bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental evolution of Escherichia coli harboring an ancient translation protein
Authors: Kaçar Betül , Ge Xueliang , Sanyal Suparna , Gaucher Eric A.
Published: February 2016

The ability to design synthetic genes and engineer biological systems at the genome scale opens new means by which to characterize phenotypic states and the responses of biological systems to perturbations. One emerging method involves inserting artificial genes into bacterial genomes, and examining how the genome and its new genes adapt to each other. Here we report the development and implementation of a modified approach to this method, in which phylogenetically inferred genes are inserted into a microbial genome, and laboratory evolution is then used to examine the adaptive potential of the resulting hybrid genome. Specifically, we engineered an approximately 700-million-year old inferred ancestral variant oftufB, an essential gene encoding Elongation Factor Tu, and inserted it in a modernEscherichia coligenome in place of the nativetufBgene. While the ancient homolog was not lethal to the cell, it did cause a two-fold decrease in organismal fitness, mainly due to reduced protein dosage. We subsequently evolved replicate hybrid bacterial populations for 2,000 generations in the laboratory, and examined the adaptive response via fitness assays, whole-genome sequencing, proteomics and biochemical assays. Hybrid lineages exhibit a general adaptive strategy in which the fitness cost of the ancient gene was ameliorated in part by up-regulation of protein production. We expect that this ancient-modern recombinant method may pave the way for the synthesis of organisms that exhibit ancient phenotypes, and that laboratory evolution of these organisms may prove useful in elucidating insights into historical adaptive processes.
Laue lens to focus an X-ray beam for radiation therapy
Authors: Paternò Gianfranco , Marziani Michele , Camattari Riccardo , Bellucci Valerio , Mazzolari Andrea , Gambaccini Mauro , Guidi Vincenzo
Published: February 2016

A Laue lens is an optical component composed of a set of crystals that produce a convergent beam exploiting X-ray diffraction in transmission geometry. Employment of a system formed by a properly designed Laue lens coupled with an X-ray unit to selectively irradiate tumours is proposed. A convergent beam leads to a depth dose profile with a pronounced peak at the focal depth, which may result in a high precision of the dose delivery. Using a custom-made Monte Carlo code and the GAMOS code, we carried out a design study to determine the geometry and the optimal features of the crystals composing the lens. As an application, a Laue lens capable of focusing a 80 keV beam 50 cm downstream of the lens has been designed. The lens is composed of an ensemble of Si crystals with curved diffracting planes. The lens produces a focal spot of 2 mm enclosing 7.64 × 106 photons for an electron charge of 1 mC impinging on the surface of the X-ray tube anode. The combination of these important figures of merit makes the proposed system suitable for irradiating both sub-cm and larger tumour masses efficiently. A dose of 2 Gy can be delivered to a small tumour in a few seconds, sparing at the same time the surrounding tissues.
X-ray crystal structure analysis of magnetically oriented microcrystals of lysozyme at 1.8 Å resolution
Authors: Tsukui Shu , Kimura Fumiko , Garman Elspeth F. , Baba Seiki , Mizuno Nobuhiro , Mikami Bunzo , Kimura Tsunehisa
Published: February 2016

Microcrystals of lysozyme (5–10 µm) suspended in an ultraviolet-light-curable resin were aligned three dimensionally under a non-uniformly rotating magnetic field, and then the resin was consolidated by photopolymerization to obtain a composite in which microcrystals were three-dimensionally aligned. The obtained composite (MOMA: magnetically oriented microcrystal array) was analysed using a synchrotron X-ray source. A resolution of 1.8 Å was obtained, which is in marked contrast to the resolution of 3 Å previously reported for these composites, obtained by using an in-house X-ray diffractometer. These results show that a combination of MOMAs with conventional synchrotron beamlines may have valuable potential for crystal analyses of protein crystals that do not grow to larger sizes.
Sodium dipotassium citrate, NaK2C6H5O7
Authors: Rammohan Alagappa , Kaduk James A.
Published: February 2016

The crystal structure of sodium dipotassium citrate, Na+·2K+·C6H5O73−, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The Na+and one of the K+cations are six-coordinate, with bond-valence sums of 1.13 and 0.92 valence units, respectively, while another crystallographically independent K+cation is seven-coordinate with a bond-valence sum of 1.20. The [KO6] and [KO7] polyhedra share edges and corners to form layers perpendicular to thebaxis. The distorted [NaO6] octahedra share edges to form chains along theaaxis. The result is a three-dimensional network. The only O—H...O hydrogen bond is an intramolecular one between the hydroxy group and a terminal carboxylate group.
Crystal structure oftrans-dichlorido(1,4,8,11-tetraazaundecane-κ4N)chromium(III) perchlorate determined from synchrotron data
Authors: Moon Dohyun , Choi Jong-Ha
Published: February 2016

The structure of the title complex, [CrCl2(2,3,2-tet)]ClO4(2,3,2-tet is 1,4,8,11-tetraazaundecane, C7H20N4), has been determined from synchrotron data. The CrIIIion is coordinated by the four N atoms of the 1,4,8,11-tetraazaundecane ligand in the equatorial plane and two chloride ions in an axial arrangement, displaying a slightly distorted octahedral coordination environment. The two H atoms of the secondary amines are grouped on the same side of the equatorial N4plane (meso-RSconformation). The Cr—N bond lengths range from 2.069 (2) to 2.084 (2) Å, while the mean Cr—Cl bond length is 2.325 (2) Å. The crystal structure is stabilized by intermolecular hydrogen-bonding interactions between the primary and secondary amine groups of the 2,3,2-tet ligands, the Cl ligands and the O atoms of the perchlorate counter-anion, forming corrugated layers parallel to (010).
Diethyl 3-amino-6-methyl-4-[(E)-2-phenylethenyl]thieno[2,3-b]pyridine-2,5-dicarboxylate
Authors: Mague Joel T. , Mohamed Shaaban K. , Akkurt Mehmet , Bakhite Etify A. , Albayati Mustafa R.
Published: February 2016

