bluuebunny/crossref_metadata_2025 huggingface dataset:
Chlamydia trachomatis Type III Secretion Proteins Regulate Transcription
Authors: Hanson Brett R. , Slepenkin Anatoly , Peterson Ellena M. , Tan Ming
Published: July 2015

The Scc4 protein (CT663) of the pathogenic bacterium
Chlamydia
has been described as a type III secretion (T3S) chaperone as well as an inhibitor of RNA polymerase. To examine if these roles are connected, we first investigated physical interactions between
Chlamydia trachomatis
Scc4 and the T3S chaperone Scc1 and a T3S substrate, CopN. In a yeast 3-hybrid assay, Scc4, Scc1, and CopN were all required to detect an interaction, which suggests that these proteins form a trimolecular complex. We also detected interactions between any two of these three T3S proteins in a pulldown assay using only recombinant proteins. We next determined whether these interactions affected the function of Scc4 as an inhibitor of RNA transcription. Using
Escherichia coli
as a heterologous
in vivo
system, we demonstrated that expression of
C. trachomatis
Scc4 led to a drastic decrease in transcript levels for multiple genes. However, coexpression of Scc4 with Scc1, CopN, or both alleviated Scc4-mediated inhibition of transcription. Scc4 expression also severely impaired
E. coli
growth, but this growth defect was reversed by coexpression of Scc4 with Scc1, CopN, or both, suggesting that the inhibitory effect of Scc4 on transcription and growth can be antagonized by interactions between Scc4, Scc1, and CopN. These findings suggest that the dual functions of Scc4 may serve as a bridge to link T3S and the regulation of gene expression in
Chlamydia
.

IMPORTANCE
This study investigates a novel mechanism for regulating gene expression in the pathogenic bacterium
Chlamydia
. The
Chlamydia
type III secretion (T3S) chaperone Scc4 has been shown to inhibit transcription by RNA polymerase. This study describes physical interactions between Scc4 and the T3S proteins Scc1 and CopN. Furthermore,
Chlamydia
Scc1 and CopN antagonized the inhibitory effects of Scc4 on transcription and growth in a heterologous
Escherichia coli
system. These results provide evidence that transcription in
Chlamydia
can be regulated by the T3S system through interactions between T3S proteins.
CovRS-Regulated Transcriptome Analysis of a Hypervirulent M23 Strain of Group A Streptococcus pyogenes Provides New Insights into Virulence Determinants
Authors: Bao Yun-Juan , Liang Zhong , Mayfield Jeffrey A. , Lee Shaun W. , Ploplis Victoria A. , Castellino Francis J.
Published: July 2015

The two-componentcontrolofvirulence (Cov) regulator (R)-sensor (S) (CovRS) regulates the virulence ofStreptococcus pyogenes(group AStreptococcus[GAS]). Inactivation of CovS during infection switches the pathogenicity of GAS to a more invasive form by regulating transcription of diverse virulence genes via CovR. However, the manner in which CovRS controls virulence through expression of extended gene families has not been fully determined. In the current study, the CovS-regulated gene expression profiles of a hypervirulentemm23GAS strain (M23ND/CovS negative [M23ND/CovS−]) and a noninvasive isogenic strain (M23ND/CovS+), under different growth conditions, were investigated. RNA sequencing identified altered expression of ∼349 genes (18% of the chromosome). The data demonstrated that M23ND/CovS−achieved hypervirulence by allowing enhanced expression of genes responsible for antiphagocytosis (e.g.,hasABC), by abrogating expression of toxin genes (e.g.,speB), and by compromising gene products with dispensable functions (e.g.,sfb1). Among these genes, several (e.g.,parEandparC) were not previously reported to be regulated by CovRS. Furthermore, the study revealed that CovS also modulated the expression of a broad spectrum of metabolic genes that maximized nutrient utilization and energy metabolism during growth and dissemination, where the bacteria encounter large variations in available nutrients, thus restructuring metabolism of GAS for adaption to diverse growth environments. From constructing a genome-scale metabolic model, we identified 16 nonredundant metabolic gene modules that constitute unique nutrient sources. These genes were proposed to be essential for pathogen growth and are likely associated with GAS virulence. The genome-wide prediction of genes associated with virulence identifies new candidate genes that potentially contribute to GAS virulence.

IMPORTANCEThe CovRS system modulates transcription of ∼18% of the genes in theStreptococcus pyogenesgenome. Mutations that inactivate CovR or CovS enhance the virulence of this bacterium. We determined complete transcriptomes of a naturally CovS-inactivated invasive deep tissue isolate of anemm23strain ofS. pyogenes(M23ND) and its complemented avirulent variant (CovS+). We identified diverse virulence genes whose altered expression revealed a genetic switching of a nonvirulent form of M23ND to a highly virulent strain. Furthermore, we also systematically uncovered for the first time the comparative levels of expression of a broad spectrum of metabolic genes, which reflected different metabolic needs of the bacterium as it invaded deeper tissue of the human host.
A Sham-Controlled Trial of Acupressure on the Quality of Sleep and Life in Haemodialysis Patients
Authors: Arab Zahra , Shariati Ali Reza , Asayesh Hamid , Vakili Mohammad Ali , Bahrami-Taghanaki Hamidreza , Azizi Hoda
Published: July 2015

Background

Sleep disorder in haemodialysis patients can lead to disturbance in their psychosocial function and interpersonal relations, and reduced quality of life. The aim of the present study was to investigate the effect of acupressure on the quality of sleep of haemodialysis patients.

