bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiscale electrostatic embedding simulations for modeling structure and dynamics of molecules in solution: A tutorial review
Authors: Dohn Asmus O.
Published: July 2020

The main concepts and important technical details of electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) simulations are explained and illustrated with the intent of assisting newcomers in performing and gauging the accuracy of such simulations, focused on smaller molecules in solution. Beginners are advised on how to increase the reliability and accuracy of the simulations through benchmarking. Central considerations on methodologies for QM/MM Molecular Dynamics (MD) simulations are presented, alongside technical fundamentals regarding the construction and manipulation of simulation systems using the python‐based Atomic Simulation Environment (ASE). A worked example of QM/MM Born–Oppenheimer MD is included, and a flowchart summarizing the most salient decisions and tasks within the methodology is presented.
Bronchial varices in a child with tricuspid atresia six years post Fontan correction
Authors: Bhushan Shreya , Goyal Vikas , Ward Cameron , Rashid Muddassir , Kapur Nitin
Published: July 2020

Tracheal and bronchial varices are rarely found in children. However, they have been described in adults with failing Fontan circuits or secondary to vascular pathology, such as portal and pulmonary hypertension. We report the presentation of haemoptysis and bronchial varices in a child, six years after a Fontan procedure for tricuspid atresia. She had tortuous mediastinal and transpleural arterial collaterals on computed tomography (CT) angiography and cardiac catheterization and subsequently underwent embolization of these collaterals. While the haemoptysis settled post embolization, the bronchial varices persisted on repeat bronchoscopy. She has since been clinically well with no further haemoptysis.
Incomplete metalloptysis linger pneumonia after a wedge resection of the lung for organizing pneumonia
Authors: Shai Sen‐Ei , Lai Yi‐Ling , Tang Hsiao‐Wen , Hung Shih‐Chieh
Published: July 2020

A 40‐year‐old man had considered himself to be robust, with the exception of an earlier diagnosis of hepatitis C. He underwent a wedge resection of the lung, at the left upper lobe (LUL), mimicking an anterior mediastinal tumor. A pathology report showed a 5 × 5 × 2.5 cm grey‐brown and yellowish lesion in a resected 9 × 6 × 3 cm of the lung, with a subsequent diagnosis of organizing pneumonia. The patient recovered uneventfully and was discharged while in a stable condition. One month later, he was admitted and given empiric antibiotic treatment for a lung abscess due to a compound symptom for three weeks after discharge. Although his symptom improved readily, a computed tomography (CT) of the chest disclosed a steady consolidation over the LUL. The fluctuation with haemoptysis and a productive cough spanned 11 months, until a bout of aggravated symptoms including foul and blood‐tinged sputum which mingled with an intermittent high fever became evident. The patient then underwent a bronchoscopy, which surprisingly revealed a metal material impacted over the orifice of the LUL bronchus, requiring biopsy forceps removal. The patient readily recovered with his symptoms thoroughly subsiding thereafter.
Why the elderly appear to be more severely affected by COVID‐19: The potential role of immunosenescence and CMV
Authors: Kadambari Seilesh , Klenerman Paul , Pollard Andrew J.
Published: July 2020

The significantly higher mortality rates seen in the elderly compared with young children during the coronavirus disease 2019 (Covid‐19) pandemic is likely to be driven in part by an impaired immune response in older individuals. Cytomegalovirus (CMV) seroprevalence approaches 80% in the elderly. CMV has been shown to accelerate immune ageing by affecting peripheral blood T cell phenotypes and increasing inflammatory mediated cytokines such as IL‐6. The elderly with pre‐existing but clinically silent CMV infection may therefore be particularly susceptible to severe Covid‐19 disease and succumb to a cytokine storm which may have been promoted by CMV. Here, we evaluate the potential role of CMV in those with severe Covid‐19 disease and consider how this relationship can be investigated in current research studies.
In‐situ probe spacing calibration improves the heat pulse method for measuring soil heat capacity and water content
Authors: Zhang Meng , Lu Yili , Ren Tusheng , Horton Robert
Published: July 2020

Heat pulse (HP) sensors have been used extensively to measure soil thermal properties and volumetric water content (θ) simultaneously. Probe spacing (R), the distance between heater probe and temperature probe, is routinely calibrated in agar solution before making HP measurements. In reality,Rmay change due to probe deflection at insertion into soil, causing uncertainties in HP measured volumetric heat capacity (C) and θ. In this paper, we present a simple on‐site calibration method for determining in‐situRby using theoreticalCvalues estimated from soil bulk density and θ values of intact soil cores collected near the sensor locations at the end of experiment. The proposed approach was tested on two field soils whereCand θ were monitored continuously. Inconsistent results were observed between agar‐calibratedRvalues (Ragar) andRvalues obtained from in‐situ calibration (Rin‐situ). Maximum difference betweenRagarandRin‐situreached 20% ofRagar. Compared to TDR measured θ, usingRagarled to root mean square errors (RMSEs) of 0.26 MJ m−3K−1inCand 0.06 m3m−3in θ on average. ForRin‐situ, the RMSE ofCwas less than 0.16 MJ m−3K−1and RMSE of θ was within 0.04 m3m−3. Thus, the use of in‐situ probe spacing calibration improved the accuracies of HP measuredCand θ.
Exploiting relationships between outcomes in Bayesian multivariate network meta‐analysis with an application to relapsing‐remitting multiple sclerosis
Authors: Waddingham Ed , Matthews Paul M. , Ashby Deborah
Published: July 2020

In multivariate network meta‐analysis (NMA), the piecemeal nature of the evidence base means that there may be treatment‐outcome combinations for which no data is available.

