bluuebunny/crossref_metadata_2025 huggingface dataset:
Circulating levels of the anti‐angiogenic thrombospondin 2 are elevated in pre‐eclampsia
Authors: STENCZER BALÁZS , MOLVAREC ATTILA , VERESH ZOLTÁN , GULLAI NÓRA , NAGY GYULA RICHÁRD , WALENTIN SZILVIA , SZIJÁRTÓ JÁNOS , RIGÓ JÁNOS
Published: June 2011

An imbalance of maternal circulating pro‐ and anti‐angiogenic factors may play a role in the pathogenesis of pre‐eclampsia. Thrombospondin 2 (TSP‐2) is a protein expressed mainly by activated endothelial cells, which acts as a potent anti‐angiogenic agent. Our aim was to determine whether serum TSP‐2 levels are altered in pre‐eclampsia. We enrolled 35 pre‐eclamptic patients and 35 healthy pregnant women in the study. Thrombospondin 2 levels were determined by enzyme‐linked immunosorbent assay, while soluble fms‐like tyrosine kinase‐1 (sFlt‐1) and placental growth factor (PlGF) concentrations were determined by electrochemiluminescence immunoassay. In patients with PE, we demonstrated 1.7‐fold higher TSP‐2 [13.2 (9.4–18.1) vs. 7.9 (7.2–11.2) ng/ml, p<0.001], 3.8‐fold higher sFlt‐1 and 4.3‐fold lower PlGF levels compared with the control group. There were no associations between TSP‐2 and sFlt‐1 or PlGF concentrations. We suggest that circulating TSP‐2 levels may contribute to the pathogenesis of PE via its anti‐angiogenic properties, but in a distinct way from sFlt‐1 and PlGF.
Patient perceptions of the potential lethality associated with deliberate self‐poisoning
Authors: Vlad Ioana A , Fatovich Daniel M , Fenner Stephen G , Daly Frank F , Soderstrom Jessamine Hui‐Min , Burrows Sally A
Published: June 2011

Introduction: Little is known about patient perceptions of the lethality of their overdose. Our aim was to compare patient perceptions with the risk assessment of clinical toxicologists.

Methods: A prospective observational study of overdose patients presenting to a tertiary hospital. Eligible patients were surveyed once they were medically fit for psychiatric evaluation. Descriptive data were collected, including the Pierce Suicide Intent Scale (SIS). In response to ‘how dangerous did you think this overdose was when you took the tablets?’ patients marked a 10 cm VAS, with 0 = would be harmless, 10 = certain to cause death. A panel of clinical toxicologists independently made a risk assessment on a 10 cm VAS, with 0 = non‐toxic ingestion and 10 = uniform lethality even with full medical intervention.

Results: Of 202 patients enrolled, 118 (58.4%, 95% CI 51–65) were female; median age 33 years (interquartile range [IQR] 24–42). One hundred and three (51%, 95% CI 44–58) stated it was their intention to kill themselves and 44 (21.8%, 95% CI 16–28) wrote a suicide note. They most commonly used their own prescription medications (141, 69.8%, 95% CI 63–76). The median patient visual analog scale (VAS) was 5.8 (IQR 2.3–8.3) and median toxicology VAS was 1.4 (IQR 0.6–2.8); this difference was statistically significant (P < 0.0001). The correlation between the patient visual analog scale (VAS) and Pierce SIS (median 8.5/25 [IQR 4–12]) was strong (r= 0.73, P < 0.0001).

Conclusions: Patient perceptions of the lethality of their overdose are correlated with their suicidal intent as measured on the Pierce SIS, with a significant mismatch between patient perceptions and the toxicological risk assessment.
Functions and Application of the AP2/ERF Transcription Factor Family in Crop ImprovementF
Authors: Xu Zhao‐Shi , Chen Ming , Li Lian‐Cheng , Ma You‐Zhi
Published: June 2011

You‐Zhi Ma (Corresponding author)

Plants have acquired sophisticated stress response systems to adapt to changing environments. It is important to understand plants’ stress response mechanisms in the effort to improve crop productivity under stressful conditions. The AP2/ERF transcription factors are known to regulate diverse processes of plant development and stress responses. In this study, the molecular characteristics and biological functions of AP2/ERFs in a variety of plant species were analyzed. AP2/ERFs, especially those in DREB and ERF subfamilies, are ideal candidates for crop improvement because their overexpression enhances tolerances to drought, salt, freezing, as well as resistances to multiple diseases in the transgenic plants. The comprehensive analysis of physiological functions is useful in elucidating the biological roles of AP2/ERF family genes in gene interaction, pathway regulation, and defense response under stress environments, which should provide new opportunities for the crop tolerance engineering.
A Transgenic Study on Affecting Potato Tuber Yield by Expressing the Rice Sucrose Transporter Genes OsSUT5Z and OsSUT2MF
Authors: Sun Aijun , Dai Yan , Zhang Xinsheng , Li Chunmin , Meng Kun , Xu Honglin , Wei Xiaoli , Xiao Guifang , Ouwerkerk Pieter B.F. , Wang Mei , Zhu Zhen
Published: June 2011