In the title molecule, C22H22N2O4S, the bicyclic core is slightly folded [1.9 (1)°], while pairwise intermolecular N—H...O hydrogen bonding forms dimers across centers of symmetry. The dihedral angle between the phenyl ring an the six-membered ring of the bicyclic core is 75.50 (4)°. The molecular conformation is stabilized by an intramolecular N—H...O hydrogen bond with graph-set motifS(6) and by a weak C—H...O contact, forming anS(7) motif. In the crystal, π–π interactions [centroid-to-centroid distance = 3.7484 (10) Å] between phenyl rings and two weak C—H...π interactions are also observed.
Benchmarking of product recovery alternatives in reverse logistics
Authors: Sharma S. K. , Mahapatra S.S. , Parappagoudar M.B.
Published: February 2016

Purpose

– Selection of best product recovery alternative in reverse logistics (RL) has gained great attention in supply chain community. The purpose of this paper is to provide a robust group decision-making tool to select the best product recovery alternative.

Design/methodology/approach

– In this paper, fuzzy values, assigned to various criteria and alternatives by a number of decision makers, are converted into crisp values and then aggregated scores are evaluated. After obtaining experts’ scores, objective and subjective weights of the criteria have been calculated using variance method and analytic hierarchy process, respectively. Then integrated weights of criteria are evaluated using different proportions of the two weights. The superiority and inferiority ranking (SIR) method is then employed to achieve the final ranking of alternatives. An example is presented to demonstrate the methodology.

Findings

– The proposed methodology provides decision makers a systematic, flexible and realistic approach to effectively rank the product recovery alternatives in RL. The alternatives can easily be benchmarked and best recovery strategy can be obtained. The sensitivity analysis carried out by changing different proportion of objective and subjective weights reveals that best ranking alternative never changes and proves the robustness of the methodology. The present benchmarking framework can also be used by decision makers to simplify any problem which encounters multi-attribute decision making and multiple decision makers.

Research limitations/implications

– The proposed methodology should be tested in different situations having varied operational and environmental conditions dealing with different products. A real case study from an industrial set up can help to assess the behavior of the proposed methodology. The presented methodology however can deal with such multi-disciplinary and multi-criteria issues in a simple and structured manner and ease the managers to select the best alternative.

Originality/value

– A novel approach for decision making taking into account both objective and subjective weights for criteria has been proposed to rank the best recovery alternatives in RL. The proposed methodology uses SIR method to prioritize the alternatives. As RL alternative selection is an important issue and involves both technical and managerial criteria as well as multiple decision makers, the proposed robust methodology can provide guidelines for the practicing managers.
Ownership, size, and efficiency: evidence from software companies in India
Authors: Sahoo Bimal Kishore
Published: February 2016

Purpose

– The purpose of this paper is to discuss the trends in relative efficiency of software companies in India during 1999-2008 by applying input-oriented data envelopment analysis (DEA) model. Based upon the PROWESS Database of Centre for Monitoring Indian Economy (CMIE), the efficiencies were estimated for the Indian, multinational and group companies. Also, relationship between efficiency and size is examined.

Design/methodology/approach

– The study applied DEA to measure relative efficiencies of software companies and two different DEA models, CCR and BCC, were applied to evaluate the relative efficiency of the sample software companies in India. Comparisons of efficiency scores based on ownership were carried out by applying ANOVA andt-statistics.

Findings

– The mean overall technical efficiency (OTE) of the software industry in India during 1999-2008 was low at 0.477. The mean pure technical efficiency for the industry for the study period was found to be 0.654 suggesting that software firms, on an average, were wasting 35 per cent of their inputs. It was observed that the Indian-owned companies have relatively high OTE score as compared to foreign owned and group owned companies. The mean OTE score of PI companies was found to be greater than the other two categories. In terms of, size it is observed that medium sized companies performance better.

Practical implications

– Software companies can use DEA to examine their performance against the best performers in the industry. Software industry in India, which is doted by large number of small firms in the lower part of the size pyramid, needs to increase their size to improve their efficiency.

Originality/value

– Research on measurement of service sector export oriented industry efficiency is limited. This paper is one of the few published studies examined service sector performance. This paper fills the gap in the literature by applying DEA in software industry in India and compares performance in terms of ownership and size.
Objectives priority in university strategy map for resource allocation
Authors: Rahimnia Fariborz , Kargozar Naghmeh
Published: February 2016

Purpose

– The purpose of this paper is to provide a model for Ferdowsi University of Mashhad (FUM) to prioritize its objectives. This will be achieved by providing strategy map using balanced score card (BSC) method.

Design/methodology/approach

– This research result is based on 21 managers’ opinion about relation among university objectives, gathered by questionnaire. DEMATHEL method which is a structural decision-making model is used to process data in questionnaires and discover casual relationship between university objectives.

Findings

– According to this research result “Having productive competent human resource that are committed to Islamic values and professional ethic” has the highest priority among FUM objectives while “Achieving educating excellence especially in graduate programs and research” has the lowest.

