Miracle-dz/UniFAR-FTUs huggingface dataset:
Cooperativity of co-factor NR2F2 with Pioneer Factors GATA3, FOXA1 in promoting ERα function

Estrogen receptor α (ERα) drives growth in the majority of human breast cancers by binding to regulatory elements and inducing transcriptional events that promote tumor growth. ERα binding activity largely depends on access to binding sites on chromatin, which is facilitated in part by Pioneer Factors (PFs). Transcription factors operate in complexes through thousands of genomic binding sites in a combinatorial fashion to control the expression of genes. However, the extent of crosstalk and cooperation between ERα pioneer factors and more collaborative transcription factors in breast cancer still remains to be elucidated systematically. Methods: Here, we determined the genomic binding information of 40 transcription-related factors and histone modifications with ChIP-seq in ENCODE and integrated it with other genomic information (RNA-seq, ATAC-seq, Gene microarray, 450k methylation chip, GRO-seq), forming a multi-dimension network to illuminate ERα associated transcription. Results: We show that transcription factor, NR2F2 binds to most sites independently of estrogen. Perturbation of NR2F2 expression decreases ERα DNA binding, chromatin openning, and estrogen-dependent cell growth. In the genome-wide analysis, we show that most binding events of NR2F2 and known pioneer factors FOXA1, GATA3 occur together, covering 85% of the ERα binding sites. Regions bound by all the three TFs appeared to be the most active, to have the strongest ERα binding and to be enriched for the super enhancers. Conclusions: The ERα binds to pre-accessible sites containing ERE elements bound by the three transcription factors (NR2F2, FOXA1 and GATA3). The three genes were also identified to correlate with decreased metastatic potential in patient cohorts and co-regulate each other. Together, our results suggest that NR2F2 is a cofactor with FOXA1 and GATA3 in ERα-mediated transcription.
Assessment of constraints and opportunities in small-scale beef cattle fattening business: Evidence from the West Hararghe Zone of Ethiopia

The study was conducted in Gemachis and Doba districts of West Hararghe Zone of Ethiopia to investigate the major constraints and opportunities of small-scale cattle fattening practices, and identify cattle selection criteria used for fattening purpose. Multi stage sampling procedure was employed to obtain a total of 171 cattle fatteners.
PHYSICAL REVIEW C 97 , 054303 ( 2018 ) Phase diagram of an extended Agassi model

J. E. García-Ramos,1,2,3 J. Dukelsky,4 P. Pérez-Fernández,2,5 and J. M. Arias2,6 1Departamento de Ciencias Integradas y Centro de Estudios Avanzados en Física, Matemática y Computación, Universidad de Huelva, 21071 Huelva, Spain 2Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Fuentenueva s/n, 18071 Granada, Spain 3Unidad Asociada de la Universidad de Huelva al IEM (CSIC), Madrid, Spain 4Instituto de Estructura de la Materia, CSIC, Serrano 123, 28006 Madrid, Spain 5Departamento de Física Aplicada III, Escuela Técnica Superior de Ingeniería, Universidad de Sevilla, Sevilla, Spain 6Departamento de Física Atómica, Molecular y Nuclear, Facultad de Física, Universidad de Sevilla, Apartado 1065, 41080 Sevilla, Spain
Efficient Falsification of Motion Planners for Autonomous Vehicles Using Rapidly-Exploring Random Trees

Verification of motion planners is often performed by testing the software with predefined test cases. These test cases usually cannot evaluate every corner case, since many corner cases are not known during development. In contrast, formal methods guarantee safety with respect to a specification, but the motion planner can still have implementation mistakes. Therefore, a general test approach is necessary which is able to test all possible operating scenarios of a vehicle and which works efficiently.
SIMD Acceleration of SpMV Kernel on Multi-core CPU Architecture

