bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and Detection Experiment of Scanning Stage for High-throughput Gene Sequencer
Authors: Zhao Yanyan , Cao Yue , Tan Wenjun , Yang Tianshi , Chen Hao 
Published: March 2023

Abstract
In order to meet the requirements of large stroke, high precision, and high acceleration step scanning imaging of the worktable of a high-throughput gene sequencer, a mechanical ultra-precision positioning platform is designed. The XY translation table has a significant impact on the fluxes and accuracy of gene sequencing detection. Using the finite element method to analyze the structural modal and obtain the first-order natural frequency; Then using the vibration test system and laser interferometer to test the first-order natural frequency and the repeat positioning accuracy of the XY translation table. The test results show that the first-order natural frequencies of the platform in X, y and Z directions are 175Hz, 111Hz and 191Hz respectively, which is much higher than the upper-frequency limit of 16.7Hz step scanning servo bandwidth. The two-way repeat positioning accuracy of XY translation table are ± 0.462 µ m and ± 0.429 µ m, meet ± 0.6 µm. So the scanning stage can meet the index requirements of a high-throughput gene sequencers under the specified working conditions, and the measured test data combined with the modal analysis model can provide a research basis for the optimal design of the subsequent platform.
Research on Near Field Signal Behaviour of Localizer Antenna System
Authors: Qu Chunqing 
Published: March 2023

Abstract
Near-field (NF) signal distribution behavior with a radius of 150 meters was studied to compare with far-field (FF) distribution characteristics. It can be found more flexible and detailed in NF than the signal from an NF monitor with only a single location. The origin of the measured value and signal detection method on the equipment was introduced in detail. The three-dimensional model was established and optimized by phase analysis as well as the measured data on-site. There was little difference between a measured distribution and a theoretical calculation in space. The change of directional weakening of the Log Periodic Dipole Antenna (LPDA) was proposed. Unequal amplitude signal synthesis together with Fresnel loss was considered to research and explain the incredible power gain. The modified 3D model is in good agreement with the measured results.
Optical Set up for Scanning System in Manufacturing Inspection
Authors: Salah Yosri Ben , Liu Weiguo , Tian Ailing , Sellami Lamia , Hamida Ahmed Ben 
Published: March 2023

Abstract
Essentially, 3D scanning systems are fundamental in today’s industry, since there is a necessity for the automation of the whole manufacturing process with the aim to achieve better results in terms of accuracy, quality, and manufacturing time. Indeed, experts move towards the integration of high-resolution sensors, and optical devices alongside software, which may offer several advantages for large manufacturing units. In this paper, a stereo vision system is demonstrated in detail while performing a scan. The developed model could be used to carry out several measurement experiments, and the measurement results are analyzed, which proved the correctness and feasibility of the method. Delivered results and outcomes are discussed.
Experimental studies on the propagation of whistler-mode waves in a magnetized plasma structure with a non-uniform density
Authors: SANG Longlong , LU Quanming , XIE Jinlin , ZHANG Qiaofeng , DING Weixing , KE Yangguang , GAO Xinliang , ZHENG Jian 
Published: March 2023

Abstract
Propagation of whistler-mode waves in a magnetized plasma structure is investigated in the Keda linear magnetized plasma device. The magnetized plasma structure has its density peak in the center, and the background magnetic field is homogeneous along the axial direction. A whistler-mode wave with a frequency of 0.3 times of electron cyclotron frequency (f
ce) is launched into the plasma structure. The wave normal angle (WNA) is about 25°, and the wavefront exhibits a wedge structure. During propagation of the whistler wave, both the propagating angle and WNA slowly approach zero, and then the wave is converged toward the center of the structure. Therefore, the wave tends to be trapped in the plasma structure. The results present observational evidence of the propagation of a whistler-mode wave trapped in the enhanced-density structure in a laboratory plasma. This trapping effect is consistent with satellite observations in the inner magnetosphere.
Inversion techniques to obtain local rotation velocity and ion temperature profiles for the x-ray crystal spectrometer on EAST
Authors: LIN Zichao , ZHANG Hongming , WANG Fudi , BAE Cheonho , FU Jia , JIN Yifei , LU Di’an , FU Shengyu , LI Jiankang , LYU Bo 
Published: March 2023

