Miracle-dz/UniFAR-FTUs huggingface dataset:
Clonal expansion in follicular lymphoma occurs subsequent to antigenic selection

The genesis of human follicular lymphoma (FL) is a multistep process. The initial event is thought to be the chromosomal translocation t(14;18)(q32;q21) juxtaposing the bcl-2 proto-oncogene with the immunoglobulin (Ig) H chain locus joining segment (JH) as an error of D- J or V-D joining in the pre-B cell. However, FL is recognized clinically as a tumor of surface Ig (sIg)-positive B cells with morphologic and phenotypic similarities to the centrocyte of the secondary immune response. Thus, additional steps must be involved in the clonal expansion of the FL tumor cell beyond the activation of bcl- 2 as a consequence of the t(14;18) translocation. Like the normal centrocyte, somatic mutations accumulate in the variable (V) genes of FL tumor B cells. To determine if clonal expansion of FL occurs before or after the development of the malignant follicle, we sought to examine the evolution of the FL V gene from its unmutated germline (GL) counterpart. To obtain the GL gene we first cloned the productively rearranged V gene of patient MT FL and obtained the clone rMTF. A hybridization probe derived from the 2.1-kb region upstream of the V gene in clone rMTF identified a single band in Southern blot hybridization of GL DNA. This probe was used to screen a size-selected library, and candidate GL V genes were isolated. Two identical clones, MTGL1 and 2, proved to have upstream regions (USRs) that were colinear with the USR of the rMTF. Thus, the MTGL clones represent the unmutated GL V genes, which were productively rearranged in the MT FL. Comparison of the GL V gene sequence to a consensus of MT FL V gene sequences revealed 42 mutations, demonstrating that malignant clonal expansion occurred subsequent to the activation of somatic mutation, presumably in the malignant follicle. Furthermore, the individual FL V gene sequences segregated into two distinct patterns of mutation. The major population represented 71% of the clones, and the minor population 29%. To investigate possible mechanisms for the parallel selection of distinct tumor cell populations, we analyzed the pattern of silent and replacement mutations within the V gene sequences. We found that in the framework regions (FRs) of both populations there were significantly fewer replacement changes than expected, suggesting that negative selective pressure was maintaining the structural integrity of the sIg. In contrast, the complementarity determining regions (CDRs), which make up the antigen binding domain of Ig, had an excess of replacement changes, suggesting positive selection for altered ligand binding.
ON FINDING MELODIC LINES IN AUDIO RECORDINGS

The paper presents our approach to the problem of finding melodic line(s) in polyphonic audio recordings. The approach is composed of two different stages, partially rooted in psychoacoustic theories of music perception: the first stage is dedicated to finding regions with strong and stable pitch (melodic fragments), while in the second stage, these fragments are grouped according to their properties (pitch, loudness.) into clusters which represent melodic lines of the piece. Expectation Maximization algorithm is used in both stages to find the dominant pitch in a region, and to train Gaussian Mixture Models that group fragments into melodies. The paper presents the entire process in more detail and provides some initial results.
The Hamilton-Jacobi skeleton

The eikonal equation and variants of it are of significant interest for problems in computer vision and image processing. It is the basis for continuous versions of mathematical morphology, stereo, shape-from-shading and for recent dynamic theories of shape. Its numerical simulation can be delicate, owing to the formation of singularities in the evolving front, and is typically based or, level set methods. However there are more classical approaches rooted in Hamiltonian physics, which have received little consideration in computer vision. In this paper we first introduce a new algorithm for simulating the eikonal equation, which offers a number of computational and conceptual advantages over the earlier methods when it comes to shock tracking. Next, we introduce a very efficient algorithm for shock detection, where the key idea is to measure the net outward flux of a vector field per unit volume, and to detect locations where a conservation of energy principle is violated. We illustrate the approach with several numerical examples including skeletons of complex 2D and 3D shapes.
adults: a randomized controlled trial of exercise Etiology and modification of gait instability in older

[PDF] [Full Text] [Abstract] , March 1, 2002; 57 (3): B115-125. J. Gerontol. A Biol. Sci. Med. Sci. L. A. Lipsitz Dynamics of Stability: The Physiologic Basis of Functional Health and Frailty [Full Text] , May 1, 2002; 57 (5): M262-282. J. Gerontol. A Biol. Sci. Med. Sci. M. A. F. Singh Prescription Exercise Comes of Age: Rationale and Recommendations for a Geriatric Exercise [Full Text] [Abstract] , December 1, 2003; 95 (6): 2248-2256. J Appl Physiol D. Malatesta, D. Simar, Y. Dauvilliers, R. Candau, F. Borrani, C. Prefaut and C. Caillaud Energy cost of walking and gait instability in healthy 65and 80-yr-olds [Full Text] [Abstract] , April 21, 2004; 2004 (16): pe16-pe16. Sci. Aging Knowl. Environ. L. A. Lipsitz Physiological Complexity, Aging, and the Path to Frailty [PDF] [Full Text] [Abstract] , May 1, 2005; 60 (5): 627-632. J. Gerontol. A Biol. Sci. Med. Sci. Y. Laufer Accelerated Walking Speed Effect of Age on Characteristics of Forward and Backward Gait at Preferred and
CT image reconstruction using hexagonal grids

