bluuebunny/crossref_metadata_2025 huggingface dataset:
QCD flux tubes across the deconfinement phase transition
Authors: Cea Paolo , Cosmai Leonardo , Cuteri Francesca , Papa Alessandro
Published: March 2018

We study the behavior across the deconfinement phase transition of the chro-moelectric flux tube generated by a static quark and a static antiquark for several distances between them. We present preliminary results for distances up to 1.33 fm and temperatures up to 1.5Tc.
Instanton effects on CP-violating gluonic correlators
Authors: Mori Shingo , Frison Julien , Kitano Ryuichiro , Matsufuru Hideo , Yamada Norikazu
Published: March 2018

In order to better understand the role played by instantons behind nonperturbative dynamics, we investigate the instanton contributions to the gluonic two point correlation functions in the SU(2) YM theory. Pseudoscalar-scalar gluonic correlation functions are calculated on the lattice at various temperatures and compared with the instanton calculus. We discuss how the instanton effects emerge or disappear with temperature and try to provide the interpretation behind it.
Pion decay in magnetic fields
Authors: Bali Gunnar S. , Brandt Bastian B. , Endrődi Gergely , Gläße Benjamin
Published: March 2018

The leptonic decay of the charged pion in the presence of background magnetic fields is investigated using quenched Wilson fermions. It is demonstrated that the magnetic field opens up a new channel for this decay. The magnetic field-dependence of the decay constants for both the ordinary and the new channel is determined. Using these inputs from QCD, we calculate the total decay rate perturbatively.
calculation of B → D*lv form factor at zero recoil using the Oktay-Kronfeld action
Authors: Bailey Jon A. , Bhattacharya Tanmoy , Gupta Rajan , Jang Yong-Chull , Lee Weonjong , Leem Jaehoon , Park Sungwoo , Yoon Boram
Published: March 2018

We present the first preliminary results for the semileptonic form factor hA1 (w = 1)/ρAj at zero recoil for the B → D*lv decay using lattice QCD with four flavors of sea quarks. We use the HISQ staggered action for the light valence and sea quarks (the MILC HISQ configurations), and the Oktay-Kronfeld (OK) action for the heavy valence quarks.
The KL - KS Mass Difference
Authors: Bai Ziyuan , Christ Norman H. , Sachrajda Christopher T.
Published: March 2018

We review the status of the RBC-UKQCD collaborations’ computations of the KL-KS mass difference. After a brief discussion of the theoretical framework which had been developed previously by the collaboration, we describe our latest computation, performed at physical quark masses, and present our preliminary result mKL - mKS = (5.5 ± 1.70) × 10-12 MeV.
Leptonic decay constants for D-mesons from 3-flavour CLS ensembles
Authors: Collins Sara , Eckert Kevin , Heitger Jochen , Hofmann Stefan , Söldner Wolfgang
Published: March 2018

e report on the status of an ongoing effort by the RQCD and ALPHA Collaborations, aimed at determining leptonic decay constants of charmed mesons. Our analysis is based on large-volume ensembles generated within the CLS effort, employing Nf = 2 + 1 non-perturbatively O(a) improved Wilson quarks, tree-level Symanzik-improved gauge action and open boundary conditions. The ensembles cover lattice spac-ings from a ≈ 0.09 fm to a ≈ 0.05 fm, with pion masses varied from 420 to 200 MeV. To extrapolate to the physical masses, we follow both the (2ml + ms) = const. and the ms = const. lines in parameter space.
Progress in the improved lattice calculation of direct CP-violation in the Standard Model
Authors: Kelly Christopher
Published: March 2018

We discuss the ongoing effort by the RBC & UKQCD collaborations to improve our lattice calculation of the measure of Standard Model direct CP violation, ∊’, with physical kinematics. We present our progress in decreasing the (dominant) statistical error and discuss other related activities aimed at reducing the systematic errors.
HQE parameters from unquenched lattice data on pseudoscalar and vector heavy-light meson masses
Authors: Gambino Paolo , Melis Aurora , Simula Silvano
Published: March 2018

We present a new lattice determination of some of the parameters appearing both in the Operator Product Expansion (OPE) analysis of the inclusive semileptonic B-meson decays and in the Heavy Quark Expansion (HQE) of the pseudoscalar (PS) and vector (V) heavy-light meson masses. We perform a lattice QCD (LQCD) computation of PS and V heavy-light meson masses for heavy-quark masses mh in the range from [see formula in PDF] to ≃ [see formula in PDF]. We employed the Nf = 2 + 1 + 1 gauge configurations of the European Twisted Mass Collaboration (ETMC) at three values of the lattice spacing a ≃ (0.062,0.082,0.089) fm with pion masses in the range Mπ ≃ (210 - 450) MeV. The heavy-quark mass is simulated directly on the lattice up to ≃ [see formula in PDF]. The interpolation to the physical [see formula in PDF] is performed using the ETMC ratio method and adopting the kinetic mass scheme. We obtain [see formula in PDF] (1 GeV) = 4.61(20) GeV (m̅b(m̅b) = 4.26(18) GeV in the MS scheme). The lattice data are analyzed in terms of the HQE and the matrix elements of dimension-4 and dimension-5 operators are extracted with good precision, namely: [see formula in PDF] and [see formula in PDF]. The data also allow for an estimate of the dimension-6 operator matrix elements.
Singlet vs Nonsinglet Perturbative Renormalization factors of Staggered Fermion Bilinears
Authors: Panagopoulos Haralambos , Spanoudes Gregoris
Published: March 2018

