bluuebunny/crossref_metadata_2025 huggingface dataset:
Phase Diagram Visualization via Continuously-Fed Crystallization: Experiments and Model
Authors: Sugiyama Masano T. , Barocas Victor H.
Published: November 2013

A protein’s atomic level three-dimensional structure is typically determined by X-ray diffraction of a high-quality protein crystal (Figure 1a). The X-ray bream is diffracted inside the crystal producing spots at various locations (Figure 1b) which can be used to back out the location of the electron cloud of the protein which is used to solve the structure (Figure 1c). The current bottleneck in these structural determination projects is in growing a diffraction quality protein crystal. Current growth methods involve testing hundreds of conditions in this multi-parametric process without knowledge of the protein phase diagram (PD). In this work, a microfluidic crystallization chamber is manufactured to allow phase diagram visualization to predict the PD of a protein in a single experiment. This phase diagram visualizer (PDV) screens a large range of protein and salt concentrations by controlling the transport mechanism (convection and diffusion) of both salt and protein. The PDV has been fabricated and its flow and concentration profiles have been determined using a computational model. The PDV has predicted the metastable line of the phase diagram for tetragonal lysozyme (known PD) and the solubility line for triclinic lysozyme (unknown PD).
In Vivo Quantification of Human Coronary Artery Deformation From Cardiac-Gated Computed Tomography Data
Authors: Choi Gilwoo , Dusch Marie N. , Xiong Guanglei , Xiao Nan , Cheng Christopher P. , Taylor Charles A.
Published: November 2013

Despite significant advances in percutaneous coronary interventions (PCI), bifurcation lesions still remain technically challenging for treatment. In an attempt to treat bifurcation lesions, innovative interventional techniques such as T-stenting, V-stenting and crush stenting have been developed. However, stenting both main and branch vessels inherently involves geometrical constraint on the devices at the site of a branch junction. Moreover, dynamic cardiac motion may cause significant deformation of the coronary artery (Fig. 1) and hence may adversely impact the functionality as well as durability of stents. This critical issue has been emphasized by recent studies on stent strut fracture-induced restenosis in a bifurcation lesion [1]. Although it has been hypothesized that cardiac motion causes significant mechanical stress on coronary stents, three-dimensional (3D) characteristics of the coronary artery deformation are not well understood. The purpose of this study was to quantify the change in the bifurcation angle between the left anterior descending coronary artery (LAD) and left circumflex artery (LCX), and the curvature change of the LAD during the cardiac cycle.
A Realistic Representation of the Rabbit Aorta for Use in Computational Haemodynamic Studies
Authors: Vincent Peter E. , Hunt Anthony A. E. , Grinberg Leopold , Sherwin Spencer J. , Weinberg Peter D.
Published: November 2013

Atherosclerosis is a common cardiovascular disease, characterised by the formation of lipid rich lesions within the walls of large arteries. Onset of atherosclerosis is observed to occur in a spatially heterogeneous fashion, with lesion sites located in regions of arterial branching and high curvature. Since blood flow patterns are also spatially heterogeneous within arteries, it has been postulated that flow may play an important role in modulating atherogenesis.
Design Optimization of an In Vitro Shear Stress and Mass Transfer Modifier for Endothelial Cell Culture
Authors: Van Doormaal Mark A. , Ethier C. Ross
Published: November 2013

Atherosclerosis, a disease of the large and medium arteries, is the leading cause of death in Western countries. Fluid dynamic and mass transfer phenomena are thought to play a role in the initiation and progression of atherosclerosis [1–3]. Atherosclerotic lesions are known to localize to areas such as bifurcations and curved arterial segments where shear stress and mass transfer patterns differ from those in straight arteries. However, the precise roles of wall shear stress and mass transfer in the localization of atherosclerotic lesions are not known, and this remains an active area of research. Determining the separate roles of wall shear stress and mass transfer in atherosclerosis is made more difficult because areas of abnormal wall shear stress often co-localize with areas of abnormal mass transfer.
Elasticity and Strength of Beta-Sheet Protein Materials: Geometric Confinement and Size Effects
Authors: Keten Sinan , Buehler Markus J.
Published: November 2013

Elasticity and strength of proteins influence their biological functions. Under external forces, many proteins exhibit entropic elasticity with a characteristic stiffening elastic behavior and unravel due to the rupture of interstrand H-bonds. We develop a fracture mechanics based theoretical framework that considers the free energy competition between entropic elasticity of polypeptide chains and rupture of peptide hydrogen bonds, which we use here to provide an explanation for the intrinsic strength limit of protein domains at vanishing rates [1, 2]. Our analysis predicts that individual protein domains stabilized only by hydrogen bonds cannot exhibit rupture forces larger than 100–300 pN in the asymptotic quasi-static limit. This result explains earlier experimental and computational observations that suggest such a universal, asymptotic strength limit at vanishing pulling rates. We show that the rupture strength of H-bond assemblies in beta-sheets is governed by geometric confinement effects, suggesting that clusters of at most 3–4 H-bonds break concurrently, even under uniform shear loading of a much larger number of H-bonds. These strength, elasticity and size effect predictions all agree well with recent experimental findings and proteomics data. Our model confirms that fracture mechanics concepts, previously primarily applied to macroscale fracture phenomena, can also be directly applied at nanoscale, to be used for describing failure mechanisms in protein materials. Our strength and optimal size predictions lead to a key hypothesis: confined H-bond clusters are prevalent in alpha helices, beta-sheets and beta-solenoids, perhaps as an evolutionary design principle that derives from generic mechanical properties of the fundamental building blocks of life.
Autonomous Effects of Shear Stress and Cyclic Circumferential Stretch Regarding Endothelial Dysfunction and Oxidative Stress: An Ex Vivo Arterial Model
Authors: Thacher Tyler , da Silva Rafaela , Silacci Paolo , Stergiopulos Nikos
Published: November 2013

