bluuebunny/crossref_metadata_2025 huggingface dataset:
Reoperative Surgery After Repair of Postcholecystectomy Bile Duct Injuries: Is it Worthwhile?
Authors: Addeo Pietro , Oussoultzoglou Elie , Fuchshuber Pascal , Rosso Edoardo , Nobili Cinzia , Souche Regis , Jaeck Daniel , Bachellier Philippe
Published: November 2012

Background

Repeat repair of bile duct injuries (BDIs) after cholecystectomy is technically challenging, and its success remains uncertain. We retrospectively evaluated the short‐ and long‐term outcomes of patients requiring reoperative surgery for BDI at a major referral center for hepatobiliary surgery.

Methods

Between January 1991 and May 2011, we performed surgical BDI repairs in 46 patients. Among them, 22 patients had undergone a previous surgical repair elsewhere (group 1), and 24 patients had no previous repair (group 2). We compared the early and late outcomes in the two groups.

Results

The patients in group 1 were younger (48.6 vs. 54.8 years, p = 0.0001) and were referred after a longer interval (>1 month) from BDI (72.7 vs. 41.7 %, p = 0.042). Intraoperative diagnosis of BDI (59.1 vs. 12.5 %, p = 0.001), ongoing cholangitis (45.4 vs. 12.5 %; p = 0.02), and delay of repair after referral to our institution (116 ± 34 days vs. 23 ± 9 days; p = 0.001) were significantly more frequent in group 1 than in group 2. No significant differences were found for postoperative mortality, morbidity, or length of stay between the groups. Patients with associated vascular injuries had a higher postoperative morbidity rate (p = 0.01) and associated hepatectomy rate (p = 0.045). After a mean follow‐up of 96.6 ± 9.7 months (range 5–237.2 months, median 96 months), the rate of recurrent cholangitis (6.5 %) was comparable in the two groups.

Conclusions

This study demonstrates that short‐ and long‐term outcomes after surgical repair of BDI are comparable regardless of whether the patient requires reoperative surgery for a failed primary repair. Associated vascular injuries increase postoperative morbidity and the need for liver resection.
Short and Long‐Term Mortality After Appendectomy in Sweden 1987 to 2006. Influence of Appendectomy Diagnosis, Sex, Age, Co‐morbidity, Surgical Method, Hospital Volume, and Time Period. A National Population‐Based Cohort Study
Authors: Andersson Roland E.
Published: November 2012

Background

Avoiding mortality is the ultimate goal when managing patients with suspected appendicitis. Previous studies have shown high mortality after negative appendectomy. This national cohort study analyzes short‐ and long‐term mortality after appendectomy in relation to appendectomy diagnosis, age, co‐morbidity, surgical method, hospital volume, and time period.

Method

A total of 223,543 appendectomy patients treated from 1987 to 2006 were identified from the Swedish National Patient Register and followed up via the Swedish Cause of Death Register. Analysis of mortality was conducted as Standardized Mortality Ratio (SMR) and by Cox multivariate regression.

Results

Negative appendectomy was followed by a higher mortality in the short term (30‐day Standardized Mortality Ratio (SMR30d) 8.95, confidence interval (CI) 6.68–12.61) than after perforated appendicitis (SMR30d 6.39, CI 5.44–7.48), and remained increased for up to 5 years (SMR5yr 1.31, CI 1.16–1.47). Non‐perforated appendicitis had a lower than expected long‐term mortality (SMR5yr 0.72, CI 0.68–0.76). These differences remained after adjustment for covariates. Laparoscopic appendectomy had similar short‐term mortality as open appendectomy but lower than expected long‐term morality (SMR5yr 0.70, CI 0.62–0.78). Mortality was decreasing during the study period. Hospital volume had no influence on mortality.

Conclusions

Negative appendectomy is associated with excess short‐ and long‐term mortality that remains after adjustment for known confounders, suggesting an association with underlying undetected morbidity. This motivates an improved preoperative diagnosis to avoid the additional trauma from unnecessary surgical interventions, but further studies are needed to investigate the cause of the increased long‐term mortality and if this can be prevented by an improved follow‐up of patients with negative appendectomy. Laparoscopic and open appendectomy have similar short‐term mortality. The lower long‐term mortality after non‐perforated appendicitis and laparoscopic appendectomy suggest selection of healthier patients for these interventions. This possibility should be taken into account when comparing mortality after open and laparoscopic appendectomy.
Low Expression of PAI‐2 as a Novel Marker of Portal Vein Tumor Thrombosis and Poor Prognosis in Hepatocellular Carcinoma
Authors: Zhou Li , Jin Ye , Cui Quan‐Cai , Jin Ke‐Min , Zhou Wei‐Xun , Xing Bao‐Cai
Published: November 2012

Background

Plasminogen activator inhibitor (PAI)‐2 was previously shown to be less frequently expressed in hepatocellular carcinoma (HCC). The present study was designed to investigate the clinical, pathological, and prognostic significance of PAI‐2 expression in HCC.

Methods

Expression of PAI‐2 was detected immunohistochemically for specimens from 78 patients with HCC after hepatic resection and correlated with clinicopathological features and patient survival. Risk factors of portal vein tumor thrombosis (PVTT) were also analyzed.

