bluuebunny/crossref_metadata_2025 huggingface dataset:
Evidence for the principle of minimal frustration in the evolution of protein folding landscapes
Authors: Tzul Franco O. , Vasilchuk Daniel , Makhatadze George I.
Published: February 2017

Significance

A detailed understanding of how different sequences that fold into the same structure affect the folding energy landscape presents one of the current challenges of the protein folding field. The principle of minimal frustration suggests that naturally evolved proteins with the same structure should have similar folding rates and that modulation of thermodynamic stability should occur via unfolding rates. We experimentally tested this hypothesis using 15 different thioredoxins, with sequences either obtained from the extant organisms or resurrected using ancestral sequence reconstruction. We show that all of these proteins fold with similar rates and that their dramatic differences in stability are because of the differences in the unfolding rates.
Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning
Authors: Klesmith Justin R. , Bacik John-Paul , Wrenbeck Emily E. , Michalczyk Ryszard , Whitehead Timothy A.
Published: February 2017

Significance

Enzymes find utility as therapeutics and for the production of specialty chemicals. Changing the amino acid sequence of an enzyme can increase solubility, but many such mutations disrupt catalytic activity. To evaluate this trade-off, we developed an experimental system to evaluate the relative solubility for nearly all possible single point mutants for two model enzymes. We find that the tendency for a given solubility-enhancing mutation to disrupt catalytic activity depends, among other factors, on how far the position is from the catalytic active site and whether that mutation has been sampled during evolution. We develop predictive models to identify mutations that enhance solubility without disrupting activity with an accuracy of 90%. These results have biotechnological applications.
Functional genomics analysis of vitamin D effects on CD4+ T cells in vivo in experimental autoimmune encephalomyelitis ‬
Authors: Zeitelhofer Manuel , Adzemovic Milena Z. , Gomez-Cabrero David , Bergman Petra , Hochmeister Sonja , N'diaye Marie , Paulson Atul , Ruhrmann Sabrina , Almgren Malin , Tegnér Jesper N. , Ekström Tomas J. , Guerreiro-Cacais André Ortlieb , Jagodic Maja
Published: February 2017

Significance

Vitamin D has been suggested to be associated with beneficial immunomodulation in autoimmune diseases. We demonstrate that the protective effect of vitamin D in an animal model of multiple sclerosis (MS) is linked to multiple signaling and metabolic pathways critical for T-cell activation and differentiation into pathogenic T helper (Th) 1 and Th17 subsets in vivo. This effect is mediated by epigenetic mechanisms as reflected by genome-wide reduction of DNA methylation and upregulation of microRNAs, with concomitant downregulation of their protein-coding target genes. Our data support the role of vitamin D in modulating risk for human disease, because orthologues of nearly 50% of MS candidate risk genes changed their expression in vivo in CD4+ T cells upon vitamin D supplementation.
DYNC1H1 mutations associated with neurological diseases compromise processivity of dynein–dynactin–cargo adaptor complexes
Authors: Hoang Ha Thi , Schlager Max A. , Carter Andrew P. , Bullock Simon L.
Published: February 2017

Significance

Mutations in microtubule motors and their cofactors are associated with several neurological diseases in humans. How disease-associated mutations affect motor function, and consequently have neuropathological effects, is largely unknown. We take advantage of recent advances in the ability to activate transport of the human dynein complex in vitro to functionally characterize 17 disease-associated mutations in the gene encoding its heavy chain. The vast majority of mutations do not affect the ability of dynein to bind a cargo adaptor but do compromise long-range motion of the motor complex. Our findings suggest that defective motility of cargo–motor complexes contributes to dynein-associated neurological phenotypes and highlight several regions of the enigmatic motor that orchestrate its ability to walk over long distances.
Phosphorylation of αB-crystallin supports reactive astrogliosis in demyelination
Authors: Kuipers Hedwich F. , Yoon Jane , van Horssen Jack , Han May H. , Bollyky Paul L. , Palmer Theo D. , Steinman Lawrence
Published: February 2017

Significance

αB-crystallin (CRYAB) is a protein involved in the protection of cells from stress and cell death, and is very highly produced in brain lesions in multiple sclerosis (MS). Astrocytes are the main non-neuronal cell type in the central nervous system. Although they are involved in many processes in health and injury, their precise role in MS is poorly understood. Using a mouse model of MS, as well as brain tissue from MS patients, we found that CRYAB enables astrocytes to become activated and that these activated astrocytes play a pathogenic role in MS, worsening injury. Furthermore, we found that a specific stress-induced modification of CRYAB supports its role in astrocyte activation and affects the intracellular signaling pathways it regulates.
Critical Foraging Habitat of Atlantic Sturgeon Based on Feeding Habits, Prey Distribution, and Movement Patterns in the Saco River Estuary, Maine
Authors: Novak Ashleigh J. , Carlson Amy E. , Wheeler Carolyn R. , Wippelhauser Gail S. , Sulikowski James A.
Published: February 2017