As the field of Sparse Matrix vector multiplication (SpMV) matures and its breadth of application increases, the need for parallel implementation becomes necessary. SpMV is proved to be a bottleneck due to its irregular access patterns. Various storage formats for sparse matrices have been proposed to solve this issue. The Quad tree-Compressed Row Storage (QCSR) format shows good performance improvement over other formats such as Compressed Row Storage (CSR) and Blocked CSR (BCSR) for SpMV. This paper extends QCSR format to exploit the Single Instruction Multiple Data (SIMD) registers which are available in current processors. Programming with SIMD registers in a single core processor achieves parallelism with reduced power and without any additional hardware requirement, as in the case of Graphics Processing Unit (GPU) computing. To program effectively in SIMD units Intel’s Streaming SIMD Extension (SSE) instructions are used. In this paper computational performance of QCSR-SpMV is determined for over a collection of 10 benchmark matrices on SIMD units of X86 architecture. Experimental results demonstrate QCSR-SIMD achieves significant average speedup of 2.0 x compared to CSR-SIMD.
Range of motion and functional results in three different designs of primary knee arthroplasty Comparative study

264 Abstract Introduction: The aim of this study was to analyze functional results and range of motion and compare them between three groups of patients with total knee arthroplasty: two with high-flex prosthesis and another one with a conventional design. Materials and Methods: Sixty-four patients were operated on with Zimmer® NexGen® total knee prostheses and 34, with high-flex Optetrack®. After patients exclusion, 22 (Group A) were treated with a high-flex Zimmer® design; 21 (Group B) with a conventional Zimmer® prosthesis and 25 (Group C) with an Optetrack ® PS prosthesis. Functional evaluation was carried out with the Knee Society Score, the Western Ontario and McMaster Universities Osteoarthritis index and the visual analogue scale. Results: After the surgery, average maximal flexion went from 99o to 113o in Group A, with an average improvement of 14o; from 106o to 118o in Group B, with an average gain of 12o; and from 110o to 111o in Group C, with a gain of 1o. Functional results evaluated using the two scores improved in the three groups. Conclusions: Functional evaluation is favorable in the three designs we evaluated. This study shows that there is no significant difference in reached final flexion, nor is there in functional results between the two first designs; however, these ones are significantly higher than the third group design after one-year follow-up.
An ELMo-inspired approach to SemDeep-5’s Word-in-Context task

This paper describes a submission to the Word-in-Context competition for the IJ-CAI 2019 SemDeep-5 workshop. The task is to determine whether a given focus word is used in the same or diﬀerent senses in two contexts. We took an ELMo-inspired approach similar to the baseline model in the task description paper, where contex-tualized representations are obtained for the focus words and a classiﬁcation is made according to the degree of similarity between these representations. Our model had a few simple diﬀerences, notably joint training of the forward and back-ward LSTMs, a diﬀerent choice of states for the contextualized representations and a new similarity measure for them. These changes yielded a 3.5% improvement on the ELMo baseline.
ARTHUR ’ S MULTIPLICITY FORMULA FOR GSp 4 AND RESTRICTION TO Sp 4 by

— We prove the classification of discrete automorphic representations of GSp4 explained in [Art04], as well as a compatibility between the local Langlands correspondences for GSp4 and Sp4. Résumé (La formule de multiplicité d’Arthur pour GSp4 et restriction à Sp4) Nous donnons une preuve de la classification des représentations automorphes discrètes de GSp4 expliquée dans [Art04], ainsi que de la compatibilité avec les correspondances de Langlands locales pour GSp4 et Sp4.
Genetic typing of bovine viral diarrhea virus isolates from Costa Rica

Sixteen bovine viral diarrhea virus (BVDV) isolates collected in Costa Rica between 1987 and 2006 from dairycattle were analyzed by RT-PCR and determined to belong to BVDV species 1. Furthermore, eleven of theseisolates were genotyped using the nucleotide sequences of the Npro region of the viral genome. Phylogeneticanalysis indicated that all samples examined clustered within the BVDV-1b subtype.
The Impact of Uncertain Revenues and Costs on Time-to-Build Projects : a Real Options Approach