Results

Positive PAI‐2 staining was observed in tumor and non‐tumor tissues from 21 (26.9 %) and 56 (71.8 %) patients, respectively. Plasminogen activator inhibitor‐2 negativity in tumor tissues was significantly associated with PVTT, with a high sensitivity not only in univariate analysis but also in multivariate analysis. In addition, positive PAI‐2 staining was related to smaller tumor size and prolonged patient survival. The Cox regression model identified intratumoral PAI‐2 staining as an independent prognosticator in patients with HCC after resection.

Conclusions

Our data demonstrated that low expression of PAI‐2 serves as a novel marker of PVTT and poor prognosis in HCC.
The Evolving Role of Laparoscopy in Colonic Diverticular Disease: A Systematic Review
Authors: Gaertner Wolfgang B. , Kwaan Mary R. , Madoff Robert D. , Willis David , Belzer George E. , Rothenberger David A. , Melton Genevieve B.
Published: November 2012

Background

A PubMed search of the biomedical literature was carried out to systematically review the role of laparoscopy in colonic diverticular disease. All original reports comparing elective laparoscopic, hand‐assisted, and open colon resection for diverticular disease of the colon, as well as original reports evaluating outcomes after laparoscopic lavage for acute diverticulitis, were considered. Of the 21 articles chosen for final review, nine evaluated laparoscopic versus open elective resection, six compared hand‐assisted colon resection versus conventional laparoscopic resection, and six considered laparoscopic lavage. Five were randomized controlled trials.

Results

Elective laparoscopic colon resection for diverticular disease is associated with increased operative time, decreased postoperative pain, fewer postoperative complications, less paralytic ileus, and shorter hospital stay compared to open colectomy. Laparoscopic lavage and drainage appears to be a safe and effective therapy for selected patients with complicated diverticulitis.

Conclusions

Elective laparoscopic colectomy for diverticular disease is associated with decreased postoperative morbidity compared to open colectomy, leading to shorter hospital stay and fewer costs. Laparoscopic lavage has an increasing but poorly defined role in complicated diverticulitis.
Use of GPS location clusters analysis to study predation, feeding, and maternal behavior of the Eurasian lynx
Authors: Krofel Miha , Skrbinšek Tomaž , Kos Ivan
Published: November 2012

Analysis of global positioning system (GPS) location clusters (GLCs) is becoming increasingly popular in studies of carnivore ecology. While promising, this application of GPS technology is still poorly developed for most species. We applied this method to study predation and maternal behavior of the Eurasian lynx (Lynx lynx) in the Dinaric Mountains. Low population densities, rugged terrain, dense vegetation, and administrative borders make studies of this endangered population using traditional methods and a limited budget very challenging. We used the geographic information system and linear mixed‐effects models to understand the movement of lynx during the consumption process and denning period and estimate lynx kill rates. A total of 99 % of kills were found at GLCs longer than 30 h and with minimum two locations within 300 m. We confirmed 86 % of potential kills and all potential dens that were searched for in the field. High success in predicting kill and den sites showed that the Eurasian lynx is a suitable species for application of the GLC analysis methods. Comparison of field‐confirmed kills with model predictions showed the possibility for remote estimation of approximate kill rates in Eurasian lynx. Movements of the lynx were primarily affected by daytime period, time since the last kill/den translocation, lynx category, and their interactions. Based on the empirical data, we programmed simulations of lynx movements and elaborated recommendations for more efficient field procedures and study designs (GPS schedules) for future studies. We believe that our findings and approach will also benefit studies of other species with similar behavior.
Factor Analysis with EM Algorithm Never Gives Improper Solutions when Sample Covariance and Initial Parameter Matrices Are Proper
Authors: Adachi Kohei
Published: November 2012

Rubin and Thayer (Psychometrika, 47:69–76, 1982) proposed the EM algorithm for exploratory and confirmatory maximum likelihood factor analysis. In this paper, we prove the following fact: the EM algorithm always gives a proper solution with positive unique variances and factor correlations with absolute values that do not exceed one, when the covariance matrix to be analyzed and the initial matrices including unique variances and inter-factor correlations are positive definite. We further numerically demonstrate that the EM algorithm yields proper solutions for the data which lead the prevailing gradient algorithms for factor analysis to produce improper solutions. The numerical studies also show that, in real computations with limited numerical precision, Rubin and Thayer’s (Psychometrika, 47:69–76, 1982) original formulas for confirmatory factor analysis can make factor correlation matrices asymmetric, so that the EM algorithm fails to converge. However, this problem can be overcome by using an EM algorithm in which the original formulas are replaced by those guaranteeing the symmetry of factor correlation matrices, or by formulas used to prove the above fact.
New Approaches to Human Mobility: Using Mobile Phones for Demographic Research
Authors: Palmer John R. B. , Espenshade Thomas J. , Bartumeus Frederic , Chung Chang Y. , Ozgencil Necati Ercan , Li Kathleen
Published: November 2012

This article explores new methods for gathering and analyzing spatially rich demographic data using mobile phones. It describes a pilot study (the Human Mobility Project) in which volunteers around the world were successfully recruited to share GPS and cellular tower information on their trajectories and respond to dynamic, location-based surveys using an open-source Android application. The pilot study illustrates the great potential of mobile phone methodology for moving spatial measures beyond residential census units and investigating a range of important social phenomena, including the heterogeneity of activity spaces, the dynamic nature of spatial segregation, and the contextual dependence of subjective well-being.
Residential Integration on the New Frontier: Immigrant Segregation in Established and New Destinations
Authors: Hall Matthew
Published: November 2012