In many plants, sucrose transporters are essential for both sucrose exports from sources and imports into sinks, indicating a function in assimilate partitioning. To investigate whether sucrose transporters can improve the yield of starch plant, potato plants (Solanum tuberosum L. cv. Désirée) were transformed with cDNAs of the rice sucrose transporter genes OsSUT5Z and OsSUT2M under the control of a tuber‐specific, class‐I patatin promoter. Compared to the controls, the average fructose content of OsSUT5Z transgenic tubers significantly increased. However, the content of the sugars and starch in the OsSUT2M transgenic potato tubers showed no obvious difference. Correspondingly, the average tuber yield, average number of tubers per plant and average weight of single tuber showed no significant difference in OsSUT2M transgenic tubers with controls. In the OsSUT5Z transgenic lines, the average tuber yield per plant was 1.9‐fold higher than the controls, and the average number of tubers per plant increased by more than 10 tubers on average, whereas the average weight of a single tuber did not increase significantly. These results suggested that the average number of tubers per plant showed more contribution than the average weight of a single tuber to the tuber yield per plant.
Why become speckled? Ontogeny and function of speckling in Shark Bay bottlenose dolphins (Tursiops sp.)1
Authors: Krzyszczyk Ewa , Mann Janet
Published: June 2011

Abstract

To date, color patterns have been used to assess cetacean age and taxonomic status, but few studies have determined precise correlates of coloration with known age or investigated its function. Here, we examine the ontogeny of speckling in 88 bottlenose dolphins (Tursiops sp.) in Shark Bay, Australia, of known age, tracked from birth to age 34. Ventral speckles first appear in the genital area at a mean age of 10.2 ± 0.35 yr (range = 7.6–12.7 yr). Throughout their life span, speckles increase in number and density, particularly along the ventral and lateral sides. The timing of speckle onset does not significantly differ by sex but is related to sexual maturity in females. The age of speckle onset in the genital area correlates with the age of first known parturition. In terms of speckle function, we discuss two hypotheses commonly proffered to explain color variation, concealment, and communication. Concealment from predators or prey is unlikely to explain speckle development in Shark Bay Tursiops because the onset occurs long after peak predation risk and initial hunting success (at 3 mo of age). We suggest that speckle patterns offer reliable cues on reproductive status and/or condition and could, thus, serve a communicative or some other function.
Minimal similarity in songs suggests limited exchange between humpback whales (Megaptera novaeangliae) in the southern Indian Ocean
Authors: Murray Anita , Cerchio Salvatore , McCauley Robert , Jenner Curt S. , Razafindrakoto Yvette , Coughran Douglas , McKay Shannon , Rosenbaum Howard
Published: June 2011

Abstract

Comparing humpback whale song from different breeding assemblages can reveal similarities in song due to acoustically interacting males, and therefore indirectly test whether males from different breeding sites are mixing. Northern Hemisphere song comparisons illustrated that whales within ocean basins share similar songs and are subpopulations within a larger population, whereas whales in different ocean basins are isolated populations and therefore do not share songs. During the 2006 breeding season, recordings were collected in Madagascar and Western Australia, and were compared visually plus aurally. Both regions shared one theme, whereas each region had four and six private themes, respectively. This study had a substantially low number of shared themes. The co‐occurrence of one theme was interpreted as an indication of limited exchange between these breeding assemblages, and we speculate that limited song similarity is due to inter‐oceanic interactions. Male(s) from an Indian Ocean breeding group could be exposed to novel song when they geographically overlap, and acoustically interact, with males from a different ocean basin. Novel song could induce rapid temporal changes as new song content is incorporated, thereby minimizing song similarities between that breeding group and other Indian Ocean breeding groups that were not exposed to the novel song.
Effects of research disturbance on the behavior and abundance of Steller sea lions (Eumetopias jubatus) at two rookeries in Alaska
Authors: Wilson Kenady , Fritz Lowell , Kunisch Erin , Chumbley Kathryn , Johnson Devin
Published: June 2011

Abstract

We examined the effects of research disturbance on the behavior and abundance of Steller sea lions (Eumetopias jubatus) at rookeries on Marmot and Ugamak Islands in Alaska. During 3 of 6 yr, researchers intentionally drove all adult and juvenile sea lions off at least part of the beach in order to permanently mark and measure sea lion pups. The research disturbance occurred after the majority of females had bred and when most pups were 1 mo old. We used generalized linear models to determine the relationship between research disturbance and sea lion behavior or abundance. Research disturbance was related to changes in the proportion of sea lions exhibiting two to three of nine behavior metrics: agonistic and resting females and active males at Marmot, and active and resting males and females at Ugamak. Model results indicated that changes lasted between 3 and 20 d depending on the sex, behavior, and rookery. Inclusion of research disturbance into Marmot abundance models did not improve the fit to the data, if variability between years was permitted. Optimally timed, low‐frequency research disturbance did not appear to have long‐term effects on sea lion behavior or abundance and was largely associated with changes that were similar to natural variation.
Bacterial and archaeal communities involved in the in situ degradation of 13C‐labelled straw in the rice rhizosphere
Authors: Shrestha Minita , Shrestha Pravin Malla , Conrad Ralf
Published: June 2011

