Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular evolution, systematics, and zoogeography of the rockfish subgenus Sebastomus (Sebastes, Scorpaenidae) based on mitochondrial cytochrome b and control region sequences.

Sebastomus is one of the most species-rich subgenera of Sebastes, whose monophyly is well supported by morphological and molecular data. We present the first description of the complete nucleotide sequence of the mitochondrial cytochrome b gene and the partial sequence of the control region of the 14 species of Sebastomus. We used these data in phylogenetic analyses to investigate their evolutionary relationships. Extremely low levels of sequence divergence indicated a recent ancestry of these species, suggesting a very rapid radiation within the last million years. The molecular data revealed two main clades within Sebastomus, each with species of different affinities that invaded new habitats from the subgeneric center of distribution. The rapid speciation in this lineage was manifested in the poor resolution of some nodes in the phylogeny. Internal fertilization and viviparity in Sebastes may have played an important role in the sudden acquisition of reproductive barriers during its radiation. The mitochondrial DNA data suggest that prolific speciation in Sebastomus may have been associated with rapid lineage sorting punctuated by allopatric reproductive isolation subsequent to dispersal events and, perhaps, by sympatric reproductive isolation associated with internal fertilization.
Investigation on passivity based control for electrical applications

Passivity based control (PBC) method is an energy based control method. The total energy of the system is expressed as a sum of stored energy and dissipated energy. This technique deals with energy shaping as well as damping injection and tracking which is achieved via Hamiltonian operator. Passivity based control is developed by satisfying dissipation matching condition. In this paper the types of passivity based control namely Energy Shaping Damping Injection (ESDI), Exact Tracking Error Dynamics Passive Output Feedback (ETEDPOF), Interconnection and damping assignment passivity based control (IDA-PBC) and Exact Static Error Dynamics Passive Output Feedback (ESEDPOF) are analysed. The journey of PBC from 1989 and the electrical applications of the method are also reviewed.
Validation of an accelerated ‘demons’ algorithm for deformable image registration in radiation therapy

A greyscale-based fully automatic deformable image registration algorithm, originally known as the ‘demons’ algorithm, was implemented for CT image-guided radiotherapy. We accelerated the algorithm by introducing an ‘active force’ along with an adaptive force strength adjustment during the iterative process. These improvements led to a 40% speed improvement over the original algorithm and a high tolerance of large organ deformations. We used three methods to evaluate the accuracy of the algorithm. First, we created a set of mathematical transformations for a series of patient's CT images. This provides a ‘ground truth’ solution for quantitatively validating the deformable image registration algorithm. Second, we used a physically deformable pelvic phantom, which can measure deformed objects under different conditions. The results of these two tests allowed us to quantify the accuracy of the deformable registration. Validation results showed that more than 96% of the voxels were within 2 mm of their intended shifts for a prostate and a head-and-neck patient case. The mean errors and standard deviations were 0.5 mm ± 1.5 mm and 0.2 mm ± 0.6 mm, respectively. Using the deformable pelvis phantom, the result showed a tracking accuracy of better than 1.5 mm for 23 seeds implanted in a phantom prostate that was deformed by inflation of a rectal balloon. Third, physician-drawn contours outlining the tumour volumes and certain anatomical structures in the original CT images were deformed along with the CT images acquired during subsequent treatments or during a different respiratory phase for a lung cancer case. Visual inspection of the positions and shapes of these deformed contours agreed well with human judgment. Together, these results suggest that the accelerated demons algorithm has significant potential for delineating and tracking doses in targets and critical structures during CT-guided radiotherapy.
On quality trade-off control for approximate computing using iterative training

