bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Branch Point Distribution on the Radius of Gyration in Batch Free‐Radical Polymerization with Chain Transfer to Polymer
Authors: Tobita Hidetaka 
Published: July 2020

AbstractFree‐radical polymerization is irreversible, and the primary chains formed earlier are expected to possess larger branching density compared with those formed later, leading to a branching density distribution (BDD) among primary chains. In addition to the BDD, the primary chain length distribution (CLD) may change during polymerization. For a primary CLD with a shift toward smaller chain length during polymerization, the expected g‐ratio for a given number k of branch points can be approximated reasonably well with that for the random branched polymers having the accumulated primary CLD. On the other hand, when the primary CLD moves toward larger chain length during polymerization, the expected g‐ratio may become smaller than the corresponding random branched polymers, due to an “unnatural” combination in the length of backbone and branch chains. The compactness of branched architecture could be controlled through the consideration of the maximum end‐to‐end path length.
Dosimetry modeling of focused kV x‐ray radiotherapy for wet age‐related macular degeneration
Authors: Yan Huagang , Sun Weiyuan , Mruthyunjaya Prithvi , Beadle Beth , Yu Weihong , Kanwal Bushra , MacDonald Carolyn A. , Liu Wu 
Published: July 2020

PurposeWet (neovascular) age‐related macular degeneration (AMD) is the leading cause of blindness in the United States. The mainstay treatment requires monthly intravitreal injection of anti‐vascular endothelial growth factor (anti‐VEGF) drugs, associated with multiple visits, high cost, and the risk of procedural injury and infection. Anti‐VEGF drugs inhibit the formation of neovasculature but do not directly attack it. Radiotherapy can destroy neovasculature and potentially also inhibit wet‐AMD associated inflammation and fibrosis not addressed by VEGF inhibitors. However, the current collimation‐based radiotherapy device uses fixed 4 mm beams, which are prone to overtreat or undertreat the choroidal neovascularization (CNV) lesions because of their various sizes and shapes. This simulation study evaluates personalized conformal treatment with focused kV radiation using cutting‐edge polycapillary x‐ray optics.MethodsSimulation of the polycapillary optics was achieved via Monte Carlo (MC)‐based three‐dimensional (3D) geometric ray tracing. Phase‐space files modeling the focused photons were generated. The method was previously verified by phantom measurements. The ultrasmall ~0.2 mm beam focal spot perpendicular to the beam direction enables spatially fractionated grid therapy, which has been shown to preferentially damage abnormal neovascular blood vessels vs normal ones. Geant4‐based MC simulations of scanning while rotating beam delivery were performed to conformally treat three clinical cases of large, medium, and small CNV lesions with regular and grid deliveries. Dose delivery uncertainties due to positioning errors were analyzed, including ±0.75 mm displacement in the three orthogonal directions and ±5° vertical/horizontal rotation of the eyeball.ResultsThe simulated CNV treatments by 60‐kVp focused x‐ray beams show highly conformal delivery of dose to the lesion plus margin (0.75 mm) with sharp dose fall‐offs and controllable spatial modulation patterns. The 90%–10% isodose penumbra is <0.5 mm. With a prescription dose of 16 Gy to the lesions, the critical structure doses are well below the tolerance. The average CNV dose varies within 10% (mostly within 4%) due to 0.75‐mm linear displacements and 5‐degree gaze angle rotation of the eyeball.ConclusionFocused kV technique allows personalized treatment of CNV lesions and reduces unwanted radiation to adjacent healthy tissue. The simulated dose distribution is superior to currently available techniques.
Deep learning using a biophysical model for robust and accelerated reconstruction of quantitative, artifact‐free and denoised images
Authors: Torop Max , Kothapalli Satya V. V. N. , Sun Yu , Liu Jiaming , Kahali Sayan , Yablonskiy Dmitriy A. , Kamilov Ulugbek S. 
Published: July 2020

