bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation functions, mean first passage times, and the Kemeny constant
Authors: Kells Adam , Koskin Vladimir , Rosta Edina , Annibale Alessia
Published: March 2020

Markov processes are widely used models for investigating kinetic networks. Here, we collate and present a variety of results pertaining to kinetic network models in a unified framework. The aim is to lay out explicit links between several important quantities commonly studied in the field, including mean first passage times (MFPTs), correlation functions, and the Kemeny constant. We provide new insights into (i) a simple physical interpretation of the Kemeny constant, (ii) a relationship to infer equilibrium distributions and rate matrices from measurements of MFPTs, and (iii) a protocol to reduce the dimensionality of kinetic networks based on specific requirements that the MFPTs in the coarse-grained system should satisfy. We prove that this protocol coincides with the one proposed by Hummer and Szabo [J. Phys. Chem. B 119, 9029 (2014)], and it leads to a variational principle for the Kemeny constant. Finally, we introduce a modification of this protocol, which preserves the Kemeny constant. Our work underpinning the theoretical aspects of kinetic networks will be useful in applications including milestoning and path sampling algorithms in molecular simulations.
Heat-induced degradation of fibrils: Exponential vs logistic kinetics
Authors: Co Nguyen Truong , Lan Pham Dang , Quoc Huy Pham Dinh , Li Mai Suan
Published: March 2020

The degradation of fibrils under the influence of thermal fluctuations was studied experimentally by various groups around the world. In the first set of experiments, it was shown that the decay of fibril content, which can be measured by the ThT fluorescence assay, obeys a bi-exponential function. In the second series of experiments, it was demonstrated that when the monomers separated from the aggregate are not recyclable, the time dependence of the number of monomers belonging to the dominant cluster is described by a single-exponential function if the fraction of bound chains becomes less than a certain threshold. Note that the time dependence of the fraction of bound chains can be measured by tryptophan fluorescence. To understand these interesting experimental results, we developed a phenomenological theory and performed molecular simulation. According to our theory and simulations using the lattice and all-atom models, the time dependence of bound chains is described by a logistic function, which slowly decreases at short time scales but becomes a single exponential function at large time scales. The results, obtained by using lattice and all-atom simulations, ascertained that the time dependence of the fibril content can be described by a bi-exponential function that decays faster than the logistic function on short time scales. We have uncovered the molecular mechanism for the distinction between the logistic and bi-exponential behavior. Since the dissociation of the chain from the fibrils requires the breaking of a greater number of inter-chain contacts as compared to the breaking of the beta sheet structure, the decrease in the number of connected chains is slower than the fibril content. Therefore, the time dependence of the aggregate size is logistic, while the two-exponential behavior is preserved for the content of fibrils. Our results are in agreement with the results obtained in both sets of experiments.
Influence of local surface defects on the minority-carrier lifetime of passivating-contact solar cells
Authors: Cattin Jean , Haschke Jan , Ballif Christophe , Boccard Mathieu
Published: March 2020

Unlocking the full potential of passivating contacts, increasingly popular in the silicon solar cell industry, requires determining the minority carrier lifetime. Minor passivation drops limit the functioning of solar cells; however, they are not detected in devices with open-circuit voltages below 700 mV. In this work, simulations and experiments were used to show the effect of localized surface defects on the overall device performance. Although the defects did not significantly affect lifetime measurements prior to electrode deposition or open-circuit voltage measurements at standard-test conditions, they had a significant impact on the point of operation and, in turn, device efficiency (up to several percent efficiency drop). Furthermore, this study demonstrates that localized defects can have a detrimental effect on well-passivated areas located several centimeters away through electrical connection by the electrode. This leads to a low-injection lifetime drop after electrode deposition. Thus, commonly measured lifetime curves before metallization (and therefore internal voltage) are usually not representative of their respective values after metallization. The low-injection lifetime drop often observed after electrode deposition can be derived from such local surface defects and not from a homogeneous passivation drop.
Maximum deformation of charged dielectric droplets
Authors: Xu Weiwei , Luo Jianfei , Qin Jun , Zhang Yongming
Published: March 2020

In this study, the maximum deformation of micrometer sized droplet of dielectric water-based paint impact onto a flat steel surface and exposed to a constant and uniform electric field was investigated by simulation based on the level-set method within the framework of Navier-Stokes. Upon a series experiments for droplet impacting and spreading of water-based paint on dielectric solid substrate with different initial impacting velocities in external electric field, results demonstrated that the maximum deformation ratio increases with the increase of initial impacting velocity, and can scale as We1/4 where We is the Weber number. The effect of electric field intensity to the final shape of droplet of water-based paint on a hydrophobic surface was investigated. It was found that the eccentricity of droplet can scale as E where E is the electric field intensity, and a prediction model of droplet between the deformation ratio (ξF) of droplet at final equilibrium contact angle and E was presented. Finally, the effect of applied voltage and equilibrium contact angle was studied.
Ultrafast excited state dynamics of biliverdin dimethyl ester
coordinate with zinc ions
Authors: Chen Zhuang , Liu Yang-yi , He Xiao-xiao , Chen Jin-quan
Published: March 2020

