bluuebunny/crossref_metadata_2025 huggingface dataset:
Crystal organometal halide perovskites with promising optoelectronic applications
Authors: Chen Junnian , Zhou Shasha , Jin Shengye , Li Huiqiao , Zhai Tianyou
Published: November 2015

Crystal organometal halide perovskites with specific morphologies and unique optoelectronic properties have extended their applications into the whole optoelectronic field.
Informed shuffled belief‐propagation decoding for low‐density parity‐check codes
Authors: Gong Yi , Liu Xingcheng , Han Guojun , Wu Bin
Published: November 2015

Shuffled belief propagation (SBP), as a sequential belief propagation (BP) algorithm, speeds up the convergence of BP decoding, and maintains the least complexity of flooding BP. However, its performance is remarkably inferior to informed dynamic scheduling (IDS) BP algorithms. The authors design an informed dynamic location method, based on the residuals of variable node log‐likelihood ratio values, to reorder variable nodes of SBP to be updated. The location method significantly accelerates the convergence of SBP algorithm from two aspects: the unstable variable node with the largest residual to be updated first, and selecting the largest residual locally. Simulation results show that the proposed algorithm performs nearly the same as the best performance of IDS BP algorithms, and behaves prominently at high signal‐to‐noise ratios.
Energy‐efficient link selection scheme in a two‐hop relay scenario with considering a mobile relay
Authors: Li Xian , Tang Qiuling , Sun Changyin
Published: November 2015

Recently researches show that significant energy saving can be achieved by introducing mobile relays into wireless sensor networks. However, due to the extra transceiver circuit energy and the mobility energy consumed by the mobile relay, it is not always better to pass data through the relay rather than to send it from source to destination directly. In this study, the authors study a novel link selection problem in a two‐hop relay scenario where the relay has the ability to move. In this scenario, data from source can be passed through three kinds of links: the direct link, the initial relay link and the adjusted relay link. From the energy‐saving perspective, the optimal moving direction, the position adjustment criterion and the optimal position of the mobile relay are firstly studied through mathematical analysis. Based on a comprehensive discussion of the energy performances of these three kinds of links, and energy‐efficient link selection scheme is then presented. Both the amount of data to be sent and the distance between source and destination are shown to be closely related to the link selection scheme. Finally numerical simulations are carried out to verify the theoretical results.
Cardiovascular Risk in Primary Hyperaldosteronism
Authors: Warchoł-Celińska E. , Lenders J. W. M. , Januszewicz A. , Prejbisz A.
Published: November 2015

After the first cases of primary aldosteronism were described and characterized by Conn, a substantial body of experimental and clinical evidence about the long-term effects of excess aldosterone on the cardiovascular system was gathered over the last 5 decades. The prevalence of primary aldosteronism varies considerably between different studies among hypertensive patients, depending on patient selection, the used diagnostic methods, and the severity of hypertension. Prevalence rates vary from 4.6 to 16.6% in those studies in which confirmatory tests to diagnose primary aldosteronism were used. There is also growing evidence indicating that prolonged exposure to elevated aldosterone concentrations is associated with target organ damage in the heart, kidney, and arterial wall, and high cardiovascular risk in patients with primary aldosteronism. Therefore, the aim of treatment should not be confined to BP normalization and hypokalemia correction, but rather should focus on restoring the deleterious effects of excess aldosterone on the cardiovascular system. Current evidence convincingly demonstrates that both surgical and medical treatment strategies beneficially affect cardiovascular outcomes and mortality in the long term. Further studies can be expected to provide better insight into the relationship between cardiovascular risk and complications and the genetic background of primary aldosteronism.
Research Update: Facile synthesis of CoFe2O4 nano-hollow spheres for efficient bilirubin adsorption
Authors: Rakshit Rupali , Pal Monalisa , Chaudhuri Arka , Mandal Madhuri , Mandal Kalyan
Published: November 2015

Herein, we report an unprecedented bilirubin (BR) adsorption efficiency of CoFe2O4 (CFO) nanostructures in contrast to the commercially available activated carbon and resin which are generally used for haemoperfusion and haemodialysis. We have synthesized CFO nanoparticles of diameter 100 nm and a series of nano-hollow spheres of diameter 100, 160, 250, and 350 nm using a simple template free solvothermal technique through proper variation of reaction time and capping agent, oleylamine (OLA), respectively, and carried out SiO2 coating by employing Stöber method. The comparative BR adsorption study of CFO and SiO2 coated CFO nanostructures indicates that apart from porosity and hollow configuration of nanostructures, the electrostatic affinity between anionic carboxyl group of BR and cationic amine group of OLA plays a significant role in adsorbing BR. Finally, we demonstrate that the BR adsorption capacity of the nanostructures can be tailored by varying the morphology as well as size of the nanostructures. We believe that our developed magnetic nanostructures could be considered as a potential material towards therapeutic applications against hyperbilirubinemia.
Photothermally excited force modulation microscopy for broadband nanomechanical property measurements
Authors: Wagner Ryan , Killgore Jason P.
Published: November 2015