In the transversal plane CT exhibits a nearly rotational symmetric point spread function. Pixel sampling is typically done on Cartesian grids which are not ideal from a signal processing point of view. It is advantageous to use a hexagonal grid which can capture the same signal components with 13% fewer sampling points. In 3D one can even save 29%. We developed an efficient scheme to allow for arbitrarily shaped field of views and a hierarchical memory layout. The latter divides the images into small hexagonal subimages, similar to honeycombs, whose size is small enough to avoid cache misses on CPU-based algorithms or to be used on dedicated signal processing hardware such as GPUs (graphics processing units) or CBEs (cell broadband engines) that may be memory limited. As the final step a resampling algorithm converts from the hex domain to the Cartesian domain before storing images. We implemented a hyperfast CBE-based Feldkamp algorithm for the hexagonal lattice and compared its performance and its image quality to reconstructions using the standard Feldkamp algorithm. Both algorithms were run on the Dual Cell Based System (DCBS, Mercury Computer Systems, Berlin, Germany) on two CBEs with 3.2 GHz each. A 5123 volume was reconstructed from 720 projections of 5122 detector pixels. Image quality of the hexagonal approach was identical to the direct approach using the Cartesian lattice: the maximum relative difference between the MTFs was 1% and image noise differed by not more than 3%. The improvement in reconstruction speed was approximately 12% for the hexagonal grid which is slightly lower than the expectation. The complete reconstruction finished in about 10 s. With identical image quality reconstruction on the hexagonal grid is a simple and effective approach to significantly reduce memory consumption and reconstruction time. Existing reconstruction algorithms can be easily modified to operate in the hexagonal domain.
Determination of swell index and swelling pressure from suction tests – a case study of Neogene clays from Warsaw (Poland)

The paper presents the results of swell index, swelling pressure and soil suction tests carried out on Neogene clays from Warsaw, depending on the water content, clay fraction, liquid limit, plasticity index, cation exchange capacity, and content of clay minerals and beidellite. These clays are considered expansive soils in Poland, as they are vulnerable to water content variations in the active zone, which result in their volume change and, in consequence, cause damage of foundations and other construction elements. A number of physical, chemical and mineral properties were determined for these clays. The swelling tests were carried out on samples precompacted in Proctor apparatus, at various initial values of water content. The analyses have shown exponential relation of swell index, swelling pressure and suction versus water content. In addition, the investigated relationship between the suction and swell characteristics of tested clays shows good correlation as a power function between these parameters. In addition, validity of correlations between fitting parameters of obtained relationships and soil index properties, such as clay fraction, liquid limit, plasticity index, cation exchange capacity, and content of clay minerals and beidellite, have been demonstrated. The empirical relations are characterized by high values of the correlation coefficient. A very high fit has also been found for a proposed relationship between the swell index and swelling pressure for tested clays
Identifying multiple infection sources in a network

Estimating which nodes are the infection sources that introduce a virus or rumor into a network, or the locations of pollutant sources, plays a critical role in limiting the potential damage to the network through timely quarantine of the sources. In this paper, we derive estimators for the infection sources and their infection regions based on the infection network geometry. We show that in a geometric tree with at most two sources, our estimator identifies these sources with probability going to one as the number of infected nodes increases. We extend and generalize our methods to general graphs, where the number of infection sources are unknown and there may be multiple sources. Numerical results are presented to verify the performance of our proposed algorithms under different types of graph structures.
The Role of Spirituality in the Lives of Mothers of Breast Cancer Survivors

Breast cancer impacts an entire family system. The mothers of breast cancer patients are likely impacted in a variety of ways by their daughters’ diagnoses. To date, few researchers have investigated the experiences and perspectives of this population. In the present study, the authors explored how mothers of breast cancer survivors managed adversities associated with this disease and illness. Using secondary data and narrative analysis, the investigators analyzed data gathered from 30 mothers. Findings indicate that participants relied on their spirituality for the management of stress and hardship related to having a loved one with breast cancer.
Investigating the relation between stochastic differentiation and homeostasis in intestinal crypts via multiscale modeling

