bluuebunny/crossref_metadata_2025 huggingface dataset:
H-BLAST: a fast protein sequence alignment toolkit on heterogeneous computers with GPUs
Authors: Ye Weicai , Chen Ying , Zhang Yongdong , Xu Yuesheng
Published: December 2016

Motivation

The sequence alignment is a fundamental problem in bioinformatics. BLAST is a routinely used tool for this purpose with over 118 000 citations in the past two decades. As the size of bio-sequence databases grows exponentially, the computational speed of alignment softwares must be improved.

Results

We develop the heterogeneous BLAST (H-BLAST), a fast parallel search tool for a heterogeneous computer that couples CPUs and GPUs, to accelerate BLASTX and BLASTP—basic tools of NCBI-BLAST. H-BLAST employs a locally decoupled seed-extension algorithm for better performance on GPUs, and offers a performance tuning mechanism for better efficiency among various CPUs and GPUs combinations. H-BLAST produces identical alignment results as NCBI-BLAST and its computational speed is much faster than that of NCBI-BLAST. Speedups achieved by H-BLAST over sequential NCBI-BLASTP (resp. NCBI-BLASTX) range mostly from 4 to 10 (resp. 5 to 7.2). With 2 CPU threads and 2 GPUs, H-BLAST can be faster than 16-threaded NCBI-BLASTX. Furthermore, H-BLAST is 1.5–4 times faster than GPU-BLAST.

Availability and Implementation

https://github.com/Yeyke/H-BLAST.git

Supplementary information

Supplementary data are available at Bioinformatics online.
The ecological profile of Atlantic salmon escapees entering a river throughout an entire season: diverse in escape history and genetic background, but frequently virus-infected
Authors: Madhun Abdullah S. , Wennevik Vidar , Skilbrei Ove T. , Karlsbakk Egil , Skaala Øystein , Fiksdal Ingrid U. , Meier Sonnich , Tang Yongkai , Glover Kevin A.
Published: December 2016

In 2014, 129 farmed salmon escapees captured in an upstream-migration trap located in the river Etne, western Norway, were investigated for viral infections, age at escape, size, and genetic composition. The frequency of escapees positive for salmonid alphavirus (SAV), piscine orthoreovirus (PRV), and infectious salmon anaemia virus (ISAV) was 12, 79, and <1%, respectively. Fatty acid analysis demonstrated that the individuals had escaped from farms at different stages of the production cycle, although the majority had probably escaped from farms in the same year as their capture in the river. Genetic analyses demonstrated that the escapees originated from multiple farms. This was also supported by the distribution of fish size and timing of entry into the river. A combination of genetic, fatty acid and viral infection analyses showed that in the river Etne in 2014: (i) most of the fish entering the river were infected with one or more viruses, (ii) the majority of them had escaped in the same year that they entered the river, (ii) they originated from multiple farm sources, and (iv) two of the identified genetic groups likely originated from two recent and distinct escape events. This is the first study to integrate results from multiple analytical methods in order to reveal the ecological and genetic diversity of escaped farmed fish entering a river with native salmon population throughout an entire season.
Upper limits on the mass and luminosity of Population III-dominated galaxies
Authors: Yajima Hidenobu , Khochfar Sadegh
Published: December 2016

We here derive upper limits on the mass and luminosity of Population III (POPIII) dominated proto-galaxies based on the collapse of primordial gas under the effect of angular momentum loss via Lyα radiation drag and the gas accretion on to a galactic centre. Our model predicts that POPIII-dominated galaxies at z ∼ 7 are hosted by haloes with Mh ∼ 1.5 × 108–1.1 × 109 M⊙, that they have Lyα luminosities of LLyα ∼ 3.0 × 1042–2.1 × 1043  erg s− 1, stellar mass of Mstar ∼ 0.8 × 105–2.5 × 106 M⊙ and outflowing gas with velocities Vout ∼ 40 km s− 1 due to Lyα radiation pressure. We show that the POPIII galaxy candidate CR7 violates the derived limits on stellar mass and Lyα luminosity and thus is unlikely to be a POPIII galaxy. POPIII-dominated galaxies at z ∼ 7 have He ii line emission that is ∼1–3 orders of magnitude lower than that of Lyα, they have high Lyα equivalent width of ≳ 300 Å and should be found close to bright star-forming galaxies. The He ii 1640 Å line is in comfortable reach of next generation telescopes, like the James Webb Space Telescope (JWST) or Thirty Meter Telescope (TMT).
How much a galaxy knows about its large-scale environment?: An information theoretic perspective
Authors: Pandey Biswajit , Sarkar Suman
Published: December 2016

The small-scale environment characterized by the local density is known to play a crucial role in deciding the galaxy properties but the role of large-scale environment on galaxy formation and evolution still remain a less clear issue. We propose an information theoretic framework to investigate the influence of large-scale environment on galaxy properties and apply it to the data from the Galaxy Zoo project that provides the visual morphological classifications of ∼1 million galaxies from the Sloan Digital Sky Survey. We find a non-zero mutual information between morphology and environment that decreases with increasing length-scales but persists throughout the entire length-scales probed. We estimate the conditional mutual information and the interaction information between morphology and environment by conditioning the environment on different length-scales and find a synergic interaction between them that operates up to at least a length-scales of ∼30  h−1 Mpc. Our analysis indicates that these interactions largely arise due to the mutual information shared between the environments on different length-scales.
AKARI near-infrared background fluctuations arise from normal galaxy populations
Authors: Helgason K. , Komatsu E.
Published: December 2016

