Miracle-dz/UniFAR-FTUs huggingface dataset:
Animal Cell Differentiation Patterns Suppress Somatic Evolution

Cell differentiation in multicellular organisms has the obvious function during development of creating new cell types. However, in long-lived organisms with extensive cell turnover, cell differentiation often continues after new cell types are no longer needed or produced. Here, we address the question of why this is true. It is believed that multicellular organisms could not have arisen or been evolutionarily stable without possessing mechanisms to suppress somatic selection among cells within organisms, which would otherwise disrupt organismal integrity. Here, we propose that one such mechanism is a specific pattern of ongoing cell differentiation commonly found in metazoans with cell turnover, which we call “serial differentiation. ” This pattern involves a sequence of differentiation stages, starting with self-renewing somatic stem cells and proceeding through several (non–self-renewing) transient amplifying cell stages before ending with terminally differentiated cells. To test the hypothesis that serial differentiation can suppress somatic evolution, we used an agent-based computer simulation of cell population dynamics and evolution within tissues. The results indicate that, relative to other, simpler patterns, tissues organized into serial differentiation experience lower rates of detrimental cell-level evolution. Self-renewing cell populations are susceptible to somatic evolution, while those that are not self-renewing are not. We find that a mutation disrupting differentiation can create a new self-renewing cell population that is vulnerable to somatic evolution. These results are relevant not only to understanding the evolutionary origins of multicellularity, but also the causes of pathologies such as cancer and senescence in extant metazoans, including humans.
Linear and Nonlinear Optical Properties of Aligned Elongated Silver Nanoparticles Embedded in Silica

Nanotechnology will be soon required in most engineering and science curricula. It cannot be questioned that cutting-edge applications based on nanoscience are having a considerable impact in nearly all fields of research, from basic to more problem-solving scientific enterprises. In this sense, books like “Silver Nanoparticles” aim at filling the gaps for comprehensive information to help both newcomers and experts, in a particular fast-growing area of research. Besides, one of the key features of this book is that it could serve both academia and industry. “Silver nanoparticles” is a collection of eighteen chapters written by experts in their respective fields. These reviews are representative of the current research areas within silver nanoparticle nanoscience and nanotechnology.
Prosody change and response timing analysis in spontaneously spoken dialogs and their modeling in a spoken dialog system

If a dialog system were to respond to a user as naturally as a human, interaction would be smoother. Imitating the human prosodic behavior of utterances is important in computer-human natural conversations. In this paper, to develop a cooperative/friendly spoken dialog system, we analyzed the correlations between F0 synchrony tendency or overlap frequency and subjective measures: “liveliness,” “familiarity,” and “informality” in human-human dialogs. We also modeled the properties of these features and implemented the model on our dialog system that generated the response timing of aizuchi (back-channel), turn-taking based on a decision tree in real time, and dynamical F0 changes to realize chat-like conversations. Index Terms: spoken dialog system, prosody control, response timing
Impact of Multi-Targeted Antiretroviral Treatment on Gut T Cell Depletion and HIV Reservoir Seeding during Acute HIV Infection

