Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative analysis examining patterns of genomic differentiation across multiple episodes of population divergence in birds

Heterogeneous patterns of genomic differentiation are commonly documented between closely related populations and there is considerable interest in identifying factors that contribute to their formation. These factors could include genomic features (e.g., areas of low recombination) that promote processes like linked selection (positive or purifying selection that affects linked neutral sites) at specific genomic regions. Examinations of repeatable patterns of differentiation across population pairs can provide insight into the role of these factors. Birds are well suited for this work, as genome structure is conserved across this group. Accordingly, we re-estimated relative (FST) and absolute (dXY) differentiation between eight sister pairs of birds that span a broad taxonomic range using a common pipeline. Across pairs, there were modest but significant correlations in window-based estimates of differentiation (up to 3% of variation explained for FST and 26% for dXY), supporting a role for processes at conserved genomic features in generating heterogeneous patterns of differentiation. This suggestion was reinforced by linear models identifying several genomic features (e.g., gene densities) as significant predictors of FST and dXY repeatability. FST repeatability was higher among pairs that were further along the speciation continuum (i.e., more reproductively isolated), suggesting that early stages of speciation may be dominated by positive selection that is different between pairs and replaced by processes acting according to shared genomic features as speciation proceeds.
T‐SAH: Animation Optimized Bounding Volume Hierarchies

We propose a method for creating a bounding volume hierarchy (BVH) that is optimized for all frames of a given animated scene. The method is based on a novel extension of surface area heuristic to temporal domain (T‐SAH). We perform iterative BVH optimization using T‐SAH and create a single BVH accounting for scene geometry distribution at different frames of the animation. Having a single optimized BVH for the whole animation makes our method extremely easy to integrate to any application using BVHs, limiting the per‐frame overhead only to refitting the bounding volumes. We evaluated the T‐SAH optimized BVHs in the scope of real‐time GPU ray tracing. We demonstrate, that our method can handle even highly complex inputs with large deformations and significant topology changes. The results show, that in a vast majority of tested scenes our method provides significantly better run‐time performance than traditional SAH and also better performance than GPU based per‐frame BVH rebuild.
A Functional Genetic Variant in microRNA-196a2 Is Associated with Increased Susceptibility of Lung Cancer in Chinese

microRNAs (miRNA) are a new class of non-protein-coding, small RNAs that function as tumor suppressors or oncogenes. They participate in diverse biological pathways and function as gene regulators. Recently, we conducted a survey of common single nucleotide polymorphisms (SNP) in miRNA sequences and reported that, among four SNPs (rs2910164, rs2292832, rs11614913, and rs3746444) in pre-miRNAs, rs11614913 in miR-196a2 might affect mature miR-196a expression and target mRNA-binding activity and was significantly associated with non-small cell lung cancer survival. However, it remains largely unknown whether miRNA SNPs may alter lung cancer susceptibility. In the current study, we evaluated associations between the above four SNPs in pre-miRNAs and lung cancer susceptibility in a case-control study of 1,058 incident lung cancer patients and 1,035 cancer-free controls in a Chinese population. We found that miR-196a2 rs11614913 variant homozygote CC was associated with ∼25% significantly increased risk of lung cancer compared with their wild-type homozygote TT and heterozygote TC (odds ratio, 1.25; 95% confidence interval, 1.01-1.54). However, no significant effects were observed on the association between the other three SNPs and lung cancer risk. These findings suggest that functional SNP rs11614913 in miR-196a2 could also contribute to lung cancer susceptibility. (Cancer Epidemiol Biomarkers Prev 2009;18(4):1183–7)
Structure Elucidation of Azotobactin 87, Isolated from Azotobacter vinelandii ATCC 12837*, **

