bluuebunny/crossref_metadata_2025 huggingface dataset:
Ultrafast dynamics of highly constrained azobenzene macrocycles
Authors: Slavov Chavdar , Yang Chong , Schweighauser Luca , Heindl Andreas H. , Stauch Tim , Wegner Herman A. , Dreuw Andreas , Wachtveitl Josef
Published: April 2019

The ultrafast photoisomerization of model azobenzene macrocycles was studied by transient absorption spectroscopy. Our results reveal a strong dependence of the dynamics and the overall molecular properties on the geometric constraints and the intramolecular strain.
Symmetry-breaking charge transfer dynamics of 9,9’-bianthracene revealed by experiment and theory
Authors: Lee Changmin , Lyu Taecheon , Choi Cheol Ho , Joo Taiha
Published: April 2019

Symmetry-breaking charge transfer reaction of 9,9’-bianthracene is driven exclusively by the rotational fluctuation of solvents, not including the inertial component in the solvation dynamics. Torsional motion and bond shortening during the reaction were observed.
Ultrafast Photolysis of o-Nitrophenol Studied by Time-Resolved Photoelectron Spectroscopy
Authors: Nitta Yuki , Schalk Oliver , Kaneshima Keisuke , Sekikawa Taro
Published: April 2019

The formation of nitrous acid (HONO) through photolysis of o-nitrophenol was captured in real time by time-resolved photoelectron spectroscopy using single-order high harmonic probe pulses. HONO is released 250 fs after photoexcitation.
UV-induced DNA self-repair mechanism traced with quantum chemistry
Authors: Reiter Sebastian , Keefer Daniel , Besel Vitus , de Vivie-Riedle Regina
Published: April 2019

Recently, UV radiation was found to promote the self-repair of a damaged DNA nucleobase sequence. The proposed mechanism after photoexcitation of an adjacent guanine adenine sequence is now validated by our quantum chemical calculations.
Directional control of dissociative ionization by a two-colour laser field
Authors: Wanie Vincent , Ibrahim Heide , Beaulieu Samuel , Thiré Nicolas , Schmidt Bruno E. , Deng Yunpei , Alnaser Ali S. , Litvinyuk Igor V. , Tong Xiao-Min , Légaré François
Published: April 2019

Using asymmetric two-color laser fields composed of 1800 and 900nm, we have simultaneously controlled four well identified fragmentation channels in dissociative ionization of the hydrogen molecule, resulting in enhanced electron-localization sensitivities of up to 65%.
Direct Measurement of Intramolecular Electron Transfer in a Series of Artificial Photosynthesis Processes
Authors: Onda Ken , Ohkubo Kei , Yamazaki Yasuomi , Koike Kazuhide , Tanaka Sei’ichi , Ishitani Osamu
Published: April 2019

We have directly determined the intramolecular electron transfer rate and revealed its mechanism in supramolecular complexes during CO2 photoreduction by time-resolved infrared spectroscopic measurements over a wide temporal range.
Mapping the ultrafast vibrational dynamics of all-trans and 13-Cis retinal isomerization in Anabaena Sensory Rhodopsin
Authors: Roy Partha Pratim , Youshizumi Rei , Kandori Hideki , Buckup Tiago
Published: April 2019

The ground and excited state evolution of fingerprint vibrational modes of all-trans-and 13-cis-retinal are mapped by impulsive vibrational spectroscopy. All-trans-retinal shows slower frequency shift dynamics in the excited state in comparison to 13-cis-retinal.
Anabaena Sensory Rhodopsin: Effect of point mutations on PSBR photo-isomerization speed
Authors: Agathangelou Damianos , Orozco-Gonzalez Yoelvis , del Carmen Marin Pérez Marí , Brazard Johanna , Kandori Hideki , Jung Kwan-Hwang , Léonard Jérémie , Ferré Nicolas , Olivucci Massimo , S. Haacke
Published: April 2019

We report new experimental results on the ultrafast photo-isomerization of ASR - PSBR where, unlike other retinal proteins, point mutations lead to a 2-fold increase of the photo-isomerization speed for the all-trans isomer. Prominent low-frequency vibrational coherences are reported for both the excited and photo-product ground states.
Conical intersection dynamics of pyrimidine nucleosides tracked with sub-20-fs UV pulses
Authors: Borrego-Varillas Rocío , Nenov Artur , Ganzer Lucia , Oriana Aurelio , Conti Irene , Delfino Ines , Manzoni Cristian , Garavelli Marco , Cerullo Giulio
Published: April 2019

By combining transient absorption spectroscopy with sub-20-fs UV pulses and ab initio numerical simulations we follow the ultrafast dynamics in pyrimidine nucleosides and visualize the passage through conical intersections presiding excited state deactivation.
Coherent wavepackets in the Fenna-Matthews-Olson complex are robust to excitonic-structure perturbations caused by mutagenesis
Authors: Maiuri Margherita , Ostroumov Evgeny E. , Saer Raphael G. , Blankenship Robert E. , Scholes Gregory
Published: April 2019

The photosynthetic FMO complex is probed by femtosecond pump-probe spectroscopy and compared with a series of genetically modified mutants with distinct excitonic interactions. These experiments allow us to identify vibrational contributions to the coherence.
New Synthetic Route to Tucatinib
Authors: Yin Lingfeng , Mao Yongjun , Liu Yaowei , Bu Lehao , Zhang Long , Chen Wenxin
Published: April 2019

