bluuebunny/crossref_metadata_2025 huggingface dataset:
Relaxed Selection Drives a Noisy Noncoding Transcriptome in Members of the Mycobacterium tuberculosis Complex
Authors: Dinan Adam M. , Tong Pin , Lohan Amanda J. , Conlon Kevin M. , Miranda-CasoLuengo Aleksandra A. , Malone Kerri M. , Gordon Stephen V. , Loftus Brendan J.
Published: August 2014

Related species are often used to understand the molecular underpinning of virulence through examination of a shared set of biological features attributable to a core genome of orthologous genes. An important but insufficiently studied issue, however, is the extent to which the regulatory architectures are similarly conserved. A small number of studies have compared the primary transcriptomes of different bacterial species, but few have compared closely related species with clearly divergent evolutionary histories. We addressed the impact of differing modes of evolution within the genus
Mycobacterium
through comparison of the primary transcriptome of
M. marinum
with that of a closely related lineage,
M. bovis
. Both are thought to have evolved from an ancestral generalist species, with
M. bovis
and other members of the
M. tuberculosis
complex having subsequently undergone downsizing of their genomes during the transition to obligate pathogenicity.
M. marinum
, in contrast, has retained a large genome, appropriate for an environmental organism, and is a broad-host-range pathogen. We also examined changes over a shorter evolutionary time period through comparison of the primary transcriptome of
M. bovis
with that of another member of the
M. tuberculosis
complex (
M. tuberculosis
) which possesses an almost identical genome but maintains a distinct host preference.

IMPORTANCE
Our comparison of the transcriptional start site (TSS) maps of
M. marinum
and
M. bovis
uncovers a pillar of conserved promoters, noncoding RNA (NCRNA), and a genome-wide signal in the −35 promoter regions of both species. We identify evolutionarily conserved transcriptional attenuation and highlight its potential contribution to multidrug resistance mediated through the transcriptional regulator
whiB7
. We show that a species population history is reflected in its transcriptome and posit relaxed selection as the main driver of an abundance of canonical −10 promoter sites in
M. bovis
relative to
M. marinum
. It appears that transcriptome composition in mycobacteria is driven primarily by the availability of such sites and that their frequencies diverge significantly across the mycobacterial clade. Finally, through comparison of
M. bovis
and
M. tuberculosis
, we illustrate that single nucleotide polymorphism (SNP)-driven promoter differences likely underpin many of the transcriptional differences between
M. tuberculosis
complex lineages.
Novel Entries in a Fungal Biofilm Matrix Encyclopedia
Authors: Zarnowski Robert , Westler William M. , Lacmbouh Ghislain Ade , Marita Jane M. , Bothe Jameson R. , Bernhardt Jörg , Lounes-Hadj Sahraoui Anissa , Fontaine Joël , Sanchez Hiram , Hatfield Ronald D. , Ntambi James M. , Nett Jeniel E. , Mitchell Aaron P. , Andes David R.
Published: August 2014

Virulence of
Candida
is linked with its ability to form biofilms. Once established, biofilm infections are nearly impossible to eradicate. Biofilm cells live immersed in a self-produced matrix, a blend of extracellular biopolymers, many of which are uncharacterized. In this study, we provide a comprehensive analysis of the matrix manufactured by
Candida albicans
both
in vitro
and in a clinical niche animal model. We further explore the function of matrix components, including the impact on drug resistance. We uncovered components from each of the macromolecular classes (55% protein, 25% carbohydrate, 15% lipid, and 5% nucleic acid) in the
C. albicans
biofilm matrix. Three individual polysaccharides were identified and were suggested to interact physically. Surprisingly, a previously identified polysaccharide of functional importance, β-1,3-glucan, comprised only a small portion of the total matrix carbohydrate. Newly described, more abundant polysaccharides included α-1,2 branched α-1,6-mannans (87%) associated with unbranched β-1,6-glucans (13%) in an apparent mannan-glucan complex (MGCx). Functional matrix proteomic analysis revealed 458 distinct activities. The matrix lipids consisted of neutral glycerolipids (89.1%), polar glycerolipids (10.4%), and sphingolipids (0.5%). Examination of matrix nucleic acid identified DNA, primarily noncoding sequences. Several of the
in vitro
matrix components, including proteins and each of the polysaccharides, were also present in the matrix of a clinically relevant
in vivo
biofilm. Nuclear magnetic resonance (NMR) analysis demonstrated interaction of aggregate matrix with the antifungal fluconazole, consistent with a role in drug impedance and contribution of multiple matrix components.

IMPORTANCE
This report is the first to decipher the complex and unique macromolecular composition of the
Candida
biofilm matrix, demonstrate the clinical relevance of matrix components, and show that multiple matrix components are needed for protection from antifungal drugs. The availability of these biochemical analyses provides a unique resource for further functional investigation of the biofilm matrix, a defining trait of this lifestyle.
Association between red cell distribution width and acute pancreatitis: a cross-sectional study
Authors: Yao Jinmei , Lv Guocai
Published: August 2014

Objective

We investigated whether red cell distribution width (RDW) was associated with mortality in patients with acute pancreatitis (AP).

Design

A cross-sectional study.

