Miracle-dz/UniFAR-FTUs huggingface dataset:
Direct Forcing for Lagrangian Rigid-Fluid Coupling

We propose a novel boundary handling algorithm for particle-based fluids. Based on a predictor-corrector scheme for both velocity and position, one- and two-way coupling with rigid bodies can be realized. The proposed algorithm offers significant improvements over existing penalty-based approaches. Different slip conditions can be realized and non-penetration is enforced. Direct forcing is employed to meet the desired boundary conditions and to ensure valid states after each simulation step. We have performed various experiments in 2D and 3D. They illustrate one- and two-way coupling of rigid bodies and fluids, the effects of hydrostatic and dynamic forces on a rigid body as well as different slip conditions. Numerical experiments and performance measurements are provided.
Gait generation via unified learning optimal control of Hamiltonian systems

SUMMARY This paper proposes a repetitive control type optimal gait generation framework by executing learning control and parameter tuning. We propose a learning optimal control method of Hamiltonian systems unifying iterative learning control (ILC) and iterative feedback tuning (IFT). It allows one to simultaneously obtain an optimal feedforward input and tuning parameter for a plant system, which minimizes a given cost function. In the proposed method, a virtual constraint by a potential energy prevents a biped robot from falling. The strength of the constraint is automatically mitigated by the IFT part of the proposed method, according to the progress of trajectory learning by the ILC part.
Blockade of chloride intracellular ion channel 1 stimulates Aβ phagocytosis

In amyloid‐β (Aβ)‐stimulated microglial cells, blockade of chloride intracellular ion channel 1 (CLIC1) reverts the increase in tumor necrosis factor‐α and nitric oxide (NO) production and results in neuroprotection of cocultured neurons. This effect could be of therapeutic efficacy in Alzheimer's disease (AD), where microglial activation may contribute to neurodegeneration, but it could reduce Aβ phagocytosis, which could facilitate amyloid plaque removal. Here, we analyzed the CLIC1 blockade effect on Aβ‐stimulated mononuclear phagocytosis. In the microglial cell line BV‐2, Aβ25–35 treatment enhanced fluorescent bead phagocytosis, which persisted also in the presence of IAA‐94, a CLIC1 channel blocker. The same result was obtained in rat primary microglia and in BV2 cells, where CLIC1 expression had been knocked down with a plasmid producing small interfering RNAs. To address specifically the issue of Aβ phagocytosis, we treated BV‐2 cells with biotinylated Aβ1–42 and measured intracellular amyloid by morphometric analysis. IAA‐94‐treated cells showed an increased Aβ phagocytosis after 24 hr and efficient degradation of ingested material after 72 hr. In addition, we tested Aβ1–42 phagocytosis in adult rat peritoneal macrophages. Also, these cells actively phagocytosed Aβ1–42 in the presence of IAA‐94. However, the increased expression of inducible NO synthase (iNOS), stimulated by Aβ, was reverted by IAA‐94. In parallel, a decrease in NO release was detected. These results suggest that blockade of CLIC1 stimulates Aβ phagocytosis in mononuclear phagocytes while inhibiting the induction of iNOS and further point to CLIC1 as a possible therapeutic target in AD. © 2008 Wiley‐Liss, Inc.
Influence of school playground size and equipment on the physical activity of students during recess

