Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved search heuristics find 20 000 new alignments between human and mouse genomes

Sequence similarity search is a fundamental way of analyzing nucleotide sequences. Despite decades of research, this is not a solved problem because there exist many similarities that are not found by current methods. Search methods are typically based on a seed-and-extend approach, which has many variants (e.g. spaced seeds, transition seeds), and it remains unclear how to optimize this approach. This study designs and tests seeding methods for inter-mammal and inter-insect genome comparison. By considering substitution patterns of real genomes, we design sets of multiple complementary transition seeds, which have better performance (sensitivity per run time) than previous seeding strategies. Often the best seed patterns have more transition positions than those used previously. We also point out that recent computer memory sizes (e.g. 60 GB) make it feasible to use multiple (e.g. eight) seeds for whole mammal genomes. Interestingly, the most sensitive settings achieve diminishing returns for human–dog and melanogaster–pseudoobscura comparisons, but not for human–mouse, which suggests that we still miss many human–mouse alignments. Our optimized heuristics find ∼20 000 new human–mouse alignments that are missing from the standard UCSC alignments. We tabulate seed patterns and parameters that work well so they can be used in future research.
TLM-G-a grid-enabled time-domain transmission-line-matrix system for the analysis of complex electromagnetic structures

A Grid-enabled time-domain transmission line matrix (TLM-G) system for full-wave analysis of complex electromagnetic (EM) structures is presented. The emerging Grid technology enables distributed EM simulations in a virtual organization. An introduction to Grid computing is given and a detailed description of the layout of the TLM-G system is made. Furthermore, the measured EM performance, scalability, and accuracy of the TLM-G system are shown.
A unified interpretation of adaptation approaches based on a macroscopic time evolution system and indirect/direct adaptation approaches

Incremental adaptation techniques for speech recognition are aimed at adjusting acoustic models quickly and stably to time-variant acoustic characteristics due to temporal changes of speaker, speaking style, noise source, etc. We proposed a novel incremental adaptation framework based on a macroscopic time evolution system, which models the time-variant characteristics by successively updating posterior distributions of acoustic model parameters. In this paper, we provide a unified interpretation of the proposal and the two major conventional approaches of indirect adaptation via transformation parameters (e.g. maximum likelihood linear regression (MLLR)) and direct adaptation of classifier parameters (e.g. maximum a posteriori (MAP)). We reveal analytically and experimentally that the proposed incremental adaptation involves both the conventional and their combinatorial approaches, and simultaneously possesses their quick and stable adaptation characteristics.
Script N=2 SO(N) SYM theory from matrix model

We study =2 SO(2N+1) SYM theory in the context of matrix model. By adding a superpotential of the scalar multiplet, W(Φ), of degree 2N+2, we reduce the theory to =1. The 2N+1 distinct critical points of W(Φ) allow us to choose a vacuum in such a way to break the gauge group to its maximal abelian subgroup. We compute the free energy of the corresponding matrix model in the planar limit and up to two vertices. This result is then used to work out the effective superpotential of =1 theory up to one-instanton correction. At the final step, by scaling the superpotential to zero, the effective U(1) couplings and the prepotential of the =2 theory are calculated which agree with the previous results.
Renewing the resource base in line with the dynamic capabilities view: a key to sustained competitive advantage in the IT industry

The purpose of this paper is to indicate that firms which renew their resource base in line with the dynamic capabilities view can generate and sustain a competitive advantage and thus the related firm performance. In order to investigate the relationships involved, in-depth interviews were conducted in six representative IT firms. The results suggest that firms with a stronger commitment to deploying dynamic capabilities are more successful and hold the potential for a sustained competitive advantage. We also found that innovation capability, managerial capability and human resource capability are the most relevant capabilities that allow firms to successfully adapt to a changing environment and the highly demanding IT market.
Spatial Correlation for Correlated Scatterers

This paper investigates the correlations between sensor signals in multipath environments created by correlated scatterers. We derive a closed form expression for the correlation in fields created by arbitrary scatterer correlations and scatterer powers, using Fourier techniques, and propose reasonable function forms for scatterer correlation. Simulations show notable differences from the uncorrelated scatterer case
Past, present, and future of social TV: A categorization

Social Television constitutes a fundamental shift in how people interact and socialize around television content. Websites are starting to combine streaming services with social networking sites such as Facebook and Twitter. Media software like Boxee allows users to recommend and share favorite television programs, and friends can jointly watch television remotely as demonstrated by Motorola's Social TV. The purpose of this paper is to provide a structured overview of current developments in this emerging field. Current offerings can be categorized based on the social purpose: content selection and recommendation, communication, community building, and status update. The framework proposed in this article is useful for better understanding the current situation and for identifying future developments.
DNA-mediated adjuvant immunotherapy extends survival in two different mouse models of myeloid malignancies