PurposeTo introduce a novel deep learning method for Robust and Accelerated Reconstruction (RoAR) of quantitative and B0‐inhomogeneity‐corrected

maps from multi‐gradient recalled echo (mGRE) MRI data.MethodsRoAR trains a convolutional neural network (CNN) to generate quantitative

maps free from field inhomogeneity artifacts by adopting a self‐supervised learning strategy given (a) mGRE magnitude images, (b) the biophysical model describing mGRE signal decay, and (c) preliminary‐evaluated F‐function accounting for contribution of macroscopic B0 field inhomogeneities. Importantly, no ground‐truth

images are required and F‐function is only needed during RoAR training but not application.ResultsWe show that RoAR preserves all features of

maps while offering significant improvements over existing methods in computation speed (seconds vs. hours) and reduced sensitivity to noise. Even for data with SNR = 5 RoAR produced

maps with accuracy of 22% while voxel‐wise analysis accuracy was 47%. For SNR = 10 the RoAR accuracy increased to 17% vs. 24% for direct voxel‐wise analysis.ConclusionsRoAR is trained to recognize the macroscopic magnetic field inhomogeneities directly from the input magnitude‐only mGRE data and eliminate their effect on

measurements. RoAR training is based on the biophysical model and does not require ground‐truth

maps. Since RoAR utilizes signal information not just from individual voxels but also accounts for spatial patterns of the signals in the images, it reduces the sensitivity of

maps to the noise in the data. These features plus high computational speed provide significant benefits for the potential usage of RoAR in clinical settings.
Lippmann‐Schwinger solvers for the computational homogenization of materials with pores
Authors: Schneider Matti 
Published: July 2020

SummaryWe show that under suitable hypotheses on the nonporous material law and a geometric regularity condition on the pore space, Moulinec‐Suquet's basic solution scheme converges linearly. We also discuss for which derived solvers a (super)linear convergence behavior may be obtained, and for which such results do not hold, in general. The key technical argument relies on a specific subspace on which the homogenization problem is nondegenerate, and which is preserved by iterations of the basic scheme. Our line of argument is based in the nondiscretized setting, and we draw conclusions on the convergence behavior for discretized solution schemes in FFT‐based computational homogenization. Also, we see how the geometry of the pores' interface enters the convergence estimates. We provide computational experiments underlining our claims.
First‐trimester screening based on cell‐free DNA vs combined screening: A randomized clinical trial on women's experience
Authors: Migliorini Sonia , Saccone Gabriele , Silvestro Fiora , Massaro Giulia , Arduino Bruno , D'Alessandro Pietro , Petti Maria Teresa , Paino Jessica Anna Cinzia , Guida Maurizio , Locci Mariavittoria , Zullo Fulvio 
Published: July 2020

AbstractObjectiveTo compare women's experience of first‐trimester combined screening (FTCS), with women's experience of an approach that uses the combination of a detailed early anatomy scan and cell‐free DNA (cfDNA) analysis.MethodsThis was single‐center, open label, parallel group, randomized clinical trial. Pregnant women were randomized at the time of their first prenatal visit to either a policy of first‐trimester risk assessment based on FTCS, or to a policy of first‐trimester risk assessment based on ultrasound findings and cfDNA. FTCS included ultrasound evaluation with crown‐rump length, nuchal translucency (NT) measurement, and a detailed ultrasound scan, along with biochemistry (PAPP‐A and free beta hCG). In this group, invasive diagnostic testing was offered to patients with risk >1 in 100, or NT >3.5 mm, or any fetal abnormalities on ultrasound. Women randomized in the intervention group received an approach of first‐trimester risk assessment based on ultrasound findings and cfDNA. cfDNA analysis included a simultaneous microarray‐based assay of non‐polymorphic (chromosomes 13, 18, 21, X and Y) and polymorphic loci to estimate chromosome proportion and fetal fraction. In the intervention group, invasive diagnostic testing was offered to patients with abnormal cfDNA screening results, or NT >3.5 mm, or any fetal abnormalities on ultrasound. Participants received pre‐test and post‐test questionnaires regarding to measure reassurance, satisfaction, and anxiety. The primary outcome was the post‐test reassurance, defined as mean score of reassurance post‐test questionnaire. The effect of the assigned screening test on the mean of each outcome was quantified as mean difference (MD) with 95% confidence interval (CI).ResultsForty women with singleton gestations were enrolled in the trial. Mean score for reassurance was significantly higher in the cfDNA group compared to the FTCS group in the pre‐test questionnaire (MD 0.80 points, 95% CI 0.27 to 1.33) and in the post‐test questionnaire (MD 16.50 points, 95% CI 2.18 to 30.82). Women randomized to the cfDNA group had higher satisfaction and lower mean anxiety score as assessed in the STAI pre‐test questionnaire.ConclusionsFirst‐trimester risk assessment for fetal aneuploidy with a combination of a detailed ultrasound examination and cfDNA is associated with better maternal reassurance and better maternal satisfaction compared to the standard first‐trimester combined screening with nuchal translucency, and biochemistry.Trial registrationClinicaltrials.gov NCT04077060.
Image‐based root phenotyping links root architecture to micronutrient concentration in cassava
Authors: Busener Natalie , Kengkanna Jitrana , Saengwilai Patompong Johns , Bucksch Alexander 
Published: July 2020

