bluuebunny/crossref_metadata_2025 huggingface dataset:
The FACT Complex Promotes Avian Leukosis Virus DNA Integration
Authors: Winans Shelby , Larue Ross C. , Abraham Carly M. , Shkriabai Nikolozi , Skopp Amelie , Winkler Duane , Kvaratskhelia Mamuka , Beemon Karen L.
Published: January 2017

All retroviruses need to integrate a DNA copy of their genome into the host chromatin. Cellular proteins regulating and targeting lentiviral and gammaretroviral integration in infected cells have been discovered, but the factors that mediate alpharetroviral avian leukosis virus (ALV) integration are unknown. In this study, we have identified the FACT protein complex, which consists of SSRP1 and Spt16, as a principal cellular binding partner of ALV integrase (IN). Biochemical experiments with purified recombinant proteins show that SSRP1 and Spt16 are able to individually bind ALV IN, but only the FACT complex effectively stimulates ALV integration activity
in vitro
. Likewise, in infected cells, the FACT complex promotes ALV integration activity, with proviral integration frequency varying directly with cellular expression levels of the FACT complex. An increase in 2-long-terminal-repeat (2-LTR) circles in the depleted FACT complex cell line indicates that this complex regulates the ALV life cycle at the level of integration. This regulation is shown to be specific to ALV, as disruption of the FACT complex did not inhibit either lentiviral or gammaretroviral integration in infected cells.

IMPORTANCE
The majority of human gene therapy approaches utilize HIV-1- or murine leukemia virus (MLV)-based vectors, which preferentially integrate near genes and regulatory regions; thus, insertional mutagenesis is a substantial risk. In contrast, ALV integrates more randomly throughout the genome, which decreases the risks of deleterious integration. Understanding how ALV integration is regulated could facilitate the development of ALV-based vectors for use in human gene therapy. Here we show that the FACT complex directly binds and regulates ALV integration efficiency
in vitro
and in infected cells.
Monoclonal Antibodies Specific for the V2, V3, CD4-Binding Site, and gp41 of HIV-1 Mediate Phagocytosis in a Dose-Dependent Manner
Authors: Musich Thomas , Li Liuzhe , Liu Lily , Zolla-Pazner Susan , Robert-Guroff Marjorie , Gorny Miroslaw K.
Published: January 2017

In light of the weak or absent neutralizing activity mediated by anti-V2 monoclonal antibodies (MAbs), we tested whether they can mediate Ab-dependent cellular phagocytosis (ADCP), which is an important element of anti-HIV-1 immunity. We tested six anti-V2 MAbs and compared them with 21 MAbs specific for V3, the CD4-binding site (CD4bs), and gp41 derived from chronically HIV-1-infected individuals and produced by hybridoma cells. ADCP activity was measured by flow cytometry using uptake by THP-1 monocytic cells of fluorescent beads coated with gp120, gp41, BG505 SOSIP.664, or BG505 DS-SOSIP.664 complexed with MAbs. The measurement of ADCP activity by the area under the curve showed significantly higher activity of anti-gp41 MAbs than of the members of the three other groups of MAbs tested using beads coated with monomeric gp41 or gp120; anti-V2 MAbs were dominant compared to anti-V3 and anti-CD4bs MAbs against clade C gp120ZM109. ADCP activity mediated by V2 and V3 MAbs was positive against stabilized DS-SOSIP.664 trimer but negligible against SOSIP.664 targets, suggesting that a closed envelope conformation better exposes the variable loops. Two IgG3 MAbs against the V2 and V3 regions displayed dominant ADCP activity compared to a panel of IgG1 MAbs. This superior ADCP activity was confirmed when two of three recombinant IgG3 anti-V2 MAbs were compared to their IgG1 counterparts. The study demonstrated dominant ADCP activity of anti-gp41 against monomers but not trimers, with some higher activity of anti-V2 MAbs than of anti-V3 and anti-CD4bs MAbs. The ability to mediate ADCP suggests a mechanism by which anti-HIV-1 envelope Abs can contribute to protective efficacy.

IMPORTANCEAnti-V2 antibodies (Abs) correlated with reduced risk of HIV-1 infection in recipients of the RV144 vaccine, suggesting that they play a protective role, but a mechanism providing such protection remains to be determined. The rare and weak neutralizing activities of anti-V2 MAbs prompted us to study Fc-mediated activities. We compared anti-V2 MAbs with other MAbs specific for V3, CD4bs, and gp41 for Ab-dependent cellular phagocytosis (ADCP) activity, implicated in protective immunity. The anti-V2 MAbs displayed stronger activity than other anti-gp120 MAbs in screening against one of two gp120s and against DS-SOSIP, which mimics the native trimer. The activity of anti-gp41 MAbs was superior in targeting monomeric gp41 but was comparable to that seen against trimers, which may not adequately expose gp41 epitopes. While anti-envelope MAbs in general mediated ADCP activity, anti-V2 MAbs displayed some dominance compared to other MAbs. Our demonstration that anti-V2 MAbs mediate ADCP activity suggests a functional mechanism for their contribution to protective efficacy.
Role of the PB2 627 Domain in Influenza A Virus Polymerase Function
Authors: Nilsson Benjamin E. , te Velthuis Aartjan J. W. , Fodor Ervin
Published: January 2017

