bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of metabolic alterations in Arabidopsis following changes in the carbon dioxide and oxygen partial pressures
Authors: Florian Alexandra , Timm Stefan , Nikoloski Zoran , Tohge Takayuki , Bauwe Hermann , Araújo Wagner L. , Fernie Alisdair R.
Published: July 2014

As sessile organisms, plants are subject to a multitude of environmental variations including several which directly affect their interaction with the atmosphere. Given the indiscriminant nature of Rubisco, the relative rates of photosynthesis and photorespiration are known to be responsive to changes in gas composition. However, comprehensive profiling methods have not yet been applied in order to characterize the wider consequences of these changes on primary metabolism in general. Moreover, although transcriptional profiling has revealed that a subset of photorespiratory enzymes are co‐expressed, whether transcriptional responses play a role in short‐term responses to atmospheric compositional changes remains unknown. To address these questions, plants Arabidopsis thaliana (Arabidopsis) ecotype Columbia (Col‐O) grown under normal air conditions were transferred to different CO2 and O2 concentrations and characterized at the physiological, molecular, and metabolic levels following this transition. The results reveal alterations in the components, which are directly involved in, or supporting, photorespiration, including transcripts and metabolite levels. The results further highlight that the majority of the regulation of these pathways is not mediated at the level of transcription and that the photorespiratory pathway is essential also in conditions in which flux through the pathway is minimized, yet suggest that flux through this pathway is not mediated at the level of transcription.
Accessing osteocyte lacunar geometrical properties in human jaw bone on the submicron length scale using synchrotron radiation μCT
Authors: HESSE BERNHARD , MÄNNICKE NILS , PACUREANU ALEXANDRA , VARGA PETER , LANGER MAX , MAURER PETER , PEYRIN FRANCOISE , RAUM KAY
Published: July 2014

The architectural properties of the osteocyte cell network provide a valuable basis for understanding the mechanisms of bone remodelling, mineral homeostasis, ageing and pathologies. Recent advances in synchrotron microtomography enable unprecedented three‐dimensional imaging of both the bone lacunar network and the extracellular matrix. Here, we investigate the three‐dimensional morphological properties of osteocyte lacunae in human healthy and bisphosphonate‐related osteonecrotic jaw bone based on synchrotron X‐ray computed tomography images, with a spatial isotropic voxel size of 300 nm. Bisphosphonate‐related osteonecrosis of the jaw is a relatively new disease with increasing incidence, which remains poorly understood. A step forward in elucidating this malady is to assess whether, and how, the morphology of the osteocyte lacunar network is modified in the affected jaw tissue. We evaluate thousands of cell lacunae from five specimens of which three originate from patients diagnosed with bisphosphonate‐associated osteonecrosis. In this exploratory study, we report three‐dimensional quantitative results on lacunar volumes (296–502 μm3), shape (approximated by an ellipsoidal shape with principal axes a > b > c, such that a = 2.2b and a = 4c) and spatial distribution (i.e., 50% of the mineralized matrix volume is located within 12 μm to the closest lacunar boundary) at submicron resolution on such specimens. We observe that the average lacunar volumes of the bisphosphonate‐related osteonecrotic jaw specimens were within the range of volumes found in the two specimens originating from healthy donors and conclude that lacunar volumes are not the key element in the course of bisphosphonate‐related osteonecrotic jaw. In three out of five specimens we observe lacunar volume sizes in segmented osteons to be significantly different compared to lacunar volumes in the adjacent tissue regions. Furthermore, we quantify the number of lacunae containing small dense objects (on average 9%). In contrast to lacunar morphology we report the lacunar density (16 000–50 000 per mm3) to be different in jaw bone tissue compared to what has been reported in femoral sites.
Competition for pollination by the lesser short‐tailed bat and its influence on the flowering phenology of some New Zealand endemics
Authors: Cummings G. , Anderson S. , Dennis T. , Toth C. , Parsons S.
Published: July 2014

The lesser short‐tailed bat, Mystacina tuberculata, is the only native mammalian pollinator in New Zealand and the only fully temperate bat pollinator in the world. Although this unique status as a pollinator is well recognized, its reduced abundance and cryptic behaviour means little research has been undertaken to assess the contribution of the lesser short‐tailed bat (hereafter ‘short‐tailed bat’) to pollination in New Zealand. Accordingly, pollination by short‐tailed bats has been assumed to be comparatively inconsequential, and the potential impacts of the bat's widespread extirpation have been overlooked. The recent discovery that the short‐tailed bat is a major pollinator for at least some of the plants it visits emphasizes the importance of exploring this species' role as a pollinator. Here, our aim was to provide an assessment of the competition for short‐tailed bat pollination through study of the temporal variation of flowering. Bats were sampled for pollen, and phenology surveys were conducted simultaneously. We found that the amount and type of pollen carried by the bats varied temporally, with one pollen type dominating samples at any given time. The two plants most consistently observed in the pollen samples flowered sequentially with little temporal overlap, suggesting that their flowering phenology may be adapted to minimize competition for the pollination services of the short‐tailed bat.
Sparse Principal Component Analysis in Hilbert Space
Authors: Qi Xin , Luo Ruiyan
Published: July 2014