Methods

In a randomised controlled trial, 108 haemodialysis patients were randomly divided into three groups: true acupressure, placebo acupressure, and no treatment. The two acupressure groups received treatment three times a week for 4 weeks during dialysis. Routine care only was provided for the no treatment group. The main study outcome was sleep quality.

Results

The total Pittsburgh Sleep Quality Index score decreased significantly from 11.9±3.13 to 6.2±1.93 in the true acupressure group, from 11.3±3.69 to 10.6±3.82 in the sham acupressure group, and from 10.9±4.10 to 10.7±3.94 in the no treatment group. There was a significant difference between groups (p<0.001).

Conclusions

Acupressure seems to have a positive effect on the sleep quality in haemodialysis patients.

Clinical Trial Registration

IRCT201106145864N2.
Arthritis as presenting manifestation of acute lymphoblastic leukaemia in children
Authors: Brix Ninna , Rosthøj Steen , Herlin Troels , Hasle Henrik
Published: July 2015

Background

At disease onset, children with acute lymphoblastic leukaemia (ALL) may present with arthralgia or even signs of arthritis. This might cause misdiagnosis and thereby lead to prolonged diagnostic delay. The present study aimed to identify children with ALL with joint involvement and to compare their characteristics and outcome with children with ALL without joint involvement.

Methods

Case records of 286 children diagnosed with ALL between 1992 and 2013 were reviewed and analysed in this retrospective, descriptive study.

Results

Fifty-three (18.5%) children with ALL presented with localised joint pain, and half of them had objective signs of arthritis. The mean number of joints involved was 2.5, most frequently presenting as asymmetric oligoarthritis. The suspected misdiagnosis were reactive arthritis (19/53), osteomyelitis (9/53) and juvenile idiopathic arthritis (8/53). Children with joint involvement had less objective signs of haematological disease. Cytopenia was absent in 24% in children with joint involvement (vs 8% without, p=0.001), 50% had only one cell line affected (vs 21%, p=0.0005) and 44% had no organomegaly (vs 29%, p=0.05). Median diagnostic delay was 4 vs 2 weeks. The 5-year event-free and overall survival was superior for children with joint involvement: 94% vs 87% (p=0.049), and 96% vs 83% (p=0.044).

Conclusions

ALL with joint involvement is a frequent finding (18.5%). The clinical signs of leukaemia are less prominent, but non-articular pain should alert the clinician of a possible diagnosis of leukaemia. The overall and event-free survivals were superior compared with the children without joint involvement.
Systemic and venous thromboembolism: think about paradoxical embolism
Authors: Cachia Monique , Pace Bardon Michael , Fsadni Peter , Montefort Stephen
Published: July 2015

Patent foramen ovale (PFO) is one of the most important causes of paradoxical embolism; it is found in about 25–30% of the population. In most patients, it is asymptomatic and diagnosis is usually made during routine echocardiography. In a small proportion of patients, PFO is diagnosed after paradoxical embolism is suspected. We present a case of a middle-aged smoker who was admitted with lower limb deep vein thrombosis and pulmonary embolism, who developed acute upper limb ischaemia during his inpatient stay. Since doctors might dismiss such cases as routine, this report highlights the importance of detailed history taking and examination in patients with venous thromboembolism. Paradoxical embolism should always be considered as a possible diagnosis when managing patients with concomitant venous and arterial embolism.
A drawing pin, drill bit, several staples and a magnet: definitely not a simple case of appendicitis
Authors: Coles Claire
Published: July 2015

The sequalae of foreign body ingestion may present in a number of manners and are even more prone to difficulties when a history of foreign body ingestion is not apparent. An 8-year-old boy with a short history of abdominal pain and vomiting presented to the hospital after seeing his general practitioner. He had a history of developmental delay. Examination revealed lower abdominal peritonism and his blood tests revealed elevated inflammatory markers. The patient was initially diagnosed with acute appendicitis and proceeded to theatre. At operation, the patient had a normal appendix but two perforations of the small bowel were incidentally discovered. After theatre, the patient underwent an abdominal X-ray, which revealed a number of radiopaque objects in the rectum. He returned to theatre where a number of metallic objects and a magnet were manually retrieved from the patient's rectum. He made a full recovery and was discharged home a few days later.
“Anybody on this list that you're more worried about?” Qualitative analysis exploring the functions of questions during end of shift handoffs
Authors: O'Brien Colleen M , Flanagan Mindy E , Bergman Alicia A , Ebright Patricia R , Frankel Richard M
Published: July 2015

Background

Shift change handoffs are known to be a point of vulnerability in the quality, safety and outcomes of healthcare. Despite numerous efforts to improve handoff reliability, few interventions have produced lasting change. Although the opportunity to ask questions during patient handoff has been required by some regulatory bodies, the function of questions during handoff has been less well explored and understood.