A new and improved synthetic route to tucatinib is described that involves three key intermediates. The first of these, 4-([1,2,4]triazolo[1,5-a]pyridin-7-yloxy)-3-methylaniline, was prepared on a 100 g scale in 33% yield over five steps and 99% purity. Next, N
4-(4-([1,2,4]triazolo[1,5-a]pyridin-7-yloxy)-3-methylphenyl)quinazoline-4,6-diamine was isolated in 67% yield over three steps and >99% purity. Then, 4,4-dimethyl-2-(methylthio)-4,5-dihydrooxazole trifluoromethanesulfonate was prepared under mild conditions in 67% yield over two steps. Finally, tucatinib was obtained in 17% yield over nine steps and in >99% purity (HPLC). Purification methods used to isolate the product and the intermediates involved in the route are also reported.
SENTINEL1: Two-Season Study of Respiratory Syncytial Virus Hospitalizations among U.S. Infants Born at 29 to 35 Weeks' Gestational Age Not Receiving Immunoprophylaxis
Authors: Anderson Evan J. , DeVincenzo John P. , Simões Eric A. F. , Krilov Leonard R. , Forbes Michael L. , Pannaraj Pia S. , Espinosa Claudia M. , Welliver Robert C. , Wolkoff Leslie I. , Yogev Ram , Checchia Paul A. , Domachowske Joseph B. , Halasa Natasha , McBride Scott J. , Kumar Veena R. , McLaurin Kimmie K. , Rizzo Christopher P. , Ambrose Christopher S.
Published: April 2019

Objective The SENTINEL1 observational study characterized confirmed respiratory syncytial virus hospitalizations (RSVH) among U.S. preterm infants born at 29 to 35 weeks' gestational age (wGA) not receiving respiratory syncytial virus (RSV) immunoprophylaxis (IP) during the 2014 to 2015 and 2015 to 2016 RSV seasons.

Study Design All laboratory-confirmed RSVH at participating sites during the 2014 to 2015 and 2015 to 2016 RSV seasons (October 1–April 30) lasting ≥24 hours among preterm infants 29 to 35 wGA and aged <12 months who did not receive RSV IP within 35 days before onset of symptoms were identified and characterized.

Results Results were similar across the two seasons. Among infants with community-acquired RSVH (N = 1,378), 45% were admitted to the intensive care unit (ICU) and 19% required invasive mechanical ventilation (IMV). There were two deaths. Infants aged <6 months accounted for 78% of RSVH observed, 84% of ICU admissions, and 91% requiring IMV. Among infants who were discharged from their birth hospitalization during the RSV season, 82% of RSVH occurred within 60 days of birth hospitalization discharge.

Conclusion Among U.S. preterm infants 29 to 35 wGA not receiving RSV IP, RSVH are often severe with almost one-half requiring ICU admission and about one in five needing IMV.
Intraoperative Tilted Posteroanterior View for the Measurement of Distal Radius Articular Step-Off
Authors: Beldner Steven , Rabinovich Remy V. , Polatsch Daniel B.
Published: April 2019

The purpose of this study is to more accurately determine distal radius articular step-off in the posteroanterior (PA) view. A cadaveric forearm was osteotomized with varying amounts of articular displacement. A second osteotomy was made through the distal radius metaphysis to create four positions of tilt in the lateral plane (5° and 15° dorsal tilt; 5° and 15° volar tilt). Using fluoroscopy, the beam was positioned in the lateral plane from 25° volar to 20° dorsal, separated by 5° increments, obtaining modified PA images of the distal radius in its various configurations. The images were randomly evaluated for step-off by three hand surgeons in a blinded fashion. Statistical analysis was performed to determine the accuracy between estimated and actual step-off and was demonstrated to be greater when the PA view was parallel to the distal radius tilt in the lateral plane, for all four configurations of distal radius tilt. Data pertaining to the distal radius with 0 mm of step-off did not demonstrate the PA view, parallel to the distal radius tilt, to be superior than the PA views not parallel to the tilt; reaffirming that with anatomic reduction, any fluoroscopic image exhibits good alignment. This study confirms that the most accurate method of accessing PA step-off is to first determine the tilt of the radius on a lateral film and then align the beam in the PA plane to match this tilt.
Effect of Trial of Labor before Cesarean and Risk of Subsequent Placenta Accreta Spectrum Disorders
Authors: O'Malley Katharine N. , Norton Mary E. , Osmundson Sarah S.
Published: April 2019

Objective This study aimed to examine whether labor before cesarean affects the risk of placenta accreta spectrum (PAS) disorders in a subsequent pregnancy.

Study Design This is a secondary analysis of the Cesarean Registry, a prospective cohort study of women undergoing cesarean between 1999 and 2002. Women with one prior cesarean with known indications, which were categorized as likely associated with labor (labored cesarean) versus likely not associated with labor (unlabored cesarean), were included. Primary outcome was PAS disorder.

Results Of 34,224 women, 60% had a “labored cesarean” and 40% had an “unlabored cesarean.” Women with prior unlabored cesarean were more likely to have subsequent PAS disorder compared with women with a prior labored cesarean after adjusting for confounders (0.28 vs. 0.13%; adjusted odds ratio: 2.03; 95% confidence interval: 1.22–3.38).

