bluuebunny/crossref_metadata_2025 huggingface dataset:
Judgement of unvoiced and voiced pronunciation based on sparse feature with DCT dictionary
Authors: Wang Lianzi , Mastorakis Nikos , Zhuang Xiaodong
Published: September 2019

The judgment of unvoiced and voiced sound based on sparse representation in DCT dictionary is implemented. Human pronunciation can be mainly divided into unvoiced and voiced sound. Sparse representation can represent the signal with as few coefficients as possible on a set of over-complete vectors, which can reveal the most representative features of signals. In this paper, the difference between the sparse representation of unvoiced and voiced sound is studied, based on which a method is proposed to distinguish unvoiced and voiced sound in words. The experimental results prove that the proposed method is effective.
Recent Developments in Direct C–H Functionalization of Quinoxalin-2(1H)-ones via Radical Addition Processes
Authors: Monika Monika , Selvakumar Sermadurai
Published: September 2019

This review article covers the recent developments in direct C–H functionalization of quinoxalin-2(1H)-one derivatives via radical additions at the C3 position. Reaction types have been categorized depending on the kind of radical used, with representative examples and insightful mechanistic details provided.

1 Introduction

2 Reactions with Alkyl Radicals

3 Reactions with Acyl Radicals

4 Reactions with Aryl Radicals

5 Reactions with Perfluoroalkyl Radicals

6 Reactions with Alkoxycarbonyl Radicals

7 Reactions with Nitrogen Radicals

8 Reactions with Oxygen Radicals

9 Reactions with Phosphorus Radicals

10 Conclusion
Discovery of Novel Approach for Regioselective Synthesis of Thioxotriaza-Spiro Derivatives via Oxalic Acid
Authors: Gopinatha Vindya K. , Swarup Hassan A. , Raghavan Sathees C. , Mantelingu Kempegowda , Rangappa Kanchugarakoppal S.
Published: September 2019

A vital approach for the synthesis of a range of novel thioxotriaza-spiro derivatives is described. These new heterocyclic systems are obtained via oxalic acid catalyzed reaction of α,β-unsaturated ketones in the presence of 5,6-diamino-2-mercaptopyrimidine-4-ols; thus, spiro rings are constructed in one step. Notably, this transformation involves condensation of an amino group followed by enamine reaction with alkenes and subsequent reaction promoted by oxalic acid to afford spiro compounds with excellent regioselectivity.
Divergent Nickel-Catalysed Ring-Opening–Functionalisation of Cyclobutanone Oximes with Organozincs
Authors: Angelini Lucrezia , Malet Sanz Laia , Leonori Daniele
Published: September 2019

The development of a nickel-catalysed strategy for the remote alkylation, arylation, vinylation and alkynylation of nitriles is presented. The methodology uses electron-poor O-Ar cyclic oximes and organozincs as coupling partners. This redox process proceeds through the generation of an iminyl radical and its following ring-opening reaction.
Anti-Markovnikov Hydroazidation of Activated Olefins via Organic Photoredox Catalysis
Authors: Onuska Nicholas P. R. , Schutzbach-Horton Megan E. , Rosario Collazo José L. , Nicewicz David. A.
Published: September 2019

Organic azides serve as synthetically useful surrogates for primary amines, a functional group which is ubiquitous in bioactive and medicinally relevant molecules. Historically, the formal hydroazidation of simple activated olefins and styrenes has proven difficult due to the inherent propensity of these compounds to oligomerize. Herein is disclosed a method for the anti-Markovnikov hydroazidation of activated olefins, catalyzed by an organic acridinium salt under irradiation from blue LEDs. This method is applicable to a variety of substituted and terminal styrenes and several vinyl ethers, yielding synthetically versatile hydroazidation products in moderate to excellent yield.
Cyanide-Mediated Synthesis of Sulfones and Sulfonamides from Vinyl Sulfones
Authors: Roy Tamal , Lee Ji-Woong
Published: September 2019

We report a facile synthesis of sulfones, β-keto sulfones, and sulfonamides from vinyl sulfones via an addition–elimination sequence where in situ generation of nucleophilic sulfinate ion is mediated by cyanide. The use vinyl sulfones renders high selectivity for S-alkylation to produce sulfones in high yields. In the presence of N-bromosuccinimide, primary and secondary amines underwent sulfonamide formation. A preliminary mechanistic study showed the formation of acrylonitrile as an innocent byproduct, without interfering with the desired reaction pathway while generating a sulfinate nucleophile.
Interlude of metastability in the melting of polymer crystals
Authors: Iyer Kiran , Margossian Marzbed , Muthukumar Murugappan
Published: September 2019