Within the vasculature endothelial cells are constantly exposed to dynamic mechanical forces generated by pulsatile blood flow. Two stimuli known to modulate endothelial function are shear stress and cyclic circumferential strain. Yet, in most studies these two stimuli are simultaneously coupled in-vivo, making it very difficult to understand their individual contributions to vascular disease. Some attempts have been made to de-couple stretch and shear stress in-vitro by using different cell lines in a variety of stretch systems and flow chambers, straying from reality and making it hard to draw definitive conclusions. In this study we wish to find a compromise between the in-vivo and in-vitro work of the past by studying the independent effects of shear stress and cyclic stretch and how they contribute to endothelial dysfunction.
Micro-Meso Scale Model of Electrospun Poly (Ester Urethane) Urea Scaffolds
Authors: D’Amore Antonio , Stella John A. , Schmidt David E. , Wagner William R. , Sacks Michael S.
Published: November 2013

Soft tissue engineering applications require accurate descriptions of native and engineered tissue microstructure and their contributions to global mechanical behavior [1–6]. Moreover, micro scale based mechanical models can be used to: (1) guide tissue engineering scaffold design, (2) provide a better understanding of cellular mechanical and metabolic response to local micro-structural deformations, and (3) investigate structural changes as a function of deformation across multiple scales. We present a novel approach to automatically collect micro-architectural data (fibers overlaps, fiber connectivity, and fiber orientation) from SEM images of electrospun poly (ester urethane) urea (PEUU) to recreate statistically equivalent scaffold mechanical models. More importantly, an appropriate representative volume element (RVE) size was selected to fully capture both critical micro-scale architectural information, as well as reproducing the larger-scale directional long fiber mechanical behavior. This approach produced material models by specifying fiber overlap density, fiber orientation, and connectivity allowing the bulk mechanical response to be determined at the meso and micro scale via FEM simulations.
Collagen Molecular Conformation Exhibits Strain-Rate Dependent Response to Axial Deformation in Silico
Authors: Bourne Jonathan W. , Torzilli Peter A.
Published: November 2013

Fibrillar collagens are a group of structural proteins that self assemble into a complex ordered structure of interconnected molecules to form supramolecular fibril structures. These collagens have three subgroups based on sequence similarity, of which clade A includes the most abundant fibrillar collagens, types I, II, and III. The fibrous hierarchical structures starts with individual collagen molecules that are crosslinked by enzymes to other collagen molecules to form micro fibrils, which aggregate and link to form sub fibrils, then larger fibrils and in some tissues continuing to assemble into larger levels of fascicles and above.
In-Vivo Force Estimation of the Anterior Cruciate Ligament
Authors: Hosseini Ali , Gill Thomas J. , Li Guoan
Published: November 2013

The knowledge of in-vivo ACL forces is instrumental for understanding ACL injury mechanisms and for improving surgical ACL reconstruction techniques. Several in-vitro investigations have measured ACL forces in response to various loads applied to the knee. However, in-vivo ACL forces in response to controlled loading are still unknown. The objective of this study was to estimate the force of healthy ACL as well as the possible upper bound of ACL forces under an increasing axial tibial loading in living subjects using a non-invasive method.
Identifying the Effects of Knee Anatomy Variation on the Envelope of Knee Motion (Varus-Valgus) Using Principal Components
Authors: Mane Amit M. , Clary Chadd W. , Reeve Amber N. , Maletsky Lorin P. , FitzPatrick David
Published: November 2013

The motion patterns of the human knee joint depend on its passive motion characteristics, which are described by the ligamentious and articular constraints. Since active motions, like walking and squatting are believed to fall within a passive envelope, the basis for the understanding of the knee joint kinematics lies in the description of its passive constraint characteristics [1]. Although several authors studied passive envelope characteristics of a knee, it is not clear from the literature which anatomical structures guide the knee in passive or active motion and how their geometric arrangement produces the unique path of passive knee motion [1–3]. A few mathematical models have been developed to study the structures that guide the passive knee motion [1, 2]. However, their hypotheses were not supported by a sufficiently detailed ligament bundle model, soft tissue properties, ligament insertion-origin sites and their intra-subject variability. To explain the relationship between knee anatomy and its variability with three-dimensional knee motion completely, new methodology must be developed. The objective of the present study was to estimate the effects of variation in knee anatomical factors on the tibiofemoral passive envelope using a multivariate analysis technique, principal component (PC) analysis.
A Dynamic Stochastic Model of Frequency-Dependent Stress Fiber Alignment Induced by Cyclic Stretch
Authors: Hsu Hui-Ju , Lee Chin-Fu , Kaunas Roland
Published: November 2013