Rice straw is a major substrate for the production of methane in flooded rice fields and results in increase of CH4 emission into the atmosphere. We investigated the bacteria and archaea involved in straw degradation by adding 13C‐labelled straw to the rhizosphere of planted rice microcosms in the greenhouse. The degradation of added straw resulted in the production of 13C‐labelled CH4 as end‐product, which was detected in the pore water. The incorporation of 13C into ribosomal RNA of Bacteria and Archaea present in the rhizospheric soil and on the roots was assessed by stable isotope probing (SIP) followed by terminal restriction fragment polymorphism (T‐RFLP) fingerprinting and cloning/sequencing of RNA fractions with different buoyant densities. Members of the Clostridium cluster I, III and XIVa were actively involved in straw degradation both in rhizospheric soil and on roots. However, on roots, Proteobacteria, Bacilli, Actinobacteria, Bacteroidetes and Chlorobi were also involved in the straw degradation process. Mostly Methanosarcina and to a less degree also Methanobacteriaceae were the dominant Archaea that assimilated straw‐derived carbon in the rhizospheric soil. Both Bacteria and Archaea together were most likely responsible for the conversion of rice straw to CH4. In conclusion, this study tackled the important and interesting issue of linking active microorganisms responsible for the straw degradation process to CH4 emission into the atmosphere.
Sustained virological response of patients with hepatitis C virus genotype 2 depends on pegylated interferon compliance
Authors: Watanabe Takao , Konishi Ichiro , Shigematsu Shuichiro , Uesugi Kazuhiro , Joko Kouji , Seike Hirotaka , Okada Shinichi , Miyaoka Hiroaki , Nakanishi Seiji , Abe Masanori , Matsuura Bunzo , Michitaka Kojiro , Horiike Norio , Hiasa Yoichi , Onji Morikazu
Published: June 2011

Aim:  Patients infected with hepatitis C virus (HCV) genotype 2 are more sensitive to interferon (IFN) therapy than those infected with genotype 1, but 10–20% of patients do not achieve a sustained viral response (SVR) to combination therapy with pegylated (PEG) IFN and ribavirin (RBV). This study examines the prognostic factors associated with SVR in patients infected with HCV genotype 2 treated with PEG IFN and RBV.

Methods:  We treated 149 patients with chronic hepatitis C caused by HCV genotype 2. The patients received s.c. PEG IFN‐α‐2b (1.5 µg/kg) and a weekly weight‐adjusted dose of RBV (600, 800 and 1000 mg per <60, 60–80 and >80 kg, respectively) for 24 weeks and then prognostic factors associated with the SVR were examined.

Results:  Among the 149 patients, 138 completed the combination therapy and a sustained viral response was achieved in 71.8% of them. Univariate analysis showed that age, as well as mean RBV and PEG IFN doses were factors affecting the SVR (P = 0.012, =0.021, =0.014). Multivariate analysis identified age and mean PEG IFN dose (P = 0.021, =0.018, respectively) as factors involved in the SVR, but not mean RBV dose.

Conclusion:  The SVR of patients infected with HCV genotype 2 depended on the dosage of PEG IFN, but not of RBV. Selecting sufficient doses of PEG IFN for combination with RBV is critical for treating such patients.
Molecular characteristics of non‐cancerous liver tissue in non‐B non‐C hepatocellular carcinoma
Authors: Utsunomiya Tohru , Shimada Mitsuo
Published: June 2011

Although chronic infection with hepatitis B virus (HBV) and/or hepatitis C virus (HCV) are the most important risk factors for the development of hepatocellular carcinoma (HCC) worldwide, the proportion of HCC patients negative for the hepatitis B surface antigen and hepatitis C antibody, so‐called “non‐B non‐C HCC”, is rapidly increasing, especially in Japan. The background liver diseases of non‐B non‐C HCC patients can be multifactorial, including occult HBV infection and non‐alcoholic steatohepatitis. It is reasonable to investigate the non‐cancerous liver tissues to identify the potential molecular mechanisms responsible for the processes of hepatocarcinogenesis of non‐B non‐C HCC. However, to date, only a few studies have focused on this research concept based on the idea of “field cancerization”. This review highlights the potential importance of the molecular analysis of non‐cancerous liver tissues to clarify the molecular characteristics in patients with non‐B non‐C HCC. A better understanding of the molecular mechanisms underlying the individual predisposition to non‐B non‐C HCC will lead to improvements in the prevention, early diagnosis and treatment of this neoplastic disease.
Therapeutic effects of the oriental herbal medicine Sho‐saiko‐to on liver cirrhosis and carcinoma
Authors: Lee Jun‐Kyoung , Kim Jung‐Hoon , Shin Hyeun Kyoo
Published: June 2011

The traditional Chinese herbal medicine Sho‐saiko‐to is a mixture of seven herbal preparations that has long been used in the treatment of chronic liver disease. Various clinical trials have shown that Sho‐saiko‐to protects against the development of hepatocellular carcinoma in cirrhotic patients. However, the mechanism by which Sho‐saiko‐to protects hepatocytes against hepatic fibrosis and carcinoma is not yet known. Basic science studies have demonstrated that Sho‐saiko‐to reduces hepatocyte necrosis and enhances liver function. Sho‐saiko‐to significantly inhibits hepatic fibrosis by inhibiting the activation of stellate cells, the major producers of collagen in the liver, as well as by inhibiting hepatic lipid peroxidation, promoting matrix degradation, and suppressing extracellular matrix (ECM) accumulation. Furthermore, clinical trials have shown that Sho‐saiko‐to lowers the rate of hepatocellular carcinoma (HCC) development in patients with cirrhosis and increases the survival of patients with HCC. Unfortunately, some case reports have shown the side effects of Sho‐saiko‐to. Most of the side effects were interstitial pneumonia and acute respiratory failure induced by Sho‐saiko‐to in Japan. As a result of analyzing these case reports, the incidence and risk are increased by co‐administration of interferon, duration of medication, and, high in an elderly population. This review discusses the properties of Sho‐saiko‐to with regards to the treatment of chronic liver diseases and suggests the side effects of Sho‐saiko‐to
So What Difference Does it Make? Mapping the Outcomes of Citizen Engagement
Authors: Gaventa John , Barrett Gregory
Published: June 2011

Over the last two decades, the idea that citizen engagement and participation can contribute to improved governance and development outcomes has been mainstreamed in development policy and discourse. Yet despite the normative beliefs that underpin this approach, the impact of participation on improved democratic and developmental outcomes has proved difficult to assess. Where previous research studies have attempted to demonstrate impact, they tend to be limited to single interventions, a small number of country contexts or by various conceptual and methodological constraints.

