bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes of Color and Fluorescence of Resin Composites Immersed in Beer
Authors: Antonov Milica , Lenhardt Lea , Manojlović Dragica , Milićević Bojana , Zeković Ivana , Dramićanin Miroslav D.
Published: July 2016

Objective

The aim of this study was to evaluate changes of color and fluorescence of resin based composite exposed to beer.

Materials and Methods

84 samples (13 mm in diameter and 1.5 mm thick) of microhybrid composite Gradia DirectTM extra bleach white were immersed in 5 different beers (dark and light) or distilled water. Color and fluorescence were measured prior and after 1‐, 7‐, and 14‐day immersion by Spectrophotometer Thermo Evolution 600 and Fluorolog‐3‐221 spectrofluorometer.

Results

Resin based composites changed color after immersion in beers of different types. Beers with higher optical absorption induced greater color changes. The fluorescence intensity of composites was decreased after immersion in beer, but the shape of fluorescence spectra was not changed. 14‐day immersion in Bernard dark beer caused the greatest changes in optical properties of composite: ΔE*=9.0 and 57.6% reduced fluorescence.

Conclusion

Dark and light beers changed optical properties of resin based composite. The color change come exclusively from the change of chroma.

Clinical Significance

To fully meet esthetic criteria when using dental materials in restoration it is crucial to match optical properties of teeth and dental restoration at the moment of placement, but also to keep the match over the time. Considering that staining in beer causes changes in color and fluorescence of composites and that discoloration is a frequent reason for replacement of composite restorations, the data and conclusions on discoloration of dental restorations caused by beer consumption should aid dental professionals when reaching for high esthetics of modern dentistry.(J Esthet Restor Dent 28:330–338, 2016)
Assessing the element of surprise of record‐breaking flood events
Authors: Kjeldsen T.R. , Prosdocimi I.
Published: July 2016

The occurrence of record‐breaking flood events continues to cause damage and disruption despite significant investments in flood defences, suggesting that these events are in some sense surprising. This study develops a new statistical test to help assess if a flood event can be considered surprising or not. The test statistic is derived from annual maximum series (AMS) of extreme events, and Monte Carlo simulations were used to derive critical values for a range of significance levels based on a Generalised Logistic distribution. The method is tested on a national data set of AMS of peak flow from the United Kingdom, and is found to correctly identify recent large events that have been identified elsewhere as causing a significant change in UK flood management policy. No temporal trend in the frequency or magnitude of surprising events was identified, and no link could be established between the occurrences of surprising events and large‐scale drivers. Finally, the implications of the findings for future research examining the most extreme flood events are discussed.
Accurate stochastic reconstruction of heterogeneous microstructures by limited x‐ray tomographic projections
Authors: LI HECHAO , KAIRA SHASHANK , MERTENS JAMES , CHAWLA NIKHILESH , JIAO YANG
Published: July 2016

An accurate knowledge of the complex microstructure of a heterogeneous material is crucial for its performance prediction, prognosis and optimization. X‐ray tomography has provided a nondestructive means for microstructure characterization in 3D and 4D (i.e. structural evolution over time), in which a material is typically reconstructed from a large number of tomographic projections using filtered‐back‐projection (FBP) method or algebraic reconstruction techniques (ART). Here, we present in detail a stochastic optimization procedure that enables one to accurately reconstruct material microstructure from a small number of absorption contrast x‐ray tomographic projections. This discrete tomography reconstruction procedure is in contrast to the commonly used FBP and ART, which usually requires thousands of projections for accurate microstructure rendition. The utility of our stochastic procedure is first demonstrated by reconstructing a wide class of two‐phase heterogeneous materials including sandstone and hard‐particle packing from simulated limited‐angle projections in both cone‐beam and parallel beam projection geometry. It is then applied to reconstruct tailored Sn‐sphere‐clay‐matrix systems from limited‐angle cone‐beam data obtained via a lab‐scale tomography facility at Arizona State University and parallel‐beam synchrotron data obtained at Advanced Photon Source, Argonne National Laboratory. In addition, we examine the information content of tomography data by successively incorporating larger number of projections and quantifying the accuracy of the reconstructions. We show that only a small number of projections (e.g. 20–40, depending on the complexity of the microstructure of interest and desired resolution) are necessary for accurate material reconstructions via our stochastic procedure, which indicates its high efficiency in using limited structural information. The ramifications of the stochastic reconstruction procedure in 4D materials science are also discussed.
The clinical value of controlled attenuation parameter for the noninvasive assessment of liver steatosis
Authors: Ferraioli Giovanna , Tinelli Carmine , De Silvestri Annalisa , Lissandrin Raffaella , Above Elisabetta , Dellafiore Carolina , Poma Gianluigi , Di Gregorio Marta , Maiocchi Laura , Maserati Renato , Filice Carlo
Published: July 2016

Background & Aims

Ultrasound is the imaging modality most widely utilized in the general population for diagnostic purposes. Controlled attenuation parameter is a novel noninvasive method for assessing steatosis. Our aim was to investigate whether the clinical value of controlled attenuation parameter in patients referred for abdominal ultrasound examinations is affected by liver fibrosis.