Quality control plays a key role in approximate computing to save the energy and guarantee that the quality of the computation outcome satisfies users' requirement. Previous works proposed a hybrid architecture, composed of a classifier for error prediction and an approximate accelerator for approximate computing using well trained neural-networks. Only inputs predicted to meet the quality are executed by the accelerator. However, the design of this hybrid architecture, relying on one-pass training process, has not been fully explored. In this paper, we propose a novel optimization framework. It advocates an iteratively training process to coordinate the training of the classifier and the accelerator with a judicious selection of training data. It integrates a dynamic threshold tuning algorithm to maximize the invocation of the accelerator (i.e., energy-efficiency) under the quality requirement. At last, we propose an efficient algorithm to explore the topologies of the accelerator and the classifier comprehensively. Experimental results shows significant improvement on the quality and the energy-efficiency compared to the conventional one-pass training method.
An approach to vowel recognition using 2DDWT based visual information of the lip region

In this paper, a vowel recognition scheme using visual information is proposed based on two dimensional discrete wavelet transform (2D-DWT). First, a video frame corresponding to a steady vowel zone is selected utilizing the speech characteristics of audio frames. Next, a pixel-based method is proposed to identify the lip region of a given video frame, where intensity variation of different color planes is utilized. The 2D-DWT is then employed on a combined image plane extracted by using the weighted sum of red and green plane pixels of the lip image. Lower order wavelet coefficients obtained after second level decomposition and differences among those coefficients are used as proposed features. Leave one out cross validation technique is used to test the classification accuracy where a distance based classifier is used. Performance of the proposed method is tested on a publicly available standard audiovisual database and a high level of recognition accuracy is achieved using only extracted visual features.
Stereo vision based pedestrian detection using B-spline modeling

This paper presents a new approach for pedestrian detection in the vehicle environment using stereo vision. The segmented pedestrians, represented as a set of equal disparity attributed segments, are refined using B-spline arithmetic. These segments are obtained from a non-dense disparity map. The disparity map is estimated using a new developed algorithm relying on the contour-following algorithm. The approximated segments are then matched with preexisting pedestrian model. The pedestrian model is generated by utilizing B-spline functions, which can refine the human body contour extracted in a digitized image. Some attributes of the approximated segments like concavity, convexity, and local curvature are considered to perform the matching process.
The Saccharomyces cerevisiae MFS Superfamily SGE1 Gene Confers Resistance to Cationic Dyes

A gene from Saccharomyces cerevisiae whose overexpression confers resistance to 10‐N‐nonyl acridine orange (NAO) has been isolated. This cationic dye binds acidic phospholipids and more specifically cardiolipin (Petit, J. M., Maftah, A., Ratinaud, M. H. and Julien, R. Eur. J. Biochem. 209, 267–273, 1992). The isolated gene was found to be identical to SGE1, a partial multicopy suppressor of the gal11 mutation (Amakasu, H., Suzuki, Y., Nishizawa, M. and Fukasawa, T. Genetics 134, 675–683, 1993), that also confers crystal violet resistance to a supersensitive strain (Ehrenhofer‐Murray, A. E., Wurgler, F. E. and Sengstag, C. Mol. Gen. Genet. 244, 287–294, 1994). The data presented in this paper show that the SGE1 gene product, a member of the major facilitator superfamily, confers a pleiotropic drug‐resistance phenotype when present in high copy number. The results also demonstrate that Sge1p acts as an extrusion permease whose specificity seems restricted to dye molecules possessing a large unsaturated domain that stabilizes a permanent positive charge such as NAO, crystal violet, ethidium bromide or malachite green. © 1997 John Wiley & Sons, Ltd.
Rensching cats and dogs: feeding ecology and fecundity trends explain variation in the allometry of sexual size dimorphism

The tendency for sexual size dimorphism (SSD) to increase with body mass in taxa where males are larger, and to decrease when females are larger, is known as Rensch's rule. In mammals, where the trend occurs, it is believed to be the result of a competitive advantage for larger males, while female mass is constrained by the energetics of reproduction. Here, we examine the allometry of SSD within the Felidae and Canidae, demonstrating distinctly different patterns: in felids, there is positive allometric scaling, while there is no trend in canids. We hypothesize that feeding ecology, via its effect on female spacing patterns, is responsible for the difference; larger male mass may be advantageous only where females are dispersed such that males can defend access to them. This is supported by the observation that felids are predominately solitary, and all are obligate carnivores. Similarly, carnivorous canids are more sexually dimorphic than insectivores and omnivores, but carnivory does not contribute to a Rensch effect as dietary variation occurs across the mass spectrum. The observed inter-familial differences are also consistent with reduced constraints on female mass in the canids, where litter size increases with body mass, versus no observable allometry in the felids.
Macroautophagy is dispensable for intracellular replication of Legionella pneumophila in Dictyostelium discoideum

