bluuebunny/crossref_metadata_2025_split huggingface dataset:
Piped water supplies managed by civic bodies in medieval English towns
Authors: LEE JOHN S. 
Published: February 2014

ABSTRACTWhen John Leland toured England in the 1540s, he observed water conduits in several towns, including a number of smaller urban centres. Subsequent historians and archaeologists, however, have seriously understated the number and importance of piped water systems in English towns. This article uses studies of individual towns, together with civic records and Leland'sItinerary, to examine the sources and technologies of urban water supplies, the origins of civic piped water systems, their relationships to other local systems, finance, management and oversight. It will argue that the growth in piped supplies by civic bodies in the later Middle Ages reflects the importance of charitable provision and the efforts of civic authorities to establish, maintain and regulate them. An appendix lists medieval English towns known to have provided public access to piped water supplies byc. 1550.
An accountability framework to promote healthy food environments
Authors: Kraak Vivica I , Swinburn Boyd , Lawrence Mark , Harrison Paul 
Published: February 2014

AbstractObjectiveTo review the available literature on accountability frameworks to construct a framework that is relevant to voluntary partnerships between government and food industry stakeholders.DesignBetween November 2012 and May 2013, a desk review of ten databases was conducted to identify principles, conceptual frameworks, underlying theories, and strengths and limitations of existing accountability frameworks for institutional performance to construct a new framework relevant to promoting healthy food environments.SettingFood policy contexts within high-income countries to address obesity and diet-related non-communicable diseases.SubjectsEligible resources (n 26) were reviewed and the guiding principles of fifteen interdisciplinary frameworks were used to construct a new accountability framework.ResultsStrengths included shared principles across existing frameworks, such as trust, inclusivity, transparency and verification; government leadership and good governance; public deliberations; independent bodies recognizing compliance and performance achievements; remedial actions to improve accountability systems; and capacity to manage conflicts of interest and settle disputes. Limitations of the three-step frameworks and ‘mutual accountability’ approach were an explicit absence of an empowered authority to hold all stakeholders to account for their performance.ConclusionsWe propose a four-step accountability framework to guide government and food industry engagement to address unhealthy food environments as part of a broader government-led strategy to address obesity and diet-related non-communicable diseases. An independent body develops clear objectives, a governance process and performance standards for all stakeholders to address unhealthy food environments. The empowered body takes account (assessment), shares the account (communication), holds to account (enforcement) and responds to the account (improvements).
Capturing changes in dietary patterns among older adults: a latent class analysis of an ageing Irish cohort
Authors: Harrington Janas M , Dahly Darren L , Fitzgerald Anthony P , Gilthorpe Mark S , Perry Ivan J 
Published: February 2014

AbstractObjectiveData-driven approaches to dietary patterns are under-utilized; latent class analyses (LCA) are particularly rare. The present study used an LCA to identify subgroups of people with similar dietary patterns, explore changes in dietary patterns over a 10-year period and relate these dynamics to sociodemographic factors and health outcomes.DesignThe 1998 baseline and 2008 follow-up of the Cork and Kerry Diabetes and Heart Disease Study. Diets were assessed with a standard FFQ. LCA, under the assumption of conditional independence, was used to identify mutually exclusive subgroups with different dietary patterns, based on food group consumption.SettingRepublic of Ireland.SubjectsMen and women aged 50–69 years at baseline (n 923) and at 10-year follow-up (n 320).ResultsThree dietary classes emerged: Western, Healthy and Low-Energy. Significant differences in demographic, lifestyle and health outcomes were associated with class membership. Between baseline and follow-up most people remained ‘stable’ in their dietary class. Most of those who changed class moved to the Healthy class. Higher education was associated with transition to a healthy diet; lower education was associated with stability in an unhealthy pattern. Transition to a healthy diet was associated with higher CVD risk factors at baseline: respondents were significantly more likely to be smokers, centrally obese and to have hypertension (non-significant).ConclusionsLCA is useful for exploring dietary patterns transitions. Understanding the predictors of longitudinal stability/transitions in dietary patterns will help target public health initiatives by identifying subgroups most/least likely to change and most/least likely to sustain a change.
243 GHz low-noise amplifier MMICs and modules based on metamorphic HEMT technology
Authors: Tessmann Axel , Hurm Volker , Leuther Arnulf , Massler Hermann , Weber Rainer , Kuri Michael , Riessle Markus , Stulz Hans-Peter , Zink Martin , Schlechtweg Michael , Ambacher Oliver , Närhi Tapani 
Published: February 2014

