bluuebunny/crossref_metadata_2025 huggingface dataset:
Planning low-carbon electricity systems under uncertainty considering operational flexibility and smart grid technologies
Authors: Moreno Rodrigo , Street Alexandre , Arroyo José M. , Mancarella Pierluigi
Published: July 2017

Electricity grid operators and planners need to deal with both the rapidly increasing integration of renewables and an unprecedented level of uncertainty that originates from unknown generation outputs, changing commercial and regulatory frameworks aimed to foster low-carbon technologies, the evolving availability of market information on feasibility and costs of various technologies, etc. In this context, there is a significant risk of locking-in to inefficient investment planning solutions determined by current deterministic engineering practices that neither capture uncertainty nor represent the actual operation of the planned infrastructure under high penetration of renewables. We therefore present an alternative optimization framework to plan electricity grids that deals with uncertain scenarios and represents increased operational details. The presented framework is able to model the effects of an array of flexible, smart grid technologies that can efficiently displace the need for conventional solutions. We then argue, and demonstrate via the proposed framework and an illustrative example, that proper modelling of uncertainty and operational constraints in planning is key to valuing operationally flexible solutions leading to optimal investment in a smart grid context. Finally, we review the most used practices in power system planning under uncertainty, highlight the challenges of incorporating operational aspects and advocate the need for new and computationally effective optimization tools to properly value the benefits of flexible, smart grid solutions in planning. Such tools are essential to accelerate the development of a low-carbon energy system and investment in the most appropriate portfolio of renewable energy sources and complementary enabling smart technologies.

This article is part of the themed issue ‘Energy management: flexibility, risk and optimization’.
Isoflurane reduces feedback in the fruit fly brain
Authors: Cohen Dror , Swinderen Bruno van , Tsuchiya Naotsugu
Published: July 2017

Hierarchically organized brains communicate through feedforward and feedback pathways. In mammals, feedforward and feedback are mediated by higher and lower frequencies during wakefulness. Feedback is preferentially impaired by general anesthetics. This suggests feedback serves critical functions in waking brains. The brain ofDrosophila melanogaster(fruit fly) is also hierarchically organized, but the presence of feedback in these brains is not established. Here we studied feedback in the fruit fly brain, by simultaneously recording local field potentials (LFPs) from low-order peripheral structures and higher-order central structures. Directed connectivity analysis revealed that low frequencies (0.1-5Hz) mediated feedback from the center to the periphery, while higher frequencies (10-45Hz) mediated feedforward in the opposite direction. Further, isoflurane anesthesia preferentially reduced feedback. Our results imply that similar spectral characteristics of feedforward and feedback may be a signature of hierarchically organized brains and that general anesthetics may induce unresponsiveness by targeting the mechanisms that support feedback.
Chitozyme: First Peroxidase-like Activity of Chitosan for Multiplexed Visual Detection of H2O2, Glucose and Lactate on Paper-based Device
Authors: Ahmed Syed Rahin , Weng Xuan , Neethirajan Suresh
Published: July 2017

Visual read-out diagnostics tools are promising candidates for field applicable medical devices. Current colorimetric biosensors require introduction of natural enzymes or nanozymes, which has some serious drawbacks for practical applications. Chitosan, a natural polymer, provides safe and efficient compound in medical and pharmaceutical technology. Herein, we report on a simple, cost-efficient, field-portable, environmental friendly and ultra-sensitive multiplex detection platform based on peroxidase-like activity of chitosan in the presence of 3,3’,5,5’-Tetramethylbenzidine (TMBZ) and H2O2. This straight forward signal amplification strategy was successfully applied to detect H2O2, glucose and lactate with the limit of detection (LOD) of 2.64 pM, 0.104 μM and 2.8 nM respectively, represents the lowest LOD of H2O2, glucose and lactate with visual read-out. The chitosan-based assay performance was also retained in complex biological media for glucose and lactate detection. Furthermore, the proposed assay was successfully demonstrated as a paper-based colorimetric biosensor. Most importantly, the simplicity, biocompatibility and sensitivity of the proposed assay will open new doors for instrument free naked eye visual detection of H2O2, glucose and lactate detection.
Case-control analysis identifies shared properties of rare germline variation in cancer predisposing genes
Authors: Artomov Mykyta , Joseph Vijai , Tiao Grace , Thomas Tinu , Schrader Kasmintan , Klein Robert J. , Kiezun Adam , Gupta Namrata , Margolin Lauren , Stratigos Alexander J. , Kim Ivana , Shannon Kristen , Ellisen Leif W. , Haber Daniel , Getz Gad , Tsao Hensin , Lipkin Steven M. , Altshuler David , Offit Kenneth , Daly Mark J.
Published: July 2017