We have studied the process of melting of polymer crystals using Langevin dynamics simulations with a coarse-grained united atom model. We have considered two ideal situations: one in which a single crystal melts and the other in which a multichain crystal melts. We show that the melting of the single crystal proceeds through a globular metastable state, which is followed by expansion to a more random coil-like state. Similarly, the melting of the multichain crystal reveals a special mechanism comprising two steps: one in which a long-lived partially molten metastable state is formed, followed by a second step in which the chains peel off from the crystalline core to a free state. We elucidate the nature of the metastable state close to the equilibrium melting temperature and show that the multichain crystals equilibrate to states of intermediate order, with the extent of ordering decreasing as we increase the melting temperature. We quantify the kinetics of melting by estimating a free energy landscape using parallel tempering Langevin dynamics simulations. These simulations reveal a metastable state in the single molecule systems, allowing us to estimate the free energy barriers. Additionally, the melting of the multichain crystals reveals the existence of two barriers, with the preference for the intermediate state reducing with increasing temperature. We compare our findings to the existing experimental evidence and find qualitative agreements.
Damage evolution in LiNbO3 due to electronic energy deposition below the threshold for direct amorphous track formation
Authors: Wesch W. , Rensberg J. , Schmidt M. , Wendler E.
Published: September 2019

Ionization-induced defect formation and amorphization were investigated in x- and z-cut LiNbO3 crystals irradiated with Si and O ions at energies yielding an electronic energy deposition Se close to the threshold value for melting. The evolution of radiation damage was analyzed using Rutherford Backscattering Spectrometry in channeling configuration. Damage peaks occur which are caused by the electronic energy loss of the incoming ions. From the difference in the evolution of these peaks observed along the x- and z-directions, the contribution of point defects/clusters and amorphous regions to the total amount of damage was separated. The analysis of the fluence dependences in the framework of a common defect accumulation and amorphization model revealed cross sections of the damage evolution processes involved. The cross sections for the point defect production were compared quantitatively with those calculated on the basis of the exciton decay model in combination with the analytical thermal spike concept. Very good agreement between measured and calculated cross sections was obtained when assuming a certain threshold value nvthresh of the relative concentration of primary defects for the formation of stable point defects/defect clusters remaining after irradiation. The occurrence of nvthresh provides a threshold value of the electronic energy deposition Se ≈ 2.5 keV nm−1 below which no defects are detected and which very well agrees with the threshold value for the defect formation in the subthreshold irradiation regime reported in the literature. The small values of the cross sections for direct amorphization within a single impact indicate that continuous amorphous ion tracks are hardly formed, but that at best, few amorphous pockets may be created along the trajectories of individual ions, which grow with ongoing irradiation. A comparison of the experimental data with inelastic thermal spike calculations shows that the formation of amorphous pockets starts when the electronic energy loss just reaches the threshold value for melting. The steep increase of the defect concentration up to complete damage within a narrow ion fluence range is mainly determined by the stimulated growth of defect clusters and amorphous regions. The corresponding parameters do not correlate with Se but with the energy density deposited per ion and unit volume, which is inversely proportional to the ion velocity. In summary, the investigations provide a consistent explanation of the damage formation in ion irradiated LiNbO3 in the near-melting threshold regime, taking into account the role of point defects, influence of partial melting, and velocity effect.
Resistance fluctuation spectroscopy of thin films of 3D topological insulator BiSbTeSe1.6
Authors: Biswas Sangram , Gopal R. K. , Singh Sourabh , Kant Raushan , Mitra Chiranjib , Bid Aveek
Published: September 2019

Despite several years of studies, the origin of slow-kinetics of charge-carriers at the surface-states of strong topological insulators remains abstruse. In this article, we report on studies of charge dynamics of thin films of the 3-dimensional strong topological insulator material BiSbTeSe1.6 grown by pulsed laser deposition (PLD). The bulk of the films was insulating, making them suitable for transport studies of topological surface-states. Despite being disordered and granular, the films show definite signatures of the presence of topological surface-states with electronic transport coherence lengths comparable to those of high-quality grown films grown by molecular beam epitaxy (MBE). At high temperatures, the resistance fluctuations in these films were found to be dominated by trapping-detrapping of charge carriers from multiple defect-levels of the bulk. At low temperatures, fluctuations in the resistance of surface-states, arising due to the coupling of surface transport with defect dynamics in bulk, determine the noise. We thus confirm that the measured low-frequency fluctuations in these films, over the entire temperature range of 20 mK–300 K, are determined primarily by bulk defect density. The magnitude of noise was comparable to that measured on bulk-exfoliated films but was slightly higher than that in MBE grown films. Our studies establish PLD as a viable route to develop high-quality topological insulator materials.
Interactions of intrinsic defects formed in ZnO and their contribution to electric conductivity
Authors: Shimizu H. , Sato W.
Published: September 2019

The formation process of lattice defects in single crystals of ZnO and their contribution to electric conduction were investigated by means of electric conductivity measurements and positron annihilation lifetime spectroscopy (PALS). For the ZnO samples once heated at high temperatures between 1073 K and 1273 K, we observed defect-induced n-type conductivity by sample warming or light irradiation to the sample, suggesting that interstitial zinc atoms (Zni) and oxygen vacancies (VO) as shallow and deep donors, respectively, were formed by the high-temperature heating. After heat treatment at 1373 K, however, the conductivity arises only from thermal excitation by sample warming, demonstrating that only Zni contributes to the conductivity but VO does not. Based on the above observation and the results of PALS measurements for the samples heated at high temperature, we propose a mechanism of the n-type conduction in ZnO that carrier electrons are provided by interstitial zinc atoms as a result of electron-hole cancellation through interaction between zinc vacancies (VZn) and VO.
Generics designate kinds but not always essences
Authors: Noyes Alexander , Keil Frank C.
Published: September 2019