We show that measurements of the fluctuations in the near-infrared background (NIRB) from the AKARI satellite can be explained by faint galaxy populations at low redshifts. We demonstrate this using reconstructed images from deep galaxy catalogues (Hawk-I UDS/GOODS Survey and S-Cosmic Assembly Deep Near-Infrared Extragalactic Legacy Survey) and two independent galaxy population models. In all cases, we find that the NIRB fluctuations measured by AKARI are consistent with faint galaxies and there is no need for a contribution from unknown populations. We find that a steep Rayleigh–Jeans spectrum for the underlying sources is not required as previously reported. The apparent Rayleigh–Jeans spectrum at large angular scales is likely a consequence of galaxies being removed systematically to deeper levels in the longer wavelength channels.
Outcomes Associated With Antimicrobial De-escalation of Treatment for Pneumonia Within the Veterans Healthcare Administration
Authors: Bohan Jefferson G. , Remington Richard , Jones Makoto , Samore Matthew , Madaras-Kelly Karl
Published: December 2016

De-escalation, an antimicrobial stewardship concept, involves narrowing broad-spectrum empiric antimicrobial therapy based on clinical data. Current health outcomes evidence is lacking to support de-escalation. Studying Veterans Healthcare Administration pneumonia patients, de-escalation was associated with improved length of stay without affecting 30-day readmission or 30-day Clostridium difficile infection rates.
The Glycosylphosphatidylinositol Anchor Biosynthesis Genes GPI12, GAA1, and GPI8 Are Essential for Cell-Wall Integrity and Pathogenicity of the Maize Anthracnose Fungus Colletotrichum graminicola
Authors: Oliveira-Garcia Ely , Deising Holger B.
Published: December 2016

Glycosylphosphatidylinositol (GPI) anchoring of proteins is one of the most common posttranslational modifications of proteins in eukaryotic cells and is important for associating proteins with the cell surface. In fungi, GPI-anchored proteins play essential roles in cross-linking of β-glucan cell-wall polymers and cell-wall rigidity. GPI-anchor synthesis is successively performed at the cytoplasmic and the luminal face of the ER membrane and involves approximately 25 proteins. While mutagenesis of auxiliary genes of this pathway suggested roles of GPI-anchored proteins in hyphal growth and virulence, essential genes of this pathway have not been characterized. Taking advantage of RNA interference (RNAi) we analyzed the function of the three essential genes GPI12, GAA1 and GPI8, encoding a cytoplasmic N-acetylglucosaminylphosphatidylinositol deacetylase, a metallo-peptide-synthetase and a cystein protease, the latter two representing catalytic components of the GPI transamidase complex. RNAi strains showed drastic cell-wall defects, resulting in exploding infection cells on the plant surface and severe distortion of in planta–differentiated infection hyphae, including formation of intrahyphal hyphae. Reduction of transcript abundance of the genes analyzed resulted in nonpathogenicity. We show here for the first time that the GPI synthesis genes GPI12, GAA1, and GPI8 are indispensable for vegetative development and pathogenicity of the causal agent of maize anthracnose, Colletotrichum graminicola.
A Synoptic Analysis of the Temporal and Spatial Aspects of Grapevine Leafroll Disease in a Historic Napa Vineyard and Experimental Vine Blocks
Authors: Arnold K. , Golino D. A. , McRoberts N.
Published: December 2016

Five Grapevine leafroll-associated virus 3 (GLRaV-3) epidemics were analyzed utilizing a standardized approach to robustly characterize the temporal and spatial parameters. Published data included in the analysis are from Spain, New Zealand, and Napa Valley, CA together with new data from a historic vineyard in Napa Valley, CA. Linear regression analyses of logit-transformed incidence data indicated a maximum average increase of 11% per year in disease incidence, with considerable variation among locations. Spatial analyses, including distribution fitting, examination of the effective sample size, and evaluation of the parameters of the binary power law fitted to variance data for disease incidence, indicated a high degree of consistency among the data sets. In all cases, except at very low disease incidence, a high degree of spatial aggregation was noted, with evidence that the degree of aggregation varied as a function of mean disease incidence. The polyetic dynamics of disease follow a logistic-like pattern over multiple seasons, consistent with limitation by inoculum availability (infected vines) at low incidence and limitation by disease-free vines at high incidence.
The DinJ/RelE Toxin-Antitoxin System Suppresses Bacterial Proliferation and Virulence of Xylella fastidiosa in Grapevine
Authors: Burbank Lindsey P. , Stenger Drake C.
Published: December 2016