Traditionally, genetic studies in cancer are focused on somatic mutations found in tumors and absent from the normal tissue. Identification of shared attributes in germline variation could aid discrimination of high-risk from likely benign mutations and narrow the search space for new cancer predisposing genes. Extraordinary progress made in analysis of common variation with GWAS methodology does not provide sufficient resolution to understand rare variation. To fulfil missing classification for rare germline variation we assembled datasets of whole exome sequences from >2,000 patients with different types of cancers: breast cancer, colon cancer and cutaneous and ocular melanomas matched to more than 7,000 non-cancer controls and analyzed germline variation in known cancer predisposing genes to identify common properties of disease associated mutations and new candidate cancer susceptibility genes. Lists of all cancer predisposing genes were divided into subclasses according to the mode of inheritance of the related cancer syndrome or contribution to known major cancer pathways. Out of all subclasses only genes linked to dominant syndromes presented significant rare germline variants enrichment in cases. Separate analysis of protein-truncating and missense variation in this subclass of genes confirmed significant prevalence of protein-truncating variants in cases only in loss-of-function tolerant genes (pLI<0.1), while ultra-rare missense mutations were significantly overrepresented in cases only in constrained genes (pLI>0.9). Taken together, our findings provide insights into the distribution and types of mutations underlying inherited cancer predisposition.
Working memory implements distinct maintenance mechanisms depending on task goals
Authors: Fahrenfort Johannes J. , Van Leeuwen Jonathan , Foster Joshua J. , Awh Edward , Olivers Christian N.L.
Published: July 2017

Working memory is the function by which we temporarily maintain information to achieve current task goals. Models of working memory typically debate where this information is stored, rather than how it is stored. Here we ask instead what neural mechanisms are involved in storage, and how these mechanisms change as a function of task goals. Participants either had to reproduce the orientation of a memorized bar (continuous recall task), or identify the memorized bar in a search array (visual search task). The sensory input and retention interval were identical in both tasks. Next, we used decoding and forward modeling on multivariate electroencephalogram (EEG) and time-frequency decomposed EEG to investigate which neural signals carry more informational content during the retention interval. In the continuous recall task, working memory content was preferentially carried by induced oscillatory alpha-band power, while in the visual search task it was more strongly carried by the distribution of evoked (consistently elevated and non-oscillatory) EEG activity. To show the independence of these two signals, we were able to remove informational content from one signal without affecting informational content in the other. Finally, we show that the tuning characteristics of both signals change in opposite directions depending on the current task goal. We propose that these signals reflect oscillatory and elevated firing-rate mechanisms that respectively support location-based and object-based maintenance. Together, these data challenge current models of working memory that place storage in particular regions, but rather emphasize the importance of different distributed maintenance signals depending on task goals.

Significance statement (120 words)

Without realizing, we are constantly moving things in and out of our mind’s eye, an ability also referred to as ‘working memory’. Where did I put my screwdriver? Do we still have milk in the fridge? A central question in working memory research is how the brain maintains this information temporarily. Here we show that different neural mechanisms are involved in working memory depending on what the memory is used for. For example, remembering what a bottle of milk looks like invokes a different neural mechanism from remembering how much milk it contains: the first one primarily involved in being able to find the object, and the other one involving spatial position, such as the milk level in the bottle.
The beneficial effects of vaccination on the evolution of seasonal influenza
Authors: Wen Frank T. , Malani Anup , Cobey Sarah
Published: July 2017

1

Although vaccines against seasonal influenza are designed to protect against circulating strains, by affecting the emergence and transmission of antigenically divergent strains, they might also change the rate of antigenic evolution. Vaccination might slow antigenic evolution by increasing immunity, reducing the chance that even antigenically diverged strains can survive. Vaccination also reduces prevalence, decreasing the supply of potentially beneficial mutations and increasing the probability of stochastic extinction. But vaccination might accelerate antigenic evolution by increasing the transmission advantage of more antigenically diverged strains relative to less diverged strains (i.e., by positive selection). Such evolutionary effects could affect vaccination’s direct benefits to individuals and indirect benefits to the host population (i.e., the private and social benefits). To investigate these potential impacts, we simulated the dynamics of an influenza-like pathogen with seasonal vaccination. On average, more vaccination decreased the rate of viral antigenic evolution and the incidence of disease. Notably, this decrease was driven partly by a vaccine-induced decline in the rate of antigenic evolution. To understand how the evolutionary effects of vaccines might affect their social and private benefits, we fitted linear panel models to simulated data. By slowing evolution, vaccination increased the social benefit and decreased the private benefit. Thus, in the long term, vaccination’s potential social and private benefits may differ from current theory, which omits evolutionary effects. These results suggest that conventional seasonal vaccines against influenza, if protective against transmission and given to the appropriate populations, could further reduce disease burden by slowing antigenic evolution.
Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism
Authors: Stewart Robert , Auffret Marc D. , Warr Amanda , Snelling Tim , Dewhurst Richard , Walker Alan W. , Roehe Rainer , Watson Mick
Published: July 2017