Conclusion Prior unlabored cesarean is associated with an increased risk of PAS disorders in a subsequent pregnancy. This association may aid in risk stratification in women with suspected PAS disorders and help counsel about risks associated with cesarean on maternal request.
Two sides of the same coin? An investigation of the effects of frames on tax compliance and charitable giving
Authors: Castiglioni Cinzia , Lozza Edoardo , van Dijk Eric , van Dijk Wilco W.
Published: April 2019

Despite tax compliance being mandatory and charitable giving being voluntary, both can be seen as two sides of the same coin. Paying taxes and making monetary donations are two complementary ways to financially provide for the common good. Using goal-framing theory, an experimental study with a mixed-factorial design (N = 435) was conducted to test the effects of different frames on the intention to pay taxes and make charitable donations. Our results showed that for real taxpayers (i.e., for employees, self-employed, and entrepreneurs, but not for students) using a gain goal frame as a support to the normative goal frame was only effective in increasing intended tax compliance, whereas a supporting hedonic goal frame was only effective in increasing donation intention. In addition, it was found that gain and hedonic goal frames worked differently according to the prevailing motivation behind tax compliance and charitable giving. When the intrinsic motivation was already high, frames were ineffective (in the tax context) or even counter-productive (in the charitable giving context). In the presence of extrinsic motivations, instead, frames are especially effective.
Magnetic field sensing with the kinetic inductance of a high-Tc superconductor
Authors: Vesterinen V. , Ruffieux S. , Kalaboukhov A. , Sipola H. , Kiviranta M. , Winkler D. , Schneiderman J. F. , Hassel J.
Published: April 2019

We carry out an experimental feasibility study of a magnetic field sensor based on the kinetic inductance of the high critical temperature (high-Tc) superconductor yttrium barium copper oxide. We pattern thin superconducting films into radio-frequency resonators that feature a magnetic field pick-up loop. At 77 K and for film thicknesses down to 75 nm, we observe the persistence of screening currents that modulate the loop kinetic inductance. We report on a device with a magnetic field sensitivity of 4 pT/Hz, an instantaneous dynamic range of 11 μT, and operability in magnetic fields up to 28 μT. According to the experimental results the device concept appears attractive for sensing applications in ambient magnetic field environments.
In situ investigation of light soaking in organolead halide perovskite films
Authors: Zhong Yu , Luna Carlos Andres Melo , Hildner Richard , Li Cheng , Huettner Sven
Published: April 2019

Organolead halide perovskite solar cells (PSCs) have generated extensive attention recently with power conversion efficiency (PCE) exceeding 23%. However, these PSCs exhibit photoinduced instability in the course of their current-voltage measurements. In this work, we study the light-induced behavior in CH3NH3PbI3−xClx films in situ, by employing wide-field photoluminescence (PL) microscopy to obtain both the spatially and temporally resolved PL images simultaneously. Along with the increase in the PL intensity under continuous illumination, some areas render PL inactive. By characterizing the excitation energy dependent long-time PL decay behavior, we suggest that the PL quenching can be ascribed to a localized accumulation of iodide ions driven by the optical field. This ion localization leads to an enhancement of non-radiative recombination. The appearance of the PL inactive areas in the perovskite film impedes its photovoltaic device performance approaching the theoretical maximum PCE. Therefore, the herein presented real-time investigation of the light soaking of perovskite films is a versatile and adaptable method providing more details to improve the performance of PSCs.
Tuning the optical bandgap in layered hybrid perovskites through variation of alkyl chain length
Authors: Sichert Jasmina A. , Hemmerling Annick , Cardenas-Daw Carlos , Urban Alexander S. , Feldmann Jochen
Published: April 2019

Recently, layered hybrid perovskites have been attracting huge interest due to a wide range of possible chemical compositions and the resulting tunability of the materials’ properties. In this study, we investigate the effect of the chain length of the organic ligands on the optical properties of stacks of two-dimensional perovskite layers consisting of alkylammonium lead iodide (CnH2n+1NH3)2PbI4 with n = 4, …, 18. Photoluminescence and absorption spectroscopy reveal a blueshift with increasing chain length n including a jump of 110 meV between the n = 10 and n = 12 ligands due to a change in octahedral tilting. Using X-ray diffraction, we determine the crystal structure and find the octahedral tilting to be the main cause of this blueshift. However, for very short chain lengths, additional effects further reduce the transition energy. Results of effective mass approximation model calculations show good agreement between the expected reduction of transition energy and measured photoluminescence emission wavelength for these samples. This highlights how octahedral tilting plays a major role in determining the optical bandgap and suggests that miniband formation plays only a minor role in this material.
Numerical modeling of InGaN/GaN p-i-n solar cells under temperature and hydrostatic pressure effects
Authors: Chouchen Bilel , Gazzah Mohamed Hichem , Bajahzar Abdullah , Belmabrouk Hafedh
Published: April 2019

The present paper deals with the modeling of the simultaneous impact of temperature and applied hydrostatic pressure on the electronic characteristics and electrical parameters in In0.2Ga0.8N/GaN p-i-n solar cells. The energy conduction band is calculated with a self-consistent model coupled with the photovoltaic parameters taking into consideration the spontaneous and piezoelectric polarizations. A new efficient numerical model based on the difference finite method is well suited to theoretical and experimental data. The results reveal that the hydrostatic pressure has a beneficial effect on the behavior of cells on the N-face configuration, whereas the elevated temperature has a destructive impact on these devices.
Celebrating women conducting research in freshwater ecology … and how the citation game is damaging them
Authors: Downes Barbara J. , Lancaster Jill
Published: April 2019

