bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic prevention of hepatitis C virus‐induced liver fibrosis by allele‐specific downregulation of MERTK
Authors: Cavalli Marco , Pan Gang , Nord Helena , Wallén Arzt Emelie , Wallerman Ola , Wadelius Claes
Published: August 2016

Aim

Infection by hepatitis C virus (HCV) can result in the development of liver fibrosis and may eventually progress into cirrhosis and hepatocellular carcinoma. However, the molecular mechanisms for this process are not fully known. Several genome‐wide association studies have been carried out to pinpoint causative variants in HCV‐infected patient cohorts, but these variants are usually not the functional ones. The aim of this study was to identify the regulatory single nucleotide polymorphism associated with the risk of HCV‐induced liver fibrosis and elucidate its molecular mechanism.

Methods

We utilized a bioinformatics approach to identify a non‐coding regulatory variant, located in an intron of the MERTK gene, based on differential transcription factor binding between the alleles. We validated the results using expression reporter assays and electrophoresis mobility shift assays.

Results

Chromatin immunoprecipitation sequencing indicated that transcription factor(s) bind stronger to the A allele of rs6726639. Electrophoresis mobility shift assays supported these findings and suggested that the transcription factor is interferon regulatory factor 1 (IRF1). Luciferase report assays showed lower enhancer activity from the A allele and that IRF1 may act as a repressor.

Conclusions

Treatment of hepatitis C with interferon‐α results in increased IRF1 levels and our data suggest that this leads to an allele‐specific downregulation of MERTK mediated by an allelic effect on the regulatory element containing the functional rs6726639. This variant also shows the hallmarks for being the driver of the genome‐wide association studies for reduced risk of liver fibrosis and non‐alcoholic fatty liver disease at MERTK.
Ambiguous Loss and Complicated Grief: Understanding the Grief of Parents of the Disappeared in Northern Uganda
Authors: Hollander Theo
Published: August 2016

In the bereavement literature, prolonged grief, described in the new DSM‐5 as persistent complex bereavement disorder, is considered a pathological disorder affecting a small but significant minority of bereaved persons. In the ambiguous loss literature, in contrast, prolonged grief is viewed as inevitably linked to the ambiguity of the bereaved person, and its causes are linked to the ambiguity, such as persistent hope, the absence of cultural and religious rituals to provide meaning to a loss, and the grief being so large as to disenfranchise community members. Based on a literature review and qualitative fieldwork with parents of missing persons in Uganda, this article examines the emotional, social, cultural, and socioeconomic aspects of the ambiguity that relatives of missing persons experience in the aftermath of wartime disappearances. I argue that, in such contexts, explanations of prolonged grief as a pathological disorder cannot be sustained.
Substitution of modified starch with hydrogen peroxide‐modified rice bran in salad dressing formulation: physicochemical, texture, rheological and sensory properties
Authors: Maani Bahareh , Alimi Mazdak , Shokoohi Shirin , Fazeli Fatemeh
Published: August 2016

Rice bran samples were treated under different conditions including hydrogen peroxide content (1, 4, and 7 wt%) and media pH (10.5, 11.5, and 12.5). Water holding capacity and color measurement results showed acceptable improvements compared with the untreated native bran confirmed by Fourier transform infrared analysis. Optimization of modification conditions upon characterization results suggested the introduction of 7% hydrogen peroxide at pH = 12.5. Accordingly, 1, 2 and 3 wt% of the rice bran treated under the optimized conditions, was used in salad dressing formulation; as for .3 wt% of modified starch in the formulation of blank sample, 1 wt% of treated rice bran dietary fiber was substituted. Biopolymer swelling and formation of a stable viscous gel network promoted by the chemical treatment of lignocellulosic rice bran restrict the mobility of oil droplets dispersed in the continuous phase which would consequently retard the emulsion instability phenomena. This effect was also confirmed by flow behavior and viscoelastic characterization results. Salad dressing samples containing 1 and 2 wt% treated rice bran showed acceptable physicochemical, rheological and organoleptic properties besides superior nutritional characteristics compared with the commercial modified starch traditionally used in salad dressing formulations.

Practical applications

Despite recommended consumption of dietary fibers, addition of unprocessed lignocellulosic materials to food products usually raise negative effects in sensory, color, and texture quality. This study investigates the modification of rice bran, the byproduct of brown rice milling, to substitute modified starch traditionally used in salad dressing formulations to achieve optimum properties desirable for the final product. Optimization of modification conditions upon characterization of the formulated samples in this study would suggest new improved formulation for the commercial product.
Microbiome changes through ontogeny of a tick pathogen vector
Authors: Zolnik Christine P. , Prill Robert J. , Falco Richard C. , Daniels Thomas J. , Kolokotronis Sergios‐Orestis
Published: September 2016

