Miracle-dz/UniFAR-FTUs huggingface dataset:
Calibration-free eye tracking by reconstruction of the pupil ellipse in 3D space

Most video-based eye trackers require a calibration procedure before measurement onset. In this work a stereo approach is presented that yields the position and orientation of the pupil in 3D space. This is achieved by analyzing the pupil images of two calibrated cameras and by a subsequent closed-form stereo reconstruction of the original pupil surface. Under the assumption that the gaze-vector is parallel to the pupil normal vector, the line of sight can be calculated without the need for the usual calibration that requires the user to fixate targets with known spatial locations.
The Sarcolemmal Calcium Pump Inhibits the Calcineurin/Nuclear Factor of Activated T-cell Pathway via Interaction with the Calcineurin A Catalytic Subunit*

The calcineurin/nuclear factor of activated T-cell (NFAT) pathway represents a crucial transducer of cellular function. There is increasing evidence placing the sarcolemmal calcium pump, or plasma membrane calcium/calmodulin ATPase pump (PMCA), as a potential modulator of signal transduction pathways. We demonstrate a novel interaction between PMCA and the calcium/calmodulin-dependent phosphatase, calcineurin, in mammalian cells. The interaction domains were located to the catalytic domain of PMCA4b and the catalytic domain of the calcineurin A subunit. Endogenous calcineurin activity, assessed by measuring the transcriptional activity of its best characterized substrate, NFAT, was significantly inhibited by 60% in the presence of ectopic PMCA4b. This inhibition was notably reversed by the co-expression of the PMCA4b interaction domain, demonstrating the functional significance of this interaction. PMCA4b was, however, unable to confer its inhibitory effect in the presence of a calcium/calmodulin-independent constitutively active mutant calcineurin A suggesting a calcium/calmodulin-dependent mechanism. The modulatory function of PMCA4b is further supported by the observation that endogenous calcineurin moves from the cytoplasm to the plasma membrane when PMCA4b is overexpressed. We suggest recruitment by PMCA4b of calcineurin to a low calcium environment as a possible explanation for these findings. In summary, our results offer strong evidence for a novel functional interaction between PMCA and calcineurin, suggesting a role for PMCA as a negative modulator of calcineurin-mediated signaling pathways in mammalian cells. This study reinforces the emerging role of PMCA as a molecular organizer and regulator of signaling transduction pathways.
Compilation à la Carte

In previous work, we proposed a new approach to the problem of implementing compilers in a modular manner, by combining earlier work on the development of modular interpreters using monad transformers with the à la carte approach to modular syntax. In this article, we refine and extend our existing framework in a number of directions. In particular, we show how generalised algebraic datatypes can be used to support a more modular approach to typing individual language features, we increase the expressive power of the framework by considering mutable state, variable binding, and the issue of noncommutative effects, and we show how the Zinc Abstract Machine can be adapted to provide a modular universal target machine for our modular compilers.
Efficient multicast support in large IP routers

We investigate techniques for the support of multicast traffic in IP routers that have a large number of switch fabric ports (from 128 to 1024) and internally operate on relatively small fixed-size data units (cells of 64 bytes each). In small packet switches, multicast traffic is typically handled by prepending a local multicast label (LML) to each cell. The LML consists of a bitmap with as many bits as switch ports. The bitmap identifies the set of ports to which copies of the cell must be transferred. The bitmap approach is no longer feasible in switches with 128 ports or more, where the LML length cannot be smaller than 16 bytes, an intolerable overhead when the internal cell payload is only 64 bytes. We devise several compression algorithms, both static and adaptive, to reduce the size of the LML's to be attached to multicast cells. The algorithms define compressed representations of the distribution sets of the multicast cells, trading the additional bandwidth needed to transfer redundant cell copies (i.e., copies directed to outputs that do not belong to the actual distribution sets) for the cell header overhead otherwise needed to deliver the cells only to the proper outputs. We use simulation experiments to compare the performance of the compression algorithms.
Bioengineering Strategies for Polymeric Scaffold for Tissue Engineering an Aortic Heart Valve: An Update