This article explores patterns and determinants of immigrant segregation for 10 immigrant groups in established, new, and minor destination areas. Using a group-specific typology of metropolitan destinations, this study finds that without controls for immigrant-group and metropolitan-level characteristics, immigrants in new destinations are more segregated and immigrants in minor destinations considerably more segregated than their counterparts in established destinations. Neither controls for immigrant-group acculturation or socioeconomic status nor those for demographic, housing, and economic features of metropolitan areas can fully account for the heightened levels of segregation observed in new and minor destinations. Overall, the results offer support for arguments that a diverse set of immigrant groups face challenges to residential incorporation in the new areas of settlement.
Migration Selection, Protection, and Acculturation in Health: A Binational Perspective on Older Adults
Authors: Riosmena Fernando , Wong Rebeca , Palloni Alberto
Published: November 2012

In this article, we test for four potential explanations of the Hispanic Health Paradox (HHP): the “salmon bias,” emigration selection, and sociocultural protection originating in either destination or sending country. To reduce biases related to attrition by return migration typical of most U.S.-based surveys, we combine data from the Mexican Health and Aging Study in Mexico and the U.S. National Health Interview Survey to compare self-reported diabetes, hypertension, current smoking, obesity, and self-rated health among Mexican-born men ages 50 and older according to their previous U.S. migration experience, and U.S.-born Mexican Americans and non-Hispanic whites. We also use height, a measure of health during childhood, to bolster some of our tests. We find an immigrant advantage relative to non-Hispanic whites in hypertension and, to a lesser extent, obesity. We find evidence consistent with emigration selection and the salmon bias in height, hypertension, and self-rated health among immigrants with less than 15 years of experience in the United States; we do not find conclusive evidence consistent with sociocultural protection mechanisms. Finally, we illustrate that although ignoring return migrants when testing for the HHP and its mechanisms, as well as for the association between U.S. experience and health, exaggerates these associations, they are not fully driven by return migration-related attrition.
Dynamical degree, arithmetic entropy, and canonical heights for dominant rational self-maps of projective space
Authors: SILVERMAN JOSEPH H.
Published: November 2012

Let φ:ℙN⤏ℙN be a dominant rational map. The dynamical degree of φ is the quantity δφ=lim (deg φn)1/n. When φ is defined over ${\bar {{\mathbb {Q}}}}$, we define the arithmetic degree of a point $P\in {\mathbb {P}}^N({\bar {{\mathbb {Q}}}})$ to be αφ(P)=lim sup h(φn(P))1/n and the canonical height of P to be $\hat {h}_\varphi (P)=\limsup \delta _\varphi ^{-n}n^{-\ell _\varphi }h(\varphi ^n(P))$ for an appropriately chosen ℓφ. We begin by proving some elementary relations and making some deep conjectures relating δφ, αφ(P) , ${\hat h}_\varphi (P)$, and the Zariski density of the orbit 𝒪φ(P) of P. We then prove our conjectures for monomial maps.
A sunward propagating fast wave in the magnetosheath observed after the passage of an interplanetary shock
Authors: Pallocchia G.
Published: November 2012

The interaction of an interplanetary (IP) shock with the terrestrial magnetosphere causes some noticeable effects on the global scale structure of the magnetosphere itself. One of these effects is given by an earthward motion of the bow shock followed, some minutes later, by a sunward displacement. As demonstrated by past observational studies, in agreement with the theory of the shock‐shock collision, the earthward motion of the bow shock is due directly to the interplanetary shock impact on it. Differently, the origin of the sunward motion of the bow shock is still not well understood. In this regard, on the basis of some issues of the present observational study, we suggest a possible mechanism to account for the aforementioned outward displacement. Our event, observed by the Cluster SC3 spacecraft on day 7 November 2004, is related to a magnetosheath perturbation triggered by an IP shock impact. The main result of the data analysis is the first identification of a reverse (i.e., sunward directed) fast magnetosonic wave just after the IP shock passage. The identification has been performed via a direct comparison of the observations with the MHD equations of nonlinear magnetosonic waves. The reverse fast wave consists of a smooth compression, approximately 2 min long, which is most of the magnetosheath plasma density increase produced by the entire perturbation. We point out that signatures of this reverse wave are observable in two other events as well as in a three‐dimensional MHD simulation reported in the literature on the topic. Moreover, we provide a possible interpretation of this reverse wave in terms of a transient pressure build‐up in the magnetosheath due to the post‐shock reconfiguration of the plasma flow around the magnetopause obstacle.
Black carbon and other light‐absorbing impurities in snow across Northern China
Authors: Wang Xin , Doherty Sarah J. , Huang Jianping
Published: November 2012