Actin stress fibers (SFs) are bundles of actin filaments anchored at each end via focal adhesions. Myosin-generated contraction leads to the development of tension, which extends SFs beyond their unloaded lengths. In human aortic ECs, the level of SF extension is maintained at a set-point level of ∼1.10 (1). SFs are also dynamic structures and their continuous assembly and disassembly is critical to cellular functions involving changes in cell shape. Further, deformation of the extracellular matrix perturbs SF extension, leading to compensatory responses such as the gradual alignment of SFs perpendicular to the principal direction of cyclic stretch. The extent of cell alignment has been shown to depend on the pattern of matrix stretch; however, it is unclear how cells distinguish between different patterns of stretch to determine their unique responses.
Applying Controlled Non-Homogeneous Deformation for In Vitro Mechanobiological Studies
Authors: Balestrini Jenna L. , Skorinko Jeremy K. , Gaudette Glenn R. , Billiar Kristen L.
Published: November 2013

The goal of this work is to develop and validate an experimental system to produce non-uniform strain patterns for studying the effects of strain magnitude, anisotropy, and gradients on cells culture. A commercially available cell stretching system was modified by affixing a 5 mm diameter glass coverslip to the center of each 35mm diameter flexible-bottomed well. The two-dimensional strain field was measured using high density mapping (HDM). Dermal fibroblasts were plated in the wells and cycled at 0.2 Hz for 2 days, stained for cytoskeletal observation, and their orientation was examined with respect to the local principle strain directions. Preliminary results indicate that the addition of the rigid inclusion creates strong radial and circumferential strain gradients with simultaneous regions of strip biaxial and equibiaxial stretch in a single well. As expected from previous work, the cells oriented themselves perpendicular to the direction of principal strain. This study demonstrates the potential utility of using non-homogeneous but symmetric and reproducible strain fields for studying mechanobiology.
Texture analysis improves level set segmentation of the anterior abdominal wall
Authors: Xu Zhoubing , Allen Wade M. , Baucom Rebeccah B. , Poulose Benjamin K. , Landman Bennett A.
Published: November 2013

Purpose:

The treatment of ventral hernias (VH) has been a challenging problem for medical care. Repair of these hernias is fraught with failure; recurrence rates ranging from 24% to 43% have been reported, even with the use of biocompatible mesh. Currently, computed tomography (CT) is used to guide intervention through expert, but qualitative, clinical judgments, notably, quantitative metrics based on image‐processing are not used. The authors propose that image segmentation methods to capture the three‐dimensional structure of the abdominal wall and its abnormalities will provide a foundation on which to measure geometric properties of hernias and surrounding tissues and, therefore, to optimize intervention.

Methods:

In this study with 20 clinically acquired CT scans on postoperative patients, the authors demonstrated a novel approach to geometric classification of the abdominal. The authors’ approach uses a texture analysis based on Gabor filters to extract feature vectors and follows a fuzzy c‐means clustering method to estimate voxelwise probability memberships for eight clusters. The memberships estimated from the texture analysis are helpful to identify anatomical structures with inhomogeneous intensities. The membership was used to guide the level set evolution, as well as to derive an initial start close to the abdominal wall.

Results:

Segmentation results on abdominal walls were both quantitatively and qualitatively validated with surface errors based on manually labeled ground truth. Using texture, mean surface errors for the outer surface of the abdominal wall were less than 2 mm, with 91% of the outer surface less than 5 mm away from the manual tracings; errors were significantly greater (2–5 mm) for methods that did not use the texture.

Conclusions:

The authors’ approach establishes a baseline for characterizing the abdominal wall for improving VH care. Inherent texture patterns in CT scans are helpful to the tissue classification, and texture analysis can improve the level set segmentation around the abdominal region.
Translating the Brain-Machine Interface
Authors: Thakor Nitish V.
Published: November 2013

Brain-machine interfaces hold promise for the recovery of sensory and motor functions, but translational challenges remain.
Specificity Residues Determine Binding Affinity for Two-Component Signal Transduction Systems
Authors: Willett Jonathan W. , Tiwari Nitija , Müller Susanne , Hummels Katherine R. , Houtman Jon C. D. , Fuentes Ernesto J. , Kirby John R.
Published: November 2013