Significance

How people reason about “kinds” (richly structured categories with high inductive potential) is at the heart of theories of cognition. One theory characterizes people as biased to essentialize, concluding that people are biased to infer that kinds are naturally determined by internal properties (essences). Generic statements (“men like sports”) are purported to evoke this bias. We advance methods by contrasting beliefs that a category is a kind with beliefs that a category has essential structure. We reveal flexibility in the presence of generics: Across varied domains and property content, generic statements increased participants’ belief that a category is richly structured with high inductive potential. Generics caused essentialism in interaction with other cues (e.g., biological properties) that reasonably prompt essentialist explanation.
Optimal compressed sensing strategies for an array of nonlinear olfactory receptor neurons with and without spontaneous activity
Authors: Qin Shanshan , Li Qianyi , Tang Chao , Tu Yuhai
Published: September 2019

Significance

Natural odors are typically mixtures of a few odorants from a large number of possible odorants, each with a broad distribution of concentrations. Here, we study how a relatively small number of neurons with a limited response range can optimize transmission of such high-dimensional sparse odor mixture information. For neurons without basal activity, we find that the optimal coding matrix is “sparse”—a fraction of ligand-receptor sensitivities are zero and the nonzero sensitivities follow a broad distribution matching the odor mixture statistics. We show that this maximum entropy code enhances performances of the downstream reconstruction and classification tasks. For neurons with a finite spontaneous activity, we show that introducing odor-evoked inhibition further enhances coding capacity.
Factors driving the seasonal and hourly variability of sea-spray aerosol number in the North Atlantic
Authors: Saliba Georges , Chen Chia-Li , Lewis Savannah , Russell Lynn M. , Rivellini Laura-Helena , Lee Alex K. Y. , Quinn Patricia K. , Bates Timothy S. , Haëntjens Nils , Boss Emmanuel S. , Karp-Boss Lee , Baetge Nicholas , Carlson Craig A. , Behrenfeld Michael J.
Published: September 2019

Four North Atlantic Aerosol and Marine Ecosystems Study (NAAMES) field campaigns from winter 2015 through spring 2018 sampled an extensive set of oceanographic and atmospheric parameters during the annual phytoplankton bloom cycle. This unique dataset provides four seasons of open-ocean observations of wind speed, sea surface temperature (SST), seawater particle attenuation at 660 nm (
c
p,660
, a measure of ocean particulate organic carbon), bacterial production rates, and sea-spray aerosol size distributions and number concentrations (
N
SSA
). The NAAMES measurements show moderate to strong correlations (0.56 <
R
< 0.70) between
N
SSA
and local wind speeds in the marine boundary layer on hourly timescales, but this relationship weakens in the campaign averages that represent each season, in part because of the reduction in range of wind speed by multiday averaging.
N
SSA
correlates weakly with seawater c
p,660
(
R
= 0.36,
P
<< 0.01), but the correlation with c
p,660
, is improved (
R
= 0.51,
P
< 0.05) for periods of low wind speeds. In addition, NAAMES measurements provide observational dependence of SSA mode diameter (
d
m
) on SST, with
d
m
increasing to larger sizes at higher SST (
R
= 0.60,
P
<< 0.01) on hourly timescales. These results imply that climate models using bimodal SSA parameterizations to wind speed rather than a single SSA mode that varies with SST may overestimate SSA number concentrations (hence cloud condensation nuclei) by a factor of 4 to 7 and may underestimate SSA scattering (hence direct radiative effects) by a factor of 2 to 5, in addition to overpredicting variability in SSA scattering from wind speed by a factor of 5.
The role of multilevel selection in host microbiome evolution
Authors: van Vliet Simon , Doebeli Michael
Published: September 2019

Animals are associated with a microbiome that can affect their reproductive success. It is, therefore, important to understand how a host and its microbiome coevolve. According to the hologenome concept, hosts and their microbiome form an integrated evolutionary entity, a holobiont, on which selection can potentially act directly. However, this view is controversial, and there is an active debate on whether the association between hosts and their microbiomes is strong enough to allow for selection at the holobiont level. Much of this debate is based on verbal arguments, but a quantitative framework is needed to investigate the conditions under which selection can act at the holobiont level. Here, we use multilevel selection theory to develop such a framework. We found that selection at the holobiont level can in principle favor a trait that is costly to the microbes but that provides a benefit to the host. However, such scenarios require rather stringent conditions. The degree to which microbiome composition is heritable decays with time, and selection can only act at the holobiont level when this decay is slow enough, which occurs when vertical transmission is stronger than horizontal transmission. Moreover, the host generation time has to be short enough compared with the timescale of the evolutionary dynamics at the microbe level. Our framework thus allows us to quantitatively predict for what kind of systems selection could act at the holobiont level.
Tunable spin and orbital polarization in SrTiO3-based heterostructures
Authors: Ho Cong Son , Kong Weilong , Yang Ming , Rusydi Andrivo , Jalil Mansoor B A
Published: September 2019

