Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of Conjoined Genes: Another Mechanism for Gene Regulation in Eukaryotes

From the ENCODE project, it is realized that almost every base of the entire human genome is transcribed. One class of transcripts resulting from this arises from the conjoined gene, which is formed by combining the exons of two or more distinct (parent) genes lying on the same strand of a chromosome. Only a very limited number of such genes are known, and the definition and terminologies used for them are highly variable in the public databases. In this work, we have computationally identified and manually curated 751 conjoined genes (CGs) in the human genome that are supported by at least one mRNA or EST sequence available in the NCBI database. 353 representative CGs, of which 291 (82%) could be confirmed, were subjected to experimental validation using RT-PCR and sequencing methods. We speculate that these genes are arising out of novel functional requirements and are not merely artifacts of transcription, since more than 70% of them are conserved in other vertebrate genomes. The unique splicing patterns exhibited by CGs reveal their possible roles in protein evolution or gene regulation. Novel CGs, for which no transcript is available, could be identified in 80% of randomly selected potential CG forming regions, indicating that their formation is a routine process. Formation of CGs is not only limited to human, as we have also identified 270 CGs in mouse and 227 in drosophila using our approach. Additionally, we propose a novel mechanism for the formation of CGs. Finally, we developed a database, ConjoinG, which contains detailed information about all the CGs (800 in total) identified in the human genome. In summary, our findings reveal new insights about the functionality of CGs in terms of another possible mechanism for gene regulation and genomic evolution and the mechanism leading to their formation.
Hierarchical sliding mode control of paralleling single-phase UPS inverters

In this paper a novel control method for parallel UPS inverters has been proposed. UPS units paralleling reduces cost of installation and increases reliability of system. This new method is based on sliding mode control and has the benefits of sliding mode control such as robustness against disturbances and fast response. We use hierarchical model of sliding mode control for parallel inverters control. The performance of this method has been investigated through simulation and comparison with common methods of parallel inverters control. Simulation was done for two parallel inverters. Simulation results certified the sliding mode control possibility for parallel inverters control.
Newsroom Convergence in Slovenia: Newswork Environments of the Media Organizations Delo and Žurnal media

Newsroom convergence is a gradual global process of increasing cooperation, collaboration and combination of technologies, staff and spaces between formerly distinct editorial teams of print, television and online media that has its evolutional origins in the United States and Great Britain. However, after theoretically reconsidering the notion of newsroom convergence, doing participant observation in two Slovenian media organizations for a month, and conducting 29 problem-centered interviews with their chairmen, editors and journalists, the author suggests that newsroom convergence is not a universal, linear and technology-driven process and concludes that models of newsroom convergence vary from country to country, from medium to medium, and derive from politically, economically and culturally specific social contexts. Delo and Žurnal media originate from different newsroom traditions, play different roles in the Slovenian media ecosystem, have varying shares of the media market and differ in demography of news staff and size of news production. As a result they have adopted specific newsroom convergence models with different spatial organization and hierarchal structures that reflect a diverse relationship between journalistic norms, market norms and technology.
Planning and execution of dynamic whole-body locomotion for a hydraulic quadruped on challenging terrain

We present a framework for dynamic quadrupedal locomotion over challenging terrain, where the choice of appropriate footholds is crucial for the success of the behaviour. We build a model of the environment on-line and on-board using an efficient occupancy grid representation. We use Any-time-Repairing A* (ARA*) to search over a tree of possible actions, choose a rough body path and select the locally-best footholds accordingly. We run a n-step lookahead optimization of the body trajectory using a dynamic stability metric, the Zero Moment Point (ZMP), that generates natural dynamic whole-body motions. A combination of floating-base inverse dynamics and virtual model control accurately executes the desired motions on an actively compliant system. Experimental trials show that this framework allows us to traverse terrains at nearly 6 times the speed of our previous work, evaluated over the same set of trials.
HULA: Scalable Load Balancing Using Programmable Data Planes