In this paper we present the perturbative computation of the difference between the renormalization factors of flavor singlet ([see formula in PDF], f : flavor index) and nonsinglet ([see formula in PDF]) bilinear quark operators (where Γ = 𝟙, γ5, γ µ, γ5 γ µ, γ5 σµv on the lattice. The computation is performed to two loops and to lowest order in the lattice spacing, using Symanzik improved gluons and staggered fermions with twice stout-smeared links. The stout smearing procedure is also applied to the definition of bilinear operators. A significant part of this work is the development of a method for treating some new peculiar divergent integrals stemming from the staggered formalism. Our results can be combined with precise simulation results for the renormalization factors of the nonsinglet operators, in order to obtain an estimate of the renormalization factors for the singlet operators. The results have been published in Physical Review D [1].
Fast algorithms for chiral fermions in 2 dimensions
Authors: Hyka (Xhako) Dafina , Osmanaj (Zeqirllari) Rudina
Published: March 2018

In lattice QCD simulations the formulation of the theory in lattice should be chiral in order that symmetry breaking happens dynamically from interactions. In order to guarantee this symmetry on the lattice one uses overlap and domain wall fermions. On the other hand high computational cost of lattice QCD simulations with overlap or domain wall fermions remains a major obstacle of research in the field of elementary particles. We have developed the preconditioned GMRESR algorithm as fast inverting algorithm for chiral fermions in U(1) lattice gauge theory. In this algorithm we used the geometric multigrid idea along the extra dimension.The main result of this work is that the preconditioned GMRESR is capable to accelerate the convergence 2 to 12 times faster than the other optimal algorithms (SHUMR) for different coupling constant and lattice 32x32. Also, in this paper we tested it for larger lattice size 64x64. From the results of simulations we can see that our algorithm is faster than SHUMR. This is a very promising result that this algorithm can be adapted also in 4 dimension.
Getting even with CLE
Authors: Aarts Gert , Boguslavski Kirill , Scherzer Manuel , Seiler Erhard , Sexty Dénes , Stamatescu Ion-Olimpiu
Published: March 2018

In the landscape of approaches toward the simulation of Lattice Models with complex action the Complex Langevin (CL) appears as a straightforward method with a simple, well defined setup. Its applicability, however, is controlled by certain specific conditions which are not always satisfied. We here discuss the procedures to meet these conditions and the estimation of systematic errors and present some actual achievements.
Computation of parton distributions from the quasi-PDF approach at the physical point
Authors: Alexandrou Constantia , Bacchio Simone , Cichy Krzysztof , Constantinou Martha , Hadjiyiannakou Kyriakos , Jansen Karl , Koutsou Giannis , Scapellato Aurora , Steffens Fernanda
Published: March 2018

We show the first results for parton distribution functions within the proton at the physical pion mass, employing the method of quasi-distributions. In particular, we present the matrix elements for the iso-vector combination of the unpolarized, helicity and transversity quasi-distributions, obtained with Nf = 2 twisted mass cloverimproved fermions and a proton boosted with momentum [see formula in PDF] = 0.83 GeV. The momentum smearing technique has been applied to improve the overlap with the proton boosted state. Moreover, we present the renormalized helicity matrix elements in the RI’ scheme, following the non-perturbative renormalization prescription recently developed by our group.
Colour fields of the quark-antiquark excited flux tube
Authors: Bicudo Pedro , Cardoso Marco , Cardoso Nuno
Published: March 2018

We present colour field density profiles for some of the first SU(3) gluonic excitations of the flux tube in the presence of a static quark-antiquark pair. The results are obtained from a large set of gluonic operators.
Lattice calculation of hadronic tensor of the nucleon
Authors: Liang Jian , Liu Keh-Fei , Yang Yi-Bo
Published: March 2018

We report an attempt to calculate the deep inelastic scattering structure functions from the hadronic tensor calculated on the lattice. We used the Backus-Gilbert reconstruction method to address the inverse Laplace transformation for the analytic continuation from the Euclidean to the Minkowski space.
bb̅ud̅ four-quark systems in the Born-Oppenheimer approximation: prospects and challenges
Authors: Peters Antje , Bicudo Pedro , Wagner Marc
Published: March 2018

We summarize previous work on b̅b̅ud four-quark systems in the Born-Oppenheimer approximation and discuss first steps towards an extension to the theoretically more challenging bb̅ud̅ system. Strategies to identify a possibly existing bb̅ud̅ bound state are discussed and first numerical results are presented.
Community-Acquired Respiratory Viruses
Authors: Gottlieb Jens
Published: March 2018

The incidence of community-acquired respiratory viruses (CARVs) is ∼15 cases per 100 patient-years after lung transplantation (LTx). Paramyxoviruses account for almost 50% of the cases of CARV infection in LTx. Most patients will be symptomatic with a mean decline of 15 to 20% in forced expiratory volume in 1 second. The attributable death rate is low in recent years 15 to 25% CARV infected LTx patients will develop chronic lung allograft dysfunction within a year after CARV infection. This risk seems to be increased in comparison to the noninfected LTx recipient.

