bluuebunny/crossref_metadata_2025 huggingface dataset:
TMEM132A ensures mouse caudal neural tube closure and regulates integrin-based mesodermal migration
Authors: Li Binbin , Brusman Liza , Dahlka Jacob , Niswander Lee A.
Published: August 2022

Coordinated migration of the mesoderm is essential for accurate organization of the body plan during embryogenesis. However, little is known about how mesoderm migration influences posterior neural tube closure in mammals. Here, we show that spinal neural tube closure and lateral migration of the caudal paraxial mesoderm depend on transmembrane protein 132A (TMEM132A), a single-pass type I transmembrane protein, the function of which is not fully understood. Our study in Tmem132a-null mice and cell models demonstrates that TMEM132A regulates several integrins and downstream integrin pathway activation as well as cell migration behaviors. Our data also implicates mesoderm migration in elevation of the caudal neural folds and successful closure of the caudal neural tube. These results suggest a requirement for paraxial mesodermal cell migration during spinal neural tube closure, disruption of which may lead to spina bifida.
The dynamic proteome in Arabidopsis thaliana early embryogenesis
Authors: Huang Yingzhang , Zhou Limeng , Hou Chunhui , Guo Dianjing
Published: August 2022

The morphology of the flowering plant is established during early embryogenesis. In recent years, many studies have focused on transcriptional profiling in plant embryogenesis, but the dynamic landscape of the Arabidopsis thaliana proteome remains elusive. In this study, Arabidopsis embryos at 2/4-cell, 8-cell, 16-cell, 32-cell, globular and heart stages were collected for nanoproteomic analysis. In total, 5386 proteins were identified. Of these, 1051 proteins were universally identified in all developmental stages and a range of 27 to 2154 proteins was found to be stage specific. These proteins could be grouped into eight clusters according to their expression levels. Gene Ontology enrichment analysis showed that genes involved in ribosome biogenesis and auxin-activated signalling were enriched during early embryogenesis, indicating that active translation and auxin signalling are important events in Arabidopsis embryo development. Combining RNA-sequencing data with the proteomics analysis, the correlation between mRNA and protein was evaluated. An overall positive correlation was found between mRNA and protein. This work provides a comprehensive landscape of the Arabidopsis proteome in early embryogenesis. Some important proteins/transcription factors identified through network analysis may serve as potential targets for future investigation.
Deltex modulates Dpp morphogen gradient formation and affects Dpp signaling in Drosophila
Authors: Sharma Vartika , Sarkar Bappi , Mutsuddi Mousumi , Mukherjee Ashim
Published: August 2022

Deltex (Dx) is a context-dependent regulator of Notch signaling that can act in a non-canonical fashion by facilitating the endocytosis of the Notch receptor. In an RNAi-based modifier screen of kinases and phosphatases, we identified Thickveins (Tkv), the receptor of Decapentaplegic (Dpp), as one of the interactors of Dx. Dpp, a Drosophila homolog of TGF-β and bone morphogenetic proteins, acts as a morphogen to specify cell fate along the anterior–posterior axis of the wing. Tight regulation of Dpp signaling is thus indispensable for its proper functioning. Here, we present Dx as a novel modulator of Dpp signaling. We show evidence for the very first time that dx genetically interacts with dpp and its pathway components. Immunocytochemical analysis revealed that Dx colocalizes with Dpp and its receptor Tkv in Drosophila third-instar larval tissues. Furthermore, Dx was also seen to modulate the expression of dpp and its target genes, and we attribute this modulation to the involvement of Dx in the endocytosis and trafficking of Dpp. This study thus presents a whole new avenue of Dpp signaling regulation via the cytoplasmic protein Dx.

This article has an associated First Person interview with the first author of the paper.
Interaction between VPS13A and the XK scramblase is important for VPS13A function in humans
Authors: Park Jae-Sook , Hu Yiying , Hollingsworth Nancy M. , Miltenberger-Miltenyi Gabriel , Neiman Aaron M.
Published: August 2022

VPS13 family proteins form conduits between the membranes of different organelles through which lipids are transferred. In humans, there are four VPS13 paralogs, and mutations in the genes encoding each of them are associated with different inherited disorders. VPS13 proteins contain multiple conserved domains. The Vps13 adaptor-binding (VAB) domain binds to adaptor proteins that recruit VPS13 to specific membrane contact sites. This work demonstrates the importance of a different domain in VPS13A function. The pleckstrin homology (PH) domain at the C-terminal region of VPS13A is required to form a complex with the XK scramblase and for the co-localization of VPS13A with XK within the cell. Alphafold modeling was used to predict an interaction surface between VPS13A and XK. Mutations in this region disrupt both complex formation and co-localization of the two proteins. Mutant VPS13A alleles found in patients with VPS13A disease truncate the PH domain. The phenotypic similarities between VPS13A disease and McLeod syndrome caused by mutations in VPS13A and XK, respectively, argue that loss of the VPS13A–XK complex is the basis of both diseases.
Early exposure to UV radiation causes telomere shortening and poorer condition later in life
Authors: Lundsgaard Niclas U. , Cramp Rebecca L. , Franklin Craig E.
Published: August 2022