The occurrence of dysfunctional aortic valves is increasing every year, and current replacement heart valves, although having been shown to be clinically successful, are only short-term solutions and suffer from many agonizing long-term drawbacks. The tissue engineering of heart valves is recognized as one of the most promising answers for aortic valve disease therapy, but overcoming current shortcomings will require multidisciplinary efforts. The use of a polymeric scaffold to guide the growth of the tissue is the most common approach to generate a new tissue for an aortic heart valve. However, optimizing the design of the scaffold, in terms of biocompatibility, surface morphology for cell attachments and the correct rate of degradation is critical in creating a viable tissue-engineered aortic heart valve. This paper highlights the bioengineering strategies that need to be followed to construct a polymeric scaffold of sufficient mechanical integrity, with superior surface morphologies, that is capable of mimicking the valve dynamics in vivo. The current challenges and future directions of research for creating tissue-engineered aortic heart valves are also discussed.
Predictive Simulation of Reaching Moving Targets Using Nonlinear Model Predictive Control

This article investigates the application of optimal feedback control to trajectory planning in voluntary human arm movements. A nonlinear model predictive controller (NMPC) with a finite prediction horizon was used as the optimal feedback controller to predict the hand trajectory planning and execution of planar reaching tasks. The NMPC is completely predictive, and motion tracking or electromyography data are not required to obtain the limb trajectories. To present this concept, a two degree of freedom musculoskeletal planar arm model actuated by three pairs of antagonist muscles was used to simulate the human arm dynamics. This study is based on the assumption that the nervous system minimizes the muscular effort during goal-directed movements. The effects of prediction horizon length on the trajectory, velocity profile, and muscle activities of a reaching task are presented. The NMPC predictions of the hand trajectory to reach fixed and moving targets are in good agreement with the trajectories found by dynamic optimization and those from experiments. However, the hand velocity and muscle activations predicted by NMPC did not agree as well with experiments or with those found from dynamic optimization.
Human Hp1-1 and Hp2-2 phenotype-specific haptoglobin therapeutics are both effective in vitro and in guinea pigs to attenuate hemoglobin toxicity.

AIMS Infusion of purified haptoglobin (Hp) functions as an effective hemoglobin (Hb) scavenging therapeutic in animal models of hemolysis to prevent cardiovascular and renal injury. Epidemiologic studies demonstrate the phenotype heterogeneity of human Hp proteins and suggest differing vascular protective potential imparted by the dimeric Hp1-1 and the polymeric Hp2-2. RESULTS In vitro experiments and in vivo studies in guinea pigs were performed to evaluate phenotype-specific differences in Hp therapeutics. We found no differences between the two phenotypes in Hb binding and intravascular compartmentalization of Hb in vivo. Both Hp1-1 and Hp2-2 attenuate Hb-induced blood pressure response and renal iron deposition. These findings were consistent with equal prevention of Hb endothelial translocation. The modulation of oxidative Hb reactions by the two Hp phenotypes was not found to be different. Both phenotypes stabilize the ferryl (Fe(4+)) Hb transition state, provide heme retention within the complex, and prevent Hb-driven low-density lipoprotein (LDL) peroxidation. Hb-mediated peroxidation of LDL resulted in endothelial toxicity, which was equally blocked by the addition of Hp1-1 and Hp2-2. INNOVATION AND CONCLUSION The present data do not provide support for the concept that phenotype-specific Hp therapeutics offer differential efficacy in mitigating acute Hb toxicity.
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