Xylella fastidiosa, the causal agent of Pierce’s disease of grapes, is a slow-growing, xylem-limited, bacterial pathogen. Disease progression is characterized by systemic spread of the bacterium through xylem vessel networks, causing leaf-scorching symptoms, senescence, and vine decline. It appears to be advantageous to this pathogen to avoid excessive blockage of xylem vessels, because living bacterial cells are generally found in plant tissue with low bacterial cell density and minimal scorching symptoms. The DinJ/RelE toxin-antitoxin system is characterized here for a role in controlling bacterial proliferation and population size during plant colonization. The DinJ/RelE locus is transcribed from two separate promoters, allowing for coexpression of antitoxin DinJ with endoribonuclease toxin RelE, in addition to independent expression of RelE. The ratio of antitoxin/toxin expressed is dependent on bacterial growth conditions, with lower amounts of antitoxin present under conditions designed to mimic grapevine xylem sap. A knockout mutant of DinJ/RelE exhibits a hypervirulent phenotype, with higher bacterial populations and increased symptom development and plant decline. It is likely that DinJ/RelE acts to prevent excessive population growth, contributing to the ability of the pathogen to spread systemically without completely blocking the xylem vessels and increasing probability of acquisition by the insect vector.
Cox-nnet: an artificial neural network method for prognosis prediction on high-throughput omics data
Authors: Ching Travers , Zhu Xun , Garmire Lana X.
Published: December 2016

Artificial neural networks (ANN) are computing architectures with massively parallel interconnections of simple neurons and has been applied to biomedical fields such as imaging analysis and diagnosis. We have developed a new ANN framework called Cox-nnet to predict patient prognosis from high throughput transcriptomics data. In over 10 TCGA RNA-Seq data sets, Cox-nnet achieves a statistically significant increase in predictive accuracy, compared to the other three methods including Cox-proportional hazards (Cox-PH), Random Forests Survival and CoxBoost. Cox-nnet also reveals richer biological information, from both pathway and gene levels. The outputs from the hidden layer node can provide a new approach for survival-sensitive dimension reduction. In summary, we have developed a new method for more accurate and efficient prognosis prediction on high throughput data, with functional biological insights. The source code is freely available atgithub.com/lanagarmire/cox-nnet.
Cell-to-cell variability in the yeast pheromone response: Cytoplasmic microtubule function stabilizes signal generation and promotes accurate fate choice
Authors: Pesce C.G. , Zdraljevic S. , Bush A. , Repetto V. , Peria W. , Yu R.C. , Colman-Lerner A. , Brent R.
Published: December 2016

In a companion paper, we carried out a high-throughput screen to identify genes that suppressed cell-to-cell variability in signaling in yeast. Two genes affected cytoplasmic microtubules that can connect the nucleus to a signaling site on the membrane. Here, we show that microtubule perturbations that affected polymerization and depolymerization, membrane attachment, and force generation increased variability. For some perturbations, "outlier" cells drove the increased variability. Bypass experiments that activated the PRS ectopically at downstream points indicated that microtubule-dependent processes might stabilize the membrane-recruited scaffold protein Ste5. The variability caused by microtubule perturbations required the MAP kinase Fus3. Microtubule perturbations hindered stable scaffold formation and decreased the accuracy of a polarity-dependent fate choice. Our experiments suggest that membrane-attached microtubules stabilize signaling by scaffold-bound Fus3, and are consistent with a model in which signaling irregularities from changes in microtubule function are amplified by cross-stimulatory feedbacks among PRS proteins. The fact that microtubule perturbations also cause aberrant fate and polarity decisions during embryonic development and cancer initiation suggests that similar variation-reducing processes might also operate in metazoans.
Deploying dengue-suppressingWolbachia:robust models predict slow but effective spatial spread inAedes aegypti
Authors: Turelli Michael , Barton Nicholas H.
Published: December 2016

A novel strategy for controlling the spread of arboviral diseases such as dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressingWolbaehia. In general,Wolbachiatransinfected into mosquitoes induce fitness costs through lower viability or fecundity. These maternally inherited bacteria also produce a frequency-dependent advantage for infected females by inducing cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected females mated to infected males. These competing effects, a frequency-dependent advantage and frequency-independent costs, produce bistableWolbachiafrequency dynamics. Above a threshold frequency, denotedp̂, CI drives fitness-decreasingWolbachiatransinfections through local populations; but belowp̂, infection frequencies tend to decline to zero. Ifp̂is not too high, CI also drives spatial spread once infections become established over sufficiently large areas. We illustrate how simple models provide testable predictions concerning the spatial and temporal dynamics ofWolbachiaintroductions, focusing on rate of spatial spread, the shape of spreading waves, and the conditions for initiating spread from local introductions. First, we consider the robustness of diffusion-based predictions to incorporating two important features ofwMel-Aedes aegyptibiology that may be inconsistent with the diffusion approximations, namely fast local dynamics induced by complete CI (i.e., all embryos produced from incompatible crosses die) and long-tailed, non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed dispersal changes wave-width predictions only slightly; but it can significantly reduce wave speed relative to the diffusion prediction; it also allows smaller local introductions to initiate spatial spread. Second, we use approximations forp̂and dispersal distances to predict the outcome of 2013 releases ofwMel-infectedAedes aegyptiin Cairns, Australia, Third, we describe new data fromAedes aegyptipopulations near Cairns, Australia that demonstrate long-distance dispersal and provide an approximate lower bound onp̂forwMel in northeastern Australia. Finally, we apply our analyses to produce operational guidelines for efficient transformation of vector populations over large areas. We demonstrate that even very slow spatial spread, on the order of 10-20 m/month (as predicted), can produce area-wide population transformation within a few years following initial releases covering about 20-30% of the target area.
Polymeric structure of a coproporphyrin I ruthenium(II) complex: a powder diffraction study
Authors: Andreev Sergey V. , Zverev Sergey A. , Zamilatskov Ilya A. , Kurochkina Nadezhda M. , Ponomarev Gelii V. , Fitch Andrew N. , Chernyshev Vladimir V.
Published: December 2016