Abstract
Inversion techniques are conducted based on the tangential x-ray crystal spectroscopy (TXCS) geometry on EAST to obtain the local profiles of ion temperature (T
i) and toroidal rotation velocity (v
t). Firstly, local emissivity profiles of the impurity argon are obtained using the asymmetrical Abel inversion. Then, the local v
t and T
i profiles are calculated by considering the local emissivity profiles and the TXCS detailed geometry. In addition, how the changes in the v
t profiles affect the accuracy in the T
i profiles is discussed in detail. It is also found that the line-integrated T
i profiles are becoming less accurate with the increase in the radial gradient in the local v
t profiles. Nonetheless, accurate T
i radial profiles are reconstructed after considering the effects of the emissivity and velocity, which are verified by comparing the inverted v
t and T
i profiles with those local profile measurements from the Charge eXchange Recombination Spectroscopy (CXRS) on EAST.
Adaptive sampling for accelerating neutron diffraction-based strain mapping
*
Authors: Venkatakrishnan S V , Fancher Chris M , Ziatdinov Maxim , Vasudevan Rama , Saleeby Kyle , Haley James , Yu Dunji , An Ke , Plotkowski Alex 
Published: March 2023

Abstract
Neutron diffraction is a useful technique for mapping residual strains in dense metal objects. The technique works by placing an object in the path of a neutron beam, measuring the diffracted signals and inferring the local lattice strain values from the measurement. In order to map the strains across the entire object, the object is stepped one position at a time in the path of the neutron beam, typically in raster order, and at each position a strain value is estimated. Typical dwell times at neutron diffraction instruments result in an overall measurement that can take several hours to map an object that is several tens of centimeters in each dimension at a resolution of a few millimeters, during which the end users do not have an estimate of the global strain features and are at risk of incomplete information in case of instruments outages. In this paper, we propose an object adaptive sampling strategy to measure the significant points first. We start with a small initial uniform set of measurement points across the object to be mapped, compute the strain in those positions and use a machine learning technique to predict the next position to measure in the object. Specifically, we use a Bayesian optimization based on a Gaussian process regression method to infer the underlying strain field from a sparse set of measurements and predict the next most informative positions to measure based on estimates of the mean and variance in the strain fields estimated from the previously measured points. We demonstrate our real-time measure-infer-predict workflow on additively manufactured steel parts—demonstrating that we can get an accurate strain estimate even with 30%–40% of the typical number of measurements—leading the path to faster strain mapping with useful real-time feedback. We emphasize that the proposed method is general and can be used for fast mapping of other material properties such as phase fractions from time-consuming point-wise neutron measurements.
Quantification of Waning Immunity After Measles Vaccination—Evidence From a Seroprevalence Study
Authors: Zibolenová Jana , Hudečková Henrieta , Chladná Zuzana , Malobická Eva , Novák Martin , Waczulíková Iveta , Mikas Ján , Mečochová Adriana 
Published: March 2023

Abstract
We aimed to quantify rates of waning immunity after measles vaccination from seroprevalence data collected in a study of a population with high vaccination coverage and a fixed vaccination schedule. Data were collected during a national survey (the Immunological Survey) carried out in the Slovak Republic in 2018. The average rate of waning immunity against measles after the first dose of measles, mumps, and rubella (MMR) vaccine (ages 1.5–10 years) was 9.7% per year from the geometric mean titer value of 2,634 mUI/mL. The average waning rate after the second dose of MMR vaccine (ages 10–33 years) was significantly lower: 4.8% per year from the lower geometric mean titer of 1,331 mUI/mL. This decline in antibody levels suggests that vaccine-induced protection may be compromised and results in an increase in the proportion of seronegative/borderline individuals. These outcomes may provide a valuable source for critical assessment of direct and indirect effects of MMR vaccination.
The effects of ecology and behavior on the evolution of coloration in Coraciiformes
Authors: Babarović Frane , Cooney Christopher R , Varley Zoë K , Nouri Lara O , Nadeau Nicola J , Thomas Gavin H 
Published: March 2023