Two-component systems (TCS) comprise histidine kinases and their cognate response regulators and allow bacteria to sense and respond to a wide variety of signals. Histidine kinases (HKs) phosphorylate and dephosphorylate their cognate response regulators (RRs) in response to stimuli. In general, these reactions appear to be highly specific and require an appropriate association between the HK and RR proteins. The
Myxococcus xanthus
genome encodes one of the largest repertoires of signaling proteins in bacteria (685 open reading frames [ORFs]), including at least 127 HKs and at least 143 RRs. Of these, 27 are
bona fide
NtrC-family response regulators, 21 of which are encoded adjacent to their predicted cognate kinases. Using system-wide profiling methods, we determined that the HK-NtrC RR pairs display a kinetic preference during both phosphotransfer and phosphatase functions, thereby defining cognate signaling systems in
M. xanthus
. Isothermal titration calorimetry measurements indicated that cognate HK-RR pairs interact with dissociation constants (
K

d

) of approximately 1 µM, while noncognate pairs had no measurable binding. Lastly, a chimera generated between the histidine kinase, CrdS, and HK1190 revealed that residues conferring phosphotransfer and phosphatase specificity dictate binding affinity, thereby establishing discrete protein-protein interactions which prevent cross talk. The data indicate that binding affinity is a critical parameter governing system-wide signaling fidelity for bacterial signal transduction proteins.

IMPORTANCE
Using
in vitro
phosphotransfer and phosphatase profiling assays and isothermal titration calorimetry, we have taken a system-wide approach to demonstrate specificity for a family of two-component signaling proteins in
Myxococcus xanthus
. Our results demonstrate that previously identified specificity residues dictate binding affinity and that phosphatase specificity follows phosphotransfer specificity for cognate HK-RR pairs. The data indicate that preferential binding affinity is the basis for signaling fidelity in bacterial two-component systems.
Sequence-Defined Transposon Mutant Library of Burkholderia thailandensis
Authors: Gallagher Larry A. , Ramage Elizabeth , Patrapuvich Rapatbhorn , Weiss Eli , Brittnacher Mitch , Manoil Colin
Published: November 2013

We constructed a near-saturation transposon mutant library for
Burkholderia thailandensis
, a low-virulence surrogate for the causative agent of melioidosis (
Burkholderia pseudomallei
). A primary set of nearly 42,000 unique mutants (~7.5 mutants/gene) was generated using transposon Tn
5
derivatives. The strains carry insertions in 87% of the predicted protein-coding genes of the organism, corresponding to nearly all of those nonessential for growth on nutrient agar. To achieve high genome coverage, we developed procedures for efficient sequence identification of insertions in extremely GC-rich regions of DNA. To facilitate strain distribution, we created a secondary library with two mutants per gene for which most transposon locations had been confirmed by resequencing. A map of mutations in the two-allele library and procedures for obtaining strains can be found at
http://tools.nwrce.org/tn_mutants/
and
http://www.gs.washington.edu/labs/manoil/
. The library should facilitate comprehensive mutant screens and serve as a source of strains to test predicted genotype-phenotype associations.

IMPORTANCE
The Gram-negative bacterium
Burkholderia pseudomallei
is a biothreat agent due to its potential for aerosol delivery and intrinsic antibiotic resistance and because exposure produces pernicious infections. Large-scale studies of
B. pseudomallei
are limited by the fact that the organism must be manipulated under biological safety level 3 conditions. A close relative of
B. pseudomallei
called
Burkholderia thailandensis
, which can be studied under less restrictive conditions, has been validated as a low-virulence surrogate in studies of virulence, antibiotic resistance and other traits. To facilitate large-scale studies of
B. thailandensis
, we created a near-saturation, sequence-defined transposon mutant library of the organism. The library facilitates genetic studies that identify genotype-phenotype associations conserved in
B. pseudomallei
.
Two Distinct N-Glycosylation Pathways Process the Haloferax volcanii S-Layer Glycoprotein upon Changes in Environmental Salinity
Authors: Kaminski Lina , Guan Ziqiang , Yurist-Doutsch Sophie , Eichler Jerry
Published: November 2013

N-glycosylation in
Archaea
presents aspects of this posttranslational modification not seen in either
Eukarya
or
Bacteria
. In the haloarchaeon
Haloferax volcanii
, the surface (S)-layer glycoprotein can be simultaneously modified by two different N-glycans. Asn-13 and Asn-83 are modified by a pentasaccharide, whereas Asn-498 is modified by a tetrasaccharide of distinct composition, with N-glycosylation at this position being related to environmental conditions. Specifically, N-glycosylation of Asn-498 is detected when cells are grown in the presence of 1.75 but not 3.4 M NaCl. While deletion of genes encoding components of the pentasaccharide assembly pathway had no effect on the biosynthesis of the tetrasaccharide bound to Asn-498, deletion of genes within the cluster spanning
HVO
_
2046
to
HVO
_
2061
interfered with the assembly and attachment of the Asn-498-linked tetrasaccharide. Transfer of the “low-salt” tetrasaccharide from the dolichol phosphate carrier upon which it is assembled to S-layer glycoprotein Asn-498 did not require AglB, the oligosaccharyltransferase responsible for pentasaccharide attachment to Asn-13 and Asn-83. Finally, although biogenesis of the low-salt tetrasaccharide is barely discernible upon growth at the elevated salinity, this glycan was readily detected under such conditions in strains deleted of pentasaccharide biosynthesis pathway genes, indicative of cross talk between the two N-glycosylation pathways.