Two compact H-band (220–325 GHz) low-noise millimeter-wave monolithic integrated circuit (MMIC) amplifiers have been developed, based on a grounded coplanar waveguide (GCPW) technology utilizing 50 and 35 nm metamorphic high electron mobility transistors (mHEMTs). For low-loss packaging of the circuits, a set of waveguide-to-microstrip transitions has been realized on 50-μm-thick GaAs substrates demonstrating an insertion loss of <0.5 dB at 243 GHz. By applying the 50 nm gate-length process, a four-stage cascode amplifier module achieved a small-signal gain of 30.6 dB at 243 GHz and more than 28 dB in the bandwidth from 218 to 280 GHz. A second amplifier module, based on the 35-nm mHEMT technology, demonstrated a considerably improved gain of 34.6 dB at 243 GHz and more than 32 dB between 210 and 280 GHz. At the operating frequency, the two broadband low-noise amplifier modules achieved a room temperature noise figure of 5.6 dB (50 nm) and 5.0 dB (35 nm), respectively.
A plant factory for moth pheromone production
Authors: Ding Bao-Jian , Hofvander Per , Wang Hong-Lei , Durrett Timothy P. , Stymne Sten , Löfstedt Christer 
Published: February 2014

AbstractMoths depend on pheromone communication for mate finding and synthetic pheromones are used for monitoring or disruption of pheromone communication in pest insects. Here we produce moth sex pheromone, using Nicotiana benthamiana as a plant factory, by transient expression of up to four genes coding for consecutive biosynthetic steps. We specifically produce multicomponent sex pheromones for two species. The fatty alcohol fractions from the genetically modified plants are acetylated to mimic the respective sex pheromones of the small ermine moths Yponomeuta evonymella and Y. padella. These mixtures are very efficient and specific for trapping of male moths, matching the activity of conventionally produced pheromones. Our long-term vision is to design tailor-made production of any moth pheromone component in genetically modified plants. Such semisynthetic preparation of sex pheromones is a novel and cost-effective way of producing moderate to large quantities of pheromones with high purity and a minimum of hazardous waste.
Angiotensin-converting enzyme 2 is subject to post-transcriptional regulation by miR-421
Authors: Lambert Daniel W. , Lambert Louise A. , Clarke Nicola E. , Hooper Nigel M. , Porter Karen E. , Turner Anthony J. 
Published: February 2014

ACE2 (angiotensin converting enzyme 2) plays a critical role in the local tissue RAS (renin–angiotensin system) by hydrolysing the potent hypertensive and mitogenic peptide AngII (angiotensin II). Changes in the levels of ACE2 have been observed in a number of pathologies, including cardiovascular disease, but little is known of the mechanisms regulating its expression. In the present study, therefore, the potential role of miRNAs in the regulation of ACE2 expression in primary human cardiac myofibroblasts was examined. Putative miRNA-binding sites were identified in the 3′-UTR of the ACE2 transcript using online prediction algorithms. Two of these, miR-200b and miR-421, were selected for further analysis. A reporter system using the 3′-UTR of ACE2 fused to the coding region of firefly luciferase was used to determine the functionality of the identified binding sites in vitro. This identified miR-421, but not miR-200b, as a potential regulator of ACE2. The ability of miR-421, an miRNA implicated in the development of thrombosis, to down-regulate ACE2 expression was subsequently confirmed by Western blot analysis of both primary cardiac myofibroblasts and transformed cells transfected with a synthetic miR-421 precursor. Real-time PCR analysis of miR-421 revealed widespread expression in human tissues. miR-421 levels in cardiac myofibroblasts showed significant inter-patient variability, in keeping with the variability of ACE2 expression we have observed previously. In conclusion, the present study is the first to demonstrate that ACE2 may be subject to post-transcriptional regulation and reveals a novel potential therapeutic target, miR-421, which could be exploited to modulate ACE2 expression in disease.
Study of gene transfection enhancement and parameters optimisation using electroporation microchip
Authors: Chung Yung‐Chiang , Liao Wei‐Jie , Huang Yu‐Tzu , Wu Cheng‐Yuan 
Published: February 2014