Black carbon (BC), organic carbon (OC), and mineral dust (MD) are the most important light‐absorbing particulate impurities in snow. A field campaign was conducted in January and February 2010 to measure light‐absorbing particles in snow across northern China. About 400 snow samples were collected at 46 sites in six provinces. A spectrophotometer was used to separate snow particulate absorption by BC and non‐BC constituents, based on the different spectral dependences of their light absorption. Light absorption by MD is due to iron oxides, so iron concentration was determined by chemical analysis. Using assumed mass absorption efficiencies for BC, OC, and iron, the fractional contribution of each to total absorption was estimated. BC is a product of combustion and iron is associated with MD, but OC in snow can be associated with either combustion products deposited to snow or from soil mixed into snow. The lowest concentrations of BC were in the remote northeast on the border of Siberia, with a median concentration in surface snow of 117 ng g–1. South of this, in the industrial northeast, the median snow BC concentration was 1220 ng g–1. In the northeast, snow particulate light absorption was dominated by BC. Across the grassland of Inner Mongolia, OC, likely mostly from local soil, dominates light absorption, with median BC concentrations of 340 ng g–1 responsible for only about one third of total particulate light absorption. In the Qilian Mountains, at the northern boundary of the Tibetan Plateau, snow particulate light absorption is dominated by local soil and desert dust.
Influence of daily variations in baseline ozone on urban air quality in the United States Pacific Northwest
Authors: Wigder Nicole L. , Jaffe Daniel A. , Herron‐Thorpe Farren L. , Vaughan Joseph K.
Published: November 2012

We examine the influence of daily variations in baseline ozone (O3) on urban air quality in the U.S. Pacific Northwest (PNW) during 2004 to 2010 through two analyses: (1) transport of free tropospheric (FT) O3 from Mount Bachelor Observatory (MBO) to Boise, Idaho; and (2) transport of marine boundary layer (MBL) O3 from Cheeka Peak (CP) to Enumclaw, Washington. Both Boise and Enumclaw experience days with maximum daily 8 hour averages of O3 (MDA8) exceeding U.S. standards. Backward trajectory cluster analyses identify days when FT and MBL O3 strongly influence MDA8 in Boise and Enumclaw. On these days, MBO and CP O3 observations explain 40% and 69% of the variations in Boise and Enumclaw MDA8, respectively. Bivariate regressions for Boise/MBO and Enumclaw/CP have slopes of 0.52 ± 0.16 and 1.04 ± 0.08, respectively, representing the differing interplay of O3 dilution, production, and loss during FT to boundary layer transport (Boise/MBO) and fast boundary layer transport (Enumclaw/CP). AIRPACT‐3/CMAQ (Air Indicator Report for Public Access and Community Tracking version 3/Community Multi‐scale Air Quality model) high‐resolution air‐quality simulation results demonstrate how transport of O3 from the FT above MBO contributes to elevated O3 at Boise. Average MDA8 O3 in Boise is higher than in Enumclaw due to site elevation and greater entrainment of FT air masses, a finding likely applicable to other PNW sites. Days with high baseline influence at Boise and Enumclaw have lower average MDA8 O3 than other days; however, some of these days would still exceed the U.S. standard if it is substantially tightened in 2013, highlighting the increasing importance of FT O3 influence on urban MDA8.
Evaluation of vegetation cover and land‐surface albedo in MPI‐ESM CMIP5 simulations
Authors: Brovkin V. , Boysen L. , Raddatz T. , Gayler V. , Loew A. , Claussen M.
Published: November 2012

Key Points

Two metrics are proposed to evaluate vegetation cover simulated by ESMs

On a global scale, tree cover is satisfactory simulated by MPI‐ESM

Land‐surface albedois evaluated using the net surface radiation
4th Australasian Vaccines and Immunotherapeutic Development Meeting
Authors: Engwerda Christian , Belz Gabrielle
Published: November 2012

This report describes advances in the understanding of how we might intervene in destructive processes, such as autoimmunity, infectious disease and cancer, through the development of innovative vaccines and immunotherapeutics.
Reducing bias in bacterial community analysis of lower respiratory infections
Authors: Rogers Geraint B , Cuthbertson Leah , Hoffman Lucas R , Wing Peter A C , Pope Christopher , Hooftman Danny A P , Lilley Andrew K , Oliver Anna , Carroll Mary P , Bruce Kenneth D , van der Gast Christopher J
Published: November 2012

High-throughput pyrosequencing and quantitative PCR (Q-PCR) analysis offer greatly improved accuracy and depth of characterisation of lower respiratory infections. However, such approaches suffer from an inability to distinguish between DNA derived from viable and non-viable bacteria. This discrimination represents an important step in characterising microbial communities, particularly in contexts with poor clearance of material or high antimicrobial stress, as non-viable bacteria and extracellular DNA can contribute significantly to analyses. Pre-treatment of samples with propidium monoazide (PMA) is an effective approach to non-viable cell exclusion (NVCE). However, the impact of NVCE on microbial community characteristics (abundance, diversity, composition and structure) is not known. Here, adult cystic fibrosis (CF) sputum samples were used as a paradigm. The effects of PMA treatment on CF sputum bacterial community characteristics, as analysed by pyrosequencing and enumeration by species-specific (Pseudomonas aeruginosa) and total bacterial Q-PCR, were assessed. At the local community level, abundances of both total bacteria and of P. aeruginosa were significantly lower in PMA-treated sample portions. Meta-analysis indicated no overall significant differences in diversity; however, PMA treatment resulted in a significant alteration in local community membership in all cases. In contrast, at the metacommunity level, PMA treatment resulted in an increase in community evenness, driven by an increase in diversity, predominately representing rare community members. Importantly, PMA treatment facilitated the detection of both recognised and emerging CF pathogens, significantly influencing ‘core’ and ‘satellite’ taxa group membership. Our findings suggest failure to implement NVCE may result in skewed bacterial community analyses.
Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community
Authors: Handley Kim M , VerBerkmoes Nathan C , Steefel Carl I , Williams Kenneth H , Sharon Itai , Miller Christopher S , Frischkorn Kyle R , Chourey Karuna , Thomas Brian C , Shah Manesh B , Long Philip E , Hettich Robert L , Banfield Jillian F
Published: November 2012