Setting

Patients with AP were recruited in the emergency department and healthy individuals were recruited in healthcare centre in the First Affiliated Hospital of Zhejiang University.

Participants

A total of 106 patients with AP and 204 healthy individuals were enrolled.

Primary and secondary outcome measures

Haematology and biochemistry results of the first test after admission were collected. The significance of the differences in RDW values among healthy individuals, non-survivors of patients with AP, and survivors of patients with AP was determined using one-way analysis of variance. Patients with AP were divided into three groups according to RDW tertiles. All patients with AP were followed up for at least 3 months. Receiver-operating characteristic (ROC) curve analysis and Kaplan-Meier analysis were used to evaluate RDW values to predict mortality of patients with AP.

Results

The RDW values were non-survivors of patients with AP>healthy individuals>survivors of patients with AP. Patients with AP with the highest RDW tertiles had the lowest levels of Ca, total protein, albumin, haemoglobin, white and red blood cell count, but the highest mortality. The area under the ROC curve of RDW was 0.846 (95% CI 0.727 to 0.964, p<0.001). With a cut-off value of 14.2 for RDW, sensitivity and specificity of RDW to predict mortality were 75.0% and 89.8%, and Kaplan-Meier analysis showed an increase in probability of death with high RDW values.

Conclusions

There is significant association between RDW and mortality of patients with AP.
What is the data-defined length for short time from diagnosis to death that is associated with a low rate of palliative care enrolment for persons with colorectal cancer?
Authors: Roach Sheri , Steenbeek Audrey , Abdolell Mohamed , Urquhart Robin , Johnston Grace
Published: August 2014

Objective

Prior research has demonstrated that people who die shortly after receiving a cancer diagnosis are at increased risk for not being referred to palliative care. No previous studies have empirically derived the length of time between diagnosis and death associated with increased risk. The objective of this study was to identify the length of time between diagnosis and death associated with increased risk for non-enrolment in a palliative care programme.

Methods

Binary recursive partitioning was employed to derive the cut-point for the number of days from colorectal cancer diagnosis to death predictive of a high risk for non-enrolment in a palliative care programme in two health districts in Nova Scotia, Canada. The study included all adults (≥20 years) who were diagnosed with colorectal cancer in the two districts between 1 January 2001 and 31 December 2005 and who died between 1 January 2001 and 31 December 2008 (n=894).

Results

Individuals who died within 18.5 days following diagnosis were at highest risk for non-enrolment in palliative care. Of the 60 adults who died in <18.5 days, 16.7% were enrolled in a palliative care programme; of the 835 adults who died ≥18.5 days after diagnosis, 65.9% were enrolled.

Conclusions

This data-driven approach may be used to define the short diagnosis-to-death time frame at which individuals are at increased risk for non-enrolment in palliative care programmes. This approach allows researchers to further investigate and compare empirically-derived cut-points that identify those who die quickly and are at risk of not receiving palliative care.
Renal denervation and blood pressure reduction in resistant hypertension: a systematic review and meta-analysis
Authors: Kwok Chun Shing , Loke Yoon K , Pradhan Shiva , Keavney Bernard , El-Omar Magdi , Mamas Mamas A
Published: August 2014

Objective

The objective of this study is to evaluate the efficacy and safety of renal denervation in patients with resistant hypertension.

Methods

We searched MEDLINE and EMBASE for studies that evaluated the use of catheter-based renal sympathetic denervation compared to a control group and reported blood pressure results at follow-up. Data was extracted from relevant studies and pooled estimates for blood pressure were determined using the inverse variance method for meta-analysis with mean difference.

Results

We identified 12 studies (three randomised controlled trials (n=688), eight prospective observational studies (n=478) and one observational study with matched controls (n=310)). Data from SYMPLICITY HTN-3, the only high-quality blinded randomised control trial suggests that there is no significant difference in change in systolic (−2.30 95% CI −6.90 to 2.30 mm Hg) or diastolic (−1.96 95% CI −4.98 to 1.06 mm Hg) blood pressure at 6 months. The pooled data from two unblinded trials of lower quality showed significant reduction in change in systolic (−27.36 95% CI −37.08 to −24.61 mm Hg) and diastolic blood pressure (−9.62 95% CI −14.51 to −4.72 mm Hg). In terms of safety, SYMPLICITY HTN-3 found no significant differences between treatment and control group in terms of death, myocardial infarction, new onset renal disease, stroke and hypertensive emergencies.

Conclusions

In conclusion, while poor quality unblinded studies provide evidence that renal denervation using catheter-based systems is effective in reducing systolic and diastolic blood pressure in resistant hypertension, the largest randomised controlled trial to date (SYMPLICITY HTN-3) failed to demonstrate any benefit.
Trends in left ventricular assist device use and outcomes among Medicare beneficiaries, 2004–2011
Authors: Lampropulos Julianna F , Kim Nancy , Wang Yun , Desai Mayur M , Barreto-Filho José Augusto S , Dodson John A , Dries Daniel L , Mangi Abeel A , Krumholz Harlan M
Published: August 2014

Objective

To characterise the trends in the left ventricular assist device (LVAD) implantation rates and outcomes between 2004 and 2011 in the Medicare population. Since the approval of the HeartMate II in 2008, the use of LVADs has steadily climbed. Given the increase in LVAD use, issues around discharge disposition, post-implant hospitalisations and costs require further understanding.

