bluuebunny/crossref_metadata_2025 huggingface dataset:
CD32 is expressed on cells with transcriptionally active HIV but does not enrich for HIV DNA in resting T cells
Authors: Abdel-Mohsen Mohamed , Kuri-Cervantes Leticia , Grau-Exposito Judith , Spivak Adam M. , Nell Racheal A. , Tomescu Costin , Vadrevu Surya Kumari , Giron Leila B. , Serra-Peinado Carla , Genescà Meritxell , Castellví Josep , Wu Guoxin , Del Rio Estrada Perla M. , González-Navarro Mauricio , Lynn Kenneth , King Colin T. , Vemula Sai , Cox Kara , Wan Yanmin , Li Qingsheng , Mounzer Karam , Kostman Jay , Frank Ian , Paiardini Mirko , Hazuda Daria , Reyes-Terán Gustavo , Richman Douglas , Howell Bonnie , Tebas Pablo , Martinez-Picado Javier , Planelles Vicente , Buzon Maria J. , Betts Michael R. , Montaner Luis J.
Published: April 2018

CD32 is associated with highly activated T cells harboring HIV RNA transcripts and does not enrich for HIV DNA in resting T cells.
Cholesterol, cancer, and rebooting a treatment for athlete’s foot
Authors: Chua Ngee Kiat , Coates Hudson W. , Brown Andrew J.
Published: April 2018

A key enzyme in cholesterol synthesis is placed firmly on the oncogenic map and demonstrated to be a potential therapeutic target in liver cancer by repurposing a common antifungal agent (Liu
et al
., this issue).
Retained Activity of an O25b-Specific Monoclonal Antibody against an Mcr-1-Producing Escherichia coli Sequence Type 131 Strain
Authors: Guachalla Luis M. , Ramoni Katharina , Varga Cecilia , Mutti Michele , Ghazawi Akela , Pál Tibor , Nagy Eszter , Sonnevend Ágnes , Nagy Gábor , Szijártó Valéria
Published: April 2018

Plasmid-encoded colistin resistance is emerging among extraintestinal pathogenic
Escherichia coli
strains, including those of the epidemic clone sequence type 131 (ST131)-H30. Mcr-1 transfers a phosphoethanolamine to the lipid A portion of lipopolysaccharide (LPS), conferring resistance to polymyxins. We investigated whether this modification changed the activity of the monoclonal antibody ASN-4, specific to the O25b side chain of ST131 LPS. We confirmed that, unlike colistin, ASN-4 retained its bactericidal and endotoxin-neutralizing activities and therefore offers a treatment option against extremely drug-resistant ST131 isolates.
Genomic Inference of Recombination-Mediated Evolution in Xanthomonas euvesicatoria and X. perforans
Authors: Jibrin Mustafa O. , Potnis Neha , Timilsina Sujan , Minsavage Gerald V. , Vallad Gary E. , Roberts Pamela D. , Jones Jeffrey B. , Goss Erica M.
Published: April 2018

Recombination is a major driver of evolution in bacterial populations, because it can spread and combine independently evolved beneficial mutations. Recombinant lineages of bacterial pathogens of plants are typically associated with the colonization of novel hosts and the emergence of new diseases. Here we show that recombination between evolutionarily and phenotypically distinct plant-pathogenic lineages generated recombinant lineages with unique combinations of pathogenicity and virulence factors.
Xanthomonas euvesicatoria
and
Xanthomonas perforans
are two closely related lineages causing bacterial spot disease on tomato and pepper worldwide. We sequenced the genomes of atypical strains collected from tomato in Nigeria and observed recombination in the type III secretion system and effector genes, which showed alleles from both
X. euvesicatoria
and
X. perforans
. Wider horizontal gene transfer was indicated by the fact that the lipopolysaccharide cluster of one strain was most similar to that of a distantly related
Xanthomonas
pathogen of barley. This strain and others have experienced extensive genomewide homologous recombination, and both species exhibited dynamic open pangenomes. Variation in effector gene repertoires within and between species must be taken into consideration when one is breeding tomatoes for disease resistance. Resistance breeding strategies that target specific effectors must consider possibly dramatic variation in bacterial spot populations across global production regions, as illustrated by the recombinant strains observed here.

IMPORTANCE
The pathogens that cause bacterial spot of tomato and pepper are extensively studied models of plant-microbe interactions and cause problematic disease worldwide. Atypical bacterial spot strains collected from tomato in Nigeria, and other strains from Italy, India, and Florida, showed evidence of genomewide recombination that generated genetically distinct pathogenic lineages. The strains from Nigeria and Italy were found to have a mix of type III secretion system genes from
X. perforans
and
X. euvesicatoria
, as well as effectors from
Xanthomonas gardneri
. These genes and effectors are important in the establishment of disease, and effectors are common targets of resistance breeding. Our findings point to global diversity in the genomes of bacterial spot pathogens, which is likely to affect the host-pathogen interaction and influence management decisions.
Cross Talk between Calcium and Reactive Oxygen Species Regulates Hyphal Branching and Ganoderic Acid Biosynthesis in Ganoderma lucidum under Copper Stress
Authors: Gao Tan , Shi Liang , Zhang Tianjun , Ren Ang , Jiang Ailiang , Yu Hanshou , Zhao Mingwen
Published: April 2018