Blacklegged ticks (Ixodes scapularis) are one of the most important pathogen vectors in the United States, responsible for transmitting Lyme disease and other tick‐borne diseases. The structure of a host's microbial community has the potential to affect the ecology and evolution of the host. We employed high‐throughput sequencing of the 16S rRNA gene V3‐V4 hypervariable regions in the first study to investigate the tick microbiome across all developmental stages (larvae, nymphs, adults). In addition to field‐collected life stages, newly hatched laboratory‐reared larvae were studied to determine the baseline microbial community structure and to assess transovarial transmission. We also targeted midguts and salivary glands due to their importance in pathogen maintenance and transmission. Over 100 000 sequences were produced per life stage replicate. Rickettsia was the most abundant bacterial genus across all sample types matching mostly the Ixodes rickettsial endosymbionts, and its proportion decreased as developmental stage progressed, with the exception of adult females that harboured a mean relative abundance of 97.9%. Laboratory‐reared larvae displayed the lowest bacterial diversity, containing almost exclusively Rickettsia. Many of the remaining bacteria included genera associated with soil, water and plants, suggesting environmental acquisition while off‐host. Female organs exhibited significantly different β‐diversity than the whole tick from which they were derived. Our results demonstrate clear differences in both α‐ and β‐diversity among tick developmental stages and between tick organs and the tick as a whole. Furthermore, field‐acquired bacteria appear to be very important to the overall internal bacterial community of this tick species, with influence from the host bloodmeal appearing limited.
Deep sequencing of mycovirus‐derived small RNAs from Botrytis species
Authors: Donaire Livia , Ayllón María A.
Published: August 2016

RNA silencing is an ancient regulatory mechanism operating in all eukaryotic cells. In fungi, it was first discovered in Neurospora crassa, although its potential as a defence mechanism against mycoviruses was first reported in Cryphonectria parasitica and, later, in several fungal species. There is little evidence of the antiviral potential of RNA silencing in the phytopathogenic species of the fungal genus Botrytis. Moreover, little is known about the RNA silencing components in these fungi, although the analysis of public genome databases identified two Dicer‐like genes in B. cinerea, as in most of the ascomycetes sequenced to date. In this work, we used deep sequencing to study the virus‐derived small RNA (vsiRNA) populations from different mycoviruses infecting field isolates of Botrytis spp. The mycoviruses under study belong to different genera and species, and have different types of genome [double‐stranded RNA (dsRNA), (+)single‐stranded RNA (ssRNA) and (–)ssRNA]. In general, vsiRNAs derived from mycoviruses are mostly of 21, 20 and 22 nucleotides in length, possess sense or antisense orientation, either in a similar ratio or with a predominance of sense polarity depending on the virus species, have predominantly U at their 5′ end, and are unevenly distributed along the viral genome, showing conspicuous hotspots of vsiRNA accumulation. These characteristics reveal striking similarities with vsiRNAs produced by plant viruses, suggesting similar pathways of viral targeting in plants and fungi. We have shown that the fungal RNA silencing machinery acts against the mycoviruses used in this work in a similar manner independent of their viral or fungal origin.
Collapsing of Non‐centred Parameterized MCMC Algorithms with Applications to Epidemic Models
Authors: Neal Peter , Xiang Fei
Published: September 2016

Data augmentation is required for the implementation of many Markov chain Monte Carlo (MCMC) algorithms. The inclusion of augmented data can often lead to conditional distributions from well‐known probability distributions for some of the parameters in the model. In such cases, collapsing (integrating out parameters) has been shown to improve the performance of MCMC algorithms. We show how integrating out the infection rate parameter in epidemic models leads to efficient MCMC algorithms for two very different epidemic scenarios, final outcome data from a multitype SIR epidemic and longitudinal data from a spatial SI epidemic. The resulting MCMC algorithms give fresh insight into real‐life epidemic data sets.
Generation of chromosomal deletions in dicotyledonous plants employing a user‐friendly genome editing toolkit
Authors: Ordon Jana , Gantner Johannes , Kemna Jan , Schwalgun Lennart , Reschke Maik , Streubel Jana , Boch Jens , Stuttmann Johannes
Published: August 2016

Genome editing facilitated by Cas9‐based RNA‐guided nucleases (RGNs) is becoming an increasingly important and popular technique for reverse genetics in both model and non‐model species. So far, RGNs were mainly applied for the induction of point mutations, and one major challenge consists in the detection of genome‐edited individuals from a mutagenized population. Also, point mutations are not appropriate for functional dissection of non‐coding DNA. Here, the multiplexing capacity of a newly developed genome editing toolkit was exploited for the induction of inheritable chromosomal deletions at six different loci in Nicotiana benthamiana and Arabidopsis. In both species, the preferential formation of small deletions was observed, suggesting reduced efficiency with increasing deletion size. Importantly, small deletions (<100 bp) were detected at high frequencies in N. benthamiana T0 and Arabidopsis T2 populations. Thus, targeting of small deletions by paired nucleases represents a simple approach for the generation of mutant alleles segregating as size polymorphisms in subsequent generations. Phenotypically selected deletions of up to 120 kb occurred at low frequencies in Arabidopsis, suggesting larger population sizes for the discovery of valuable alleles from addressing gene clusters or non‐coding DNA for deletion by programmable nucleases.
Cuerpos anfibios: metamorfosis y anfientidad sexual en XXY (2007) de Lucía Puenzo
Authors: Fradinger Moira
Published: September 2016