Stimulation of subsurface microorganisms to induce reductive immobilization of metals is a promising approach for bioremediation, yet the overall microbial community response is typically poorly understood. Here we used proteogenomics to test the hypothesis that excess input of acetate activates complex community functioning and syntrophic interactions among autotrophs and heterotrophs. A flow-through sediment column was incubated in a groundwater well of an acetate-amended aquifer and recovered during microbial sulfate reduction. De novo reconstruction of community sequences yielded near-complete genomes of Desulfobacter (Deltaproteobacteria), Sulfurovum- and Sulfurimonas-like Epsilonproteobacteria and Bacteroidetes. Partial genomes were obtained for Clostridiales (Firmicutes) and Desulfuromonadales-like Deltaproteobacteria. The majority of proteins identified by mass spectrometry corresponded to Desulfobacter-like species, and demonstrate the role of this organism in sulfate reduction (Dsr and APS), nitrogen fixation and acetate oxidation to CO2 during amendment. Results indicate less abundant Desulfuromonadales, and possibly Bacteroidetes, also actively contributed to CO2 production via the tricarboxylic acid (TCA) cycle. Proteomic data indicate that sulfide was partially re-oxidized by Epsilonproteobacteria through nitrate-dependent sulfide oxidation (using Nap, Nir, Nos, SQR and Sox), with CO2 fixed using the reverse TCA cycle. We infer that high acetate concentrations, aimed at stimulating anaerobic heterotrophy, led to the co-enrichment of, and carbon fixation in Epsilonproteobacteria. Results give an insight into ecosystem behavior following addition of simple organic carbon to the subsurface, and demonstrate a range of biological processes and community interactions were stimulated.
Quartz tuning fork-based frequency modulation atomic force spectroscopy and microscopy with all digital phase-locked loop
Authors: An Sangmin , Hong Mun-heon , Kim Jongwoo , Kwon Soyoung , Lee Kunyoung , Lee Manhee , Jhe Wonho
Published: November 2012

We present a platform for the quartz tuning fork (QTF)-based, frequency modulation atomic force microscopy (FM-AFM) system for quantitative study of the mechanical or topographical properties of nanoscale materials, such as the nano-sized water bridge formed between the quartz tip (∼100 nm curvature) and the mica substrate. A thermally stable, all digital phase-locked loop is used to detect the small frequency shift of the QTF signal resulting from the nanomaterial-mediated interactions. The proposed and demonstrated novel FM-AFM technique provides high experimental sensitivity in the measurement of the viscoelastic forces associated with the confined nano-water meniscus, short response time, and insensitivity to amplitude noise, which are essential for precision dynamic force spectroscopy and microscopy.
Calibration and performance assessment of a temperature sensor prototype using a 1-point calibration procedure
Authors: Chapon P. A. , Gauthier A. , Bulla J. , Moussay S.
Published: November 2012

This study aims to assess the relevance of 1-point calibration procedure, within the framework of the development of a new telemetric temperature sensor. The criteria used for performance assessment were the level of accuracy, and the time of inertia of the temperature sensor prototype (TSP) tested. First, the stability of the calibration bath was assessed. Then, the accuracy of 16 prototypes was evaluated for 7 target temperatures (ranging from 29 °C to 45 °C). Finally, the inertia of TSP response was evaluated while increasing and decreasing the bath temperature. The difference between prototype and target temperature increases as bath temperature moves away from 37 °C; however, the accuracy of the sensor conforms to applicable standards. Most TSP remain in the range of ±0.2 °C for each temperature level tested, but a linear, decreasing slope is observed; prototypes underestimate high temperatures and overestimate low temperatures. Data from time of inertia assessment show that probes were within the range of ±0.2 °C from the target temperature with a maximal delay of 150 s which satisfy standard norms. However, results indicate that a 1-point calibration procedure of the sensors appears non optimal, a 2-point calibration procedure should be performed to avoid the observed temperature data slope.
Work-based criterion for particle motion and implication for turbulent bed-load transport
Authors: Lee Hyungoo , Ha Man Yeong , Balachandar S.
Published: November 2012