Background Limited knowledge exists on early HIV events that may inform preventive and therapeutic strategies. This study aims to characterize the earliest immunologic and virologic HIV events following infection and investigates the usage of a novel therapeutic strategy. Methods and Findings We prospectively screened 24,430 subjects in Bangkok and identified 40 AHI individuals. Thirty Thais were enrolled (8 Fiebig I, 5 Fiebig II, 15 Fiebig III, 2 Fiebig IV) of whom 15 completed 24 weeks of megaHAART (tenofovir/emtricitabine/efavirenz/raltegravir/maraviroc). Sigmoid biopsies were completed in 24/30 at baseline and 13/15 at week 24. At baseline, the median age was 29 years and 83% were MSM. Most were symptomatic (87%), and were infected with R5-tropic (77%) CRF01_AE (70%). Median CD4 was 406 cells/mm3. HIV RNA was 5.5 log10 copies/ml. Median total blood HIV DNA was higher in Fiebig III (550 copy/106 PBMC) vs. Fiebig I (8 copy/106 PBMC) (p = 0.01) while the median %CD4+CCR5+ gut T cells was lower in Fiebig III (19%) vs. Fiebig I (59%) (p = 0.0008). After 24 weeks of megaHAART, HIV RNA levels of <50 copies were achieved in 14/15 in blood and 13/13 in gut. Total blood HIV DNA at week 0 predicted reservoir size at week 24 (p<0.001). Total HIV DNA declined significantly and was undetectable in 3 of 15 in blood and 3 of 7 in gut. Frequency of CD4+CCR5+ gut T cells increased from 41% at baseline to 64% at week 24 (p>0.050); subjects with less than 40% at baseline had a significant increase in CD4+CCR5+ T cells from baseline to week 24 (14% vs. 71%, p = 0.02). Conclusions Gut T cell depletion and HIV reservoir seeding increases with progression of AHI. MegaHAART was associated with immune restoration and reduced reservoir size. Our findings could inform research on strategies to achieve HIV drug-free remission.
Modeling spatially-varying reflectance based on Kernel Nyström

We present a new method for modeling real-world surface reflectance, described with non-parametric spatially-varying bidirectional reflectance distribution functions(SVBRDF). Our method seeks to achieve high reconstruction accuracy, compactness and "editability" of representation meanwhile speeding up both the SVBRDF capturing and modeling processes. For a planar surface, we 1) design a fast capturing device to acquire reflectance samples at dense surface locations; 2) propose a Laplacian-based angular interpolation scheme for a 2D slice of BRDF at a given surface location, and then a Kernel Nyström method for SVBRDF data matrix reconstruction; 3) propose a practical algorithm to extract linear-independent basis BRDFs, and to calculate blending weights through projecting reconstructed reflectance onto these bases. Results demonstrate that our approach models real-world reflectance with both high accuracy and high visual fidelity for real-time virtual environment rendering.
Lyapunov Based Control of Flexible Joint Manipulator with Experimental Validation by Using Chaotic Gyroscope Synchronization

This paper presents a nonlinear control for trajectory tracking and vibration control of a flexible joint manipulator by using chaotic gyroscope synchronization. To study the effectiveness of the controllers, designed controller is developed for tip angular position control of a flexible joint manipulator. Based on Lyapunov stability theory, the nonlinear controller and some generic sufficient conditions for global asymptotic control are attained. In this study, the anti-control is applied to reduce the deflection angle of flexible joint system. To achieve this goal, the chaos dynamic must be created in the flexible joint system. So, the flexible joint system has been synchronized to chaotic gyroscope system. In this study, control and anti-control concepts are applied to achieve the high quality performance of flexible joint system. It is trying to design a controller which is capable to satisfy the control and anti-control aims. The performances of the proposed control are examined in terms of input tracking capability and level of vibration reduction. Finally, the efficacy of the proposed method is validated through experimentation on QUANSER's flexible joint manipulator.
Senseval-3 logic forms: A system and possible improvements

Logic Forms, particular powerful logic representations presented in Moldovan and Rus (2001), are simple yet highly effective. In this paper, the structure of Logic Forms and their generation from input text are described. The results of an evaluation comparing the Logic Forms generated by hand with those generated automatically are also reported. Finally, we suggest some improvements to the representation used in the LFI task based on our results.
Statistical inferences under the Null hypothesis: common mistakes and pitfalls in neuroimaging studies