IMPORTANCE
In the haloarchaeon
Haloferax volcanii
, originally from the Dead Sea, the pathway responsible for the assembly and attachment of a pentasaccharide to the S-layer glycoprotein, a well-studied glycoprotein in this species, has been described. More recently, it was shown that in response to growth in low salinity, the same glycoprotein is modified by a novel tetrasaccharide. In the present study, numerous components of the pathway used to synthesize this “low-salt” tetrasaccharide are described. As such, this represents the first report of two N-glycosylation pathways able to simultaneously modify a single protein as a function of environmental salinity. Moreover, and to the best of our knowledge, the ability to N-glycosylate the same protein with different and unrelated glycans has not been observed in either
Eukarya
or
Bacteria
or indeed beyond the halophilic archaea, for which similar dual modification of the
Halobacterium salinarum
S-layer glycoprotein was reported.
Sp100 Provides Intrinsic Immunity against Human Papillomavirus Infection
Authors: Stepp Wesley H. , Meyers Jordan M. , McBride Alison A.
Published: November 2013

Most DNA viruses associate with, and reorganize, nuclear domain 10 (ND10) bodies upon entry into the host nucleus. In this study, we examine the roles of the ND10 components PML, Sp100, and Daxx in the establishment of human papillomavirus type 18 (HPV18) infection of primary human keratinocytes. HPV18 DNA or HPV18 quasivirus was introduced into primary human keratinocytes depleted of each ND10 protein by small interfering RNA technology, and genome establishment was determined by using a quantitative immortalization assay and measurements of viral transcription and DNA replication. Keratinocyte depletion of Sp100 resulted in a substantial increase in the number of HPV18-immortalized colonies and a corresponding increase in viral transcription and DNA replication. However, Sp100 repressed viral transcription and replication only during the initial stages of viral establishment, suggesting that Sp100 acts as a repressor of incoming HPV DNA.

IMPORTANCEThe intrinsic immune system provides a first-line defense against invading pathogens. Host cells contain nuclear bodies (ND10) that are important for antiviral defense, yet many DNA viruses localize here upon cell entry. However, viruses also disrupt, reorganize, and modify individual components of the bodies. In this study, we show that one of the ND10 components, Sp100, limits the infection of human skin cells by human papillomavirus (HPV). HPVs are important pathogens that cause many types of infection of the cutaneous and mucosal epithelium and are the causative agents of several human cancers. Understanding how host cells counteract HPV infection could provide insight into antimicrobial therapies that could limit initial infection.
Analysis of Interspike Interval of Dorsal Horn Neurons Evoked by Different Needle Manipulations at St36
Authors: Zhou Tao , Wang Jiang , Han Chun-Xiao , Torao Ishida , Guo Yi
Published: November 2013

Objectives

Previous research has suggested that different manual acupuncture (MA) manipulations may have different physiological effects. Recent studies have demonstrated that neural electrical signals are generated or changed when acupuncture is administered. In order to explore the effects of different MA manipulations on the neural system, an experiment was designed to record the discharges of wide dynamic range (WDR) neurons in the spinal dorsal horn evoked by MA at different frequencies (0.5, 1, 2 and 3 Hz) at ST36.

Methods

Microelectrode extracellular recordings were used to record the discharges of WDR neurons evoked by different MA manipulations. Approximate firing rate and coefficient of variation of interspike interval (ISI) were used to extract the characteristic parameters of the neural electrical signals after spike sorting, and the neural coding of the evoked discharges by different MA manipulations was obtained.

Results

Our results indicated that the neuronal firing rate and time sequences of ISI showed distinct clustering properties for different MA manipulations, which could distinguish them effectively.

Conclusions

The combination of firing rate and ISI codes carries information about the acupuncture stimulus frequency. Different MA manipulations appear to change the neural coding of electrical signals in the spinal dorsal horn through WDR neurons.
Gag Reflex Control through Acupuncture: A Case Series
Authors: Bilello Giuseppa , Fregapane Antonella
Published: November 2013

Background

Many patients avoid dental appointments because of severe gagging when they have work performed, such as taking impressions. There are several methods known to alleviate gagging, and some studies have suggested that acupuncture may be effective in reducing gag reflex. The aim of the present study therefore was to evaluate whether acupuncture can produce a reduction of the gag reflex.

Methods

A total of 20 patients, aged between 19 and 80 years, with history of gag reflex on taking dental impressions, were recruited. All patients fulfilling the inclusion criteria had an upper and lower dental alginate impression taken without acupuncture, and a second upper and lower alginate impression taken immediately after acupuncture based on traditional Chinese medicine. After each impression, the patients recorded their emetic sensation using a visual analogue scale (VAS).

Results

The results showed a significant (p<0.05) reduction in the gag reflex scores after acupuncture. For upper impressions, they fell from 6.8 (1.1) to 1.1 (1.1); and for lower impressions, from 5.45 (1.0) to 0.4 (0.7) (mean (SD)).

