bluuebunny/crossref_metadata_2025 huggingface dataset:
Forms of n‐3 (ALA, C18:3n‐3 or DHA, C22:6n‐3) Fatty Acids Affect Carcass Yield, Blood Lipids, Muscle n‐3 Fatty Acids and Liver Gene Expression in Lambs
Authors: Ponnampalam Eric N. , Lewandowski Paul A. , Fahri Fahri T. , Burnett Viv F. , Dunshea Frank R. , Plozza Tim , Jacobs Joe L.
Published: September 2015

The effects of supplementing diets with n‐3 alpha‐linolenic acid (ALA) and docosahexaenoic acid (DHA) on plasma metabolites, carcass yield, muscle n‐3 fatty acids and liver messenger RNA (mRNA) in lambs were investigated. Lambs (n = 120) were stratified to 12 groups based on body weight (35 ± 3.1 kg), and within groups randomly allocated to four dietary treatments: basal diet (BAS), BAS with 10.7 % flaxseed supplement (Flax), BAS with 1.8 % algae supplement (DHA), BAS with Flax and DHA (FlaxDHA). Lambs were fed for 56 days. Blood samples were collected on day 0 and day 56, and plasma analysed for insulin and lipids. Lambs were slaughtered, and carcass traits measured. At 30 min and 24 h, liver and muscle samples, respectively, were collected for determination of mRNA (FADS1, FADS2, CPT1A, ACOX1) and fatty acid composition. Lambs fed Flax had higher plasma triacylglycerol, body weight, body fat and carcass yield compared with the BAS group (P < 0.001). DHA supplementation increased carcass yield and muscle DHA while lowering plasma insulin compared with the BAS diet (P < 0.01). Flax treatment increased (P < 0.001) muscle ALA concentration, while DHA treatment increased (P < 0.001) muscle DHA concentration. Liver mRNA FADS2 was higher and CPT1A lower in the DHA group (P < 0.05). The FlaxDHA diet had additive effects, including higher FADS1 and ACOX1 mRNA than for the Flax or DHA diet. In summary, supplementation with ALA or DHA modulated plasma metabolites, muscle DHA, body fat and liver gene expression differently.
Socio‐structural and behavioral risk factors associated with trafficked history of female bar/spa entertainers in the sex trade in the Philippines
Authors: Urada Lianne A. , Halterman Sonja , Raj Anita , Tsuyuki Kiyomi , Pimentel‐Simbulan Nymia , Silverman Jay G.
Published: September 2015

Objective

To explore factors associated with trafficking (deceptive/coercive entry to sex trade) among female bar/spa entertainers who traded sex in the Philippines.

Method

Female bar/spa entertainers who traded sex in the past 6 months were recruited from 25 bar/spa venues in Metro Manila (April 2009–January 2010) and assessed via cross‐sectional survey data collection for HIV‐risk‐related socio‐structural factors associated with deceptive/coercive entry into the sex trade. The study employed hierarchical linear modeling.

Results

Of 166 bar/spa entertainers assessed, 19 (11.4%) reported being deceived/coerced (i.e. trafficked) into their first jobs. Trafficking history was independently associated with current drug use (adjusted odds ratio [AOR] 2.05; 95% confidence interval [CI] 1.00–3.97) decreased availability of condoms at venues for entertainers (AOR 0.18; 95% CI 0.05–0.71) and, conversely, increased peer support for practicing safer sex behaviors (AOR 3.08; 95% CI 1.63–5.09). Those deceived/coerced into their positions were more likely than non‐trafficked women to have been recruited by an agency who came to their rural province (AOR 12.07; 95% CI 1.77–82.25) as opposed to getting the job from advertisement (AOR 0.10; 95% CI 0.02–0.65) or a friend/acquaintance (AOR 0.02; 95% CI 0.00–0.48).

Conclusion

The findings have implications for designing interventions to prevent and target trafficked women in the Philippines who may be more vulnerable to substance use and, potentially, HIV infection.
Experimental Evidence for the Existence of an External World
Authors: SCHWITZGEBEL ERIC , MOORE ALAN T.
Published: September 2015

In this essay I attempt to refute radical solipsism by means of a series of empirical experiments. In the first experiment, I exhibit unreliable judgment about the primeness or divisibility of four-digit numbers, in contrast to a seeming Excel program. In the second experiment, I exhibit an imperfect memory for seemingly arbitrary three-digit number and letter combinations, in contrast to my seeming collaborator with seemingly hidden notes. In the third experiment, I seem to suffer repeated defeats at chess. In all three experiments, the most straightforward interpretation of the experiential evidence is that something exists in the universe that is superior in the relevant respects—theoretical reasoning (about primes), memorial retention (for digits and letters), or practical reasoning (at chess)—to my own solipsistically conceived self.
How A-theoretic Deprivationists Should Respond to Lucretius
Authors: DENG NATALJA
Published: September 2015

What, if anything, makes death bad for the deceased themselves? Deprivationists hold that death is bad for the deceased iff it deprives them of intrinsic goods they would have enjoyed had they lived longer. This view faces the problem that birth too seems to deprive one of goods one would have enjoyed had one been born earlier, so that it too should be bad for one. There are two main approaches to the problem. In this paper, I explore the second approach, by Anthony Brueckner and John Martin Fischer, and suggest that it can be developed so as to meet deprivationists’ needs. On the resulting view, metaphysical differences between the future and the past give rise to a corresponding axiological difference in the intrinsic value of future and past experiences. As experiences move into the past, they lose their intrinsic value for the person.
Fugitive Pleasure and the Meaningful Life: Nietzsche on Nihilism and Higher Values
Authors: KATSAFANAS PAUL
Published: September 2015