Societal Impact StatementMicronutrient deficiency or “hidden hunger” is estimated to affect two billion people worldwide and increasing the micronutrient concentration of food could play an important role in tackling this global challenge. Using a combination of imaging techniques and atomic absorption spectroscopy, we describe a link between root phenotype and micronutrient concentration in cassava, which could enable new phenotypic selection strategies for breeding. This approach could be used with existing breeding infrastructure to enhance the micronutrient concentration of cassava and hence, benefit the health of people, particularly in low‐income countries where cassava is consumed as a staple crop.Summary

Cassava storage roots are a staple food in low‐income countries of South‐East Asia and sub‐Saharan Africa, where growth stunting is prevalent as a consequence of micronutrient deficiencies. We aim to link phenotypes of field‐grown cassava roots to micronutrient concentration in the edible storage roots as a simple way to improve phenotypic selection for nutritional value in cassava.

We used existing and newly developed imaging techniques to quantify root phenotypes of the cassava root architecture over time and used flame atomic absorption spectroscopy to measure micronutrient concentration in storage roots. Both together allow the association of root phenotypes with micronutrient concentration in mature cassava roots.

We show that early and late bulking genotypes in cassava exhibit distinct foraging behaviors that are associated with micronutrient concentration in the edible storage root. Our observations suggest that late bulking cassava is a key to provide sufficient micronutrients in the edible storage root.

The association between root phenotype and micronutrient concentration with imaging techniques allows phenotypic selection for enhanced micronutrient concentration. Therefore, implementing image‐based phenotyping into cassava breeding programs in sub‐Saharan Africa and South‐East Asia could be an essential element to resolve micronutrient deficiencies that puts individuals at a higher risk of growth stunting.
Review of the Wedge Test and Single Curve Initiation Principle Applied to Aluminized High Explosives
Authors: Elia Thomas , Chuzeville Vincent , Baudin Gérard , Genetier Marc , Lefrançois Alexandre , Osmont Antoine , Boulanger Rémi 
Published: July 2020

AbstractThe experiments have a key role in the initiation and transition studies of solid high explosives. Detonic has forced scientist to improve their experimental approach by designing relevant set‐up and developing accurate metrological devices. For example, the wedge or pop‐plot test was developed in the 50’s and remains a legacy experiment in the characterization of high explosive. However, for 70 years, it has been widely improved, because of the accurate measurements need. This paper aims to review the main improvements performed on the pop‐plot test and analyze a series of results acquired on melt‐cast and cast‐cured high explosives. We first describe the current set‐up with its new metrological devices. Then, we discuss the results and limitations of this test.
A humanized antibody inhibitor for cathepsin L
Authors: Shi Xiaojing , Zhang Yong 
Published: July 2020