Children’s physical activity (PA) is increasingly restricted by the fast pace of modern life. Schools are the opportune setting in which to increase PA during daily recess. The purpose of this study was to record the degree of PA of 6th grade primary school students during recess and determine whether the playground size and available equipment can influence the degree of students’ PA. The study sample comprised of 625 12-year-old students, 324 (51.8%) boys and 301 (48.2%) girls. The PA during recess was calculated by Metabolic Equivalent Time (MET*min) using a self-reference questionnaire. The impact of schoolyard size and equipment on MET*min was evaluated by Kruskal–Wallis analysis of variance (ANOVA). The students’ PA (MET*min) during recess was higher at schools with a large schoolyard (197.55±133.15 MET*min), compared with medium size (152.65±109.23 MET*min) and small ones (117.69±104.22 MET*min), (χ2=50.629, p<0.001). Moreover, students were more physically active during recess in adequately equipped schools (187.11±124.21 MET*min), compared with partially (158.84±128.61 MET*min) or inadequately equipped ones (114.19±89.13 MET*min). This indicates a strong positive relationship between PA and equipment (χ2=21.277, p<0.001). An encouraging school environment can motivate pre-adolescent children to be more physically active and therefore healthier. These data reveal that spacious schoolyards rich in outdoor facilities can lead to more physically active behaviour among students during recess.
AsicBoost - A Speedup for Bitcoin Mining

AsicBoost is a method to speed up Bitcoin mining by a factor of approximately 20%. The performance gain is achieved through a high-level optimization of the Bitcoin mining algorithm which allows for drastic reduction in gate count on the mining chip. AsicBoost is applicable to all types of mining hardware and chip designs. This paper presents the idea behind the method and describes the information flow in implementations of AsicBoost.
Temporal Dynamics in Neuromorphic Systems

The hallmark of cognitive behavior is the ability of an agent to select an economically advantageous action based on immediate external stimuli as well as on their longer-term context. Neuromorphic cognition refers to the cognitive abilities of systems or agents implemented in neuromorphic electronic VLSI technology whose processing architecture is similar to the distributed, asynchronous one of biological brains. Neuromorphic agents are typically real-time behaving systems composed of multiple asynchronous event-based VLSI chips that integrate networks of silicon neurons and dynamic synapses together and that are interfaced to event-based neuromorphic sensors and robotic actuators. In order to express cognitive performance, these agents require a hardware infrastructure that supports local learning and decision making, for distributed communication and for the elaboration of state-dependent processing. We describe examples of such mechanisms and present a method for efficiently implementing neuromorphic cognition in these agents.
Mechanical and Architectural Bone Adaptation in Early Stage Experimental Osteoarthritis

The purpose of this study was to quantify mechanical and architectural changes to knee joint periarticular subchondral cancellous bone in early stage experimental osteoarthritis (OA). Unilateral anterior cruciate ligament transection (ACLX) was performed on 10 dogs that were assigned randomly to two groups: 3 weeks or 12 weeks post‐ACLX. Cylindrical bone cores excised from the medial condyle of the distal femur after death were scanned using high‐resolution microcomputed tomography (μCT) and subsequently failed under unconstrained uniaxial compression. The apparent‐level elastic modulus was less in the ACLX femur compared with the contralateral control, and the decrease was significant (−45%; p < 0.05) by 12‐weeks post‐ACLX. A finite element (FE) analysis based on μCT data simulated the uniaxial compression tests on a specimen‐by‐specimen basis to determine tissue modulus. No change in tissue modulus was detected, and a single tissue modulus of 5100 MPa (95% CI, ±600 MPa) explained the apparent‐level modulus changes observed in the disease‐related bone adaptation. The three‐dimensional (3D) connectivity was evaluated from the original μCT data to quantify architectural alterations in contrast to tissue alterations. Significantly increased connectivity (through plate perforations) occurred as early as 3 weeks post‐ACLX and was as high as 127% by 12 weeks post‐ACLX in the distal femur. These measured changes indicated that architectural adaptation predominated over tissue modulus changes affecting apparent‐level elastic modulus in the early stage of experimental OA and suggests that to maintain normal cancellous bone after a traumatic injury, early intervention should focus on preventing the substantial architectural alterations.
State Capacity and Long-Run Economic Performance

We present new evidence about the long-run relationship between state capacity -- the fiscal and administrative power of states -- and economic performance. Our database is novel and spans 11 European countries and 4 centuries from the Old Regime to World War I. We argue that national governments undertook two political transformations over this period: fiscal centralization and limited government. We find a significant direct relationship between fiscal centralization and economic growth. Furthermore, we find that an increase in the state's capacity to extract greater tax revenues was one mechanism through which both political transformations improved economic performance. Our analysis shows systematic evidence that state capacity is an important determinant of long-run economic growth.
Effective Protein Separation by Coupling Hydrophobic Interaction and Reverse Phase Chromatography for Top-down Proteomics

