bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design of a tunable turnstile mode converter for high-power microwave applications
Authors: Wang Xiaoyu , Fan Yuwei , Yang Baoping , Shu Ting , Xu Xu , Li Ankun , Liu Zeyang 
Published: October 2021

This study investigates the frequency tunability of a coaxial transverse electromagnetic mode (TEM)–linear-polarized TE11 mode tunable turnstile mode converter (TTMC) for high-power microwave applications using a combination of simulation and experiment. In the proposed structure, the sliding folded waveguide can be moved radially to meet the requirement of linear polarization, and the matching structure is designed to eliminate the undesired reflection. The simulation shows that the conversion efficiency of the TTMC can reach over 99% in the frequency range of 1.45–2.35 GHz, corresponding to a frequency tuning bandwidth of about 47.4%. Moreover, the TTMC can maintain a continuous high conversion efficiency at different frequency points by changing the tuning mechanism. The experimental investigation shows that the TTMC can convert the coaxial TEM mode into a circular waveguide TE11 mode with a conversion efficiency of above 95% in the frequency range of 1.55–2.35 GHz. The experimental measurements agree well with the simulation results, implying feasibility of the TTMC design and its superior performance.
Coexisting vortices and antivortices generated by dually gauged harmonic maps
Authors: Han Xiaosen , Huang Genggeng , Yang Yisong 
Published: October 2021

In this paper, we first formulate a dually gauged harmonic map model, suggested from a product Abelian Higgs field theory arising in impurity-inspired field theories, and obtain a new BPS system of equations governing coexisting vortices and antivortices, which are topologically characterized by the first Chern classes of the underlying Hermitian bundles and the Thom classes of their associated dual bundles. We then establish existence and uniqueness theorems for such vortices. For the equations over a compact surface, we obtain necessary and sufficient conditions for the existence of solutions. For the equations over the full plane, we obtain all finite-energy solutions. In addition, we also present precise expressions giving the values of various physical quantities of the solutions, including magnetic charges and energies, in terms of the total numbers of vortices and antivortices, of two species and the coupling parameters involved.
Switchover phenomenon induced by epidemic seeding on geometric networks
Authors: Ódor Gergely , Czifra Domonkos , Komjáthy Júlia , Lovász László , Karsai Márton 
Published: October 2021

Significance
Initial seeding of an epidemic from the best-connected nodes of a network would intuitively lead to the largest outbreak. We challenge this picture and explore a switchover phenomenon: Epidemics started from the central part of a geometric metapopulation network can reach more individuals only if the basic reproduction number is small, but if the epidemic is more infectious, it reaches a larger population when seeded from uniformly selected nodes. We identify spatial geometry to amplify this effect in both data-driven and synthetic epidemic models, and we give rigorous proofs that this phenomenon appears in various random networks. Our results help us understand why real epidemics started from seemingly similar conditions may have significantly different outcomes.
A mutation-mediated evolutionary adaptation of Zika virus in mosquito and mammalian host
Authors: Yu Xi , Shan Chao , Zhu Yibin , Ma Enhao , Wang Jinglin , Wang Penghua , Shi Pei-Yong , Cheng Gong 
Published: October 2021

SignificanceZika virus (ZIKV) circulated undetectably for decades until its recent outbreak from 2015 to 2017. Our study demonstrated that a mutation in the ZIKV capsid protein (C-T106A) significantly increased the epidemic potential of ZIKV over its transmission cycle by promoting the efficient assembly of ZIKV virions. Our results offer additional evidence about the evolutionary enhancement of ZIKV infectivity in mammalian hosts and mosquitoes, potentially improving our understanding of the potential relationships between ZIKV evolution and the occasional widespread reemergence in nature.
Use of liquid lithography to form in vitro intestinal crypts with varying microcurvature surrounding the stem cell niche
Authors: Howard R Logan , Wang Yuli , Allbritton Nancy L 
Published: October 2021