Most existing multivariate evidence synthesis models are either unable to estimate the missing treatment‐outcome combinations, or can only do so under particularly strong assumptions, such as perfect between‐study correlations between outcomes or constant effect size across outcomes. Many existing implementations are also limited to two treatments or two outcomes, or rely on model specification that is heavily tailored to the dimensions of the dataset. We present a Bayesian multivariate NMA model that estimates the missing treatment‐outcome combinations via mappings between the population mean effects, while allowing the study‐specific effects to be imperfectly correlated. The method is designed for aggregate‐level data (rather than individual patient data) and is likely to be useful when modeling multiple sparsely reported outcomes, or when varying definitions of the same underlying outcome are adopted by different studies. We implement the model via a novel decomposition of the treatment effect variance, which can be specified efficiently for an arbitrary dataset given some basic assumptions regarding the correlation structure. The method is illustrated using data concerning the efficacy and liver‐related safety of eight active treatments for relapsing‐remitting multiple sclerosis. The results indicate that fingolimod and interferon beta‐1b are the most efficacious treatments but also have some of the worst effects on liver safety. Dimethyl fumarate and glatiramer acetate perform reasonably on all of the efficacy and safety outcomes in the model.
Role of Solidification in Submerged Entry Nozzle Clogging During Continuous Casting of Steel
Authors: Barati Hadi , Wu Menghuai , Kharicha Abdellah , Ludwig Andreas
Published: July 2020

Metallurgists are embroiled in a debate on the role of solidification in submerged entry nozzle (SEN) clogging during continuous casting of steel: does clogging originate from solidification, or does clogging cause the solidification? This study tries to clarify this debate. An enthalpy‐based mixture continuum model is used to simulate solidification in a clog structure. The 3D structure of the clog is reconstructed using X‐ray tomography images of an as‐clogged piece in an SEN, and is directly used in the numerical model. The flow and solidification in the open pores/channels of the clog structure are then calculated. The modeling results demonstrate that although solidification does occur deep in the clog structure as the melt flow is stopped, a gap remains between the solidification and clog fronts. This gap signifies an open‐channel clog region, and the clog structure in this region needs to be mechanically strong to withstand the impact of the melt flow; otherwise, fragmentation occurs. The study verifies that the solidification cannot occur before clogging if the molten steel has sufficient superheat and the SEN is properly preheated. A SEN made of an isolating refractory material can postpone the clogging, thereby extending its service life.
Design of As‐Cast Structures of Continuously Cast Steel Grades: Modeling and Prediction
Authors: Fix Carolin , Elixmann Sina-Maria , Senk Dieter Georg
Published: July 2020

The prediction of the solidification structure by means of calculations and simulation programs is of great importance for controlling the quality of continuous casting (CC) semis. Plant components, different process control options, and the chemical composition of the as‐cast product require optimized coordination of those factors to be able to set the optimum structure. As the simulation of temperature fields to predict the crater end during final solidification is already state of the art, the precise simulation of the solidification zones in CC semis is the important next step. Therefore, a circular arc caster is simulated with nucleation, grain growth, and sedimentation considered. The asymmetric as‐cast structure is calculated with a good accuracy providing a good base for the implementation of microsegregation in the next development step.
A methodology for identifying flexible design opportunities in large‐scale systems
Authors: Allaverdi David , Browning Tyson R.
Published: July 2020

Despite many uncertainties, industrial fields such as energy (eg, oil rigs), utilities infrastructure (eg, telecommunications), space systems, transportation systems, construction, and manufacturing make large and mostly irreversible investments in systems with potentially long life cycles. The life cycle value of such systems may be increased significantly by designing in the flexibility to make future changes. This paper presents a systematic methodology for designers to identify flexible design opportunities (FDOs) more comprehensively and earlier in the system design process. The methodology guides designers to generate flexible design concepts that can be assessed, selected, and integrated into a design during an early stage of the design process. We demonstrate and validate the FDO methodology on a case in the offshore drilling industry.
The impact of system specifics on systems thinking
Authors: Mambrey Sophia , Timm Justin , Landskron Jana Julia , Schmiemann Philipp
Published: July 2020

