bluuebunny/crossref_metadata_2025_split huggingface dataset:
ON TENSOR PRODUCTS OF WEAK MIXING VECTOR SEQUENCES AND THEIR APPLICATIONS TO UNIQUELY E-WEAK MIXING C*-DYNAMICAL SYSTEMS
Authors: MUKHAMEDOV FARRUKH 
Published: October 2011

AbstractWe prove that, under certain conditions, uniform weak mixing (to zero) of the bounded sequences in Banach space implies uniform weak mixing of their tensor product. Moreover, we prove that ergodicity of tensor product of the sequences in Banach space implies their weak mixing. As applications of the results obtained, we prove that the tensor product of uniquely E-weak mixing C*-dynamical systems is also uniquely E-weak mixing.
Combining meteorites and missions to explore Mars
Authors: McCoy Timothy J. , Corrigan Catherine M. , Herd Christopher D. K. 
Published: October 2011

Laboratory studies of meteorites and robotic exploration of Mars reveal scant atmosphere, no evidence of plate tectonics, past evidence for abundant water, and a protracted igneous evolution. Despite indirect hints, direct evidence of a martian origin came with the discovery of trapped atmospheric gases in one meteorite. Since then, the study of martian meteorites and findings from missions have been linked. Although the meteorite source locations are unknown, impact ejection modeling and spectral mapping of Mars suggest derivation from small craters in terrains of Amazonian to Hesperian age. Whereas most martian meteorites are young (< 1.3 Ga), the spread of whole rock isotopic compositions results from crystallization of a magma ocean > 4.5 Ga and formation of enriched and depleted reservoirs. However, the history inferred from martian meteorites conflicts with results from recent Mars missions, calling into doubt whether the igneous histor y inferred from the meteorites is applicable to Mars as a whole. Allan Hills 84001 dates to 4.09 Ga and contains fluid-deposited carbonates. Accompanying debate about the mechanism and temperature of origin of the carbonates came several features suggestive of past microbial life in the carbonates. Although highly disputed, the suggestion spurred interest in habitable extreme environments on Earth and throughout the Solar System. A flotilla of subsequent spacecraft has redefined Mars from a volcanic planet to a hydrologically active planet that may have harbored life. Understanding the history and habitability of Mars depends on understanding the coupling of the atmosphere, surface, and subsurface. Sample return that brings back direct evidence from these diverse reservoirs is essential.
Ultrahigh resolution protein structures using NMR chemical shift tensors
Authors: Wylie Benjamin J. , Sperling Lindsay J. , Nieuwkoop Andrew J. , Franks W. Trent , Oldfield Eric , Rienstra Chad M. 
Published: October 2011

NMR chemical shift tensors (CSTs) in proteins, as well as their orientations, represent an important new restraint class for protein structure refinement and determination. Here, we present the first determination of both CST magnitudes and orientations for
13
C
α
and
15
N (peptide backbone) groups in a protein, the β1 IgG binding domain of protein G from
Streptococcus
spp., GB1. Site-specific
13
C
α
and
15
N CSTs were measured using synchronously evolved recoupling experiments in which
13
C and
15
N tensors were projected onto the
1
H-
13
C and
1
H-
15
N vectors, respectively, and onto the
15
N-
13
C vector in the case of
13
C
α
. The orientations of the
13
C
α
CSTs to the
1
H-
13
C and
13
C-
15
N vectors agreed well with the results of ab initio calculations, with an rmsd of approximately 8°. In addition, the measured
15
N tensors exhibited larger reduced anisotropies in α-helical versus β-sheet regions, with very limited variation (18 ± 4°) in the orientation of the
z
-axis of the
15
N CST with respect to the
1
H-
15
N vector. Incorporation of the
13
C
α
CST restraints into structure calculations, in combination with isotropic chemical shifts, transferred echo double resonance
13
C-
15
N distances and vector angle restraints, improved the backbone rmsd to 0.16 Å (PDB ID code 2LGI) and is consistent with existing X-ray structures (0.51 Å agreement with PDB ID code 2QMT). These results demonstrate that chemical shift tensors have considerable utility in protein structure refinement, with the best structures comparable to 1.0-Å crystal structures, based upon empirical metrics such as Ramachandran geometries and
χ
1
/
χ
2
distributions, providing solid-state NMR with a powerful tool for de novo structure determination.
Structure determination of an intercalating ruthenium dipyridophenazine complex which kinks DNA by semiintercalation of a tetraazaphenanthrene ligand
Authors: Hall James P. , O’Sullivan Kyra , Naseer Abeer , Smith Jayden A. , Kelly John M. , Cardin Christine J. 
Published: October 2011

