Miracle-dz/UniFAR-FTUs huggingface dataset:
Global predictions and tests of erythroid regulatory regions.

of the genomic DNA sequences of human , mouse, and other organisms are landmark achievements , but the major changes in biology and medicine anticipated as a result (Lander 1996) require that a function be assigned to all the important segments within those genomes (Collins et al. 2003). It has long been realized that functional sequences change more slowly than non-functional (neutral) DNA sequences over evolutionary time (Kimura 1968; Li et al. 1981). Some gene prediction and assessment algorithms incorporate interspecies sequence alignments into their analysis (see, e.g., Korf et al. 2001; Wiehe et al. 2001; Nekrutenko et al. 2002). This slower rate also can be predictive for sequences involved in gene regulation. One of the early approaches for finding critical sequences within bacteriophage promoters used sequence comparison (Pribnow 1975), and highly conserved noncoding DNA sequences are now commonly used as guides for potential gene regulatory elements (for review, see Hardison 2000; Pennacchio and Rubin 2001). In this paper, we address two complications to the large-scale application of genomic sequence alignments to predicting cis-regulatory modules (CRMs), i.e., discrete sequences such as promoters, enhancers, and silencers that control gene expression. The rate at which neutral DNA changes is highly variable within a genome (Wolfe et al. 1989; Hardison et al. 2003), and thus the amount of change observed needs to be corrected for local variation in the neutral rate. Such a corrected score can be used to compute a probability that a sequence is conserved because of purifying selection (Waterston et al. 2002; Chiaromonte et al., this volume). The second complication is that DNA sequences which do not code for protein (noncoding DNA) can be selected for functions other than a role in regulating gene expression. Examples include genes for noncoding RNAs such as tRNAs and microRNAs. Sequences involved in chromosome dynamics may also be under selection. We describe an approach to find patterns characteristic of gene regulatory sequences within the alignments (Elnitski et al. 2003). We are applying these analyses of whole-genome sequence alignments to predict regulatory elements of genes expressed during late erythroid differentiation. This is a particularly attractive somatic cell model for mammalian differentiation because morphologically distinct cell types are made during the progress of differentiation and maturation, and several abundant red cell proteins , such as hemoglobins and cytoskeletal proteins, are well-characterized markers of later maturation (Migliac-cio and Papayannopoulou 2001). Furthermore, cultured cell lines such as murine …
Analysis and Development of Antigen-specific T Cells Derived from Peripheral Blood Mononuclear Cells of Healthy Donors.

BACKGROUND/AIM Adoptive cell therapy using antigen-specific T cells is a promising treatment modality for cancer patients. Various methods to isolate specific T cells and identify corresponding T cell receptor (TCR) sequences are known. This study aimed to identify antigen-specific TCR from T cells isolated using carboxyfluorescein succinimidyl ester (CFSE), which marks proliferating activated T cells. MATERIALS AND METHODS CFSE stained healthy donor peripheral blood mononuclear cells (PBMCs) were treated with cytomegalovirus (CMV) or Epstein-Barr virus (EBV) peptides for seven days. Then, proliferating T cells with decreased CFSE staining were isolated and single cell VDJ sequencing was performed on isolated T cells to identify antigen-specific TCRs. RESULTS As antigen-specific TCR candidates, ten TCR clones were selected for the CMV antigen and five for the EBV antigen. The reactivity of ten CMV TCR-transduced T cells and one EBV TCR-transduced T cell toward T2 cells pulsed with CMV or EBV peptide was confirmed via NFAT-luciferase, IFN-γ ELISA, and cytotoxicity assays. CONCLUSION Identification of antigen-specific TCRs with CFSE staining is a valid method for the development of effective immunotherapy. The identified CMV- or EBV-specific TCRs can be used for adoptive cell therapy to treat cancer.
Thermoelasticity of Iron‐ and Aluminum‐Bearing MgSiO3 Postperovskite

