bluuebunny/crossref_metadata_2025 huggingface dataset:
Circularly polarized lasing in chiral modulated semiconductor microcavity with GaAs quantum wells
Authors: Demenev A. A. , Kulakovskii V. D. , Schneider C. , Brodbeck S. , Kamp M. , Höfling S. , Lobanov S. V. , Weiss T. , Gippius N. A. , Tikhodeev S. G.
Published: October 2016

We report close to circularly polarized lasing at ℏω=1.473 and 1.522 eV from an AlAs/AlGaAs Bragg microcavity, with 12 GaAs quantum wells in the active region and chirally etched upper distributed Bragg refractor under optical pump at room temperature. The advantage of using the chiral photonic crystal with a large contrast of dielectric permittivities is its giant optical activity, allowing to fabricate a very thin half-wave plate, with a thickness of the order of the emitted light wavelength, and to realize the monolithic control of circular polarization.
Contactless microparticle control via ultrahigh frequency needle type single beam acoustic tweezers
Authors: Fei Chunlong , Li Ying , Zhu Benpeng , Chiu Chi Tat , Chen Zeyu , Li Di , Yang Yintang , Kirk Shung K. , Zhou Qifa
Published: October 2016

This paper reports on contactless microparticle manipulation including single-particle controlled trapping, transportation, and patterning via single beam acoustic radiation forces. As the core component of single beam acoustic tweezers, a needle type ultrasonic transducer was designed and fabricated with center frequency higher than 300 MHz and −6 dB fractional bandwidth as large as 64%. The transducer was built for an f-number close to 1.0, and the desired focal depth was achieved by press-focusing technology. Its lateral resolution was measured to be better than 6.7 μm by scanning a 4 μm tungsten wire target. Tightly focused acoustic beam produced by the transducer was shown to be capable of manipulating individual microspheres as small as 3 μm. “USC” patterning with 15 μm microspheres was demonstrated without affecting nearby microspheres. These promising results may expand the applications in biomedical and biophysical research of single beam acoustic tweezers.
Induction of Marangoni convection in pure water drops
Authors: Kita Yutaku , Askounis Alexandros , Kohno Masamichi , Takata Yasuyuki , Kim Jungho , Sefiane Khellil
Published: October 2016

We report on experimental observations/visualization of thermocapillary or Marangoni flows in a pure water drop via infrared thermography. The Marangoni flows were induced by imposing a temperature gradient on the drop by locally heating the substrate directly below the center with a laser. Evidently, a temperature gradient along the liquid-air interface of ca. 2.5 °C was required for the Marangoni flows to be initiated as twin vortices and a subsequent gradient of ca. 1.5 °C to maintain them. The vortices exhibited an oscillatory behavior where they merged and split in order for the drop to compensate for the non-uniform heating and cooling. The origin of these patterns was identified by comparing the dimensionless Marangoni and Rayleigh numbers, which showed the dominance of the Marangoni convection. This fact was further supported by a second set of experiments where the same flow patterns were observed when the drop was inverted (pendant drop).
Synthesis of atomic layers of hybridized h-BNC by depositing h-BN on graphene via ion beam sputtering
Authors: Meng J. H. , Zhang X. W. , Liu H. , Yin Z. G. , Wang D. G. , Wang Y. , You J. B. , Wu J. L.
Published: October 2016

We report the deposition of hexagonal boron nitride (h-BN) on graphene by ion beam sputtering deposition. Both graphene domains and films synthesized by chemical vapor deposition were used as substrates. In the case of graphene domains, it was found that the h-BN domains were preferentially grown on the baked Cu surface instead of graphene due to the highly catalytic activity of Cu. On the other hand, the higher ejection energy of sputtered particles leads to the mixing of boron/nitrogen atoms and carbon atoms. Consequently, the h-BNC films consisting of the hybrid atomic layers of h-BN and graphene domains were formed when the graphene films were used as substrates. This work provides a promising and accessible route for the synthesis of hybridized h-BNC material.
Strain-controlled interfacial magnetization and orbital splitting in La2/3Sr1/3MnO3/tetragonal BiFeO3 heterostructures
Authors: Yin Li , Zhang Qian , Mi Wenbo , Wang Xiaocha
Published: October 2016

The electronic and magnetic properties of La2/3Sr1/3MnO3(LSMO)/tetragonal BiFeO3(BFO) heterostructures with the xy-plane biaxial strain were investigated by first-principles calculations. As the xy-plane lattice constant is ranging from 3.619 to 3.921 Å, a large interfacial magnetoelectric coupling (IMEC) appears in the LaO/Fe-O2 and LaO/O2-Fe models. Particularly, the interfacial Mn in the LaO/O2-Fe model shows a large spin-down t2g orbital splitting at a strain from −2% to 6%, where the maximum splitting energy is 283 meV at 2%. Additionally, the LaO/O2-Fe model is half-metallic at a strain of 2%, 4%, and 6%. The results demonstrate that IMEC, orbital occupancy, and half-metallicity of LSMO/BFO heterostructures can be effectively engineered by the interfacial coupling and in-plane strain, which paves a way for designing the novel magnetoelectric devices.
An integrated wind-forecast system based on the weather research and forecasting model, Kalman filter, and data assimilation with nacelle-wind observation
Authors: Che Yuzhang , Xiao Feng
Published: October 2016