Methods

Consecutive patients referred for abdominal ultrasound examinations were enrolled. Controlled attenuation parameter and liver stiffness were assessed with the FibroScan (Echosens, France). Liver fibrosis was staged according to published cutoffs of liver stiffness measurements. Pearson's or Spearman's rank correlation coefficient was used to test the association between two study variables. Optimal cutoff of controlled attenuation parameter for diagnosing liver steatosis (S≥2) was 256 dB/m. The diagnostic performance and accuracy of dichotomized controlled attenuation parameter, ultrasound and body mass index were analysed using the imperfect gold standard methodology.

Results

A total of 726 subjects (464 males and 262 females) were studied. Five hundred and eight‐nine (81.1%) patients were affected by chronic viral hepatitis. Correlation of controlled attenuation parameter with ultrasound score was 0.48 and 0.57 in patients with and without chronic viral hepatitis respectively. In patients with chronic viral hepatitis, ultrasound, dichotomized controlled attenuation parameter and body mass index showed performance of 58.2%, 82.3% and 46.7%, respectively, whereas in patients without chronic viral hepatitis, the performance was 86.4%, 68.6% and 48.6% respectively.

Conclusions

In patients with chronic viral hepatitis and advanced liver fibrosis, controlled attenuation parameter performs better than ultrasound for assessing liver steatosis, whereas in patients without viral hepatitis and with nonsignificant liver disease ultrasound shows the best performance.
Integrated low‐intensity biofeedback therapy in fecal incontinence: evidence that “good” in‐home anal sphincter exercise practice makes perfect
Authors: Vasant D. H. , Solanki K. , Balakrishnan S. , Radhakrishnan N. V.
Published: July 2016

Background

Biofeedback therapy (BFT) is an established treatment for fecal incontinence (FI), with access often being restricted to tertiary centers due to resources and the perceived requirement for high‐intensity regimes. However, the optimal regime remains unknown. We evaluated outcomes from our low‐intensity integrated BFT program in a secondary care center.

Methods

Outcomes of our BFT service for FI were evaluated retrospectively. Response was defined by ≥50% improvement in FI frequency from baseline or complete continence. Responders were compared to non‐responders for factors including symptoms, manometry data, sphincter exercise technique and duration of practice, and the number and frequency of sessions. Where patients dropped out, outcomes and the reason for dropout were obtained retrospectively.

Key Results

Fecal incontinence patients (n=205, median 62 years, 72% female) attended a median (IQR) 3 (2) BFT sessions with 55 (36) days between visits. Overall, 146/205 (71%) responded with 97/205 (47%) achieving continence. Fecal incontinence frequency improved dramatically in completed cases (P=0.000). While non‐response was associated with males (P=0.03) and dropout (P=0.000), “good” anal sphincter exercise technique (P=0.008) and longer in‐home practice (P=0.007) and more sessions (P=0.04) were associated with response. Dropout rate was 80/205 (39%), with the reason for dropout being obtained in 80%.

Conclusions & Inferences

Despite low‐intensity BFT, comparable outcomes to data from tertiary centers were achieved. Our data emphasize the importance of technique and in‐home practice of anal sphincter exercises. Customizing BFT intensity based on predictive factors and encouraging in‐home practice may optimize outcomes, reduce dropout rates, and rationalize resources.
Taxonomic similarity, more than contact opportunity, explains novel plant–pathogen associations between native and alien taxa
Authors: Bufford Jennifer L. , Hulme Philip E. , Sikes Benjamin A. , Cooper Jerry A. , Johnston Peter R. , Duncan Richard P.
Published: July 2016

Novel associations between plants and pathogens can have serious impacts on managed and natural ecosystems world‐wide. The introduction of alien plants increases the potential for biogeographically novel plant–pathogen associations to arise when pathogens are transmitted from native to alien plant species and vice versa.

We quantified biogeographically novel associations recorded in New Zealand over the last 150 yr between plant pathogens (fungi, oomycetes and plasmodiophorids) and vascular plants. We examined the extent to which taxonomic similarity, pathogen traits, contact opportunity and sampling effort could explain the number of novel associates for host and pathogen species.

Novel associations were common; approximately one‐third of surveyed plants and pathogens were recorded with at least one biogeographically novel associate. Native plants had more alien pathogens than vice versa. Taxonomic similarity between the native and alien flora and the total number of recorded associations (a measure of sampling effort) best explained the number of novel associates among species.

The frequency of novel associations and the importance of sampling effort as an explanatory variable emphasize the need for effective monitoring and risk assessment tools to mitigate the potential environmental and economic impact of novel pathogen associations.
Establishment of an international database for genetic variants in esophageal cancer
Authors: Vihinen Mauno
Published: July 2016

The establishment of a database has been suggested in order to collect, organize, and distribute genetic information about esophageal cancer. The World Organization for Specialized Studies on Diseases of the Esophagus and the Human Variome Project will be in charge of a central database of information about esophageal cancer–related variations from publications, databases, and laboratories; in addition to genetic details, clinical parameters will also be included. The aim will be to get all the central players in research, clinical, and commercial laboratories to contribute. The database will follow established recommendations and guidelines. The database will require a team of dedicated curators with different backgrounds. Numerous layers of systematics will be applied to facilitate computational analyses. The data items will be extensively integrated with other information sources. The database will be distributed as open access to ensure exchange of the data with other databases. Variations will be reported in relation to reference sequences on three levels––DNA, RNA, and protein—whenever applicable. In the first phase, the database will concentrate on genetic variations including both somatic and germline variations for susceptibility genes. Additional types of information can be integrated at a later stage.
Household‐Level Coastal Adaptation and Its Drivers: A Systematic Case Study Review
Authors: Koerth Jana , Vafeidis Athanasios T. , Hinkel Jochen
Published: July 2016