The Gram‐negative bacterium Legionella pneumophila is a facultative intracellular pathogen of free‐living amoebae and mammalian phagocytes. L. pneumophila is engulfed in phagosomes that initially avoid fusion with lysosomes. The phagosome associates with endoplasmic reticulum (ER) and mitochondria and eventually resembles ER. The morphological similarity of the replication vacuole to autophagosomes, and enhanced bacterial replication in response to macroautophagy‐inducing starvation, led to the hypothesis that L. pneumophila infection requires macroautophagy. As L. pneumophila replicates in Dictyostelium discoideum, and macroautophagy genes have been identified and mutated in D. discoideum, we have taken a genetic and cell biological approach to evaluate the relationship between host macroautophagy and intracellular replication of L. pneumophila. Mutation of the apg1, apg5, apg6, apg7 and apg8 genes produced typical macroautophagy defects, including reduced bulk protein degradation and cell viability during starvation. We show that L. pneumophila replicates normally in D. discoideum macroautophagy mutants and produces replication vacuoles that are morphologically indistinguishable from those in wild‐type D. discoideum. Furthermore, a green fluorescent protein (GFP)‐tagged marker of autophagosomes, Apg8, does not systematically co‐localize with DsRed‐labelled L. pneumophila. We conclude that macroautophagy is dispensable for L. pneumophila intracellular replication in D. discoideum.
Apoptosis in Mycobacterium tuberculosis infection in mice exhibiting varied immunopathology

This study examined mechanisms contributing to pulmonary immunopathology following acute Mycobacterium tuberculosis (MTB) infection in vivo in a murine model. A/J and C57BL/6 mice were intravenously infected with MTB (Erdman). Pathological differences were found between strains, unrelated to pulmonary load of bacilli. A/J mice developed progressive interstitial pneumonitis, while C57BL/6 mice maintained granuloma formation. The contribution of FAS and FAS ligand‐mediated apoptosis was assessed via bioluminescent reverse transcription‐polymerase chain reaction (RT‐PCR), immunohistochemical staining, and TUNEL assessment of DNA fragmentation. Cytokine messages for pulmonary tumour necrosis factor‐α (TNF‐α) and interferon‐γ (IFN‐γ), as well as for the lytic molecules perforin and granzyme B, were quantified. Immunohistochemical staining for CD3 receptor was performed to monitor lymphocytic lung infiltration. Soon after infection, A/J mice exhibited increased pulmonary IFN‐γ message, concurrent with the appearance of CD3+ lymphocytes distributed throughout the lung. C57BL/6 mice exhibited perivascular cuffing, with no accompanying increase in IFN‐γ message. A/J mice also had elevated levels of FAS and FAS ligand message and protein early after infection, while the C57BL/6 mice had no increased expression of these molecules. Both strains exhibited qualitatively similar numbers of TUNEL‐positive cells throughout infection, with a marked increase on day 7. Apoptotic cells appeared to co‐localize with acid fast bacilli. It is therefore proposed that apoptosis during initial granuloma formation following MTB infection may occur through a FAS/FAS ligand‐independent pathway. Moreover, a failure of completion of the FAS/FAS ligand‐mediated apoptosis pathway in the A/J mice may contribute to inefficient elimination of lymphocytes, thus further aggravating pulmonary pathology. Copyright © 2000 John Wiley & Sons, Ltd.
Vulnerability and Social Justice as Factors in Emergent U.S. Nanotechnology Risk Perceptions