Objective

To investigate questions and the functions they serve in nursing and medicine handoffs.

Research design

Qualitative thematic analysis based on audio recordings of nurse-to-nurse, medical resident-to-resident and surgical intern-to-intern handoffs.

Subjects

Twenty-seven nurse handoff dyads and 18 medical resident and surgical intern handoff dyads at one VA Medical Center.

Results

Our analysis revealed that the vast majority of questions were asked by the Incoming Providers. Although topics varied widely, the bulk of Incoming Provider questions requested information that would best help them understand individual patient conditions and plan accordingly. Other question types sought consensus on clinical reasoning or framing and alignment between the two professionals.

Conclusions

Handoffs are a type of socially constructed work. Questions emerge with some frequency in virtually all handoffs but not in a linear or predictable way. Instead, they arise in the moment, as necessary, and without preplanning. A checklist cannot model this process element because it is a static memory aid and questions occur in a relational context that is emergent. Studying the different functions of questions during end of shift handoffs provides insights into the interface between the technical context in which information is transferred and the social context in which meaning is created.
Determination of a shear rate threshold for thrombus formation in intracranial aneurysms
Authors: Ribeiro de Sousa Daniel , Vallecilla Carolina , Chodzynski Kamil , Corredor Jerez Ricardo , Malaspinas Orestis , Eker Omer Faruk , Ouared Rafik , Vanhamme Luc , Legrand Alexandre , Chopard Bastien , Courbebaisse Guy , Zouaoui Boudjeltia Karim
Published: July 2015

Background

Particular intra-aneurysmal blood flow conditions, created naturally by the growth of an aneurysm or induced artificially by implantation of a flow diverter stent (FDS), can potentiate intra-aneurysmal thrombosis. The aim of this study was to identify hemodynamic indicators, relevant to this process, which could be used as a prediction of the success of a preventive endovascular treatment.

Method

A cross sectional study on 21 patients was carried out to investigate the possible association between intra-aneurysmal spontaneous thrombus volume and the dome to neck aspect ratio (AR) of the aneurysm. The mechanistic link between these two parameters was further investigated through a Fourier analysis of the intra-aneurysmal shear rate (SR) obtained by computational fluid dynamics (CFD). This analysis was first applied to 10 additional patients (4 with and 6 without spontaneous thrombosis) and later to 3 patients whose intracranial aneurysms only thrombosed after FDS implantation.

Results

The cross sectional study revealed an association between intra-aneurysmal spontaneous thrombus volume and the AR of the aneurysm (R2=0.67, p<0.001). Fourier analysis revealed that in cases where thrombosis occurred, the SR harmonics 0, 1, and 2 were always less than 25/s, 10/s, and 5/s, respectively, and always greater than these values where spontaneous thrombosis was not observed.

Conclusions

Our study suggests the existence of an SR threshold below which thrombosis will occur. Therefore, by analyzing the SR on patient specific data with CFD techniques, it may be potentially possible to predict whether or the intra-aneurysmal flow conditions, after FDS implantation, will become prothrombotic.
Lactoferrin attenuates fatty acid-induced lipotoxicity via Akt signaling in hepatocarcinoma cells
Authors: Morishita Satoru , Tomita Keiko , Ono Tomoji , Murakoshi Michiaki , Saito Kenji , Sugiyama Keikichi , Nishino Hoyoku , Kato Hisanori
Published: July 2015

Nonalcoholic fatty liver disease (NAFLD) describes a spectrum of lesions ranging from simple steatosis to non-alcoholic steatohepatitis (NASH). The excess influx of fatty acids (FAs) into the liver is recognized as a main cause of simple steatosis formation and progression to NASH. Recently, administration of lactoferrin (LF), a glycoprotein present in milk, was suggested to prevent NAFLD development. However, the effect of LF on the contribution of FA to NAFLD development remains unclear. In this study, the effects of LF on FA mixture (FAm)-induced lipotoxicity using human hepatocarcinoma G2 cells were assessed. FAm significantly decreased cell viability and increased intracellular lipid accumulation, whereas LF significantly recovered cell viability without affecting lipid accumulation. FAm-induced lactic dehydrogenase (LDH) and caspase-3/7 activities were significantly decreased by LF and SP600125, a c-Jun N-terminal kinase (JNK) specific inhibitor. We also found that LF added to FAm-treated cells induced Akt phosphorylation, which contributed to inhibition of JNK signaling pathway-dependent apoptosis. Akt inhibitor VIII, an allosteric Akt inhibitor, significantly attenuated the effect of LF on LDH activity and abrogated the ones on cell viability and caspase-3/7 activity. In summary, the present study has revealed that LF has a protective effect on FAm-induced lipotoxicity in a HepG2 model of NAFLD and identified the activation of the Akt signaling pathway as a possibly major mechanism.
Influence of initial fines content on fabric of soils subjected to internal erosion
Authors: Ouyang Mao , Takahashi Akihiro
Published: July 2015