In this paper, we report on a meta‐case study analysis of a ten‐year research programme on citizenship, participation and accountability which analysed a non‐randomised sample of 100 research studies of four types of citizen engagement in 20 countries. By mapping the observable effects of citizen participation through a close reading of these studies, we created a typology of four democratic and developmental outcomes, including (a) the construction of citizenship, (b) the strengthening of practices of participation, (c) the strengthening of responsive and accountable states, and (d) the development of inclusive and cohesive societies.

We find that citizen participation produces positive effects across these outcome types, though in each category there are also examples of negative outcomes of citizen participation. We also find that these outcomes vary according to the type of citizen engagement and to political context. These findings have important implications for the design of and support for participatory programmes meant to improve state responsiveness and effectiveness.
On thinning of chains in MCMC
Authors: Link William A. , Eaton Mitchell J.
Published: June 2011

1. Markov chain Monte Carlo (MCMC) is a simulation technique that has revolutionised the analysis of ecological data, allowing the fitting of complex models in a Bayesian framework. Since 2001, there have been nearly 200 papers using MCMC in publications of the Ecological Society of America and the British Ecological Society, including more than 75 in the journal Ecology and 35 in the Journal of Applied Ecology.

2. We have noted that many authors routinely ‘thin’ their simulations, discarding all but every kth sampled value; of the studies we surveyed with details on MCMC implementation, 40% reported thinning.

3. Thinning is often unnecessary and always inefficient, reducing the precision with which features of the Markov chain are summarised. The inefficiency of thinning MCMC output has been known since the early 1990’s, long before MCMC appeared in ecological publications.

4. We discuss the background and prevalence of thinning, illustrate its consequences, discuss circumstances when it might be regarded as a reasonable option and recommend against routine thinning of chains unless necessitated by computer memory limitations.
Predicting Dynamic Barite Sag in Newtonian-Oil Based Drilling Fluids in Pipe
Authors: Nguyen Tan , Miska Stefan , Yu Mengjiao , Takach Nicholas
Published: June 2011

Barite Sag is the settling of barite particles in the wellbore (or other weighting materials), which results in undesirable fluctuations in drilling fluid density. A variety of major drilling problems including lost circulation, well control difficulties, poor cement jobs, and stuck pipe can result from uncontrolled barite sag. Study of this phenomenon and how to mitigate its effects has long been of interest. This paper describes a fundamental mathematical approach to analyze the settling of barite particles in shear flow of Newtonian fluids. A set of four coupled partial differential equations to describe dynamic barite sag in Newtonian fluids in pipe flow is obtained by applying mass and momentum conservation for solid and liquid phase. Solid concentration in axial and radial directions as a function of time is calculated by using an explicit numerical method to solve these equations. A number of experiments in a flow loop were conducted to verify the mathematical model. Two mass flow meters were installed at the inlet and outlet of the flow loop’s test section. Differences in the density measurements over time were converted to the solid accumulation, which was compared with results from the modeling. In addition, based on the experimental results, three different stages of barite accumulation due to the settling and bed pickup of barite particles during circulation will be presented. The proposed methodology and results of this study will help drillers have a better understanding in terms of undesirable density fluctuations and barite bed characteristics.
Temperature Control of a SOFC and MGT Hybrid System
Authors: Wu Xiao-Juan , Huang Qi , Zhu Xin-Jian , Zhang Chang-Hua
Published: June 2011

Transients in a load have a significant impact on the performance and durability of a solid oxide fuel cell (SOFC) integrated into a micro gas turbine (MGT) hybrid power system. One of the main reasons is that the SOFC operating temperature and turbine inlet temperature change drastically due to the load change. Therefore, in order to guarantee the temperature to operate within a specified range, an adaptive proportional-integral-derivative (PID) decoupling control strategy based on a dynamic radial basis function (RBF) neural network is presented to control the temperature of a natural gas fueled, tubular SOFC/MGT hybrid with internal reforming in this paper. Using the self-learning ability of the dynamic RBF neural network, the proportional, integral, and differential factor of the PID controller are tuned on-line. The simulation results show that it is feasible to build the adaptive PID decoupling controller for temperature control of the SOFC/MGT hybrid system.
Experimental Technique of Measuring Dynamic Fluid Shear Stress on the Aortic Surface of the Aortic Valve Leaflet
Authors: Yap Choon Hwai , Saikrishnan Neelakantan , Tamilselvan Gowthami , Yoganathan Ajit P.
Published: June 2011