Porphyrin complexes of ruthenium are widely used as models for the heme protein system, for modelling naturally occurring iron–porphyrin systems and as catalysts in epoxidation reactions. The structural diversity of ruthenium complexes offers an opportunity to use them in the design of multifunctional supramolecular assemblies. Coproporphyrins and metallocoproporphyrins are used as sensors in bioassay and the potential use of derivatives as multiparametric sensors for oxygen and H+is one of the main factors driving a growing interest in the synthesis of new porphyrin derivatives. In the coproporphyrin I RuIIcomplexcatena-poly[[carbonylruthenium(II)]-μ-2,7,12,17-tetrakis[2-(ethoxycarbonyl)ethyl]-3,8,13,18-tetramethylporphyrinato-κ5N,N′,N′′,N′′′:O], [Ru(C44H52N4O8)(CO)]n, the RuIIcentre is coordinated by four N atoms in the basal plane, and by axial C (carbonyl ligand) and O (ethoxycarbonylethyl arm from a neighbouring complex) atoms. The complex adopts a distorted octahedral geometry. Self-assembly of the molecules during crystallization from a methylene chloride–ethanol (1:10v/v) solution at room temperature gives one-dimensional polymeric chains.
Control chart for high-quality processes based on Six Sigma quality
Authors: Joghee Ravichandran
Published: December 2016

Purpose

The purpose of this paper is to develop an innovative and quite new Six Sigma quality control (SSQC) chart for the benefit of Six Sigma practitioners. A step-by-step procedure for the construction of the chart is also given.

Design/methodology/approach

Under the assumption of normality, in this paper, the construction of SSQC chart is proposed in which the population mean and standard deviation are drawn from the process specification from the perspective of Six Sigma quality (SSQ). In this chart, the concept of target range is used to restrict the shift in the process within plus or minus 1.5 times of standard deviation. This control chart is useful in monitoring the process to ensure that the process is well maintained within the specification limits with minimum variation (shift).

Findings

A step-by-step procedure is given for the construction of the proposed SSQC chart. It can be easily understood and its application is also simple for Six Sigma practitioners. The proposed chart suggests for timely improvements in process mean and variation. The illustrative example shows the improved performance of the proposed new procedure.

Research limitations/implications

The proposed approach assumes a normal population described by the known specification of the process/product characteristics though it may not be in all cases. This may call for a thorough study of the population before applying the chart.

Practical implications

The proposed SSQC chart is an innovative approach and is quite new for the practitioners. The paper assumes that the population standard deviation is known and is drawn from the specification of the process/product characteristics. The proposed chart helps in fine-tuning the process mean and bringing the process standard deviation to the satisfactory level from the perspective of SSQ.

Originality/value

The paper is the first of its kind. It is innovative and quite new to the Six Sigma practitioners who will find its application interesting.
Development and evaluation of android-based library stocktaking application using NFC Technology: a case study in Bina Nusantara University
Authors: Wibisurya Aswin , Karya San , Heriyanni Eileen
Published: December 2016

Purpose

The purpose of this paper is to develop and evaluate a mobile application to facilitate stocktaking in libraries implementing radio frequency identification. The case of Bina Nusantara University’s library is used in this study. In this kind of library, near field communication (NFC) tags are placed in the book for getting book information, borrowing or returning and theft prevention, so the application. Stocktaking is an important process to be performed periodically to monitor and maintain the quality of collections and to make these collections easily accessible for library users. However, stocktaking in libraries takes too much effort and needs to be more efficient.

Design/methodology/approach

The design of the mobile application using entity relationship diagram (ERD) includes a diagram and flowchart. An evaluation is done by comparing the stocktaking effort of the latest semester and the previous semester. In the latest semester, the stocktaking is done by a hybrid of the proposed mobile application and a legacy desktop application, whereas the stocktaking of the previous semester is done only using the legacy desktop application.

Findings

Evaluation of the usage of this mobile stocktaking application is 43 per cent more efficient compared to an older desktop application.

Originality/value

The authors report the development of Android-based mobile stocktaking application by using Android’s NFC feature and evaluate it in a real environment.
Commissioning Human Services: Lessons from Australian Convict Contracting
Authors: Sturgess Gary L. , Argyrous George , Rahman Sara
Published: December 2016

The transportation of convicts to the British penal colony at New South Wales in the late 18th and early 19th centuries was largely undertaken by private merchants under contract to government. In the early years, the outcomes of this system, as measured by mortality rates, were mixed, but by the turn of the century, public officials had refined its operation, resulting in a significant decline in convict deaths. Close study of the evolution of this system reveals that government officials were grappling with many of the same issues encountered by public service commissioners today – trade‐offs between price and quality, the use of transactional versus relational contracting forms, and heavy reliance on financial incentives as opposed to intrinsic motivation. Government's success in reducing mortality on the convict ships highlights the importance of system design, effective monitoring and management when public services are delivered under contract.
Effect of different treatments on the stability of lysozyme, lactoferrin and β‐lactoglobulin in donkey's milk
Authors: Ozturkoglu‐Budak Sebnem
Published: December 2016