An overall lack of information prompted the recent listing of Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus under the Endangered Species Act. Key to the restoration of the species and of particular importance is the need to characterize the use of critical habitat across the region, specifically in the Gulf of Maine, where the population was listed as threatened. Much of the research to date has focused on large river systems able to support remnant spawning populations; however, the role of small coastal river systems for Atlantic Sturgeon is not well documented. Several of these systems are being reinhabited, and to facilitate new knowledge about the Gulf of Maine population, a long‐term (2009–2014) acoustic telemetry study for 51 Atlantic Sturgeon tagged in the Saco River was evaluated. Results suggested that the majority of fish were aggregating near the natural mouth of the estuary across the 6 years. Gastric lavage samples from 163 (91 juvenile and 72 adult) fish (65.0–171.5 cm fork length) during 2013 and 2014 demonstrated that American Sand Lance Ammodytes americanus was the most common prey (the index of relative importance for 2013 and 2014 was 93.5% and 85.4%, respectively), a finding unique to this river system. In addition, benthic sediment grabs, beam trawls, otter trawls, and beach seines conducted in 2013 and 2014 indicated that the distribution of American Sand Lances was comparable to the aggregation area observed for Atlantic Sturgeon. The combined results suggest that the Saco River estuary provides critical foraging habitat imperative for the future recovery of the Gulf of Maine Atlantic Sturgeon population.

Received May 24, 2016; accepted November 17, 2016 Published online February 15, 2017
Physicochemical properties of giant embryo rice Seonong 17 and Keunnunjami
Authors: Chung Soo Im , Lee Sang Chul , Kang Mi Young
Published: February 2017

This study was carried out to determine the physicochemical properties of giant embryo rice “Seonong 17” and “Keunnunjami” in comparison with the normal embryo rice. Scanning electron microscopy revealed that Seonong 17 and Keunnunjami have larger embryo and that starch granules from Keunnunjami were more tightly packed with smaller air spaces between granules. Seonong 17 exhibited the lowest amylose content. Keunnunjami showed the highest protein content, pasting temperature, peak and breakdown viscosities, and gelatinization temperature and enthalpy. Both giant embryo rice samples contained significantly higher amounts of essential amino acids and unsaturated fatty acids than the normal rice. Proteomic analysis using two-dimensional gel electrophoresis revealed differences in the protein profile of Seonong 17 and Keunnunjami. The results could serve as baseline information in evaluating the quality of these two giant embryo rice cultivars and provide a better understanding of their potential uses and food industry applications.
Gating ring strengthens marriage of BK channel voltage sensing to pore opening
Authors: Sedwick Caitlin
Published: February 2017

A new JGP study shows that the gating ring helps the voltage-sensing domain open the BK channel’s pore.
Final report on the torque supplementary comparison COOMET.M.T-S1 measurand torque: 0 N·m, 100 N·m, 500 kN·m, 1500 N·m, 2500 N·m
Authors: Cherepanov Boris , Röske Dirk
Published: February 2017

This publication presents results of a supplementary comparison using national reference machines of the Russian Federation and Germany in field of torque.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Strong hypercontractivity and logarithmic Sobolev inequalities on stratified complex Lie groups
Authors: Eldredge Nathaniel , Gross Leonard , Saloff-Coste Laurent
Published: February 2017

We show that for a hypoelliptic Dirichlet form operator

A
A

on a stratified complex Lie group, if the logarithmic Sobolev inequality holds, then a holomorphic projection of

A
A

is strongly hypercontractive in the sense of Janson. This extends previous results of Gross to a setting in which the operator

A
A

is not holomorphic.
Balancing the Health Risks and Benefits of Seafood: How Does Available Guidance Affect Consumer Choices?
Authors: Uchida Hirotsugu , Roheim Cathy A. , Johnston Robert J.
Published: February 2017

Seafood species vary in their health benefits (e.g., from omega‐3 fatty acids) and risks (e.g., from methylmercury or polychlorobiphenyls). Reflecting these risks and benefits, multiple public and private organizations offer guidance to consumers on seafood consumption. The effect of this guidance is unknown; previous literature has been unable to disentangle the effects of messages with differing health information, provided by different sources, on demand for different types of seafood. The result is ambiguity regarding the drivers of observed changes in seafood demand. This study investigates the effect of health risk and benefit information on preferences for wild and farmed salmon and swordfish, three species targeted by consumer guidance. The analysis applies an experimental auction with seafood consumers informed by a Bayesian risk‐learning model. The model provides a systematic way to disentangle effects on seafood demand, for example, by evaluating whether changes in demand for different species are due to information content or source. Using this approach, we test the effect of guidance provided by four different public and private groups in the United States. Difference‐in‐difference tests find no impact of health benefit information regardless of source or message, but find multiple effects of health risk information that vary across different types of guidance. These findings suggest that current guidance does not improve consumers’ ability to balance health risks and benefits. We also identify potential avenues to improve the efficacy of this guidance.
Cumulative Exposure to Systolic Blood Pressure During Young Adulthood Through Midlife and the Urine Albumin-to-Creatinine Ratio at Midlife
Authors: Kramer Holly , Colangelo Laura , Lewis Cora E. , Jacobs David R. , Pletcher Mark , Bibbins-Domingo Kirstin , Chang Alex , Siscovick David , Shlipak Michael , Peralta Carmen A. , Bansal Nisha , Muntner Paul , Liu Kiang
Published: February 2017

BACKGROUND

Higher blood pressure during young adulthood may increase cardiovascular and kidney disease risk later in life. This study examined the association of cumulative systolic blood pressure (SBP) exposure during young adulthood through midlife with urine albumin-to-creatinine ratios (ACR) measured during midlife.

