bluuebunny/crossref_metadata_2025 huggingface dataset:
Recognition of Streptococcuspseudoporcinus Colonization in Women as a Consequence of Using Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Group B Streptococcus Identification
Authors: Suwantarat Nuntra , Grundy Maureen , Rubin Mayer , Harris Renee , Miller Jo-Anne , Romagnoli Mark , Hanlon Ann , Tekle Tsigereda , Ellis Brandon C. , Witter Frank R. , Carroll Karen C.
Published: October 2015

During a 14-month period of using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) for group B streptococcus (GBS) identification, we recovered 32 (1%)
Streptococcus
pseudoporcinus
isolates from 3,276 GBS screening cultures from female genital sources (25 isolates from pregnant women and 7 from nonpregnant women). An additional two
S. pseudoporcinus
isolates were identified from a urine culture and a posthysterectomy wound culture. These isolates were found to cross-react with three different GBS antigen agglutination kits, PathoDx (Remel) (93%), Prolex (Pro-Lab Diagnostics) (38%), and Streptex (Remel) (53%). New approaches to bacterial identification in routine clinical microbiology laboratories may affect the prevalence of
S. pseudoporcinus
.
pH-Dependent Formation and Disintegration of the Influenza A Virus Protein Scaffold To Provide Tension for Membrane Fusion
Authors: Batishchev O. V. , Shilova L. A. , Kachala M. V. , Tashkin V. Y. , Sokolov V. S. , Fedorova N. V. , Baratova L. A. , Knyazev D. G. , Zimmerberg J. , Chizmadzhev Y. A.
Published: October 2015

Influenza virus is taken up from a pH-neutral extracellular milieu into an endosome, whose contents then acidify, causing changes in the viral matrix protein (M1) that coats the inner monolayer of the viral lipid envelope. At a pH of ∼6, M1 interacts with the viral ribonucleoprotein (RNP) in a putative priming stage; at this stage, the interactions of the M1 scaffold coating the lipid envelope are intact. The M1 coat disintegrates as acidification continues to a pH of ∼5 to clear a physical path for the viral genome to transit from the viral interior to the cytoplasm. Here we investigated the physicochemical mechanism of M1's pH-dependent disintegration. In neutral media, the adsorption of M1 protein on the lipid bilayer was electrostatic in nature and reversible. The energy of the interaction of M1 molecules with each other in M1 dimers was about 10 times as weak as that of the interaction of M1 molecules with the lipid bilayer. Acidification drives conformational changes in M1 molecules due to changes in the M1 charge, leading to alterations in their electrostatic interactions. Dropping the pH from 7.1 to 6.0 did not disturb the M1 layer; dropping it lower partially desorbed M1 because of increased repulsion between M1 monomers still stuck to the membrane. Lipid vesicles coated with M1 demonstrated pH-dependent rupture of the vesicle membrane, presumably because of the tension generated by this repulsive force. Thus, the disruption of the vesicles coincident with M1 protein scaffold disintegration at pH 5 likely stretches the lipid membrane to the point of rupture, promoting fusion pore widening for RNP release.

IMPORTANCE
Influenza remains a top killer of human beings throughout the world, in part because of the influenza virus's rapid binding to cells and its uptake into compartments hidden from the immune system. To attack the influenza virus during this time of hiding, we need to understand the physical forces that allow the internalized virus to infect the cell. In particular, we need to know how the protective coat of protein inside the viral surface reacts to the changes in acid that come soon after internalization. We found that acid makes the molecules of the protein coat push each other while they are still stuck to the virus, so that they would like to rip the membrane apart. This ripping force is known to promote membrane fusion, the process by which infection actually occurs.
Crystal Structure of the Conserved Amino Terminus of the Extracellular Domain of Matrix Protein 2 of Influenza A Virus Gripped by an Antibody
Authors: Cho Ki Joon , Schepens Bert , Moonens Kristof , Deng Lei , Fiers Walter , Remaut Han , Saelens Xavier
Published: October 2015

We report the crystal structure of the M2 ectodomain (M2e) in complex with a monoclonal antibody that binds the amino terminus of M2. M2e extends into the antibody binding site to form an N-terminal β-turn near the bottom of the paratope. This M2e folding differs significantly from that of M2e in complex with an antibody that binds another part of M2e. This suggests that M2e can adopt at least two conformations that can elicit protective antibodies.
Respiratory Syncytial Virus Attachment Glycoprotein Contribution to Infection Depends on the Specific Fusion Protein
Authors: Meng Jia , Hotard Anne L. , Currier Michael G. , Lee Sujin , Stobart Christopher C. , Moore Martin L.
Published: October 2015

Human respiratory syncytial virus (RSV) is an important pathogen causing acute lower respiratory tract disease in children. The RSV attachment glycoprotein (G) is not required for infection, as G-null RSV replicates efficiently in several cell lines. Our laboratory previously reported that the viral fusion (F) protein is a determinant of strain-dependent pathogenesis. Here, we hypothesized that virus dependence on G is determined by the strain specificity of F. We generated recombinant viruses expressing G and F, or null for G, from the laboratory A2 strain (Katushka RSV-A2GA2F [kRSV-A2GA2F] and kRSV-GstopA2F) or the clinical isolate A2001/2-20 (kRSV-2-20G2-20F and kRSV-Gstop2-20F). We quantified the virus cell binding, entry kinetics, infectivity, and growth kinetics of these four recombinant viruses
in vitro
. RSV expressing the 2-20 G protein exhibited the greatest binding activity. Compared to the parental viruses expressing G and F, removal of 2-20 G had more deleterious effects on binding, entry, infectivity, and growth than removal of A2 G. Overall, RSV expressing 2-20 F had a high dependence on G for binding, entry, and infection.