Technical advances in many areas have produced more complicated high‐dimensional data sets than the usual high‐dimensional data matrix, such as the fMRI data collected in a period for independent trials, or expression levels of genes measured in different tissues. Multiple measurements exist for each variable in each sample unit of these data. Regarding the multiple measurements as an element in a Hilbert space, we propose Principal Component Analysis (PCA) in Hilbert space. The principal components (PCs) thus defined carry information about not only the patterns of variations in individual variables but also the relationships between variables. To extract the features with greatest contributions to the explained variations in PCs for high‐dimensional data, we also propose sparse PCA in Hilbert space by imposing a generalized elastic‐net constraint. Efficient algorithms to solve the optimization problems in our methods are provided. We also propose a criterion for selecting the tuning parameter.
Dual Band Slot Antenna for 3.5 WiMAX and 5.8 WLAN
Authors: Chagharvand Sahar , Hamid M. R. B. , Kamarudin M. R. , Khalily Mohsen
Published: July 2014

This paper presents a single layer planar slot antenna for dual band operation. The antenna is fed by a coplanar waveguide (CPW) with two inverted C-shaped resonators to achieve the dual band operation. The impedance bandwidth for ǀS11ǀ < -10dB is 14% in lower band and 7% in higher band. The antenna prototype’s electromagnetic performance, impedance bandwidth, radiation pattern, and antenna gain were measured. The proposed configuration offers a relatively compact, easy to fabricate and dual band performance providing gain between 2 and 4 dBi. The designed antenna has good dual bandwidth covering 3.5 WiMAX and 5.8 WLAN tasks. Experimental and numerical results also showed good agreement after comparison.
Constructing an Adoption Model for e-Government Services
Authors: Shajari Maziar , Ismail Zuraini
Published: July 2014

The frequent use of e-Government services and the ability of the government to successfully implement e-Government to match the needs of the citizens remain to be understood. The purpose of this study is to construct an adoption model for the e-Government services by considering renowned technology adoption models. This model considered trustworthiness in shaping the adoption model. To test the model, questionnaire was designed, adapted from previous studies which were distributed to employees of public organizations in Esfahan, Iran. The proposed model was thoroughly analyzed using Structured Equation Modeling (SEM). The new adoption model modified and the final model consist of ten constructs including intention to use, trustworthiness, perceived usefulness, perceived ease of use, compatibility, social influence, job relevant, output quality, and image. The results affirmed that relationships between the model variables suggested good model fit. The fitted model of this study may be applied to other e-Government services of other countries.
Development of Training Kit for Learning Taguchi Method and Design of Experiments
Authors: Jamaluddin Haris , A. Ghani Jaharah , Ab. Rahman Mohd Nizam , Md. Deros Baba
Published: July 2014

This study focused on designing a training kit for learning design of experiment (DoE). A model has been established to provide a platform and facilities to conduct design of experiment. A system of ball rolling on a designated track has been made to fulfill this objective. Several factors could be set up to conduct real experiments repetitively. To verify the feasibility of this training kit, four different kind of experiments have been used to test the reliability of the factors levels and their response quality characteristics. Taguchi L8 and L9 matrices are used to find the optimum response time for a ball to complete the full travelling cycle, with quality objective of smaller the better, the conducted experiments achieved some results between Taguchi and Factorial designs that were used to confirm the experiments. The corresponded travelling time for Taguchi experiment and experimental solution of 24 factorial designs are 11.25 s and 11.43 s respectively, both falls within 90% confidence interval.
Dynamic Response Optimization for Cemented Carbide Injection Molding
Authors: M. Amin Sri Yulis , Muhamad Norhamidi , Jamaludin Khairur Rijal
Published: July 2014

The need to optimize the injection molding parameters for producing cemented carbide parts via Metal Injection Molding process is crucial to ensure the system’s robustness towards manufacturer and customer’s satisfactions. Defect free product with best density can be produced while reducing time and cost in manufacturing. In this work, the feedstock consisting of WC-Co powders, mixed with palm stearin and polyethylene binder system was injection molded to produce green parts. Several processing variables, namely powder loading, injection temperature, holding pressure and flowrate, were optimized towards the density of the green body, as the response factor. By considering humidity level at morning and evening conditions as the noise factor, the results show the optimum combination of injection molding parameters that produces best green density. The green part exhibited best density by following this optimum processing parameters, A2B3C1D1, that are flowrate at 20 ccm/s, powder loading at 63% vol., injection temperature at 140°C, and holding pressure at 1700 bar.
Optimization of 67% Powder Loading Co-30Cr-6Mo µMIM Part by Taguchi Method
Authors: Wahi Azizah , Muhamad Norhamidi , Zakaria Hafizawati
Published: July 2014

This research studies the effect of injection moulding parameters on the density of green body of Cobalt-30Chromium-6Molybdenum (Co-30Cr-6Mo) for powder injection moulding (PIM) feedstock. In this paper 20 micron Co-Cr-Mo powder was mixed with a palm stearin and polyethylene binder system. L18 orthogonal array by Taguchi Method was used to optimize and predict the future performance. Several injection parameters were optimized such as injection temperature, holding pressure, injection temperature, and mould temperature and injection time. The result shows that the optimum combination of these parameters will produce higher density micro parts. The optimum parameters for 67% powder loading of 20µm Co-30Cr-6Mo powder is 180oC injection temperature, while injection pressure, mold temperature, packing time and injection time are 10 bar, 100oC, 5 s and 7 s respectively.
Precipitation of Cellulase and Xylanase for Cross-Linked Enzyme Aggregates
Authors: Sulaiman Nurul Jannah , A. Rahman Roshanida , Ngadi Norzita
Published: July 2014

