Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical approaches for DNA barcoding.

Cantino, P. D. , and K. de Queiroz. 2004. PhyloCode: A phylogenetic code of biological nomenclature. [http://www.ohiou. edu/phylocode/] de Queiroz, K. 1992. Phylogenetic definitions and taxonomic philosophy. Biol. Philos. 7:295-313. de Queiroz, K. 1997. The Linnaean hierarchy and the evolutionization of taxonomy, with emphasis on the problem of nomenclature. Aliso 15:125-144. de Queiroz, K. 2005. Linnaean, rank-based, and phylogenetic nomenclature: Restoring primacy to the link between names and taxa. Symb. Bot. Ups. 33(3):127-140. de Queiroz, K. , and P. D. Cantino. 2001. Phylogenetic nomenclature and the PhyloCode. Bull. Zool. Nomencl. 58:254-271. de Queiroz, K. , and J. Gauthier. 1990. Phylogeny as a central principle in taxonomy: Phylogenetic definitions of taxon names. Syst. Zool. 39:307-322. de Queiroz, K. , and J. Gauthier. 1992. Phylogenetic taxonomy. Annu. Rev. Ecol. Syst. 23:449-480. de Queiroz, K. , and J. Gauthier. 1994. Toward a phylogenetic system of biological nomenclature. Trends Ecol. Evol. 9:27-31. International Botanical Congress. 2000. International Code of Botanical Nomenclature. Edition adopted by the Sixteenth International Botanical Congress, St. Louis, Missouri, July-August 1999. Koeltz Scientific Books, Konigstein. International Commission on Zoological Nomenclature. 1999. International Code of Zoological Nomenclature, 4th edition. International Trust for Zoological Nomenclature, London. International Union of Microbiological Societies. 1992. International Code of Nomenclature of Bacteria and Statutes of the International Committee on Systematic Bacteriology and Statutes of the Bacteriology and Applied Microbiology Section of The International Union of Microbiological Societies. American Society for Microbiology, Washington. Laurin, M. , K. de Queiroz, P. Cantino, N. Cellinese, and R. Olmstead. 2005. The PhyloCode, types, ranks, and monophyly: A response to Pickett. Cladistics 21:605-607. Pickett, K. M. 2005. The new and improved PhyloCode, now with types, ranks, and even polyphyly: A conference report from the First International Phylogenetic Nomenclature Meeting. Cladistics 21:7982.
Staggered transverse tripoles with quadripolar lateral anodes using percutaneous and surgical leads in spinal cord stimulation.

BACKGROUND In spinal cord stimulation for low-back pain, the use of electrode arrays with both low-power requirements and selective activation of target dorsal column (DC) fibers is desired. The aligned transverse tripolar lead configuration offers the best DC selectivity. Electrode alignment of the same configuration using 3 parallel percutaneous leads is possible, but compromised by longitudinal migration, resulting in loss of DC selectivity. This loss might be repaired by using the adjacent anodal contacts on the lateral leads. OBJECTIVE To investigate if stimulation using adjacent anodal contacts on the lateral percutaneous leads of a staggered transverse tripole can restore DC selectivity. METHODS Staggered transverse tripoles with quadripolar lateral anodes were modeled on the low-thoracic vertebral region (T10-T12) of the spinal cord using (a) percutaneous lead with staggered quadripolar lateral anodal configuration (PERC QD) and (b) laminotomy lead with staggered quadripolar lateral anodal configuration (LAM QD), of the same contact dimensions. The commercially available LAM 565 surgical lead with 16 widely spaced contacts was also modeled. For comparison with PERC QD, staggered transverse tripoles with dual lateral anodes were modeled by using percutaneous lead with staggered dual lateral anodal configuration (PERC ST). RESULTS The PERC QD improved the depth of DC penetration and enabled selective recruitment of DCs in comparison with PERC ST. Mediolateral selectivity of DCs could not be achieved with the LAM 565. CONCLUSION Stimulation using PERC QD improves anodal shielding of dorsal roots and restores DC selectivity. Based on our modeling study, we hypothesize that, in clinical practice, LAM QD can provide an improved performance compared with the PERC QD. Our model also predicts that the same configuration realized on the commercial LAM 565 surgical lead with widely spaced contacts cannot selectively stimulate DCs essential in treating low-back pain.
Heschl gyrus and its included primary auditory cortex: Structural MRI studies in healthy and diseased subjects