To forecast wind speed at hub-height is a challenging task for wind energy application, especially in Japan where the terrain feature is very complex and large fluctuations are observed in surface wind field. In this study, an integrated system to predict the hub-height wind speed has been developed by combining data assimilation and Kalman filter with the high resolution Weather Research and Forecasting (WRF) model. Assimilating the nacelle wind data (quality-controlled) and the Kalman filter algorithm effectively improves accuracy of the WRF model forecast by optimizing initial condition and post-processing the model output, respectively. It is found that the WRF model forecasts can be markedly improved after assimilating the nacelle wind data through the Gridpoint Statistical Interpolation analysis system, with the relative improvements of 34.3%, 23.9%, and 8.8% in ME (mean error), RMSE (root mean square error), and IA (index of agreement), respectively. The implementation of the Kalman filter can significantly reduce ME and RMSE while increases the value of IA as well. Further improvement can be achieved if the Kalman filter and nacelle wind data assimilation are implemented simultaneously. It is observed that the role of the Kalman filter is more dominant for the wind band of rated out speeds, while data assimilation is effective in reducing the random errors and becomes more important in rare or extreme weather conditions. Both data assimilation and Kalman filter modules apply the nacelle wind data which is routinely available, so the system can be easily adopted in different wind farm sites for operational use.
Abscisic acid controlled sex before transpiration in vascular plants
Authors: McAdam Scott A. M. , Brodribb Timothy J. , Banks Jo Ann , Hedrich Rainer , Atallah Nadia M. , Cai Chao , Geringer Michael A. , Lind Christof , Nichols David S. , Stachowski Kye , Geiger Dietmar , Sussmilch Frances C.
Published: October 2016

Significance

Since the dawn of land plants, the phytohormone abscisic acid (ABA) has played a critical role in regulating plant responses to water availability. Here we seek to explain the origins of the core ABA signaling pathway found in modern seed plants. Using the characterization of mutants and gene silencing in a fern species, we find that the same hormone signaling components are used in sex determination of ferns as are used for the control of seed dormancy and transpiration in seed plants. Ferns are shown to lack downstream functionality of stomatal components, suggesting that the origins of the core ABA signaling pathway in seed plants may lie in the sexual differentiation of ferns.
Chronic use of PAH‐specific therapy in World Health Organization Group III Pulmonary Hypertension: a systematic review and meta‐analysis
Authors: Prins Kurt W. , Duval Sue , Markowitz Jeremy , Pritzker Marc , Thenappan Thenappan
Published: October 2016

Pulmonary hypertension (PH) complicating chronic obstructive pulmonary disease (COPD‐PH) and interstitial lung disease (ILD‐PH) (World Health Organization [WHO] Group III PH) increases medical costs and reduces survival. Despite limited data, many clinicians are using pulmonary arterial hypertension (PAH)‐specific therapy to treat WHO Group III PH patients. To further investigate the utility of PAH‐specific therapy in WHO Group III PH, we performed a systematic review and meta‐analysis. Relevant studies from January 2000 through May 2016 were identified in the MEDLINE, EMBASE, and COCHRANE electronic databases and www.clinicaltrials.gov. Change in six‐minute walk distance (6MWD) was estimated using random effects meta‐analysis techniques. Five randomized controlled trials (RCTs) in COPD‐PH (128 placebo or standard treatment and 129 PAH‐medication treated patients), two RCTs in ILD‐PH (23 placebo and 46 treated patients), and four single‐arm clinical trials (50 patients) in ILD‐PH were identified. Treatment in both COPD‐PH and ILD‐PH did not worsen hypoxemia. Symptomatic burden was not consistently reduced but there were trends for reduced pulmonary artery pressures and pulmonary vascular resistance with PAH‐specific therapy. As compared to placebo, 6MWD was not significantly improved with PAH‐specific therapy in the five COPD‐PH RCTs (42.7 m; 95% confidence interval [CI], –1.0 – 86.3). In the four single‐arm studies in ILD‐PH patients, there was a significant improvement in 6MWD after PAH‐specific treatment (46.2 m; 95% CI, 27.9–64.4), but in the two ILD‐PH RCTs there was not an improvement (21.6 m; 95% CI, –17.8 – 61.0) in exercise capacity when compared to placebo. Due to the small numbers of patients evaluated and inconsistent beneficial effects, the utility of PAH‐specific therapy in WHO Group III PH remains unproven. A future clinical trial that is appropriately powered is needed to definitively determine the efficacy of this widely implemented treatment approach.
Key comparison BIPM.RI(I)-K3 of the air-kerma standards of the VSL, The Netherlands and the BIPM in medium-energy x-rays
Authors: Burns D T , Kessler C , Pooter J A de , Jansen B J
Published: October 2016

A key comparison has been made between the air-kerma standards of the VSL, The Netherlands and the BIPM in the medium-energy x-ray range. The results show the standards to be in agreement at the level of the standard uncertainty of the comparison of 3.2 parts in 103. The results are analysed and presented in terms of degrees of equivalence, suitable for entry in the BIPM key comparison database.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Factors Affecting the Development and Severity of Goss’s Bacterial Wilt and Leaf Blight of Corn, Caused by Clavibacter michiganensis subsp. nebraskensis
Authors: Langemeier Craig B. , Robertson Alison E. , Wang Dong , Jackson-Ziems Tamra A. , Kruger Greg R.
Published: October 2016