We highlight women’s contributions to freshwater ecology by firstly considering the historical context and gender-based barriers faced by women attempting to gain an education and secure research jobs in science over the past 100+ years. The stories of four remarkable, pioneering women in freshwater ecology (Kathleen Carpenter, Ann Chapman, Rosemary Lowe-McConnell and Ruth Patrick) illustrate the impact of barriers, emphasise the significance of their contributions and provide inspiration for the challenges ahead. Women still face barriers to participation in science, and the second part of the paper focuses on a current form of discrimination, which is citation metrics used to measure the ‘quality’ or ‘impact’ of research. We show that arguments that citation metrics reflect research quality are logically flawed, and that women are directly disadvantaged by this practice. Women are also indirectly disadvantaged in ecology because they are more likely to carry out empirical than theoretical research, and publications are generated more slowly from empirical research. Surveys of citation patterns in ecology reveal also that women are less likely to be authors of review papers, which receive three times more citations than do original articles. Unless unfettered use of citation metrics is stopped, research will be damaged, and women will be prominent casualties.
Interaction of elementary waves with a weak discontinuity in an isothermal drift-flux model of compressible two-phase flows
Authors: Minhajul  , Raja Sekhar T.
Published: April 2019

In this paper, we study the interaction of elementary waves of the Riemann problem with a weak discontinuity for an isothermal no-slip compressible gas-liquid drift flux equation of two-phase flows. We construct the solution of the Riemann problem in terms of a one parameter family of curves. Using the properties of elementary waves, we prove a necessary and sufficient condition on initial data for which the solution of the Riemann problem consists of a left shock, contact discontinuity, and a right shock. Moreover, we derive the amplitudes of weak discontinuity and discuss the interactions of weak discontinuity with shocks and contact discontinuity. Finally, we carry out some tests to investigate the effect of shock strength and initial data on the jump in shock acceleration and the amplitudes of reflected and transmitted waves.
PHANOTATE: a novel approach to gene identification in phage genomes
Authors: McNair Katelyn , Zhou Carol , Dinsdale Elizabeth A , Souza Brian , Edwards Robert A
Published: April 2019

Motivation

Currently there are no tools specifically designed for annotating genes in phages. Several tools are available that have been adapted to run on phage genomes, but due to their underlying design, they are unable to capture the full complexity of phage genomes. Phages have adapted their genomes to be extremely compact, having adjacent genes that overlap and genes completely inside of other longer genes. This non-delineated genome structure makes it difficult for gene prediction using the currently available gene annotators. Here we present PHANOTATE, a novel method for gene calling specifically designed for phage genomes. Although the compact nature of genes in phages is a problem for current gene annotators, we exploit this property by treating a phage genome as a network of paths: where open reading frames are favorable, and overlaps and gaps are less favorable, but still possible. We represent this network of connections as a weighted graph, and use dynamic programing to find the optimal path.

Results

We compare PHANOTATE to other gene callers by annotating a set of 2133 complete phage genomes from GenBank, using PHANOTATE and the three most popular gene callers. We found that the four programs agree on 82% of the total predicted genes, with PHANOTATE predicting more genes than the other three. We searched for these extra genes in both GenBank’s non-redundant protein database and all of the metagenomes in the sequence read archive, and found that they are present at levels that suggest that these are functional protein-coding genes.

Availability and implementation

https://github.com/deprekate/PHANOTATE

Supplementary information

Supplementary data are available at Bioinformatics online.
DeepPASTA: deep neural network based polyadenylation site analysis
Authors: Arefeen Ashraful , Xiao Xinshu , Jiang Tao
Published: April 2019

Motivation

Alternative polyadenylation (polyA) sites near the 3′ end of a pre-mRNA create multiple mRNA transcripts with different 3′ untranslated regions (3′ UTRs). The sequence elements of a 3′ UTR are essential for many biological activities such as mRNA stability, sub-cellular localization, protein translation, protein binding and translation efficiency. Moreover, numerous studies in the literature have reported the correlation between diseases and the shortening (or lengthening) of 3′ UTRs. As alternative polyA sites are common in mammalian genes, several machine learning tools have been published for predicting polyA sites from sequence data. These tools either consider limited sequence features or use relatively old algorithms for polyA site prediction. Moreover, none of the previous tools consider RNA secondary structures as a feature to predict polyA sites.

Results

In this paper, we propose a new deep learning model, called DeepPASTA, for predicting polyA sites from both sequence and RNA secondary structure data. The model is then extended to predict tissue-specific polyA sites. Moreover, the tool can predict the most dominant (i.e. frequently used) polyA site of a gene in a specific tissue and relative dominance when two polyA sites of the same gene are given. Our extensive experiments demonstrate that DeepPASTA signisficantly outperforms the existing tools for polyA site prediction and tissue-specific relative and absolute dominant polyA site prediction.

Availability and implementation

https://github.com/arefeen/DeepPASTA

Supplementary information

Supplementary data are available at Bioinformatics online.
Religious service attendance, health behaviors and well-being—an outcome-wide longitudinal analysis
Authors: Pawlikowski Jakub , Białowolski Piotr , Węziak-Białowolska Dorota , VanderWeele Tyler J
Published: April 2019

Background

Previous studies of relationship between religiosity, health behaviors and well-being have showed mainly positive relationships, however, are very often limited to results of associative nature and subject to unmeasured confounding. This study focused on evaluating evidence for a positive association between religious service attendance (RSA), health behaviors and well-being in a longitudinal setting and robustness of these associations to unmeasured confounding.