IMPORTANCE
RSV is the leading cause of childhood acute respiratory disease requiring hospitalization. As with other paramyxoviruses, two major RSV surface viral glycoproteins, the G attachment protein and the F fusion protein, mediate virus binding and subsequent membrane fusion, respectively. Previous work on the RSV A2 prototypical strain demonstrated that the G protein is functionally dispensable for
in vitro
replication. This is in contrast to other paramyxoviruses that require attachment protein function as a prerequisite for fusion. We reevaluated this requirement for RSV using G and F proteins from clinical isolate 2-20. Compared to the laboratory A2 strain, the G protein from 2-20 had greater contributions to virus binding, entry, infectivity, and
in vitro
growth kinetics. Thus, the clinical isolate 2-20 F protein function depended more on its G protein, suggesting that RSV has a higher dependence on G than previously thought.
Single-Genome Sequencing of Hepatitis C Virus in Donor-Recipient Pairs Distinguishes Modes and Models of Virus Transmission and Early Diversification
Authors: Li Hui , Stoddard Mark B. , Wang Shuyi , Giorgi Elena E. , Blair Lily M. , Learn Gerald H. , Hahn Beatrice H. , Alter Harvey J. , Busch Michael P. , Fierer Daniel S. , Ribeiro Ruy M. , Perelson Alan S. , Bhattacharya Tanmoy , Shaw George M.
Published: October 2015

Despite the recent development of highly effective anti-hepatitis C virus (HCV) drugs, the global burden of this pathogen remains immense. Control or eradication of HCV will likely require the broad application of antiviral drugs and development of an effective vaccine. A precise molecular identification of transmitted/founder (T/F) HCV genomes that lead to productive clinical infection could play a critical role in vaccine research, as it has for HIV-1. However, the replication schema of these two RNA viruses differ substantially, as do viral responses to innate and adaptive host defenses. These differences raise questions as to the certainty of T/F HCV genome inferences, particularly in cases where multiple closely related sequence lineages have been observed. To clarify these issues and distinguish between competing models of early HCV diversification, we examined seven cases of acute HCV infection in humans and chimpanzees, including three examples of virus transmission between linked donors and recipients. Using single-genome sequencing (SGS) of plasma vRNA, we found that inferred T/F sequences in recipients were identical to viral sequences in their respective donors. Early in infection, HCV genomes generally evolved according to a simple model of random evolution where the coalescent corresponded to the T/F sequence. Closely related sequence lineages could be explained by high multiplicity infection from a donor whose viral sequences had undergone a pretransmission bottleneck due to treatment, immune selection, or recent infection. These findings validate SGS, together with mathematical modeling and phylogenetic analysis, as a novel strategy to infer T/F HCV genome sequences.

IMPORTANCE
Despite the recent development of highly effective, interferon-sparing anti-hepatitis C virus (HCV) drugs, the global burden of this pathogen remains immense. Control or eradication of HCV will likely require the broad application of antiviral drugs and the development of an effective vaccine, which could be facilitated by a precise molecular identification of transmitted/founder (T/F) viral genomes and their progeny. We used single-genome sequencing to show that inferred HCV T/F sequences in recipients were identical to viral sequences in their respective donors and that viral genomes generally evolved early in infection according to a simple model of random sequence evolution. Altogether, the findings validate T/F genome inferences and illustrate how T/F sequence identification can illuminate studies of HCV transmission, immunopathogenesis, drug resistance development, and vaccine protection, including sieving effects on breakthrough virus strains.
Pan-ebolavirus and Pan-filovirus Mouse Monoclonal Antibodies: Protection against Ebola and Sudan Viruses
Authors: Holtsberg Frederick W. , Shulenin Sergey , Vu Hong , Howell Katie A. , Patel Sonal J. , Gunn Bronwyn , Karim Marcus , Lai Jonathan R. , Frei Julia C. , Nyakatura Elisabeth K. , Zeitlin Larry , Douglas Robin , Fusco Marnie L. , Froude Jeffrey W. , Saphire Erica Ollmann , Herbert Andrew S. , Wirchnianski Ariel S. , Lear-Rooney Calli M. , Alter Galit , Dye John M. , Glass Pamela J. , Warfield Kelly L. , Aman M. Javad
Published: October 2015

The unprecedented 2014-2015 Ebola virus disease (EVD) outbreak in West Africa has highlighted the need for effective therapeutics against filoviruses. Monoclonal antibody (MAb) cocktails have shown great potential as EVD therapeutics; however, the existing protective MAbs are virus species specific. Here we report the development of pan-ebolavirus and pan-filovirus antibodies generated by repeated immunization of mice with filovirus glycoproteins engineered to drive the B cell responses toward conserved epitopes. Multiple pan-ebolavirus antibodies were identified that react to the Ebola, Sudan, Bundibugyo, and Reston viruses. A pan-filovirus antibody that was reactive to the receptor binding regions of all filovirus glycoproteins was also identified. Significant postexposure efficacy of several MAbs, including a novel antibody cocktail, was demonstrated. For the first time, we report cross-neutralization and
in vivo
protection against two highly divergent filovirus species, i.e., Ebola virus and Sudan virus, with a single antibody. Competition studies indicate that this antibody targets a previously unrecognized conserved neutralizing epitope that involves the glycan cap. Mechanistic studies indicated that, besides neutralization, innate immune cell effector functions may play a role in the antiviral activity of the antibodies. Our findings further suggest critical novel epitopes that can be utilized to design effective cocktails for broad protection against multiple filovirus species.