Determining the contribution of elevated ultraviolet-B radiation (UVBR; 280–315 nm) to amphibian population declines is being hindered by a lack of knowledge about how different acute UVBR exposure regimes during early life-history stages might affect post-metamorphic stages via long-term carryover effects. We acutely exposed tadpoles of the Australian green tree frog (Litoria caerulea) to a combination of different UVBR irradiances and doses in a multi-factorial laboratory experiment, and then reared them to metamorphosis in the absence of UVBR to assess carryover effects in subsequent juvenile frogs. Dose and irradiance of acute UVBR exposure influenced carryover effects into metamorphosis in somewhat opposing manners. Higher doses of UVBR exposure in larvae yielded improved rates of metamorphosis. However, exposure at a high irradiance resulted in frogs metamorphosing smaller in size and in poorer condition than frogs exposed to low and medium irradiance UVBR as larvae. We also demonstrate some of the first empirical evidence of UVBR-induced telomere shortening in vivo, which is one possible mechanism for life-history trade-offs impacting condition post-metamorphosis. These findings contribute to our understanding of how acute UVBR exposure regimes in early life affect later life-history stages, which has implications for how this stressor may shape population dynamics.
Descriptive analysis of clinical and laboratory findings in relation to changes in SARS-CoV-2 viral dynamics and cyclic threshold: a retrospective, single center observational study in patients treated with Hydroxychloroquine/Azithromycin combination therapy
Authors: Alamri Maha M. , Devol Edward B. , Al-Otaibi Anwar B. , Albaiz Faisal A. , Alabdely Mayyadah H. , Althawadi Sahar I. , Mutabagani Maysoon S. , Alhamlan Fatimah S. , Alrabiah Fahad A. , Almaghrabi Reem S.
Published: August 2022

Background: Cases of undiagnosed pneumonia have emerged, and sequencing of respiratory samples indicated the presence of SARS-CoV-2 causing COVID-19.  Patients with higher viral load and lower Ct values tend to have progressive disease and severe lung injury. The objective of this study is to describe the clinical manifestation and disease outcomes of COVID-19 patients in relation to their Ct values.

Methods: A retrospective, single center observational study was performed, including patients admitted to King Faisal Specialist Hospital and Research Centre (KFSH&RC) Riyadh between March 1st-29th, 2020 and have a confirmed diagnosis of COVID-19. The Ct value was identified to determine the viral load. All patients were treated according to KFSH&RC guidelines.  Patients were divided into HCQ/AZI and non HCQ/AZI treated groups.

Results: There were many days where Ct values were not available. An attempt at imputing information for missing Ct values was made using logic.  The logic leads to an ordinal Ct score 1, 2, 3, or 4. As a result, complete Ct score profiles were available. There was no evidence of statistically significant difference between the two groups in regard to clinical severity, duration to negative test or changes in Ct values. 

Conclusion: There is little knowledge known to the time profile of Ct values and their relation to disease course of COVID-19. This study provides insight on how Ct values might be used to determine treatment efficacy. As it might be difficult to obtain Ct values at all times, this study provides an imputation method that may be used with conservative statistical assumptions for analyses of Ct profiles.
METHOD OF CALCULATION OF CARBON DIOXIDE EMISSION BY MACHINE-TRACTOR UNITS IN TECHNOLOGICAL OPERATIONS, TAKING INTO ACCOUNT THE INFLUENCE OF THE PARAMETERS OF THE UNITS ON THE FORMED CROP OF GRAIN CROPS
Authors: Khafizov Kamil , Khafizov Ramil , Nurmiev Azat
Published: August 2022