One of the challenges in proteomics is the proteome’s complexity, which necessitates the fractionation of proteins prior to the mass spectrometry (MS) analysis. Despite recent advances in top-down proteomics, separation of intact proteins remains challenging. Hydrophobic interaction chromatography (HIC) appears to be a promising method that provides high-resolution separation of intact proteins, but unfortunately the salts conventionally used for HIC are incompatible with MS. In this study, we have identified ammonium tartrate as a MS-compatible salt for HIC with comparable separation performance as the conventionally used ammonium sulfate. Furthermore, we found that the selectivity obtained with ammonium tartrate in the HIC mobile phases is orthogonal to that of reverse phase chromatography (RPC). By coupling HIC and RPC as a novel two-dimensional chromatographic method, we have achieved effective high-resolution intact protein separation as demonstrated with standard protein mixtures and a complex cell lysate. Subsequently, the separated intact proteins were identified by high-resolution top-down MS. For the first time, these results have shown the high potential of HIC as a high-resolution protein separation method for top-down proteomics.
Human Microbiota of the Argentine Population- A Pilot Study

The human microbiota is the collection of microorganisms living in or on the human body. An imbalance or dysbiosis in these microbial communities can be associated with a wide variety of human diseases (Petersen and Round, 2014; Pham and Lawley, 2014; Zaura et al., 2014). Moreover, when the microbiota of the same body sites is compared between different healthy individuals, specific microbial community features are apparent (Li et al., 2012; Yatsunenko et al., 2012; Oh et al., 2014; Relman, 2015). In addition, specific selective pressures are found at distinct body sites leading to different patterns in microbial community structure and composition (Costello et al., 2009; Consortium, 2012b; Zhou et al., 2013). Because of these natural variations, a comprehensive characterization of the healthy microbiota is critical for predicting alterations related to diseases. This characterization should be based on a broad healthy population over time, geography, and culture (Yatsunenko et al., 2012; Shetty et al., 2013; Leung et al., 2015; Ross et al., 2015). The study of healthy individuals representing different ages, cultural traditions, and ethnic origins will enable to understand how the associated microbiota varies between populations and respond to different lifestyles. It is important to address these natural variations in order to later detect variations related to disease.
High-Frequency Hippocampal Oscillations Activated by Optogenetic Stimulation of Transplanted Human ESC-Derived Neurons

After transplantation, individual stem cell-derived neurons can functionally integrate into the host CNS; however, evidence that neurons derived from transplanted human embryonic stem cells (hESCs) can drive endogenous neuronal network activity in CNS tissue is still lacking. Here, using multielectrode array recordings, we report activation of high-frequency oscillations in the β and γ ranges (10–100 Hz) in the host hippocampal network via targeted optogenetic stimulation of transplanted hESC-derived neurons.
First report of cystic fibrosis mutations in Libyan cystic fibrosis patients

Background: There are few data on the molecular basis of Cystic Fibrosis (CF) in North Africa, probably due to under-diagnosis. Aim: This is the first study of cystic fibrosis transmembrane conductance regulator (CFTR) mutations in the Libyan population. Subjects and methods: This study analysed the complete coding region and flanking intronic sequences of the CFTR gene in 10 unrelated Libyan CF patients. Results: This study identified four mutations (F508del, c.1670delC, N1303K and E1104X), with a high frequency of the latter. Conclusion: Identification of CF mutations facilitates molecular investigation of cystic fibrosis in the Libyan population and helps to provide effective genetic counselling among CF families.
Leveraging disturbance observer based torque control for improved impedance rendering with series elastic actuators