AbstractCathepsin L (CTSL) is a cysteine protease involved in a variety of physiological and pathological processes. Potent inhibitors against CTSL have long been sought for drug development. Due to insufficient specificity and suboptimal pharmacological properties for current CTSL inhibitors, novel agents are still required for selectively blocking CTSL activity. Here we generated a humanized antibody inhibitor of CTSL by genetically fusing the inhibitory propeptide of procathepsin L to the N‐terminus of the light chain of a humanized antibody. The resulting antibody fusion could be stably expressed and displays highly potent inhibition activity and specificity toward CTSL. This work demonstrates a new approach for the rapid generation of antibody inhibitors of CTSL. It can possibly be extended to create inhibitory antibodies targeting other cathepsin proteases, providing novel research and therapeutic tools.
Tight junction protein claudin‐1 is downregulated by TGF‐β1 via MEK signaling in benign prostatic epithelial cells
Authors: Wang Ke , Pascal Laura E. , Li Feng , Chen Wei , Dhir Rajiv , Balasubramani Goundappa K. , DeFranco Donald B. , Yoshimura Naoki , He Dalin , Wang Zhou 
Published: July 2020

AbstractBackgroundBenign prostatic hyperplasia (BPH) is arguably the most common disease in aging men. Although the etiology is not well understood, chronic prostatic inflammation is thought to play an important role in BPH initiation and progression. Our recent studies suggest that the prostatic epithelial barrier is compromised in glandular BPH tissues. The proinflammatory cytokine transforming growth factor beta 1 (TGF‐β1) impacts tight junction formation, enhances epithelial barrier permeability, and suppresses claudin‐1 messenger RNA expression in prostatic epithelial cells. However, the role of claudin‐1 in the prostatic epithelial barrier and its regulation by TGF‐β1 in prostatic epithelial cells are not clear.MethodsThe expression of claudin‐1 was analyzed in 22 clinical BPH specimens by immunohistochemistry. Human benign prostate epithelial cell lines BPH‐1 and BHPrE1 were treated with TGF‐β1 and transfected with small interfering RNAs specific to claudin‐1. Epithelial monolayer permeability changes in the treated cells were measured using trans‐epithelial electrical resistance (TEER). The expression of claudin‐1, E‐cadherin, N‐cadherin, snail, slug, and activation of mitogen‐activated proteins kinases (MAPKs) and AKT was assessed following TGF‐β1 treatment using Western blot analysis.ResultsClaudin‐1 expression was decreased in glandular BPH tissue compared with adjacent normal prostatic tissue in patient specimens. TGF‐β1 treatment or claudin‐1 knockdown in prostatic epithelial cell lines increased monolayer permeability. TGF‐β1 decreased levels of claudin‐1 and increased levels of snail and slug as well as increased phosphorylation of the MAPK extracellular signal‐regulated kinase‐1/2 (ERK‐1/2) in both BPH‐1 and BHPrE1 cells. Overexpression of snail or slug had no effect on claudin‐1 expression. In contrast, PD98059 and U0126, inhibitors of the upstream activator of ERK‐1/2 (ie, MEK‐1/2) restored claudin‐1 expression level as well as the epithelial barrier.ConclusionOur findings suggest that downregulation of claudin‐1 by TGF‐β1 acting through the noncanonical MEK‐1/2/ERK‐1/2 pathway triggers increased prostatic epithelial monolayer permeability in vitro. These findings also suggest that elevated TGF‐β1 may contribute to claudin‐1 downregulation and compromised epithelial barrier in clinical BPH specimens.
Residue interaction dynamics in Vaucheria aureochrome1 light‐oxygen‐voltage: Bridging theory and experiments
Authors: Deb Anwesha , Grewal Rajdeep Kaur , Roy Soumen , Mitra Devrani 
Published: July 2020

AbstractAllosteric communication is the basis of signaling and information transfer. Collective interactions between amino acid residues, which are spatially distributed in the three dimensional structure of a protein molecule, form the basis of allosteric network. While the construction of residue interaction graphs (RIG) is based on static crystal structures of proteins, it is important to extract information on protein dynamics to understand allostery. Therefore, quantitative analysis of RIG based on the framework of differential network (DN), is immensely helpful in identifying key amino acid residue interactions within such communication pathways. While the simultaneous availability of protein structures from two different states is essential for DN, there are additional challenges. Crystallographic artifacts like nonbiological dimeric arrangements within the crystal lattice automatically influence the construction and eventually the interpretation of RIG. Therefore, experimental validation of predictions from the analyses of RIG is naturally scarce in the literature. Herein, we study the photo sensor domain of the signaling photoreceptor transcription factor, aureochrome1, to understand light‐driven signaling. We perform direct experiments to verify the predictions from RIG using the machinery of DN. However, the agreement leaves scope for improvement. We then discuss the notion of quaternary structure alignment to obtain a biologically meaningful dimer. Thence, we reconstruct the RIG and reanalyze the modified structure. Results of these reanalyses render far superior agreement with experiments. Therefore, this notion of addressing crystallographic biases provides a fresh yet general approach for reconciliation of theory and experiments. It is applicable beyond the present case to all signaling proteins in general.
Identification of potential allosteric binding sites in cathepsin K based on intramolecular communication
Authors: Rocha Gisele V. , Bastos Leonardo S. , Costa Mauricio G. S. 
Published: July 2020