Researches were conducted for the purpose of development of a method of calculation of emission of carbon dioxide by machine and tractor units on technological operations in crop production at cultivation of grain crops. The criterion of optimization of parameters and operating modes of soil-cultivating, sowing and other units – the minimum emission of carbon dioxide in the atmosphere at their production, maintenance and production operation is offered. Feature of the offered method is the fact that it considers the influence of parameters of the equipment on losses of a potential harvest which to avoid at today's level of development of the equipment and technologies it is impossible. Formation of a harvest results from absorption by carbon dioxide plants from the atmosphere and, partially, from the soil. Carbon dioxide (CO2) which the lost harvest could absorb from the atmosphere is removed from a circulation, so remains in the air, and in our technique it is attributed to CO2 released into the atmosphere at production, service and operation of the unit. In article the method of calculation of the amount of the carbon dioxide necessary for the formation of unit of a grain part of a harvest and not grain part accompanying it is in detail considered. The formula which allows to calculate the mass of carbon dioxide in kg for the formation of grain weighing 1 kg is offered. It became clear that from grain crops on formation of unit of a harvest, most of all CO2 from the atmosphere is absorbed by winter rye (about 3 kg/kg), further corn (2.8 kg/kg by theoretical calculations). Leaning on these researches, the mathematical model of operation of machine and tractor units on technological operations on preparation of the soil for crops and crops by the offered criterion of optimization is developed. An inspection of operability of the offered method by carrying out computing experiments with use of the created mathematical model on technological operation – preparation of the soil heavy disk harrows is carried out. During calculations of influence weight of the tractor, power of its engine, width of capture of the unit and working speed of the unit on carbon dioxide emission became clear. The minimum emission of carbon dioxide, for conditions of carrying out a computing experiment, is provided weighing tractor of 145 kN. The tractor weight deviation towards increase or reduction leads to growth of emission of carbon dioxide in the atmosphere.
MECHANISMS OF INFLUENCE OF SOCIO-ECONOMIC FACTORS OF RURAL AREAS ON THE RESULTS OF AGRICULTURAL PRODUCTION
Authors: Gazetdinov Mirsharip , Gazetdinov Shamil , Semicheva Ol'ga
Published: August 2022

The article examines the mechanism of influence on the economic efficiency of agricultural production of socio-economic factors that determine the development of rural areas at the present stage. The purpose of the study is to identify and substantiate those forms of interrelations in rural areas that contribute to improving the efficiency of agricultural production. It is established that the whole set of socio-economic factors (elimination of seasonality, increase and uniform income generation, development of social activity, etc.) can be considered as a separate element of the organizational and economic mechanism of innovative development of agricultural production. It is argued that the role of territorial contractual relations in the field of joint production and social activities of business entities and their interaction with municipal government bodies is increasing. It is established that social factors have a twofold impact on the level of costs. On the one hand, they contribute to their growth, on the other – to increase the economic effect, thereby ensuring the payback of the costs incurred. It is proposed to form certain forms of contractual territorial and economic structures for the development of rural territories and socio-economic ties of business entities. Such as economic associations created within the framework of individual administrative-territorial units in order to develop the entire economic complex, and also associations for coordination and cooperation, created not for the purpose of conducting any economic activity, but as an organizational tool for developing and implementing a common strategy of coordinated actions to solve certain problems affecting the interests of several rural areas
COST APPROACH TO SUSTAINABILITY ASSESSMENT THE FUNCTIONING OF THE ECONOMY OF ORGANIZATIONS
Authors: Il'in Sergey
Published: August 2022

Abstract. The prepared article is devoted to the study of the category of "stability" in relation to the activities of legal entities (organizations), which is based on the stability of its identifiable qualitative indicators. The purpose of such a study is to propose by the author a list of indicators and methods for calculating them for organizations to obtain objective information about the development (functioning) of their activities (economy) in statics and dynamics, which helps to develop the most effective economic measures. To achieve it the author has chosen a cost (monetary) approach to assessing the sustainability of the functioning of the economy of organizations. The priority given to it is due to the dominance of commodity-money relations in all sectors of the national and world economy, including in the agricultural sector (one of the most important spheres of the national economy of any state), and the universal property of monetary meters, manifested in the universal equivalence of accounting and analysis of economic transactions. The composition of static indicators includes result-effectiveness and expenses-effectiveness, characterizing the efficiency functioning of the economy over a specific time interval, and the composition of dynamic indicators – the change under their influence of the result and influence of the expenses over a number of time intervals, meaning the financial benefit derived by organizations from this process, determining economic prospects (competitiveness) in the long term. Upon the construction methods for calculating such indicators was used a rational-constructive method in combination with mathematical analysis and logarithm. In their unity they give the exact parameters of the calculated indicators. The methods formed through the selected methods have been tested on the example of one of the agricultural organizations (LLC "AE "Moscow"), in which there is a practical significance of the study. The analysis of indicators is carried out, conclusions made and the directions of increasing the stability of the functioning of its economy are recommended on the its materials.
AUDIT OF THE EFFECTIVENESS OF NATIONAL PROJECTS
Authors: Kashirskaya Lyudmila , Zurnadzh'yanc Yu.
Published: August 2022