Cross-linked enzyme aggregate is a promising strategy among other enzyme immobilization technologies such as solid matrix linking and gel entrapping. Despite of having the advantage of being reused, cross-linked enzyme aggregate (CLEA) also offers greater stability during operation and storage. Preparation of CLEA involves two steps which are precipitation and cross-linking of the enzymes. The purpose of this study is to find the best precipitant for cross-linked enzyme aggregate of cellulase and xylanase. The tested precipitants were acetone, ammonium sulphate, dimethoxyethane (DME), n-propanol, polyethyleneglycol (PEG), and tert-butanol. The enzymes were precipitated and cross-linked using glutaraldehyde. The enzyme activities were determined through DNS method and the relative activities for resulted CLEA were compared. It was found that PEG was the best precipitant for CLEA-cellulase while DME, ammonium sulphate and tert-butanol contributed the highest activity retention for CLEA-cellulase-xylanase under cellulase and xylanase assay, and CLEA-xylanase, respectively.
MR-deDuster: A Dust Emission Separator in Air Pollution Control
Authors: Norelyza H. , Rashid M. , Hajar S. , Nurnadia A.
Published: July 2014

There are many technologies developed to control dust emission in industry. A multi-cyclones separator is one of the commonly available technologies for dust emission control from a gas stream. However, it is usually used as a pre-cleaner unit installed prior to a more efficient air pollution control system such as fabric filters or baghouse. In this respect, a study has been carried out to investigate and theoretically predict the performance of a MR-deDuster, a newly developed multi-cyclones dust emission separator system. The MR-deDuster performance was measured by its collection efficiency based on the particle size distribution of two selected adsorbent material commonly used as flue gas cleaning agent, i.e., lime and activated carbon, as a representative of dust particles. The study illustrates that the unit manages to capture dust sized 2.4µm at 50% collection efficiency with reasonably low pressure drop. The unit also capable of achieving more than 95% total dust collection efficiency for all dust tested.
Optimization of Protein Extraction from Fermented and Non Fermented Perah Seed by using Response Surface Methodology
Authors: Mazlan Hamimah Satirah , Muhamad , Ida Idayu , Hassan Nor Diana , Hadi Tan Nuraimi Azlan
Published: July 2014

The optimum protein extraction from fermented and non-fermented Perah seed (Elateriospermumtapos) was investigated using the response surface methodology (RSM). A box-behnken design with three independent variables which are NaOH concentration (6, 8 and 10%), extraction time (10, 20 and 30 minutes) and solvent/meal ratio (50:1, 100:1 and 150:1, v/w) was used to study the response of protein yield. A second-degree equation for independent and response variables was produced from simulation to obtain the contour plot graphs. The best protein extraction procedure from both fermented and non-fermented Perah seed was obtained at 5.5% of solvent extraction, 40:1 ratio of solvent/meal and at 32 minutes of reaction time. Surface concentration and ratio of solvent/meal were found to influence the protein yield from fermented seed; meanwhile only the solvent concentration influenced protein yield from non-fermented seed. The maximum protein yields for both fermented and non-fermented Perah seeds were 18.0 g/100g and 5.0 g/100g seed meal respectively.
Plants in Antarctica: Current and Future Phytoremediation Potential
Authors: Abd Manan Fazilah , Ibrahim Zaharah , Shahir Shafinaz
Published: July 2014

As an extremely cold, dry and windy part of the world, Antarctica is a unique continent that can only be inhabit by limited number of organisms. For a long time, Antarctica was a pristine area. But nowadays, it has been invaded with many kinds of pollutants derived from human activities such as solid, liquid and metal wastes. To prevent further deterioration in Antarctic environment, remediation process is strongly needed. Phytoremediation is an environmentally clean technique to remove pollutants using plants. This is an alternative to the current physical and chemical remediation method. The success of phytoremediation technique is influenced by plant species and various environmental parameters. Unlike in the temperate and tropical region, an extremely low temperature in Antarctica does not permit the growth of many types of vegetations. Thus, phytoremediation process is scarce. Despite this limitation, there are growing interests among scientists to investigate the potential of phytoremediation to occur in tremendously harsh condition. This paper reviews current pollution problems in the Antarctic region and the possibility of phytoremediation technique to be implemented in this continent.
The Effects of Nanoparticle Addition in Bi-2212 Superconductors
Authors: Suazlina M. A. , Yusainee S. Y. S. , Azhan H. , Abd-Shukor R. , Mustaqim R. M.
Published: July 2014

The effect of Y2O3 nanoparticle addition on the superconducting properties of Bi1.6Pb0.4Sr 2CaCu 2Oy have been investigated. The samples were prepared using high purity oxide powders via solid state reaction method. Y2O3 nanoparticle with 0.0-1.0 wt. % was systematically added to the well balanced Bi1.6Pb0.4 Sr2CaCu2Oy before sinter in order to trace the existense of nanoparticle addition in the system. The samples were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM) and critical current density, Jc. The current density measurement was done via four-point probe method under zero magnetic fields. The critical current density, Jc and superconductivity transition temperature, Tc for sample with addition of Y2O3 nanoparticle were found to be higher than the pure sample. The optimal addition of Y2O3 nanoparticle to the sample Bi-2212 system was found at 0.7 wt. %. The crystallographic structure of all samples was evidenced to be orthorhombic where a ≠ b ≠ c. Changes in superconducting properties of Y2O3 nanoparticle added Bi-2212 system were discussed.
A Review of Fingerprint Image Pre-processing
Authors: Abbood Alaa Ahmed , Sulong Ghazali , U. Peters Sabine
Published: July 2014