IMPORTANCE
Filoviruses represent a major public health threat in Africa and an emerging global concern. Largely driven by the U.S. biodefense funding programs and reinforced by the 2014 outbreaks, current immunotherapeutics are primarily focused on a single filovirus species called Ebola virus (EBOV) (formerly Zaire Ebola virus). However, other filoviruses including Sudan, Bundibugyo, and Marburg viruses have caused human outbreaks with mortality rates as high as 90%. Thus, cross-protective immunotherapeutics are urgently needed. Here, we describe monoclonal antibodies with cross-reactivity to several filoviruses, including the first report of a cross-neutralizing antibody that exhibits protection against Ebola virus and Sudan virus in mice. Our results further describe a novel combination of antibodies with enhanced protective efficacy. These results form a basis for further development of effective immunotherapeutics against filoviruses for human use. Understanding the cross-protective epitopes are also important for rational design of pan-ebolavirus and pan-filovirus vaccines.
TRIM5 Retroviral Restriction Activity Correlates with the Ability To Induce Innate Immune Signaling
Authors: Lascano Josefina , Uchil Pradeep D. , Mothes Walther , Luban Jeremy
Published: October 2015

Host restriction factor TRIM5 inhibits retroviral transduction in a species-specific manner by binding to and destabilizing the retroviral capsid lattice before reverse transcription is completed. However, the restriction mechanism may not be that simple since TRIM5 E3 ubiquitin ligase activity, the proteasome, autophagy, and TAK1-dependent AP-1 signaling have been suggested to contribute to restriction. Here, we show that, among a panel of seven primate and Carnivora TRIM5 orthologues, each of which has potential for potent retroviral restriction activity, all activated AP-1 signaling. In contrast, TRIM family paralogues most closely related to TRIM5 did not. While each primate species has a single TRIM5 gene, mice have at least seven TRIM5 homologues that cluster into two groups, Trim12a, -b, and -c and Trim30a, -b, -c, and -d. The three Trim12 proteins activated innate immune signaling, while the Trim30 proteins did not, though none of the murine Trim5 homologues restricted any of a panel of cloned retroviruses. To determine if any mouse TRIM5 homologues had potential for restriction activity, each was fused to the human immunodeficiency virus type 1 (HIV-1) CA binding protein cyclophilin A (CypA). The three Trim12-CypA fusions all activated AP-1 and restricted HIV-1 transduction, whereas the Trim30-CypA fusions did neither. AP-1 activation and HIV-1 restriction by the Trim12-CypA fusions were inhibited by disruption of TAK1. Overall then, these experiments demonstrate that there is a strong correlation between TRIM5 retroviral restriction activity and the ability to activate TAK1-dependent innate immune signaling.

IMPORTANCE
The importance of retroviruses for the evolution of susceptible host organisms cannot be overestimated. Eight percent of the human genome is retrovirus sequence, fixed in the germ line during past infection. Understanding how metazoa protect their genomes from mutagenic retrovirus infection is therefore of fundamental importance to biology. TRIM5 is a cellular protein that protects host genome integrity by disrupting the retroviral capsid as it transports viral nucleic acid to the host cell nucleus. Previous data suggest that innate immune signaling contributes to TRIM5-mediated restriction. Here, we show that activation of innate immune signaling is conserved among primate and carnivore TRIM5 orthologues and among 3 of the 7 mouse Trim5 homologues and that such activity is required for TRIM5-mediated restriction activity.
Multiple calcified brain metastases in a man with invasive ductal breast cancer
Authors: Ressl Nadine , Oberndorfer Stefan
Published: October 2015

We report a case of a 52-year-old Caucasian man with invasive ductal carcinoma of the breast. One year after initial diagnosis, he developed a generalised epileptic seizure and neuroimaging showed multiple, calcified intracerebral lesions. Owing to these atypical cerebral imaging findings, comprehensive serological and cerebrospinal fluid analysis was conducted and a latent toxoplasmosis was suspected. In order to distinguish between metastases and an infectious disease, a cerebral biopsy was performed, which verified brain metastases. The patient received whole-brain radiotherapy. The last cerebral CT scan, 18 months later showed stable disease. Calcification of brain metastases in patients with breast cancer is very rare. Owing to their non-characteristic radiological appearance with a lack of contrast enhancement, diagnosis of metastases can be difficult. Infectious diseases should be considered within the diagnostic work up. Owing to possible pitfalls, we recommend a widespread differential diagnostic work up in similar cases, and even in cases with a confirmed primary tumour.
Do patients with gastrointestinal cancer want to decide where they have tests and surgery? A questionnaire study of provider choice
Authors: Byrne Ben E , Faiz Omar D , Vincent Charles
Published: October 2015

Backgrounds

Choice of provider has been an important strategy among policy makers, intended, in part, to drive improvements in quality and efficiency of healthcare. This study examined the information requirements, and decision-making experiences and preferences of patients who have had surgery for gastrointestinal cancer, to assess the status of provider choice in current practice.