Abstract
Objective. The role of the crypt microarchitecture and surrounding tissue curvature on intestinal stem/proliferative cell physiology is unknown. The utility of liquid lithography in creating polydimethylsiloxane (PDMS) micropillar stamps with controlled tip curvature was assessed. Using these stamps, the impact of microcurvature at the crypt base on intestinal cell and cytoskeletal behavior was studied. Approach. An SU-8 master mold as a support, polyols of varying surface energies as sacrificial liquids, and liquid PDMS as the solidifiable material were combined using liquid lithography to form PDMS micropillar arrays. Vapor phase deposition of organosilane onto the master mold was used to modify the surface energy of the master mold to shape the micropillar tips. Collagen was molded using the micropillar arrays forming a scaffold for culture of human primary colonic epithelial cells. Cell proliferation and cytoskeletal properties were assessed using fluorescent stains. Main results. Liquid lithography using low surface energy polyols (<55 dynes cm−1) generated convex-tipped PDMS micropillars, while polyols with higher surface energies (>55 dynes cm−1) yielded concave-tipped PDMS micropillars. Gradients of octyltrichlorosilane deposition across a master mold with an array of microwells yielded a PDMS micropillar array with a range of tip curvatures. Human primary colonic epithelial cells cultured on micropillar-molded collagen scaffolds demonstrated a stem/proliferative cell compartment at the crypt base. Crypts with a convex base demonstrated significantly lower cell proliferation at the crypt base than that of cells in crypts with either flat or concave bases. Crypts with a convex base also displayed higher levels of G-actin activity compared to that of crypts with flat or concave bases. Significance. Liquid lithography enabled creation of arrays of in vitro colonic crypts with programmable curvature. Primary cells at the crypt base sensed and responded to surface curvature by altering their proliferation and cytoskeletal properties.
Ultrafast dynamics of exciton–polariton in optically tailored potential landscapes at room temperature
Authors: Chen Fei , Li Hui , Zhou Hang , Ye Ziyu , Luo Song , Sun Zheng , Sun Fenghao , Wang Jiawei , Xu Huailiang , Xu Hongxing , Chen Zhanghai , Wu Jian 
Published: October 2021

Abstract
In this work, by using femtosecond angle-resolved spectroscopic imaging technique, the ultrafast dynamics of confined exciton–polaritons in an optical induced potential well based on a ZnO whispering-gallery microcavity is explicitly visualized. The sub-picosecond transition between succeeding quantum harmonic oscillator states can be experimentally distinguished. The landscape of the potential well can be modified by the pump power, the spatial distance and the time delay of the two input laser pulses. Clarifying the underlying mechanism of the polariton harmonic oscillator is interesting for the applications of polariton-based optoelectronic devices and quantum information processing.
Real-time multi-class signal quality assessment of photoplethysmography using machine learning technique
Authors: Prasun Pratyush , Mukhopadhyay Sumitra , Gupta Rajarshi 
Published: October 2021

Abstract
Photoplethysmography (PPG) signal quality assessment (SQA) ensures improved measurements of various surrogate cardiovascular measurements like heart rate, SpO2, blood pressure, cardiac output and many more and as well reduces false alrams in ambulatory measurements. Although PPG SQA (PSQA) is a well researched area, but multiclass prediction of signal quality and its hardware implementation is limited. In this paper, a new non-segmenting approach for multiclass PSQA is presented with an optimal set of seven time-frequency domain features in conjuction with supervised classifiers to identify clean, partly clean and corrupted PPG data. The present work was carried out in three major stages- signal (dataset) acquisition, feature extraction and 3-class classification using random forest classifier. The technique was evaluated with volunteers’ data, MIMIC-III data from PhysioNet, CSL data, and combined data and achieved an overall average accuracy of 96.8% with good (0.98 or above) sensitivity, specificity, F1 score, precision and recall. On-device implementation of the proposed PSQA was accomplished using 7.2 h of PPG dataset on a quad-core Broadcom BCM 2837 controller with 1.2 GHz, supported by 1 GB RAM-based standalone device, with an accuracy of 97.09%. The latency and the peak memory requirement of the implementation was 0.81 s and 19 kB respectively to process 3 s PPG data. The present technique may be integrated as a part of a remote healthcare system using wearable sensors.
Thermodynamic properties for Ar-Al, Ar-Cu and Ar-Fe mixtures from 0.3 kK up to 4 kK for 1 atm
Authors: Coufal O 
Published: October 2021

