressions and relations expressed in text, is an important part of temporal relation extraction. To capture the variations found in this setting, we employ a distant supervision approach, modeling the task as multi-class text classification. There are two main challenges with distant supervision: (1) noise generated by incorrect heuristic labeling, and (2) distribution mismatch between the target and distant supervision examples. We are particularly interested in addressing the second problem and propose a sampling approach to handle the distribution mismatch. Our prior-informed distant supervision approach improves over basic distant supervision and outperforms a purely supervised approach when evaluated on TAC-KBP data, both on classification and end-to-end metrics.
MAGMA: Multi-level accelerated gradient mirror descent algorithm for large-scale convex composite minimization

Composite convex optimization models arise in several applications, and are especially prevalent in inverse problems with a sparsity inducing norm and in general convex optimization with simple constraints. The most widely used algorithms for convex composite models are accelerated first order methods, however they can take a large number of iterations to compute an acceptable solution for large-scale problems. In this paper we propose to speed up first order methods by taking advantage of the structure present in many applications and in image processing in particular. Our method is based on multi-level optimization methods and exploits the fact that many applications that give rise to large scale models can be modelled using varying degrees of fidelity. We use Nesterov's acceleration techniques together with the multi-level approach to achieve $\mathcal{O}(1/\sqrt{\epsilon})$ convergence rate, where $\epsilon$ denotes the desired accuracy. The proposed method has a better convergence rate than any other existing multi-level method for convex problems, and in addition has the same rate as accelerated methods, which is known to be optimal for first-order methods. Moreover, as our numerical experiments show, on large-scale face recognition problems our algorithm is several times faster than the state of the art.
On-chip MRAM as a High-Bandwidth, Low-Latency Replacement for DRAM Physical Memories

Impediments to main memory performance have traditionally been due to the divergence in processor versus memory speed and the pin bandwidth limitations of modern packaging technologies. In this paper we evaluate a magneto-resistive memory (MRAM)-based hierarchy to address these future constraints. MRAM devices are nonvolatile, and have the potential to be faster than DRAM, denser than embedded DRAM, and can be integrated into the processor die in layers above those of conventional wiring. We describe basic MRAM device operation, develop detailed models for MRAM banks and layers, and evaluate an MRAM-based memory hierarchy in which all off-chip physical DRAM is replaced by on-chip MRAM. We show that this hierarchy offers extremely high bandwidth, resulting in a 15% improvement in end-program performance over conventional DRAM-based main memory systems. Finally, we compare the MRAM hierarchy to one using a chipstacked DRAM technology and show that the extra bandwidth of MRAM enables it to outperform this nearer-term technology. We expect that the advantage of MRAM-like technologies will increase with the proliferation of chip multiprocessors due to increased memory bandwidth demands.
Cuffless and Noninvasive Tonometry Mean Arterial Pressure Measurement by Physiological Characteristics and Applied Pressure

We developed a cuffless and noninvasive measurement technique of blood pressure using tonometric pressure sensor. With observation that the maximum value of a pulse pressure is not obtained at mean arterial pressure (MAP), we have figured out MAP based on the physiological characteristic including the elasticity of wrist tissue, the depth of blood vessel. Through an analysis of 198 clinic data, we have induced the regression equation of the MAP. The probability of the elasticity, depth and APM to explain MAP was 92.1%. The mean difference and the standard deviation between the MAP predicted from the regression equation and the MAP measured by commercial cuff type BP meter were Z-3.183 mmHg and 5.133 mmHg respectively. Comparing the results with the American national standard for electronic or automated sphygmomanometers, we can conclude that the results are quite reliable and promising. Detecting only one part of the body and using only one device are quite advantageous over other BP measurement technique. Our technique makes new way for the cuffless BP measurement
The impact of image descriptions on user tagging behavior: A study of the nature and functionality of crowdsourced tags