Practical implications

– FUM managers need to focus on their human resources and enhance their competency in order to achieve academic excellence.

Originality/value

– Achieving superiority in university competitive position based on its education and research activities is FUM vision. As a non-profit organization due to resource restriction and environmental circumstances it has to fulfill this goal with higher productivity. BSC as a performance management system will help it to achieve this goal by translating vision into objectives and defining casual relationship between them. This method is rarely studied in the context of universities especially in Iranian universities. This research applied strategy map, one of BSC implementation stages, in a public university in Iran to illustrate series of objectives that leads to mission accomplishment.
Masses of Fluid for Cylindrical Tanks in Rock With Partial Uplift of Bottom Plate
Authors: Taniguchi Tomoyo , Katayama Yukihiro
Published: February 2016

This study proposes the use of a slice model consisting of a set of thin rectangular tanks for evaluating the masses of fluid contributing to the rocking motion of cylindrical tanks; the effective mass of fluid for rocking motion, that for rocking–bulging interaction, effective moment inertia of fluid for rocking motion and its centroid. They are mathematically or numerically quantified, normalized, tabulated, and depicted as functions of the aspect of tanks for different values of the ratio of the uplift width of the tank bottom plate to the diameter of tank for the designer's convenience.
Geometrical Parameters Influencing the Aerodynamic Efficiency of a Small-Scale Self-Pitch High-Solidity VAWT
Authors: Xisto Carlos M. , Páscoa José C. , Trancossi Michele
Published: February 2016

In this paper, four key design parameters with a strong influence on the performance of a high-solidity variable pitch vertical axis wind turbine (VAWT) operating at low tip-speed-ratio (TSR) are addressed. To this aim, a numerical approach, based on a finite-volume discretization of two-dimensional (2D) unsteady Reynolds-averaged Navier–Stokes (URANS) equations, on a multiple sliding mesh, is proposed and validated against experimental data. The self-pitch VAWT design is based on a straight-blade Darrieus wind turbine with blades that are allowed to pitch around a feathering axis, which is also parallel to the axis of rotation. The pitch angle amplitude and periodic variation are dynamically controlled by a four-bar linkage system. We only consider the efficiency at low and intermediate TSR; therefore, the pitch amplitude is chosen to be a sinusoidal function with a considerable amplitude. The results of this parametric analysis will contribute to define the guidelines for building a full-size prototype of a small-scale wind turbine of increased efficiency.
Quantification of Age-Related Tissue-Level Failure Strains of Rat Femoral Cortical Bones Using an Approach Combining Macrocompressive Test and Microfinite Element Analysis
Authors: Fan Ruoxun , Gong He , Zhang Rui , Gao Jiazi , Jia Zhengbin , Hu Yanjuan
Published: February 2016

Bone mechanical properties vary with age; meanwhile, a close relationship exists among bone mechanical properties at different levels. Therefore, conducting multilevel analyses for bone structures with different ages are necessary to elucidate the effects of aging on bone mechanical properties at different levels. In this study, an approach that combined microfinite element (micro-FE) analysis and macrocompressive test was established to simulate the failure of male rat femoral cortical bone. Micro-FE analyses were primarily performed for rat cortical bones with different ages to simulate their failure processes under compressive load. Tissue-level failure strains in tension and compression of these cortical bones were then back-calculated by fitting the experimental stress–strain curves. Thus, tissue-level failure strains of rat femoral cortical bones with different ages were quantified. The tissue-level failure strain exhibited a biphasic behavior with age: in the period of skeletal maturity (1–7 months of age), the failure strain gradually increased; when the rat exceeded 7 months of age, the failure strain sharply decreased. In the period of skeletal maturity, both the macro- and tissue-levels mechanical properties showed a large promotion. In the period of skeletal aging (9–15 months of age), the tissue-level mechanical properties sharply deteriorated; however, the macromechanical properties only slightly deteriorated. The age-related changes in tissue-level failure strain were revealed through the analysis of male rat femoral cortical bones with different ages, which provided a theoretical basis to understand the relationship between rat cortical bone mechanical properties at macro- and tissue-levels and decrease of bone strength with age.
Dynamic Recrystallization of Al Alloy 7075 in Turning
Authors: Tabei A. , Shih D. S. , Garmestani H. , Liang S. Y.
Published: February 2016

This work investigates the effects of turning process parameters on recrystallization behavior in Al alloy 7075. To realize this purpose, samples were machined under different cutting speeds and material feed rates at two extreme levels. Microscopy imaging reveals that activation of dynamic recrystallization or grain growth depends on the combination of applied cutting parameters. Increasing the cutting speed intensifies recrystallization, while the feed rate governs the grain growth. Adjusting the cutting parameters enables one to obtain a desired average grain size below the machined surface, up to a ∼180 μm depth. The average grain size of the initial material was 31.6 μm. The imposed processing parameters successfully yielded average grain sizes in the range from 19 to 44 μm. Additionally, a computational framework work consisting of finite-element analysis (FEA) coupled with kinetic-based modeling of recrystallization was developed, which is capable of following the trend of change in the average grain size and acceptably predicts the evolved average grain size.
Real Area of Contact in a Soft Transparent Interface by Particle Exclusion Microscopy
Authors: Schulze Kyle D. , Bennett Alex I. , Marshall Samantha , Rowe Kyle G. , Dunn Alison C.
Published: February 2016