Detection rate of CARV dependent on clinical awareness, sampling, and diagnostic method with nucleic acid testing by polymerase chain reaction in bronchoalveolar lavage is the gold standard after LTx.

There is no approved treatment for paramyxoviruses, most centers use ribavirin by various routes. Toxicity of systemic ribavirin is of concern and some patients will have contraindication to this treatment modality. Treatment may reduce the risk to develop chronic lung allograft dysfunction and respiratory failure. Agents under development are inhibiting viral attachment and use silencing mechanisms of viral replication.
Surveillance Bronchoscopy: Is It Still Relevant?
Authors: Benzimra Mark
Published: March 2018

The performance of bronchoscopy with bronchoalveolar lavage and transbronchial biopsy is an essential tool and skill required by any clinician caring for patients postlung transplantation. Making a confident diagnosis is crucial in initiating different treatment strategies which may be in turn hazardous to the patient in light of an inaccurate diagnosis. Having more information available for evaluation optimizes the chances of tailoring appropriate therapeutic options in this complex patient population. Performing a bronchoscopy with bronchoalveolar lavage and transbronchial biopsy indeed provides a wealth of information via microbiological, cytological, and histological samples that assist us to differentiate infection from rejection, or to confirm the presence of both. This review aims to discuss the utility of bronchoscopy postlung transplantation in the diagnosis of rejection, infection, and airway complications, as well as looking into the ongoing controversy regarding monitoring practices worldwide and safety concerns.
Defining Success in Lung Transplantation: From Survival to Quality of Life
Authors: Singer Jonathan , Kolaitis Nicholas
Published: March 2018

Lung transplantation (LT) has the potential to extend survival and improve quality of life (QOL) for patients suffering from end-stage lung disease. This review describes the many ways in which success can be defined in LT. It evaluates the improvements in survival outcomes after LT over time, and describes ways to measure the success of LT other than survival after transplantation. It also addresses the importance of patient-centered outcomes and how improvements in health-related quality of life (HRQL) are pivotal to defining success within LT.
Surgical Site Infection in a Tertiary Neonatal Surgery Centre
Authors: Woldemicael Adiam , Bradley Sarah , Pardy Caroline , Richards Justin , Trerotoli Paolo , Giuliani Stefano
Published: March 2018

Introduction Surgical site infection (SSI) is a key performance indicator to assess the quality of surgical care. Incidence and risk factors for SSI in neonatal surgery are lacking in the literature.

Aim To define the incidence of SSI and possible risk factors in a tertiary neonatal surgery centre.

Materials and Methods This is a prospective cohort study of all the neonates who underwent abdominal and thoracic surgery between March 2012 and October 2016. The variables analyzed were gender, gestational age, birth weight, age at surgery, preoperative stay in neonatal intensive care unit, type of surgery, length of stay, and microorganisms isolated from the wounds. Statistical analysis was done with chi-square, Student's t- or Mann–Whitney U-tests. A logistic regression model was used to evaluate determinants of risk for SSI; variables were analyzed both with univariate and multivariate models. For the length of hospital stay, a logistic regression model was performed with independent variables.

Results A total of 244 neonates underwent 319 surgical procedures. The overall incidence of SSIs was 43/319 (13.5%). The only statistical differences between neonates with and without SSI were preoperative stay (<4 days vs. ≥4 days, p < 0.01) and length of hospital stay (<30 days vs. ≥30 days, p < 0.01). A pre-operative stay longer than 4 days was associated with almost three times increased risk of SSI (odds ratio [OR] 2.96, 95% confidence interval [CI] 1.05–8.34, p = 0.0407). Gastrointestinal procedures were associated with more than ten times the risk of SSI compared with other procedures (OR 10.17, 95% CI 3.82–27.10, p < 0.0001). Gastroschisis closure and necrotizing enterocolitis (NEC) laparotomies had the highest incidence SSI (54% and 62%, respectively). The risk of longer length of hospital stay after SSI was more than three times higher (OR = 3.36, 95%CI 1.63–6.94, p = 0.001).

Conclusion This is the first article benchmarking the incidence of SSI in neonatal surgery in the United Kingdom. A preoperative stay ≥4 days and gastrointestinal procedures were independent risk factors for SSI. More research is needed to develop strategies to reduce SSI in selected neonatal procedures.
Future cities: moving from technical to human needs
Authors: Caprotti Federico
Published: March 2018

The article argues for a foregrounding of human needs at the heart of urban societal futures. While economic, technical and environmental imperatives are understandably the focus of policymaking and governance arrangements at national and supra-national scales, defining and targeting priorities in the ‘ordinary’ city is key. The argument is that it is now time to place basic human needs (as enshrined both in international agreements and in the more prosaic conditions of specific cities) at the centre of thinking and planning for future cities. The piece therefore proposes that plans for urban futures start from an elaboration of contextually sensitive as well as internationally negotiated needs rather than from macro-scale and potentially ephemeral visions of glittering technological future metropoles.
Design, development, and reliability assessment of dual output converters for SPV based DC nanogrid
Authors: Gupta Nikita , Garg Rachana
Published: March 2018