Goss’s bacterial wilt and leaf blight, which is caused by Clavibacter michiganensis subsp. nebraskensis, is a disease of corn (Zea mays) that has been increasingly reported across the Midwest since its reemergence in western Nebraska, northeastern Colorado, and southeastern Wyoming during the 2006 growing season. The objective of this study was to identify environmental and agronomic factors contributing to the incidence of the disease across the Corn Belt through a multistate survey conducted during the 2011 growing season. Of the 2,400 surveys distributed throughout nine states, 486 were returned with corn leaf samples, of which 70% tested positive for C. michiganensis subsp. nebraskensis using an enzyme-linked immunosorbent assay. The agronomic data associated with each field were analyzed using classification and regression tree and random forest analyses to identify the factors that contributed most to Goss’s bacterial wilt and leaf blight development. A χ2 test of independence was also done to determine relationships between certain variables and disease incidence. The two best predictors of Goss’s bacterial wilt and leaf blight were hybrid resistance to Goss’s bacterial wilt and leaf blight, as indicated by the seed companies’ score and a planting population density >67,500 plants ha−1. Other important predictors included longitude, planting date, crop rotation, percent residue, yield history, tillage, and growth stage. Relationships between glyphosate applications, foliar fungicide applications, and corn rootworm beetle with samples testing positive for C. michiganensis subsp. nebraskensis were also detected. These data contribute to our understanding of factors that increase the risk of Goss’s bacterial wilt and leaf blight, and should enable more effective management practices to be adopted or developed.
Overview of ATX-101 (Deoxycholic Acid Injection): A Nonsurgical Approach for Reduction of Submental Fat
Authors: Dayan Steven H. , Humphrey Shannon , Jones Derek H. , Lizzul Paul F. , Gross Todd M. , Stauffer Karen , Beddingfield Frederick C.
Published: October 2016

In 2015, ATX-101 (deoxycholic acid injection; Kybella in the United States and Belkyra in Canada; Kythera Biopharmaceuticals, Inc., Westlake Village, CA [an affiliate of Allergan plc, Dublin, Ireland]) was approved as a first-in-class injectable drug for improvement in the appearance of moderate to severe convexity or fullness associated with submental fat. ATX-101 has been evaluated in a clinical development program that included 18 Phase 1 to 3 studies supporting the current indication. Since 2007, the toxicity and safety profiles of ATX-101 have been characterized in numerous preclinical studies, its pharmacokinetics, pharmacodynamics, and optimal treatment paradigm have been defined in multiple Phase 1 and 2 studies, and its efficacy and clinical safety have been confirmed in 4 large Phase 3 trials (2 conducted in Europe and 2 in the United States and Canada [REFINE-1 and REFINE-2]). As subcutaneous injection of deoxycholic acid has been shown to cause adipocytolysis, the reduction in submental fat achieved after ATX-101 treatment is expected to be long lasting. This prediction is confirmed by data from long-term follow-up studies of up to 4 years after last treatment with ATX-101, which demonstrate that the treatment response is maintained over time in most subjects. ATX-101 offers a durable, minimally invasive alternative to liposuction and surgery for addressing submental fullness.
Pembrolizumab
Authors: Nguyen Catherine M. , Jacob Sharon E.
Published: October 2016

Drugs are medications or substances that are used to modify physiologic responses and alleviate associated symptoms. In dermatology, medications and substances are utilized on a daily basis and include topical treatments to anesthetics in micrographic surgery to biologic-acting immunologic agents. The purposes of this section are to focus on drug, specifically how it works and how it is utilized, and to discuss routine alternatives (if available). In this column, we will focus on the uses, mechanism of action, adverse effects, and alternatives to pembrolizumab, a new immunotherapy used for advanced melanoma.
Surgeon-Controlled Study and Meta-Analysis Comparing FlexHD and AlloDerm in Immediate Breast Reconstruction Outcomes
Authors: Sobti Nikhil , Liao Eric C.
Published: October 2016

Background:

The use of acellular dermal matrix has facilitated immediate prosthesis-based breast reconstruction. However, few studies directly compare surgical outcomes following acellular dermal matrix–based reconstruction with two of the most commonly available materials, AlloDerm and FlexHD. Those studies that are available often do not adequately control for the surgeon as a variable. The authors hypothesize that complication rates will not differ significantly between AlloDerm and FlexHD when practice and surgeon variables are properly controlled.

Methods:

Retrospective review was conducted to identify consecutive implant-based reconstruction procedures performed at a tertiary academic medical institution by a single plastic surgeon over 6 years. Univariate and binomial regression analyses were conducted to compare patient characteristics and clinical endpoints across acellular dermal matrix groups (AlloDerm/AlloDerm ready-to-use versus FlexHD Pliable/Perforated).

Results:

Of the 233 patients that underwent matrix-based breast reconstruction, 11 (4.7 percent) developed surgical-site infection. The infection rate was not statistically different between patients who received FlexHD [n = 5 (5.0 percent)] versus AlloDerm [n = 6 (4.6 percent)] on either univariate (p = 0.89) or binomial regression analysis (p = 0.56). Likewise, there were no statistical differences in rates of seroma, hematoma, explantation, or delayed wound healing.