The fidelity with which series elastic actuators (SEAs) render desired impedances is important. Numerous approaches to SEA impedance control have been developed under the premise that high-precision actuator torque control is a prerequisite. Indeed, the design of an inner torque compensator has a significant impact on actuator impedance rendering. The disturbance observer (DOB) based torque control implemented in NASA's Valkyrie robot is considered here and a mathematical model of this torque control, cascaded with an outer impedance compensator, is constructed. While previous work has examined the impact a disturbance observer has on torque control performance, little has been done regarding DOBs and impedance rendering accuracy. Both simulation and a series of experiments are used to demonstrate the significant improvements possible in an SEA's ability to render desired dynamic behaviors when utilizing a DOB. Actuator transparency at low impedances is improved, closed loop hysteresis is reduced, and the actuator's dynamic response to both commands and interaction torques more faithfully matches that of the desired model. All of this is achieved by leveraging DOB based control rather than increasing compensator gains, thus making improved SEA impedance control easier to achieve in practice.
RNA Sequencing Reveals Upregulation of RUNX1-RUNX1T1 Gene Signatures in Clear Cell Renal Cell Carcinoma

In the past few years, therapies targeted at the von Hippel-Lindau (VHL) and hypoxia-inducible factor (HIF) pathways, such as sunitinib and sorafenib, have been developed to treat clear cell renal cell carcinoma (ccRCC). However, the majority of patients will eventually show resistance to antiangiogenesis therapies. The purpose of our study was to identify novel pathways that could be potentially used as targets for new therapies. Whole transcriptome sequencing (RNA-Seq) was conducted on eight matched tumor and adjacent normal tissue samples. A novel RUNX1-RUNX1T1 pathway was identified which was upregulated in ccRCC through gene set enrichment analysis (GSEA). We also confirmed the findings based on previously published gene expression microarray data. Our data shows that upregulated of the RUNX1-RUNX1T1 gene set maybe an important factor contributing to the etiology of ccRCC.
The role of molecular genetic analysis within the diagnostic haemato‐oncology laboratory

The identification of the molecular genetic basis to many haematological malignancies along with the increased use of molecularly targeted therapy has heralded an increasing role for molecular genetic–based techniques. Demonstration of acquired changes such as the JAK2 V617F mutation within myeloproliferative neoplasms has quickly moved from a research setting to the diagnostic laboratory. Disease‐specific genetic markers, such as the BCR–ABL1 fusion gene in chronic myeloid leukaemia, enable sensitive molecular genetic methods to be applied for the detection and quantification of low‐level residual disease, allowing early identification of relapse. Consequently, molecular genetics now plays a crucial role in diagnosis, the identification of prognostic markers and monitoring of haematological malignancies. The development of high‐throughput whole‐genome approaches offers the potential to rapidly screen newly diagnosed patients for all disease‐associated molecular genetic changes.
Neurobehavioral Correlates of Familism and Adolescent Risk Taking

Risk taking underlies many health problems that contribute to the public health burden during the adolescent period. Recent advances in developmental neuroscience have identified key neurobiological underpinnings of adolescent risk taking, but there is little understanding of how these neural processes interact with social processes in order to promote or prevent risk taking. In this dissertation, I use a multi-method, longitudinal program of research, including daily diaries, experimental tasks, and neuroimaging, to examine the mechanisms by which a culturally meaningful type of family relationship - familism - buffers Mexican youth from drug use and risk taking. Familism is a fundamental aspect of family life, which implies children's role in the support and assistance of their family. Results of Study 1 suggest that family obligation values are protective, relating to dampened substance use, largely due to the links with decreased association with deviant peers and increased disclosure to parents. In contrast, family assistance behaviors are a source of risk within high parent-child conflict homes, relating to higher levels of substance use. In study 2, I examine whether familism is protective by influencing neural regions involved in reward processing and cognitive control, neural processes implicated in adolescent risk taking. Results indicate that family obligation values are associated with reduced ventral striatum (VS) activation when receiving monetary rewards and increased prefrontal cortex (PFC) activation when inhibiting behavioral responses. Reduced VS activation correlates with less real-life risk taking behavior and enhanced PFC activation correlates with better decision-making skills. Thus, family obligation may decrease reward sensitivity and enhance cognitive control, thereby reducing adolescent risk taking. In Study 3, I examine whether the meaningful and rewarding nature of family assistance may be an asset for adolescents. Results show that enhanced VS activation when contributing to the family predicts decreases in adolescents' risk taking behavior over the next year. Thus, family relationships that are personally meaningful can provide adolescents with a sense of reward, and this reward may lead to positive, healthy outcomes. Results of this dissertation indicate that traditional family values and practices play a critical role in shaping Mexican adolescents' risk for substance use and risk taking.
Shape recovery of collision zones for obstacle avoidance