Abstract
The subject of the article is the thermodynamic properties (tdp) of mixtures of Ar-Al, Ar-Cu and Ar-Fe in thermodynamic equilibrium state. In current published works the metals in the mixture are assumed to be in the gaseous state. In the present work, the metals are at a temperature of 0.3 kK crystalline substances which with increasing temperature change to liquid and gaseous substances. The proportion of metal in the mixture is in the interval from 0 to 100 mass%. The calculation results are presented in the figures and in detailed tables in the TDPtables.txt in the Supplementary material. The physical model of the calculation of tdp is a simplification of reality. The results of tdp calculation are affected not only by this simplification but also by the inaccuracy of input data. Attention is devoted to these simplifications and inaccuracies. The discontinuities of thermodynamic properties caused by phase transitions are analysed.
An approach for numerical simulating and processing of measured electrical signals from board sensors installed on wheeled electro-mechanical platforms
Authors: Mamalis A.G. , Nevliudov I. , Romashov Yu. 
Published: October 2021

Abstract
The generalized approaches of mathematical modelling for
numerical simulating and processing of measured electrical signals
from board sensors installed on wheeled electro-mech­an­ical platforms
are developed in this research. The mathematical backgrounds of the
developed approaches are elaborated on the basis of especially
formulated initial-value problems need to be solved numerically or
the identification procedure need to be applied. It is shown that
using the Lagrange's formalism and the electro-mechanical analogies
for constructing the improved coupled mathematical models both the
mechanics and electrics and electronics of the wheeled platforms and
the installed board sensors and the measuring electronic transducers
allows having the more information if processing of the measured
signals will be on the basis of such improved mathematical
models. It is considered the particular example of using the
proposed approaches dealt with simulating and processing the
measured electric signals from the board accelerometer installed on
the four wheeled electro-mechanic platform. Due to this example it
was shown that using of the improved mathematical models allows the
significantly wider possibilities of accelerometer measuring, so
that the different parameters can be estimated by means processing
the direct accelerometer measures using the corresponded
mathematical models. It was shown that, the most difficulties of
identification problems for processing the measured signals from the
board sensors installed on the wheeled platforms are due to inherent
them the mathematical incorrectness according to Hadamard. The
effectiveness of using the filtering of the results of processing
the measured signals is shown for the considered particular example
of the identification problem also.
Sensitivity analysis towards trace-uranium detection with γ-γ coincidence NAA
Authors: Tsang R.H.M. , Nusair O. , Piepke A. 
Published: October 2021

Abstract
We present an improved approach for detection of trace
amounts of 238U by means of neutron activation analysis (NAA).
The analysis enhancement is obtained by utilizing γ-γ
coincidence counting. An empirical method for evaluating the
sensitivity gain in the presence of a large source-related
background is presented. A comparison of detection limits is made
between two counting schemes; namely, counting single gammas using
one HPGe detector versus counting coincident gammas using two HPGe
detectors placed face-to-face. A data-validated radiation transport
model, created in GEANT4 for a single HPGe detector, is extended to
handle the two-detector setup. In this counting scheme, a
238U-detection sensitivity enhancement of about a factor of 8
is predicted for a sample of Saint-Gobain G3 Sapphire when compared
to the simpler singles counting approach.
The world’s largest heliothermal lake newly formed in the Aral Sea basin
Authors: Izhitskiy Alexander S , Kirillin Georgiy B , Goncharenko Igor V , Kurbaniyazov Abilgazy K , Zavialov Peter O 
Published: October 2021

Abstract
The Aral Sea desiccation is one of the worst aquatic ecological disasters of the last century, important for understanding the worldwide trends to degradation of arid lakes under water use and climate change. Formerly the fourth largest lake worldwide, the Aral Sea has lost ∼90% of its water since the early 1960s due to irrigation in its drainage basin. Our survey on the seasonal thermal and mixing regime in Chernyshev—a semi-isolated hypersaline part of the Aral Sea—revealed a newly formed two-layered structure with strong gradients of salinity and water transparency at mid-depths. As a result, the Chernyshev effectively accumulates solar energy, creating a temperature maximum at the water depth of ∼5 m with temperatures up to 37 °C. Herewith, this part of the Aral Sea has evolved to an unprecedently large (∼80 km2) heliothermal lake akin to artificial solar ponds used for ‘green energy’ production. The newly formed heliothermal lake, with transparent and freshened layer on top of the hypersaline and nutrient-rich deep water, acts as a solar energy trap and facilitates intense biogeochemical processes. The latter reveal themselves in practically 100% opacity of the deep layer to the solar light, permanent deep anoxia, and growing methane concentrations. The recent emergence of the Chernyshev as a heliothermal lake provides an opportunity for tracing the biogeochemical and ecological response of aquatic ecosystems to suddenly changed environmental conditions.
Multi-material digital light processing bioprinting of hydrogel-based microfluidic chips
Authors: Bhusal Anant , Dogan Elvan , Nguyen Hai-Anh , Labutina Olga , Nieto Daniel , Khademhosseini Ali , Miri Amir K 
Published: October 2021