The cow rumen is a specialised organ adapted for the efficient breakdown of plant material into energy and nutrients, and it is the rumen microbiome that encodes the enzymes responsible. Many of these enzymes are of huge industrial interest. Despite this, rumen microbes are under-represented in the public databases. Here we present 220 high quality bacterial and archaeal genomes assembled directly from 768 gigabases of rumen metagenomic sequence data. Comparative analysis with current publicly available genomes reveals that the majority of these represent previously unsequenced strains and species of bacteria and archaea. The genomes contain over 13,000 proteins predicted to be involved in carbohydrate metabolism, over 90% of which do not have a good match in the public databases. Inclusion of the 220 genomes presented here improves metagenomic read classification by 2-3-fold, both in our data and in other publicly available rumen datasets. This release improves the coverage of rumen microbes in the public databases, and represents a hugely valuable resource for biomass-degrading enzyme discovery and studies of the rumen microbiome
Consensus on Molecular Subtypes of Ovarian Cancer
Authors: Chen Gregory M , Kannan Lavanya , Geistlinger Ludwig , Kofia Victor , Safikhani Zhaleh , Gendoo Deena M A , Parmigiani Giovanni , Birrer Michael , Haibe-Kains Benjamin , Waldron Levi
Published: July 2017

INTRODUCTION

Various computational methods for gene expression-based subtyping of high-grade serous (HGS) ovarian cancer have been proposed. This resulted in the identification of molecular subtypes that are based on different datasets and were differentially validated, making it difficult to achieve consensus on which definitions to use in follow-up studies. We assess three major subtype classifiers for their robustness and association to outcome by a meta-analysis of publicly available expression data, and provide a classifier that represents their consensus.

METHODS

We use a compendium of 15 microarray datasets consisting of 1,774 HGS ovarian tumors to assess 1) concordance between published subtyping algorithms, 2) robustness of those algorithms to re-clustering across datasets, and 3) association of subtypes with overall survival. A consensus classifier is trained on concordantly classified samples, and validated by leave-one-dataset-out validation.

RESULTS

Each subtyping classifier identified subsets significantly differing in overall survival, but were not robust to re-fitting in independent datasets and grouped only approximately one third of patients concordantly into four subtypes. We propose a consensus classifier to identify the minority of unambiguously classifiable tumors across multiple gene expression platforms, using a 100-gene signature. The resulting consensus subtypes correlate with patient age, survival, tumor purity, and lymphocyte infiltration.

CONCLUSIONS

Our analysis demonstrates that most HGS ovarian cancers are not able to be subtyped. A minority of tumors can be classified and our proposed consensus classifier consolidates and improves on the robustness of three previously proposed subtype classifiers. It provides reliable stratification of patients with HGS ovarian tumors of clearly defined subtype, and will assist in studying the role of polyclonality in the majority of tumors that are not robustly classifiable.
Sequanix: A Dynamic Graphical Interface for Snakemake Workflows
Authors: Desvillechabrol Dimitri , Legendre Rachel , Rioualen Claire , Bouchier Christiane , Helden Jacques van , Kennedy Sean , Cokelaer Thomas
Published: July 2017

We designed a PyQt graphical user interface – Sequanix – aiming at democratizing the use of Snakemake pipelines. Although the primary goal of Sequanix was to facilitate the execution of NGS Snakemake pipelines available in the Sequana project (http://sequana.readthedocs.io), it can also handle any Snakemake pipelines. Therefore, Sequanix should be useful to all Snakemake developers willing to expose their pipelines to a wider audience.

Availability

Source code available onhttp://github.com/sequana/sequanaand standalone onhttp://bioconda.github.io(sequana package).
AMP-activated protein kinase protects against anoxia inDrosophila melanogaster
Authors: Evans Justin J. , Xiao Chengfeng , Robertson R. Meldrum
Published: July 2017

During anoxia, proper energy maintenance is essential in order to maintain neural operation. Starvation activates AMP-activated protein kinase (AMPK), an evolutionarily conserved indicator of cellular energy status, in a cascade which modulates ATP production and consumption. We investigated the role of energetic status on anoxia tolerance inDrosophilaand discovered that starvation or AMPK activation increases the speed of locomotor recovery from an anoxic coma. Using temporal and spatial genetic targeting we found that AMPK in the fat body contributes to starvation-induced fast locomotor recovery, whereas, under fed conditions, disrupting AMPK in oenocytes prolongs recovery. By evaluating spreading depolarization in the fly brain during anoxia we show that AMPK activation reduces the severity of ionic disruption and prolongs recovery of electrical activity. Further genetic targeting indicates that glial, but not neuronal, AMPK affects locomotor recovery. Together, these findings support a model in which AMPK is neuroprotective inDrosophila.
cAMP Signaling Regulates DNA Demethylation by Augmenting the Intracellular Labile Ferrous Iron Pool
Authors: Camarena Vladimir , Sant David W. , Huff Tyler C. , Mustafi Sushmita , Muir Ryan K. , Renslo Adam R. , Monje Paula , Wang Gaofeng
Published: July 2017

It is widely accepted that cAMP regulates gene transcription principally by activating the protein kinase A (PKA)-targeted transcription factors. Here, we show that cAMP enhances the generation of 5-hydroxymethylcytosine (5hmC) in multiple cell types. 5hmC is converted from 5-methylcytosine (5mC) by Tet methylcytosine dioxygenases, for which Fe(II) is an essential cofactor. The promotion of 5hmC was mediated by a prompt increase of the intracellular labile Fe(II) pool (LIP). cAMP enhanced the acidification of endosomes for Fe(II) release to the LIP likely through RapGEF2. The effect of cAMP on Fe(II) and 5hmC was confirmed by adenylate cyclase activators, phosphodiesterase inhibitors, and most notably by stimulation of G protein-coupled receptors (GPCR). The transcriptomic changes caused by cAMP occurred in concert with 5hmC elevation in differentially transcribed genes. Collectively, these data show a previously unrecognized regulation of gene transcription by GPCR-cAMP signaling through augmentation of the intracellular labile Fe(II) pool and DNA demethylation.
Rapid and scalable preparation of bacterial lysates for cell-free gene expression
Authors: Didovyk Andriy , Tonooka Taishi , Tsimring Lev , Hasty Jeff
Published: July 2017