We demonstrate photothermally excited force modulation microscopy (PTE FMM) for mechanical property characterization across a broad frequency range with an atomic force microscope (AFM). Photothermal excitation allows for an AFM cantilever driving force that varies smoothly as a function of drive frequency, thus avoiding the problem of spurious resonant vibrations that hinder piezoelectric excitation schemes. A complication of PTE FMM is that the sub-resonance cantilever vibration shape is fundamentally different compared to piezoelectric excitation. By directly measuring the vibrational shape of the cantilever, we show that PTE FMM is an accurate nanomechanical characterization method. PTE FMM is a pathway towards the characterization of frequency sensitive specimens such as polymers and biomaterials with frequency range limited only by the resonance frequency of the cantilever and the low frequency limit of the AFM.
A framework for administrative claim data to explore healthcare coordination and collaboration
Authors: Uddin Shahadat , Kelaher Margaret , Srinivasan Uma
Published: November 2015

Previous studies have documented the application of electronic health insurance claim data for health services research purposes. In addition to administrative and billing details of healthcare services, insurance data reveal important information regarding professional interactions and/or links that emerge among healthcare service providers through, for example, informal knowledge sharing. By using details of such professional interactions and social network analysis methods, the aim of the present study was to develop a research framework to explore health care coordination and collaboration. The proposed framework was used to analyse a patient-centric care coordination network and a physician collaboration network. The usefulness of this framework and its applications in exploring collaborative efforts of different healthcare professionals and service providers is discussed. What is known about the topic? Application of methods and measures of social network analytics in exploring different health care collaboration and coordination networks is a comparatively new research direction. It is apparent that no other study in the present healthcare literature proposes a generic framework for examining health care collaboration and coordination using an administrative claim dataset. What does this paper add? Using methods and measures of social network analytics, this paper proposes a generic framework for analysing various health care collaboration and coordination networks extracted from an administrative claim dataset. What are the implications for the practitioners? Healthcare managers or administrators can use the framework proposed in the present study to evaluate organisational functioning in terms of effective collaboration and coordination of care in their respective healthcare organisations.
Advance care planning in Australia: what does the law say?
Authors: Carter Rachel Z. , Detering Karen M. , Silvester William , Sutton Elizabeth
Published: November 2015

Advance care planning (ACP) assists people to plan for their future health and personal care. ACP encourages a person to legally appoint a substitute decision maker (SDM) and to document any specific wishes regarding their future health care in an advance care directive (ACD). Formal documentation of wishes increases the chances that a person’s wishes will be known and followed. However, one of the biggest impediments for doctors following the person’s wishes is uncertainty surrounding the law, which is complicated and varies between the states and territories of Australia. SDM legislation varies regarding who can be appointed, how they are appointed, the powers that an SDM can be given and the decision-making principles that the SDM needs to follow. In circumstances where an SDM has not been appointed, the hierarchy for determining the default SDM for a person also varies between states. Although many states have legislated ACD forms allowing for documentation of a person’s health care wishes, these forms allow for different things to be documented and have different requirements to be valid. The Australian population is mobile, with patients frequently moving between states. The status of ACP documentation created in a state other than the state in which a patient requires treatment also varies, with some states recognising interstate ACDs whereas others do not. This article outlines the legal status of ACDs, within Australian jurisdictions, including the legal validity of interstate ACDs, and argues that uniform laws and documents would assist with awareness and understanding of, and compliance with, ACDs.
A novel approach for managing the growing demand for ambulance services by low-acuity patients
Authors: Eastwood Kathryn , Morgans Amee , Smith Karen , Hodgkinson Angela , Becker Gareth , Stoelwinder Johannes
Published: November 2015