Conclusions

The findings from our study suggest that acupuncture may be useful for preventing and treating gag reflex, and justifies further study.
Chronostratigraphy of Eocene volcanism, central British Columbia
Authors: Bordet Esther , Mihalynuk Mitchell G. , Hart Craig J.R. , Mortensen Jim K. , Friedman Richard M. , Gabites Janet
Published: November 2013

Onset and termination of Eocene felsic volcanism in the Chilcotin Plateau of central British Columbia is constrained between 54.6 and 46.6 Ma by 33 new U–Pb and 40Ar/39Ar isotopic age determinations. Dates were obtained from representative felsic coherent and fragmental volcanic rocks that comprise the Ootsa Lake Group. The resulting chronostratigraphy shows that magma compositions evolved from felsic to intermediate, with no spatial migration of the volcanic activity. Rhyolitic compositions are oldest; and are overlain by dacitic rocks with varied phenocrysts assemblages. In many parts of the Chilcotin Plateau, the Eocene stratigraphy is capped by distinctive vitreous black dacite lavas, which are contemporaneous with andesitic lavas of the Endako Group in the Nechako Plateau to the north. Crystallization ages from Ootsa Lake Group rocks of the Chilcotin Plateau overlap age determinations from correlative rocks of the Nechako Plateau and southern BC. Collectively, this geochronological dataset supports previous suggestions of a voluminous Early Eocene-aged (∼55–46 Ma) period of volcanism in the Intermontane Belt. The abrupt initiation of volcanism, as well as the wide extent, thickness, and compositions that characterize Eocene volcanic rocks may be explained by cessation of subduction and formation of a slab gap beneath British Columbia in the Early Eocene.
A vlHMM approach to context-aware search
Authors: Liao Zhen , Jiang Daxin , Pei Jian , Huang Yalou , Chen Enhong , Cao Huanhuan , Li Hang
Published: November 2013

Capturing the context of a user's query from the previous queries and clicks in the same session leads to a better understanding of the user's information need. A context-aware approach to document reranking, URL recommendation, and query suggestion may substantially improve users' search experience. In this article, we propose a general approach to context-aware search by learning avariable length hidden Markov model(vlHMM) from search sessions extracted from log data. While the mathematical model is powerful, the huge amounts of log data present great challenges. We develop several distributed learning techniques to learn a very large vlHMM under themap-reduceframework. Moreover, we construct feature vectors for each state of the vlHMM model to handle users' novel queries not covered by the training data. We test our approach on a raw dataset consisting of 1.9 billion queries, 2.9 billion clicks, and 1.2 billion search sessions before filtering, and evaluate the effectiveness of the vlHMM learned from the real data on three search applications: document reranking, query suggestion, and URL recommendation. The experiment results validate the effectiveness of vlHMM in the applications of document reranking, URL recommendation, and query suggestion.
Architecture customization of on-chip reconfigurable accelerators
Authors: Yoon Jonghee W. , Lee Jongeun , Park Sanghyun , Kim Yongjoo , Lee Jinyong , Paek Yunheung , Cho Doosan
Published: November 2013

Integrating coarse-grained reconfigurable architectures (CGRAs) into a System-on-a-Chip (SoC) presents many benefits as well as important challenges. One of the challenges is how to customize the architecture for the target applications efficiently and effectively without performing explicit design space exploration. In this article we present a novel methodology for incremental interconnect customization of CGRAs that can suggest a new interconnection architecture which is able to maximize the performance for a given set of application kernels while minimizing the hardware cost. In our methodology, we translate the problem of interconnect customization into that of inexact graph matching, and we devised a heuristic for A* search algorithm to efficiently solve the inexact graph matching problem. Our experimental results demonstrate that our customization method can quickly find application-optimized interconnections that exhibit 80% higher performance on average compared to the base architecture which has mesh interconnections, with little energy and hardware increase in interconnections and muxes.
A bottom-up, knowledge-aware approach to integrating and querying web data services
Authors: Quarteroni Silvia , Brambilla Marco , Ceri Stefano
Published: November 2013

As a wealth of data services is becoming available on the Web, building and querying Web applications that effectively integrate their content is increasingly important. However, schema integration and ontology matching with the aim of registering data services often requires a knowledge-intensive, tedious, and error-prone manual process.

We tackle this issue by presenting a bottom-up, semi-automatic service registration process that refers to an external knowledge base and uses simple text processing techniques in order to minimize and possibly avoid the contribution of domain experts in the annotation of data services. The first by-product of this process is a representation of the domain of data services as an entity-relationship diagram, whose entities are named after concepts of the external knowledge base matching service terminology rather than being manually created to accommodate an application-specific ontology. Second, a three-layer annotation of service semantics (service interfaces, access patterns, service marts) describing how services “play” with such domain elements is also automatically constructed at registration time. When evaluated against heterogeneous existing data services and with a synthetic service dataset constructed using Google Fusion Tables, the approach yields good results in terms of data representation accuracy.