Methods

The single-item Control Preferences Scale was used to determine patients’ experiences and preferences when being referred for tests, and choosing where to have surgery. Participants used a Likert scale to rate the importance of 23 information items covering a variety of structures, processes and outcomes at the hospital level and the department level. Participants were recruited by post and online.

Results

463 responses were analysed. Patients reported very low levels of involvement in provider choice, with their doctor deciding where they underwent tests or surgery in 77.0% and 81.8% of cases, respectively. Over two-thirds of participants would have preferred greater involvement in provider choice than they experienced. Of note, patient age and education were not associated with reported preferences. Information on how long patients with cancer wait for treatment, annual operative volume and postoperative mortality rate, as well as retained foreign bodies and infection rates were considered very important.

Conclusions

There was a substantial unmet desire for greater involvement in provider choice among study participants. Respondents attached particular importance to surgery-specific information. Efforts should be made to increase involvement of patients with gastrointestinal cancer in provider decisions, across primary and secondary care, to deliver more patient-centred care. The reported lack of patient involvement in provider choice suggests it is unlikely to be working as an effective lever to drive quality improvement at present.
Underlying risk factors for prescribing errors in long-term aged care: a qualitative study
Authors: Tariq Amina , Georgiou Andrew , Raban Magdalena , Baysari Melissa Therese , Westbrook Johanna
Published: October 2015

Objective(s)

To identify system-related risk factors perceived to contribute to prescribing errors in Australian long-term care settings, that is, residential aged care facilities (RACFs).

Design and setting

The study used qualitative methods to explore factors that contribute to unsafe prescribing in RACFs. Data were collected at three RACFs in metropolitan Sydney, Australia between May and November 2011. Participants included RACF managers, doctors, pharmacists and RACF staff actively involved in prescribing-related processes. Methods included non-participant observations (74 h), in-depth semistructured interviews (n=25) and artefact analysis. Detailed process activity models were developed for observed prescribing episodes supplemented by triangulated analysis using content analysis methods.

Results

System-related factors perceived to increase the risk of prescribing errors in RACFs were classified into three overarching themes: communication systems, team coordination and staff management. Factors associated with communication systems included limited point-of-care access to information, inadequate handovers, information storage across different media (paper, electronic and memory), poor legibility of charts, information double handling, multiple faxing of medication charts and reliance on manual chart reviews. Team factors included lack of established lines of responsibility, inadequate team communication and limited participation of doctors in multidisciplinary initiatives like medication advisory committee meetings. Factors related to staff management and workload included doctors’ time constraints and their accessibility, lack of trained RACF staff and high RACF staff turnover.

Conclusions

The study highlights several system-related factors including laborious methods for exchanging medication information, which often act together to contribute to prescribing errors. Multiple interventions (eg, technology systems, team communication protocols) are required to support the collaborative nature of RACF prescribing.
Expression of EphB6 in ovarian serous carcinoma is associated with grade, TNM stage and survival
Authors: Gu Yun , Li Fengshan , Qian Ning , Chen Xiao , Wang Hai , Wang Jiandong
Published: October 2015

Background

Ovarian serous carcinoma (OSC) is the most common ovarian epithelial malignancy. Despite new medical and surgical advances, the overall 5-year survival for OSC remains poor. There is an important need to determine diagnostic and prognostic markers for this disease. Eph receptors are the largest known family of receptor tyrosines characterised in humans. These receptors are involved in the development and progression of various diseases including cancer. EphB6 contains kinase domains that are altered in several conserved amino acids and is catalytically inactive. The aim of the present study was to correlate the immunohistological expression of EphB6 in a cohort of patients with epithelial ovarian tumours with clinicopathological parameters and survival.

Methods

In this study we examined the expression of EphB6 protein in 55 cases of OSC, 24 cases of benign ovarian serous tumours, 37 cases of serous borderline tumours and 20 cases with normal fallopian tubes by immunohistochemical staining with a polyclonal anti-EphB6 antibody. The relationship between EphB6 expression and pathological parameters was analysed. Kaplan–Meier survival function was used to analyse the prognosis.

Results

High expression of EphB6 was observed in 100% (20/20) of normal fallopian tube samples, 100% (24/24) of benign epithelial ovarian tumours, 78% (29/37) of ovarian serous borderline tumours and 18% (10/55) of OSCs (p<0.001). The expression of EphB6 was significantly associated with grade (p<0.001) and TNM stage (p=0.017). EphB6 expression was reversely related to Ki-67 (p=0.021). The survival analysis showed that patients with negative or weak expression of EphB6 protein had a poorer outcome than those with positive expression (p=0.046).

Conclusions

Our results show that EphB6 is a new biomarker for distinguishing high- and low-grade OSC, and may be a potential prognostic marker in OSCs.
Sociodemographic risk factors of alcohol drinking in Hong Kong adolescents
Authors: Huang Rong , Ho Sai Yin , Wang Man Ping , Lo Wing Sze , Lam Tai Hing
Published: October 2015

Background

Adolescent drinking in Western countries has been associated with older age and high socioeconomic status, but the association with family structure was inconsistent.