Objective The aim of the present study was to describe the Ambulance Victoria (AV) secondary telephone triage service, called the Referral Service (RS), for low-priority patients calling triple zero. This service provides alternatives to ambulance dispatch, such as doctor or nurse home visits. Methods A descriptive epidemiological review of all the cases managed between 2009 and 2012 was conducted, using data from AV case records, the Victorian Admitted Episodes Dataset and the Australian Bureau of Statistics. Cases were reviewed for patient demographics, condition, final disposition and RS outcome. Results In all, 107148 cases were included in the study, accounting for 10.3% of the total calls for ambulance attendance. Median patient age was 54 years and 55% were female. Geographically based socioeconomic status was associated with the rate of calls to the RS (r = –0.72; 95% confidence interval CI –0.104, –0.049; P < 0.001). Abdominal pain and back symptoms were the most common patient problems. Although 68% of patients were referred to the emergency department, only 27.6% of the total cases were by emergency ambulance; the remainder were diverted to non-emergency ambulance or the patient’s own private transport. The remaining 32% of cases were referred to alternative service providers or given home care advice. Conclusions This paper describes the use of an ongoing secondary triage service, providing an effective strategy for managing emergency ambulance demand. What is known about the topic? Some calls to emergency services telephone numbers for ambulance assistance consist of cases deemed to be low-acuity that could potentially be better managed in the primary care setting. The demand on ambulance resources is increasing each year. Secondary telephone triage systems have been trialled in ambulance services in the US and UK with minimal success in terms of overall impact on ambulance resourcing. What does this paper add? This study describes a model of secondary telephone triage in the ambulance setting that has provided an effective way to divert patients to more suitable forms of health care to meet their needs. What are the implications for practitioners? The implications for practitioners are vast. Some of the issues that currently face paramedics include: fatigue because of high workloads; skills decay because of a lack of exposure to patients requiring intervention with skills the paramedics have, as well as a lack of time for paramedics to practice these skills during their downtime; and decreasing job satisfaction linked to both these factors. Implications for patients include quicker response times because more ambulances will be available to respond and increased patient safety because of decreased fatigue and higher skill levels in paramedics.
Effects of sulfur on arsenic accumulation in seedlings of the mangrove Aegiceras conrniculatum
Authors: Wu Guirong , Lu Haoliang , Liu Jingchun , Yan Chongling
Published: November 2015

Levels of arsenic (As) contamination are generally increasing in the sediments of mangrove forests, which represent some of the world’s most threatened marine habitats. The highly anaerobic soils of these important coastal ecosystems are sulfide-rich, yet the potential role of sulfur (S) in the accumulation of As within mangrove tissues is poorly understood. To investigate those dynamics, the present study evaluated the effect of supplemental S on the accumulation of As in mangrove (Aegiceras conrniculatum L.) seedlings. We applied treatments in a 4 × 4 completely randomised factorial design that consisted of four S concentrations (0, 1, 2 and 4 g kg–1, in the form of S monomer) combined with four As concentrations (0, 30, 60 and 150 mg kg–1, in the form of Na2HAsO4·7H2O). Three replicates of each treatment combination were conducted. The experiment demonstrated that the effect of S was inversely related to As accumulation in the seedlings; it enhanced As accumulation when applied at low concentrations, and decreased its accumulation when applied at high concentrations. Moreover, supplying S altered the relative concentration of the different forms of As in seedlings, namely As (V) and As (III), and significantly decreased their concentration in roots (P < 0.01). Taken together, our results suggest that the addition of exiguous S can mitigate the toxicity of As to mangrove seedlings, which has implications for the remediation of polluted coastal areas that are vegetated with mangrove forests.
Synthesis of Non-Symmetrical and Atropisomeric Dibenzo[1,3]diazepines: Pd/CPhos-Catalysed Direct Arylation of Bis-Aryl Aminals
Authors: Wezeman Tim , Hu Yuling , McMurtrie John , Bräse Stefan , Masters Kye-Simeon
Published: November 2015

Pd/CPhos-catalysis provides direct arylation/cyclisation of methylene-linked bis-anilines to dibenzo[1,3]diazepines v, which are both non-(C2)-symmetrical and axially chiral. Synthesis of the direct arylation substrates commences with substitution of (N-acyl)anilines to methylene methyl sulfide derivatives, followed by halogenation/de-thiomethylation to N-(chloromethyl)anilines. These are substituted with a second aniline derivative, allowing modular preparation of (ortho-halo)aryl-aminal-linked arenes 4. The C–H functionalising direct arylation conditions were adapted from Fagnou and co-workers: substrates and potassium carbonate were heated in dimethylacetamide in the presence of palladium acetate and an electron-rich and sterically hindered biarylphosphine ligand, here CPhos 5. These conditions delivered the C1-(a)symmetric dibenzo[1,3]diazepine targets, which, due to torsion around the axis of the newly formed biaryl bond, are also intrinsically atropisomeric. The axially twisted scaffold is known to impart special properties to ligands/catalysts when the products are further converted into the corresponding seven-membered ring-containing N-heterocyclic carbenes (e.g. xii and xiv).
Potential impact of the human papillomavirus vaccine on the incidence proportion of genital warts in French women (EFFICAE study): a multicentric prospective observational study
Authors: Judlin Philippe , Jacquard Anne-Carole , Carcopino Xavier , Aubin François , Dahlab André , Mistretta Frédéric , Not Didier , Boelle Pierre-Yves , Aynaud Olivier , Soubeyrand Benoît
Published: November 2015