Soft matter mechanics are characterized by high strains and time-dependent elastic properties, which complicate contact mechanics for emerging applications in biomedical surfaces and flexible electronics. In addition, hydrated soft matter precludes using interferometry to observe real areas of contact. In this work, we present a method for measuring the real area of contact in a soft, hydrated, and transparent interface by excluding colloidal particles from the contact region. We confirm the technique by presenting a Hertz-like quasi-static indentation (loading time > 1.4 hrs) by a polyacrylamide probe into a stiff flat surface in a submerged environment. The real contact area and width were calculated from in situ images of the interface processed to reduce image noise and thresholded to define the perimeter of contact. This simple technique of in situ particle exclusion microscopy (PEM) may be widely applicable for determining real areas of contact of soft, transparent interfaces.
Results and problems in the construction phase of the SuperKEKB vacuum system
Authors: Suetsugu Yusuke , Kanazawa Ken-ichi , Shibata Kyo , Ishibashi Takuya , Hisamatsu Hiromi , Shirai Mitsuru , Terui Shinji
Published: February 2016

The SuperKEKB, the upgrade of the KEKB, is an electron–positron collider with asymmetric energies, that is, 7.0 GeV electrons and 4.0 GeV positrons, designed for a luminosity of 8 × 1035 cm−2 s−1. As a key item of the upgrade project, a new vacuum system for the SuperKEKB has been in construction since 2010. Over 1000 beam pipes, vacuum pumps, bellows chambers, and other various vacuum components had almost been fabricated in 2014. All the new beam pipes were baked as a general rule before being installed in the KEKB tunnel. A thin TiN film with a low secondary-electron yield was coated on the inside of the beam pipes for the positron ring as a countermeasure against the electron cloud effect. The performance of the new built-in nonevaporable getter (NEG) pumps and the step-less connection flanges met the expectation. Although several problems such as damage to the bellows chambers due to a large earthquake, cracking of the welding lines of the aluminum beam pipes, and a relatively high air-leak rate at the connection flanges occurred during the construction work, approximately 99% of the beam pipes were successfully installed by the end of October 2015. The activation of the NEG pumps in the tunnel started at the beginning of 2015 and has also been completed in approximately 97% of the ring. The installed beam pipes and the bellows chambers in the tunnel were aligned to their specified positions as the final step of the installation work. The vacuum system was ready in 2015 with the aim of starting the first commissioning in 2016. The various experiences during the construction phase reported here will be a useful reference for the design and construction of other accelerators in the future.
At the edge between metal organic chemical vapor deposition and atomic layer deposition: Fast Atomic Sequential Technique, for high throughput conformal deposition
Authors: Piallat Fabien , Vitiello Julien
Published: February 2016

A comparison of the metal organic chemical vapor deposition (MOCVD), atomic layer deposition (ALD), and a new deposition method, the Fast Atomic Sequential Technique (FAST®), was completed. Within all the materials which can be deposited by the FAST technique, the case study of TiN thin film deposition by reaction of tetrakis(diethylamino)titanium precursor with NH3 reactant gas is presented here. The thickness and resistivity measurements revealed that while the FAST deposition is five times faster than the ALD, the lowest resistivity achieved is four times lower than MOCVD minimum resistivity, thus equivalent to ALD at 100 μΩ cm. Moreover, a 25% gain toward lower action energy of the FAST deposition compared to the MOCVD tends to support a different reaction mechanism between the two techniques. Additionally, the FAST technique introduces new process parameters offering the possibility to change the deposition technique to either a MOCVD-like or to an ALD-like deposition in the same tool, thus allowing to choose between high throughput and high conformality or for a compromise of the two. Then, using high aspect ratio vias, the higher conformality of FAST compared to MOCVD is shown. Evolution of the conformality on different aspect ratios devices shows that while ALD is conformal whatever the aspect ratio, MOCVD is not suitable for vias with an aspect ratio higher than 5:1, whereas FAST can achieve a conformality higher than 60% in aspect ratios of 35:1.
Functionalization of poly(ε-caprolactone) surface with lactose-modified chitosan via alkaline hydrolysis: ToF-SIMS characterization
Authors: Tortora Luca , Concolato Sofia , Urbini Marco , Giannitelli Sara Maria , Basoli Francesco , Rainer Alberto , Trombetta Marcella , Orsini Monica , Mozetic Pamela
Published: February 2016

Functionalization of poly(ε-caprolactone) (PCL) was performed via hydrolysis and subsequent grafting of lactose-modified chitosan (chitlac) at two different degrees of derivatization (9% and 64%). Time of flight secondary ion mass spectrometry (ToF-SIMS) and multivariate analysis (principal component analysis) were successfully applied to the characterization of PCL surface chemistry, evidencing changes in the biopolymer surface following base-catalyzed hydrolysis treatment. ToF-SIMS analysis also confirmed positive EDC/NHS-catalyzed (EDC: N-ethyl-N′-(3-(dimethylamino)propyl)carbodiimide; NHS: N-hydroxysuccinimide) immobilization of chitlac onto activated PCL surface, with formation of amide bonds between PCL surface carboxyl groups and amine residues of chitlac. Yield of grafting reaction was also shown to be dependent upon the lactosilation degree of chitlac.
Trehalose inhibits solute carrier 2A (SLC2A) proteins to induce autophagy and prevent hepatic steatosis
Authors: DeBosch Brian J. , Heitmeier Monique R. , Mayer Allyson L. , Higgins Cassandra B. , Crowley Jan R. , Kraft Thomas E. , Chi Maggie , Newberry Elizabeth P. , Chen Zhouji , Finck Brian N. , Davidson Nicholas O. , Yarasheski Kevin E. , Hruz Paul W. , Moley Kelle H.
Published: February 2016