Abstract Chromopeptide siderophores (azotobactin 87-1 and -II) were isolated from an iron deficient culture medium of Azotobacter vinelandii ATCC 12837 (=DSM 87). Their structures were elu cidated by chemical degradation studies and spectroscopic methods, especially 2D-NMR-tech-niques. Total assignments of 1H-, 13C-, and 15N-resonances based on 2D-HOHAHA-, 1H/13C-HMQC-, 1H /13C-HMBC-, 1H /15N-HMQC/TOCSY-, and 1H/15N-HMBC-experiments are given as well as sequential information derived from 1H/1H-NOESY-, 1H /13C-HMBC-and 1H/ 13N-HMBC-experiments. Both Az 87-1 and Az 87-11 consist of a tetracyclic chromophore -(1S)8,9-dihydroxy-4-oxo-2,3,4,5-tetrahydro-1H,10cH-3a,5,10b-triazaacephenantrylene-1-carb-oxylic acid -and a decapeptide chain linked with the N-terminus to the carboxy group of the chromophore containing also modified, non-proteinogenic amino acids. The sequence L-Ser-D-Ser-L-Hse-Gly-D-threo-OHAsp-Hse-Hse-Hse-D-N5OH-N5-R-Hbu-Om-L-Hse was determined for Az 87-1, while Az 87-11 contains a C-terminal L-Hse-lactone instead. Iron is chelated by the catecholic group of the chromophore, the β-hydroxy aspartic acid, and the hydroxamate function formed by N5-hydroxyornithine and R-β-hydroxybutyric acid.
Safety and Efficacy of Oxcarbazepine: Results of Randomized, Double‐Blind Trials

Oxcarbazepine is approved as monotherapy and adjunctive therapy for partial seizures with and without secondarily generalized seizures in adults and as adjunctive therapy for partial‐onset seizures in children aged 4–16 years. The clinical development of oxcarbazepine is different from the newer antiepileptic drugs (AEDs) in the extent and concordance of results across clinical trials. The safety and efficacy of oxcarbazepine was evaluated in adjunctive therapy trials, in comparative monotherapy trials with classic AEDs in adults and children with newly diagnosed epilepsy, in monotherapy therapeutic failure design trials in patients with refractory partial seizures, and in trigeminal neuralgia and affective disorder. The results of oxcarbazepine in treating epilepsy are discussed.
Developing a Flood Monitoring System From Remotely Sensed Data for the Limpopo Basin

This paper describes the application of remotely sensed precipitation to the monitoring of floods in a region that regularly experiences extreme precipitation and flood events, often associated with cyclonic systems. Precipitation data, which are derived from spaceborne radar aboard the National Aeronautics and Space Administration's Tropical Rainfall Measuring Mission and from National Oceanic and Atmospheric Administration's infrared-based products, are used to monitor areas experiencing extreme precipitation events that are defined as exceedance of a daily mean areal average value of 50 mm over a catchment. The remotely sensed precipitation data are also ingested into a hydrologic model that is parameterized using spatially distributed elevation, soil, and land cover data sets that are available globally from remote sensing and in situ sources. The resulting streamflow is classified as an extreme flood event when flow anomalies exceed 1.5 standard deviations above the short-term mean. In an application in the Limpopo basin, it is demonstrated that the use of satellite-derived precipitation allows for the identification of extreme precipitation and flood events, both in terms of relative intensity and spatial extent. The system is used by water authorities in Mozambique to proactively initiate independent flood hazard verification before generating flood warnings. The system also serves as a supplementary information source when in situ gauging systems are disrupted. This paper concludes that remotely sensed precipitation and derived products greatly enhance the ability of water managers in the Limpopo basin to monitor extreme flood events and provide at-risk communities with early warning information
A Complete Processing Chain for Shadow Detection and Reconstruction in VHR Images

