Miracle-dz/UniFAR-FTUs huggingface dataset:
Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

Using genetic data to resolve the evolutionary relationships of species is of major interest in evolutionary and systematic biology. However, reconstructing the sequence of speciation events, the so-called species tree, in closely related and potentially hybridizing species is very challenging. Processes such as incomplete lineage sorting and interspecific gene flow result in local gene genealogies that differ in their topology from the species tree, and analyses of few loci with a single sequence per species are likely to produce conflicting or even misleading results. To study these phenomena on a full phylogenomic scale, we use whole-genome sequence data from 200 individuals of four black-and-white flycatcher species with so far unresolved phylogenetic relationships to infer gene tree topologies and visualize genome-wide patterns of gene tree incongruence. Using phylogenetic analysis in nonoverlapping 10-kb windows, we show that gene tree topologies are extremely diverse and change on a very small physical scale. Moreover, we find strong evidence for gene flow among flycatcher species, with distinct patterns of reduced introgression on the Z chromosome. To resolve species relationships on the background of widespread gene tree incongruence, we used four complementary coalescent-based methods for species tree reconstruction, including complex modeling approaches that incorporate post-divergence gene flow among species. This allowed us to infer the most likely species tree with high confidence. Based on this finding, we show that regions of reduced effective population size, which have been suggested as particularly useful for species tree inference, can produce positively misleading species tree topologies. Our findings disclose the pitfalls of using loci potentially under selection as phylogenetic markers and highlight the potential of modeling approaches to disentangle species relationships in systems with large effective population sizes and post-divergence gene flow.
Outliers handling in the structure-from-motion algorithm

Structure from motion (SfM) is an important task in computer vision. Nowadays, most SfM algorithms are based on feature points, while the outliers from the feature points extraction will limit the accuracy of the SfM algorithms. To eliminate outliers, the RANSAC-style methods are widely used but they have high time complexity. In this paper, a soft-weight-assign method is proposed for the iterative SfM methods to handle outliers. Simulation and experimental results show that the effect of outliers can be strongly reduced by the proposed soft-weight-assign method.
Code-Based Neighbor Discovery Protocols in Mobile Wireless Networks

In mobile wireless networks, the emerging proximity-based applications have led to the need for highly effective and energy-efficient neighbor discovery protocols. However, existing works cannot realize the optimal worst-case latency in the symmetric case, and their performances with asymmetric duty cycles can still be improved. In this paper, we investigate asynchronous neighbor discovery through a code-based approach, including the symmetric and asymmetric cases. We derive the tight worst-case latency bound in the case of symmetric duty cycle. We design a novel class of symmetric patterns called Diff-Codes, which is optimal when the Diff-Code can be extended from a perfect difference set. We further consider the asymmetric case and design ADiff-Codes. To evaluate (A)Diff-Codes, we conduct both simulations and testbed experiments. Both simulation and experiment results show that (A)Diff-Codes significantly outperform existing neighbor discovery protocols in both the median case and worst case. Specifically, in the symmetric case, the maximum worst-case improvement is up to 50%; in both symmetric and asymmetric cases, the median case gain is as high as 30%.
Creating Effective Collaborative Learning Groups in an Online Environment

Collaborative learning in an online classroom can take the form of discussion among the whole class or within smaller groups. This paper addresses the latter, examining first whether assessment makes a difference to the level of learner participation and then considering other factors involved in creating effective collaborative learning groups. Data collected over a three year period (15 cohorts) from the Foundations course in the Master of Distance Education (MDE) program offered jointly by University of Maryland University College (UMUC) and the University of Oldenburg does not support the authors‟ original hypothesis that assessment makes a significant difference to learner participation levels in small group learning projects and leads them to question how much emphasis should be placed on grading work completed in study groups to the exclusion of other strategies. Drawing on observations of two MDE courses, including the Foundations course, their extensive online teaching experience, and a review of the literature, the authors identify factors other than grading that contribute positively to the effectiveness of small collaborative learning groups in the online environment. In particular, the paper focuses on specific instructional strategies that facilitate learner participation in small group projects, which result in an enhanced sense of community, increased skill acquisition, and better learning outcomes.
A Sensitive Hepatocytemediated Assay for the Metabolism of Nitrosamines to Mutagens for Mammalian Cells1