Lagging public-sector investment in infrastructure and the deregulation of most industries mean that decisions will have to be made increasingly by the private sector under multiple sources of uncertainty. We enhance the traditional real options approach to analysing investment under uncertainty by accounting for both multiple sources of uncertainty and the time-to-build aspect. The latter feature arises in the energy and transportation sectors because investors can decide the rate at which the project is completed. Furthermore, two explicit sources of uncertainty represent the discounted cash inflows and outflows of the completed project. We use a finite-difference scheme to solve numerically for both the option value and the free boundary that characterises the optimal investment strategy. Somewhat counterintuitively, we find that with a relatively long time to build, a reduction in the growth rate of the operating cost may actually lower the investment threshold. This is contrary to the outcome when the time-to-build aspect is ignored in a model with uncertain price and cost. Hence, research and development efforts to enhance emerging technologies may be more relevant in infrastruc∗Corresponding author Email address: afzal.siddiqui@ucl.ac. uk (Afzal S. Siddiqui) 27 January 2016 ture projects with long lead times.
Robust and Traffic Aware Medium Access Control Mechanisms for Energy-Efficient mm-Wave Wireless Network-on-Chip Architectures

To cater to the performance/watt needs, processors with multiple processing cores on the same chip have become the de facto design choice. In such multicore systems, Network-on-Chip (NoC) serves as a communication infrastructure for data transfer among the cores on the chip. However, conventional metallic interconnect based NoCs are constrained by their long multi-hop latencies and high power consumption, limiting the performance gain in these systems. Among, different alternatives, due to the CMOS compatibility and energy-efficiency, low-latency wireless interconnect operating in the millimeter wave (mm-wave) band is nearer term solution to this multi-hop communication problem. This has led to the recent exploration of millimeter-wave (mmwave) wireless technologies in wireless NoC architectures (WiNoC). To realize the mm-wave wireless interconnect in a WiNoC, a wireless interface (WI) equipped with on-chip antenna and transceiver circuit operating at 60GHz frequency range is integrated to the ports of some NoC switches. The WIs are also equipped with a medium access control (MAC) mechanism that ensures a collision free and energy-efficient communication among the WIs located at different parts on the chip. However, due to shrinking feature size and complex integration in CMOS technology, high-density chips like multicore systems are prone to manufacturing defects and dynamic faults during chip operation. Such failures can result in
STEREOPHONIC ACOUSTIC ECHO CANCELLATION USING BLIND SOURCE SEPARATION AS POST-PROCESSING

Stereophonic or multi-channel acoustic echo cancellation systems suffer from cross-talk [1, 2]. This problem is also common to other multi-channel sound systems. Almost all attempts made to solve this problem are based on pre-processing techniques, which decorrelate the multi-channel input signals [3, 4]. However, preprocessing of these signals leads to a degradation of the audio quality, and further attempts need to be made to improve the audio quality [5]. Conversely, postprocessing has the potential of avoiding these problems and producing a natural sound. This paper investigates post-processing in stereophonic acoustic echo cancellation (SAEC) using the blind source separation (BSS) technique. It is demonstrated through computer simulation that reasonable results are obtained with this proposed method.
Electronic Communications of the EASST Volume 23 ( 2009 ) Proceedings of the Ninth International Workshop on Automated Verification of Critical Systems ( AVOCS 2009 ) High-level Proofs about Low-level Programs

Functional verification of low-level code requires abstractions over the memory model to be effective, since the number of side-conditions induced by byteaddressed memory is prohibitive even with modern automated reasoners. We propose a flexible solution to this challenge: assertions contain explicit memory layouts which carry the necessary side-conditions as invariants. The memory-related proof obligations arising during verification can then be solved using specialized automatic proof procedures. The remaining verification conditions about the content of data structures directly reflect a developer’s understanding. The development is formalized in Isabelle/HOL.
Chaotic Behavior of Financial Time Series-An Empirical Assessment

Financial Time Series often exhibit either chaotic or persistent or mean reversing behaviour. This behaviour could be quantified through Chaotic Exponent which ranges from zero to one. The rescaled range technique developed for hydrology by Hurst is applied in financial time series to estimate chaotic exponents which determines whether financial time series behaviour is purely chaotic white noise or any pattern exists. We have computed Chaotic Exponent coefficient for nine shares traded in Kula Lumpur Stock Exchange, nine popular stock market indices and nine selected exchange rates. As per theory pure random time series which behaves in a chaotic form cannot be forecasted, but somewhat skewed or non-normal financial time series could be forecasted. The forecasts could be used in several financial decisions like pricing of derivatives and very useful in hedging decisions. Our results indicate that the chaotic exponent of the selected financial time series is not consistent. They are either mean reversing or persistent, occasionally they show pure randomness. This proves that the forecasting of financial time series is relevant for hedging decisions.
A Test of the Effect of Macro-economic Variables on Volatility of Securities Prices : Evidence from Nairobi Securities Exchange Konyango