As one of the biological endogenous pigments, biliverdin (BV) and its dimethyl ester (BVE) have extremely weak fluorescence in solution with quantum yield less than 0.01%. However, the situation reverses with the addition of zinc ions. The strength for fluorescence of BVE-Zn2+ complex is greatly enhanced and fluorescence quantum yield can increase to 5%. Herein, we studied ultrafast excited state dynamics of BVE-Zn2+ complex in ethanol, n-propanol, and DMSO solutions in order to reveal the mechanism of fluorescence quantum yield enhancement. The results show that BVE can form a stable coordination complex with zinc with 1:1 stoichiometry in solution. BVE is structurally and energetically more stable in the complex. Using picosecond time-resolve fluorescence and femtosecond transient absorption spectroscopy, we show that smaller non-radiative rate constant of BVE-Zn2+ complex in DMSO is the key to increasing its fluorescence quantum yield and the excited state decay mechanism is also revealed. These results provide valuable information about the fluorescence property change after BVE binding to metal ions and may provide a guidance for the study of phytochromes or other fluorescence proteins in which BV/BVE acts as chromophores.
Volatile depletion in planet-forming disks
Authors: Du Fujun
Published: March 2020

Newly born stars are surrounded by gas and dust with a flattened axisymmetric distribution termed protoplanetary disk, in which planets are formed. Observations of these objects are necessary for understanding the formation and early evolution of stars and planets, and for revealing the composition of the raw material from which planets are made. Numerical models can extract important parameters from the observational data, including the gas and dust mass of the disk. These parameters are used as input for further modeling, e.g., to calculate the chemical composition of the disk. A consistent thermochemical model should be able to reproduce the abundances of different species in the disk. However, this good wish has been challenged for many disks: models over-predict the emission line intensity of some species; namely, they are depleted (with respect to expectations from canonical models). In this review we show how this disparity indicates that dust evolution has significant effects on gas chemistry, and may indicate the earliest stages of planet formation.
Correction of the Fan factor
Authors: Ullrich Bruno , Xi Haowen , Bhowmick Mithun
Published: March 2020

The theory of Fan describes the thermally provoked shift of the energy bandgap of semiconductors. Part of the theory is the Fan factor, which depends on the microscopic material parameters, such as the dielectric constants and effective masses. Herein, employing data of GaP, we show that the originally published Fan factor was missing one multiplicative numerical factor, which turned out to be the high frequency dielectric constant.
PIMMS43 is required for malaria parasite immune evasion and sporogonic development in the mosquito vector
Authors: Ukegbu Chiamaka V. , Giorgalli Maria , Tapanelli Sofia , Rona Luisa D. P. , Jaye Amie , Wyer Claudia , Angrisano Fiona , Blagborough Andrew M. , Christophides George K. , Vlachou Dina
Published: March 2020

After being ingested by a female
Anopheles
mosquito during a bloodmeal on an infected host, and before they can reach the mosquito salivary glands to be transmitted to a new host,
Plasmodium
parasites must establish an infection of the mosquito midgut in the form of oocysts. To achieve this, they must first survive a series of robust innate immune responses that take place prior to, during, and immediately after ookinete traversal of the midgut epithelium. Understanding how parasites may evade these responses could highlight new ways to block malaria transmission. We show that an ookinete and sporozoite surface protein designated as PIMMS43 (
Plasmodium
Infection of the Mosquito Midgut Screen 43) is required for parasite evasion of the
Anopheles coluzzii
complement-like response. Disruption of PIMMS43 in the rodent malaria parasite
Plasmodium berghei
triggers robust complement activation and ookinete elimination upon mosquito midgut traversal. Silencing components of the complement-like system through RNAi largely restores ookinete-to-oocyst transition but oocysts remain small in size and produce a very small number of sporozoites that additionally are not infectious, indicating that PIMMS43 is also essential for sporogonic development in the oocyst. Antibodies that bind PIMMS43 interfere with parasite immune evasion when ingested with the infectious blood meal and significantly reduce the prevalence and intensity of infection. PIMMS43 genetic structure across African
Plasmodium falciparum
populations indicates allelic adaptation to sympatric vector populations. These data add to our understanding of mosquito–parasite interactions and identify PIMMS43 as a target of malaria transmission blocking.
Squeezed metallic droplet with tunable Kubo gap and charge injection in transition metal dichalcogenides
Authors: Yuan Jiaren , Chen Yuanping , Xie Yuee , Zhang Xiaoyu , Rao Dewei , Guo Yandong , Yan Xiaohong , Feng Yuan Ping , Cai Yongqing
Published: March 2020