A DC nanogrid for residential and commercial purposes supplies both AC and DC output voltages at different utilization levels to meet the load requirements. In this paper, the author(s) have developed a Solar Photovoltaic based DC nanogrid using dual output converter configurations which aims to improve both reliability and efficiency. The converter configurations are developed and analyzed for different levels of DC and AC output voltages in a nanogrid. Further, the performance characterization models of these converters such as sensitivity and reliability models are developed to test the robustness and effects when there is parametric variation. Markov reliability models are developed to estimate the mean time to system failure, as assessed in the Military Handbook for Reliability Prediction of Electronic Equipment (MIL-HDBK-217F). Also, the developed converter configurations are investigated in detail using MATLAB along with Simulink toolbox. Finally, the converter configurations are experimentally validated using a 100 W prototype, built, and tested in the laboratory for practical applications. The prototype model is a basic building block for further study and practical implementation for Power System designers and is useful in the areas where there is no grid. Also, the developed dual output-based system has improved energy security and reliability.
Theoretical insights into the minority carrier lifetime of doped Si—A computational study
Authors: Iyakutti K. , Lavanya R. , Rajeswarapalanichamy R. , Mathan Kumar E. , Kawazoe Y.
Published: March 2018

Using density functional theory, we have analyzed the ways and means of improving the minority carrier lifetime (MCL) by calculating the band structure dependent quantities contributing to the MCL. We have computationally modeled silicon doped with different elements like B, C, N, O, P, Ti, Fe, Ga, Ge, As, In, Sn, Sb, and Pt and looked at the effect of doping on MCL. In co-doping, the systems Si-B-Ga, Si-B-Ge, Si-B-2Ge, Si-B-Pt, Si-Ga-Ge, Si-Ga-2Ge, and Si-Ga-Pt are investigated. From our calculation, it is found that by doping and co-doping of Si with suitable elements having “s” and “p” electrons, there is a decrease in the recombination activity. The predicted effective minority carrier lifetime indicates the possibility of significant improvements. Based on the above studies, it is now maybe possible, with suitable choice of dopant and co-dopant material, to arrive at part of a standard production process for solar grade Si material.
A grid-side reactive power control strategy for highly offshore wind power penetrated systems
Authors: Huang Fuyuan , Wang Huaiyuan , Wen Buying
Published: March 2018

A grid-side reactive power control strategy is proposed in this paper, which aims to enhance the voltage stability of highly offshore wind power penetrated systems. The basic idea of the strategy is to establish an evaluating system including the voltage stability index (VSI), VSI sensitivity index, and reactive power residual adjustment capability index (RPRACI). The indexes can be applied to identify the voltage dangerous nodes, locate the compensation nodes, and determine each node's amount of compensation. The strategy is particularly suitable for large-scale offshore wind power integrated systems because it is designed to deal with large disturbances such as offshore wind power fluctuations. This strategy can be specified in three steps. First, voltage dangerous nodes are identified by the nodal VSI. Next, adjustable nodes are chosen according to the sensitivities of each node to the dangerous nodes and RPRACI of each node. Finally, reactive power compensation of each adjustable node is allocated depending on the magnitudes of the sensitivity indexes. The simulation results in the IEEE 14-bus system indicate that the proposed strategy can effectively improve the local grid voltage stability when large-scale offshore wind power is injected into the system.
Increasing the effective absorption of Eu3+-doped luminescent materials towards practical light emitting diodes for illumination applications
Authors: van de Haar Marie Anne , Werner Jan , Kratz Nadja , Hilgerink Tom , Tachikirt Mohamed , Honold Jürgen , Krames Michael R.
Published: March 2018

White light emitting diodes (LEDs) composed of a blue LED and a green/yellow downconverter material (phosphor) can be very efficient, but the color is often not considered very pleasant. Although the color rendering can be improved by adding a second, red-emitting phosphor, this generally results in significantly reduced efficacy of the device due to the broad emission of available conventional red-emitting phosphors. Trivalent europium is well-known for its characteristic narrow-band emission in the red region, with little radiation outside the eye sensitivity area, making it an ideal candidate for enabling high color quality as well as a high lumen equivalent of radiation from a spectrum point of view. However, a thorough study of the practical potential and challenges of Eu3+ as a red emitter for white LEDs has remained elusive so far due to the low excitation probability in the blue spectral range which is often even considered a fundamental limitation. Here, we show that the absorption in the blue region can be brought into an interesting regime for white LEDs and show that it is possible to increase both the color rendering and efficacy simultaneously using Eu3+ as a red emitter, compared to warm white LEDs comprising conventional materials.
Enhanced optical-to-THz conversion efficiency of photoconductive antenna using dielectric nano-layer encapsulation
Authors: Gupta Abhishek , Rana Goutam , Bhattacharya Arkabrata , Singh Abhishek , Jain Ravikumar , Bapat Rudheer D. , Duttagupta S. P. , Prabhu S. S.
Published: March 2018