Motivation: PSORTb has remained the most precise bacterial protein subcellular localization (SCL) predictor since it was first made available in 2003. However, the recall needs to be improved and no accurate SCL predictors yet make predictions for archaea, nor differentiate important localization subcategories, such as proteins targeted to a host cell or bacterial hyperstructures/organelles. Such improvements should preferably be encompassed in a freely available web-based predictor that can also be used as a standalone program. Results: We developed PSORTb version 3.0 with improved recall, higher proteome-scale prediction coverage, and new refined localization subcategories. It is the first SCL predictor specifically geared for all prokaryotes, including archaea and bacteria with atypical membrane/cell wall topologies. It features an improved standalone program, with a new batch results delivery system complementing its web interface. We evaluated the most accurate SCL predictors using 5-fold cross validation plus we performed an independent proteomics analysis, showing that PSORTb 3.0 is the most accurate but can benefit from being complemented by Proteome Analyst predictions. Availability: http://www.psort. org/psortb (download open source software or use the web interface). Contact: psort-mail@sfu.ca Supplementary Information: Supplementary data are availableat Bioinformatics online.
Importance of Hydrogen Bonding for Efficiency and Specificity of the Human Mitochondrial DNA Polymerase*

To assess the contribution to discrimination afforded by base pair hydrogen bonding during DNA replication by the human mitochondrial DNA polymerase, we examined nucleoside mimics lacking hydrogen bond forming capability but retaining the overall steric shape of the natural nucleotide. We employed oligonucleotide templates containing either a deoxyadenosine shape mimic (dQ) or a deoxythymidine shape mimic (dF). Additionally, the nucleoside triphosphate analogs difluorotoluene deoxynucleoside triphosphate, 9-methyl-1-H-imidazo[(4,5)-b]pyridine deoxyribose triphosphate, and 4-methylbenzimidazole deoxyribose triphosphate (dZTP; another dATP shape mimic) were assayed. We used pre-steady state methods to determine the kinetic parameters governing nucleotide incorporation, kpol and Kd. In general, the loss of hydrogen bonding potential led to 2–3 kcal/mol reduction in ground state binding free energy, whereas effects on the maximum rate of polymerization were quite variable, ranging from negligible (dATP:dF) to nearly 4 kcal/mol (dZTP:dT). Although we observed only a 46-fold reduction in discrimination when dF was present in the template, there was a complete elimination of discrimination when dQ was present in the template. Our data with dF indicate that hydrogen bonding contributes 2.2 kcal/mol toward the efficiency of incorporation, whereas data with dQ (which may overestimate the effect due to poor steric mimicry) suggest a contribution of up to 6.8 kcal/mol. Taken together, the data suggest that sterics are necessary but not sufficient to achieve optimal efficiency and fidelity for DNA polymerase. Base pair hydrogen bonding contributes at least a third of the energy underlying nucleoside incorporation efficiency and specificity.
Prevalence and distribution of Eimeria species in broiler chicken farms of different capacities

We conducted a survey in broiler farms from Romania to establish prevalence and distribution of Eimeria species using single PCR assay. We found Eimeria spp. in 21 (91%) out of 23 flocks, and in 11 (92%) out of 12 farms. Four species of Eimeria were identified: E. acervulina (21/23; 91%), E. tenella (14/23; 61%), E. maxima (5/23; 22%) and E. praecox (3/23; 13%). Infection with a single species (E. acervulina) was detected in 6 (26%) infected flocks originated from large farms. Mixed infections were found in 15 (65%) flocks and the most prevalent combination was E. acervulina + E. tenella (8/23; 35%). Four flocks (17%) harboured mixed infection with E. acervulina + E. tenella + E. maxima. E. acervulina was significantly more prevalent in flocks that received ionophores as anticoccidial feed additives.
Simulation of human respiration in fMRI with a mechanical model

Obtaining functional magnetic resonance images of the brain is a challenging measurement process having a low characteristic signal-to-noise ratio. Images contain various forms of noise, including those induced by physiologic processes. One of the prevalent disturbances is hypothesized to result from susceptibility fluctuations caused by abdominal volume changes during respiration. To test this hypothesis and characterize the contribution of respiration noise to both magnitude and phase images, a mechanical model of a respiring human was constructed. The model was tested by comparing data from the model with that of a resting human. Power spectrum analyses show that the model induces both phase and magnitude disturbances similar to those in the human. The disturbances are directly related to the frequency of the respiration, with the noise most prevalent in the phase images. Though magnitude image noise is hard to identify in the human, the manikin demonstrates the presence of this disturbance. The construction of the manikin rules out motion as the primary source of the observed fluctuations and variation of the electrical properties of the manikin also indicates that signal fluctuations are not primarily due to eddy currents. Therefore, the changes are most probably induced by bulk susceptibility changes correlating with respiration.
Modeling adsorption properties of structurally deformed metal–organic frameworks using structure–property map