Present and future social and ecological challenges are complex both to understand and to attempt to solve. To comprehend the complex systems underlying these issues, students need systems thinking skills. However, in science education, a uniform delineation of systems thinking across contexts has yet to be established. While there seems to be consensus on a number of key skills from a theoretical perspective, it remains uncertain whether it is possible to distinguish levels of systems thinking, and if so, how they would be determined. In this study, we investigated the impact of the specifics of a system on the skills and levels of systems thinking. We administered a 36‐item multiple‐choice test to 196 Grade 5 and 6 students. For our analysis, we followed a quantitative approach, applying a systems thinking model that incorporates the latest insights on the levels and skills of systems thinking in geography to the context of ecology. By following an Item Response Theory approach, we confirmed a set of systems thinking skills that are necessary to understand complex systems in ecology: identifying system organization, analyzing system behavior, and system modeling. We examined whether individual skill levels can be distinguished to determine whether a system's general principle or system‐specific features cause difficulty for students. Our results indicate that system specifics, such as type of relation within ecosystems (e.g., predator–prey), appear to determine the formation of levels. Students struggled most with the difference between basic, direct cause‐and‐effect relationships and indirect effects. Once they understood the relevance of indirect relationships in moderately complex systems, a further increase in complexity caused little additional difficulty. Accordingly, we suggest that systems thinking should be examined from a variety of perspectives. To promote interdisciplinary learning, a systems thinking model that defines key commonalities across fields while leaving space for system specifics is needed.
Is location of urethral kinking a confounder of association between urethral closure pressure and stress urinary incontinence?
Authors: Ling C. , Shek K. L. , Gillor M. , Caudwell‐Hall J. , Dietz H. P.
Published: July 2020

Objectives

Intact urethral support and normal sphincter function are deemed important for urinary continence. We aimed to test whether the location of urethral kinking (as the probable anatomical correlate of maximal pressure transmission) is associated with stress urinary incontinence and/or urodynamic stress incontinence.

Methods

This was a retrospective study of women seen at a tertiary urogynecological center in 2017. Patients had undergone an interview, multichannel urodynamic testing and four‐dimensional translabial ultrasound examination. Those with a history of anti‐incontinence surgery, absence of urethral kinking on ultrasound and/or missing or inadequate ultrasound volume data were excluded. Volume data were used to assess urethral mobility using a semi‐automated Excel® urethral motion profile program. Mobility vectors were calculated using the formula √((x
valsalva − x
rest)2 + (y
valsalva − y
rest)2), where x and y are the coordinates of six equidistant points along the length of the urethra from the bladder neck to the external urethral meatus. The location of urethral kinking was identified as a concave contour of the urethra on the vaginal side in the midsagittal plane on maximum Valsalva maneuver. The distance between the center of the kink and the bladder neck was measured and expressed as a centile in relation to the total length of the urethra, using the formula: (distance from bladder neck/total length of urethra) × 100. Univariate and multivariate analyses were performed to test the associations of stress urinary incontinence and urodynamic stress incontinence with age, maximum urethral pressure, urethral mobility vectors and location of urethral kinking.

Results

Of 450 women seen during the study period, 61 were excluded owing to previous incontinence surgery and 82 owing to absence of urethral kinking, inadequate volume data or missing data, leaving 307 women included, of whom 227 (74%) complained of stress urinary incontinence and 211 (69%) complained of urgency urinary incontinence. 190 (62%) of the women were diagnosed with urodynamic stress incontinence. On multivariate analysis, maximum urethral pressure (36 vs 50 cmH2O; P < 0.001), mid‐urethral mobility (2.27 vs 2.03 cm; P = 0.003) and location of urethral kinking (63.1st vs 59.7th centile; P = 0.002) were associated significantly with urodynamic stress incontinence. The location of urethral kinking was associated with stress urinary incontinence on univariate analysis (P = 0.026) but not on multivariate analysis (P = 0.21).

Conclusions

The location of urethral kinking is associated with urodynamic stress incontinence. The further urethral kinking is from the mid urethra, the more likely is urodynamic stress incontinence. This provides circumstantial evidence for the pressure‐transmission theory of stress urinary continence. © 2020 International Society of Ultrasound in Obstetrics and Gynecology.
Multi-attribute optimization-based system decomposition considering several value chain stakeholder perspectives
Authors: Suh Eun Suk , Sinha Kaushik , Ahn Jaemyung
Published: July 2020

The final architecture of a complex system reflect preferences of several value chain stakeholders on system attributes, also called “ilities”. Owing to differences in their individual roles and responsibilities, different stakeholders prefer different approaches to architect and decompose a system to optimize their attributes of interest. However, owing to increasing complexity of modern engineering systems, optimizing multiple attributes of complex systems has become challenging; moreover, very few researches have been published in this regard. Thus, to address this gap in available literature, this paper presents a multi-attribute optimization framework for complex system decomposition. The proposed framework primarily optimizes two attributes—system robustness (to the perspective of the stakeholder), and modularity—while system maintainability is considered an optimization constraint. Feasibility of the proposed framework has been demonstrated through a case study, wherein system attributes of three different mechanical clock models having different architectures were optimized.
Superdiffusive limits for deterministic fast–slow dynamical systems
Authors: Chevyrev Ilya , Friz Peter K. , Korepanov Alexey , Melbourne Ian
Published: July 2020

We consider deterministic fast–slow dynamical systems on $$\mathbb {R}^m\times Y$$