Nietzsche's discussions of nihilism are meant to bring into view an intriguing pathology of modern culture: that it is unable to sustain ‘higher values’. This paper attempts to make sense of the nature and import of higher values. Higher values are a subset of final values and are distinct from foundational values. Higher values are characterized by six features: demandingness, susceptibility toward creating tragic conflicts, recruitment of a characteristic set of powerful emotions, perceived import, exclusionary nature, and their tendency to instantiate a community. The paper considers Nietzsche's arguments for the claim that we are committed to instituting some set of higher values. The cost of not doing so is vitiating our deepest aim and precluding a central form of happiness.
Estimating Post-Emergency Fertility Among Disaster-Affected Adolescents: Findings From a Case-Control Study in Aceh Province, Indonesia
Authors: Kinoshita Mari , Suhardan Suhardan , Danila Danila Damsyik , Chiang Chifa , Aoyama Atsuko
Published: September 2015

Objective

We aimed to retrospectively estimate adolescent fertility rates before and after a large-scale natural disaster.

Methods

A case-control study was conducted in Aceh Province, Indonesia, 2 years after the Indian Ocean tsunami in 2004. The age-specific fertility rates of 15–19-year-old-women (ASFR 15–19) was estimated each year from 2004 to 2006 by creating hypothetical age cohorts. The results were compared with data from the closest edition of the Indonesian Demographic Health Survey (IDHS).

Results

The pre-disaster ASFR 15–19 (4.4% in 2004) was not significantly different from the 2002–2003 IDHS data (P=0.49), whereas the post-disaster ASFR 15–19 (1.1% in 2005–2006) was significantly lower than the provincial estimation in the 2007 IDHS (P<0.01). ASFR 15–19 was reduced by 76% in the post-disaster period compared with the pre-disaster period (rate ratio: 0.24, P=0.02).

Conclusions

The creation of hypothetical age cohorts enabled valid and useful estimation of the ASFR in disaster-affected areas where reliable vital statistics are not available. For pre-disaster fertility estimation, however, we suggest excluding data from the 40-week period preceding the disaster, because the data may be biased by excess mortality in childbearing mothers and newborn babies in the disaster. (Disaster Med Public Health Preparedness. 2016;10:80–86)
The epigraphy of Sidi Khrebish, Benghazi (Berenice): an update
Authors: Reynolds Joyce , Kenrick Philip
Published: September 2015

The excavations at Sidi Khrebish, Benghazi, within the Hellenistic and Roman city of Berenice, yielded a considerable variety of inscriptions on portable objects in addition to monumental epigraphy. An account of the latter was published in the first volume of the final reports in 1977, together with a very short and preliminary list of the former. Following the detailed studies of various classes of material, it seemed opportune to bring together an updated account of the inscriptions on ‘minor objects’, which range from missiles to transport amphorae, table wares, kitchen wares, and lamps.
Contribution of dietary advanced glycation end products (AGE) to circulating AGE: role of dietary fat
Authors: Davis Kathleen E. , Prasad Chandan , Vijayagopal Parakat , Juma Shanil , Adams-Huet Beverley , Imrhan Victorine
Published: September 2015

The purpose of this pilot study was to determine whether macronutrient content (low-fat v. high-fat diet) influences an indicator of advanced glycation end products (AGE), Nε carboxymethyl-lysine (CML), in the context of a 1-d, high-AGE diet. The effect of the diets on inflammatory markers was also assessed. A total of nineteen overweight and obese adults (nine men and ten women) without known disease were recruited to participate in a crossover challenge of a high-fat, high-AGE (HFHA) and low-fat, high-AGE (LFHA) diet. In each phase patients had fasting blood drawn, followed by consumption of a high-fat or low-fat breakfast test meal, then three postprandial blood draws at 1, 2 and 3 h after consuming the test meal. After consuming high-AGE meals for the remainder of the day, participants returned the next day for a follow-up analysis. A different pattern in the 3-h post-meal CML and soluble receptor for AGE response to the two diets was observed (P=0·01 and 0·05, respectively). No change in serum CML was observed following consumption of a LFHA breakfast (535 (25th–75th percentile 451–790) to 495 (25th–75th percentile 391–682) ng/ml; P=0·36), whereas a rise in CML occurred after the HFHA breakfast (463 (25th–75th percentile 428–664) to 578 (25th–75th percentile 474–865) ng/ml; P=0·05). High sensitivity C-reactive protein and high molecular weight adiponectin were not affected by either diet. These findings suggest that dietary CML may not be as important in influencing serum CML as other dietary factors. In addition, acute exposure to dietary CML may not influence inflammation in adults without diabetes or kidney disease. This is contrary to previous findings.
Political Competition and Ethnic Riots in Democratic Transition: A Lesson from Indonesia
Authors: Toha Risa J.
Published: September 2015

Conventional wisdom recognizes the prevalence of intergroup clashes during political transition. Most explanations of ethnic riots, however, are based on clashes in mature democracies, and are therefore silent on the dynamics at work during democratic transition. Using district-level data in Indonesia from 1990 through 2005, this article argues that riots tend to occur in ethnically divided districts with low electoral competition because uncompetitiveness in the first democratic elections signals continued regime entrenchment and local political exclusion. As such, riots often follow uncompetitive elections, and dissipate after elections become more competitive and opposition candidates secure electoral victory.
Ten years’ experience with Felix tympanoplasty: analysis of anatomical and functional results
Authors: Castelli M L , Vitiello R , Ponzo S , Evangelista A
Published: September 2015

Objective:

This paper presents our 10 years’ experience with Felix tympanoplasty. This surgical procedure is designed to repair large perforations of unhealthy tympanic membranes, providing good graft stability without blunting of the anterior tympanomeatal angle.

