bluuebunny/crossref_metadata_2025 huggingface dataset:
Expression and control of an operon from an intracellular symbiont which is homologous to the groE operon
Authors: Sato S , Ishikawa H
Published: November 2016

Members of the genus Buchnera are intracellular symbionts harbored by the aphid bacteriocyte which selectively synthesize symbionin, a homolog of the Escherichia coli GroEL protein, in vivo. Symbionin and SymS, a GroES homolog, are encoded in the symSL operon. Northern blotting and primer extension analyses revealed that the symSL operon invariably gives rise to a bicistronic mRNA under the control of a heat shock promoter, though the amount of the symSL mRNA in the isolated symbiont did not increase in response to heat shock. The sigma32 protein that recognizes the heat shock promoter in E. coli was scarcely detected in Buchnera cells even after heat shock. Although the functionally essential regions of the Buchnera sigma32 protein were well conserved, the Buchnera rpoH gene did not complement an E. coli delta rpoH mutant. On the one hand, the A-T evolutionary pressure imposed on the Buchnera genome may have not only decreased the activity of its sigma32 but also ruined the nucleotide sequences necessary for the expression of rpoH; on the other hand, it may have facilitated expression of the symSL operon without activation by sigma32.
Influence of different rol gene products on the chain length of Shigella dysenteriae type 1 lipopolysaccharide O antigen expressed by Shigella flexneri carrier strains
Authors: Klee S R , Tzschaschel B D , Timmis K N , Guzman C A
Published: November 2016

Introduction of the rol genes of Shigella dysenteriae 1 and Escherichia coli K-12 into Shigella flexneri carrier strains expressing the heterologous S. dysenteriae type 1 lipopolysaccharide resulted in the formation of longer chains of S. dysenteriae 1 O antigen. In bacteria producing both homologous and heterologous O antigen, this resulted in a reduction of the masking of heterologous O antigen by homologous lipopolysaccharide and an increased immune response induced by intraperitoneal immunization of mice by recombinant bacteria. The rol genes of S. dysenteriae 1 and E. coli K-12 were sequenced, and their gene products were compared with the S. flexneri Rol protein. The primary sequence of S. flexneri Rol differs from both E. coli K-12 and S. dysenteriae 1 Rol proteins only at positions 267 and 270, which suggests that this region may be responsible for the difference in biological activities.
The rtn gene of Proteus vulgaris is actually from Escherichia coli
Authors: Hall B G
Published: November 2016

The rtn gene, identified as coming from Proteus vulgaris ATCC 13315, is present in Escherichia coli K-12, and over a 440-bp region of rtn is identical to the published Proteus sequence, with the exception of a single G insertion. It was not possible to verify the presence of rtn in P. vulgaris.
Identification and characterization of IS1381, a new insertion sequence in Streptococcus pneumoniae
Authors: Sánchez-Beato A R , García E , López R , García J L
Published: November 2016

A new insertion sequence (IS1381) was identified in the genome of Streptococcus pneumoniae R6 as an 846-bp segment containing 20-bp terminal inverted repeats and flanked by 7-bp direct repeats. The three sequenced copies of this element have two overlapping open reading frame (ORF) genes named orfA and orfB. However, significant variations between individual copies were found, suggesting that inactivating mutations have occurred in an original single ORF. Accordingly, the consensus IS1381 element derived from the comparison of the three available copies should contain a single ORF sufficient to encode a basic protein of 267 amino acids which exhibited high similarity to the putative transposases of ISL2 from Lactobacillus helveticus and of IS702 from the cyanobacterium Calothrix sp. strain PCC 7601. A minimum of five to seven copies were detected by hybridization experiments in the R6 genome. In remarkable contrast with the two previously reported pneumococcal insertion sequences, several copies of IS1381 have been detected in all of the clinical isolates tested so far. Interestingly, Streptococcus oralis NCTC 11427 (type strain), a close relative of pneumococcus, does not contain this element, but its occurrence in the type strain of Streptococcus mitis (NCTC 12261) suggests that this species has exchanged DNA with S. pneumoniae directly or through an intermediate species.
Cnr protein, the negative regulator of bacteriophage P4 replication, stimulates specific DNA binding of its initiator protein alpha
Authors: Ziegelin G , Calendar R , Ghisotti D , Terzano S , Lanka E
Published: November 2016

Bacteriophage P4 DNA replication depends upon the phage-encoded alpha protein, which has DNA helicase and DNA primase activity and can specifically bind to the replication origin (ori) and to the cis replicating region (crr). The P4 Cnr protein functions as a negative regulator of P4 replication, and P4 does not replicate in cells that overexpress cnr. We searched for P4 mutants that suppressed this phenotype (Cnr resistant [alpha cr]). Eight independent mutants that grew in the presence of high levels of Cnr were obtained. None of these can establish the plasmid state. Each of these mutations lies in the DNA binding domain of gp alpha that occupies the C terminus of the protein. Five different sequence changes were found: T675M, G732V (three times), G732W (twice), L733V, and L737V. A TrxA-Cnr fusion protein does not bind DNA by itself but stimulates the ori and crr binding abilities of alpha protein in vitro. The alpha cr mutant proteins were still able to bind specifically to ori or crr, but specific DNA binding was less stimulated by the TrxA-Cnr protein. We present evidence that Cnr protein interacts with the gp alpha domain that binds specifically to DNA and that gp(alpha)cr mutations impair this interaction. We hypothesize that gp alpha-Cnr interaction is essential for the control of P4 DNA replication.
Promoter mapping and transcriptional regulation of the iron-regulated Neisseria gonorrhoeae fbpA gene
Authors: Forng R Y , Ekechukwu C R , Subbarao S , Morse S A , Genco C A
Published: November 2016