Evidence‐based information on household‐level adaptation is an important element of integrated management of vulnerable coastal regions. A growing number of empirical studies deal with household‐level adaptation at the coast in different regions. This article provides a systematic review of these studies. We analyze studies according to how households in different parts of the world are currently adapting, or how they are intending to adapt, and identify explanatory factors for adaptation behavior and intention. We find that households implement a broad range of adaptation measures and that adaptation behavior is explained by individual factors such as socioeconomic and cognitive variables, experience, and perceived responsibilities. Nonpersonal characteristics have also been used to explain adaptation behavior and intention but have not been extensively investigated. Few studies employ qualitative research methods and use inductive approaches as well as models stemming from behavioral economics. Our findings suggest that coastal risk management policies should communicate the efficacy of household‐level adaptation, in addition to information about flood risk, in order to encourage coastal households in their adaptation activities. In this context, we discuss the role of resources and responsibility of households for their adaptation behavior. We describe the lessons learnt and formulate a research agenda on household‐level adaptation to coastal flood risk. In practice, coastal risk management policies should further promote individually driven adaptation by integrating it in adaptation strategies and processes.
A novel HLA‐A*24 allele, A*24:337, was identified by sequencing‐based typing
Authors: Hu B. , Han B. , Chi X.‐Y. , Jiao S.‐X.
Published: July 2016

A novel allele A*24:337 was identified in a Chinese individual by sequence‐based typing.
Characterization of Anaplasma marginale subsp. centrale Strains by Use of
msp1aS
Genotyping Reveals a Wildlife Reservoir
Authors: Khumalo Zamantungwa T. H. , Catanese Helen N. , Liesching Nicole , Hove Paidashe , Collins Nicola E. , Chaisi Mamohale E. , Gebremedhin Assefaw H. , Oosthuizen Marinda C. , Brayton Kelly A.
Published: July 2016

Bovine anaplasmosis caused by the intraerythrocytic rickettsial pathogen
Anaplasma marginale
is endemic in South Africa.
Anaplasma marginale
subspecies
centrale
also infects cattle; however, it causes a milder form of anaplasmosis and is used as a live vaccine against
A. marginale
. There has been less interest in the epidemiology of
A. marginale
subsp.
centrale
, and, as a result, there are few reports detecting natural infections of this organism. When detected in cattle, it is often assumed that it is due to vaccination, and in most cases, it is reported as coinfection with
A. marginale
without characterization of the strain. A total of 380 blood samples from wild ruminant species and cattle collected from biobanks, national parks, and other regions of South Africa were used in duplex real-time PCR assays to simultaneously detect
A. marginale
and
A. marginale
subsp.
centrale.
PCR results indicated high occurrence of
A. marginale
subsp.
centrale
infections, ranging from 25 to 100% in national parks. Samples positive for
A. marginale
subsp.
centrale
were further characterized using the
msp1aS
gene, a homolog of
msp1
α of
A. marginale
, which contains repeats at the 5′ ends that are useful for genotyping strains. A total of 47 Msp1aS repeats were identified, which corresponded to 32
A. marginale
subsp.
centrale
genotypes detected in cattle, buffalo, and wildebeest. RepeatAnalyzer was used to examine strain diversity. Our results demonstrate a diversity of
A. marginale
subsp.
centrale
strains from cattle and wildlife hosts from South Africa and indicate the utility of
msp1aS
as a genotypic marker for
A. marginale
subsp.
centrale
strain diversity.
First Evaluation of GenoType MTBDR
plus
2.0 Performed Directly on Respiratory Specimens in Central America
Authors: Lanzas Fedora , Ioerger Thomas R. , Shah Harita , Acosta William , Karakousis Petros C.
Published: July 2016

The turnaround times for conventional methods used to detect
Mycobacterium tuberculosis
in sputum samples and to obtain drug susceptibility information are long in many developing countries, including Panama, leading to delays in appropriate treatment initiation and continued transmission in the community. We evaluated the performance of a molecular line probe assay, the Genotype MTBDR
plus
version 2.0 assay, in detecting
M. tuberculosis
complex directly in respiratory specimens from smear-positive tuberculosis cases from four different regions in Panama, as well as the most frequent mutations in genes conferring resistance to isoniazid (
katG
and
inhA
) and rifampin (
rpoB
). Our results were confirmed with the nitrate reductase assay and genomic sequencing.
M. tuberculosis
complex was detected by the Genotype MTBDR
plus
2.0 assay with 100% sensitivity and specificity. The sensitivity and specificity for rifampin resistance were 100% and 100%, respectively, and those for isoniazid resistance were 90.7% and 100%. Isoniazid monoresistance was detected in 5.2% of new cases. Genotype MTBDR
plus
2.0 is highly accurate in detecting
M. tuberculosis
complex in respiratory specimens and is able to discriminate isoniazid-monoresistant cases from multidrug-resistant cases within 2 days.
Human Cathelicidin Compensates for the Role of Apolipoproteins in Hepatitis C Virus Infectious Particle Formation
Authors: Puig-Basagoiti Francesc , Fukuhara Takasuke , Tamura Tomokazu , Ono Chikako , Uemura Kentaro , Kawachi Yukako , Yamamoto Satomi , Mori Hiroyuki , Kurihara Takeshi , Okamoto Toru , Aizaki Hideki , Matsuura Yoshiharu
Published: July 2016