Analizo la película XXY de Lucía Puenzo (Argentina, 2007) desde el punto de vista de la relación entre la materia viviente de la zona costera uruguaya y la propuesta del film con respecto a la diversidad sexual. Sugiero la expresión “anfientidad sexual” para distinguir la manera en que el film representa la relación entre cuerpo, sexo y género al ficcionalizar un caso intersex a través de asociaciones entre los animales humanos y los anfibios y reptiles del ambiente costero, en especial las tortugas marinas que migran cruzando el Atlántico y que se encuentran en peligro de extinción. En tanto las tortugas determinan su sexo dependiendo de la temperatura del ambiente, representan un dinamismo relacional singular de la materia viviente, que corre peligro de extinguirse en nuestra era y que el film asocia con la variación sexual. 
Stuart Hall desde/en América Latina
Authors: Mato Daniel
Published: September 2016

Este artículo analiza cómo las ideas de Stuart Hall han sido adoptadas de manera rigurosa y crítica por los académicos e intelectuales latinoamericanos que pueden considerarse pioneros de los estudios culturales en América Latina y quienes los siguieron; por los que realizan estudios críticos, pero rechazan la etiqueta estudios culturales, y por aquellos cuyo trabajo puede claramente ubicarse dentro del campo de los estudios culturales, aun cuando hasta ahora no se ha asumido como tal. Este análisis lleva a la conclusión de que sería simplista limitar la discusión acerca de la importancia de las ideas de Hall en América Latina exclusivamente al campo de los llamados estudios culturales latinoamericanos y plantea, más bien, la necesidad de analizar su importancia de una manera más abarcante. 
Ultrasonographic diagnosis of stenosis of native arteriovenous fistulas in haemodialysis patients
Authors: Tirinescu Dacian Călin , Bondor Cosmina Ioana , Vlăduțiu Dan Ştefan , Pațiu Ioan Mihai , Moldovan Diana , Orășan Remus , Kacsó Ina Maria
Published: August 2016

Aims: Ultrasound (US) examination is an important tool in the diagnosis of arteriovenous (AVF) stenoses; different US measures are available for assessing the severity of stenoses. The aim of our study was to analyse risk factors and consequences of AVF stenosis and its severity and to compare the usefulness of different US measures of stenoses’ severity. Material and methods:  Ninety-seven prevalent patients from a single dialysis centre with patent AVF were included. We recorded history of disease, clinical and laboratory data. US was used to diagnosis the stenosis and to measure blood flow in the brachial artery, resistivity index (RI), and the diameter of the vessels (arteries, anastomosis, venous outflow). Results: Stenosis was present in 54.64% of the patients (59.6% juxtaanastomotic). Stenosis patients had higher age, lower diameter of the brachial artery, lower anastomosis diameter, and lower diastolic blood pressure (DBP). Atherosclerosis, delayed maturation of AVF, and statin treatment were more prominent in the stenosis group. Logistic regression disclosed delayed maturation, cholesterol, atherosclerosis, and DBP as significant predictors of stenosis. When severe stenosis was measured by the diameter reduction, stenosis patients had higher age, lower HDL cholesterol, and poorer dialysis efficacy. Flow in the brachial artery and RI were less useful for identifying risk factors or differences in outcome. Conclusions: Prevalence of stenosis was high in our cohort, more than half of the patients having some degree of stenosis. Risk factors for stenosis were related to atherosclerosis, low DBP, and delayed maturation of AVF. Diameter of stenosis is the most useful marker of severity.
Layer-specific myocardial strain analysis: investigation of regional deformation in a rabbit model of diabetes mellitus during different stages.
Authors: Qiao Ying-Yan , Zeng Mu , Li Rong-Juan , Leng Zhao-Ting , Yang Jiao , Yang Ya
Published: August 2016

Aim: The purpose of the present study was to determine the characteristics of myocardial damage at different stages of diabetes mellitus (DM) using layer-specific myocardial strain. Material and methods: Thirty six New Zealand white rabbits were randomly divided into either the control group (n =18) or the DM group (induced with alloxan) (n=18). For the myocardial deformation studies echocardiography and layer-specific strain were performed at baseline and after 3, 6, and 9 months in all of the rabbits. Three-layer longitudinal strain (LS) was calculated in the apical 4-chamber view, and three-layer circumferential strain (CS) in the short-axis view at the level of mitral valve. Layer-specific longitudinal and circumferential strains were assessed from endocardium, mid-myocardium and epicardium. For histomorphological study of the heart structure, the rabbits were sacrificed at 3, 6 and 9 months. Routine hematoxylin and eosin staining was performed. Results: The highest absolute values of left ventricular longitudinal strain (LS) and circumferential strain (CS) were registered in the endocardium and the lowest in the epicardium in both groups. At 3 months, there was no significant difference in three-layer LS and CS (p>0.05), but at 6 months the LS of endocardium (LSendo) and CS of endocardium (CSendo) were lower in the DM group compared with the control group; at 9 months, the rest of the parameters were also decreased (p<0.05). Moreover, in ROC analysis at 6 months LSendo yielded better sensitivity and specificity in the detection of diabetic cardiomyopathy (AUC of LSendo was 0.897 and AUC of CSendo was 0.617). With the progression of untreated diabetes, the histopathological abnormalities intensified gradually beginning at 6 months. Conclusion: The progressive impairments in LV myocardial deformation and structure occurs early in diabetic rabbits, the myocardial damage may be nontransmural, and endocardial function is more susceptible to be affected by DM. Layer-specific myocardial strain echocardiography may identify subtle myocardial dysfunction in the early stages of DM.
Targeting BCL-2 and ABL/LYN in Philadelphia chromosome–positive acute lymphoblastic leukemia
Authors: Leonard Jessica T. , Rowley Joelle S. J. , Eide Christopher A. , Traer Elie , Hayes-Lattin Brandon , Loriaux Marc , Spurgeon Stephen E. , Druker Brian J. , Tyner Jeffrey W. , Chang Bill H.
Published: August 2016