The RNA genome of influenza A viruses is transcribed and replicated by the viral RNA-dependent RNA polymerase, composed of the subunits PA, PB1, and PB2. High-resolution structural data revealed that the polymerase assembles into a central polymerase core and several auxiliary highly flexible, protruding domains. The auxiliary PB2 cap-binding and the PA endonuclease domains are both involved in cap snatching, but the role of the auxiliary PB2 627 domain, implicated in host range restriction of influenza A viruses, is still poorly understood. In this study, we used structure-guided truncations of the PB2 subunit to show that a PB2 subunit lacking the 627 domain accumulates in the cell nucleus and assembles into a heterotrimeric polymerase with PB1 and PA. Furthermore, we showed that a recombinant viral polymerase lacking the PB2 627 domain is able to carry out cap snatching, cap-dependent transcription initiation, and cap-independent ApG dinucleotide extension
in vitro
, indicating that the PB2 627 domain of the influenza virus RNA polymerase is not involved in core catalytic functions of the polymerase. However, in a cellular context, the 627 domain is essential for both transcription and replication. In particular, we showed that the PB2 627 domain is essential for the accumulation of the cRNA replicative intermediate in infected cells. Together, these results further our understanding of the role of the PB2 627 domain in transcription and replication of the influenza virus RNA genome.

IMPORTANCE
Influenza A viruses are a major global health threat, not only causing disease in both humans and birds but also placing significant strains on economies worldwide. Avian influenza A virus polymerases typically do not function efficiently in mammalian hosts and require adaptive mutations to restore polymerase activity. These adaptations include mutations in the 627 domain of the PB2 subunit of the viral polymerase, but it still remains to be established how these mutations enable host adaptation on a molecular level. In this report, we characterize the role of the 627 domain in polymerase function and offer insights into the replication mechanism of influenza A viruses.
Innate Immune Responses of Bat and Human Cells to Filoviruses: Commonalities and Distinctions
Authors: Kuzmin Ivan V. , Schwarz Toni M. , Ilinykh Philipp A. , Jordan Ingo , Ksiazek Thomas G. , Sachidanandam Ravi , Basler Christopher F. , Bukreyev Alexander
Published: January 2017

Marburg (MARV) and Ebola (EBOV) viruses are zoonotic pathogens that cause severe hemorrhagic fever in humans. The natural reservoir of MARV is the Egyptian rousette bat (Rousettus aegyptiacus); that of EBOV is unknown but believed to be another bat species. The Egyptian rousette develops subclinical productive infection with MARV but is refractory to EBOV. Interaction of filoviruses with hosts is greatly affected by the viral interferon (IFN)-inhibiting domains (IID). Our study was aimed at characterization of innate immune responses to filoviruses and the role of filovirus IID in bat and human cells. The study demonstrated that EBOV and MARV replicate to similar levels in all tested cell lines, indicating that permissiveness for EBOV at cell and organism levels do not necessarily correlate. Filoviruses, particularly MARV, induced a potent innate immune response in rousette cells, which was generally stronger than that in human cells. Both EBOV VP35 and VP24 IID were found to suppress the innate immune response in rousette cells, but only VP35 IID appeared to promote virus replication. Along with IFN-α and IFN-β, IFN-γ was demonstrated to control filovirus infection in bat cells but not in human cells, suggesting host species specificity of the antiviral effect. The antiviral effects of bat IFNs appeared not to correlate with induction of IFN-stimulated genes 54 and 56, which were detected in human cells ectopically expressing bat IFN-α and IFN-β. As bat IFN-γ induced the type I IFN pathway, its antiviral effect is likely to be partially induced via cross talk.

IMPORTANCEBats serve as reservoirs for multiple emerging viruses, including filoviruses, henipaviruses, lyssaviruses, and zoonotic coronaviruses. Although there is no evidence for symptomatic disease caused by either Marburg or Ebola viruses in bats, spillover of these viruses into human populations causes deadly outbreaks. The reason for the lack of symptomatic disease in bats infected with filoviruses remains unknown. The outcome of a virus-host interaction depends on the ability of the host immune system to suppress viral replication and the ability of a virus to counteract the host defenses. Our study is a comparative analysis of the host innate immune response to either MARV or EBOV infection in bat and human cells and the role of viral interferon-inhibiting domains in the host innate immune responses. The data are useful for understanding the interactions of filoviruses with natural and accidental hosts and for identification of factors that influence filovirus evolution.
Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product
Authors: Dailey Harry A. , Dailey Tamara A. , Gerdes Svetlana , Jahn Dieter , Jahn Martina , O'Brian Mark R. , Warren Martin J.
Published: January 2017