Crowdsourcing has emerged as a way to harvest social wisdom from thousands of volunteers to perform a series of tasks online. However, little research has been devoted to exploring the impact of various factors such as the content of a resource or crowdsourcing interface design on user tagging behavior. Although images' titles and descriptions are frequently available in image digital libraries, it is not clear whether they should be displayed to crowdworkers engaged in tagging. This paper focuses on offering insight to the curators of digital image libraries who face this dilemma by examining (i) how descriptions influence the user in his/her tagging behavior and (ii) how this relates to the (a) nature of the tags, (b) the emergent folksonomy, and (c) the findability of the images in the tagging system. We compared two different methods for collecting image tags from Amazon's Mechanical Turk's crowdworkers—with and without image descriptions. Several properties of generated tags were examined from different perspectives: diversity, specificity, reusability, quality, similarity, descriptiveness, and so on. In addition, the study was carried out to examine the impact of image description on supporting users' information seeking with a tag cloud interface. The results showed that the properties of tags are affected by the crowdsourcing approach. Tags from the “with description” condition are more diverse and more specific than tags from the “without description” condition, while the latter has a higher tag reuse rate. A user study also revealed that different tag sets provided different support for search. Tags produced “with description” shortened the path to the target results, whereas tags produced without description increased user success in the search task.
A joint intelligibility evaluation of French text-to-speech synthesis systems: the EvaSy SUS/ACR campaign

The EVALDA/EvaSy project is dedicated to the evaluation of text-to-speech synthesis systems for the French language. It is subdivided into four components: evaluation of the grapheme-to-phoneme conversion module (Boula de Mareüil et al., 2005), evaluation of prosody (Garcia et al., 2006), evaluation of intelligibility, and global evaluation of the quality of the synthesised speech. This paper reports on the key results of the intelligibility and global evaluation of the synthesised speech. It focuses on intelligibility, assessed on the basis of semantically unpredictable sentences, but a comparison with absolute category rating in terms of e.g. pleasantness and naturalness is also provided. Three diphone systems and three selection systems have been evaluated. It turns out that the most intelligible system (diphone-based) is far from being the one which obtains the best mean opinion score.
Stratospheric ozone in boreal fire plumes – the 2013 smoke season over central Europe

Abstract. In July 2013 very strong boreal fire plumes were observed at the northern rim of the Alps by lidar and ceilometer measurements of aerosol, ozone and water vapour for about 3 weeks. In addition, some of the lower-tropospheric components of these layers were analysed at the Global Atmosphere Watch laboratory at the Schneefernerhaus high-altitude research station (2650 m a.s.l., located a few hundred metres south-west of the Zugspitze summit). The high amount of particles confirms our hypothesis that fires in the Arctic regions of North America lead to much stronger signatures in the central European atmosphere than the multitude of fires in the USA. This has been ascribed to the prevailing anticyclonic advection pattern during favourable periods and subsidence, in contrast to warm-conveyor-belt export, rainout and dilution frequently found for lower latitudes. A high number of the pronounced aerosol structures were positively correlated with elevated ozone. Chemical ozone formation in boreal fire plumes is known to be rather limited. Indeed, these air masses could be attributed to stratospheric air intrusions descending from remote high-latitude regions, obviously picking up the aerosol on their way across Canada. In one case, subsidence from the stratosphere over Siberia over as many as 15–20 days without increase in humidity was observed although a significant amount of Canadian smoke was trapped. These coherent air streams lead to rather straight and rapid transport of the particles to Europe.
Performance Analysis of Coherent Optical OFDM Applied to UAV Mobile FSO Systems

