Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing

Heliconius butterflies represent a recent radiation of species, in which wing pattern divergence has been implicated in speciation. Several loci that control wing pattern phenotypes have been mapped and two were identified through sequencing. These same gene regions play a role in adaptation across the whole Heliconius radiation. Previous studies of population genetic patterns at these regions have sequenced small amplicons. Here, we use targeted next-generation sequence capture to survey patterns of divergence across these entire regions in divergent geographical races and species of Heliconius. This technique was successful both within and between species for obtaining high coverage of almost all coding regions and sufficient coverage of non-coding regions to perform population genetic analyses. We find major peaks of elevated population differentiation between races across hybrid zones, which indicate regions under strong divergent selection. These ‘islands’ of divergence appear to be more extensive between closely related species, but there is less clear evidence for such islands between more distantly related species at two further points along the ‘speciation continuum’. We also sequence fosmid clones across these regions in different Heliconius melpomene races. We find no major structural rearrangements but many relatively large (greater than 1 kb) insertion/deletion events (including gain/loss of transposable elements) that are variable between races.
Fast speaker verification on mobile phone data using boosted slice classifiers

In this work, we investigate a novel computationally efficient speaker verification (SV) system involving boosted ensembles of simple threshold-based classifiers. The system is based on a novel set of features called “slice features”. Both the system and the features were inspired by the recent success of pixel comparison-based ensemble approaches in the computer vision domain. The performance of the proposed system was evaluated through speaker verification experiments on the MOBIO corpus containing mobile phone speech, according to a challenging protocol. The system was found to perform reasonably well, compared to multiple state-of-the-art SV systems, with the benefit of significantly lower computational complexity. Its dual characteristics of good performance and computational efficiency could be important factors in the context of SV system implementation on portable devices like mobile phones.
On the Existence of Perfect Space–Time Codes

Perfect space-time codes are codes for the coherent multiple-input multiple-output (MIMO) channel. They have been called so since they satisfy a large number of design criteria that makes their performances outmatch many other codes. In this correspondence, we discuss the existence of such codes (or more precisely, the existence of perfect codes with optimal signal complexity).
Data composites of airborne observations of tropospheric ozone and its precursors

Tropospheric data from a number of aircraft campaigns have been gridded onto global maps, forming “data composites” of chemical species important in ozone photochemistry. Although these are not climatologies in the sense of a long temporal average, these data summaries are useful for providing a picture of the global distributions of these species and are a start to creating observations-based climatologies. Using aircraft measurements from a number of campaigns, we have averaged observations of O3, CO, NO, NOx, HNO3, PAN, H2O2, CH3OOH, HCHO, CH3COCH3, C2H6, and C3H8 onto a 5° latitude by 5° longitude horizontal grid with a 1-km vertical resolution. These maps provide information about the distributions at various altitudes, but also clearly show that direct observations of the global troposphere are still very limited. A set of regions with 10°–20° horizontal extent has also been chosen wherein there is sufficient data to study vertical profiles. These profiles are particularly valuable for comparison with model results, especially when a full suite of chemical species can be compared simultaneously. The O3 and NO climatologies generated from measurements obtained during commercial aircraft flights associated writh the MOZAIC and NOXAR programs are incorporated with the data composites at 10–11 km. As an example of the utility of these data composites, observations are compared to results from two global chemical transport models, MOZART and IMAGES, to help identify incorrect emission sources, incorrect strength of convection, and missing chemistry in the models. These comparisons suggest that in MOZART the NOx biomass burning emissions may be too low and convection too weak and that the transport of ozone from the stratosphere in IMAGES is too great. The ozone profiles from the data composites are compared with ozonesonde climatologies and show that in some cases the aircraft data agree with the long-term averages, but in others, such as in the western Pacific during PEM-Tropics-A, agreement is lacking. Finally, the data composites provide temporal and spatial information, which can help identify the locations and seasons where new measurements would be most valuable. All of the data composites presented here are available via the Internet (http://aoss.engin.umich.edu/SASSarchive/).
Starting SCF calculations by superposition of atomic densities