AbstractNetwork theory methods and molecular dynamics (MD) simulations are accepted tools to study allosteric regulation. Indeed, dynamic networks built upon correlation analysis of MD trajectories provide detailed information about communication paths between distant sites. In this context, we aimed to understand whether the efficiency of intramolecular communication could be used to predict the allosteric potential of a given site. To this end, we performed MD simulations and network theory analyses in cathepsin K (catK), whose allosteric sites are well defined. To obtain a quantitative measure of the efficiency of communication, we designed a new protocol that enables the comparison between properties related to ensembles of communication paths obtained from different sites. Further, we applied our strategy to evaluate the allosteric potential of different catK cavities not yet considered for drug design. Our predictions of the allosteric potential based on intramolecular communication correlate well with previous catK experimental and theoretical data. We also discuss the possibility of applying our approach to other proteins from the same family.
Overestimated acceleration of the advective Brewer–Dobson circulation due to stratospheric cooling
Authors: Eichinger Roland , Šácha Petr 
Published: July 2020

AbstractTropospheric warming and stratospheric cooling influence the vertical structure of the atmosphere. Numerous studies have analysed the thermal expansion of the troposphere, however, stratospheric cooling reverses the sign of this shift in the middle stratosphere, causing a downward shift in the upper stratosphere and mesosphere. This is a robust feature in transient climate model simulations, but its impact is commonly unappreciated. Here, we quantify the trend difference of the residual mean vertical velocity (), a proxy for diagnosing the advective Brewer–Dobson circulation (BDC) strength, which arises from implicit neglect of the shrinking distance between stratospheric pressure levels in the CCMI‐1 (Chemistry‐Climate Model Initiative part 1) data request. There, a log‐pressure formula with constant scale height is recommended to compute . However, stratospheric cooling in transient climate simulations causes a reduction of the geometrical distance between pressure levels and thereby also the scale height significantly decreases over time. Using the general scale height definition for the transformation, the trends are therefore smaller. In both cases, the units are m·s−1, but in the latter case it is the constant measure of length geopotential metres and not log‐pressure metres. We quantify that, due to the temperature dependence of log‐pressure metres, past studies that based trend analyses on log‐pressure overestimated the advective BDC acceleration by ∼ 20%. This result is consistent among the CCMI‐1 projections over the 1960–2100 period. We highlight that other diagnostics can also be affected by the neglect of the declining stratospheric pressure level distance. A detailed description of the diagnostics is necessary for consistent assessments of trends. Data processing tools should generally not include the constant scale height assumption if the data are used for trend analyses.
DevOpRET: Continuous reliability testing in DevOps
Authors: Bertolino Antonia , Angelis Guglielmo De , Guerriero Antonio , Miranda Breno , Pietrantuono Roberto , Russo Stefano 
Published: July 2020

AbstractTo enter the production stage, in DevOps practices candidate software releases have to pass quality gates, where they are assessed to meet established target values for key indicators of interest. We believe software reliability should be an important such indicator, as it greatly contributes to the end‐user satisfaction. We propose DevOpRET, an approach for reliability testing as part of the acceptance testing stage in DevOps. DevOpRET relies on operational‐profile–based testing, a common reliability assessment technique. DevOpRET leverages usage and failure data monitored in operations to continuously refine its estimate. We evaluate accuracy and efficiency of DevOpRET through controlled experiments with a real‐world open source platform and with a microservice architectures benchmark. The results show that DevOpRET provides accurate and efficient estimates of the true reliability over subsequent DevOps cycles.