Shrinking the size of a bulk metal into nanoscale leads to the discreteness of electronic energy levels, the so-called Kubo gap δ. Renormalization of the electronic properties with a tunable and size-dependent δ renders fascinating photon emission and electron tunneling. In contrast with usual three-dimensional (3D) metal clusters, here we demonstrate that Kubo gap δ can be achieved with a two-dimensional (2D) metallic transition metal dichalcogenide (i.e., 1T′-phase MoTe
2
) nanocluster embedded in a semiconducting polymorph (i.e., 1H-phase MoTe
2
). Such a 1T′/1H MoTe
2
nanodomain resembles a 3D metallic droplet squeezed in a 2D space which shows a strong polarization catastrophe while simultaneously maintaining its bond integrity, which is absent in traditional δ-gapped 3D clusters. The weak screening of the host 2D MoTe
2
leads to photon emission of such pseudometallic systems and a ballistic injection of carriers in the 1T′/1H/1T′ homojunctions which may find applications in sensors and 2D reconfigurable devices.
Electrically powered motions of toron crystallites in chiral liquid crystals
Authors: Sohn Hayley R. O. , Smalyukh Ivan I.
Published: March 2020

Significance

Topological solitons exhibit particle-like behavior and, similar to colloids, allow one to model out-of-equilibrium processes like crystallization, melting, and defect motions in molecular and atomic systems. We now show that such soft solitonic particles can also exhibit dynamics not accessible to their atomic and molecular counterparts. These dynamics arise from facile responses of the liquid crystal host medium to external fields, causing nonreciprocal shearing-like deformations of quasi-hexagonal lattices of torons in a periodically tilted director background. Collective motions of crystallites of these solitons prompt fascinating evolution of grain boundaries and five–seven defects within them. Our findings reveal rich active-matter behavior of topologically protected objects at both the building-block and crystal lattice scales.
Suppression of age-related salivary gland autoimmunity by glycosylation-dependent galectin-1-driven immune inhibitory circuits
Authors: Martínez Allo Verónica C. , Hauk Vanesa , Sarbia Nicolas , Pinto Nicolás A. , Croci Diego O. , Dalotto-Moreno Tomás , Morales Rosa M. , Gatto Sabrina G. , Manselle Cocco Montana N. , Stupirski Juan C. , Deladoey Ángel , Maronna Esteban , Marcaida Priscila , Durigan Virginia , Secco Anastasia , Mamani Marta , Dos Santos Alicia , Catalán Pellet Antonio , Pérez Leiros Claudia , Rabinovich Gabriel A. , Toscano Marta A.
Published: March 2020

Significance

Different immune inhibitory circuits act in concert to prevent and limit the extent of deleterious autoimmune reactions occurring during the aging process. An in-depth understanding of these pathways is critical for implementation of more selective and powerful immunomodulatory modalities capable of attenuating autoimmune inflammation. Here we show that lack of galectin-1 (an endogenous β-galactoside-binding protein) or specific N-glycosylated ligands leads to a gradual breakdown of tolerogenic programs and to the establishment of age-related salivary gland autoimmunity. This study emphasizes the role of lectin–glycan interactions in the maintenance and restoration of immune tolerance and highlights their clinical relevance and therapeutic potential in chronic inflammatory disorders.
Learning to perceive, produce and recognise words in a non-native language
Authors: Elvin Jaydene , Williams Daniel , Escudero Paola
Published: March 2020

This chapter investigates three important skills that facilitate L2 communication: (1) perception (listening), (2) spoken word recognition (understanding) and (3) production (speaking) and their interrelation. In Part One, we present a review of the literature pertaining to L2 acquisition in Portuguese, with a particular focus on phonological acquisition. In Part Two, we review a series of recent studies that investigated the acquisition of Brazilian Portuguese vowels by naïve Australian English (AusE) and European Spanish (ES) listeners at the initial stage of learning. Each study targets one of the aforementioned skills and we will discuss the interrelation between them at the initial stage of L2 acquisition. We conclude the chapter by discussing the implications of this research for second-language learners and teachers of Portuguese.
The changing rhythm of Yucatan Spanish
Authors: Michnowicz Jim , Hyler Alex
Published: March 2020

This is a real time sociolinguistic analysis of the changing rhythm of Yucatan Spanish (YS), measured by four rhythm metrics: %V, ΔC, Vnpvi and Crpvi. We compare apparent time data, previously collected in 2005, with real time data collected 11 years later, in 2016, analyzing the prosodic rhythm of YS across three age groups (2005 older vs. younger; 2016 younger) and two language groups (Maya-Spanish bilinguals vs. Spanish monolinguals). Results indicate that younger speakers are moving away from the Maya-influenced rhythm of traditional YS, and are instead adopting a rhythm similar to Mexico City Spanish. These changes are explained as a process of new dialect formation/koineization, as the dialect stabilizes after a period of intense dialect and language contact.
The unstressed vowel system of Asturian Spanish
Authors: Barnes Sonia
Published: March 2020

Influenced by the minority language of the region, speakers of Asturian Spanish vary in their production of final back vowels in the masculine singular morpheme, with realizations that range from Spanish [-o] (e.g., perro) to Asturian [-u] (e.g., perru). In this study, I compare the acoustic properties of [o] and [u] in unstressed final and non-final position using the Pillai-Barlett Statistic in R. The results show that young speakers and women have significantly lower pillai scores word-finally, indicating a higher degree of merger between the two vowels in that position. I propose that these speakers are producing a “neutral” variant that allows them to minimize the social risk of using a stigmatized form, while being able to index regional identity.
Portuguese remnants in the Spanish of Olivenza (Extremadura)
Authors: Gabriel Christoph , Grünke Jonas , Kireva Elena
Published: March 2020