We describe the procedure to start an SCF calculation of the general type from a sum of atomic electron densities, as implemented in GAMESS‐UK. Although the procedure is well known for closed‐shell calculations and was already suggested when the Direct SCF procedure was proposed, the general procedure is less obvious. For instance, there is no need to converge the corresponding closed‐shell Hartree–Fock calculation when dealing with an open‐shell species. We describe the various choices and illustrate them with test calculations, showing that the procedure is easier, and on average better, than starting from a converged minimal basis calculation and much better than using a bare nucleus Hamiltonian. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 926–932, 2006
The Use of Plasma-Derived Complement C1-Esterase Inhibitor Concentrate (Berinert®) in the Treatment of Angiotensin Converting Enzyme-Inhibitor Related Angioedema

Angioedema of the upper airways is a severe and potentially life-threatening condition. The incidence has been increasing in the past two decades, primarily due to pharmaceuticals influencing the generation or degradation of the vasoactive molecule bradykinin. Plasma-derived C1-esterase inhibitor concentrate is a well-established treatment option of hereditary and acquired complement C1-esterase inhibitor deficiency, which are also mediated by an increased level of bradykinin resulting in recurrent angioedema. We here present a case of severe angiotensin converting enzyme-inhibitor related angioedema (ACEi-AE) of the hypopharynx that completely resolved rapidly after the infusion of plasma-derived C1-inhibitor concentrate adding to the sparse reports in the existing literature.
Vision-based road detection via on-line video registration

Road segmentation is an essential functionality for supporting advanced driver assistance systems (ADAS) such as road following and vehicle and pedestrian detection. Significant efforts have been made in order to solve this task using vision-based techniques. The major challenge is to deal with lighting variations and the presence of objects on the road surface. In this paper, we propose a new road detection method to infer the areas of the image depicting road surfaces without performing any image segmentation. The idea is to previously segment manually or semi-automatically the road region in a traffic-free reference video record on a first drive. And then to transfer these regions to the frames of a second video sequence acquired later in a second drive through the same road, in an on-line manner. This is possible because we are able to automatically align the two videos in time and space, that is, to synchronize them and warp each frame of the first video to its corresponding frame in the second one. The geometric transform can thus transfer the road region to the present frame on-line. In order to reduce the different lighting conditions which are present in outdoor scenarios, our approach incorporates a shadowless feature space which represents an image in an illuminant-invariant feature space. Furthermore, we propose a dynamic background subtraction algorithm which removes the regions containing vehicles in the observed frames which are within the transferred road region.
A Real Time Predictive Maintenance System of Aluminium Electrolytic Capacitors Used in Uninterrupted Power Supplies

This paper presents a low cost method to realize a real time condition monitoring and a predictive maintenance system of an electrolytic capacitor used in uninterrupted power supplies (UPS). This method consists in detecting the changes on real time in equivalent series resistance (ESR) and the capacitance C values of the electrolytic capacitors. Simulation and experimental results are presented to illustrate the proposed monitoring technique. The proposed method can be used in UPS where waveforms are continuously varying in amplitude, frequency and versus temperature. The proposed on line failure prediction method has the merits of using only the existent resources in UPS and with the use of knower algorithms.
Venus topography and kilometer‐scale slopes

During the first 8 months of the Magellan mission, the radar altimeter has made some three million measurements of the surface of Venus covering the latitude range from 85°N to 80°S. Methods involving range correlation, Doppler filtering, multi-burst summation, and range migration are used to focus the observations and to achieve high surface resolution. Results are presented as maps of the global distribution of topography, meter-scale roughness, and power reflection coefficient. The results are similar to those reported in previous experiments (surface heights exhibit a unimodal distribution with more than 80% of the surface lying within 1 km of the 6051.84-km mean radius) but the higher resolution of the Magellan altimeter has disclosed several surprisingly steep features, e.g. the southwest face of the Maxwell Montes, the southern face of the Danu Montes, and the chasmata to the east of Thetis Regio, where average kilometer-scale slopes of greater than 30° are not uncommon. This conclusion is corroborated by close inspection of synthetic aperture radar imagery.
Polyphase implementation of a video scalar