Methods:

From January 2001 to December 2011, 64 Felix tympanoplasties were performed, conducted as the only surgical procedure. This paper describes the surgical technique and analyses the functional results.

Results:

Graft take was achieved in 61 ears (95.31 per cent). There was air–bone gap improvement in 84.6 per cent of cases.

Conclusion:

Felix tympanoplasty was effective in repairing unhealthy tympanic membranes with large perforations; the avoidance of blunting at the anterior tympanomeatal angle achieved good functional results.
Diagnostic value of the wideband acoustic absorbance test in middle-ear effusion
Authors: Terzi S , Özgür A , Erdivanli Ö Ç , Coşkun Z Ö , Ogurlu M , Demirci M , Dursun E
Published: September 2015

Objectives:

This study aimed to investigate the diagnostic value of wideband acoustic absorbance testing in otitis media with effusion.

Methods:

This prospective study compared middle-ear wideband acoustic absorbance rates in three paediatric patient groups: a healthy group of 34 volunteers; 48 patients diagnosed with otitis media with effusion; and 28 patients with chronic effusion but no sign of effusion during myringotomy. The diagnostic value of absorbance testing was analysed with the receiver operating characteristic test.

Results:

The wideband acoustic absorbance rate was significantly lower in the otitis media with effusion group than in both the otitis media and healthy groups at the 0.375–2 kHz averaged mean absorbance (p < 0.017 and p < 0.001, respectively). Receiver operating characteristic analysis showed the highest diagnostic value for the 0.375–2 kHz averaged mean (area under the curve 0.984), followed by those at 1 and 1.5 kHz (area under the curve: 0.973 and 0.967, respectively).

Conclusion:

The wideband acoustic absorbance test is more accurate for detecting middle-ear effusion compared with conventional 226-Hz tympanometry. Its practicality and objectivity suggest that the wideband acoustic absorbance test may be a better alternative for diagnosing otitis media with effusion.
Prevalence of allergic rhinitis among elementary and middle school students in Changsha city and its impact on quality of life
Authors: Song Y , Wang M , Xie J , Li W , Zhang X , Wang T , Tan G
Published: September 2015

Objectives:

To investigate the prevalence of allergic rhinitis among elementary and middle school students and examine its impact on their quality of life.

Methods:

Stratified sampling and cluster sampling surveys were performed among 10–17-year-old students in Changsha city from June 2011 to April 2012.

Results:

In the stratified sampling survey, the self-reported allergic rhinitis rate was 42.5 per cent. Further examination demonstrated that the average prevalence of allergic rhinitis was 19.4 per cent. The cluster sampling survey demonstrated that 214 of 814 students appeared to be atopic (26.3 per cent). The prevalence of allergic rhinitis and asthma was 17.2 and 2.1 per cent, respectively. In total, 71 atopic individuals (8.7 per cent) were without any symptoms of allergic disease. Further analysis showed that allergic rhinitis influenced the students' sleep, emotions and memory (p < 0.001).

Conclusion:

The prevalence of allergic rhinitis was 15.8 –19.4 per cent, showing an increase with age. Allergic rhinitis affected students' sleep, emotions and memory.
DYNAMIC PANEL ANDERSON-HSIAO ESTIMATION WITH ROOTS NEAR UNITY
Authors: PHILLIPS PETER C. B.
Published: September 2015

Limit theory is developed for the dynamic panel IV estimator in the presence of an autoregressive root near unity. In the unit root case, Anderson–Hsiao lagged variable instruments satisfy orthogonality conditions but are well known to be irrelevant. For a fixed time series sample size (T) IV is inconsistent and approaches a shifted Cauchy-distributed random variate as the cross-section sample sizen→ ∞. But whenT→ ∞, either for fixednor asn→ ∞, IV is$\sqrt T$consistent and its limit distribution is a ratio of random variables that converges to twice a standard Cauchy asn→ ∞. In this case, the usual instruments are uncorrelated with the regressor but irrelevance does not prevent consistent estimation. The same Cauchy limit theory holds sequentially and jointly as (n,T) → ∞ with no restriction on the divergence rates ofnandT.When the common autoregressive root$\rho = 1 + c/\sqrt T$the panel comprises a collection of mildly integrated time series. In this case, the IV estimator is$\sqrt n$consistent for fixedTand$\sqrt {nT}$consistent with limit distributionN(0, 4) when (n,T) → ∞ sequentially or jointly. These results are robust for common roots of the formρ= 1+c/Tγfor allγ∈ (0, 1) and joint convergence holds. Limit normality holds but the variance changes whenγ= 1. Whenγ> 1 joint convergence fails and sequential limits differ with different rates of convergence. These findings reveal the fragility of conventional Gaussian IV asymptotics to persistence in dynamic panel regressions.
Education Sector as a Stakeholder of Destination Management Organizations: Cooperation of Local DMOs with Educational Institutions
Authors: Borzyszkowski Jacek , Marczak Mirosław
Published: September 2015