As an emerging domain of risk research, nanotechnologies engender novel research questions, including how new technologies are encountered given different framing and contextual detail. Using data from a recent U.S. national survey of perceived risks (N= 1,100), risk versus benefit framings and the specific social positions from which people encounter or perceive new technologies are explored. Results indicate that vulnerability and attitudes toward environmental justice significantly influenced risk perceptions of nanotechnology as a broad class, while controlling for demographic and affective factors. Comparative analyses of different examples of nanotechnology applications demonstrated heightened ambivalence across acceptability when risk versus benefit information was provided with application descriptions (described in short vignettes as compared to the general category “nanotechnology,” absent of risk or benefit information). The acceptability of these nano‐specific vignettes varied significantly in only some cases given indexes of vulnerability and attitudes toward environmental justice. However, experimental narrative analyses, using longer, more comprehensive descriptive passages, show how assessments of risks and benefits are tied to the systematically manipulated psychometric qualities of the application (its invasiveness and controllability), risk messaging from scientists, and the social implications of the technology with regard to justice. The article concludes with discussion of these findings for risk perception research and public policy related to nanotechnology and possibly other emerging technologies.
Epigenetic determinism in science and society

The epigenetic “revolution” in science cuts across many disciplines, and it is now one of the fastest-growing research areas in biology. Increasingly, claims are made that epigenetics research represents a move away from the genetic determinism that has been prominent both in biological research and in understandings of the impact of biology on society. We discuss to what extent an epigenetic framework actually supports these claims. We show that, in contrast to the received view, epigenetics research is often couched in language as deterministic as genetics research in both science and the popular press. We engage the rapidly emerging conversation about the impact of epigenetics on public discourse and scientific practice, and we contend that the notion of epigenetic determinism – or the belief that epigenetic mechanisms determine the expression of human traits and behaviors – matters for understandings of the influence of biology and society on population health.
Cores and Peripheries: Spatial Analysis of Housing Choice Voucher Distribution in the San Francisco Bay Area Region, 2000–2010

Abstract This study uses spatial regressions and spatial statistics to examine the changes in the distribution of Housing Choice Voucher (HCV) households within an expanded San Francisco Bay Area region. From 2000 to 2010, the density of HCV households grew disproportionately across the region, and areas of significant increase emerged in both the region’s urban cores and its rural periphery. Furthermore, the destination communities shared a set of common characteristics. In 2010 HCV households were more likely to locate in areas with lower housing prices, lower percentages of educated people, higher rates of poverty, and higher percentages of African American households when compared with the region as a whole. These findings suggest that voucher holders locate where housing is affordable. We conclude that in regions with tight housing markets, supply matters. This study also introduces housing researchers and policy makers to a methodological approach that addresses what is known in geostatistics as a change of support problem.
Cystic fibrosis, disease severity, and a macrophage migration inhibitory factor polymorphism.

RATIONALE Macrophage migration inhibitory factor (MIF) is a key proinflammatory mediator. It contributes toward an exaggerated gram-negative inflammatory response via its ability to induce Toll-like receptor-4 expression. Studies have shown that MIF knockout mice have less aggressive Pseudomonas infection (compared with wild-type). OBJECTIVES To assess whether a novel functional MIF polymorphism was associated with clinical prognosis in a patient cohort with chronic gram-negative infection, namely cystic fibrosis (CF). METHODS Collected genomic DNA was analyzed via polymerase chain reaction amplification for the polymorphic region for the CATT repeat polymorphism. Individuals may have a 5-, 6-, 7-, or 8-CATT tetranucleotide repeat unit on each allele. The 5-CATT repeat allele exhibits the lowest MIF promoter activity. MEASUREMENTS AND MAIN RESULTS Patients with stable CF (n = 167) and a matched control group (n = 166) were enrolled. In patients with CF, the MIF5(+) group had a decreased incidence of Pseudomonas aeruginosa colonization (odds ratio, 0.25; 95% confidence interval, 0.09-0.65; p = 0.004) and a significant reduction in the risk of pancreatic insufficiency (odds ratio, 0.27; 95% confidence interval, 0.07-1.0; p = 0.05). A trend toward milder disease activity in the MIF5(+) group was seen with all other parameters. CONCLUSIONS The results support the concept of a regulatory role for MIF in CF.
Recombinant factor VIII Fc fusion protein: extended‐interval dosing maintains low bleeding rates and correlates with von Willebrand factor levels