R

m

×
Y

of the form $$\begin{aligned} {\left\{ \begin{array}{ll} x_{k+1}^{(n)} = x_k^{(n)} + n^{-1} a\big (x_k^{(n)}\big ) + n^{-1/\alpha } b\big (x_k^{(n)}\big ) v(y_k), \\ y_{k+1} = f(y_k), \end{array}\right. } \end{aligned}$$

x

k
+
1

(
n
)

=

x
k

(
n
)

+

n

-
1

a

(

x
k

(
n
)

)

+

n

-
1
/
α

b

(

x
k

(
n
)

)

v

(

y
k

)

,

y

k
+
1

=
f

(

y
k

)

,

where $$\alpha \in (1,2)$$

α
∈
(
1
,
2
)

. Under certain assumptions we prove convergence of the m-dimensional process $$X_n(t)= x_{\lfloor nt \rfloor }^{(n)}$$

X
n

(
t
)

=

x

⌊
n
t
⌋

(
n
)

to the solution of the stochastic differential equation $$\begin{aligned} \mathrm {d} X = a(X)\mathrm {d} t + b(X) \diamond \mathrm {d} L_\alpha , \end{aligned}$$

d
X
=
a

(
X
)

d
t
+
b

(
X
)

⋄
d

L
α

,

where $$L_\alpha $$

L
α

is an $$\alpha $$
α
-stable Lévy process and $$\diamond $$
⋄
indicates that the stochastic integral is in the Marcus sense. In addition, we show that our assumptions are satisfied for intermittent maps f of Pomeau–Manneville type.
Relationships between ground motion parameters and macroseismic intensity for Italy
Authors: Gomez-Capera Augusto Antonio , D’Amico Maria , Lanzano Giovanni , Locati Mario , Santulin Marco
Published: July 2020

The relation between macroseismic intensity and ground shaking makes it possible to transform instrumental Ground Motion Parameters (GMPs) in macroseismic intensity and vice versa, and is therefore useful for making comparisons between estimates of seismic hazard determined in terms of GMPs and macroseismic intensity, and for other engineering and seismological applications. Empirical relationships between macroseismic intensity and different recorded GMPs for the Italian territory are presented in this paper. The coefficients are calibrated using a dataset of horizontal geometrical mean GMPs, i.e. peak ground acceleration, peak ground velocity, spectral acceleration at 0.2, 0.3, 1.0 and 2.0 s from the ITalian ACcelerometric Archive (ITACA; Luzi et al. in Italian Accelerometric Archive v3.0, Istituto Nazionale di Geofisica e Vulcanologia, Dipartimento della Protezione Civile Nazionale, 2019.10.13127/itaca.3.0), and macroseismic intensity at Mercalli–Cancani–Sieberg (MCS) scale from the database DBMI15 (Locati et al. in Database Macrosismico Italiano (DBMI15), versione 2.0, Istituto Nazionale di Geofisica e Vulcanologia (INGV), 2019.10.13127/DBMI/DBMI15.2). A dataset is obtained that corresponds to 240 pairs of macroseismic intensity-GMPs from 67 Italian earthquakes in the time window 1972–2016 with moment magnitude ranging from 4.2 to 6.8 and macroseismic intensity in the range [2, 10–11]. The final dataset  correlates strong motion stations and macroseismic intensity observations generally within 2 km from each other, and each association is manually validated through an expert judgement. The adopted functional form is non-linear, predicting macroseismic intensity as a function of LogGMPs and vice versa by performing separate regressions. The set of empirical conversion relationships GMP–IMCS–GMP and the associated standard deviations are compared with previous models. In order to verify the proposed model, a map in terms of PGA is obtained, starting from the PSHA in terms of intensities (Gomez Capera et al. in Bull Seismol Soc Am 100(4):614–1631, 2010.10.1785/0120090212) and then using the empirical relationship here proposed in PGA, and compared with the National Italian seismic hazard map (Stucchi et al. in Bull Seismol Soc Am 101(4):1885–1911, 2011.10.1785/0120100130).
Docosahexaenoic Acid Protects Traumatic Brain Injury by Regulating NOX2 Generation via Nrf2 Signaling Pathway
Authors: Zhu Wei , Cui Guangqiang , Li Tuo , Chen Hongguang , Zhu Jian , Ding Yuexia , Zhao Li
Published: July 2020

Docosahexaenoic acid (DHA) is verified to have neuroprotective effects on traumatic brain injury (TBI) rats by activating Nrf2 signaling pathway, but the role of NOX2 in this effect has not been illuminated. So this study explored the role of NOX2 in TBI models treated with DHA, aiming to complete the mechanism of DHA. TBI rat models were constructed with or without DHA treatment, and H2O2-induced hippocampal neurons were pretreated with DHA alone or in combination with Nrf2 inhibitor brusatol. The neurological function, cognitive ability, and cerebral edema degree of rats were assessed. The apoptosis rate and viability of cells was measured. The generation of NOX2, Nrf2, HO-1 and NQO-1 expression levels, and ROS content in hippocampal CA1 region and hippocampal neurons were detected. DHA could not only improve the neurological function, brain edema and cognitive ability in TBI rats, but also decrease effectively the contents of NOX2 and ROS in hippocampal CA1 region and hippocampal neurons. DHA promoted the nuclear transposition of Nrf2 and the expression levels of HO-1 and NQO-1 in hippocampal CA1 region and hippocampal neurons. On the contrary, Nrf2 inhibitor brusatol inhibited the nuclear transposition of Nrf2 and the expression levels of HO-1 and NQO-1 in hippocampal neurons, promoted the generation of ROS and NOX2, and accelerated cell apoptosis. Both in vivo and in vitro experiments demonstrated that DHA treated TBI by reducing NOX2 generation that might function on Nrf2 signaling pathway, providing a potential evidence for its clinical application.
Reply to “Consequences of dike breaches and dike overflow in a bifurcating river system”
Authors: Bomers A. , Schielen R. M. J. , Hulscher S. J. M. H.
Published: July 2020