The Free Space Optical (FSO) communication links is a promising and cost-effective solution for the provision of high data rate point to point communications. Due to their huge bandwidth, license free spectrum and multipath fading mitigation, the FSO links combined with Orthogonal Frequency Division Multiplexing (OFDM) modulation technique provide an ideal communication solution between Unmanned Aerial Vehicles (UAVs) and fixed Ground Station (GS). In order to design a high performance communication link, it is important to characterize the quality of the optical channel with a proper model, considering the interesting challenges of environmental conditions, such as turbulence and visibility conditions. In this paper we are studying the performance of a mobile link among co-moving UAVs, UAV and GS at different fixed altitudes and link ranges via Optisystem simulation platform, in terms of Bit Error Rate (BER), Optical Signal to Noise Ratio (OSNR) and constellation diagrams. An extensive, comparative analysis among different FSO configurations links considering various characteristics of the OFDM modulation, link ranges, Bit Rates (BR) and the atmospherical conditions is provided.
Electrohydrodynamics of Three-Dimensional Vesicles: A Numerical Approach

A three-dimensional numerical model of vesicle electrohydrodynamics in the presence of DC electric fields is presented. The vesicle membrane is modeled as a thin capacitive interface through the use of a semi-implicit level set Jet scheme. The enclosed volume and surface area are conserved both locally and globally by a new Navier-Stokes projection method. The electric field calculations explicitly take into account the capacitive interface by an implicit Immersed Interface Method formulation, which calculates the electric potential field and the trans-membrane potential simultaneously. The results match well with previously published experimental, analytic and two-dimensional computational works.
Graphons, mergeons, and so on!

In this work we develop a theory of hierarchical clustering for graphs. Our modeling assumption is that graphs are sampled from a graphon, which is a powerful and general model for generating graphs and analyzing large networks. Graphons are a far richer class of graph models than stochastic blockmodels, the primary setting for recent progress in the statistical theory of graph clustering. We define what it means for an algorithm to produce the "correct" clustering, give sufficient conditions in which a method is statistically consistent, and provide an explicit algorithm satisfying these properties.
Stem cell therapy for muscular dystrophy

Muscular dystrophy is a heterogeneous group of neuromuscular disorders that manifests as progressive muscle weakness, muscle wasting and, in many cases, death. Although there has been enormous progress in the molecular understanding of muscular dystrophy, there is still no cure. There are, however, several different therapeutic options under investigation, including adult-derived stem cell transplantation. Encouraging and pioneering experiments in mouse models for Duchenne’s muscular dystrophy (DMD) demonstrated that myoblasts could be transplanted into dystrophic muscle; these myoblasts repaired a small proportion of damaged myofibres. Subsequent work has been devoted to optimisation of this technique. In doing so, a number of adult-derived stem cells have been isolated, characterised and used in promising animal transplantation experiments. Further research is ongoing, and is clearly necessary to make this therapy a viable treatment option for patients with muscular dystrophy.
Automated Network Analysis Identifies Core Pathways in Glioblastoma

Background Glioblastoma multiforme (GBM) is the most common and aggressive type of brain tumor in humans and the first cancer with comprehensive genomic profiles mapped by The Cancer Genome Atlas (TCGA) project. A central challenge in large-scale genome projects, such as the TCGA GBM project, is the ability to distinguish cancer-causing “driver” mutations from passively selected “passenger” mutations. Principal Findings In contrast to a purely frequency based approach to identifying driver mutations in cancer, we propose an automated network-based approach for identifying candidate oncogenic processes and driver genes. The approach is based on the hypothesis that cellular networks contain functional modules, and that tumors target specific modules critical to their growth. Key elements in the approach include combined analysis of sequence mutations and DNA copy number alterations; use of a unified molecular interaction network consisting of both protein-protein interactions and signaling pathways; and identification and statistical assessment of network modules, i.e. cohesive groups of genes of interest with a higher density of interactions within groups than between groups. Conclusions We confirm and extend the observation that GBM alterations tend to occur within specific functional modules, in spite of considerable patient-to-patient variation, and that two of the largest modules involve signaling via p53, Rb, PI3K and receptor protein kinases. We also identify new candidate drivers in GBM, including AGAP2/CENTG1, a putative oncogene and an activator of the PI3K pathway; and, three additional significantly altered modules, including one involved in microtubule organization. To facilitate the application of our network-based approach to additional cancer types, we make the method freely available as part of a software tool called NetBox.