A sensitive cell-mediated assay has been developed for testing mutagenesis in Chinese hamster V79 cells by carcino genic nitrosamines. Mutations were characterized by resist ance to ouabain and 6-thioguanine. Since V79 cells do not metabolize nitrosamines, mutagenesis in the V79 cells was tested in the presence of primary hepatocytes capable of metabolizing nitrosamines. The hepatocytes were isolated after collagenase and hyaluronidase digestion of liver slices. All seven liver carcinogens of the nine tested nitrosamines ex hibited a mutagenic response in this cell-mediated assay. The potent liver carcinogens nitrosodimethylamine, nitrosodieth ylamine, nitrosoethylmethylamine, and nitrosodipropylamine could be detected with doses as low as 1 @M.The noncarcin ogenic nitrosodiphenylamine was not mutagenic. Nitrosome thoxymethylamine was the only nitrosamine that exhibited mu tagenic activity in the absence of hepatocytes, and this activity was diminished in the presence of hepatocytes. It is suggested that the use of hepatocytes prepared by the slicing method for carcinogen metabolism and mutable V79 cells offers a highly sensitive assay for determining the mutagenic potential of carcinogenic nitrosamines and probably of other classes of hazardous chemicals occurring in the environment.
How Random are Intrinsically Disordered Proteins? A Small Angle Scattering Perspective

While the crucial role of intrinsically disordered proteins (IDPs) in the cell cycle is now recognized, deciphering their molecular mode of action at the structural level still remains highly challenging and requires a combination of many biophysical approaches. Among them, small angle X-ray scattering (SAXS) has been extremely successful in the last decade and has become an indispensable technique for addressing many of the fundamental questions regarding the activities of IDPs. After introducing some experimental issues specific to IDPs and in relation to the latest technical developments, this article presents the interest of the theory of polymer physics to evaluate the flexibility of fully disordered proteins. The different strategies to obtain 3-dimensional models of IDPs, free in solution and associated in a complex, are then reviewed. Indeed, recent computational advances have made it possible to readily extract maximum information from the scattering curve with a special emphasis on highly flexible systems, such as multidomain proteins and IDPs. Furthermore, integrated computational approaches now enable the generation of ensembles of conformers to translate the unique flexible characteristics of IDPs by taking into consideration the constraints of more and more various complementary experiment. In particular, a combination of SAXS with high-resolution techniques, such as x-ray crystallography and NMR, allows us to provide reliable models and to gain unique structural insights about the protein over multiple structural scales. The latest neutron scattering experiments also promise new advances in the study of the conformational changes of macromolecules involving more complex systems.
Commentary on Land Settlement in the Peten

Nancy Peckenham's "Land Settlement in the Peten" is a generally unsubstantiated and undocumented, emotional response to what is indubitably an outrageous situation. Her sweeping generalizations, her ignorance of Peten history, and her numerous factual errors of commission, omission, and implication blur the reader's perception of the true setting and hinder understanding of the struggle currently being fought in Guatemala's jungle frontier. Peckenham repeatedly claims that the Kekchi Maya are "the traditional inhabitants of the Peten" (1980: 174, 175). This is not true. After the decline of the Mayan Empire's Classic Period (around 1100 AD), the Peten was virtually abandoned except for small pockets of Mayan Indians, including the Lacandon, Yucatecan, and the Mopain, but not the Kekchi. The historical and cultural antecedents of the Peten are found more in the (overwhelmingly Mexican) Yucatan peninsula than in Guatemala itself, where the Kekchi have always resided, (see, for example, Reina, 1961). While these Mayan groups of the Peten and their cultures have long been exposed to and interacted with other cultural groups (Reina, 1961), not only did they not include Kekchf Mayan, but they did not even have intercourse with the Kekchf until very recently. It was not until the late 1950s that large numbers of Kekchf began permanently migrating to Peten from their native region, the departments of Alta and Baja Verapaz (Adams, 1965). Peckenham (1980Q 169-170) writes,
Unsupervised Feature Selection for Accurate Recommendation of High-Dimensional Image Data

Content-based image suggestion (CBIS) targets the recommendation of products based on user preferences on the visual content of images. In this paper, we motivate both feature selection and model order identification as two key issues for a successful CBIS. We propose a generative model in which the visual features and users are clustered into separate classes. We identify the number of both user and image classes with the simultaneous selection of relevant visual features using the message length approach. The goal is to ensure an accurate prediction of ratings for multidimensional non-Gaussian and continuous image descriptors. Experiments on a collected data have demonstrated the merits of our approach.
MIMO-Assisted MPR-Aware MAC Design for Asynchronous WLANs

The use of multiple-packet reception (MPR) in wireless networks is known to improve throughput especially in high-traffic conditions. The lack of synchronization among the nodes in random access systems introduces significant challenges toward the adoption of MPR in the PHY and the MAC design for systems using MPR. In this paper, we propose an asynchronous MPR method for the PHY and also design a compatible random access MAC for wireless local area networks (WLANs). Relying on space-time coding techniques, our MPR method detects multiple asynchronous packets while providing diversity and low bit error rates at the PHY layer. Extending the design of IEEE 802.11, our MPR MAC design encourages simultaneous packet transmissions and handles multiple packet receptions. Simulation results show that the throughput of a WLAN significantly improves in many scenarios of operation using our proposed PHY/MAC MPR framework.
Extensions to Pairwise Similarity Calculation of Information Networks