Abstract
What drives the evolution of plumage color in birds? Bird color is likely to be under both natural and sexual selection where natural selection may favor evolution toward crypsis or camouflage whereas sexual selection may favor evolution toward conspicuousness. The responses to selection are predicted to relate to species’ ecology, behavior, and life history. Key hypotheses have focused on habitat and light environment, breeding strategy, territoriality, and hunting behavior. We tested these potential causes of color variation in the Coraciiformes, a colorful clade of non-passerine birds, using phylogenetic comparative methods and data on chromatic and achromatic properties of plumage coloration measured from museum specimens. We found that correlates of color evolution in Coraciiformes vary across body regions and depend on the focal color property (chromatic or achromatic properties of plumage coloration). While the light environment showed widespread effects on coloration in multiple body regions for both color properties, selection pressures related to behavioral characteristics had more spatially localized effects (e.g. territoriality on achromatic properties of wing feathers and hunting strategy on chromatic properties of belly feathers). Our results reveal both general patterns that may hold across other bird clades and more nuanced effects of selection that are likely to be mediated through the visual ecology of the signaler and receiver and the behavioral characteristics of Coraciiform species.
Motif elucidation in ChIP-seq datasets with a knockout control
Authors: Denisko Danielle , Viner Coby , Hoffman Michael M 
Published: March 2023

Abstract

Summary
Chromatin immunoprecipitation-sequencing is widely used to find transcription factor binding sites, but suffers from various sources of noise. Knocking out the target factor mitigates noise by acting as a negative control. Paired wild-type and knockout (KO) experiments can generate improved motifs but require optimal differential analysis. We introduce peaKO—a computational method to automatically optimize motif analyses with KO controls, which we compare to two other methods. PeaKO often improves elucidation of the target factor and highlights the benefits of KO controls, which far outperform input controls.

Availability and implementation
PeaKO is freely available at https://peako.hoffmanlab.org.

Contact
michael.hoffman@utoronto.ca
PATO: genome-wide prediction of lncRNA–DNA triple helices
Authors: Amatria-Barral Iñaki , González-Domínguez Jorge , Touriño Juan 
Published: March 2023

AbstractMotivationLong non-coding RNA (lncRNA) plays a key role in many biological processes. For instance, lncRNA regulates chromatin using different molecular mechanisms, including direct RNA–DNA hybridization via triplexes, cotranscriptional RNA–RNA interactions, and RNA–DNA binding mediated by protein complexes. While the functional annotation of lncRNA transcripts has been widely studied over the last 20 years, barely a handful of tools have been developed with the specific purpose of detecting and evaluating lncRNA–DNA triple helices. What is worse, some of these tools have nearly grown a decade old, making new triplex-centric pipelines depend on legacy software that cannot thoroughly process all the data made available by next-generation sequencing (NGS) technologies.ResultsWe present PATO, a modern, fast, and efficient tool for the detection of lncRNA–DNA triplexes that matches NGS processing capabilities. PATO enables the prediction of triple helices at the genome scale and can process in as little as 1 h more than 60 GB of sequence data using a two-socket server. Moreover, PATO’s efficiency allows a more exhaustive search of the triplex-forming solution space, and so PATO achieves higher levels of prediction accuracy in far less time than other tools in the state of the art.Availability and implementationSource code, user manual, and tests are freely available to download under the MIT License at https://github.com/UDC-GAC/pato.
Causal inference with misspecified exposure mappings: separating definitions and assumptions
Authors: Sävje F 
Published: March 2023