Methods

In a 2012–2013 school-based survey in Hong Kong, 23 096 students (mean age 14.7 years, SD 1.8 years) completed an anonymous questionnaire. Current drinking was defined as any drinking and binge drinking as consuming at least 5 drinks on one occasion, both in the past 30 days. Multilevel logistic regression was used to examine the association of sociodemographic characteristics with current drinking, binge drinking and type of alcohol consumed.

Results

Current drinking was associated with age (≥15 vs ≤14 years) (adjusted OR 1.87, 95% CI 1.74 to 2.02), higher perceived family affluence versus low affluence (1.11, 1.02 to 1.21 for medium affluence; 1.55, 1.38 to 1.75 for high affluence), private housing versus public housing (1.11, 1.01 to 1.21) and non-intact family versus intact family (1.31, 1.19 to 1.45 for separated/divorced parents; 1.40, 1.21 to 1.62 for one or both deceased parents). Similar risk factors were observed for binge drinking. Girls were more likely to drink fruit wine (1.48, 1.36 to 1.62), while they were less likely to drink beer (0.85, 0.79 to 0.92) and spirits (0.69, 0.54 to 0.87). Students who reported high family affluence were more likely to drink wine (1.91, 1.59 to 2.30) and spirits (2.23, 1.54 to 3.24).

Conclusions

Generally, adolescents who were older and had higher socioeconomic status were more likely to drink. High family affluence was associated with wine and spirits drinking. Beer and spirits were preferred more by boys, and fruit wine by girls. These results indicated high-risk groups for adolescent alcohol interventions.
Syntheses of Mg–Al–NO3layered double hydroxides with high crystallinity in the presence of amines
Authors: Nejati Kamellia , Mokhtari Azam , Khodam Fatemeh , Rezvani Zolfaghar
Published: October 2015

In the present work, layered double hydroxides of Mg–Al were synthesized with nitrate interlayer anions in the presence of different types of amines such as ethylenediamine, dimethylamine, and trimethylamine, without a N2atmosphere, from a homogeneous solution using the coprecipitation method. The concentration of the different types of amines and pH of the solution were adjusted to produce high-purity and -crystallinity samples. The structure and morphology of layered double hydroxides were characterized and investigated by powder X-ray Diffraction, Fourier transform infrared spectroscopy, field emission scanning electron microscopy, and thermogravimetric analysis techniques. The analyses showed that with increasing amine concentration, both crystallinity and purity of the samples increase at pH 10.5.
Study on the homology of the genomes of tetraploid Asiatic lilies (Lilium) using FISH
Authors: Zhou Shujun , Zhong Lei , Zhang Lu , Xu Zhenghua , Liu Xuxin , Li Kehu , Zhou Guixue
Published: October 2015

Asiatic lily cultivars, bred by hybridization and (or) chromosome doubling of species of section Sinomartagon of Lilium, are diploid, triploid, or tetraploid, but the homology of the genomes among species of section Sinomartagon and Asiatic lilies remains unclear. In the present research, two tetraploid Asiatic cultivars were analyzed, using 45S rDNA as probe, for their FISH karyotypes and their chromosomal association, anaphase I, telophase II, and pollen viability were surveyed to assess the multivalent segregation. Chromosomal assortment of six progenies of the two tetraploid cultivars were also investigated. The results showed that the tetraploid cultivars had similar FISH karyotypes, they predominantly formed multivalents, and these were equally separated because their anaphase I, telophase II, and pollen viability were similar to those of diploid species. Apart from minor variations, FISH karyotypes of progenies were similar to each other and to their parents. Based on these results and considering the high crossability among species of section Sinomartagon and (or) Asiatic lilies, we concluded that species of section Sinomartagon and their resulting cultivars share a common genome; thus, polyploidy Asiatic lilies are autopolyploid.
Genomics innovation: transforming healthcare, business, and the global economy
Authors: Jimenez-Sanchez Gerardo
Published: October 2015

The genomics revolution has generated an unprecedented number of assets to propel innovation. Initial availability of genomics-based applications show a significant potential to contribute addressing global challenges, such as human health, food security, alternative sources of energies, and environmental sustainability. In the last years, most developed and emerging nations have established bioeconomy agendas where genomics plays a major role to meet their local needs. Genomic medicine is one of the most visible areas where genomics innovation is likely to contribute to a more individualized, predictive, and preventive medical practice. Examples in agriculture, dairy and beef, fishery, aquaculture, and forests industries include the effective selection of genetic variants associated to traits of economic value. Some, in addition to producing more and better foods, already represent an important increase in revenues to their respective industries. It is reasonable to predict that genomics applications will lead to a paradigm shift in our ability to ease significant health, economic, and social burdens. However, to successfully benefit from genomics innovations, it is imperative to address a number of hurdles related to generating robust scientific evidence, developing lower-cost sequencing technologies, effective bioinformatics, as well as sensitive ethical, economical, environmental, legal, and social aspects associated with the development and use of genomics innovations.
Low-Voltage Wide Tuning Range Membership Function Generator and Its Application
Authors: Ghanavati B. , Mohammadzadeh S. , Noshad B. , Ahmadzadeh M. , Falahat A.
Published: October 2015