METHODS

We used data from the Coronary Artery Risk Development in Young Adults (CARDIA) study, a biracial cohort recruited in 4 urban areas during years 1985–1986. Cumulative SBP was calculated as the average SBP between 2 exams multiplied by years between exams over 20 year years. ACR was measured 20 years after baseline when participants were age 43–50 years (midlife). A generalized additive model was used to examine the association of log ACR as a function of cumulative SBP with adjustment for covariates including SBP measured concurrently with ACR.

RESULTS

Cumulative SBP ranged from a low of 1,671 to a high of 3,260 mm Hg. Participants in the highest cumulative SBP quartile were more likely to be male (61.4% vs. 20.7%; P < 0.001), Black (61.5% vs. 25.6%; P < 0.001) and have elevated ACR (18.7% vs. 4.8%; P < 0.001) vs. lowest quartile. Spline regression curves of ACR vs. cumulative SBP demonstrated an inflection point in ACR with cumulative SBP levels >2,350 mm Hg with linear increases in ACR above this threshold. Adjusted geometric mean ACR values were significantly higher with cumulative SBP ≥2,500 vs. <2500 (9.18 [1.06] vs. 6.92 [1.02]; P < 0.0001).

CONCLUSION

Higher SBP during young adulthood through midlife is associated with higher ACR during midlife.
Associations of Proatrial Natriuretic Peptide with Components of the Metabolic Syndrome in Adolescents and Young Adults from the General Population
Authors: Goharian Tina S. , Goetze Jens P. , Faber Jens , Andersen Lars B. , Grøntved Anders , Jeppesen Jørgen L.
Published: February 2017

BACKGROUND

In middle-aged and elderly populations, circulating natriuretic peptide concentrations are negatively associated with several components of the metabolic syndrome. Whether these negative associations are also present in healthy adolescents and young adults from the general population are unknown.

METHODS

In a cross-sectional setting, we measured plasma concentrations of mid-regional proatrial natriuretic peptide (MR-proANP) in 343 adolescents (age 14–16 years) and 616 young adults (age 20–28 years) from the Danish site of the European Youth Heart Study, which is a population-based study of cardiovascular disease risk factors in children, adolescents and young adults. We used linear regression analysis to examine the associations, expressed as standardized regression coefficients, of various variables of interest with MR-proANP stratified according to age group, adjusting for age and gender.

RESULTS

Among the young adults, MR-proANP was negatively associated with body mass index (BMI) (β = −0.10, P = 0.02), waist circumference (WC) (β = −0.14, P < 0.001), systolic blood pressure (BP) (β = −0.08, P = 0.03), diastolic BP (β = −0.23, P < 0.001), insulin (β = −0.15, P < 0.001), and triglycerides (β = −0.14, P < 0.001). Among the adolescents a somehow different pattern was observed since MR-proANP was not significantly associated with BMI (β = −0.00, P = 0.98), WC (β = −0.01, P = 0.90) and insulin (β = −0.02, P = 0.69). Nevertheless, among the adolescents, MR-proANP was negatively associated with triglycerides (β = −0.13, P = 0.01), diastolic BP (β = −0.12, P = 0.01) and systolic BP (β = −0.10, P = 0.10), although the latter association was of borderline significance.

CONCLUSIONS

The young adults displayed significant negative associations between MR-proANP and several components of the metabolic syndrome, whereas such associations were not found among the adolescents besides triglycerides and diastolic BP.
Association of Blood Pressure Trajectory With Mortality, Incident Cardiovascular Disease, and Heart Failure in the Cardiovascular Health Study
Authors: Smitson Christopher C. , Scherzer Rebecca , Shlipak Michael G. , Psaty Bruce M. , Newman Anne B. , Sarnak Mark J. , Odden Michelle C. , Peralta Carmen A.
Published: February 2017

BACKGROUND

Common blood pressure (BP) trajectories are not well established in elderly persons, and their association with clinical outcomes is uncertain.

METHODS

We used hierarchical cluster analysis to identify discrete BP trajectories among 4,067 participants in the Cardiovascular Health Study using repeated BP measures from years 0 to 7. We then evaluated associations of each BP trajectory cluster with all-cause mortality, incident cardiovascular disease (CVD, defined as stroke or myocardial infarction) (N = 2,837), and incident congestive heart failure (HF) (N = 3,633) using Cox proportional hazard models.

RESULTS

Median age was 77 years at year 7. Over a median 9.3 years of follow-up, there were 2,475 deaths, 659 CVD events, and 1,049 HF events. The cluster analysis identified 3 distinct trajectory groups. Participants in cluster 1 (N = 1,838) had increases in both systolic (SBP) and diastolic (DBP) BPs, whereas persons in cluster 2 (N = 1,109) had little change in SBP but declines in DBP. Persons in cluster 3 (N = 1,120) experienced declines in both SBP and DBP. After multivariable adjustment, clusters 2 and 3 were associated with increased mortality risk relative to cluster 1 (hazard ratio = 1.21, 95% confidence interval: 1.06–1.37 and hazard ratio = 1.20, 95% confidence interval: 1.05–1.36, respectively). Compared to cluster 1, cluster 3 had higher rates of incident CVD but associations were not statistically significant in demographic-adjusted models (hazard ratio = 1.16, 95% confidence interval: 0.96–1.39). Findings were similar when stratified by use of antihypertensive therapy.