The main purpose of this article is to present the activities of local DMOs (destination management organizations) in the context of the development of the tourist education sector in Poland. The article provides the results of the authors’ research on the collaboration between DMOs and the representatives of the educational sector in Poland, especially in the area of the training of professionally prepared personnel for the operation of the market of tourist services.
Reforming Property Law in Kosovo: A Clash of Legal Orders
Authors: Roccia Marco
Published: September 2015

The legal framework regulating property in Kosovo has been defined as ‘A jumble of laws, regulations, administrative instructions, court practices and directives combine to create a complicated and seemingly impenetrable system for determining contests over immovable property ownership in Kosovo. At the highest level, international human rights standards affect property rights…’1 As in other areas of legislation, laws addressing property issues derive from different periods in Kosovo’s history, that is to say the Yugoslav time, the so-called discriminatory period of the 1990s, UNMIK’s rule of the first decade of the 2000s and, finally, independent Kosovo. Laws are scattered through several legal texts, regulate different aspects of property rights, and often refer to institutions that no longer exist. This paper focuses on the specific issues affecting property law in Kosovo, a sector where international organizations and bilateral cooperation are massively intervening. While assessing legal acts in force and data collected on the field, the author argues how, for an effective reformation of the sector, a clear and coordinated strategy will have to be adopted by the two main donors which, in the next few years, will be launching several technical assistance contracts. Comparing European best practices with the proposed intervention suggested by the European Union and USAID will also give the chance to illustrate how a strict adherence to ECHR standards in the field of property, as the Constitution of Kosovo requires, will bring to light problems already seen in other European countries, that is to say a clash between domestic civil legislation on property, on the one hand, and the case-law of the European Court of Human Rights on Article 1 Protocol 1, on the other. The author will also notice that the tendency to adopt a too political approach, typical of international organizations and donors, in an area characterized by legal principles of a more technical nature, will be cause for additional confusion.
Executive Dysfunction 25 Years after Treatment with Cranial Radiotherapy for Pediatric Lymphoid Malignancies
Authors: Schuitema Ilse , de Sonneville Leo , Kaspers Gertjan , van der Pal Helena , Uyttebroeck Anne , van den Bos Cor , Veerman Anjo
Published: September 2015

The first cohorts to survive childhood lymphoid malignancies treated with cranial irradiation are now aging into adulthood, and concerns are growing about the development of radiotherapy-induced cognitive deficits in the aging brain. These deficits are hypothesized to increase over time. Their impact on daily functioning of older survivors, and the accompanying need for interventions, should be anticipated. By describing a detailed profile of executive function deficits and their associations with age, specific targets for neuropsychological intervention can be identified. Fifty survivors of childhood lymphoid malignancies and 58 related controls were assessed with the Amsterdam Neuropsychological Tasks program. The survivors were on average 31.1 (4.9) years old, treated with 22.5 (6.8) Gy cranial irradiation, and examined on average 25.5 (3.1) years after diagnosis. The survivors showed significantly decreased response speed, irrespective of the task at hand. Furthermore, we found deficits in working memory capacity, inhibition, cognitive flexibility, executive visuomotor control, attentional fluctuations, and sustained attention. Older age was associated with poorer performance on executive visuomotor control and inhibition. On executive visuomotor control, 50% of female survivors performed more than 1.5 SD below average, versus 15.4% of male survivors. The combination of visuospatial working memory problems and decreasing executive visuomotor control could result in difficulty with learning new motor skills at older ages, like walking with a cane. Deterioration of executive control and inhibition may result in decreased behavioral and emotional regulation in aging survivors. Especially the deficiency in executive visuomotor control in female survivors should be considered for (prophylactic) intervention. (JINS, 2015, 21, 657–669)
Affordability of public pension benefit: a historical and empirical analysis of US state and local government pension contributions
Authors: PENG JUN , WANG QIUSHI
Published: September 2015

As a result of the two severe stock market declines since 2000, there has been a steady debate about the affordability of state and local public pension benefits. We measured the affordability of pension benefits in terms of governments’ ability to make the required contributions based on existing tax and revenue bases. We conducted a historical analysis of government pension contributions at national and state level over a 20-year period 1992–2011 and found that the real pension burdens have increased over this period. We also found substantial variation in pension burdens among the 50 states. The results of our empirical analysis showed that employee contribution share, investment return, size of the public workforce, and pension benefit level had significant effects on pension burdens. Based on these findings, we proposed several strategies for reducing pension burdens, including increasing employee pension contribution, reducing size of workforce, and improving pension investment performance.
Lethal giant larvae‐1 deficiency enhances the CD8+ effector T‐cell response to antigen challenge in vivo
Authors: Ramsbottom Kelly M , Sacirbegovic Faruk , Hawkins Edwin D , Kallies Axel , Belz Gabrielle T , Van Ham Vanessa , Haynes Nicole M , Durrant Michael J , Humbert Patrick O , Russell Sarah M , Oliaro Jane
Published: September 2015