Exchangeable apolipoproteins (ApoA, -C, and -E) have been shown to redundantly participate in the formation of infectious hepatitis C virus (HCV) particles during the assembly process, although their precise role in the viral life cycle is not well understood. Recently, it was shown that the exogenous expression of only short sequences containing amphipathic α-helices from various apolipoproteins is sufficient to restore the formation of infectious HCV particles in ApoB and ApoE double-gene-knockout Huh7 (BE-KO) cells. In this study, through the expression of a small library of human secretory proteins containing amphipathic α-helix structures, we identified the human cathelicidin antimicrobial peptide (CAMP), the only known member of the cathelicidin family of antimicrobial peptides (AMPs) in humans and expressed mainly in bone marrow and leukocytes. We showed that CAMP is able to rescue HCV infectious particle formation in BE-KO cells. In addition, we revealed that the LL-37 domain in CAMP containing amphipathic α-helices is crucial for the compensation of infectivity in BE-KO cells, and the expression of CAMP in nonhepatic 293T cells expressing claudin 1 and microRNA miR-122 confers complete propagation of HCV. These results suggest the possibility of extrahepatic propagation of HCV in cells with low-level or no expression of apolipoproteins but expressing secretory proteins containing amphipathic α-helices such as CAMP.

IMPORTANCE
Various exchangeable apolipoproteins play a pivotal role in the formation of infectious HCV during the assembly of viral particles, and amphipathic α-helix motifs in the apolipoproteins have been shown to be a key factor. To the best of our knowledge, we have identified for the first time the human cathelicidin CAMP as a cellular protein that can compensate for the role of apolipoproteins in the life cycle of HCV. We have also identified the domain in CAMP that contains amphipathic α-helices crucial for compensation and show that the expression of CAMP in nonhepatic cells expressing claudin 1 and miR-122 confers complete propagation of HCV. We speculate that low levels of HCV propagation might be possible in extrahepatic tissues expressing secretory proteins containing amphipathic α-helices without the expression of apolipoproteins.
Analysis of Major Histocompatibility Complex-Bound HIV Peptides Identified from Various Cell Types Reveals Common Nested Peptides and Novel T Cell Responses
Authors: Rucevic Marijana , Kourjian Georgio , Boucau Julie , Blatnik Renata , Garcia Bertran Wilfredo , Berberich Matthew J. , Walker Bruce D. , Riemer Angelika B. , Le Gall Sylvie
Published: July 2016

Despite the critical role of epitope presentation for immune recognition, we still lack a comprehensive definition of HIV peptides presented by HIV-infected cells. Here we identified 107 major histocompatibility complex (MHC)-bound HIV peptides directly from the surface of live HIV-transfected 293T cells, HIV-infected B cells, and primary CD4 T cells expressing a variety of HLAs. The majority of peptides were 8 to 12 amino acids (aa) long and mostly derived from Gag and Pol. The analysis of the total MHC-peptidome and of HLA-A02-bound peptides identified new noncanonical HIV peptides of up to 16 aa that could not be predicted by HLA anchor scanning and revealed an heterogeneous surface peptidome. Nested sets of surface HIV peptides included optimal and extended HIV epitopes and peptides partly overlapping or distinct from known epitopes, revealing new immune responses in HIV-infected persons. Surprisingly, in all three cell types, a majority of Gag peptides derived from p15 rather than from the most immunogenic p24. The cytosolic degradation of peptide precursors in corresponding cells confirmed the generation of identified surface-nested peptides. Cytosolic degradation revealed peptides commonly produced in all cell types and displayed by various HLAs, peptides commonly produced in all cell types and selectively displayed by specific HLAs, and peptides produced in only one cell type. Importantly, we identified areas of proteins leading to common presentations of noncanonical peptides by several cell types with distinct HLAs. These peptides may benefit the design of immunogens, focusing T cell responses on relevant markers of HIV infection in the context of HLA diversity.