The purpose of the study is to improve the methodology for auditing the effectiveness of national projects through the use of standard audit elements. The tasks of developing and supplementing approaches to the standardization of the audit of the effectiveness of national projects were set and solved, in particular, a strategy, program, checklist and risk assessment were proposed as the basis of the audit methodology using the example of the national project “Housing and Urban Environment”. The methodological basis of the research is the system and process approaches to the problem under study. In the course of the research, general scientific methods of logical analysis and synthesis were used, in particular, analogies, typologies, generalizations. Based on the study of extensive empirical material, the results of the implementation of national projects, their financing and the possibility of making changes and adjustments to them are investigated. As a result, it was concluded that the Project Passports included insufficiently justified and resourced values of target indicators, and the values of indicators set by regions were not supported by sufficient organizational measures. In addition, regulatory and methodological documents do not include full-fledged methodological support for their development and implementation, being limited to general approaches and principles. Also, the parameters of the mutual influence of the national project “Housing and urban environment” on other national projects are not specified in the Passport of the national project and in other regulatory and methodological documents, and therefore it is not possible to fully assess the quality of such influence. The practical significance of the article is that the conclusions obtained on the basis of the proposed elements of the methodology for auditing the effectiveness of national projects, in particular, the procedure for drawing up a strategy, audit program, checklist and audit risk assessment, will allow us to develop optimal positions in the regulation and determination of financing of national projects.
Is the grass elsewhere really greener? A study on the place marketing activity of Polish self-governments
Authors: Sokołowicz Mariusz E. , Lewandowska-Gwarda Karolina , Przygodzki Zbigniew
Published: August 2022

The role of place marketing and branding as a modus for enhancing public sector efficiency is growing, especially in territorial self-government units (TSGUs). A growing proportion maintains the relevant responsible agencies. We compared the place marketing activities of Polish TSGUs, focusing on their maturity in this matter. We associate maturity with the awareness that one should not be ashamed of territorial uniqueness but, on the contrary, highlight it as a source of merit. We based our study on self-evaluation carried out by marketing practitioners operating in Polish TSGUs. The results reveal that most of them do not yet fully exploit state-of-the-art place marketing to strengthen development policies. However, they vary significantly by disclosing many interesting local specificities.
Neighbourhood (dis)satisfaction in a former closed Soviet city: the case of Dnipro(petrovsk), Ukraine
Authors: Havryliuk Oleksii
Published: August 2022

This paper describes and analyses the geography and factors of the neighbourhood satisfaction of the residents of a former post-WWII Soviet closed city in Ukraine – the post-Soviet city of Dnipro (population ca. one million). It is based on a questionnaire survey (n=1248) among adult (18+) inhabitants in Dnipro conducted in early 2018. The results show that the current inner-urban pattern is characterised by semi-peripheralised neighbourhood satisfaction, which is a consequence of the significant influence of (among other factors): infrastructure availability in the neighbourhood, the social and natural environmental in the neighbourhood, and the set of Soviet-legacy factors (the “Soviet” factor). Surprisingly, the highest level of neighbourhood satisfaction in the city of Dnipro is observed in one of the peripheral neighbourhoods (with predominant detached housing), in which the residents’ evaluation of their residential neighbourhood follows the proximity effect.
Gauging the possibility of using property tax to respond to the rapid expansion of built-up area in Depok Municipality
Authors: Fikri Arie , Pravitasari Andrea , Indraprahasta Galuh
Published: August 2022

Over the last three decades, Depok Municipality has experienced rapid expansion of built-up area, due to the city’s strategic location as a satellite city of Jakarta that functions primarily as a dormitory town. Agricultural, plantation and vacant lands have been largely converted into different forms of built-up area. Some efforts should therefore be made to control this extensive land-use conversion. In particular, a fiscal instrument such as a property tax can be used not only as a source of city revenue, but also as a means for urban environmental control. In this study, we aim to gauge the potentiality of property tax in addressing large scale expansion of built-up area. In doing so, we employed Pearson Correlation and Moran’s Index analyses by comparing built-up area development and property tax performance in 2014 and 2019. The results indicate that property tax has not functioned very effectively as an instrument to steer built-up area expansion in Depok.
Krok w kierunku syntezy dziejów i kultury średniowiecznej Europy Wschodniej – kompendium Florina Curty Eastern Europe in the Middle Ages (500–1300)
Authors: Paroń Aleksander
Published: August 2022

W artykule przedstawione zostało najnowsze kompendium historii i kultury średniowiecznej Europy Wschodniej (500–1300). Krytyczna analiza obszernej publikacji pozwala uznać ją za ważne, choć w wielu kwestiach dyskusyjne, studium, które narusza dotychczasowe schematy opisywania przeszłości tego regionu i toruje drogę dla nowych i innowacyjnych opracowań.
Adoption of FasTrak on San Francisco Bay Area Bridges: Impact of Operations Research Models in Relieving Congestion
Authors: Bollapragada Ramesh , Kakar Venoo , Goodwin John , Fremier Andrew
Published: August 2022

Bay Area toll bridges are the main transportation link across the nine-county San Francisco Bay Area. These bridges experience extreme congestion and become bottlenecks during peak hours with long backups at the toll plazas. A solution to ensure smooth vehicle throughput at toll plazas is the widespread adoption of the electronic toll collection system called FasTrak. However, the FasTrak system has experienced low usage rates since its inception relative to other toll collection systems in the country. Forecasting, marketing, and operations research models were utilized to make recommendations and collaborate with transportation authorities to increase FasTrak usage during peak hours (5–10 a.m. and 3–7 p.m.) to address traffic congestion. After these recommendations were implemented, FasTrak usage increased from 40% in 2006 to the long-term target of 70% by 2016. This paper presents a synthesis of the challenges and the implementation of the FasTrak Strategic Plan. Furthermore, econometric models are presented that capture the effect on traffic volumes of increased FasTrak usage achieved through congestion pricing. Saved travel time resulted in productivity gains of approximately $569 million per year. This study contributes to an understanding of the role of effective transportation policies in reducing congestion and improving productivity.