The combination of venetoclax and dasatinib is synergistically effective in treating Philadelphia chromosome–positive ALL.
Fast Mechanically Driven Daughter Cell Separation Is Widespread in
Actinobacteria
Authors: Zhou Xiaoxue , Halladin David K. , Theriot Julie A.
Published: August 2016

Dividing cells of the coccoid Gram-positive bacterium
Staphylococcus aureus
undergo extremely rapid (millisecond) daughter cell separation (DCS) driven by mechanical crack propagation, a strategy that is very distinct from the gradual, enzymatically driven cell wall remodeling process that has been well described in several rod-shaped model bacteria. To determine if other bacteria, especially those in the same phylum (
Firmicutes
) or with similar coccoid shapes as
S. aureus
, might use a similar mechanically driven strategy for DCS, we used high-resolution video microscopy to examine cytokinesis in a phylogenetically wide range of species with various cell shapes and sizes. We found that fast mechanically driven DCS is rather rare in the
Firmicutes
(low G+C Gram positives), observed only in
Staphylococcus
and its closest coccoid relatives in the
Macrococcus
genus, and we did not observe this division strategy among the Gram-negative
Proteobacteria
. In contrast, several members of the high-G+C Gram-positive phylum
Actinobacteria
(
Micrococcus luteus
,
Brachybacterium faecium
,
Corynebacterium glutamicum
, and
Mycobacterium smegmatis
) with diverse shapes ranging from coccoid to rod all undergo fast mechanical DCS during cell division. Most intriguingly, similar fast mechanical DCS was also observed during the sporulation of the actinobacterium
Streptomyces venezuelae
.

IMPORTANCE
Much of our knowledge on bacterial cytokinesis comes from studying rod-shaped model organisms such as
Escherichia coli
and
Bacillus subtilis
. Less is known about variations in this process among different bacterial species. While cell division in many bacteria has been characterized to some extent genetically or biochemically, few species have been examined using video microscopy to uncover the kinetics of cytokinesis and daughter cell separation (DCS). In this work, we found that fast (millisecond) DCS is exhibited by species in two independent clades of Gram-positive bacteria and is particularly prevalent among the
Actinobacteria
, a diverse group that includes significant pathogens as well as bacteria that generate medically important antibiotics.
Colistin- and Carbapenem-Resistant Escherichia coli Harboring
mcr-1
and
bla
NDM-5
, Causing a Complicated Urinary Tract Infection in a Patient from the United States
Authors: Mediavilla José R. , Patrawalla Amee , Chen Liang , Chavda Kalyan D. , Mathema Barun , Vinnard Christopher , Dever Lisa L. , Kreiswirth Barry N.
Published: August 2016

Colistin is increasingly used as an antibiotic of last resort for the treatment of carbapenem-resistant Gram-negative infections. The plasmid-borne colistin resistance gene
mcr-1
was initially identified in animal and clinical samples from China and subsequently reported worldwide, including in the United States. Of particular concern is the spread of
mcr-1
into carbapenem-resistant bacteria, thereby creating strains that approach pan-resistance. While several reports of
mcr-1
have involved carbapenem-resistant strains, no such isolates have been described in the United States. Here, we report the isolation and identification of an
Escherichia coli
strain harboring both
mcr-1
and carbapenemase gene
bla
NDM-5
from a urine sample in a patient without recent travel outside the United States. The isolate exhibited resistance to both colistin and carbapenems, but was susceptible to amikacin, aztreonam, gentamicin, nitrofurantoin, tigecycline, and trimethoprim-sulfamethoxazole. The
mcr-1
- and
bla
NDM-5
-harboring plasmids were completely sequenced and shown to be highly similar to plasmids previously reported from China. The strain in this report was first isolated in August 2014, highlighting an earlier presence of
mcr-1
within the United States than previously recognized.

IMPORTANCE
Colistin has become the last line of defense for the treatment of infections caused by Gram-negative bacteria resistant to multiple classes of antibiotics, in particular carbapenem-resistant
Enterobacteriaceae
(CRE). Resistance to colistin, encoded by the plasmid-borne gene
mcr-1
, was first identified in animal and clinical samples from China in November 2015 and has subsequently been reported from numerous other countries. In April 2016,
mcr-1
was identified in a carbapenem-susceptible
Escherichia coli
strain from a clinical sample in the United States, followed by a second report from a carbapenem-susceptible
E. coli
strain originally isolated in May 2015. We report the isolation and identification of an
E. coli
strain harboring both colistin (
mcr-1
) and carbapenem (
bla
NDM-5
) resistance genes, originally isolated in August 2014 from urine of a patient with recurrent urinary tract infections. To our knowledge, this is the first report in the United States of a clinical bacterial isolate with both colistin and carbapenem resistance, highlighting the importance of active surveillance efforts for colistin- and carbapenem-resistant organisms.
The Nucleoid Binding Protein H-NS Biases Genome-Wide Transposon Insertion Landscapes
Authors: Kimura Satoshi , Hubbard Troy P. , Davis Brigid M. , Waldor Matthew K.
Published: August 2016