A versatile low-voltage CMOS circuit with a trapezoidal transconductance characteristic and independently programmable slope, height and horizontal position is designed in 0.18[Formula: see text][Formula: see text]m standard CMOS technology. The proposed circuit is constructed from combination of two linearization methods to enhance the linearity in low voltage applications. A [Formula: see text]118[Formula: see text]dB THD was obtained for a 400[Formula: see text]mV peak to peak differential input voltage at 125[Formula: see text]KHz. Simulation results using HSPICE that verify the functionality of circuit with 1.5[Formula: see text]V supply are presented. The total power consumption is only 120[Formula: see text][Formula: see text]W. The circuit can find application in the implementation of membership functions in analogue and mixed-signal neuro-fuzzy systems.
An Aggregated Process-Based Traffic Generator for Network Performance Evaluation
Authors: Wang Xiaoting , Wang Yiwen , Li Ping
Published: October 2015

Nowadays, it is desirable to generate traffic which can reflect realistic network traffic environment for performance evaluation of network equipments. Existing traffic generation solutions mainly include special test equipments, software traffic generators and field programmable gate array (FPGA)-based traffic generators. However, special test equipments are generally too expensive, software traffic generators could not achieve high data rates and FPGA-based traffic generators mostly lack flexibility. This paper presents a novel traffic generation solution according to an aggregated process-based model to overcome the weakness of above methods. The traffic generator can generate real-time Poisson, two-state Markov-modulated Poisson process (MMPP-2) and self-similar traffic by hardware. The main structure of the traffic generator is presented and statistical properties of the generated traffic have been evaluated. Experiment results indicate that the proposed traffic generation solution can achieve better performance of the generated traffic compared with existing FPGA-based traffic generators while the required date rates can be up to Gbps line rate.
k-Centerpoints Conjectures for Pointsets in ℝd
Authors: Mustafa Nabil H. , Ray Saurabh , Shabbir Mudassir
Published: October 2015

In this paper, we introduce the notion of [Formula: see text]-centerpoints for any set [Formula: see text] of [Formula: see text] points in [Formula: see text]. These unify and generalize previous results such as the classical centerpoint theorem,1 and the recently-proven ray-shooting theorem.2 We define two variants: affine [Formula: see text]-centerpoints, and topological [Formula: see text]-centerpoints. We prove their equivalence in [Formula: see text], and conjecture that these are in fact equivalent in any dimension. We present the first non-trivial bounds for these problems in [Formula: see text], as well as present several conjectures related to them.
Spread: A Measure of the Size of Metric Spaces
Authors: Willerton Simon
Published: October 2015

Motivated by Leinster-Cobbold measures of biodiversity, the notion of the spread of a finite metric space is introduced. This is related to Leinster’s magnitude of a metric space. Spread is generalized to infinite metric spaces equipped with a measure and is calculated for spheres and straight lines. For Riemannian manifolds the spread is related to the volume and total scalar curvature. A notion of scale-dependent dimension is introduced and seen for approximations to certain fractals to be numerically close to the Minkowski dimension of the original fractals.
Minimum Dominating Set Problem for Unit Disks Revisited
Authors: Carmi Paz , Das Gautam K. , Jallu Ramesh K. , Nandy Subhas C. , Prasad Prajwal R. , Stein Yael
Published: October 2015

In this article, we study approximation algorithms for the problem of computing minimum dominating set for a given set [Formula: see text] of [Formula: see text] unit disks in [Formula: see text]. We first present a simple [Formula: see text] time 5-factor approximation algorithm for this problem, where [Formula: see text] is the size of the output. The best known 4-factor and 3-factor approximation algorithms for the same problem run in time [Formula: see text] and [Formula: see text] respectively [M. De, G. K. Das, P. Carmi and S. C. Nandy, Approximation algorithms for a variant of discrete piercing set problem for unit disks, Int. J. of Computational Geometry and Appl., 22(6):461–477, 2013]. We show that the time complexity of the in-place 4-factor approximation algorithm for this problem can be improved to [Formula: see text]. A minor modification of this algorithm produces a [Formula: see text]-factor approximation algorithm in [Formula: see text] time. The same techniques can be applied to have a 3-factor and a [Formula: see text]-factor approximation algorithms in time [Formula: see text] and [Formula: see text] respectively. Finally, we propose a very important shifting lemma, which is of independent interest, and it helps to present [Formula: see text]-factor approximation algorithm for the same problem. It also helps to improve the time complexity of the proposed PTAS for the problem.
Primordial black holes and the observable features of the universe
Authors: Belotsky K. M. , Kirillov A. A. , Rubin S. G.
Published: October 2015

Here, we briefly discuss the possibility to solve simultaneously with primordial black holes (PBHs) the problems of dark matter (DM), reionization of the universe, origin of positron line from Galactic center and supermassive black hole (BH) in it. Discussed scenario can naturally lead to a multiple-peak broad-mass-range distribution of PBHs in mass, which is necessary for simultaneous solution of the problems.
Analysis of instability of systems composed by dark and baryonic matter
Authors: Kremer Gilberto M. , André Raíla
Published: October 2015