Fingerprints are the most widely used form of human identification and verification due to their uniqueness and permanence. For that reason, many Automatic Fingerprint Identification Systems (AFIS) have been commercially produced and accepted by the international community. Though their performance is good, there is still room for improvement. One of the main concerns is poor fingerprint images that are caused by capturing devices. Thus, to improve the efficiency of AFIS, both image enhancement and feature extraction methods are required to be implemented. An effective feature extraction depends on the quality of its image whereby high image quality would normally produce genuine features. On the other hand, poor quality would lead to fake features that will result in false acceptance. This paper reviews several state-of-the-art methods of fingerprint image pre-processing including gray level normalization, noise removal and segmentation.
Computerized detection of noncalcified plaques in coronary CT angiography: Evaluation of topological soft gradient prescreening method and luminal analysis
Authors: Wei Jun , Zhou Chuan , Chan Heang‐Ping , Chughtai Aamer , Agarwal Prachi , Kuriakose Jean , Hadjiiski Lubomir , Patel Smita , Kazerooni Ella
Published: July 2014

Purpose:

The buildup of noncalcified plaques (NCPs) that are vulnerable to rupture in coronary arteries is a risk for myocardial infarction. Interpretation of coronary CT angiography (cCTA) to search for NCP is a challenging task for radiologists due to the low CT number of NCP, the large number of coronary arteries, and multiple phase CT acquisition. The authors conducted a preliminary study to develop machine learning method for automated detection of NCPs in cCTA.

Methods:

With IRB approval, a data set of 83 ECG‐gated contrast enhanced cCTA scans with 120 NCPs was collected retrospectively from patient files. A multiscale coronary artery response and rolling balloon region growing (MSCAR‐RBG) method was applied to each cCTA volume to extract the coronary arterial trees. Each extracted vessel was reformatted to a straightened volume composed of cCTA slices perpendicular to the vessel centerline. A topological soft‐gradient (TSG) detection method was developed to prescreen for NCP candidates by analyzing the 2D topological features of the radial gradient field surface along the vessel wall. The NCP candidates were then characterized by a luminal analysis that used 3D geometric features to quantify the shape information and gray‐level features to evaluate the density of the NCP candidates. With machine learning techniques, useful features were identified and combined into an NCP score to differentiate true NCPs from false positives (FPs). To evaluate the effectiveness of the image analysis methods, the authors performed tenfold cross‐validation with the available data set. Receiver operating characteristic (ROC) analysis was used to assess the classification performance of individual features and the NCP score. The overall detection performance was estimated by free response ROC (FROC) analysis.

Results:

With our TSG prescreening method, a prescreening sensitivity of 92.5% (111/120) was achieved with a total of 1181 FPs (14.2 FPs/scan). On average, six features were selected during the tenfold cross‐validation training. The average area under the ROC curve (AUC) value for training was 0.87 ± 0.01 and the AUC value for validation was 0.85 ± 0.01. Using the NCP score, FROC analysis of the validation set showed that the FP rates were reduced to 3.16, 1.90, and 1.39 FPs/scan at sensitivities of 90%, 80%, and 70%, respectively.

Conclusions:

The topological soft‐gradient prescreening method in combination with the luminal analysis for FP reduction was effective for detection of NCPs in cCTA, including NCPs causing positive or negative vessel remodeling. The accuracy of vessel segmentation, tracking, and centerline identification has a strong impact on NCP detection. Studies are underway to further improve these techniques and reduce the FPs of the CADe system.
Age-Related Loss of Muscle Mass, Strength, and Power and Their Association With Mobility in Recreationally-Active Older Adults in the United Kingdom
Authors: Maden-Wilkinson Thomas M. , McPhee Jamie S. , Jones David A. , Degens Hans
Published: July 2014

To investigate reasons for the age-related reduction in physical function, we determined the relationships between muscle size, strength, and power with 6-min walk distance (6MWD) and timed up-and-go performance in 49 young (23 ± 3.1 years) and 66 healthy, mobile older adults (72 ± 5 years). While muscle mass, determined by DXA and MRI, did not correlate with performance in the older adults, power per body mass, determined from a countermovement jump, did correlate. The 40% lower jumping power observed in older adults (p < .05) was due to a lower take-off velocity, which explained 34% and 42% of the variance in 6MWD in older women and men, respectively (p < .01). The lower velocity was partly attributable to the higher body mass to maximal force ratio, but most was due to a lower intrinsic muscle speed. While changes in muscle function explain part of the age-related reduction in functional performance, ~60% of the deficit remains to be explained.
Conceptualization and Measurement of Fan Engagement: Empirical Evidence From a Professional Sport Context
Authors: Yoshida Masayuki , Gordon Brian , Nakazawa Makoto , Biscaia Rui
Published: July 2014