We formulate the effective Hamiltonian of Rashba spin–orbit coupling (RSOC) in

LaAlO

3

/

SrTiO

3

(LAO/STO) heterostructures. We derive analytical expressions of properties, e.g. Rashba parameter, effective mass, band edge energy and orbital occupancy, as functions of material and tunable heterostructure parameters. While linear RSOC is dominant around the Γ-point, cubic RSOC becomes significant at the higher-energy anti-crossing region. We find that linear RSOC stems from the structural inversion asymmetry (SIA), while the cubic term is induced by both SIA and bulk asymmetry. Furthermore, the SOC strength shows a striking dependence on the tunable heterostructure parameters such as STO thickness and the interfacial electric field which is ascribed to the quantum confinement effect near the LAO/STO interface. The calculated values of the linear and cubic RSOC are in agreement with previous experimental results.
Post-surgical hydropneumopericardium: a case report of dramatic increase in the apparent size of pericardial effusion with positional changes
Authors: Ali Yehia Z , Aung Htin , Doll Nathan J , Pislaru Sorin V
Published: September 2019

Background

Pneumopericardium is an uncommon clinical finding. It most commonly occurs after chest trauma but can also emerge as a complication following interventional or surgical procedures and can result in life-threatening complications. A high index of clinical suspicion should be present and once the condition is recognized, it should be managed promptly. Paucity of literature on pneumopericardium makes outlining any new case of paramount importance to emphasize the aspects of diagnosis and management of this rare condition.

Case summary

A 59-year-old woman with severe mitral valve and moderate tricuspid valve regurgitation underwent mitral and tricuspid valve repair with uneventful post-operative in-hospital stay. She presented 10 days after discharge with progressive shortness of breath. Chest X-ray revealed right hydropneumothorax. Transthoracic echocardiography (TTE) performed in the emergency department showed an apparently small pericardial effusion with patient in supine position; the effusion size increased substantially when imaging in left lateral decubitus, with presence of intrapericardial air bubbles. Computed tomography scan of the chest confirmed the presence of right hydropneumothorax and hydropneumopericardium, with a communicating pleuro-pericardial tract. The patient underwent chest tube placement which successfully decompressed both pleural and pericardial space.

Discussion

Hydropneumopericardium is a rare post-operative complication. Comprehensive TTE with imaging from multiple acoustic windows is mandatory when evaluating the extent of pericardial effusion. Presence of cardiac tamponade is crucial in determining the management plan.
Towards an equitable digital public health era: promoting equity through a health literacy perspective
Authors: Azzopardi-Muscat Natasha , Sørensen Kristine
Published: September 2019

Digital technologies shape the way in which individuals and health systems interact to promote health and treat illness. Their propensity to exacerbate inequalities is increasingly being highlighted as a concern for public health. Personal, contextual and technological factors all interact and determine uptake and consequent use of digital technologies for health. This article reviews evidence on the impact of digital technologies on health equity. Health literacy is presented as a lens through which to approach research and policy on access, uptake and use of digital technologies. In the short term, based on our review of published literature, we conclude that it is likely that digital technologies will increase health inequities associated with increased age, lower level of educational attainment and lower socio-economic status. Geographical inequity may increase as a result of poor infrastructure but may decrease if digital technologies can be effectively widely deployed to compensate for health workforce and health system deficiencies. Programmes to enhance health and digital literacy and monitoring of access, utilization and impact across all groups in society can help to ensure that digital technologies act to reduce rather than reproduce or exacerbate existent health inequalities.
Less Severe Preoperative Synovitis is Associated With Higher Self-reported Pain Intensity 12 Months After Total Knee Arthroplasty—An Exploratory Prospective Observational Study
Authors: Petersen Kristian K. , Arendt-Nielsen Lars , Vela Jonathan , Skou Søren T. , Eld Mikkel , Al-Mashkur Nasir M. , Boesen Mikael , Riis Robert G.C. , Simonsen Ole
Published: September 2019

Objectives:

Synovitis is one of the possible pain generators in osteoarthritis (OA) and is associated with upregulation of proinflammatory cytokines, which can lead to worsening of the postoperative pain. This exploratory study aimed to investigate the association between perioperative synovitis and self-reported pain 12 months after total knee arthroplasty (TKA) in patients with OA.

Materials and Methods:

Twenty-six knee OA patients were included in this analysis. The perioperative volume of synovitis in predefined locations was assessed by contrast-enhanced magnetic resonance imaging (CE-MRI) and dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). Perioperative synovitis was assessed histologically from biopsies of the synovium. Highest pain intensity within the last 24 hours (Visual Analog Scale, VAS, 0 to 100) was assessed before and 12 months after TKA. Patients were divided into a low-pain intensity (VAS≤30) and a high-pain intensity (VAS>30) group on the basis of 12 months postoperative VAS.