Photoconductive antennas (PCAs) are among the most conventional devices used for emission as well as detection of terahertz (THz) radiation. However, due to their low optical-to-THz conversion efficiencies, applications of these devices in out-of-laboratory conditions are limited. In this paper, we report several factors of enhancement in THz emission efficiency from conventional PCAs by coating a nano-layer of dielectric (TiO2) on the active area between the electrodes of a semi-insulating GaAs-based device. Extensive experiments were done to show the effect of thicknesses of the TiO2 layer on the THz power enhancement with different applied optical power and bias voltages. Multiphysics simulations were performed to elucidate the underlying physics behind the enhancement of efficiency of the PCA. Additionally, this layer increases the robustness of the electrode gaps of the PCAs with high electrical insulation as well as protect it from external dust particles.
Effect of surfaces similarity on contact resistance of fractal rough surfaces under cyclic loading
Authors: Gao Yuanwen , Liu Limei , Ta Wurui , Song Jihua
Published: March 2018

Although numerous studies have shown that contact resistance depends significantly on roughness and fractal dimension, it remains elusive how they affect contact resistance between rough surfaces. The interface similarity index is first proposed to describe the similarity of the contact surfaces, which gives a good indication of the actual contact area between surfaces. We reveal that the surfaces’ similarity be an origin of contact resistance variation. The cyclic loading can increase the contact stiffness, and the contact stiffness increases with the increase of the interface similarity index. These findings explain the mechanism of surface roughness and fractal dimension on contact resistance, and also provide reference for the reliability design of the electrical connection.
Inter-population variability in growth and reproduction of invasive bleak Alburnus alburnus (Linnaeus, 1758) across the Iberian Peninsula
Authors: Latorre D. , Masó G. , Hinckley A. , Verdiell-Cubedo D. , Tarkan A. S. , Vila-Gispert A. , Copp G. H. , Cucherousset J. , da Silva E. , Fernández-Delgado C. , García-Berthou E. , Miranda R. , Oliva-Paterna F. J. , Ruiz-Navarro A. , Serrano J. M. , Almeida D.
Published: March 2018

The native European freshwater cyprinid fish, common bleak Alburnus alburnus (Linnaeus, 1758), is an invasive non-native fish in the Iberian Peninsula, where it threatens the valuable endemic fish fauna. Despite the bleak’s invasive status, there is a dearth of studies on the biological traits of non-native populations in Europe’s Mediterranean region, and the present study aimed to compare bleak growth and reproductive traits across the principal rivers of Iberia with those from a native ‘reference’ bleak population in France. Non-native bleak from the River Tagus had the highest back-calculated total lengths (TLs), growth rate and body condition, but the lowest reproductive investment and smallest egg size of all studied populations. Whereas, these latter two traits were the highest in the River Ebro, where fecundity was the lowest for all Iberian rivers. The youngest age and the smallest TL at maturity were observed in the River Ebro. The River Segura had the lowest back-calculated TLs and growth rate, the highest fecundity and proportion of females, and the oldest age at maturity. Population traits of bleak in the River Saône (the native ‘reference’ population) were generally different from those in Iberian rivers, except for the River Ebro. This wide inter-population variability contributes to the species’ successful establishment in novel habitats.
Defining the importance of ecological processes for monitoring aquatic habitats for conservation and rehabilitation objectives at the Ranger uranium mine, Kakadu Region, Australia
Authors: Bartolo Renee E. , Harford Andrew J. , Humphrey Chris L. , George Amy K. , van Dam Rick A.
Published: March 2018

Key ecological processes must be present and maintained in ecosystems to ensure the success of ecological restoration and conservation programs. The present paper identifies and defines key ecological processes operating at various spatial scales within aquatic ecosystems of the Magela Creek catchment, within Kakadu National Park, and prioritises those that may be vulnerable to potential mine-derived stressors. This assessment was required to ensure that current and future environmental monitoring programs are in place to safeguard the protection of these processes, particularly in the context of rehabilitation of Ranger uranium mine. Ecological processes within riparian habitats and biotic interactions across all habitats were at a higher risk of exposure to potential stressors. Generally, the selected assessment endpoints used for the operational phase of the mine are sufficient to measure and assess ecological processes. However, biological endpoints require additional suitable early detection indicators because marked lags exist in their response, which will be more important during the rehabilitation phase of the mine because of the longer timeframes to be assessed. The lags would otherwise allow potential impacts to underpinning processes to pass undetected. Risk identification allows monitoring programs to move beyond simple measurement variables to full evaluation of underlying ecological processes, which maintain both structure and function in ecosystems.
Rainwater harvesting for drinking: a physiochemical assessment in Port Vila, Vanuatu
Authors: Kotra Krishna K. , Samanta Sailesh , Prasad Surendra
Published: March 2018