Lethal giant larvae‐1 (Lgl‐1) is an evolutionary conserved protein that regulates cell polarity in diverse lineages; however, the role of Lgl‐1 in the polarity and function of immune cells remains to be elucidated. To assess the role of Lgl‐1 in T cells, we generated chimeric mice with a hematopoietic system deficient for Lgl‐1. Lgl‐1 deficiency did not impair the activation or function of peripheral CD8+ T cells in response to antigen presentation in vitro, but did skew effector and memory T‐cell differentiation. When challenged with antigen‐expressing virus or tumor, Lgl‐1‐deficient mice displayed altered T‐cell responses. This manifested in a stronger antiviral and antitumor effector CD8+ T‐cell response, the latter resulting in enhanced control of MC38‐OVA tumors. These results reveal a novel role for Lgl‐1 in the regulation of virus‐specific T‐cell responses and antitumor immunity.
Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers
Authors: Spencer Sarah J , Tamminen Manu V , Preheim Sarah P , Guo Mira T , Briggs Adrian W , Brito Ilana L , A Weitz David , Pitkänen Leena K , Vigneault Francois , Virta Marko P Juhani , Alm Eric J
Published: September 2015

Many microbial communities are characterized by high genetic diversity. 16S ribosomal RNA sequencing can determine community members, and metagenomics can determine the functional diversity, but resolving the functional role of individual cells in high throughput remains an unsolved challenge. Here, we describe epicPCR (Emulsion, Paired Isolation and Concatenation PCR), a new technique that links functional genes and phylogenetic markers in uncultured single cells, providing a throughput of hundreds of thousands of cells with costs comparable to one genomic library preparation. We demonstrate the utility of our technique in a natural environment by profiling a sulfate-reducing community in a freshwater lake, revealing both known sulfate reducers and discovering new putative sulfate reducers. Our method is adaptable to any conserved genetic trait and translates genetic associations from diverse microbial samples into a sequencing library that answers targeted ecological questions. Potential applications include identifying functional community members, tracing horizontal gene transfer networks and mapping ecological interactions between microbial cells.
Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants
Authors: Berni Canani Roberto , Sangwan Naseer , Stefka Andrew T , Nocerino Rita , Paparo Lorella , Aitoro Rosita , Calignano Antonio , Khan Aly A , Gilbert Jack A , Nagler Cathryn R
Published: September 2015

Dietary intervention with extensively hydrolyzed casein formula supplemented with Lactobacillus rhamnosus GG (EHCF+LGG) accelerates tolerance acquisition in infants with cow’s milk allergy (CMA). We examined whether this effect is attributable, at least in part, to an influence on the gut microbiota. Fecal samples from healthy controls (n=20) and from CMA infants (n=19) before and after treatment with EHCF with (n=12) and without (n=7) supplementation with LGG were compared by 16S rRNA-based operational taxonomic unit clustering and oligotyping. Differential feature selection and generalized linear model fitting revealed that the CMA infants have a diverse gut microbial community structure dominated by Lachnospiraceae (20.5±9.7%) and Ruminococcaceae (16.2±9.1%). Blautia, Roseburia and Coprococcus were significantly enriched following treatment with EHCF and LGG, but only one genus, Oscillospira, was significantly different between infants that became tolerant and those that remained allergic. However, most tolerant infants showed a significant increase in fecal butyrate levels, and those taxa that were significantly enriched in these samples, Blautia and Roseburia, exhibited specific strain-level demarcations between tolerant and allergic infants. Our data suggest that EHCF+LGG promotes tolerance in infants with CMA, in part, by influencing the strain-level bacterial community structure of the infant gut.
Growth rates and rRNA content of four marine bacteria in pure cultures and in the Delaware estuary
Authors: Lankiewicz Thomas S , Cottrell Matthew T , Kirchman David L
Published: September 2015

Interpretation of 16S ribosomal RNA (rRNA) to 16S rRNA gene ratios (rRNA:rDNA) is based on a limited number of studies with rapidly growing copiotrophic bacteria. The most abundant bacteria in the ocean are oligotrophs, which probably grow more slowly than those bacteria whose rRNA:rDNA versus growth rate relationships are known. To examine whether rRNA:rDNA varies differently in oligotrophic marine bacteria than in copiotrophic bacteria, we used quantitative PCR and reverse transcriptase quantitative PCR to measure rRNA:rDNA in two marine copiotrophs and in two marine oligotrophs, including Candidatus Pelagibacter ubique HTCC1062, a coastal isolate of SAR11, the most abundant bacterial clade in the ocean. The rRNA:rDNA ratios for the two copiotrophs were similar to those expected on the basis of an analysis of previously studied copiotrophic bacteria, while the ratios for the two oligotrophs were substantially lower than predicted even given their slow growth rates. The rRNA:rDNA ratios determined along a transect in the Delaware estuary suggested that SAR11 bacteria grow at rates close to the growth rate in culture, while rates of the two copiotrophs were far below those observed in laboratory cultures. Our results have implications for interpreting rRNA:rDNA from natural communities, understanding growth strategies and comparing regulatory mechanisms in copiotrophs and oligotrophs.
Metagenomic reconstructions of bacterial CRISPR loci constrain population histories
Authors: Sun Christine L , Thomas Brian C , Barrangou Rodolphe , Banfield Jillian F
Published: September 2015