Seepage-induced internal erosion often happens in earth structures. This paper presents experimental investigations on the influence of initial fines content on fabric of soils subjected to internal erosion. The tested materials were the binary mixtures of silica No. 3 and silica No. 8, which correspond to the coarse and fine fractions, respectively. One group of specimens was prepared with initial fines contents of 0, 15%, 25%, and 35% by weight. The undrained monotonic compression tests were performed on this group to examine the influence of fines content on the undrained behavior. The other group was prepared with initial fines contents of 15%, 25%, and 35% by weight, on which the seepage tests and subsequent undrained compression tests were carried out to demonstrate the mechanical influence of the internal erosion. The undrained behavior of the first group of specimens reveals that the presence of fines would decrease the peak and residual strengths. A comparison between the undrained behavior of soils with erosion and that of soils without erosion shows that the soils become less contractive after the internal erosion. When the axial strain is less than 0.4%, the undrained secant stiffness of soils with erosion is larger than that without erosion at the same axial strain. Meanwhile, the undrained peak strength and residual strength are larger for soils with erosion than that for soils without erosion. The less amount of excess pore-water pressure is generated during the undrained compression for the eroded soils comparing to those of the uneroded soils. Furthermore, the eroded soils show a wider instability zone than that of the uneroded soils, which suggests that the instability zone be enlarged by the internal erosion. Besides, one-dimensional upward seepage tests were performed to investigate the change of fabric of the mixed sand with 15%, 25%, and 35% fines contents due to internal erosion. The recorded microscopic images of soils before and after erosion reveal that the fabric is altered by the internal erosion.
Statistical characterization of random field parameters using frequentist and Bayesian approaches
Authors: Ching Jianye , Wu Shih-Shuan , Phoon Kok-Kwang
Published: July 2015

Because information collected in a site investigation is limited, it is not possible to obtain actual values for the mean, standard deviation, and scale of fluctuation for a soil property of interest. The deviation between the estimated values and the actual values is called the statistical uncertainty. There are at least two schools of thought on how to model the statistical uncertainty: frequentist thought and Bayesian thought. The purpose of this paper is to discuss their philosophical difference, to show how to quantify the statistical uncertainty based on these two distinct schools of thought, and to compare their performances. To quantify the statistical uncertainty, the confidence interval will be used for the frequentist school of thought, whereas the posterior probability distribution will be used for the Bayesian school of thought. Examples will be presented to compare the performances of these two schools of thought in terms of their consistencies. The results show that, in general, the Bayesian thought performs better in terms of consistency. In particular, the Markov chain Monte Carlo method is recommended when the amount of information available is very limited.
Characterization of resistance to ascochyta blight of selected wild Cicer germplasm
Authors: Armstrong-Cho Cheryl , Lulsdorf Monika M. , Hashemi Parvaneh , Banniza Sabine
Published: July 2015

The resistance of 24 perennial Cicer accessions to Ascochyta rabiei (Pass.) Labr. was assessed under field and greenhouse conditions. Two perennial and two annual Cicer accessions with superior resistance were examined and compared with susceptible (‘CDC Xena’) and resistant (‘CDC Frontier’) domesticated Cicer arietinum L. (chickpea) cultivars in terms of pathogen colonization, symptom development, host autofluorescence, and hydrogen peroxide generation. Colonizing hyphae on the four wild Cicer genotypes were pigmented, but hyaline on cultivated chickpea. The morphology of colonizing hyphae differed on the six genotypes, with wider hyphae observed on the most resistant genotype, Cicer anatolicum Alef. PI 383626. Inoculation of leaves of the top five nodes indicated that infection rates were highest on the youngest unfurled leaf for C. anatolicum PI 383626, Cicer oxyodon Boiss. & Hoh. PI 561103, Cicer bijugum Rech.f. ILWC 260, and ‘CDC Frontier’. Observations of hyphal pigmentation, modified hyphal growth, and low infection rates on fully developed leaves of wild Cicer plants suggest that components of the plant surface play an important role in disease resistance. Localized autofluorescence in response to infection was observed in the two perennials, but not in the other genotypes examined. The distinct resistance strategy observed in these perennial accessions make them interesting but challenging candidates for introgression of resistance into cultivated chickpea.
Mass discrimination using the inferred depth of maximum through the particle densities measured at observation level
Authors: Rastegarzadeh G. , Khoshabadi S.
Published: July 2015

In the present work, the shower depth of maximum (X max e) and (X max μ) (the depth at which the number of muons of shower get their maximum) has been calculated from the particles densities at the observation level. It is noteworthy that these are both mass sensitive parameters. Based on CORSIKA simulations a relationship between slope of the lateral distribution functions (η) of electrons and muons (at the observation level) and their X max have been investigated. An accurate linear relationship between them is found. The higher the energy, the deeper the X max and the steeper the distribution function is. Simulations have been done for heavy and light primaries in the energy range of 1014–1015 eV. Better ability for mass discrimination of η of the muons, due to less deflection of muons with the atmosphere is demonstrated. This method has got better results for low energies. Therefore a mass sensitive parameter, with good potential for mass discriminating between light and heavy primaries is presented.
The effect of heat transfer on the nonlinear peristaltic transport of a Jeffrey fluid through a finite vertical porous channel
Authors: Vajravelu K. , Sreenadh S. , Lakshminarayana P. , Sucharitha G.
Published: July 2015