In the sport management literature, limited attention has been devoted to the conceptualization and measurement of fan engagement. Two quantitative studies were completed to validate the proposed fan-engagement scale composed of three defining elements (management cooperation, prosocial behavior, and performance tolerance). The results from Study 1 provide evidence of convergent and discriminant validity for the threefactor model of fan engagement. In Study 2, we assess nomological validity by examining the antecedents and consequences of fan engagement and found that team identification and basking in reflected glory played a particularly important role in increasing the three dimensions of fan engagement. Furthermore, the results indicate that performance tolerance has a positive effect on purchase intention. These findings highlight the importance of the sequential relationships between team identification, performance tolerance, and purchase intention.
New Insight into the Mechanism of Accumulation and Intraerythrocytic Compartmentation of Albitiazolium, a New Type of Antimalarial
Authors: Wein Sharon , Tran Van Ba Christophe , Maynadier Marjorie , Bordat Yann , Perez Julie , Peyrottes Suzanne , Fraisse Laurent , Vial Henri J.
Published: July 2014

Bis-thiazolium salts constitute a new class of antihematozoan drugs that inhibit parasite phosphatidylcholine biosynthesis. They specifically accumulate in
Plasmodium
- and
Babesia
-infected red blood cells (IRBC). Here, we provide new insight into the choline analogue albitiazolium, which is currently being clinically tested against severe malaria. Concentration-dependent accumulation in
P. falciparum
-infected erythrocytes reached steady state after 90 to 120 min and was massive throughout the blood cycle, with cellular accumulation ratios of up to 1,000. This could not occur through a lysosomotropic effect, and the extent did not depend on the food vacuole pH, which was the case for the weak base chloroquine. Analysis of albitiazolium accumulation in
P. falciparum
IRBC revealed a high-affinity component that was restricted to mature stages and suppressed by pepstatin A treatment, and thus likely related to drug accumulation in the parasite food vacuole. Albitiazolium also accumulated in a second high-capacity component present throughout the blood cycle that was likely not related to the food vacuole and also observed with
Babesia divergens
-infected erythrocytes. Accumulation was strictly glucose dependent, drastically inhibited by H
+
/K
+
and Na
+
ionophores upon collapse of ionic gradients, and appeared to be energized by the proton-motive force across the erythrocyte plasma membrane, indicating the importance of transport steps for this permanently charged new type of antimalarial agent. This specific, massive, and irreversible accumulation allows albitiazolium to restrict its toxicity to hematozoa-infected erythrocytes. The intraparasitic compartmentation of albitiazolium corroborates a dual mechanism of action, which could make this new type of antimalarial agent resistant to parasite resistance.
In Vitro
Synergism Observed with Azithromycin, Clarithromycin, Minocycline, or Tigecycline in Association with Antifungal Agents against Pythium insidiosum
Authors: Jesus Francielli P. K. , Ferreiro Laerte , Loreto Érico S. , Pilotto Maiara B. , Ludwig Aline , Bizzi Karine , Tondolo Juliana S. M. , Zanette Régis A. , Alves Sydney H. , Santurio Janio M.
Published: July 2014

We describe here the
in vitro
activities of azithromycin, clarithromycin, minocycline, or tigecycline alone and in combination with amphotericin B, itraconazole, terbinafine, voriconazole, anidulafungin, caspofungin, or micafungin against 30 isolates of the oomycete
Pythium insidiosum
. The assays were based on the CLSI M38-A2 technique and the checkerboard microdilution method. The main synergisms observed were through the combination of minocycline with amphotericin B (73.33%), itraconazole (70%), and micafungin (70%) and of clarithromycin with micafungin (73.33%).
Pyocyanin Production by Pseudomonas aeruginosa Confers Resistance to Ionic Silver
Authors: Muller Michael , Merrett Neil D.
Published: July 2014

Silver in its ionic form (Ag
+
), but not the bulk metal (Ag
0
), is toxic to microbial life forms and has been used for many years in the treatment of wound infections. The prevalence of bacterial resistance to silver is considered low due to the nonspecific nature of its toxicity. However, the recent increased use of silver as an antimicrobial agent for medical, consumer, and industrial products has raised concern that widespread silver resistance may emerge.
Pseudomonas aeruginosa
is a common pathogen that produces pyocyanin, a redox toxin and a reductant for molecular oxygen and ferric (Fe
3+
) ions. The objective of this study was to determine whether pyocyanin reduces Ag
+
to Ag
0
, which may contribute to silver resistance due to lower bioavailability of the cation. Using surface plasmon resonance spectroscopy and scanning electron microscopy, pyocyanin was confirmed to be a reductant for Ag
+
, forming Ag
0
nanoparticles and reducing the bioavailability of free Ag
+
by >95% within minutes. Similarly, a pyocyanin-producing strain of
P. aeruginosa
(PA14) reduced Ag
+
but not a pyocyanin-deficient (Δ
phzM
) strain of the bacterium. Challenge of each strain with Ag
+
(as AgNO
3
) gave MICs of 20 and 5 μg/ml for the PA14 and Δ
phzM
strains, respectively. Removal of pyocyanin from the medium strain PA14 was grown in or its addition to the medium that Δ
phzM
mutant was grown in gave MICs of 5 and 20 μg/ml, respectively. Clinical isolates demonstrated similar pyocyanin-dependent resistance to Ag
+
. We conclude that pseudomonal silver resistance exists independently of previously recognized intracellular mechanisms and may be more prevalent than previously considered.
Binding Mode Characterization of NBD Series CD4-Mimetic HIV-1 Entry Inhibitors by X-Ray Structure and Resistance Study
Authors: Curreli Francesca , Kwon Young Do , Zhang Hongtao , Yang Yongping , Scacalossi Daniel , Kwong Peter D. , Debnath Asim K.
Published: July 2014