Despite the fact that the Heschl gyrus (HG) is a crucial brain structure as it contains the primary auditory cortex (PAC), relatively few structural MRI studies have concentrated upon it. We propose that this may be attributed in part to the considerable variability of this structure and, most importantly, to the lack of unified criteria for defining the extent of the PAC along the MRI‐determined landmarks of the HG, which ultimately affects the reliability and reproducibility of these studies. This review highlights three aspects: first, the standard and variant anatomy of the HG and PAC with particular focus on MRI definition of these regions; second, the importance of studying the HG and PAC in health and disease using structural MRI; and, third, the problem of MRI localization of the PAC. The scientific community should be aware that the HG and its included PAC are not synonyms. Additionally, owing to the great complexity and variability of these regions, future MRI studies should be cautious when using single brain‐based atlas or maps generated by simply averaging across individuals to localize these regions. Instead, and while waiting for future in vivo microstructural localization of the PAC, the use of probabilistic and functional maps is advantageous but not without shortcomings. J. Magn. Reson. Imaging 2008;28:287–299. © 2008 Wiley‐Liss, Inc.
Model predictive position/force control of an anthropomorphic robotic arm

When a robotic manipulator executes a task in restricted and unknown environments, it is necessary to implement a position/force control in free space and constrained space. In classic controllers, position/force control may be carried out by means a controller switching, once the contact point has been reached. In this paper, a new position/force predictive controller for an anthropomorphic robotic arm is proposed. This work proposes an unique control law for controlling both variables (position or force). In a model predictive framework, where several goals have to be reached, it is known that cost function includes several parameters (weights) whose modification allows to prioritize goals to achieve. This fact has been taken into account to set up the controller. The proposed control law is validated by experiments involving a 7-dof anthropomorphic robotic arm executing a trajectory tracking task in a restricted environment. As experimental results show, it is possible to control position and force by adjusting controller weights.
Meta-material based on an Ideal Spring Lattice: A Linear Elastic Isotropic Material with Zero Poisson's Ratio over Large Strains

A lot of scientiﬁc effort is put into changing mechanical material properties by creating micro-structural architectures instead of chemical composition. This results in meta-materials, which are future materials tuned to the needs of the user. To change the Poisson’s ratio and Young’s modulus, most current designs exploit mechanisms and hinges to obtain the desired behavior. However, this leads to non-linear material properties and anisotropy, especially for large strains. In this work a method is proposed that makes use of specially curved leaf springs (ideal springs) in a planar lattice. The spring characteristics directly determine the Young’s modulus, furthermore is the Poisson’s ratio designed to be zero. These properties are isotropic and linear up to large compressive and tensile strains. The spring designs may not only be used in a lattice, but also could be used as ideal springs or zero free length springs in the field of static balancing.
Synchrotron Radiation Based Multi-Scale Structural Characterization of CoPt3 Colloidal Nanoparticles

Bimetallic CoPt3 nanoparticles represent a category of colloidal nanoparticles with high application potentials in, e.g., heterogeneous catalysis, sensor technology, and magnetic storage media. Deposition of this system on functionalized supports delivers opportunities for controlled immobilization of the nanoparticles. In this work, self-assembled monolayers (SAMs) of n-alkanethiol molecules served as functionalizing material for the Au covered Si substrates. Deposition of the ligand-terminated nanoparticles took place by means of spin and dip coating and has been optimized for each of the mentioned methods so that monolayers of nanoparticles on supports were fabricated with a well-controlled coverage The morphology of the nanoparticle film arranged is addressed by grazing-incidence small angle x-ray scattering (GISAXS). This together with x-ray standing waves in total external reflection (TER-XSW) enables a 3D structural characterization of such nanoparticle films, so that the mean particle size, mean distance of the arranged nanoparticle films to the substrate, as well as the mean particle-particle distance in lateral direction have been determined. TER-XSW, being an element-specific position-sensitive method, also reveals the elemental distribution of the particles which complementary provides a fundamental understanding of their internal structure. The CoPt3 nanoparticles investigated here exhibit a core-shell-like structure with cores of CoPt3 and shells mainly comprise Co. The results regarding the internal structure of the nanoparticles were then verified by extended X-ray absorption fine structure (EXAFS) measurements.
Removing Mistracking of Multibody Motion Video Database Hopkins155