Cell-free gene expression systems are emerging as an important platform for a diverse range of synthetic biology and biotechnology applications, including production of robust field-ready biosensors. Here, we combine programmed cellular autolysis with a freeze-thaw or freeze-dry cycle to create a practical, reproducible, and a labor- and cost-effective approach for rapid production of bacterial lysates for cell-free gene expression. Using this method, ro-bust and highly active bacterial cell lysates can be produced without specialized equipment at a wide range of scales, making cell-free gene expression easily and broadly accessible. More-over, live autolysis strain can be freeze-dried directly and subsequently lysed upon rehydration to produce active lysate. We demonstrate the utility of autolysates for synthetic biology by reg-ulating protein production and degradation, implementing quorum sensing, and showing quan-titative protection of linear DNA templates by GamS protein. To allow versatile and sensitive β-galactosidase (LacZ) based readout we produce autolysates with no detectable background LacZ activity and use them to produce sensitive mercury(II) biosensors with LacZ-mediated colorimetric and fluorescent outputs. The autolysis approach can facilitate wider adoption of cell-free technology for cell-free gene expression as well as other synthetic biology and biotechnology applications, such as metabolic engineering, natural product biosynthesis, or proteomics.
SQUID: Transcriptomic Structural Variation Detection from RNA-seq
Authors: Ma Cong , Shao Mingfu , Kingsford Carl
Published: July 2017

Transcripts are frequently modified by structural variations, which leads to a fused transcript of either multiple genes (known as a fusion gene) or a gene and a previously non-transcribing sequence. Detecting these modifications (called transcriptomic structural variations, or TSVs), especially in cancer tumor sequencing, is an important and challenging computational problem. We introduce SQUID, a novel algorithm to accurately predict both fusion-gene and non-fusion-gene TSVs from RNA-seq alignments. SQUID unifies both concordant and discordant read alignments into one model, and doubles the accuracy on simulation data compared to other approaches. With SQUID, we identified novel non-fusion-gene TSVs on TCGA samples.
Long-term adaptive evolution of genomically recodedEscherichia coli
Authors: Wannier Timothy M. , Kunjapur Aditya M. , Rice Daniel P. , McDonald Michael J. , Desai Michael M. , Church George M.
Published: July 2017

Efforts are underway to construct several recoded genomes anticipated to exhibit multi-virus resistance, enhanced non-standard amino acid (NSAA) incorporation, and capability for synthetic biocontainment. Though we succeeded in pioneering the first genomically recoded organism (Escherichia colistrain C321.ΔA), its fitness is far lower than that of its non-recoded ancestor, particularly in defined media. This fitness deficit severely limits its utility for NSAA-linked applications requiring defined media such as live cell imaging, metabolic engineering, and industrial-scale protein production. Here, we report adaptive evolution of C321.ΔA for more than 1,000 generations in independent replicate populations grown in glucose minimal media. Evolved recoded populations significantly exceed the growth rates of both the ancestral C321.ΔA and non-recoded strains, permitting use of the recoded chassis in several new contexts. We use next-generation sequencing to identify genes mutated in multiple independent populations, and we reconstruct individual alleles in ancestral strains via multiplex automatable genome engineering (MAGE) to quantify their effects on fitness. Several selective mutations occur only in recoded evolved populations, some of which are associated with altering the translation apparatus in response to recoding, whereas others are not apparently associated with recoding, but instead correct for off-target mutations that occurred during initial genome engineering. This report demonstrates that laboratory evolution can be applied after engineering of recoded genomes to streamline fitness recovery compared to application of additional targeted engineering strategies that may introduce further unintended mutations. In doing so, we provide the most comprehensive insight to date into the physiology of the commonly used C321.ΔA strain.

Significance Statement

After demonstrating construction of an organism with an altered genetic code, we sought to evolve this organism for many generations to improve its fitness and learn what unique changes natural selection would bestow upon it. Although this organism initially had impaired fitness, we observed that adaptive laboratory evolution resulted in several selective mutations that corrected for insufficient translation termination and for unintended mutations that occurred when originally altering the genetic code. This work further bolsters our understanding of the pliability of the genetic code, it will help guide ongoing and future efforts seeking to recode genomes, and it results in a useful strain for non-standard amino acid incorporation in numerous contexts relevant for research and industry.
Mobile shopping among young consumers: an empirical study in an emerging market
Authors: Mahapatra Sabita
Published: July 2017

Purpose

Superior functionality of smartphones makes them a potential retailing channel, despite their slow adoption. The purpose of this paper is to identify convenience factors that influence consumption experience and intention to continue shopping on a mobile phone.