The advent of heme during evolution allowed organisms possessing this compound to safely and efficiently carry out a variety of chemical reactions that otherwise were difficult or impossible. While it was long assumed that a single heme biosynthetic pathway existed in nature, over the past decade, it has become clear that there are three distinct pathways among prokaryotes, although all three pathways utilize a common initial core of three enzymes to produce the intermediate uroporphyrinogen III. The most ancient pathway and the only one found in the
Archaea
converts siroheme to protoheme via an oxygen-independent four-enzyme-step process. Bacteria utilize the initial core pathway but then add one additional common step to produce coproporphyrinogen III. Following this step, Gram-positive organisms oxidize coproporphyrinogen III to coproporphyrin III, insert iron to make coproheme, and finally decarboxylate coproheme to protoheme, whereas Gram-negative bacteria first decarboxylate coproporphyrinogen III to protoporphyrinogen IX and then oxidize this to protoporphyrin IX prior to metal insertion to make protoheme. In order to adapt to oxygen-deficient conditions, two steps in the bacterial pathways have multiple forms to accommodate oxidative reactions in an anaerobic environment. The regulation of these pathways reflects the diversity of bacterial metabolism. This diversity, along with the late recognition that three pathways exist, has significantly slowed advances in this field such that no single organism's heme synthesis pathway regulation is currently completely characterized.
Qualitative study of primary care clinicians’ views on point-of-care testing for C-reactive protein for acute respiratory tract infections in family medicine
Authors: Hardy Victoria , Thompson Matthew , Keppel Gina A , Alto William , Dirac M Ashworth , Neher Jon , Sanford Christopher , Hornecker Jaime , Cole Allison
Published: January 2017

Objective

To explore clinicians views of the barriers and facilitators to use of C-reactive protein (CRP) point-of-care tests (POCT) in US family medicine clinics for the management of acute respiratory tract infections (ARTIs) in adults.

Setting

Five family medicine clinics across two US states.

Participants

30 clinicians including 18 physicians, 9 physician residents, 2 physician assistants and 1 nurse practitioner, took part in the study.

Design

A qualitative study using a grounded theory approach to thematically analyse focus group interviews.

Results

These clinicians had limited access to diagnostic tests for patients with ARTI, and very little knowledge of CRP POCT. Three major themes were identified and included the potential clinical role of CRP POCT, concerns related to implementing CRP POCT and evidence needed prior to wider adoption in family medicine. Clinicians believed CRP POCT could support decision-making for some presentations of ARTIs and patient populations when used in conjunction with clinical criteria. Clinicians had concerns about possible overuse and inaccuracy of CRP POCT which they believed might increase antibiotic prescribing rates. Other concerns identified included integration of the test with clinic workflows and cost-effectiveness.

Conclusions

Clinicians stand at the forefront of antibiotic stewardship efforts, but have few diagnostic tests to help them confidently manage ARTIs. CRP POCT may facilitate some aspects of clinical practice. Incorporating CRP POCT with clinical guidelines may strengthen utility of this test, when there is diagnostic uncertainty.
Risk of disseminated intravascular coagulation in patients with type 2 diabetes mellitus: retrospective cohort study
Authors: Nogami Kenichiro , Muraki Isao , Imano Hironori , Iso Hiroyasu
Published: January 2017

Objectives

To determine quantitatively the association between type 2 diabetes mellitus (T2DM) and disseminated intravascular coagulation (DIC).

Design

Retrospective cohort study using a claims database.

Setting

Medical care institutions representing 9% of all secondary hospitals (acute care hospitals) in Japan.

Participants

In total, 797 324 admissions, comprising 435 354 patients aged 18–79 years at the time of admission, were enrolled between January 2010 and September 2014. All patients were diagnosed with diabetes or admitted to hospitals that provided laboratory data.

Main outcome measures

Incidence of DIC reported by physicians in claims data.

Results

Logistic regression analysis found that the risk of DIC was significantly higher in T2DM patients than in non-DM patients (fully adjusted OR: 1.39 (95% CI 1.32 to 1.45)), independent of age, sex, admission year and potential underlying diseases. The higher risk of DIC in T2DM patients was apparent in those who were treated with insulin within the 30-day period prior to admission (1.53 (1.37 to 1.72)). When stratified by the potential underlying diseases, the risk of DIC was higher in T2DM patients with non-septic severe infection (1.67 (1.41 to 1.97)) and with solid tumour (1.59 (1.47 to 1.72)) than in non-DM patients with those underlying diseases. The risk was similar between T2DM and non-DM patients with sepsis (0.98 (0.90 to 1.08)) and lower in T2DM patients with acute leukaemia (0.70 (0.59 to 0.84)).

Conclusions

T2DM was associated with a higher risk of DIC, particularly when recently treated with insulin, as well as among admissions with solid tumour or non-septic severe infection.
Patients' views on the causes of their polymyalgia rheumatica: a content analysis of data from the PMR Cohort Study
Authors: Tshimologo Maatla , Saunders Benjamin , Muller Sara , Mallen Christian D , Hider Samantha L
Published: January 2017

Objective

To explore primary care polymyalgia rheumatica (PMR) patient beliefs about the causes of their PMR.

Design

Qualitative content analysis was conducted on patients' written responses to the question of what they thought had caused their PMR. All data were coded and emergent categories of causal beliefs identified.

Setting

Community patients receiving primary care at general practitioner (GP) practices across England.