Olivenza Spanish (OS), spoken in the border zone between Extremadura and Alentejo, is characterized by salient phonological features that can plausibly be interpreted as long-term effects of Portuguese-Spanish bilingualism. We present the results of a formant analysis of unstressed /o/, which is raised to [u] in a quarter of OS cases, and discuss selected outcomes of recent (supra)segmental studies on the variety in question. It is argued that the respective findings speak in favor of interpreting OS as the result, first, of L1 transfer that occurred during the processes of L2 acquisition by the inhabitants of Olivenza after its incorporation into Spain in 1801, and second, of the local dialect’s subsequent convergence with the dominant variety, Castilian Spanish.
A cognitive approach to the grammaticalization of the epistemic marker
fijo
Authors: Lavale-Ortiz Ruth María
Published: March 2020

The present paper has as its aim to show the semantic
evolution of the form fijo through which it has acquired
increasingly pragmatic uses and functions until it became an epistemic
marker. Within this grammaticalization process, the cognitive procedures of
metaphor and metonymy, as well as the general mechanism of subjectification,
explain the semantic change experienced by this unit thanks to its
appearance in certain contextual patterns which have conventionalized the
epistemic value. Taking de fijo que, de fijo, and a
punto fijo/fixo as our reference, the corpus study reveals that
the variants of fijo code both the speaker’s epistemic
commitment and evidential contents, even though each one of them
conceptualizes the scene from a different perspective.
Identification and functional characterization of Penicillium marneffei major facilitator superfamily (MFS) transporters
Authors: Utami Setyowati T , Indriani Carissa I , Bowolaksono Anom , Yaguchi Takashi , Chen Xinyue , Niimi Kyoko , Niimi Masakazu , Kajiwara Susumu
Published: March 2020

Penicillium marneffei is a thermally dimorphic fungus that causes penicilliosis, and become the third-most-common opportunistic fungal infection in immunocompromised patients in Southeast Asia. Azoles and amphotericin B have been introduced for the treatment, however, it is important to investigate possible mechanisms of azole resistance for future treatment failure. We identified 177 putative MFS transporters and classified into 17 subfamilies. Among those, members of the Drug:H+ antiporter 1 subfamily are known to confer resistance to antifungals. Out of 39 paralogs, three (encoded by PmMDR1, PmMDR2, and PmMDR3) were heterologously overexpressed in S. cerevisiae AD∆ conferred resistance to various drugs and compounds including azoles, albeit to different degrees. PmMDR1-expressing strain showed resistance to the broadest range of drugs, followed by the PmMDR3, and PmMDR2 conferred weak resistance to a limited range of drugs. We conclude that PmMDR1 and PmMDR3, may be able to serve as multidrug efflux pumps.
Polymer compaction and bridging-induced clustering of protein-inspired patchy particles
Authors: Brackley C A
Published: March 2020

There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to be able to compact DNA in vitro, and many others have been observed in foci or puncta when fluorescently labelled and imaged in vivo. In this work we study, using coarse-grained Langevin dynamics simulations, the compaction of polymers by simple model proteins and a phenomenon known as the ‘bridging-induced attraction’. The latter is a mechanism observed in previous simulations [Brackley et al 2013 Proc. Natl Acad. Sci. USA
110 E3605], where proteins modelled as spheres form clusters via their multivalent interactions with a polymer, even in the absence of any explicit protein–protein attractive interactions. Here we extend this concept to consider more detailed model proteins, represented as simple ‘patchy particles’ interacting with a semi-flexible bead-and-spring polymer. We find that both the compacting ability and the effect of the bridging-induced attraction depend on the valence of the model proteins. These effects also depend on the shape of the protein, which determines its ability to form bridges.
Quantification of 3D spatial correlations between state variables and distances to the grain boundary network in full-field crystal plasticity spectral method simulations
Authors: Kühbach Markus , Roters Franz
Published: March 2020

Deformation microstructure heterogeneities play a pivotal role during dislocation patterning and interface network restructuring. Thereby, they affect indirectly how the microstructure recrystallizes. Given this relevance, it has become common practice to study the evolution of deformation microstructure heterogeneities with 3D experiments and full-field crystal plasticity computer simulations including tools such as the spectral method. Quantifying material point to grain or phase boundary distances, though, is a practical challenge with spectral method crystal plasticity models because these discretize the material volume rather than mesh explicitly the grain and phase boundary interface network. This limitation calls for specific data post-processing methods to quantify the spatial correlations between state variable values at each material point and the points’ corresponding distance to the closest grain or phase boundary. This work contributes to the development of advanced such post-processing routines. Specifically, two grain reconstruction and three distancing methods are developed for solving above challenge. The individual strengths and limitations of these methods surplus the efficiency of their parallel implementation is assessed with an exemplary Düsseldorf Advanced Material Simulation Kit large scale crystal plasticity study. We apply the new tool to assess the evolution of subtle stress and disorientation gradients towards grain boundaries.
Threshold for blowup for the supercritical cubic wave equation
Authors: Glogić Irfan , Maliborski Maciej , Schörkhuber Birgit
Published: March 2020