A simple work-based criterion for the onset of downstream migration of a particle sitting on a rough bed in a turbulent flow is developed in the present work. The criterion is motivated by the fact that the geometric pocket formed by other bed particles within which the mobile particle is sitting can be viewed as a potential well and the gravitational and frictional mechanisms impose an energy barrier for the particle to fully escape the pocket and initiate irreversible downstream migration. The energy barrier is clearly a statistical quantity, as it depends on the shape, size, and other details of the mobile particle and the geometry of the pocket. The energy barrier imposes a threshold value for the hydrodynamic work that must be done on the particle in order to initiate downstream migration. The simple work-based criterion developed here is related to the critical force and critical impulse criteria that have been advanced in the past. The fluctuating nature of the effective hydrodynamic force that works towards dislodging the particle out of the pocket and migrating it downstream is explored with data from a direct numerical simulation of turbulent channel flow and the probabilities of instances when the force, impulse, and work-based criteria for particle motion are satisfied and computed. The work-based criterion for particle migration is used to obtain an expression for the bed load transport that can be applied on an instantaneous basis at any local region of the bed. The average nondimensional bed load transport rate, or Einstein number, computed based on the present work-based model is shown to compare well with existing experimental data and empirical models. In particular, at low mobility regime, the present model is able to naturally recover the well-accepted rapid increase in bed load transport as 16th power of average bed shear stress and at high mobility regime the present model captures the slower increase in bed load transport with increasing average bed shear stress.
Effect of orifice inner lip radius on synthetic jet efficiency
Authors: Nani David J. , Smith Barton L.
Published: November 2012

A synthetic jet is formed by periodic oscillation of a fluid through an orifice. The oscillatory motion is driven by a diaphragm or other driver. Previous studies have demonstrated that synthetic jet formation and time-averaged cavity pressure are a function of the orifice shape. Traditionally, the performance of the jet is evaluated with varying configurations of fixed driver input voltage or fixed driver displacement. Neither of these measures accurately reflect the efficiency of the actuator. Defining efficiency as “desired output divided by required input,” these traditional measures may not account for increase in required driving current or force. A sharp inside edge of a thin synthetic jet orifice can result in separated flow and increased momentum flux (due to the decreased flow area) for a fixed driver displacement. This can lead one to believe that efficiency has been improved, when, in reality, much more power was required for the driver. Acoustic power, which is the time-average of volume flow rate through the orifice multiplied by the driving pressure, accurately accounts for the power required to drive the actuator. For any synthetic jet actuator, the power to the driver is the power to the fluid (acoustic power) divided by the driver efficiency. If we assume that the driver efficiency is not a strong function of the load, any change to the acoustic power will result in the same proportional change in the driver input power. This study investigates the efficiency of a round (axisymmetric) synthetic jet actuator as a function of the radius of curvature of the interior edge of the orifice. Simultaneous particle image velocimetry measurements at the jet exit and cavity pressure measurements are used to measure the acoustic power required to generate the jet. The resultant momentum flux of the jet is used as a measure of output of the jet. Results are obtained for a range of displacement amplitudes (or stroke lengths) and radii of curvature, while Reynolds number is held fixed.
Static and dynamic properties of multi-section InGaN-based laser diodes
Authors: Sulmoni L. , Lamy J.-M. , Dorsaz J. , Castiglia A. , Carlin J.-F. , Scheibenzuber W. G. , Schwarz U. T. , Zeng X. , Boïko D. L. , Grandjean N.
Published: November 2012

We have studied multi-section InGaN multiple-quantum-well (MQW) laser diodes grown on c-plane freestanding GaN substrate consisting of an absorber section (AS) and an amplifier gain section. As a result of the interplay between external bias applied to the AS and the internal piezoelectric and spontaneous polarization fields inherent to c-plane InGaN MQWs, the devices exhibit non-linear non-monotonic variations of the threshold current due to the quantum-confined Stark effect that takes place in the AS MQWs. We report on how this effect tailors the lasing characteristics and lasing dynamics, leading from a steady-state cw lasing regime for an unbiased AS to self-pulsation and Q-switching regimes at high negative absorber bias.
A first-principles-based correlation functional for harmonious connection of short-range correlation and long-range dispersion
Authors: Modrzejewski Marcin , Lesiuk Michał , Rajchel Łukasz , Szczęśniak Małgorzata M. , Chałasiński Grzegorz
Published: November 2012

We present a physically motivated correlation functional belonging to the meta-generalized gradient approximation (meta-GGA) rung, which can be supplemented with long-range dispersion corrections without introducing double-counting of correlation contributions. The functional is derived by the method of constraint satisfaction, starting from an analytical expression for a real-space spin-resolved correlation hole. The model contains a position-dependent function that controls the range of the interelectronic correlations described by the semilocal functional. With minimal empiricism, this function may be adjusted so that the correlation model blends with a specific dispersion correction describing long-range contributions. For a preliminary assessment, our functional has been combined with an atom-pairwise dispersion correction and full Hartree-Fock (HF)-like exchange. Despite the HF-exchange approximation, its predictions compare favorably with reference interaction energies in an extensive set of non-covalently bound dimers.
Color filters for reflective display with wide viewing angle and high reflectivity based on metal dielectric multilayer
Authors: Chung Deukseok , Shin Changgyun , Song Byonggwon , Jung Myonghoon , Yun Youngjun , Hyun Nam Sung , Noh Changho , Kim Jungwoo , Lee Sangyoon
Published: November 2012

We report high performance reflective color filters based on one-dimensional metal-dielectric multilayer. Wide viewing angle of ±50°, far beyond that with conventional all-dielectric multilayers, is achieved while maintaining approximately 100% peak reflectance and color reproducibility. Reflectance of 40% in white mode and color gamut of 47% to the United States National Television Systems Committee (NTSC) standard is demonstrated. The proposed color filter is integrated into 3.5-in. color reflective display and shows 30% increase in brightness than conventional dye color filters.
The effect of electron beam pitch angle and density gradient on solar type III radio bursts
Authors: Pechhacker R. , Tsiklauri D.
Published: November 2012