CONCLUSIONS

Among community-dwelling elders, distinct BP trajectories were identified by integrating both SBP and DBP. These clusters were found to have differential associations with outcomes.
An Assessment of the Robustness of the COSHH-Essentials (C-E) Target Airborne Concentration Ranges 15 Years on, and Their Usefulness for Determining Control Measures
Authors: Vaughan Nicholas P. , Rajan-Sithamparanadarajah Rajadurai
Published: February 2017

The Health and Safety Executive (HSE) in Great Britain (GB), in association with its stakeholders, developed the Control of Substances Hazardous to Health (COSHH)-Essentials (C-E) control banding tool in 1998. The objective was to provide a simple tool for employers, particularly small and medium-sized enterprises (SMEs), to help select and apply appropriate measures for the adequate control of exposure to hazardous substances. The tool used hazard classification information (R-phrases) to assign substances to one of five health hazard groups, each with its respective ‘target airborne concentration range’. The validity of the allocation of substances to a target airborne concentration range was demonstrated at the time using 111 substances that had a current health-based Occupational Exposure Limit (OEL) in GB. The C-E control banding approach remains an important tool to complement exposure assessment/monitoring and the selection and use of suitable control measures for hazardous substances. These include engineering controls and personal protective equipment (PPE). The C-E based control banding approach has been adopted around the world. This paper extends the original validation exercise, using a greater number of chemical substances, to establish whether the target airborne concentration ranges remain appropriate. This is of particular interest in light of the introduction of the Globally Harmonized System (GHS) for classification, in which R-phrases have now been replaced by hazard-statements (H-statements). The validation exercise includes substances with OELs published by nine bodies internationally; and the Derived No-Effect Levels (DNELs) assigned by registrants under the European Union—Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) Regulations. When compared against 8-hour TWA OELs for 850 substances drawn from nine bodies and a limited number of DNELS, the C-E target airborne concentration ranges remain valid. This comparative work also informs a wider consideration around the practicality and the applicability of the C-E generic approach to facilitate the implementation of good practice control for a wide range of substances (more than 95%) which do not have any recognized OEL.
A multi-scale convolutional neural network for phenotyping high-content cellular images
Authors: Godinez William J , Hossain Imtiaz , Lazic Stanley E , Davies John W , Zhang Xian
Published: February 2017

Motivation

Identifying phenotypes based on high-content cellular images is challenging. Conventional image analysis pipelines for phenotype identification comprise multiple independent steps, with each step requiring method customization and adjustment of multiple parameters.

Results

Here, we present an approach based on a multi-scale convolutional neural network (M-CNN) that classifies, in a single cohesive step, cellular images into phenotypes by using directly and solely the images’ pixel intensity values. The only parameters in the approach are the weights of the neural network, which are automatically optimized based on training images. The approach requires no a priori knowledge or manual customization, and is applicable to single- or multi-channel images displaying single or multiple cells. We evaluated the classification performance of the approach on eight diverse benchmark datasets. The approach yielded overall a higher classification accuracy compared with state-of-the-art results, including those of other deep CNN architectures. In addition to using the network to simply obtain a yes-or-no prediction for a given phenotype, we use the probability outputs calculated by the network to quantitatively describe the phenotypes. This study shows that these probability values correlate with chemical treatment concentrations. This finding validates further our approach and enables chemical treatment potency estimation via CNNs.

Availability and Implementation

The network specifications and solver definitions are provided in Supplementary Software 1.

Supplementary information

Supplementary data are available at Bioinformatics online.
Empirical comparison of web-based antimicrobial peptide prediction tools
Authors: Gabere Musa Nur , Noble William Stafford
Published: February 2017

Motivation

Antimicrobial peptides (AMPs) are innate immune molecules that exhibit activities against a range of microbes, including bacteria, fungi, viruses and protozoa. Recent increases in microbial resistance against current drugs has led to a concomitant increase in the need for novel antimicrobial agents. Over the last decade, a number of AMP prediction tools have been designed and made freely available online. These AMP prediction tools show potential to discriminate AMPs from non-AMPs, but the relative quality of the predictions produced by the various tools is difficult to quantify.

Results

We compiled two sets of AMP and non-AMP peptides, separated into three categories—antimicrobial, antibacterial and bacteriocins. Using these benchmark data sets, we carried out a systematic evaluation of ten publicly available AMP prediction methods. Among the six general AMP prediction tools—ADAM, CAMPR3(RF), CAMPR3(SVM), MLAMP, DBAASP and MLAMP—we find that CAMPR3(RF) provides a statistically significant improvement in performance, as measured by the area under the receiver operating characteristic (ROC) curve, relative to the other five methods. Surprisingly, for antibacterial prediction, the original AntiBP method significantly outperforms its successor, AntiBP2 based on one benchmark dataset. The two bacteriocin prediction tools, BAGEL3 and BACTIBASE, both provide very good performance and BAGEL3 outperforms its predecessor, BACTIBASE, on the larger of the two benchmarks.