Design/methodology/approach

This study was carried out on students using a survey method. This study was conducted in the National Capital Region of India due to its large and diverse population. A purposive sampling technique was used to contact 380 respondents.

Findings

The data were analysed using a structural equation model. The results indicate search and possession convenience to be positively related to consumption experience while search, evaluation and post-purchase convenience are positively related to continuance usage intention. The findings of this study provide evidence that mobile phone is an effective channel for shopping due to search, evaluation, possession and post-purchase convenience.

Research limitations/implications

This study used student population between the age group of 20 and 30 years, thereby limiting the generality of the results.

Practical implications

This study provides insights to retailers and brand managers for crafting their mobile marketing strategies.

Originality/value

This study explores and uncovers, for the first time, convenience dimensions of a mobile shopping channel across various stages of consumers’ purchase cycle.
Ethnographic inquiry in colonial India: Herbert Risley, William Crooke, and the study of tribes and castes
Authors: Fuller C.J.
Published: July 2017

Sir Herbert Risley and William Crooke, both officials in the colonial government, published the first two handbooks of tribes and castes in British India in the 1890s, each containing a lengthy ethnographic glossary with entries for individual tribes and castes. The handbooks are rarely consulted by modern anthropologists of India and have been criticized as colonialist misrepresentation. This article, which reassesses Risley's and Crooke's handbooks as contributions to anthropological knowledge, examines their collection and presentation of ethnographic information, particularly Risley's inquiry into caste ranking. It discusses criticism of the handbooks and their elitist bias, as well as the collaborative contribution made by Indian assistants. It briefly considers why Risley's and Crooke's work was uninteresting to leading metropolitan anthropologists and notes the greater interest of European sociologists.
What Sorts of Things are Public Morals? A Liberal Cosmopolitan Approach to Article XX GATT
Authors: Suttle Oisin
Published: July 2017

Existing theories of WTO law cannot adequately explain the form or content of the GATT exceptions, in particular Article XX(a) Public Morals. Nor, in consequence, can they satisfactorily answer the interpretive questions they raise. This article explains Article XX in terms of self‐determination as a political and moral value, and the choices it mandates peoples make for themselves. Drawing on debates in contemporary political philosophy, it distinguishes three categories of argument for self‐determination: intrinsic, expressive and instrumental, each having implications for the scope of the choices a self‐determining community must make for itself. This account of self‐determination in trade regulation is used to reconstruct Article XX, both explaining the individual provisions, and suggesting how these might be developed and interpreted. It concludes by examining Article XX(a) in detail, highlighting the interpretive questions public morals pose, and how understanding Article XX in terms of self‐determination suggests these should be answered.
The effect of laparoscopic resection of large niches in the uterine caesarean scar on symptoms, ultrasound findings and quality of life: a prospective cohort study
Authors: Vervoort AJMW , Vissers J , Hehenkamp WJK , Brölmann HAM , Huirne JAF
Published: July 2017

Objective

To evaluate the effectiveness of a laparoscopic niche resection on niche‐related symptoms and/or fertility‐related problems, ultrasound findings and quality of life.

Design

Prospective cohort study.

Setting

University hospital.

Population

Women with a large niche (residual myometrium <3 mm) and complaints of either postmenstrual spotting, dysmenorrhoea, intrauterine fluid accumulation and/or difficulties with embryo transfer due to distorted anatomy.

Methods

Women filled out questionnaires and a validated menstrual score chart at baseline and 6 months after the laparoscopic niche resection. At baseline and between 3 and 6 months follow up niches were evaluated by transvaginal ultrasound.

Main outcome measures

The primary outcome was reduction of the main problem 6 months after the intervention. Secondary outcomes were complications, menstrual characteristics, dysmenorrhoea, niche measurements, intrauterine fluid, surgical outcomes, satisfaction and quality of life.

Results

In all, 101 women underwent a laparoscopic niche resection. In 80 women (79.2%) the main problem was improved or resolved. Postmenstrual spotting was significantly reduced by 7 days at 6 months follow up compared with baseline. Dysmenorrhoea and discomfort related to spotting was also significantly reduced. The residual myometrium was increased significantly at follow up. The intrauterine fluid was resolved in 86.9% of the women with intrauterine fluid at baseline; 83.3% of women were (very) satisfied. The physical component of quality of life increased, the mental component did not change.

Conclusions

A laparoscopic niche resection reduced postmenstrual spotting, discomfort due to spotting, dysmenorrhoea and the presence of intrauterine fluid in the majority of women and increased the residual myometrium.

