Miracle-dz/UniFAR-FTUs huggingface dataset:
A robust technique for motion correction in fMRI

A major source of error in the analysis of functional Magnetic Resonance images is the presence of spurious activation arising on account of patient head movement at the time of image acquisition. This makes it imperative for the images to be subjected to motion correction through registration. A number of solutions to the problem currently do exist though there is always the need for faster approaches which produce better estimates of the motion parameters. In this paper, we propose a signal model for fMRI images with possible relative movement between scans and show how the least trimmed squares estimator, which is well-known in the statistical literature for its robustness, can be used. Since data obtained from actual fMRI studies do not provide the “correct” values of the motion parameters with which the performances of various estimators may be compared, computer simulations are set up where these parameters may be controlled. Our simulations indicate that the proposed method produces smaller error in the estimated motion parameters, when compared to the existing estimators, including another robust estimator.
Genome-wide Pathway Analysis Using Gene Expression Data of Colonic Mucosa in Patients with Inflammatory Bowel Disease

Background:Ulcerative colitis (UC) and Crohn's disease (CD) share some pathogenetic features. To provide new steps on the role of altered gene expression, and the involvement of gene networks, in the pathogenesis of these diseases, we performed a genome-wide analysis in 15 patients with CD and 14 patients with UC by comparing the RNA from inflamed and noninflamed colonic mucosa. Methods:Two hundred ninety-eight differentially expressed genes in CD and 520 genes in UC were identified. By bioinformatic analyses, 34 pathways for CD, 6 of them enriched in noninflamed and 28 in inflamed tissues, and 19 pathways for UC, 17 in noninflamed and 2 in inflamed tissues, were also highlighted. Results:In CD, the pathways included genes associated with cytokines and cytokine receptors connection, response to external stimuli, activation of cell proliferation or differentiation, cell migration, apoptosis, and immune regulation. In UC, the pathways were associated with genes related to metabolic and catabolic processes, biosynthesis and interconversion processes, leukocyte migration, regulation of cell proliferation, and epithelial-to-mesenchymal transition. Conclusions:In UC, the pattern of inflammation of colonic mucosa is due to a complex interaction network between host, gut microbiome, and diet, suggesting that bacterial products or endogenous synthetic/catabolic molecules contribute to impairment of the immune response, to breakdown of epithelial barrier, and to enhance the inflammatory process. In patients with CD, genes encoding a large variety of proteins, growth factors, cytokines, chemokines, and adhesion molecules may lead to uncontrolled inflammation with ensuing destruction of epithelial cells, inappropriate stimulation of antimicrobial and T cells differentiation, and inflammasome events.
Quantification of cytomegalovirus DNA in BAL fluid: a longitudinal study in lung transplant recipients.

STUDY OBJECTIVES Cytomegalovirus (CMV) infection is common in patients receiving solid organ transplants, and it is associated with increased morbidity as well as risk for development of chronic rejection. A rapid and sensitive diagnostic method would improve the therapeutic management of CMV infection, including the monitoring of treatment effects. We investigated whether longitudinal determinations of CMV DNA quantities in BAL fluid could be useful for this purpose. DESIGN CMV DNA levels in 340 BAL samples from 35 consecutive lung transplant recipients were studied during a median of 18 months. Seventeen (49%) of the patients developed CMV disease with pneumonitis. Twenty-seven CMV disease episodes were diagnosed. RESULTS Patients with CMV disease had a significantly higher mean level of CMV copies per milliliter BAL fluid (1,120 +/- 4,379) compared with those without (180 +/- 1,177, p < 0.01). Viral load as well as acute rejection requiring treatment (>/= A2) were independent risk factors associated with CMV disease. Differences between the groups concerning HLA-DR matching, basic immunosuppressive therapy, and CMV serologic status D/R -/+ vs D/R +/+ were not significant. A diagnostic definition of normality based on the mean level of all episodes without CMV disease +2 SD would discriminate only 9 of the 27 CMV episodes. CONCLUSIONS Although the viral load is increased during episodes of clinical CMV disease in lung transplant recipients, the quantitative PCR assessment of CMV DNA in BAL fluid is not discriminative enough to be useful as a diagnostic tool for CMV disease.
Are All Managers Created Equal?