A design for improving gene transfection efficiency, which provides simple fabrication, low voltage and power consumptions, and easy implementation is developed; this design entails combining high and low electric fields, adjusting the voltage, using different numbers of pulses with varying durations, and different types of buffers with differing conductivities. The human embryonic kidney 293 (293T) cells were used. It was shown that a combination of two units of high electric field (1600 V/cm) for 0.6 ms and three units of low electric field (800 V/cm) for 1.2 ms is the optimum combination. This combination yielded a survival rate greater than 70% and a transfection rate of approximately 45%. The transfection rate of this combination was 80–100% greater than that obtained using two pulses, and the transfection rate obtained using two pulses was 40–50% greater than that obtained using single pulses. However, the survival rate decreases when the pulse duration is considerably long, even for low electric fields; therefore the number of pulses and their durations should be limited. The hypoosmolar buffer yielded the largest transfection rate. It was shown that the conductivity of the buffer solution is an important parameter, with the appropriate value ranging within 1.0–3.6 mS/cm. The transfection rate of the 293T cells using a cytoporation buffer could be enhanced by adding potassium ions in concentration lower than 2 μg/ml.
Instability of the Vertebrae Remains following Balloon Kyphoplasty
Authors: Tarukado Kiyoshi , Tono Osamu , Ikuta Ko , Harimaya Katsumi , Matsumoto Yoshihiro , Okada Seiji , Hayashida Mitsumasa , Iwamoto Yukihide , Doi Toshio 
Published: February 2014

Study Design Retrospective cohort study. Objectives The mechanism underlying the pain relief observed following balloon kyphoplasty (BKP) to vertebral compression fractures is reported to involve stabilization of the fractured vertebrae. However, whether fixation of the vertebrae was achieved immediately after BKP has not been investigated. The purpose of this study was to assess fixation of the vertebrae immediately after BKP and whether the instability was related to visual analog scale (VAS) scores. Methods Thirty-eight patients with vertebrae that were evaluated on lateral roentgenkymography within 1 week after BKP were recruited. Instability was defined as a cleft observed between the cement and end plate of the vertebra in the supine position that disappeared in the sitting position, and the posterior wall height of the vertebra was reduced in the sitting position. Results Instability of the vertebrae immediately after BKP was observed in 17 cases. VAS scores improved in all cases, and no significant differences were observed with or without instability. Conclusions The mechanism of rapid pain relief following BKP was not strong fixation but some degree of stabilization or other factors. We suggest that more research is needed about the mechanism of pain relief following BKP in the future.
How fragmentation and corridors affect wind dynamics and seed dispersal in open habitats
Authors: Damschen Ellen I. , Baker Dirk V. , Bohrer Gil , Nathan Ran , Orrock John L. , Turner Jay R. , Brudvig Lars A. , Haddad Nick M. , Levey Douglas J. , Tewksbury Joshua J. 
Published: February 2014

Significance
Understanding how widespread human-induced global changes are affecting the movement and dispersal of organisms is critical for maintaining species diversity and making sound land management decisions. In contrast with animal-dispersed species, little is known about how wind-dispersed species are affected by conservation strategies such as corridors. We use a combination of mechanistic models and field data to show that habitat corridors alter wind dynamics in a way that promotes seed dispersal and appears to increase plant diversity. Wind direction also interacts with landscape orientation to determine when corridors can provide connectivity.
Designer receptor manipulations reveal a role of the locus coeruleus noradrenergic system in isoflurane general anesthesia
Authors: Vazey Elena M. , Aston-Jones Gary 
Published: February 2014

