bluuebunny/crossref_metadata_2025 huggingface dataset:
Phase-transforming metamaterial with magnetic interactions
Authors: Liang Xudong , Fu Hongbo , Crosby Alfred J.
Published: January 2022

Significance

Material phase transitions offer promise for driving motion and managing high-rate energy transfer events; however, engineering conventional phase transitions at a molecular or atomic level is challenging. We overcome this challenge by coupling multiple interacting fields within a metamaterial framework. Specifically, we embed magnetic domains, with nonlinear, orientationally dependent force interactions, within elastic structures to control reversible phase transitions and program high–strain-rate deformation. The resulting high-rate energy transformations are used to enhance elastic recoil, which could be used to drive high-power motion and to quickly dampen impact loading events. The developed Landau free energy–based model for this material system broadens the impact of this advance, setting the stage for metamaterials with wide-ranging compositions, interacting fields, and engineered properties.
A multidimensional approach to identifying the physical qualities of male English regional academy rugby union players; considerations of position, chronological age, relative age and maturation
Authors: Owen Cameron , Till Kevin , Phibbs Padraic , Read Dale J. , Weakley Jonathon , Atkinson Mark , Cross Matt , Kemp Simon , Sawczuk Thomas , Stokes Keith , Williams Sean , Jones Ben
Published: January 2022

Interpreting the physical qualities of youth athletes is complex due to the effects of growth, maturation and development. This study aimed to evaluate the effect of position, chronological age, relative age and maturation on the physical qualities of elite male academy rugby union players. 1,424 participants (n = 2,381 observations) from nine Rugby Football Union regional academies prospectively completed a physical testing battery at three time points, across three playing seasons. Anthropometrics, body composition, muscular power, muscular strength, speed, aerobic capacity and running momentum were assessed. Positional differences were identified for all physical qualities. The largest effect sizes were observed for the associations between chronological age (d = 0.65–0.73) and maturation (d = −0.77 to −0.69) and body mass related variables (i.e. body mass and running momentum). Relative strength, maximum velocity and aerobic capacity were the only models to include two fixed effects with all other models including at least three fixed effects (i.e. position and a combination of chronological age, relative age and maturation). These findings suggest a multidimensional approach considering position, chronological age, relative age and maturation is required to effectively assess the physical qualities of male age grade rugby union players. Therefore practitioners should use regression equations rather than traditional descriptive statistic tables to provide individualised normative comparisons thus enhancing the application of testing results for talent identification and player development.

Highlights

Practitioners should record and incorporate position, chronological age, relative age and maturation into the physical evaluation of elite academy rugby union players.

The regression equations provided within this study offer highly generalisable comparative values that are specific to a players chronological and biological development.

Through the use of enhanced player evaluation practitioners will be able to make more informed decisions surrounding talent identification and athlete development.
Direct demonstration of complete combustion of gas-suspended powder metal fuel using bomb calorimetry
Authors: Tran Quan , Altman Igor , Dube Pascal , Malkoun Mark , Sadangi R , Koch Robert , Pantoya Michelle L
Published: January 2022

Off-the-shelf calorimeters are typically used for hydrocarbon-based fuels and not designed for simulating metal powder oxidation in gaseous environments. We have developed a method allowing a typical bomb calorimeter to accurately measure heat released during combustion and achieve nearly 100% of the reference heat of combustion from powder fuels such as aluminum. The modification uses a combustible organic dispersant to suspend the fuel particles and promote more complete combustion. The dispersant is a highly porous organic starch-based material (i.e. packing peanut) and allows the powder to burn as discrete particles thereby simulating dust-type combustion environments. The demonstrated closeness of measured Al heat of combustion to its reference value is evidence of complete metal combustion achieved in our experiment. Beyond calorific output under conditions simulating real reactive systems, we demonstrate that the calorimeter also allows characterization of the temporal heat release from the reacting material and this data can be extracted from the instrument. The rate of heat release is an important additional parameter characterizing the combustion process. The experimental approach described will impact future measurements of heat released during combustion from solid fuel powders and enable scientists to quantify the energetic performance of metal fuel more accurately as well as the transient thermal behavior from combusting metal powders.
Imaging the electrostatic landscape of unstrained self-assemble GaAs quantum dots
Authors: Martin Lanzoni Evandro , Covre da Silva Saimon F , Knopper Matthijn Floris , Garcia Ailton J , Costa Carlos Alberto Rodrigues , Deneke Christoph
Published: January 2022