Rainwater harvesting for drinking purpose has been a great source for survival by many societies since ages and now scarcity in water resources has been forcing many others to follow. Even though, rainwater harvesting is an exploitative practice where there is abundance of rainfall, but the methods in which harvesting process are carried needs to be studied in detail. The present study was a systematic physiochemical analysis of harvested rainwater for drinking purpose in Port Vila, Vanuatu where 22 sites were studied for two consecutive seasons. Notable mean variations were observed in total dissolved solids (TDS) with 63.84 mg/L, pH 0.4 and electrical conductivity (EC) with 98.9 µS/Cm. The mean standard deviation of 3.6 mg/L in acidity of pre and post monsoon seasons was also been a noted concern. Timing, extent of rainfall along with the usage had shown variations in the constituent’s concentrations. The study revealed that the standards for the harvested drinking water are compromised at some sites either in one or multiple physiochemical parameters. People in Port Vila continue to consume the harvested water due to cultural practices and beliefs related to rainwater. It was observed that proper management and adaptation to new technologies would yield better quality of the harvested water.
Digital energy monitor: design, simulations and prototype
Authors: Sharma N. , Kumar P. , Singh N. , Mehta U.
Published: March 2018

This paper demonstrates the design and implementation of a GSM based digital energy monitoring device. Firstly fuzzy based model is developed to replicate the characteristic of current and voltage sensors. The entire system is also studied and simulated in terms of utility side supply, load, microcontroller digitization and GSM communication. A virtual data sharing technic is also studied for the proposed system using state flow logic. A prototype system is verified real-time with its test and verification phase results. In this work, remote monitoring of electricity has been made easier for the utility. Demand side management is also presented as customers can instantly get their electricity consumptions when requested. Further, an effective overcurrent monitoring system has been embedded along with a backup battery source. Results obtained from the experiments prove that with this emerging technology it is possible to move towards a smarter grid at a rapid and cost effective way.
LSD1 activates a lethal prostate cancer gene network independently of its demethylase function
Authors: Sehrawat Archana , Gao Lina , Wang Yuliang , Bankhead Armand , McWeeney Shannon K. , King Carly J. , Schwartzman Jacob , Urrutia Joshua , Bisson William H. , Coleman Daniel J. , Joshi Sunil K. , Kim Dae-Hwan , Sampson David A. , Weinmann Sheila , Kallakury Bhaskar V. S. , Berry Deborah L. , Haque Reina , Van Den Eeden Stephen K. , Sharma Sunil , Bearss Jared , Beer Tomasz M. , Thomas George V. , Heiser Laura M. , Alumkal Joshi J.
Published: March 2018

Significance

Medical castration or interference with androgen receptor (AR) function is the principal treatment for advanced prostate cancer. However, progression is universal, and therapies following the emergence of castration resistance do not offer durable control of the disease. Lysine-specific demethylase 1 (LSD1) is an important regulator of gene expression, including in cancer. Here, we show that LSD1 is highly expressed in tumors of patients with lethal castration-resistant prostate cancer (CRPC) and that LSD1 promotes AR-independent survival in CRPC cells in a noncanonical, demethylase-independent manner. We determined that the drug SP-2509 acts as an allosteric inhibitor of LSD1–blocking demethylase-independent functions. Our demonstration of tumor suppression with this inhibitor in CRPC preclinical models provides the rationale for clinical trials with LSD1 inhibitors.
Dependence of the evolution of carbon dynamics in the northern permafrost region on the trajectory of climate change
Authors: McGuire A. David , Lawrence David M. , Koven Charles , Clein Joy S. , Burke Eleanor , Chen Guangsheng , Jafarov Elchin , MacDougall Andrew H. , Marchenko Sergey , Nicolsky Dmitry , Peng Shushi , Rinke Annette , Ciais Philippe , Gouttevin Isabelle , Hayes Daniel J. , Ji Duoying , Krinner Gerhard , Moore John C. , Romanovsky Vladimir , Schädel Christina , Schaefer Kevin , Schuur Edward A. G. , Zhuang Qianlai
Published: March 2018

Significance

We applied regional and global-scale biogeochemical models that coupled thaw depth with soil carbon exposure to evaluate the dependence of the evolution of future carbon storage in the northern permafrost region on the trajectory of climate change. Our analysis indicates that the northern permafrost region could act as a net sink for carbon under more aggressive climate change mitigation pathways. Under less aggressive pathways, the region would likely act as a source of soil carbon to the atmosphere, but substantial net losses would not occur until after 2100. These results suggest that effective mitigation efforts during the remainder of this century could attenuate the negative consequences of the permafrost carbon–climate feedback.
Processes and patterns of interaction as units of selection: An introduction to ITSNTS thinking
Authors: Doolittle W. Ford , Inkpen S. Andrew
Published: March 2018

Many practicing biologists accept that nothing in their discipline makes sense except in the light of evolution, and that natural selection is evolution’s principal sense-maker. But what natural selection actually is (a force or a statistical outcome, for example) and the levels of the biological hierarchy (genes, organisms, species, or even ecosystems) at which it operates directly are still actively disputed among philosophers and theoretical biologists. Most formulations of evolution by natural selection emphasize the differential reproduction of entities at one or the other of these levels. Some also recognize differential persistence, but in either case the focus is on lineages of material things: even species can be thought of as spatiotemporally restricted, if dispersed, physical beings. Few consider—as “units of selection” in their own right—the processes implemented by genes, cells, species, or communities. “It’s the song not the singer” (ITSNTS) theory does that, also claiming that evolution by natural selection of processes is more easily understood and explained as differential persistence than as differential reproduction. ITSNTS was formulated as a response to the observation that the collective functions of microbial communities (the songs) are more stably conserved and ecologically relevant than are the taxa that implement them (the singers). It aims to serve as a useful corrective to claims that “holobionts” (microbes and their animal or plant hosts) are aggregate “units of selection,” claims that often conflate meanings of that latter term. But ITSNS also seems broadly applicable, for example, to the evolution of global biogeochemical cycles and the definition of ecosystem function.
S
-nitrosylation drives cell senescence and aging in mammals by controlling mitochondrial dynamics and mitophagy
Authors: Rizza Salvatore , Cardaci Simone , Montagna Costanza , Di Giacomo Giuseppina , De Zio Daniela , Bordi Matteo , Maiani Emiliano , Campello Silvia , Borreca Antonella , Puca Annibale A. , Stamler Jonathan S. , Cecconi Francesco , Filomeni Giuseppe
Published: March 2018