In this paper we analyze the influence of free convection on nonlinear peristaltic transport of a Jeffrey fluid in a finite vertical porous stratum using the Brinkman model. Heat is generated within the fluid by both viscous and Darcy dissipations. The coupled nonlinear governing equations are solved analytically. The expressions for the temperature, the axial velocity, the local wall shear stress and the pressure gradient are obtained. The effects of various physical parameters such as the Jeffrey parameter [Formula: see text], the permeability parameter [Formula: see text] and the heat source/sink parameter [Formula: see text] are analyzed through graphs, and the results are discussed in detail. It is observed that the velocity field increases with increasing values of the Jeffrey parameter but it decreases with increasing values of the permeability parameter. It is found that the pressure rise increases with decreasing Jeffrey parameter and increasing permeability parameter. We notice that the effect of the permeability parameter [Formula: see text] is the strongest on the bolus trapping phenomenon. For [Formula: see text] [Formula: see text] the results of the present study reduce to the results of Tripathi [Math. Comput. Modelling 57 (2013) 1270–1283]. Further the effect of viscous and Darcy dissipations is to reduce the rate of heat transfer in the finite vertical porous channel under peristalsis.
Pressure induced stiffening, thermal softening of bulk modulus and brittle nature of mercury chalcogenides
Authors: Varshney Dinesh , Shriya Swarna , Sapkale Raju , Varshney Meenu , Ameri M.
Published: July 2015

The pressure and temperature dependent elastic properties of mercury chalcogenides ( Hg X; X = S , Se and Te ) with pressure induced structural transition from ZnS -type (B3) to NaCl -type (B1) structure have been analyzed within the framework of a model interionic interaction potential with long-range Coulomb and charge transfer interactions, short-range overlap repulsion and van der Waals (vdW) interactions as well as zero point energy effects. Emphasis is on the evaluation of the Bulk modulus with pressure and temperature dependency to yield the Poisson's ratio ν, the Pugh ratio ϕ, anisotropy parameter, Shear and Young's modulus, Lamé's constant, Klein man parameter, elastic wave velocity and Debye temperature. The Poisson's ratio behavior infers that Hg X are brittle in nature. To our knowledge this is the first quantitative theoretical prediction of the pressure dependence of elastic and thermodynamical properties explicitly the ductile (brittle) nature of Hg X and still awaits experimental confirmations.
Ophiolitic rocks of the Indo-Myanmar Ranges, NE India: relicts of an inverted and tectonically imbricated hyper-extended continental margin basin?
Authors: Soibam I. , Khuman M. Ch. , Subhamenon S. S.
Published: July 2015

The Indo-Myanmar Ranges (IMR) of NE India are host to various ophiolitic rocks, including metamorphosed Alpine-type harzburgite and lherzolite. Compared to abyssal peridotites of normal oceanic lithosphere, these ultramafic rocks are enriched in trace and rare earth elements. Spilitic pillow lavas along with mafic dykes and sills locally intruded into the serpentinized ultramafic rocks and associated pelagic sediments exhibit alkaline compositional affinities. Ophiolite formation and emplacement were by a process analogous to that described for mantle exhumation in hyper-extended continental margin settings and ophiolites in parts of the European Alps, involving very slow passive continental margin rifting accompanied by slow upwelling or extensional unroofing of the subcontinental upper mantle up to the seafloor. Preliminary palaeomagnetic measurements conducted on ultramafic rocks within the IMR ophiolite belt give a virtual geomagnetic pole (VGP) at 47° N, 045° E for thermal demagnetization (TDM) measurements and 33° N, 013° E for the alternating field demagnetization (AfD) measurements, requiring an anticlockwise rotation of the ultramafic bodies by 14° during the subduction process. The original trend of the spreading axis of the ophiolites was probably NE–SW, with spreading directed NW–SE. Computation of palaeolatitude of the ultramafic rocks gives an average value of 24.67°. Comparison between the palaeolatitude and the present latitude of the sample sites provides a mere latitudinal shift of less than 1°.

Field studies, combined with an analysis of structural and tectonic features in the IMR, suggest a generalized WNW–ESE (east–west) compression and NNE–SSW (north–south) extension contradictory to the NNE–SSW contraction indicated by seismic data. Area balancing techniques employed along sections orientated perpendicular to regional tectonic strike in the IMR reveal systematic variations in the amount of crustal shortening, with a maximum of approximately 60% recorded in the Nagaland–Manipur segment along 25.644° N, 93.826° E–25.076° N, 95.897° E. The amount of shortening gradually decreases away from the axis of maximum shortening and on both sides. Calculations of relative plate motion based on rotation vectors given by different workers for various plate pairs represented in the region reveal that the interaction between the Indian and Myanmar plates can ideally produce the structural and tectonic features of this range. Dextral shear coupled to oblique subduction of the Indian Plate below the Myanmar Plate can best explain all of the structural and tectonic features present in the IMR.
Smart Colonography for Distributed Medical Databases with Group Kernel Feature Analysis
Authors: Motai Yuichi , Ma Dingkun , Docef Alen , Yoshida Hiroyuki
Published: July 2015