Ganoderma lucidumis among the best known medicinal basidiomycetes due to its production of many pharmacologically active compounds. To study the regulatory networks involved in its growth and development, we analyzed the relationship between reactive oxygen species (ROS) and Ca2+signaling in the regulation of hyphal branching and ganoderic acid (GA) biosynthesis after Cu2+treatment. Our results revealed that Cu2+treatment decreased the distance between hyphal branches and increased the GA content and the intracellular levels of ROS and Ca2+. Further research revealed that the Cu2+-induced changes in hyphal branch distance, GA content, and cytosolic Ca2+level were dependent on increases in cytosolic ROS. Our results also showed that increased cytosolic Ca2+could reduce cytosolic ROS by activating antioxidases and modulating Cu2+accumulation, resulting in feedback to adjust hyphal growth and GA biosynthesis. These results indicated that cytosolic ROS and Ca2+levels exert important cross talk in the regulation of hyphal growth and GA biosynthesis induced by Cu2+. Taken together, our results provide a reference for analyzing the interactions among different signal transduction pathways with regard to the regulation of growth and development in other filamentous fungi.

IMPORTANCEGanoderma lucidum, which is known as an important medicinal basidiomycete, is gradually becoming a model organism for studying environmental regulation and metabolism. In this study, we analyzed the relationship between reactive oxygen species (ROS) and Ca2+signaling in the regulation of hyphal branching and ganoderic acid (GA) biosynthesis under Cu2+stress. The results revealed that the Cu2+-induced changes in the hyphal branch distance, GA content, and cytosolic Ca2+level were dependent on increases in cytosolic ROS. Furthermore, the results indicated that increased cytosolic Ca2+could reduce cytosolic ROS levels by activating antioxidases and modulating Cu2+accumulation. The results in this paper indicate that there was important cross talk between cytosolic ROS and Ca2+levels in the regulation of hyphal growth and GA biosynthesis induced by Cu2+.
Draft Genome Sequence of “Nocardia suismassiliense” Strain S-137 (CSUR P4007)
Authors: Fellag Mustapha , Levasseur Anthony , Delerce Jérémy , Bittar Fadi , Marié Jean-Lou , Davoust Bernard , Drancourt Michel
Published: April 2018

“
Nocardia suismassiliense
” strain S-137 isolated from
Sus scrofa
feces exhibits a 9.4-Mb (67.1% GC content) draft genome sequence containing 8,658 protein-coding genes, 66 tRNAs, and 9 rRNAs.
In silico
DNA-DNA hybridization confirmed strain S-137 as representative of a new species, “
Nocardia suismassiliense
,” closely related to
N. tenerifensis
and
N. brasiliensis
.
Near-Complete Genome Sequence of Pseudomonas palleroniana MAB3, a Beneficial 1-Aminocyclopropane-1-Carboxylate Deaminase-Producing Bacterium Able To Promote the Growth of Mushrooms and Plants
Authors: Urón Paola , Giachini Admir J. , Glick Bernard R. , Rossi Márcio J. , Nascimento Francisco X.
Published: April 2018

The near-complete genome sequence of
Pseudomonas palleroniana
MAB3, a 1-aminocyclopropane-1-carboxylate deaminase-producing bacterium isolated from an environmental soil
Amanita
mushroom, is presented here. The genome of
P. palleroniana
MAB3 contains a single circular chromosome of 6.29 Mb and an average GC content of 60.5%.
Complete Genome Sequence of Shewanella sp. WE21, a Rare Isolate with Multiple Novel Large Genomic Islands
Authors: Castillo Daniel , Gram Lone , Dailey Frank E.
Published: April 2018

We present here the whole-genome sequence of
Shewanella
sp. WE21, an unusual omega-3 fatty acid-producing bacterium isolated from the gastrointestinal tract of the freshwater fish
Sander vitreus
(walleye). This genome contains a number of unique, large genomic islands with genes not present in other
Shewanella
bacteria.
Draft Genome Sequence of Burkholderia gladioli Coa14, a Bacterium with Petroleum Bioremediation Potential Isolated from Coari Lake, Amazonas, Brazil
Authors: Lopes Eraldo Ferreira , Da Costa Josemar Gurgel , Wolf Ivan Rodrigo , Lima José Paulo de Araújo , Astolfi-Filho Spartaco
Published: April 2018

Burkholderia gladioli
Coa14 is a bacterium isolated from water collected from Coari Lake (Amazonas, Brazil) that shows a capacity for survival in a medium containing only oil as a carbon source. Here, we report its draft genome sequence, highlighting some genes involved with petroleum derivative degradation.
Gut Microbiome Analysis Identifies Potential Etiological Factors in Acute Gastroenteritis
Authors: Castaño-Rodríguez Natalia , Underwood Alexander P. , Merif Juan , Riordan Stephen M. , Rawlinson William D. , Mitchell Hazel M. , Kaakoush Nadeem O.
Published: April 2018