Results:

The high-pain intensity group had significantly lower perioperative contrast-enhanced-synovitis (P=0.025), DCE-synovitis (P<0.04), and a trend toward lower histologically assessed synovitis (P=0.077) compared with the low-pain intensity group. Perioperative synovitis scores were inversely correlated with pain intensity 12 months after TKA (P<0.05), indicating that more severe perioperative synovitis is associated with less severe pain intensity at 12 months.

Discussion:

Higher degrees of perioperative synovitis scores are found to be associated with less postoperative pain 12 months after TKA. Further, correlation analysis revealed that less severe perioperative CE-MRI and DCE-MRI synovitis was associated with higher pain intensity 12 months after TKA, suggesting that CE-MRI and DCE-MRI synovitis grades could be used as imaging markers for prediction of chronic postoperative pain after TKA.
Etymology of Letheon
Authors: Haridas Rajesh P. , Gionfriddo Michael , Bause George S.
Published: September 2019

In late 1846, following his successful public demonstrations of surgical anesthesia, Boston dentist William T. G. Morton selected Letheon as the commercial name for the ether-based “preparation” he had used to produce insensibility to pain. We have not identified a first-hand account of the coinage of Letheon. Although the name ultimately derives from the Greek Lēthē, the adjective Lethean, much in use in the mid-19th century, may have influenced Morton and those he called on to assist in finding a commercial name. By one unverified account, the name Letheon might have been coined independently by both Augustus Addison Gould, M.D., and Henry Jacob Bigelow, M.D.
NEW OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY FINDINGS ON AN INTRARETINAL VASCULAR PROCESS SECONDARY TO TOXOPLASMA RETINOCHOROIDITIS: 2 CASE REPORTS
Authors: Toutée Adélaïde , Orès Raphaëlle , Mrejen Sarah , Bodaghi Bahram , Kobal Alfred , Merabet Lilia , Brignole-Baudouin Françoise , Sahel José-Alain , Nghiem-Buffet Sylvia , Errera Marie-Hélène
Published: September 2019

Background/Purpose:

To determine which retinal layer is primarily involved in intraretinal vascular processes associated with Toxoplasma retinochoroiditis using multimodal imaging, including optical coherence tomography angiography (OCTA).

Methods:

Toxoplasma retinal lesions were analyzed through multimodal imaging, including color fundus photographs, fluorescein angiography, indocyanine green angiography, spectral-domain OCT, and OCTA.

Results:

Two patients with atypical features of Toxoplasma retinochoroiditis are described in the acute phase. The first patient presented with a primary episode of acute Toxoplasma retinitis associated with an intraretinal abnormal vascular process that was detected at the acute phase by indocyanine green angiography and was better delineated by OCTA. Seven months later, the intraretinal vascular process had fully resolved on OCTA imaging. The second patient presented with a recurrence of active Toxoplasma retinochoroiditis adjacent to a pre-existing pigmented scar. He had a similar abnormal intraretinal vascular process that was identified on both fluorescein angiography at the early phase and indocyanine green angiography, which was also confirmed by OCTA imaging.

Conclusion:

We report a new finding associated with Toxoplasma chorioretinitis: an abnormal intraretinal vascular process that resolved without anti–vascular endothelial growth factor therapy but after toxoplasmosis treatment alone.
Cross-Cultural Validity: Canadian Norm Values of the Alberta Infant Motor Scale Evaluated for Dutch Infants
Authors: Suir Imke , Boonzaaijer Marike , Nijmolen Petra , Westers Paul , Nuysink Jacqueline
Published: September 2019

Purpose:

To examine whether the Canadian normative values of the Alberta Infant Motor Scale (AIMS) are appropriate for Dutch infants.

Method:

In a cross-sectional study, 499 infants developing typically (0.5-19 months) were assessed using the AIMS home video method. The scaling method was used for calculating item locations of the Dutch sample, and Welch test to compare Canadian and Dutch raw scores.

Results: The

AIMS items (45 of 58) met the criterion for stable regression to calculate item locations of the Dutch data set and compare these with the Canadian data set. Dutch infants passed 42 of 45 items at an older age. Most monthly age groups of Dutch infants had lower mean AIMS scores.

Conclusion:

The Canadian norms are not appropriate for the Dutch study sample. Dutch infants appear to develop in a similar sequence but at a slower rate. This has implications regarding the clinical use of the AIMS in the Netherlands.
Dose-dependent morbidity of freshwater turtle hatchlings, Emydura macquarii krefftii, inoculated with Ranavirus isolate (Bohle iridovirus, Iridoviridae)
Authors: Wirth Wytamma , Schwarzkopf Lin , Skerratt Lee F. , Tzamouzaki Anna , Ariel Ellen
Published: September 2019