Supplementary information

Supplementary data are available at Bioinformatics online.
SANA: simulated annealing far outperforms many other search algorithms for biological network alignment
Authors: Mamano Nil , Hayes Wayne B
Published: February 2017

Every alignment algorithm consists of two orthogonal components: an objective function M measuring the quality of an alignment, and a search algorithm that explores the space of alignments looking for ones scoring well according to M. We introduce a new search algorithm called SANA (Simulated Annealing Network Aligner) and apply it to protein-protein interaction networks using S3 as the topological measure. Compared against 12 recent algorithms, SANA produces 5–10 times as many correct node pairings as the others when the correct answer is known. We expose an anti-correlation in many existing aligners between their ability to produce good topological vs. functional similarity scores, whereas SANA usually outscores other methods in both measures. If given the perfect objective function encoding the identity mapping, SANA quickly converges to the perfect solution while many other algorithms falter. We observe that when aligning networks with a known mapping and optimizing only S3, SANA creates alignments that are not perfect and yet whose S3 scores match that of the perfect alignment. We call this phenomenon saturation of the topological score. Saturation implies that a measure’s correlation with alignment correctness falters before the perfect alignment is reached. This, combined with SANA’s ability to produce the perfect alignment if given the perfect objective function, suggests that better objective functions may lead to dramatically better alignments. We conclude that future work should focus on finding better objective functions, and offer SANA as the search algorithm of choice.

Availability and Implementation

Software available at http://sana.ics.uci.edu.

Supplementary information

Supplementary data are available at Bioinformatics online.
Penalized likelihood estimation of a trivariate additive probit model
Authors: Filippou Panagiota , Marra Giampiero , Radice Rosalba
Published: February 2017

This article proposes a penalized likelihood method to estimate a trivariate probit model, which accounts for several types of covariate effects (such as linear, nonlinear, random, and spatial effects), as well as error correlations. The proposed approach also addresses the difficulty in estimating accurately the correlation coefficients, which characterize the dependence of binary responses conditional on covariates. The parameters of the model are estimated within a penalized likelihood framework based on a carefully structured trust region algorithm with integrated automatic multiple smoothing parameter selection. The relevant numerical computation can be easily carried out using the SemiParTRIV() function in a freely available R package. The proposed method is illustrated through a case study whose aim is to model jointly adverse birth binary outcomes in North Carolina.
A reference gene set construction using RNA-seq of multiple tissues of Chinese giant salamander, Andrias davidianus
Authors: Geng Xiaofang , Li Wanshun , Shang Haitao , Gou Qiang , Zhang Fuchun , Zang Xiayan , Zeng Benhua , Li Jiang , Wang Ying , Ma Ji , Guo Jianlin , Jian Jianbo , Chen Bing , Qiao Zhigang , Zhou Minghui , Wei Hong , Fang Xiaodong , Xu Cunshuan
Published: February 2017

Background

Chinese giant salamander (CGS) is the largest extant amphibian species in the world. Owing to its evolutionary position and four peculiar phenomenon of life (longevity, starvation tolerance, regenerative ability, and hatch without sunshine), it is an invaluable model species for research. However, lack of genomic resources leads to fewer study progresses in these fields, due to its huge genome of ~50 GB making it extremely difficult to be assembled.

Results

We reported the sequenced transcriptome of more than 20 tissues from adult CGS using Illumina Hiseq 2000 technology, and a total of 93 366 no-redundancy transcripts with a mean length of 1326 bp were obtained. We developed for the first time an efficient pipeline to construct a high-quality reference gene set of CGS and obtained 26 135 coding genes. BUSCO and homologous assessment showed that our assembly captured 70.6% of vertebrate universal single-copy orthologs, and this coding gene set had a higher proportion of completeness CDS with comparable quality of the protein sets of Tibetan frog.

Conclusions

These highest quality data will provide a valuable reference gene set to the subsequent research of CGS. In addition, our strategy of de novo transcriptome assembly and protein identification is applicable to similar studies.
Seasonal and annual calcification rates of the Hawaiian reef coral, Montipora capitata, under present and future climate change scenarios
Authors: Bahr Keisha D. , Jokiel Paul L. , Rodgers Ku‘ulei S.
Published: February 2017

The response of corals to future conditions of global warming and ocean acidification (OA) is a topic of considerable interest. However, little information is available on the seasonal interaction between temperature, pCO2, and irradiance under ecologically relevant experimental conditions. Controlled experiments were performed in continuous-flow mesocosms under full solar radiation to describe the direct and interactive effects of temperature, irradiance, and pCO2 on growth of a Hawaiian reef building coral (Montipora capitata) over an annual cycle. Corals were subjected to 12 experimental treatments consisting of two pCO2 levels (present-day levels, 2× present), two temperature regimes (ambient, heated +2°C), and three conditions of irradiance (ambient, 50 and 90% reduction). A multiple polynomial regression model with full factorial fixed factors (temperature, pCO2, irradiance) was developed. Temperature and irradiance were the primary factors driving net calcification (Gnet) rates of M. capitata, with pCO2 playing a lesser role. Gnet showed a curvilinear response to irradiance and temperature, which defines thresholds at the end members. Also, high irradiance regimes under elevated temperatures showed a negative synergistic effect on Gnet. Therefore, decreasing irradiance penetration resulting from greater depth and/or higher turbidity will lower the impact of ocean warming on M. capitata. Results suggest that under future climate conditions, the interaction of environmental parameters may shift seasonal patterns in Gnet and timing of growth optima for M. capitata. Ocean warming in shallow water environments with high irradiance poses a more immediate threat to coral growth than acidification for this dominant coral species. In the future, increased temperature and the interaction between high irradiance and high temperature will be the main factors controlling Gnet with OA playing a less important role. This observation is congruent with other reports that high temperature combined with high irradiance is the main cause of high coral mortality during mass bleaching events.
Managing marine socio-ecological systems: picturing the future
Authors: Thébaud Olivier , Link Jason S. , Kohler Bas , Kraan Marloes , López Romain , Poos Jan Jaap , Schmidt Jörn O. , Smith David C.
Published: February 2017