Unstrained GaAs quantum dots are promising candidates for quantum information devices due to their optical properties, but their electronic properties have remained relatively unexplored until now. In this work, we systematically investigate the electronic structure and natural charging of GaAs quantum dots at room temperature using Kelvin probe force microscopy (KPFM). We observe a clear electrical signal from these structures demonstrating a lower surface potential in the middle of the dot. We ascribe this to charge accumulation and confinement inside these structures. Our systematical investigation reveals that the change in surface potential is larger for a nominal dot filling of 2 nm and then starts to decrease for thicker GaAs layers. Using k · p calculation, we show that the confinement comes from the band bending due to the surface Fermi level pinning. We find a correlation between the calculated charge density and the KPFM signal indicating that k · p calculations could be used to estimate the KPFM signal for a given structure. Our results suggest that these self-assembled structures could be used to study physical phenomena connected to charged quantum dots like Coulomb blockade or Kondo effect.
Au-on-Ag nanostructure for in-situ SERS monitoring of catalytic reactions
Authors: He Shuyue , Wu Di , Chen Siwei , Liu Kai , Yang Eui-Hyeok , Tian Fei , Du Henry
Published: January 2022

Dual-functionality Au-on-Ag nanostructures (AOA) were fabricated on a silicon substrate by first immobilizing citrate-reduced Ag nanoparticles (Ag NPs, ∼43 nm in diameter), followed by depositing ∼7 nm Au nanofilms (Au NFs) via thermal evaporation. Au NFs were introduced for their catalytic activity in concave-convex nano-configuration. Ag NPs underneath were used for their significant enhancement factor (EF) in surface-enhanced Raman scattering (SERS)-based measurements of analytes of interest. Rhodamine 6G (R6G) was utilized as the Raman-probe to evaluate the SERS sensitivity of AOA. The SERS EF of AOA is ∼37 times than that of Au NPs. Using reduction of 4-nitrothiophenol (4-NTP) by sodium borohydride (NaBH4) as a model reaction, we demonstrated the robust catalytic activity of AOA as well as its capacity to continuously monitor via SERS the disappearance of reactant 4-NTP, emergence and disappearance of intermediate 4,4′-DMAB, and the appearance of product 4-ATP throughout the reduction process in real-time and in situ.
3D-printed bio-inspired zero Poisson’s ratio graded metamaterials with high energy absorption performance
Authors: Hamzehei Ramin , Zolfagharian Ali , Dariushi Soheil , Bodaghi Mahdi
Published: January 2022