History: This paper was refereed.

Supplemental Material: The online appendix is available at https://doi.org/10.1287/inte.2022.1127 .
Higher Education Teachers´ Conceptions of Professional Development and Change: A Longitudinal Case Study of University Pedagogy Prospects
Authors: Karjalainen Asko , Nissilä Säde-Pirkko
Published: August 2022

The aim of this research is to find out how higher education (HE) teachers reflect on the possibilities of personal development and evaluate the institutional promotion of academic teaching in an HE community. The purpose was thus to understand how university employed teachers experienced and reflected on the benefits of their pedagogical education and pedagogical fellowship during and after the studies. To obtain information regarding the current situations and prospects for the future of the research persons, questionnaires were used, and unstructured essays were written through their study time and subsequently. The research methods were qualitative content analysis and deep analysing methods. The teachers possess cognitive thinking skills of the highest level. Pedagogical and transformative thinking are not at the same level. The research persons express their views tactfully when outlining how teaching should be realized in the future. Still, they criticized the resistance to changes in academic teaching, especially before they themselves were part of the administration.
Numerical simulation of scalar wave scattering by a circular cylinder buried in a planar substrate
Authors: Tsermaa Baatarchuluun , Kim Jin Seung , Park Byong Chon , Myung-Whun Kim
Published: August 2022

We report numerical simulation results based on rigorous analytic solutions of scalar wave scattering caused by a cylinder buried in a planar substrate. As there are multiple interactions between the planar substrate and the cylinder, theoretical solutions were expressed in the form of coupled sets of infinite series, with each term within the series explicitly reflecting the effect of multiple scattering of increasing order. We determined the near- and far-field distributions of (1) the reflected field in the air, (2) the scattered and transmitted fields in the substrate, and (3) the transmitted field within the cylinder. Our results indicate that the effects of higher-order multiple scattering depend on the size, location, and refractive index of the cylinder, especially in the near-field region. The simulation is generalizable, as it places no restrictions on the physical and geometrical qualities of the cylinder or the planar substrate.
Field correlations of a partially coherent optical Gaussian wave in tissue turbulence
Authors: Baykal Yahya
Published: August 2022

For a partially coherent Gaussian optical wave, field correlations in turbulent tissues are examined. Changes in the field correlations are evaluated when the degree of source coherence, diagonal length from the receiver point, transverse receiver coordinate, tissue type, tissue length, source size, characteristic length of heterogeneity, strength coefficient of the refractive-index fluctuations, fractal dimension, and the small length-scale factor of the turbulent tissue vary. Investigated turbulent tissue types are liver parenchyma (mouse), upper dermis (human), intestinal epithelium (mouse), and deep dermis (mouse). For all the examined tissue types, field correlations are found to increase as the degree of source coherence, fractal dimension, and small length-scale factor increase and as the diagonal length from the receiver point, transverse receiver coordinate, tissue length, characteristic length of heterogeneity, and strength coefficient of the refractive-index fluctuations decrease. For the coherent source, an increase in the source size will increase the field correlations; however, for the partially coherent source, this trend is reversed.
Tailoring the light absorption of monolayer graphene via accidental quasi-bound states in the continuum
Authors: Yang Chaoyu , Sang Tian , Li Shi , Wang Yueke , Cao Guoyang , Hu Lian
Published: August 2022

Bound states in the continuum (BICs) have drawn fundamental and technological interests due to their distinct features such as infinite quality factor and extremely localized fields. Recently, it has been shown that the light absorption of graphene can be effectively enhanced by using symmetry-protected quasi-BICs; however, the important role of the counterparts of accidental quasi-BICs for light absorption enhancement of ultrathin films has not been studied, to our knowledge. Herein, light absorption enhancement of graphene is demonstrated through the excitation of accidental quasi-BICs based on a simple silicon grating metasurface (SGM). Highly efficient light absorption of monolayer graphene can be achieved at over-coupled resonance, and the locations of the absorption peaks and their peak values can be dynamically tuned by varying the incident angle. The enhanced light absorption of graphene is originated mainly from the hybrid toroidal dipole and electric quadrupole mode according to the far-field multiple decompositions and near-field distributions of the unit cell of the structure. In addition, the absorption responses of the SGM with graphene are robust to the variation of structural parameters, and their optical performances can be highly modulated as the Fermi level of graphene is altered.
Adaptive sparse reconstruction for lensless digital holography via PSF estimation and phase retrieval
Authors: Pacheco Carolina , McKay Gregory N. , Oommen Anisha , Durr Nicholas J. , Vidal René , Haeffele Benjamin D.
Published: August 2022