In this work, the dynamics of self-gravitating systems composed by dark and baryonic matter is analyzed. Searching for a description of this dynamics, a system of collisionless Boltzmann equations for the two constituents and the Poisson equation for the gravitational field are employed. Through the solution of these equations, the collapse criterion is determined from a dispersion relation. The collapse occurs in an unstable region where the solutions grow exponentially with time. It is shown that the unstable region becomes larger if the dispersion velocity of dark matter becomes larger than the one of the baryonic matter. The results obtained are also compared with the case where only the dark matter is present. The model of the present work has a higher limit of instability and therefore exhibited an advantage in the structure formation.
GENERATING FRACTAL PATTERNS BY USING p-CIRCLE INVERSION
Authors: RAMÍREZ JOSÉ L. , RUBIANO GUSTAVO N. , ZLOBEC BORUT JURČIČ
Published: October 2015

In this paper, we introduce the [Formula: see text]-circle inversion which generalizes the classical inversion with respect to a circle ([Formula: see text]) and the taxicab inversion [Formula: see text]. We study some basic properties and we also show the inversive images of some basic curves. We apply this new transformation to well-known fractals such as Sierpinski triangle, Koch curve, dragon curve, Fibonacci fractal, among others. Then we obtain new fractal patterns. Moreover, we generalize the method called circle inversion fractal be means of the [Formula: see text]-circle inversion.
Dynamical Behavior of an Epidemic Model in a Fuzzy Transmission
Authors: Mondal Prasanta Kumar , Jana Soovoojeet , Haldar Palash , Kar T. K.
Published: October 2015

In this paper, we have formulated a simple SIS type epidemic model in the presence of treatment control, and we have discussed the dynamical behavior of the system. The system is modified by considering both the disease transmission rate and the treatment function as fuzzy numbers, and also the fuzzy expected value of the infected individuals is calculated. Furthermore, the fuzzy basic reproduction number is investigated and a threshold condition of pathogen is obtained at which the system undergoes a transcritical bifurcation.
An Efficient Clustering for Anonymizing Data and Protecting Sensitive Labels
Authors: Nayahi J. Jesu Vedha , Kavitha V.
Published: October 2015

Sharing data to a third party for the mutual benefit of the data owners plays a vital need in all computer applications. Ensuring the privacy of sensitive data is an important issue in data sharing and hence there is a need for privacy preserving data mining algorithms. Traditional privacy preserving algorithms are prone to attacks, have high information loss and sometimes fail to achieve the privacy constraints. In this paper, a (G,S) clustering algorithm is proposed to achieve clusters each with S diverse sensitive values for the sensitive attribute. The number of distinct sensitive values in each cluster would be exactly equal to the number of sensitive values in the given data set. The clusters’ formed are anonymized by replacing the actual values with the centroid(G) of the cluster. The algorithm achieves the maximum possible diverse sensitive values in each cluster making it resilient to similarity attack. The method guarantees high degree of privacy with very minimal loss of information. The privacy degree of the clusters formed is at least equal to the number of distinct values in the sensitive attribute. The worst case linking probability would be as low as 0.5. The significance of this algorithm is its resilience to similarity attack. The performance of the algorithm is proved to be better than the existing algorithms in terms of KL Divergence, Discernibility metric and few other metrics.
Archimedean Aggregation Operators Based on Dual Hesitant Fuzzy Set and Their Application to GDM
Authors: Yu Dejian
Published: October 2015

Many information fusion methods have been widely investigated to tackle group decision making (GDM) problem under dual hesitant fuzzy (DHF) environment. Nevertheless, traditional DHF information fusion methods are not quite perfect and they could be improved. In this study, we introduce the Archimedean t-conorm and t-norm (ATT) to DHF environment. We first introduce the ATT operations for DHF information, some existing operations are proved to be the exceptional cases of the proposed ones. Then, several new aggregation operators for DHF information are proposed based on ATT operations. Finally, an actual case about the selection of cooperative hospital as an emergency hospital for a company is studied based on the proposed methods.
Linear Programming Method for Solving Semi-Latticized Fuzzy Relation Geometric Programming with Max-Min Composition
Authors: Yang Xiao-Peng
Published: October 2015

Motivated by application in BitTorrent-like Peer-to-Peer resource sharing system, we introduce the maximization and minimization semi-latticized fuzzy relation geometric programming problems with max-min composition in this paper. The objective function in the proposed problem in nonlinear and the feasible domain is non-convex. The maximization problem is converted into a fuzzy relation monomial geometric programming and then solved. However, this approach is not effective for the minimization one. The linear programming method is applied to deal with the minimization problem. A step-to-step algorithm is develop to carried out the linear programming method and tow illustrative examples are provided at last.
Interlaminar Stresses Calculation Using a Stacked-Shell Finite Element Modeling Approach
Authors: Lampeas G. , Fotopoulos K.
Published: October 2015