We previously identified two small-molecule CD4 mimetics—NBD-556 and NBD-557—and synthesized a series of NBD compounds that resulted in improved neutralization activity in a single-cycle HIV-1 infectivity assay. For the current investigation, we selected several of the most active compounds and assessed their antiviral activity on a panel of 53 reference HIV-1 Env pseudoviruses representing diverse clades of clinical isolates. The selected compounds inhibited tested clades with low-micromolar potencies. Mechanism studies indicated that they act as CD4 agonists, a potentially unfavorable therapeutic trait, in that they can bind to the gp120 envelope glycoprotein and initiate a similar physiological response as CD4. However, one of the compounds, NBD-09027, exhibited reduced agonist properties, in both functional and biophysical studies. To understand the binding mode of these inhibitors, we first generated HIV-1-resistant mutants, assessed their behavior with NBD compounds, and determined the X-ray structures of two inhibitors, NBD-09027 and NBD-10007, in complex with the HIV-1 gp120 core at ∼2-Å resolution. Both studies confirmed that the NBD compounds bind similarly to NBD-556 and NBD-557 by inserting their hydrophobic groups into the Phe43 cavity of gp120. The basic nitrogen of the piperidine ring is located in close proximity to D368 of gp120 but it does not form any H-bond or salt bridge, a likely explanation for their nonoptimal antagonist properties. The results reveal the structural and biological character of the NBD series of CD4 mimetics and identify ways to reduce their agonist properties and convert them to antagonists.
Latitudinal Distribution of Ammonia-Oxidizing Bacteria and Archaea in the Agricultural Soils of Eastern China
Authors: Jiang Hongchen , Huang Liuqin , Deng Ye , Wang Shang , Zhou Yu , Liu Li , Dong Hailiang
Published: July 2014

The response of soil ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to individual environmental variables (e.g., pH, temperature, and carbon- and nitrogen-related soil nutrients) has been extensively studied, but how these environmental conditions collectively shape AOB and AOA distributions in unmanaged agricultural soils across a large latitudinal gradient remains poorly known. In this study, the AOB and AOA community structure and diversity in 26 agricultural soils collected from eastern China were investigated by using quantitative PCR and bar-coded 454 pyrosequencing of the
amoA
gene that encodes the alpha subunit of ammonia monooxygenase. The sampling locations span over a 17° latitude gradient and cover a range of climatic conditions. The
Nitrosospira
and
Nitrososphaera
were the dominant clusters of AOB and AOA, respectively; but the subcluster-level composition of
Nitrosospira
-related AOB and
Nitrososphaera
-related AOA varied across the latitudinal gradient. Variance partitioning analysis showed that geography and climatic conditions (e.g., mean annual temperature and precipitation), as well as carbon-/nitrogen-related soil nutrients, contributed more to the AOB and AOA community variations (∼50% in total) than soil pH (∼10% in total). These results are important in furthering our understanding of environmental conditions influencing AOB and AOA community structure across a range of environmental gradients.
Developmental Cell Fate and Virulence Are Linked to Trehalose Homeostasis in Cryptococcus neoformans
Authors: Botts Michael R. , Huang Mingwei , Borchardt Regen K. , Hull Christina M.
Published: July 2014

Among pathogenic environmental fungi, spores are thought to be infectious particles that germinate in the host to cause disease. The meningoencephalitis-causing yeast
Cryptococcus neoformans
is found ubiquitously in the environment and sporulates in response to nutrient limitation. While the yeast form has been studied extensively, relatively little is known about spore biogenesis, and spore germination has never been evaluated at the molecular level. Using genome transcript analysis of spores and molecular genetic approaches, we discovered that trehalose homeostasis plays a key role in regulating sporulation of
C. neoformans
, is required for full spore viability, and influences virulence. Specifically, we found that genes involved in trehalose metabolism, including a previously uncharacterized secreted trehalase (
NTH2
), are highly overrepresented in dormant spores. Deletion of the two predicted trehalases in the
C. neoformans
genome,
NTH1
and
NTH2
, resulted in severe defects in spore production, a decrease in spore germination, and an increase in the production of alternative developmental structures. This shift in cell types suggests that trehalose levels modulate cell fate decisions during sexual development. We also discovered that deletion of the
NTH2
trehalase results in hypervirulence in a murine model of infection. Taken together, these data show that the metabolic adaptations that allow this fungus to proliferate ubiquitously in the environment play unexpected roles in virulence in the mammalian host and highlight the complex interplay among the processes of metabolism, development, and pathogenesis.
Retinoid Levels Influence Enterohemorrhagic Escherichia coli Infection and Shiga Toxin 2 Susceptibility in Mice
Authors: Cabrera Gabriel , Fernández-Brando Romina J. , Abrey-Recalde María Jimena , Baschkier Ariela , Pinto Alipio , Goldstein Jorge , Zotta Elsa , Meiss Roberto , Rivas Marta , Palermo Marina S.
Published: July 2014

