Miracle-dz/UniFAR-FTUs huggingface dataset:
Leveraging distant relatedness to quantify human mutation and gene conversion rates

The rate at which human genomes mutate is a central biological parameter that has many implications for our ability to understand demographic and evolutionary phenomena. We present a method for inferring mutation and gene conversion rates using the number of sequence differences observed in identical-by-descent (IBD) segments together with a reconstructed model of recent population size history. This approach is robust to, and can quantify, the presence of substantial genotyping error, as validated in coalescent simulations. We applied the method to 498 trio-phased Dutch individuals from the Genome of the Netherlands (GoNL) project, sequenced at an average depth of 13x. We infer a point mutation rate of 1.66 ± 0.04 × 10−8 per base per generation, and a rate of 1.26 ± 0.06 × 10−9 for < 20 bp indels. Our estimated average genome-wide mutation rate is higher than most pedigree-based estimates reported thus far, but lower than estimates obtained using substitution rates across primates. By quantifying how estimates vary as a function of allele frequency, we infer the probability that a site is involved in non-crossover gene conversion as 5.99 ± 0.69 × 10−6, consistent with recent reports. We find that recombination does not have observable mutagenic effects after gene conversion is accounted for, and that local gene conversion rates reflect recombination rates. We detect a strong enrichment for recent deleterious variation among mismatching variants found within IBD regions, and observe summary statistics of local IBD sharing to closely match previously proposed metrics of background selection, but find no significant effects of selection on our estimates of mutation rate. We detect no evidence for strong variation of mutation rates in a number of genomic annotations obtained from several recent studies.
Indoor multiple sound source localization using a novel data selection scheme

The multiple sound source localization problem in reverberant environments is studied by using a circular microphone array. The problem is approached by performing single source localization at each of the selected time-frequency (TF) data points from the received signals followed by a histogram technique to achieve robust localization. A novel TF data point selection scheme is proposed based on the ratio of the power of a TF point to that of its adjacent preceding TF point at the same frequency. The method introduces little extra computation and is suitable for real-time implementation. The proposed algorithm is compared with the algorithm in [1] to show its effectiveness and efficiency using extensive simulations.
A G2 Continuous Path-smoothing Algorithm Using Modified Quadratic Polynomial Interpolation

Path searching algorithm is one of the main topics in studies on path planning. These algorithms are used to avoiding obstacles and find paths from starting point to target point. There are dynamic problems that must be addressed when these paths are applied in real environments. In order to be applicable in actual situations, the path must be a smooth path. A smooth path is a path that maintains continuity. Continuity is decided by the differential values of the path. In order to be G2 continuous, the secondary differential values of the path must be connected throughout the path. In this paper, the interpolation method is used to construct continuous paths. The quadratic polynomial interpolation is a simple method for obtaining continuous paths about three points. The proposed algorithm makes a connection of three points with curves and the proposed path is rotated using the parametric method in order to make the path optimal and smooth. The polynomials expand to the next three points and they merge into the entire path using the membership functions with G2 continuity.
Deterministic MDPs with Adversarial Rewards and Bandit Feedback

We consider a Markov decision process with deterministic state transition dynamics, adversarially generated rewards that change arbitrarily from round to round, and a bandit feedback model in which the decision maker only observes the rewards it receives. In this setting, we present a novel and efficient online decision making algorithm named MarcoPolo. Under mild assumptions on the structure of the transition dynamics, we prove that MarcoPolo enjoys a regret of O(T3/4 √log T) against the best deterministic policy in hindsight. Specifically, our analysis does not rely on the stringent unichain assumption, which dominates much of the previous work on this topic.
Middleware and Management Support for Programmable QoS-Network Architectures

This paper focuses on management and middleware support for incremental updating of code and policies on various levels of granularity in time and space and on code deployment in vastly large distributed systems such as a networking infrastructure. In particular, we describe a middleware for programmable Differentiated Service (DiffServ) architectures. DiffServ architectures are envisaged by the standardization body of the IETF to be open to an evolutionary process and to facilitate adjustments to local conditions. The middleware we suggest for enabling openness and programmability of future DiffServ QoS architectures uses XML in the definition of specific policy languages, provides XML extensions to satisfy new needs and the management of deployed policies on different active nodes. Based on our middleware, router packet forwarding policies may be flexibly defined and, in an extreme case, even dynamically updated at run-time on the active nodes as a function of the network/router status. Based on a two-level language approach, the middleware decouples policy management, which is handled through XML interpretation, from packet forwarding that is implemented in more efficient languages. The two-level language approach allows a compilation of highly efficient executable code from an intermediate XML virtual machine level representation.
Sub-operating systems: a new approach to application security