Methods

We examined LVAD implantation rates and short-term and long-term outcomes among Medicare fee-for-service beneficiaries hospitalised for LVAD implantation. We also conducted analyses among survivors 1-year post-discharge to examine rehospitalisation rates. Lastly, we reported Centers for Medicare & Medicaid Services (CMS) payments for both index hospitalisation and rehospitalisations 1 year post-discharge.

Results

A total of 2152 LVAD implantations were performed with numbers increasing from 107 in 2004 to 612 in 2011. The 30-day mortality rate decreased from 52% to 9%, and 1-year mortality rate decreased from 69% to 31%. We observed no change in overall length of stay, but post-procedure length of stay increased. We also found an increase in home discharge dispositions from 26% to 53%. Between 2004 and 2010, the rehospitalisation rate increased and the number of hospital days decreased. The adjusted CMS payment for the index hospitalisation increased from $188 789 to $225 697 over time but decreased for rehospitalisation from $60 647 to $53 630.

Conclusions

LVAD implantations increased over time. We found decreasing 30-day and 1-year mortality rates and increasing home discharge disposition. The proportion of patients rehospitalised among 1-year survivors remained high with increasing index hospitalisation cost, but decreasing post-implantation costs over time.
Clinical and prognostic implications of serum and tissue prolactin levels in canine mammary tumours
Authors: Queiroga F. L. , Pérez‐Alenza M. D. , González Gil A. , Silvan G. , Peña L. , Illera J. C.
Published: August 2014

The biological implications of serum and tissue prolactin levels in canine mammary tumours (CMT) have been previously described although the influence of this hormone on inflammatory mammary carcinomas as well as its value as prognostic indicator remains to be properly clarified. Prolactin determinations were carried out by enzyme immunoassay in tumour tissue and serum of 39 female dogs with spontaneous CMT and in normal mammary gland and serum of 10 controls. Prolactin levels were higher in the case of CMT compared to controls (P<0.05). In malignant CMT, higher levels of tissue prolactin were associated with the occurrence of tumour relapse and/or distant metastasis (P<0.05). Inflammatory mammary carcinomas presented the highest values for tissue prolactin concentrations with concentrations significantly higher than other malignant non‐inflammatory mammary carcinoma tumours (P<0.05). The high levels of prolactin found in cases with poor clinical prognoses, including inflammatory mammary carcinoma, open the possibility of being able to better stratify clinical cases in malignant CMT with a view to tailoring treatment appropriately.
Adverse events associated with chloramphenicol use in dogs: a retrospective study (2007–2013)
Authors: Short J. , Zabel S. , Cook C. , Schmeitzel L.
Published: August 2014

Chloramphenicol is a broad spectrum antibiotic that has been increasingly utilised since the emergence of methicillin‐resistant staphylococcal infections. Due to toxicities in humans, use of the drug has been limited. In dogs, gastrointestinal signs are common adverse events described, and bone marrow suppression is possible. The aim of this study was to evaluate the adverse events associated with chloramphenicol in dogs seen by one specialty practice from January 2007 through June 2013. The database was searched for all dogs prescribed chloramphenicol during the time period. Dosage, length of treatment, age and body weight of the dogs were recorded as well as any adverse events that occurred during treatment. A total of 105 cases were evaluated. Thirty‐nine dogs experienced at least one adverse event while on the medication. The most commonly noted were gastrointestinal signs and hindlimb weakness. The mean body weight for dogs with hindlimb weakness was 35.3 kg, which was significant. Resolution was documented in 54 per cent of cases when the drug was discontinued. Methicillin‐resistant Staphylococcus pseudintermedius on bacterial culture was listed as the reason for chloramphenicol use in 76 per cent of the cases. Based on this information, further prospective studies are recommended to evaluate the reproducibility of this report.
Cosmic ray modulation in high and middle latitudes during solar cycles 22 and 23
Authors: Okpala Kingsley Chukwudi , Okeke Francisca Nneka , Ugwuoke Anselem Ikechukwu
Published: August 2014

Galactic cosmic rays are modulated in the heliosphere primarily by the global merged interaction regions with intense magnetic fields, which leads to a decrease in galactic cosmic rays throughout the heliosphere. Using long-term averages of solar wind (SW) component parameters in addition to cosmic ray count rates of four neutron monitors with different rigidity cutoffs, we analyzed the effect of these SW components on the count rates under different interplanetary magnetic field (IMF) disturbance levels. From first-order partial correlation, we found that the IMF-B was the most dominant modulating parameter, especially during quiet conditions and the SW dynamic pressure was more effective during disturbed conditions. The influence of more subtle parameters like wind speed, Bz component, and proton density were masked by these dominant parameters: IMF total B, and SW dynamic pressure.
Influence of pulse duration on above-threshold ionization in intensive circularly polarized laser field
Authors: Yuan Minghu , Wang Dandan , Chen Junsheng , Fu Aiping , Tian Fenghui , Chu Tianshu
Published: August 2014