In this study, we have mapped the promoter region of the Neisseria gonorrhoeae ferric iron binding protein-encoding gene fbpA, determined the start point of transcription, and examined the accumulation of fbpA mRNA Primer extension analysis of the fbpA promoter region indicated a single transcriptional start site located 51 bp upstream of the ATG translational start site. Northern blot analysis with a 200-bp fbpA structural gene probe detected one transcript of 1.0 kb in RNAs extracted from gonococcal cultures grown under iron-restricted conditions; the 1.0-kb transcript was observed to accumulate at a steady rate throughout the growth cycle. In comparison, in cultures grown under iron-sufficient conditions, the intensity of the 1.0-kb transcript was reduced considerably. Isolation of total RNA from rifampin-treated cells indicated that the half-life of the 1.0-kb fbpA transcript in cells grown under iron-restricted conditions was 1.2 +/- 0.2 min, while that of the 1.0-kb fbpA transcript obtained from cultures grown under iron-sufficient conditions was 0.5 +/- 0.1 min. Taken together, our results indicate that the fbpA promoter is regulated by iron and that transcription and translation of FbpA are closely linked.
Sinorhizobium teranga bv. acaciae ORS1073 and Rhizobium sp. strain ORS1001, two distantly related Acacia-nodulating strains, produce similar Nod factors that are O carbamoylated, N methylated, and mainly sulfated
Authors: Lorquin J , Lortet G , Ferro M , Mear N , Promé J C , Boivin C
Published: November 2016

We have determined the structures of Nod factors produced by strains representative of Sinorhizobium teranga bv. acaciae and the so-called cluster U from the Rhizobium loti branch, two genetically different symbionts of particular Acacia species. Compounds from both strains were found to be similar, i.e., mainly sulfated, O carbamoylated, and N methylated, indicating a close relationship between host specificity and Nod factor structure, regardless of the taxonomy of the bacterial symbiont.
Impact of Genetic Diversity on the Biology of
Mycobacterium tuberculosis
Complex Strains
Authors: Niemann Stefan , Merker Matthias , Kohl Thomas , Supply Philip
Published: November 2016

Tuberculosis (TB) remains the most deadly bacterial infectious disease worldwide. Its treatment and control are threatened by increasing numbers of multidrug-resistant (MDR) or nearly untreatable extensively drug-resistant (XDR) strains. New concepts are therefore urgently needed to understand the factors driving the TB epidemics and the spread of different strain populations, especially in association with drug resistance. Classical genotyping and, more recently, whole-genome sequencing (WGS) revealed that the world population of tubercle bacilli is more diverse than previously thought. Several major phylogenetic lineages can be distinguished, which are associated with their sympatric host population. Distinct clonal (sub)populations can even coexist within infected patients. WGS is now used as the ultimate approach for differentiating clinical isolates and for linking phenotypic to genomic variation from lineage to strain levels. Multiple lines of evidence indicate that the genetic diversity of TB strains translates into pathobiological consequences, and key molecular mechanisms probably involved in differential pathoadaptation of some main lineages have recently been identified. Evidence also accumulates on molecular mechanisms putatively fostering the emergence and rapid expansion of particular MDR and XDR strain groups in some world regions. However, further integrative studies will be needed for complete elucidation of the mechanisms that allow the pathogen to infect its host, acquire multidrug resistance, and transmit so efficiently. Such knowledge will be key for the development of the most effective new diagnostics, drugs, and vaccination strategies.
Conservative treatments for greater trochanteric pain syndrome: a systematic review
Authors: Barratt Paul A , Brookes Nathan , Newson Annalisa
Published: November 2016

Background

Greater trochanteric pain syndrome (GTPS) can have a significant effect on quality of life.

Aim

To evaluate the conservative treatments for GTPS.

Design

This systematic review assessed risk of bias using the Cochrane Risk of Bias Tool and Cochrane Risk of Bias Tool for non-randomised studies of interventions.

Data sources

On 13 January 2016, a comprehensive search was conducted, with no limit on year of publication for relevant studies in the MEDLINE, CINAHL, AMED and EMBASE databases.

Eligibility criteria for selecting studies

English language randomised controlled trials, case–control or cohort studies reporting outcome data for conservative treatments for adults having a diagnosis of GTPS, or trochanteric bursitis, were included.

Results

8 studies (n=696) were eligible for inclusion in the review; corticosteroid injections (CSI) (n=6), shockwave therapy (n=2), home training (n=1) and orthotics (n=1). Based on pain, CSI demonstrated superior outcomes for up to 3 months compared with home training, radial shockwave therapy (RSWT) and usual care, in 4 studies demonstrating either a low or moderate risk of bias. Fluoroscopy-guided injections failed to show additional benefit. RSWT and home training had limited evidence. No conclusions can be drawn regarding the use of orthotics due to the serious risk of bias and methodological flaws within that study.