The morbidity and mortality resulting from acute gastroenteritis and associated chronic sequelae represent a substantial burden on health care systems worldwide. Few studies have investigated changes in the gut microbiome following an episode of acute gastroenteritis. By using nondirected 16S rRNA gene amplicon sequencing, the fecal microbiota of 475 patients with acute gastroenteritis was examined. Patient age was correlated with the overall microbial composition, with a decrease in the abundance of
Faecalibacterium
being observed in older patients. We observed the emergence of a potential
Escherichia-Shigella
-dominated enterotype in a subset of patients, and this enterotype was predicted to be more proinflammatory than the other common enterotypes, with the latter being dominated by
Bacteroides
or
Faecalibacterium
. The increased abundance of
Escherichia-Shigella
did not appear to be associated with infection with an agent of a similar sequence similarity. Stool color and consistency were associated with the diversity and composition of the microbiome, with deviations from the norm (not brown and solid) showing increases in the abundances of bacteria such as
Escherichia-Shigella
and
Veillonella
. Analysis of enriched outliers within the data identified a range of genera previously associated with gastrointestinal diseases, including
Treponema
,
Proteus
,
Capnocytophaga
,
Arcobacter
,
Campylobacter
,
Haemophilus
,
Aeromonas
, and
Pseudomonas
. Our data represent the first in-depth analysis of gut microbiota in acute gastroenteritis. Phenotypic changes in stool color and consistency were associated with specific changes in the microbiota. Enriched bacterial taxa were detected in cases where no causative agent was identified by using routine diagnostic tests, suggesting that in the future, microbiome analyses may be utilized to improve diagnostics.
Retrospective Evaluation of Infants Aged 1 to 60 Days with Residual Cerebrospinal Fluid (CSF) Tested Using the FilmArray Meningitis/Encephalitis (ME) Panel
Authors: Blaschke Anne J. , Holmberg Kristen M. , Daly Judy A. , Leber Amy L. , Dien Bard Jennifer , Korgenski Ernest K. , Bourzac Kevin M. , Kanack Kristen J.
Published: April 2018

In pediatric practice it is common for infants under 2 months of age to undergo evaluation for sepsis when they are ill, often including lumbar puncture to assess for central nervous system (CNS) infection. The FilmArray Meningitis/Encephalitis (ME) panel is a newly approved test for rapid identification of CNS pathogens. Our objective was to study the epidemiology of CNS infection in young infants and the potential impact of rapid multiplex PCR on their care. A performance evaluation of the FilmArray ME panel was conducted from February 2014 to September 2014 at 11 sites. FilmArray ME panel results were compared to reference standards but not shared with providers. In our study, medical records for infants (aged 1 to 60 days) enrolled at three sites were reviewed for clinical, laboratory, and outcome data. A total of 145 infants were reviewed. The median age was 25 days. Most of the infants were hospitalized (134/145 [92%]) and received antibiotics (123/145 [85%]), and almost half (71/145 [49%]) received acyclovir. One infant had a bacterial pathogen, likely false positive, identified by the FilmArray ME panel. Thirty-six infants (25%) had a viral pathogen detected, including 21 enteroviruses. All infants with enteroviral meningitis detected by the FilmArray ME panel and conventional PCR were hospitalized, but 20% were discharged in less than 24 h when conventional PCR results became available. The FilmArray ME panel may play a role in the evaluation of young infants for CNS infection. Results may be used to guide management, possibly resulting in a decreased length of stay and less antimicrobial exposure for infants with low-risk viral infection detected.
Generation of Recombinant Rotaviruses Expressing Fluorescent Proteins by Using an Optimized Reverse Genetics System
Authors: Komoto Satoshi , Fukuda Saori , Ide Tomihiko , Ito Naoto , Sugiyama Makoto , Yoshikawa Tetsushi , Murata Takayuki , Taniguchi Koki
Published: April 2018

An entirely plasmid-based reverse genetics system for rotaviruses was established very recently. We improved the reverse genetics system to generate recombinant rotavirus by transfecting only 11 cDNA plasmids for its 11 gene segments under the condition of increasing the ratio of the cDNA plasmids for NSP2 and NSP5 genes. Utilizing this highly efficient system, we then engineered infectious recombinant rotaviruses expressing bioluminescent (NanoLuc luciferase) and fluorescent (enhanced green fluorescent protein [EGFP] and mCherry) reporters. These recombinant rotaviruses expressing reporters remained genetically stable during serial passages. Our reverse genetics approach and recombinant rotaviruses carrying reporter genes will be great additions to the tool kit for studying the molecular virology of rotavirus and for developing future next-generation vaccines and expression vectors.

IMPORTANCERotavirus is one of the most important pathogens causing severe gastroenteritis in young children worldwide. In this paper, we describe a robust and simple reverse genetics system based on only rotavirus cDNAs and its application for engineering infectious recombinant rotaviruses harboring bioluminescent (NanoLuc) and fluorescent (EGFP and mCherry) protein genes. This highly efficient reverse genetics system and recombinant group A rotaviruses expressing reporters could be powerful tools for the study of different aspects of rotavirus replication. Furthermore, they may be useful for next-generation vaccine production for this medically important virus.
Electroacupuncture Reduces Hypothalamic and Medullary Expression of Orexins and their Receptors in a Rat Model of Chronic Obstructive Pulmonary Disease
Authors: Zhang Xin-Fang , Qin Qin , Geng Wen-Ye , Jiang Chuan-Wei , Liu Yong , Liu Xiao-Li , Li Jing , Liu Zi-Bing
Published: April 2018

Objectives

Decreased lung function in chronic obstructive pulmonary disease (COPD) is correlated with abnormal excitability of the respiratory centre where orexin neuropeptides from the hypothalamus are responsible for regulating respiration. We hypothesised that improvements in pulmonary function with electroacupuncture (EA) may be related to orexins in a rat model of COPD.