Published studies using functional and structural MRI include many errors in the way data are analyzed and conclusions reported. This was observed when working on a comprehensive review of the neural bases of synesthesia, but these errors are probably endemic to neuroimaging studies. All studies reviewed had based their conclusions using Null Hypothesis Significance Tests (NHST). NHST have yet been criticized since their inception because they are more appropriate for taking decisions related to a Null hypothesis (like in manufacturing) than for making inferences about behavioral and neuronal processes. Here I focus on a few key problems of NHST related to brain imaging techniques, and explain why or when we should not rely on “significance” tests. I also observed that, often, the ill-posed logic of NHST was even not correctly applied, and describe what I identified as common mistakes or at least problematic practices in published papers, in light of what could be considered as the very basics of statistical inference. MRI statistics also involve much more complex issues than standard statistical inference. Analysis pipelines vary a lot between studies, even for those using the same software, and there is no consensus which pipeline is the best. I propose a synthetic view of the logic behind the possible methodological choices, and warn against the usage and interpretation of two statistical methods popular in brain imaging studies, the false discovery rate (FDR) procedure and permutation tests. I suggest that current models for the analysis of brain imaging data suffer from serious limitations and call for a revision taking into account the “new statistics” (confidence intervals) logic.
A new reconfigurable mixerless polar transmitter for multi-standard and SDR applications

A mixerless polar transmitter architecture using an analog RF variable gain amplifier (VGA) and an analog phase shifter is proposed and implemented. This architecture avoids the use of nonlinear switching mixers and quadrature modulator circuits for frequency up-conversion. Thus, spurs and distortion common to mixer circuits are absent and therefore the proposed architecture does not require any filtering at its RF output. Hence, the proposed topology can be implemented for wider RF bandwidths and is more reconfigurable for multi-standard and Software Defined Radio applications. The unusual nonlinear behavior of the proposed polar transmitter was analyzed and mitigated using a new modified memory polynomial model. The proposed architecture achieved an EVM of 0.92 % for an LTE signal of 1.4 MHz bandwidth with 64 QAM constellation.
Genomic Analysis Reveals the Molecular Heterogeneity of Ovarian Clear Cell Carcinomas

Purpose: Ovarian clear cell carcinomas (OCCC) are a drug-resistant and aggressive type of epithelial ovarian cancer. We analyzed the molecular genetic profiles of OCCCs to determine whether distinct genomic subgroups of OCCCs exist. Experimental design: Fifty pure primary OCCCs were subjected to high-resolution microarray-based comparative genomic hybridization (aCGH). Unsupervised hierarchical clustering using Ward's linkage analysis was performed to identify genomic subgroups of OCCCs. Survival analysis was performed using Kaplan–Meier method and log-rank test. Cox-regression analysis was used to identify independent predictors of outcome. Differentially amplified regions between genomic subgroups of OCCCs were identified using a multi-Fisher's exact test. Results: Hierarchical cluster analysis revealed two distinct clusters of OCCCs with different clinical outcomes. Patients from cluster-1 had a significantly shorter median progression-free survival (PFS) than those from cluster-2 (11 vs. 65 months, P = 0.009), although estimates for ovarian cancer–specific survival (OCS) did not reach statistical significance (P = 0.065). In multivariate analysis, suboptimal debulking surgery and genomic cluster were independently prognostic for PFS. Recurrently amplified genomic regions with a significantly higher prevalence in cluster-1 than cluster-2 OCCCs were identified and validated. HER2 gene amplification and protein overexpression was observed in 14% of OCCCs, suggesting that this may constitute a potential therapeutic target for a subgroup of these tumors. Conclusions: OCCCs constitute a heterogeneous disease at the genomic level despite having similar histological features. The pattern of genomic aberrations in subgroups of OCCCs is of clinical significance. We have identified recurrently amplified regions that may harbor potential therapeutic targets for subgroups of OCCCs. Clin Cancer Res; 17(6); 1521–34. ©2011 AACR.
An approach of optimal designing of nonwoven air filter media: Effect of fibre fineness

