High-confidence Models Research Articles

Unmanned Aerial Vehicle Object Tracking by Correlation Filter with Adaptive Appearance Model.

With the increasing availability of low-cost, commercially available unmanned aerial vehicles (UAVs), visual tracking using UAVs has become more and more important due to its many new applications, including automatic navigation, obstacle avoidance, traffic monitoring, search and rescue, etc. However, real-world aerial tracking poses many challenges due to platform motion and image instability, such as aspect ratio change, viewpoint change, fast motion, scale variation and so on. In this paper, an efficient object tracking method for UAV videos is proposed to tackle these challenges. We construct the fused features to capture the gradient information and color characteristics simultaneously. Furthermore, cellular automata is introduced to update the appearance template of target accurately and sparsely. In particular, a high confidence model updating strategy is developed according to the stability function. Systematic comparative evaluations performed on the popular UAV123 dataset show the efficiency of the proposed approach.

A New Approach for Train Driver Tracking in Real Time

Find the main driver in the train cab and keep tracking him is the primary step for driver activity analysis in real time. But long-term robust human tracking is still a challenging task due to many practical factors. Most template-based tracking algorithms of templates often fail when encountering occlusion, pose variation and motion blur. In this paper, we propose a real-time algorithm based on correlation filters for long-term human tracking. To restore the false model caused by occlusion, we construct a conditional target re-detection mechanism. We adopted a high-confidence model update strategy to ensure the correct detection and avoid model drift problem. The experimental results indicate that the proposed algorithm is robust and accurate to variations in pose and heavy occlusion while runs at speed in real-time.

Genome assembly of the Pink Ipê (Handroanthus impetiginosus, Bignoniaceae), a highly valued, ecologically keystone Neotropical timber forest tree.

Background Handroanthus impetiginosus (Mart. ex DC.) Mattos is a keystone Neotropical hardwood tree widely distributed in seasonally dry tropical forests of South and Mesoamerica. Regarded as the “new mahogany,” it is the second most expensive timber, the most logged species in Brazil, and currently under significant illegal trading pressure. The plant produces large amounts of quinoids, specialized metabolites with documented antitumorous and antibiotic effects. The development of genomic resources is needed to better understand and conserve the diversity of the species, to empower forensic identification of the origin of timber, and to identify genes for important metabolic compounds.FindingsThe genome assembly covers 503.7 Mb (N50 = 81 316 bp), 90.4% of the 557-Mbp genome, with 13 206 scaffolds. A repeat database with 1508 sequences was developed, allowing masking of ∼31% of the assembly. Depth of coverage indicated that consensus determination adequately removed haplotypes assembled separately due to the extensive heterozygosity of the species. Automatic gene prediction provided 31 688 structures and 35 479 messenger RNA transcripts, while external evidence supported a well-curated set of 28 603 high-confidence models (90% of total). Finally, we used the genomic sequence and the comprehensive gene content annotation to identify genes related to the production of specialized metabolites.ConclusionsThis genome assembly is the first well-curated resource for a Neotropical forest tree and the first one for a member of the Bignoniaceae family, opening exceptional opportunities to empower molecular, phytochemical, and breeding studies. This work should inspire the development of similar genomic resources for the largely neglected forest trees of the mega-diverse tropical biomes.

HAMP Domain Rotation and Tilting Movements Associated with Signal Transduction in the PhoQ Sensor Kinase.

ABSTRACTHAMP domains are α-helical coiled coils that often transduce signals from extracytoplasmic sensing domains to cytoplasmic domains. Limited structural information has resulted in hypotheses that specific HAMP helix movement changes downstream enzymatic activity. These hypotheses were tested by mutagenesis and cysteine cross-linking analysis of the PhoQ histidine kinase, essential for resistance to antimicrobial peptides in a variety of enteric pathogens. These results support a mechanistic model in which periplasmic signals which induce an activation state generate a rotational movement accompanied by a tilt in α-helix 1 which activates kinase activity. Biochemical data and a high-confidence model of the PhoQ cytoplasmic domain indicate a possible physical interaction of the HAMP domain with the catalytic domain as necessary for kinase repression. These results support a model of PhoQ activation in which changes in the periplasmic domain lead to conformational movements in the HAMP domain helices which disrupt interaction between the HAMP and the catalytic domains, thus promoting increased kinase activity.