Ranaviral infections cause mass die-offs in wild and captive turtle populations. Two experimental studies were performed to first determine the susceptibility of an Australian turtle species (Emydura macquarii krefftii) to different routes of infection and second examine the effect of viral titre on the morbidity in hatchlings. All inoculation routes (intracoelomic, intramuscular and oral) produced disease, but the clinical signs, histopathology and time to onset of disease varied with the route. The median infectious and lethal doses for intramuscularly inoculated hatchlings were 102
.
52 (1.98–2.93) and 104.43 (3.81–5.19) TCID50 ml−1, respectively. Clinical signs began 14 to 29 days post-inoculation and the median survival time was 22 days (16–25) across all dose groups. For every 10-fold increase in dose, the odds of developing any clinical signs or severe clinical signs increased by 3.39 [P<0.01, 95 % confidence interval (CI): 1.81–6.36] and 3.71 (P<0.01, 95 % CI: 1.76–7.80), respectively. Skin lesions, previously only reported in ranaviral infection in lizards, were observed in the majority of intramuscularly inoculated hatchlings that developed ranaviral disease. The histological changes were consistent with those in previous reports for reptiles and consisted of necrosis at or near the site of injection, in the spleen, liver and oral cavity. Systemic inflammation was also observed, predominantly affecting necrotic organs. The estimates reported here can be used to model ranaviral disease and quantify and manage at-risk populations.
Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes
Authors: De Maio Nicola , Shaw Liam P. , Hubbard Alasdair , George Sophie , Sanderson Nicholas D. , Swann Jeremy , Wick Ryan , AbuOun Manal , Stubberfield Emma , Hoosdally Sarah J. , Crook Derrick W. , Peto Timothy E. A. , Sheppard Anna E. , Bailey Mark J. , Read Daniel S. , Anjum Muna F. , Walker A. Sarah , Stoesser Nicole ,   on behalf of the REHAB consortium
Published: September 2019

Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Long-read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid assembly). However, it is not clear how different long-read sequencing methods affect hybrid assembly accuracy. Relative automation of the assembly process is also crucial to facilitating high-throughput complete bacterial genome reconstruction, avoiding multiple bespoke filtering and data manipulation steps. In this study, we compared hybrid assemblies for 20 bacterial isolates, including two reference strains, using Illumina sequencing and long reads from either Oxford Nanopore Technologies (ONT) or SMRT Pacific Biosciences (PacBio) sequencing platforms. We chose isolates from the family Enterobacteriaceae, as these frequently have highly plastic, repetitive genetic structures, and complete genome reconstruction for these species is relevant for a precise understanding of the epidemiology of antimicrobial resistance. We de novo assembled genomes using the hybrid assembler Unicycler and compared different read processing strategies, as well as comparing to long-read-only assembly with Flye followed by short-read polishing with Pilon. Hybrid assembly with either PacBio or ONT reads facilitated high-quality genome reconstruction, and was superior to the long-read assembly and polishing approach evaluated with respect to accuracy and completeness. Combining ONT and Illumina reads fully resolved most genomes without additional manual steps, and at a lower consumables cost per isolate in our setting. Automated hybrid assembly is a powerful tool for complete and accurate bacterial genome assembly.
Long non-coding RNA Neat1 regulates adaptive behavioural response to stress in mice
Authors: Kukharsky Michail S. , Ninkina Natalia N. , An Haiyan , Telezhkin Vsevolod , Wei Wenbin , de Meritens Camille Rabesahala , Cooper-Knock Johnathan , Nakagawa Shinichi , Hirose Tetsuro , Buchman Vladimir L. , Shelkovnikova Tatyana A.
Published: September 2019

Abstract

NEAT1 is a highly and ubiquitously expressed long non-coding RNA (lncRNA) which serves as an important regulator of cellular stress response. However, the physiological role of NEAT1 in the central nervous system (CNS) is still poorly understood. In the current study, we addressed this by characterising the CNS function in the Neat1 knockout mouse model (Neat1-/- mice), using a combination of behavioural phenotyping, electrophysiology and expression analysis. RNAscope® in situ hybridisation revealed that in wild-type mice, Neat1 is expressed evenly across the CNS, with high expression in glial cells and low expression in neurons. Loss of Neat1 in mice results in an inadequate reaction to physiological stress manifested as hyperlocomotion and panic escape response. In addition, Neat1-/- mice display deficits in social interaction and rhythmic patterns of activity but retain normal motor function and memory. Neat1-/- mice do not present with neuronal loss, overt neuroinflammation or gross synaptic dysfunction in the brain. However, cultured Neat1-/- neurons are characterised by hyperexcitability and dysregulated calcium homeostasis, and stress-induced neuronal activity is also augmented in Neat1-/- mice in vivo. Gene expression analysis showed that Neat1 may act as a weak positive regulator of multiple genes in the brain. Furthermore, loss of Neat1 affects alternative splicing of genes important for the CNS function and implicated in neurological diseases. Overall, our data suggest that Neat1 is involved in stress signaling in the brain and fine-tunes the CNS functions to enable adaptive behaviour in response to physiological stress.
Deciphering anomalous heterogeneous intracellular transport with neural networks
Authors: Han Daniel S , Korabel Nickolay , Chen Runze , Johnston Mark , Allan Viki J. , Fedotov Sergei , Waigh Thomas A.
Published: September 2019