Significance

The free radical theory of aging remains controversial. Accumulation of mitochondrial damage is commonly accepted as an age-related phenomenon associated with the inescapable side effects of oxidative metabolism. However, to date, molecular determinants of this phenomenon have not been identified. Previous evidence indicates that engineered mice deficient in the denitrosylase
S
-nitrosoglutathione reductase (GSNOR) show features of aging. Here, we show that due to epigenetic events, GSNOR expression declines with age, ultimately resulting in the accumulation of damaged mitochondria. By contrast, centenarians maintain high GSNOR expression. Collectively, these data suggest that GSNOR may act as a longevity protein countering defects in mitochondrial physiology that arise from age-related epigenetic deregulation.
An Inclusive History for a Divided World?
Authors: Frolova-Walker Marina
Published: March 2018

The article discusses various historiographical problems created by Soviet music and, more broadly, music under the so-called ‘totalitarian’ regimes for the conventional modernism-driven narrative of the twentieth century. It reviews a number of existing challenges to the dominant narrative within musicology and related fields such as art and architectural history, and it proposes ways in which we can move forward. In conclusion, the author considers the new challenges to the breaking down of cold-war barriers, not only in a historical sense, but also today, in the midst of a new cold war.
‘Che soave zeffiretto’ and the Structure of Act 3 of Le nozze di Figaro
Authors: Woodfield Ian
Published: March 2018

‘Che soave zeffiretto’, the letter duettino sung by the Countess and Susanna in Le nozze di Figaro, has achieved iconic status as a perfect example of the transcendental beauty of Mozart's music. An examination of the extant sources suggests that the composer and his librettist regarded it as a key moment in the opera: the crux of a developing relationship between the two women. A late change of plan over its location led to a reconfiguration of Act 3, resulting in the minor inconsistencies that Robert Moberly and Christopher Raeburn sought to explain in their celebrated double-casting hypothesis. The various versions of the text and a complete continuity draft of the score reveal the meticulous craftsmanship that went into its creation, in particular the development of its comedic potential as a vaudeville.
SimPhospho: a software tool enabling confident phosphosite assignment
Authors: Suni Veronika , Suomi Tomi , Tsubosaka Tomoya , Imanishi Susumu Y , Elo Laura L , Corthals Garry L
Published: March 2018

Motivation

Mass spectrometry combined with enrichment strategies for phosphorylated peptides has been successfully employed for two decades to identify sites of phosphorylation. However, unambiguous phosphosite assignment is considered challenging. Given that site-specific phosphorylation events function as different molecular switches, validation of phosphorylation sites is of utmost importance. In our earlier study we developed a method based on simulated phosphopeptide spectral libraries, which enables highly sensitive and accurate phosphosite assignments. To promote more widespread use of this method, we here introduce a software implementation with improved usability and performance.

Results

We present SimPhospho, a fast and user-friendly tool for accurate simulation of phosphopeptide tandem mass spectra. Simulated phosphopeptide spectral libraries are used to validate and supplement database search results, with a goal to improve reliable phosphoproteome identification and reporting. The presented program can be easily used together with the Trans-Proteomic Pipeline and integrated in a phosphoproteomics data analysis workflow.

Availability and implementation

SimPhospho is open source and it is available for Windows, Linux and Mac operating systems. The software and its user’s manual with detailed description of data analysis as well as test data can be found at https://sourceforge.net/projects/simphospho/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Integrating long-range connectivity information into de Bruijn graphs
Authors: Turner Isaac , Garimella Kiran V , Iqbal Zamin , McVean Gil
Published: March 2018

Motivation

The de Bruijn graph is a simple and efficient data structure that is used in many areas of sequence analysis including genome assembly, read error correction and variant calling. The data structure has a single parameter k, is straightforward to implement and is tractable for large genomes with high sequencing depth. It also enables representation of multiple samples simultaneously to facilitate comparison. However, unlike the string graph, a de Bruijn graph does not retain long range information that is inherent in the read data. For this reason, applications that rely on de Bruijn graphs can produce sub-optimal results given their input data.

Results

We present a novel assembly graph data structure: the Linked de Bruijn Graph (LdBG). Constructed by adding annotations on top of a de Bruijn graph, it stores long range connectivity information through the graph. We show that with error-free data it is possible to losslessly store and recover sequence from a Linked de Bruijn graph. With assembly simulations we demonstrate that the LdBG data structure outperforms both our de Bruijn graph and the String Graph Assembler (SGA). Finally we apply the LdBG to Klebsiella pneumoniae short read data to make large (12 kbp) variant calls, which we validate using PacBio sequencing data, and to characterize the genomic context of drug-resistance genes.