This study aims at introducing a number of two-dimensional (2D) re-entrant based zero Poisson’s ratio (ZPR) graded metamaterials for energy absorption applications. The metamaterials’ designs are inspired by the 2D image of a DNA molecule. This inspiration indicates how a re-entrant unit cell must be patterned along with the two orthogonal directions to obtain a ZPR behavior. Also, how much metamaterials’ energy absorption capacity can be enhanced by taking slots and horizontal beams into account with the inspiration of the DNA molecule’s base pairs. The ZPR metamaterials comprise multi-stiffness unit cells, so-called soft and stiff re-entrant unit cells. The variability in unit cells’ stiffness is caused by the specific design of the unit cells. A finite element analysis (FEA) is employed to simulate the deformation patterns of the ZPRs. Following that, meta-structures are fabricated with 3D printing of TPU as hyperelastic materials to validate the FEA results. A good correlation is observed between FEA and experimental results. The experimental and numerical results show that due to the presence of multi-stiffness re-entrant unit cells, the deformation mechanisms and the unit cells’ densifications are adjustable under quasi-static compression. Also, the structure designed based on the DNA molecule’s base pairs, so-called structure F‴, exhibits the highest energy absorption capacity. Apart from the diversity in metamaterial unit cells’ designs, the effect of multi-thickness cell walls is also evaluated. The results show that the diversity in cell wall thicknesses leads to boosting the energy absorption capacity. In this regard, the energy absorption capacity of structure ‘E’ enhances by up to 33% than that of its counterpart with constant cell wall thicknesses. Finally, a comparison in terms of energy absorption capacity and stability between the newly designed ZPRs, traditional ZPRs, and auxetic metamaterial is performed, approving the superiority of the newly designed ZPR metamaterials over both traditional ZPRs and auxetic metamaterials.
Gravitational waves × HI intensity mapping: cosmological and astrophysical applications
Authors: Scelfo Giulio , Spinelli Marta , Raccanelli Alvise , Boco Lumen , Lapi Andrea , Viel Matteo
Published: January 2022

Two of the most rapidly growing observables in cosmology and astrophysics are gravitational waves (GW) and the neutral hydrogen (HI) distribution.
In this work, we investigate the cross-correlation between resolved gravitational wave detections and HI signal from intensity mapping (IM) experiments.
By using a tomographic approach with angular power spectra, including all projection effects, we explore possible applications of the combination of the Einstein Telescope and the SKAO intensity mapping surveys.
We focus on three main topics:
(i) statistical inference of the observed redshift distribution of GWs;
(ii) constraints on dynamical dark energy models as an example of cosmological studies;
(iii) determination of the nature of the progenitors of merging binary black holes, distinguishing between primordial and astrophysical origin.
Our results show that:
(i) the GW redshift distribution can be calibrated with good accuracy at low redshifts, without any assumptions on cosmology or astrophysics, potentially providing a way to probe astrophysical and cosmological models;
(ii) the constrains on the dynamical dark energy parameters are competitive with IM-only experiments, in a complementary way and potentially with less systematics;
(iii) it will be possible to detect a relatively small abundance of primordial black holes within the gravitational waves from resolved mergers.
Our results extend towards GW × IM the promising field of multi-tracing cosmology and astrophysics, which has the major advantage of allowing scientific investigations in ways that would not be possible by looking at single observables separately.
Inflation and dark matter after spontaneous Planck scale generation by hidden chiral symmetry breaking
Authors: Aoki Mayumi , Kubo Jisuke , Yang Jinbo
Published: January 2022

Dynamical chiral symmetry breaking in a QCD-like hidden
sector is used to generate the Planck mass and the electroweak scale
including the heavy right-handed neutrino mass. A real scalar field
transmits the energy scale of the hidden sector to the visible
sectors, playing besides a role of inflaton in the early Universe
while realizing a Higgs-inflation-like model. Our dark matter
candidates are hidden pions that raise due to dynamical chiral
symmetry breaking. They are produced from the decay of inflaton.
Unfortunately, it will be impossible to directly detect them,
because they are super heavy (109 ∼ 12 GeV), and moreover
the interaction with the visible sector is extremely suppressed.
Simultaneous control of natural and extra degrees of freedom by isometric force and electromyographic activity in the muscle-to-force null space
Authors: Gurgone Sergio , Borzelli Daniele , de Pasquale Paolo , Berger Denise Jennifer , Lisini Baldi Tommaso , D’Aurizio Nicole , Prattichizzo Domenico , d’Avella Andrea
Published: January 2022