What do you get when a lawyer, a modeller, an economist, a social scientist and an ecologist talk about the ocean? Besides an interesting conversation, it is likely there will be some consideration of how to solve many of the problems facing marine ecosystems around the world. That is precisely what the MSEAS 2016 symposium on understanding marine socio-ecological systems aimed to do. From 30 May to 3 June in Brest, France, the symposium gathered over 230 participants from around the world and from multiple disciplines to discuss the challenge of explicitly considering the human component in producing synoptic assessments of marine social-ecological systems. The symposium fostered dynamic debates on the inter-disciplinary collaborations needed to support management of ongoing and anticipated growth in multiple ocean uses, with particular consideration of the triple bottom line of ecological, economic and social sustainability. Building on the illustrations produced by a professional cartoonist during the meeting, this graphic novel summarizes the key challenges ahead in understanding marine socio-ecological systems and draws a path for future research endeavours in this domain.
New Perspectives on Collective Labour Law: Trade Union Recognition and Collective Bargaining
Authors: Ewing Keith , Hendy John
Published: February 2017

Drawing on the Manifesto for Labour Law published earlier this year, we consider Kahn-Freund’s assessment of British labour law (for the first three quarters of the twentieth century) as voluntarist, abstentionist collective laissez faire as espoused by Bob Simpson. In contrast (and utilising Simpson’s tool of ‘law in context’), we point up the role of the state during this period in implementing labour law policy in support of extensive collective bargaining by the use of public law powers (in the contemporaneous sense in which such law was understood). Drawing on this legacy, we set out the measures by which collective bargaining, in particular at sectoral level, might be restored. We deal with the establishment of Sectoral Employment Commissions consisting of equal numbers of employers and union representatives (similar to the old Joint Industrial Councils). In default, tripartite bodies based on the extinct Wages Councils would be established. We propose the (re) use of ‘fair wages clauses’ (ie public procurement arrangements) to require participation in collective bargaining and the observance of collective agreements. We consider the reciprocal issues of representation at the workplace, union access thereto and reform of the recognition machinery, taking in Simpson’s analysis of the current and earlier recognition legislation.
A ward-based time study of paper and electronic documentation for recording vital sign observations
Authors: Wong David , Bonnici Timothy , Knight Julia , Gerry Stephen , Turton James , Watkinson Peter
Published: February 2017

Objective: To investigate time differences in recording observations and an early warning score using traditional paper charts and a novel e-Obs system in clinical practice.

Methods: Researchers observed the process of recording observations and early warning scores across 3 wards in 2 university teaching hospitals immediately before and after introduction of the e-Obs system. The process of recording observations included both measurement and documentation of vital signs. Interruptions were timed and subtracted from the measured process duration. Multilevel modeling was used to compensate for potential confounding factors.

Results: In all, 577 nurse events were observed (281 paper, 296 e-Obs). The geometric mean time to take a complete set of vital signs was 215 s (95% confidence interval [CI], 177 s–262 s) on paper, and 150 s (95% CI, 130 s–172 s) electronically. The treatment effect ratio was 0.70 (95% CI, 0.57–0.85, P < .001). The treatment effect ratio in ward 1 was 0.37 (95% CI, 0.26–0.53), in ward 2 was 0.98 (95% CI, 0.70–1.38), and in ward 3 was 0.93 (95% CI, 0.66–1.33).

Discussion: Introduction of an e-Obs system was associated with a statistically significant reduction in overall time to measure and document vital signs electronically compared to paper documentation. The reductions in time varied among wards and were of clinical significance on only 1 of 3 wards studied.