Background
The objective was to evaluate the effect of a HPV vaccination program on the incidence proportion of a proxy, genital warts (GW), in women in France. Methods: The number of primary GW cases was prospectively recorded over two 4-month periods before (T0: Dec 2008 to March 2009) and after (T1: Dec 2011 to March 2012) a HPV vaccination program. A total of 160 gynaecologists participated in T0 and 189 in T1. Primary genital herpes (HSV) infection was used as a control. Results: During T0, 39 190 15- to 26 year-old women were seen, of whom 176 were diagnosed with GW (incidence proportion: 0.45%) and 155 with primary HSV infection (incidence proportion: 0.39%). During T1, 45 628 females were seen [229 with GW (incidence proportion: 0.50%) and 202 with HSV (incidence proportion: 0.44%)]. In the 15–20 years age category, the incidence proportion of primary GW decreased from 0.41% to 0.30% (P = 0.128) between T0 and T1, and the proportion of women newly diagnosed with primary genital herpes diseases slightly increased from 0.34% to 0.38% (P = 0.620). In the 15–18 years age group, this decrease became significant (0.34% to 0.18%; P = 0.048). Conclusions: A trend for a non-significant decreased incidence proportion of GW was observed in young women below 20 years who are more frequently vaccinated. This may be the result of HPV vaccination and suggests that a substantial increase in vaccine coverage could lead to a more pronounced decreased incidence proportion of GW in the future.
Costs of pleasure and the benefits of pain: self-perceived genital sensation, anatomy and sexual dysfunction
Authors: Callens Nina , Bronselaer Guy , De Sutter Petra , De Cuypere Griet , T'Sjoen Guy , Hoebeke Piet , Cools Martine
Published: November 2015

Background
Research has highlighted the complex association between female sexual dysfunction (FSD) and distress regarding sexual activity, with decreased physical pleasure being an important mediator. The current study aims to elucidate the association between pleasurable and painful genital sensitivity and FSD, and to further investigate whether FSD may be distressing because it prevents the experience of sexual pleasure, induces pain or both. Methods: Sexually active women (n = 256; median, 22 years; range, 18–49 years) completed web-based questionnaires, including the Self-Assessment of Genital Anatomy and Sexual Function, the Female Sexual Function Index and the Female Sexual Distress Scale. Results: Women reported their clitoris to be more sensitive than their vagina in terms of having more pleasurable responses (P < 0.001), but not more painful responses (P = 0.49). In women with FSD (n = 36), impaired self-perceived genital sensation was found: they reported significantly less sexual pleasure and orgasm intensity, and more orgasm effort and discomfort within the clitoral and vaginal area than women without FSD (n = 220) (P-value < 0.05). The odds of having FSD were significantly greater in women with perceived increased discomfort in the vaginal area during stimulation (odds ratio = 5.59, P = 0.009, 95% confidence interval: 1.53–20.39), but not in the clitoral area. Conclusions: The data provide evidence of the relevance of self-perceived genital sensitivity to sexual pleasure and overall sexual experience. Enhancing the pleasurableness of genital sensations, especially during partnered sex, could decrease the likelihood of experiencing pain and concomitant FSD.
Anuran developmental plasticity loss: the cost of constant salinity stress
Authors: Kearney Brian D. , Byrne Phillip G. , Reina Richard D.
Published: November 2015

In animals with a complex life cycle, changes in biotic and abiotic conditions during development can alter growth and maturation rates, causing carry-over effects in postmetamorphic phenotypes. In anurans, this developmental plasticity can result in a trade-off between length of larval period and body size at metamorphosis in stressful environments. Secondary salinisation has been identified as a substantial stressor to amphibians; however, little is known about how salinity-induced developmental plasticity differs between anuran populations. We examined differences in survival, time to metamorphosis, size at metamorphosis (mass and snout–vent length) and body condition at metamorphosis in response to elevated salinity in three populations of the brown tree frog (Litoria ewingii). Significant differences in size at metamorphosis between salinity treatments were observed in tadpoles sourced from freshwater wetlands and ephemeral wetlands, with tadpoles showing a reduced mass and snout–vent length at metamorphosis in the higher-salinity treatment. There were no significant differences in metamorphic traits between salinity treatments in tadpoles sourced from a consistently brackish wetland, suggesting either an erosion of developmental plasticity in response to elevated salinity, or the magnitude of salinity required to alter developmental traits is higher in this population. Our results indicate that environmental conditions of source populations need to be considered when studying life-history adaptations in response to environmental change.
For freedom alone: Secession after the Scottish referendum
Authors: Waters Timothy William
Published: November 2015

