bluuebunny/crossref_metadata_2025_split huggingface dataset:
M42 aminopeptidase catalytic site: the structural and functional role of a strictly conserved aspartate residue
Authors: Dutoit Raphaël , Brandt Nathalie , Van Gompel Tom , Van Elder Dany , Van Dyck Jeroen , Sobott Frank , Droogmans Louis 
Published: July 2020

AbstractThe M42 aminopeptidases are a family of dinuclear aminopeptidases widely distributed in Prokaryotes. They are potentially associated to the proteasome, achieving complete peptide destruction. Their most peculiar characteristic is their quaternary structure, a tetrahedron‐shaped particle made of twelve subunits. The catalytic site of M42 aminopeptidases is defined by seven conserved residues. Five of them are involved in metal ion binding which is important to maintain both the activity and the oligomeric state. The sixth conserved residue, a glutamate, is the catalytic base deprotonating the water molecule during peptide bond hydrolysis. The seventh residue is an aspartate whose function remains poorly understood. This aspartate residue, however, must have a critical role as it is strictly conserved in all MH clan enzymes. It forms some kind of catalytic triad with the histidine residue and the metal ion of the M2 binding site. We assess its role in TmPep1050, an M42 aminopeptidase of Thermotoga maritima, through a mutational approach. Asp‐62 was substituted with alanine, asparagine, or glutamate residue. The Asp‐62 substitutions completely abolished TmPep1050 activity and impeded dodecamer formation. They also interfered with metal ion binding as only one cobalt ion is bound per subunit instead of two. The structure of Asp62Ala variant was solved at 1.5 Å showing how the substitution has an impact on the active site fold. We propose a structural role for Asp‐62, helping to stabilize a crucial loop in the active site and to position correctly the catalytic base and a metal ion ligand of the M1 site.
Reliability assessment for systems suffering common cause failure based on Bayesian networks and proportional hazards model
Authors: Li Yan‐Feng , Liu Yang , Huang Tudi , Huang Hong‐Zhong , Mi Jinhua 
Published: July 2020

AbstractThe Bayesian network (BN) is an efficient tool for probabilistic modeling and causal inference, and it has gained considerable attentions in the field of reliability assessment. The common cause failure (CCF) is simultaneous failure of multiple elements in a system under a common cause, and it is a common phenomenon in engineering systems with dependent elements. Several models and methods have been proposed for modeling and assessment of complex systems with CCF. In this paper, a new reliability assessment method is proposed for the systems suffering from CCF in a dynamic environment. The CCF among components is characterized by a BN, which allows for bidirectional reasoning. A proportional hazards model is applied to capture the dynamic working environment of components and then the reliability function of the system is obtained. The proposed method is validated through an illustrative example, and some comparative studies are also presented.
Theoretical study of propylene epoxidation heterogeneous‐homogeneous mechanism over MoOx/SiO2 catalyst
Authors: Wan Zhehong , Lin Zenan , Peng Jiahui , Chen Wei , Li Xiaohan , Chen Xiaohui 
Published: July 2020

AbstractThe green direct propylene (C3H6) epoxidation on MoOx is well studied by experimental methods, but detailed molecular reaction mechanism studies using in‐silico experiments method are few. Here, the different oxidation heterogeneous‐homogeneous pathways for MoOx/SiO2 catalyst are calculated, mainly involving Mo=O on di‐oxo tetracoordinate MoOx, allyl peroxy (C3H5OO•), and allyloxy (C3H5O•) radicals. The results show that, for surface reaction mechanism with Mo=O, the barriers of propylene oxide (PO) and acetone generation are too high; in comparison, the byproduct acrolein is more beneficial product with a lower barrier. In heterogeneous‐homogeneous pathways, the desorbed allyl (C3H5•) from the surface can easily combine with O2 to synthesize C3H5OO• radical, and in the partial oxidation of propylene with C3H5OO• as an oxidant, PO is more beneficial with a low barrier compared to byproducts such as propanal, acetone, acetaldehyde, etc. These indicate that (a) gas‐phase free radical reactions have important effects on PO generation, in which C3H5OO• is the main active species; (b) on MoOx surface, Mo=O is difficult to be used as the active O species for PO production. Further research is needed on other active sites such as Mo‐O‐Mo or defective sites.
Multiscale electrostatic embedding simulations for modeling structure and dynamics of molecules in solution: A tutorial review
Authors: Dohn Asmus O. 
Published: July 2020

AbstractThe 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

AbstractTracheal 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

AbstractA 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

SummaryThe 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

AbstractHeat 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.
A methodology for identifying flexible design opportunities in large‐scale systems
Authors: Allaverdi David , Browning Tyson R. 
Published: July 2020

AbstractDespite 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

AbstractPresent 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

ABSTRACTObjectivesIntact 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.MethodsThis 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.ResultsOf 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).ConclusionsThe 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

AbstractThe 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

AbstractWe 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

(
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=

x
k

(
n
)

+

n

-
1

a

(

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)

+

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1
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α

b

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)

)

v

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)

,

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+
1

=
f

(

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k

)

,

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

α
∈
(
1
,
2
)

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

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n

(
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=

x

⌊
n
t
⌋

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

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=
a

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⋄
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,

where $$L_\alpha $$

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is an $$\alpha $$
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-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

AbstractThe 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).