Image scaling is important in the conversion between different formats such as NTSC, PAL, HDTV and between the CCIR 601 video resolution to the various sizes included in MPEG coding. The change of the resolution proves specially beneficial for improving the coding efficiency. The scaling operation can be generalized by decimation by a factor of M followed by filtering and then interpolation by a factor of L where M and L are integers. The choice of the digital filter depends on the values of L and M. For certain resolution changes, M and L can be rather large integers. Conventional implementation of the filter may result in huge memory and computational requirements. To reduce this factor for practical applications, a polyphase implementation of the digital filter for the video scalar is presented. Some factors determining the choice of the digital filter are discussed. Finally, examples are shown for different resolution scaling of an image.
The SRE Motif in the Human PNPLA3 Promoter (−97 to −88 bp) Mediates Transactivational Effects of SREBP‐1c

Patatin‐like phospholipase domain containing 3 (PNPLA3) is a non‐secreted protein primarily expressed in liver and adipose tissue. Recently, numerous genetic studies have shown that PNPLA3 is a major susceptibility gene for nonalcoholic fatty liver disease (NAFLD). However, the mechanism involved in transcriptional regulation of the PNPLA3 gene remains unknown. We performed a detailed analysis of the human PNPLA3 gene promoter and identified two novel cis‐acting elements (SRE and NFY binding motifs) located at −97/−88 and −26/−22 bp, respectively. Overexpression of SREBP‐1c in HepG2 cells significantly increased PNPLA3 promoter activity. Mutation of either of the putative SRE or NFY binding motifs blocked the transactivation effects of SREBP‐1c on the promoter. Overexpression of SREBP‐1c and NFY together increased PNPLA3 promoter activity twice as much as that of SREBP‐1c or NFY expression alone. This result suggests that SREBP‐1c and NFY synergistically transactivate the human PNPLA3 gene. The ability of SREBP‐1c and NFY to bind these cis‐elements was confirmed using gel shift analysis. Putative SRE and NFY motifs also mediated synergistic insulin‐induced transactivation of the PNPLA3 promoter in HepG2 cells. Additionally, the ability of SREBP‐1c to bind to the PNPLA3 promoter was increased by insulin in a dose‐dependent manner. Moreover, the treatment of HepG2 cells with the PI3K inhibitor LY294002 led to reduced insulin promoter‐activating ability accompanied by a decrease in PNPLA3 and SREBP‐1c protein expression. These results demonstrate that SREBP‐1c is a direct activator of the human PNPLA3 gene and insulin transactivates the PNPLA3 gene via the PI3K‐SREBP‐1c/NFY pathway in HepG2 cells. J. Cell. Physiol. 230: 2224–2232, 2015. © 2015 Wiley Periodicals, Inc.
Unsupervised Acquisition of Predominant Word Senses