Participants

Participants were recruited from a primary care PMR inception cohort (n=654). Between June 2012 and June 2014 GPs referred 739 people with a new PMR diagnosis in the past 3 years into the study. Patients were mailed a baseline self-completion questionnaire, which included the question, ‘What do you think caused your PMR?’. Responses to this question form the data set for the present study.

Results

296 (45%) patients gave a possible cause for their PMR, while 276 (42%) respondents wrote ‘no idea’. Common attributions include ageing (45, 18%), medication (18, 5%) and personal stress (53, 14%). 24 respondents (6%) thought their PMR was as a result of another medical condition.

Conclusions

This is the first study to examine causation beliefs in PMR, identifying a number of possible causes such as ageing, stress and as a complication of other medical problems. Understanding these patient beliefs may impact on treatment adherence and patient outcome.
Associations between prescribed Chinese herbal medicine and risk of hepatocellular carcinoma in patients with chronic hepatitis B: a nationwide population-based cohort study
Authors: Tsai Tzung-Yi , Livneh Hanoch , Hung Tsung-Hsing , Lin I -Hsin , Lu Ming-Chi , Yeh Chia-Chou
Published: January 2017

Objective

Patients with chronic hepatitis B (CHB) are reported to exhibit higher risk of subsequent hepatocellular carcinoma (HCC). However, it remains unclear if Chinese herbal medicine (CHM), an important category of traditional Chinese medicine (TCM), may lower HCC risk in this population. So this study aimed to investigate the effects of CHM on HCC risk among patients with CHB.

Methods

This cohort study used the Taiwanese National Health Insurance Research Database to identify 21 020 newly diagnosed patients with CHB from 1998 to 2007. Among them, 8640 received CHM products after CHB onset (CHM users), and the remaining 12 380 patients were designated as a control group (non-CHM users). All enrolees were followed until the end of 2012 to measure the incidence rate and HR of HCC.

Results

During 15 years of follow-up, 371 CHM users and 958 non-CHM users developed HCC, representing an incidence rate of 5.28% and 10.18% per 1000 person-years, respectively. CHM users had significantly lower HCC risk compared with non-CHM users (adjusted HR=0.63, 95% CI 0.56 to 0.72). The predominant effect was observed in those receiving CHM products for more than 180 days (adjusted HR=0.52). Some CHM products, such asHedyotis diffusa, Scutellaria barbata,Rehmannia glutinosa, Isatis tinctoria,Yi Guan Jian, Xiao Chai Hu Tang, Wu Ling San and Gan Lu Yin, were significantly associated with lower risk of HCC.

Conclusions

The use of CHM was associated with a significantly reduced HCC risk in patients with CHB, which supports the integration of TCM with CHM into clinical practice to influence a favourable prognosis.
The prevalence of visual symptoms in poppers users: a global survey
Authors: Davies Andrew J , Borschmann Rohan , Kelly Simon P , Ramsey John , Ferris Jason , Winstock Adam R
Published: January 2017

Introduction and aims

The use of ‘poppers’ (volatile alkyl nitrites) has been associated with the development of visual symptoms secondary to the development of maculopathy. There are currently no data regarding the prevalence of this condition among poppers users. The aim of this study was to quantify the presence of visual symptoms among poppers users from a global cohort.

Design and methods

The Global Drug Survey (GDS) conducts annual anonymous online surveys of drug and alcohol use. Within the 2012 GDS, questions were inserted regarding the presence of visual symptoms in poppers users.

Results

The GDS received a total of 21 575 valid responses, with a total of 17 479 from the UK, Australia, USA and Eurozone. Within these areas, 5152 (29.5%) had used poppers within their lifetime and 1322 (7.6%) within the previous year. Of the ‘last year’ users, when asked the question: ‘Do you think poppers use has affected your eyesight?’, 29 (2.2%) people responded ‘yes’, 130 (10.0%) responded ‘maybe’ and 1146 (87.8%) responded ‘no (17 people did not answer). Both multiple choice and free-text responses regarding the nature of visual symptoms correlated with the central visual disturbance that would be expected from maculopathy. There was significant increased symptom prevalence with age (likelihood ratio (χ2)=19.0; p<0.001).

Discussion and conclusions

This study demonstrates that a small, yet significant from a public health perspective, proportion of poppers users have visual symptoms. Clinical correlation is required to determine whether these reported symptoms are due to poppers associated maculopathy, or an alternative cause.
Decreased left ventricular stroke volume is associated with low-grade exercise tolerance in patients with chronic obstructive pulmonary disease
Authors: Inoue Sumito , Shibata Yoko , Kishi Hiroyuki , Nitobe Joji , Iwayama Tadateru , Yashiro Yoshinori , Nemoto Takako , Sato Kento , Sato Masamichi , Kimura Tomomi , Igarashi Akira , Tokairin Yoshikane , Kubota Isao
Published: January 2017

Background

Low-grade exercise tolerance is associated with a poor prognosis in patients with chronic obstructive pulmonary disease (COPD). The 6 min walk test (6MWT) is commonly used to evaluate exercise tolerance in patients with COPD. However, little is known regarding the relationship between cardiac function and exercise tolerance in patients with COPD. The aim of this study was to identify predictive factors in cardiac function for low-grade exercise tolerance in patients with stable COPD.