Users regularly exchange apparently innocuous data files using email and ftp. While the users view these data as passive, there are situations when they are interpreted as code by some system application. In that case the data become "active". Some examples of such data are Java, JavaScript and Microsoft Word attachments, each of which are executed within the security context of the user, allowing potentially arbitrary machine access. The structure of current operating systems and user applications makes solving this problem challenging.We propose a new protection mechanism to address active content, which applies fine-grained access controls at the level of individual data objects. All data objects arriving from remote sources are tagged with a non-removable identifier. This identifier dictates its permissions and privileges rather than the file owner's user ID. Since users possess many objects, the system provides far more precise access control policies to be enforced, and at a far finer granularity than previous designs.
Reliability and Validity of the “Personal Well-Being Index – Adult” in Mothers of Mentally Retarded Students in North of Tehran-Iran

Objective: Having a good quality of life has always been desirable for humans and the concept of a good life and the ways of achieving it have been focused over the years. Personal wellbeing is the mental component of quality of life. Thus, the current study was conducted to estimate psychometric characteristics of “personal well-being index-adult” (PWI-A) in mothers of mentally retarded students of exceptional schools in northern districts of Tehran. Methods: From 358 mothers of mentally retarded students in north of Tehran (districts 1, 2 and 3), 200 mothers were selected by systematic random sampling. The collected data using PWI-A was analyzed by inferential statistics (Cronbach’s alpha coefficient for test reliability and linear multivariate regression for test validity). Results: Results showed acceptable reliability and validity for PWI-A in mothers of mentally retarded students of exceptional schools in north districts of Tehran. The Correlation between seven items was significant (P<0.001) and this index had the most extensive coverage of construct validity. Conclusion: This study showed that this scale could be applied to measure personal wellbeing in mothers of mentally retarded students.
Statistical machine translation based text normalization with crowdsourcing

In [1], we have proposed systems for text normalization based on statistical machine translation (SMT) methods which are constructed with the support of Internet users and evaluated those with French texts. Internet users normalize text displayed in a web interface in an annotation process, thereby providing a parallel corpus of normalized and non-normalized text. With this corpus, SMT models are generated to translate non-normalized into normalized text. In this paper, we analyze their efficiency for other languages. Additionally, we embedded the English annotation process for training data in Amazon Mechanical Turk and compare the quality of texts thoroughly annotated in our lab to those annotated by the Turkers. Finally, we investigate how to reduce the user effort by iteratively applying an SMT system to the next sentences to be edited, built from the sentences which have been annotated so far.
AN OVERVIEW OF MOBILE ROBOTIC AGENTS MOTION PLANNING IN DYNAMIC ENVIRONMENTS

An overview of Mobile Robotic Agents’ Motion Planning (RMP) and Trajectory Planning Problem (TPP) in Dynamic Environment is presented. We have focused on the area of mobile robots, in an environment in which obstacles may change their location in space-time and henceforth it does not cover the same for environment comprising only non-moving, stationary obstacles. Comparative graphs and charts, demonstrating the directions, major contributions and distribution of works over the past 23 years have been provided in conclusion section.
Parallel feed travelling wave distributed pin photodetectors with integrated MMI couplers

The fabrication and performance of a parallel feed travelling wave photodetector with pin diodes operating at 1550 nm is presented. A parallel optical feed using an integrated multimode interference (MMI) power splitter helps increase the maximum linear photocurrent through a more uniform distribution of photocurrent. The maximum DC linear current measured is 52.2 mA. Maximum linear RF power at 10 GHz was 9 dBm.
MusaWRKY71 Overexpression in Banana Plants Leads to Altered Abiotic and Biotic Stress Responses

WRKY transcription factors are specifically involved in the transcriptional reprogramming following incidence of abiotic or biotic stress on plants. We have previously documented a novel WRKY gene from banana, MusaWRKY71, which was inducible in response to a wide array of abiotic or biotic stress stimuli. The present work details the effects of MusaWRKY71 overexpression in transgenic banana plants. Stable integration and overexpression of MusaWRKY71 in transgenic banana plants was proved by Southern blot analysis and quantitative real time PCR. Transgenic banana plants overexpressing MusaWRKY71 displayed enhanced tolerance towards oxidative and salt stress as indicated by better photosynthesis efficiency (Fv/Fm) and lower membrane damage of the assayed leaves. Further, differential regulation of putative downstream genes of MusaWRKY71 was investigated using real-time RT-PCR expression analysis. Out of a total of 122 genes belonging to WRKY, pathogenesis-related (PR) protein genes, non-expressor of pathogenesis-related genes 1 (NPR1) and chitinase families analyzed, 10 genes (six belonging to WRKY family, three belonging to PR proteins family and one belonging to chitinase family) showed significant differential regulation in MusaWRKY71 overexpressing lines. These results indicate that MusaWRKY71 is an important constituent in the transcriptional reprogramming involved in diverse stress responses in banana.
Smart-Its - communication and sensing technology for UbiComp environments