Some managers are better than others. Using the cognitive hierarchy framework of Camerer, Ho, and Chong (2004), the authors develop a structural econometric model that estimates the level of strategic thinking. In the model, firms with a high level of strategic thinking are more likely to correctly conjecture the expected actions of their competitors. The authors apply this model to decisions by managers at 2233 Internet service providers of whether to offer their customers access through 56K modems in 1997. The model is validated by showing that firms with a higher estimated probability of strategic thinking were more likely to have survived through April 2007. The estimation results show considerable heterogeneity in the degree to which firms behave strategically and suggest that strategic ability affects marketing outcomes; specifically, a simulated increase in strategic ability means that fewer firms offer the technology to their customers.
Flying KIWI: Design of Approximate Query Processing Engine for Interactive Data Analytics at Scale

This paper introduces the design of hybrid SQL-on-Hadoop system, which supports dual-mode (interactive and deep) analytics. We present an architecture of approximate query processing engine using horizontal and vertical sampling of the original database for interactive big data analytics. A key novelty of our approach is that we can support interactive analytics as well as deep analytics at scale in the unified manner.
Circuit Lower Bounds, Help Functions, and the Remote Point Problem

We investigate the power of Algebraic Branching Programs (ABPs) augmented with help polynomials, and constant-depth Boolean circuits augmented with help functions. We relate the problem of proving explicit lower bounds in both these models to the Remote Point Problem (introduced by Alon, Panigrahy, and Yekhanin (RANDOM '09)). More precisely, proving lower bounds for ABPs with help polynomials is related to the Remote Point Problem w.r. t. the rank metric, and for constant-depth circuits with help functions it is related to the Remote Point Problem w.r. t. the Hamming metric. For algebraic branching programs with help polynomials with some degree restrictions we show exponential size lower bounds for explicit polynomials.
Implicit B-Spline Surface Reconstruction

This paper presents a fast and flexible curve, and surface reconstruction technique based on implicit B-spline. This representation does not require any parameterization and it is locally supported. This fact has been exploited in this paper to propose a reconstruction technique through solving a sparse system of equations. This method is further accelerated to reduce the dimension to the active control lattice. Moreover, the surface smoothness and user interaction are allowed for controlling the surface. Finally, a novel weighting technique has been introduced in order to blend small patches and smooth them in the overlapping regions. The whole framework is very fast and efficient and can handle large cloud of points with very low computational cost. The experimental results show the flexibility and accuracy of the proposed algorithm to describe objects with complex topologies. Comparisons with other fitting methods highlight the superiority of the proposed approach in the presence of noise and missing data.
Cardiac melanocytes influence atrial reactive oxygen species involved with electrical and structural remodeling in mice

Cardiac melanocyte‐like cells (CMLCs) contribute to atrial arrhythmias when missing the melanin synthesis enzyme dopachrome tautomerase (Dct). While scavenging reactive oxygen species (ROS) in Dct‐null mice partially suppressed atrial arrhythmias, it remains unclear if CMLCs influence atrial ROS and structure or if the electrical response of CMLCs to ROS differs from that of atrial myocytes. This study is designed to determine if CMLCs contribute to overall atrial oxidative stress or structural remodeling, and if ROS affects the electrophysiology of CMLCs differently than atrial myocytes. Immunohistochemical analysis showed higher expression of the oxidative marker 8‐hydroxy‐2′‐deoxyguanosine in Dct‐null atria versus Dct‐heterozygous (Dct‐het) atria. Exposing isolated CMLCs from Dct‐het and Dct‐null mice to hydrogen peroxide increased superoxide anion more in Dct‐null CMLCs. Trichrome staining showed increased fibrosis in Dct‐null atria, and treating Dct‐null mice with the ROS scavenger Tempol reduced atrial fibrosis. Action potential recordings from atrial myocytes and isolated Dct‐het and Dct‐null CMLCs in response to hydrogen peroxide showed that the EC50 for action potential duration (APD) prolongation of Dct‐null CMLCs was 8.2 ± 1.7 μmol/L versus 16.8 ± 2.0 μmol/L for Dct‐het CMLCs, 19.9 ± 2.1 μmol/L for Dct‐null atrial myocytes, and 20.5 ± 1.9 μmol/L for Dct‐het atrial myocytes. However, APD90 was longer in CMLCs versus atrial myocytes in response to hydrogen peroxide. Hydrogen peroxide also induced more afterdepolarizations in CMLCs compared to atrial myocytes. These studies suggest that Dct within CMLCs contributes to atrial ROS balance and remodeling. ROS prolongs APD to a greater extent and induces afterdepolarizations more frequently in CMLCs than in atrial myocytes.
Obstacle detection by means of stereo feature matching