Tweetable abstract

Laparoscopic niche resection reduces niche‐related problems and enlarges the residual myometrium.
The functional potential and active populations of the pit mud microbiome for the production of Chinese strong‐flavour liquor
Authors: Tao Yong , Wang Xiang , Li Xiangzhen , Wei Na , Jin Hong , Xu Zhancheng , Tang Qinglan , Zhu Xiaoyu
Published: July 2017

The popular distilled Chinese strong‐flavour liquor (CSFL) is produced by solid fermentation in the ground pit. Microbes inhabiting in the pit mud (PM) on the walls of the fermentation pit are responsible for the production of caproic acid (CA) that determines the quality of CSFL to a large degree. However, little is known about the active microbial populations and metabolic potential of the PM microbiome. Here, we investigated the overall metabolic features of the PM microbiome and its active microbial components by combining metagenomics and MiSeq‐sequencing analyses of the 16S rRNA genes from DNA and RNA (cDNA). Results showed that prokaryotes were predominant populations in the PM microbiome, accounting for 95.3% of total metagenomic reads, while eukaryotic abundance was only 1.8%. The dominant prokaryotic phyla were Firmicutes, Euryarchaeota, Bacteroidetes, Actinobacteria and Proteobacteria, accounting for 48.0%, 19.0%, 13.5%, 2.5% and 2.1% of total metagenomic reads respectively. Most genes encoding putative metabolic pathways responsible for the putative CA production via chain elongation pathway were detected. This indicated that the PM microbiome owned functional potential for synthesizing CA from ethanol or lactate. Some key genes encoding enzymes involved in hydrogenotrophic and acetoclastic methanogenesis pathways were detected in the PM metagenome, suggesting the possible occurrence of interspecies hydrogen transfer between CA‐producing bacteria and methanogens. The 16S rDNA and 16S rRNA profiles showed that the Clostridial cluster IV, Lactobacillus, Caloramator, Clostridium, Sedimentibacter, Bacteroides and Porphyromonas were active populations in situ, in which Clostridial cluster IV and Clostridium were likely involved in the CA production. This study improved our understandings on the active populations and metabolic pathways of the PM microbiome involved in the CA synthesis in the CSFL fermentation.
A matter of hierarchy: activation of orfamide production by the post‐transcriptional Gac‐Rsm cascade of Pseudomonas protegens CHA0 through expression upregulation of the two dedicated transcriptional regulators
Authors: Sobrero Patricio Martín , Muzlera Andrés , Frescura Julieta , Jofré Edgardo , Valverde Claudio
Published: July 2017

In this work, we surveyed the genome of P. protegens CHA0 in order to identify novel mRNAs possibly under the control of the Gac‐Rsm cascade that might, for their part, serve to elucidate as‐yet‐unknown functions involved in the biocontrol of plant pathogens and/or in cellular processes required for fitness in natural environments. In view of the experimental evidence from former studies on the Gac‐Rsm cascade, we developed a computational screen supported by a combination of sequence, structural and evolutionary constraints that led to a dataset of 43 potential novel mRNA targets. We then confirmed several mRNA targets experimentally and next focused on two of the respective genes that are physically linked to the orfamide biosynthetic gene cluster and whose predicted open‐reading frames resembled cognate LuxR‐type transcriptional regulators of cyclic lipopeptide clusters in related pseudomonads. In this report, we demonstrate that in strain CHA0, orfamide production is stringently dependent on a functional Gac‐Rsm cascade and that both mRNAs encoding transcriptional regulatory proteins are under direct translational control of the RsmA/E proteins. Our results have thus revealed a hierarchical control over the expression of orfamide biosynthetic genes with the final transcriptional control subordinated to the global Gac‐Rsm post‐transcriptional regulatory system.
Impact of pre‐operative health‐related quality of life on outcomes after heart surgery
Authors: Norkienė Ieva , Urbanaviciute Indre , Kezyte Greta , Vicka Vaidas , Jovaisa Tomas
Published: July 2017

Background

Long‐term improvement in health‐related quality of life (HRQOL) is one of the most important outcomes of cardiac surgery. The aim of this study is to define the impact of perioperative patient and procedural variables on HRQOL dynamics, a year after cardiac surgery.

Methods

Consecutive patients undergoing elective on‐pump cardiac surgery were enrolled in this prospective observational cohort study. Patients completed the Medical Outcomes Study 36‐Item Short‐Form Health Survey (SF‐36) questionnaire a day before surgery and once again a year after surgery. The effect size method was used to determine whether treatment resulted in the improvement of HRQOL.

Results

A total of 67.3% of patients achieved long‐term improvement in HRQOL. Significant negative association was identified between Physical and Mental Component Summary scores (PCS/MCS) and long‐term outcomes. Pre‐operative PCS were 40.7 ± 13.7 for improvers and 56.6 ± 14.4 for non‐improvers; MCS were 45.8 ± 12.1 and 65.2 ± 13.7, respectively (P < 0.001 for all). There were no statistically significant differences in pre‐operative risk factors, demographics, operative factors or post‐operative variables between the two groups.