In September 2014, the people of Scotland voted on whether or not to become an independent state. The consequences of independence would have been complex –decisions about accession to the EU, currency union, defense. Seemingly less dramatic, yet no less important, are the consequences of Scotland not seceding — the effects in global law and politics of the very fact that the referendum happened, and that it failed. Many elements of the Scottish case find close parallels in claims for secession elsewhere in the world. Yet those claims more often meet less welcoming receptions. Indeed, it is not the attempt to secede, but the existing state's acquiescence that marks this case as different: The UK is the rare country that acknowledges the possibility of its own division. Great Britain's acquiescence both made Scottish secession possible and made it an outlier, whose precedential value must be closely interrogated. The key missing element is any evidence that the process was shaped by a sense of international legal obligation — indeed, the pathways of Scottish secession have been an insular affair, a function of particularly British law and politics, in which international law played little role. This article argues that the Scottish referendum provides little precedent for a changing legal norm — yet also offers a compelling model for how such a new norm ought to look. This article is about something that did not happen, and why it does not matter — but also why precisely that is so important.
Proportionality in Investor-State Arbitration
Authors: Bücheler Gebhard
Published: November 2015

While international investment law is one of the most dynamic and thriving fields of international law, it is increasingly criticized for failing to strike a fair balance between private property rights and the public interest. Proportionality is a tool to resolve conflicts between competing rights and interests. This book assesses its current role, its potential, and its limits in investor–State arbitration. Proportionality is often lauded for reconciling colliding interests. This book identifies three factors arbitrators should consider before engaging in a proportionality analysis: the rule of law, the risk of judicial law-making, and the availability of a value system that guides the proportionality analysis. Apart from making suggestions of when arbitrators should apply proportionality and when not, the book outlines what States can do to recalibrate the balance between private property rights and the public interest if they wish to do so without dismantling the current system of investor–State arbitration. The book considers whether and to what extent the notion of general principles of law within the meaning of Article 38(1)(c) of the ICJ Statute and the concept of systemic integration enshrined in Article 31(3)(c) of the Vienna Convention on the Law of Treaties provide a valid legal foundation for applying proportionality in investor–State arbitration.
Proportionality and Expropriation
Authors: Bücheler Gebhard
Published: November 2015

This chapter examines whether and under what circumstances international investment agreement (IIA) provisions on expropriation involve a proportionality analysis. The chapter is organized as follows. Section I explains the differences between direct and indirect expropriations. It also provides a brief overview of the jurisprudence resulting from the Argentine crisis on direct expropriation. Section II introduces the different approaches of determining an indirect expropriation and their use by the tribunals in the Argentine cases. Section III discusses some policy rationales for determining the existence of an indirect expropriation by applying the principle of proportionality. Section IV examines the legal reasoning in Tecmed, which is often adduced as the ‘leading case’ when it comes to the relevance of proportionality in the context of indirect expropriation. It shows that the methodology adopted by the Tecmed tribunal is insufficient reason to resort to proportionality analysis in interpreting each and every IIA provision on expropriation. Still, the different means of treaty interpretation reflected in Article 31 of the Vienna Convention on the Law of Treaties (VCLT) may justify the application of the principle of proportionality under certain circumstances, as Section V illustrates.
Proportionality and NPM Clauses
Authors: Bücheler Gebhard
Published: November 2015

This chapter addresses one of the most effective means for States to ensure they are not liable to foreign investors when they adopt (proportionate) measures in furtherance of governmental goals in the public interest: non-precluded measures clauses (NPMs). An increasing number of international investment agreements (IIAs) contain such exception clauses for the protection of specific values such as international peace and security, labour standards, or the stability of financial systems. One of these clauses is Article XI of the USA–Argentina bilateral investment treaty (BIT), which played a key role in several of the Argentina cases. The chapter begins with an overview of the jurisprudence of arbitral tribunals and annulment committees that have analysed Article XI. It then examines the most important interpretative issues that arose in the context of Article XI, in particular whether the term ‘necessary’ in this provision triggers a proportionality analysis. It considers the consequences of a successful invocation of Article XI and analyses whether a State has to compensate foreign investors for measures that meet the requirements of Article XI and for how long a State can rely on Article XI.
Introduction to optical gain
Authors: Blood Peter
Published: November 2015

This chapter provides an introduction to optical gain and to the requirements for a semiconductor structure that enables this gain to be translated into laser action. The basis of laser action is the coherent amplification of light by stimulated emission, made possible when the population of states is inverted. Although such a system is far from thermal equilibrium, the energy distributions of carriers in a semiconductor laser are in quasi-equilibrium at room temperature described by Fermi functions. The amplification process is quantified by the gain coefficient and the gain spectrum. The gain is positive when the separation of the quasi-Fermi energies for electrons and holes exceeds the photon energy; the material is transparent where the photon energy is equal to the quasi-Fermi level separation. The chapter ends with the key requirements for a laser diode structure.
Laser action
Authors: Blood Peter
Published: November 2015