Conclusions:

Clinical endpoints of interest were all equivalent between acellular dermal matrix types. This study uniquely reports a single-surgeon case series comparing outcomes between different acellular dermal matrix types. Instead of focusing on acellular dermal matrix as a predictor of outcome, other patient and surgeon factors should be addressed to improve results and innovate better alternatives.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
Determining the Cost of Incidental Findings for Patients Undergoing Preoperative Planning for Abdominally Based Perforator Free Flap Breast Reconstruction with Computed Tomographic Angiography
Authors: Agarwal Shailesh , Talia Jordan , Liu Peter S. , Momoh Adeyiza O. , Kozlow Jeffrey H.
Published: October 2016

Background:

Computed tomographic angiography is increasingly used during surgical planning for abdominally based microvascular breast reconstruction. Cost-analysis studies have demonstrated a benefit to the use of computed tomographic angiography, although the secondary costs of incidental findings have not been previously reported. This study investigates the cost of computed tomographic angiography, taking into account the cost of incidental findings found during imaging.

Methods:

Patients undergoing preoperative computed tomographic angiography in preparation for autologous abdominally based breast reconstruction from July of 2010 through May of 2014 were included in this study. Patient medical records were reviewed for imaging findings, need for follow-up, and any additional procedures. Costs were determined using the publicly available Healthcare Bluebook.

Results:

A total of 135 patients underwent computed tomographic angiography in preparation for abdominally based microvascular breast reconstruction. Twenty-eight patients (21 percent) were noted to have clinically significant incidental findings recommended for follow-up imaging or procedures. Inclusion of chest imaging with computed tomographic angiography of the abdomen/pelvis to assess for internal mammary and/or thoracodorsal artery patency increased the incidental findings approximately five-fold. The mean cost of computed tomographic angiography increased by 32 percent, from $1267 to $1677 per patient, when incidental findings were included.

Conclusions:

Computed tomography angiography is a tool for the preoperative evaluation of patients desiring autologous breast reconstruction. The true cost of preoperative computed tomographic angiography is likely 30 percent greater than the baseline cost when the subsequent evaluation of incidental findings is included and should be accounted for in future cost-analysis studies.
Nostrilplasty by Manipulating the Dilator Naris Muscles: A Pilot Study
Authors: Jung Jae-A , Jung Su-Young , Han Seung-Kyu , Dhong Eun-Sang , Kim Woo Kyung
Published: October 2016

The present study was undertaken to determine whether a more aesthetically acceptable nostril shape could be created by manipulating the dilator naris muscles. Patients who had round or horizontally shaped nostrils were treated by resecting the dilator naris muscle to attenuate the dilating and lateral pulling effect of the muscles. The resected muscle segments were inserted into the nasal tip area to project the nasal tip. Manipulating the dilator muscle shaped the nostril more vertically and enhanced nasal tip augmentation. The ratio of the short axis to the long axis of the nostril was improved significantly. The interaxial angle became more acute. The patient satisfaction score was also increased. A more aesthetically pleasing nostril shape can be produced by resecting and grafting the dilator naris muscle segments.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
Surgical Outcome after Penile Inversion Vaginoplasty: A Retrospective Study of 475 Transgender Women
Authors: Buncamper Marlon E. , van der Sluis Wouter B. , van der Pas Roos S. D. , Özer Müjde , Smit Jan Maerten , Witte Birgit I. , Bouman Mark-Bram , Mullender Margriet G.
Published: October 2016

Background:

For many transgender women, vaginoplasty is the final stage in the gender-confirming process. Penile inversion vaginoplasty is considered the gold standard for vaginal construction in transgender women. In this study, the authors assessed intraoperative and postoperative complications after penile inversion vaginoplasty.

Methods:

All patients who underwent penile inversion vaginoplasty between January of 2000 and January of 2014 were identified retrospectively from the authors’ hospital registry. A retrospective chart review was conducted. Outcome measures were intraoperative and postoperative complications, reoperations, secondary surgical procedures, and possible risk factors.

Results:

Between January of 2000 and January of 2014, 475 patients underwent penile inversion vaginoplasty, 405 of whom did not have and 70 of whom did have additional full-thickness skin grafts. The median patient age at surgery was 38.6 years (range, 18.1 to 70.8 years). Median follow-up was 7.8 years (range, 1.0 to 15.9 years). The most frequently observed intraoperative complication was rectal injury [n = 11 (2.3 percent)]. Short-term postoperative bleeding that required transfusion [n = 23 (4.8 percent)], reoperation [n = 7 (1.5 percent)] or both [n = 2 (0.4 percent)] occurred in some cases. Major complications comprised three (0.6 percent) rectoneovaginal fistulas, which were successfully treated. Revision vaginoplasty was performed in 14 patients (2.9 percent). Comorbid diabetes was associated with a higher risk of local infection (OR, 9.8; p = 0.003; 95 percent CI, 2.8 to 34.4), and use of psychotropic medication predisposed to postoperative urinary retention (OR, 2.1; p = 0.006; 95 percent CI, 1.2 to 3.5).