The disaccharide trehalose blocks glucose uptake in hepatocytes and induces autophagy that prevents fatty liver disease.
Epidermal signals confine dendrites
Authors: Ferrarelli Leslie K.
Published: February 2016

Intercellular signaling from the epidermis maintains proper dendritic patterning in
Drosophila
sensory neurons.
Bacteria give that full feeling
Authors: Gough Nancy R.
Published: February 2016

Peptides produced by stationary phase bacteria trigger satiety signals.
New connections: Interpreting calcium signals
Authors: Gough Nancy R.
Published: February 2016

Single-cell and computational analysis reveals how cells decode calcium signals.
Protein Network of the Pseudomonas aeruginosa Denitrification Apparatus
Authors: Borrero-de Acuña José Manuel , Rohde Manfred , Wissing Josef , Jänsch Lothar , Schobert Max , Molinari Gabriella , Timmis Kenneth N. , Jahn Martina , Jahn Dieter
Published: February 2016

Oxidative phosphorylation using multiple-component, membrane-associated protein complexes is the most effective way for a cell to generate energy. Here, we systematically investigated the multiple protein-protein interactions of the denitrification apparatus of the pathogenic bacterium
Pseudomonas aeruginosa
. During denitrification, nitrate (Nar), nitrite (Nir), nitric oxide (Nor), and nitrous oxide (Nos) reductases catalyze the reaction cascade of NO
3−
→ NO
2−
→ NO → N
2
O → N
2
. Genetic experiments suggested that the nitric oxide reductase NorBC and the regulatory protein NosR are the nucleus of the denitrification protein network. We utilized membrane interactomics in combination with electron microscopy colocalization studies to elucidate the corresponding protein-protein interactions. The integral membrane proteins NorC, NorB, and NosR form the core assembly platform that binds the nitrate reductase NarGHI and the periplasmic nitrite reductase NirS via its maturation factor NirF. The periplasmic nitrous oxide reductase NosZ is linked via NosR. The nitrate transporter NarK2, the nitrate regulatory system NarXL, various nitrite reductase maturation proteins, NirEJMNQ, and the Nos assembly lipoproteins NosFL were also found to be attached. A number of proteins associated with energy generation, including electron-donating dehydrogenases, the complete ATP synthase, almost all enzymes of the tricarboxylic acid (TCA) cycle, and the Sec system of protein transport, among many other proteins, were found to interact with the denitrification proteins. This deduced nitrate respirasome is presumably only one part of an extensive cytoplasmic membrane-anchored protein network connecting cytoplasmic, inner membrane, and periplasmic proteins to mediate key activities occurring at the barrier/interface between the cytoplasm and the external environment.

IMPORTANCE
The processes of cellular energy generation are catalyzed by large multiprotein enzyme complexes. The molecular basis for the interaction of these complexes is poorly understood. We employed membrane interactomics and electron microscopy to determine the protein-protein interactions involved. The well-investigated enzyme complexes of denitrification of the pathogenic bacterium
Pseudomonas aeruginosa
served as a model. Denitrification is one essential step of the universal N cycle and provides the bacterium with an effective alternative to oxygen respiration. This process allows the bacterium to form biofilms, which create low-oxygen habitats and which are a key in the infection mechanism. Our results provide new insights into the molecular basis of respiration, as well as opening a new window into the infection strategies of this pathogen.
Regulation of Growth, Cell Shape, Cell Division, and Gene Expression by Second Messengers (p)ppGpp and Cyclic Di-GMP in Mycobacterium smegmatis
Authors: Gupta Kuldeepkumar Ramnaresh , Baloni Priyanka , Indi Shantinath S. , Chatterji Dipankar
Published: February 2016

The alarmone (p)ppGpp regulates transcription, translation, replication, virulence, lipid synthesis, antibiotic sensitivity, biofilm formation, and other functions in bacteria. Signaling nucleotide cyclic di-GMP (c-di-GMP) regulates biofilm formation, motility, virulence, the cell cycle, and other functions. In
Mycobacterium smegmatis
, both (p)ppGpp and c-di-GMP are synthesized and degraded by bifunctional proteins Rel
Msm
and DcpA, encoded by
rel
Msm
and
dcpA
genes, respectively. We have previously shown that the Δ
rel
Msm
and Δ
dcpA
knockout strains are antibiotic resistant and defective in biofilm formation, show altered cell surface properties, and have reduced levels of glycopeptidolipids and polar lipids in their cell wall (K. R. Gupta, S. Kasetty, and D. Chatterji, Appl Environ Microbiol 81:2571–2578, 2015,
http://dx.doi.org/10.1128/AEM.03999-14
). In this work, we have explored the phenotypes that are affected by both (p)ppGpp and c-di-GMP in mycobacteria. We have shown that both (p)ppGpp and c-di-GMP are needed to maintain the proper growth rate under stress conditions such as carbon deprivation and cold shock. Scanning electron microscopy showed that low levels of these second messengers result in elongated cells, while high levels reduce the cell length and embed the cells in a biofilm-like matrix. Fluorescence microscopy revealed that the elongated Δ
rel
Msm
and Δ
dcpA
cells are multinucleate, while transmission electron microscopy showed that the elongated cells are multiseptate. Gene expression analysis also showed that genes belonging to functional categories such as virulence, detoxification, lipid metabolism, and cell-wall-related processes were differentially expressed. Our results suggests that both (p)ppGpp and c-di-GMP affect some common phenotypes in
M. smegmatis
, thus raising a possibility of cross talk between these two second messengers in mycobacteria.