The presence of shadows in very high resolution (VHR) images can represent a serious obstacle for their full exploitation. This paper proposes to face this problem as a whole through the proposal of a complete processing chain, which relies on various advanced image processing and pattern recognition tools. The first key point of the chain is that shadow areas are not only detected but also classified to allow their customized compensation. The detection and classification tasks are implemented by means of the state-of-the-art support vector machine approach. A quality check mechanism is integrated in order to reduce subsequent misreconstruction problems. The reconstruction is based on a linear regression method to compensate shadow regions by adjusting the intensities of the shaded pixels according to the statistical characteristics of the corresponding nonshadow regions. Moreover, borders are explicitly handled by making use of adaptive morphological filters and linear interpolation for the prevention of possible border artifacts in the reconstructed image. Experimental results obtained on three VHR images representing different shadow conditions are reported, discussed, and compared with two other reconstruction techniques.
Joint Downlink User Association and Interference Management in Two-Tier HetNets With Dynamic Resource Partitioning

We investigate a joint user association and interference management problem in two-tier downlink heterogeneous networks where pico base stations (BSs) are densely deployed in areas of high traffic demand. We employ macro almost blanking subframes (ABSs) to mitigate cross-tier interference. To manage co-tier interference among picocells, we introduce pico operation mode (POM): During each POM, a distinct subset of picocells serve users simultaneously; different POMs operate at different times at different durations. We formulate the problem as maximizing the network utility under proportional fairness with the optimization over user association and resource partitioning (RP) (including the macro ABS and the amount of time allocated to each POM). As an exhaustive search over all possible POMs in the optimization may become computationally infeasible, we propose a method of preselecting favorable POMs to reduce the dimension of the optimization. With the selected POMs, we explicitly examine the structure of the optimal solutions and show that 1) the optimal user association is load-aware and can be determined by rate bias values of each BS, and 2) all the POMs and the macro BSs have balanced load in the sense that the ratios of the number of associated users to the allocated time are the same. Based on the analysis, an alternating algorithm is developed to obtain the RP and the biases. We demonstrate through numerical examples that 1) the proposed POM selection method does not incur significant performance loss, compared with the case where all possible POMs are considered; 2) the alternating algorithm provides near-optimal cell association and RP solutions; 3) by applying the proposed framework, significant network performance improvement can be achieved with dense pico deployments, compared with baselines without co-tier interference management and baselines with sparse pico deployments.
Packing d-Dimensional Bins in d Stages

We consider the d-dimensional bin-packing problem, the most relevant generalization of classical bin packing, and show a general result about the asymptotic worst-case ratio of a wide class of approximation algorithms that construct solutions in d stages, containing many heuristics previously considered in the literature. Moreover, we give the exact value of the asymptotic worst-case ratio between the optimal solution and the best solution obtainable by packing the items in d stages, showing how to achieve such a ratio efficiently. The key property behind our result is the asymptotic optimality of the fractional relaxation of (one-dimensional) bin packing, an important by-product of the approximation schemes for the problem from the 1980s, which, to the best of our knowledge, is used here for the first time only for the sake of the analysis. For the two-dimensional case, we push the approximablity threshold below 2 after more than 20 years (reaching 1.691.), but also improve and widely simplify the analysis of the previous best method from the 1980s. Moreover, for d ≥ 3 we improve the previous approximability threshold by a factor of 1.691. , a notable improvement when d is small.
Benchmark : Stratified Controllers of Tank Networks

We present a new model of a tank network used to transfer liquid. Tanks are connected by channels. The throughput velocity of every particular channel is governed by the controller. We consider a special class of stratified controllers which are organized in several phases. Every phase can be further partitioned into multiple options. This structure makes it easy to generate a variety of benchmark instances ranging in the size, branching factor and generally analysis complexity. We provide a flexible benchmark generator for this class of benchmarks and a sample benchmark suite built by the generator. Finally, we use the Hyst model transformation framework to convert the original model in a format compatible with several reachability tools. Category: academic Difficulty: high 1 Context and Origins The area of hybrid automata [9] has undergone a rapid development in the last decade. In particular, several extensible frameworks [6, 3] for the analysis of hybrid automata are now available. Such frameworks provide an excellent environment to develop new analysis algorithms in a timely manner. However, an extensive testing suite is necessary to ensure the correctness of the developed algorithms and furthermore evaluate their performance against other available algorithms and tools. Unfortunately, only a few benchmark suites are publicly available [5]. Furthermore, the available benchmark instances are hard-coded and cannot be easily adjusted. In this paper, we suggest a new extensible class of benchmarks inspired by the work of Frehse et al. [7]. ∗Air Force Research Laboratory, Rome, NY, USA stanleybak@gmail.com †IST Austria sergiy.bogomolov@ist.ac. at ‡University of Freiburg, Germany greitsch@informatik.uni-freiburg.de §University of Texas at Arlington, USA taylor.johnson@gmail.com ¶DISTRIBUTION A. Approved for public release; Distribution unlimited. (Approval AFRL PA #88ABW-2015-0432, 06 FEB 2015)
Tracking and Analyzing Individual Distress Following Terrorist Attacks Using Social Media Streams