We have previously shown that a specific promyelocytic leukemia-retinoic acid receptor alpha (PML-RARA) DNA vaccine combined with all-trans retinoic acid (ATRA) increases the number of long term survivors with enhanced immune responses in a mouse model of acute promyelocytic leukemia (APL). This study reports the efficacy of a non-specific DNA vaccine, pVAX14Flipper (pVAX14), in both APL and high risk myelodysplastic syndrome (HR-MDS) models. PVAX14 is comprised of novel immunogenic DNA sequences inserted into the pVAX1 therapeutic plasmid. APL mice treated with pVAX14 combined with ATRA had increased survival comparable to that obtained with a specific PML-RARA vaccine. Moreover, the survival advantage correlated with decreased PML-RARA transcript levels and increase in anti-RARA antibody production. In HR-MDS mice, pVAX14 significantly improved survival and reduced biomarkers of leukemic transformation such as phosphorylated mitogen-activated protein/extracellular signal-regulated kinase kinase (MEK) 1. In both preclinical models, pVAX14 vaccine significantly increased interferon gamma (IFNγ) production, memory T-cells (memT), reduced the number of colony forming units (CFU) and increased expression of the adapter molecule signalling to NF-κB, MyD88. These results demonstrate the adjuvant properties of pVAX14 providing thus new approaches to improve clinical outcome in two different models of myeloid malignancies, which may have potential for a broader applicability in other cancers.
Thermal infrared observations of heterogeneous soil-vegetation systems

Heterogeneous soil-foliage systems are characterized under most conditions by large differences in surface temperature between foliage and soil. Two radiometric methods in the thermal infrared spectral region can be used to observe these effects: observations at very high spatial resolution to capture individual leaves or observations at multiple view and illumination angles. The latter is applicable at any spatial resolution, although the anisotropy of emittance is a secondary effect due to thermal heterogeneity and requires high precision radiometric measurements. This chapter reviews the experimental evidence on the anisotropy of emittance by the soil-vegetation system and describes the interpretation of this signal in terms of the thermal heterogeneity and geometry of the canopy space. Observations of the dependence of exitance on view angle by means of ground-based goniometers, airborne and spaceborne imaging radiometers are reviewed first to conclude that under most conditions a two-components, i.e. soil and foliage, model of observed Top Of Canopy (TOC) brightness temperature is adequate to interpret observations. Modeling approaches to describe radiative transfer in the soil-vegetation-atmosphere system, with emphasis on Correspondence/Reprint request: Prof. Dr. Massimo Menenti, D Delft Institute of Earth and Planetary Observation Systems (DEOS), Delft University of Technology, 2629 HS Delft, The Netherlands. E-mail: m.menenti@tudelft.nl L. Jia and M. Menenti 2 the thermal infrared region, are reviewed. Given the dependence of observed TOC brightness temperature on leaf-level radiation and heat balance, energy and water transfer in the soil-vegetation-atmosphere system must be included to construct a realistic model of exitance by soil-vegetation systems. Algorithms to estimate foliage and soil temperatures by inverse modeling of multi-angular measurements of exitance are described and evaluated against both synthetic and experimental data.
Optimum Planning of Hybrid Energy System using HOMER for Rural Electrification

large proportion of the world's population lives in remote rural areas that are geographically isolated and sparsely populated. This paper discussed the efficient system of sustainable renewable energy for domestic use and its total cost for the off-grid area; taking Sandip-para as model which is in Raujan upzila of Chittagong district. Method of this paper is collecting the basic data of solar radiation, wind speed and other required input data, and then hybrid optimization. Simulation model was developed using the HOMER energy modeling software. Simulation model has been used to find out the best technically viable renewable based energy efficient system for different numbers of household. Results have been presented as the most efficient economic way for electrifying the area.
Managing risk of construction projects : a case study of Iran