IMPORTANCE
Our work has expanded the horizon of (p)ppGpp and c-di-GMP signaling in Gram-positive bacteria. We have come across a novel observation that
M. smegmatis
needs (p)ppGpp and c-di-GMP for cold tolerance. We had previously shown that the Δ
rel
Msm
and Δ
dcpA
strains are defective in biofilm formation. In this work, the overproduction of (p)ppGpp and c-di-GMP encased
M. smegmatis
in a biofilm-like matrix, which shows that both (p)ppGpp and c-di-GMP are needed for biofilm formation. The regulation of cell length and cell division by (p)ppGpp was known in mycobacteria, but our work shows that c-di-GMP also affects the cell size and cell division in mycobacteria. This is perhaps the first report of c-di-GMP regulating cell division in mycobacteria.
Large leiomyoma of the bladder masquerading as an enlarged prostate gland
Authors: Itam Sarah , Elhage Oussama , Khan Muhammad Shamim
Published: February 2016

A 56-year-old man was admitted to hospital with shortness of breath and subsequently sustained a cardiac arrest. In the recovery period, he developed acute urinary retention and haematuria. Imaging suggested an enlarged prostate and he was started on clean intermittent catheterisation. Following further imaging and a transurethral biopsy, he was found to have a bladder leiomyoma. This was treated with laparotomy, cystotomy and enucleation of the tumour. At his 6-week follow-up appointment, he had a satisfactory cystogram and a successful void without catheter.
Spontaneous hyphaemas requiring a closer look
Authors: Goetz Reinold Kirton , Cosgrave Edel
Published: February 2016

We present four cases of acute blurred vision that presented to the Ophthalmology Emergency Department of University Hospital Waterford. All four patients were found to have a spontaneous hyphaema with neither neovascular cause nor traumatic history. The pathophysiology was initially uncertain. On closer investigation, these patients were found to have rare iris microhaemangiomas (IMs) or Cobb's haemangiomas. They were all treated conservatively and made full recoveries. Though some reports recommend treating IM prior to intraocular surgery, one of these patients proceeded to have uncomplicated cataract surgery at a later date with no need for prior intervention.
Unusual case of spinal epidermoid cyst and a concomitant spinal arachnoid cyst
Authors: Celik Ahmet Orhan , Baris Mustafa Mahmut , Demirtas Hakan , Umul Ayşe
Published: February 2016

A 38-year-old woman presented with a 12-month history of subjective weakness and pain in her legs. Thoracolumbar MRI revealed two spinal intradural cystic lesions at T5–6 and T11 levels, respectively. The lesion located at the T5–6 level was heterogeneously hyperintense on T2-weighted images and heterogeneously hypointense on T1-weighted images. This lesion showed high signal intensity on diffusion weighted MRI (DWI) and low signal intensity on apparent diffusion coefficient images (ADC). According to the MRI findings, we reported this tumour as a spinal epidermoid cyst. The pathology result suggested that the lesion was an epidermoid cyst. The second intradural lesion, at the T11 level, showed a hypointense signal on T1 and hyperintense signal on T2 images. However, in contrast to the superior lesion, this lesion was hypointense on DWI and hyperintense on ADC. We evaluated the second lesion as an arachnoid cyst according to the MRI findings.
Combined pulmonary fibrosis and emphysema: effect of pulmonary rehabilitation in comparison with chronic obstructive pulmonary disease
Authors: Tomioka Hiromi , Mamesaya Nobuaki , Yamashita Shyuji , Kida Yoko , Kaneko Masahiro , Sakai Hideki
Published: February 2016

Objective

To evaluate the effectiveness of short-term comprehensive inpatient pulmonary rehabilitation for patients with combined pulmonary fibrosis and emphysema (CPFE), and to compare responses with those of patients with chronic obstructive pulmonary disease (COPD) who underwent an identical programme.

Design

Retrospective analysis of several outcome measures.

Setting

Pulmonary ward at a 358-bed community teaching hospital.

Methods

3-week inpatient pulmonary rehabilitation programme assessed by pulmonary function tests, 6 min walk test and health-related quality of life (HRQL) using the Short Form-36 (SF-36).

Results

17 patients with CPFE and 49 patients with COPD were referred to and completed the programme between March 2007 and February 2015. Age, sex, smoking status, body mass index and the Medical Research Council dyspnoea grade were comparable between groups. In the CPFE group, improvement from the start of the programme to the programme end was observed in forced expiratory volume in 1 s (FEV1) (from 1.7±0.4 to 1.8±0.4, p=0.034); however, there was no significant improvement in the 6 min walk test (distance, SpO2nadir and Borg scale on exercise). With regard to HRQL, improvement was observed in physical function (p=0.015) whereas deterioration was observed in social functioning (p=0.044). In the COPD group, significant improvement was observed after the programme in the FEV1, 6 min walk test and 4 of the 8 SF-36 subscales. There was a significant difference in changes in the 6 min walk distance: −16.6±58.4 in CPFE versus 30.2±55.6 in COPD (p=0.009). In 2 domains, there was a significant difference in SF-36 scores between groups: Δvitality, −6.3±22.4 in CPFE versus 11.3±21.1 in COPD, p=0.009; and Δsocial functioning, −18.8±34.2 in CPFE versus 5.3±35.9 in COPD, p=0.027.