IMPORTANCEThe recognition of HIV-infected cells by immune T cells relies on the presentation of HIV-derived peptides by diverse HLA molecules at the surface of cells. The landscape of HIV peptides displayed by HIV-infected cells is not well defined. Considering the diversity of HLA molecules in the human population, it is critical for vaccine design to identify HIV peptides that may be displayed despite the HLA diversity. We identified 107 HIV peptides directly from the surface of three cell types infected with HIV. They corresponded to nested sets of HIV peptides of canonical and novel noncanonical lengths not predictable by the presence of HLA anchors. Importantly, we identified areas of HIV proteins leading to presentation of noncanonical peptides by several cell types with distinct HLAs. Including such peptides in vaccine immunogen may help to focus immune responses on common markers of HIV infection in the context of HLA diversity.
Characterization of Viral Populations by Using Circular Sequencing
Authors: Whitfield Zachary J. , Andino Raul
Published: July 2016

With the enormous sizes viral populations reach, many variants are at too low a frequency to be detected by conventional next-generation sequencing (NGS) methods. Circular sequencing (CirSeq) is a method by which the error rate of next-generation sequencing is decreased so that even low-frequency viral variants can be accurately detected. The ability to visualize almost the entire genetic makeup of a viral swarm has implications for epidemiology, viral evolution, and vaccine design. Here we discuss experimental planning, analysis, and recent insights using CirSeq.
Herpes Simplex Virus 1 Interaction with Myeloid CellsIn Vivo
Authors: Shivkumar Maitreyi , Lawler Clara , Milho Ricardo , Stevenson Philip G.
Published: July 2016

Herpes simplex virus 1 (HSV-1) enters mice via olfactory epithelial cells and then colonizes the trigeminal ganglia (TG). Most TG nerve endings are subepithelial, so this colonization implies subepithelial viral spread, where myeloid cells provide an important line of defense. The outcome of infection of myeloid cells by HSV-1in vitrodepends on their differentiation state; the outcomein vivois unknown. Epithelial HSV-1 commonly infected myeloid cells, and Cre-Lox virus marking showed nose and lung infections passing through LysM-positive (LysM+) and CD11c+cells. In contrast, subcapsular sinus macrophages (SSMs) exposed to lymph-borne HSV-1 were permissive only when type I interferon (IFN-I) signaling was blocked; normally, their infection was suppressed. Thus, the outcome of myeloid cell infection helped to determine the HSV-1 distribution: subepithelial myeloid cells provided a route of spread from the olfactory epithelium to TG neurons, while SSMs blocked systemic spread.

IMPORTANCEHerpes simplex virus 1 (HSV-1) infects most people and can cause severe disease. This reflects its persistence in nerve cells that connect to the mouth, nose, eye, and face. Established infection seems impossible to clear. Therefore, we must understand how it starts. This is difficult in humans, but mice show HSV-1 entry via the nose and then spread to its preferred nerve cells. We show that this spread proceeds in part via myeloid cells, which normally function in host defense. Myeloid infection was productive in some settings but was efficiently suppressed by interferon in others. Therefore, interferon acting on myeloid cells can stop HSV-1 spread, and enhancing this defense offers a way to improve infection control.
Molecular Determinants Directing HIV-1 Gag Assembly to Virus-Containing Compartments in Primary Macrophages
Authors: Inlora Jingga , Chukkapalli Vineela , Bedi Sukhmani , Ono Akira
Published: July 2016

The subcellular sites of HIV-1 assembly, determined by the localization of the structural protein Gag, vary in a cell-type-dependent manner. In T cells and transformed cell lines used as model systems, HIV-1 assembles at the plasma membrane (PM). The binding and localization of HIV-1 Gag to the PM are mediated by the interaction between the matrix (MA) domain, specifically the highly basic region, and a PM-specific acidic phospholipid, phosphatidylinositol-4,5-bisphosphate [PI(4,5)P
2
]. In primary macrophages, prominent accumulation of assembling or assembled particles is found in the virus-containing compartments (VCCs), which largely consist of convoluted invaginations of the PM. To elucidate the molecular mechanism of HIV-1 Gag targeting to the VCCs, we examined the impact of overexpression of polyphosphoinositide 5-phosphatase IV (5ptaseIV), which depletes cellular PI(4,5)P
2
, in primary macrophages. We found that the VCC localization and virus release of HIV-1 are severely impaired upon 5ptaseIV overexpression, suggesting an important role for the MA-PI(4,5)P
2
interaction in HIV-1 assembly in primary macrophages. However, our analysis of HIV-1 Gag derivatives with MA changes showed that this interaction contributes to Gag membrane binding but is dispensable for specific targeting of Gag to the VCCs
per se
. We further determined that deletion of the NC domain abolishes VCC-specific localization of HIV-1 Gag. Notably, HIV-1 Gag localized efficiently to the VCCs when the NC domain was replaced with a leucine zipper dimerization motif that promotes Gag multimerization. Altogether, our data revealed that targeting of HIV-1 Gag to the VCCs requires NC-dependent multimerization.

IMPORTANCE
In T cells and model cell lines, HIV-1 Gag localizes to the PM in a manner dependent on the MA-PI(4,5)P
2
interaction. On the other hand, in primary macrophages, HIV-1 Gag localizes to convoluted intracellular membrane structures termed virus-containing compartments (VCCs). Although these compartments have been known for decades, and despite the implication of viruses in VCCs being involved in virus reservoir maintenance and spread, the viral determinant(s) that promotes Gag targeting to VCCs is unknown. In this study, we found that the MA-PI(4,5)P
2
interaction facilitates efficient Gag membrane binding in macrophages but is not essential for Gag targeting to VCCs. Rather, our results revealed that NC-dependent multimerization promotes VCC targeting. Our findings highlight the differential roles played by MA and NC in HIV-1 Gag membrane binding and targeting and suggest a multimerization-dependent mechanism for Gag trafficking in primary macrophages similar to that for Gag localization to uropods in polarized T cells.
Guinea Pig Prion Protein Supports Rapid Propagation of Bovine Spongiform Encephalopathy and Variant Creutzfeldt-Jakob Disease Prions
Authors: Watts Joel C. , Giles Kurt , Saltzberg Daniel J. , Dugger Brittany N. , Patel Smita , Oehler Abby , Bhardwaj Sumita , Sali Andrej , Prusiner Stanley B.
Published: July 2016