The above-threshold ionization (ATI) process of argon in intensive circularly polarized laser field has been investigated by solving the time-dependent Schrödinger equation in length gauge with emphasis on pulse duration effect. It is shown that the influence of pulse duration is obvious on the transition between multiple-photon and tunneling ionization regimes when the Keldysh parameter is no more than 3.25. That is, photoelectron ionization by shorter pulse occurs in the tunneling regime mainly, and yet the multiple-photon absorption appears more easily with longer pulse. However, such influence disappears when the Keldysh parameter is sufficiently large and the ATI always appears in the multiple-photon ionization regime.
Protective effect of co-administration of rosuvastatin and probucol on atherosclerosis in rats
Authors: Chen Zuoyuan , Li Shan , Zhao Wenna , Chen Xiuhua , Wang Xiaxia
Published: August 2014

This study aimed to study the combined effect of rosuvastatin and probucol on atherosclerosis (AS) in rats. In total, 95 male Wistar rats were divided into 5 groups: 25 in the control group (A), 25 in the model group (B), 15 in the rosuvastatin group (C), 15 in the probucol group (D), and 15 in the rosuvastatin combined probucol group (E). A high-lipid diet and vitamin D3 were administered to establish AS rat model. Groups C, D, and E received corresponding drugs. Blood lipids, oxidized low-density lipoprotein (OX-LDL), malonaldehyde (MDA), superoxide dismutase (SOD), adiponectin (APN), and vascular endothelial cadherin (VE-cadherin) were measured. Platelet endothelial cell adhesion molecule-1 (PECAM-1) was detected by immune histochemistry. In groups B–E, AS rat models were successfully constructed. In groups C–E, blood lipids, OX-LDL, VE-cadherin, MDA, PECAM-1, and intimal thickness were decreased (p < 0.01), while SOD and APN were increased (p < 0.05), compared with that in group B. Furthermore, group E had lower levels of OX-LDL, MDA, and PECAM-1 but higher levels of SOD and APN and attenuated intimal thickening compared with groups C or D (p < 0.05). Administering rosuvastatin and probucol could attenuate AS lesions through modulation of oxidative stress, PECAM-1, and APN. Both drugs might help slow the progression of AS.
The group theoretical description of the three-body problem
Authors: Nikonov V. A. , Nyiri J.
Published: August 2014

The group theoretical description of the three-particle problem provides successful techniques for the solution of different questions. We present here a review of this approach.
On sinh–Gordon thermodynamic Bethe ansatz and fermionic basis
Authors: Negro Stefano
Published: August 2014

We review the construction of the fermionic basis for sinh–Gordon model and investigate numerically the ultraviolet limit of the one-point functions. We then compare the predictions obtained from this formalism against previously established results.
Energy carries information
Authors: Ilgin Irfan , Yang I.-Sheng
Published: August 2014

We show that for every qubit of quantum information, there is a well-defined notion of "the amount of energy that carries it," because it is a conserved quantity. This generalizes to larger systems and any conserved quantities: the eigenvalue spectrum of conserved charges has to be preserved while transferring quantum information. It is possible to "apparently" violate these conservations by losing a small fraction of information, but that must invoke a specific process which requires a large scale coherence. We discuss its implication regarding the black hole information paradox.
Zero-one-only process: A correlated random walk with a stochastic ratchet
Authors: Baek Seung Ki , Jeong Hawoong , Son Seung-Woo , Kim Beom Jun
Published: August 2014

The investigation of random walks is central to a variety of stochastic processes in physics, chemistry and biology. To describe a transport phenomenon, we study a variant of the one-dimensional persistent random walk, which we call a zero-one-only process. It makes a step in the same direction as the previous step with probability p, and stops to change the direction with 1 − p. By using the generating-function method, we calculate its characteristic quantities such as the statistical moments and probability of the first return.
The structural and elastic properties of TMB4(TM =V,Cr,Mn) under pressure: A first-principles study
Authors: Wu Xiao-Long , Zhou Xiao-Lin , Chang Jing
Published: August 2014

The structural and elastic properties of 3d transition metal tetraboride TM B4(TM = V , Cr , Mn ) have been studied by using density functional theory (DFT) within the local density approximation (LDA) and generalized gradient approximation (GGA) for exchange-correlation function. Our results are in agreement well with available experimental data and previous theoretical studies. The full elastic constants and bulk shear modulus of TM B4(TM = V , Cr , Mn ) are obtained in the wide pressure range. Results indicated that these phases of TM B4(TM = V , Cr , Mn ) are strongly pressure dependent. And the CrB4in Immm structure is the most ultraincompressible among the considered phases at 0 GPa. By the mechanical stability criteria, it is predicted that these phases of TM B4(TM = V , Cr , Mn ) compounds are stable up to 100 GPa. In addition, the calculated B/G ratio indicated that all the structures of TM B4(TM = V , Cr , Mn ) possess brittle nature in the range of pressure from 0 GPa to 100 GPa except the Pnnm structure of MnB4, which is higher than 1.75, indicating that the Pnnm structure of MnB4is prone to ductility when the pressure is above 73 GPa.
Mixing for invertible dynamical systems with infinite measure
Authors: Melbourne Ian
Published: August 2014

In a recent paper, Melbourne and Terhesiu [Operator renewal theory and mixing rates for dynamical systems with infinite measure, Invent. Math.189 (2012) 61–110] obtained results on mixing and mixing rates for a large class of noninvertible maps preserving an infinite ergodic invariant measure.