We describe a crystal structure, at atomic resolution (1.1 Å, 100 K), of a ruthenium polypyridyl complex bound to duplex DNA, in which one ligand acts as a wedge in the minor groove, resulting in the 51° kinking of the double helix. The complex cation Λ-[Ru(1,4,5,8-tetraazaphenanthrene)
2
(dipyridophenazine)]
2+
crystallizes in a 1∶1 ratio with the oligonucleotide d(TCGGCGCCGA) in the presence of barium ions. Each complex binds to one duplex by intercalation of the dipyridophenazine ligand and also by semiintercalation of one of the orthogonal tetraazaphenanthrene ligands into a second symmetrically equivalent duplex. The result is noncovalent cross-linking and marked kinking of DNA.
Evidence of denser MgSiO3glass above 133 gigapascal (GPa) and implications for remnants of ultradense silicate melt from a deep magma ocean
Authors: Murakami Motohiko , Bass Jay D. 
Published: October 2011

Ultralow velocity zones are the largest seismic anomalies in the mantle, with 10–30% seismic velocity reduction observed in thin layers less than 20–40 km thick, just above the Earth’s core-mantle boundary (CMB). The presence of silicate melts, possibly a remnant of a deep magma ocean in the early Earth, have been proposed to explain ultralow velocity zones. It is, however, still an open question as to whether such silicate melts are gravitationally stable at the pressure conditions above the CMB. Fe enrichment is usually invoked to explain why melts would remain at the CMB, but this has not been substantiated experimentally. Here we report in situ high-pressure acoustic velocity measurements that suggest a new transformation to a denser structure of MgSiO3glass at pressures close to those of the CMB. The result suggests that MgSiO3melt is likely to become denser than crystalline MgSiO3above the CMB. The presence of negatively buoyant and gravitationally stable silicate melts at the bottom of the mantle, would provide a mechanism for observed ultralow seismic velocities above the CMB without enrichment of Fe in the melt. An ultradense melt phase and its geochemical inventory would be isolated from overlying convective flow over geologic time.
Crystal structure of the octameric pore of staphylococcal γ-hemolysin reveals the β-barrel pore formation mechanism by two components
Authors: Yamashita Keitaro , Kawai Yuka , Tanaka Yoshikazu , Hirano Nagisa , Kaneko Jun , Tomita Noriko , Ohta Makoto , Kamio Yoshiyuki , Yao Min , Tanaka Isao 
Published: October 2011

Staphylococcal γ-hemolysin is a bicomponent pore-forming toxin composed of LukF and Hlg2. These proteins are expressed as water-soluble monomers and then assemble into the oligomeric pore form on the target cell. Here, we report the crystal structure of the octameric pore form of γ-hemolysin at 2.5 Å resolution, which is the first high-resolution structure of a β-barrel transmembrane protein composed of two proteins reported to date. The octameric assembly consists of four molecules of LukF and Hlg2 located alternately in a circular pattern, which explains the biochemical data accumulated over the past two decades. The structure, in combination with the monomeric forms, demonstrates the elaborate molecular machinery involved in pore formation by two different molecules, in which interprotomer electrostatic interactions using loops connecting β2 and β3 (loop A: Asp43-Lys48 of LukF and Lys37-Lys43 of Hlg2) play pivotal roles as the structural determinants for assembly through unwinding of the N-terminal β-strands (amino-latch) of the adjacent protomer, releasing the transmembrane stem domain folded into a β-sheet in the monomer (prestem), and interaction with the adjacent protomer.
Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines
Authors: Savojardo Castrense , Fariselli Piero , Casadio Rita 
Published: October 2011