The validity and reliability of modelled neural and tissue properties of the ankle muscles in children with cerebral palsy

Spastic cerebral palsy (CP) is characterized by increased joint resistance, caused by a mix of increased tissue stiffness, as well as involuntary reflex and background muscle activity. These properties can be quantified using a neuromechanical model of the musculoskeletal complex and instrumented assessment. The construct validity of the neuromechanical parameters was examined (i.e. the internal model validity, effect of knee angle, speed and age, sensitivity to patients versus controls, spasticity severity and treatment), together with the repeatability. We included 38 children with CP and 35 controls. A motor driven footplate applied two slow (15°/s) and two fast (100°/s) rotations around the ankle joint, at two different knee angles. Ankle angle, torque and EMG of the gastrocnemius (GA), soleus (SO) and tibialis anterior (TA) muscle were used to optimize a nonlinear neuromuscular model. Outcome measures were tissue stiffness, reflex and background activity for GA, SO and TA. The internal model validity showed medium to high parameter confidence and good model fits. All parameter could discriminate between patients with CP and controls according to CP pathology. Other measures of external model validity (effect of test position, speed and age) showed behaviour along the lines of current knowledge of physiology. GA/SO background activity was sensitive to spasticity severity, but reflex activity was not. Preliminary data indicated that reflex activity was reduced after spasticity treatment. The between-trial and -day repeatability was moderate to good. The large variance between patients in the ratio of stiffness and neural resistance indicates that the method could potentially contribute to patient-specific treatment selection.

High-Confidence Vertical Positioning for Extended-Reach Wells

This article, written by Senior Technology Editor Dennis Denney, contains highlights of paper SPE 151441, ’High-Confidence Vertical Positioning for Extended-Reach Wells,’ by Nelson Mohammed, SPE, and Michael Terpening, SPE, Schlumberger, prepared for the 2012 IADC/SPE Drilling Conference and Exhibition, San Diego, California, 6-8 March. The paper has not been peer reviewed. Establishing confidence in the vertical thickness of the hydrocarbon column is critical in development-project economics. True-vertical-depth (TVD) uncertainty associated with the hydrocarbon column, in the absence of vertical-appraisal-well data, may be dominated by the propagation of inclination error in nonvertical or horizontal pilot wells. The challenges associated with establishing reliable hydrocarbon-column height can be extreme if high-step-out extended-reach (ER) wells are the primary source of appraisal data. Also, thin reservoirs targeted by ER wells often have a limited vertical target on the basis of standard TVD-error-propagation models. Three complementary elements were integrated to improve the TVD uncertainty associated with ER well paths. Application Challenge The application was made in an offshore field near Sakhalin Island in eastern Russia. The structure has several appraisal wells drilled by various operators through the 1980s. A recent development-drilling campaign with ER wells was conducted that enabled evaluating and testing of the proposed high-confidence error models. Vintage appraisal wells proved the presence of oil and provided information on the hydraulic regime with flow tests. However, there was no full penetration in a single well of the hydrocarbon column in the main sands, resulting in large gas/oil-contact (GOC) and oil/water-contact (OWC) uncertainties that precluded an economically reliable measure of oil-in-place volumes. The quality of available seismic data was poor, and environmental and economic limitations existed for upgrading data or further appraisal drilling to address uncertainties. The chosen development option was to drill from a shore location and use extended-reach-drilling (ERD) techniques with horizontal production holes to reach the reservoirs. Hence, certainty of the OWCs and GOCs was essential for proper placement of the horizontal production holes within the oil column. The vertical uncertainty associated with ERD would need to be minimized to assess the hydrocarbon column and to place the horizontal production wells properly. As Fig. 1 shows, the first two production wells were designed to use separate pilot holes, downward through water (Well-1) and upward through gas (Well-2), to acquire formation-pressure-while-drilling data to characterize the hydraulic regime better. The primary objective was a direct determination of the fluid-column contacts, or an accurate inference of the contacts through a well- defined pressure-gradient profile. TVD Assurance Through Synergy Redundant data from two separate but comparable inclination sensors in the same bottomhole assembly (BHA) [in the measurement-while-drilling (MWD) and rotary-steering-system (RSS) tools, respectively] were used to permit a statistical reduction in the error from multiple independent measurements. Because the sensors are in separate sections of the same BHA, the data enable a robust cross check to ensure that the sag corrections for each sensor are simultaneously consistent.