In-line lensless digital holography has great potential in multiple applications; however, reconstructing high-quality images from a single recorded hologram is challenging due to the loss of phase information. Typical reconstruction methods are based on solving a regularized inverse problem and work well under suitable image priors, but they are extremely sensitive to mismatches between the forward model and the actual imaging system. This paper aims to improve the robustness of such algorithms by introducing the adaptive sparse reconstruction method, ASR, which learns a properly constrained point spread function (PSF) directly from data, as opposed to solely relying on physics-based approximations of it. ASR jointly performs holographic reconstruction, PSF estimation, and phase retrieval in an unsupervised way by maximizing the sparsity of the reconstructed images. Like traditional methods, ASR uses the image formation model along with a sparsity prior, which, unlike recent deep learning approaches, allows for unsupervised reconstruction with as little as one sample. Experimental results in synthetic and real data show the advantages of ASR over traditional reconstruction methods, especially in cases where the theoretical PSF does not match that of the actual system.
Simulation of traveling-wave resonant tunneling diode oscillator waveguides
Authors: Jéhn Zoltán
Published: August 2022

In a traveling-wave resonant tunneling diode oscillator, the gain medium is encapsulated in a metallic waveguide. The geometrical parameters of the system and the skin penetration depth in the metal layers are of similar length scales. It confirms the need for a full-wave simulation, where the impedance boundary conditions can not be applied in a straightforward manner. In this work, a method of moments-based electromagnetic wave solver was developed and used to illustrate different traveling-wave RTD oscillator structures.
Integrated polarization mode interferometer in 220-nm silicon-on-insulator technology
Authors: Schweikert Christian , Tsianaka Anastasia , Hoppe Niklas , Klenk Rouven H. , Elster Raik , Greul Markus , Kaschel Mathias , Southan Alexander , Vogel Wolfgang , Berroth Manfred
Published: August 2022

A compact integrated and high-efficiency polarization mode interferometer in the 220-nm silicon-on-insulator platform is presented. Due to the operation with two polarization modes in a single waveguide, low propagation losses and high sensitivities combined with a small footprint are achieved. The designed and fabricated system with a 5-mm-long sensing region shows a measured excess loss of only 1.5 dB with an extinction ratio up to 30 dB, while its simulated homogeneous bulk sensitivity can exceed 8000 rad/RIU. The combination with a 90° hybrid readout system offers single wavelength operation with unambiguousness for phase shifts up to 2π and constant sensitivity.
Fully connected aperture array design of the segmented planar imaging system
Authors: Liu Gang , Wen Desheng , Fan Wenhui , Song Zongxi , Sun Zhonghan
Published: August 2022

Compared with the traditional imaging systems, segmented planar imaging technology has the advantages of low mess, small size, and low power in the same resolution situation. To obtain relatively complete frequency domain coverage, the lenslet array requires a large number of lenslets, and the photonic integrated circuit board requires a large number of optical devices, which limits the application and development of the segmented planar imaging technology. In this paper, we introduce a novel, to the best of our knowledge, design of the photonic integrated circuit to ensure that each lenslet in the lenslet array can form a baseline with any other lenslets. This breaks the barrier between segmented planar imaging technology and the traditional synthetic aperture, giving segmented planar imaging technology a sufficient number of frequency domain samples and a concise photonic integrated circuit structure.
Scelestial: Fast and accurate single-cell lineage tree inference based on a Steiner tree approximation algorithm
Authors: Foroughmand-Araabi Mohammad-Hadi , Goliaei Sama , McHardy Alice C.
Published: August 2022

Single-cell genome sequencing provides a highly granular view of biological systems but is affected by high error rates, allelic amplification bias, and uneven genome coverage. This creates a need for data-specific computational methods, for purposes such as for cell lineage tree inference. The objective of cell lineage tree reconstruction is to infer the evolutionary process that generated a set of observed cell genomes. Lineage trees may enable a better understanding of tumor formation and growth, as well as of organ development for healthy body cells. We describe a method, Scelestial, for lineage tree reconstruction from single-cell data, which is based on an approximation algorithm for the Steiner tree problem and is a generalization of the neighbor-joining method. We adapt the algorithm to efficiently select a limited subset of potential sequences as internal nodes, in the presence of missing values, and to minimize cost by lineage tree-based missing value imputation. In a comparison against seven state-of-the-art single-cell lineage tree reconstruction algorithms—BitPhylogeny, OncoNEM, SCITE, SiFit, SASC, SCIPhI, and SiCloneFit—on simulated and real single-cell tumor samples, Scelestial performed best at reconstructing trees in terms of accuracy and run time. Scelestial has been implemented in C++. It is also available as an R package named RScelestial.
Deep learning prediction of chemical-induced dose-dependent and context-specific multiplex phenotype responses and its application to personalized alzheimer’s disease drug repurposing
Authors: Wu You , Liu Qiao , Qiu Yue , Xie Lei
Published: August 2022