Methods

The COPD model was established by cigarette smoke exposure and lipopolysaccharide injection. Modelled rats received EA at BL13 and ST36 for two weeks, after which lung function was tested. Orexin levels in the hypothalamus and medulla were detected by ELISA, while mRNA/protein expression and localisation of orexins and their receptors were investigated using real time PCR, Western blotting and immunohistochemistry, respectively.

Results

The decrease in lung function observed in COPD rats was improved after EA treatment. Orexin levels in the hypothalamus and medulla were significantly higher in COPD rats than in normal rats, but were significantly reduced in the EA-treated group. There was a negative correlation between orexin content and lung function. In the hypothalamus, mRNA and protein expression and immunoreactivity of orexins were significantly higher in the COPD group than in the normal group, but a significant decrease was observed after EA. In the medulla, the expression and immunoreactivity of orexin receptors were significantly higher in the COPD group than in the normal group, but a significant decrease was observed after EA.

Conclusions

The positive effect of EA on pulmonary function in COPD rats may be related to downregulation of orexins and their receptors in the medulla.
Outcome of paediatric cataract surgery in Northwest Ethiopia: a retrospective case series
Authors: Asferaw Mulusew , Mekonen Sisay Yoseph , Woodruff Geoffrey , Gilbert Clare E , Tesfaye Samson
Published: April 2018

Aim

To assess visual acuity outcomes, and factors associated with the outcome, of paediatric cataract surgery at the Child Eye Health Tertiary Facility, Gondar, Northwest Ethiopia.

Methods

The medical records of children aged below 16 years who underwent cataract surgery between September 2010 and August 2014 were reviewed for preoperative, surgical and postoperative data.

Results

One hundred and seventy-six eyes of 142 children (mean age 7.9 years±4.2 SD, 66% male) who had cataract surgery were included. Twenty-five per cent (35/142) of children had bilateral cataract, 18 (13%) had unilateral non-traumatic cataracts and 89 (63%) had unilateral traumatic cataracts. An intraocular lens was implanted in 93% of eyes. Visual acuities at last follow-up: bilateral cases in the better eye: good (≥6/18 or fix and follow) in 21/34 eyes (62%), borderline (<6/18–6/60) in 4 eyes (12%) and poor (<6/60) in 9 eyes (26%). In unilateral non-traumatic cases: good in 6 eyes (33%), borderline in 3 eyes (17%) and poor in 9 eyes (50%). In unilateral traumatic cases: good in 36 eyes (40%), borderline in 20 eyes (23%) and poor in 33 eyes (37%). In bilateral cataract, worse outcomes were associated with preoperative nystagmus/strabismus. In traumatic cases, worse outcomes were associated with the preoperative trauma-related complications.

Conclusions

Visual acuity improved significantly after surgery, with better outcomes in bilateral cases. Early detection and surgery by a trained surgeon with good follow-up and postoperative rehabilitation can lead to better visual outcomes.
Addressing the third delay: implementing a novel obstetric triage system in Ghana
Authors: Goodman David M , Srofenyoh Emmanuel K , Ramaswamy Rohit , Bryce Fiona , Floyd Liz , Olufolabi Adeyemi , Tetteh Cecilia , Owen Medge D
Published: April 2018

Institutional delivery has been proposed as a method for reducing maternal morbidity and mortality, but little is known about how referral hospitals in low-resource settings can best manage the expected influx of patients. In this study, we assess the impact of an obstetric triage improvement programme on reducing hospital-based delay in a referral hospital in Accra, Ghana. An Active Implementation Framework is used to describe a 5-year intervention to introduce and monitor obstetric triage capabilities. Baseline data, collected from September to November 2012, revealed significant delays in patient assessment on arrival. A triage training course and monitoring of quality improvement tools occurred in 2013 and 2014. Implementation barriers led to the construction of a free-standing obstetric triage pavilion, opened January 2015, with dedicated midwives. Data were collected at three time intervals following the triage pavilion opening and compared with baseline including: referral indications, patient and labour characteristics, waiting time from arrival to assessment and the documentation of a care plan. An obstetric triage improvement programme reduced the median (IQR) patient waiting time from facility arrival to first assessment by a midwife from 40 min (15–100) to 5 min (2–6) (p<0.001) over the 5-year intervention. The triage pavilion enhanced performance resulting in the elimination of previous delays associated with the time of admission and disease acuity. Care plan documentation increased from 51% to 96%. Obstetric triage, when properly implemented, reduced delay in a busy, low-resource hospital. The implementation process was sustained under local leadership during transition to a new hospital.
Optimal relieffor pain at the end of life: a caregiver’s tale
Authors: Morris David B
Published: April 2018