We present ab initio (LDA + Usc) studies of high‐temperature and high‐pressure elastic properties of pure as well as iron‐bearing (ferrous, Fe2+, and ferric, Fe3+) and aluminum‐bearing MgSiO3 postperovskite, the likely dominant phase in the deep lower mantle of the Earth. Thermal effects are addressed within the quasiharmonic approximation by combining vibrational density of states and static elastic coefficients. Aggregate elastic moduli and sound velocities for the Mg end members are successfully compared with scarce experimental data available. Effects of iron (Fe) and aluminum (Al) substitutions on elastic properties and their pressure and temperature dependence have been thoroughly investigated. At the observed perovskite to postperovskite transition (P = 125 GPa and T = 2,500 K), compressional and shear velocities increase by 0–1% and 1.5–3.75%, respectively. This observation is consistent with some seismic studies of the D′′ discontinuity beneath the Caribbean, which suggests that our robust estimates of elastic properties of the postperovskite phase will be very helpful to understand lateral velocity variations in the deep lower mantle region and to constrain its composition and thermal structure.
Realistic Biomechanical Simulation and Control of Human Swimming

We address the challenging problem of controlling a complex biomechanical model of the human body to synthesize realistic swimming animation. Our human model includes all of the relevant articular bones and muscles, including 103 bones (163 articular degrees of freedom) plus a total of 823 muscle actuators embedded in a finite element model of the musculotendinous soft tissues of the body that produces realistic deformations. To coordinate the numerous muscle actuators in order to produce natural swimming movements, we develop a biomimetically motivated motor control system based on Central Pattern Generators (CPGs), which learns to produce activation signals that drive the numerous muscle actuators.
Factors Influencing Students' Behavioural Intention to Adopt and use Mobile Learning in Higher Educational Institutions in Nigeria: An Example of Ekiti State University, Ado-Ekiti

Rapid explosion of mobile technologies and its services in Nigeria has provided a new platform for higher institutions to widen access to education through mobile learning. Mobile technologies provide learners with flexibility and ubiquity to learn anytime and anywhere via wireless Internet. However, few researches have been conducted to investigate factors that contribute towards students' adoption and use of mobile learning in Nigeria. Therefore, this study applied the Unified Theory of Acceptance and Use of Technology (UTAUT) model to investigate students' behavioural intention to adopt and use mobile learning in higher educational institutions in Nigeria. This study follows a quantitative approach and a survey questionnaire was developed and utilised as the main instrument for data collection. A sample of 250 students was selected from five different schools and four hypotheses are formulated. The data collected was tested against the research model using regression analysis. The results showed that, three factors with the exception of facilitating conditions: performance expectancy, effort expectancy and social influence had significant positive effects on students' intention to adopt and use mobile learning with performance expectancy being the strongest predictor. Further, the findings show that the developed model explains 48.2% of the variance in the adoption intention to use M-Learning. Based on these findings, M-Learning services that based on students' suggestions in order to meet their performance expectations must be developed and the M-Learning content must be compatible with different mobile devices along with their operating system. Educational institutions should increase students' awareness about the expected benefits and advantages of using M-Learning system. Mobile learning providers should conduct training and awareness to early adopters who are already using various mobile services. These early adopters have the potential to persuade their colleagues and friends to adopt to use mobile learning.
Publicly verifiable proofs of sequential work