More and more Ubiquitous computing scenarios arise where computers are embedded into everyday objects as secondary ariefacts. The need for a generic platform to enhance such artifacts is addressed by the Smart-Its project. TecO’s Smart-Its are small-scale embedded computer devices that can be easily attached to everyday objects and simply programmed for a special task. Just like paper Post-Its are able to add some information to an object a Smart-Its could add some computing, perception and communication capability to an object. All this capability was integrated into the tiny Smart-Its board itself that is able to operate without any additional infrastructure. This paper introduces the architecture of the Smart-Its hardware, the design decisions for the hardware itself and presents experiences we made while constructing and operating these devices; some of these experience are also based on the deployment and use of the first 160 Smart-Its devices.
Travelling Waves in some Reaction-diffusion-aggregation Models

We deal with the reaction-diffusion-aggregation equation vt = h D(v)vx i x + f(v) t 0, x 2 R, where f is a monostable (i.e., Fisher-type) nonlinear reaction term and D(v) is a changing-sign nonlinear term, modeling repulsive-attractive population dynamic. We prove the existence of travelling fronts having speed varying in a half-line and provide an estimate for the minimal speed c . We also investigate the possible existence of fronts reaching the equilibria at finite values.
Bayesian Search Algorithms for Decomposable Gaussian Graphical Models

In this report, we are interested in the cases when the dependence among variables is sparse. The independence among the variables is reflected in structural zeros in precision matrix Σ [Dem72]. We now describe a prior which forces sparsity in precision matrix, while maintaining positive-definiteness of covariance matrix. A positive definite matrix A has an inverse Wishart (IW) density, if the density is of the following form,
Monetary and Financial Sector Reforms in India : A Practitioner ’ s Perspective

The objectives of this paper are to review the monetary and financial sector reforms in India, identify the emerging issues and explore the prospects for further reform. The first part is devoted to a brief background on the need for reforms taken up in 1991-92. The second part is devoted to the institutional aspects of the reform. Issues relating to ownership, competition and regulation in the financial sector as a whole, but primarily in the banking sector are analysed. The third part relating to policy framework focuses on monetary policy and credit delivery. The fiscal policy insofar as it impacts on the financial sector is also analysed. The fourth part focuses on managing process of reform in its various dimensions and perspective is that of the Reserve Bank of India (RBI). The concluding part identifies the critical elements that would possibly determine the progress of reform.
Optimising large scale public transport network design problems using mixed-mode parallel multi-objective evolutionary algorithms

In this paper we present a novel tool, using both OpenMP and MPI protocols, for optimising the efficiency of Urban Transportation Systems within a defined catchment, town or city. We build on a previously presented model which uses a Genetic Algorithm with novel genetic operators to optimise route sets and provide a transport network for a given problem set. This model is then implemented within a Parallel Multi-Objective Genetic Algorithm and demonstrated to be scalable to within the scope of real world, [city-wide], problems. This paper compares and contrasts three methods of parallel distribution of the Genetic Algorithm's computational workload: a job farming algorithm and two variations on an `Islands' approach. Results are presented in the paper from both single and mixed mode strategies. The results presented are from a range of previously published academic problem sets. Additionally a real world inspired problem set is evaluated and a visualisation of the optimised output is given.
Video analysis and synthesis based on a retinal-inspired frame

This paper introduces a novel retinal-inspired filter which is applied on video streams. We mathematically prove that under specific assumptions the spatiotemporal convolution turns into a spatial convolution with a short lifespan temporal kernel. As a consequence, the filter is applied on each image of the video stream separately. We analyze how each image is decomposed into a group of subbands, each one of which approximates the image providing different kind of information. Afterwords, we propose an algorithm to reconstruct each image by exploiting the group of subbands. Finally, we defend our mathematical proofs by providing numerical simulations which show the relevance of our study.
Older adults' experience of psychological therapy

The portfolio examines the older adult experience of psychological therapy. The research study is from the older adult perspective and it provides a rich narrative and strengthens theory and practice links. This research explored older adult service users’ retrospective accounts of Psychological Therapy within a secondary care service. The aim was to enhance the knowledge base and understanding of what is known about older adults’ subjective experiences of the processes involved when receiving Psychological Therapy. A qualitative methodology was chosen to allow the older adult participants to express their thoughts and feelings using unstructured interviews. The Grounded Theory analysis revealed categories and themes which produced a theory that explains the process of therapy. Nine older adult participants volunteered to take part and a grounded theory analysis of the data yielded a core category of ‘moving towards equanimity’. The category can be understood as contributing to the older adult participants regaining emotional stability, mental calm and balance. Within the Professional Practice section the case study features the complexity of the therapeutic work with an older adult who experienced depression and insomnia. The case examines the flexibility in the use of the therapeutic model and the core skills required within a strong therapeutic relationship which helped the older adult hold onto hope. The final part of the portfolio is a critical review about older adults and the therapeutic alliance. The review examines studies that have explored this extensive research area to raise awareness of the factors that influence the development of the alliance with older adults.
Cache coherence enabled adaptive refresh for volatile STT-RAM