In this reply, we would like to comment on the discussion paper of AlQasimi and Mahdi (Nat Hazards 97:1–4, 2020. 10.1007/s11069-020-03904-1). We discuss their view and possible improvements of the paper of Bomers et al. (Nat Hazards 97(1):309–334, 2019b. 10.1007/s11069-019-03643-y) in more detail and explain how large-flood modelling methods can benefit from the suggestions given by AlQasimi and Mahdi (2020).
Dynamics of price level changes in the Visegrad group: comparative study
Authors: Białek Jacek , Roszko-Wójtowicz Elżbieta
Published: July 2020

In Poland, as in many other countries, to measure inflation, expressed both by the CPI and HICP, the Laspeyres price index with weights from the base period is used. Thus calculated index does not take into account changes in the consumption structure which are caused by changes in prices in the analysed time interval (i.e.: a year). Therefore, in countries where the CPI is determined based on the Laspeyres index, there is a high probability of its bias due to substitution of goods, but not only. The value of the CPI or HICP should approximate the real inflation as accurately as possible, among others, because these indicators are used to index nominal values in the economy, which in turn is important in price decisions made by enterprises. Searching for an answer to the question about the possibility of effective reduction of the measurement bias in measuring inflation, the authors conducted an empirical study whose main aim was to assess diversity of the level of inflation in the Visegrad countries at different levels of aggregation, with particular emphasis on the scale of the bias in measuring inflation resulting from substitution of goods. The study concentrated on determining the size of differences arising from the change in the index formula used when estimating the level of inflation. The article consists of six parts in which sources and types of bias in inflation measurement are discussed, index formulas divided into weighted and unweighted ones are reviewed, statistics on inflation in the Visegrad countries are presented in a dynamic approach, and the results of empirical research are presented and discussed. For the purpose of the research part and the need to perform a comparative analysis, data on the HICP value from the Eurostat database from the years 2011–2018 were used. Therefore, it seems that both the choice of the calculation formula and the level of data aggregation in the analysis of inflation is significant in its estimates.
Neuro-Doping as a Means to Avert Fascistoid Ideology in Elite Sport
Authors: Tännsjö Torbjörn
Published: July 2020

Assume that neuro-doping is safe and efficient. This means that the use of it, and similar future safe methods of enhancement in sport, may help those who are naturally weak to catch up with those who are naturally strong and sometimes even defeat them. The rationale behind anti-doping measures seem to presuppose that this is unfair. But the idea that those who are naturally strong should defeat those who are naturally weak rests on a fascistoid ideology that sport had better leave behind. Neuro-doping may be seen as a means to undermine the fascistoid notion of fairness. The conjecture is that, given that society adopts what will be characterized as a policy of biological egalitarianism, this will happen. Then people will compete in society in general and in sport in particular on more equal biological terms. The fascination with natural strength, and the cheering for the winners, can then go away. Instead we see a liberated sport where we take part in it for the sheer fun of doing so. Neuro-doping, and similar techniques, may be a means that helps to liberate elite sport from its perverse view of fairness.
Rare earth elements (REE) in biology and medicine
Authors: Ascenzi P. , Bettinelli M. , Boffi A. , Botta M. , De Simone G. , Luchinat C. , Marengo E. , Mei H. , Aime S.
Published: July 2020

This survey reports on topics that were presented at the workshop on “Challenges with Rare Earth Elements. The Periodic Table at work for new Science & Technology” hold at the Academia dei Lincei in November 2019. The herein reported materials refer to presentations dealing with studies and applications of rare earth elements (REE) in several areas of Biology and Medicine. All together they show the tremendous impact REE have in relevant fields of living systems and highlight, on one hand, the still existing knowledge gap for an in-depth understanding of their function in natural systems as well as the very important role they already have in providing innovative scientific and technological solutions in a number of bio-medical areas and in fields related to the assessment of the origin of food and on their manufacturing processes. On the basis of the to-date achievements one expects that new initiatives will bring, in a not too far future, to a dramatic increase of our understanding of the REE involvement in living organisms as well as a ramp-up in the exploitation of the peculiar properties of REE for the design of novel applications in diagnostic procedures and in the set-up of powerful medical devices. This scenario calls the governmental authorities for new responsibilities to guarantee a continuous availability of REE to industry and research labs together with providing support to activities devoted to their recovery/recycling.
Imperfect food markets in times of crisis: economic consequences of supply chain disruptions and fragmentation for local market power and urban vulnerability
Authors: Ihle Rico , Rubin Ofir D. , Bar-Nahum Ziv , Jongeneel Roel
Published: July 2020