The construction industry is one of the most dynamic, risky, and challenging businesses. Due to construction projects’ complexity and uniqueness, the number of risks present invariably goes beyond those found in other industries. Therefore, risk management should be applied as an integral part of project management for managing these risks – in particular in developing countries. Contingency theory was selected as the theoretical framework of this thesis. Since the environment has been considered as one of the important contextual variables being focused on in this theory, the research was situated within a specific environment. Considering the unstable social, economic and political conditions in Iran today in comparison with many other countries, it was found to be a suitable case to be evaluated in this thesis. A questionnaire was designed and twenty-five risks were identified and categorized in five main categories as follows: Political and Governmental, Managerial and Technical, Economic and Financial, Cultural and Social, and Natural. For each of these risks, relevant mitigation strategies were also proposed. Criticality of risks along with effectiveness of mitigation strategies were evaluated via 100 questionnaires which were distributed to the three key categories of actors associated with construction projects namely clients, contractors, and consultants. Out of 76 valid responses received, interviews were conducted with 24 of the participants in order to extract the knowledge and understand how these groups manage the identified risks. Findings of the research revealed that Economic and Financial risks have the greatest influence on construction projects in Iran. Moreover, there is a serious lack of risk management knowledge and expertise among all the three key categories of actors. The conclusion drawn from the evaluation of risk management strategies was that due to high volatility of the economic and political situation of the country, reactive risk management is practiced more than proactive risk management. The results of the case study about the risks and their management strategies have also implications for contingency theory; modifying the theory from a conceptual theory to a more meaningful theory. There is a mixture of proactive and reactive management while utilizing the theory for managing any situation and existence of this mixture needs to be made explicit in the theory. Likewise, utilization of contingency plan needs to be made more explicit in the theory. Moreover, employment of contingency theory for managing situations has been stated to be unique for each particular situation and therefore the situation should be defined in order to refer to a more specific concept. This eventually may lead to a more specific and detailed theory for any situation and hence instead of saying ‘it all depends’, it can be stated that ‘it depends on this and that’.
Working at the interface of phylogenetics and population genetics: a biogeographical analysis of Triaenops spp. (Chiroptera: Hipposideridae)

New applications of genetic data to questions of historical biogeography have revolutionized our understanding of how organisms have come to occupy their present distributions. Phylogenetic methods in combination with divergence time estimation can reveal biogeographical centres of origin, differentiate between hypotheses of vicariance and dispersal, and reveal the directionality of dispersal events. Despite their power, however, phylogenetic methods can sometimes yield patterns that are compatible with multiple, equally well‐supported biogeographical hypotheses. In such cases, additional approaches must be integrated to differentiate among conflicting dispersal hypotheses. Here, we use a synthetic approach that draws upon the analytical strengths of coalescent and population genetic methods to augment phylogenetic analyses in order to assess the biogeographical history of Madagascar's Triaenops bats (Chiroptera: Hipposideridae). Phylogenetic analyses of mitochondrial DNA sequence data for Malagasy and east African Triaenops reveal a pattern that equally supports two competing hypotheses. While the phylogeny cannot determine whether Africa or Madagascar was the centre of origin for the species investigated, it serves as the essential backbone for the application of coalescent and population genetic methods. From the application of these methods, we conclude that a hypothesis of two independent but unidirectional dispersal events from Africa to Madagascar is best supported by the data.
Sexual behaviour patterns in South Africa and their association with the spread of HIV: insights from a mathematical model

This paper aims to quantify the effects of different types of sexual risk behaviour on the spread of HIV in South Africa. A mathematical model is developed to simulate changes in numbers of sexual partners, changes in marital status, changes in commercial sex activity and changes in the frequency of unprotected sex over the life course. This is extended to allow for the transmission of HIV, and the model is fitted to South African HIV prevalence data and sexual behaviour data. Results suggest that concurrent partnerships and other non-spousal partnerships are major drivers of the HIV/AIDS epidemic in South Africa.
Consistent Synchronization of Action Order with Least Noticeable Delays in Fast-Paced Multiplayer Online Games

When running multiplayer online games on IP networks with losses and delays, the order of actions may be changed when compared to the order run on an ideal network with no delays and losses. To maintain a proper ordering of events, traditional approaches either use rollbacks to undo certain actions or local lags to introduce additional delays. Both may be perceived by players because their changes are beyond the just-noticeable-difference (JND) threshold. In this article, we propose a novel method for ensuring a strongly consistent completion order of actions, where strong consistency refers to the same completion order as well as the same interval between any completion time and the corresponding ideal reference completion time under no network delay. We find that small adjustments within the JND on the duration of an action would not be perceivable, as long as the duration is comparable to the network round-trip time. We utilize this property to control the vector of durations of actions and formulate the search of the vector as a multidimensional optimization problem. By using the property that players are generally more sensitive to the most prominent delay effect (with the highest probability of noticeability Pnotice or the probability of correctly noticing a change when compared to the reference), we prove that the optimal solution occurs when Pnotice of the individual adjustments are equal. As this search can be done efficiently in polynomial time ( ∼ 5ms) with a small amount of space ( ∼ 160KB), the search can be done at runtime to determine the optimal control. Last, we evaluate our approach on the popular open-source online shooting game BZFlag.
The Approach Being Explored—projection Reduction Exposure with Variable Axis Immersion Lenses (prevail)—combines the High Exposure Efficiency of Massively Parallel Pixel Projection with Scanning-probe-forming Systems to Dynamically Correct for Aberrations. in Contrast to Optical Lithography Systems,