The innovative stacked-shell modeling approach is investigated in the frame of an explicit finite element method for the prediction of laminated structural elements' static response, focusing on the interlaminar stress calculation. The main advantage of the investigated stacked-shell modeling technique is the lower computational cost compared to conventional methods, for the same accuracy in displacement and stress results. A laminated plate under sinusoidally distributed transverse loading, a laminated strip under three-point bending and a laminated cylindrical shell under cylindrical bending have been used in the assessment of the developed methodology; static results referring to displacement and both in-plane and out-of-plane stresses of the investigated cases have shown that the proposed technique is highly efficient in the calculation of interlaminar stresses of composite structures, which provides the background for an accurate and efficient delamination prediction.
A computational model of flow and species transport in the mesangium
Authors: Hunt Sarah E. , Dorfman Kevin D. , Segal Yoav , Barocas Victor H.
Published: October 2015

A variety of macromolecules accumulate in the glomerular mesangium in many different diseases, but the physics of the transport of these molecules within the mesangial matrix has not been extensively studied. We present a computational model of convection and diffusion within the porous mesangial matrix and apply this model to the specific instance of immunoglobulin A (IgA) transport in IgA nephropathy. We examine the influence of physiological factors including glomerular basement membrane (GBM) thickness and mesangial matrix density on the total accumulation of IgA. Our results suggest that IgA accumulation can be understood by relating convection and diffusion, thus demonstrating the importance of intrinsic glomerular factors.
Erythropoietin protects the tubular basement membrane by promoting the bone marrow to release extracellular vesicles containing tPA-targeting miR-144
Authors: Zhou Yang , Fang Li , Yu Yanting , Niu Jing , Jiang Lei , Cao Hongdi , Sun Qi , Zen Ke , Dai Chunsun , Yang Junwei
Published: October 2015

Renal fibrosis is an inevitable outcome of chronic kidney disease (CKD). Erythropoietin (EPO) has been recently reported to be able to mitigate renal fibrosis. The mechanism underlying the protective effect of EPO, however, remains elusive. In the present study, employing a mouse model of renal tubulointerstitial fibrosis induced by unilateral ureteral obstruction (UUO), we demonstrated that EPO markedly reduced the disruption of the tubular basement membrane (TBM) through attenuating the activation of tissue plasminogen activator (tPA) and matrix metalloproteinase 9 (MMP9), the major matrix proteolytic network in the obstructed kidney. Instead of acting directly on tPA in the kidney, EPO strongly increased the level of circulating microRNA (miR)-144, which was delivered to the injured renal fibroblasts via extracellular vesicles (EVs) to target the tPA 3′-untranslated region and suppress tPA expression. The protective effect of EPO on mouse TBM was inhibited by miR-144 antagomir. Furthermore, in vitro results confirmed that EPO could stimulate bone marrow-derived Sca-1+CD44+CD11b−CD19−cells to secrete miR-144-containing EVs, which markedly suppressed tPA expression, as well as metalloproteinase 9 (MMP9) level and activity, in cultured renal fibroblasts. In conclusion, our study provides the first evidence that EPO protects mouse renal TBM through promoting bone marrow cells to generate and secrete miR-144, which, in turn, is efficiently delivered into the mouse kidney via EVs to inhibit the activation of the tPA/MMP9-mediated proteolytic network. This finding thus suggests that EPO, a hormone widely used to treat anemia in CKD, is a potential therapeutic strategy for renal fibrosis.
Dynamics of individual perceptual decisions
Authors: Merfeld Daniel M. , Clark Torin K. , Lu Yue M. , Karmali Faisal
Published: October 2015

Perceptual decision making is fundamental to a broad range of fields including neurophysiology, economics, medicine, advertising, law, etc. Although recent findings have yielded major advances in our understanding of perceptual decision making, decision making as a function of time and frequency (i.e., decision-making dynamics) is not well understood. To limit the review length, we focus most of this review on human findings. Animal findings, which are extensively reviewed elsewhere, are included when beneficial or necessary. We attempt to put these various findings and data sets, which can appear to be unrelated in the absence of a formal dynamic analysis, into context using published models. Specifically, by adding appropriate dynamic mechanisms (e.g., high-pass filters) to existing models, it appears that a number of otherwise seemingly disparate findings from the literature might be explained. One hypothesis that arises through this dynamic analysis is that decision making includes phasic (high pass) neural mechanisms, an evidence accumulator and/or some sort of midtrial decision-making mechanism (e.g., peak detector and/or decision boundary).
Nanomaterial Synthesis Using Plasma Generation in Liquid
Authors: Saito Genki , Akiyama Tomohiro
Published: October 2015

Over the past few decades, the research field of nanomaterials (NMs) has developed rapidly because of the unique electrical, optical, magnetic, and catalytic properties of these materials. Among the various methods available today for NM synthesis, techniques for plasma generation in liquid are relatively new. Various types of plasma such as arc discharge and glow discharge can be applied to produce metal, alloy, oxide, inorganic, carbonaceous, and composite NMs. Many experimental setups have been reported, in which various parameters such as the liquid, electrode material, electrode configuration, and electric power source are varied. By examining the various electrode configurations and power sources available in the literature, this review classifies all available plasma in liquid setups into four main groups: (i) gas discharge between an electrode and the electrolyte surface, (ii) direct discharge between two electrodes, (iii) contact discharge between an electrode and the surface of surrounding electrolyte, and (iv) radio frequency and microwave plasma in liquid. After discussion of the techniques, NMs of metal, alloy, oxide, silicon, carbon, and composite produced by techniques for plasma generation in liquid are presented, where the source materials, reaction media, and electrode configurations are discussed in detail.