Abstract
Motivation: Transmembrane β-barrels (TMBBs) are extremely important proteins that play key roles in several cell functions. They cross the lipid bilayer with β-barrel structures. TMBBs are presently found in the outer membranes of Gram-negative bacteria and of mitochondria and chloroplasts. Loop exposure outside the bacterial cell membranes makes TMBBs important targets for vaccine or drug therapies. In genomes, they are not highly represented and are difficult to identify with experimental approaches. Several computational methods have been developed to discriminate TMBBs from other types of proteins. However, the best performing approaches have a high fraction of false positive predictions.
Results: In this article, we introduce a new machine learning approach for TMBB detection based on N-to-1 Extreme Learning Machines that significantly outperforms previous methods achieving a Matthews correlation coefficient of 0.82, a probability of correct prediction of 0.92 and a sensitivity of 0.73.
Availability: The method and the cross-validation sets are available at the web page http://betaware.biocomp.unibo.it/BetAware.
Contact: piero.fariselli@unibo.it
MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories
Authors: Schmidtke Peter , Bidon-Chanal Axel , Luque F. Javier , Barril Xavier 
Published: October 2011

AbstractMotivation: A variety of pocket detection algorithms are now freely or commercially available to the scientific community for the analysis of static protein structures. However, since proteins are dynamic entities, enhancing the capabilities of these programs for the straightforward detection and characterization of cavities taking into account protein conformational ensembles should be valuable for capturing the plasticity of pockets, and therefore allow gaining insight into structure–function relationships.Results: This article describes a new method, called MDpocket, providing a fast, free and open-source tool for tracking small molecule binding sites and gas migration pathways on molecular dynamics (MDs) trajectories or other conformational ensembles. MDpocket is based on the fpocket cavity detection algorithm and a valuable contribution to existing analysis tools. The capabilities of MDpocket are illustrated for three relevant cases: (i) the detection of transient subpockets using an ensemble of crystal structures of HSP90; (ii) the detection of known xenon binding sites and migration pathways in myoglobin; and (iii) the identification of suitable pockets for molecular docking in P38 Map kinase.Availability: MDpocket is free and open-source software and can be downloaded at http://fpocket.sourceforge.net.Contact: pschmidtke@ub.eduSupplementary Information: Supplementary data are available at Bioinformatics online.
Shoulder Pain in Amyotrophic Lateral Sclerosis
Authors: Ho Doreen T , Ruthazer Robin , Russell James A 
Published: October 2011

Abstract

Objective:
To determine the frequency of shoulder pain in our amyotrophic lateral sclerosis (ALS) population and to explore potential associations with demographic and clinical features.

Methods:
We retrospectively reviewed the medical records of 193 patients with ALS patients seen at the Lahey Clinic between 2005 and 2009. Patients were categorized by the predominance of upper and lower motor neuron signs and the body regions initially involved. The frequency of shoulder pain was identified in each of these subgroups.

Results:
Forty-five (23%) of the 193 patients reported shoulder pain at some time during the course of their illness. Age, gender, manual labor, prior shoulder problems, ALS phenotype, and initial region of involvement were not correlated with shoulder pain. Patients with shoulder pain were more likely to develop proximal arm weakness during their illness and to report pain elsewhere.

Conclusions:
Despite the limitations posed by this retrospective study, it underscores the prevalence of shoulder pain in patients with ALS. Further studies to identify risk factors, mechanisms of, and treatments for shoulder pain in patients with ALS may benefit this population.
A Novel Biodegradable Septal Defect Occluder the “Chinese Lantern” Design, Proof of Concept
Authors: Wu Wei , Yip James , Tang Yong-Dan , Khoo Vincent , Kong Jen Fong , Duong-Hong Duc , Boey Freddy , Venkatraman Subbu S. 
Published: October 2011