We construct a publicly verifiable protocol for proving computational work based on collision-resistant hash functions and a new plausible complexity assumption regarding the existence of "inherently sequential" hash functions. Our protocol is based on a novel construction of time-lock puzzles. Given a sampled "puzzle" P getsr Dn, where $n$ is the security parameter and Dn is the distribution of the puzzles, a corresponding "solution" can be generated using N evaluations of the sequential hash function, where N>n is another parameter, while any feasible adversarial strategy for generating valid solutions must take at least as much time as Ω(N) serial evaluations of the hash function after receiving $P$. Thus, valid solutions constitute a "proof" that Ω(N) parallel time elapsed since p was received. Solutions can be publicly and efficiently verified in time poly(n) ⋅ polylog(N). Applications of these "time-lock puzzles" include noninteractive timestamping of documents (where the distribution over the possible documents corresponds to the puzzle distribution Dn) and universally verifiable CPU benchmarks. Our construction is secure in the standard model under complexity assumptions (collision-resistant hash functions and inherently sequential hash functions), and makes black-box use of the underlying primitives. Consequently, the corresponding construction in the random oracle model is secure unconditionally. Moreover, as it is a public-coin protocol, it can be made non-interactive in the random oracle model using the Fiat-Shamir Heuristic. Our construction makes a novel use of "depth-robust" directed acyclic graphs---ones whose depth remains large even after removing a constant fraction of vertices---which were previously studied for the purpose of complexity lower-bounds. The construction bypasses a recent lower-bound of Mahmoody, Moran, and Vadhan (CRYPTO '11) for time-lock puzzles in the random oracle model, which showed that it is impossible to have time-lock puzzles like ours in the random oracle model if the puzzle generator also computes a solution together with the puzzle.
Geothermal energy for heating and cooling in agricultural greenhouses

Geothermal source is a perspective technology able to use the ground as a thermal sink or heat source. It is one of the energy resources in Iran that can be used with long-term investment. This study provided a new idea to use of this energy for heating and cooling of buildings. Two wells were used for heating and cooling due to the constant temperature of the water in depth of 12 m underground (approximately is equal to the annual temperature environment during the year). Water flowed in six speeds: 10, 11.5, 13, 16, 29 and 34 lit/min using a hydraulic pump (12 meters hydraulic height and 2 inch diameter) from first well, and after passing through radiator, discharge to other well. The outdoor temperature was 9oC, 40 ° C and 15.5-16 ° C for heating, cooling and well water respectively. An axial fan is used to passing the air in six speeds: 0.5, 1.1, 2.2, 3.3, 4.4 and 7.4 m/s through the radiator. The results showed that the use of water from this well can reduce the required power about 25% for heating and increase the air temperature from 9 to 25 ° C. Also this system can reduce the required power between 38 to 60% for cooling and decrease the air temperature from 40 to 25 ° C.
Aerial Survey Estimates of Abundance of the Eastern Chukchi Sea Stock of Beluga Whales ( Delphinapterus leucas ) in 2012

The eastern Chukchi Sea (ECS) stock of beluga whales is one of three stocks in western Alaska that are co-managed by the National Marine Fisheries Service and the Alaska Beluga Whale Committee. Abundance of this stock was estimated as 3710 in 1991 from incomplete data. Analysis of data from satellite-linked time-depth recorders (SDRs) attached to belugas in summer concentration areas of the ECS and Beaufort Sea (BS) stocks provided an overview of beluga distribution and movements and allowed the identification of an area (140˚ W to 157˚ W in the BS) and a time period (19 July – 20 August) in which the distributions of the two stocks do not overlap. Aerial survey data were collected by the Aerial Surveys of Arctic Marine Mammals (ASAMM) project in that region and time period in 2012. We used those data in a line transect analysis that estimated there were 5547 (CV = 0.22) surface-visible belugas in the study area. Data from SDRs were used to develop correction factors to account for animals that were missed because they were either outside of the study area or diving too deep to be seen, resulting in a total abundance estimate of 20 752 (CV = 0.70). The average annual Alaska Native subsistence harvest from the ECS stock (57) is about 0.3% of the population estimate. Without data collected by the ASAMM project and from satellite-linked tags, this analysis would not have been possible. Additional surveys and tagging of ECS belugas are warranted.
A Summary of Common Assumptions and Relative Costs Across Different Methods of Discrete Text Categorization

Previous methods of analyzing the substance of political attention have had to make several restrictive assumptions or been prohibitively costly when applied to large-scale political texts. Here, we describe a topic model for legislative speech, a statistical learning model that uses word choices to infer topical categories covered in a set of speeches and to identify the topic of specific speeches. Our method estimates, rather than assumes, the substance of topics, the keywords that identify topics, and the hierarchical nesting of topics. We use the topic model to examine the agenda in the U.S. Senate from 1997 to 2004. Using a new database of over 118,000 speeches (70,000,000 words) from the Congressional Record, our model reveals speech topic categories that are both distinctive and meaningfully interrelated and a richer view of democratic agenda dynamics than had previously been possible.
The dependency locality theory: A distance-based theory of linguistic complexity.