The aim of this study was to investigate the effects of freezing and heat treatments at different temperatures on the stability of the main whey proteins of donkey milk in comparison with those obtained from colostrum and raw milk. Samples subjected to heat treatment at 85 °C showed greater loss of stability, with levels decreasing by 60% and 87% for lysozyme and β‐lactoglobulin, respectively. Lactoferrin completely disappeared at heat treatments higher than 65 °C. Colostrum contained the highest lactoferrin and β‐lactoglobulin concentrations, however, lysozyme was found to be present at similar concentrations in colostrum, raw, frozen and heat‐treated milk at temperatures lower than 85 °C.
Genomic investigation of piglet resilience following porcine epidemic diarrhea outbreaks
Authors: Bertolini F. , Harding J. C. S. , Mote B. , Ladinig A. , Plastow G. S. , Rothschild M. F.
Published: December 2016

Porcine epidemic diarrhea virus (PEDV) belongs to the Coronaviridae family and causes malabsorptive watery diarrhea, vomiting, dehydration and imbalanced blood electrolytes in pigs. Since the 1970s, PED outbreaks have become a source of problems in pig producing countries all over the world, causing large economic losses for pig producers. Although the infection in adults is not fatal, in naïve suckling piglets mortality is close to 100%. In this study, we investigated genome‐wide differences between dead and recovered suckling piglets from commercial farms after PED outbreaks. Samples from 262 animals (156 dead and 106 recovered) belonging to several commercial lines were collected from five different farms in three different countries (USA, Canada and Germany) and genotyped with the porcine 80K SNP chip. Mean Fst value was calculated in 1‐Mb non‐overlapping windows between dead and recovered individuals, and the results were normalized to find differences within the comparison. Seven windows with high divergence between dead and recovered were detected—five on chromosome 2, one on chromosome 4 and one on chromosome 15—in total encompassing 152 genes. Several of these genes are either under‐ or overexpressed in many virus infections, including Coronaviridae (such as SARS‐CoV). A total of 32 genes are included in one or more Gene Ontology terms that can be related to PED development, such as Golgi apparatus, as well as mechanisms generally linked to resilience or diarrhea development (cell proliferation, ion transport, ATPase activity). Taken together this information provides a first genomic picture of PEDV resilience in suckling piglets.
Race, Representation, and the Voting Rights Act
Authors: Schuit Sophie , Rogowski Jon C.
Published: December 2016

Despite wide scholarly interest in the Voting Rights Act, surprisingly little is known about how its specific provisions affected Black political representation. In this article, we draw on theories of electoral accountability to evaluate the effect of Section 5 of the Voting Rights Act, the preclearance provision, on the representation of Black interests in the 86th to 105th congresses. We find that members of Congress who represented jurisdictions subject to the preclearance requirement were substantially more supportive of civil rights–related legislation than legislators who did not represent covered jurisdictions. Moreover, we report that the effects were stronger when Black voters composed larger portions of the electorate and in more competitive districts. This result is robust to a wide range of model specifications and empirical strategies, and it persists over the entire time period under study. Our findings have especially important implications given the Supreme Court's recent decision in Shelby County v. Holder.
Exhuming the Dead and Talking to the Living: The 1914 Fire at the Florida Industrial School for Boys—Invoking the Uncanny as a Site of Analysis
Authors: Jackson Antoinette T.
Published: December 2016

This article revisits the 1914 fire at the Florida Industrial School for Boys in Marianna, Florida. It resulted in the deaths of ten people and led to increased levels of public focus on the school's mission, purpose, and its day‐to‐day operational practices. Those who burned in the fire were buried on campus in the area known as “Boot Hill Cemetery.” Very little documentation about the history of the cemetery, or who is buried there, exists; and the exact locations of individual burials were never documented. In 2013, a University of South Florida (USF) research team began excavation of the burials located in the area of Boot Hill. Their efforts have been justified by requests from family members to learn about missing loved ones. Exhuming bodies of those who perished in the fire, as well as those who died at other times, demands that we think critically about what is recovered, what is invoked, and what is next and for whom. I introduce Freud's concept of “the uncanny” as a frame of reference for talking about things that surface when one recovers human remains or in some way revisits the site of a past, perhaps long‐hidden, traumatic event.
A Dermal Equivalent Engineered with TGF‐β3 Expressing Bone Marrow Stromal Cells and Amniotic Membrane: Cosmetic Healing of Full‐Thickness Skin Wounds in Rats
Authors: Samadikuchaksaraei Ali , Mehdipour Ahmad , Habibi Roudkenar Mehryar , Verdi Javad , Joghataei Mohammad Taghi , As'adi Kamran , Amiri Fatemeh , Dehghan Harati Mozhgan , Gholipourmalekabadi Mazaher , Karkuki Osguei Nushin
Published: December 2016