The biochemical and neuropathological properties of bovine spongiform encephalopathy (BSE) and variant Creutzfeldt-Jakob disease (vCJD) prions are faithfully maintained upon transmission to guinea pigs. However, primary and secondary transmissions of BSE and vCJD in guinea pigs result in long incubation periods of ∼450 and ∼350 days, respectively. To determine if the incubation periods of BSE and vCJD prions could be shortened, we generated transgenic (Tg) mice expressing guinea pig prion protein (GPPrP). Inoculation of Tg(GPPrP) mice with BSE and vCJD prions resulted in mean incubation periods of 210 and 199 days, respectively, which shortened to 137 and 122 days upon serial transmission. In contrast, three different isolates of sporadic CJD prions failed to transmit disease to Tg(GPPrP) mice. Many of the strain-specified biochemical and neuropathological properties of BSE and vCJD prions, including the presence of type 2 protease-resistant PrP
Sc
, were preserved upon propagation in Tg(GPPrP) mice. Structural modeling revealed that two residues near the N-terminal region of α-helix 1 in GPPrP might mediate its susceptibility to BSE and vCJD prions. Our results demonstrate that expression of GPPrP in Tg mice supports the rapid propagation of BSE and vCJD prions and suggest that Tg(GPPrP) mice may serve as a useful paradigm for bioassaying these prion isolates.

IMPORTANCE
Variant Creutzfeldt-Jakob disease (vCJD) and bovine spongiform encephalopathy (BSE) prions are two of the prion strains most relevant to human health. However, propagating these strains in mice expressing human or bovine prion protein has been difficult because of prolonged incubation periods or inefficient transmission. Here, we show that transgenic mice expressing guinea pig prion protein are fully susceptible to vCJD and BSE prions but not to sporadic CJD prions. Our results suggest that the guinea pig prion protein is a better, more rapid substrate than either bovine or human prion protein for propagating BSE and vCJD prions.
An RNA Element That Facilitates Programmed Ribosomal Readthrough in Turnip Crinkle Virus Adopts Multiple Conformations
Authors: Kuhlmann Micki M. , Chattopadhyay Maitreyi , Stupina Vera A. , Gao Feng , Simon Anne E.
Published: July 2016

Ribosome recoding is used by RNA viruses for translational readthrough or frameshifting past termination codons for the synthesis of extension products. Recoding sites, along with downstream recoding stimulatory elements (RSEs), have long been studied in reporter constructs, because these fragments alone mediate customary levels of recoding and are thus assumed to contain complete instructions for establishment of the proper ratio of termination to recoding. RSEs from the
Tombusviridae
and
Luteoviridae
are thought to be exceptions, since they contain a long-distance RNA-RNA connection with the 3′ end. This interaction has been suggested to substitute for pseudoknots, thought to be missing in tombusvirid RSEs. We provide evidence that the phylogenetically conserved RSE of the carmovirus
Turnip crinkle virus
(TCV) adopts an alternative, smaller structure that extends an upstream conserved hairpin and that this alternative structure is the predominant form of the RSE within nascent viral RNA in plant cells and when RNA is synthesized
in vitro
. The TCV RSE also contains an internal pseudoknot along with the long-distance interaction, and the pseudoknot is not compatible with the phylogenetically conserved structure. Conserved residues just past the recoding site are important for recoding, and these residues are also conserved in the RSEs of gammaretroviruses. Our data demonstrate the dynamic nature of the TCV RSE and suggest that studies using reporter constructs may not be effectively recapitulating RSE-mediated recoding within viral genomes.

IMPORTANCE
Ribosome recoding is used by RNA viruses to enable ribosomes to extend translation past termination codons for the synthesis of longer products. Recoding sites and a downstream recoding stimulatory element (RSE) mediate expected levels of recoding when excised and placed in reporter constructs and thus are assumed to contain complete instructions for the establishment of the proper ratio of termination to recoding. We provide evidence that most of the TCV RSE adopts an alternative structure that extends an upstream conserved hairpin and that this alternative structure, and not the phylogenetically conserved structure, is the predominant form of the RSE in RNA synthesized
in vitro
and in plant cells. The TCV RSE also contains an internal pseudoknot that is not compatible with the phylogenetically conserved structure and an RNA bridge to the 3′ end. These data suggest that the TCV RSE is structurally dynamic and that multiple conformations are likely required to regulate ribosomal readthrough.
Simulations in undergraduate nursing programmes in New Zealand: current status and next steps
Authors: Lesa Raewyn , Daniel Ben
Published: July 2016

Introduction

There is an increasing global tendency to use simulations in nursing education. This research examined the current status of simulation programs in undergraduate nursing schools in New Zealand. The goal was to gain a better understanding of how simulations are currently implemented in nursing schools and to identify the associated opportunities and challenges.