Aortic valve (AV) calcification is a highly prevalent disease with serious impact on mortality and morbidity. The exact cause and mechanism of the progression of AV calcification is unknown, although mechanical forces have been known to play a role. It is thus important to characterize the mechanical environment of the AV. In the current study, we establish a methodology of measuring shear stresses experienced by the aortic surface of the AV leaflets using an in vitro valve model and adapting the laser Doppler velocimetry (LDV) technique. The valve model was constructed from a fresh porcine aortic valve, which was trimmed and sutured onto a plastic stented ring, and inserted into an idealized three-lobed sinus acrylic chamber. Valve leaflet location was measured by obtaining the location of highest back-scattered LDV laser light intensity. The technique of performing LDV measurements near to biological surfaces as well as the leaflet locating technique was first validated in two phantom flow systems: (1) steady flow within a straight tube with AV leaflet adhered to the wall, and (2) steady flow within the actual valve model. Dynamic shear stresses were then obtained by applying the techniques on the valve model in a physiologic pulsatile flow loop. Results show that aortic surface shear stresses are low during early systole (<5dyn/cm2) but elevated to its peak during mid to late systole at about 18–20 dyn/cm2. Low magnitude shear stress (<5dyn/cm2) was observed during early diastole and dissipated to zero over the diastolic duration. Systolic shear stress was observed to elevate only with the formation of sinus vortex flow. The presented technique can also be used on other in vitro valve models such as congenitally geometrically malformed valves, or to investigate effects of hemodynamics on valve shear stress. Shear stress data can be used for further experiments investigating effects of fluid shear stress on valve biology, for conditioning tissue engineered AV, and to validate numerical simulations.
Finite Element Lumbar Spine Facet Contact Parameter Predictions are Affected by the Cartilage Thickness Distribution and Initial Joint Gap Size
Authors: Woldtvedt Daniel J. , Womack Wesley , Gadomski Benjamin C. , Schuldt Dieter , Puttlitz Christian M.
Published: June 2011

Current finite element modeling techniques utilize geometrically inaccurate cartilage distribution representations in the lumbar spine. We hypothesize that this shortcoming severely limits the predictive fidelity of these simulations. Specifically, it is unclear how these anatomically inaccurate cartilage representations alter range of motion and facet contact predictions. In the current study, cadaveric vertebrae were serially sectioned, and images were taken of each slice in order to identify the osteochondral interface and the articulating surface. A series of custom-written algorithms were utilized in order to quantify each facet joint’s three-dimensional cartilage distribution using a previously developed methodology. These vertebrae-dependent thickness cartilage distributions were implemented on an L1 through L5 lumbar spine finite element model. Moments were applied in three principal planes of motion, and range of motion and facet contact predictions from the variable thickness and constant thickness distribution models were determined. Initial facet gap thickness dimensions were also parameterized. The data indicate that the mean and maximum cartilage thickness increased inferiorly from L1 to L5, with an overall mean thickness value of 0.57 mm. Cartilage distribution and initial facet joint gap thickness had little influence on the lumbar range of motion in any direction, whereas the mean contact pressure, total contact force, and total contact area predictions were altered considerably. The data indicate that range of motion predictions alone are insufficient to establish model validation intended to predict mechanical contact parameters. These data also emphasize the need for the careful consideration of the initial facet joint gap thickness with respect to the spinal condition being studied.
Optical transparency and electrical conductivity of nonstoichiometric ultrathin InxOy films
Authors: Joseph Shay , Berger Shlomo
Published: June 2011

The effect of thickness and composition on the electrical conductivity and optical transparency, mainly in the infrared, of ultrathin InxOy films was studied. InxOy films 35–470 Å thick with oxygen atomic fractions of ∼0.3 and ∼0.5 were prepared via dc magnetron sputtering. All films were polycrystalline, consisting of only the cubic bixbiyte phase of In2O3. The average grain size of the films increased from 30 to 95 nm as the film thickness increased. The weak dependence of the electrical conductivity on the frequency and the low activation energies for conduction, a few hundredths of an eV, provided an indication that free band conduction was the primary electrical conduction mechanism in the case of all ultrathin InxOy films. It was found that introducing a high degree of nonstoichiometry in the form of oxygen deficiency did not help improve the electrical conductivity, since not all vacancies contributed two free electrons for conduction and due to impurity scattering. The optical nature of these films, studied mainly by ellipsometry, was found to be dependent on the film’s composition and thickness. In the infrared, the dielectric function of all InxOy films was consistent with the Drude model, inferring that the transparency loss in this region was a result of free charge carriers. In the visible however, InxOy films under 170 Å, which had an oxygen atomic fraction of ∼0.5, were modeled by extending the Drude model to the shorter wavelengths. Films over 170 Å, with the same composition, were modeled using the Cauchy dispersion model, meaning that no absorption was measured. These results indicate that, optically, under specific compositions, ultrathin InxOy films undergo a transition from metalliclike behavior to dielectric behavior with increasing film thickness. Using a figure of merit approach, it was determined that a nonstoichiometric 230 Å thick InxOy film, with an oxygen atomic fraction of ∼0.3, had the best combination of conductivity and transparency, namely, absorption of less than 20% in the infrared, about 10% in the visible, and electrical resistance of only 230 Ω at 20 kHz. Such a film may be classified as a highly conductive transparent oxide even in the infrared.
Angular dependence of the nanoDot OSL dosimeter
Authors: Kerns James R. , Kry Stephen F. , Sahoo Narayan , Followill David S. , Ibbott Geoffrey S.
Published: June 2011