Significance Modeling amorphous materials using the conventional molecular simulation method is exceedingly difficult because structural information of the material is absent. Here, we present a way to indirectly model structurally deformed metal–organic frameworks using a large number of simulation data for crystalline metal–organic frameworks. Our experimental/computational results demonstrate that computed adsorption properties of crystalline metal–organic frameworks can be transferred onto those of structurally deformed, amorphous metal–organic frameworks. This opens up a way to understand adsorption properties of amorphous materials. Structural deformation and collapse in metal-organic frameworks (MOFs) can lead to loss of long-range order, making it a challenge to model these amorphous materials using conventional computational methods. In this work, we show that a structure–property map consisting of simulated data for crystalline MOFs can be used to indirectly obtain adsorption properties of structurally deformed MOFs. The structure–property map (with dimensions such as Henry coefficient, heat of adsorption, and pore volume) was constructed using a large data set of over 12000 crystalline MOFs from molecular simulations. By mapping the experimental data points of deformed SNU-200, MOF-5, and Ni-MOF-74 onto this structure–property map, we show that the experimentally deformed MOFs share similar adsorption properties with their nearest neighbor crystalline structures. Once the nearest neighbor crystalline MOFs for a deformed MOF are selected from a structure–property map at a specific condition, then the adsorption properties of these MOFs can be successfully transformed onto the degraded MOFs, leading to a new way to obtain properties of materials whose structural information is lost.
Genetic variability of HIV type 1 in Kenya.

The AIDS epidemic is a rapidly growing problem in Nairobi, where the seroprevalence in pregnant women increased from 4% in 1988 to over 10% in 1991. 22 HIV-1-seropositive pregnant women and 1 HIV-1-infected baby (K88) attending the Pumwani Maternity Hospital of Nairobi between 1990 and 1992 were studied as part of a cohort study of maternal risk factors in mother-to-child transmission. A 250-base pair (bp) fragment of the env gene encoding C2V3 was amplified mostly from DNA isolated from primary peripheral blood mononuclear cells and subsequently sequenced. The 23 newly determined HIV env sequences were aligned with 23 previously known sequences of HIV-1 isolates of diverse geographical origin and the sequence of the HIV-1-related chimpanzee isolate SIVcpz-gab, on the basis of primary structure. Distance calculation, tree construction, and bootstrap analysis were realized with the software package TREECON. In the tree, 8 major branches could be observed containing sequences representative of 8 different subtypes A, B, C, D, E, F, G, and H, besides the outlier group O. 19 of 23 Kenyan isolates clustered with D687, Z321, U455, and SF170, which were members of genetic subtype A. Phylogenetic analyses favored positioning of K976 as a divergent A subtype strain. For 4 strains (K29, K88, K98, and K112) the subtype A classification based on the gag gene was also observed on the basis of phylogenetic analysis of the C2V3 coding part of the env gene. The predicted amino acid sequence of the V3 region for these strains was also presented. The finding that among 23 HIV-1 isolates collected in Nairobi, 19 were classified in subtype A versus 3 in subtype D, together with a much larger variation between subtype A strains as compared to subtype D strains, suggests an earlier introduction of a subtype A strain, multiple introductions of subtype A strains, and/or faster diversification of subtype A strains as compared to subtype D strains.
Betting Strategies, Market Selection, and the Wisdom of Crowds