This article reports on an optimal design of nonwoven air filter media produced from fibres of different finenesses. A series of nonwoven filter media was prepared from polypropylene fibres of three different finenesses. The entire media were evaluated for filtration efficiency and pressure drop. A three-component augmented simplex lattice design was used for media preparation, and response surface methodology was employed for data analysis. A set of expressions was obtained for predicting the filtration efficiency and pressure drop of nonwoven filter media as a function of fibre composition. The composition in the media was optimized by desirability function approach to achieve maximum filtration efficiency and minimum pressure drop simultaneously.
Compact and Accurate 3-D Face Modeling Using an RGB-D Camera: Let's Open the Door to 3-D Video Conference

We present a method for producing an accurate and compact 3-D face model in real time using a low cost RGB-D sensor like the Kinect camera. We extend and use Bump Images for highly accurate and low memory consumption 3-D reconstruction of the human face. Bump Images are generated by representing the Cartesian coordinates of points on the face in the spherical coordinate system whose origin is the center of the head. After initialization, the Bump Images are updated in real time with every RGB-D frame with respect to the current viewing direction and head pose that are estimated using the frame-to-global-model registration strategy. While high accuracy of the representation allows to recover fine details, low memory use opens new possible applications of consumer depth cameras such as 3-D video conferencing. We validate our approach by quantitatively comparing our result with the result obtained by a commercial high resolution laser scanner. We also discuss the potential of our proposed method for a 3-D video conferencing application with existing internet speeds.
Specular 3 D Object Tracking by View Generative Learning

This paper proposes a novel specular 3D object tracking method. Our method works with texture-less specular objects and objects with background reflections on the surface. It is a keypoint-based tracking using a view generative learning. Conventional local features are robust to scale and rotation, but keypoint matching fails when the viewpoint significantly changes. We apply a view generative learning to improve the robustness to viewpoint changes. To be robust to large appearance changes, our method does viewdependent rendering for generating views and stores all the descriptors of the keypoints on the generated images and its 3D-position in the reference database called ”feature table”. We conducted quantitative evaluation on the object pose and showed our method outperforms compared with the other view generative learning methods in terms of tracking accuracy and learning process.
Growth Factor Production and Speed of Engraftment Correlate with Vascular Endothelial Frequency of Apoptotic Cells in Solid Tumors and Efficiency Diabetic / Severe Combined Immunodeficiency Mouse Model : Human Myeloid and Lymphoid Malignancies in the Non-Obese

Recent studies have suggested that non-obese diabetic/severe combined immunodeficiency (NOD/SCID) mice transplanted with human hematological malignancies show higher levels of engraftment compared with other strains. We used this model to compare xenotransplantability of human leukemia and lymphoma cell lines and to investigate angiogenesis in hematopoietic malignancies. Ten of 12 evaluated cell lines were able to engraft NOD/SCID mice within 120 days. A strong correlation was observed between the amount of vascular endothelial growth factor (VEGF) produced in vitro by cultured cells and the efficiency of tumor engraftment (r 5 0.808; P 5 0.001), and an inverse correlation was found between VEGF production and the time of tumor engraftment (r 5 20.792; P 5 0.006) and between VEGF production and the frequency of apoptotic/ dead cells in solid tumors (r 5 20.892; P 5 0.007). Moreover, VEGF production correlated with the frequency of endothelial (CD311/CD341) cells in solid tumors (r 5 0.897;P 5 0.001). Taken together within vitro data presented here and indicating that the VEGF antagonist Flt-1/Fc chimera inhibits leukemia and lymphoma cell proliferation, our findings support a role for tumor-derived VEGF in leukemia and lymphoma progression. Furthermore, the present study confirms previous observations indicating that VEGF expression may play a crucial role in xenotransplantability of human solid malignancies in SCID mice. The NOD/ SCID model is promising for future evaluations of antiangiogenic drugs, alone or in combination with established chemoor immunotherapy regimens.
Decentralizing the optimal multi-cell beamforming via large system analysis