Methods

We recruited 57 patients with stable COPD (men 54, women 3) to perform the 6MWT. Patients with underlying orthopaedic disease or heart failure were excluded. Cardiac function was evaluated by echocardiography and contrast-enhanced cardiac CT. We also measured pulmonary function and the 6MWT distance.

Results

Forced expiratory volume in 1 s (FEV1) and per cent predicted FEV, along with left ventricular end diastolic volume and left ventricular cardiac output as measured by cardiac CT, were significantly related to the 6MWT distance. On multivariate analysis, left ventricular stroke volume was the factor most closely associated with a decreased walked distance in the 6MWT.

Conclusions

Decreased left ventricular stroke volume was associated with low-grade exercise tolerance in patients with stable COPD without heart failure.
Predator–prey interactions in the face of management regulations: changes in Mediterranean small pelagic species are not due to increased tuna predation
Authors: Van Beveren Elisabeth , Fromentin Jean-Marc , Bonhommeau Sylvain , Nieblas Anne-Elise , Metral Luisa , Brisset Blandine , Jusup Marko , Bauer Robert Klaus , Brosset Pablo , Saraux Claire
Published: January 2017

Recently, the abundance of young Atlantic bluefin tuna (Thunnus thynnus) tripled in the northwestern Mediterranean following effective management measures. We investigated whether its predation on sardine (Sardina pilchardus) and anchovy (Engraulis encrasicolus) could explain their concurrent size and biomass decline, which caused a fishery crisis. Combining the observed diet composition of bluefin tuna, their modelled daily energy requirements, their population size, and the abundance of prey species in the area, we calculated the proportion of the prey populations that were consumed by bluefin tuna annually over 2011–2013. To assess whether tuna could alter the size structure of the three small pelagic fish populations (anchovy, sardine, and sprat (Sprattus sprattus)), the size distributions of the consumed prey species were compared with those of the wild populations. We estimated that the annual consumption of small pelagic fish by bluefin tuna is less than 2% of the abundance of these populations. Furthermore, size selectivity patterns were not observed. We thus concluded that tuna predation is unlikely to be the main cause of major changes in the small pelagic fish populations from this area.
Understanding inter-reach variation in brown trout (Salmo trutta) mortality rates using a hierarchical Bayesian state-space model
Authors: Bret Victor , Capra Hervé , Gouraud Véronique , Lamouroux Nicolas , Piffady Jérémy , Tissot Laurence , Rivot Etienne
Published: January 2017

Successful management and protection of wild animal populations relies on good understanding of their life cycles. Because population dynamics depends on intricate interactions of biological and ecological processes at various scales, new approaches are needed that account for the variability of demographic processes and associated parameters in a hierarchy of spatial scales. A hierarchical Bayesian model for the resident brown trout (Salmo trutta) life cycle was built to assess the relative influence of local and general determinants of mortality. The model was fitted to an extensive data set collected in 40 river reaches, combining abundance and environmental data (hydraulics, water temperature). Density-dependent mortality of juveniles increased at low water temperatures and decreased with shelter availability. High water temperature increased density-dependent mortality in adults. The model could help to predict monthly juvenile and adult mortality under scenarios of global warming and changes in shelter availability due to habitat degradation or restoration.
Practical quantum teleportation of an unknown quantum state
Authors: Amin Syed Tahir , Khalique Aeysha
Published: January 2017

We present our model to teleport an unknown quantum state using entanglement between two distant parties. Our model takes into account experimental limitations due to contribution of multi-photon pair production of parametric down conversion source, inefficiency, dark counts of detectors, and channel losses. We use a linear optics setup for quantum teleportation of an unknown quantum state by the sender performing a Bell state measurement. Our theory successfully provides a model for experimentalists to optimize the fidelity by adjusting the experimental parameters. We apply our model to a recent experiment on quantum teleportation and the results obtained by our model are in good agreement with the experimental results.
Enhancement of single guide RNA transcription for efficient CRISPR/Cas-based genomic engineering
Authors: Ui-Tei Kumiko , Maruyama Shohei , Nakano Yuko
Published: January 2017

Genomic engineering using clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) protein is a promising approach for targeting the genomic DNA of virtually any organism in a sequence-specific manner. Recent remarkable advances in CRISPR/Cas technology have made it a feasible system for use in therapeutic applications and biotechnology. In the CRISPR/Cas system, a guide RNA (gRNA), interacting with the Cas protein, recognizes a genomic region with sequence complementarity, and the double-stranded DNA at the target site is cleaved by the Cas protein. A widely used gRNA is an RNA polymerase III (pol III)-driven single gRNA (sgRNA), which is produced by artificial fusion of CRISPR RNA (crRNA) and trans-activation crRNA (tracrRNA). However, we identified a TTTT stretch, known as a termination signal of RNA pol III, in the scaffold region of the sgRNA. Here, we revealed that sgRNA carrying a TTTT stretch reduces the efficiency of sgRNA transcription due to premature transcriptional termination, and decreases the efficiency of genome editing. Unexpectedly, it was also shown that the premature terminated sgRNA may have an adverse effect of inducing RNA interference. Such disadvantageous effects were avoided by substituting one base in the TTTT stretch.
Hirzebruch-type inequalities and plane curve configurations
Authors: Pokora Piotr
Published: January 2017