Conclusions:

Successful vaginal construction without the need for secondary functional reoperations was achieved in the majority of patients. Intraoperative complications are scarce. Postoperative complications occur frequently but are generally minor and easily treated.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
The Stanford-ReSurge Burn Scar Contracture Scale for Neck: Development and Initial Validation for Burn Scar Contracture
Authors: Cai Lawrence , Puri Vinita , Dangol Mohan Krishna , Mannan Iftekhar Ibne , Khundkar Shafquat Hussain , Le Thua Trung-Hau , Muguti Godfrey , Rai Shankar Man , Karanas Yvonne , Chang James
Published: October 2016

Background:

Burn contractures can cause significant disability, particularly in patients in resource-limited settings. However, a gap exists in our ability to measure outcomes in patients with burn contractures of the neck. The objective of this study was to develop and validate the Stanford-ReSurge Burn Scar Contracture Scale–Neck to longitudinally assess functional status and measure functional improvement following contracture release of the neck.

Methods:

A literature review was performed to identify scales used in neck assessment and burn assessment. Items were then removed from the pool based on redundancy, feasibility, cultural appropriateness, and applicability to patients in international resource-limited environments. Remaining items were administered to patients with burn contracture of the neck.

Results:

The initial literature review found 33 scales that were combined to create an initial pool of 714 items, which was first reduced to 40 items. Feedback from field testing then yielded a 20-item outcome tool to assess appearance, activities of daily living, somatosensation, satisfaction, and range of motion, with a floor of 20 and a ceiling score of 100 points. Preliminary testing with 10 patients showed an average preoperative score of 58 points and an average 1-month postoperative score of 42 points.

Conclusions:

The authors have created an outcome tool for measuring functional status following burn contracture release of the neck, which can easily be implemented in resource-limited settings where the burden of burn injuries and morbidities is disproportionately high. Ongoing work includes a multicountry study to evaluate validity and reliability.
Chronic Psychosocial Stress and Gut Health in Children: Associations With Calprotectin and Fecal Short-Chain Fatty Acids
Authors: Michels Nathalie , Van de Wiele Tom , De Henauw Stefaan
Published: October 2016

Objectives

The mechanisms underpinning the association between chronic stress and gut health are poorly understood. We aimed to investigate the relationship between bacterial produced short-chain fatty acids, gut barrier function, and stress measures.

Methods

A fecal sample, hair sample, and questionnaire data were collected from 113 Belgian children (8–16 years old). Biological measures of stress included hair cortisol (most proximal 3 cm) and 5-minute heart rate variability (high frequency). Self-report measures of stress included emotional problems and negative events. Fecal calprotectin was determined as a marker of intestinal inflammation and an indirect indicator of gut barrier integrity. Fecal short-chain fatty acids (butyrate, propionate, acetate, valerate, isobutyrate, and isovalerate) were measured with gas chromatography. Linear regression analyses were adjusted for sex, age, socioeconomic status, body mass index, fiber intake, and protein intake.

Results

Emotional problems were significantly associated with higher butyrate (β = 0.263), valerate (β = 0.230), isovalerate (β = 0.231), and isobutyrate (β = 0.233). Heart rate variability reflecting higher parasympathetic activity was related to lower valerate levels (β = −0.217). Hair cortisol was not associated with the short-chain fatty acids. None of the stress measures and none of the fecal short-chain fatty acids were significantly related to fecal calprotectin.

Conclusions

In healthy children, the impact of chronic stress is manifested more obviously in short-chain fatty acids than in intestinal inflammation as measured by levels of calprotectin. Despite the rather counterintuitive associations with butyrate, these results point to the need for further research on gut microbiome composition.
CancerGD: a resource for identifying and interpreting genetic dependencies in cancer
Authors: Bridgett Stephen , Campbell James , Lord Christopher J. , Ryan Colm J.
Published: October 2016

Genes whose function is selectively essential in the presence of cancer associated genetic aberrations represent promising targets for the development of precision therapeutics. Here we present CancerGD (www.cancergd.org), a resource that integrates genotypic profiling with large-scale loss-of-function genetic screens in tumor cell lines to identify such genetic dependencies. CancerGD provides tools for searching, visualizing, and interpreting these genetic dependencies through the integration of functional interaction networks.
Applying Corrections in Single-Molecule FRET
Authors: Ingargiola Antonino
Published: October 2016

Single-molecule Förster resonance energy transfer (smFRET) experiments can detect the distance between a donor and an acceptor fluorophore on the 3-10nm scale. In ratiometric smFRET experiments, the FRET efficiency is estimated from the ratio of acceptor and total signal (donor + acceptor). An excitation scheme involving two alternating lasers (ALEX) is often employed to discriminate between singly– and doubly-labeled populations thanks to a second ratiometric parameter, the stoichiometryS. Accurate FRET andSestimations requires applying three well-known correction factors: donor emission leakage into the acceptor channel, acceptor direct excitation by the donor excitation laser and the “gamma factor” (i.e. correction for the imbalance between donor and acceptor signals due to different fluorophore’s quantum yields and photon detection effciencies).