Conclusion: Our results suggest that introduction of an e-Obs system could lower nursing workload as well as increase documentation quality.
Effect of acute millimeter wave exposure on dopamine metabolism of NGF-treated PC12 cells
Authors: Haas Alexis J. , Le Page Yann , Zhadobov Maxim , Sauleau Ronan , Dréan Yves Le , Saligaut Christian
Published: February 2017

Several forthcoming wireless telecommunication systems will use electromagnetic frequencies at millimeter waves (MMWs), and technologies developed around the 60-GHz band will soon know a widespread distribution. Free nerve endings within the skin have been suggested to be the targets of MMW therapy which has been used in the former Soviet Union. So far, no studies have assessed the impact of MMW exposure on neuronal metabolism. Here, we investigated the effects of a 24-h MMW exposure at 60.4 GHz, with an incident power density (IPD) of 5 mW/cm², on the dopaminergic turnover of NGF-treated PC12 cells. After MMW exposure, both intracellular and extracellular contents of dopamine (DA) and 3,4-dihydroxyphenylacetic acid (DOPAC) were studied using high performance liquid chromatography. Impact of exposure on the dopamine transporter (DAT) expression was also assessed by immunocytochemistry. We analyzed the dopamine turnover by assessing the ratio of DOPAC to DA, and measuring DOPAC accumulation in the medium. Neither dopamine turnover nor DAT protein expression level were impacted by MMW exposure. However, extracellular accumulation of DOPAC was found to be slightly increased, but not significantly. This result was related to the thermal effect, and overall, no evidence of non-thermal effects of MMW exposure were observed on dopamine metabolism.
Stylometry and collaborative authorship: Eddy, Lovecraft, and ‘The Loved Dead’
Authors: Eldin Addison , Lavin Matthew J. , Look Daniel M.
Published: February 2017

The authorship of the 1924 short story ‘The Loved Dead’ has been contested by family members of Clifford Martin Eddy, Jr. and Sunand Tryambak Joshi, a leading scholar on Howard Phillips Lovecraft. The authors of this article use stylometric methods to provide evidence for a claim about the authorship of the story and to analyze the nature of Eddy’s collaboration with Lovecraft. Further, we extend Rybicki, Hoover, and Kestemont’s (Collaborative authorship: Conrad, Ford, and rolling delta. Literary and Linguistic Computing, 2014; 29, 422–31) analysis of stylometry as it relates to collaborations in order to reveal the necessary considerations for employing a stylometric approach to authorial collaboration.
Direct evidence for Ly$\boldsymbol{\alpha }$ depletion in the protocluster core
Authors: Shimakawa Rhythm , Kodama Tadayuki , Hayashi Masao , Tanaka Ichi , Matsuda Yuichi , Kashikawa Nobunari , Shibuya Takatoshi , Tadaki Ken-ichi , Koyama Yusei , Suzuki Tomoko L. , Yamamoto Moegi
Published: February 2017

We have carried out panoramic Lyα narrow-band imaging with Suprime-Cam on Subaru towards the known protocluster USS1558−003 at z = 2.53. Our previous narrow-band imaging in the near-infrared identified multiple dense groups of Hα emitters (HAEs) within the protocluster. We have now identified the large-scale structures across a ∼50 comoving Mpc scale traced by Lyα emitters (LAEs) in which the protocluster traced by the HAEs is embedded. On a smaller scale, however, there are remarkably few LAEs in the regions of HAE overdensities. Moreover, the stacking analyses of the images show that HAEs in higher-density regions show systematically lower escape fractions of Lyα photons than those of HAEs in lower-density regions. These phenomena may be driven by the extra depletion of Lyα emission lines along our line of sight by more intervening cold circumgalactic/intergalactic medium and/or dust in the dense core. We also caution that all the previous high-z protocluster surveys using LAEs as tracers would have largely missed galaxies in the very dense cores of the protoclusters where we would expect to see any early environmental effects.
Concordance cosmology without dark energy
Authors: Rácz Gábor , Dobos László , Beck Róbert , Szapudi István , Csabai István
Published: February 2017

According to the separate universe conjecture, spherically symmetric sub-regions in an isotropic universe behave like mini-universes with their own cosmological parameters. This is an excellent approximation in both Newtonian and general relativistic theories. We estimate local expansion rates for a large number of such regions, and use a scale parameter calculated from the volume-averaged increments of local scale parameters at each time step in an otherwise standard cosmological N-body simulation. The particle mass, corresponding to a coarse graining scale, is an adjustable parameter. This mean field approximation neglects tidal forces and boundary effects, but it is the first step towards a non-perturbative statistical estimation of the effect of non-linear evolution of structure on the expansion rate. Using our algorithm, a simulation with an initial Ωm = 1 Einstein–de Sitter setting closely tracks the expansion and structure growth history of the Λ cold dark matter (ΛCDM) cosmology. Due to small but characteristic differences, our model can be distinguished from the ΛCDM model by future precision observations. Moreover, our model can resolve the emerging tension between local Hubble constant measurements and the Planck best-fitting cosmology. Further improvements to the simulation are necessary to investigate light propagation and confirm full consistency with cosmic microwave background observations.
Intramedullary Lesion Length on Postoperative Magnetic Resonance Imaging is a Strong Predictor of ASIA Impairment Scale Grade Conversion Following Decompressive Surgery in Cervical Spinal Cord Injury
Authors: Aarabi Bizhan , Sansur Charles A. , Ibrahimi David M. , Simard J. Marc , Hersh David S. , Le Elizabeth , Diaz Cara , Massetti Jennifer , Akhtar-Danesh Noori
Published: February 2017

BACKGROUND: Evidence indicates that, over time, patients with spinal cord injury (SCI) improve neurologically in various degrees. We sought to further investigate indicators of grade conversion in cervical SCI.

OBJECTIVE: To detect predictors of ASIA impairment scale (AIS) grade conversion in SCI following surgical decompression.

METHODS: In a retrospective study, demographics, clinical, imaging, and surgical data from 100 consecutive patients were assessed for predictors of AIS grade conversion.