Significance
Thousands of people each day receive general anesthesia. Recovery from the anesthetic state is a passive process that can be variable and unpredictable. Identifying neural systems involved in recovery of consciousness after general anesthesia is fundamental to optimizing anesthetic safety and our knowledge of anesthetic action. We examined how norepinephrine from the nucleus locus coeruleus (LC) affects general anesthesia, and found that blocking the action of norepinephrine, particularly in the CNS, delayed recovery from general anesthesia. Using genetic tools to selectively activate only LC neurons, we found that LC activation was sufficient to alter EEG measurements of anesthetic depth and accelerate recovery of consciousness. Our data show that LC activity can alter the anesthetic state, and that noradrenergic medications may affect clinical responses to anesthetic agents.
Commanding Legality
Authors: Kawar Leila 
Published: February 2014

AbstractThe emergence of constitutional review in France has attracted substantial attention from scholars of public law. Yet little has been written about the political implications of the expansion of rights-based review on the part of France’s highest administrative jurisdiction, the Conseil d’Etat. The argument is made in this article that repeat litigation by French lawyers defending the cause of immigrants is an important site for observing the symbolic power of legal forms. The analysis focuses on cases challenging immigration-related administrative regulations and shows how the process of repeatedly adjudicating these issues has focused attention away from litigants and their claims at the same time that it has reinforced the centrality of the Conseil d’Etat and its formalist jurisprudence in administrative governance. This detailed examination of the practical operation of France’s highest administrative jurisdiction leads to the surprising conclusion that this distinctly nonadversarial form of adjudication has contributed over the long term to institutionalizing a juridification of immigration-related administrative policy making.
Improved protein–ligand binding affinity prediction by using a curvature-dependent surface-area model
Authors: Cao Yang , Li Lei 
Published: February 2014

Motivation: Hydrophobic effect plays a pivotal role in most protein–ligand binding. State-of-the-art protein–ligand scoring methods usually treat hydrophobic free energy as surface tension, which is proportional to interfacial surface area for simplicity and efficiency. However, this treatment ignores the role of molecular shape, which has been found very important by either experimental or theoretical studies.
Results: We propose a new empirical scoring function, named Cyscore. Cyscore improves the prediction accuracy by using a novel curvature-dependent surface-area model, which is able to distinguish convex, planar and concave surface in hydrophobic free energy calculation. Benchmark tests show that this model significantly improves the protein–ligand scoring and Cyscore outperforms a variety of well established scoring functions using PDBbind benchmark sets for binding affinity correlation and ranking tests. We expect the curvature-dependent surface-area model and Cyscore would contribute to the study of protein–ligand interactions.
Availability: Cyscore is available to non-commercial users at http://clab.labshare.cn/software/cyscore.html.
Contact: cao@scu.edu.cn
Supplementary information: Supplementary Data is available at Bioinformatics online.
Getting all information out of logbooks: estimating banana prawn fishable biomass, catchability, and fishing power increase, with a focus on natural mortality
Authors: Zhou Shijie , Buckworth Rik C. , Ellis Nick , Deng Roy A. , Pascoe Sean 
Published: February 2014