Transforming growth factor beta‐3 (TGF‐β3) has been shown to decrease scar formation after scheduled topical applications to the cutaneous wounds. This study aimed to continuously deliver TGF‐β3, during the early phase of wound healing, by engineering a dermal equivalent (DE) using TGF‐β3 expressing bone marrow stromal cells (BM‐SCs) and human dehydrated amniotic membrane (hDAM). To engineer a DE, rat BM‐SCs were seeded on the hDAM and TGF‐β3 was transiently transfected into the BM‐SCs using a plasmid vector. Pieces of the dermal equivalent were transplanted onto the full‐thickness excisional skin wounds in rats. The process of wound healing was assessed by image analysis, Manchester Scar Scale (MSS), and histopathological studies 7, 14, 21, and 85 days after the excision. The results confirmed accurate construction of recombinant pcDNA3.1‐TGF‐β3 expression system and showed that the transfected BM‐SCs seeded on hDAM expressed TGF‐β3 mRNA and protein from day 3 through day 7 after transfection. After implantation of the DE, contraction of the wounds was measured from day 7 through 21 and analyzed by linear regression, which revealed that the rate of wound contraction in all experimental groups was similar. Histologic evaluation demonstrated that transfected BM‐SCs decreased retention and recruitment of the cells during the early stage of wound healing, decreased the formation of vascular structures and led to formation of uniformly parallel collagen bundles. MSS scores showed that TGF‐β3 secreting cells significantly improved the cosmetic appearance of the healed skin and decreased the scar formation. From these results, it could be concluded that transient secretion of TGF‐β3, during the early phase of healing, by BM‐SCs seeded on hDAM can improve the cosmetic appearance of the scar in cutaneous wounds without negatively affecting the process of wound repair.
Involvement of viperin in prevention of intrauterine transmission of hepatitis B virus
Authors: Bai Xiaoxia , Yang Huiyan , Wan Liuxia , Wang Peng , Wang Hanzhi , Yang Xiaofu , Wang Zhengping , Dong Minyue
Published: December 2016

The aim of this study was to explore the role of viperin in the prevention of intrauterine infection of hepatitis B virus (HBV). Placental samples were collected from seven HBV‐positive pregnant women with their infants infected via intrauterine transmission (infected group), 30 HBV‐positive women with non‐infected infants (non‐infected group), and 30 HBV‐negative women (controls). The expression of viperin in placenta was analyzed with immunohistochemistry and Western blotting. The expression of viperin of placental trophoblast cell line Swan71 was determined after exposed to HBV. Viperin was localized to syncytiotrophoblast, and there was a significant difference in placental viperin levels among control, non‐infected group and infected group (F = 12.824, p < 0.001). The expression of viperin was significantly higher in non‐infected group than in control (p = 0.019) and in infected group (p < 0.001), and viperin expression was significantly lower in infected group than in control (p = 0.001). The exposure to HBV significantly increased the expression of viperin in Swan 71 (p < 0.001). Exposure to HBV up‐regulates viperin expression in vivo and in vitro in placental trophoblast, and lack of this up‐regulation is associated with intrauterine transmission of HBV.
Letter: reduction in chronic hepatitis B‐related hepatocellular carcinoma with anti‐viral therapy, including low‐risk patients – more questions than answers
Authors: Wei T.‐Y. , Wang C.‐C.
Published: December 2016

Linked Content

This article is linked to Lin et al papers. To view these articles visit https://doi.org/10.1111/apt.13774 and https://doi.org/10.1111/apt.13859.
Changing ethnographic mediums: the place‐based contingency of smartphones and scratchnotes
Authors: Gorman Richard
Published: December 2016

The medium by which ethnographic notes are taken within the field is changing. Increasingly researchers are turning to jotting short notes using smartphone notation apps, leaving pen and paper behind. While this has practical benefits, there is a need to recognise explicitly how the medium by which notes are taken can influence the content, style and practice of contemporaneous ethnographic note‐taking. There is a place‐based contingency to the acceptability of the smartphone as a research tool; phones carry different social connotations to paper notebooks, and can act to reinforce difference, making statements of privilege, power and culture. The medium by which fieldnotes are taken actively impacts the field and is capable of influencing relationships with participants and altering the power dynamic of research. The changing tools of note‐taking also result in a changing visibility of the act of writing, bringing additional challenges to managing consent and ensuring the ethicality of research.
In Good Times but Not in Bad: The Role of Managerial Discretion in Moderating the Stakeholder Management and Financial Performance Relationship
Authors: Shahzad Ali M. , Rutherford Matthew A. , Sharfman Mark P.
Published: December 2016

We examine the role of managers in controlling the positive impact of stakeholder management (SM) on firm financial performance (FP) in the long term. We develop and test competing hypotheses on whether managers act as “good citizens” or engage in “self‐dealing” when allowed greater discretion. We test our assertions using dynamic panel data analysis of a sample of 806 U.S. public firms operating in 34 industries over 5 years (2005–2009). Our results indicate a nuanced influence of managerial discretion contexts on the SM‐FP relationship. We infer that given more latitude in decision making, as long as the “going is good” managers act as good citizens, but otherwise they revert to managerial self‐dealing. In light of our results, firms designing governance mechanisms to encourage managers to balance the needs of both shareholders and stakeholders must remain cognizant of contextual contingencies.
Osteopontin‐deficiency disturbs direct osteogenesis in the process of achieving osseointegration following immediate placement of endosseous implants
Authors: Makishi Sanako , Saito Kotaro , Ohshima Hayato
Published: December 2016

Background

The role of osteopontin (OPN) in the process of achieving osseointegration following implantation remains to be clarified.

