bluuebunny/crossref_metadata_2025 huggingface dataset:
Defining and assessing an anisotropic delineation margin for modern radiotherapy
Authors: Bell L. R. , Pogson E. M. , Metcalfe P. E. , Holloway L. C.
Published: November 2016

Purpose:

Uncertainty in target volume delineation for modern radiotherapy impacts dosimetry and patient outcomes. Delineation uncertainty is generally overlooked in practice as a source of error, potentially since historically, other uncertainties have been the main focus. This work defined and assessed an anisotropic delineation margin in both polar and spherical coordinate systems in order to account for the spatially varying nature of this uncertainty using a whole breast radiotherapy cohort as a proof of concept.

Methods:

A cohort of 21 whole breast radiotherapy patient datasets with clinical target volumes delineated by eight independent observers was utilized. Patients were divided into categories based on target volume and laterality. An anisotropic delineation margin for each category was determined by multiplying the average standard deviation in observer contours in each category by a factor of two. Standard deviation was determined in both polar and spherical coordinates at angular increments. This anisotropic approach was compared to a conventional clinical approach, where the delineation margin was applied in the cardinal directions only. The assessment of the delineation margin was undertaken by comparing the encompassment of the observer volumes by the target volume with added margin. The extra, presumed healthy tissue included in the margin and the malignant tissue missed by the margin were determined.

Results:

The proposed delineation margin is effective at accounting for inter‐observer variation, producing >95% coverage of all CTVs for polar, spherical, and Cartesian margins in 82%, 79%, and 92% of cases, respectively. Additionally, <1% malignant tissue was missed for 65%, 70%, and 91% of cases and <37% healthy tissue was included in 95%, 89%, and 97% of cases. A conventional delineation margin approach is most appropriate for small and gold standard target volumes. However, for large target volumes, an anisotropic margin is necessary, producing significantly greater coverage of CTVs, including significantly less presumed healthy tissue and missing significantly less malignant tissue.

Conclusions:

All delineation margin methods that account for target volume and laterality proved to be adequate, with appropriate encompassment of interobserver variation and minimal inclusion of extra excess healthy tissue and exclusion of possible malignant tissue. The anisotropic approach was found to be superior to a conventional approach for target volumes >1400 cm3 only with significantly greater encompassment of interobserver variation, less missed malignant tissue and less included healthy tissue. This methodology has been validated for a whole breast radiotherapy cohort as a proof of concept, however could be applied to other anatomical sites.
Gas changes signal eruptions
Authors: Rosen Julia
Published: November 2016

Shifting gas mix warns that magma is on the rise.
Mechanisms linking circadian clocks, sleep, and neurodegeneration
Authors: Musiek Erik S. , Holtzman David M.
Published: November 2016

Disruptions of normal circadian rhythms and sleep cycles are consequences of aging and can profoundly affect health. Accumulating evidence indicates that circadian and sleep disturbances, which have long been considered symptoms of many neurodegenerative conditions, may actually drive pathogenesis early in the course of these diseases. In this Review, we explore potential cellular and molecular mechanisms linking circadian dysfunction and sleep loss to neurodegenerative diseases, with a focus on Alzheimer’s disease. We examine the interplay between central and peripheral circadian rhythms, circadian clock gene function, and sleep in maintaining brain homeostasis, and discuss therapeutic implications. The circadian clock and sleep can influence a number of key processes involved in neurodegeneration, suggesting that these systems might be manipulated to promote healthy brain aging.
Circadian clocks: Not your grandfather’s clock
Authors: Turek Fred W.
Published: November 2016

The last 20 years have seen the rapid evolution of our understanding of the molecular genes and networks that enable almost all forms of life to generate 24-hour—or circadian—rhythms. One finding has been particularly exciting: that the molecular circadian clock resides in almost all of the cells of the body and that the clock regulates the timing of many cellular and signaling pathways associated with multiple disease states. Such advances represent a new frontier for medicine: circadian medicine.
Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods
Authors: Huang Andrew D. , Luo Chengwei , Pena-Gonzalez Angela , Weigand Michael R. , Tarr Cheryl L. , Konstantinidis Konstantinos T.
Published: November 2016

Diagnostic testing for foodborne pathogens relies on culture-based techniques that are not rapid enough for real-time disease surveillance and do not give a quantitative picture of pathogen abundance or the response of the natural microbiome. Powerful sequence-based culture-independent approaches, such as shotgun metagenomics, could sidestep these limitations and potentially reveal a pathogen-specific signature on the microbiome that would have implications not only for diagnostics but also for better understanding disease progression and pathogen ecology. However, metagenomics have not yet been validated for foodborne pathogen detection. Toward closing these gaps, we applied shotgun metagenomics to stool samples collected from two geographically isolated (Alabama and Colorado) foodborne outbreaks, where the etiologic agents were identified by culture-dependent methods as distinct strains of
Salmonella enterica
subsp.
enterica
serovar Heidelberg. Metagenomic investigations were consistent with the culture-based findings and revealed, in addition, the
in situ
abundance and level of intrapopulation diversity of the pathogen, the possibility of coinfections with
Staphylococcus aureus
, overgrowth of commensal
Escherichia coli
, and significant shifts in the gut microbiome during infection relative to reference healthy samples. Additionally, we designed our bioinformatics pipeline to deal with several challenges associated with the analysis of clinical samples, such as the high frequency of coeluting human DNA sequences and assessment of the virulence potential of pathogens. Comparisons of these results to those of other studies revealed that in several, but not all, cases of diarrheal outbreaks, the disease and healthy states of the gut microbial community might be distinguishable, opening new possibilities for diagnostics.