Methods

Three waves (2009, 2011 and 2015) of the biennial longitudinal Polish household panel study with response from 6400 respondents were analyzed. Evidence for a positive and robust association between RSA and outcome variables was evaluated using outcome-wide regression analysis with control of all variables temporally prior to the exposure and sensitivity measures (E-values) to give information on the extent to which an unmeasured confounder would need to be associated with both the exposure and the outcomes.

Results

RSA is associated with reduced risk of unhealthy behaviors (smoking, alcohol use) and higher emotional well-being. These relationships are robust to substantial unmeasured confounding and difficult to explain by reference to other, unknown, variables. Evidence for a positive relationship between RSA and other well-being variables (social, physical) was less clear.

Conclusions

Religiosity may play an important role in public health, particularly in prevention of non-communicable diseases. The strong and robust associations between RSA and some health behaviors (i.e. tobacco use, alcohol abuse) and emotional well-being should arguably be taken into account in health education, health promotion programs, health prevention policy and psychotherapeutic approaches, particularly in more religious populations.
Commemorating Jules Michelet, 1876, 1882, 1898: The productivity of banality
Authors: Creyghton Camille
Published: April 2019

Between 1870 and 1900 three commemorative events for Jules Michelet took place in France: his burial at the Père Lachaise cemetery in 1876, the unveiling of his monument in 1882 and the national commemoration of his centenary in 1898. The republican historian was thus a major figure in Third Republic memory culture, while he was also considered one of its sources of inspiration. This article examines how throughout successive commemorations Michelet’s legacy was appropriated and popularized by the regime and how this resulted in what can be called a ‘banalizing of memory’. Furthermore, it argues that this banalizing process, despite criticism based on Michelet’s own work, was productive and led to an expansion of the public’s awareness of Michelet. Rather than being a sign of declining memory, banality in some contexts was the most viable option for realizing the aims of a commemoration.
Barents Sea cod (Gadus morhua) diet composition: long-term interannual, seasonal, and ontogenetic patterns
Authors: Holt Rebecca E , Bogstad Bjarte , Durant Joël M , Dolgov Andrey V , Ottersen Geir
Published: April 2019

Atlantic cod (Gadus morhua) is an ecologically and commercially important species in the North-Atlantic region. Cod is a top predator and information on its trophic ecology is integral for understanding predator–prey relationships and food-web dynamics. We present an analysis of the trophic patterns of Barents Sea (BS) cod using a unique 33-year time-series of stomach-content data from 1984 to 2016. We assessed patterns in diet (prey) composition across years, between seasons, as well as ontogenetic trends in diet, including predator–prey size relationships. Ontogenetic shifts in diet were observed, with fish becoming more important prey with increasing cod size. A very early onset of piscivory was found in <20 cm cod. Cannibalism was found in cod > 20 cm and increased with size. Juvenile cod exhibit a tendency towards consuming prey up to 33% of their body length, whereas larger cod feed on all prey sizes, resulting in asymmetric predator–prey size distributions. Diet varied significantly during 1984–2016, consistent with changes in both prey, cod abundance, and distribution. Seasonal differences were observed; capelin dominated the winter diet, whereas cod, polar cod, and other fish species were prevalent in summer/autumn months. This work represents an important step towards understanding trophic linkages that determine BS ecosystem dynamics.
Impact of ART-induced viral suppression on the HIV epidemic in Italy
Authors: Papa Federico , Felici Giovanni , Franzetti Marco , Gandolfi Alberto , Sinisgalli Carmela
Published: April 2019

The present study aims to clarify the role of the fraction of patients under antiretroviral therapy (ART) achieving viral suppression (VS) (i.e. having plasma viral load below the detectability threshold) on the human immunodeficiency virus (HIV) epidemic in Italy. Based on the hypothesis that VS makes the virus untransmittable, we extend a previous model and we develop a time-varying ordinary differential equation model with immigration and treatment, where the naive and non-naive populations of infected are distinguished, and different compartments account for treated subjects virally suppressed and not suppressed. Moreover, naive and non-naive individuals with acquired immune deficiency syndrome (AIDS) are considered separately. Clinical data stored in the nationwide database Antiviral Response Cohort Analysis are used to reconstruct the history of the fraction of virally suppressed patients since highly active ART introduction, as well as to assess some model parameters. Other parameters are set according to the literature and the final model calibration is obtained by fitting epidemic data over the years 2003–2015. Predictions on the evolution of the HIV epidemic up to the end of 2035 are made assuming different future trends of the fraction of virally suppressed patients and different eligibility criteria for treatment. Increasing the VS fraction is found to reduce the incidence, the new cases of AIDS and the deaths from AIDS per year, especially in combination with early ART initiation. The asymptotic properties of a time-invariant formulation of the model are studied, and the existence and global asymptotic stability of a unique positive equilibrium are proved.
Linezolid resistance in patients with drug-resistant TB and treatment failure in South Africa
Authors: Wasserman Sean , Louw Gail , Ramangoaela Limpho , Barber Garrick , Hayes Cindy , Omar Shaheed Vally , Maartens Gary , Barry Clifton , Song Taeksun , Meintjes Graeme
Published: April 2019

Objectives

Limited data exist on clinical associations and genotypic correlates of linezolid resistance in Mycobacterium tuberculosis. We aimed to describe mutations and clinical factors associated with phenotypic linezolid resistance from patients with drug-resistant TB at two public sector facilities in South Africa.