Purpose

This study aimed to analyze the healing patterns of the bone‐implant interface after immediate placement of implants in the maxillae of 4‐week‐old Opn‐knockout (KO) and wild‐type (WT) mice.

Materials and Methods

After maxillary first molars were extracted, cavities were prepared with a drill and titanium implants blasted with ceramic abrasives containing hydroxyapatite/β‐tricalcium phosphate were placed. Following fixation at 3, 5, 7, and 28 days after implantation, the samples were analyzed using immunohistochemistry, in situ hybridization, and an electron probe micro analyzer.

Results

Two types of bone healing were observed in the process of achieving osseointegration: “direct osteogenesis,” where bone formation occurs at the implant surface, and “indirect osteogenesis,” where it does at the pre‐existing damaged bone surface in the WT mice. Direct osteogenesis occurred after the recruitment of tartrate resistant acid phosphatase‐positive cells and the deposition of OPN on the implant surface. In contrast, the rate of osseointegration or direct osteogenesis was significantly low, and cell proliferation was disturbed in the Opn‐KO mice.

Conclusions

These results suggest that Opn‐deficiency disturbs direct osteogenesis to lead the delayed osseointegration after immediate placement of endosseous implants.
Molecular evolution of Zika virus as it crossed the Pacific to the Americas
Authors: de Bernardi Schneider Adriano , Malone Robert W. , Guo Jun‐Tao , Homan Jane , Linchangco Gregorio , Witter Zachary L. , Vinesett Dylan , Damodaran Lambodhar , Janies Daniel A.
Published: December 2016

Zika virus was previously considered to cause only a benign infection in humans. Studies of recent outbreaks of Zika virus in the Pacific, South America, Mexico and the Caribbean have associated the virus with severe neuropathology. Viral evolution may be one factor contributing to an apparent change in Zika disease as it spread from Southeast Asia across the Pacific to the Americas. To address this possibility, we have employed computational tools to compare the phylogeny, geography, immunology and RNA structure of Zika virus isolates from Africa, Asia, the Pacific and the Americas. In doing so, we compare and contrast methods and results for tree search and rooting of Zika virus phylogenies. In some phylogenetic analyses we find support for the hypothesis that there is a deep common ancestor between African and Asian clades (the “Asia/Africa” hypothesis). In other phylogenetic analyses, we find that Asian lineages are descendent from African lineages (the “out of Africa” hypothesis). In addition, we identify and evaluate key mutations in viral envelope protein coding and untranslated terminal RNA regions. We find stepwise mutations that have altered both immunological motif sets and regulatory sequence elements. Both of these sets of changes distinguish viruses found in Africa from those in the emergent Asia–Pacific–Americas lineage. These findings support the working hypothesis that mutations acquired by Zika virus in the Pacific and Americas contribute to changes in pathology. These results can inform experiments required to elucidate the role of viral genetic evolution in changes in neuropathology, including microcephaly and other neurological and skeletomuscular issues in infants, and Guillain‐Barré syndrome in adults.
Evaluating an Outcomes‐based Standardized Homeownership Education Program
Authors: Eschbach Cheryl L. , Weber Robert , Tobe Erica , Hale Lauren , Washington Vivian
Published: December 2016

A statewide education program provided prospective homebuyers with information to support long‐term preservation of affordable homeownership. Between 2012 and 2015, a sample of 1,561 Michigan residents completed pre‐ and post program evaluation surveys. The surveys measured 12 outcomes of the homeownership education program. Change scores were calculated for participants, and paired t‐tests were used to compare pre‐ and postsurvey means for each of the 12 outcome measures. The results of both change scores and t‐tests showed that homeownership education increased the participants’ knowledge of financial requirements for buying a home and practices to prevent predatory lending and foreclosure. The financial practices in which the largest percentage of participants reported an intention to change were as follows: tracking spending, creating a budget, calculating a reasonable housing payment, identifying patterns to adjust, and developing a plan to change financial habits.
Chronic Conditions, Medical Out‐of‐Pocket Expenditure Burden, and Perceived Health
Authors: Anong Sophia T. , Ajongwen Patience , Chandwani Sheenu
Published: December 2016

This study examined the impact of medical out‐of‐pocket expenditure burden on being in a state of poor or fair health. Expenditures were self‐reported payments for premiums, coinsurance, deductibles, and health services and supplies not covered by health insurance. The burden was measured as a ratio of total medical expenditures relative to family income. Supported by literature, several cutoffs (as opposed to just one threshold) were proposed to determine the critical point of increased health risk of medical financial burden. A treatment effects model was estimated recognizing that ratios are jointly influenced by other confounding factors such as chronic conditions. Data on 16,907 adults in the 2011 Medical Expenditure Panel Survey were analyzed. The researchers concluded that ratios exceeding 10% increased the probability of reporting poor or fair health status. However, estimating this relationship while accounting for insurance but ignoring the presence of chronic conditions completely reversed this relationship. Sensitivity analysis suggested that insurance for those with chronic conditions does not lessen the negative impact of high out‐of‐pocket burdens, which seem to affect their perceived health. Implications are discussed relative to the goals of the Affordable Care Act.
Theses and Dissertations Completed in Family and Consumer Sciences: 2015
Authors: Kabaci M.J.
Published: December 2016