Conclusions

This review demonstrates a paucity of high-quality research for the conservative treatments of GTPS. The risk of bias was low in only one study, demonstrating no additional benefit with fluoroscopically guided injections. Risk of bias in all remaining studies was varied. Standardisation of diagnostic criteria and outcome measures is essential to enable more powerful analysis.
Can wheat germ have a beneficial effect on human health? A study protocol for a randomised crossover controlled trial to evaluate its health effects
Authors: Moreira-Rosário André , Pinheiro Helder , Calhau Conceição , Azevedo Luís Filipe
Published: November 2016

Introduction

Cardiovascular diseases (CVD) are the leading cause of mortality worldwide and diet is an important contributor to CVD risk. Thus, several food derivatives are being investigated for their beneficial impact on reducing cardiometabolic risk factors, either in risk groups or in healthy population as a preventive measure. Wheat germ is a food by-product with high nutritional value, especially as a concentrated source of dietary fibre and essential fatty acids, but its incorporation into the diet has been rare up to now. Previous studies do not clarify the hypothesised potential causal relationship between the consumption of wheat germ and benefits for human health.

Methods and analysis

We are conducting a randomised, double-blinded, crossover, placebo-controlled clinical trial designed to assess the physiological effects of daily consumption of wheat germ-enriched bread (containing 6 g of wheat germ) compared with non-enriched bread, over a 4-week period with a 15-week follow-up, in a healthy human population. A total of 55 participants (healthy volunteers, aged 18–60) have been recruited from the Porto metropolitan area in northern Portugal. Our aim is to evaluate the health effects of wheat germ on blood cholesterol and triglycerides, postprandial glycaemic response, gastrointestinal function and discomfort, and changes in intestinal microbiota and insulin resistance as secondary outcomes. The study follows the best practices for evaluating health claims in food according to the European Food Safety Authority (EFSA) scientific opinion, namely random allocation, double blinding, reporting methods to measure and maximise compliance, and validated outcomes with beneficial physiological effects as recommended by EFSA.

Ethics and dissemination

The study has been approved by the Health Ethics Committee of São João Hospital Centre (156-15) and the Ethics Committee of Faculty of Medicine of the University of Porto (PCEDCSS-FMUP07/2015). Results will be disseminated through peer-reviewed publications and presentations at international scientific meetings.

Trial registration number

NCT02405507; pre-results.
Operationalising the Lean principles in maternity service design using 3P methodology
Authors: Smith Iain
Published: November 2016

The last half century has seen significant changes to Maternity services in England. Though rates of maternal and infant mortality have fallen to very low levels, this has been achieved largely through hospital admission. It has been argued that maternity services may have become over-medicalised and service users have expressed a preference for more personalised care. NHS England's national strategy sets out a vision for a modern maternity service that continues to deliver safe care whilst also adopting the principles of personalisation. Therefore, there is a need to develop maternity services that balance safety with personal choice.

To address this challenge, a maternity unit in North East England considered improving their service through refurbishment or building new facilities. Using a design process known as the production preparation process (or 3P), the Lean principles of understanding user value, mapping value-streams, creating flow, developing pull processes and continuous improvement were applied to the design of a new maternity department. Multiple stakeholders were engaged in the design through participation in a time-out (3P) workshop in which an innovative pathway and facility for maternity services were co-designed. The team created a hybrid model that they described as “wrap around care” in which the Lean concept of pull was applied to create a service and facility design in which expectant mothers were put at the centre of care with clinicians, skills, equipment and supplies drawn towards them in line with acuity changes as needed.

Applying the Lean principles using the 3P method helped stakeholders to create an innovative design in line with the aspirations and objectives of the National Maternity Review. The case provides a practical example of stakeholders applying the Lean principles to maternity services and demonstrates the potential applicability of the Lean 3P approach to design healthcare services in line with policy requirements.
Social capital interventions targeting older people and their impact on health: a systematic review
Authors: Coll-Planas Laura , Nyqvist Fredrica , Puig Teresa , Urrútia Gerard , Solà Ivan , Monteserín Rosa
Published: November 2016

Background

Observational studies show that social capital is a protective health factor. Therefore, we aim to assess the currently unclear health impact of social capital interventions targeting older adults.

Methods

We conducted a systematic review based on a logic model. Studies published between January 1980 and July 2015 were retrieved from MEDLINE, EMBASE, CINAHL, PsycINFO, Cochrane Central Register of Controlled Trials and Web of Science. We included randomised controlled trials targeting participants over 60 years old and focused on social capital or its components (eg, social support and social participation). The comparison group should not promote social capital. We assessed risk of bias and impact on health outcomes and use of health-related resources applying a procedure from the Canadian Agency for Drugs and Technologies in Health (CADTH) based on vote-counting and standardised decision rules. The review protocol was registered in PROSPERO (reference number CRD42014015362).

Results

We examined 17 341 abstracts and included 73 papers reporting 36 trials. Trials were clinically and methodologically diverse and reported positive effects in different contexts, populations and interventions across multiple subjective and objective measures. According to sufficiently reported outcomes, social capital interventions showed mixed effects on quality of life, well-being and self-perceived health and were generally ineffective on loneliness, mood and mortality. Eight trials with high quality showed favourable impacts on overall, mental and physical health, mortality and use of health-related resources.