Methods

Adults and adolescents with treatment failure (culture positivity ≥4 months) on a linezolid-containing regimen were retrospectively identified. Phenotypic resistance, as defined by a linezolid MIC >1 mg/L, was assessed for retrieved isolates using broth microdilution. Targeted sequencing of rrl and rplC was performed, irrespective of growth on subculture.

Results

Thirty-nine patients with linezolid-based treatment failure were identified, 13 (33%) of whom had phenotypic or genotypic linezolid resistance after a median duration of 22 months (range = 7–32) of linezolid therapy. Paired MIC testing and genotyping was performed on 55 unique isolates. All isolates with phenotypic resistance (n = 16) were associated with known resistance mutations, most frequently due to the T460C substitution in rplC (n = 10); rrl mutations included G2814T, G2270C/T and A2810C. No mutations were detected in isolates with MICs at or below the critical concentration.

Conclusions

Linezolid resistance occurred in a third of patients with drug-resistant TB and treatment failure. Resistance occurred late and was predicted by a limited number of mutations in rrl and rplC. Screening for genotypic resistance should be considered for patients with a positive culture after 4 months of linezolid therapy in order to optimize treatment and avoid the toxicity of ineffective linezolid therapy.
Determination of Quinolone Antibiotic Residues in Human Serum and Urine Using High-Performance Liquid Chromatography/Tandem Mass Spectrometry
Authors: Wang Xiaoli , Guo Tao , Wei Yunbo , Xu Guiju , Li Na , Feng Jinhong , Zhao Rusong
Published: April 2019

Quinolone antibiotic residues may pose potential threat to human health. A rapid and sensitive method was developed for the determination of quinolone residues in human serum and urine. After solid phase extraction (SPE) process, eight quinolone residues were analyzed by high-performance liquid chromatography/tandem mass spectrometry (HPLC-MS/MS) using ciprofloxacin-d8 as the internal standard. The relative standard deviation of intra-day and inter-day precision for the eight quinolones were less than 7.52% and the accuracies ranged from 95.8% to 103% in human serum, and from 94.1% to 104% in human urine. The extraction recoveries for the eight quinolones varied from 80.2% to 113% in human serum and 83.4% to 117% in human urine. The limit of detection for the eight quinolones was 0.50–1.00 ng/mL. Quinolone antibiotic residues in human serum and urine from 12 volunteers were successfully analyzed with the validated method. The SPE-HPLC-MS/MS method was useful for accurate determination of quinolone antibiotic residues in human body.
Trends in the Evolution of Floodplain Management in Australia: Risk Assessment, Precautionary and Robust Decision-Making
Authors: England Philippa
Published: April 2019

This article tracks the evolution of floodplain development policy in Australia and analyses some recent case law in the light of that policy. Although the dominant policy paradigm promotes strategic risk management combined with affordable and proportionate risk mitigation, the case law analysed adopts a more risk averse and normative tone. There seems to be a clear dichotomy between the preferred risk management approach of the main policy documents and actual practice, at least in the courts. The reasons for this divergence and some reflections on the future of the precautionary principle in the light of this evidence are discussed in the final sections.
Noninvasive Sampling Reveals Short-Term Genetic Rescue in an Insular Red Fox Population
Authors: Quinn Cate B , Alden Preston B , Sacks Benjamin N
Published: April 2019

Genetic factors in the decline of small populations are extremely difficult to study in nature. We leveraged a natural experiment to investigate evidence of inbreeding depression and genetic rescue in a remnant population of subalpine-specialized Sierra Nevada red foxes (Vulpes vulpes necator) using noninvasive genetic monitoring during 2010–2017. Only 7 individuals were detected in the first 2 years. These individuals assigned genetically to the historical population and exhibited genetic hallmarks of inbreeding and no evidence of reproduction. Two years into the study, we detected 2 first-generation immigrant males from a recently expanding population of red foxes in the Great Basin Desert. Through annual resampling of individuals (634 red fox DNA samples, 41 individuals) and molecular reconstruction of pedigrees, we documented 1–3 litters/year for 5 years, all descended directly or indirectly from matings involving immigrant foxes. The observed heterozygosity and allelic richness of the population nearly doubled in 2 years. Abundance increased, indicative of a rapidly expanding population. Throughout the study, adult survival was high. Restoration of gene flow apparently improved the demographic trajectory of this population in the short term. Whether these benefits continue in the longer term could depend on numerous factors, such as maintenance of any locally adapted alleles. This study highlights the value of noninvasive genetic monitoring to assess rapidly shifting conditions in small populations. Uncertainties about the longer-term trajectory of this population underscore the need to continue monitoring and to research potential for both negative and positive aspects of continued genetic infusion.
From positive PDL to its non-classical extensions
Authors: Sedlár Igor , Punčochář Vít
Published: April 2019

We provide a complete binary implicational axiomatization of the positive fragment of propositional dynamic logic (PDL). The intended application of this result are completeness proofs for non-classical extensions of positive PDL. Two examples are discussed in this article, namely, a paraconsistent extension with modal De Morgan negation and a substructural extension with the residuated operators of the non-associative Lambek calculus. Informal interpretations of these two extensions are outlined.
Tracking reasons with extensions of relevant logics
Authors: Standefer Shawn
Published: April 2019