Structural Characterization of Novel Pseudomonas aeruginosa Type IV Pilins

Pseudomonas aeruginosa type IV pili, composed of PilA subunits, are used for attachment and twitching motility on surfaces. P. aeruginosa strains express one of five phylogenetically distinct PilA proteins, four of which are associated with accessory proteins that are involved either in pilin posttranslational modification or in modulation of pilus retraction dynamics. Full understanding of pilin diversity is crucial for the development of a broadly protective pilus-based vaccine. Here, we report the 1.6-Å X-ray crystal structure of an N-terminally truncated form of the novel PilA from strain Pa110594 (group V), which represents the first non-group II pilin structure solved. Although it maintains the typical T4a pilin fold, with a long N-terminal α-helix and four-stranded antiparallel β-sheet connected to the C-terminus by a disulfide-bonded loop, the presence of an extra helix in the αβ-loop and a disulfide-bonded loop with helical character gives the structure T4b pilin characteristics. Despite the presence of T4b features, the structure of PilA from strain Pa110594 is most similar to the Neisseria gonorrhoeae pilin and is also predicted to assemble into a fiber similar to the GC pilus, based on our comparative pilus modeling. Interactions between surface-exposed areas of the pilin are suggested to contribute to pilus fiber stability. The non-synonymous sequence changes between group III and V pilins are clustered in the same surface-exposed areas, possibly having an effect on accessory protein interactions. However, based on our high-confidence model of group III PilA PA14, compensatory changes allow for maintenance of a similar shape.

Model-building strategies for low-resolution X-ray crystallographic data

The interpretation of low-resolution X-ray crystallographic data proves to be challenging even for the most experienced crystallographer. Ambiguity in the electron-density map makes main-chain tracing and side-chain assignment difficult. However, the number of structures solved at resolutions poorer than 3.5 A is growing rapidly and the structures are often of high biological interest and importance. Here, the challenges faced in electron-density interpretation, the strategies that have been employed to overcome them and developments to automate the process are reviewed. The methods employed in model generation from electron microscopy, which share many of the same challenges in providing high-confidence models of macromolecular structures and assemblies, are also considered.

Crystal Structure of the Herpes Simplex Virus 1 DNA Polymerase

Herpesviruses are the second leading cause of human viral diseases. Herpes Simplex Virus types 1 and 2 and Varicella-zoster virus produce neurotropic infections such as cutaneous and genital herpes, chickenpox, and shingles. Infections of a lymphotropic nature are caused by cytomegalovirus, HSV-6, HSV-7, and Epstein-Barr virus producing lymphoma, carcinoma, and congenital abnormalities. Yet another series of serious health problems are posed by infections in immunocompromised individuals. Common therapies for herpes viral infections employ nucleoside analogs, such as Acyclovir, and target the viral DNA polymerase, essential for viral DNA replication. Although clinically useful, this class of drugs exhibits a narrow antiviral spectrum, and resistance to these agents is an emerging problem for disease management. A better understanding of herpes virus replication will help the development of new safe and effective broad spectrum anti-herpetic drugs that fill an unmet need. Here, we present the first crystal structure of a herpesvirus polymerase, the Herpes Simplex Virus type 1 DNA polymerase, at 2.7 A resolution. The structural similarity of this polymerase to other alpha polymerases has allowed us to construct high confidence models of a replication complex of the polymerase and of Acyclovir as a DNA chain terminator. We propose a novel inhibition mechanism in which a representative of a series of non-nucleosidic viral polymerase inhibitors, the 4-oxo-dihydroquinolines, binds at the polymerase active site interacting non-covalently with both the polymerase and the DNA duplex.