As these lines were written, the Covid-19 pandemic crisis was continuing to threaten countries around the globe. The worldwide consensus that physical distancing is an effective instrument for mitigating the spread of the virus has led policymakers to temporarily limit the freedom of movement of people between and within countries, cities, and even neighborhoods. These public health-related restrictions on human mobility yielded an unprecedented fragmentation of international and national food distribution systems. Focusing on food retailing - usually being modestly oligopolistic - we take a micro-economic perspective as we analyze the potential consequences this disruption has for the physical as well as for the economic access of households to food at the local level. As the mobility constraints implemented substantially reduced competition, we argue that food retailers might have been tempted to take advantage of the implied fragmentation of economic activity by exploiting their temporarily raised market power at the expense of consumers and farmers. We illustrate our point by providing empirical evidences of rising wholesale-retail as well as farm-retail price margins observed during the Covid-19 crisis. Subsequently, we review existing empirical approaches that can be used to quantify and decompose the micro-economic effects of crises on food demand and supply as well as the size and structure of the market, costs of trade, and economic welfare. The employment of such approaches facilitates policymakers’ understanding of micro-economic effects of public health-induced mobility restrictions on economic activity.
The Design of Early-Stage Plant Breeding Trials Using Genetic Relatedness
Authors: Cullis Brian R. , Smith Alison B. , Cocks Nicole A. , Butler David G.
Published: July 2020

The use of appropriate statistical methods has a key role in improving the accuracy of selection decisions in a plant breeding program. This is particularly important in the early stages of testing in which selections are based on data from a limited number of field trials that include large numbers of breeding lines with minimal replication. The method of analysis currently recommended for early-stage trials in Australia involves a linear mixed model that includes genetic relatedness via ancestral information: non-genetic effects that reflect the experimental design and a residual model that accommodates spatial dependence. Such analyses have been widely accepted as they have been found to produce accurate predictions of both additive and total genetic effects, the latter providing the basis for selection decisions. In this paper, we present the results of a case study of 34 early-stage trials to demonstrate this type of analysis and to reinforce the importance of including information on genetic relatedness. In addition to the application of a superior method of analysis, it is also critical to ensure the use of sound experimental designs. Recently, model-based designs have become popular in Australian plant breeding programs. Within this paradigm, the design search would ideally be based on a linear mixed model that matches, as closely as possible, the model used for analysis. Therefore, in this paper, we propose the use of models for design generation that include information on genetic relatedness and also include non-genetic and residual models based on the analysis of historic data for individual breeding programs. At present, the most commonly used design generation model omits genetic relatedness information and uses non-genetic and residual models that are supplied as default models in the associated software packages. The major reasons for this are that preexisting software is unacceptably slow for designs incorporating genetic relatedness and the accuracy gains resulting from the use of genetic relatedness have not been quantified. Both of these issues are addressed in the current paper. An updating scheme for calculating the optimality criterion in the design search is presented and is shown to afford prodigious computational savings. An in silico study that compares three types of design function across a range of ancillary treatments shows the gains in accuracy for the prediction of total genetic effects (and thence selection) achieved from model-based designs using genetic relatedness and program specific non-genetic and residual models.

Supplementary materials accompanying this paper appear online.
Analytic approximation to Bessel function $$J_{0}(x)$$
Authors: Maass F. , Martin P. , Olivares J.
Published: July 2020

Three analytic approximations for the Bessel function $$J_{0}(x)$$

J
0

(
x
)

have been determined, valid for every positive value of the variable x. The three approximations are very precise. The technique used here is based on the multipoint quasi-rational approximation method, MPQA, but here the procedure has been improved and extended. The structure of the approximation is derived considering simultaneously both the power series and asymptotic expansion of $$J_{0}(x)$$

J
0

(
x
)

. The analytic approximation is like a bridge between both expansions. The accuracy of the zeros of each approximant is even higher than the functions itself. The maximum absolute error of the best approximation is 0.00009. The maximum relative error is in the first zero and it is 0.00004.
Procalcitonin for Antibiotic Prescription in Chronic Obstructive Pulmonary Disease Exacerbations: Systematic Review, Meta-Analysis, and Clinical Perspective
Authors: Chen Ken , Pleasants Katherine A. , Pleasants Roy A. , Beiko Tatsiana , Washburn Ronald G. , Yu Zhiheng , Zhai Suodi , Drummond M. Bradley
Published: July 2020