Purpose: Optically stimulated luminescent detectors (OSLDs) are quickly gaining popularity as passive dosimeters, with applications in medicine for linac output calibration verification, brachytherapy source verification, treatment plan quality assurance, and clinical dose measurements. With such wide applications, these dosimeters must be characterized for numerous factors affecting their response. The most abundant commercial OSLD is the InLight/OSL system from Landauer, Inc. The purpose of this study was to examine the angular dependence of the nanoDot dosimeter, which is part of the InLight system.Methods: Relative dosimeter response data were taken at several angles in 6 and 18 MV photon beams, as well as a clinical proton beam. These measurements were done within a phantom at a depth beyond the build‐up region. To verify the observed angular dependence, additional measurements were conducted as well as Monte Carlo simulations in MCNPX.Results: When irradiated with the incident photon beams parallel to the plane of the dosimeter, the nanoDot response was 4% lower at 6 MV and 3% lower at 18 MV than the response when irradiated with the incident beam normal to the plane of the dosimeter. Monte Carlo simulations at 6 MV showed similar results to the experimental values. Examination of the results in Monte Carlo suggests the cause as partial volume irradiation. In a clinical proton beam, no angular dependence was found.Conclusions: A nontrivial angular response of this OSLD was observed in photon beams. This factor may need to be accounted for when evaluating doses from photon beams incident from a variety of directions.
Management of the baseline shift using a new and simple method for respiratory‐gated radiation therapy: Detectability and effectiveness of a flexible monitoring system
Authors: Tachibana Hidenobu , Kitamura Nozomi , Ito Yasushi , Kawai Daisuke , Nakajima Masaru , Tsuda Akihisa , Shiizuka Hisao
Published: June 2011

Purpose: In respiratory‐gated radiation therapy, a baseline shift decreases the accuracy of target coverage and organs at risk (OAR) sparing. The effectiveness of audio‐feedback and audio‐visual feedback in correcting the baseline shift in the breathing pattern of the patient has been demonstrated previously. However, the baseline shift derived from the intrafraction motion of the patient's body cannot be corrected by these methods. In the present study, the authors designed and developed a simple and flexible system.Methods: The system consisted of a web camera and a computer running our in‐house software. The in‐house software was adapted to template matching and also to no preimage processing. The system was capable of monitoring the baseline shift in the intrafraction motion of the patient's body. Another marker box was used to monitor the baseline shift due to the flexible setups required of a marker box for gated signals. The system accuracy was evaluated by employing a respiratory motion phantom and was found to be within AAPM Task Group 142 tolerance (positional accuracy <2 mm and temporal accuracy <100 ms) for respiratory‐gated radiation therapy. Additionally, the effectiveness of this flexible and independent system in gated treatment was investigated in healthy volunteers, in terms of the results from the differences in the baseline shift detectable between the marker positions, which the authors evaluated statistically.Results: The movement of the marker on the sternum [1.599 ± 0.622 mm (1 SD)] was substantially decreased as compared with the abdomen [6.547 ± 0.962 mm (1 SD)]. Additionally, in all of the volunteers, the baseline shifts for the sternum [−0.136 ± 0.868 (2 SD)] were in better agreement with the nominal baseline shifts than was the case for the abdomen [−0.722 ± 1.56 mm (2 SD)]. The baseline shifts could be accurately measured and detected using the monitoring system, which could acquire the movement of the marker on the sternum. The baseline shift‐monitoring system with the displacement‐based methods for highly accurate respiratory‐gated treatments should be used to make most of the displacement‐based gating methods.Conclusions: The advent of intensity modulated radiation therapy and volumetric modulated radiation therapy facilitates margin reduction for the planning target volumes and the OARs, but highly accurate irradiation is needed to achieve target coverage and OAR sparing with a small margin. The baseline shifts can affect treatment not only with the respiratory gating system but also without the system. Our system can manage the baseline shift and also enables treatment irradiation to be undertaken with high accuracy.
Transient diffraction grating measurements of molecular diffusion in the undergraduate laboratory
Authors: Spiegel Daniel R. , Tuli Santona
Published: June 2011

Diffusion is a central process in many biological, chemical, and physical systems. We describe an experiment that employs the interference of laser beams to allow the measurement of molecular diffusion on submillimeter length scales. The interference fringes of two intersecting pump beams within a dye solution create a sinusoidal distribution of long-lived molecular excited states. A third probe beam is incident at a wavelength at which the indices of refraction of the ground and excited states are different, so the probe beam diffracts from the spatially periodic excited-state pattern. After the pump beams are switched off, the excited-state periodicity washes out as the system diffuses back to equilibrium. The molecular diffusion constant is obtained from the rate constant of the exponential decay of the diffracted beam. It is also possible to measure the excited-state lifetime.
The Gibbs paradox and the distinguishability of identical particles
Authors: Versteegh Marijn A. M. , Dieks Dennis
Published: June 2011

Identical classical particles are distinguishable. This distinguishability affects the number of ways W a macrostate can be realized on the microlevel, and from the relation S=k ln W leads to a nonextensive expression for the entropy. This result is usually considered incorrect because of its inconsistency with thermodynamics. It is sometimes concluded from this inconsistency that identical particles are fundamentally indistinguishable and that quantum mechanics is indispensable for making sense of this inconsistency. In contrast, we argue that the classical statistics of distinguishable particles and the resulting nonextensive entropy function are perfectly acceptable from both a theoretical and an experimental perspective. The inconsistency with thermodynamics can be removed by taking into account that the entropy concept in statistical mechanics is not completely identical to the thermodynamical one. We observe that even identical quantum particles are in some cases distinguishable, and conclude that quantum mechanics is irrelevant to the Gibbs paradox.
β-Glucuronidase as a Sensitive and Versatile Reporter in Actinomycetes
Authors: Myronovskyi Maksym , Welle Elisabeth , Fedorenko Viktor , Luzhetskyy Andriy
Published: June 2011