Objective. Muscle activation patterns in the muscle-to-force null space, i.e. patterns that do not generate task-relevant forces, may provide an opportunity for motor augmentation by allowing to control additional end-effectors simultaneously to natural limbs. Here we tested the feasibility of muscular null space control for augmentation by assessing simultaneous control of natural and extra degrees of freedom. Approach. We instructed eight participants to control translation and rotation of a virtual 3D end-effector by simultaneous generation of isometric force at the hand and null space activity extracted in real-time from the electromyographic signals recorded from 15 shoulder and arm muscles. First, we identified the null space components that each participant could control more naturally by voluntary co-contraction. Then, participants performed several blocks of a reaching and holding task. They displaced an ellipsoidal cursor to reach one of nine targets by generating force, and simultaneously rotated the cursor to match the target orientation by activating null space components. We developed an information-theoretic metric, an index of difficulty defined as the sum of a spatial and a temporal term, to assess individual null space control ability for both reaching and holding. Main results. On average, participants could reach the targets in most trials already in the first block (72%) and they improved with practice (maximum 93%) but holding performance remained lower (maximum 43%). As there was a high inter-individual variability in performance, we performed a simulation with different spatial and temporal task conditions to estimate those for which each individual participants would have performed best. Significance. Muscular null space control is feasible and may be used to control additional virtual or robotics end-effectors. However, decoding of motor commands must be optimized according to individual null space control ability.
Prototype characterization of a charge-integration pixel detector readout chip with in-pixel A/D conversion
Authors: Li M. , Wei W. , Jiang X. , Cui S. , Zhang J. , Lu B. , Liu Z.
Published: January 2022

HYLITE (High dYmamic range free electron Laser Imaging deTEctor) is a hybrid pixel detector readout chip, which is designed for advanced light sources such as X-ray Free Electron Laser (XFEL) and diffraction-limited storage rings. It is a charge-integration readout chip which has three gains for different dynamic ranges and automatic gain-switching function. The full dynamic range covered by HYLITE is 1 ∼ 104 photons with an energy of 12 keV for each pixel in every shot. In-pixel ADC is designed to achieve front-end digitization and a 10 kHz continuous frame rate.

HYLITE0.1 is the first prototype chip for functional verification that was produced in CMOS 0.13 μm technology. It consists of a pixel array with 6 × 12 pixels and a periphery with full standalone operation features. The size of each pixel is 200 μm × 200 μm. Three design variations of pixels with different integrating capacitance and structures were designed to optimize between area and performance. A 10-bit Wilkinson ADC is integrated in each pixel to digitize the outputs of the pre-amplifier. Therefore, analog signal transmission of long distance is avoided and a frame rate of 10 kHz can be achieved. In this paper, we present the design of HYLITE0.1 and the test results of this prototype chip.
Design and optimization of a breast-dedicated SPECT scanner with multi-lofthole collimation
Authors: Saed M. , Sadremomtaz A. , Mahani H.
Published: January 2022

Background: the need for simultaneous
high-sensitivity and high-resolution breast SPECT imaging mandates
to design and optimize dedicated scanners. Therefore, this work aims
to design and optimize a novel breast-dedicated SPECT system with
multi-lofthole collimator.

Materials and Methods: in this research, a novel
breast-dedicated scanner is designed and then optimized. The scanner
is equipped with a single full-ring multi-lofthole collimation long
with modular NaI(Tl) detectors. The step-and-shoot data acquisition
was considered with two steps. Then, an analytic optimization was
conducted to balance the existing sensitivity-resolution
tradeoff. To do so, several scanner geometries were
investigated. The optimal configuration maximized the system
sensitivity at a given system resolution. Furthermore, the scanner
was also modeled within the GATE simulator. Then, detector energy
resolution, septal penetration and scattering, and system
sensitivity were calculated. Analytic findings were also compared
with the simulated ones.

Results: the results showed that high sensitivity of about
2 cps/kBq can be obtained for a diameter of lofthole 3.05 mm with
a 75° opening angle. Results of GATE simulations showed
clinically acceptable performance of the system offering 9% energy
resolution for a point source. The septal penetration and scattering
were approximately 0.5% and 0.2%, respectively, for cylindrical
water phantom and tungsten as collimator material.