A major issue in understanding how language is implemented in the brain involves understanding the use of language in language comprehension and production. However, before we look to the brain to see what areas are associated with language processing phenomena, it is necessary to have good psychological theories of the relevant behavioral phenomena. Recent results have suggested that constructing an interpretation for a sentence involves the moment-by-moment integration of a variety of different information sources, constrained by the available computational resources (see, e.g., Ford, Bresnan, and Kaplan 1982; MacDonald, Pearlmutter, and Seidenberg 1994; Trueswell, Tanenhaus, and Garnsey 1994; Trueswell1996; Tyler and MarslenWilson 1977; McClelland, St. John, and Taraban 1989; Pearlmutter and MacDonald 1992; Crain and Steedman 1985; Altmann and Steedman, 1988; Ni , Crain, and Shankweiler 1996; see Gibson and Pearlmutter 1998 and Tanenhaus and Trueswell 1995 for summaries). This chapter presents evidence for one theory of resource use in sentence co"mprehension: the dependency locality theory (DLT ). If the evidence for a theory such as this one accumulates, it will then make sense to look for neural correlates of the theory (see Kaan et ale 1998; Harris 1998, for some initial attempts to find event-related potential measurements of brain activity corresponding to the components of the DLT ). An important part of a theory of sentence comprehension is a theory of how sentence structures are assembledsentence parsingas words are input one at a time. Two important components of sentence parsing consume computational resources:
Network anomaly detection and localization

With the increasing scale and complexity of the network, how to maintain a level of network performance and robustness for network operators to satisfy customers becomes more and more challenging. Network anomaly detection and localization are critical for ensuring network performance. In this paper, a novel framework for detecting and localizing network anomalies using active measurements is presented. The framework is composed of three steps: the first step is to detect network anomalies on network path under monitoring, the second step is to cluster destination IPs on the monitored path using unsupervised learning methods, the last step is to localize network anomalies that induce anomalous network performance and behaviors. The last step is designed to reveal the possible cause for each IP set clustered in the second step and localize root cause at every moment by analyzing the inclusion relation between detected anomalous destination IPs and clustered IP sets. The efficacy of the framework to diagnose network anomalies is demonstrated by several real-world cases, which have been recorded in three years of network monitoring experience.
A novel FK506- and rapamycin-binding protein (FPR3 gene product) in the yeast Saccharomyces cerevisiae is a proline rotamase localized to the nucleolus