IMPORTANCE
Diagnostic testing for enteric pathogens has relied for decades on culture-based techniques, but a total of 38.4 million cases of foodborne illness per year cannot be attributed to specific causes. This study describes new culture-independent metagenomic approaches and the associated bioinformatics pipeline to detect and type the causative agents of microbial disease with unprecedented accuracy, opening new possibilities for the future development of health technologies and diagnostics. Our tools and approaches should be applicable to other microbial diseases in addition to foodborne diarrhea.
Whole-Genome Relationships among Francisella Bacteria of Diverse Origins Define New Species and Provide Specific Regions for Detection
Authors: Challacombe Jean F. , Petersen Jeannine M. , Gallegos-Graves La Verne , Hodge David , Pillai Segaran , Kuske Cheryl R.
Published: November 2016

Francisella tularensis
is a highly virulent zoonotic pathogen that causes tularemia and, because of weaponization efforts in past world wars, is considered a tier 1 biothreat agent. Detection and surveillance of
F. tularensis
may be confounded by the presence of uncharacterized, closely related organisms. Through DNA-based diagnostics and environmental surveys, novel clinical and environmental
Francisella
isolates have been obtained in recent years. Here we present 7 new
Francisella
genomes and a comparison of their characteristics to each other and to 24 publicly available genomes as well as a comparative analysis of 16S rRNA and
sdhA
genes from over 90
Francisella
strains. Delineation of new species in bacteria is challenging, especially when isolates having very close genomic characteristics exhibit different physiological features—for example, when some are virulent pathogens in humans and animals while others are nonpathogenic or are opportunistic pathogens. Species resolution within
Francisella
varies with analyses of single genes, multiple gene or protein sets, or whole-genome comparisons of nucleic acid and amino acid sequences. Analyses focusing on single genes (16S rRNA,
sdhA
), multiple gene sets (virulence genes, lipopolysaccharide [LPS] biosynthesis genes, pathogenicity island), and whole-genome comparisons (nucleotide and protein) gave congruent results, but with different levels of discrimination confidence. We designate four new species within the genus;
Francisella opportunistica
sp. nov. (MA06-7296),
Francisella salina
sp. nov. (TX07-7308),
Francisella uliginis
sp. nov. (TX07-7310), and
Francisella frigiditurris
sp. nov. (CA97-1460). This study provides a robust comparative framework to discern species and virulence features of newly detected
Francisella
bacteria.

IMPORTANCE
DNA-based detection and sequencing methods have identified thousands of new bacteria in the human body and the environment. In most cases, there are no cultured isolates that correspond to these sequences. While DNA-based approaches are highly sensitive, accurately assigning species is difficult without known near relatives for comparison. This ambiguity poses challenges for clinical cases, disease epidemics, and environmental surveillance, for which response times must be short. Many new
Francisella
isolates have been identified globally. However, their species designations and potential for causing human disease remain ambiguous. Through detailed genome comparisons, we identified features that differentiate
F. tularensis
from clinical and environmental
Francisella
isolates and provide a knowledge base for future comparison of
Francisella
organisms identified in clinical samples or environmental surveys.
Enhanced Glucose Consumption and Organic Acid Production by Engineered Corynebacterium glutamicum Based on Analysis of a
pfkB1
Deletion Mutant
Authors: Hasegawa Satoshi , Tanaka Yuya , Suda Masako , Jojima Toru , Inui Masayuki
Published: November 2016

In the analysis of a carbohydrate metabolite pathway, we found interesting phenotypes in a mutant strain of
Corynebacterium glutamicum
deficient in
pfkB1
, which encodes fructose-1-phosphate kinase. After being aerobically cultivated with fructose as a carbon source, this mutant consumed glucose and produced organic acid, predominantly
l
-lactate, at a level more than 2-fold higher than that of the wild-type grown with glucose under conditions of oxygen deprivation. This considerably higher fermentation capacity was unique for the combination of
pfkB1
deletion and cultivation with fructose. In the metabolome and transcriptome analyses of this strain, marked intracellular accumulation of fructose-1-phosphate and significant upregulation of several genes related to the phosphoenolpyruvate:carbohydrate phosphotransferase system, glycolysis, and organic acid synthesis were identified. We then examined strains overexpressing several of the identified genes and demonstrated enhanced glucose consumption and organic acid production by these engineered strains, whose values were found to be comparable to those of the model
pfkB1
deletion mutant grown with fructose.
l
-Lactate production by the
ppc
deletion mutant of the engineered strain was 2,390 mM (i.e., 215 g/liter) after 48 h under oxygen deprivation, which was a 2.7-fold increase over that of the wild-type strain with a deletion of
ppc
.