We focus on extensions to the pairwise similarity calculation of information networks. By considering both inand out-link relationships, we propose Additiveand Multiplicative-SimRank to calculate the similarity score. Then we discuss the loop/cycles problem of information networks and propose a method to address this problem. Our extensive experimental results conducted on eight food web data sets show that our approach performs significantly better than earlier approaches.
Tupleware: Redefining Modern Analytics

There is a fundamental discrepancy between the targeted and actual users of current analytics frameworks. Most systems are designed for the data and infrastructure of the Googles and Facebooks of the world---petabytes of data distributed across large cloud deployments consisting of thousands of cheap commodity machines. Yet, the vast majority of users operate clusters ranging from a few to a few dozen nodes, analyze relatively small datasets of up to a few terabytes, and perform primarily compute-intensive operations. Targeting these users fundamentally changes the way we should build analytics systems. This paper describes the design of Tupleware, a new system specifically aimed at the challenges faced by the typical user. Tupleware's architecture brings together ideas from the database, compiler, and programming languages communities to create a powerful end-to-end solution for data analysis. We propose novel techniques that consider the data, computations, and hardware together to achieve maximum performance on a case-by-case basis. Our experimental evaluation quantifies the impact of our novel techniques and shows orders of magnitude performance improvement over alternative systems.
Implicit parallelism with ordered transactions

Implicit Parallelism with Ordered Transactions (IPOT) is an extension of sequential or explicitly parallel programming models to support speculative parallelization. The key idea is to specify opportunities for parallelization in a sequential program using annotations similar to transactions. Unlike explicit parallelism, IPOT annotations do not require the absence of data dependence, since the parallelization relies on runtime support for speculative execution. IPOT as a parallel programming model is determinate, i.e., program semantics are independent of the thread scheduling. For optimization, non-determinism can be introduced selectively. We describe the programming model of IPOT and an online tool that recommends boundaries of ordered transactions by observing a sequential execution. On three example HPC workloads we demonstrate that our method is effective in identifying opportunities for fine-grain parallelization. Using the automated task recommendation tool, we were able to perform the parallelization of each program within a few hours.
A Cone-Beam Reconstruction Algorithm Based on Nutating Line Filtration for Single Circular Trajectory

Traditionally, projection data are filtered along the horizontal lines on the detector plane for the FDK algorithm. This makes it impossible that the same voxels involved in the filtering at one projection angle are also filtered together at the other projection angles. To keep filtering together as much as possible for the same voxels at different projection angle, a cone-beam algorithm is presented based on the nutating line by modifying a result due to Turbell. Unlike Turbell's method, the proposed algorithm avoids the process step of rebinning the cone-beam data to 3D parallel-beam data. In addition, to further enlarge reconstruction volume and make the short-scan reconstruction, another FBP term suggested by Zhuang et al. is also modified into the final formula. The performance of the proposed algorithms is compared with other related algorithms through computer simulation using the Shepp-Logan phantom. The experiment results show that the proposed algorithm can substantially compensate for the low density drop inherent to the FDK-type algorithm
PRL‐3 promotes migration and invasion and is associated with poor prognosis in salivary adenoid cystic carcinoma

Background PRL‐3 had been found to be involved in tumorigenesis in various malignancies. In this study, we investigated the role of PRL‐3 in the development, migration, and invasion of salivary adenoid cystic carcinoma (SACC). Methods Immunohistochemistry (IHC) was used to analyze the role of PRL‐3 in the development and prognosis of SACC. Then, we overexpressed or inhibited the expression of PRL‐3 in paired SACC cells to analyze the role of PRL‐3 in the migration and invasion of SACC. In vitro migration and invasion assays were used. Western blotting was used to detect metastasis‐related protein levels. Results IHC results confirmed that the deregulation of PRL‐3 was a frequent event in SACC; the upregulation of PRL‐3 was related to clinical stages, vital status, and distant metastasis, which was associated with reduced overall survival and disease‐free survival. SACC‐LM cells with higher migratory and invasive abilities had more robust PRL‐3 protein expression than SACC‐83 cells with lower migratory and invasive abilities. PRL‐3 overexpression promoted cell migration, invasion, and proliferation, led to simultaneous upregulation of phosphorylated PRL‐3, pERK1/2, Slug, vimentin, and downregulation of E‐cadherin in SACC‐83 cells. However, the inhibition of PRL‐3 by PRL‐3 inhibitor or PRL‐3 siRNA in SACC‐LM cells inhibited cell migration, invasion, and proliferation, resulted in simultaneous downregulation of phosphorylated PRL‐3, pERK1/2, Slug, vimentin, and upregulation of E‐cadherin. Conclusions Our results confirm that PRL‐3 plays an important role in the development of SACC and contributes to the migratory and invasive abilities of SACC.
Perceptual Learning of Interrupted Speech