This paper is an overview of work in the IBM Microelectronics Division to extend electronbeam lithography technology to the projection level for use in next-generation lithography. The approach being explored—Projection Reduction Exposure with Variable Axis Immersion Lenses (PREVAIL)—combines the high exposure efficiency of massively parallel pixel projection with scanning-probe-forming systems to dynamically correct for aberrations. In contrast to optical lithography systems, electron-beam lithography systems are not diffraction-limited, and their ultimate attainable resolution is, for practical purposes, unlimited. However, their throughput has been—and continues to be—the major challenge in electron-beam lithography. The work described here, currently continuing, has been undertaken to address that challenge. Novel electron optical methods have been used and their feasibility ascertained by means of a Proof-Of-Concept (POC) system containing a Curvilinear Variable Axis Lens (CVAL) for achieving large-distance (>20 mm at a reticle) beam scanning at a resolution of <100 nm, and a high-emittance electron source for achieving uniform illumination of a 1-mm section of the reticle. A production-level prototype PREVAIL system, an “alpha” system, for the 100-nm node has been under development jointly with the Nikon Corporation. At the writing of this paper, its electron-optics subsystem had been brought up to basic operation and was being prepared for integration with its mechanical and vacuum subsystem, under development at Nikon facilities.
Process Examination of Executive Function in ADHD: Sex and Subtype Effects

To examine effects of group (Attention-Deficit/Hyperactivity Disorder [ADHD] versus Typically Developing [TD]), sex, and ADHD subtype on “process/optional” measures of executive functioning, children ( n = 123; 54 ADHD, 69 TD) aged 8–16 completed subtests from the D-KEFS. No group, sex, or ADHD subtype effects were found on optional measures from the Trail Making, Color–Word Interference, and Tower tests. A significant interaction was found for Verbal Fluency Total Repetition Errors; boys with Combined/Hyperactive-Impulsive (ADHD-C/HI) type ADHD performed better than ADHD-C/HI girls, whereas girls with Inattentive type ADHD (ADHD-I) performed better than ADHD-I boys. Overall, children with ADHD did not differ from TD on most optional measures from the D-KEFS. When sex and ADHD subtype were considered, children with the subtype of ADHD less common for sex were at greater risk for poorer performance.
Computer Vision and Image Understanding Improved Scene Identification and Object Detection on Egocentric Vision of Daily Activities

This work investigates the relationship between scene and associated objects on daily activities under egocentric vision constraints. Daily activities are performed in prototypical scenes that share a lot of visual appearances independent of where or by whom the video was recorded. The intrinsic characteristics of egocentric vision suggest that the location where the activity is conducted remains consistent throughout frames. This paper shows that egocentric scene identification is improved by taking the temporal context into consideration. Moreover, since most of the objects are typically associated with particular types of scenes, we show that a generic object detection method can also be improved by re-scoring the results of the object detection method according to the scene content. We first show the case where the scene identity is explicitly predicted to improve object detection, and then we show a framework using Long Short-Term Memory (LSTM) where no labeling of the scene type is needed. We performed experiments in the Activities of Daily Living (ADL) public dataset (Pirsiavash and Ramanan,2012), which is a standard benchmark for egocentric vision.
GLOBAL-SCALE OBJECT DETECTION USING SATELLITE IMAGERY

: In recent years, there has been a substantial increase in the availability of high-resolution commercial satellite imagery, enabling a variety of new remote-sensing applications. One of the main challenges for these applications is the accurate and efﬁcient extraction of semantic information from satellite imagery. In this work, we investigate an important instance of this class of challenges which involves automatic detection of multiple objects in satellite images. We present a system for large-scale object training and detection, leveraging recent advances in feature representation and aggregation within the bag-of-words paradigm. Given the scale of the problem, one of the key challenges in learning object detectors is the acquisition and curation of labeled training data. We present a crowd-sourcing based framework that allows efﬁcient acquisition of labeled training data, along with an iterative mechanism to overcome the label noise introduced by the crowd during the labeling process. To show the competence of the presented scheme, we show detection results over several object-classes using training data captured from close to 200 cities and tested over multiple geographic locations.