Methods

16 nursing schools in New Zealand deliver undergraduate nursing education. 10 of these schools selected a nursing leader who was involved in the schools’ simulation program to complete an online survey. The survey questions were designed to explore the nature of simulations in nursing schools, and the opportunities and challenges experienced in the implementation of these programmes.

Data analysis

Survey data were analysed and presented as summary statistics (frequencies and percentages). Responses to short questions were thematically analysed and common themes were identified. The analysis was divided into demographic characterises and main results.

Results

The key outcomes of the study have shown the prevalence of various simulation modalities in nursing schools in New Zealand. The analysis also suggests that the current practices associated with the integration of simulations into nursing education in New Zealand are fragmented and sporadic. Challenges shared across all institutions include inadequate resourcing of simulation programs, poor curriculum integration and programme alignment; a lack of shared understanding of what constitutes simulation and the extent to which simulation modalities achieve learning outcomes.

Conclusions

The outcome of this study has contributed to a better understanding of the prevalence and nature of simulation programs in undergraduate nursing schools in New Zealand. It has also provided insights into the different opportunities and challenges associated with implementing these programmes in nursing schools. Furthermore, the research has identified important conceptual and theoretical issues related to the broad discourse on the use of simulations in undergraduate nursing education.
Taxonomy and developmental morphology of Rogersiomyces malaysianus comb. nov. (Cantharellales, Agaricomycetes)
Authors: Psurtseva Nadezhda V. , Zmitrovich Ivan V. , Malysheva Vera F.
Published: July 2016

A basidiomycete fungus from Vietnam, grown in a moist chamber on bark (as substrate) was identified as Hyphobasidiofera malaysiana. The isolation of this fungus into axenic culture allowed for investigations such as culture morphology, large and small subunit molecular phylogenies, life cycle karyology, and mating experiments. Comparative morphological data revealed that this species belongs to Rogersiomyces and the name Rogersiomyces malaysianus comb. nov. is proposed. Molecular studies revealed close relationships of Rogersiomyces, Sistotrema sensu lato, and Hydnum sensu stricto (Cantharellales, Agaricomycetes). The fungus produces binucleate basidiospores that germinate to form clamped and dikaryotic mycelium. The cultural characters and reproductive structures of this unusual sistotremoid fungus are described. It was concluded that the characteristic of dikaryotization into basidium, ephemeral basidiomata, and statismosporic basidia represent an adaptation of this fungus to irregular, but plentiful moistening during monsoon climate.
The derived length of the unit group of a group algebra — The case G′ = Sylp(G)
Authors: Juhász Tibor
Published: July 2016

Let [Formula: see text] be an odd prime, and let [Formula: see text] be a nilpotent group, whose commutator subgroup is finite abelian satisfying [Formula: see text] and [Formula: see text]. In this contribution, an upper bound is given on the derived length of the group of units of the group algebra of [Formula: see text] over a field of characteristic [Formula: see text]. Furthermore, we show that this bound is achieved, whenever [Formula: see text] is cyclic.
Random Walks That Find Perfect Objects and the Lovász Local Lemma
Authors: Achlioptas Dimitris , Iliopoulos Fotis
Published: July 2016

We give an algorithmic local lemma by establishing a sufficient condition for the uniform random walk on a directed graph to reach a sink quickly. Our work is inspired by Moser’s entropic method proof of the Lovász Local Lemma (LLL) for satisfiability and completely bypasses the Probabilistic Method formulation of the LLL. In particular, our method works when the underlying state space is entirely unstructured. Similarly to Moser’s argument, the key point is that the inevitability of reaching a sink is established by bounding the entropy of the walk as a function of time.
Floorplanning and Topology Synthesis for Application-Specific Network-on-Chips with RF-Interconnect
Authors: Huang Jinglei , Chen Song , Zhong Wei , Zhang Wenchao , Diao Shengxi , Lin Fujiang
Published: July 2016

Application-specific Network-on-Chip (ASNoC) has been proposed as a promising solution to address the global communication challenges in System-on-Chips. However, with the number of cores increasing, the on-chip communication becomes more and more complex and the power consumption imposes the major challenge for designing ASNoCs. In this article, we propose a four-stage floorplanning and topology synthesis approach for ASNoCs with Radio-Frequency Interconnect (RF-I). First, considering the advantage of RF-I in long-distance on-chip communication, we integrate the floorplanning and clustering to explore the proper clustering of cores, where the cores belonging to the same cluster will share the same switch for communications, form an island, and occupy a contiguous physical region. After the switches and network interfaces are inserted into the floorplan, the allocation of routing paths and the RF-I logical channels are integrated in an iterative procedure to generate fine-grained dynamically reconfigurable ASNoC topologies. Finally, considering the signal integrity of RF-I, we adjust the placement of the switches by a simulated annealing-based method to reduce the number of RF-I routing corners. To evaluate the placement of switches, we propose a dynamical programming-based method to route the transmission line with the minimized number of routing corners in linear time. The results show that, using the RF-I, we can reduce the power consumption of ASNoCs by 20% to 26%.
Convex Sparse PCA for Unsupervised Feature Learning
Authors: Chang Xiaojun , Nie Feiping , Yang Yi , Zhang Chengqi , Huang Heng
Published: July 2016