Transposon insertion sequencing (TIS; also known as TnSeq) is a potent approach commonly used to comprehensively define the genetic loci that contribute to bacterial fitness in diverse environments. A key presumption underlying analyses of TIS datasets is that loci with a low frequency of transposon insertions contribute to fitness. However, it is not known whether factors such as nucleoid binding proteins can alter the frequency of transposon insertion and thus whether TIS output may systematically reflect factors that are independent of the role of the loci in fitness. Here, we investigated whether the histone-like nucleoid structuring (H-NS) protein, which preferentially associates with AT-rich sequences, modulates the frequency of Mariner transposon insertion in the
Vibrio cholerae
genome, using comparative analysis of TIS results from wild-type (wt) and
Δhns V. cholerae
strains. These analyses were overlaid on gene classification based on GC content as well as on extant genome-wide identification of H-NS binding loci. Our analyses revealed a significant dearth of insertions within AT-rich loci in wt
V. cholerae
that was not apparent in the
Δhns
insertion library. Additionally, we observed a striking correlation between genetic loci that are overrepresented in the
Δhns
insertion library relative to their insertion frequency in wt
V. cholerae
and loci previously found to physically interact with H-NS. Collectively, our findings reveal that factors other than genetic fitness can systematically modulate the frequency of transposon insertions in TIS studies and add a cautionary note to interpretation of TIS data, particularly for AT-rich sequences.

IMPORTANCE
Transposon insertion sequencing (TIS) is often used to assess the relative frequency with which genetic loci can be disrupted, which is taken as an indicator of their importance for bacterial fitness. Here, we report that biological factors other than the relative levels of fitness of insertion mutants can influence TIS output. We found that the presence of the DNA binding protein H-NS, which preferentially recognizes AT-rich sequences, is linked to significant underrepresentation of mutations within AT-rich loci in transposon insertion libraries. Furthermore, there is a marked correspondence between loci bound by H-NS and loci with an increased frequency of disruption in a Δ
hns
insertion library relative to a wt library. Our data suggest that factors other than genetic fitness (e.g., DNA binding proteins such as H-NS) can systematically modulate the frequency of transposon insertions in TIS studies and add a note of caution for interpretation of TIS data.
Sleeping Beauty and the Story of the Bacille Calmette-Guérin Vaccine
Authors: Fletcher Helen A.
Published: August 2016

Mycobacterium bovis
BCG is the only available vaccine for protection against tuberculosis (TB). While BCG protects children from severe disease, it has little impact on pulmonary disease in adults. A recombinant BCG vaccine BCG Δ
ureC
::
hly
(strain VPM1002) is in advanced clinical trials and shows promise for improved vaccine safety but little change in efficacy in animal models. A second-generation recombinant BCG vaccine with an additional deletion of the
nuoG
gene (BCG Δ
ureC
::
hly
Δ
nuoG
) shows improved efficacy in a mouse model compared to that of VPM1002. BCG was first used in humans in 1921 and, like Sleeping Beauty pricked by the spinning wheel, we have slept for 100 years, showing a reluctance to invest in clinical development or in biomanufacturing capacity for TB vaccines. The advance of recombinant BCGs should awaken us from our sleep and call us to invest in new-generation TB vaccines and to protect the biomanufacture of our current BCG vaccine.
Predicting mortality in patients treated differently: updating and external validation of a prediction model for nursing home residents with dementia and lower respiratory infections
Authors: Rauh Simone P , Heymans Martijn W , Mehr David R , Kruse Robin L , Lane Patricia , Kowall Neil W , Volicer Ladislav , van der Steen Jenny T
Published: August 2016

Objective

To evaluate whether a model that was previously developed to predict 14-day mortality for nursing home residents with dementia and lower respiratory tract infection who received antibiotics could be applied to residents who were not treated with antibiotics. Specifically, in this same data set, to update the model using recalibration methods; and subsequently examine the historical, geographical, methodological and spectrum transportability through external validation of the updated model.

Design

1 cohort study was used to develop the prediction model, and 4 cohort studies from 2 countries were used for the external validation of the model.

Setting

Nursing homes in the Netherlands and the USA.

Participants

157 untreated residents were included in the development of the model; 239 untreated residents were included in the external validation cohorts.

Outcome

Model performance was evaluated by assessing discrimination: area under the receiver operating characteristic curves; and calibration: Hosmer and Lemeshow goodness-of-fit statistics and calibration graphs. Further, reclassification tables allowed for a comparison of patient classifications between models.

Results

The original prediction model applied to the untreated residents, who were sicker, showed excellent discrimination but poor calibration, underestimating mortality. Adjusting the intercept improved calibration. Recalibrating the slope did not substantially improve the performance of the model. Applying the updated model to the other 4 data sets resulted in acceptable discrimination. Calibration was inadequate only in one data set that differed substantially from the other data sets in case-mix. Adjusting the intercept for this population again improved calibration.