We subsequently demonstrate that natural language processing methods can be used to decompose and match simple queries to the data services represented in three layers according to the preceding methodology with satisfactory results. We show how semantic annotations are used at query time to convert the user's request into an executable logical query. Globally, our findings show that the proposed registration method is effective in creating a uniform semantic representation of data services, suitable for building Web applications and answering search queries.
Making Decisions about Privacy
Authors: Knijnenburg Bart P. , Kobsa Alfred
Published: November 2013

Recommender systems increasingly use contextual and demographical data as a basis for recommendations. Users, however, often feel uncomfortable providing such information. In a privacy-minded design of recommenders, users are free to decide for themselves what data they want to disclose about themselves. But this decision is often complex and burdensome, because the consequences of disclosing personal information are uncertain or even unknown. Although a number of researchers have tried to analyze and facilitate such information disclosure decisions, their research results are fragmented, and they often do not hold up well across studies. This article describes a unified approach to privacy decision research that describes the cognitive processes involved in users’ “privacy calculus” in terms of system-related perceptions and experiences that act as mediating factors to information disclosure. The approach is applied in an online experiment with 493 participants using a mock-up of a context-aware recommender system. Analyzing the results with a structural linear model, we demonstrate that personal privacy concerns and disclosure justification messages affect the perception of and experience with a system, which in turn drive information disclosure decisions. Overall, disclosure justification messages do not increase disclosure. Although they are perceived to be valuable, they decrease users’ trust and satisfaction. Another result is that manipulating the order of the requests increases the disclosure of items requested early but decreases the disclosure of items requested later.
Rating Bias and Preference Acquisition
Authors: Freyne Jill , Berkovsky Shlomo , Smith Gregory
Published: November 2013

Personalized systems and recommender systems exploit implicitly and explicitly provided user information to address the needs and requirements of those using their services. User preference information, often in the form of interaction logs and ratings data, is used to identify similar users, whose opinions are leveraged to inform recommendations or to filter information. In this work we explore a different dimension of information trends in user bias and reasoning learned from ratings provided by users to a recommender system. Our work examines the characteristics of a dataset of 100,000 user ratings on a corpus of recipes, which illustrates stable user bias towards certain features of the recipes (cuisine type, key ingredient, and complexity). We exploit this knowledge to design and evaluate a personalized rating acquisition tool based on active learning, which leverages user biases in order to obtain ratings bearing high-value information and to reduce prediction errors with new users.
Common-source-line array
Authors: Zhao Bo , Yang Jun , Zhang Youtao , Chen Yiran , Li Hai
Published: November 2013

Traditional array organization of bipolar nonvolatile memories such as STT-MRAM and memristor utilizes two bitlines for cell manipulations. With technology scaling, such bitline pair will soon become the bottleneck for further density improvement. In this article we propose a novel common-source-line array architecture, which uses a shared source-line along the row, leaving only one bitline per column. We elaborate the array design to ensure reliability, and demonstrate its effectiveness on STT-MRAM and memristor memory arrays. Our study results show that with comparable latency and energy, the proposed common-source-line array can save 34% and 33% area for Memristor-RAM and STT-MRAM respectively, compared with corresponding dual-bitline arrays.
Adaptive virtual channel partitioning for network-on-chip in heterogeneous architectures
Authors: Lee Jaekyu , Li Si , Kim Hyesoon , Yalamanchili Sudhakar
Published: November 2013

Current heterogeneous chip-multiprocessors (CMPs) integrate a GPU architecture on a die. However, the heterogeneity of this architecture inevitably exerts different pressures on shared resource management due to differing characteristics of CPU and GPU cores. We consider how to efficiently share on-chip resources between cores within the heterogeneous system, in particular the on-chip network. Heterogeneous architectures use an on-chip interconnection network to access shared resources such as last-level cache tiles and memory controllers, and this type of on-chip network will have a significant impact on performance.

In this article, we propose a feedback-directed virtual channel partitioning (VCP) mechanism for on-chip routers to effectively share network bandwidth between CPU and GPU cores in a heterogeneous architecture. VCP dedicates a few virtual channels to CPU and GPU applications with separate injection queues. The proposed mechanism balances on-chip network bandwidth for applications running on CPU and GPU cores by adaptively choosing the best partitioning configuration. As a result, our mechanism improves system throughput by 15% over the baseline across 39 heterogeneous workloads.
Deflection routing in 3D network-on-chip with limited vertical bandwidth
Authors: Lee Jinho , Lee Dongwoo , Kim Sunwook , Choi Kiyoung
Published: November 2013

This article proposes a deflection routing for 3D NoC with serialized TSVs for vertical links. Compared to buffered routing, deflection routing provides area- and power-efficient communication and little loss of performance under low to medium traffic load. Under 3D environments, the deflection routing can yield even better performance than buffered routing when key aspects are properly taken into account. However, the existing deflection routing technique cannot be directly applied because the serialized TSV links will take longer time to send data than ordinary planar links and cause many problems. A naive deflection through a TSV link can cause significantly longer latency and more energy consumption even for communications through planar links. This article proposes a method to mitigate the effect and also solve arising deadlock and livelock problems. Evaluation of the proposed scheme shows its effectiveness in throughput, latency, and energy consumption.
"Mind the gap"
Authors: Huang Hui , Yin Kangxue , Gong Minglun , Lischinski Dani , Cohen-Or Daniel , Ascher Uri , Chen Baoquan
Published: November 2013