Here we describe a versatile and sensitive reporter system for actinomycetes that is based on
gusA
, which encodes the β-glucuronidase enzyme. A series of
gusA-
containing transcriptional and translational fusion vectors were constructed and utilized to study the regulatory cascade of the phenalinolactone biosynthetic gene cluster. Furthermore, these vectors were used to study the efficiency of translation initiation at the ATG, GTG, TTG, and CTG start codons. Surprisingly, constructs using a TTG start codon showed the best activity, whereas those using ATG or GTG were approximately one-half or one-third as active, respectively. The CTG fusion showed only 5% of the activity of the TTG fusion. A suicide vector, pKGLP2, carrying
gusA
in its backbone was used to visually detect merodiploid formation and resolution, making gene targeting in actinomycetes much faster and easier. Three regulatory genes,
plaR1
,
plaR2
, and
plaR3
, involved in phenalinolactone biosynthesis were efficiently replaced with an apramycin resistance marker using this system. Finally, we expanded the genetic code of actinomycetes by introducing the nonproteinogenic amino acid
N
-epsilon-cyclopentyloxycarbonyl-
l
-lysine with the GusA protein as a reporter.
Novel Family of Carbohydrate-Binding Modules Revealed by the Genome Sequence of Spirochaeta thermophila DSM 6192
Authors: Angelov Angel , Loderer Christoph , Pompei Susanne , Liebl Wolfgang
Published: June 2011

Spirochaeta thermophila
is a thermophilic, free-living, and cellulolytic anaerobe. The genome sequence data for this organism have revealed a high density of genes encoding enzymes from more than 30 glycoside hydrolase (GH) families and a noncellulosomal enzyme system for (hemi)cellulose degradation. Functional screening of a fosmid library whose inserts were mapped on the
S. thermophila
genome sequence allowed the functional annotation of numerous GH open reading frames (ORFs). Seven different GH ORFs from the
S. thermophila
DSM 6192 genome, all putative β-glycanase ORFs according to sequence similarity analysis, contained a highly conserved novel GH-associated module of unknown function at their C terminus. Four of these GH enzymes were experimentally verified as xylanase, β-glucanase, β-glucanase/carboxymethylcellulase (CMCase), and CMCase. Binding experiments performed with the recombinantly expressed and purified GH-associated module showed that it represents a new carbohydrate-binding module (CBM) that binds to microcrystalline cellulose and is highly specific for this substrate. In the course of this work, the new CBM type was only detected in
Spirochaeta
, but recently we found sequences with detectable similarity to the module in the draft genomes of
Cytophaga fermentans
and
Mahella australiensis
, both of which are phylogenetically very distant from
S. thermophila
and noncellulolytic, yet inhabit similar environments. This suggests a possibly broad distribution of the module in nature.
Evidence of Burkholderia pseudomallei-Specific Immunity in Patient Sera Persistently Nonreactive by the Indirect Hemagglutination Assay
Authors: Harris Patrick N. A. , Williams Natasha L. , Morris Jodie L. , Ketheesan Natkunam , Norton Robert E.
Published: June 2011

The indirect hemagglutination assay (IHA) is the most frequently used serological test to confirm exposure toBurkholderia pseudomallei. Patients with culture-confirmed disease often have a nonreactive IHA at presentation and occasionally fail to seroconvert on serial testing. We investigated whether using antigens derived from the cultured isolates of persistently IHA-nonreactive patient sera improved the sensitivity of the IHA. In addition, we assessed the antigen-specific lymphocyte response in this group of patients to a panel ofB. pseudomalleiantigens, including those derived from their own cultured isolates. Eleven patients with culture-proven melioidosis were identified as having persistently IHA-nonreactive sera. A modified IHA using erythrocytes sensitized with patient isolate-derived antigen tested against convalescent-phase serum was performed. The majority (82%) of sera showed a negative (≤1:5) result, one was borderline (1:20), and one was positive at the cutoff value (1:40). IHA-nonreactive sera were also tested by enzyme immunoassay (EIA), with 73% (8/11) demonstrating IgG positivity. In addition, lymphocytes isolated from persistently IHA-nonreactive patient sera demonstrated significantly increased proliferation in response toB. pseudomalleiantigens compared to controls. These studies demonstrate the presence ofB. pseudomallei-specific antibody by EIA andB. pseudomallei-specific lymphocytes in patient sera categorized as persistently nonreactive according to the IHA. New immunoassays are required and should incorporateB. pseudomalleiantigens that are immunoreactive for this subset of IHA-nonreactive patient sera.
Functional Dissection of a Candida albicans Zinc Cluster Transcription Factor, the Multidrug Resistance Regulator Mrr1
Authors: Schubert Sabrina , Popp Christina , Rogers P. David , Morschhäuser Joachim
Published: June 2011