Principal component analysis (PCA) has been widely applied to dimensionality reduction and data pre-processing for different applications in engineering, biology, social science, and the like. Classical PCA and its variants seek for linear projections of the original variables to obtain the low-dimensional feature representations with maximal variance. One limitation is that it is difficult to interpret the results of PCA. Besides, the classical PCA is vulnerable to certain noisy data. In this paper, we propose a Convex Sparse Principal Component Analysis (CSPCA) algorithm and apply it to feature learning. First, we show that PCA can be formulated as a low-rank regression optimization problem. Based on the discussion, the
l
2, 1
-normminimization is incorporated into the objective function to make the regression coefficients sparse, thereby robust to the outliers. Also, based on the sparse model used in CSPCA, an optimal weight is assigned to each of the original feature, which in turn provides the output with good interpretability. With the output of our CSPCA, we can effectively analyze the importance of each feature under the PCA criteria. Our new objective function is convex, and we propose an iterative algorithm to optimize it. We apply the CSPCA algorithm to feature selection and conduct extensive experiments on seven benchmark datasets. Experimental results demonstrate that the proposed algorithm outperforms state-of-the-art unsupervised feature selection algorithms.
Sampling for Nyström Extension-Based Spectral Clustering
Authors: Zhang Xianchao , Zong Linlin , You Quanzeng , Yong Xing
Published: July 2016

Sampling is the key aspect for Nyström extension based spectral clustering. Traditional sampling schemes select the set of landmark points on a whole and focus on how to lower the matrix approximation error. However, the matrix approximation error does not have direct impact on the clustering performance. In this article, we propose a sampling framework from an incremental perspective, i.e., the landmark points are selected one by one, and each next point to be sampled is determined by previously selected landmark points. Incremental sampling builds explicit relationships among landmark points; thus, they work together well and provide a theoretical guarantee on the clustering performance. We provide two novel analysis methods and propose two schemes for selecting-the-next-one of the framework. The first scheme is based on clusterability analysis, which provides a better guarantee on clustering performance than schemes based on matrix approximation error analysis. The second scheme is based on loss analysis, which provides maximized predictive ability of the landmark points on the (implicit) labels of the unsampled points. Experimental results on a wide range of benchmark datasets demonstrate the superiorities of our proposed incremental sampling schemes over existing sampling schemes.
Automatic Analysis of Naturalistic Hand-Over-Face Gestures
Authors: Mahmoud Marwa , Baltrušaitis Tadas , Robinson Peter
Published: July 2016

One of the main factors that limit the accuracy of facial analysis systems is hand occlusion. As the face becomes occluded, facial features are lost, corrupted, or erroneously detected. Hand-over-face occlusions are considered not only very common but also very challenging to handle. However, there is empirical evidence that some of these hand-over-face gestures serve as cues for recognition of cognitive mental states. In this article, we present an analysis of automatic detection and classification of hand-over-face gestures. We detect hand-over-face occlusions and classify hand-over-face gesture descriptors in videos of natural expressions using multi-modal fusion of different state-of-the-art spatial and spatio-temporal features. We show experimentally that we can successfully detect face occlusions with an accuracy of 83%. We also demonstrate that we can classify gesture descriptors (
hand shape
,
hand action
, and
facial region occluded
) significantly better than a naïve baseline. Our detailed quantitative analysis sheds some light on the challenges of automatic classification of hand-over-face gestures in natural expressions.
Compiling Affine Loop Nests for a Dynamic Scheduling Runtime on Shared and Distributed Memory
Authors: Dathathri Roshan , Mullapudi Ravi Teja , Bondhugula Uday
Published: July 2016

Current de-facto parallel programming models like OpenMP and MPI make it difficult to extract
task-level dataflow parallelism
as opposed to
bulk-synchronous parallelism
. Task parallel approaches that use point-to-point synchronization between dependent tasks in conjunction with dynamic scheduling dataflow runtimes are thus becoming attractive. Although good performance can be extracted for both shared and distributed memory using these approaches, there is little compiler support for them.

In this article, we describe the design of compiler--runtime interaction to automatically extract coarse-grained dataflow parallelism in affine loop nests for both shared and distributed-memory architectures. We use techniques from the polyhedral compiler framework to extract tasks and generate components of the runtime that are used to dynamically schedule the generated tasks. The runtime includes a distributed decentralized scheduler that dynamically schedules tasks on a node. The schedulers on different nodes cooperate with each other through asynchronous point-to-point communication, and all of this is achieved by code automatically generated by the compiler. On a set of six representative affine loop nest benchmarks, while running on 32 nodes with 8 threads each, our compiler-assisted runtime yields a geometric mean speedup of 143.6× (70.3× to 474.7× ) over the sequential version and a geometric mean speedup of 1.64× (1.04× to 2.42× ) over the state-of-the-art automatic parallelization approach that uses
bulk synchronization
. We also compare our system with past work that addresses some of these challenges on shared memory, and an emerging runtime (Intel Concurrent Collections) that demands higher programmer input and effort in parallelizing. To the best of our knowledge, ours is also the first automatic scheme that allows for dynamic scheduling of affine loop nests on a cluster of multicores.