Biological intracellular transport is predominantly heterogeneous in both time and space, exhibiting varying non-Brownian behaviour. Characterisation of this movement through averaging methods over an ensemble of trajectories or over the course of a single trajectory often fails to capture this heterogeneity adequately. Here, we have developed a deep learning feedforward neural network trained on fractional Brownian motion, which provides a novel, accurate and efficient characterization method for resolving heterogeneous behaviour of intracellular transport both in space and time. Importantly, the neural network requires significantly fewer data points compared to established methods, such as mean square displacements, rescaled range analysis and sequential range analysis. This enables robust estimation of Hurst exponents for very short time series data, making possible direct, dynamic segmentation and analysis of experimental tracks of rapidly moving cellular structures such as endosomes and lysosomes. By using this analysis, we were able to interpret anomalous intracellular dynamics as fractional Brownian motion with a stochastic Hurst exponent.
Experimental system and image analysis software for high throughput phenotyping of mycorrhizal growth response inBrachypodium distachyon
Authors: Maviane-Macia Felicia , Ribeyre Camille , Buendia Luis , Gaston Mégane , Khafif Mehdi , Devoilles Fabrice , Peeters Nemo , Lefebvre Benoit
Published: September 2019

Plant growth response to Arbuscular Mycorrhizal (AM) fungi is variable and depends on genetic and environment factors that still remain largely unknown. Identification of these factors can be envisaged using high-throughput and accurate plant phenotyping.

We setup experimental conditions based on a two-compartment system allowing to measureBrachypodium distachyonmycorhizal growth response (MGR) in an automated phenotyping greenhouse. We developed a new image analysis software“IPSO Phen”to estimate ofB. distachyonaboveground biomass.

We found a positive MGR in theB. distachyonBd3-1 genotype inoculated with the AM fungiRhizophagus irregularisonly if nitrogen and phosphorus were added together in the compartment restricted to AM fungi. Using this condition, we found genetic diversity inB. distachyonfor MGR ranging from positive to negative MGR depending on the plant genotype tested.

Our result on the interaction between nitrogen and phosphorus for MGR inB. distachyonopens new perspectives about AM functioning. In addition, our open-source software allowing to test and run image analysis parameters on large amount of images generated by automated plant phenotyping facilities, will help to screen large panels of genotypes and environmental conditions to identify the factors controlling the MGR.
Single Cell Spatial Chromatin Analysis of Fixed Immunocytochemically Identified Neuronal Cells
Authors: Lee Jaehee , Lu Youtao , Wang Jinchun , Li Jifen , Fisher Stephen A. , Nordgren C. Erik , Rosario Jean G. , Anderson Stewart A. , Ulyanova Alexandra V. , Brem Steven , Chen H. Isaac , Wolf John A. , Grady M. Sean , Healy Mimi , Kim Junhyong , Eberwine James
Published: September 2019

Assays examining the open-chromatin landscape in single cells require isolation of the nucleus, resulting in the loss of spatial/microenvironment information. Here we describe CHEX-seq (CHromatin EXposed) for identifying single-stranded open-chromatin DNA regions in paraformaldehyde-fixed single cells. CHEX-seq uses light-activated DNA probes that binds to single-stranded DNA in open chromatin. In situ laser activation of the annealed probes’ 3’-Lightning Terminator™ in selected cells permits the probe to act as a primer for in situ enzymatic copying of single-stranded DNA that is then sequenced. CHEX-seq is benchmarked with human K562 cells and its utility is demonstrated in dispersed primary mouse and human brain cells, and immunostained cells in mouse brain sections. Further, CHEX-seq queries the openness of mitochondrial DNA in single cells. Evaluation of an individual cell’s chromatin landscape in its tissue context enables “spatial chromatin analysis”.

One Sentence Summary

A new method, CHEX-seq (CHromatin eXposed), identifies the open-chromatin landscape in single fixed cells thereby allowing spatial chromatin analysis of selected cells in complex cellular environments.
Structure of an RNA helix with pyrimidine mismatches and cross-strand stacking
Authors: Montemayor Eric J. , Virta Johanna M. , Hagler Lauren D. , Zimmerman Steven C. , Butcher Samuel E.
Published: September 2019

The structure of a 22-base-pair RNA helix with mismatched pyrimidine base pairs is reported. The helix contains two symmetry-related CUG sequences: a triplet-repeat motif implicated in myotonic dystrophy type 1. The CUG repeat contains a U–U mismatch sandwiched between Watson–Crick pairs. Additionally, the center of the helix contains a dimerized UUCG motif with tandem pyrimidine (U–C/C–U) mismatches flanked by U–G wobble pairs. This region of the structure is significantly different from previously observed structures that share the same sequence and neighboring base pairs. The tandem pyrimidine mismatches are unusual and display sheared, cross-strand stacking geometries that locally constrict the helical width, a type of stacking previously associated with purines in internal loops. Thus, pyrimidine-rich regions of RNA have a high degree of structural diversity.
At the heart of controversies
Authors: Amilien Virginie , Tocco Barbara , Strandbakken Paal
Published: September 2019

Purpose

The purpose of this paper is to discuss and evaluate the role of hybrid forums as tools to address specific controversies related to sustainable practices in localized agro-food systems (LAFS).