The annual survey of graduate programs at U.S. universities and colleges was conducted in the spring of 2016 to compile a list of theses and dissertations completed in 2015 in family and consumer sciences areas of interest. For the survey, requests for the titles and authors were sent via email to institutions three times within a seven‐week period. Thirty‐five colleges and universities responded to the survey. A total of 310 theses and 174 dissertations were reported. A report of those submissions, by subject category, author, title, and name of student's advisor (if given), is provided.
Comprehension of Indirect Meaning in Spanish as a Foreign Language
Authors: Taguchi Naoko , Gomez‐Laich Maria Pia , Arrufat‐Marques Maria‐Jose
Published: December 2016

This study investigated comprehension of indirect meaning among learners of L2 Spanish via an original computer‐delivered multimedia listening test. The comprehension of implied speaker intention is a type of indirect communication that involves the ability to understand implied intention by using linguistic knowledge, contextual cues, and the assumption of relevance (Taguchi, 2005, 2011). Since inferential processing involves parallel processing of all available signals, both linguistic and nonlinguistic, to interpret the indirect utterance (Sperber & Wilson, 1995), it is essential to incorporate multimedia input. By creating a multimedia comprehension test in Spanish, the study examined theoretical claims about inferential mechanisms and their applicability to L2 comprehension. Thirty‐two L2 Spanish learners in intermediate/advanced Spanish classes at a private U.S. university and 21 native Spanish speakers completed a listening test that assessed comprehension of three types of indirect meaning: indirect refusals, indirect opinions, and irony. These item types differed in terms of the degree of conventionality encoded and the extent of inferencing required for comprehension. Participants’ comprehension was analyzed for accuracy and comprehension speed. Results revealed a significant difference in L2 Spanish learners’ comprehension accuracy scores and response times across the three item types. Irony was the most difficult to comprehend for L2 Spanish learners. Conventionality did not facilitate comprehension because indirect refusals and opinions had the same accuracy scores. In terms of response times, indirect opinions were faster to comprehend than indirect refusals and irony items. Posthoc retrospective verbal interviews revealed that learners used a wide a range of verbal, nonverbal, and contextual cues to make inferences of indirect meaning.
Harder Roads to Trek? Paradoxical Slowing of an Atrioventricular Reentrant Tachycardia With Contralateral Bundle Branch Block
Authors: DIVAKARA MENON SYAMKUMAR M. , AYATI MARYAM , HEALEY JEFF S.
Published: December 2016

Slowing of the tachycardia with increase in cycle length and increase in VA time with ipsilateral bundle branch block is a characteristic feature of accessory pathway mediated AVRT. Contralateral bundle branch block has no effect on the tachycardia as it is not a part of the tachycardia circuit. We present an interesting phenomenon in which contralateral bundle branch block resulted in tachycardia slowing in a case of WPW syndrome.
Catheter Ablation for Atrial Fibrillation in Patients With Watchman Left Atrial Appendage Occlusion Device: Results from a Multicenter Registry
Authors: TURAGAM MOHIT K. , LAVU MADHAV , AFZAL MUHAMMAD R. , VUDDANDA VENKAT , JAZAYERI MOHAMMAD‐ALI , PARIKH VALAY , ATKINS DONITA , BOMMANA SUDHARANI , DI BIASE LUIGI , HORTON RODNEY , BAI RONG , SWARUP VIJAY , CHENG JIE , NATALE ANDREA , LAKKIREDDY DHANUNJAYA
Published: December 2016

AF Ablation After Watchman

Background

There have been an increasing number of atrial fibrillation (AF) patients with Watchman left atrial appendage occlusion (LAAO) device, requiring catheter ablation (CA) for maintenance of normal sinus rhythm. In this study, we describe our experience with the feasibility and safety of CA in patients with a preexisting Watchman LAAO device.

Methods

This was a retrospective multicenter AF registry of 60 patients with Watchman LAAO device who underwent CA for AF. Baseline clinical and procedural characteristics of the included subjects were retrieved from review of medical records and were analyzed.

Results

The mean age was 72.7 ± 4.9 years and the mean CHADS2 score was 2.3 ± 0.6. All patients had successful pulmonary vein isolation (PVI). The left atrial appendage (LAA) was electrically active in 34 (56%) while reentrant tachycardia and AF triggers were seen in 17 (28%) patients. Electrical isolation was attempted in these 17 patients with only 10 achieving complete LAA isolation. Repeat imaging showed new peri‐device leaks in 30% (12/40) patients, while new significant peri‐device leaks (≥5 mm) were noted in 10% (10/40) of patients after RFA, respectively, requiring continuation of oral anticoagulation. There were a higher proportion of patients with severe peri‐device leaks (≥5 mm) after LAA isolation. However, >50% of those leaks sealed off on follow‐up transesophageal echocardiogram.

Conclusion

AF ablation is a feasible and safe in patients with preexisting Watchman LAAO device. Electrical isolation of the LAA could be difficult and when attempted can result in increased risk of short‐term peri‐device leak and recurrence of AT/AF in almost all patients.