The current opioid crisis—driven partly by medical overprescription and partly by illegal drug abuse—is a significant cultural and professional dilemma in the USA and elsewhere. It has produced a strong reaction in favour of restricting medical use of opioids for pain, especially chronic pain. The author for a quarter century has written about pain from a biocultural perspective, and in this essay—based on his experience as primary caregiver for his late wife—he approaches the question of appropriate opioid use at the end of life.
Experimental tobacco marketplace: substitutability of e-cigarette liquid for cigarettes as a function of nicotine strength
Authors: Pope Derek A , Poe Lindsey , Stein Jeffrey S , Kaplan Brent A , Heckman Bryan W , Epstein Leonard H , Bickel Warren K
Published: April 2018

Background

The experimental tobacco marketplace (ETM) provides a method to estimate, prior to implementation, the effects of new products or policies on purchasing across various products in a complex tobacco marketplace. We used the ETM to examine the relationship between nicotine strength and substitutability of alternative products for cigarettes to contribute to the literature on regulation of e-liquid nicotine strength.

Methods

The present study contained four sampling and four ETM purchasing sessions. During sampling sessions, participants were provided 1 of 4 e-liquid strengths (randomised) to sample for 2 days followed by an ETM purchasing session. The nicotine strength sampled in the 2 days prior to an ETM session was the same strength available for purchase in the next ETM. Each participant sampled and could purchase 0 mg/mL, 6 mg/mL, 12 mg/mL and 24 mg/mL e-liquid, among other products, during the study.

Results

Cigarette demand was unaltered across e-liquid strength. E-liquid was the only product to substitute for cigarettes across more than one e-liquid strength. Substitutability increased as a function of e-liquid strength, with the 24 mg/mL displaying the greatest substitutability of all products.

Conclusions

The present study found that e-liquid substitutability increased with nicotine strength, at least up to 24 mg/mL e-liquid. However, the effects of e-liquid nicotine strength on cigarette purchasing were marginal and total nicotine purchased increased as e-liquid nicotine strength increased.
Fracture analysis of a central crack in a long cylindrical superconductor with exponential model
Authors: Zhao Yu Feng , Xu Chi
Published: April 2018

The fracture behavior of a long cylindrical superconductor is investigated by modeling a central crack that is induced by electromagnetic force. Based on the exponential model, the stress intensity factors (SIFs) with the dimensionless parameter p and the length of the crack a/R for the zero-field cooling (ZFC) and field-cooling (FC) processes are numerically simulated using the finite element method (FEM) and assuming a persistent current flow. As the applied field [Formula: see text] decreases, the dependence of p and a/R on the SIFs in the ZFC process is exactly opposite to that observed in the FC process. Numerical results indicate that the exponential model exhibits different characteristics for the trend of the SIFs from the results obtained using the Bean and Kim models. This implies that the crack length and the trapped field have significant effects on the fracture behavior of bulk superconductors. The obtained results are useful for understanding the critical-state model of high-temperature superconductors in crack problem.
Triassic fault reactivation in eastern Saudi Arabia: implications for shear and fluid systems on the southern margin of Neotethys
Authors: Stewart S.A. , Muslem A.S. , Wibisono G.
Published: April 2018

Early to Mid-Triassic fault reactivation in eastern Saudi Arabia is shown using three-dimensional seismic reflection data. The geometry and timing of these fault systems are constrained by the interpretation of reflectors in the Khuff, Sudair and Jilh formations, tied to deep wells. The faults terminate upwards in the Sudair and Jilh formations, dating this event to 250–240 Ma. The fault systems generally trend north–south to NE–SW and in places consist of isolated systems several hundred kilometres long, whereas other areas show pervasive, evenly spaced faults 5–10 km apart. The north–south-trending structures control Triassic isopach variations, whereas the NE–SW-trending systems contain localized highs and lows in relay zones, indicating strike-slip kinematics with the maximum horizontal stress, restored for post-Triassic plate rotation, trending 030–210°. These fault systems link Lower Paleozoic source rocks with the Khuff Formation reservoirs, often retaining topseal integrity due to the presence of upper fault tips in the sealing units. The faults are interpreted to be reactivations of Precambrian basement lineaments. The fault timing correlates with a cusp in the African–Arabian plate motion path relative to Tethyan terranes. These local- and plate-scale observations can be explained by Early to Mid-Triassic dextral shear along the Arabian continental margin.
Interactive Sound Propagation and Rendering for Large Multi-Source Scenes
Authors: Schissler Carl , Manocha Dinesh
Published: April 2018

We present an approach to generate plausible acoustic effects at interactive rates in large dynamic environments containing many sound sources. Our formulation combines listener-based backward ray tracing with sound source clustering and hybrid audio rendering to handle complex scenes. We present a new algorithm for dynamic late reverberation that performs high-order ray tracing from the listener against spherical sound sources. We achieve sublinear scaling with the number of sources by clustering distant sound sources and taking relative visibility into account. We also describe a hybrid convolution-based audio rendering technique that can process hundreds of thousands of sound paths at interactive rates. We demonstrate the performance on many indoor and outdoor scenes with up to 200 sound sources. In practice, our algorithm can compute more than 50 reflection orders at interactive rates on a multicore PC, and we observe a 5x speedup over prior geometric sound propagation algorithms.
A Compressed Representation for Ray Tracing Parametric Surfaces
Authors: Selgrad Kai , Lier Alexander , Martinek Magdalena , Buchenau Christoph , Guthe Michael , Kranz Franziska , Schäfer Henry , Stamminger Marc
Published: April 2018