Conclusion

Patients with COPD derived greater benefits than those with CPFE, from the relatively short periods of inpatient pulmonary rehabilitation.
Management of children with type 1 diabetes during illness: a national survey
Authors: Soni Astha , Agwu Juliana Chizo , Wright Neil Peter , Moudiotis Christopher , Kershaw Melanie , Edge Julie , Drew Josephine Helen , Ng Sze May
Published: February 2016

Aim

Adequate sick-day management at home can reduce the risk of progression to diabetic ketoacidosis and admission to hospital. The aim of this project was to review the management of diabetes during illness.

Method

The Association of Children's Diabetes Clinicians (ACDC) carried out a questionnaire survey of all paediatric diabetes units. In addition, parents of children with type 1 diabetes completed an online questionnaire.

Results

The survey of 127 units had a 73% response rate. Sick-day management guidelines were in place in 93%. All guidelines advised giving extra insulin during illness. In 67%, the extra dose was based on a fraction of total daily dose. 22% used units per kg body weight (U/kg). 21% used locally derived formulae to calculate extra dose of insulin. 3% of units advised only blood ketone monitoring. Although all units had an out-of-hours access policy for the families, 45% received advice from the general paediatric registrar. Only in 15%, the advice was directly from a member of the paediatric diabetes team. 680 parents completed the questionnaire. 86% reported receiving training on managing sick days. The majority (52.2%) receiving an informal session at diagnosis. 40% did not know what to do in the presence of raised blood glucose and high blood ketones.

Conclusions

There was a wide variation in the practice of monitoring and advice given during illness. Both surveys highlight need for national guidance as well and to improve quality of sick-day rule education programmes for parents of children with type 1 diabetes.
Sensitive detection of bisphenol A based on a ratiometric electrochemical aptasensor
Authors: Liu Yunqing , Zhang Xia , Yang Junshuai , Xiong Erhu , Zhang Xiaohua , Chen Jinhua
Published: February 2016

A new ratiometric electrochemical aptasensor has been developed for highly sensitive and selective detection of bisphenol A (BPA). The double-stranded DNA (dsDNA), consisting of the BPA aptamer (DNA1) and methylene blue (MB)-labeled complementary DNA (cDNA), was immobilized on a gold nanoparticle (AuNP) modified glassy carbon (GC) electrode. In the presence of BPA, the specific BPA–aptamer interaction drove the release of the MB-labeled cDNA from the electrode surface. As a result, the oxidation peak current of MB (IMB) decreased and that of BPA (IBPA) increased. The peak current ratio (IBPA/IMB) of BPA and MB was linear with the concentration of BPA in the range from 1 to 100 pmol/L with a detection limit of 0.6 pmol/L. The detection limit is much lower than that obtained by most of the reported electrochemical methods. On the other hand, the developed aptasensor possesses good selectivity, reproducibility, and stability, and the related sensing structure is very simple, showing promising practical applications in BPA assays.
Are brown trout replacing or displacing bull trout populations in a changing climate?
Authors: Al-Chokhachy Robert , Schmetterling David , Clancy Chris , Saffel Pat , Kovach Ryan , Nyce Leslie , Liermann Brad , Fredenberg Wade , Pierce Ron
Published: February 2016

Understanding how climate change may facilitate species turnover is an important step in identifying potential conservation strategies. We used data from 33 sites in western Montana to quantify climate associations with native bull trout (Salvelinus confluentus) and non-native brown trout (Salmo trutta) abundance and population growth rates (λ). We estimated λ using exponential growth state-space models and delineated study sites based on bull trout use for either spawning and rearing (SR) or foraging, migrating, and overwintering (FMO) habitat. Bull trout abundance was negatively associated with mean August stream temperatures within SR habitat (r = −0.75). Brown trout abundance was generally highest at temperatures between 12 and 14 °C. We found bull trout λ were generally stable at sites with mean August temperature below 10 °C but significantly decreasing, rare, or extirpated at 58% of the sites with temperatures exceeding 10 °C. Brown trout λ were highest in SR and sites with temperatures exceeding 12 °C. Declining bull trout λ at sites where brown trout were absent suggest brown trout are likely replacing bull trout in a warming climate.
Molecular characterization and expression pattern of sorbitol transporter genePbSOT2in Pear (Pyrus bretschneideriRehd.) fruit
Authors: Wang Lifen , Qi Xiaoxiao , Yang Yanan , Zhang Shaoling
Published: February 2016

Sorbitol is a primary photosynthetic product and the principal photosynthetic transport substance in plants of the Rosaceae. Sorbitol transporters in the major facilitator superfamily (MFS) are important for phloem loading and sorbitol uptake into sink tissues. Here we report the cloning, localization, and expression analysis of a sorbitol transporter in fruit of Pyrus bretschneideri Rehd. cv. “Yali.” This clone, named PbSOT2, encoded a 537-aa protein with a calculated molecular mass of 57.92 kDa. The predicted protein had 12 transmembrane domains and belonged to the MFS carriers. PbSOT2 was sub-cellularly targeted to the plasma membrane. The expression of PbSOT2 was highest during the rapid enlargement phase of fruit (100 days after full bloom). In addition, the sorbitol content in fruit fluctuated within certain limits, but its proportion of total sugars decreased continuously. This work shows that PbSOT2 may play a role in fruit enlargement and the accumulation of hexose during fruit development.
Finite-size effects on semi-directed Barabási–Albert networks
Authors: Radwan M. A. , Sumour Muneer A. , Elbitar A. M. , Shabat M. M. , Lima F. W. S.
Published: February 2016