Volatility as an erratic rise and fall in the stock returns with a lot of demerits especially when it comes to valuation of equities at the stock exchange in that it may cause the bourse to value the securities incorrectly. All it may act as a cold shoulder to investors confidence due to increased uncertainty and hence risk which subsequently may lead to limited investment as a result of the high capital cost emanating from high premium, demanded by shareholders in their investment. This will eventually lead to a slow growth and development of an economy. The main objective of this study is to establish the effect of macroeconomic variables on volatility of securities prices in the Nairobi Securities Exchange (NSE). To achieve the objective of the study, models were developed using annual inflation rate, exchange rate, interest rate, money supply, broad money supply and general money supply as the independent variables and the stock returns as the dependent
Ženíšek The use of semiregular finite elements In :

This text is extended Equadiff 9 plenary lecture. Sections 1–4 contain a survey of published results which concern triangular and quadrilateral finite elements. Sections 1 and 2 are devoted to interpolation problems. These two sections contain also results of other authors. The analysis of both the effect of numerical integration and approximation of a boundary is restricted to triangular elements with linear polynomials and to quadrilateral elements with four-node isoparametric functions. The corresponding results in the case of smooth solutions are introduced in Section 3, where the rate of convergence O(h) is proved; the case of nonsmooth solutions is studied in Section 5. This section is restricted to triangular elements. In Sections 3 and 5 the domain considered has a form of a narrow ring with a great diameter. In this case the elements cannot be arbitrarily narrow. In Section 4 a composite domain indicated in Fig. 5 is approximated by triangular elements and applications of the finite element method in magnetostatical problems are introduced. In this case the triangular elements can be arbitrarily narrow. Section 6 is an Appendix where a special form of a discrete Friedrichs’ inequality, suitable for semiregular elements, is proved. Sections 5 and 6, which complete the survey introduced in Sections 1–4, have not yet been published and were written specially for Equadiff 9. The notation of derivatives and Sobolev spaces is identical with the notation used in [9]. As to the notion of semiregular elements, semiregular triangles can have one angle arbitrarily small. Triangles with two arbitrarily small angles are irregular. A semiregular quadrilateral K can be arbitrarily narrow and it satisfies the condition | cos θi| ≤ σ < 1 (i = 1, . . . , 4), where θ1, . , θ4 are the angles of K. AMS Subject Classification. 65N30
Gesture controlled X-RHex (2.0) robot

In this paper, the authors describe the design of Gesture controlled X-RHex (2.0) Robot. X-RHex (2.0) has only six actuators, one motor located at each hip, achieving mechanical simplicity that promotes reliable and robust operation in real-world tasks. The paper is also about improving controlling the robot and accurate handling. Gesture controlling is the solution for easy handling and giving the desired direction to robot effectively. Empirically stable and highly maneuverable locomotion arises from a very simple clock-driven, open loop tripod gait. The main area of paper is to operate the wireless X-RHex (2.0) Robot more efficiently by using an accelerometer sensor.
Distributed Implementations of Dependency Discovery Algorithms

We analyze the problem of discovering dependencies from distributed big data. Existing (non-distributed) algorithms focus on minimizing computation by pruning the search space of possible dependencies. However, distributed algorithms must also optimize communication costs, especially in shared-nothing settings, leading to a more complex optimization space. To understand this space, we introduce six primitives shared by existing dependency discovery algorithms, corresponding to data processing steps separated by communication barriers. Through case studies, we show how the primitives allow us to analyze the design space and develop communication-optimized implementations. Finally, we support our analysis with an experimental evaluation on real datasets.
Effect of Biochar Application Rates on the Hydraulic Properties of an Agricultural-Use Boreal Podzol