1.5D particle-in-cell simulations of a hot, low density electron beam injected into magnetized, maxwellian plasma were used to further explore the alternative non-gyrotropic beam driven electromagnetic (EM) emission mechanism, first studied in Tsiklauri, Phys. Plasmas 18, 052903 (2011). Variation of beam injection angle and background density gradient showed that the emission process is caused by the perpendicular component of the beam injection current, whereas the parallel component only produces Langmuir waves, which play no role in the generation of EM waves in our mechanism. Particular emphasis was put on the case, where the beam is injected perpendicularly to the background magnetic field, as this turned off any electrostatic wave generation along the field and left a purely electromagnetic signal in the perpendicular components. The simulations establish the following key findings: (i) Initially, waves at a few ωce/γ are excited, mode converted and emitted at ≈ωpe (ii) The emission intensity along the beam axis is proportional to the respective component of the kinetic energy of the beam; (iii) The frequency of the escaping EM emission is independent of the injection angle; (iv) A stronger background density gradient causes earlier emission; (v) The beam electron distribution function in phase space shows harmonic oscillation in the perpendicular components at the relativistic gyrofrequency; (vi) The requirement for cyclotron maser emission, ∂f∂v⊥>0, is fulfilled; (vii) The degree of linear polarization of the emission is strongly dependent on the beam injection angle; (viii) The generated electromagnetic emission is left-hand elliptically polarized as the pitch angle tends to 90°; and (ix) The generated electromagnetic energy is of the order of 0.1% of the initial beam kinetic energy.
Guide-star-based computational adaptive optics for broadband interferometric tomography
Authors: Adie Steven G. , Shemonski Nathan D. , Graf Benedikt W. , Ahmad Adeel , Scott Carney P. , Boppart Stephen A.
Published: November 2012

We present a method for the numerical correction of optical aberrations based on indirect sensing of the scattered wavefront from point-like scatterers (“guide stars”) within a three-dimensional broadband interferometric tomogram. This method enables the correction of high-order monochromatic and chromatic aberrations utilizing guide stars that are revealed after numerical compensation of defocus and low-order aberrations of the optical system. Guide-star-based aberration correction in a silicone phantom with sparse sub-resolution-sized scatterers demonstrates improvement of resolution and signal-to-noise ratio over a large isotome. Results in highly scattering muscle tissue showed improved resolution of fine structure over an extended volume. Guide-star-based computational adaptive optics expands upon the use of image metrics for numerically optimizing the aberration correction in broadband interferometric tomography, and is analogous to phase-conjugation and time-reversal methods for focusing in turbid media.
Single-molecule dissection of the high-affinity cohesin–dockerin complex
Authors: Stahl Stefan W. , Nash Michael A. , Fried Daniel B. , Slutzki Michal , Barak Yoav , Bayer Edward A. , Gaub Hermann E.
Published: November 2012

Cellulose-degrading enzyme systems are of significant interest from both a scientific and technological perspective due to the diversity of cellulase families, their unique assembly and substrate binding mechanisms, and their potential applications in several key industrial sectors, notably cellulose hydrolysis for second-generation biofuel production. Particularly fascinating are cellulosomes, the multimodular extracellular complexes produced by numerous anaerobic bacteria. Using single-molecule force spectroscopy, we analyzed the mechanical stability of the intermolecular interfaces between the cohesin and the dockerin modules responsible for self-assembly of the cellulosomal components into the multienzyme complex. The observed cohesin–dockerin rupture forces (>120 pN) are among the highest reported for a receptor–ligand system to date. Using an atomic force microscope protocol that quantified single-molecule binding activity, we observed force-induced dissociation of calcium ions from the duplicated loop–helix F-hand motif located within the dockerin module, which in the presence of EDTA resulted in loss of affinity to the cohesin partner. A cohesin amino acid mutation (D39A) that eliminated hydrogen bonding with the dockerin’s critically conserved serine residues reduced the observed rupture forces. Consequently, no calcium loss occurred and dockerin activity was maintained throughout multiple forced dissociation events. These results offer insights at the single-molecule level into the stability and folding of an exquisite class of high-affinity protein–protein interactions that dictate fabrication and architecture of cellulose-degrading molecular machines.
Developing a broader scientific foundation for river restoration: Columbia River food webs
Authors: Naiman Robert J. , Alldredge J. Richard , Beauchamp David A. , Bisson Peter A. , Congleton James , Henny Charles J. , Huntly Nancy , Lamberson Roland , Levings Colin , Merrill Erik N. , Pearcy William G. , Rieman Bruce E. , Ruggerone Gregory T. , Scarnecchia Dennis , Smouse Peter E. , Wood Chris C.
Published: November 2012