Datacenter networks employ multi-rooted topologies (e.g., Leaf-Spine, Fat-Tree) to provide large bisection bandwidth. These topologies use a large degree of multipathing, and need a data-plane load-balancing mechanism to effectively utilize their bisection bandwidth. The canonical load-balancing mechanism is equal-cost multi-path routing (ECMP), which spreads traffic uniformly across multiple paths. Motivated by ECMP's shortcomings, congestion-aware load-balancing techniques such as CONGA have been developed. These techniques have two limitations. First, because switch memory is limited, they can only maintain a small amount of congestion-tracking state at the edge switches, and do not scale to large topologies. Second, because they are implemented in custom hardware, they cannot be modified in the field. This paper presents HULA, a data-plane load-balancing algorithm that overcomes both limitations. First, instead of having the leaf switches track congestion on all paths to a destination, each HULA switch tracks congestion for the best path to a destination through a neighboring switch. Second, we design HULA for emerging programmable switches and program it in P4 to demonstrate that HULA could be run on such programmable chipsets, without requiring custom hardware. We evaluate HULA extensively in simulation, showing that it outperforms a scalable extension to CONGA in average flow completion time (1.6 x at 50% load, 3 x at 90% load).
New insights from the analysis of free flow vehicular traffic in highways

Building vehicular networks in roads and highways is a challenging research topic with a large number of applications ranging from traffic jams and car collisions prevention to efficient route planning. The analysis of the distance between vehicles in roads is a key factor in, e.g., designing vehicular networks protocols or planning a supporting infrastructure to improve vehicular connectivity. This work proposes a Gaussian-exponential mixture model to characterize the time distance between vehicles in a highway lane, based on measurements collected at different locations in several highways of the city of Madrid, in Spain. The model arises from the observed behavior that some vehicles travel very close together, like in a burst mode, showing Gaussian inter-arrival times, while other vehicles are somehow isolated, showing exponentially distributed inter-arrival times. The experiments show that such a Gaussian-exponential mixture model accurately characterizes inter-vehicle times observed from real traces.
Developments in low-resolution biological X-ray crystallography

Despite the recent substantial technological developments in X-ray crystallography, solving and refining structures at low resolutions remain substantial challenges. Many macromolecular crystals, especially those of large molecules or multicomponent assemblies, diffract X-rays to resolutions that are worse than 3. 5Å. This report summarizes several recent advances aiding low resolution crystallographic work.
Finding HeavyPaths in Weighted Graphs and a Case-Study on Community Detection

A heavy path in a weighted graph represents a notion of connectivity and ordering that goes beyond two nodes. The heaviest path of length l in the graph, simply means a sequence of nodes with edges between them, such that the sum of edge weights is maximum among all paths of length l. It is trivial to state the heaviest edge in the graph is the heaviest path of length 1, that represents a heavy connection between (any) two existing nodes. This can be generalized in many different ways for more than two nodes, one of which is finding the heavy weight paths in the graph. In an influence network, this represents a highway for spreading information from a node to one of its indirect neighbors at distance l. Moreover, a heavy path implies an ordering of nodes. For instance, we can discover which ordering of songs (tourist spots) on a playlist (travel itinerary) is more pleasant to a user or a group of users who enjoy all songs (tourist spots) on the playlist (itinerary). This can also serve as a hard optimization problem, maximizing different types of quantities of a path such as score, flow, probability or surprise, defined as edge weight. Therefore, if one can solve the Heavy Path Problem (HPP) efficiently, they can as well use HPP for modeling and reduce other complex problems to it.
Finding the shortest node-disjoint pair of paths that are allowed to share resilient arcs