Risk research has theorized a number of mechanisms that might trigger, prolong, or potentially alleviate individuals' distress following terrorist attacks. These mechanisms are difficult to examine in a single study, however, because the social conditions of terrorist attacks are difficult to simulate in laboratory experiments and appropriate preattack baselines are difficult to establish with surveys. To address this challenge, we propose the use of computational focus groups and a novel analysis framework to analyze a social media stream that archives user history and location. The approach uses time‐stamped behavior to quantify an individual's preattack behavior after an attack has occurred, enabling the assessment of time‐specific changes in the intensity and duration of an individual's distress, as well as the assessment of individual and social‐level covariates. To exemplify the methodology, we collected over 18 million tweets from 15,509 users located in Paris on November 13, 2015, and measured the degree to which they expressed anxiety, anger, and sadness after the attacks. The analysis resulted in findings that would be difficult to observe through other methods, such as that news media exposure had competing, time‐dependent effects on anxiety, and that gender dynamics are complicated by baseline behavior. Opportunities for integrating computational focus group analysis with traditional methods are discussed.
Two fast X-ray transients in archival Chandra data

We present the discovery of two new X-ray transients in archival Chandra data. The first transient, XRT 110103, occurred in January 2011 and shows a sharp rise of at least three orders of magnitude in count rate in less than 10 s, a flat peak for about 20 s and decays by two orders of magnitude in the next 60 s. We find no optical or infrared counterpart to this event in preexisting survey data or in an observation taken by the SIRIUS instrument at the Infrared Survey Facility 2.1 yr after the transient, providing limiting magnitudes of J>18.1, H>17.6 and Ks>16.3. This event shows similarities to the transient previously reported in Jonker et al. which was interpreted as the possible tidal disruption of a white dwarf by an intermediate mass black hole. We discuss the possibility that these transients originate from the same type of event. If we assume these events are related a rough estimate of the rates gives 1.4*10^5 per year over the whole sky with a peak 0.3-7 keV X-ray flux greater than 2*10^-10 erg cm^-2 s^-1 . The second transient, XRT 120830, occurred in August 2012 and shows a rise of at least three orders of magnitude in count rate and a subsequent decay of around one order of magnitude all within 10 s, followed by a slower quasi-exponential decay over the remaining 30 ks of the observation. We detect a likely infrared counterpart with magnitudes J=16.70+/-0.06, H=15.92+/-0.04 and Ks=15.37+/-0.06 which shows an average proper motion of 74+/-19 milliarcsec per year compared to archival 2MASS observations. The JHKs magnitudes, proper motion and X-ray flux of XRT 120830 are consistent with a bright flare from a nearby late M or early L dwarf.
A Comparative Analysis of Real-Time Algorithms for Power Signal Decomposition in Multiple Synchronous Reference Frames

The monitoring and rejection of voltage and current harmonics in power electronics applications such as power quality conditioners or distributed generation systems require correct estimation algorithms especially if the harmonic amplitudes are time varying. Power signal decomposition in multiple synchronous rotating reference frames (MSRFs) is considered one of the best solutions. The most commonly employed implementations of this signal transformation are based on phase-locked loops (PLLs), recursive discrete Fourier transforms (RDFT), or discrete Kalman filtering (DKF). In this paper, a rigorous analysis of the performance of these implementations has been carried out. Complete tests have been performed to evaluate the computational burden, the frequency domain response, and the tolerance to low frequency amplitude variations. The results make it possible to select the proper method depending on the requirements of each application.
Bilateral A1 fenestrations: Report of two cases and literature review