Conclusions

Our review highlights the lack of evidence and the diversity among trials, while supporting the potential of social capital interventions to reach comprehensive health effects in older adults.
Beneficial effects of nontoxic ozone on H2O2-induced stress and inflammation
Authors: Kucukgul Altug , Erdogan Suat , Gonenci Ramazan , Ozan Gonca
Published: November 2016

In this study, the anti-oxidant and anti-inflammatory efficacy of ozone oxidative preconditioning (OOP) were investigated on hydrogen peroxide (H2O2)-induced human lung alveolar cells. In MTT and trypan blue viability tests, while 100 μmol/L H2O2caused a 17.3% and 21.9% decrease in the number of living cells, respectively, ozone at 20 μmol/L regenerated cell proliferation and prevented 9.6% and 11.0% of cell loss, respectively. In addition, H2O2decreased the transcription levels of catalase (CAT), glutathione peroxidase (GPx), and superoxide dismutase (SOD) 5.43-, 2.89-, and 5.33-fold, respectively, while it increased Bax, NF-κβ, TNF-α, and iNOS expression 1.57-, 1.32-, 1.40-, and 1.41-fold, respectively. Ozone pretreatment, however, increased CAT, GPx, and SOD transcription levels 7.08-, 5.17-, and 6.49-fold and decreased Bax, NF-κβ, TNF-α, and iNOS transcriptions by 1.25-, 0.76-, 3.63-, and 7.91-fold, respectively. Moreover, intracellular glutathione (GSH) level and SOD activity were decreased by 46.2% and 45.0% in the H2O2treatment group, and OOP recovered 58.5% and 20.1% of the decreases caused by H2O2. H2O2also increased nitrite levels 7.84-fold, and OOP reduced this increase by half. Consequently, OOP demonstrated potent anti-oxidant and anti-inflammatory effects on in vitro model of oxidative stress-induced lung injury.
[2.2]Paracyclophane-based single molecular wire consisting of four π-electron systems
Authors: Morisaki Yasuhiro , Shibata Shotaro , Chujo Yoshiki
Published: November 2016

A [2.2]paracyclophane-based through-space–conjugated tetramer comprising four partially stacked π-electron systems was designed and synthesized, with a large overlap integral between the photoluminescence spectrum of the terminal π-electron system of the through-space–conjugated trimer and the absorption band of the fourth π-electron system. Efficient unidirectional photoexcited energy transfer in the tetramer occurred by the Förster mechanism; the energy transfer efficiency and related rate constants were found to be >0.999 and >1012 s–1, respectively, and stepwise energy transfer was found to be dominant. The [2.2]paracyclophane-based tetramer acted as a single molecular wire for efficient unidirectional photoexcited energy transfer.
Gravitational radiation observations
Authors: Glass E.N.
Published: November 2016

A discussion of the details of recent gravitational radiation detection by LIGO is given.
N-acetylcysteine a possible protector against indomethacin-induced peptic ulcer: crosstalk between antioxidant, anti-inflammatory, and antiapoptotic mechanisms
Authors: Soliman Nema Ali , Zineldeen Doaa Hussein , Katary Mohamed Alaa , Ali Darin Abd
Published: November 2016

This study investigated the gastroprotective effects of N-acetylcysteine (NAC) against indomethacin-induced gastric ulcer in rats. Ulceration was induced by a single oral administration of indomethacin (30 mg/kg). 50 male albino rats were allocated into 5 equal groups: control group received normal saline orally, indomethacin group rats received normal saline orally for 5 days and indomethacin (50 mg/kg) on the last day, ranitidine group received ranitidine (reference drug) orally for 5 days (50 mg/kg) before receiving indomethacin (50 mg/kg) on the last day, and NAC groups received NAC orally at 300 and 500 mg/kg, respectively, for 5 days before receiving indomethacin (50 mg/kg) on the last day. Gastric tissue interleukin-1β (IL-1β), interferon-γ (IFN-γ), and caspase-3 levels were immunoassayed. Total thiol (T-SH), myeloperoxidase (MPO), and glucose-6-phosphate dehydrogenase (G6PD) were determined by spectrophotometry. Cytokine-induced neutrophil chemoattractant 2α (CINC-2α) gene expression was evaluated in addition to Bcl-2 immunohistochemistry. Pretreatment with NAC improved the inflammatory, apoptotic, and redox status in a dose-dependent manner particularly in NAC 500 mg/kg pretreated group. These results show a role for NAC in improving indomethacin-induced gastric ulceration via antioxidative, antiapoptotic, and anti-inflammatory interactive mechanisms.
Nuclear DNA content correlates with depth, body size, and diversification rate in amphipod crustaceans from ancient Lake Baikal, Russia
Authors: Jeffery Nicholas W. , Yampolsky Lev , Gregory T. Ryan
Published: November 2016