Parametric surfaces are an essential modeling tool in computer aided design and movie production. Even though their use is well established in industry, generating ray-traced images adds significant cost in time and memory consumption. Ray tracing such surfaces is usually accomplished by subdividing the surfaces on the fly, or by conversion to a polygonal representation. However, on-the-fly subdivision is computationally very expensive, whereas polygonal meshes require large amounts of memory. This is a particular problem for parametric surfaces with displacement, where very fine tessellation is required to faithfully represent the shape. Hence, memory restrictions are the major challenge in production rendering. In this article, we present a novel solution to this problem. We propose a compression scheme for a priori Bounding Volume Hierarchies (BVHs) on parametric patches, that reduces the data required for the hierarchy by a factor of up to 48. We further propose an approximate evaluation method that does not require leaf geometry, yielding an overall reduction of memory consumption by a factor of 60 over regular BVHs on indexed face sets and by a factor of 16 over established state-of-the-art compression schemes. Alternatively, our compression can simply be applied to a standard BVH while keeping the leaf geometry, resulting in a compression rate of up to 2:1 over current methods. Although decompression generates additional costs during traversal, we can manage very complex scenes even on the memory restrictive GPU at competitive render times.
Momentum-Mapped Inverted Pendulum Models for Controlling Dynamic Human Motions
Authors: Kwon Taesoo , Hodgins Jessica K.
Published: April 2018

Designing a unified framework for simulating a broad variety of human behaviors has proven to be challenging. In this article, we present an approach for control system design that can generate animations of a diverse set of behaviors including walking, running, and a variety of gymnastic behaviors. We achieve this generalization with a balancing strategy that relies on a new form of inverted pendulum model (IPM), which we call the momentum-mapped IPM (MMIPM). We analyze reference motion capture data in a pre-processing step to extract the motion of the MMIPM. To compute a new motion, the controller plans a desired motion, frame by frame, based on the current pendulum state and a predicted pendulum trajectory. By tracking this time-varying trajectory, the controller creates a character that dynamically balances, changes speed, makes turns, jumps, and performs gymnastic maneuvers.
Retrieval on Parametric Shape Collections
Authors: Schulz Adriana , Shamir Ariel , Baran Ilya , Levin David I. W. , Sitthi-Amorn Pitchaya , Matusik Wojciech
Published: April 2018

While collections of parametric shapes are growing in size and use, little progress has been made on the fundamental problem of shape-based matching and retrieval for parametric shapes in a collection. The search space for such collections is both discrete (number of shapes) and continuous (parameter values). In this work, we propose representing this space using descriptors that have shown to be effective for single shape retrieval. While single shapes can be represented as points in a descriptor space, parametric shapes are mapped into larger continuous regions. For smooth descriptors, we can assume that these regions are bounded low-dimensional manifolds where the dimensionality is given by the number of shape parameters. We propose representing these manifolds with a set of primitives, namely, points and bounded tangent spaces. Our algorithm describes how to define these primitives and how to use them to construct a manifold approximation that allows accurate and fast retrieval. We perform an analysis based on curvature, boundary evaluation, and the allowed approximation error to select between primitive types. We show how to compute decision variables with no need for empirical parameter adjustments and discuss theoretical guarantees on retrieval accuracy. We validate our approach with experiments that use different types of descriptors on a collection of shapes from multiple categories.
Antialiasing Complex Global Illumination Effects in Path-Space
Authors: Belcour Laurent , Yan Ling-Qi , Ramamoorthi Ravi , Nowrouzezahrai Derek
Published: April 2018

We present the first method to efficiently predict antialiasing footprints to pre-filter color-, normal-, and displacement-mapped appearance in the context of multi-bounce global illumination. We derive Fourier spectra for radiance and importance functions that allow us to compute spatial-angular filtering footprints at path vertices for both uni- and bi-directional path construction. We then use these footprints to antialias reflectance modulated by high-resolution maps (such as color and normal maps) encountered along a path. In doing so, we also unify the traditional path-space formulation of light transport with our frequency-space interpretation of global illumination pre-filtering. Our method is fully compatible with all existing single bounce pre-filtering appearance models, not restricted by path length, and easy to implement atop existing path-space renderers. We illustrate its effectiveness on several radiometrically complex scenarios where previous approaches either completely fail or require orders of magnitude more time to arrive at similarly high-quality results.
Fast Weather Simulation for Inverse Procedural Design of 3D Urban Models
Authors: Garcia-Dorado Ignacio , Aliaga Daniel G. , Bhalachandran Saiprasanth , Schmid Paul , Niyogi Dev
Published: April 2018

We present the first realistic, physically based, fully coupled, real-time weather design tool for use in urban procedural modeling. We merge designing of a 3D urban model with a controlled long-lasting spatiotemporal interactive simulation of weather. Starting from the fundamental dynamical equations similar to those used in state-of-the-art weather models, we present a novel simplified urban weather model for interactive graphics. Control of physically based weather phenomena is accomplished via an inverse modeling methodology. In our results, we present several scenarios of forward design, inverse design with high-level and detailed-level weather control and optimization, and comparisons of our method against well-known weather simulation results and systems.
Functional Characterization of Intrinsic and Extrinsic Geometry
Authors: Corman Etienne , Solomon Justin , Ben-Chen Mirela , Guibas Leonidas , Ovsjanikov Maks
Published: April 2018