Spin-Transfer Torque RAM (STT-RAM) is extensively studied in recent years. Recent work proposed to improve the write performance of STT-RAM through relaxing the retention time of STT-RAM cell, magnetic tunnel junction (MTJ). Unfortunately, frequent refresh operations of volatile STT-RAM could dissipate significantly extra energy. In addition, refresh operations can severely conflict with normal read/write operations and results in degraded cache performance. This paper proposes Cache Coherence Enabled Adaptive Refresh (CCear) to minimize refresh operations for volatile STT-RAM. Through novel modifications to cache coherence protocol, CCear can effectively minimize the number of refresh operations on volatile STT-RAM. Full-system simulation results show that CCear approaches the performance of the ideal refresh policy with negligible overhead.
Hydrology and Earth System Sciences Hydroclimatology of the Nile: Results from a Regional Climate Model

This paper presents the result of the regional coupled climatic and hydrologic model of the Nile Basin. For the first time the interaction between the climatic processes and the hydrological processes on the land surface have been fully coupled. The hydrological model is driven by the rainfall and the energy available for evaporation generated in the climate model, and the runoff generated in the catchment is again routed over the wetlands of the Nile to supply moisture for atmospheric feedback. The results obtained are quite satisfactory given the extremely low runoff coefficients in the catchment. The paper presents the validation results over the sub-basins: Blue Nile, White Nile, Atbara river, the Sudd swamps, and the Main Nile for the period 1995 to 2000. Observational datasets were used to evaluate the model results including radiation, precipitation, runoff and evaporation data. The evaporation data were derived from satellite images over a major part of the Upper Nile. Limitations in both the observational data and the model are discussed. It is concluded that the model provides a sound representation of the regional water cycle over the Nile. The sources of atmospheric moisture to the basin, and location of conver-gence/divergence fields could be accurately illustrated. The model is used to describe the regional water cycle in the Nile basin in terms of atmospheric fluxes, land surface fluxes and land surface-climate feedbacks. The monthly moisture recycling ratio (i.e. locally generated/total precipitation) over the Nile varies between 8 and 14%, with an annual mean of 11%, which implies that 89% of the Nile water resources originates from outside the basin physical boundaries. The monthly precipitation efficiency varies between 12 and 53%, and the annual mean is 28%. The mean annual result of the Nile regional water cycle is compared to that of the Amazon and the Mississippi basins.
Zigzag Generalized Lévy Walk: the In Vivo Search Strategy of Immunocytes

Immune responses are based on the coordinated searching behaviors of immunocytes that are aimed at tracking down specific targets. The search efficiency of immunocytes significantly affects the speed of initiation and development of immune responses. Previous studies have shown that not only the intermittent walk but also the zigzag turning preference of immunocytes contributes to the search efficiency. However, among existing models describing immunocytes' search strategy, none has captured both features. Here we propose a zigzag generalized Lévy walk model to describe the search strategy of immunocytes more accurately and comprehensively by considering both the intermittent and the zigzag-turning walk features. Based on the analysis of the searching behaviors of typical immune cell types, dendritic cells and leukocytes, in their native physiological environment, we demonstrate that the model can describe the in vivo search strategy of immunocytes well. Furthermore, by analyzing the search efficiency, we find that this type of search strategy enables immunocytes to capture rare targets in approximately half the time than the previously proposed generalized Lévy walk. This study sheds new light on the fundamental mechanisms that drive the efficient initiation and development of immune responses and in turn may lead to the development of novel therapeutic approaches for diseases ranging from infection to cancer.
Pricing Theater Seats: The Value of Price Commitment and Monotone Discounting

We examine the value of price commitment in a nonprofit organization using individual level purchases over a series of concert performances. To decide on a pricing policy, the performing arts organization must be able to accurately measure when each ticket will be sold and what type of audience will purchase the tickets for each performance. We use a competing hazards framework to model the timing of ticket purchases when customer segments differ in their valuations and arrival times. We show that the customer purchase likelihoods change based on the prices observed earlier in the season. Hence, price commitment can aid in improving sales, revenues, and customer visits. In particular, we show that price commitment to a decreasing monotone discount policy can improve the revenues in the range of 2.1%-6.7% per concert.