Computer-Aided Detection (CAD) of polyps in Computed Tomographic (CT) colonography is currently very limited since a single database at each hospital/institution doesn't provide sufficient data for training the CAD system's classification algorithm. To address this limitation, we propose to use multiple databases, (e.g., big data studies) to create multiple institution-wide databases using distributed computing technologies, which we call smart colonography. Smart colonography may be built by a larger colonography database networked through the participation of multiple institutions via distributed computing. The motivation herein is to create a distributed database that increases the detection accuracy of CAD diagnosis by covering many true-positive cases. Colonography data analysis is mutually accessible to increase the availability of resources so that the knowledge of radiologists is enhanced. In this article, we propose a scalable and efficient algorithm called Group Kernel Feature Analysis (GKFA), which can be applied to multiple cancer databases so that the overall performance of CAD is improved. The key idea behind the proposed GKFA method is to allow the feature space to be updated as the training proceeds with more data being fed from other institutions into the algorithm. Experimental results show that GKFA achieves very good classification accuracy.
Improving light field camera sample design with irregularity and aberration
Authors: Wei Li-Yi , Liang Chia-Kai , Myhre Graham , Pitts Colvin , Akeley Kurt
Published: July 2015

Conventional camera designs usually shun sample irregularities and lens aberrations. We demonstrate that such irregularities and aberrations, when properly applied, can improve the quality and usability of light field cameras. Examples include spherical aberrations for the mainlens, and misaligned sampling patterns for the microlens and photosensor elements. These observations are a natural consequence of a key difference between conventional and light field cameras: optimizing for a single captured 2D image versus a range of reprojected 2D images from a captured 4D light field. We propose designs in mainlens aberrations and microlens/photosensor sample patterns, and evaluate them through simulated measurements and captured results with our hardware prototype.
Data-driven finite elements for geometry and material design
Authors: Chen Desai , Levin David I. W. , Sueda Shinjiro , Matusik Wojciech
Published: July 2015

Crafting the behavior of a deformable object is difficult---whether it is a biomechanically accurate character model or a new multimaterial 3D printable design. Getting it right requires constant iteration, performed either manually or driven by an automated system. Unfortunately, Previous algorithms for accelerating three-dimensional finite element analysis of elastic objects suffer from expensive precomputation stages that rely on
a priori
knowledge of the object's geometry and material composition. In this paper we introduce Data-Driven Finite Elements as a solution to this problem. Given a material palette, our method constructs a metamaterial library which is reusable for subsequent simulations, regardless of object geometry and/or material composition. At runtime, we perform fast coarsening of a simulation mesh using a simple table lookup to select the appropriate metamaterial model for the coarsened elements. When the object's material distribution or geometry changes, we do not need to update the metamaterial library---we simply need to update the metamaterial assignments to the coarsened elements. An important advantage of our approach is that it is applicable to non-linear material models. This is important for designing objects that undergo finite deformation (such as those produced by multimaterial 3D printing). Our method yields speed gains of up to two orders of magnitude while maintaining good accuracy. We demonstrate the effectiveness of the method on both virtual and 3D printed examples in order to show its utility as a tool for deformable object design.
Single-view reconstruction via joint analysis of image and shape collections
Authors: Huang Qixing , Wang Hai , Koltun Vladlen
Published: July 2015

We present an approach to automatic 3D reconstruction of objects depicted in Web images. The approach reconstructs objects from single views. The key idea is to jointly analyze a collection of images of different objects along with a smaller collection of existing 3D models. The images are analyzed and reconstructed together. Joint analysis regularizes the formulated optimization problems, stabilizes correspondence estimation, and leads to reasonable reproduction of object appearance without traditional multi-view cues.
Perceptually based downscaling of images
Authors: Öztireli A. Cengiz , Gross Markus
Published: July 2015

We propose a perceptually based method for downscaling images that provides a better apparent depiction of the input image. We formulate image downscaling as an optimization problem where the difference between the input and output images is measured using a widely adopted perceptual image quality metric. The downscaled images retain perceptually important features and details, resulting in an accurate and spatio-temporally consistent representation of the high resolution input. We derive the solution of the optimization problem in closed-form, which leads to a simple, efficient and parallelizable implementation with sums and convolutions. The algorithm has running times similar to linear filtering and is orders of magnitude faster than the state-of-the-art for image downscaling. We validate the effectiveness of the technique with extensive tests on many images, video, and by performing a user study, which indicates a clear preference for the results of the new algorithm.
Computational interlocking furniture assembly
Authors: Fu Chi-Wing , Song Peng , Yan Xiaoqi , Yang Lee Wei , Jayaraman Pradeep Kumar , Cohen-Or Daniel
Published: July 2015