Colorectal tumors originate and develop within intestinal crypts. Even though some of the essential phenomena that characterize crypt structure and dynamics have been effectively described in the past, the relation between the differentiation process and the overall crypt homeostasis is still partially understood. We here investigate this relation and other important biological phenomena by introducing a novel multiscale model that combines a morphological description of the crypt with a gene regulation model: the emergent dynamical behavior of the underlying gene regulatory network drives cell growth and differentiation processes, linking the two distinct spatio-temporal levels. The model relies on a few a priori assumptions, yet accounting for several key processes related to crypt functioning, such as: dynamic gene activation patterns, stochastic differentiation, signaling pathways ruling cell adhesion properties, cell displacement, cell growth, mitosis, apoptosis and the presence of biological noise. We show that this modeling approach captures the major dynamical phenomena that characterize the regular physiology of crypts, such as cell sorting, coordinate migration, dynamic turnover, stem cell niche maintenance and clonal expansion. All in all, the model suggests that the process of stochastic differentiation might be sufficient to drive the crypt to homeostasis, under certain crypt configurations. Besides, our approach allows to make precise quantitative inferences that, when possible, were matched to the current biological knowledge and it permits to investigate the role of gene-level perturbations, with reference to cancer development. We also remark the theoretical framework is general and may applied to different tissues, organs or organisms.
Deterministic prefetching for container-managed persistence

Modern information system architectures place applications in an application server and persistent objects in a relational database. In this setting, we consider the problem of improving application throughput; our proposed solution uses data prefetching to minimize the total data-access time of an application, in a manner that affects neither the application code nor the backend DBMS. Our methodology is based on analyzing and automatically merging SQL queries to produce query sequences with low total response time, in ways that exploit the application’s data-access patterns. The proposed approach is independent of the application domain and can be viewed as a component of container-managed persistence that can be implemented in middleware. This paper describes our proposed framework for using generic data-access patterns in merging queries, to derive query sequences with improved total data-access time. For each guideline that is discovered, we list the rules to determine when the specific guideline is applicable, its key parameters, and the experimental results in terms of the improved dataaccess time. The approach is evaluated in the context of financial and manufacturing domains, which support the kinds of natural conceptual relationships where this approach is valuable. This research is supported under NCSU CACC Grant 11019
Design Space Exploration of L1 Data Caches for FPGA-Based Multiprocessor Systems

Combining multi-processing with the high level of configurability possible with FPGA-based soft-processors, this paper presents a multiprocessing framework based on the MicroBlaze soft-processor that provides multicore support and fully coherent, independently configurable Level 1 Caches with Linux multicore support. This architecture allows for fine-grain configurability of the system, allowing for FPGA resources to be better optimized for a specific embedded application. We use our framework to explore the L1 Data Cache configuration, developing a metric for efficiency based on resource usage and static application runtime. We find that a Pseudo-Random replacement policy is consistently the more efficient choice for FPGA systems.
Protein phosphatase 2A Cα regulates osteoblast differentiation and the expressions of bone sialoprotein and osteocalcin via osterix transcription factor

Serine/threonine protein phosphatase 2A (PP2A) participates in regulating many important physiological processes such as cell cycle, growth, apoptosis, and signal transduction. Osterix is a zinc‐finger‐containing transcription factor that is essential for osteoblast differentiation and regulation of many bone‐related genes. We have recently reported that decrease in α‐isoform of PP2A catalytic subunit (PP2A Cα) accelerates osteoblast differentiation through the expression of bone‐related genes. In this study, we further examined the role of PP2A Cα in osteoblast differentiation by establishing the stable cell lines that overexpress PP2A Cα. Overexpression of PP2A Cα reduced alkaline phosphatase (ALP) activity. Osteoblast differentiation and mineralization were also decreased in PP2A Cα‐overexpressing cells, with reduction of bone‐related genes including osterix, bone sialoprotein (Bsp), and osteocalcin (OCN). Luciferase assay showed that the transcriptional activity of the Osterix promoter region was decreased in PP2A Cα‐overexpressing cells. Introduction of ectopic Osterix rescued the expression of Bsp and OCN in PP2A Cα‐overexpressing cells. These results indicate that PP2A Cα and its activity play a negative role in osteoblast differentiation and Osterix is a key factor responsible for regulating the expressions of Bsp and OCN during PP2A Cα‐mediated osteoblast differentiation. J. Cell. Physiol. © 2012 Wiley Periodicals, Inc.
VideoMark: A video-based learning analytic technique for MOOCs

The massive online open course (MOOC) revolution offers opportunities for learning analytics regarding the diversity in learning activities of MOOCs. In MOOCs, video lectures represent the principal learning resource, and learners spend most of their time engaged in self-paced, independent learning. Therefore, MOOCs present an innovative form of video-based learning. How to improve this learning environment by adding additional features to video lectures represents a path for progress. Few studies have investigated the interaction between learners and the video content; however, improvement in this domain is necessary. This paper proposes a video-based learning analysis approach called VideoMark, which enables learners to judiciously review, consolidate, and clarify specific concepts introduced in MOOCs. This analytical approach can be applied to MOOC-style ShareCourse programs in Taiwan. Finally, this analytical approach is presented as a visual keyword cloud for learners to clarify specific learning concepts in the MOOC learning process.
The Development of a Monolithic Shape Memory Alloy Actuator