Lake Baikal in Russia is a large, ancient lake that has been the site of a major radiation of amphipod crustaceans. Nearly 400 named species are known in this single lake, and it is thought that many more await description. The size and depth of Lake Baikal, in particular, may have contributed to the radiation of endemic amphipods by providing a large number of microhabitats for species to invade and subsequently experience reproductive isolation. Here we investigate the possibility that large-scale genomic changes have also accompanied diversification in these crustaceans. Specifically, we report genome size estimates for 36 species of Baikal amphipods, and examine the relationship between genome size, body size, and the maximum depths at which the amphipods are found in the lake. Genome sizes ranged nearly 8-fold in this sample of amphipod species, from 2.15 to 16.63 pg, and there were significant, positive, phylogenetically corrected relationships between genome size, body size, maximum depth, and diversification rate among these species. Our results suggest that major genomic changes, including transposable element proliferation, have accompanied speciation that was driven by selection for differences in body size and habitat preference in Lake Baikal amphipods.
Switchable soliton mode-locked and multi-wavelength operation in thulium-doped all-fiber ring laser
Authors: Latiff A. A. , Shamsudin H. , Tiu Z. C. , Ahmad H. , Harun S. W.
Published: November 2016

A switchable soliton mode-locked and multi-wavelength operation in thulium-doped fiber laser (TDFL) is demonstrated based on nonlinear polarization rotation (NPR) technique. The TDFL produces a soliton pulse operating at 1917.66[Formula: see text]nm using a 5[Formula: see text]m long thulium-doped fiber (TDF) as a gain medium as well as nonlinear medium. The solitonic behavior is further identified with two orders of Kelly sidebands in the output spectrum. The mode-locked emission is obtained from threshold pump power of 522–1052[Formula: see text]mW with consistent pulse repetition rate of 14.7[Formula: see text]MHz. Maximum pulse energy is calculated as 0.89[Formula: see text]nJ at pump power of 1052[Formula: see text]mW, whereas the maximum pulse width is estimated to be approximately 1.36[Formula: see text]ps corresponding to sech2 pulse profile. By shifting the polarization orientation, the cavity can change to multi-wavelength operation with signal-to-noise ratio (SNR) higher than 53[Formula: see text]dB. At pump power of 1037[Formula: see text]mW, three stable peak wavelengths are generated with a power fluctuation and constant spacing of [Formula: see text] dB and 7.4[Formula: see text]nm, respectively.
Spin coherence control of optical bistability via light hole transition in multiple quantum well waveguide embedded in a dielectric medium
Authors: Solookinejad Gh. , Panahi M. , Sangachin E. Ahmadi , Asadpour Seyyed Hossein
Published: November 2016

In this study, we explore the optical bistability (OB) and multistability (OM) features of probe light propagating in a multiple quantum well (MQW) nanostructure embedded in a dielectric medium. It is realized that via light hole (LH) transition between valance bands and conduction band of MQWs with different electron states, the electron spin coherence can be created which can be used to controlling the OB and OM properties. It is realized that the thickness of dielectric slab can lead to adjusting the threshold of OB in different intensities of input field. Moreover, it is found that the transition from OB to OM or vice versa can be possible by selection of suitable quantity of slab thickness. In addition, the role of relative phase of applied fields on OB and OM manners is discussed in different quantities of thickness. Our results may be suitable for developing nanoscale devices in quantum information science and technologies for future applications.
Simultaneous acquisition of microscale reflectance and normals
Authors: Nam Giljoo , Lee Joo Ho , Wu Hongzhi , Gutierrez Diego , Kim Min H.
Published: November 2016

Acquiring microscale reflectance and normals is useful for digital documentation and identification of real-world materials. However, its simultaneous acquisition has rarely been explored due to the difficulties of combining both sources of information at such small scale. In this paper, we capture both spatially-varying material appearance (diffuse, specular and roughness) and normals
simultaneously
at the
microscale
resolution. We design and build a microscopic light dome with 374 LED lights over the hemisphere, specifically tailored to the characteristics of microscopic imaging. This allows us to achieve the highest resolution for such combined information among current state-of-the-art acquisition systems. We thoroughly test and characterize our system, and provide microscopic appearance measurements of a wide range of common materials, as well as renderings of novel views to validate the applicability of our captured data. Additional applications such as bi-scale material editing from real-world samples are also demonstrated.
Birefractive stereo imaging for single-shot depth acquisition
Authors: Baek Seung-Hwan , Gutierrez Diego , Kim Min H.
Published: November 2016

We propose a novel
birefractive
depth acquisition method, which allows for single-shot depth imaging by just placing a birefringent material in front of the lens. While most transmissive materials present a single refractive index per wavelength, birefringent crystals like calcite posses two, resulting in a double refraction effect. We develop an imaging model that leverages this phenomenon and the information contained in the ordinary and the extraordinary refracted rays, providing an effective formulation of the geometric relationship between scene depth and double refraction. To handle the inherent ambiguity of having two sources of information overlapped in a single image, we define and combine two different cost volume functions. We additionally present a novel calibration technique for birefringence, carefully analyze and validate our model, and demonstrate the usefulness of our approach with several image-editing applications.
Sphere-meshes for real-time hand modeling and tracking
Authors: Tkach Anastasia , Pauly Mark , Tagliasacchi Andrea
Published: November 2016