Conclusion

Among those completing this study, one in three patients did not experience long‐term HRQOL improvements following cardiac surgery. Multivariate analysis confirmed that higher pre‐operative PCS and MCS are independent predictors of worse HRQOL a year after surgery. Further research should focus on establishing the prevalence of this phenomenon worldwide and develop targeted interventions to improve long‐term self‐perceived quality of life for patients with relatively good pre‐operative health.
Robotic mitral valve plasty for mitral regurgitation after blunt chest trauma in Barlow's disease
Authors: Ishikawa Norihiko , Watanabe Go , Tarui Tatsuya , Horikawa Takahumi , Seguchi Ryuta , Kiuchi Ryuta , Tomita Shigeyuki , Ohtake Hiroshi , Kawachi Kenji
Published: July 2017

We successfully treated a case of mitral regurgitation due to chest trauma in Barlow's disease. A 71‐year‐old man was admitted with severe mitral regurgitation after blunt compression of the chest by a heavy object 5 months earlier. Preoperative examination revealed wide chordae tendineae rupture and myxomatous changes to the bileaflets. Neo‐chordae reconstruction of the anterior mitral leaflet using loop technique, triangular resection of the posterior mitral leaflet, and ring annuloplasty was performed via surgical robot. Robotic mitral valve plasty for severe mitral regurgitation due to chest trauma in Barlow's disease was achieved safely with good clinical and excellent cosmetic results.
Cardiac vagal tone, a non‐invasive measure of parasympathetic tone, is a clinically relevant tool in Type 1 diabetes mellitus
Authors: Brock C. , Jessen N. , Brock B. , Jakobsen P. E. , Hansen T. K. , Rantanen J. M. , Riahi S. , Dimitrova Y. K. , Dons‐Jensen A. , Aziz Q. , Drewes A. M. , Farmer A. D.
Published: July 2017

Aims

To compare a novel index of parasympathetic tone, cardiac vagal tone, with established autonomic variables and to test the hypotheses that (1) cardiac vagal tone would be associated with established time and frequency domain measures of heart rate and (2) cardiac vagal tone would be lower in people with Type 1 diabetes than in a matched healthy cohort and lower still in people with established neuropathy.

Methods

Cardiac vagal tone is a validated cardiometrically derived index of parasympathetic tone. It is measured using a standard three‐lead electrocardiogram which connects, via Bluetooth, to a smartphone application. A 5‐min resting recording of cardiac vagal tone was undertaken and observational comparisons were made between 42 people with Type 1 diabetes and peripheral neuropathy and 23 without peripheral neuropathy and 65 healthy people. In those with neuropathy, 24‐h heart rate variability values were compared with cardiac vagal tone. Correlations between cardiac vagal tone and clinical variables were also made.

Results

Cardiac vagal tone was lower in people with established neuropathy and Type 1 diabetes in comparison with healthy participants [median (interquartile range) linear vagal scale 3.4 (1.6–5.5 vs 7.0 (5.5–9.6); P < 0.0001]. Cardiac vagal tone was positively associated with time (r = 0.8, P < 0.0001) and frequency domain markers of heart rate variability (r = 0.75, P < 0.0001), representing established measures of parasympathetic function. Cardiac vagal tone was negatively associated with age (r=–0.32, P = 0.003), disease duration (r=–0.43, P < 0.0001) and cardiovascular risk score (r=–0.32, P = 0.006).

Conclusions

Cardiac vagal tone represents a convenient, clinically relevant method of assessing parasympathetic nervous system tone, potentially facilitating the earlier identification of people with Type 1 diabetes who should undergo formal autonomic function testing.
Diabetes and risk of occupational injury: a cohort study
Authors: Kouvonen A. , Kivimäki M. , Pentti J. , Aalto V. , Oksanen T. , Virtanen M. , Vahtera J.
Published: July 2017

Aims

To investigate if diabetes is associated with a higher risk of occupational (workplace or commuting) injury.

Methods

Medication data from the Finnish Prescription Register were used to identify diabetes cases in 2004 in a large employee cohort (the Finnish Public Sector study). These data were linked to injury records obtained from the Federation of Accident Insurance Institutions. A total of 1020 diabetes cases (median age 52 years, range 20 to 65 years; 66% women) and their 5234 age‐ and sex‐matched controls were followed up until 2011. Sex‐stratified Cox proportional hazards models, adjusting for age, occupational status, obesity and health behaviours, were applied. Because of the small number of men in the cohort, injury types and locations were only examined among women.

Results

During the median follow‐up of 6.7 years, 25% of the participants with diabetes (n=252) and 20% of those without (n=1051) experienced an occupational injury. The association between diabetes and injury was stronger in women than men (P=0.048). Diabetes was associated with a higher risk of workplace (hazard ratio 1.37, 95% CI 1.11 to 1.69) and commuting (hazard ratio 1.36, 95% CI 1.03 to 1.79) injury in women. With regard to different injury types and locations, diabetes was associated with bone fractures, dislocations, sprains and strains, and injuries to upper and lower extremities. In men, there was an association between insulin‐treated diabetes and commuting injury (hazard ratio 3.14, 95% CI 1.52 to 6.49).

Conclusions

Diabetes was associated with workplace and commuting injuries in women. Men with insulin‐treated diabetes had a higher risk of commuting injuries.
Prevalence and characteristics of paediatric Type 2 diabetes in the Republic of Ireland
Authors: O'Dea M. I. , O'Connell S. M. , O'Grady M. J.
Published: July 2017

Objective

To establish the prevalence of paediatric Type 2 diabetes in the Republic of Ireland and describe patient demographics, initial presentation, management, outcomes, comorbidities and complications.

Methods

Using a standardized proforma we conducted a cross‐sectional survey of children and adolescents aged < 16 years with a diagnosis of Type 2 diabetes between October and December 2015 in each of the 19 centres in the Republic of Ireland responsible for the care of children with diabetes.