Shape memory alloys (SMAs) provide exciting opportunities for miniature actuation systems. As SMA actuators are scaled down in size, cooling increases and bandwidth improves. However, the inclusion of a bias element with which to cycle the SMA actuator becomes difficult at very small scales. One technique used to avoid the necessity of having to include a separate bias element is the use of local annealing to fabricate a monolithic device out of nickel titanium (NiTi). The actuator geometry is machined out of a single piece of nonannealed NiTi. After locally annealing a portion of the complete device, that section exhibits the shape memory effect while the remainder acts as structural support and provides the bias force required for cycling. This work proposes one such locally-annealed monolithic SMA actuator for future incorporation in a device that navigates the digestive tract. After detailing the derivation of lumped electro-mechanical models for the actuator, a description of the prototyping procedure, including fabrication and local annealing of the actuator, is provided. This thesis presents the experimental prototype actuator behaviour and compares it with simulations generated using the developed models.
Contact force-guided catheter ablation for the treatment of atrial fibrillation: a meta-analysis of randomized, controlled trials

Contact force (CF) sensing technology allows real-time monitoring during catheter ablation for atrial fibrillation (AF). However, the effect of CF sensing technology on procedural parameters and clinical outcomes still needs clarification. Because of the inconsistent results thus far in this area, we performed a meta-analysis to determine whether CF sensing technology can improve procedural parameters and clinical outcomes for the treatment of AF. Studies examining the benefits of CF sensing technology were identified in English-language articles by searching the MEDLINE, Web of Science, and Cochrane Library databases (inception to May 2015). Ten randomized, controlled trials involving 1834 patients (1263 males, 571 females) were included in the meta-analysis (681 in the CF group, 1153 in the control group). Overall, the ablation time was significantly decreased by 7.34 min (95%CI=-12.21 to -2.46; P=0.003, Z test) in the CF group compared with the control group. CF sensing technology was associated with significantly improved freedom from AF after 12 months (OR=1.55, 95%CI=1.20 to 1.99; P=0.0007) and complications were significantly lower in the CF group than in the control group (OR=0.50, 95%CI=0.29 to 0.87; P=0.01). However, fluoroscopy time analysis showed no significantly decreased trend associated with CF-guided catheter ablation (weighted mean difference: -2.59; 95%CI=-9.06 to 3.88; P=0.43). The present meta-analysis shows improvement in ablation time and freedom from AF after 12 months in AF patients treated with CF-guided catheter ablation. However, CF-guided catheter ablation does not decrease fluoroscopy time.
Nanoparticle risk management and cost evaluation: a general framework

Industrial production of nano-objects has been growing fast during the last decade and a wide range of products containing nanoparticles (NPs) is proposed to the public in various markets (automotive, electronics, textiles…). The issues encountered in monitoring the presence of nano-objects in any media cause a major difficulty for controlling the risk associated to the production stage. It is therefore very difficult to assess the efficiency of prevention and mitigation solutions, which potentially leads to overestimate the level of the protection barriers that are recommended. The extra costs in adding nano-objects to the process, especially that of nanosafety, must be estimated and optimized to ensure the competitiveness of the future production lines and associated products. The risk management and cost evaluation methods presented herein have been designed for application in a pilot production line of injection-moulded nanocomposites.
Field Testing of an Integrated Surface/Subsurface Modeling Technique for Planetary Exploration

While there has been much interest in developing ground-penetrating radar (GPR) technology for rover-based planetary exploration, relatively little work has been done on the data collection process. Starting from the manual method, we fully automate GPR data collection using only sensors typically found on a rover. Further, we produce two novel data products: (1) a three-dimensional, photorealistic surface model coupled with a ribbon of GPR data, and (2) a two-dimensional, topography-corrected GPR radargram with the surface topography plotted above. Each result is derived from only the onboard sensors of the rover, as would be required in a planetary exploration setting. These techniques were tested using data collected in a Mars analogue environment on Devon Island in the Canadian High Arctic. GPR transects were gathered over polygonal patterned ground similar to that seen on Mars by the Phoenix Lander. Using the techniques developed here, scientists may remotely explore the interaction of the surface topography and subsurface structure as if they were on site.
10-702 Project Report : Parallel LDA , Truth or Dare ?

Latent Dirichlet Allocation (LDA) is a popular topic model, which can be learned using Collapsed Gibbs Sampling. Although Collapsed Gibbs Sampling is inherently sequential, we show that parallel approximation of the original algorithm is able to learn as good models as the exact algorithm. We studied the problem with real datasets, simulated data and statistical analysis.