Automated obstacle detection is required in a number of applications. It is a challenging task because there is no prior knowledge about the appearance of ground, or the locations and appearance of obstacles in the scene. In this paper, an obstacle detection system based on matching the color edge features in stereo images is presented. The paper also presents an enhanced adaptive local-cross based stereo matching method used in the system. The system has been extensively evaluated. The result of evaluation allows the usage of system for automatic detection of moderately sized obstacles within a distance range of 2-15 meters with sufficient accuracy.
Inter-joint dynamic interaction 5 during constrained human quiet standing 6 examined by induced acceleration analysis 7 8

225 words] 33 34 Recent studies have demonstrated that human quiet standing is a multi-joint movement, 35 whereby the central nervous system (CNS) is required to deal with dynamic interactions 36 among the joints to achieve optimal motor performance. The purpose of this study was to 37 investigate how the CNS deals with such inter-joint interaction during quiet standing by 38 examining the relationship between the kinetics (torque) and kinematics (angular 39 acceleration) within the multi-degree-of-freedom system. We modeled quiet standing as a 40 double-link inverted pendulum involving both ankle and hip joints and conducted an 41 “induced acceleration analysis. ” We found that the net ankle and hip torques induced 42 angular accelerations of comparable magnitudes to the ankle (3.8 ± 1.4 deg/s2 and 3.3 ± 1.2 43 deg/s2) and hip (9.1 ± 3.2 deg/s2 and 10.5 ± 3.5 deg/s2) joints, respectively. Angular 44 accelerations induced by the net ankle and hip torques were modulated in a temporally 45 anti-phase pattern to one another in each of the two joints. These quantitative and temporal 46 relationships allowed the angular accelerations induced by the two net torques to 47 counter-compensate one another, thereby substantially (~70%) reducing the resultant 48 angular accelerations of the individual joints. These results suggest that, by taking 49 advantage of the inter-joint interaction, the CNS prevents the net torques from producing 50 large amplitudes of the resultant angular accelerations when combined with the kinematic 51 effects of all other torques in the chain. 52
Comparison of the Hα Equivalent Width of H II Regions in a Flocculent and a Grand-Design Galaxy: Possible Evidence for Initial Mass Function Variations

We present here a study of the Hα equivalent widths of the flocculent galaxy NGC 4395 and the grand-design galaxy NGC 5457. A difference between the mean values of the Hα equivalent widths for the two galaxies has been found. Several hypotheses are presented in order to explain this difference: differences in age, metallicity, star formation rate, photon leakage, and initial mass function. Various tests and Monte Carlo models are used to find out the most probable cause of this difference. The results show that the possible cause for the difference could be a variation in the initial mass function. This difference is such that it seems to favor a fraction of more massive stars in the grand-design galaxy when compared with the flocculent galaxy. This could be due to a change of the environmental conditions due to a density wave.
Children’s relationships with the opposite sex inside peer culture: the case of rural children in Turkey