Expressions to directly correct both raw FRET and S values have been reported in [1] in the context of freely-diffusing smFRET. Here we extend Leeet al.work providing several expressions for the direct excitation coeffcient and highlighting a clear interpretation in terms of physical parameters and experimental quantities. Moreover, we derive a more complete set of analytic expressions for correcting FRET andS. We aim to provide a clear and concise reference for different definitions of correction coeffcients and correction formulas valid for any smFRET experiment both in immobilized and freely-diffusing form.
PlantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters
Authors: Kautsar Satria A. , Duran Hernando G. Suarez , Blin Kai , Osbourn Anne , Medema Marnix H.
Published: October 2016

Plant specialized metabolites are chemically highly diverse, play key roles in host-microbe interactions, have important nutritional value in crops and are frequently applied as medicines. It has recently become clear that plant biosynthetic pathway-encoding genes are sometimes densely clustered in specific genomic loci: biosynthetic gene clusters (BGCs). Here, we introduce plantiSMASH, a versatile online analysis platform that automates the identification of candidate plant BGCs. Moreover, it allows integration of transcriptomic data to prioritize candidate BGCs based on the coexpression patterns of predicted biosynthetic enzyme-coding genes, and facilitates comparative genomic analysis to study the evolutionary conservation of each cluster. Applied on 48 high-quality plant genomes, plantiSMASH identifies a rich diversity of candidate plant BGCs. These results will guide further experimental exploration of the nature and dynamics of gene clustering in plant metabolism. Moreover, spurred by the continuing decrease in costs of plant genome sequencing, they will allow genome mining technologies to be applied to plant natural product discovery.

The plantiSMASH web server, precalculated results and source code are freely available fromhttp://plantismash.secondarymetabolites.org.
Respectable femininity: a significant panel of glass ceiling for career women
Authors: Ansari Nighat
Published: October 2016

Purpose

This study aims to explicate the role of “respectable femininity” norms in the work lives of professional women and investigate the extent to which they impact female career advancement (or lack thereof) by way of creating a clash with the traditional career management techniques of accumulating social capital and managing desirable impression.

Design/methodology/approach

The qualitative research design was deemed appropriate for the study to gain an insight of the incumbents’ work experiences. The opinions, thoughts, experiences and expressions of the participants were gauged through in-depth, semi-structured interviews to ensure the coverage of all the relevant aspects while retaining the flexibility to obtain rich and detailed data beyond the preconceived questions.

Findings

It was found that working women in Pakistan feeling guilty of violating the norm of “confinement to private spheres” appeared obliged to abide by the respectable femininity principles of “domesticity”, “restrained networking” and “toning down their femininity” to maintain an “honourable” reputation/image in the society; however, these norms, in turn, created a significant hurdle in their career advancement by way of constraining their capacity to exploit the career management techniques of accumulating “social capital” and employing “impression management” tactics.

Originality/value

This research will add credence to the scant literature pertaining to the role of “respectable femininity” in the professional lives of working women. The study showcases the female’s enigmatic struggle of becoming a “good woman” and a “successful careerist” at the same time which culminates in to a series of subtle barriers in their professional careers mounting ultimately to become a significant panel of “glass ceiling” in their progression.
Integrated framework for early warning system in UAE
Authors: Alhmoudi Abdulla Ali , Aziz Zeeshan
Published: October 2016

Purpose

The impacts and costs of natural disasters on people, properties and environment are often severe when these occur on a large scale and with no warning system in place. The lack of deployment of an early warning system (EWS), low risk and hazard knowledge and impact of natural hazard experienced by some communities in the UAE have emphasised the need for more effective EWSs. This work focuses on developing an integrated framework for EWSs for communities prone to the impact of natural hazards to reduce their vulnerability and improve emergency management arrangements in the UAE.

Design/methodology/approach

The essential elements of effective EWS were identified through literature review to develop an integrated framework for EWS. Semi-structured interviews and questionnaires were also used to identify and confirm hindering factors to deployment of effective EWSs in Abu Dhabi and Fujairah Emirates, while areas that require further development were also identified through this means.

Findings

The outcome of this research revealed that the warning for natural hazards in the UAE lacked the required elements for effective EWS, whereas the elements which are present are insufficient to mitigate the impacts of natural hazards. The information in this work emphasises the need to improve two elements, and to develop the other two essential elements of EWS in the UAE.

Originality/value

The outcome of this research revealed that the warning for natural hazards in the UAE lacked the required elements for effective EWS, whereas the elements which are present are insufficient to mitigate the impacts of natural hazards. The information in this work emphasises the need to improve two elements and to develop the other two essential elements of EWS in the UAE.
Multi-library union, promoting ILL/DD of the Chinese science digital library
Authors: Xi Qingkui , Mao Liju , Zhang Bin , Shi Wen , Bao Ping
Published: October 2016

Purpose

This study aims to describe and analyse interlibrary loans and document delivery (ILL/DD) in the Chinese Academy of Sciences and to evaluate the ILL/DD service quality of one particular library.

Design/methodology/approach

ILL/DD at the Chinese Science Digital Library (CSDL) is described. The success of ILL/DD at CSDL is analysed. Finally, the service quality of one library’s ILL/DD based on LibQUAL+ is evaluated.

Findings

ILL/DD at CSDL can be improved through a multi-library union, and a modified LibQUAL+ model can be used to evaluate a library’s ILL/DD service quality.

Social implications

More patrons can access a better service, and the work efficiency of librarians can be improved.