We consider the focusing cubic wave equation in the energy supercritical case, i.e. in dimensions

. For this model an explicit nontrivial self-similar blowup solution was recently found by the first and third author in Glogić and Schörkhuber (2018 (arXiv:1810.07681)). Furthermore, the solution is proven to be co-dimension one stable in d  =  7. In this paper, we study the equation from a numerical point of view. For d  =  5 and d  =  7 in the radial case, we provide evidence that this solution is at the threshold between generic ODE blowup and dispersion. In addition, we investigate the spectral problem that underlies the stability analysis and compute the spectrum in general supercritical dimensions.
Nonlinear patterns shaping the domain on which they live
Authors: Ruppert Mirko , Ziebert Falko , Zimmermann Walter
Published: March 2020

Nonlinear stripe patterns in two spatial dimensions break the rotational symmetry and generically show a preferred orientation near domain boundaries, as described by the famous Newell–Whitehead–Segel (NWS) equation. We first demonstrate that, as a consequence, stripes favour rectangular over quadratic domains. We then investigate the effects of patterns ‘living’ in deformable domains by introducing a model coupling a generalized Swift–Hohenberg model to a generic phase field model describing the domain boundaries. If either the control parameter inside the domain (and therefore the pattern amplitude) or the coupling strength (‘anchoring energy’ at the boundary) are increased, the stripe pattern self-organizes the domain on which it ‘lives’ into anisotropic shapes. For smooth phase field variations at the domain boundaries, we simultaneously find a selection of the domain shape and the wave number of the stripe pattern. This selection shows further interesting dynamical behavior for rather steep variations of the phase field across the domain boundaries. The here-discovered feedback between the anisotropy of a pattern and its orientation at boundaries is relevant e.g. for shaken drops or biological pattern formation during development.
Minimal seesaw extension for neutrino mass and mixing, leptogenesis and dark matter: FIMPzillas through the right-handed neutrino portal
Authors: Chianese Marco , Fu Bowen , King Stephen F.
Published: March 2020

We propose a minimal seesaw extension to simultaneously account for realistic neutrino mass and mixing, the baryon asymmetry of the Universe via leptogenesis and a viable dark matter relic density, in which two right-handed neutrinos are coupled to a dark Dirac fermion and complex scalar field, both charged under a global U(1)
D
symmetry. As a concrete example, we consider the Littlest Seesaw model which describes neutrino mass and mixing and accounts for leptogenesis, thereby fixing the neutrino Yukawa couplings and right-handed neutrino masses. By considering the freeze-in production mechanism of dark matter, we explore the parameter space of right-handed neutrino portal couplings and dark particle masses which give the correct dark matter relic abundance, focussing on the case of a superheavy Dirac fermion dark matter particle, with a mass around 1010 GeV. Such a FIMPzilla can provide a successful explanation of the dark matter relic abundance, with its production reliant on neutrino Yukawa couplings over much of the parameter space, depending on the assumed dark particle masses, and the reheat temperature.
Accounting for polarization–related effects in the measurement of the bidirectional reflectance distribution function
Authors: Calderón A , Ferrero A , Campos J
Published: March 2020

When measuring the Bidirectional Reflectance Distribution Function (BRDF) to characterize typical materials, the effect of the polarization of the light source or the dependence of the detector on the polarization is not usually considered, even though many studies have proven their impact in the uncertainty of the BRDF of most materials, including diffuse reflectance standards. A methodology to assess polarization-related effects proposed by other authors has been tested in this work for the measurement of the BRDF of four typical materials used for realizing white diffuse reflectance standards (ceramic tile, barium sulfate, Spectralon and Russian opal glass). Relative systematic error due to polarizing conditions is calculated as a combination of the instrument polarization bias and sample-based coefficients, and the impact of the proposed methodology on the uncertainty is discussed.
African Americans, Haiti, and the Incessant Common Wind
Authors: Byrd Brandon R.
Published: March 2020

The 2018 publication of Julius S. Scott’s The Common Wind: Afro-American Currents in the Age of the Haitian Revolution inspired a renewed focus on the reverberations of the Haitian Revolution. Here, six scholars of the Atlantic World and the Age of Revolutions consider the historiographical implications of The Common Wind and remind us how the Haitian upheaval belongs at the very center of the ripples of modernity that spread across the globe from the revolutionary Atlantic.
A Quantitative General Population Job Exposure Matrix for Occupational Noise Exposure
Authors: Stokholm Zara Ann , Erlandsen Mogens , Schlünssen Vivi , Basinas Ioannis , Bonde Jens Peter , Peters Susan , Brandt Jens , Vestergaard Jesper Medom , Kolstad Henrik Albert
Published: March 2020