IMPORTANCE
Enhancement of glycolytic flux is important for improving microbiological production of chemicals, but overexpression of glycolytic enzymes has often resulted in little positive effect. That is presumably because the central carbon metabolism is under the complex and strict regulation not only transcriptionally but also posttranscriptionally, for example, by the ATP/ADP ratio. In contrast, we studied a mutant strain of
Corynebacterium glutamicum
that showed markedly enhanced glucose consumption and organic acid production and, based on the findings, identified several genes whose overexpression was effective in enhancing glycolytic flux under conditions of oxygen deprivation. These results will further understanding of the regulatory mechanisms of glycolytic flux and can be widely applied to the improvement of the microbial production of useful chemicals.
Environmental Pseudomonads Inhibit Cystic Fibrosis Patient-Derived Pseudomonas aeruginosa
Authors: Chatterjee Payel , Davis Elizabeth , Yu Fengan , James Sarah , Wildschutte Julia H. , Wiegmann Daniel D. , Sherman David H. , McKay Robert M. , LiPuma John J. , Wildschutte Hans
Published: November 2016

Pseudomonas aeruginosa
is an opportunistic pathogen which is evolving resistance to many currently used antibiotics. While much research has been devoted to the roles of pathogenic
P. aeruginosa
in cystic fibrosis (CF) patients, less is known of its ecological properties.
P. aeruginosa
dominates the lungs during chronic infection in CF patients, yet its abundance in some environments is less than that of other diverse groups of pseudomonads. Here, we sought to determine if clinical isolates of
P. aeruginosa
are vulnerable to environmental pseudomonads that dominate soil and water habitats in one-to-one competitions which may provide a source of inhibitory factors. We isolated a total of 330 pseudomonads from diverse habitats of soil and freshwater ecosystems and competed these strains against one another to determine their capacity for antagonistic activity. Over 900 individual inhibitory events were observed. Extending the analysis to
P. aeruginosa
isolates revealed that clinical isolates, including ones with increased alginate production, were susceptible to competition by multiple environmental strains. We performed transposon mutagenesis on one isolate and identified an ∼14.8-kb locus involved in antagonistic activity. Only two other environmental isolates were observed to carry the locus, suggesting the presence of additional unique compounds or interactions among other isolates involved in outcompeting
P. aeruginosa
. This collection of strains represents a source of compounds that are active against multiple pathogenic strains. With the evolution of resistance of
P. aeruginosa
to currently used antibiotics, these environmental strains provide opportunities for novel compound discovery against drug-resistant clinical strains.

IMPORTANCE
We demonstrate that clinical CF-derived isolates of
P. aeruginosa
are susceptible to competition in the presence of environmental pseudomonads. We observed that many diverse environmental strains exhibited varied antagonistic profiles against a panel of clinical
P. aeruginosa
isolates, suggesting the presence of distinct mechanisms of inhibition among these ecological strains. Understanding the properties of these antagonistic events offers the potential for discoveries of antimicrobial compounds or metabolic pathways important to the development of novel treatments for
P. aeruginosa
infections.
Complete Genome Sequence of Mycobacterium chimaera Strain AH16
Authors: Hasan Nabeeh A. , Honda Jennifer R. , Davidson Rebecca M. , Epperson L. Elaine , Bankowski Matthew J. , Chan Edward D. , Strong Michael
Published: November 2016

Mycobacterium chimaera
is a nontuberculous mycobacterial species that causes cardiovascular, pulmonary, and postsurgical infections. Here, we report the first complete genome sequence of
M. chimaera
. This genome is 6.33 Mbp, with a G+C content of 67.56%, and encodes 4,926 protein-coding genes, as well as 74 tRNAs, one ncRNA, and three rRNA genes.
Draft Genome Sequences of Four Alteromonas macleodii Strains Isolated from Copper Coupons and Grown Long-Term at Elevated Copper Levels
Authors: Cusick Kathleen D. , Dale Jason R. , Little Brenda J. , Biffinger Justin C.
Published: November 2016

Alteromonas macleodii
is a marine bacterium involved in the early stages of biofouling on ship hulls treated with copper as an antifouling agent. We report here the draft genome sequences of an
A. macleodii
strain isolated from copper coupons and three laboratory mutants grown long-term at elevated copper levels.
Performance Characteristics of a New Consensus Commercial Kit for Hepatitis D Virus RNA Viral Load Quantification
Authors: Le Gal Frédéric , Dziri Samira , Gerber Athenaïs , Alloui Chakib , Ben Abdesselam Zahia , Roulot Dominique , Brichler Ségolène , Gordien Emmanuel
Published: November 2016

Hepatitis D virus (HDV) is responsible for fulminant hepatitis and liver failure and accelerates evolution toward cirrhosis and hepatocellular carcinoma in hepatitis B virus (HBV)-infected patients. To date, treatment relies upon long-term administration of pegylated alpha-interferon with a sustained virological response in 30% of the patients. Very recently, new, promising anti-HDV therapies have been developed and are already being used in clinical trials. HDV RNA viral load (HDVL) monitoring must be an integral part of the management of the infected patients. However, HDV genus is characterized by a high genetic variability into eight genotypes (HDV-1 to -8), and most available in-house or commercial assays are useful for only a limited subset of genotypes. Results of a comparison of the performance of a new kit for HDVL quantification with the consensus in-house assay of the French National Reference Laboratory for HDV developed in 2005 are reported here. A total of 611 clinical samples of all HDV genotypes with various HDVL values, including several consecutive samples over several years from 36 patients, were studied. A specificity, sensitivity, and reproducibility evaluation was conducted using HDV-positive clinical samples, hepatitis A, B, C and E (HAV, HBV, HCV, and HEV, respectively) and HIV mono-infected samples, and the WHO HDV RNA international standard. Overall results were strictly comparable between the two assays (median difference, 0.07 log IU/ml), with high diagnosis precision and capacity. In summary, this new kit showed high performance in detection/quantification of HDVL, regardless of the genotype of the infecting strain used, and seems to be a suitable tool for patient management.
MicroRNA 373 Facilitates the Replication of Porcine Reproductive and Respiratory Syndrome Virus by Its Negative Regulation of Type I Interferon Induction
Authors: Chen Jing , Shi Xibao , Zhang Xiaozhuan , Wang Aiping , Wang Li , Yang Yanyan , Deng Ruiguang , Zhang Gai-Ping
Published: November 2016