Presents an approach to detect moving obstacles in order to define a collision zone around them. The approach uses a camera system to provide image sequences from which the dynamic aspect of the scene can be recovered. In fact, if the camera samples the observation space at some time intervals, a two-dimensional image sequence may be created, due to the relative motion. The analysis of these sequences can be useful to recovery information about the relative notion between a mobile vehicle and the navigation space. The appearance of an obstacle can be recovered using optical flow analysis. The authors compute optical flow maps to solve the problem of detecting discontinuities in the flow field in order to segment the image in different moving objects. An estimation of depth values for the segmented points is accomplished by means of optical flow and focus of expansion. Experimental results on image sequences of a real scene are presented. <<ETX>>
An integrative approach for codon repeats evolutionary analyses

The relationship between genome characteristics and several human diseases has been a central research goal in genomics. Many studies have shown that specific gene patterns, such as amino acid repetitions, are associated with human diseases. However, several open questions still remain, such as, how these tandem repeats appeared in the evolutionary path or how they have evolved in orthologous genes of related organisms. In this paper, we present a computational solution that facilitates comparative studies of orthologous genes from various organisms. The application uses various web services to gather gene sequence information, local algorithms for tandem repeats identification and similarity measures for gene clustering.
A fuzzy impulse noise detection and reduction method

Removing or reducing impulse noise is a very active research area in image processing. In this paper we describe a new algorithm that is especially developed for reducing all kinds of impulse noise: fuzzy impulse noise detection and reduction method (FIDRM). It can also be applied to images having a mixture of impulse noise and other types of noise. The result is an image quasi without (or with very little) impulse noise so that other filters can be used afterwards. This nonlinear filtering technique contains two separated steps: an impulse noise detection step and a reduction step that preserves edge sharpness. Based on the concept of fuzzy gradient values, our detection method constructs a fuzzy set impulse noise. This fuzzy set is represented by a membership function that will be used by the filtering method, which is a fuzzy averaging of neighboring pixels. Experimental results show that FIDRM provides a significant improvement on other existing filters. FIDRM is not only very fast, but also very effective for reducing little as well as very high impulse noise.
F-TCP: light-weight TCP for file transfer in high bandwidth-delay product networks

We describe F-TCP, a new TCP for file transfer in high bandwidth-delay product networks. TCP is not suitable for file transfer application in high bandwidth-delay product networks. There needs a protocol that should not take away too much bandwidth from standard TCP flows while utilizing the full bandwidth of high-speed networks. This paper presents another important constraint, namely small buffer problems. Small socket buffers at the end-hosts limit the effective window of the transfer, and the maximum throughput. Existing schemes have severe small buffer problems because high bandwidth-delay product networks need a large socket buffer. The proposed mechanism, called F-TCP, is based on direct kernel-to-kernel file transfer architecture. The key idea is that no need of in-order delivery in file transfer process. F-TCP needs only small buffer by allowing out-of-order file transfer with asynchronous loss recovery. Experimental results in several high bandwidth-delay product paths show that F-TCP provides consistently a significant throughput increase (18% to 80%) compared to previous TCP approach. We expect that F-TCP is mostly useful for application such as FTP and P2P in high-speed wide-area networks.