The 2020 Global Initiative for Obstructive Lung Disease report indicates that the blood biomarker procalcitonin (PCT) may assist in decision-making regarding the initiation of antibiotics for chronic obstructive pulmonary disease (COPD) exacerbations. PCT is an acute-phase reactant that increases in response to inflammation and infection, and has been studied in various bacterial infections for initiation and de-escalation of antibacterials. The purpose of this systematic review and meta-analysis was to evaluate the strength of the data on the use of PCT to guide antibiotic prescription in COPD exacerbations. Among the randomized clinical trials included in our meta-analysis, almost all of which were conducted exclusively in the hospital setting. PCT was found to decrease overall antibiotic exposure in COPD exacerbations by 2.01 days (p = 0.04), while no apparent effects were found on clinical outcomes (length of hospital stay, p = 0.88; treatment failure p = 0.51; all-cause mortality p = 0.28). However, the majority of blood PCT levels in COPD exacerbations were below the manufacturer-recommended cutoff for antibiotics, and the use of this marker was associated with worse outcomes in the intensive care setting. Further, based on additional sensitivity analysis excluding studies with high risk of bias or with converted outcome value, the effect of PCT on antibiotic duration in RCTs was no longer significant (MD = −1.88 days, 95% CI [−3.95, 0.19] days, p = 0.08, and MD = −1.72 days, 95% CI [−4.28, 0.83] days, p = 0.19, respectively). Our review and analysis does not support the use of PCT to guide antibiotic prescription in COPD exacerbations.
Gradient Wetting Transition from the Wenzel to Robust Cassie-Baxter States along Nanopillared Cicada Wing and Underlying Mechanism
Authors: Xie Heng , Huang Hanxiong
Published: July 2020

Gradient wettability is important for some living organisms. Herein, the dynamic responses of water droplets impacting on the surfaces of four regions along the wing vein of cicada Cryptotympana atrata fabricius are investigated. It is revealed that a gradient wetting behavior from hydrophilicity (the Wenzel state) to hydrophobicity and further to superhydrophobicity (the Cassie-Baxter state) appears from the foot to apex of the wing. Water droplets impacting on the hydrophilic region of the wing cannot rebound, whereas those impacting on the hydrophobic region can retract and completely rebound. The hydrophobic region exhibits robust water-repelling performance during the dynamic droplet impact. Moreover, a droplet sitting on the hydrophobic region can recover its spherical shape after squeezed to a water film as thin as 0.45 mm, and lossless droplet transportation can be achieved at the region. Based on the geometric parameters of the nanopillars at the hydrophilic and hydrophobic regions on the cicada wing, two wetting models are developed for elucidating the mechanism for the gradient wetting behavior. This work directs the design and fabrication of surfaces with gradient wetting behavior by mimicking the nanopillars on cicada wing surface.
Proteomic Analysis of Uterine Tissues During Peri-Implantation Period in Mice with Experimentally Induced Adenomyosis that Treated with anti-Ngf: Implications for Cell-Cell Adhesion and Metabolic Processes
Authors: Li Yan , Zhang Dan , Jin Bailing , Xia Lan , Zhang Aijun
Published: July 2020

Nerve growth factor (NGF) has been verified to be expressed with higher level in adenomyosis uteri, and its neutralizing antibody has a strong inhibitory influence on inflammation. The present study aimed to explore the effect of anti-NGF on the expression of proteins in uteri of mice-induced adenomyosis and assessed its potential role in improving pregnancy rate. In this study, we established a mouse model of adenomyosis and administrated NGF-neutralizing antibody into mice. The mass spectrometry (MS) analysis of the uteri during the implantation window was performed to explore the essential proteins participating in therapy. Besides, embryos of healthy mice were transferred into the uteri to assess the implantation rate. The results of MS analysis demonstrated that 119 proteins were changed in the adenomyosis group compared with control group, and 126 proteins were differentially expressed in the anti-NGF group compared with the adenomyosis group (fold change > 1.5, P < 0.05. After performing cluster analysis using Mfuzz package, we found that a group of proteins participated in cell-cell adhesion and metabolic processes, which were attenuated in the adenomyosis group, while those were successfully recovered by anti-NGF treatment. Western blotting confirmed that the expression levels of integrin alpha-1 (ITGA1), integrin beta-1 (ITGB1), laminin subunit gamma-1 (LAMC1), and creatine kinase M-type (CKM) were decreased in adenomyosis group, whereas those levels were elevated after anti-NGF treatment. Embryo implantation rate in the adenomyosis group was significantly decreased compared with that in the control group (2.31% vs. 26.15%, P < 0.001) and anti-NGF treatment slightly enhanced the embryo implantation rate in mice with experimentally induced adenomyosis (9.23% vs. 2.31%, P = 0.017). Our results revealed that anti-NGF therapy can improve fertility of mice with experimentally induced adenomyosis, possibly through promoting integrin-related proteins.
IC4R-2.0: Rice Genome Reannotation Using Massive RNA-Seq Data
Authors: Sang Jian , Zou Dong , Wang Zhennan , Wang Fan , Zhang Yuansheng , Xia Lin , Li Zhaohua , Ma Lina , Li Mengwei , Xu Bingxiang , Liu Xiaonan , Wu Shuangyang , Liu Lin , Niu Guangyi , Li Man , Luo Yingfeng , Hu Songnian , Hao Lili , Zhang Zhang
Published: July 2020