Here, we are concerned with extending these results to the invertible setting. Mixing is established for a large class of infinite measure invertible maps. Assuming additional structure, in particular exponential contraction along stable manifolds, it is possible to obtain good results on mixing rates and higher order asymptotics.
Weighted PI index of corona product of graphs
Authors: Pattabiraman K. , Kandan P.
Published: August 2014

In this paper, we present exact formula for the weighted PI index of corona product of two connected graphs in terms of other graph invariants including the PI index, first Zagreb index and second Zagreb index. Then, we apply our result to compute the weighted PI indices of t-fold bristled graph, bottleneck graph, sunlet graph, star graph, fan graph, wheel graph and some classes of bridge graphs.
Statistical analysis of road–vehicle–driver interaction as an enabler to designing behavioral models
Authors: Chakravarty T. , Chowdhury A. , Ghose A. , Bhaumik C. , Balamuralidhar P.
Published: August 2014

Telematics form an important technology enabler for intelligent transportation systems. One application of the same is that by deploying on-board diagnostic devices, the signatures of vehicle vibration along with its location and time are recorded. Detailed analyses of the collected signatures offer deep insights into the state of the objects under study. Towards that objective, we carried out experiments by deploying telematics device in one of the office bus that ferries employees to office and back. Data is collected from 3-axis accelerometer, GPS speed and the time for all the journeys. In this paper, we present initial results of the above exercise by applying statistical methods to derive information through systematic analysis of the data collected over four months. It is demonstrated that the higher order derivative of the measured Z-axis acceleration samples display the properties of Weibull distribution when the time axis is replaced by the amplitude of such processed acceleration data. Such an observation offers us a method to predict future behavior where deviations from prediction are classified as context-based aberrations or progressive degradation of the system. In addition, we capture the relationship between speed of the vehicle and median of the jerk energy samples using regression analysis. That analysis is further used to identify low, normal and high JE values for a velocity and classify journey at a micro-trip (small section of a trip) level. Such results offer an opportunity to develop a robust method to model road–vehicle interaction thereby enabling us to predict such like driving behavior and condition-based maintenance, etc.
Framing It Right: China–EU Relations and Patterns of Interaction on Climate Change
Authors: GIPPNER Olivia
Published: August 2014

In the field of Climate Change China has been an increasingly important member of the UN Framework Convention on Climate Change (UNFCCC) process and since the mid-2000s, a key target of European engagement policies in the broader framework of the "EU–China strategic partnership". But how do Chinese decision-makers perceive these efforts? The way or "frame" they use to look at climate change also determines their mutual perceptions of each other's efforts on climate change. In order to better understand and evaluate how Chinese climate elites see the EU, the article first details the nascent theoretical debate on diagnostic, prognostic, and motivational framing and critically assesses the Chinese discourse on climate change. As an empirical, qualitative study, the article draws on interviews carried out in Beijing, Bonn, and Warsaw in 2012 and 2013. The article's main argument is that the Chinese frame toward the issue of climate change has been converging toward the European frame in the 2000s. During these years increasing energy intensity and environmental pollution raised awareness of climate change effects and vulnerability within the population. The Chinese ascent to the status of the second biggest world economy and increasing engagement in multilateral cooperation has a further effect on its framing of climate change. Located in the discourse post-Copenhagen, it attempts to capture the new global dynamics that have been integral to the subsequent rounds of negotiation and epitomized by the Chinese position during the 2011 COP17 Summit in Durban.
Efficient High-Rate Secret Key Extraction in Wireless Sensor Networks Using Collaboration
Authors: Premnath Sriram Nandha , Croft Jessica , Patwari Neal , Kasera Sneha Kumar
Published: August 2014

Secret key establishment is a fundamental requirement for private communication between two entities. In this article, we propose and evaluate a new approach for secret key extraction where multiple sensors collaborate in exchanging probe packets and collecting channel measurements. Essentially, measurements from multiple channels have a substantially higher differential entropy compared to the measurements from a single channel, thereby resulting in more randomness in the information source for key extraction, and this in turn produces
stronger
secret keys. We also explore the fundamental trade-off between the quadratic increase in the number of measurements of the channels due to multiple nodes per group versus a linear reduction in the sampling rate and a linear increase in the time gap between bidirectional measurements. To experimentally evaluate collaborative secret key extraction in wireless sensor networks, we first build a simple yet flexible testbed with multiple TelosB sensor nodes. Next, we perform large-scale experiments with different configurations of collaboration. Our experiments show that in comparison to the 1 × 1 configuration, collaboration among sensor nodes significantly increases the secret bit extraction per second, per probe, as well as per millijoule of transmission energy. In addition, we show that the collaborating nodes can improve the performance further when they exploit both space and frequency diversities.
Engineering Parallel Algorithms
Authors: Sanders Peter
Published: August 2014