MicroRNAs (miRNAs) play an important role in the regulation of immune responses. Previous studies have indicated that dysregulating the miRNAs leads to the immunosuppression of porcine reproductive and respiratory syndrome virus (PRRSV). However, it is not clear how PRRSV regulates the expression of host miRNA, which may lead to immune escape or promote the replication of the virus. The present work suggests that PRRSV upregulated the expression of miR-373 through elevating the expression of specificity protein 1 (Sp1) in MARC-145 cells. Furthermore, this work demonstrated that miR-373 promoted the replication of PRRSV, since miR-373 was a novel negative miRNA for the production of beta interferon (IFN-β) by targeting nuclear factor IA (NFIA), NFIB, interleukin-1 receptor-associated kinase 1 (IRAK1), IRAK4, and interferon regulatory factor 1 (IRF1). We also found that both NFIA and NFIB were novel proteins for inducing the production of IFN-β, and both of them could inhibit the replication of PRRSV. In conclusion, PRRSV upregulated the expression of miR-373 by elevating the expression of Sp1 and hijacked the host miR-373 to promote the replication of PRRSV by negatively regulating the production of IFN-β.

IMPORTANCEPRRSV causes one of the most economically devastating diseases of swine, and there is no effective method for controlling PRRSV. It is not clear how PRRSV inhibits the host's immune response and induces persistent infection. Previous studies have shown that PRRSV inhibited the production of type I IFN, and the treatment of type I IFN could efficiently inhibit the replication of PRRSV, so it will be helpful to design new methods of controlling PRRSV by understanding the molecular mechanism by which PRRSV modulated the production of IFN. The current work shows that miR-373, upregulated by PRRSV, promotes PRRSV replication, since miR-373 impaired the production of IFN-β by targeting NFIA, NFIB, IRAK1, IRAK4, and IRF1, and both NFIA and NFIB were antiviral proteins to PRRSV. In conclusion, this paper revealed a novel mechanism of PRRSV that impaired the production of type I IFN by upregulating miR-373 expression in MARC-145 cells.
Inclusion Body Fusion of Human Parainfluenza Virus Type 3 Regulated by Acetylated α-Tubulin Enhances Viral Replication
Authors: Zhang Shengwei , Jiang Yanliang , Cheng Qi , Zhong Yi , Qin Yali , Chen Mingzhou
Published: November 2016

Viral inclusion bodies (IBs), or replication factories, are unique structures generated by viral proteins together with some cellular proteins as a platform for efficient viral replication, but little is known about the mechanism underlying IB formation and fusion. Our previous study demonstrated that the interaction between the nucleoprotein (N) and phosphoprotein (P) of human parainfluenza virus type 3 (HPIV3), an enveloped virus with great medical impact, can form IBs. In this study, we found that small IBs can fuse with each other to form large IBs that enhance viral replication. Furthermore, we found that acetylated α-tubulin interacts with the N-P complex and colocalizes with IBs of HPIV3 but does not interact with the N-P complex of human respiratory syncytial virus or vesicular stomatitis virus and does not colocalize with IBs of human respiratory syncytial virus. Most importantly, enhancement of α-tubulin acetylation using the pharmacological inhibitor trichostatin A (TSA), RNA interference (RNAi) knockdown of the deacetylase enzymes histone deacetylase 6 (HDAC6) and sirtuin 2 (SIRT2), or expression of α-tubulin acetyltransferase 1 (α-TAT1) resulted in the fusion of small IBs into large IBs and effective viral replication. In contrast, suppression of acetylation of α-tubulin by overexpressing HDAC6 and SIRT2 profoundly inhibited the fusion of small IBs and viral replication. Our findings offer previously unidentified mechanistic insights into the regulation of viral IB fusion by acetylated α-tubulin, which is critical for viral replication.

IMPORTANCE
Inclusion bodies (IBs) are unique structures generated by viral proteins and some cellular proteins as a platform for efficient viral replication. Human parainfluenza virus type 3 (HPIV3) is a nonsegmented single-stranded RNA virus that mainly causes lower respiratory tract disease in infants and young children. However, no vaccines or antiviral drugs for HPIV3 are available. Therefore, understanding virus-host interactions and developing new antiviral strategies are increasingly important. Acetylation on lysine (K) 40 of α-tubulin is an evolutionarily conserved modification and plays an important role in many cellular processes, but its role in viral IB dynamics has not been fully explored. To our knowledge, our findings are the first to show that acetylated α-tubulin enhances viral replication by regulating HPIV3 IB fusion.
Phylogenetic Diversity of Koala Retrovirus within a Wild Koala Population
Authors: Chappell K. J. , Brealey J. C. , Amarilla A. A. , Watterson D. , Hulse L. , Palmieri C. , Johnston S. D. , Holmes E. C. , Meers J. , Young P. R.
Published: November 2016