Bacterial CRISPR-Cas systems provide insight into recent population history because they rapidly incorporate, in a unidirectional manner, short fragments (spacers) from coexisting infective virus populations into host chromosomes. Immunity is achieved by sequence identity between transcripts of spacers and their targets. Here, we used metagenomics to study the stability and dynamics of the type I-E CRISPR-Cas locus of Leptospirillum group II bacteria in biofilms sampled over 5 years from an acid mine drainage (AMD) system. Despite recovery of 452 686 spacers from CRISPR amplicons and metagenomic data, rarefaction curves of spacers show no saturation. The vast repertoire of spacers is attributed to phage/plasmid population diversity and retention of old spacers, despite rapid evolution of the targeted phage/plasmid genome regions (proto-spacers). The oldest spacers (spacers found at the trailer end) are conserved for at least 5 years, and 12% of these retain perfect or near-perfect matches to proto-spacer targets. The majority of proto-spacer regions contain an AAG proto-spacer adjacent motif (PAM). Spacers throughout the locus target the same phage population (AMDV1), but there are blocks of consecutive spacers without AMDV1 target sequences. Results suggest long-term coexistence of Leptospirillum with AMDV1 and periods when AMDV1 was less dominant. Metagenomics can be applied to millions of cells in a single sample to provide an extremely large spacer inventory, allow identification of phage/plasmids and enable analysis of previous phage/plasmid exposure. Thus, this approach can provide insights into prior bacterial environment and genetic interplay between hosts and their viruses.
Erratum: Riverbed methanotrophy sustained by high carbon conversion efficiency
Authors: Trimmer Mark , Shelley Felicity C , Purdy Kevin J , Maanoja Susanna T , Chronopoulou Panagiota-Myrsini , Grey Jonathan
Published: September 2015

Correction to: The ISME Journal (2015) 9, 2304–2314; doi:10.1038/ismej.2015.98 Since the publication of this paper, the author has discovered the incorrect spelling of an author’s name. ‘Grey Jonathan’ should be ‘Jonathan Grey’. The publisher would like to apologize for any inconvenience this may have caused.
Erratum: Making pathogens sociable: the emergence of high relatedness through limited host invasibility
Authors: van Leeuwen Edwin , O’Neill Sarah , Matthews Andrew , Raymond Ben
Published: September 2015

Correction to: The ISME Journal 2015; doi: 10.1038/ismej.2015.111 After the publication of this paper, the authors noticed an error in the title. The correct title is ‘Making pathogens sociable: the emergence of high relatedness through limited host invasibility’. The publisher would like to apologise for any inconvenience this may have caused.
Sub-microWatt threshold nanoisland lasers
Authors: Jang Hoon , Karnadi Indra , Pramudita Putu , Song Jung-Hwan , Soo Kim Ki , Lee Yong-Hee
Published: September 2015

Ultralow threshold nanolasers have been sought after as power efficient light sources in photonic integrated circuits. Here a single-cell nanobeam laser with a nanoisland quantum well is proposed and demonstrated. Continuous operation at 1.5 μm is achieved at room temperature with an ultralow lasing threshold of 210 nW in absorbed power. The size of the active medium is reduced to 0.7 × 0.25 × 0.02 μm3 by removing the absorptive quantum well region surrounding the central cavity. Relatively thick (420 nm) InP slabs are employed to improve the thermal and mechanical characteristics. The nanoisland-based structures will provide a new platform to engineer fundamental light–matter interactions by controlling the size and the location of the nanoemitters, allowing the realization of highly efficient nanophotonic devices.
Real-time fluorescence imaging with 20 nm axial resolution
Authors: Stabley Daniel R. , Oh Thomas , Simon Sanford M. , Mattheyses Alexa L. , Salaita Khalid
Published: September 2015

Measuring the nanoscale organization of protein structures near the plasma membrane of live cells is challenging, especially when the structure is dynamic. Here we present the development of a two-wavelength total internal reflection fluorescence method capable of real-time imaging of cellular structure height with nanometre resolution. The method employs a protein of interest tagged with two different fluorophores and imaged to obtain the ratio of emission in the two channels. We use this approach to visualize the nanoscale organization of microtubules and endocytosis of the epidermal growth factor receptor.
Lack of association of the iNOS gene polymorphism with risk of cancer: a systematic review and Meta-Analysis
Authors: Jiao Jinghua , Wu Jingyang , Huang Desheng , Liu Lei
Published: September 2015

In order to investigate the association between the iNOS gene polymorphisms and susceptibility to cancer, a search of English papers was done using Pubmed, the Cochrane Library, Embase, ISI Web of Science, Google (scholar) database and all Chinese reports were conducted using CBMDisc, Chongqing VIP database and CNKI database. A total of eight studies were included in this meta-analysis including 1,920 cases and 2,373 controls. The results indicated that the polymorphisms in iNOS gene (C150T(Ser608 Leu) polymorphism and polymorphic (CCTTT)n repeats) had no association with cancer risk for all genetic models. This meta-analysis suggested that the polymorphisms in the iNOS gene were not associated with cancer risk.
A comprehensive study on different modelling approaches to predict platelet deposition rates in a perfusion chamber
Authors: Pallarès Jordi , Senan Oriol , Guimerà Roger , Vernet Anton , Aguilar-Mogas Antoni , Vilahur Gemma , Badimon Lina , Sales-Pardo Marta , Cito Salvatore
Published: September 2015