Occupational noise exposure is a known risk factor for hearing loss and also adverse cardiovascular effects have been suggested. A job exposure matrix (JEM) would enable studies of noise and health on a large scale. The objective of this study was to create a quantitative JEM for occupational noise exposure assessment of the general working population. Between 2001–2003 and 2009–2010, we recruited workers from companies within the 10 industries with the highest reporting of noise-induced hearing loss according to the Danish Working Environment Authority and in addition workers of financial services and children day care to optimize the range in exposure levels. We obtained 1343 personal occupational noise dosimeter measurements among 1140 workers representing 100 different jobs according to the Danish version of the International Standard Classification of Occupations 1988 (DISCO 88). Four experts used 35 of these jobs as benchmarks and rated noise levels for the remaining 337 jobs within DISCO 88. To estimate noise levels for all 372 jobs, we included expert ratings together with sex, age, occupational class, and calendar year as fixed effects, while job and worker were included as random effects in a linear mixed regression model. The fixed effects explained 40% of the total variance: 72% of the between-jobs variance, −6% of the between-workers variance and 4% of the within-worker variance. Modelled noise levels showed a monotonic increase with increasing expert score and a 20 dB difference between the highest and lowest exposed jobs. Based on the JEM estimates, metal wheel-grinders were among the highest and finance and sales professionals among the lowest exposed. This JEM of occupational noise exposure can be used to prioritize preventive efforts of occupational noise exposure and to provide quantitative estimates of contemporary exposure levels in epidemiological studies of health effects potentially associated with noise exposure.
Quantification of light interception within image-based 3-D reconstruction of sole and intercropped canopies over the entire growth season
Authors: Zhu Binglin , Liu Fusang , Xie Ziwen , Guo Yan , Li Baoguo , Ma Yuntao
Published: March 2020

Background and Aims

Light interception is closely related to canopy architecture. Few studies based on multi-view photography have been conducted in a field environment, particularly studies that link 3-D plant architecture with a radiation model to quantify the dynamic canopy light interception. In this study, we combined realistic 3-D plant architecture with a radiation model to quantify and evaluate the effect of differences in planting patterns and row orientations on canopy light interception.

Methods

The 3-D architectures of maize and soybean plants were reconstructed for sole crops and intercrops based on multi-view images obtained at five growth dates in the field. We evaluated the accuracy of the calculated leaf length, maximum leaf width, plant height and leaf area according to the measured data. The light distribution within the 3-D plant canopy was calculated with a 3-D radiation model. Finally, we evaluated canopy light interception in different row orientations.

Key Results

There was good agreement between the measured and calculated phenotypic traits, with an R2 >0.97. The light distribution was more uniform for intercropped maize and more concentrated for sole maize. At the maize silking stage, 85 % of radiation was intercepted by approx. 55 % of the upper canopy region for maize and by approx. 33 % of the upper canopy region for soybean. There was no significant difference in daily light interception between the different row orientations for the entire intercropping and sole systems. However, for intercropped maize, near east–west orientations showed approx. 19 % higher daily light interception than near south–north orientations. For intercropped soybean, daily light interception showed the opposite trend. It was approx. 49 % higher for near south–north orientations than for near east–west orientations.

Conclusions

The accurate reconstruction of 3-D plants grown in the field based on multi-view images provides the possibility for high-throughput 3-D phenotyping in the field and allows a better understanding of the relationship between canopy architecture and the light environment.
Females of a solitary bee reject males to collect food for offspring
Authors: Dutra Ana Laura , Schlindwein Clemens , Oliveira Reisla
Published: March 2020

The time dedicated to courtship and copulation is the most general cost of mating for females. However, quantitative estimates of this cost and the consequences for female mating behavior have been investigated for only a few model organisms and mostly under laboratory conditions. We determined the costs of copulations and persistent courtship by males in terms of time for females of the solitary bee Anthrenoides micans. We estimated the rate and duration of male mating behaviors and the consequences for sexual interactions for females with respect to the loss of foraging opportunity in the wild. Males invested most of their time searching for mates and intercepted foraging females every 3 min. Copulas lasted, on average, 10 times longer than the time females took to resist male mating attempts. Despite the high frequency of these rejections (82%), females spent 3-fold more time copulating than rejecting males. Considering the rate of encounters with males and the mean duration of flower visits by females, we estimated that females would perform 64% fewer flower visits per hour if they accepted all copulation attempts. The loss of time is especially significant in the natural habitat of the species, where host cacti blossom for extraordinary short periods of time and females compete with other cacti-specialized bees and conspecifics. Because the offspring production of a female solitary bee depends on its pollen collection capacity, reduced foraging performance directly influences female reproductive success.
GlycoGlyph: a glycan visualizing, drawing and naming application
Authors: Mehta Akul Y , Cummings Richard D
Published: March 2020

Motivation

Glycan structures are commonly represented using symbols or linear nomenclature such as that from the Consortium for Functional Glycomics (also known as modified IUPAC-condensed nomenclature). No current tool allows for writing the name in such format using a graphical user interface (GUI); thus, names are prone to errors or non-standardized representations.