The overexpression of the
MDR1
gene, which encodes a multidrug efflux pump of the major facilitator superfamily, is a frequent cause of resistance to the widely used antimycotic agent fluconazole and other toxic compounds in the pathogenic yeast
Candida albicans
. The zinc cluster transcription factor Mrr1 controls
MDR1
expression in response to inducing chemicals, and gain-of-function mutations in
MRR1
are responsible for the constitutive
MDR1
upregulation in fluconazole-resistant
C. albicans
strains. To understand how Mrr1 activity is regulated, we identified functional domains of this transcription factor. A hybrid protein consisting of the N-terminal 106 amino acids of Mrr1 and the transcriptional activation domain of Gal4 from
Saccharomyces cerevisiae
constitutively induced
MDR1
expression, demonstrating that the DNA binding domain is sufficient to target Mrr1 to the
MDR1
promoter. Using a series of C-terminal truncations and systematic internal deletions, we could show that Mrr1 contains multiple activation and inhibitory domains. One activation domain (AD1) is located in the C terminus of Mrr1. When fused to the tetracycline repressor TetR, this distal activation domain induced gene expression from a TetR-dependent promoter. The deletion of an inhibitory region (ID1) located near the distal activation domain resulted in constitutive activity of Mrr1. The additional removal of AD1 abolished the constitutive activity, but the truncated Mrr1 still could activate the
MDR1
promoter in response to the inducer benomyl. These results demonstrate that the activity of Mrr1 is regulated in multiple ways and provide insights into the function of an important mediator of drug resistance in
C. albicans
.
Alterations in the β Flap and β′ Dock Domains of the RNA Polymerase Abolish NusA-Mediated Feedback Regulation of the
metY
-
nusA
-
infB
Operon
Authors: Bylund Göran O. , Nord Stefan , Lövgren J. Mattias , Wikström P. Mikael
Published: June 2011

The RimM protein in
Escherichia coli
is important for the
in vivo
maturation of 30S ribosomal subunits and a Δ
rimM
mutant grows poorly due to assembly and translational defects. These deficiencies are suppressed partially by mutations that increase the synthesis of another assembly protein, RbfA, encoded by the
metY-nusA-infB
operon. Among these suppressors are mutations in
nusA
that impair the NusA-mediated negative-feedback regulation at internal intrinsic transcriptional terminators of the
metY-nusA-infB
operon. We describe here the isolation of two new mutations, one in
rpoB
and one in
rpoC
(encoding the β and β′ subunits of the RNA polymerase, respectively), that increase the synthesis of RbfA by preventing NusA from stimulating termination at the internal intrinsic transcriptional terminators of the
metY-nusA-infB
operon. The
rpoB2063
mutation changed the isoleucine in position 905 of the β flap-tip helix to a serine, while the
rpoC2064
mutation duplicated positions 415 to 416 (valine-isoleucine) at the base of the β′ dock domain. These findings support previously published
in vitro
results, which have suggested that the β flap-tip helix and β′ dock domain at either side of the RNA exit tunnel mediate the binding to NusA during transcriptional pausing and termination.
Crystal Structure of Bacillus anthracis Phosphoglucosamine Mutase, an Enzyme in the Peptidoglycan Biosynthetic Pathway
Authors: Mehra-Chaudhary Ritcha , Mick Jacob , Beamer Lesa J.
Published: June 2011

Phosphoglucosamine mutase (PNGM) is an evolutionarily conserved bacterial enzyme that participates in the cytoplasmic steps of peptidoglycan biosynthesis. As peptidoglycan is essential for bacterial survival and is absent in humans, enzymes in this pathway have been the focus of intensive inhibitor design efforts. Many aspects of the structural biology of the peptidoglycan pathway have been elucidated, with the exception of the PNGM structure. We present here the crystal structure of PNGM from the human pathogen and bioterrorism agent
Bacillus anthracis
. The structure reveals key residues in the large active site cleft of the enzyme which likely have roles in catalysis and specificity. A large conformational change of the C-terminal domain of PNGM is observed when comparing two independent molecules in the crystal, shedding light on both the apo- and ligand-bound conformers of the enzyme. Crystal packing analyses and dynamic light scattering studies suggest that the enzyme is a dimer in solution. Multiple sequence alignments show that residues in the dimer interface are conserved, suggesting that many PNGM enzymes adopt this oligomeric state. This work lays the foundation for the development of inhibitors for PNGM enzymes from human pathogens.
Draft Genome Sequence of the Thermoalkaliphilic Caldalkalibacillus thermarum Strain TA2.A1
Authors: Kalamorz Falk , Keis Stefanie , McMillan Duncan G. G. , Olsson Karen , Stanton Jo-Ann , Stockwell Peter , Black Mik A. , Klingeman Dawn M. , Land Miriam L. , Han Cliff S. , Martin Stanton L. , Becher S. Anette , Peddie Catherine J. , Morgan Hugh W. , Matthies Doreen , Preiß Laura , Meier Thomas , Brown Steven D. , Cook Gregory M.
Published: June 2011

The genes and molecular machines that allow for a thermoalkaliphilic lifestyle have not been defined. To address this goal, we report on the improved high-quality draft genome sequence of
Caldalkalibacillus thermarum
strain TA2.A1, an obligately aerobic bacterium that grows optimally at pH 9.5 and 65 to 70°C on a wide variety of carbon and energy sources.
Genome Sequence of the Chlamydophila abortus Variant Strain LLG
Authors: Sait Michelle , Clark Ewan M. , Wheelhouse Nick , Livingstone Morag , Spalding Lucy , Siarkou Victoria I. , Vretou Evangelia , Smith David G. E. , Lainson F. Alex , Longbottom David
Published: June 2011

Chlamydophila abortus
is a common cause of ruminant abortion. Here we report the genome sequence of strain LLG, which differs genotypically and phenotypically from the wild-type strain S26/3. Genome sequencing revealed differences between LLG and S26/3 to occur in pseudogene content, in transmembrane head/inc family proteins, and in biotin biosynthesis genes.