In relevant logics, necessary truths need not imply each other. In justification logic, necessary truths need not all be justified by the same reason. There is an affinity to these two approaches that suggests their pairing will provide good logics for tracking reasons in a fine-grained way. In this paper, I will show how to extend relevant logics with some of the basic operators of justification logic in order to track justifications or reasons. I will define and study three kinds of frames for these logics. For the first kind of frame, I show soundness and highlight a difficulty in proving completeness. This motivates two alternative kinds of frames, with respect to which completeness results are obtained. Axioms to strengthen the justification logic portions of these logics are considered. I close by developing an analogy between the dot operator of justification logic and theory fusion in relevant logics.
Partiality and its dual in natural implicative expansions of Kleene’s strong 3-valued matrix with only one designated value
Authors: Robles Gemma , Méndez José M
Published: April 2019

Equivalent overdetermined and underdetermined bivalent Belnap–Dunn type semantics for the logics determined by all natural implicative expansions of Kleene’s strong 3-valued matrix with only one designated value are provided.
A unified-models analysis of the development of sexual size dimorphism in Damaraland mole-rats, Fukomys damarensis
Authors: Thorley Jack , Clutton-Brock Tim H
Published: April 2019

Individual variation in growth rates often generates variation in fitness. However, the ability to draw meaningful inferences from growth data depends on the use of growth models that allow for direct comparisons of growth between the sexes, between populations, and between species. Unlike traditional sigmoid functions, a recently parameterized family of unified growth models provides a reliable basis for comparisons since each parameter affects a single curve characteristic and parameters are directly comparable across the unified family. Here, we use the unified-models approach to examine the development of sexual size dimorphism in Damaraland mole-rats (Fukomys damarensis), where breeding males are larger than breeding females. Using skeletal measurements, we show here that the larger size of male Damaraland mole-rats arises from an increased growth rate across the entire period of development, rather than through sex differences in the duration or timing of growth. Male-biased skeletal size dimorphism is not unusual among rodents, and our measures of sex differences in size in captive mole-rats are close to sexual size differences in the wild, where size dimorphism = 1.04 (male:female). We hope our study will encourage the wide use of unified growth models by mammalogists.
ALGORITHMS, MACHINE LEARNING, AND COLLUSION
Authors: Schwalbe Ulrich
Published: April 2019

This paper discusses whether self-learning price-setting algorithms can coordinate their pricing behavior to achieve a collusive outcome that maximizes the joint profits of the firms using them. Although legal scholars have generally assumed that algorithmic collusion is not only possible but also exceptionally easy, computer scientists examining cooperation between algorithms as well as economists investigating collusion in experimental oligopolies have countered that coordinated, tacitly collusive behavior is not as rapid, easy, or even inevitable as often suggested. Research in experimental economics has shown that the exchange of information is vital to collusion when more than two firms operate within a given market. Communication between algorithms is also a topic in research on artificial intelligence, in which some scholars have recently indicated that algorithms can learn to communicate, albeit in somewhat limited ways. Taken together, algorithmic collusion currently seems far more difficult to achieve than legal scholars have often assumed and is thus not a particularly relevant competitive concern at present. Moreover, there are several legal problems associated with algorithmic collusion, including questions of liability, of auditing and monitoring algorithms, and of enforcing competition law.
The Extended Disc Galaxy Exploration Science Survey: description and surface brightness profile properties
Authors: Staudaher Shawn M , Dale Daniel A , van Zee Liese
Published: April 2019

The survey description and near-infrared properties for 92 galaxies are presented for the Extended Disc Galaxy Exploration Science (EDGES) Survey, along with an investigation into the properties of the stellar haloes of these galaxies. EDGES is a Spitzer Space Telescope Warm Mission program designed to reach the surface brightness limit (∼0.5 kJy sr−1 or 29 AB mag arcsec−2) of the Infrared Array Camera (IRAC) 3.6 and 4.5 ${\rm \mu}$m bands for a wide range of galaxy types found within the local volume. The surface brightness profiles exhibit a large range in disc scale length, with breaks more frequently seen than in previous studies, owing in large part to the extremely deep near-infrared imaging. A number of these surface brightness profile breaks may be due to stellar haloes, up to seven galaxies out of the full sample of 92 galaxies, and we explore these implications in relation to current cosmological models. We also report the discovery of a new tidal stream near NGC 3953.
Observation of a possible superflare on Proxima Centauri
Authors: Kielkopf John F , Hart Rhodes , Carter Bradley D , Marsden Stephen C
Published: April 2019

We report the observation on ut 2017 July 1 of an unusually powerful flare detected in near-infrared continuum photometry of Proxima Centauri. During a campaign monitoring the star for possible exoplanet transits, we identified an increase in Sloan i’ flux leading to an observed peak at BJD 2457935.996 that was at least 10 per cent over pre-flare flux in this band. It was followed by a two-component rapid decline in the first 100 s that became a slower exponential decay with time constant of 1350 s. A smaller flare event 1300 s after the first added an incremental peak flux increase of 1 per cent of pre-flare flux. Since the onset of the flare was not fully time resolved at a cadence of 62 s, its actual peak value is unknown but greater than the time average over a single exposure of 20 s. The i’ band is representative of broad optical and near-IR continuum flux over which the integrated energy of the flare is 100 times the stellar luminosity. This meets the criteria that established the concept of superflares on similar stars. The resulting implied ultraviolet flux and space weather could have had an extreme effect on the atmospheres of planets within the star’s otherwise habitable zone.
Adaptive Changes in Hemoglobin Function in High-Altitude Tibetan Canids Were Derived via Gene Conversion and Introgression
Authors: Signore Anthony V , Yang Ying-Zhong , Yang Quan-Yu , Qin Ga , Moriyama Hideaki , Ge Ri-Li , Storz Jay F
Published: April 2019