The intelligibility of periodically interrupted speech improves once the silent gaps are filled with noise bursts. This improvement has been attributed to phonemic restoration, a top-down repair mechanism that helps intelligibility of degraded speech in daily life. Two hypotheses were investigated using perceptual learning of interrupted speech. If different cognitive processes played a role in restoring interrupted speech with and without filler noise, the two forms of speech would be learned at different rates and with different perceived mental effort. If the restoration benefit were an artificial outcome of using the ecologically invalid stimulus of speech with silent gaps, this benefit would diminish with training. Two groups of normal-hearing listeners were trained, one with interrupted sentences with the filler noise, and the other without. Feedback was provided with the auditory playback of the unprocessed and processed sentences, as well as the visual display of the sentence text. Training increased the overall performance significantly, however restoration benefit did not diminish. The increase in intelligibility and the decrease in perceived mental effort were relatively similar between the groups, implying similar cognitive mechanisms for the restoration of the two types of interruptions. Training effects were generalizable, as both groups improved their performance also with the other form of speech than that they were trained with, and retainable. Due to null results and relatively small number of participants (10 per group), further research is needed to more confidently draw conclusions. Nevertheless, training with interrupted speech seems to be effective, stimulating participants to more actively and efficiently use the top-down restoration. This finding further implies the potential of this training approach as a rehabilitative tool for hearing-impaired/elderly populations.
Location, Location, Location and Location Facility Location Incorporating Demand Uncertainty, Logistic Network Design, Product Heterogeneity and Competition Location, Location, Location and Location Facility Location Incorporating Demand Uncertainty, Logistic Network De- Sign, Product Heterogeneity 

Choosing locations to provide service under various constraints and objectives is an essential logistic activity in several contexts. Manufacturers choose locations for facilities and sales depots, government agencies choose locations for fire stations and other service installations, politicians choose ideological positions in the space of political agendas, etc. The field of location theory is devoted to the analysis and development of strategies for choosing locations to optimize certain objectives while meeting various requirements. Traditional models of location involve a fixed set of constraints with fully specified data and a relatively simple set of location points. Examples of such models include the uncapacitated facility location problem and the k-center problem. Real-world location, however, often involves several other imponderables. This research addresses some of these extraneous issues in location analysis: • Demand uncertainty: Locations have to be chosen before the demand is fully revealed, although forecasts are available. • Logistic network design: Transshipment networks have to be constructed in addition to choosing locations. • Product heterogeneity: Demand for several different products has to be served, with economies of scale in manufacturing multiple commodities at the same location. • Competition: More than one agent is competing for the same demand, so locations have to be chosen strategically. Barring the last chapter, all of our work is from the perspective of approximation algorithms. We provide polynomial time approximation algorithms for various location models in the contexts described above. For the competitive location model, we provide bounds for payoffs of the agents choosing the locations, and strategies for achieving those payoffs.
Strategies in syllogistic reasoning

This paper is about syllogistic reasoning, i.e., reasoning from such pairs of premises as, All the chefs are musicians; some of the musicians are painters. We present a computer model that implements the latest account of syllogisms, which is based on the theory of mental models. We also report four experiments that were designed to test this account. Experiments 1 and 2 examined the strategies revealed by the participants’ use of paper and pencil as aids to reasoning. Experiment 3 used a new technique to externalize thinking. The participants had to refute, if possible, putative conclusions by constructing external models that were examples of the premises but counterexamples of the conclusions. Experiment 4 used the same techniques to examine the participants’ strategies as they drew their own conclusions from syllogistic premises. The results of the experiments showed that individuals not trained in logic can construct counterexamples, that they use similar operations to those implemented in the computer model, but that they rely on a much greater variety of interpretations of premises and of search strategies than the computer model does. We re-evaluates current theories of syllogistic reasoning in the light of these results.
COLEPL and COLSLM: An Unsupervised WSD Approach to Multilingual Lexical Substitution, Tasks 2 and 3 SemEval 2010

In this paper, we present a word sense disambiguation (WSD) based system for multilingual lexical substitution. Our method depends on having a WSD system for English and an automatic word alignment method. Crucially the approach relies on having parallel corpora. For Task 2 (Sinha et al., 2009) we apply a supervised WSD system to derive the English word senses. For Task 3 (Lefever & Hoste, 2009), we apply an unsupervised approach to the training and test data. Both of our systems that participated in Task 2 achieve a decent ranking among the participating systems. For Task 3 we achieve the highest ranking on several of the language pairs: French, German and Italian.