Genome reannotation aims for complete and accurate characterization of gene models and thus is of critical significance for in-depth exploration of gene function. Although the availability of massive RNA-seq data provides great opportunities for gene model refinement, few efforts have been made to adopt these precious data in rice genome reannotation. Here we reannotate the rice (Oryza sativa L. ssp. japonica) genome based on integration of large-scale RNA-seq data and release a new annotation system IC4R-2.0. In general, IC4R-2.0 significantly improves the completeness of gene structure, identifies a number of novel genes, and integrates a variety of functional annotations. Furthermore, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are systematically characterized in the rice genome. Performance evaluation shows that compared to previous annotation systems, IC4R-2.0 achieves higher integrity and quality, primarily attributable to massive RNA-seq data applied in genome annotation. Consequently, we incorporate the improved annotations into the Information Commons for Rice (IC4R), a database integrating multiple omics data of rice, and accordingly update IC4R by providing more user-friendly web interfaces and implementing a series of practical online tools. Together, the updated IC4R, which is equipped with the improved annotations, bears great promise for comparative and functional genomic studies in rice and other monocotyledonous species. The IC4R-2.0 annotation system and related resources are freely accessible at http://ic4r.org/.
Optimal stopping for measure-valued piecewise deterministic Markov processes
Authors: Cloez Bertrand , de Saporta Benoîte , Joubaud Maud
Published: July 2020

This paper investigates the random horizon optimal stopping problem for measure-valued piecewise deterministic Markov processes (PDMPs). This is motivated by population dynamics applications, when one wants to monitor some characteristics of the individuals in a small population. The population and its individual characteristics can be represented by a point measure. We first define a PDMP on a space of locally finite measures. Then we define a sequence of random horizon optimal stopping problems for such processes. We prove that the value function of the problems can be obtained by iterating some dynamic programming operator. Finally we prove via a simple counter-example that controlling the whole population is not equivalent to controlling a random lineage.
Finite-time ruin probabilities under large-claim reinsurance treaties for heavy-tailed claim sizes
Authors: Albrecher Hansjörg , Chen Bohan , Vatamidou Eleni , Zwart Bert
Published: July 2020

We investigate the probability that an insurance portfolio gets ruined within a finite time period under the assumption that the r largest claims are (partly) reinsured. We show that for regularly varying claim sizes the probability of ruin after reinsurance is also regularly varying in terms of the initial capital, and derive an explicit asymptotic expression for the latter. We establish this result by leveraging recent developments on sample-path large deviations for heavy tails. Our results allow, on the asymptotic level, for an explicit comparison between two well-known large-claim reinsurance contracts, namely LCR and ECOMOR. Finally, we assess the accuracy of the resulting approximations using state-of-the-art rare event simulation techniques.
Spatiotemporal variations and implications of luminescence sensitivity of quartz grains on the Chinese Loess Plateau since the last interglaciation
Authors: Lü Tongyan , Sun Jimin , Feathers James K. , Sun Dongxia
Published: July 2020

Although luminescence sensitivity of quartz grains of desert sands has been used in discriminating provenance, it still remains unclear about its spatiotemporal variations and climatic implications. In this paper, the luminescence sensitivity of quartz grains from the northern margin of the Chinese Loess Plateau (CLP) was studied using single-aliquot optically stimulated luminescence (OSL) and “pseudo” single-grain OSL measurements. Our results indicate that the OSL sensitivities have lower values in sand/loess beds and higher values in paleosols. We suggest that the variations in OSL sensitivity of quartz grains with depth on the CLP are mainly influenced by the origin of the quartz grains as they are related to the loess-sized material production processes and the migration of desert regions. More quartz grains of glacial origin with lower luminescence sensitivity, together with the reduced durations of irradiation and exposure cycles induced by shorter transport distance due to desert expansion, account for the lower luminescence sensitivity of glacial periods. Moreover, both the mountain processes and the retreat–advance of deserts are ultimately related to climatic changes, therefore, the orbital scale variations of luminescence sensitivity are controlled by glacial–interglacial oscillations on the CLP.
Behavioural strategy of the ectosymbiotic crab (Sestrostomasp.) during ecdysis of the crab and its upogebiid shrimp host
Authors: Shiozaki Yuto , Itani Gyo
Published: July 2020

Moulting is essential for crustacean growth, but is one of the causes of mortality, because a crustacean cannot move during and just after its ecdysis. In the cases of ectosymbiotic crabs, escape from the host's hostile response may also be a problem during its own ecdysis. In this study,Sestrostomasp. (Varunidae), an ectosymbiotic crab which clings to the ventral abdomen of upogebiid shrimps with legs that can walk, was studied to clarify how the crab moults and maintains association with the host. Five cases of crab ecdysis were observed, where the crab moulted with its legs clinging to the host abdomen, without detaching from the host body. Time required for moulting was 14–21 min. Shedding of the old exoskeleton (active phase) took only 40–59 s.Sestrostomasp. detached from the host abdomen and waited in the burrow tube during shrimp ecdysis. The crab then reattached at the same location on the host when shrimp moulting was complete. Our results suggest thatSestrostomasp. are able to maintain a symbiotic relationship with the same shrimp host after its own ecdysis as well after ecdysis of its host.