Thrombus formation is a multiscale phenomenon triggered by platelet deposition over a protrombotic surface (eg. a ruptured atherosclerotic plaque). Despite the medical urgency for computational tools that aid in the early diagnosis of thrombotic events, the integration of computational models of thrombus formation at different scales requires a comprehensive understanding of the role and limitation of each modelling approach. We propose three different modelling approaches to predict platelet deposition. Specifically, we consider measurements of platelet deposition under blood flow conditions in a perfusion chamber for different time periods (3, 5, 10, 20 and 30 minutes) at shear rates of 212 s−1, 1390 s−1 and 1690 s−1. Our modelling approaches are: i) a model based on the mass-transfer boundary layer theory; ii) a machine-learning approach; and iii) a phenomenological model. The results indicate that the three approaches on average have median errors of 21%, 20.7% and 14.2%, respectively. Our study demonstrates the feasibility of using an empirical data set as a proxy for a real-patient scenario in which practitioners have accumulated data on a given number of patients and want to obtain a diagnosis for a new patient about whom they only have the current observation of a certain number of variables.
Investigation of the methylation of Numb by the SET8 protein lysine methyltransferase
Authors: Weirich Sara , Kusevic Denis , Kudithipudi Srikanth , Jeltsch Albert
Published: September 2015

It has been reported that the Numb protein is methylated at lysine 158 and 163 and that this methylation is introduced by the SET8 protein lysine methyltransferase [Dhami et al., (2013) Molecular Cell 50, 565–576]. We studied this methylation in vitro using peptide arrays and recombinant Numb protein as substrates. Numb peptides and protein were incubated with recombinant SET8 purified after expression in E. coli or human HEK293 cells. However, no methylation of Numb by SET8 was detectable. SET8 methylation of Histone H4 and p53 peptides and proteins, which were used as positive controls, was readily observed. While SET8 methylation of Numb in cells cannot be ruled out, based on our findings, more evidence is needed to support this claim. It appears likely that another not yet identified PKMT is responsible for the reported methylation of Numb in cells.
Statin-activated nuclear receptor PXR promotes SGK2 dephosphorylation by scaffolding PP2C to induce hepatic gluconeogenesis
Authors: Gotoh Saki , Negishi Masahiko
Published: September 2015

Statin therapy is known to increase blood glucose levels in humans. Statins utilize pregnane X receptor (PXR) and serum/glucocorticoid regulated kinase 2 (SGK2) to activate phosphoenolpyruvate carboxykinase 1 (PEPCK1) and glucose-6-phosphatase (G6Pase) genes, thereby increasing glucose production in human liver cells. Here, the novel statin/PXR/SGK2-mediated signaling pathway has now been characterized for hepatic gluconeogenesis. Statin-activated PXR scaffolds the protein phosphatase 2C (PP2C) and SGK2 to stimulate PP2C to dephosphorylate SGK2 at threonine 193. Non-phosphorylated SGK2 co-activates PXR-mediated trans-activation of promoters of gluconeogenic genes in human liver cells, thereby enhancing gluconeogenesis. This gluconeogenic statin-PXR-SGK2 signal is not present in mice, in which statin treatment suppresses hepatic gluconeogenesis. These findings provide the basis for statin-associated side effects such as an increased risk for Type 2 diabetes.
Fabrication of efficient planar perovskite solar cells using a one-step chemical vapor deposition method
Authors: Tavakoli Mohammad Mahdi , Gu Leilei , Gao Yuan , Reckmeier Claas , He Jin , Rogach Andrey L. , Yao Yan , Fan Zhiyong
Published: September 2015

Organometallic trihalide perovskites are promising materials for photovoltaic applications, which have demonstrated a rapid rise in photovoltaic performance in a short period of time. We report a facile one-step method to fabricate planar heterojunction perovskite solar cells by chemical vapor deposition (CVD), with a solar power conversion efficiency of up to 11.1%. We performed a systematic optimization of CVD parameters such as temperature and growth time to obtain high quality films of CH3NH3PbI3 and CH3NH3PbI3-xClx perovskite. Scanning electron microscopy and time resolved photoluminescence data showed that the perovskite films have a large grain size of more than 1 micrometer and carrier life-times of 10 ns and 120 ns for CH3NH3PbI3 and CH3NH3PbI3-xClx, respectively. This is the first demonstration of a highly efficient perovskite solar cell using one step CVD and there is likely room for significant improvement of device efficiency.
Role of Viscous Dissipative Processes on the Wetting of Textured Surfaces
Authors: Grewal H. S. , Nam Kim Hong , Cho Il-Joo , Yoon Eui-Sung
Published: September 2015

We investigate the role of viscous forces on the wetting of hydrophobic, semi-hydrophobic and hydrophilic textured surfaces as second-order effects. We show that during the initial contact, the transition from inertia- to viscous-dominant regime occurs regardless of their surface topography and chemistry. Furthermore, we demonstrate the effect of viscosity on the apparent contact angle under quasi-static conditions by modulating the ratio of a water/glycerol mixture and show the effect of viscosity, especially on the semi-hydrophobic and hydrophobic textured substrates. The reason why the viscous force does not affect the apparent contact angle of the hydrophilic surface is explained based on the relationship between the disjoining pressure and surface chemistry. We further propose a wetting model that can predict the apparent contact angle of a liquid drop on a textured substrate by incorporating a viscous force component in the force balance equation. This model can predict apparent contact angles on semi-hydrophobic and hydrophobic textured surfaces exhibiting Wenzel state more accurately than the Wenzel model, indicating the importance of viscous forces in determining the apparent contact angle. The modified model can be applied for estimating the wetting properties of arbitrary engineered surfaces.
Introduction of Methyl Groups at C2 and C6 Positions Enhances the Antiangiogenesis Activity of Curcumin
Authors: Koo Hyun-Jung , Shin Sarah , Choi Joon Young , Lee Kyung-Han , Kim Byung-Tae , Choe Yearn Seong
Published: September 2015