Conclusions

The discriminative performance of the model seems robust for differences between settings. To improve calibration, we recommend adjusting the intercept when applying the model in settings where different mortality rates are expected. An impact study may evaluate the usefulness of the two prediction models for treated and untreated residents and whether it supports decision-making in clinical practice.
Is poor oral health a risk marker for incident cardiovascular disease hospitalisation and all-cause mortality? Findings from 172 630 participants from the prospective 45 and Up Study
Authors: Joshy Grace , Arora Manish , Korda Rosemary J , Chalmers John , Banks Emily
Published: August 2016

Objective

To investigate the relationship between oral health and incident hospitalisation for ischaemic heart disease (IHD), heart failure (HF), ischaemic stroke and peripheral vascular disease (PVD) and all-cause mortality.

Design

Prospective population-based study of Australian men and women aged 45 years or older, who were recruited to the 45 and Up Study between January 2006 and April 2009; baseline questionnaire data were linked to hospitalisations and deaths up to December 2011. Study exposures include tooth loss and self-rated health of teeth and gums at baseline.

Setting

New South Wales, Australia.

Participants

Individuals aged 45–75 years, excluding those with a history of cancer/cardiovascular disease (CVD) at baseline; n=172 630.

Primary outcomes

Incident hospitalisation for IHD, HF, ischaemic stroke and PVD and all-cause mortality.

Results

During a median follow-up of 3.9 years, 3239 incident hospitalisations for IHD, 212 for HF, 283 for ischaemic stroke and 359 for PVD, and 1908 deaths, were observed. Cox proportional hazards models examined the relationship between oral health indicators and incident hospitalisation for CVD and all-cause mortality, adjusting for potential confounding factors. All-cause mortality and incident CVD hospitalisation risk increased significantly with increasing tooth loss for all outcomes except ischaemic stroke (ptrend<0.05). In those reporting no teeth versus ≥20 teeth left, risks were increased for HF (HR, 95% CI 1.97, 1.27 to 3.07), PVD (2.53, 1.81 to 3.52) and all-cause mortality (1.60, 1.37 to 1.87). The risk of IHD, PVD and all-cause mortality (but not HF or ischaemic stroke) increased significantly with worsening self-rated health of teeth and gums (ptrend<0.05). In those reporting poor versus very good health of teeth and gums, risks were increased for IHD (1.19, 1.03 to 1.38), PVD (1.66, 1.13 to 2.43) and all-cause mortality (1.76, 1.50 to 2.08).

Conclusions

Tooth loss and, to a lesser extent, self-rated health of teeth and gums, are markers for increased risk of IHD, PVD and all-cause mortality. Tooth loss is also a marker for increased risk of HF.
Tributary effects in rivers: interactions of spatial scale, network structure, and landscape characteristics
Authors: Jones Nicholas E. , Schmidt Bastian J.
Published: August 2016

Landscape characteristics in combination with the physical structure of branched stream networks define the environmental conditions available for lotic biota. From simple stream network “laws” can emerge a spatially explicit understanding of habitat heterogeneity. Based on geographic information system analyses, we explore how stream networks integrate spatial heterogeneity of the landscape and form new characteristics as stream segments accumulate into progressively larger drainages and how these changes in landscape characteristics relate to confluence symmetry ratio and drainage size. Simple expectations for stream networks include the following: (i) abrupt changes in longitudinal patterns are more probable among the numerous small and diverse headwater streams than in large, rare, and characteristically similar tributaries, (ii) the many small tributaries flowing into large mainstem channels cause individually small, yet collectively gradual, changes in longitudinal patterns. Such a spatial understanding of where change is likely to occur helps to reconcile gradual river continuum and abrupt discontinuum views of patterns in rivers and predict the locations of important confluences, ecological transitions, longitudinal gradients, and patterns of biodiversity in stream networks.
Numerical study of S1 zero group velocity Lamb modes for nonlinear functionally graded materials
Authors: Zagrouba Mouldi , Bouhdima Mohamed Shili
Published: August 2016

This paper presents detailed theoretical investigation of the first-order symmetric zero group velocity (S1-ZGV) modes propagating in functionally graded material (FGM) plates. Governing equations for the Lamb waves are derived and the power series technique (PST) is employed to solve the recursive equations associated with any power law and its gradient coefficient. The convergence criteria relative to PST have been discussed. Then, the dispersion curves are obtained on the basis of PST. Additionally, the impact of the FGM base materials and the gradient coefficient on S1-ZGV frequency is investigated. Numerical results show that S1-ZGV frequency is comparatively more sensitive to the shear modulus than to the Lamé parameter λ. Additionally, the variations of S1-ZGV frequency as a function of the Poisson ratio of various FGM plates are clarified.
On formation of long-living states
Authors: Ivlev Boris I.
Published: August 2016

The motion of a particle in a potential well is studied when the particle is attached to an infinite elastic string. This is generic with the problem of dissipative quantum mechanics investigated by Caldeira and Leggett (Ann. Phys. 149, 374 (1983). doi: 10.1016/0003-4916(83)90202-6 ). Besides the dissipative motion there is another scenario of interaction of the string with the particle attached. Stationary particle–string states exist with string deformations accompanying the particle. This is like polaronic states in solids. Our polaronic states in the well are non-decaying and have a continuous energy spectrum. These states may have a link to quantum electrodynamics.
Dynamic cancellation of a cosmological constant and approach to the Minkowski vacuum
Authors: Klinkhamer F. R. , Volovik G. E.
Published: August 2016