Modern systems for real-time hand tracking rely on a combination of discriminative and generative approaches to robustly recover hand poses. Generative approaches require the specification of a geometric model. In this paper, we propose a the use of sphere-meshes as a novel geometric representation for real-time generative hand tracking. How tightly this model fits a specific user heavily affects tracking precision. We derive an optimization to non-rigidly deform a template model to fit the user data in a number of poses. This optimization jointly captures the user's static and dynamic hand geometry, thus facilitating high-precision registration. At the same time, the limited number of primitives in the tracking template allows us to retain excellent computational performance. We confirm this by embedding our models in an open source real-time registration algorithm to obtain a tracker steadily running at 60Hz. We demonstrate the effectiveness of our solution by qualitatively and quantitatively evaluating tracking precision on a variety of complex motions. We show that the improved tracking accuracy at high frame-rate enables stable tracking of extended and complex motion sequences without the need for per-frame re-initialization. To enable further research in the area of high-precision hand tracking, we publicly release source code and evaluation datasets.
Eulerian solid-fluid coupling
Authors: Teng Yun , Levin David I. W. , Kim Theodore
Published: November 2016

We present a new method that achieves a two-way coupling between deformable solids and an incompressible fluid where the underlying geometric representation is entirely Eulerian. Using the recently developed Eulerian Solids approach [Levin et al. 2011], we are able to simulate multiple solids undergoing complex, frictional contact while simultaneously interacting with a fluid. The complexity of the scenarios we are able to simulate surpasses those that we have seen from any previous method. Eulerian Solids have previously been integrated using explicit schemes, but we develop an implicit scheme that allows large time steps to be taken. The in-compressibility condition is satisfied in both the solid and the fluid, which has the added benefit of simplifying collision handling.
Mesh denoising via cascaded normal regression
Authors: Wang Peng-Shuai , Liu Yang , Tong Xin
Published: November 2016

We present a data-driven approach for mesh denoising. Our key idea is to formulate the denoising process with cascaded non-linear regression functions and learn them from a set of noisy meshes and their ground-truth counterparts. Each regression function infers the normal of a denoised output mesh facet from geometry features extracted from its neighborhood facets on the input mesh and sends the result as the input of the next regression function. Specifically, we develop a
filtered facet normal descriptor (FND)
for modeling the geometry features around each facet on the noisy mesh and model a regression function with neural networks for mapping the FNDs to the facet normals of the denoised mesh. To handle meshes with different geometry features and reduce the training difficulty, we cluster the input mesh facets according to their FNDs and train neural networks for each cluster separately in an offline learning stage. At runtime, our method applies the learned cascaded regression functions to a noisy input mesh and reconstructs the denoised mesh from the output facet normals.

Our method learns the non-linear denoising process from the training data and makes no specific assumptions about the noise distribution and geometry features in the input. The runtime denoising process is fully automatic for different input meshes. Our method can be easily adapted to meshes with arbitrary noise patterns by training a dedicated regression scheme with mesh data and the particular noise pattern. We evaluate our method on meshes with both synthetic and real scanned noise, and compare it to other mesh denoising algorithms. Results demonstrate that our method outperforms the state-of-the-art mesh denoising methods and successfully removes different kinds of noise for meshes with various geometry features.
Block assembly for global registration of building scans
Authors: Yan Feilong , Nan Liangliang , Wonka Peter
Published: November 2016

We propose a framework for global registration of building scans. The first contribution of our work is to detect and use portals (e.g., doors and windows) to improve the local registration between two scans. Our second contribution is an optimization based on a linear integer programming formulation. We abstract each scan as a block and model the blocks registration as an optimization problem that aims at maximizing the overall matching score of the entire scene. We propose an efficient solution to this optimization problem by iteratively detecting and adding local constraints. We demonstrate the effectiveness of the proposed method on buildings of various styles and that our approach is superior to the current state of the art.
Sparse-as-possible SVBRDF acquisition
Authors: Zhou Zhiming , Chen Guojun , Dong Yue , Wipf David , Yu Yong , Snyder John , Tong Xin
Published: November 2016

We present a novel method for capturing real-world, spatially-varying surface reflectance from a small number of object views (
k
). Our key observation is that a specific target's reflectance can be represented by a small number of custom basis materials (
N
) convexly blended by an even smaller number of non-zero weights at each point (
n
). Based on this
sparse basis/sparser blend
model, we develop an SVBRDF reconstruction algorithm that jointly solves for
n
,
N
, the basis BRDFs, and their spatial blend weights with an alternating iterative optimization, each step of which solves a linearly-constrained quadratic programming problem. We develop a numerical tool that lets us estimate the number of views required and analyze the effect of lighting and geometry on reconstruction quality. We validate our method with images rendered from synthetic BRDFs, and demonstrate convincing results on real objects of pre-scanned shape and lit by uncontrolled natural illumination, from very few or even a single input image.
Burst photography for high dynamic range and low-light imaging on mobile cameras
Authors: Hasinoff Samuel W. , Sharlet Dillon , Geiss Ryan , Adams Andrew , Barron Jonathan T. , Kainz Florian , Chen Jiawen , Levoy Marc
Published: November 2016