Results

Twelve cases of Type 2 diabetes were identified, giving a prevalence in children aged <16 years of 1.2/100 000 (95% CI 0.6 to 2). Six of these children (50%) were white, two (33%) of whom were members of the travelling community. Four (33%) were of black ethnicity. The prevalence of Type 2 diabetes in traveller children was 16.1/100 000 (95% CI 1.9 to 58.1) and was similar to that in black children, a known high‐risk group, which was 13.3/100 000 (95% CI 3.6 to 34.1). The median current HbA1c value was 51 mmol/mol (6.8%) and four (33%) of the children achieved the International Society for Pediatric and Adolescent Diabetes target HbA1c of ≤48 mmol/mol (6.5%). Seven (59%) children were managed on metformin monotherapy, three (25%) were managed on insulin and metformin in combination, and two (16%) were receiving dietary management.

Conclusion

This was the first national study to estimate the prevalence of childhood Type 2 diabetes in Ireland. Despite their white ethnicity, traveller children appear to be a high‐risk group, but this finding requires further study.
Effects of adding biochar on the properties and nitrogen bioavailability of an acidic soil
Authors: Wang Z. Y. , Chen L. , Sun F. L. , Luo X. X. , Wang H. F. , Liu G. C. , Xu Z. H. , Jiang Z. X. , Pan B. , Zheng H.
Published: July 2017

Biochar has attracted global attention because of its widespread application to improve soil quality and enhance soil productivity. Five types of biochar were prepared from peanut shells at 200–600°C by slow pyrolysis, and their physicochemical properties were investigated. Biochar was produced at 300 and 400°C, PBC300 and PBC400, respectively. The two forms of biochar were evaluated as soil amendments with an incubation and a pot experiment in a soil that had become acidified because of excessive use of nitrogen (N) fertilizers. The PBC300 and PBC400 additions significantly decreased the soil bulk density and increased the pH, cation exchange capacity (CEC) and soil organic matter (SOM) content. Both types of biochar significantly decreased NH4+‐N and NO3−‐N contents as a result of N immobilization, reduced nitrification because of the enhanced microbial activity (determined by the fluorescein diacetate method) and reduced the abundance of ammonia‐oxidizing bacteria (AOB). The growth of maize (Zea mays L.) was stimulated and, compared with the unamended soil, the biomass increased by 15.2–32.7% following the addition of PBC300 or PBC400. Maize root morphology (e.g. length and tips) and the properties of the rhizosphere soil (e.g. CEC and pH) were improved by the addition of biochar, leading to enhance N bioavailability by decreasing NAE (N accumulation efficiency) and increasing NUE (N utilization efficiency). In general, the ameliorating effects of PBC400 on the acidic soil were superior to those of PBC300. These results indicate that producing a specific type of biochar based on pyrolytic temperature might be an alternative strategy for selecting the most appropriate biochar for a specific soil.

Highlights

Biochar was selected for an acidic soil based on the pyrolytic temperature.

Biochar decreased the soil bulk density and increased the soil pH, CEC and SOM.

Biochar slowed nitrification by decreasing the abundance of ammonia‐oxidizing bacteria (AOB).

Adding biochar stimulated maize growth and improved N bioavailability.
Predictors of cognitive function in patients with hypothalamic hamartoma following stereotactic radiofrequency thermocoagulation surgery
Authors: Sonoda Masaki , Masuda Hiroshi , Shirozu Hiroshi , Ito Yosuke , Akazawa Kohei , Asano Eishi , Kameyama Shigeki
Published: July 2017

Objective

To determine the predictors of cognitive function in patients with drug‐resistant gelastic seizures (GS) related to hypothalamic hamartoma (HH) before and after stereotactic radiofrequency thermocoagulation surgery (SRT).

Methods

We studied 88 patients with HH who underwentSRTbetween October 1997 and December 2014. Patients received neuropsychological tests preoperatively and postoperatively. Based on the preoperative measures, patients were categorized as “high‐functioning” (full‐scale intelligence quotient [FSIQ] ≥70; n = 48) and “low‐functioning” group (FSIQ<70; n = 40). Univariate and multivariate linear regression analyses determined the clinical, electroencephalography (EEG), and imaging factors associated with preoperative cognitive function as well as postoperative cognitive change.

Results

Eighty‐seven patients (98.8%) were followed postoperatively for an average of 3.3 years, and 75 (85.2%) of them achievedGSremission at the last hospital visit. Neuropsychological performance was significantly improved after surgery in both groups. Multivariate linear regression analysis showed that a smallerHHsize (p = 0.002) and a smaller number of antiepileptic drugs (p < 0.001) were preoperatively associated with better neuropsychological performance. Multivariate linear regression analysis showed that better postoperative improvement in cognition was associated with a shorter duration of epilepsy (p = 0.03).

Significance

Cognitive impairment related to epileptic encephalopathy may improve followingSRTin substantial proportions ofHHpatients. Reduced improvement in postoperative cognitive function in patients with longer duration of epilepsy warrants further studies to determine if earlierSRTprovides a greater chance of postoperative cognitive improvement in patients withHH.