A key question in evolutionary biology concerns the relative importance of different sources of adaptive genetic variation, such as de novo mutations, standing variation, and introgressive hybridization. A corollary question concerns how allelic variants derived from these different sources may influence the molecular basis of phenotypic adaptation. Here, we use a protein-engineering approach to examine the phenotypic effect of putatively adaptive hemoglobin (Hb) mutations in the high-altitude Tibetan wolf that were selectively introgressed into the Tibetan mastiff, a high-altitude dog breed that is renowned for its hypoxia tolerance. Experiments revealed that the introgressed coding variants confer an increased Hb–O2 affinity in conjunction with an enhanced Bohr effect. We also document that affinity-enhancing mutations in the β-globin gene of Tibetan wolf were originally derived via interparalog gene conversion from a tandemly linked β-globin pseudogene. Thus, affinity-enhancing mutations were introduced into the β-globin gene of Tibetan wolf via one form of intragenomic lateral transfer (ectopic gene conversion) and were subsequently introduced into the Tibetan mastiff genome via a second form of lateral transfer (introgression). Site-directed mutagenesis experiments revealed that the increased Hb–O2 affinity requires a specific two-site combination of amino acid replacements, suggesting that the molecular underpinnings of Hb adaptation in Tibetan mastiff (involving mutations that arose in a nonexpressed gene and which originally fixed in Tibetan wolf) may be qualitatively distinct from functionally similar changes in protein function that could have evolved via sequential fixation of de novo mutations during the breed’s relatively short duration of residency at high altitude.
A Virtual-Reality, 360-Degree Fly-Through of an Arteriovenous Malformation Resection: 2-Dimensional Operative Video
Authors: Steinberger Jeremy , Nistal Dominic , Schlachter Leslie , Costa Anthony , Oemke Holly , Bederson Joshua B
Published: April 2019

The application of navigation integrated virtual reality (VR) in neurosurgery is an emerging paradigm that may offer improved situational awareness for the surgeon. Here, we present a case of a complex arteriovenous malformation (AVM) with complex venous drainage and observe how VR impacted structural delineation during approach, resection, and overall strategic planning. The patient was a 30-yr-old female with no past medical history who presented with headaches and a generalized tonic clonic seizure. Workup included computed tomography, computed tomography angiography, magnetic resonance imaging, magnetic resonance angiography, and magnetic resonance venography; a high flow right frontal AVM was found. The AVM was safely resected using navigation integrated with VR; careful arterial devascularization preceded resection of the draining veins and then the AVM nidus. Postoperative scans confirmed complete resection of the AVM. This case outlines the application of a current state-of-the-art VR platform to assist the craniotomy for resection of an AVM.
Successful classification of macrophage-mannose receptor CD206 in severity of anti-MDA5 antibody positive dermatomyositis associated ILD
Authors: Horiike Yasuoki , Suzuki Yuzo , Fujisawa Tomoyuki , Yasui Hideki , Karayama Masato , Hozumi Hironao , Furuhashi Kazuki , Enomoto Noriyuki , Nakamura Yutaro , Inui Naoki , Ogawa Noriyoshi , Suda Takafumi
Published: April 2019

Objectives

Macrophage-mannose receptor, CD206, is a marker of alternatively activated macrophages. Activated macrophages play key roles in DM. Interstitial lung disease (ILD) is a leading cause of mortality in patients with DM/clinically amyopathic DM (CADM). In particular, patients with the anti-melanoma differential gene 5 antibody (MDA5) frequently develop fatal rapid progressive ILD. This study aimed to evaluate the clinical implications of alternatively activated macrophages in patients with CADM/DM-ILD with anti-MDA5 antibody (MDA5-CADM/DM-ILD).

Methods

We measured serum concentrations of soluble CD206 (sCD206) in 33 patients with MDA5-CADM/DM-ILD and 36 age- and sex-matched control subjects. Expression levels of CD206 in the lungs from MDA5-CADM/DM-ILD were also examined.

Results

Patients with MDA5-CADM/DM-ILD had higher levels of sCD206 than those in controls (P < 0.0001). Of the 33 patients, 10 MDA5-CADM/DM-ILD patients developed fatal respiratory failure. Concentrations of sCD206 in patients with fatal ILD cases were significantly higher than those in the survivors, and increased sCD206 levels were associated with a higher mortality rate (Log-rank test, P = 0.0009). Age- and gender-adjusted logistic regression analyses showed that sCD206 was an independent prognostic factor for MDA5-CADM/DM-ILD. Importantly, assessment by sCD206 together with PaO2 successfully divided into three groups by their prognosis (P < 0.005, respectively). Pathological analyses showed accumulations of CD206-positive macrophages in lungs from the fatal case rather than those in the non-fatal cases.

Conclusions

Levels of serum sCD206 are increased in MDA5-CADM/DM-ILD and associated with poor prognosis. sCD206 is a potential biomarker to predict the severity of MDA5-CADM/DM-ILD.