Cell phone cameras have small apertures, which limits the number of photons they can gather, leading to noisy images in low light. They also have small sensor pixels, which limits the number of electrons each pixel can store, leading to limited dynamic range. We describe a computational photography pipeline that captures, aligns, and merges a burst of frames to reduce noise and increase dynamic range. Our system has several key features that help make it robust and efficient. First, we do not use bracketed exposures. Instead, we capture frames of constant exposure, which makes alignment more robust, and we set this exposure low enough to avoid blowing out highlights. The resulting merged image has clean shadows and high bit depth, allowing us to apply standard HDR tone mapping methods. Second, we begin from Bayer raw frames rather than the demosaicked RGB (or YUV) frames produced by hardware Image Signal Processors (ISPs) common on mobile platforms. This gives us more bits per pixel and allows us to circumvent the ISP's unwanted tone mapping and spatial denoising. Third, we use a novel FFT-based alignment algorithm and a hybrid 2D/3D Wiener filter to denoise and merge the frames in a burst. Our implementation is built atop Android's Camera2 API, which provides per-frame camera control and access to raw imagery, and is written in the Halide domain-specific language (DSL). It runs in 4 seconds on device (for a 12 Mpix image), requires no user intervention, and ships on several mass-produced cell phones.
FrameFab
Authors: Huang Yijiang , Zhang Juyong , Hu Xin , Song Guoxian , Liu Zhongyuan , Yu Lei , Liu Ligang
Published: November 2016

Frame shapes, which are made of struts, have been widely used in many fields, such as art, sculpture, architecture, and geometric modeling, etc. An interest in robotic fabrication of frame shapes via spatial thermoplastic extrusion has been increasingly growing in recent years. In this paper, we present a novel algorithm to generate a feasible fabrication sequence for general frame shapes. To solve this non-trivial combinatorial problem, we develop a divide-and-conquer strategy that first decomposes the input frame shape into stable layers via a constrained sparse optimization model. Then we search a feasible sequence for each layer via a local optimization method together with a backtracking strategy. The generated sequence guarantees that the already-printed part is in a stable equilibrium state at all stages of fabrication, and that the 3D printing extrusion head does not collide with the printed part during the fabrication. Our algorithm has been validated by a built prototype robotic fabrication system made by a 6-axis KUKA robotic arm with a customized extrusion head. Experimental results demonstrate the feasibility and applicability of our algorithm.
Fabrication of freeform objects by principal strips
Authors: Takezawa Masahito , Imai Takuma , Shida Kentaro , Maekawa Takashi
Published: November 2016

Current CAD modeling techniques enable the design of objects with aesthetically pleasing smooth freeform surfaces. However, the fabrication of these freeform shapes remains challenging. Our novel method uses orthogonal principal strips to fabricate objects whose boundary consists of freeform surfaces. This approach not only lends an artistic touch to the appearance of objects, but also provides directions for reinforcement, as the surface is mostly bent along the lines of curvature. Moreover, it is unnecessary to adjust the bending of these orthogonal strips during the construction process, which automatically reforms the design shape as if it is memorized, provided the strips possess bending rigidity. Our method relies on semi-isometric mapping, which preserves the length of boundary curves, and approximates angles between boundary curves under local minimization. Applications include the fabrication of paper and sheet metal craft, and architectural models using plastic plates. We applied our technique to several freeform objects to demonstrate the effectiveness of our algorithms.
Practical 3D frame field generation
Authors: Ray Nicolas , Sokolov Dmitry , Lévy Bruno
Published: November 2016

Given a tetrahedral mesh, the algorithm described in this article produces a smooth 3D frame field, i.e. a set of three orthogonal directions associated with each vertex of the input mesh. The field varies smoothly inside the volume, and matches the normals of the volume boundary. Such a 3D frame field is a key component for some hexahedral meshing algorithms, where it is used to steer the placement of the generated elements.

We improve the state-of-the art in terms of quality, efficiency and reproducibility. Our main contribution is a non-trivial extension in 3D of the existing least-squares approach used for optimizing a 2D frame field. Our algorithm is inspired by the method proposed by Huang
et al.
[2011], improved with an initialization that directly enforces boundary conditions. Our initialization alone is a fast and easy way to generate frames fields that are suitable for remeshing applications. For better robustness and quality, the field can be further optimized using nonlinear optimization as in Li
et al
[2012]. We make the remark that sampling the field on vertices instead of tetrahedra significantly improves both performance and quality.
Power coordinates
Authors: Budninskiy Max , Liu Beibei , Tong Yiying , Desbrun Mathieu
Published: November 2016

We present a full geometric parameterization of generalized barycentric coordinates on convex polytopes. We show that these continuous and non-negative coefficients ensuring linear precision can be efficiently and exactly computed through a power diagram of the polytope's vertices and the evaluation point. In particular, we point out that well-known explicit coordinates such as Wachspress, Discrete Harmonic, Voronoi, or Mean Value correspond to simple choices of power weights. We also present examples of new barycentric coordinates, and discuss possible extensions such as power coordinates for non-convex polygons and smooth shapes.
Complexity of Two-Variable Logic on Finite Trees
Authors: Benaim Saguy , Benedikt Michael , Charatonik Witold , Kieroński Emanuel , Lenhardt Rastislav , Mazowiecki Filip , Worrell James
Published: November 2016