We investigate the limiting behavior of trader wealth and prices in a simple prediction market with a finite set of participants having heterogeneous beliefs. Traders bet repeatedly on the outcome of a binary event with fixed Bernoulli success probability. A class of strategies, including (fractional) Kelly betting and constant relative risk aversion (CRRA) are considered. We show that when traders are willing to risk only a small fraction of their wealth in any period, belief heterogeneity can persist indefinitely; if bets are large in proportion to wealth then only the most accurate belief type survives. The market price is more accurate in the long run when traders with less accurate beliefs also survive. That is, the survival of traders with heterogeneous beliefs, some less accurate than others, allows the market price to better reflect the objective probability of the event in the long run.
Alterations in GABAA receptor expression in neonatal ventral hippocampal lesioned rats: Comparison of prepubertal and postpubertal periods

Rats with neonatal ventral hippocampal lesions (NVHL) have been studied as a neurodevelopmental animal model of schizophrenia. NVHL rats exhibit postpubertal emergence of hyperresponsiveness to stress, suggesting increased mesolimbic dopamine (DA) activity. However, previous studies have not yielded clear evidence of this. Disturbances in the γ‐amino‐butyric acid (GABA)‐ergic system as well as the dopaminergic system are thought to be present in schizophrenia. To determine whether GABAA receptors play a role in the abnormal postpubertal behavior in NVHL rats, we compared changes in expression of mRNA of GABAA receptor subunits and in [35S] t‐butylbicyclophosphorothionate ([35S] TBPS) binding in the prepubertal and postpubertal periods. Male pups were lesioned with ibotenic acid at postnatal day 7 (PD 7), and in situ hybridization and quantitative autoradiography were then performed. In NVHL rats, α1 subunit mRNA expression in prefrontal cortex was decreased at PD 35 (prepubertal period; by 21.7%), but increased at PD 56 (postpubertal period; by 21.4%) when compared with sham controls. β2 subunit mRNA expression was increased in PFC in the postpubertal period (by 24.3%). β3 subunit mRNA expression was increased in the caudate‐putamen in the postpubertal period (by 37.2%). [35S] TBPS binding was increased in PFC only in the postpubertal period (by 17.7%). These findings suggest that dysfunction of the GABAergic system exists in NVHL rats. Furthermore, developmental and regional changes in GABAA receptor expression appear to occur in compensation for the attenuation of GABAergic system activity in NVHL rats. Synapse 61:357‐366, 2007. © 2007 Wiley‐Liss, Inc.
On the utility of HCI practices in improving a commercial information retrieval system

Human-computer interaction (HCI) issues are an important but often overlooked part of software application development. InRAD’s Automated Knowledge Discovery System (Basu, Merrel, Fellbaum, Talbert, Kolpack, Honeycutt, Alonso, & Bloom, 2005) featured numerous Web 2.0 and Web 3.0 components under the hood, but users of the system frequently reported difficulties in actually leveraging the power and capabilities of the system. By partnering with a team of graduate students studying HCI from a local university, InRAD was able to identify and address a wide array of usability issues and improve user satisfaction. The HCI processes that were employed as well as the result of those efforts, rebranded as the InSpire system, are described in this case study as a guide for others to follow.
What Affect Lower Grade Learner's Perceived Usefulness and Perceived Ease of Use of Mobile Digital Textbook Learning System? An Empirical Factor Analyses Investigation in China

Although perceived usefulness and perceived ease of use are two important factors which could directly influence the acceptance of technology and actual usage for digital textbook, less attention has been paid to children’s mobile digital textbook usage. Therefore, the purpose of this study is to investigate and empirically validate the perceived usefulness and the perceived ease of use by elementary school students during their usage of digital textbook. For data analyses, two questionnaires were developed using existing scales from prior TAM instruments. The sample of this study included 5,245 elementary school students in China who have experience of using digital textbook. The results indicate that students believe that using mobile digital textbook enhance their study performance, but they believe it is not very easy to use. Besides, gender, grade and parents’ attitudes towards mobile digital textbook affect the usage. Gender differences exist only in the perceived ease of use. Male students make less effort in using mobile digital textbook than female students. In addition, the students in lower grades tend to have more positive perspectives on mobile digital textbook than the students in higher grades. Furthermore, mobile digital textbook usage experience (time & frequency) has a significant effect on the students’ perceived usefulness. Finally, parents’ attitudes towards mobile digital textbook influence their children’s perceived usefulness.