Concocting a plausible composition from several non-overlapping image pieces, whose relative positions are not fixed in advance and without having the benefit of priors, can be a daunting task. Here we propose such a method, starting with a set of sloppily pasted image pieces with gaps between them. We first extract salient curves that approach the gaps from non-tangential directions, and use likely correspondences between pairs of such curves to guide a novel
tele-registration
method that simultaneously aligns all the pieces together. A
structure-driven
image completion technique is then proposed to fill the gaps, allowing the subsequent employment of standard in-painting tools to finish the job.
Bilateral blue noise sampling
Authors: Chen Jiating , Ge Xiaoyin , Wei Li-Yi , Wang Bin , Wang Yusu , Wang Huamin , Fei Yun , Qian Kang-Lai , Yong Jun-Hai , Wang Wenping
Published: November 2013

Blue noise sampling is an important component in many graphics applications, but existing techniques consider mainly the spatial positions of samples, making them less effective when handling problems with non-spatial features. Examples include biological distribution in which plant spacing is influenced by non-positional factors such as tree type and size, photon mapping in which photon flux and direction are not a direct function of the attached surface, and point cloud sampling in which the underlying surface is unknown a priori. These scenarios can benefit from blue noise sample distributions, but cannot be adequately handled by prior art.

Inspired by bilateral filtering, we propose a bilateral blue noise sampling strategy. Our key idea is a general formulation to modulate the traditional sample distance measures, which are determined by sample position in spatial domain, with a similarity measure that considers arbitrary per sample attributes. This modulation leads to the notion of
bilateral
blue noise whose properties are influenced by not only the uniformity of the sample positions but also the similarity of the sample attributes. We describe how to incorporate our modulation into various sample analysis and synthesis methods, and demonstrate applications in object distribution, photon density estimation, and point cloud sub-sampling.
Inverse volume rendering with material dictionaries
Authors: Gkioulekas Ioannis , Zhao Shuang , Bala Kavita , Zickler Todd , Levin Anat
Published: November 2013

Translucent materials are ubiquitous, and simulating their appearance requires accurate physical parameters. However, physically-accurate parameters for scattering materials are difficult to acquire. We introduce an optimization framework for measuring bulk scattering properties of homogeneous materials (phase function, scattering coefficient, and absorption coefficient) that is more accurate, and more applicable to a broad range of materials. The optimization combines stochastic gradient descent with Monte Carlo rendering and a material dictionary to invert the radiative transfer equation. It offers several advantages: (1) it does not require isolating single-scattering events; (2) it allows measuring solids and liquids that are hard to dilute; (3) it returns parameters in physically-meaningful units; and (4) it does not restrict the shape of the phase function using Henyey-Greenstein or any other low-parameter model. We evaluate our approach by creating an acquisition setup that collects images of a material slab under narrow-beam RGB illumination. We validate results by measuring prescribed nano-dispersions and showing that recovered parameters match those predicted by Lorenz-Mie theory. We also provide a table of RGB scattering parameters for some common liquids and solids, which are validated by simulating color images in novel geometric configurations that match the corresponding photographs with less than 5% error.
Reconstructing detailed dynamic face geometry from monocular video
Authors: Garrido Pablo , Valgaert Levi , Wu Chenglei , Theobalt Christian
Published: November 2013

Detailed facial performance geometry can be reconstructed using dense camera and light setups in controlled studios. However, a wide range of important applications cannot employ these approaches, including all movie productions shot from a single principal camera. For post-production, these require dynamic monocular face capture for appearance modification. We present a new method for capturing face geometry from monocular video. Our approach captures detailed, dynamic, spatio-temporally coherent 3D face geometry without the need for markers. It works under uncontrolled lighting, and it successfully reconstructs expressive motion including high-frequency face detail such as folds and laugh lines. After simple manual initialization, the capturing process is fully automatic, which makes it versatile, lightweight and easy-to-deploy. Our approach tracks accurate sparse 2D features between automatically selected key frames to animate a parametric blend shape model, which is further refined in pose, expression and shape by temporally coherent optical flow and photometric stereo. We demonstrate performance capture results for long and complex face sequences captured indoors and outdoors, and we exemplify the relevance of our approach as an enabling technology for model-based face editing in movies and video, such as adding new facial textures, as well as a step towards enabling everyone to do facial performance capture with a single affordable camera.
PatchNet
Authors: Hu Shi-Min , Zhang Fang-Lue , Wang Miao , Martin Ralph R. , Wang Jue
Published: November 2013

We introduce
PatchNets
, a compact, hierarchical representation describing structural and appearance characteristics of image regions, for use in image editing. In a PatchNet, an image region with coherent appearance is summarized by a graph node, associated with a single representative patch, while geometric relationships between different regions are encoded by labelled graph edges giving contextual information. The hierarchical structure of a PatchNet allows a coarse-to-fine description of the image. We show how this PatchNet representation can be used as a basis for interactive, library-driven, image editing. The user draws rough sketches to quickly specify editing constraints for the target image. The system then automatically queries an image library to find semantically-compatible candidate regions to meet the editing goal. Contextual image matching is performed using the PatchNet representation, allowing suitable regions to be found and applied in a few seconds, even from a library containing thousands of images.