We have solved a problem of finding the shortest node-disjoint pair of paths that can share resilient arcs. It is assumed that a network consists of a set of nodes and a set of arcs. Moreover, a number of available arcs are resilient. Our goal is to find the shortest pair of paths such that they share only those nodes that are incident to shared resilient arcs. Furthermore, we assume that the resulting paths cannot contain loops. In the paper we present two novel algorithms solving the above problem. We implement the proposed algorithms and compare them to an MIP approach.
'Technical, Objective, Equitable, and Uniform'? A Critique of the Colombian System for the Selection of Beneficiaries of Social Programmes, Sisben

Targeted poverty reduction programmes, advocated in contemporary poverty orthodoxy, heighten the importance of poverty information. Two divergent tendencies are discernible: tightened-up targeting through narrowed eligibility criteria; and a new epistemology of poverty based on qualitative and participatory methods. Statistical and qualitative analysis of findings from research in rural Colombia shows that the former approach is less "technical, objective, equitable and uniform" than it purports to be; and that the latter is more valid than is often appreciated. A good compromise is to combine the two and apply them in a spirit of "self-critical epistemological awareness" (Chambers 1997).
Insights into Eyestalk Ablation Mechanism to Induce Ovarian Maturation in the Black Tiger Shrimp

Eyestalk ablation is commonly practiced in crustacean to induce ovarian maturation in captivity. The molecular mechanism of the ablation has not been well understood, preventing a search for alternative measures to induce ovarian maturation in aquaculture. This is the first study to employ cDNA microarray to examine effects of eyestalk ablation at the transcriptomic level and pathway mapping analysis to identify potentially affected biological pathways in the black tiger shrimp (Penaeus monodon). Microarray analysis comparing between gene expression levels of ovaries from eyestalk-intact and eyestalk-ablated brooders revealed 682 differentially expressed transcripts. Based on Hierarchical clustering of gene expression patterns, Gene Ontology annotation, and relevant functions of these differentially expressed genes, several gene groups were further examined by pathway mapping analysis. Reverse-transcriptase quantitative PCR analysis for some representative transcripts confirmed microarray data. Known reproductive genes involved in vitellogenesis were dramatically increased during the ablation. Besides these transcripts expected to be induced by the ablation, transcripts whose functions involved in electron transfer mechanism, immune responses and calcium signal transduction were significantly altered following the ablation. Pathway mapping analysis revealed that the activation of gonadotropin-releasing hormone signaling, calcium signaling, and progesterone-mediated oocyte maturation pathways were putatively crucial to ovarian maturation induced by the ablation. These findings shed light on several possible molecular mechanisms of the eyestalk ablation effect and allow more focused investigation for an ultimate goal of finding alternative methods to replace the undesirable practice of the eyestalk ablation in the future.
Fusing vision-based bearing measurements and motion to localize pairs of robots

Abstract —This paper presents a method to cooperativelylocalize pairs of robots fusing bearing-only information pro-vided by a camera and the motion of the vehicles. Thealgorithm uses the robots as landmarks to estimate therelative location between the platforms. Bearings are obtaineddirectly from the camera, as opposed to measuring depthswhich would require knowledge or reconstruction of the worldstructure.We present the general recursive Bayes estimator and threedifferent implementations based on an extended Kalman ﬁlter,a particle ﬁlter and a combination of both techniques. Wehave compared the performance of the different implemen-tations using real data acquired with two platforms, oneequipped with an omnidirectional camera, and simulateddata.Keywords: Cooperative robots, bearing-only measure-ments, localization. I. I NTRODUCTION In the last years cooperative robotics has received con-siderable attention. Teams of robots are able to overcomethe limitations of single robots and allow to attack moredifﬁcult tasks. Furthermore, they increase the degree ofautonomy and robustness by introducing redundancy. How-ever, the use of teams of robots increases the complexity ofthe system. New challenges appear providing new researchareas. In this context cooperative localization is consideredone of the basic capabilities required for autonomousoperation of teams of robots.In this paper we address the problem of cooperativelylocalizing two robots using bearing-only measurementsand the motion of the robots. When the robots navigatebased on proprioceptive sensors, e.g. odometry, they buildand maintain their own, unrelated, referential frames. Byproviding exteroceptive sensors, such as omnidirectionalcameras that track other robots, the various referentialframes can be fused to a single one. The common ref-erential frame opens the way for cooperation and sharingof the information acquired by each of the robots.Omnidirectional cameras allow localizing robots in a360
Long-pore Electrostatics in Inward-rectifier Potassium Channels