Curcumin has diverse biological activities, but is known to undergo rapid metabolism via reduction of vinylic double bonds and phase II conjugation. To prevent reductive metabolism of curcumin, we introduced a methyl group at both C2 and C6 positions (compound1) or at the C2 position (compound2) of curcumin, creating steric hindrance on double bonds against metabolizing enzymes. As predicted, these compounds were resistant to reduction by alcohol dehydrogenase. Compound1was further evaluated for its antiangiogenesis activityin vitroandin vivo. It exhibited significantly greater inhibitory activity than curcumin against endothelial cell migration, invasion and tube formation. Similarly, thein vivoMatrigel plug assay in C57BL/6 mice showed more pronounced reduction of blood vessels in the plugs containing1than those containing curcumin. Moreover,1suppressed tumor growth more effectively than curcumin in a U87MG mouse xenograft model by inhibiting angiogenesis.In vivometabolite analysis by liquid chromatography/mass spectrometry demonstrated that1underwent markedly slower reductive metabolism than curcumin. Taken together, our results indicate that1has enhanced antiangiogenesis activity and suppression of tumor growth compared with curcumin, reflecting diminished reductive metabolism owing to the introduction of methyl groups at the C2 and C6 positions of curcumin.
Edges of human embryonic stem cell colonies display distinct mechanical properties and differentiation potential
Authors: Rosowski Kathryn A. , Mertz Aaron F. , Norcross Samuel , Dufresne Eric R. , Horsley Valerie
Published: September 2015

In order to understand the mechanisms that guide cell fate decisions during early human development, we closely examined the differentiation process in adherent colonies of human embryonic stem cells (hESCs). Live imaging of the differentiation process reveals that cells on the outer edge of the undifferentiated colony begin to differentiate first and remain on the perimeter of the colony to eventually form a band of differentiation. Strikingly, this band is of constant width in all colonies, independent of their size. Cells at the edge of undifferentiated colonies show distinct actin organization, greater myosin activity and stronger traction forces compared to cells in the interior of the colony. Increasing the number of cells at the edge of colonies by plating small colonies can increase differentiation efficiency. Our results suggest that human developmental decisions are influenced by cellular environments and can be dictated by colony geometry of hESCs.
RBM45 homo-oligomerization mediates association with ALS-linked proteins and stress granules
Authors: Li Yang , Collins Mahlon , Geiser Rachel , Bakkar Nadine , Riascos David , Bowser Robert
Published: September 2015

The aggregation of RNA-binding proteins is a pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). RBM45 is an RNA-binding protein that forms cytoplasmic inclusions in neurons and glia in ALS and FTLD. To explore the role of RBM45 in ALS and FTLD, we examined the contribution of the protein’s domains to its function, subcellular localization and interaction with itself and ALS-linked proteins. We find that RBM45 forms homo-oligomers and physically associates with the ALS-linked proteins TDP-43 and FUS in the nucleus. Nuclear localization of RBM45 is mediated by a bipartite nuclear-localization sequence (NLS) located at the C-terminus. RBM45 mutants that lack a functional NLS accumulate in the cytoplasm and form TDP-43 positive stress granules. Moreover, we identify a novel structural element, termed the homo-oligomer assembly (HOA) domain, that is highly conserved across species and promote homo-oligomerization of RBM45. RBM45 mutants that fail to form homo-oligomers exhibit significantly reduced association with ALS-linked proteins and inclusion into stress granules. These results show that RMB45 may function as a homo-oligomer and that its oligomerization contributes to ALS/FTLD RNA-binding protein aggregation.
Fast Episodes of West-Mediterranean-Tyrrhenian Oceanic Opening and Revisited Relations with Tectonic Setting
Authors: Savelli Carlo
Published: September 2015

Extension and calc-alkaline volcanism of the submerged orogen of alpine age (OAA) initiated in Early Oligocene (~33/32 Ma) and reached the stage of oceanic opening in Early-Miocene (Burdigalian), Late-Miocene and Late-Pliocene. In the Burdigalian (~20–16 Ma) period of widespread volcanism of calcalkaline type on the margins of oceanic domain, seafloor spreading originated the deep basins of north Algeria (western part of OAA) and Sardinia/Provence (European margin). Conversely, when conjugate margins’ volcanism has been absent or scarce seafloor spreading formed the plains Vavilov (7.5–6.3 Ma) and Marsili (1.87–1.67 Ma) within OAA eastern part (Tyrrhenian Sea). The contrast between occurrence and lack of margin’s igneous activity probably implies the diversity of the geotectonic setting at the times of oceanization. It appears that the Burdigalian calcalkaline volcanism on the continental margins developed in the absence of subduction. The WNW-directed subduction of African plate probably commenced at ~16/15 Ma (waning Burdigalian seafloor spreading) after ~18/16 Ma of rifting. Space-time features indicate that calcalkaline volcanism is not linked only to subduction. From this view, temporal gap would exist between the steep subduction beneath the Apennines and the previous, flat-type plunge of European plate with opposite direction producing the OAA accretion and double vergence.
Absence of the Electric Aharonov-Bohm Effect due to Induced Charges
Authors: Wang Rui-Feng
Published: September 2015

This paper states that the induced charge should not be neglected in the electric Aharonov-Bohm (A-B) effect. If the induced charge is taken into account, the interference pattern of the moving charge will not change with the potential difference between the two metal tubes. It means that the scalar potential itself can not affect the phase of the moving charge and the true factor affecting the phase of the moving charge is the energy of the system including the moving charge and the induced charge.