Objective Atrial septal defect (ASD) is a general term used to describe an opening in the atrial septum that divides the two atria; unless the hole is occluded, it can give rise to serious complications. Given the need for percutaneous deployment for ASD or patent foramen ovale (PFO) occluders, all currently available devices are made of metals (specifically nitinol) and synthetic fabric. However, their permanent presence in the human body is not desirable due to the risks of long-term allergy, toxicity, and complications such as thrombus formation, device arm fracture, and nickel allergy. Once the hole is covered by a newly regenerated tissue, the device is no longer needed; thus it is ideal if the device is fully absorbed by the body when healing is completed. Methods The “Chinese Lantern” device is made of fully biodegradable polymers featured with a unique pull-fold mechanism. The device was inserted across the ASD/PFO model created on Yorkshire swines through a short sheath by hybrid open surgery. X-ray imaging, echocardiography, and postmortem histopathology were obtained during the 1-month follow-up study period. Results X-ray imaging showed that the devices were in satisfactory position and stable. Echocardiography showed that there is no shunting from the right atrium to the left atrium, indicating excellent sealing. The in vitro degradation study and postmortem explantation study confirmed that the devices have good integrity during the 1-month trial. Furthermore, the devices appeared to be completely endothelialized after 1 month. Conclusions This work proves the feasibility of interventional closure of ASD or PFO with an innovative biodegradable device, which we call the “Chinese Lantern” for its symbolic design.
Image-Guided Transapical Aortic Valve Implantation Sensorless Tracking of Stenotic Valve Landmarks in Live Fluoroscopic Images
Authors: Merk Denis R. , Karar Mohamed Esmail , Chalopin Claire , Holzhey David , Falk Volkmar , Mohr Friedrich W. , Burgert Oliver 
Published: October 2011

Objective Aortic valve stenosis is one of the most frequently acquired valvular heart diseases, accounting for almost 70% of valvular cardiac surgery. Transapical transcatheter aortic valve implantation has recently become a suitable minimally invasive technique for high-risk and elderly patients with severe aortic stenosis. In this article, we aim to automatically define a target area of valve implantation, namely, the area between the coronary ostia and the lowest points of two aortic valve cusps. Therefore, we present a new image-based tracking method of these aortic landmarks to assist in the placement of aortic valve prosthesis under live 2D fluoroscopy guidance. Methods We propose a rigid intensity-based image registration technique for tracking valve landmarks in 2D fluoroscopic image sequences, based on a real-time alignment of a contrast image including the initialized manual valve landmarks to each image of sequence. The contrast image is automatically detected to visualize aortic valve features when the aortic root is filled with a contrast agent. Results Our registration-based tracking method has been retrospectively applied to 10 fluoroscopic image sequences from routine transapical aortic valve implantation procedures. Most of all tested fluoroscopic images showed a successful tracking of valve landmarks, especially for the images without contrast agent injections. Conclusions A new intraoperative image-based method has been developed for tracking aortic valve landmarks in live 2D fluoroscopic images to assist transapical aortic valve implantations and to increase the overall safety of surgery as well.
Early Experience with Robotic-Assisted Lung Resection
Authors: Fortes Daniel L. , Tomaszek Sandra C. , Wigle Dennis A. 
Published: October 2011

Objective Robotic-assisted surgery is not widely accepted for general thoracic surgical procedures, and the technical advantages, cost effectiveness, and patient benefit are in question. Few reports have been published to date regarding clinical experience with this technology. We describe our first consecutive case experience with robotic-assisted lung resection. Methods A total of 23 robotic-assisted lung resections were performed from December 1, 2008, to September 30, 2010. Patients were selected on the basis of being candidates for a minimally invasive approach to their lung resection, including criteria such as known or suspected early-stage nonsmall-cell lung cancer, no prior thoracotomy, no neoadjuvant therapy, and a body mass index (BMI) less than 40 kg/cm2. Data on patient characteristics and perioperative results were collected retrospectively. Results Overall 90-day mortality was 0%. The total postoperative complication rate was 39%. Conversion of the robotic-assisted procedure to a video-assisted procedure was necessary in four patients (17%), and to a thoracotomy in one patient (4%). We assessed operative time, chest tube duration, and length of hospital stay. Comparison to published outcomes from the Society of Thoracic Surgeons database demonstrated comparable outcomes to standard approaches. Conclusions Robotic-assisted lung resection is safe and feasible, with comparable short-term outcomes to published results from video-assisted or open approaches.
Role of Gastroesophageal Reflux in Children With Unexplained Chronic Cough
Authors: Borrelli Osvaldo , Marabotto Caterina , Mancini Valentina , Aloi Marina , Macrì Francesco , Falconieri Paola , Lindley Keith J. , Cucchiara Salvatore 
Published: October 2011