Originality/value

This study is helpful to librarians interested in ILL/DD and resource sharing in China.
An assessment of place brand potential: familiarity, favourability and uniqueness
Authors: Chan Chung-Shing , Peters Mike , Marafa Lawal M.
Published: October 2016

Purpose

This paper aims to present an approach by which to assess the potential of branding a particular type of place resource or feature.

Design/methodology/approach

A review was conducted to analyse three key periodicals (Journal of Brand Management, Place Branding and Public Diplomacy and Journal of Place Management and Development) in the field of branding and place branding between 2000 and 2011. These three periodicals are recognized as the three leading periodicals of place branding, and they followed the clear establishment and development of the field of place branding.

Findings

Familiarity, favourability and uniqueness are the three dimensions that give a quick indication of the level of place brand equity, and in turn they represent the level of place brand potential.

Research limitations/implications

In the literature, brand potential is not well conceptualized. This paper identifies this knowledge gap through a review of place branding studies, and it closes the gap by connecting brand potential with place brand equity.

Originality/value

This paper suggests practical and research directions by which to study these three dimensions to generate valuable brands for places.
Characterisation and multifaceted anisotropy assessment of Corvio sandstone for geological CO2 storage studies
Authors: Falcon‐Suarez Ismael , Canal‐Vila Jacobo , Delgado‐Martin Jordi , North Laurence , Best Angus
Published: October 2016

We present a comprehensive characterisation of the physical, mineralogical, geomechanical, geophysical, and hydrodynamic properties of Corvio sandstone. This information, together with a detailed assessment of anisotropy, is needed to establish Corvio sandstone as a useful laboratory rock‐testing standard for well‐constrained studies of thermo–hydro–mechanical–chemical coupled phenomena associated with CO2 storage practices and for geological reservoir studies in general. More than 200 core plugs of Corvio sandstone (38.1 and 50 mm diameters, 2:1 length‐to‐diameter ratio) were used in this characterisation study, with a rock porosity of 21.7 ± 1.2%, dry density 2036 ± 32 kg m−3, and unconfined compressive and tensile strengths of 41 ± 3.28 and 2.3 ± 0.14 MPa, respectively. Geomechanical tests show that the rock behaves elastically between ∼10 and ∼18 MPa under unconfined conditions with associated Young's modulus and Poisson's ratio of 11.8 ± 2.8 GPa and 0.34 ± 0.01 GPa, respectively. Permeability abruptly decreases with confining pressure up to ∼10 MPa and then stabilises at ∼1 mD. Ultrasonic P‐ and S‐wave velocities vary from about 2.8–3.8 km s−1 and 1.5–2.4 km s−1, respectively, over confining and differential pressures between 0.1 and 35 MPa, allowing derivation of associated dynamic elastic moduli. Anisotropy was investigated using oriented core plugs for electrical resistivity, elastic wave velocity and attenuation, permeability, and tracer injection tests. Corvio sandstone shows weak transverse isotropy (symmetry axis normal to bedding) of <10% for velocity and <20% for attenuation.
The Dalriada Document: Towards a Multinational Compromise that Respects Democratic Diversity in the United Kingdom
Authors: O'Leary Brendan
Published: October 2016

Northern Ireland and Scotland could and should stay within the European Union while remaining inside the United Kingdom. This proposal need not prevent, and may facilitate, England and Wales in leaving the EU, and it is in accordance with the respective preferences of the peoples of the two Unions who voted in the advisory referendum held on 23 June 2016. Prime Minister May and her Cabinet should address carefully the question of whether to trigger Article 50, or instead to give notice that only parts of the UK—England and Wales—will be leaving the EU. The price of enforcing the entirety of the UK's exit from the EU may be lasting damage to the two Unions that make up the United Kingdom of Great Britain and Northern Ireland.
Deaths Due to Child Abuse: A 6‐Year Review of Cases in The Cook County Medical Examiner's Office
Authors: Serinelli Serenella , Arunkumar Ponni , Filkins James A. , Gitto Lorenzo
Published: October 2016

Case files from the Cook County Medical Examiner's Office from 2007 to 2012 were reviewed to analyze homicides due to physical child abuse in children <3 years old. Fatal cases mostly involved younger subjects. Intracranial injuries were the leading cause of death, while death due to extracranial injuries was uncommon. Eyes were involved in most of the cases. Spinal cord was involved in about 1/3 of the cases, mostly in the thoracic area. In some cases, previous injuries were present. There were significant differences in the pattern of injuries between age groups. Subjects showing signs of impact to the head and subjects with no evidence of an impact showed no significant difference in internal injuries. The association of multiple injuries is highly suggestive of child abuse. In suspected child abuse, a postmortem examination including neuropathological, ophthalmological, and radiological information should be always evaluated, together with investigative reports and the medical history.
Flow Curves: an Intuitive Interface for Coherent Scene Deformation
Authors: Ciccone L. , Guay M. , Sumner R.
Published: October 2016