Routine prophylaxis with replacement factor VIII (FVIII) – the standard of care for severe hemophilia A – often requires frequent intravenous infusions (three or four times weekly). An FVIII molecule with an extended half‐life could reduce infusion frequency. The A‐LONG study established the safety, efficacy and prolonged pharmacokinetics of recombinant FVIII Fc fusion protein (rFVIIIFc) in previously treated adolescents and adults with severe hemophilia A.
Brain Inflammation and Alzheimer's-Like Pathology in Individuals Exposed to Severe Air Pollution

Air pollution is a complex mixture of gases (e.g., ozone), particulate matter, and organic compounds present in outdoor and indoor air. Dogs exposed to severe air pollution exhibit chronic inflammation and acceleration of Alzheimer's-like pathology, suggesting that the brain is adversely affected by pollutants. We investigated whether residency in cities with high levels of air pollution is associated with human brain inflammation. Expression of cyclooxygenase-2 (COX2), an inflammatory mediator, and accumulation of the 42-amino acid form of β-amyloid (Aβ42), a cause of neuronal dysfunction, were measured in autopsy brain tissues of cognitively and neurologically intact lifelong residents of cities having low (n:9) or high (n:10) levels of air pollution. Genomic DNA apurinic/apyrimidinic sites, nuclear factor-κB activation and apolipoprotein E genotype were also evaluated. Residents of cities with severe air pollution had significantly higher COX2 expression in frontal cortex and hippocampus and greater neuronal and astrocytic accumulation of Aβ42 compared to residents in low air pollution cities. Increased COX2 expression and Aβ42 accumulation were also observed in the olfactory bulb. These findings suggest that exposure to severe airpollution is associated with brain inflammation and Aβ 42 accumulation, two causes of neuronal dysfunction that precede the appearance of neuritic plaques and neurofibrillary tangles, hallmarks of Alzheimer's disease.
Network externalities and tariff structure*

Abstract In this paper, we show that with cost asymmetry, stronger network externalities and less differentiated goods, the uniform tariff rate set by the government of the importing country increases and the optimal discriminatory-tariff gap widens. In addition, under network externalities and good differentiation, we demonstrate that: (a) the optimal tariff policy is superior to free trade in maximizing the domestic social welfare; (b) the maximum-revenue tariff rate is always higher than the optimal tariff rate; (c) the consumer surplus and social welfare are always higher under the optimal tariff policy than under the maximum-revenue tariff policy.
NIR-based gaze tracking with fast pupil ellipse fitting for real-time wearable eye trackers

In this work, a NIR (near infrared ray) based fast pupil ellipse fitting based gaze tracking system is developed for the wearable eye tracker. By a near-field and side-view eye camera, the contour of pupil in captured images is an ellipse generally, and that of pupil shape is not always circular. After pre-processing, the pupil contour is recognized by the two-stage binarizations, and the binaried pupil contour is applied to select the possible candidate points for pupil ellipse fittings. After the Random Sample Consensus (RANSAC) based fast pupil ellipse fitting, the centers of pupils are estimated effectively, and the gaze tracking is worked efficiently after calibrations. By experiments, the average estimated errors of pupil ellipse centers are smaller than 2 pixels. At training mode, the average horizontal and vertical accuracies of gaze tracking are 0.66 and 1.84 degrees, respectively. At testing mode, the average horizontal and vertical accuracies of gaze tracking are 1.13 and 2.24 degrees, respectively. Finally, the proposed main function performs up to 266.7 frames/sec by a personal computer with 3.4GHz operational frequency.