In the past, parallel processing was a specialized approach to high-performance computing. Today, we have to rethink the computational cores of algorithmic and data structures applications. In this article we discuss how this process of rethinking can be understood using algorithm engineering.
Data Pre-Forwarding for Opportunistic Data Collection in Wireless Sensor Networks
Authors: Wu Xiuchao , Brown Kenneth N. , Sreenan Cormac J.
Published: August 2014

Opportunistic data collection in wireless sensor networks uses passing smartphones to collect data from sensor nodes, thus avoiding the cost of multiple static sink nodes. Based on the observed mobility patterns of smartphone users, sensor data should be preforwarded to the nodes that are visited more frequently with the aim of improving network throughput. In this article, we construct a formal network model and an associated theoretical optimization problem to maximize the throughput subject to energy constraints of sensor nodes. Since a centralized controller is not available in opportunistic data collection, data pre-forwarding (DPF) must operate as a distributed mechanism in which each node decides when and where to forward data based on local information. Hence, we develop a simple distributed DPF mechanism with two heuristic algorithms, implement this proposal in Contiki-OS, and evaluate it thoroughly. We demonstrate empirically, in simulations, that our approach is close to the optimal solution obtained by a centralized algorithm. We also demonstrate that this approach performs well in scenarios based on real mobility traces of smartphone users. Finally, we evaluate our proposal on a small laboratory testbed, demonstrating that the distributed DPF mechanism with heuristic algorithms performs as predicted by simulations, and thus that it is a viable technique for opportunistic data collection through smartphones.
Barrier Coverage by Sensors with Adjustable Ranges
Authors: Fan Haosheng , Li Minming , Sun Xianwei , Wan Peng-Jun , Zhao Yingchao
Published: August 2014

One of the most fundamental tasks of wireless sensor networks is to provide coverage of the deployment region. We study the coverage of a line interval with a set of wireless sensors with adjustable coverage ranges. Each coverage range of a sensor is an interval centered at that sensor whose length is decided by the power the sensor chooses. The objective is to find a range assignment with the minimum cost. There are two variants of the optimization problem. In the
discrete
variant, each sensor can only choose from a finite set of powers, whereas in the
continuous
variant, each sensor can choose power from a given interval. For the discrete variant of the problem, a polynomial-time exact algorithm is designed. For the continuous variant of the problem, NP-hardness of the problem is proved and followed by an ILP formulation. Then, constant-approximation algorithms are designed when the cost for all sensors is proportional to
r
κ
for some constant κ ≥ 1, where
r
is the covering radius corresponding to the chosen power. Specifically, if κ = 1, we give a 1.25-approximation algorithm and a fully polynomial-time approximation scheme; if κ > 1, we give a 2-approximation algorithm. We also show that the approximation analyses are tight.
Evolutionary algorithms for object-oriented test data generation
Authors: Suresh Yeresime , Rath Santanu Ku.
Published: August 2014

Identification of effective test data for testing a software application is a difficult task. The presence of a large number of decision nodes in a program makes it difficult to test all modules, and as a result consumes a lot of testers' time. The effort required for testing can be reduced by automatic generation of test data for particular modules. Out of numerous optimization algorithms, evolutionary algorithms can help in this scenario by generating relevant test data. The ability of evolutionary algorithms to obtain effective solutions from a very large search space of candidate solutions can be used for automatic test data generation. This paper explores the automatic generation of test data for object-oriented programs based on the concept of the extended control flow graph by utilizing the binary particle swarm optimization and artificial bee colony optimization algorithms. The proposed approach is applied to a bank ATM case study. The experimental results obtained, when compared with the clonal selection algorithm, reveal that the artificial bee colony optimization algorithm is more efficient for generating effective test data than the binary particle swarm optimization and clonal selection algorithms.
Why interaction between metrics should be considered in the development of software quality models
Authors: Goyal Rinkaj , Chandra Pravin , Singh Yogesh
Published: August 2014

This study examines the need to consider interactions between the measurements (metrics) of different quality factors in the development of software quality models. Though the correlation between metrics has been explored to a considerable depth in the development of these models, consideration of interactions between predictors is comparatively new in software engineering. This preliminary study is supported by statistically-proven results, differentiating interactions with correlation analysis.

The issues raised here will assist analysts to improve empirical analyses by incorporating interactions in software quality model development, where amalgamating effects between different characteristics or subcharacteristics are observed.
Skeletal muscle atrophy and the E3 ubiquitin ligases MuRF1 and MAFbx/atrogin-1
Authors: Bodine Sue C. , Baehr Leslie M.
Published: August 2014

Muscle RING finger 1 (MuRF1) and muscle atrophy F-box (MAFbx)/atrogin-1 were identified more than 10 years ago as two muscle-specific E3 ubiquitin ligases that are increased transcriptionally in skeletal muscle under atrophy-inducing conditions, making them excellent markers of muscle atrophy. In the past 10 years much has been published about MuRF1 and MAFbx with respect to their mRNA expression patterns under atrophy-inducing conditions, their transcriptional regulation, and their putative substrates. However, much remains to be learned about the physiological role of both genes in the regulation of mass and other cellular functions in striated muscle. Although both MuRF1 and MAFbx are enriched in skeletal, cardiac, and smooth muscle, this review will focus on the current understanding of MuRF1 and MAFbx in skeletal muscle, highlighting the critical questions that remain to be answered.
Expression of microRNAs and their target genes and pathways associated with ovarian follicle development in cattle
Authors: Zielak-Steciwko A. E. , Browne J. A. , McGettigan P. A. , Gajewska M. , Dzięcioł M. , Szulc T. , Evans A. C. O.
Published: August 2014