ABSTRACTObjective:The relation between respiratory symptoms and gastroesophageal reflux (GER) is a matter of contention and debate, with limited data in children to substantiate or refute cause and effect. Moreover, there are few data on the relation between nonacid reflux and chronic cough in childhood. We aimed to describe the type and physical characteristics of reflux episodes in children with unexplained chronic cough.Patients and Methods:Forty‐five children with chronic cough underwent 24‐hour multichannel intraluminal impedance‐pH monitoring (MII‐pH monitoring). Symptom association probability (SAP) characterized the reflux‐cough association. Twenty children with erosive reflux disease (ERD) served as controls.Results:Twenty‐four children had cough‐related reflux (CRR), with 19 having no gastrointestinal symptoms. Twenty‐one had cough‐unrelated reflux (CUR). CRR and ERD had increased acid (AR), weakly acidic (WAc), and weakly alkaline (WAlk) reflux. Esophageal acid exposure time and acid clearance time were higher in ERD than in CRR and CUR. In the CRR group, of 158 cough episodes related to reflux episodes, 66% involved AR, 18% WAc, and 16% WAlk. Seventeen children had positive SAP, 7 for AR, 5 for both AR and WAc, 4 for both WAc and WAlk, and 1 for WAlk.Conclusions:In children with unexplained chronic cough, asymptomatic acid and nonacid GER is a potential etiologic factor. The increased acid exposure time and delayed acid clearance characteristic of ERD are absent in cough‐related GER. MII‐pH monitoring increases the likelihood of demonstrating a temporal association between the cough and all types of reflux.
Siglec‐F Inhibition Reduces Esophageal Eosinophilia and Angiogenesis in a Mouse Model of Eosinophilic Esophagitis
Authors: Rubinstein Eitan , Cho Jae Youn , Rosenthal Peter , Chao James , Miller Marina , Pham Alexa , Aceves Seema S. , Varki Ajit , Broide David H. 
Published: October 2011

ABSTRACTObjectives:Eosinophilic esophagitis (EoE) is a disorder characterized histologically by tissue eosinophilia. Sialic acid–binding immunoglobulin‐like lectin (Siglec‐F) is a receptor highly expressed on mouse eosinophils and mediates eosinophilic apoptosis. We investigated whether administration of an anti‐Siglec‐F Ab would reduce esophageal eosinophilic inflammation and remodeling in a mouse model of egg ovalbumin (OVA)–induced EoE.Subjects and Methods:Three groups of mice were studied (no OVA, OVA + anti‐Siglec‐F Ab, and OVA + isotype control Ab). Mice were sensitized intraperitoneally and then challenged chronically with intraesophageal OVA. Levels of esophageal eosinophils and features of remodeling (angiogenesis, vascular endothelial growth factor expression, deposition of fibronectin, basal zone hyperplasia, and fibrosis) were quantitated by immunohistochemistry and image analysis.Results:Administration of an anti‐Siglec‐F Ab to OVA‐challenged mice significantly reduced levels of esophageal eosinophils, down to levels noted in non‐OVA‐challenged mice. The anti‐Siglec‐F Ab also reduced features of OVA‐induced remodeling, including angiogenesis, basal zone hyperplasia, and fibronectin deposition. The reduced angiogenesis in anti‐Siglec‐F Ab‐treated mice was associated with reduced numbers of vascular endothelial growth factor–positive cells in the esophagus. The anti‐Siglec‐F antibody did not significantly reduce esophageal fibrosis as assessed by trichrome staining.Conclusions:Administration of an anti‐Siglec‐F antibody significantly decreased the number of eosinophils in the esophagus in a mouse model of OVA‐induced EoE. The reduction in eosinophilic inflammation was associated with a significant decrease in levels of angiogenesis, deposition of fibronectin, and basal zone hyperplasia. Studies in this pre‐clinical model of EoE suggest that Siglec‐F (and its human paralog Siglec‐8) may be novel therapeutic targets to reduce eosinophilic inflammation in EoE.