Well-functioning food webs are fundamental for sustaining rivers as ecosystems and maintaining associated aquatic and terrestrial communities. The current emphasis on restoring habitat structure—without explicitly considering food webs—has been less successful than hoped in terms of enhancing the status of targeted species and often overlooks important constraints on ecologically effective restoration. We identify three priority food web-related issues that potentially impede successful river restoration: uncertainty about habitat carrying capacity, proliferation of chemicals and contaminants, and emergence of hybrid food webs containing a mixture of native and invasive species. Additionally, there is the need to place these food web considerations in a broad temporal and spatial framework by understanding the consequences of altered nutrient, organic matter (energy), water, and thermal sources and flows, reconnecting critical habitats and their food webs, and restoring for changing environments. As an illustration, we discuss how the Columbia River Basin, site of one of the largest aquatic/riparian restoration programs in the United States, would benefit from implementing a food web perspective. A food web perspective for the Columbia River would complement ongoing approaches and enhance the ability to meet the vision and legal obligations of the US Endangered Species Act, the Northwest Power Act (Fish and Wildlife Program), and federal treaties with Northwest Indian Tribes while meeting fundamental needs for improved river management.
Folding of large multidomain proteins by partial encapsulation in the chaperonin TRiC/CCT
Authors: Rüßmann Florian , Stemp Markus J. , Mönkemeyer Leonie , Etchells Stephanie A. , Bracher Andreas , Hartl F. Ulrich
Published: November 2012

The eukaryotic chaperonin, TRiC/CCT (TRiC, TCP-1 ring complex; CCT, chaperonin containing TCP-1), uses a built-in lid to mediate protein folding in an enclosed central cavity. Recent structural data suggest an effective size limit for the TRiC folding chamber of ∼70 kDa, but numerous chaperonin substrates are substantially larger. Using artificial fusion constructs with actin, an obligate chaperonin substrate, we show that TRiC can mediate folding of large proteins by segmental or domain-wise encapsulation. Single or multiple protein domains up to ∼70 kDa are stably enclosed by stabilizing the ATP-hydrolysis transition state of TRiC. Additional domains, connected by flexible linkers that pass through the central opening of the folding chamber, are excluded and remain accessible to externally added protease. Experiments with the physiological TRiC substrate hSnu114, a 109-kDa multidomain protein, suggest that TRiC has the ability to recognize domain boundaries in partially folded intermediates. In the case of hSnu114, this allows the selective encapsulation of the C-terminal ∼45-kDa domain and segments thereof, presumably reflecting a stepwise folding mechanism. The capacity of the eukaryotic chaperonin to overcome the size limitation of the folding chamber may have facilitated the explosive expansion of the multidomain proteome in eukaryotes.
A mathematical model of fluid and gas flow in nanoporous media
Authors: Monteiro Paulo J. M. , Rycroft Chris H. , Barenblatt Grigory Isaakovich
Published: November 2012

The mathematical modeling of the flow in nanoporous rocks (e.g., shales) becomes an important new branch of subterranean fluid mechanics. The classic approach that was successfully used in the construction of the technology to develop oil and gas deposits in the United States, Canada, and the Union of Soviet Socialist Republics becomes insufficient for deposits in shales. In the present article a mathematical model of the flow in nanoporous rocks is proposed. The model assumes the rock consists of two components: (
i
) a matrix, which is more or less an ordinary porous or fissurized-porous medium, and (
ii
) specific organic inclusions composed of kerogen. These inclusions may have substantial porosity but, due to the nanoscale of pores, tubes, and channels, have extremely low permeability on the order of a nanodarcy (

) or less. These inclusions contain the majority of fluid: oil and gas. Our model is based on the hypothesis that the permeability of the inclusions substantially depends on the pressure gradient. At the beginning of the development of the deposit, boundary layers are formed at the boundaries of the low-permeable inclusions, where the permeability is strongly increased and intensive flow from inclusions to the matrix occurs. The resulting formulae for the production rate of the deposit are presented in explicit form. The formulae demonstrate that the production rate of deposits decays with time following a power law whose exponent lies between

and

. Processing of experimental data obtained from various oil and gas deposits in shales demonstrated an instructive agreement with the prediction of the model.
The clean conscience at work: emotions, intuitions and morality
Authors: Schnall Simone , Cannon Peter R.
Published: November 2012

How do people decide what is right and wrong, and to what extent are their actions guided by such moral considerations? Inspired by philosophical traditions, early approaches to morality focused on rationality, and assumed that people arrive at moral standards by logical thought. More recently, however, psychologists have explored the influence of emotions and intuitions on morality, and evidence has been accumulating that moral decisions and behaviors are far from rational, but instead, are guided by intuitions and situational considerations. For example, seemingly irrelevant concerns such as keeping one’s mind and spirit clean and pure can change people’s moral judgment. Emotions can also influence behavior, and positive, uplifting emotions such as elevation and gratitude can be harnessed to produce beneficial outcomes for individuals and organizations alike. Furthermore, people appear to aspire to an equilibrium of moral self-worth, and engage in more or less ethical behavior depending on their currently perceived moral integrity. Thus, morality and ethical behavior is less likely to reside in the person than in the context, and thus, for the study of spirituality, it might be beneficial to focus on people’s situational constraints in the workplace rather than their stable dispositions. Further, because of their potential to inspire positive action, organizations might aim to make positive moral emotions, such as gratitude, elevation, and awe part of everyday work contexts. Overall, in organizations and the workplace, the goal shifts from trying to identify the moral individual to providing the contextual conditions that appeal to spiritual concerns in order to foster moral behavior.