Results

Here we present GlycoGlyph, a web application built using JavaScript, which is capable of drawing glycan structures using a GUI and providing the linear nomenclature as an output or using it as an input in a dynamic manner. GlycoGlyph also allows users to save the structures as an SVG vector graphic, and allows users to export the structure as condensed GlycoCT.

Availability and implementation

The application can be used at: https://glycotoolkit.com/Tools/GlycoGlyph/. The application is tested to work in modern web browsers such as Firefox or Chrome.

Contact

aymehta@bidmc.harvard.edu or rcummin1@bidmc.harvard.edu
First European Haplotype of Echinococcus multilocularis Identified in the United States: An Emerging Disease?
Authors: Polish Louis B , Pritt Bobbi , Barth Thomas F E , Gottstein Bruno , O’Connell Elise M , Gibson Pamela C
Published: March 2020

Background

Echinococcus multilocularis is one of the most severe and lethal parasitic diseases of humans, most often reported in Europe and Asia. Only 1 previous case has been documented in the contiguous United States from Minnesota in 1977. European haplotypes have been identified in carnivores and domestic dogs as well as recently in patients in western and central Canada.

Methods

We used immunohistochemical testing with the monoclonal antibody Em2G11 and a species-specific enzyme-linked immunosorbent assay affinity-purified antigen Em2, as well as COX1 gene sequencing.

Results

Using pathology, immunohistochemical staining, specific immunodiagnostic testing, and COX1 gene sequencing, we were able to definitively identify E. multilocularis as the causative agent of our patient’s liver and lung lesions, which clustered most closely with the European haplotype.

Conclusions

We have identified the first case of a European haplotype E. multilocularis in the United States and the first case of this parasitic infection east of the Mississippi River. Given the identification of this haplotype in Canada, this appears to be an emerging infectious disease in North America.
Out-of-Sequence Vaccinations With Measles Vaccine and Diphtheria-Tetanus-Pertussis Vaccine: A Reanalysis of Demographic Surveillance Data From Rural Bangladesh
Authors: Clipet-Jensen Clara , Andersen Andreas , Jensen Aksel Karl Georg , Aaby Peter , Zaman K
Published: March 2020

Background

Due to delays in vaccinations, diphtheria-tetanus-whole-cell-pertussis (DTP) is often given with or after measles vaccine (MV)—out of sequence. We reanalyzed data from Matlab, Bangladesh, to examine how administration of MV and DTP out-of-sequence was associated with child survival.

Methods

In sum, 36 650 children born between 1986 and 1999 were followed with registration of vaccinations and survival. Controlling for background factors using Cox proportional hazards models, survival was analyzed between 9 and 24 months of age. We measured the mortality rate ratio (MRR) to compare vaccination groups. Oral polio vaccine (OPV) campaigns, which started in 1995, reduced the mortality rate and reduced the difference between vaccination groups. In the main analysis, we therefore censored for OPV campaigns; there were 151 nonaccident deaths before the OPV campaigns.

Results

Compared with MV administered alone (MV-only), DTP administered with or after MV had MRR 2.20 (1.31–3.70), and DTP-only had MRR 1.78 (1.01–3.11). Compared with MV-only, DTP administered with MV had a female-male MRR 0.56 (0.13–2.38), significantly different to DTP administered after MV, which had MRR 14.83 (1.88–117.1), test of interaction P = .011. Compared with having DTP (no MV) as most recent vaccination, MV-only had a nonaccident MRR of 0.56 (0.32–0.99).

Conclusion

The negative effects of non-live DTP with or after live MV are not explained merely by selection bias. These observations support a live-vaccine-last policy where DTP should not be given with or after MV.
Impaired myocardial reserve underlies reduced exercise capacity and heart rate recovery in preterm-born young adults
Authors: Huckstep Odaro J , Burchert Holger , Williamson Wilby , Telles Fernando , Tan Cheryl M J , Bertagnolli Mariane , Arnold Linda , Mohamed Afifah , McCormick Kenny , Hanssen Henner , Leeson Paul , Lewandowski Adam J
Published: March 2020

Aims 

We tested the hypothesis that the known reduction in myocardial functional reserve in preterm-born young adults is an independent predictor of exercise capacity (peak VO2) and heart rate recovery (HRR).

Methods and results 

We recruited 101 normotensive young adults (n = 47 born preterm; 32.8 ± 3.2 weeks’ gestation and n = 54 term-born controls). Peak VO2 was determined by cardiopulmonary exercise testing (CPET), and lung function assessed using spirometry. Percentage predicted values were then calculated. HRR was defined as the decrease from peak HR to 1 min (HRR1) and 2 min of recovery (HRR2). Four-chamber echocardiography views were acquired at rest and exercise at 40% and 60% of CPET peak power. Change in left ventricular ejection fraction from rest to each work intensity was calculated (EFΔ40% and EFΔ60%) to estimate myocardial functional reserve. Peak VO2 and per cent of predicted peak VO2 were lower in preterm-born young adults compared with controls (33.6 ± 8.6 vs. 40.1 ± 9.0 mL/kg/min, P = 0.003 and 94% ± 20% vs. 108% ± 25%, P = 0.001). HRR1 was similar between groups. HRR2 decreased less in preterm-born young adults compared with controls (−36 ± 13 vs. −43 ± 11 b.p.m., P = 0.039). In young adults born preterm, but not in controls, EFΔ40% and EFΔ60% correlated with per cent of predicted peak VO2 (r2 = 0.430, P = 0.015 and r2 = 0.345, P = 0.021). Similarly, EFΔ60% correlated with HRR1 and HRR2 only in those born preterm (r2 = 0.611, P = 0.002 and r2 = 0.663, P = 0.001).