Conclusion: the designed SPECT scanner provides promising
results in terms of sensitivity and spatial resolution and therefore
outperforms the traditional multi-pinhole collimation by a much
higher sensitivity at a given system resolution.
Lack of vegetation exacerbates exposure to dangerous heat in dense settlements in a tropical African city
Authors: Van de Walle J , Brousse O , Arnalsteen L , Brimicombe C , Byarugaba D , Demuzere M , Jjemba E , Lwasa S , Misiani H , Nsangi G , Soetewey F , Sseviiri H , Thiery W , Vanhaeren R , Zaitchik B F , van Lipzig N P M
Published: January 2022

Both climate change and rapid urbanization accelerate exposure to heat in the city of Kampala, Uganda. From a network of low-cost temperature and humidity sensors, operational in 2018–2019, we derive the daily mean, minimum and maximum Humidex in order to quantify and explain intra-urban heat stress variation. This temperature-humidity index is shown to be heterogeneously distributed over the city, with a daily mean intra-urban Humidex Index deviation of 1.2 ∘C on average. The largest difference between the coolest and the warmest station occurs between 16:00 and 17:00 local time. Averaged over the whole observation period, this daily maximum difference is 6.4 ∘C between the warmest and coolest stations, and reaches 14.5 ∘C on the most extreme day. This heat stress heterogeneity also translates to the occurrence of extreme heat, shown in other parts of the world to put local populations at risk of great discomfort or health danger. One station in a dense settlement reports a daily maximum Humidex Index of

>

40 ∘C in 68% of the observation days, a level which was never reached at the nearby campus of the Makerere University, and only a few times at the city outskirts. Large intra-urban heat stress differences are explained by satellite earth observation products. Normalized Difference Vegetation Index has the highest (75%) power to predict the intra-urban variations in daily mean heat stress, but strong collinearity is found with other variables like impervious surface fraction and population density. Our results have implications for urban planning on the one hand, highlighting the importance of urban greening, and risk management on the other hand, recommending the use of a temperature-humidity index and accounting for large intra-urban heat stress variations and heat-prone districts in urban heat action plans for tropical humid cities.
Risk and reward of the global truffle sector under predicted climate change
Authors: Čejka Tomáš , Isaac Elizabeth L , Oliach Daniel , Martínez-Peña Fernando , Egli Simon , Thomas Paul , Trnka Miroslav , Büntgen Ulf
Published: January 2022

Climate change has been described as the main threat for the cultivation and growth of truffles, but hydroclimate variability and model uncertainty challenge regional projections and adaptation strategies of the emerging sector. Here, we conduct a literature review to define the main Périgord truffle growing regions around the world and use 20 global climate models to assess the impact of future trends and extremes in temperature, precipitation and soil moisture on truffle production rates and price levels in all cultivation regions in the Americas, Europe, South Africa, and Australasia. Climate model simulations project 2.3 million km2 of suitable land for truffle growth will experience 50% faster aridification than the rests of the global land surface, with significantly more heat waves between 2070 and 2099 CE. Overall, truffle production rates will decrease by ∼15%, while associated price levels will increase by ∼36%. At the same time, a predicted increase in summer precipitation and less intense warming over Australasia will likely alleviate water scarcity and support higher yields of more affordable truffles. Our findings are relevant for truffle farmers and businesses to adapt their irrigation systems and management strategies to future climate change.
Biofabrication of advanced in vitro 3D models to study ischaemic and doxorubicin-induced myocardial damage
Authors: Sharma Poonam , Liu Chung Ming Clara , Wang Xiaowei , Bienvenu Laura A , Beck Dominik , Figtree Gemma , Boyle Andrew , Gentile Carmine
Published: January 2022