In scale-free Barabási–Albert (BA) networks, we study the finite-size effect at different number m of neighbors. So, we investigate the effects of finite network size N for the recently developed semi-directed BA networks (SDBA1 and SDBA2) at fixed [Formula: see text]) and show and explain the gap in the distribution of the number [Formula: see text] of neighbors of the nodes i.
A Simple and Efficient Arrowhead Detection Technique in Biomedical Images
Authors: Santosh K. C. , Alam Naved , Roy Partha Pratim , Wendling Laurent , Antani Sameer , Thoma George R.
Published: February 2016

In biomedical documents/publications, medical images tend to be complex by nature and often contain several regions that are annotated using arrows. In this context, an automated arrowhead detection is a critical precursor to region-of-interest (ROI) labeling and image content analysis. To detect arrowheads, in this paper, images are first binarized using fuzzy binarization technique to segment a set of candidates based on connected component (CC) principle. To select arrow candidates, we use convexity defect-based filtering, which is followed by template matching via dynamic time warping (DTW). The DTW similarity score confirms the presence of arrows in the image. Our test results on biomedical images from imageCLEF 2010 collection shows the interest of the technique, and can be compared with previously reported state-of-the-art results.
REVIEW ON IMPROVING WEAR AND CORROSION RESISTANCE OF STEELS VIA PLASMA ELECTROLYTIC SATURATION TECHNOLOGY
Authors: LIN NAIMING , XIE RUIZHEN , ZHOU PENG , ZOU JIAOJUAN , MA YONG , WANG ZHENXIA , HAN PENGJU , WANG ZHIHUA , TANG BIN , TIAN WEI
Published: February 2016

Plasma electrolytic saturation (PES) technique which holds the advantages of short treating time and limited heating influence and immediate quenching effect is conducted under high voltage power supply in some electrolyte has been extensively applied to enhance the surface performance of metallic materials. Steel is widely used in various fields thanks to its promising merits of easy workability, plasticity, toughness and weldability. It accounts for a large proportion in the application scope of the metal materials. Steel surfaces with good corrosion resistance, promising wear resistance and high hardness would be obtained by PES. Meanwhile, uniformed coatings can be formed without special requirements for substrate geometries using the PES. This paper first presents a brief introduction of the technological principle of PES. The status on studies and applications of PES for improving surface performance of steels has been reviewed.
COMPUTER AIDED DIAGNOSIS FOR CARDIOVASCULAR DISEASES BASED ON ECG SIGNALS: A SURVEY
Authors: FAUST OLIVER , NG E. Y. K.
Published: February 2016

The interpretation of Electroencephalography (ECG) signals is difficult, because even subtle changes in the waveform can indicate a serious heart disease. Furthermore, these waveform changes might not be present all the time. As a consequence, it takes years of training for a medical practitioner to become an expert in ECG-based cardiovascular disease diagnosis. That training is a major investment in a specific skill. Even with expert ability, the signal interpretation takes time. In addition, human interpretation of ECG signals causes interoperator and intraoperator variability. ECG-based Computer-Aided Diagnosis (CAD) holds the promise of improving the diagnosis accuracy and reducing the cost. The same ECG signal will result in the same diagnosis support regardless of time and place. This paper introduces both the techniques used to realize the CAD functionality and the methods used to assess the established functionality. This survey aims to instill trust in CAD of cardiovascular diseases using ECG signals by introducing both a conceptional overview of the system and the necessary assessment methods.
DIAGNOSIS OF MULTICLASS TACHYCARDIA BEATS USING RECURRENCE QUANTIFICATION ANALYSIS AND ENSEMBLE CLASSIFIERS
Authors: DESAI USHA , MARTIS ROSHAN JOY , ACHARYA U. RAJENDRA , NAYAK C. GURUDAS , SESHIKALA G. , SHETTY K RANJAN
Published: February 2016

Atrial Fibrillation (A-Fib), Atrial Flutter (AFL) and Ventricular Fibrillation (V-Fib) are fatal cardiac abnormalities commonly affecting people in advanced age and have indication of life-threatening condition. To detect these abnormal rhythms, Electrocardiogram (ECG) signal is most commonly visualized as a significant clinical tool. Concealed non-linearities in the ECG signal can be clearly unraveled using Recurrence Quantification Analysis (RQA) technique. In this paper, RQA features are applied for classifying four classes of ECG beats namely Normal Sinus Rhythm (NSR), A-Fib, AFL and V-Fib using ensemble classifiers. The clinically significant ([Formula: see text]) features are ranked and fed independently to three classifiers viz. Decision Tree (DT), Random Forest (RAF) and Rotation Forest (ROF) ensemble methods to select the best classifier. The training and testing of the feature set is accomplished using 10-fold cross-validation strategy. The RQA coefficients using ROF provided an overall accuracy of 98.37% against 96.29% and 94.14% for the RAF and DT, respectively. The results achieved evidently ratify the superiority of ROF ensemble classifier in the diagnosis of A-Fib, AFL and V-Fib. Precision of four classes is measured using class-specific accuracy (%) and reliability of the performance is assessed using Cohen’s kappa statistic ([Formula: see text]). The developed approach can be used in therapeutic devices and help the physicians in automatic monitoring of fatal tachycardia rhythms.