In this paper, we come back to a problem proposed by F. Hirzebruch in the 1980s, namely whether there exists a configuration of smooth conics in the complex projective plane such that the associated desingularization of the Kummer extension is a ball quotient. We extend our considerations to the so-called [Formula: see text]-configurations of curves in the projective plane and we show that in most cases for a given configuration the associated desingularization of the Kummer extension is not a ball quotient. Moreover, we provide improved versions of Hirzebruch-type inequality for [Formula: see text]-configurations. Finally, we show that the so-called characteristic numbers (or [Formula: see text] numbers) for [Formula: see text]-configurations are bounded from above by [Formula: see text]. At the end of the paper we give some examples of surfaces constructed via Kummer extensions branched along conic configurations.
Molecular dynamics approach for crystal structures of methane A and B
Authors: Galván César G. , Cabrera-Trujillo José M. , Hernández-Hernández Ivonne J. , Pérez Luis A.
Published: January 2017

The carbon structures of phases A and B of methane are investigated through classical molecular dynamics simulations using optimized potentials for liquid simulations all-atom force fields as well as ReaxFF reactive force fields. Both final thermodynamic states were obtained by the proper ramping of temperature and pressure through well-known regions of methane’s phase diagram using the isothermal–isobaric (NPT) ensemble. Our calculated structures are in good agreement with very recent experimental data. The knowledge of these phases is the basis for the study of methane at high pressures.
Green’s functions theory for an interstitial magnetic impurity in a transverse Ising ferromagnet
Authors: Freire M. M. , Costa Filho Raimundo N. , Leite R. V.
Published: January 2017

A Green’s function formalism is used to calculate the spectrum of localized states associated with an interstitial magnetic impurity in a semi-infinite ferromagnet described by the transverse Ising model. The nonresonant and resonant excitations of the system due to the impurity (i.e. the defect modes outside and inside, respectively, the region of the bulk and surface spin waves (SW)) are calculated numerically for the high-temperature phase. Two situations are analyzed, depending on the position of the interstitial impurity: the impurity is in the surface ([Formula: see text]) and the impurity is in the bulk region ([Formula: see text]).
Cascading failures mechanism based on betweenness-degree ratio distribution with different connecting preferences
Authors: Wang Xiao Juan , Guo Shi Ze , Jin Lei , Chen Mo
Published: January 2017

We study the structural robustness of the scale free network against the cascading failure induced by overload. In this paper, a failure mechanism based on betweenness-degree ratio distribution is proposed. In the cascading failure model we built the initial load of an edge which is proportional to the node betweenness of its ends. During the edge random deletion, we find a phase transition. Then based on the phase transition, we divide the process of the cascading failure into two parts: the robust area and the vulnerable area, and define the corresponding indicator to measure the performance of the networks in both areas. From derivation, we find that the vulnerability of the network is determined by the distribution of betweenness-degree ratio. After that we use the connection between the node ability coefficient and distribution of betweenness-degree ratio to explain the cascading failure mechanism. In simulations, we verify the correctness of our derivations. By changing connecting preferences, we find scale free networks with a slight assortativity, which performs better both in robust area and vulnerable area.
Learning Similarity Scores by Using a Family of Distance Functions in Multiple Feature Spaces
Authors: López-Iñesta Emilia , Grimaldo Francisco , Arevalillo-Herráez Miguel
Published: January 2017

There exist a large number of distance functions that allow one to measure similarity between feature vectors and thus can be used for ranking purposes. When multiple representations of the same object are available, distances in each representation space may be combined to produce a single similarity score. In this paper, we present a method to build such a similarity ranking out of a family of distance functions. Unlike other approaches that aim to select the best distance function for a particular context, we use several distances and combine them in a convenient way. To this end, we adopt a classical similarity learning approach and face the problem as a standard supervised machine learning task. As in most similarity learning settings, the training data are composed of a set of pairs of objects that have been labeled as similar/dissimilar. These are first used as an input to a transformation function that computes new feature vectors for each pair by using a family of distance functions in each of the available representation spaces. Then, this information is used to learn a classifier. The approach has been tested using three different repositories. Results show that the proposed method outperforms other alternative approaches in high-dimensional spaces and highlight the benefits of using multiple distances in each representation space.
Approximation of Unknown Multivariate Probability Distributions by Using Mixtures of Product Components: A Tutorial
Authors: Grim Jiří
Published: January 2017

In literature the references to EM estimation of product mixtures are not very frequent. The simplifying assumption of product components, e.g. diagonal covariance matrices in case of Gaussian mixtures, is usually considered only as a compromise because of some computational constraints or limited dataset. We have found that the product mixtures are rarely used intentionally as a preferable approximating tool. Probably, most practitioners do not “trust” the product components because of their formal similarity to “naive Bayes models.” Another reason could be an unrecognized numerical instability of EM algorithm in multidimensional spaces. In this paper we recall that the product mixture model does not imply the assumption of independence of variables. It is even not restrictive if the number of components is large enough. In addition, the product components increase numerical stability of the standard EM algorithm, simplify the EM iterations and have some other important advantages. We discuss and explain the implementation details of EM algorithm and summarize our experience in estimating product mixtures. Finally we illustrate the wide applicability of product mixtures in pattern recognition and in other fields.
Spatial Error Concealment Algorithm Based on Adaptive Edge Threshold and Directional Weight
Authors: Ni Hongxia , Li Yufeng
Published: January 2017