Summary
Exposure mappings facilitate investigations of complex causal effects when units interact in experiments. Current methods require experimenters to use the same exposure mappings to define the effect of interest and to impose assumptions on the interference structure. However, the two roles rarely coincide in practice, and experimenters are forced to make the often questionable assumption that their exposures are correctly specified. This paper argues that the two roles exposure mappings currently serve can, and typically should, be separated, so that exposures are used to define effects without necessarily assuming that they are capturing the complete causal structure in the experiment. The paper shows that this approach is practically viable by providing conditions under which exposure effects can be precisely estimated when the exposures are misspecified. Some important questions remain open.
Cardiac sarcoidosis: phenotypes, diagnosis, treatment, and prognosis
Authors: Lehtonen Jukka , Uusitalo Valtteri , Pöyhönen Pauli , Mäyränpää Mikko I , Kupari Markku 
Published: March 2023

Abstract
Cardiac sarcoidosis (CS) results from epithelioid cell granulomas infiltrating the myocardium and predisposing to conduction disturbances, ventricular tachyarrhythmias, and heart failure. Manifest CS, however, constitutes only the top of an iceberg as advanced imaging uncovers cardiac involvement 4 to 5 times more commonly than what is clinically detectable. Definite diagnosis of CS requires myocardial biopsy and histopathology, but a sufficient diagnostic likelihood can be achieved by combining extracardiac histology of sarcoidosis with clinical manifestations and findings on cardiac imaging. CS can appear as the first or only organ manifestation of sarcoidosis or on top of pre-existing extracardiac disease. Due to the lack of controlled trials, the care of CS is based on observational evidence of low quality. Currently, the treatment involves corticosteroid-based, tiered immunosuppression to control myocardial inflammation with medical and device-based therapy for symptomatic atrioventricular block, ventricular tachyarrhythmias, and heart failure. Recent outcome data indicate 90% to 96% 5-year survival in manifest CS with the 10-year figures ranging from 80% to 90%. Major progress in the care of CS awaits the key to its molecular–genetic pathogenesis and large-scale controlled clinical trials.
Long-term outcomes of phenoclusters in severe tricuspid regurgitation
Authors: Rao Vishal N , Giczewska Anna , Chiswell Karen , Felker G Michael , Wang Andrew , Glower Donald D , Gaca Jeffrey G , Parikh Kishan S , Vemulapalli Sreekanth 
Published: March 2023

Abstract

Aims
Severe tricuspid regurgitation (TR) exhibits high 1-year morbidity and mortality, yet long-term cardiovascular risk overall and by subgroups remains unknown. This study characterizes 5-year outcomes and identifies distinct clinical risk profiles of severe TR.

Methods and results
Patients were included from a large US tertiary referral center with new severe TR by echocardiography based on four-category American Society of Echocardiography grading scale between 2007 and 2018. Patients were categorized by TR etiology (with lead present, primary, and secondary) and by supervised recursive partitioning (survival trees) for outcomes of death and the composite of death or heart failure hospitalization. The Kaplan–Meier estimates and Cox regression models were used to evaluate any association by (i) TR etiology and (ii) groups identified by survival trees and outcomes over 5 years. Among 2379 consecutive patients with new severe TR, median age was 70 years, 61% were female, and 40% were black. Event rates (95% confidence interval) were 30.9 (29.0–32.8) events/100 patient-years for death and 49.0 (45.9–52.2) events/100 patient-years for the composite endpoint, with no significant difference by TR etiology. After applying supervised survival tree modeling, two separate groups of four phenoclusters with distinct clinical prognoses were separately identified for death and the composite endpoint. Variables discriminating both outcomes were age, albumin, blood urea nitrogen, right ventricular function, and systolic blood pressure (all P &lt; 0.05).