Many mathematical techniques have been presented for classifying feature point trajectories over multibody motion video sequences into different motions, and most are applied to the Hopkins155 database for evaluating their performance. In this paper, we point out that Hopkins155 has problems and that correct performance evaluation is not necessarily done using it. We create a new database by removing incorrect trajectories from Hopkins155. The basic principle of mistracking removal is the fact that correct trajectories all belong to parallel 2-D affine spaces in a high-dimensional space if all motions are translational and that parallel 2-D affine spaces are included in a 3-D affine space. Noting that if the image sequence is divided into short intervals, individual motions can be regarded as approximately translational in each interval, we detect incorrect trajectories by repeated plane fitting in the 3-D space by RANSAC. We point out why conventional RANSAC voting does not work and demonstrate that out method allows us to tell in which frames incorrect trajectoires occurred. The performance of multibody motion segmentation can be correctly evaluated using our database.
Projective synchronization in drive-response dynamical networks

In this paper, the projective synchronization (characterized by a scaling factorα) in the drive-response dynamical networks whose each node is the parts of four-dimensional hyperchaotic system is studied. Using pinning control for small fraction of nodes in all the drive-response dynamical networks direct the scaling factor onto the desired value. A synchronous criterion ensuring projective synchronization in the drive-response dynamical networks is obtained. To verify the correctness of the synchronous criterion some numerical simulations are given.
Factored Proximity Models for Top-N Recommendations

In this paper, we propose EIGENREC; a simple and versatile Latent Factor framework for Top-N Recommendations, which includes the well-known PureSVD algorithm as a special case. EIGENREC builds a low dimensional model of an inter-item proximity matrix that combines a traditional similarity component, with a scaling operator, designed to regulate the effects of the prior item popularity on the final recommendation list. A comprehensive set of experiments on the MovieLens and the Yahoo datasets, based on widely applied performance metrics suggest that EIGENREC outperforms several state of-the-art algorithms, in terms of Standard and Long-Tail recommendation accuracy, while exhibiting low susceptibility to the problems caused by Sparsity, even its most extreme manifestations – the Cold-start problems.
Multistatic, MIMO and networked radar: The future of radar sensors?

A review is presented of work on multistatic, MIMO and networked radar, explaining the current high degree of interest in these subjects. The enhancement of target signatures in the forward scatter geometry is explained, and some of the principles of Passive Bistatic Radar. The challenge here is to identify applications which offer a clear advantage over conventional radar approaches. Finally, some newer, longer term ideas on networked radar as an intelligent, adaptive distributed sensor system are presented and discussed.
Rapid decline in MyHC I(β) mRNA expression in rat soleus during hindlimb unloading is associated with AMPK dephosphorylation

Inactivation of a skeletal muscle results in slow to fast myosin heavy chain (MyHC) shift. AMP‐activated protein kinase (AMPK) can be implicated in the regulation of genes encoding the slow MyHC isoform. Here we report that AMPK dephosphorylation after 24 h of mechanical unloading can contribute to histone deacetylase (HDAC) nuclear translocation; activation of AMPK prevents HDAC4 nuclear accumulation after 24 h of unloading and AMPK dephosphorylation inhibits slow MyHC expression following 24 h of unloading. Our data indicate that AMPK dephosphorylation during the first 24 h of mechanical unloading has a significant impact on the expression of MyHC isoforms in rat soleus causing a decrease in MyHC I(β) pre‐mRNA and mRNA expression as well as MyHC IIa mRNA expression.
Regional distribution of nitrergic neurons in the inner retina of the chicken