Predictive modeling of drug-induced gene expressions is a powerful tool for phenotype-based compound screening and drug repurposing. State-of-the-art machine learning methods use a small number of fixed cell lines as a surrogate for predicting actual expressions in a new cell type or tissue, although it is well known that drug responses depend on a cellular context. Thus, the existing approach has limitations when applied to personalized medicine, especially for many understudied diseases whose molecular profiles are dramatically different from those characterized in the training data. Besides the gene expression, dose-dependent cell viability is another important phenotype readout and is more informative than conventional summary statistics (e.g., IC50) for characterizing clinical drug efficacy and toxicity. However, few computational methods can reliably predict the dose-dependent cell viability. To address the challenges mentioned above, we designed a new deep learning model, MultiDCP, to predict cellular context-dependent gene expressions and cell viability on a specific dosage. The novelties of MultiDCP include a knowledge-driven gene expression profile transformer that enables context-specific phenotypic response predictions of novel cells or tissues, integration of multiple diverse labeled and unlabeled omics data, the joint training of the multiple prediction tasks, and a teacher-student training procedure that allows us to utilize unreliable data effectively. Comprehensive benchmark studies suggest that MultiDCP outperforms state-of-the-art methods with unseen cell lines that are dissimilar from the cell lines in the supervised training in terms of gene expressions. The predicted drug-induced gene expressions demonstrate a stronger predictive power than noisy experimental data for downstream tasks. Thus, MultiDCP is a useful tool for transcriptomics-based drug repurposing and compound screening that currently rely on noisy high-throughput experimental data. We applied MultiDCP to repurpose individualized drugs for Alzheimer’s disease in terms of efficacy and toxicity, suggesting that MultiDCP is a potentially powerful tool for personalized drug discovery.
Lipid levels in midlife and risk of atrial fibrillation over 3 decades—Experience from the Swedish AMORIS cohort: A cohort study
Authors: Ding Mozhu , Wennberg Alexandra , Gigante Bruna , Walldius Göran , Hammar Niklas , Modig Karin
Published: August 2022

Background

The role of cholesterol levels in the development of atrial fibrillation (AF) is still controversial. In addition, whether and to what extent apolipoproteins are associated with the risk of AF is rarely studied. In this study, we aimed to investigate the association between blood lipid levels in midlife and subsequent risk of new-onset AF.

Methods and findings

This population-based study included 65,136 individuals aged 45 to 60 years without overt cardiovascular diseases (CVDs) from the Swedish Apolipoprotein-Related Mortality Risk (AMORIS) cohort. Lipids were measured in 1985 to 1996, and individuals were followed until December 31, 2019 for incident AF (i.e., study outcome). Hazard ratios (HRs) with 95% confidence intervals (CIs) were estimated using Cox regression, adjusting for age, sex, and socioeconomic status. Over a mean follow-up of 24.2 years (standard deviation 7.5, range 0.2 to 35.9), 13,871 (21.3%) incident AF cases occurred. Higher levels of total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C) were statistically significantly associated with a lower risk of AF during the first 5 years of follow-up (HR = 0.61, 95% CI: 0.41 to 0.99, p = 0.013; HR = 0.64, 95% CI: 0.45 to 0.92, p = 0.016), but not thereafter (HR ranging from 0.94 [95% CI: 0.89 to 1.00, p = 0.038] to 0.96 [95% CI: 0.77 to 1.19, p > 0.05]). Lower levels of high-density lipoprotein cholesterol (HDL-C) and apolipoprotein A-I (ApoA-I) and higher triglycerides (TG)/HDL-C ratio were statistically significantly associated with a higher risk of AF during the entire follow-up (HR ranging from 1.13 [95% CI: 1.07 to 1.19, p < 0.001] to 1.53 [95% CI: 1.12 to 2.00, p = 0.007]). Apolipoprotein B (ApoB)/ApoA-I ratio was not associated with AF risk. The observed associations were similar among those who developed incident heart failure (HF)/coronary heart disease (CHD) and those who did not. The main limitations of this study include lack of adjustments for lifestyle factors and high blood pressure leading to potential residual confounding.

Conclusions

High TC and LDL-C in midlife was associated with a lower risk of AF, but this association was present only within 5 years from lipid measurement and not thereafter. On the contrary, low HDL-C and ApoA-I and high TG/HDL-C ratio were associated with an increased risk of AF over almost 35 years of follow-up. ApoB/ApoA-I ratio was not associated with AF risk.
Association between serum uric acid levels and colonic diverticulosis in terms of sex
Authors: Hu Je-Ming , Chang Yu-Tien , Shih Chi-Wei , Hsu Chih-Hsiung , Lin Tzu-Chiao , Lai Chung-Yu , Lin Ming-Hsun , Chen Wei-Liang
Published: August 2022

Background

The association between elevated serum uric acid (UA) levels and the risk of developing colonic diverticulosis has not yet been investigated. Thus, this cross-sectional study aimed to examine this correlation in individuals from Taiwan.