Laser action arises from round-trip, coherent amplification of light brought about by optical feedback due to reflection at the end mirrors, initiated by emission coupled into the mode specified by the spontaneous emission factor. The gain for laser action, and hence the threshold current, the emission wavelength, and the longitudinal mode spacing are given by the amplitude and phase of the laser mode in the presence of feedback. Laser action couples the photon and carrier densities through stimulated emission and this leads to a pinning of the quasi-Fermi levels and carrier density above threshold. The assumptions that underlie the definition of threshold and use of the relation between peak gain and recombination current to determine threshold are introduced. The injection efficiency, internal radiative quantum efficiency below threshold, and the internal and external differential quantum efficiencies above threshold, related by the light extraction factor, and power conversion efficiency are defined.
The classical atomic dipole oscillator
Authors: Blood Peter
Published: November 2015

Optical gain can be regarded as the growth of an electromagnetic wave propagating through a dielectric as described by Maxwell’s equations, with electric polarisation due to dipoles induced by the field of the wave in classical atomic oscillators. The real and imaginary parts of the complex susceptibility give the amplitude gain and refractive index change respectively. Over time the phase relation between oscillation of individual dipoles is lost by collisions; this loss of coherence causes the optical response of the ensemble to be broadened in energy or wavelength. The response is also broadened by gradual energy loss (damping) causing a reduction in the amplitude of the oscillating field. These effects are characterised by time constants T22 and T1 respectively, which combine to produce homogeneous broadening with Lorentzian lineshape. Absorption by an atomic ensemble is expressed as an optical cross section of each atom.
Measurement of gain and emission
Authors: Blood Peter
Published: November 2015

This chapter provides a description of methods for measurement of gain and spontaneous emission spectra on laser devices in the presence of round-trip amplification by observation of emission from the end facet and observation of true spontaneous emission spectra through a transparent contact, or a contact window in the top or back of the device. Emission from the end of the laser can be analysed as a function of cavity length to give the peak gain–current relation or the gain spectrum can be obtained from Fabry–Perot fringes on the amplified spontaneous spectrum below threshold, the Hakki–Paoli method. The window emission spectrum can be transformed to a gain spectrum provided the system is in quasi-equilibrium, and in certain circumstances may be calibrated to give the radiative recombination rate.
Single-pass measurement of gain and emission
Authors: Blood Peter
Published: November 2015

The most direct measurement of gain is given by the fractional increase in energy with distance as light makes a single pass through the medium. Amplified spontaneous emission is observed over a single pass, usually by having absorbing regions or low-reflectivity mirrors at one end of the structure. Measurements can be made on laser structures, but not while operating as a laser. The intensity of light from the end of the structure is measured as the amplifying length is varied, so these are known as ‘variable stripe length’ methods. The chapter begins with a short survey of the development of this approach, followed by a detailed account of the electrically pumped ‘segmented contact’ or ‘multi-section’ method, much of which is relevant to other realisations of the experiment, such as optical excitation. Calibration using the population inversion factor gives the radiative current and internal efficiency.
Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments
Authors: Fox Gearóid , Sievers Fabian , Higgins Desmond G.
Published: November 2015

Motivation: Multiple sequence alignments (MSAs) with large numbers of sequences are now commonplace. However, current multiple alignment benchmarks are ill-suited for testing these types of alignments, as test cases either contain a very small number of sequences or are based purely on simulation rather than empirical data.

Results: We take advantage of recent developments in protein structure prediction methods to create a benchmark (ContTest) for protein MSAs containing many thousands of sequences in each test case and which is based on empirical biological data. We rank popular MSA methods using this benchmark and verify a recent result showing that chained guide trees increase the accuracy of progressive alignment packages on datasets with thousands of proteins.

Availability and implementation: Benchmark data and scripts are available for download at http://www.bioinf.ucd.ie/download/ContTest.tar.gz.

Contact:  des.higgins@ucd.ie

Supplementary information:  Supplementary data are available at Bioinformatics online.
rHAT: fast alignment of noisy long reads with regional hashing
Authors: Liu Bo , Guan Dengfeng , Teng Mingxiang , Wang Yadong
Published: November 2015

Motivation: Single Molecule Real-Time (SMRT) sequencing has been widely applied in cutting-edge genomic studies. However, it is still an expensive task to align the noisy long SMRT reads to reference genome by state-of-the-art aligners, which is becoming a bottleneck in applications with SMRT sequencing. Novel approach is on demand for improving the efficiency and effectiveness of SMRT read alignment.