Effective composition in visual arts relies on the principle of movement, where the viewer's eye is directed along subjective curves to a center of interest. We call these curves subjective because they may span the edges and/or center‐lines of multiple objects, as well as contain missing portions which are automatically filled by our visual system. By carefully coordinating the shape of objects in a scene, skilled artists direct the viewer's attention via strong subjective curves. While traditional 2D sketching is a natural fit for this task, current 3D tools are object‐centric and do not accommodate coherent deformation of multiple shapes into smooth flows. We address this shortcoming with a new sketch‐based interface called Flow Curves which allows coordinating deformation across multiple objects. Core components of our method include an understanding of the principle of flow, algorithms to automatically identify subjective curve elements that may span multiple disconnected objects, and a deformation representation tailored to the view‐dependent nature of scene movement. As demonstrated in our video, sketching flow curves requires significantly less time than using traditional 3D editing workflows.
TSS BVHs: Tetrahedron Swept Sphere BVHs for Ray Tracing Subdivision Surfaces
Authors: Du P. , Kim Y. J. , Yoon S. E.
Published: October 2016

We present a novel, compact bounding volume hierarchy, TSS BVH, for ray tracing subdivision surfaces computed by the Catmull‐Clark scheme. We use Tetrahedron Swept Sphere (TSS) as a bounding volume to tightly bound limit surfaces of such subdivision surfaces given a user tolerance. Geometric coordinates defining our TSS bounding volumes are implicitly computed from the subdivided mesh via a simple vertex ordering method, and each level of our TSS BVH is associated with a single distance bound, utilizing the Catmull‐Clark scheme. These features result in a linear space complexity as a function of the tree depth, while many prior BVHs have exponential space complexity. We have tested our method against different benchmarks with path tracing and photon mapping. We found that our method achieves up to two orders of magnitude of memory reduction with a high culling ratio over the prior AABB BVH methods, when we represent models with two to four subdivision levels. Overall, our method achieves three times performance improvement thanks to these results. These results are acquired by our theorem that rigorously computes our TSS bounding volumes.
Foveated Real‐Time Ray Tracing for Head‐Mounted Displays
Authors: Weier Martin , Roth Thorsten , Kruijff Ernst , Hinkenjann André , Pérard‐Gayot Arsène , Slusallek Philipp , Li Yongmin
Published: October 2016

Head‐mounted displays with dense pixel arrays used for virtual reality applications require high frame rates and low latency rendering. This forms a challenging use case for any rendering approach. In addition to its ability of generating realistic images, ray tracing offers a number of distinct advantages, but has been held back mainly by its performance. In this paper, we present an approach that significantly improves image generation performance of ray tracing. This is done by combining foveated rendering based on eye tracking with reprojection rendering using previous frames in order to drastically reduce the number of new image samples per frame. To reproject samples a coarse geometry is reconstructed from a G‐Buffer. Possible errors introduced by this reprojection as well as parts that are critical to the perception are scheduled for resampling. Additionally, a coarse color buffer is used to provide an initial image, refined smoothly by more samples were needed. Evaluations and user tests show that our method achieves real‐time frame rates, while visual differences compared to fully rendered images are hardly perceivable. As a result, we can ray trace non‐trivial static scenes for the Oculus DK2 HMD at 1182 × 1464 per eye within the the VSync limits without perceived visual differences.
Direct shape optimization for strengthening 3D printable objects
Authors: Zhou Yahan , Kalogerakis Evangelos , Wang Rui , Grosse Ian R.
Published: October 2016

Recently there has been an increasing demand for software that can help designers create functional 3D objects with required physical strength. We introduce a generic and extensible method that directly optimizes a shape subject to physical and geometric constraints. Given an input shape, our method optimizes directly its input mesh representation until it can withstand specified external forces, while remaining similar to the original shape. Our method performs physics simulation and shape optimization together in a unified framework, where the physics simulator is an integral part of the optimizer. We employ geometric constraints to preserve surface details and shape symmetry, and adapt a second‐order method with analytic gradients to improve convergence and computation time. Our method provides several advantages over previous work, including the ability to handle general shape deformations, preservation of surface details, and incorporation of user‐defined constraints. We demonstrate the effectiveness of our method on a variety of prinTable 3D objects through detailed simulations as well as physical validations.
Pixel History Linear Models for Real‐Time Temporal Filtering
Authors: Iglesias‐Guitian Jose A. , Moon Bochang , Koniaris Charalampos , Smolikowski Eric , Mitchell Kenny
Published: October 2016

We propose a new real‐time temporal filtering and antialiasing (AA) method for rasterization graphics pipelines. Our method is based on Pixel History Linear Models (PHLM), a new concept for modeling the history of pixel shading values over time using linear models. Based on PHLM, our method can predict per‐pixel variations of the shading function between consecutive frames. This combines temporal reprojection with per‐pixel shading predictions in order to provide temporally coherent shading, even in the presence of very noisy input images. Our method can address both spatial and temporal aliasing problems under a unique filtering framework that minimizes filtering error through a recursive least squares algorithm. We demonstrate our method working with a commercial deferred shading engine for rasterization and with our own OpenGL deferred shading renderer. We have implemented our method in GPU and it has shown significant reduction of temporal flicker in very challenging scenarios including foliage rendering, complex non‐linear camera motions, dynamic lighting, reflections, shadows and fine geometric details. Our approach, based on PHLM, avoids the creation of visible ghosting artifacts and it reduces the filtering overblur characteristic of temporal deflickering methods. At the same time, the results are comparable to state‐of‐the‐art real‐time filters in terms of temporal coherence.