Koala populations are in serious decline across many areas of mainland Australia, with infectious disease a contributing factor. Koala retrovirus (KoRV) is a gammaretrovirus present in most wild koala populations and captive colonies. Five subtypes of KoRV (A to E) have been identified based on amino acid sequence divergence in a hypervariable region of the receptor binding domain of the envelope protein. However, analysis of viral genetic diversity has been conducted primarily on KoRV in captive koalas housed in zoos in Japan, the United States, and Germany. Wild koalas within Australia have not been comparably assessed. Here we report a detailed analysis of KoRV genetic diversity in samples collected from 18 wild koalas from southeast Queensland. By employing deep sequencing we identified 108 novel KoRV envelope sequences and determined their phylogenetic diversity. Genetic diversity in KoRV was abundant and fell into three major groups; two comprised the previously identified subtypes A and B, while the third contained the remaining hypervariable region subtypes (C, D, and E) as well as four hypervariable region subtypes that we newly define here (F, G, H, and I). In addition to the ubiquitous presence of KoRV-A, which may represent an exclusively endogenous variant, subtypes B, D, and F were found to be at high prevalence, while subtypes G, H, and I were present in a smaller number of animals.

IMPORTANCE
Koala retrovirus (KoRV) is thought to be a significant contributor to koala disease and population decline across mainland Australia. This study is the first to determine KoRV subtype prevalence among a wild koala population, and it significantly expands the total number of KoRV sequences available, providing a more precise picture of genetic diversity. This understanding of KoRV subtype prevalence and genetic diversity will be important for conservation efforts attempting to limit the spread of KoRV. Furthermore, KoRV is one of the only retroviruses shown to exist in both endogenous (transmitted vertically to offspring in the germ line DNA) and exogenous (horizontally transmitted between infected individuals) forms, a division of fundamental evolutionary importance.
Activation and Inactivation of Primary Human Immunodeficiency Virus Envelope Glycoprotein Trimers by CD4-Mimetic Compounds
Authors: Madani Navid , Princiotto Amy M. , Zhao Connie , Jahanbakhshsefidi Fatemeh , Mertens Max , Herschhorn Alon , Melillo Bruno , Smith Amos B. , Sodroski Joseph
Published: November 2016

Human immunodeficiency virus type 1 (HIV-1) entry into cells is mediated by the viral envelope glycoproteins (Env), a trimer of three gp120 exterior glycoproteins, and three gp41 transmembrane glycoproteins. The metastable Env is triggered to undergo entry-related conformational changes when gp120 binds sequentially to the receptors, CD4 and CCR5, on the target cell. Small-molecule CD4-mimetic compounds (CD4mc) bind gp120 and act as competitive inhibitors of gp120-CD4 engagement. Some CD4mc have been shown to trigger Env prematurely, initially activating Env function, followed by rapid and irreversible inactivation. Here, we study CD4mc with a wide range of anti-HIV-1 potencies and demonstrate that all tested CD4mc are capable of activating as well as inactivating Env function. Biphasic dose-response curves indicated that the occupancy of the protomers in the Env trimer governs viral activation versus inactivation. One CD4mc bound per Env trimer activated HIV-1 infection. Envs with two CD4mc bound were activated for infection of CD4-negative, CCR5-positive cells, but the infection of CD4-positive, CCR5-positive cells was inhibited. Virus was inactivated when all three Env protomers were occupied by the CD4mc, and gp120 shedding from the Env trimer was increased in the presence of some CD4mc. Env reactivity and the on rates of CD4mc binding to the Env trimer were found to be important determinants of the potency of activation and entry inhibition. Cross-sensitization of Env protomers that do not bind the CD4mc to neutralization by an anti-V3 antibody was not evident. These insights into the mechanism of antiviral activity of CD4mc should assist efforts to optimize their potency and utility.

IMPORTANCE
The trimeric envelope glycoproteins of human immunodeficiency virus type 1 (HIV-1) mediate virus entry into host cells. Binding to the host cell receptors, CD4 and CCR5, triggers changes in the conformation of the HIV-1 envelope glycoprotein trimer important for virus entry. Small-molecule CD4-mimetic compounds inhibit HIV-1 infection by multiple mechanisms: (i) direct blockade of the interaction between the gp120 exterior envelope glycoprotein and CD4; (ii) premature triggering of conformational changes in the envelope glycoproteins, leading to irreversible inactivation; and (iii) exposure of cryptic epitopes to antibodies, allowing virus neutralization. The consequences of the binding of the CD4-mimetic compound to the HIV-1 envelope glycoproteins depends upon how many of the three subunits of the trimer are bound and upon the propensity of the envelope glycoproteins to undergo conformational changes. Understanding the mechanistic factors that influence the activity of CD4-mimetic compounds can help to improve their potency and coverage of diverse HIV-1 strains.
Mechanism of Enhanced HIV Restriction by Virion Coencapsidated Cytidine Deaminases APOBEC3F and APOBEC3G
Authors: Ara Anjuman , Love Robin P. , Follack Tyson B. , Ahmed Khawaja A. , Adolph Madison B. , Chelico Linda
Published: November 2016