Abstract Using both NADPH diaphorase and anti-nNOS antibodies, we have identified—from retinal flatmounts—neuronal types in the inner retina of the chicken that are likely to be nitrergic. The two methods gave similar results and yielded a total of 15 types of neurons, comprising 9 amacrine cells, 5 ganglion cells, and 1 centrifugal midbrain neuron. Six of these 15 cell types are ubiquitously distributed, comprising 3 amacrine cells, 2 displaced ganglion cells, and a presumed orthotopic ganglion cell. The remaining nine cell types are regionally restricted within the retina. As previously reported, efferent fibers of midbrain neurons and their postsynaptic partners, the unusual axon-bearing target amacrine cells, are entirely confined to the ventral retina. Also confined to the ventral retina, though with somewhat different distributions, are the “bullwhip” amacrine cells thought to be involved in eye growth, an orthotopic ganglion cell, and two types of large axon-bearing amacrine cells whose dendrites and axons lie in stratum 1 of the inner plexiform layer (IPL). Intracellular fills of these two cell types showed that only a minority of otherwise morphologically indistinguishable neurons are nitrergic. Two amacrine cells that branch throughout the IPL are confined to an equatorial band, and one small-field orthotopic ganglion cell that branches in the proximal IPL is entirely dorsal. These findings suggest that the retina uses different processing on different regions of the visual image, though the benefit of this is presently obscure.
A Spike Train Neural Network Model for Short-term Electricity Load Forecasting

Short term load forecasting (STLF) is very important because of its essentiality in power system planning and operation. Due to the restructuring of power markets, several electric power companies need to forecast their load requirement with maximum accuracy. Though various forecasting models are developed, accurate forecasting with zero error is still a challenging task. Here in this paper, the forecast engine of the proposed strategy is a spike train based neural network. The Spiking Neural Network (SNN) uses the neural code of precisely timed spikes and exploits the rich dynamics in its structural representation. Therefore, the proposed load forecasting system is known as the SNNSTLF (Spiking Neural Network Short-term Load Forecaster). The suitability and the validation of the proposed SNNSTLF model is investigated and compared with back-propagation artificial neural network (BPANN). The method is tested based on historical load data of Hyderabad.
Enteropathogens and risk factors for diarrhea in Norwegian dairy calves

Abstract The aims of the current study were to estimate the prevalence of enteropathogens in calves in Norwegian dairy herds, evaluate the clinical consequences of protozoal infections, and identify risk factors for diarrhea. The 135 participating herds were randomly selected from those in The Norwegian Dairy Herd Recording System that had at least 15 cow-years. Each herd was followed for 1 yr. Fecal samples from calves with (n=68) or without (n=691) diarrhea were analyzed for the presence of Cryptosporidium, Giardia, and Eimeria species. Diarrheic samples (n=191) were assayed for rotavirus group A, bovine coronavirus (BCoV), Cryptosporidium, and Escherichia coli F5 by antigen ELISA. Blood samples (n=1,348) were analyzed for antibodies against BCoV and rotavirus. Potential risk factors for diarrhea were analyzed by using Cox regression analysis adjusted for herd frailty effect. Rotavirus and Cryptosporidium were the most commonly detected enteropathogens in diarrheic samples. A high level of Cryptosporidium shedding or BCoV seropositive calves in a herd was associated with an increased risk of diarrhea. Other factors found to increase the risk of diarrhea were use of slatted concrete floor in group pens versus other floor types [hazard ratio (HR)=8.9], housing of calves in free-stalls compared with tie-stalls (HR=3.7), purchasing of calves into the herd versus not purchasing calves (HR=4.1), and calves being born during winter compared with other seasons of the year (HR=1.5).
LRP: Role in Vascular Wall Integrity and Protection from Atherosclerosis