Design/methodology/approach

In contrast with other conventional public engagement methods, such as citizen juries, consensus conferences, focus groups or deliberative processes, hybrid forums entail a more dynamic and democratic mechanism to reflect and act together, with the aim of constructing a common project around a defined challenge (Callonet al., 2001, 2009). They can offer an enriching and challenging methodological approach in the context of LAFS, especially in the discussion of controversial issues around food chain sustainability. The authors present here a new generation of hybrid forums: HF 2.0.

Findings

HF 2.0. represent both a methodological tool and a real experience of dialogic democracy, two interactive aspects which are closely interlinked and rest upon each other. The authors argue that the attractiveness of HF 2.0. is notable in at least two ways: first, they provide a solid democratic and reflective mechanism to stimulate effective dialogue and knowledge-exchange among different stakeholders; second, they contribute as an important methodological evidence-based tool, which can be used as a launching pad for shaping local action groups and community partnerships’ strategies aimed at fostering local development.

Originality/value

This paper attempts to provide a methodological discussion over the experimental use of HF 2.0. in the context of LAFS and assesses their effectiveness in the co-construction of knowledge. The authors explore their pragmatic validity in addressing controversies over local and sustainable seafood via empirical applications in Norway and the UK.
Leadership in challenging times of academic libraries
Authors: Aslam Mohammad
Published: September 2019

Purpose

The purpose of this study is to explore the key challenges of academic libraries in times of changing nature of higher education system and how library leaders can manage the challenges when effective leadership is highly required for academic libraries today. As the time is changing, the kinds of challenges that library leaders face have also changed. Author of this study explores the methods and approaches, which are more effective ways of managing challenges in the reshaping environment of academic libraries. At the same time, change has become a permanent part of academic libraries and they need leaders who are able to lead and manage change efficiently, bring theories into practices, find innovative solutions to challenges, creative thinkers, effective communicators, collaborative mindset and self-motivators.

Design/methodology/approach

The selective publications have been reviewed to find the best ways to leading changes and managing challenges in academic libraries. The approaches and methods in this study are based on personal experiences of author as director of the university libraries and experiences of library leadership worldwide are conversed.

Findings

Academic libraries are facing similar challenges around the world. The author found that academic library leadership needs innovative skills and competencies, effective communication abilities and a new way of thinking to deal with challenges and create willingness to adapt the changes. Kotter’s leadership manage change model may apply for creating and implementing organizational change in academic libraries.

Originality/value

Literature on this topic is comparatively limited. Consequently, this manuscript adds value to the publications of library and information sciences and offers the literature in the field of leadership challenges and manage change in the academic libraries. It also provides guidelines to academic library leadership universally, and how can leaders work with change effectively.
An examination of chronic ill-health and lifestyle factors among inmates: searching for the healthy immigrant effect in New South Wales Prisons
Authors: Field Courtney , Zovko Alyssa , Bowman Julia
Published: September 2019

Purpose

The purpose of this paper is to compare the rates of chronic health conditions and lifestyle factors between Australian-born and overseas-born inmates and to uncover predictive relationships between lifestyle factors and health outcomes for both groups.

Design/methodology/approach

Data are presented from a cross-sectional study based on a sample of inmates from correctional sites in New South Wales (NSW). The inclusion of results here was guided by the literature relating to the healthy immigrant effect.

Findings

Results indicate that a higher proportion of Australian-born inmates consumed alcohol at higher levels and were more likely to smoke on a daily or almost daily basis than overseas-born inmates. Australian-born inmates were also more likely than overseas-born inmates to have been diagnosed with cancer, epilepsy or hepatitis C. Physical activity predicted the number of diagnoses for Australian-born inmates while physical activity and smoking frequency predicted the number of diagnoses for overseas-born inmates.

Practical implications

Overseas-born inmates make up a considerable portion of the prison population in NSW. A better understanding of those health and lifestyle factors that distinguish them from Australian-born inmates provides important insight regarding health promotion and the planning of service provision for those providing health care in this space.

Originality/value

Comparison of the health of immigrant and native-born prison inmates has not been undertaken before and promises to provide important information regarding those factors that distinguish a sizeable minority in the prison population.
Influence of non-linear radiation, Joule heating and viscous dissipation on the boundary layer flow of MHD nanofluid flow over a thin moving needle
Authors: Upreti Himanshu , Kumar Manoj
Published: September 2019

Purpose

The purpose of this paper is to examine the effect of non-linear thermal radiation, Joule heating and viscous dissipation on the mixed convection boundary layer flow of MHD nanofluid flow over a thin moving needle.

Design/methodology/approach

The equations directing the flow are reduced into ODEs by implementing similarity transformation. The Runge–Kutta–Fehlberg method with a shooting technique was implemented.

Findings

Numerical outcomes for the coefficient of skin friction and the rate of heat transfer are tabulated and discussed. Also, the boundary layer thicknesses for flow and temperature fields are addressed with the aid of graphs.

Originality/value

Till now, no numerical study investigated the combined influence of Joule heating, non-linear thermal radiation and viscous dissipation on the mixed convective MHD flow of silver-water nanofluid flow past a thin moving needle. The numerical results for existing work are new and their novelty verified by comparing them with the work published earlier.