Inward-rectifier potassium (Kir) channels differ from the canonical K+ channel structure in that they possess a long extended pore (∼85 Å) for ion conduction that reaches deeply into the cytoplasm. This unique structural feature is presumably involved in regulating functional properties specific to Kir channels, such as conductance, rectification block, and ligand-dependent gating. To elucidate the underpinnings of these functional roles, we examine the electrostatics of an ion along this extended pore. Homology models are constructed based on the open-state model of KirBac1.1 for four mammalian Kir channels: Kir1.1/ROMK, Kir2.1/IRK, Kir3.1/GIRK, and Kir6.2/KATP. By solving the Poisson-Boltzmann equation, the electrostatic free energy of a K+ ion is determined along each pore, revealing that mammalian Kir channels provide a favorable environment for cations and suggesting the existence of high-density regions in the cytoplasmic domain and cavity. The contribution from the reaction field (the self-energy arising from the dielectric polarization induced by the ion's charge in the complex geometry of the pore) is unfavorable inside the long pore. However, this is well compensated by the electrostatic interaction with the static field arising from the protein charges and shielded by the dielectric surrounding. Decomposition of the static field provides a list of residues that display remarkable correspondence with existing mutagenesis data identifying amino acids that affect conduction and rectification. Many of these residues demonstrate interactions with the ion over long distances, up to 40 Å, suggesting that mutations potentially affect ion or blocker energetics over the entire pore. These results provide a foundation for understanding ion interactions in Kir channels and extend to the study of ion permeation, block, and gating in long, cation-specific pores.
Optimal beamforming with combined channel and path CSIT for multi-cell multi-user MIMO

We consider a combined form of partial CSIT (Channel State Information at the Transmitter(s) (Tx)), comprising both channel estimates (mean CSIT) and covariance CSIT. In particular multipath induced structured low rank covariances are considered that arise in Massive MIMO and mmWave settings. For the beamforming optimization, we first revisit Weighted Sum Rate (WSR) maximization with perfect CSIT and introduce yet another equivalent approach: Weighted Sum Unbiased MSE (WSUMSE). We then turn to the partial CSIT case where we consider Expected WSR (EWSR) maximization for which EWSUMSE turns out to be a better approximation compared to the existing EWSMSE approach. These approaches also allow an uplink/downlink duality interpretation for partial CSI.
Survey of Presence of Non-Indigenous Eurytemora Carolleeae in the Gulf of Riga (Baltic Sea) Five Years After its First Discovery

Abstract In the brackish ecosystem of the Gulf of Riga, the calanoid copepod Eurytemora affinis is a key species, but recently a new non-indigenous species Eurytemora carolleeae was discovered in the region. In the present study, we aimed to validate the presence of E. carolleeae in the southern part of the Gulf of Riga five years after its first discovery. The study area is the closest region to the Rīga harbour — the main source of non-indigenous species arrival in the Gulf. Recent studies have predicted the possible potential of E. carolleeae invasion due to its physiological plasticity. Male and female specimens of Eurytemora were collected in spring, summer, and autumn of 2013, and analysed based on three morphological indicators. Despite the higher reproduction rate of E. carolleeae, this intrusive species does not seem to have succeeded in establishing during the five-year period after its first discovery in the Gulf of Riga, and hence does not present a threat to the native E. affinis population in the study area.
Ionizing radiation, part 2: some internally deposited radionuclides. Views and expert opinions of an IARC Working Group on the Evaluation of Carcinogenic Risks to Humans. Lyon, 14-21 June 2000.