Abstract
Recent advancements in digital-light-processing (DLP)-based bioprinting and hydrogel engineering have enabled novel developments in organs-on-chips. In this work, we designed and developed a multi-material, DLP-based bioprinter for rapid, one-step prototyping of hydrogel-based microfluidic chips. A composite hydrogel bioink based on poly-ethylene-glycol-diacrylate (PEGDA) and gelatin methacryloyl (GelMA) was optimized through varying the bioprinting parameters such as light exposure time, bioink composition, and layer thickness. We showed a wide range of mechanical properties of the microfluidic chips for various ratios of PEGDA:GelMA. Microfluidic features of hydrogel-based chips were then tested using dynamic flow experiments. Human-derived tumor cells were encapsulated in 3D bioprinted structures to demonstrate their bioactivity and cell-friendly environment. Cell seeding experiments then validated the efficacy of the selected bioinks for vascularized micro-tissues. Our biofabrication approach offers a useful tool for the rapid integration of micro-tissue models into organs-on-chips and high-throughput drug screening platforms.
Cardinalities of prime spectra of precompletions
Authors: Barrett Erica , Graf Emil , Loepp S. , Strong Kimball , Zhang Sharon 
Published: October 2021

Given a complete local (Noetherian) ring

T
T

, we find necessary and sufficient conditions on

T
T

such that there exists a local domain

A
A

with

|

A

|

>

|

T

|

|A| > |T|

and

A
^

=
T

\widehat {A} = T

, where

A
^

\widehat {A}

denotes the completion of

A
A

with respect to its maximal ideal. We then find necessary and sufficient conditions on

T
T

such that there exists a domain

A
A

with

A
^

=
T

\widehat {A} = T

and

|

S
p
e
c

(
A
)

|

>

|

S
p
e
c

(
T
)

|

|\mathrm {Spec}(A)| > |\mathrm {Spec}(T)|

. Finally, we use “partial completions” to create local rings

A
A

with

A
^

=
T

\widehat {A} = T

such that

S
p
e
c

(
A
)

\mathrm {Spec}(A)

has varying cardinality in different varieties.
Impact of Reverse Causation on Estimates of Cancer Risk Associated With Radiation Exposure From Computerized Tomography: A Simulation Study Modeled on Brain Cancer
Authors: Little Mark P , Patel Ankur , Lee Choonsik , Hauptmann Michael , Berrington de Gonzalez Amy , Albert Paul 
Published: October 2021

Abstract
Use of computed tomography (CT) scanning has increased substantially since its introduction in the 1990s. Several authors have reported increased risk of leukemia and brain tumors associated with radiation exposure from CT scans. However, reverse causation is a concern, particularly for brain cancer; in other words, the CT scan may have been taken because of preexisting cancer and therefore not have been a cause. We assessed the possibility of reverse causation via a simulation study focused on brain tumors, using a simplified version of the data structure for recent CT studies. Five-year–lagged and unlagged analyses implied an observed excess risk per scan up to 70% lower than the true excess risk per scan, particularly when more than 10% of persons with latent cancer had increased numbers of scans or the extra scanning rate after development of latent cancer was greater than 2 scans/year; less extreme values of these parameters imply little risk attenuation. Without a lag and when more than 20% of persons with latent cancer had increased scans—an arguably implausible scenario—the excess risk per scan was increased over the true excess risk per scan by up to 35%–40%. This study suggests that with a realistic lag, reverse causation results in downwardly biased risk, a result of induced classical measurement error, and is therefore unlikely to produce a spurious positive association between cancer and radiation dose from CT scans.
Trajectories of Prescription Opioid Utilization During Pregnancy Among Prepregnancy Chronic Users and Risk of Neonatal Opioid Withdrawal Syndrome
Authors: Straub Loreen , Huybrechts Krista F , Hernández-Díaz Sonia , Zhu Yanmin , Vine Seanna , Desai Rishi J , Gray Kathryn J , Bateman Brian T 
Published: October 2021