Development of ovarian follicles is controlled at the molecular level by several gene products whose precise expression leads to regression or ovulation of follicles. MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression through sequence-specific base pairing with target messenger RNAs (mRNAs) causing translation repression or mRNA degradation. The aim of this study was to identify miRNAs expressed in theca and/or granulosa layers and their putative target genes/pathways that are involved in bovine ovarian follicle development. By using miRCURY microarray (Exiqon) we identified 14 and 49 differentially expressed miRNAs ( P < 0.01) between dominant and subordinate follicles in theca and granulosa cells, respectively. The expression levels of four selected miRNAs were confirmed by qRT-PCR. To identify target prediction and pathways of differentially expressed miRNAs we used Union of Genes option in DIANA miRPath v.2.0 software. The predicted targets for these miRNAs were enriched for pathways involving oocyte meiosis, Wnt, TGF-beta, ErbB, insulin, P13K-Akt, and MAPK signaling pathways. This study identified differentially expressed miRNAs in the theca and granulosa cells of dominant and subordinate follicles and implicates them in having important roles in regulating known molecular pathways that determine the fate of ovarian follicle development.
Pachydermodactyly Treated with Tranilast in a Young Girl
Authors: Higuchi Chikahisa , Tomita Tetsuya , Yoshikawa Hideki
Published: August 2014

Introduction.Pachydermodactyly is a rare disease with asymptomatic swelling of proximal interphalangeal joints. This disorder should be considered in the differential diagnosis of juvenile idiopathic arthritis or rheumatoid arthritis. However, pachydermodactyly is not well recognized by many orthopaedic surgeons and rheumatologists.Case Presentation.We report herein a case of a 13-year-old girl with pachydermodactyly. She presented to our clinic with symmetrical swelling of digits II through V without functional loss for the last 4 years. X-ray examination demonstrated no bone or joint destruction and magnetic resonance images showed only thickened skin tissues. No inflammatory signs were seen with laboratory blood tests. We reached a diagnosis of pachydermodactyly by exclusion. We had administered tranilast to her for 6 months and her symptom slightly improved.Conclusion.It is important to recognize pachydermodactyly and be able to differentiate it from other causes of PIP joint swelling such as rheumatoid arthritis, although pachydermodactyly is rare and benign. Physicians including orthopaedists and rheumatologists should make a prompt diagnosis to avoid unnecessary investigations and prevent the patient from receiving inappropriate treatment with steroids or cytotoxic agents. On the other hand, tranilast might be an effective drug to pachydermodactyly.
Voice Activity Detection in Noisy Environments Based on Double-Combined Fourier Transform and Line Fitting
Authors: Park Jinsoo , Kim Wooil , Han David K. , Ko Hanseok
Published: August 2014

A new voice activity detector for noisy environments is proposed. In conventional algorithms, the endpoint of speech is found by applying an edge detection filter that finds the abrupt changing point in a feature domain. However, since the frame energy feature is unstable in noisy environments, it is difficult to accurately find the endpoint of speech. Therefore, a novel feature extraction algorithm based on the double-combined Fourier transform and envelope line fitting is proposed. It is combined with an edge detection filter for effective detection of endpoints. Effectiveness of the proposed algorithm is evaluated and compared to other VAD algorithms using two different databases, which are AURORA 2.0 database and SITEC database. Experimental results show that the proposed algorithm performs well under a variety of noisy conditions.
Opportunistic Maintenance Policy for a System with Hidden Failures: A Multicriteria Approach Applied to an Emergency Diesel Generator
Authors: Cavalcante Cristiano A. V. , Lopes Rodrigo S.
Published: August 2014

This paper aims to develop a maintenance policy to support the maintenance decisions of an emergency system that supplies electricity when failure of the primary system occurs in a health facility. An Opportunistic maintenance policy was developed, in which failures are hidden and inspections are performed to detect the state of the system and subsystems. Failure in the system can have negative consequences for the health unit. A multicriteria model that considers cost and availability criteria and preference of the maintenance manager of the health unit was developed.
Low-Complexity Transmit Antenna Selection and Beamforming for Large-Scale MIMO Communications
Authors: Qian Kun , Wang Wen-Qin , Shao Huaizong
Published: August 2014

Transmit antenna selection plays an important role in large-scale multiple-input multiple-output (MIMO) communications, but optimal large-scale MIMO antenna selection is a technical challenge. Exhaustive search is often employed in antenna selection, but it cannot be efficiently implemented in large-scale MIMO communication systems due to its prohibitive high computation complexity. This paper proposes a low-complexity interactive multiple-parameter optimization method for joint transmit antenna selection and beamforming in large-scale MIMO communication systems. The objective is to jointly maximize the channel outrage capacity and signal-to-noise (SNR) performance and minimize the mean square error in transmit antenna selection and minimum variance distortionless response (MVDR) beamforming without exhaustive search. The effectiveness of all the proposed methods is verified by extensive simulation results. It is shown that the required antenna selection processing time of the proposed method does not increase along with the increase of selected antennas, but the computation complexity of conventional exhaustive search method will significantly increase when large-scale antennas are employed in the system. This is particularly useful in antenna selection for large-scale MIMO communication systems.
A Discrete Wavelet Based Feature Extraction and Hybrid Classification Technique for Microarray Data Analysis
Authors: Bennet Jaison , Arul Ganaprakasam Chilambuchelvan , Arputharaj Kannan
Published: August 2014