Boreal agriculture struggles with soils of lower agronomic value, most of which are sandy with a low water holding capacity (WHC) and prone to nutrient leaching. Biochar amendments are associated with positive effects on soil hydraulic properties and enhanced nutrient retention. However, these effects are strongly related to feedstock type and pyrolysis parameters and depend on biochar application rates and soil types. While biochar could increase the productivity of boreal agriculture by improving water and nutrient use efficiency, little is known about its effects on hydraulic processes in podzol. In this study, we investigated the effects of biochar rates (10, 20, 40, 80 Mg carbon ha−1) and maturity on soil hydrology for an agriculturally used Podzol in Labrador, Canada. The in-situ soil water content (SWC) and weather data over an entire growing season were analysed. Hydrus 1D simulations were used to estimate changes in water fluxes. SWC showed clear differentiation among storage parameters (i.e., initial, peak and final SWC) and kinetic parameters (i.e., rate of SWC change). Storage parameters and soil wetting and drying rates were significantly affected by biochar rates and its maturity. The magnitude of the changes in SWC after either wetting or drying events was statistically not affected by the biochar rate. This confirms that biochar mostly affected the WHC. Nevertheless, reductions in cumulative lower boundary fluxes were directly related to biochar incorporation rates. Overall, biochar had positive effects on hydrological properties. The biochar rate of 40 Mg C ha−1 was the most beneficial to agriculturally relevant hydraulic conditions for the tested Podzol.
Title: MRI-Based Assessment of Lower Extremity Muscle Volumes in Patients Before and After ACL Reconstruction

Context: Study of muscle volumes in patients after anterior cruciate ligament (ACL) injury and reconstruction (ACL-R) is largely limited to cross-sectional assessment of the thigh musculature, which may inadequately describe post-traumatic and post-surgical muscle function. No studies have prospectively examined the influence of ACL injury and reconstruction on lower extremity muscle volumes. Objective: Assess magnetic resonance imaging (MRI) derived lower extremity muscle volumes, and quantify quadriceps strength and activation in patients following ACL injury and reconstruction. Design: Prospective case series. Setting: Research laboratory and MRI facility. Patients (or Other Participants): Four patients (2 males, 2 females, age=27.4±7.4, height=169.2±8.1cm, mass=74.3±18.5kg) scheduled for ACL-R. Intervention(s): 35 muscle volumes were obtained from a bilateral lower extremity MRI before and after ACL-R. Main Outcome Measures: Muscle volumes expressed relative to (1) a normative database pre-and-postsurgery, (2) limb symmetry pre-and-post-surgery, and (3) percentage change pre-to-post-surgery. Quadriceps function was quantified by normalized knee extension maximal voluntary isometric contraction (MVIC) torque and central activation ratio (CAR). Results: Involved vastus lateralis and tibialis anterior were consistently smaller than healthy individuals (Z< -1SD) pre-and-postsurgery in all patients. Involved rectus femoris and vastus lateralis were more than 15% smaller than the contralateral limb pre-surgery, whereas the involved rectus femoris, gracilis, vastus medialis, vastus intermedius, and vastus lateralis muscle volumes exceeded 20% asymmetry postoperatively. Involved gracilis and semitendinosus atrophied more than 30% from pre-to-postsurgery. Involved MVIC torque and CAR increased by 12.7% and 12.5% respectively, yet strength remained 33.2% asymmetric post-surgery. Conclusions: Adaptations in lower extremity muscle volumes are present following ACL injury and reconstruction. Anterior thigh and shank muscles were smaller than healthy individuals, and large asymmetries in quadriceps volumes were observed preand post-surgery. Selective atrophy of the semitendinosus and gracilis occurred following surgery. Volumetric deficits of the quadriceps musculature may exist despite improvements in muscle strength and activation. Word Count: 300 D ow nl oa de d by U ni ve rs ity o f A uc kl an d L ib ra ry o n 05 /1 5/ 17 , V ol um e 0, A rt ic le N um be r 0 “MRI-Based Assessment of Lower Extremity Muscle Volumes in Patients Before and After ACL Reconstruction” by Norte GE et al. et al. Journal of Sport Rehabilitation © 2017 Human Kinetics, Inc.