Enterohemorrhagic
Escherichia coli
(EHEC) is a food-borne pathogen that produces Shiga toxin (Stx) and causes hemorrhagic colitis. Under some circumstances, Stx produced within the intestinal tract enters the bloodstream, leading to systemic complications that may cause the potentially fatal hemolytic-uremic syndrome. Although retinoids like vitamin A (VA) and retinoic acid (RA) are beneficial to gut integrity and the immune system, the effect of VA supplementation on gastrointestinal infections of different etiologies has been controversial. Thus, the aim of this work was to study the influence of different VA status on the outcome of an EHEC intestinal infection in mice. We report that VA deficiency worsened the intestinal damage during EHEC infection but simultaneously improved survival. Since death is associated mainly with Stx toxicity, Stx was intravenously inoculated to analyze whether retinoid levels affect Stx susceptibility. Interestingly, while VA-deficient (VA-D) mice were resistant to a lethal dose of Stx2, RA-supplemented mice were more susceptible to it. Given that peripheral blood polymorphonuclear cells (PMNs) are known to potentiate Stx2 toxicity, we studied the influence of retinoid levels on the absolute number and function of PMNs. We found that VA-D mice had decreased PMN numbers and a diminished capacity to produce reactive oxygen species, while RA supplementation had the opposite effect. These results are in line with the well-known function of retinoids in maintaining the homeostasis of the gut but support the idea that they have a proinflammatory effect by acting, in part, on the PMN population.
Folding LacZ in the Periplasm of Escherichia coli
Authors: Dwyer Robert S. , Malinverni Juliana C. , Boyd Dana , Beckwith Jon , Silhavy Thomas J.
Published: July 2014

Targeted, translational LacZ fusions provided the initial support for the signal sequence hypothesis in prokaryotes and allowed for selection of the mutations that identified the Sec translocon. Many of these selections relied on the fact that expression of targeted, translational
lacZ
fusions like
malE-lacZ
and
lamB-lacZ42-1
causes lethal toxicity as folded LacZ jams the translocation pore. However, there is another class of targeted LacZ fusions that do not jam the translocon. These targeted, nonjamming fusions also show toxic phenotypes that may be useful for selecting mutations in genes involved in posttranslocational protein folding and targeting; however, they have not been investigated to the same extent as their jamming counterparts. In fact, it is still unclear whether LacZ can be fully translocated in these fusions. It may be that they simply partition into the inner membrane where they can no longer participate in folding or assembly. In the present study, we systematically characterize the nonjamming fusions and determine their ultimate localization. We report that LacZ can be fully translocated into the periplasm, where it is toxic. We show that this toxicity is likely due to LacZ misfolding and that, in the absence of the periplasmic disulfide bond catalyst DsbA, LacZ folds in the periplasm. Using the novel phenotype of periplasmic β-galactosidase activity, we show that the periplasmic chaperone FkpA contributes to LacZ folding in this nonnative compartment. We propose that targeted, nonjamming LacZ fusions may be used to further study folding and targeting in the periplasm of
Escherichia coli
.
Oral drug treatments in patients with erectile dysfunction and multiple comorbidities: a retrospective observational study
Authors: Zaman Huri Hasniza , Lian Choo Tee , Sulaiman Che Zuraini , Mark Raymond , Abdul Razack Azad Hassan
Published: July 2014

Objective

To investigate factors associated with demographic/clinical characteristics and drug selection in patients with erectile dysfunction (ED). The prevalence of ED is increasing worldwide. Studies have shown that ED is associated with age, lifestyle and comorbidities. However, the factors associated with patient characteristics as well as drug selection are incompletely understood.

Setting

A tertiary medical centre in Kuala Lumpur, Malaysia.

Participants

A total of 219 patients (range 23–80 years) who had received phosphodiesterase type-5 (PDE-5) inhibitors as ED treatment were evaluated.

Inclusion criteria

Adult patients aged ≥18 years, diagnosed with ED, and prescribed with sildenafil, tadalafil or vardenafil.

Exclusion criteria

Patients diagnosed with ED but who did not receive any PDE-5 inhibitor, or those with missing data.

Primary and secondary outcome measures

Factors associated with demographic and clinical characteristics as well as drug selection were assessed.

Results

Ischaemic heart disease (p=0.025), benign prostatic hyperplasia (p<0.001), obesity (p=0.005), lower urinary tract symptoms (LUTS) (p=0.006) and α-blockers (p<0.001) were significantly associated with elderly patients with ED. Additionally, LUTS (p=0.038) and α-blockers (p=0.008) were significantly associated with the selection of PDE-5 inhibitor.

Conclusions

These data showed that elderly patients with ED were significantly associated with comorbidities and α-blockers, whereas LUTS and α blockers were associated with drug selection.
Synthesis of reduction-sensitive 1,1-diarylhydrazines from 1,1-diarylamines
Authors: Bain Cheryl D. , Bayne Julia M. , Bohle D. Scott , Butler Ian S. , Poisson Joël
Published: July 2014

1-(2-Nitrophenyl)-1-phenylamine and methyl 4-((2-nitrophenyl)amino)benzoate have been transformed into their corresponding urea derivatives through the action of chlorosulfonyl isocyanate. The initial sulfimidate product from the former reaction has sufficient stability so that it can be isolated and characterized as its disodium salt, and this, as well as three other subsequent products, have been characterized by X-ray diffraction. The corresponding intermediary urea was converted into its hydrazine derivative via a Hofmann rearrangement under oxidative conditions. Density functional theory has been used to examine the nature of the intermediates and transition states for the Hofmann rearrangement. There is little theoretical indication for a cyclic aziridinonium intermediate and the transition state between the urea and the isocyanate corresponds to a reactant-like rotation of the planar singlet nitrene before migration and formation of the new N−N bond.
Biodegradation of type II pyrethroids and major degraded products by a newly isolated Acinetobacter sp. strain JN8
Authors: Jin Zhaoxia , Guo Qiong , Zhang Zongshen , Yan Tongshuai
Published: July 2014