Cancer classification by doctors and radiologists was based on morphological and clinical features and had limited diagnostic ability in olden days. The recent arrival of DNA microarray technology has led to the concurrent monitoring of thousands of gene expressions in a single chip which stimulates the progress in cancer classification. In this paper, we have proposed a hybrid approach for microarray data classification based on nearest neighbor (KNN), naive Bayes, and support vector machine (SVM). Feature selection prior to classification plays a vital role and a feature selection technique which combines discrete wavelet transform (DWT) and moving window technique (MWT) is used. The performance of the proposed method is compared with the conventional classifiers like support vector machine, nearest neighbor, and naive Bayes. Experiments have been conducted on both real and benchmark datasets and the results indicate that the ensemble approach produces higher classification accuracy than conventional classifiers. This paper serves as an automated system for the classification of cancer and can be applied by doctors in real cases which serve as a boon to the medical community. This work further reduces the misclassification of cancers which is highly not allowed in cancer detection.
Indoor Massive MIMO Channel Modelling Using Ray-Launching Simulation
Authors: Weng Jialai , Tu Xiaoming , Lai Zhihua , Salous Sana , Zhang Jie
Published: August 2014

Massive multi-input multioutput (MIMO) is a promising technique for the next generation of wireless communication networks. In this paper, we focus on using the ray-launching based channel simulation to model massive MIMO channels. We propose one deterministic model and one statistical model for indoor massive MIMO channels, both based on ray-launching simulation. We further propose a simplified version for each model to improve computational efficiency. We simulate the models in indoor wireless network deployment environments and compare the simulation results with measurements. Analysis and comparison show that these ray-launching based simulation models are efficient and accurate for massive MIMO channel modelling, especially with application to indoor network planning and optimisation.
Absorbed Radiation Dose in Radiosensitive Organs Using 64- and 320-Row Multidetector Computed Tomography: A Comparative Study
Authors: Khan Atif N. , Shuaib Waqas , Nikolic Boris , Khan Mohammad K. , Kang Jian , Khosa Faisal
Published: August 2014

Aim. To determine absorbed radiation dose (ARD) in radiosensitive organs during prospective and full phase dose modulation using ECG-gated MDCTA scanner under 64- and 320-row detector modes.Methods. Female phantom was used to measure organ radiation dose. Five DP-3 radiation detectors were used to measure ARD to lungs, breast, and thyroid using the Aquilion ONE scanner in 64- and 320-row modes using both prospective and dose modulation in full phase acquisition. Five measurements were made using three tube voltages: 100, 120, and 135 kVp at 400 mA at heart rate (HR) of 60 and 75 bpm for each protocol. Mean acquisition was recorded in milligrays (mGy).Results. Mean ARD was less for 320-row versus 64-row mode for each imaging protocol. Prospective EKG-gated imaging protocol resulted in a statistically lower ARD using 320-row versus 64-row modes for midbreast (6.728 versus 19.687 mGy,P<0.001), lung (6.102 versus 21.841 mGy,P<0.001), and thyroid gland (0.208 versus 0.913 mGy;P<0.001). Retrospective imaging using 320- versus 64-row modes showed lower ARD for midbreast (10.839 versus 43.169 mGy,P<0.001), lung (8.848 versus 47.877 mGy,P<0.001), and thyroid gland (0.057 versus 2.091 mGy;P<0.001). ARD reduction was observed at lower kVp and heart rate.Conclusions. Dose reduction to radiosensitive organs is achieved using 320-row compared to 64-row modes for both prospective and retrospective gating, whereas 64-row mode is equivalent to the same model 64-row MDCT scanner.
Recent Advances in Application of Biosensors in Tissue Engineering
Authors: Hasan Anwarul , Nurunnabi Md , Morshed Mahboob , Paul Arghya , Polini Alessandro , Kuila Tapas , Al Hariri Moustafa , Lee Yong-kyu , Jaffa Ayad A.
Published: August 2014

Biosensors research is a fast growing field in which tens of thousands of papers have been published over the years, and the industry is now worth billions of dollars. The biosensor products have found their applications in numerous industries including food and beverages, agricultural, environmental, medical diagnostics, and pharmaceutical industries and many more. Even though numerous biosensors have been developed for detection of proteins, peptides, enzymes, and numerous other biomolecules for diverse applications, their applications in tissue engineering have remained limited. In recent years, there has been a growing interest in application of novel biosensors in cell culture and tissue engineering, for example, real-time detection of small molecules such as glucose, lactose, and H2O2as well as serum proteins of large molecular size, such as albumin and alpha-fetoprotein, and inflammatory cytokines, such as IFN-g and TNF-α. In this review, we provide an overview of the recent advancements in biosensors for tissue engineering applications.