In order to improve the H.264/AVC compressed video stream error resilience in wireless channel transmission, this paper presents a spatial error concealment algorithm based on adaptive edge threshold and directional weight. Firstly, this algorithm makes use of Sobel gradient operator of image edge detection to detect the edge of adjacent macro blocks; secondly, according to specific information of adjacent macro-block of damaged macro-block, it can set gradient adaptive threshold; thirdly, it makes the direction weighted interpolation to damaged macro-block with the Sobel gradient operator of image edge detection. Experiments show that the image reconstruction quality is greatly improved by using this algorithm, which has higher application value for different video sequence as compared to the traditional spatial error concealment algorithms. This algorithm not only improves the quality of image restoration, but also has higher application value.
An Approach to Microcontroller-Based Realization of Boost Converter with Quasi-Sliding Mode Control
Authors: Almawlawe Muhanad , Mitić Darko , Antić Dragan , Icić Zoran
Published: January 2017

The paper considers a realization of quasi-sliding mode control for DC–DC boost-type converter on ATmega8 microcontroller. The proposed control law represents a combination of discrete-time sliding mode and generalized minimum variance control techniques. The control design is based on input–output converter model and only the sensed output voltage is used for generating control signal. This approach simplifies the practical realization of boost converter since there is no need for current sensors. By introducing an additional discrete-time integrator in control, the converter accuracy in steady-state under load and input voltage variations is enhanced. The experimental prototype is developed and several experiments are conducted to validate the functionalities of the proposed solution. The maximum load and line regulation errors of the proposed converter are 1.55% and 2.9%, respectively.
Calculating Blood Pressure Based on Measured Heart Sounds
Authors: Chen Lingguang , Wu Sean F. , Xu Yong , Lyman William D. , Kapur Gaurav
Published: January 2017

The current standard technique for blood pressure determination is by using cuff/stethoscope, which is not suited for infants or children. Even for adults such an approach yields 60% accuracy with respect to intra-arterial blood pressure measurements. Moreover, it does not allow for continuous monitoring of blood pressure over 24 h and days. In this paper, a new methodology is developed that enables one to calculate the systolic and diastolic blood pressures continuously in a non-invasive manner based on the heart beats measured from the chest of a human being. To this end, we must separate the first and second heart sounds, known as S1 and S2, from the directly measured heart sound signals. Next, the individual characteristics of S1 and S2 must be identified and correlated to the systolic and diastolic blood pressures. It is emphasized that the material properties of a human being are highly inhomogeneous, changing from one organ to another, and the speed at which the heart sound signals propagate inside a human body cannot be determined precisely. Moreover, the exact locations from which the heart sounds are originated are unknown a priori, and must be estimated. As such, the computer model developed here is semi-empirical. Yet, validation results have demonstrated that this semi-empirical computer model can produce relatively robust and accurate calculations of the systolic and diastolic blood pressures with high statistical merits.
SYNTHESIS OF ZnO:Mg NANOCOMPOSITE BY PULSED LASER ABLATION IN LIQUID
Authors: KHASHAN KHAWLA S. , MAHDI FARAH
Published: January 2017

ZnO:Mg nanocomposite formation by two-step laser ablation in deionized water is analyzed. Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), UV–Vis spectroscopy, scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) analysis were employed to obtain infrared spectra, crystalline structures, optical absorption spectra, morphology and spatial composition of the prepared nanocomposite. The FTIR result shows that bonds at [Formula: see text]480[Formula: see text]cm[Formula: see text] and 900[Formula: see text]cm[Formula: see text] correspond to Zn–O and Mg–O stretching modes. The XRD pattern observed the hexagonal wurtzite of ZnMgO phase at [Formula: see text] and 34.76[Formula: see text]. SEM image shows a flower-like hierarchical structure with a full array about 2[Formula: see text][Formula: see text]m. The absorption spectra demonstrate that a band gap of nanocomposite increases as the Mg content increases.
CHARACTERIZATION OF RF MAGNETRON-SPUTTERED CrCuN AND CrNiN COATINGS BY NANOINDENTATION
Authors: TAN SHUYONG , LIU XIAOHUI , ZHANG XUHAI , FANG FENG , WANG ZHANGZHONG
Published: January 2017