2.2.2 (a) (ii) – 172 In first paragraph, last line, replace 222 Ra with 224 RA. 2.2.2 (b) (ii) – 173 In last paragraph, line 9, replace: [The Working Group noted that four cases of lymphoid leukaemia were found among people treated with radium, consisting of one acute and three chronic dysplastic leukaemias. ] with: [The Working Group noted that four cases of lymphoid leukaemia were found among people treated with radium, consisting of one acute lymphoblastic and three chronic lymphocytic leukaemias. ] 2.4. 3 (b) – 208 In first paragraph, line 14, replace fibroblastic spindle-cell sarcoma with fibroblastic osteosarcoma.
Emission and fate modelling framework for engineered nanoparticles in urban aquatic systems at high spatial and temporal resolution

Trends in global urbanization and technology development have raised concerns about the associated increase in emissions to the environment, including novel contaminants such as engineered nanoparticles (ENPs). The assessment of these emissions in urban systems requires modelling approaches that integrate the complexity of urban environments as well as the high spatial and temporal variability of contaminant emissions. ENPs are emitted to urban surface waters through a variety of point and diffuse sources, with these emissions being driven by weather, usage patterns and population density. While the potential environmental and health impacts of ENPs are still not fully understood, understanding the spatial and temporal distribution of ENPs at the local scale will help to inform risk assessment. In this paper, we propose a novel modelling approach for estimating the exposure of ENPs in surface waters of urban systems. An integrative modelling framework combining an emission and a fate model for ENPs with high spatial and temporal resolution is presented and strategies for data gathering and the handling of knowledge gaps are discussed. Our framework is capable of identifying local emission hot spots and predicting exposure across a city, while generating information on the final speciation of the emitted ENPs (nano form, aggregates and other transformation products) within the studied environmental compartments over time.
Evaluating Semantic Relatedness Between Concepts

In this paper, we systematically investigate the methods of measuring semantic relatedness between concepts and categorize them into 6 types of methods: path based, information content, gloss based, vector based, corpus based and string based. Besides, we re-implement those types of methods for evaluating on the latest knowledge sources and made API, which is freely available for research purposes, called CM4J1.
Commute path bandwidth traces from 3G networks: analysis and applications

In this dataset paper, we present and make available real-world measurements of the throughput that was achieved at the application layer when adaptive HTTP streaming was performed over 3G networks using mobile devices. For the streaming sessions, we used popular commute routes in and around Oslo (Norway) traveling with different types of public transportation (metro, tram, train, bus and ferry). We also have a few logs using a car. Each log provides a times-tamp, GPS coordinates and the measured number of bytes downloaded for approximately every second of the route. The dataset can be used in several ways, but the most obvious application is to emulate the same network bandwidth behavior (on specific geographical positions) for repeated experiments.
Geo-spotting: mining online location-based services for optimal retail store placement

The problem of identifying the optimal location for a new retail store has been the focus of past research, especially in the field of land economy, due to its importance in the success of a business. Traditional approaches to the problem have factored in demographics, revenue and aggregated human flow statistics from nearby or remote areas. However, the acquisition of relevant data is usually expensive. With the growth of location-based social networks, fine grained data describing user mobility and popularity of places has recently become attainable. In this paper we study the predictive power of various machine learning features on the popularity of retail stores in the city through the use of a dataset collected from Foursquare in New York. The features we mine are based on two general signals: geographic, where features are formulated according to the types and density of nearby places, and user mobility, which includes transitions between venues or the incoming flow of mobile users from distant areas. Our evaluation suggests that the best performing features are common across the three different commercial chains considered in the analysis, although variations may exist too, as explained by heterogeneities in the way retail facilities attract users. We also show that performance improves significantly when combining multiple features in supervised learning algorithms, suggesting that the retail success of a business may depend on multiple factors.