Conclusion
Patients with newly identified severe TR have high 5-year risk for death and death or heart failure hospitalization. Partitioning patients using supervised survival tree models, but not TR etiology, discriminated clinical risk. These data aid in identifying relevant subgroups in clinical trials of TR and clinical risk/benefit analysis for TR therapies.
Robustness increases heritability: implications for familial disease
Authors: Frank Steven A 
Published: March 2023

AbstractRobustness protects organisms in two ways. Homeostatic buffering lowers the variation of traits caused by internal or external perturbations. Tolerance reduces the consequences of bad situations, such as extreme phenotypes or infections. This article shows that both types of robustness increase the heritability of protected traits. Additionally, robustness strongly increases the heritability of disease. The natural tendency for organisms to protect robustly against perturbations may partly explain the high heritability that occurs for some diseases.
The evolution of partner specificity in mutualisms
Authors: Carlson Christopher , Akçay Erol , Morsky Bryce 
Published: March 2023

AbstractMutualistic species vary in their level of partner specificity, which has important evolutionary, ecological, and management implications. Yet, the evolutionary mechanisms which underpin partner specificity are not fully understood. Most work on specialization focuses on the trade-off between generalism and specialism, where specialists receive more benefits from preferred partners at the expense of benefits from non-preferred partners, while generalists receive similar benefits from all partners. Because all mutualisms involve some degree of both cooperation and conflict between partners, we highlight that specialization to a mutualistic partner can be cooperative, increasing benefit to a focal species and a partner, or antagonistic, increasing resource extraction by a focal species from a partner. We devise an evolutionary game theoretic model to assess the evolutionary dynamics of cooperative specialization, antagonistic specialization, and generalism. Our model shows that cooperative specialization leads to bistability: stable equilibria with a specialist host and its preferred partner excluding all others. We also show that under cooperative specialization with spatial effects, generalists can thrive at the boundaries between differing specialist patches. Under antagonistic specialization, generalism is evolutionarily stable. We provide predictions for how a cooperation-antagonism continuum may determine the patterns of partner specificity that develop within mutualistic relationships.
Widespread convergent morphological evolution within the largest family of songbirds
Authors: Demery Amelia-Juliette , Burns Kevin J 
Published: March 2023

AbstractAlthough convergence is a common evolutionary phenomenon, few studies have quantified its prevalence across a large, densely sampled clade. Large-scale phylogenies and the advent of novel computational methods facilitate more robust identification of convergent events and their statistical significance. The tanagers (Aves: Thraupidae), the largest family of songbirds, offer an excellent opportunity to study the extent of phenotypic convergence in response to similar ecological pressures on a continental scale. To investigate convergence in the group, we used the largest phylogenetic and multivariate morphological dataset to date for the clade. First, we used phylogenetic comparative analyses to show a correlation between diet and aspects of bill shape. We then investigated our dataset for the presence and magnitude of convergent events and assessed significance through simulations and modeling analyses. Overall, we found that around half (45.3%) of species and clades we tested have converged in morphological space more than would be expected by chance alone. Our study shows that across Thraupidae, various bill shapes have evolved convergently to fill multiple distinct sections of ecological niche space, reflecting a signal of ecological opportunity and structural constraints.
City of Fury: Urban Violence, Dystopia and Anti-Utopia in Nuevo orden and Era Uma Vez Brasília
Authors: Paz Mariano 
Published: March 2023

Abstract
In the twenty-first century Latin America has become the most urbanized region on the planet and, at the same time, the one that has the highest level of inequality. This article discusses how this tension is expressed in cinema, an eminently urban art, through two case studies: the Mexican Nuevo orden (dir. by Michel Franco, 2020) and the Brazilian film Era uma vez Brasília (dir. by Adirley Queirós, 2017). Both works are independent films that deal with issues of urban violence and authoritarianism through a distinct style that combines the techniques of realist representation with fictional elements borrowed from dystopian and science fiction genres. While the two show a preoccupation with the economic and racialized inequality that characterizes urban space in the capital cities of Mexico and Brazil, they ultimately evoke two modes of utopian discourse. Whereas the first film can be considered anti-utopian, criticizing the impulse to seek social change, the second one, though pessimistic, retains a utopian call for political action.