The q-theory approach to the cosmological constant problem is reconsidered. The new observation is that the effective classical q-theory gets modified due to the back-reaction of quantum-mechanical particle production by spacetime curvature. Furthermore, a Planck-scale cosmological constant is added to the potential term of the action density, in order to represent the effects from zero-point energies and phase transitions. The resulting dynamical equations of a spatially-flat Friedmann–Robertson–Walker universe are then found to give a steady approach to the Minkowski vacuum, with attractor behavior for a finite domain of initial boundary conditions on the fields. The approach to the Minkowski vacuum is slow and gives rise to an inflation-type increase of the particle horizon.
The constraints on new physics from b → s transitions
Authors: Ge Zhao-Feng , Feng Tai-Fu , Zhang Hai-Bin
Published: August 2016

Assuming that the corrections to relevant Wilson coefficients from new physics (NP) contain the possible CP phases, we analyze the constraints on the NP corrections from the updated experimental data on rare B decays from LHCb, BABAR, and BELLE, etc. systematically. Through global fit among the theoretical evaluations and corresponding experimental observations, we find that the possible CP phases of the corrections to relevant Wilson coefficients from NP affect the allowed parameter space obviously.
Scalar isovector resonance photoproduction through the final state meson–meson interactions
Authors: Bibrzycki Łukasz , Kamiński Robert
Published: August 2016

We construct the amplitudes of [Formula: see text] photoproduction taking into account the effects of the [Formula: see text] interchannel coupling. The idea of our model is to describe the scalar isovectors as dynamically produced in the final state while the initial stage of the reaction being described in terms of meson exchanges. Meson loops which arise this way include not only pseudoscalars but also vector mesons. These amplitudes are used to calculate the [Formula: see text]-wave cross-sections and mass distributions in the [Formula: see text] effective mass region corresponding to the scalar resonances [Formula: see text] and [Formula: see text]. The values we obtained for [Formula: see text] are comparable with predictions of other models while the cross-section for [Formula: see text] is about an order of magnitude larger than prediction based on the quark model. We show that the amplitudes with loops containing vector mesons calculated in the on-shell approximation are not suppressed in contrast to amplitudes containing only pseudoscalar loops. We also estimate the cross-sections for the [Formula: see text]- and [Formula: see text]-waves in the [Formula: see text] channel.
The distributional zeta-function in disordered field theory
Authors: Svaiter B. F. , Svaiter N. F.
Published: September 2016

In this paper, we present a new mathematical rigorous technique for computing the average free energy of a disordered system with quenched randomness, using the replicas. The basic tool of this technique is a distributional zeta-function, a complex function whose derivative at the origin yields the average free energy of the system as the sum of two contributions: the first one is a series in which all the integer moments of the partition function of the model contribute; the second one, which cannot be written as a series of the integer moments, can be made as small as desired. This result supports the use of integer moments of the partition function, computed via replicas, for expressing the average free energy of the system. One advantage of the proposed formalism is that it does not require the understanding of the properties of the permutation group when the number of replicas goes to zero. Moreover, the symmetry is broken using the saddle-point equations of the model. As an application for the distributional zeta-function technique, we obtain the average free energy of the disordered [Formula: see text] model defined in a [Formula: see text]-dimensional Euclidean space.
The Efficiency of the 4-Out-of-5 Runs Rules Scheme for Monitoring the Ratio of Population Means of a Bivariate Normal Distribution
Authors: Tran Kim Phuc
Published: August 2016

In order to monitor the ratio of population means of a bivariate normal distribution, [K. P. Tran, P. Castagliola, and G. Celano, Monitoring the ratio of two normal variables using run rules type control charts, Int. J. Prod. Res. 54(6) (2016a) 1670–1688] recently suggested a scheme based on Runs Rules, called the RRRZ control chart, and showed how their proposed approach efficiently detects small or moderate process shifts. The goal of this paper is to investigate the one-sided RRRZ control charts with the 4-out-of-5 Runs Rules by using a Markov chain methodology. Several tables are generated and commented to show the statistical performance of the investigated charts. Also, comparisons with other competitive schemes are provided to show the statistical performance of the proposed charts. Finally, two examples illustrate the use of proposed charts on a quality control problem simulated from the food industry and a real industrial case from a plant treating batteries for recyclement.
RAPET (Reaction under Autogenic Pressure at Elevated Temperatures) Technique Assisted Synthesis of Encapsulated CdE@C [E= S, Se and Te] Nanocrystallites
Authors: George P. P. , Genish I. , Maklouf Shirly ben-david , Koltypin Y. , Gedanken A.
Published: September 2016