ABSTRACT This study investigated the relationships that children living in rural regions in Turkey have with the opposite sex and the roles of boys and girls with respect to peer culture. Qualitative data collection methods such as observation, interview, and document analysis were used and the data were analysed through qualitative data analysis methods. During the data collection process, 6-year-old pre-school children were observed for six weeks in the researcher's own classroom and the data were recorded through detailed field notes. The cultural society in which the children live, their activities in the classroom and friendship relations established outside school were found to be important factors that influence the children’s relationships with the opposite sex. Relationships with the opposite sex were observed to differ according to the type of activity in the classroom. Furthermore, the function of the material used during games was found to vary according to relationships with the opposite sex.
Learning Concept Graphs from Online Educational Data

This paper addresses an open challenge in educational data mining, i.e., the problem of automatically mapping online courses from different providers (universities, MOOCs, etc.) onto a universal space of concepts, and predicting latent prerequisite dependencies (directed links) among both concepts and courses. We propose a novel approach for inference within and across course-level and concept-level directed graphs. In the training phase, our system projects partially observed course-level prerequisite links onto directed concept-level links; in the testing phase, the induced concept-level links are used to infer the unknown course-level prerequisite links. Whereas courses may be specific to one institution, concepts are shared across different providers. The bi-directional mappings enable our system to perform interlingua-style transfer learning, e.g. treating the concept graph as the interlingua and transferring the prerequisite relations across universities via the interlingua. Experiments on our newly collected datasets of courses from MIT, Caltech, Princeton and CMU show promising results.
Applauding with Closed Hands: Neural Signature of Action-Sentence Compatibility Effects

Background Behavioral studies have provided evidence for an action–sentence compatibility effect (ACE) that suggests a coupling of motor mechanisms and action-sentence comprehension. When both processes are concurrent, the action sentence primes the actual movement, and simultaneously, the action affects comprehension. The aim of the present study was to investigate brain markers of bidirectional impact of language comprehension and motor processes. Methodology/Principal Findings Participants listened to sentences describing an action that involved an open hand, a closed hand, or no manual action. Each participant was asked to press a button to indicate his/her understanding of the sentence. Each participant was assigned a hand-shape, either closed or open, which had to be used to activate the button. There were two groups (depending on the assigned hand-shape) and three categories (compatible, incompatible and neutral) defined according to the compatibility between the response and the sentence. ACEs were found in both groups. Brain markers of semantic processing exhibited an N400-like component around the Cz electrode position. This component distinguishes between compatible and incompatible, with a greater negative deflection for incompatible. Motor response elicited a motor potential (MP) and a re-afferent potential (RAP), which are both enhanced in the compatible condition. Conclusions/Significance The present findings provide the first ACE cortical measurements of semantic processing and the motor response. N400-like effects suggest that incompatibility with motor processes interferes in sentence comprehension in a semantic fashion. Modulation of motor potentials (MP and RAP) revealed a multimodal semantic facilitation of the motor response. Both results provide neural evidence of an action-sentence bidirectional relationship. Our results suggest that ACE is not an epiphenomenal post-sentence comprehension process. In contrast, motor-language integration occurring during the verb onset supports a genuine and ongoing brain motor-language interaction.
Fuel Cells for Data Centers: Power Generation Inches From the Server

Typically, improving data center availability requires designing in more infrastructure; the antithesis of reducing costs. Is there a way to cut infrastructure, cost and emissions while improving energy efficiency and server availability? We consider and evaluate the integration of fuel cells with IT hardware with various architectural designs, essentially collapsing the entire energy supply chain, from power plant to power supply unit, into the confines of a single server cabinet. In this paper, we propose a distributed power architecture for fuel cell powered data centers to achieve high reliability and efficiency. We describe the distributed fuel cell power system design and the system components. We experimentally validate the design and demonstrate the use of a 10kW Proton Exchange Membrane Fuel Cell (PEMFC) stack and system as the distributed power source to power a server rack, eliminating the power distribution system in the data center and the grid outside of the data center. The PEMFC is found to respond quickly and reproducibly to both AC and DC load changes directly from the rack. By utilizing the fuel cell DC output, 53% energy efficiency in a single server rack can be achieved. We also carry out cost analysis to quantify the cost savings that could be achieved with fuel cells placed in each rack. We evaluate and characterize the performance and the dynamic load following capability of the fuel cell. In addition, direct DC power from the fuel cell system eliminates the capital cost and operating conversion losses from systems that use energy storage and AC/DC conversion equipment. Reducing components in the energy supply chain not only cuts cost but reduces points of maintenance and failure improving availability.
OC3MON: Flexible, Affordable, High Performance Staistics Collection