The gene (FPR3) encoding a novel type of peptidylpropyl-cis-trans- isomerase (PPIase) was isolated during a search for previously unidentified nuclear proteins in Saccharomyces cerevisiae. PPIases are thought to act in conjunction with protein chaperones because they accelerate the rate of conformational interconversions around proline residues in polypeptides. The FPR3 gene product (Fpr3) is 413 amino acids long. The 111 COOH-terminal residues of Fpr3 share greater than 40% amino acid identity with a particular class of PPIases, termed FK506-binding proteins (FKBPs) because they are the intracellular receptors for two immunosuppressive compounds, rapamycin and FK506. When expressed in and purified from Escherichia coli, both full-length Fpr3 and its isolated COOH-terminal domain exhibit readily detectable PPIase activity. Both fpr3 delta null mutants and cells expressing FPR3 from its own promoter on a multicopy plasmid have no discernible growth phenotype and do not display any alteration in sensitivity to the growth-inhibitory effects of either FK506 or rapamycin. In S. cerevisiae, the gene for a 112-residue cytosolic FKBP (FPR1) and the gene for a 135-residue ER-associated FKBP (FPR2) have been described before. Even fpr1 fpr2 fpr3 triple mutants are viable. However, in cells carrying an fpr1 delta mutation (which confers resistance to rapamycin), overexpression from the GAL1 promoter of the C-terminal domain of Fpr3, but not full-length Fpr3, restored sensitivity to rapamycin. Conversely, overproduction from the GAL1 promoter of full- length Fpr3, but not its COOH-terminal domain, is growth inhibitory in both normal cells and fpr1 delta mutants. In fpr1 delta cells, the toxic effect of Fpr3 overproduction can be reversed by rapamycin. Overproduction of the NH2-terminal domain of Fpr3 is also growth inhibitory in normal cells and fpr1 delta mutants, but this toxicity is not ameliorated in fpr1 delta cells by rapamycin. The NH2-terminal domain of Fpr3 contains long stretches of acidic residues alternating with blocks of basic residues, a structure that resembles sequences found in nucleolar proteins, including S. cerevisiae NSR1 and mammalian nucleolin. Indirect immunofluorescence with polyclonal antibodies raised against either the NH2- or the COOH-terminal segments of Fpr3 expressed in E. coli demonstrated that Fpr3 is located exclusively in the nucleolus.
Molecular Cancer Gene Expression Profiles in Primary Pancreatic Tumors and Metastatic Lesions of Ela-c-myc Transgenic Mice

Background: Pancreatic carcinoma usually is a fatal disease with no cure, mainly due to its invasion and metastasis prior to diagnosis. We analyzed the gene expression profiles of paired primary pancreatic tumors and metastatic lesions from Ela-c-myc transgenic mice in order to identify genes that may be involved in the pancreatic cancer progression. Differentially expressed selected genes were verified by semi-quantitative and quantitative RT-PCR. To further evaluate the relevance of some of the selected differentially expressed genes, we investigated their expression pattern in human pancreatic cancer cell lines with high and low metastatic potentials.
Time-of-Arrival Measurement Using Adaptive CMOS IR-UWB Range Finder With Scalable Resolution

This paper introduces an adaptive CMOS impulse-radio ultra-wideband (IR-UWB) range finder with scalable resolution for localization applications and presents a brief demonstration of its operation. The distance resolution of the proposed range finder can be adapted to the ranging environment using a two-step time-to-digital converter (TDC) with scalable delay cells. Using the scalable time resolution of the TDC, the proposed range finder can control its maximum detectable distance and range resolution without any change in hardware. The proposed CMOS IR-UWB range finder has been implemented with a 0.11-μm process; the effective areas of the transmitter and receiver are 0.065 mm2 and 0.27 mm2, respectively. The range finder has a range 8 m, with 2.9 mm scalable resolution. The power consumptions of the transmitter and receiver are 1.5 mW and 42 mW, respectively.
Census and survey of the visible internet

Prior measurement studies of the Internet have explored traffic and topology, but have largely ignored edge hosts. While the number of Internet hosts is very large, and many are hidden behind firewalls or in private address space, there is much to be learned from examining the population of visible hosts, those with public unicast addresses that respond to messages. In this paper we introduce two new approaches to explore the visible Internet. Applying statistical population sampling, we use censuses to walk the entire Internet address space, and surveys to probe frequently a fraction of that space. We then use these tools to evaluate address usage, where we find that only 3.6% of allocated addresses are actually occupied by visible hosts, and that occupancy is unevenly distributed, with a quarter of responsive /24 address blocks (subnets) less than 5% full, and only 9% of blocks more than half full. We show about 34 million addresses are very stable and visible to our probes (about 16% of responsive addresses), and we project from this up to 60 million stable Internet-accessible computers. The remainder of allocated addresses are used intermittently, with a median occupancy of 81 minutes. Finally, we show that many firewalls are visible, measuring significant diversity in the distribution of firewalled block size. To our knowledge, we are the first to take a census of edge hosts in the visible Internet since 1982, to evaluate the accuracy of active probing for address census and survey, and to quantify these aspects of the Internet.