We present an easy synthetic method for the fabrication of encapsulated nanosized semiconductor CdE [E [Formula: see text] S, Se and Te] within the core of carbon capsule. We also discuss the growth of CdSC and neat CdS nanocrystals on stainless steel coupons (SSC) by a reaction under autogenic pressure at elevated temperature (RAPET) technique. The thermal decomposition of mixture of Cd(acetate)2 and sulfur, selenium and tellurium was carried out at 750[Formula: see text]C under air for 3[Formula: see text]h. The synthesized products were systematically characterized by X-ray powder diffraction, scanning electron microscopy (SEM) and transmission electron microscopy. Carbon matrix, with an average diameter of 250[Formula: see text]nm, encapsulated several nanometric-sized CdS nanocrystals, as evidenced from high resolution SEM (HRSEM). We examined the optical properties of this core/shell CdS@C and nonencapsulated CdS nanocrystals and found that both core shell and neat CdS nanocrystals show emission in the pohotoluminescence (PL) spectrum.
Identifying cancer type specific oncogenes and tumor suppressors using limited size data
Authors: Pavel Ana B. , Vasile Cristian I.
Published: August 2016

Cancer is a complex and heterogeneous genetic disease. Different mutations and dysregulated molecular mechanisms alter the pathways that lead to cell proliferation. In this paper, we explore a method which classifies genes into oncogenes (ONGs) and tumor suppressors. We optimize this method to identify specific (ONGs) and tumor suppressors for breast cancer, lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC) and colon adenocarcinoma (COAD), using data from the cancer genome atlas (TCGA). A set of genes were previously classified as ONGs and tumor suppressors across multiple cancer types (Science 2013). Each gene was assigned an ONG score and a tumor suppressor score based on the frequency of its driver mutations across all variants from the catalogue of somatic mutations in cancer (COSMIC). We evaluate and optimize this approach within different cancer types from TCGA. We are able to determine known driver genes for each of the four cancer types. After establishing the baseline parameters for each cancer type, we identify new driver genes for each cancer type, and the molecular pathways that are highly affected by them. Our methodology is general and can be applied to different cancer subtypes to identify specific driver genes and improve personalized therapy.
Humans, Econs and Portfolio Choice
Authors: Best Michael J. , Grauer Robert R.
Published: September 2016

We compare the portfolio choices of Humans — prospect theory investors — to the portfolio choices of Econs — power utility and mean-variance (MV) investors. In a numerical example, prospect theory portfolios are decidedly unreasonable. In an in-sample asset allocation setting, the prospect theory results are consistent with myopic loss aversion. However, the portfolios are extremely unstable. The power utility and MV results are consistent with traditional finance theory, where the portfolios are stable across decision horizons. In an out-of-sample asset allocation setting, the power utility and portfolios outperform the prospect theory portfolios. Nonetheless the prospect theory portfolios with loss aversion coefficients of 2.25 and 2 perform well.
Gamma beam industrial applications at ELI-NP
Authors: Suliman Gabriel , Iancu Violeta , Ur Calin A. , Iovea Mihai , Daito Izuru , Ohgaki Hideaki
Published: August 2016

The Nuclear Physics oriented pillar of the pan-European Extreme Light Infrastructure (ELI-NP) will host an ultra-bright, energy tunable, and quasi-monochromatic gamma-ray beam system in the range of 0.2–19.5 MeV produced by laser Compton backscattering. This gamma beam satisfies the criteria for large-size product investigations with added capabilities like isotope detection through the use of nuclear resonance fluorescence (NRF) and is ideal for non-destructive testing applications. Two major applications of gamma beams are being envisaged at ELI-NP: industrial applications based on NRF and industrial radiography and tomography. Both applications exploit the unique characteristics of the gamma beam to deliver new opportunities for the industry. Here, we present the experimental setups proposed at ELI-NP and discuss their performance based on analytical calculations and GEANT4 numerical simulations. One of the main advantages of using the gamma beam at ELI-NP for applications based on NRF is the availability of an advanced detector array, which can enhance the advantages already provided by the high quality of the gamma beam.
Sedimentology and stratigraphic architecture of a Miocene retrogradational, tide-dominated delta system: Balingian Province, offshore Sarawak, Malaysia
Authors: Amir Hassan Meor H. , Johnson Howard D. , Allison Peter A. , Abdullah Wan H.
Published: August 2016

The Balingian Province of NW Borneo is a major hydrocarbon-bearing region with production dominantly from Early Miocene (cycle II) coastal to lower coastal plain deposits. A regional sedimentological synthesis is outlined from the main productive interval of three offshore oilfields, which are representative of the depositional environments and stratigraphic architecture in cycle II. Four types of vertical facies successions are recognized: (1) fluvio-tidal channel; (2) tide-dominated delta front; (3) wave-dominated shoreface; and (4) barrier lagoon. The facies successions demonstrate that cycle II consists of a tide-dominated delta system that is partly analogous to the modern Rajang Delta and Lupar Embayment of southern Sarawak. Fluvio-tidal channel and tide-dominated delta successions represent periods of river-fed progradation. Wave-dominated shoreface and barrier lagoon facies successions represent depositional systems that developed during periods of transgression and/or delta lobe abandonment. Cycle II consists of several high-order sequences stacked together into two lower-order,
c.
100–300 m thick fining-upwards, unconformity-bounded megasequences. This stratigraphic architecture reflects a combination of hinterland denudation and long-term eustatic sea-level rise. These trends were interrupted by frequent, higher-order relative sea-level falls, which were a result of movement along the West Balingian Line fault zone. Variations in the thickness of megasequences between the three oilfields reflect fluctuations in tectonically driven subsidence rates. This exerted a fundamental control on the reservoir architecture, zonation and correlation and provides a basis for comparing field behaviour.