A Gram-negative aerobic bacterium, designated as JN8, was isolated from activated sludge and soil in a pesticides factory in China. It was found that JN8 had a high capacity for degrading a broad range of type II pyrethroids and utilizing these pyrethroids as the sole carbon source for cell growth. The degradation rates of a 100 mg·L−1 concentration of β-cypermethrin, cypermethrin, fenpropathrin, fenvalerate, and deltamethrin by JN8 in mineral salt medium were 74.1%, 64.9%, 57.9%, 48.1% and 34.9%, respectively. Strain JN8 was identified as a species of Acinetobacter based on its biochemical properties and 16S rRNA sequence analysis. β-Cypermethrin was degraded by JN8 through hydrolysis of the carboxylester linkage to form 3-phenoxybenzoic acid and 3-(2,2-dichlorovinyl)-2,2-dimethylcyclopropane carboxylic acid, both of which could be further degraded by JN8. JN8 is the first strain of an Acinetobacter species in which pyrethoid-degrading activity has been detected, and such a feature makes it a potential resource for disposal of waste and effluent from pyrethroid manufacturing facilities.
Electrical conductivity and density of state of boron nitride nanotubes due to electronic correlation
Authors: Rezania H.
Published: July 2014

The temperature behavior of electrical conductivity of boron nitride nanotubes (6, 0) in the context of Hubbard model at the paramagnetic sector. The effect of electronic correlation on the energy gap of boron nitride nanotube (BNNT) is investigated. Interacting electronic Green's function matrix has been found within GW approximation. Using Kubo formula, electrical conductivity of the system has been calculated. The results show that the band gap in the density of state decreases with Coulomb repulsion strength. Moreover, the increase of electronic correlation leads to decrease electrical conductivity of BNNT. Also the electrical conductivity shows an exponential behavior in terms of temperature at all the values of electron–electron interaction parameter.
IMPROVED POINTER MACHINE AND I/O LOWER BOUNDS FOR SIMPLEX RANGE REPORTING AND RELATED PROBLEMS
Authors: AFSHANI PEYMAN
Published: July 2014

We investigate one of the fundamental areas in computational geometry: lower bounds for range reporting problems in the pointer machine and the external memory models. We develop new techniques that lead to new and improved lower bounds for simplex range reporting as well as some other geometric problems.

Simplex range reporting is the problem of storing n points in the d-dimensional space in a data structure such that the k points that lie inside a query simplex can be found efficiently. This is one of the fundamental and extensively studied problems in computational geometry. Currently, the best data structures for the problem achieve Q(n) + O(k) query time using [Formula: see text] space in which the [Formula: see text] notation either hides a polylogarithmic or an nε factor for any constant ε > 0, (depending on the data structure and Q(n)). The best lower bound on this problem is due to Chazelle and Rosenberg who showed any pointer machine data structure that can answer queries in O(nγ + k) time must use Ω(nd-ε-dγ) space. Observe that this bound is a polynomial factor away from the best known data structures.

In this article, we improve the space lower bound to [Formula: see text]. Not only this bridges the gap from polynomial to sub-polynomial, it also offers a smooth trade-off curve. For instance, for polylogarithmic values of Q(n), our space lower bound almost equals Ω((n/Q(n))d); the latter is generally believed to be the “right” bound.

By a simple geometric transformation, we also improve the best lower bounds for the halfspace range reporting problem. Furthermore, we study the external memory model and offer a new simple framework for proving lower bounds in this model. We show that answering simplex range reporting queries with Q(n)+O(k/B) I/Os requires [Formula: see text]) space or [Formula: see text] blocks, in which B is the block size.
Origin of Late Palaeozoic bauxites in the North China Craton: constraints from zircon U–Pb geochronology and
in situ
Hf isotopes
Authors: Liu Jian , Zhao Yue , Liu Ankun , Zhang Shuanhong , Yang Zhenyu , Zhuo Shengguang
Published: July 2014

Bauxite deposits that lie between Middle Ordovician limestones and Late Carboniferous clastic sediments (known as the ‘G’ layer bauxites) are widespread throughout the northern part of the North China Craton. The origin of these bauxites has remained uncertain and has been attributed either to alteration of the underlying limestone or to tephra deposited on the limestone erosional surface. We use U–Pb ages and
in situ
Hf isotopic analyses of detrital zircons from the ‘G’ layer bauxite deposits (both by laser ablation inductively coupled plasma mass spectrometry) to constrain the major source materials of the bauxites. The zircon ages are dominated by Palaeozoic ages, especially Carboniferous to Early Permian (338–291 Ma), coeval with the Palaeozoic subduction-related volcanism in the Inner Mongolia Palaeo-Uplift on the northern margin of the North China Craton. Zircon ϵ
Hf
(
t
) values range from 2.2 to −24.5 and are dominated by negative values, similar to those of Palaeozoic magmatic rocks in the Inner Mongolia Palaeo-Uplift, but distinct from those of Palaeozoic magmatic rocks in the Central Asian Orogenic Belt with positive ϵ
Hf
(
t
) values. Thus, we argue that the bauxites were derived mainly from volcanic dust produced during the Palaeozoic, particularly in the Carboniferous to Early Permian (338–291 Ma), by volcanism in the Inner Mongolia Palaeo-Uplift along the northern margin of the North China Craton, rather than in the Central Asian Orogenic Belt to the north. The underlying Middle Ordovician limestones, however, had provided only minor, if any, source materials for the bauxites.