The APOBEC3 (A3) enzymes, A3G and A3F, are coordinately expressed in CD4
+
T cells and can become coencapsidated into HIV-1 virions, primarily in the absence of the viral infectivity factor (Vif). A3F and A3G are deoxycytidine deaminases that inhibit HIV-1 replication by inducing guanine-to-adenine hypermutation through deamination of cytosine to form uracil in minus-strand DNA. The effect of the simultaneous presence of both A3G and A3F on HIV-1 restriction ability is not clear. Here, we used a single-cycle infectivity assay and biochemical analyses to determine if coencapsidated A3G and A3F differ in their restriction capacity from A3G or A3F alone. Proviral DNA sequencing demonstrated that compared to each A3 enzyme alone, A3G and A3F, when combined, had a coordinate effect on hypermutation. Using size exclusion chromatography, rotational anisotropy, and
in vitro
deamination assays, we demonstrate that A3F promotes A3G deamination activity by forming an A3F/G hetero-oligomer in the absence of RNA which is more efficient at deaminating cytosines. Further, A3F caused the accumulation of shorter reverse transcripts due to decreasing reverse transcriptase efficiency, which would leave single-stranded minus-strand DNA exposed for longer periods of time, enabling more deamination events to occur. Although A3G and A3F are known to function alongside each other, these data provide evidence for an A3F/G hetero-oligomeric A3 with unique properties compared to each individual counterpart.

IMPORTANCE
The APOBEC3 enzymes APOBEC3F and APOBEC3G act as a barrier to HIV-1 replication in the absence of the HIV-1 Vif protein. After APOBEC3 enzymes are encapsidated into virions, they deaminate cytosines in minus-strand DNA, which forms promutagenic uracils that induce transition mutations or proviral DNA degradation. Even in the presence of Vif, footprints of APOBEC3-catalyzed deaminations are found, demonstrating that APOBEC3s still have discernible activity against HIV-1 in infected individuals. We undertook a study to better understand the activity of coexpressed APOBEC3F and APOBEC3G. The data demonstrate that an APOBEC3F/APOBEC3G hetero-oligomer can form that has unique properties compared to each APOBEC3 alone. This hetero-oligomer has increased efficiency of virus hypermutation, raising the idea that we still may not fully realize the antiviral mechanisms of endogenous APOBEC3 enzymes. Hetero-oligomerization may be a mechanism to increase their antiviral activity in the presence of Vif.
Comparison of therapy persistence for fixed versus free combination antihypertensives: a retrospective cohort study
Authors: Grimmsmann Thomas , Himmel Wolfgang
Published: November 2016

Objectives

The aim of the study was to compare therapy persistence among patients who started with one of three drug regimens: a monotherapy, or combination therapy either as a fixed combination (ie, ‘single pill’) or as a free combination (ie, two separate antihypertensive agents).

Design

In a secondary data analysis, we used descriptive statistics and multivariate logistic regression to measure the effect of the three therapy regimens on therapy persistence over 4 years.

Setting

Prescription data from a large German statutory health insurance provider.

Participants

All patients who started with a new antihypertensive therapy in 2007 or 2008 (n=8032) were included and followed for 4 years.

Primary outcome measure

Therapy persistence, defined as receiving a refill prescription no later than within 180 days.

Results

The persistence rates after 4 years were nearly identical among patients who started with a monotherapy (40.3%) or a fixed combination of two drugs (39.8%). However, significantly more patients who started with free-drug combinations remained therapy persistent (56.4%), resulting in an OR of 2.00 (95% CI 1.6 to 2.5; p<0.0001) for free combinations versus fixed combinations. This trend was observed in all age groups and for men and women. At the end of the study period, the number of different antihypertensive agents was still similar between patients who started with a fixed combination (2.41) and patients who started with a free combination (2.28).

Conclusions

While single-pill combinations make it easier to take different drugs at once, the risk is high that these several substances are stopped at once. Therapy persistence was significantly better for patients who started with a free-drug combination without taking much fewer different antihypertensive drugs as those with a fixed combination.
Rationale and protocol for using a smartphone application to study autism spectrum disorders: SMARTAUTISM
Authors: Bonnot Olivier , Bonneau Dominique , Doudard Aude , Duverger Philippe
Published: November 2016

Introduction

Longitudinal studies on the evolution of autism spectrum disorder (ASD) symptoms are limited and have primarily used repeated measurements performed several months apart. However, measurements of changes in everyday life should more closely reflect the ‘real life’ of the patient and his or her family. We propose to study the child's ASD symptoms and their effect on the quality of life, psychological status and anxiety of the child's parents over a 6-month period using SMARTAUTISM, a smartphone application.

Method and analysis

This is a prospective, longitudinal, exploratory, open study with a 6-month follow-up period. Data will be recorded longitudinally over multiple weeks under natural conditions. The factors affecting the quality of life and anxiety of parents of children with ASD and the children's functional symptoms will be examined, and the feasibility of using a smartphone application designed for parents of ASD patients will be assessed.Primary objective: Explore the evolution of a child's behaviour over 6 months and the (psychological and social) effects of these changes on the family.Secondary objective: Assess the feasibility of our application by examining the filling rate and application usage by parents for 6 months. 100 families containing 1 child diagnosed with ASD will be included. At baseline, sociodemographic, psychiatric and medical data will be recorded. The correlations of the general epidemiological variables (primary outcome measure) will be evaluated via multivariate analysis. The application filling rate (relative to the ideal filling rate) will be used to assess the feasibility of the application (secondary outcome measure).