A multi-cell minimum power beamforming problem is considered. It is known that the inter-cell interference (ICI) terms couple the base stations (BS) and inter-cell coordination is required for global optimal solution. The cooperation can be realized by exchange of instantaneous channel state information (CSI) or terms related to the ICI values via a backhaul link. However, the limited backhaul capacity and delay constraints put a limit on achievable performance when the number of antennas and users grow large or when dealing with a fast fading scenario. In this work, we demonstrate that the ICI terms coupling the coordinating BSs can be approximated using the random matrix theory (RMT) tools when the problem dimensions grow large, and that the approximated ICI values depend only on channels statistics, i.e, spatial load and user specific path loss values. This leads to a significant reduction in the information exchange rate among BSs. Furthermore, processing is simplified because with a fixed approximated ICI values the beamforming vectors can be obtained locally at each BS. The proposed solution guarantees the feasibility of the target signal-to-interference-plus-noise ratios (SINR) without any major loss of performance as compared to the optimal centralized design.
Point Light Field for Point Rendering Systems

In this paper, we introduce the concept of point light fields for point based rendering systems, analogous to surface light fields for polygonal rendering systems. We evaluate two representations, namely, singular value decomposition and spherical harmonics for their representation accuracy, storage efficiency, and real-time reconstruction of point light fields. We have applied our algorithms to both real-world and synthetic point based models. We show the results of our algorithm using an advanced point based rendering system.
Study of particle trajectories, residence times and flow behavior in kneading discs of intermeshing co‐rotating twin‐screw extruders

A three-dimensional finite element model was implemented for the solution of mass and momentum conservation equations in the kneading disc section of an intermeshing co-rotating twin-screw extruder. The polymer melt was modeled with a Carreau constitutive equation. The particle tracking technique was used to obtain residence times and analyze distributive mixing for different length to diameter ratios (L/D) of kneading discs. Previous studies from Kalyon et al. (1) and Cheng and Manas-Zloczower (2) have shown that the mixing performance of intermeshing co-rotating twin-screw extruders is highly dependent on the combination of screw configuration and operating conditions. The complexity of the geometry and the transient character of the flow demand powerful computational tools to characterize the flow and to develop a prediction tool for the analysis of relative performance between different configurations. Difficulties arise in the particle tracking technique because of the time discretization and the presence of moving boundaries. Results show the importance of particle history on the evaluation of the relative performance of different configurations of kneading blocks and suggest a reevaluation of the use of average flow characteristics for the analysis of mixing. Results also confirm the importance of an accurate description of the geometry and clearances in order to obtain information about relative mixing performance. Polym. Eng. Sci. 44:779–793, 2004. © 2004 Society of Plastics Engineers.
The implementation of a first-order logic AGM belief revision system

Belief revision is increasingly being seen as central to a number of fundamental problems in artificial intelligence such as nonmonotonic reasoning, reasoning about action, truth maintenance and database update. The authors describe the first implementation of an AGM belief revision system. The system is based on classical first-order logic, and for any finitely representable belief state, it efficiently computes expansions, contractions and revision satisfying the AGM postulates for rational belief change. The system uses a finite base to represent a belief set, and interprets a partially specified entrenchment as representing a unique most conservative entrenchment-this is motivated by considerations of evidence and by the close connections between belief revision and nonmonotonic reasoning. The authors describe in detail the algorithms for belief change, and give some examples of the system's operation.
Turning Speech Into Scripts

We describe an architecture for implementing spoken natural language dialogue interfaces to semi-autonomous systems, in which the central idea is to transform the input speech signal through successive levels of representation corresponding roughly to linguistic knowledge, dialogue knowledge, and domain knowledge. The final representation is an executable program in a simple scripting language equivalent to a subset of Cshell. At each stage of the translation process, an input is transformed into an output, producing as a byproduct a "meta-output" which describes the nature of the transformation performed. We show how consistent use of the output/meta-output distinction permits a simple and perspicuous treatment of apparently diverse topics including resolution of pronouns, correction of user misconceptions, and optimization of scripts. The methods described have been concretely realized in a prototype speech interface to a simulation of the Personal Satellite Assistant.