The Internet is rapidly growing in number of users, traffic levels, and topological complexity. At the same time it is increasingly driven by economic competition. These developments render it more difficult, and yet more critical, to characterize network usage and workload trends, and point to the need for a high performance monitoring system that can provide workload data to Internet users and administrators. To ensure the practicality of using the monitor at variety of locations, implementation on low cost, commodity hardware is a necessity.
WebMining : An unsupervised parallel corpora web retrieval system

Inductive methods in multilingual natural language processing require using parallel corpora, which is not often available. Besides, Internet is an important source of parallel texts and a increasingly number of multilingual websites can be found. In this paper we present a system able to automatically collect large multilingual corpora from the web. The input of the system is a list of multilingual websites that has been manually created. For each website, the system downloads all their webpages following their links, and each new webpage is compared to all previously downloaded ones looking for possible parallel webpages. To determine if two pages are parallel, the system uses four filters based on: size, language, HTML structure and plain text. The last one extracts sentences of both pages and tries to align them using a word-to-word statistical translation model, which is trained on the fly. The final output of the system is an aligned bilingual sentence corpus. Our system has been compared to three other similar systems. Evaluation results show the high precision obtained with our system.
ESD-Protected Wideband CMOS LNAs Using Modified Resistive Feedback Techniques With Chip-on-Board Packaging

A novel modified resistive feedback structure for designing wideband low-noise amplifiers (LNAs) is proposed and demonstrated in this paper. Techniques including feedback through a source follower, an R-C feedback network, a gate peaking inductor inside the feedback loop, and neutralization capacitors are used. Bond-wire inductors and electrostatic devices (ESDs) are co-designed to improve the chip performance. Two LNAs, LNA1 and LNA2, were fabricated using a TSMC digital 90-nm CMOS technology. Both chips were tested on board using chip-on-board packages with ESD diodes added at the inputs and outputs. LNA1 achieves a 3-dB bandwidth of 9 GHz with 10 dB of power gain and a minimum noise figure (NF) of 4.2 dB. LNA2 achieves a 3-dB bandwidth of 3.2 GHz with 15.5 dB of power gain and a minimum NF of 1.76 dB. The two LNAs have third-order intermodulation intercept points of 8 and 9 dBm. Their power consumptions are 20 and 25 mW with a 1.2-V supply, respectively.
Genomic landscape of endometrial stromal sarcoma of uterus

Although recurrent gene fusions such as JAZF1-JJAZ1 are considered driver events for endometrial stromal sarcoma (ESS) development, other genomic alterations remain largely unknown. In this study, we performed whole-exome sequencing, transcriptome sequencing and copy number profiling for five ESSs (three low-grade ESS (LG-ESS) and two undifferentiated uterine sarcomas (UUSs)). All three LG-ESSs exhibited either one of JAZF1-SUZ12, JAZF1-PHF1 and MEAF6-PHF1 fusions, whereas the two UUSs did not. All ESSs except one LG-ESS exhibited copy number alterations (CNAs), many of which encompassed cancer-related genes. In UUSs, five CNAs encompassing cancer-related genes (EZR, CDH1, RB1, TP53 and PRKAR1A) accompanied their expressional changes, suggesting that they might stimulate UUS development. We found 81 non-silent mutations (35 from LG-ESSs and 46 from UUSs) that included 15 putative cancer genes catalogued in cancer-related databases, including PPARG and IRF4 mutations. However, they were non-recurrent and did not include any well-known mutations, indicating that point mutations may not be a major driver for ESS development. Our data show that gene fusions and CNAs are the principal drivers for LG-ESS and USS, respectively, but both may require additional genomic alterations including point mutations. These differences may explain the different biologic behaviors between LG-ESS and UUS. Our findings suggest that ESS development requires point mutations and CNAs as well as the gene fusions.