Ethics and dissemination

The SMARTAUTISM study has the approval of the local ethics committee, and data security will be ensured via the use of encryption and a secure medical server. The use of this application will be proposed at autism resource centres across France.
Clinicopathological features of neoplasms with neuroendocrine differentiation occurring in the liver
Authors: Nomura Yoriko , Nakashima Osamu , Akiba Jun , Ogasawara Sachiko , Fukutomi Shogo , Yamaguchi Rin , Kusano Hironori , Kage Masayoshi , Okuda Koji , Yano Hirohisa
Published: November 2016

Background/aims

We investigated the clinicopathological features of hepatic neuroendocrine tumours (NET) and neuroendocrine carcinoma (NEC), which remain largely unknown.

Material and methods

We examined 1235 tumours from 1048 patients who had undergone curative hepatectomy for liver neoplasms at Kurume University Hospital. Pathological diagnoses were based on the 2010 WHO Classification of Tumours of the Digestive System. We performed immunostaining for hepatocyte markers (eg, hepatocyte paraffin (HepPar)-1), neuroendocrine markers (eg, chromogranin A (CGA)) and the proliferation marker (Ki-67).

Results

There were four cases of NET G2 (0.38%) and five of hepatic malignant tumours with an NEC component (HNEC) (0.48%). HNEC cases were classified into three types, that is, transitional, intermediate and separate types, according to their histological and immunohistochemical features. In the former two types, the NEC component intermingled with the moderately to poorly differentiated hepatocellular carcinoma (HCC) component or intermediate component consisting of tumour cells showing the colocalisation of CGA and HepPar-1. In the separate type, the NEC and poorly differentiated HCC components were present separately, whereas the sarcomatous HCC component was detected in the vicinity of the NEC component. Ki-67 labelling indices of the NET G2, HCC and NEC components of HNEC were 6.8%, 14.9% and 58.9%, respectively.

Conclusions

Primary hepatic NET and NEC are very rare tumours. The NEC component in HNEC showed high proliferative activity and influenced patient prognoses.
Design, fiction and the medical humanities
Authors: Strachan Christopher Gordon
Published: November 2016

This paper sets out to explore the similarities between the developing discipline of speculative and critical design (SCD) and science fiction, and their relevance to the medical humanities. SCD looks beyond ‘commercial design’ to consider what sort of things we should, or should not, be designing in order to create preferable futures. It does so by extrapolating from current social, economic, political and scientific knowledge, designing artefacts, experiences and scenarios which communicate futures and alternative realities in tangible ways. By first outlying the relevance of SCD to the medical humanities, through its ability to imagine and visualise preferable healthcare futures, the paper will then discuss several recent design projects which focus on current and future ethical issues raised by emerging biotechnology. Through these projects, the paper will look at SCD's ability to provoke, engage and critique science and society, while also critically reflecting on the limitations of the evolving design discipline. Through the paper it is hoped that there can be an increased understanding of SCD and its ambitions, as well as its limitations, in order for SCD to better approach issues relating to health and wellbeing, along with other difficult and challenging issues which will affect all us today and into the (sci-fi) future.
Application of sonoelastography for evaluating the stiffness of equine superficial digital flexor tendon during healing
Authors: Tamura N. , Kuroda T. , Kotoyori Y. , Fukuda K. , Nukada T. , Kato T. , Kuwano A. , Kasashima Y.
Published: November 2016

Sonoelastography can assess the inner stiffness of tissues. Sonoelastographic evaluation of injured equine superficial digital flexor tendons (SDFTs) is considered to be useful for assessing the stiffness of a lesion even during late‐stage rehabilitation. The purpose of this study was to investigate and compare the sonoelastographic appearance of injured SDFTs over time from the onset of the injury. Eighteen horses were classified into three groups according to the length of time from injury onset: group A, within two weeks after injury; group B, approximately five months after injury; and group C, approximately nine months after injury. Longitudinal and transverse images of all injured SDFTs were obtained using grey‐scale ultrasonography and sonoelastography. Grey‐scale and sonoelastographic images were evaluated by two observers using echogenicity‐grading and colour‐grading systems, respectively. The authors evaluated the interobserver agreement and compared the grades among the three groups. The results indicated almost perfect interobserver agreement. Significant differences were found in the sonoelastography among the three groups, whereas no significant difference was found in the grey‐scale ultrasonography between groups B and C. Sonoelastography is a feasible and useful modality to evaluate the equine injured SDFTs in vivo and to distinguish between them among the different phases even during the chronic phase.
Crystal structure and DFT studies of 4-methyl-N-(1-phenylethyl)-N′-(1-phenylethylidene)benzenesulfono-hydrazide: evidence of a carbene insertion in the formation of acetophenone azine from acetophenone p-toluensulfonylhydrazone
Authors: Valencia Rocío A. , Apolonio Víctor M. , Caballero-García Guillermo , Martínez-Otero Diego , Barroso-Flores Joaquín , Cuevas-Yañez Erick
Published: November 2016

The crystal structure of 4-Methyl-N-(1-phenylethyl)-N′-(1-phenylethylidene) benzene sulfonohydrazide is disclosed, which is obtained from direct reaction between acetophenone tosylhydrazone and potassium tert-butoxide. Reaction mechanisms and the corresponding energy barriers were assessed through DFT calculations at the B3LYP/6-31G(d,p) level of theory and showed that this compound plays an important role as an intermediate in the formation of acetophenone azine from acetophenone p-toluensulfonylhydrazone through a carbene insertion on this last compound.
A cyclopenta[hi]acephenanthrylene bearing two benzoannelated [3.3.3]propellane units: extension of triptindane chemistry
Authors: Hackfort Thorsten , Neumann Beate , Stammler Hans-Georg , Kuck Dietmar
Published: November 2016