Verification of properties expressed in the two-variable fragment of first-order logic FO
2
has been investigated in a number of contexts. The satisfiability problem for FO
2
over arbitrary structures is known to be NEXPTIME-complete, with satisfiable formulas having exponential-sized models. Over words, where FO
2
is known to have the same expressiveness as unary temporal logic, satisfiability is again NEXPTIME-complete. Over finite labelled ordered trees, FO
2
has the same expressiveness as navigational XPath, a popular query language for XML documents. Prior work on XPath and FO
2
gives a 2EXPTIME bound for satisfiability of FO
2
over trees. This work contains a comprehensive analysis of the complexity of FO
2
on trees, and on the size and depth of models. We show that different techniques are required depending on the vocabulary used, whether the trees are ranked or unranked, and the encoding of labels on trees. We also look at a natural restriction of FO
2
, its guarded version,  GF
2
. Our results depend on an analysis of types in models of FO
2
formulas, including techniques for controlling the number of distinct subtrees, the depth, and the size of a witness to satisfiability for FO
2
sentences over finite trees.
Optimistic concurrency with OPTIK
Authors: Guerraoui Rachid , Trigonakis Vasileios
Published: November 2016

We introduce OPTIK, a new practical design pattern for designing and implementing fast and scalable concurrent data structures. OPTIK relies on the commonly-used technique of version numbers for detecting conflicting concurrent operations. We show how to implement the OPTIK pattern using the novel concept of OPTIK locks. These locks enable the use of version numbers for implementing very efficient optimistic concurrent data structures. Existing state-of-the-art lock-based data structures acquire the lock and then check for conflicts. In contrast, with OPTIK locks, we merge the lock acquisition with the detection of conflicting concurrency in a single atomic step, similarly to lock-free algorithms. We illustrate the power of our OPTIK pattern and its implementation by introducing four new algorithms and by optimizing four state-of-the-art algorithms for linked lists, skip lists, hash tables, and queues. Our results show that concurrent data structures built using OPTIK are more scalable than the state of the art.
Adding approximate counters
Authors: Steele Guy L. , Tristan Jean-Baptiste
Published: November 2016

We describe a general framework for adding the values of two approximate counters to produce a new approximate counter value whose expected estimated value is equal to the sum of the expected estimated values of the given approximate counters. (To the best of our knowledge, this is the first published description of any algorithm for adding two approximate counters.) We then work out implementation details for five different kinds of approximate counter and provide optimized pseudocode. For three of them, we present proofs that the variance of a counter value produced by adding two counter values in this way is bounded, and in fact is no worse, or not much worse, than the variance of the value of a single counter to which the same total number of increment operations have been applied. Addition of approximate counters is useful in massively parallel divide-and-conquer algorithms that use a distributed representation for large arrays of counters. We describe two machine-learning algorithms for topic modeling that use millions of integer counters, and confirm that replacing the integer counters with approximate counters is effective, speeding up a GPU-based implementation by over 65% and a CPU-based by nearly 50%, as well as reducing memory requirements, without degrading their statistical effectiveness.
Lease/release
Authors: Haider Syed Kamran , Hasenplaugh William , Alistarh Dan
Published: November 2016

High memory contention is generally agreed to be a worst-case scenario for concurrent data structures. There has been a significant amount of research effort spent investigating designs which minimize contention, and several programming techniques have been proposed to mitigate its effects. However, there are currently few architectural mechanisms to allow scaling contended data structures at high thread counts.

In this paper, we investigate hardware support for scalable contended data structures. We propose Lease/Release, a simple addition to standard directory-based MSI cache coherence protocols, allowing participants to lease memory, at the granularity of cache lines, by delaying coherence messages for a
short, bounded
period of time. Our analysis shows that Lease/Release can significantly reduce the overheads of contention for both non-blocking (lock-free) and lock-based data structure implementations, while ensuring that no deadlocks are introduced. We validate Lease/Release empirically on the Graphite multiprocessor simulator, on a range of data structures, including queue, stack, and priority queue implementations, as well as on transactional applications. Results show that Lease/Release consistently improves both throughput and energy usage, by up to 5x, both for lock-free and lock-based data structure designs.
Tidex
Authors: Ramalhete Pedro , Correia Andreia
Published: November 2016

Several basic mutual exclusion lock algorithms are known, with one of the simplest being the Ticket Lock. We present a new mutual exclusion lock with properties similar to the Ticket Lock but using atomic_exchange() instead of atomic_fetch_add() that can be more efficient on systems without a native instruction for atomic_fetch_add(), or in which the native instruction for atomic_exchange() is faster than the one for atomic_fetch_add(). Similarly to the Ticket Lock, our lock has small memory foot print, is extremely simple, respects FIFO order, and provides starvation freedom in architectures that implement atomic_exchange() as a single instruction, like x86.
User-assisted storage reuse determination for dynamic task graphs
Authors: Kurt Mehmet Can , Ren Bin , Krishnamoorthy Sriram , Agrawal Gagan
Published: November 2016

Models based on task graphs that operate on
single-assignment
data are attractive in several ways, but also require nuanced algorithms for scheduling and memory management for efficient execution. In this paper, we consider memory-efficient dynamic scheduling of task graphs, and present a novel approach for dynamically recycling the memory locations assigned to data items as they are produced by tasks.