Furniture typically consists of assemblies of elongated and planar parts that are connected together by glue, nails, hinges, screws, or other means that do not encourage disassembly and re-assembly. An alternative approach is to use an interlocking mechanism, where the component parts tightly interlock with one another. The challenge in designing such a network of interlocking joints is that local analysis is insufficient to guarantee global interlocking, and there is a huge number of joint combinations that require an enormous exploration effort to ensure global interlocking. In this paper, we present a computational solution to support the design of a network of interlocking joints that form a globally-interlocking furniture assembly. The key idea is to break the furniture complex into an overlapping set of small groups, where the parts in each group are immobilized by a local key, and adjacent groups are further locked with dependencies. The dependency among the groups saves the effort of exploring the immobilization of every subset of parts in the assembly, thus allowing the intensive interlocking computation to be localized within each small group. We demonstrate the effectiveness of our technique on many globally-interlocking furniture assemblies of various shapes and complexity.
Homogeneous codes for energy-efficient illumination and imaging
Authors: O'Toole Matthew , Achar Supreeth , Narasimhan Srinivasa G. , Kutulakos Kiriakos N.
Published: July 2015

Programmable coding of light between a source and a sensor has led to several important results in computational illumination, imaging and display. Little is known, however, about how to utilize energy most effectively, especially for applications in live imaging. In this paper, we derive a novel framework to maximize energy efficiency by "homogeneous matrix factorization" that respects the physical constraints of many coding mechanisms (DMDs/LCDs, lasers,
etc.
). We demonstrate energy-efficient imaging using two prototypes based on DMD and laser illumination. For our DMD-based prototype, we use fast local optimization to derive codes that yield brighter images with fewer artifacts in many transport probing tasks. Our second prototype uses a novel combination of a low-power laser projector and a rolling shutter camera. We use this prototype to demonstrate never-seen-before capabilities such as (1) capturing live structured-light video of very bright scenes---even a light bulb that has been turned on; (2) capturing epipolar-only and indirect-only live video with optimal energy efficiency; (3) using a low-power projector to reconstruct 3D objects in challenging conditions such as strong indirect light, strong ambient light, and smoke; and (4) recording live video from a projector's---rather than the camera's---point of view.
Dihedral angle-based maps of tetrahedral meshes
Authors: Paillé Gilles-Philippe , Ray Nicolas , Poulin Pierre , Sheffer Alla , Lévy Bruno
Published: July 2015

We present a geometric representation of a tetrahedral mesh that is solely based on dihedral angles. We first show that the shape of a tetrahedral mesh is completely defined by its dihedral angles. This proof leads to a set of angular constraints that must be satisfied for an immersion to exist in
R
3
. This formulation lets us easily specify conditions to avoid inverted tetrahedra and multiply-covered vertices, thus leading to locally injective maps. We then present a constrained optimization method that modifies input angles when they do not satisfy constraints. Additionally, we develop a fast spectral reconstruction method to robustly recover positions from dihedral angles. We demonstrate the applicability of our representation with examples of volume parameterization, shape interpolation, mesh optimization, connectivity shapes, and mesh compression.
Practical hex-mesh optimization via edge-cone rectification
Authors: Livesu Marco , Sheffer Alla , Vining Nicholas , Tarini Marco
Published: July 2015

The usability of hexahedral meshes depends on the degree to which the shape of their elements deviates from a perfect cube; a single concave, or
inverted
element makes a mesh unusable. While a range of methods exist for discretizing 3D objects with an initial topologically suitable hex mesh, their output meshes frequently contain poorly shaped and even inverted elements, requiring a further quality optimization step. We introduce a novel framework for optimizing hex-mesh quality capable of generating inversion-free high-quality meshes from such poor initial inputs. We recast hex quality improvement as an optimization of the shape of overlapping cones, or unions, of tetrahedra surrounding every
directed
edge in the hex mesh, and show the two to be equivalent. We then formulate cone shape optimization as a sequence of convex quadratic optimization problems, where hex convexity is encoded via simple linear inequality constraints. As this solution space may be empty, we therefore present an alternate formulation which allows the solver to proceed even when constraints cannot be satisfied exactly. We iteratively improve mesh element quality by solving at each step a set of local, per-cone, convex constrained optimization problems, followed by a global energy minimization step which reconciles these local solutions. This latter method provides no theoretical guarantees on the solution but produces inversion-free, high quality meshes in practice. We demonstrate the robustness of our framework by optimizing numerous poor quality input meshes generated using a variety of initial meshing methods and producing high-quality inversion-free meshes in each case. We further validate our algorithm by comparing it against previous work, and demonstrate a significant improvement in both worst and average element quality.
Integrable PolyVector fields
Authors: Diamanti Olga , Vaxman Amir , Panozzo Daniele , Sorkine-Hornung Olga
Published: July 2015

We present a framework for designing curl-free tangent vector fields on discrete surfaces. Such vector fields are gradients of locally-defined scalar functions, and this property is beneficial for creating surface parameterizations, since the gradients of the parameterization coordinate functions are then exactly aligned with the designed fields. We introduce a novel definition for discrete curl between unordered sets of vectors (PolyVectors), and devise a curl-eliminating continuous optimization that is independent of the matchings between them. Our algorithm naturally places the singularities required to satisfy the user-provided alignment constraints, and our fields are the gradients of an inversion-free parameterization by design.
Deformation capture and modeling of soft objects
Authors: Wang Bin , Wu Longhua , Yin KangKang , Ascher Uri , Liu Libin , Huang Hui
Published: July 2015