We propose a novel way to capture and characterize distortion between pairs of shapes by extending the recently proposed framework of shape differences built on functional maps. We modify the original definition of shape differences slightly and prove that after this change, the discrete metric is fully encoded in two shape difference operators and can be recovered by solving two linear systems of equations. Then we introduce an extension of the shape difference operators using offset surfaces to capture extrinsic or embedding-dependent distortion, complementing the purely intrinsic nature of the original shape differences. Finally, we demonstrate that a set of four operators is complete, capturing intrinsic and extrinsic structure and fully encoding a shape up to rigid motion in both discrete and continuous settings. We highlight the usefulness of our constructions by showing the complementary nature of our extrinsic shape differences in capturing distortion ignored by previous approaches. We additionally provide examples where we recover local shape structure from the shape difference operators, suggesting shape editing and analysis tools based on manipulating shape differences.
Efficient Solver for Spacetime Control of Smoke
Authors: Pan Zherong , Manocha Dinesh
Published: April 2018

We present a novel algorithm to control the physically-based animation of smoke. Given a set of keyframe smoke shapes, we compute a dense sequence of control force fields that can drive the smoke shape to match several keyframes at certain time instances. Our approach formulates this control problem as a spacetime optimization constrained by partial differential equations. In order to compute the locally optimal control forces, we alternatively optimize the velocity fields and density fields using an alternating direction method of multiplier (ADMM) optimizer. In order to reduce the high complexity of multiple passes of fluid resimulation during velocity field optimization, we utilize the coherence between consecutive fluid simulation passes. We demonstrate the benefits of our approach by computing accurate solutions on 2D and 3D benchmarks. In practice, we observe up to an order of magnitude improvement over prior optimal control methods.
Interactive Relighting in Single Low-Dynamic Range Images
Authors: Wu Jung-Hsuan , Saito Suguru
Published: April 2018

This article addresses the relighting of outdoor and large indoor scenes illuminated by nondistant lights, which has seldom been discussed in previous works. We propose a method for users to interactively edit the illumination of a scene by moving existing lights and inserting synthetic lights into the scene that requires only a small amount of user annotation and a single low-dynamic range (LDR) image. We achieve this by adopting a top-down approach that estimates the scene reflectance by fitting a diffuse illumination model to a photograph. This approach gains stability and robustness by estimating the camera, scene geometry, and light sources in sequence and by using a confidence map, which is a per-pixel weight map. The results of our evaluation demonstrates that the proposed method can estimate a scene accurately enough for realistic relighting of images. Moreover, the experimental results of our user studies show that the synthesized images are so realistic as to be almost indistinguishable from real photographs.
BundleFusion
Authors: Dai Angela , Nießner Matthias , Zollhöfer Michael , Izadi Shahram , Theobalt Christian
Published: April 2018

Real-time, high-quality, 3D scanning of large-scale scenes is key to mixed reality and robotic applications. However, scalability brings challenges of drift in pose estimation, introducing significant errors in the accumulated model. Approaches often require hours of offline processing to globally correct model errors. Recent online methods demonstrate compelling results but suffer from (1) needing minutes to perform online correction, preventing true real-time use; (2) brittle frame-to-frame (or frame-to-model) pose estimation, resulting in many tracking failures; or (3) supporting only unstructured point-based representations, which limit scan quality and applicability. We systematically address these issues with a novel, real-time, end-to-end reconstruction framework. At its core is a robust pose estimation strategy, optimizing per frame for a global set of camera poses by considering the complete history of RGB-D input with an efficient hierarchical approach. We remove the heavy reliance on temporal tracking and continually localize to the globally optimized frames instead. We contribute a parallelizable optimization framework, which employs correspondences based on sparse features and dense geometric and photometric matching. Our approach estimates globally optimized (i.e., bundle adjusted) poses in real time, supports robust tracking with recovery from gross tracking failures (i.e., relocalization), and re-estimates the 3D model in real time to ensure global consistency, all within a single framework. Our approach outperforms state-of-the-art online systems with quality on par to offline methods, but with unprecedented speed and scan completeness. Our framework leads to a comprehensive online scanning solution for large indoor environments, enabling ease of use and high-quality results.
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Interactive Design and Stability Analysis of Decorative Joinery for Furniture
Authors: Yao Jiaxian , Kaufman Danny M. , Gingold Yotam , Agrawala Maneesh
Published: April 2018