There has been a great deal of recent research into word sense disambiguation, particularly since the inception of the Senseval evaluation exercises. Because a word often has more than one meaning, resolving word sense ambiguity could benefit applications that need some level of semantic interpretation of language input. A major problem is that the accuracy of word sense disambiguation systems is strongly dependent on the quantity of manually sense-tagged data available, and even the best systems, when tagging every word token in a document, perform little better than a simple heuristic that guesses the first, or predominant, sense of a word in all contexts. The success of this heuristic is due to the skewed nature of word sense distributions. Data for the heuristic can come from either dictionaries or a sample of sense-tagged data. However, there is a limited supply of the latter, and the sense distributions and predominant sense of a word can depend on the domain or source of a document. (The first sense of star for example would be different in the popular press and scientific journals). In this article, we expand on a previously proposed method for determining the predominant sense of a word automatically from raw text. We look at a number of different data sources and parameterizations of the method, using evaluation results and error analyses to identify where the method performs well and also where it does not. In particular, we find that the method does not work as well for verbs and adverbs as nouns and adjectives, but produces more accurate predominant sense information than the widely used SemCor corpus for nouns with low coverage in that corpus. We further show that the method is able to adapt successfully to domains when using domain specific corpora as input and where the input can either be hand-labeled for domain or automatically classified.
Proteome Analysis of Dormancy-Released Seeds of Fraxinus mandshurica Rupr. in Response to Re-Dehydration under Different Conditions

Desiccation tolerance is the ability of orthodox seeds to achieve equilibrium with atmospheric relative humidity and to survive in this state. Understanding how orthodox seeds respond to dehydration is important for improving quality and long-term storage of seeds under low temperature and drought stress conditions. Long-term storage of seeds is an artificial situation, because in most natural situations a seed that has been shed may not remain in a desiccated state for very long, and if dormant it may undergo repeated cycles of hydration. Different types of seeds are differentially sensitive to desiccation and this directly affects long-term storage. For these reasons, many researchers are investigating loss of desiccation tolerance during orthodox seed development to understand how it is acquired. In this study, the orthodox seed proteome response of Fraxinus mandshurica Rupr. to dehydration (to a relative water content of 10%, which mimics seed dehydration) was investigated under four different conditions viz. 20 °C; 20 °C with silica gel; 1 °C; and 1 °C after pretreatment with Ca2+. Proteins from seeds dehydrated under different conditions were extracted and separated by two-dimensional difference gel electrophoresis (2D-DIGE). A total of 2919 protein spots were detected, and high-resolution 2D-DIGE indicated there were 27 differentially expressed. Seven of these were identified using MALDI TOF/TOF mass spectrometry. Inferences from bioinformatics annotations of these proteins established the possible involvement of detoxifying enzymes, transport proteins, and nucleotide metabolism enzymes in response to dehydration. Of the seven differentially abundant proteins, the amounts of six were down-regulated and one was up-regulated. Also, a putative acyl-coenzyme A oxidase of the glyoxylate cycle increased in abundance. In particular, the presence of kinesin-1, a protein important for regulation and cargo interaction, was up-regulated in seeds exposed to low temperature dehydration. Kinesin-1 is present in all major lineages, but it is rarely detected in seed desiccation tolerance of woody species. These observations provide new insight into the proteome of seeds in deep dormancy under different desiccation conditions.
Massive MIMO in Spectrum Sharing Networks: Achievable Rate and Power Efficiency

Massive multiple input multiple output (MIMO) is one of the key technologies for fifth generation and can substantially improve energy and spectrum efficiencies. This paper explores the potential benefits of massive MIMO in spectrum sharing networks. We consider a multiuser MIMO primary network, with <inline-formula><tex-math notation="LaTeX">$N_\texttt{P}$</tex-math></inline-formula>-antenna primary base station (PBS) and <inline-formula><tex-math notation="LaTeX">$K$</tex-math></inline-formula> single-antenna primary users (PUs), and a multiple-input–single-output secondary network, with <inline-formula><tex-math notation="LaTeX">$N_\texttt{S}$</tex-math></inline-formula>-antenna secondary base station and a single-antenna secondary user. Using the proposed model, we derive a tight closed-form expression for the lower bound on the average achievable rate, which is applicable to arbitrary system parameters. By performing large-system analysis, we examine the impact of large number of PBS antennas and large number of PUs on the secondary network. It is shown that, when <inline-formula><tex-math notation="LaTeX">$N_\texttt{P}$</tex-math></inline-formula> and <inline-formula><tex-math notation="LaTeX">$K$</tex-math></inline-formula> grow large, <inline-formula><tex-math notation="LaTeX">$N_\texttt{S}$</tex-math></inline-formula> must be proportional to <inline-formula><tex-math notation="LaTeX">$\ln K$</tex-math></inline-formula> or larger, to enable successful secondary transmission. In addition, we examine the impact of imperfect channel state information on the secondary network. It is shown that the detrimental effect of channel estimation errors is significantly mitigated as <inline-formula><tex-math notation="LaTeX">$N_\texttt{S}$</tex-math></inline-formula> grows large.
Algorithm for real time faces detection in 3D space