The McMurry reaction of triptindan-9-one (2), a three-fold benzoannelated Cs-symmetrical [3.3.3]propellane ketone, gave trans-9,9′-bitriptindanylidene (5), a sterically crowded stilbene hydrocarbon bearing two E-oriented triptindane moieties, in good yield. Photoisomerization of 5 generated the corresponding cis-stilbene 8 in a photostationary E:Z mixture (55:45), which adopts a similarly crowded C2-symmetrical conformation that is apparently static on the NMR timescale. Photocyclodehydrogenation of 5 via 8 in benzene solution afforded the title hydrocarbon 6, a 1,2,9,10-tetrahydrocyclopenta[hi]acephenanthrylene merged with two triptindane units, in 85% yield. X-ray structure analysis of 6 revealed an essentially planar phenanthrene unit but significant steric repulsion between the pairs of opposite methylene groups of the [3.3.3]propellane cores, giving rise to a C2-symmetrical conformation. Reaction of 2 under modified McMurry conditions (DME instead of THF as a solvent) gave the saturated dimer, 9,9′-bitriptindanyl 7, as a mixture of diastereomers. Attempts to synthesize “columnene” (4), an elusive barrelene derivative fused with two triptindane caps, by three-fold McMurry reaction of triptindane-9,10,11-trione (3) failed.
Empirical evidence of plasticity in life-history characteristics across climatic and fish density gradients
Authors: Ward Hillary G.M. , Post John R. , Lester Nigel P. , Askey Paul J. , Godin Theresa
Published: November 2016

Understanding how environmental productivity and resource competition influence somatic growth rates and plasticity in life-history traits is a critical component of population ecology. However, evolutionary effects often confound the relationship between plasticity in life-history characteristics and environmental productivity. We used a unique set of experimentally stocked populations of rainbow trout (Oncorhynchus mykiss) to empirically test predictions from life-history theory relating to patterns in immature growth rates, age- and size-at-maturity, and the energy allocated into reproduction across climatic and fish density gradients. Our results support theoretical predictions that plasticity in life-history characteristics is a function of environmental variables. In particular, we demonstrate that immature growth rates are best explained by climatic and density-dependent competition effects and that age-at-maturity and the energy allocated to reproduction depends on juvenile growth conditions. Empirical evidence of these relationships helps to improve our understanding of optimal life-history strategies of fish populations.
Distribution pattern of dorsal root ganglion neurons synthesizing nitric oxide synthase in different animal species
Authors: Kolesár Dalibor , Kolesárová Mária , Kyselovič Ján
Published: November 2016

The main aim of the present review is to provide at first a short survey of the basic anatomical description of sensory ganglion neurons in relation to cell size, conduction velocity, thickness of myelin sheath, and functional classification of their processes. In addition, we have focused on discussing current knowledge about the distribution pattern of neuronal nitric oxide synthase containing sensory neurons especially in the dorsal root ganglia in different animal species; hence, there is a large controversy in relation to interpretation of the results dealing with this interesting field of research.
Is there a role of inducible nitric oxide synthase activation in the delayed antiarrhythmic effect of sodium nitrite?
Authors: Demeter-Haludka Vivien , Juhász László , Kovác Mária , Gardi János , Végh Ágnes
Published: November 2016

This study aimed to examine whether inducible nitric oxide synthase (iNOS) plays a role in the delayed antiarrhythmic effect of sodium nitrite. Twenty-one dogs were infused intravenously with sodium nitrite (0.2 μmol·kg–1·min–1) for 20 min, either in the absence (n = 12) or in the presence of the iNOS inhibitor S-(2-aminoethyl)-isothiourea (AEST) (total dose 2.0 mg·kg–1 i.v., n = 9). Control dogs (n = 12) were given saline. Twenty-four hours later, all of the dogs were subjected to a 25 min period occlusion of the left anterior descending coronary artery followed by rapid reperfusion. Dogs treated with AEST and nitrite received again AEST prior to the occlusion. Compared with the controls, sodium nitrite markedly reduced the number of ectopic beats, the number and incidence of ventricular tachycardia, and the incidence of ventricular fibrillation during occlusion and increased survival (0% versus 50%) from the combined ischaemia and reperfusion insult. Although AEST completely inhibited iNOS activity, the nitrite-induced increase in NO bioavailability during occlusion was not substantially modified. Furthermore, AEST attenuated but did not completely abolish the antiarrhythmic effect of nitrite. The marked delayed antiarrhythmic effect of sodium nitrite is not entirely due to the activation of iNOS; other mechanisms may certainly play a role.
3-Manifold invariants derived from the intersecting kernels
Authors: Li Fengling , Lei Fengchun , Wu Jie
Published: November 2016

The intersecting kernel of a Heegaard splitting [Formula: see text] for a compact orientable 3-manifold [Formula: see text] is the subgroup [Formula: see text] of [Formula: see text], where [Formula: see text] is the homomorphism induced by the inclusion [Formula: see text], [Formula: see text]. In the paper, we obtain some invariants of 3-manifolds [Formula: see text] from certain quotient groups of the intersecting kernels of their Heegaard splittings. We also list two algebraic problems related to the new invariants, which might be interesting to study.