Availability and implementation

Linked de Bruijn Graphs and associated algorithms are implemented as part of McCortex, which is available under the MIT license at https://github.com/mcveanlab/mccortex.

Supplementary information

Supplementary data are available at Bioinformatics online.
ONETOOL for the analysis of family-based big data
Authors: Song Yeunjoo E , Lee Sungyoung , Park Kyungtaek , Elston Robert C , Yang Hyeon-Jong , Won Sungho
Published: March 2018

Motivation

Despite the need for separate tools to analyze family-based data, there are only a handful of tools optimized for family-based big data compared to the number of tools available for analyzing population-based data.

Results

ONETOOL implements the properties of well-known existing family data analysis tools and recently developed methods in a computationally efficient manner, and so is suitable for analyzing the vast amount of variant data available from sequencing family members, providing a rich choice of analysis methods for big data on families.

Availability and implementation

ONETOOL is freely available from http://healthstat.snu.ac.kr/software/onetool/.

Supplementary information

Supplementary data are available at Bioinformatics online.
So Close and Yet So Irritating: Negative Relations and Implications for Well-being by Age and Closeness
Authors: Birditt Kira S , Sherman Carey W , Polenick Courtney A , Becker Lucia , Webster Noah J , Ajrouch Kristine J , Antonucci Toni C
Published: March 2018

Objectives

Negative social relationships are associated with poor health, chronic illness, and mortality. Yet, we know little about the dynamics of negative aspects of relationships within individual’s closest relationships over time, how those experiences vary by age, and the implications of those relationships for well-being.

Method

A total of 592 participants (ages 25–97; M = 57.5; 63.3% women) from the Social Relations Study completed monthly web surveys for up to 12 months. Each month they reported negative relationship quality with their three closest network members and multiple dimensions of well-being (positive affect, negative affect, self-rated health, and sleep quality).

Results

Multilevel models revealed older individuals reported less negativity in their relationships than younger people, but fewer age differences in the closest tie. Greater negative relationship quality predicted poor well-being (i.e., greater negative affect, sleep problems). Links between negative relations and well-being were less strong among older individuals; especially in the closest ties.

Discussion

Results were partially consistent with the strength and vulnerability integration (SAVI) model, which proposes fewer age-related improvements in emotion regulation when individuals are unable to avoid tensions. Despite feeling just as negative as younger individuals, older individuals may be more resilient to tensions in their closest relationships.
Change of Polarization for Moduli of Sheaves on Surfaces as Bridgeland Wall-crossing
Authors: Bertram Aaron , Martinez Cristian
Published: March 2018

We prove that the “Thaddeus flips” of L-twisted sheaves constructed by Matsuki and Wentworth explaining the change of polarization for Gieseker semistable sheaves on a surface can be obtained via Bridgeland wall-crossing. Similarly, we realize the change of polarization for moduli spaces of one-dimensional Gieseker semistable sheaves on a surface by varying a family of stability conditions.
Isocitrate Dehydrogenase Mutations in Low-Grade Gliomas Correlate With Prolonged Overall Survival in Older Patients
Authors: Jones Pamela S , Carroll Kate T , Koch Matthew , DiCesare Jasmine A T , Reitz Kara , Frosch Matthew , Barker Fred G , Cahill Daniel P , Curry William T
Published: March 2018

BACKGROUND

Older age has been associated with worse outcomes in low-grade gliomas (LGGs). Given their rarity in the older population, determining optimal treatment plans and patient outcomes remains difficult.

OBJECTIVE

To retrospectively study LGG survival outcomes in an older population stratified by molecular genetic profiles.

METHODS

We included patients age ≥40 yr with pathologically confirmed World Health Organization grade II gliomas treated at a single institution between 1995 and 2015. We collected tumor genomic information when available.

RESULTS

Median overall survival for the entire group (n = 111, median age 51 yr, range 40-77 yr) was 15.75 yr with 5- and 10-yr survival rates of 84.3% and 67.7%, respectively. On univariate analysis, patients with isocitrate dehydrogenase (IDH) mutation had significantly increased survival compared to IDH wildtype (hazard ratio [HR] 0.17 [0.07-0.45], P < .001). Older age, seizure at presentation, larger tumor size, IDH wildtype, biopsy only, chemotherapy, and radiation were significantly associated with shorter survival based on univariate analyses. In patients with known IDH status (n = 73), bivariate analysis of IDH mutation status and age showed only IDH status significantly influenced overall survival (HR 0.22 [0.07-0.68], P = .008). Greater surgical resection was predictive of survival, although extent of resection significantly correlated with IDH mutation status (odds ratio 7.5; P < .001).

CONCLUSION

We show that genomic alterations in LGG patients ≥40 occur at high rates like the younger population and predict a similar survival advantage. Maximizing surgical resection may have survival benefit, although feasibility of resection is often linked to IDH status. Given the importance of molecular genetics, a redefinition of prognostic factors associated with these tumors is likely to emerge.