This paper presents the algorithm of stereo-faces detection in video sequences. A stereo-face is a face of a man presented by set of images obtained from different points of view. Such data can be used for faces structure estimation. Our algorithm is based on computationally effective method of face detection in mono image. Information about face positions is then combined using sparse stereo matching algorithm. Sparse means that stereo correspondence is estimated not for all scene points but only for points of interest. This allows obtaining the low computation cost of algorithm. We use few criteria to estimate correspondence. These are: epipolar constraint, size correspondence, 3D region of interest constraint and histogram correspondence. Object distance estimation method that does not use projective transformations of stereo planes is also considered.
Identifying Implicit Component Interactions in Distributed Cyber-Physical Systems

Modern distributed systems and networks, like those found in cyber-physical system domains such as critical infrastructures, contain many complex interactions among their constituent software and/or hardware components. Despite extensive testing of individual components, security vulnerabilities resulting from unintended and unforeseen component interactions (so-called implicit interactions) often remain undetected. This paper presents a method for identifying the existence of implicit interactions in designs of distributed cyber-physical systems using the algebraic modeling framework known as Communicating Concurrent Kleene Algebra (CKA). Experimental results verifying the applicability of CKA for identifying dependencies in system designs that would otherwise be very hard to find are also presented. More broadly, this research aims to advance the specification, design, and implementation of distributed cyber-physical systems with improved cybersecurity assurance by providing a new way of thinking about the problem of implicit interactions through the application of formal methods.
A wideband 10-bit, 20 Msps pipelined ADC using current-mode signals

A 10-b BiCMOS analog-to-digital converter (ADC) is used to demonstrate a current-mode pipeline system that overcomes some of the limitations of high-speed multiple-flash architectures. Although multistage ADCs are efficient in both die area and power, a track-and-hold amplifier (T/H) is required to prevent the input from changing while a conversion is taking place. If the ADC is pipelined (operating on more than one sample at a time), a T/H is required between each pipeline stage. Additionally, for resolution greater than about 8 b interstage amplification is required. The settling behavior of the T/Hs and amplifiers dominates the performance of these ADCs. To address these problems, a differential current-mode architecture incorporates current-mode T/Hs, obviating the need for interstage amplifiers. The prototype chip achieves 10 b of resolution at 20 Msample/s with an 80-MHz input bandwidth and dissipates 1 W. <<ETX>>
Cytologic identification of Toxoplasma gondii from subretinal aspirate

diffuse macular necrotizing retinitis in his right eye (Fig. 1A). He was put on treatment on high-dose oral corticosteroids without clinical improvement. His medical history was post-transfusional hepatitis C. At presentation, his visual acuity (VA) was counting fingers in the right eye and 20 ⁄ 20 in the left eye. Fluorescein angiography demonstrated late hypofluorescence in the area of retinitis (Fig. 1B). Routine blood tests, serology for veneral disease and a Mantoux test were within normal limits. The toxoplasma IgG titre was positive at 238 IU ⁄ml (normal,<6 IU ⁄ml);but IgM levels were not elevated. A brain computed tomography scan was normal. Because of no clinical improvement, a diagnostic pars plana vitrectomy was performed. An undiluted vitreous aspirate was obtained at the start of the procedure, and a subretinal aspirate from the area of the retinitis was taken with a 33G cannula. Vitreous