We present a data-driven method for deformation capture and modeling of general soft objects. We adopt an iterative framework that consists of one component for physics-based deformation tracking and another for spacetime optimization of deformation parameters. Low cost depth sensors are used for the deformation capture, and we do not require any force-displacement measurements, thus making the data capture a cheap and convenient process. We augment a state-of-the-art probabilistic tracking method to robustly handle noise, occlusions, fast movements and large deformations. The spacetime optimization aims to match the simulated trajectories with the tracked ones. The optimized deformation model is then used to boost the accuracy of the tracking results, which can in turn improve the deformation parameter estimation itself in later iterations. Numerical experiments demonstrate that the tracking and parameter optimization components complement each other nicely.

Our spacetime optimization of the deformation model includes not only the material elasticity parameters and dynamic damping coefficients, but also the reference shape which can differ significantly from the static shape for soft objects. The resulting optimization problem is highly nonlinear in high dimensions, and challenging to solve with previous methods. We propose a novel splitting algorithm that alternates between reference shape optimization and deformation parameter estimation, and thus enables tailoring the optimization of each subproblem more efficiently and robustly.

Our system enables realistic motion reconstruction as well as synthesis of virtual soft objects in response to user stimulation. Validation experiments show that our method not only is accurate, but also compares favorably to existing techniques. We also showcase the ability of our system with high quality animations generated from optimized deformation parameters for a variety of soft objects, such as live plants and fabricated models.
Foldabilizing furniture
Authors: Li Honghua , Hu Ruizhen , Alhashim Ibraheem , Zhang Hao
Published: July 2015

We introduce the
foldabilization
problem for space-saving furniture design. Namely, given a 3D object representing a piece of furniture, our goal is to apply a minimum amount of modification to the object so that it can be folded to save space --- the object is thus foldabilized. We focus on one instance of the problem where folding is with respect to a prescribed folding direction and allowed object modifications include hinge insertion and part shrinking.

We develop an automatic algorithm for foldabilization by formulating and solving a nested optimization problem operating at two granularity levels of the input shape. Specifically, the input shape is first partitioned into a set of integral
folding units.
For each unit, we construct a graph which encodes conflict relations, e.g., collisions, between foldings implied by various patch foldabilizations within the unit. Finding a minimum-cost foldabilization with a conflict-free folding is an instance of the maximum-weight independent set problem. In the outer loop of the optimization, we process the folding units in an optimized ordering where the units are sorted based on estimated foldabilization costs. We show numerous foldabilization results computed at interactive speed and 3D-print physical prototypes of these results to demonstrate manufacturability.
Interaction context (ICON)
Authors: Hu Ruizhen , Zhu Chenyang , van Kaick Oliver , Liu Ligang , Shamir Ariel , Zhang Hao
Published: July 2015

We introduce a
contextual descriptor
which aims to provide a
geometric
description of the
functionality
of a 3D object in the context of a given scene. Differently from previous works, we do not regard functionality as an abstract label or represent it implicitly through an agent. Our descriptor, called
interaction context or ICON
for short, explicitly represents the geometry of object-to-object interactions. Our approach to object functionality analysis is based on the key premise that functionality should mainly be derived from interactions between objects and not objects in isolation. Specifically, ICON collects geometric and structural features to encode interactions between a central object in a 3D scene and its surrounding objects. These interactions are then grouped based on feature similarity, leading to a hierarchical structure. By focusing on interactions and their organization, ICON is insensitive to the numbers of objects that appear in a scene, the specific disposition of objects around the central object, or the objects' fine-grained geometry. With a series of experiments, we demonstrate the potential of ICON in functionality-oriented shape processing, including shape retrieval (either directly or by complementing existing shape descriptors), segmentation, and synthesis.
GRIDiron
Authors: Mitchell Nathan , Cutting Court , Sifakis Eftychios
Published: July 2015

We present an interactive simulation framework for authoring surgical procedures of soft tissue manipulation using physics-based simulation to animate the flesh. This interactive authoring tool can be used by clinical educators to craft three-dimensional illustrations of the intricate maneuvers involved in craniofacial repairs, in contrast to two-dimensional sketches and still photographs which are the medium used to describe these procedures in the traditional surgical curriculum. Our virtual environment also allows surgeons-intraining to develop cognitive skills for craniofacial surgery by experimenting with different approaches to reconstructive challenges, adapting stock techniques to flesh regions with nonstandard shape, and reach preliminary predictions about the feasibility of a given repair plan. We use a Cartesian grid-based embedded discretization of nonlinear elasticity to maximize regularity, and expose opportunities for aggressive multithreading and SIMD accelerations. Using a grid-based approach facilitates performance and scalability, but constrains our ability to capture the topology of thin surgical incisions. We circumvent this restriction by hybridizing the grid-based discretization with an explicit hexahedral mesh representation in regions where the embedding mesh necessitates overlap or nonmanifold connectivity. Finally, we detail how the front-end of our system can run on lightweight clients, while the core simulation capability can be hosted on a dedicated server and delivered as a network service.