Results: We propose Regional Hashing-based Alignment Tool (rHAT), a seed-and-extension-based read alignment approach specifically designed for noisy long reads. rHAT indexes reference genome by regional hash table (RHT), a hash table-based index which describes the short tokens within local windows of reference genome. In the seeding phase, rHAT utilizes RHT for efficiently calculating the occurrences of short token matches between partial read and local genomic windows to find highly possible candidate sites. In the extension phase, a sparse dynamic programming-based heuristic approach is used for reducing the cost of aligning read to the candidate sites. By benchmarking on the real and simulated datasets from various prokaryote and eukaryote genomes, we demonstrated that rHAT can effectively align SMRT reads with outstanding throughput.

Availability and implementation: rHAT is implemented in C++; the source code is available at https://github.com/HIT-Bioinformatics/rHAT.

Contact:  ydwang@hit.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins
Authors: Lange Joanna , Wyrwicz Lucjan S. , Vriend Gert
Published: November 2015

Summary: Intrinsically disordered proteins (IDPs) lack tertiary structure and thus differ from globular proteins in terms of their sequence–structure–function relations. IDPs have lower sequence conservation, different types of active sites and a different distribution of functionally important regions, which altogether make their multiple sequence alignment (MSA) difficult. The KMAD MSA software has been written specifically for the alignment and annotation of IDPs. It augments the substitution matrix with knowledge about post-translational modifications, functional domains and short linear motifs.

Results: MSAs produced with KMAD describe well-conserved features among IDPs, tend to agree well with biological intuition, and are a good basis for designing new experiments to shed light on this large, understudied class of proteins.

Availability and implementation: KMAD web server is accessible at http://www.cmbi.ru.nl/kmad/. A standalone version is freely available.

Contact: vriend@cmbi.ru.nl
BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts
Authors: Yang Kun , Stracquadanio Giovanni , Luo Jingchuan , Boeke Jef D. , Bader Joel S.
Published: November 2015

Summary: Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment.

Availability and implementation: BioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilder.

Contact:  joel.bader@jhu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins
Authors: Heffernan Rhys , Dehzangi Abdollah , Lyons James , Paliwal Kuldip , Sharma Alok , Wang Jihua , Sattar Abdul , Zhou Yaoqi , Yang Yuedong
Published: November 2015

Motivation: Solvent exposure of amino acid residues of proteins plays an important role in understanding and predicting protein structure, function and interactions. Solvent exposure can be characterized by several measures including solvent accessible surface area (ASA), residue depth (RD) and contact numbers (CN). More recently, an orientation-dependent contact number called half-sphere exposure (HSE) was introduced by separating the contacts within upper and down half spheres defined according to the Cα-Cβ (HSEβ) vector or neighboring Cα-Cα vectors (HSEα). HSEα calculated from protein structures was found to better describe the solvent exposure over ASA, CN and RD in many applications. Thus, a sequence-based prediction is desirable, as most proteins do not have experimentally determined structures. To our best knowledge, there is no method to predict HSEα and only one method to predict HSEβ.

Results: This study developed a novel method for predicting both HSEα and HSEβ (SPIDER-HSE) that achieved a consistent performance for 10-fold cross validation and two independent tests. The correlation coefficients between predicted and measured HSEβ (0.73 for upper sphere, 0.69 for down sphere and 0.76 for contact numbers) for the independent test set of 1199 proteins are significantly higher than existing methods. Moreover, predicted HSEα has a higher correlation coefficient (0.46) to the stability change by residue mutants than predicted HSEβ (0.37) and ASA (0.43). The results, together with its easy Cα-atom-based calculation, highlight the potential usefulness of predicted HSEα for protein structure prediction and refinement as well as function prediction.

Availability and implementation: The method is available at http://sparks-lab.org.

Contact:  yuedong.yang@griffith.edu.au or yaoqi.zhou@griffith.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction
Authors: Li Nan , Ainsworth Richard I. , Wu Meixin , Ding Bo , Wang Wei
Published: November 2015

Motivation: MIEC-SVM is a structure-based method for predicting protein recognition specificity. Here, we present an automated MIEC-SVM pipeline providing an integrated and user-friendly workflow for construction and application of the MIEC-SVM models. This pipeline can handle standard amino acids and those with post-translational modifications (PTMs) or small molecules. Moreover, multi-threading and support to Sun Grid Engine (SGE) are implemented to significantly boost the computational efficiency.

Availability and implementation: The program is available at http://wanglab.ucsd.edu/MIEC-SVM.