Abstract
Biomass, catchability, and natural mortality are key parameters in fish stock assessment. Yet, it is difficult to estimate these quantities, especially natural mortality, when only fishery data are available. Using a method of population depletion analysis, we estimated these population and biological quantities for the white banana prawn (Penaeus merguiensis) in Australia's valuable Northern Prawn Fishery. In addition, we directly included fishing power change over time. The models were implemented in a Bayesian framework by incorporating process error, observation error, and random variability for the underlying parameters. The posterior median initial fishable biomass ranged from ∼2000 to 7000 t year−1, and the median catchability varied from ∼3.8 × 10−4 to 7.3 × 10−4 boat-day−1, resulting in an average fishing power increase of 2.6% per year. An unexpected result is the estimate of exponential natural mortality rate of ∼0.03 week−1. This value is substantially lower than an earlier estimate of 0.05 week−1, which was based on a single year's fishery data in one stock region and has been widely used for over four decades without validation. We attribute this low natural mortality estimate mainly to prawn aggregation behaviour.
T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data
Authors: Fiston-Lavier Anna-Sophie , Barrón Maite G. , Petrov Dmitri A. , González Josefa 
Published: February 2014

ABSTRACTTransposable elements (TEs) constitute the most active, diverse and ancient component in a broad range of genomes. Complete understanding of genome function and evolution cannot be achieved without a thorough understanding of TE impact and biology. However, in-depth analysis of TEs still represents a challenge due to the repetitive nature of these genomic entities. In this work, we present a broadly applicable and flexible tool: T-lex2. T-lex2 is the only available software that allows routine, automatic, and accurate genotyping of individual TE insertions and estimation of their population frequencies both using individual strain and pooled next-generation sequencing (NGS) data. Furthermore, T-lex2 also assesses the quality of the calls allowing the identification of miss-annotated TEs and providing the necessary information to re-annotate them. The flexible and customizable design of T-lex2 allows running it in any genome and for any type of TE insertion. Here, we tested the fidelity of T-lex2 using the fly and human genomes. Overall, T-lex2 represents a significant improvement in our ability to analyze the contribution of TEs to genome function and evolution as well as learning about the biology of TEs. T-lex2 is freely available online athttp://sourceforge.net/projects/tlex/.AbbreviationsTEtransposable elementNGSnext-generation sequencingLTRlong-terminal repeatTSDtarget site duplicationPTSputative target sitePEpaired-end
Genetic drift suppresses bacterial conjugation in spatially structured populations
Authors: Freese Peter D. , Korolev Kirill S. , Jiménez José I. , Chen Irene A. 
Published: February 2014

ABSTRACTConjugation is the primary mechanism of horizontal gene transfer that spreads antibiotic resistance among bacteria. Although conjugation normally occurs in surface-associated growth (e.g., biofilms), it has been traditionally studied in well-mixed liquid cultures lacking spatial structure, which is known to affect many evolutionary and ecological processes. Here we visualize spatial patterns of gene transfer mediated by F plasmid conjugation in a colony ofEscherichia coligrowing on solid agar, and we develop a quantitative understanding by spatial extension of traditional mass-action models. We found that spatial structure suppresses conjugation in surface-associated growth because strong genetic drift leads to spatial isolation of donor and recipient cells, restricting conjugation to rare boundaries between donor and recipient strains. These results suggest that ecological strategies, such as enforcement of spatial structure and enhancement of genetic drift, could complement molecular strategies in slowing the spread of antibiotic resistance genes.
Extensive translation of small ORFs revealed by polysomal ribo-Seq
Authors: Aspden Julie L. , Eyre-Walker Ying Chen , Philips Rose J. , Brocard Michele , Amin Unum , Couso Juan 
Published: February 2014

ABSTRACTThousands of small Open Reading Frames (smORFs) encoding small peptides of fewer than 100 amino acids exist in our genomes. Examples of functional smORFs have been characterised in a few species but the actual number of translated smORFs, and their molecular, functional and evolutionary features are not known. Here we present a genome-wide assessment of smORF translation by ribosomal profiling of polysomal fractions. This ‘polysomal ribo-Seq’ suggests that smORFs are translated at the same level and in the same relative numbers (80%) as normal proteins. The smORF peptides appear widely conserved, show activity in cells, and display a putative amino acid signature. These findings reinforce the idea that smORFs are an abundant and fundamental genome component, displaying features usually attributed to canonical proteins, including high translation levels, biological function, amino acid sequence specificity and cross-species conservation.