Background: Bilateral fenestration of the A1 segment of anterior cerebral artery (ACA) is an uncommon anomaly. Our objective is to describe two cases with this anomaly and to review the literature. Case Description: A 50-year-old woman presented with subarachnoid hemorrhage from a ruptured A1 aneurysm. Angiography revealed bilateral A1 segment fenestration as well as an aneurysm on the proximal end of fenestration on the right side. The second case is that of an 86-year-old woman who was found to have bilateral fenestration of A1 segment at autopsy. Conclusion: Bilateral A1 fenestration is an uncommon anomaly that may be associated with an aneurysm. In surgical clipping of such cases, extreme caution should be exercised to inspect both arms of the fenestration since both may have multiple perforators as demonstrated in our autopsy specimen. This will be the first published pictorial demonstration of these perforators arising from the arms of fenestration.
Bone health in children and adolescent with Turner syndrome

Abstract Low bone mineral density (BMD) in patients with Turner syndrome (TS) has been reported in a considerable number of previous studies. Cortical and trabecular bone have been involved. Osteoporosis can be overdiagnosed in TS patients with a short stature unless BMD measurements are adjusted for body size. Optimization of bone health in girls with TS requires a healthy active lifestyle, including adequate calcium, vitamin D, and hormonal replacement therapy, according to consensus guidelines.
Characterization and Pathogenicity of New Record of Anthracnose on Various Chili Varieties Caused by Colletotrichum scovillei in Korea

Abstract The anthracnose disease caused by Colletotrichum species is well-known as a major plant pathogen that primarily causes fruit rot in pepper and reduces its marketability. Thirty-five isolates representing species of Colletotrichum were obtained from chili fruits showing anthracnose disease symptoms in Chungcheongnam-do and Chungcheongbuk-do, South Korea. These 35 isolates were characterized according to morphological characteristics and nucleotide sequence data of internal transcribed spacer, glyceraldehyde-3-phosphate-dehydrogenase, and β-tubulin. The combined dataset shows that all of these 35 isolates were identified as C. scovillei and morphological characteristics were directly correlated with the nucleotide sequence data. Notably, these isolates were recorded for the first time as the causes of anthracnose caused by C. scovillei on pepper in Korea. Forty cultivars were used to investigate the pathogenicity and to identify the possible source of resistance. The result reveals that all of chili cultivars used in this study are susceptible to C. scovillei.
A framework for automatic semantic video annotation Utilizing similarity and commonsense knowledge bases

The rapidly increasing quantity of publicly available videos has driven research into developing automatic tools for indexing, rating, searching and retrieval. Textual semantic representations, such as tagging, labelling and annotation, are often important factors in the process of indexing any video, because of their user-friendly way of representing the semantics appropriate for search and retrieval. Ideally, this annotation should be inspired by the human cognitive way of perceiving and of describing videos. The difference between the low-level visual contents and the corresponding human perception is referred to as the ‘semantic gap’. Tackling this gap is even harder in the case of unconstrained videos, mainly due to the lack of any previous information about the analyzed video on the one hand, and the huge amount of generic knowledge required on the other. This paper introduces a framework for the Automatic Semantic Annotation of unconstrained videos. The proposed framework utilizes two non-domain-specific layers: low-level visual similarity matching, and an annotation analysis that employs commonsense knowledgebases. Commonsense ontology is created by incorporating multiple-structured semantic relationships. Experiments and black-box tests are carried out on standard video databases for action recognition and video information retrieval. White-box tests examine the performance of the individual intermediate layers of the framework, and the evaluation of the results and the statistical analysis show that integrating visual similarity matching with commonsense semantic relationships provides an effective approach to automated video annotation.