RF magnetron-sputtered CrCuN coatings with ultra-low Cu content (0.53–2.1 at.%) were deposited using Cr[Formula: see text]Cu3 target (at.%) by changing the substrate negative bias from 0[Formula: see text]V to [Formula: see text]200[Formula: see text]V. The CrNiN coatings with different nickel contents (0, 2.92 and 8.79 at.%) were sputtered by different-component Cr–Ni alloy targets (Cr, Cr[Formula: see text]Ni5 and Cr[Formula: see text]Ni[Formula: see text], in at.%). The effect of bias and alloying element content on coating toughness was investigated by nanoindentation. The results show that all the coatings have unsatisfied toughness because of [Formula: see text]/[Formula: see text]. With increasing bias, the toughness of CrN and CrCuN coatings improves basically due to grain refinement caused by high bias effect. Under the same bias, although CrCuN coatings have finer grains, their toughness is still lower than that of CrN coatings because of inadequate copper coverage degree as a result of ultra-low copper content. On the contrary, once there is an appropriate alloying element content of 2.92 at.% Ni, the toughness of CrNiN coatings increases with the nickel content due to relatively higher Ni coverage degree.
A GENERALIZED CONTAGION PROCESS WITH AN APPLICATION TO CREDIT RISK
Authors: DASSIOS ANGELOS , ZHAO HONGBIAO
Published: January 2017

We introduce a class of analytically tractable jump processes with contagion effects by generalizing the classical Hawkes process. This model framework combines the characteristics of three popular point processes in the literature: (1) Cox process with CIR intensity; (2) Cox process with Poisson shot-noise intensity; (3) Hawkes process with exponentially decaying intensity. Hence, it can be considered as a self-exciting and externally-exciting point process with mean-reverting stochastic intensity. Essential probabilistic properties such as moments, the Laplace transform of intensity process, and the probability generating function of point process as well as some important asymptotics have been derived. Some special cases and a method for change of measure are discussed. This point process may be applicable to modeling contagious arrivals of events for various circumstances (such as jumps, transactions, losses, defaults, catastrophes) in finance, insurance and economics with both endogenous and exogenous risk factors within one framework. More specifically, these exogenous factors could contain relatively short-lived shocks and long-lasting risk drivers. We make a simple application to calculate the default probability for credit risk and to price defaultable zero-coupon bonds.
Contactless Cardiac Activity Detection Based on Head Motion Magnification
Authors: Al-Naji Ali , Chahl Javaan
Published: January 2017

The aim of this study is to remotely measure cardiac activity (heart pulse, total cycle length and pulse width) from videos based on a head motion at different positions of the head (front, back and side). As the head motion resulting from the cardiac cycle of blood from the heart to the head via the carotid arteries is not visible to the naked eye and to preserve the signal strength in the video, we used wavelet decomposition and a Chebychev filter to develop a standard Eulerian video magnification in terms of noise removal and execution time. We used both magnification systems to measure cardiac activity and statistically compare the results using Bland–Altman method. Also, we proposed a new video quality system based on fuzzy interface system to select which magnification system has better magnification quality and gives better results for the heart pulse rate. The experimental results on several videos captured from 10 healthy subjects show that the proposed contactless system of heart pulse has an accuracy of 98.3% when magnified video based on the developing magnification system was used and an accuracy of 97.4% when magnified video based on Eulerian magnification system was used instead. The proposed system has low computational complexity, making it suitable for advancing health care applications, mobile health applications and telemedicine.
FPGA-Based Multiplier-Less Log-Based Hardware Architectures for Hybrid Color Image Enhancement System
Authors: Nnolim Uche A.
Published: January 2017

Logarithmic image processing (LIP) models provide a viable framework for image enhancement, particularly the color-based models. These techniques, due to their vector nature, avoid the problems of grayscale methods applied to RGB color image processing. Furthermore, the absence of multiply-accumulate (MAC) operations makes them amenable to hardware realization for faster operation when compared with spatial filter kernel-based approaches. However, details of image scenes are not always revealed after processing and homomorphic filters are still a popular low-complexity option for correction of images acquired under uneven illumination conditions, notwithstanding the fading that occurs when processing RGB color images. Though nonlinear color space converter hardware architectures have been implemented and reported in the literature for improving results from conventional illumination correction techniques, they add to the hardware complexity. The contributions of the work described in this paper includes original, practical, standard and logarithmic, multiplier-less high-speed architectures for a variant of the LIP model in addition to standard and log-hybrid architectures for a modified spatial homomorphic filter (MSDHF) to reduce color fading in RGB space. The modified homomorphic filter is able to enhance both faded/bright and dark low-contrast images, giving it an edge over standard illumination correction systems. A combined approach utilizing the MSDHF and simplified LIP algorithms enhances the strengths of the individual algorithms while minimizing their individual weaknesses. Comparisons of the developed systems are made with the standard homomorphic filter architecture and similar works from the literature.
An FGLM-like algorithm for computing the radical of a zero-dimensional ideal
Authors: Mora Teo
Published: January 2017

We present a linear algebra algorithm, which, given a zero-dimensional ideal via a “good” representation, produces a separating linear form, its radical, again given via the same “good” representation and also a Kronecker parametrization of it. As an irrelevant byproduct, if you like, you can also read a Gröbner basis of the radical.
Cohen–Macaulayness of trivial extensions
Authors: Mahdikhani A. , Sahandi P. , Shirmohammadi N.
Published: January 2017

Our goal is to determine when the trivial extensions of commutative rings by modules are Cohen–Macaulay in the sense of Hamilton and Marley. For this purpose, we provide a generalization of the concept of Cohen–Macaulayness of rings to modules.