High-quality hand-made furniture often employs
intrinsic joints
that geometrically interlock along mating surfaces. Such joints increase the structural integrity of the furniture and add to its visual appeal. We present an interactive tool for designing such intrinsic joints. Users draw the visual appearance of the joints on the surface of an input furniture model as groups of two-dimensional (2D) regions that must belong to the same part. Our tool automatically partitions the furniture model into a set of solid 3D parts that conform to the user-specified 2D regions and assemble into the furniture. If the input does not merit assemblable solid 3D parts, then our tool reports the failure and suggests options for redesigning the 2D surface regions so that they are assemblable. Similarly, if any parts in the resulting assembly are unstable, then our tool suggests where additional 2D regions should be drawn to better interlock the parts and improve stability. To perform this stability analysis, we introduce a novel variational static analysis method that addresses shortcomings of the equilibrium method for our task. Specifically, our method correctly detects sliding instabilities and reports the locations and directions of sliding and hinging failures. We show that our tool can be used to generate over 100 joints inspired by traditional woodworking and Japanese joinery. We also design and fabricate nine complete furniture assemblies that are stable and connected using only the intrinsic joints produced by our tool.
Learning to Schedule Control Fragments for Physics-Based Characters Using Deep Q-Learning
Authors: Liu Libin , Hodgins Jessica
Published: April 2018

Given a robust control system, physical simulation offers the potential for interactive human characters that move in realistic and responsive ways. In this article, we describe how to learn a scheduling scheme that reorders short control fragments as necessary at runtime to create a control system that can respond to disturbances and allows steering and other user interactions. These schedulers provide robust control of a wide range of highly dynamic behaviors, including walking on a ball, balancing on a bongo board, skateboarding, running, push-recovery, and breakdancing. We show that moderate-sized Q-networks can model the schedulers for these control tasks effectively and that those schedulers can be efficiently learned by the deep Q-learning algorithm.
Two-Scale Topology Optimization with Microstructures
Authors: Zhu Bo , Skouras Mélina , Chen Desai , Matusik Wojciech
Published: April 2018

In this article, we present a novel two-scale framework to optimize the structure and the material distribution of an object given its functional specifications. Our approach utilizes multi-material microstructures as low-level building blocks of the object. We start by precomputing the material property gamut—the set of bulk material properties that can be achieved with all material microstructures of a given size. We represent the boundary of this material property gamut using a level set field. Next, we propose an efficient and general topology optimization algorithm that simultaneously computes an optimal object topology and spatially varying material properties constrained by the precomputed gamut. Finally, we map the optimal spatially varying material properties onto the microstructures with the corresponding properties to generate a high-resolution printable structure. We demonstrate the efficacy of our framework by designing, optimizing, and fabricating objects in different material property spaces on the level of a trillion voxels, that is, several orders of magnitude higher than what can be achieved with current systems.
Portrait Lighting Transfer Using a Mass Transport Approach
Authors: Shu Zhixin , Hadap Sunil , Shechtman Eli , Sunkavalli Kalyan , Paris Sylvain , Samaras Dimitris
Published: April 2018

Lighting is a critical element of portrait photography. However, good lighting design typically requires complex equipment and significant time and expertise. Our work simplifies this task using a relighting technique that transfers the desired illumination of one portrait onto another. The novelty in our approach to this challenging problem is our formulation of relighting as a mass transport problem. We start from standard color histogram matching that only captures the overall tone of the illumination, and we show how to use the mass-transport formulation to make it dependent on facial geometry. We fit a three-dimensional (3D) morphable face model to the portrait, and for each pixel, we combine the color value with the corresponding 3D position and normal. We then solve a mass-transport problem in this augmented space to generate a color remapping that achieves localized, geometry-aware relighting. Our technique is robust to variations in facial appearance and small errors in face reconstruction. As we demonstrate, this allows our technique to handle a variety of portraits and illumination conditions, including scenarios that are challenging for previous methods.
Facial Expression Analysis under Partial Occlusion
Authors: Zhang Ligang , Verma Brijesh , Tjondronegoro Dian , Chandran Vinod
Published: April 2018

Automatic machine-based Facial Expression Analysis (FEA) has made substantial progress in the past few decades driven by its importance for applications in psychology, security, health, entertainment, and human–computer interaction. The vast majority of completed FEA studies are based on nonoccluded faces collected in a controlled laboratory environment. Automatic expression recognition tolerant to partial occlusion remains less understood, particularly in real-world scenarios. In recent years, efforts investigating techniques to handle partial occlusion for FEA have seen an increase. The context is right for a comprehensive perspective of these developments and the state of the art from this perspective. This survey provides such a comprehensive review of recent advances in dataset creation, algorithm development, and investigations of the effects of occlusion critical for robust performance in FEA systems. It outlines existing challenges in overcoming partial occlusion and discusses possible opportunities in advancing the technology. To the best of our knowledge, it is the first FEA survey dedicated to occlusion and aimed at promoting better-informed and benchmarked future work.
Providing Geo-Elasticity in Geographically Distributed Clouds
Authors: Guo Tian , Shenoy Prashant
Published: April 2018

Geographically distributed cloud platforms are well suited for serving a geographically diverse user base. However, traditional cloud provisioning mechanisms that make local scaling decisions are not adequate for delivering the best possible performance for modern web applications that observe both temporal and spatial workload fluctuations. We propose GeoScale, a system that provides geo-elasticity by combining model-driven proactive and agile reactive provisioning approaches. GeoScale can dynamically provision server capacity at any location based on workload dynamics. We conduct a detailed evaluation of GeoScale on Amazon’s geo-distributed cloud and show up to 40% improvement in the 95th percentile response time when compared to traditional elasticity techniques.