Contact: wei-wang@ucsd.edu

Supplementary information  :  Supplementary data available at Bioinformatics online.
PAPA: a flexible tool for identifying pleiotropic pathways using genome-wide association study summaries
Authors: Wen Yan , Wang Wenyu , Guo Xiong , Zhang Feng
Published: November 2015

Summary: Pleiotropy is common in the genetic architectures of complex diseases. To the best of our knowledge, no analysis tool has been developed for identifying pleiotropic pathways using multiple genome-wide association study (GWAS) summaries by now. Here, we present PAPA, a flexible tool for pleiotropic pathway analysis utilizing GWAS summary results. The performance of PAPA was validated using publicly available GWAS summaries of body mass index and waist-hip ratio of the GIANT datasets. PAPA identified a set of pleiotropic pathways, which have been demonstrated to be involved in the development of obesity.

Availability and implementation  : PAPA program, document and illustrative example are available at http://sourceforge.net/projects/papav1/files/.

Contact  :  fzhxjtu@mail.xjtu.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Uncovering multiloci-ordering by algebraic property of Laplacian matrix and its Fiedler vector
Authors: Cheon Mookyung , Kim Choongrak , Chang Iksoo
Published: November 2015

Motivation: The loci-ordering, based on two-point recombination fractions for a pair of loci, is the most important step in constructing a reliable and fine genetic map.

Results: Using the concept from complex graph theory, here we propose a Laplacian ordering approach which uncovers the loci-ordering of multiloci simultaneously. The algebraic property for a Fiedler vector of a Laplacian matrix, constructed from the recombination fraction of the loci-ordering for 26 loci of barley chromosome IV, 846 loci of Arabidopsisthaliana and 1903 loci of Malus domestica, together with the variable threshold uncovers their loci-orders. It offers an alternative yet robust approach for ordering multiloci.

Availability   and implementation  : Source code program with data set is available as supplementary data and also in a software category of the website (http://biophysics.dgist.ac.kr)

Contact:  crkim@pusan.ac.kr or iksoochang@dgist.ac.kr.

Supplementary information:  Supplementary data are available at Bioinformatics online.
Optimal seed solver: optimizing seed selection in read mapping
Authors: Xin Hongyi , Nahar Sunny , Zhu Richard , Emmons John , Pekhimenko Gennady , Kingsford Carl , Alkan Can , Mutlu Onur
Published: November 2015

Motivation: Optimizing seed selection is an important problem in read mapping. The number of non-overlapping seeds a mapper selects determines the sensitivity of the mapper while the total frequency of all selected seeds determines the speed of the mapper. Modern seed-and-extend mappers usually select seeds with either an equal and fixed-length scheme or with an inflexible placement scheme, both of which limit the ability of the mapper in selecting less frequent seeds to speed up the mapping process. Therefore, it is crucial to develop a new algorithm that can adjust both the individual seed length and the seed placement, as well as derive less frequent seeds.

Results: We present the Optimal Seed Solver (OSS), a dynamic programming algorithm that discovers the least frequently-occurring set of x seeds in an L-base-pair read in O(x×L) operations on average and in O(x×L2) operations in the worst case, while generating a maximum of O(L2) seed frequency database lookups. We compare OSS against four state-of-the-art seed selection schemes and observe that OSS provides a 3-fold reduction in average seed frequency over the best previous seed selection optimizations.

Availability and implementation: We provide an implementation of the Optimal Seed Solver in C++ at: https://github.com/CMU-SAFARI/Optimal-Seed-Solver

Contact:  hxin@cmu.edu, calkan@cs.bilkent.edu.tr or onur@cmu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Metabolic network-guided binning of metagenomic sequence fragments
Authors: Biggs Matthew B. , Papin Jason A.
Published: November 2015

Motivation: Most microbes on Earth have never been grown in a laboratory, and can only be studied through DNA sequences. Environmental DNA sequence samples are complex mixtures of fragments from many different species, often unknown. There is a pressing need for methods that can reliably reconstruct genomes from complex metagenomic samples in order to address questions in ecology, bioremediation, and human health.

Results: We present the SOrting by NEtwork Completion (SONEC) approach for assigning reactions to incomplete metabolic networks based on a metabolite connectivity score. We successfully demonstrate proof of concept in a set of 100 genome-scale metabolic network reconstructions, and delineate the variables that impact reaction assignment accuracy. We further demonstrate the integration of SONEC with existing approaches (such as cross-sample scaffold abundance profile clustering) on a set of 94 metagenomic samples from the Human Microbiome Project. We show that not only does SONEC aid in reconstructing species-level genomes, but it also improves functional predictions made with the resulting metabolic networks.

Availability and implementation: The datasets and code presented in this work are available at: https://bitbucket.org/mattbiggs/sorting_by_network_completion/.

Contact:  papin@virginia.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.