Abstract
Little is known about the impact of dose, duration, and timing of prenatal prescription opioid exposure on the risk of neonatal opioid withdrawal syndrome (NOWS). Using a cohort of 18,869 prepregnancy chronic opioid users nested within the 2000–2014 Medicaid Analytic eXtract, we assessed average opioid dosage within biweekly gestational age intervals, created group-based trajectory models, and evaluated the association between trajectory groups and NOWS risk. Women were grouped into 6 distinct opioid use trajectories which, based on observed patterns, were categorized as 1) continuous very low-dose use, 2) continuous low-dose use, 3) initial moderate-dose use with a gradual decrease to very low-dose/no use, 4) initial high-dose use with a gradual decrease to very low-dose use, 5) continuous moderate-dose use, and 6) continuous high-dose use. Absolute risk of NOWS per 1,000 infants was 7.7 for group 1 (reference group), 28.8 for group 2 (relative risk (RR) = 3.7, 95% confidence interval (CI): 2.8, 5.0), 16.5 for group 3 (RR = 2.1, 95% CI: 1.5, 3.1), 64.9 for group 4 (RR = 8.4, 95% CI: 5.6, 12.6), 77.3 for group 5 (RR = 10.0, 95% CI: 7.5, 13.5), and 172.4 for group 6 (RR = 22.4, 95% CI: 16.1, 31.2). Trajectory models—which capture information on dose, duration, and timing of exposure—are useful for gaining insight into clinically relevant groupings to evaluate the risk of prenatal opioid exposure.
Growth Rate in Childhood and Adolescence and the Risk of Breast and Prostate Cancer: A Population-Based Study
Authors: Haraldsdottir Alfheidur , Steingrimsdottir Laufey , Maskarinec Gertraud , Adami Hans-Olov , Aspelund Thor , Valdimarsdottir Unnur A , Bjarnason Ragnar , Thorsdottir Inga , Halldorsson Thorhallur I , Gunnarsdottir Ingibjorg , Tryggvadottir Laufey , Gudnason Vilmundur , Birgisdottir Bryndis E , Torfadottir Johanna E 
Published: October 2021

Abstract
Growth rate is regulated by hormonal pathways that might affect early cancer development. We explored the association between rate of growth in height from ages 8 to 13 years (childhood) and from age 13 to attainment of adult height (adolescence), as measured at study entry, and the risk of breast or prostate cancer. Participants were 2,037 Icelanders born during 1915–1935, who took part in the Reykjavik Study, established in 1967. Height measurements were obtained from school records and at study entry. We used multivariable Cox regression models to calculate hazard ratios with 95% confidence intervals of breast and prostate cancer by rates of growth in tertiles. During a mean follow-up of 66 years (women) and 64 years (men), 117 women were diagnosed with breast cancer and 118 men with prostate cancer (45 with advanced disease). Women in the highest growth-rate tertile in adolescence had a higher risk of breast cancer (hazard ratio = 2.4, 95% confidence interval: 1.3, 4.3) compared with women in the lowest tertile. A suggestive inverse association was observed for highest adolescent growth rate in men and advanced prostate cancer: hazard ratio = 0.4, 95% confidence interval: 0.2, 1.0. Rapid growth, particularly in adolescence may affect cancer risk later in life.
PATO: Pangenome Analysis Toolkit
Authors: Fernández-de-Bobadilla Miguel D , Talavera-Rodríguez Alba , Chacón Lucía , Baquero Fernando , Coque Teresa M , Lanza Val F 
Published: October 2021

Abstract

Motivation
We present the Pangenome Analysis Toolkit (PATO) designed to simultaneously analyze thousands of genomes using a desktop computer. The tool performs common tasks of pangenome analysis such as core-genome definition and accessory genome properties and includes new features that help characterize population structure, annotate pathogenic features and create gene sharedness networks. PATO has been developed in R to integrate with the large set of tools available for genetic, phylogenetic and statistical analysis in this environment.

Results
PATO can perform the most demanding bioinformatic analyses in minutes with an accuracy comparable to state-of-the-art software but 20–30× times faster. PATO also integrates all the necessary functions for the complete analysis of the most common objectives in microbiology studies. Finally, PATO includes the necessary tools for visualizing the results and can be integrated with other analytical packages available in R.

Availabilityand implementation
The source code for PATO is freely available at https://github.com/irycisBioinfo/PATO under the GPLv3 license.

Supplementary information
Supplementary data are available at Bioinformatics online.