RESULTS: American Spinal Injury Association motor score was 17.1. AIS grade was A in 52%, B in 29%, and C in 19% of patients. Surgical decompression took place on an average of 17.6 h following trauma (≤12 h in 51 and >12 h in 49). Complete decompression was verified by magnetic resonance imaging (MRI) in 73 patients. Intramedullary lesion length (IMLL) on postoperative MRI measured 72.8 mm, and hemorrhage at the injury epicenter was noted in 71 patients. Grade conversion took place in 26.9% of AIS grade A patients, 65.5% of AIS grade B, and 78.9% of AIS grade C. AIS grade conversion had statistical relationship with injury severity score, admission AIS grade, extent of decompression, presence of intramedullary hemorrhage, American Spinal Injury Association motor score, and IMLL. A stepwise multiple logistic regression analysis indicated IMLL was the sole and strongest indicator of AIS grade conversion (odds ratio 0.950, 95% CI 0.931-0.969). For 1- and 10-mm increases in IMLL, the model indicates 4% and 40% decreases, respectively, in the odds of AIS grade conversion.

CONCLUSION: Compared with other surrogates, IMLL remained as the only predictor of AIS grade conversion.
Histopathological Insights on Imaging Results of Intraoperative Magnetic Resonance Imaging, 5-Aminolevulinic Acid, and Intraoperative Ultrasound in Glioblastoma Surgery
Authors: Coburger Jan , Scheuerle Angelika , Pala Andrej , Thal Dietmar , Wirtz Christian Rainer , König Ralph
Published: February 2017

BACKGROUND: For appropriate use of available intraoperative imaging techniques in glioblastoma (GB) surgery, it is crucial to know the potential of the respective techniques in tumor detection.

OBJECTIVE: To assess histopathological basis of imaging results of intraoperative magnetic resonance imaging (iMRI), 5-aminolevulinic acid (5-ALA), and linear array intraoperative ultrasound (lioUS).

METHODS: We prospectively compared the imaging findings of iMRI, 5-ALA, and lioUS at 99 intraoperative biopsy sites in 33 GB patients during resection control. Histological classification of specimens, tumor load, presence of necrosis, presence of vascular malformations, and O6-methylguanin-DNA methyltransferase (MGMT) promoter state was correlated with imaging findings.

RESULTS: Solid tumor was found in 57%, infiltration zone in 42%, and no tumor in 1% of specimens. However, imaging was negative in iMRI in 49%, using 5-ALA in 17%, and in lioUS in 21%. In positive imaging results, share of solid tumor was highest in 5-ALA (65%) followed by lioUS (60%) and lowest in iMRI (55%). In comparison to 5-ALA, iMRI had a high share of solid tumor in specimens when showing intermediate results. Sensitivity for invasive tumor was higher in 5-ALA (84%) and lioUS (80%) than in iMRI (50%). We found a significant correlation of 5-ALA with classification of specimen, presence of necrosis, and microproliferations. Methylated MGMT promoter correlated with positive findings in 5-ALA. lioUS and iMRI showed no correlations with histopathological findings.

CONCLUSION: All of the assessed established imaging techniques detect infiltrating tumor only to a certain extent. Only 5-ALA showed a significant correlation with histopathological findings. Interestingly, tumor remnants in an MGMT-methylated tumor are more likely to be visible using 5-ALA as in unmethylated tumors.
A New Classification for Pathologies of Spinal Meninges—Part 2: Primary and Secondary Intradural Arachnoid Cysts
Authors: Klekamp Jörg
Published: February 2017

BACKGROUND: Spinal intradural arachnoid cysts are rare causes of radiculopathy or myelopathy. Treatment options include resection, fenestration, or cyst drainage.

OBJECTIVE: To classify intradural spinal arachnoid cysts and present results of their treatment.

METHODS: Among 1519 patients with spinal space occupying lesions, 130 patients demonstrated intradural arachnoid cysts. Neuroradiological and surgical features were reviewed and clinical data analyzed.

RESULTS: Twenty-one patients presented arachnoid cysts as a result of an inflammatory leptomeningeal reaction related to meningitis, subarachnoid hemorrhage, intrathecal injections, intradural surgery, or trauma, ie, secondary cysts. For the remaining 109 patients, no such history could be elucidated, ie, primary cysts. Forty-six percent of primary and 86% of secondary cysts were associated with syringomyelia. Patients presented after an average history of 53 ± 88 months. There were 122 thoracic and 7 lumbar cysts plus 1 cervical cyst. Fifty-nine patients with primary and 15 patients with secondary cysts underwent laminotomies with complete or partial cyst resection and duraplasty. Mean follow-up was 57 ± 52 months. In the first postoperative year, profound improvements for primary cysts were noted, in contrast to marginal changes for secondary cysts. Progression-free survival for 10 years following surgery was determined as 83% for primary compared to 15% for secondary cysts. Despite differences in clinical presentation, progression-free survival was almost identical for patients with or without syringomyelia.

CONCLUSIONS: Complete or partial resection leads to favorable short- and long-term results for primary arachnoid cysts. For secondary cysts, surgery can only provide clinical stabilization for a limited time due to the often extensive arachnoiditis.