Methods

From Jan. 1, 2010, to Dec. 31, 2016., approximately 5,605 patients (aged >20 years) from Tri-Service General Hospital who met the inclusion criteria according to colonoscopy and laboratory test findings were included in this research. The correlation between serum UA levels and colonic diverticulosis was investigated via regression analyses.

Results

Participants with elevated serum UA levels were at a higher risk of colonic diverticulosis. The area under the curve for serum UA levels was significantly higher in women than in men (0.651 [95% confidence interval: 0.596–0.707] vs. 0.55 [0.507–0.593]). There were specific trends in female-specific indicators for colonic diverticulosis across increasing quartiles of serum UA levels.

Conclusions

Patients with elevated serum UA levels should be cautious regarding the development of colonic diverticulosis disorder in female. Moreover, prospective studies may provide additional information on the relationship between elevated serum UA levels and colonic diverticulosis.
What matters most to patients with severe aortic stenosis when choosing treatment? Framing the conversation for shared decision making
Authors: Col Nananda F. , Otero Diana , Lindman Brian R. , Horne Aaron , Levack Melissa M. , Ngo Long , Goodloe Kimberly , Strong Susan , Kaplan Elvin , Beaudry Melissa , Coylewright Megan
Published: August 2022

Background

Guidelines recommend including the patient’s values and preferences when choosing treatment for severe aortic stenosis (sAS). However, little is known about what matters most to patients as they develop treatment preferences. Our objective was to identify, prioritize, and organize patient-reported goals and features of treatment for sAS.

Methods

This multi-center mixed-methods study conducted structured focus groups using the nominal group technique to identify patients’ most important treatment goals and features. Patients separately rated and grouped those items using card sorting techniques. Multidimensional scaling and hierarchical cluster analyses generated a cognitive map and clusters.

Results

51 adults with sAS and 3 caregivers with experience choosing treatment (age 36–92 years) were included. Participants were referred from multiple health centers across the U.S. and online. Eight nominal group meetings generated 32 unique treatment goals and 46 treatment features, which were grouped into 10 clusters of goals and 11 clusters of features. The most important clusters were: 1) trust in the healthcare team, 2) having good information about options, and 3) long-term outlook. Other clusters addressed the need for and urgency of treatment, being independent and active, overall health, quality of life, family and friends, recovery, homecare, and the process of decision-making.

Conclusions

These patient-reported items addressed the impact of the treatment decision on the lives of patients and their families from the time of decision-making through recovery, homecare, and beyond. Many attributes had not been previously reported for sAS. The goals and features that patients’ value, and the relative importance that they attach to them, differ from those reported in clinical trials and vary substantially from one individual to another. These findings are being used to design a shared decision-making tool to help patients and their clinicians choose a treatment that aligns with the patients’ priorities.

Trial registration

ClinicalTrials.gov, Trial ID: NCT04755426, Trial URL https://clinicaltrials.gov/ct2/show/NCT04755426.
Sculpting the Glauberg “prince”. A traceological research of the Celtic sculpture and related fragments from the Glauberg (Hesse, Germany)
Authors: Trefný Martin , Mischka Doris , Cihla Michal , Posluschny Axel. G. , Václavík František R. , Ney Wolfram , Mischka Carsten
Published: August 2022

Article presents the results of a complex traceological research of the famous statue of the „prince”of Glauberg, found in an Early La Tène funeral complex in Glauberg (Hesse). Research focused also on two other fragments of related sandstone sculptures, found together with the Glauberger prince. The sandstone „prince”of Glauberg was already in the past a subject of many archaeological studies. Nevertheless, all or absolute majority of them were focused on aspects of art historian nature or on the question of the origin, role and function of such sculptures in the Early Iron Age Central Europe. On the contrary, the aim of our research is oriented exclusively on the questions related to the manufacture of this sculpture, identification of used sculptor´s tools and applied working techniques. Our research was realised by means of digital documentation followed by the aplication of traceological methods. The character of the survived working traces on the sculpture´s surfaces was studied by mechanoscopy, while the material of used tools was determined by X-ray fluorescence. The reconstructions of used tools were compared with the existing tools as represented by the Iron Age archaeological finds. This comparison was oriented on the most relevant regions of developed La Tène culture, particularly on South Western Germany and Bohemia. However, also other relevant area, significant as the possible source of inspiration of Celtic sculptors for the creation of the monumental sculpture–Apennine peninsula, was taken into consideration. Our research revealed individual steps and phases during the sculpture´s manufacture, enabled the reconstrucion of used tools and confirmed real existence of such tools in mentioned regions. Finally it has brought first indices of the necessity of the distinguishing between ideological and technological aspects of related Celtic sculpture, when considering possible influence of Apennine peninsula on transalpine Central Europe.