Conclusions 

Impaired myocardial functional reserve underlies reductions in peak VO2 and HRR in young adults born moderately preterm. Peak VO2 and HRR may aid risk stratification and treatment monitoring in this population.
Inverted takotsubo syndrome complicated with cardiogenic shock requiring veno-arterial extracorporeal membrane oxygenation in a patient with bilateral pheochromocytoma: a case report
Authors: Faria Bebiana Manuela Monteiro , Português João , Roncon-Albuquerque Jr Roberto , Pimentel Rodrigo
Published: March 2020

Background

Takotsubo syndrome (TS) is characterized by a transient left ventricular (LV) dysfunction and rarely presents with cardiogenic shock (CS). Inverted TS (ITS) is a rare entity associated with the presence of a pheochromocytoma.

Case summary

We present a case of a young woman was admitted to the emergency department due to intense headache, chest discomfort, palpitations, and breathlessness. An ITS secondary to a pheochromocytoma crisis presenting with CS was diagnosed. The patient was managed with veno-arterial extracorporeal membrane oxygenation, until recovery of LV function. On the 35th day of hospitalization, open bilateral adrenalectomy was performed.

Discussion

Takotsubo syndrome patients presenting with CS are challenging and clinicians should be aware of underlying causes. Specific triggers such as pheochromocytoma should systematically be considered particularly if ITS was presented. Extracorporeal life support devices could provide temporary mechanical circulatory support in patients with TS on refractory CS and help to manage complex cases with TS due to pheochromocytoma.
Supracardiac atherosclerosis in embolic stroke of undetermined source: the underestimated source
Authors: Ntaios George , Wintermark Max , Michel Patrik
Published: March 2020

The term ‘embolic stroke of undetermined source’ (ESUS) is used to describe patients with a non-lacunar ischaemic stroke without any identified embolic source from the heart or the arteries supplying the ischaemic territory, or any other apparent cause. When the ESUS concept was introduced, covert atrial fibrillation was conceived to be the main underlying cause in the majority of ESUS patients. Another important embolic source in ESUS is the atherosclerotic plaque in the carotid, vertebrobasilar, and intracranial arteries, or the aortic arch—collectively described as supracardiac atherosclerosis. There is emerging evidence showing that the role of supracardiac atherosclerosis is larger than it was initially perceived. Advanced imaging methods are available to identify plaques which high embolic risk. The role of novel antithrombotic strategies in these patients needs to be assessed in randomized controlled trials. This review presents the evidence which points towards a major aetiological association between atherosclerotic plaques and ESUS, summarizes the imaging features which may aid to identify plaques more likely to be associated with ESUS, discusses strategies to reduce the associated stroke risk, and highlights the rationale for future research in this field.
Effect of hydroxylysine-O-glycosylation on the structure of type I collagen molecule: A computational study
Authors: Tang Ming , Wang Xiaocong , Gandhi Neha S , Foley Bethany Lachele , Burrage Kevin , Woods Robert J , Gu YuanTong
Published: March 2020

Collagen undergoes many types of post-translational modifications (PTMs), including intracellular modifications and extracellular modifications. Among these PTMs, glycosylation of hydroxylysine (Hyl) is the most complicated. Experimental studies demonstrated that this PTM ceases once the collagen triple helix is formed and that Hyl-O-glycosylation modulates collagen fibrillogenesis. However, the underlying atomic-level mechanisms of these phenomena remain unclear. In this study, we first adapted the force field parameters for O-linkages between Hyl and carbohydrates and then investigated the influence of Hyl-O-glycosylation on the structure of type I collagen molecule, by performing comprehensive molecular dynamic simulations in explicit solvent of collagen molecule segment with and without the glycosylation of Hyl. Data analysis demonstrated that (i) collagen triple helices remain in a triple-helical structure upon glycosylation of Hyl; (ii) glycosylation of Hyl modulates the peptide backbone conformation and their solvation environment in the vicinity and (iii) the attached sugars are arranged such that their hydrophilic faces are well exposed to the solvent, while their hydrophobic faces point towards the hydrophobic portions of collagen. The adapted force field parameters for O-linkages between Hyl and carbohydrates will aid future computational studies on proteins with Hyl-O-glycosylation. In addition, this work, for the first time, presents the detailed effect of Hyl-O-glycosylation on the structure of human type I collagen at the atomic level, which may provide insights into the design and manufacture of collagenous biomaterials and the development of biomedical therapies for collagen-related diseases.