Vascular smooth muscle cell (SMC) proliferation and migration are important events in the development of atherosclerosis. The low-density lipoprotein receptor–related protein (LRP1) mediates suppression of SMC migration induced by platelet-derived growth factor (PDGF). Here we show that LRP1 forms a complex with the PDGF receptor (PDGFR). Inactivation of LRP1 in vascular SMCs of mice causes PDGFR overexpression and abnormal activation of PDGFR signaling, resulting in disruption of the elastic layer, SMC proliferation, aneurysm formation, and marked susceptibility to cholesterol-induced atherosclerosis. The development of these abnormalities was reduced by treatment with Gleevec, an inhibitor of PDGF signaling. Thus, LRP1 has a pivotal role in protecting vascular wall integrity and preventing atherosclerosis by controlling PDGFR activation.
CallCab: A unified recommendation system for carpooling and regular taxicab services

Carpooling taxicab services hold the promise of providing additional transportation supply, especially in extreme weather or rush hour when regular taxicab services are insufficient. Although many recommendation systems about regular taxicab services have been proposed recently, little research, if any, has been done to assist passengers to find a successful taxicab ride with carpooling. In this paper, we present the first systematic work to design a unified recommendation system for both regular and carpooling services, called CallCab, based on a data driven approach. In response to a passenger's request, CallCab aims to recommend either (i) a vacant taxicab for a regular service with no detour, or (ii) an occupied taxicab heading to the similar direction for a carpooling service with less detour, yet without assuming any knowledge of destinations of passengers already on occupied taxicabs. To analyze these unknown destinations of occupied taxicabs, CallCab generates and refines taxicab trip distributions based on GPS datasets and context information collected in the existing taxicab infrastructure. To improve CallCab's efficiency to process such a big dataset, we augment the efficient MapReduce model with a Measure phase tailored for our application. We evaluate CallCab with a real world dataset of 14,000 taxicabs, and results show that compared to ground truth, CallCab can reduce 64% of the total mileage to deliver all passengers and 63% of passenger's waiting time.
Control Processes and Ultra High Data Rates for Unmanned Autonomous Systems

Advancements in the size, weight, power and cost of gigabit per second directional wireless communication networks and technologies are enabling C4ISR using a backbone of unmanned autonomous systems (UAS). In this paper, we focus on the control of a set of UASs (topology) that provide mobile base stations for tactical operations. We discuss a comprehensive control architecture based on our on-going research and development, and we provide results of simulation experiments designed to investigate the effectiveness of reconfiguration of topologies that use steerable, high data rate (gigabit per second) directional beams in terms of network performance.
Visibility constrained surface evolution

The problem of feature-based surface reconstruction is considered in this paper. Our main contribution is the ability to handle visibility constraints, obtained from the projections of points, curves and silhouettes, in the surface fitting process. While traditional methods often ignore such information, we show that visibility constraints not only give better initial surface estimates and faster convergence, but also provide an important cue for determining surface topology. The problem is cast as a variational problem with constraints within the level set framework. It is shown how to evolve the surface without violating the visibility constraints using methods from variational calculus. Applications of the theory are detailed for a number of important cases of geometric primitives: points, curves and visual hulls. Several experiments on real image sequences are given to demonstrate the performance of the approach.
Associations Between Secondhand Smoke Exposure and Sleep Patterns in Children

OBJECTIVES: The objective of this study was to investigate the relationship between exposure to secondhand smoke (SHS) and child sleep patterns among a group of children with asthma who were exposed regularly to tobacco smoke at home. METHODS: We studied 219 children who were enrolled in an asthma intervention trial and were exposed regularly to SHS. Serum cotinine levels were used to measure exposure to tobacco smoke, and sleep patterns were assessed through parent reports using the Children's Sleep Habits Questionnaire. Covariates in adjusted analyses included gender, age, race, maternal marital status, education, and income, prenatal tobacco exposure, maternal depression, Home Observation for Measurement of the Environment total score, household density, asthma severity, and use of asthma medications. RESULTS: Exposure to SHS was associated with sleep problems, including longer sleep-onset delay (P = .004), sleep-disordered breathing (P = .02), parasomnias (P = .002), daytime sleepiness (P = .022), and overall sleep disturbance (P = .0002). CONCLUSIONS: We conclude that exposure to SHS is associated with increased sleep problems among children with asthma.