Current preclinical in vitro and in vivo models of cardiac injury typical of myocardial infarction (MI, or heart attack) and drug induced cardiotoxicity mimic only a few aspects of these complex scenarios. This leads to a poor translation of findings from the bench to the bedside. In this study, we biofabricated for the first time advanced in vitro models of MI and doxorubicin (DOX) induced injury by exposing cardiac spheroids (CSs) to pathophysiological changes in oxygen (O2) levels or DOX treatment. Then, contractile function and cell death was analyzed in CSs in control verses I/R and DOX CSs. For a deeper dig into cell death analysis, 3D rendering analyses and mRNA level changes of cardiac damage-related genes were compared in control verses I/R and DOX CSs. Overall, in vitro CSs recapitulated major features typical of the in vivo MI and drug induced cardiac damages, such as adapting intracellular alterations to O2 concentration changes and incubation with cardiotoxic drug, mimicking the contraction frequency and fractional shortening and changes in mRNA expression levels for genes regulating sarcomere structure, calcium transport, cell cycle, cardiac remodelling and signal transduction. Taken together, our study supports the use of I/R and DOX CSs as advanced in vitro models to study MI and DOX-induced cardiac damge by recapitulating their complex in vivo scenario.
Energy-conserving model of hexagonal pattern in Rayleigh-Bénard convection
Authors: Mondal Hiya , Das Alaka
Published: January 2022

We have constructed an energy-conserving 16 mode dynamical system to model hexagonal pattern in Rayleigh-Bénard convection of Boussinesq fluids with symmetric stress-free thermally conducting boundaries. The model shows stable roll pattern at the onset of convection. Hexagon is found to appear in the system via sausage and (or) stationary rhombus patterns. Both up and down hexagons arise periodically or chaotically with roll, sausage and rhombus patterns. Hexagonal pattern exists for all values of the Prandtl number,

1
≤
P
r
≤
5

explored here. However, the pattern is more prominent for small Pr and

k

<

k
c

, where k denotes the wave number. The plot of Nusselt number matches with previous theoretical result. In dissipationless limit, the total energy and the unavailable energy are constants though the kinetic energy, the potential energy and the available energy vary with time. The derived model does not diverge for large values of Rayleigh number Ra.
CO2 capture by alcohol ammonia based deep eutectic solvents with different water content
Authors: Liu Xiangwei , Ao Qian , Shi Shengyou , Li Shuie
Published: January 2022

The existing CO2 absorption by deep eutectic solvents is limited by the unavoidable water absorption problem during use. In this study, we prepared three deep eutectic solvents with different alcohol aminations and added different water contents to discuss the effect of water content on the absorption of carbon dioxide by deep eutectic solvents. All deep eutectic solvents have a low melting point at room temperature as a liquid and have high thermal stability, where the choline chloride-diethanolamine deep eutectic solvents have a high viscosity. Anhydrous choline chloride-monoethanolamine deep eutectic solvents have the largest CO2 absorption, reaching 0.2715 g g−1, and the absorption of CO2 by anhydrous choline chloride-N-methyldiethanolamine deep eutectic solvents is only 0.0611 g g−1. Water content inhibited the absorption of CO2 in primary amine and secondary amine systems, whereas it enhanced the absorption of CO2 in tertiary amine systems, which was related to the reaction process of deep eutectic solvent and CO2.
Effect of sintering temperature on microstructures and mechanical properties of ZK60 magnesium alloys
Authors: Ma Luosheng , Ma Lili , Jin Peipeng , Feng Xinya , Jia Lei
Published: January 2022

In this study, ZK60 Mg alloys were prepared via hot-press sintering under a constant pressure of 30 MPa as well as Ar atmosphere. The sintering temperature was determined to be in the range of 450 °C–600 °C with an interval of 50 °C. The effect of sintering temperature on the microstructures and mechanical properties of the alloys was investigated. All the four sintered alloys mainly exhibited an α-Mg-phase structure and equiaxed grain microstructure. However, a specific amount of melt, enriched in Zn element, formed when the sintering temperature reached 500 °C. Thus, only the alloy sintered at 450 °C maintained the nominal composition of the alloy powder, and exhibited the favorable yield strength and hardness, which was 135.1 MPa and 57 HV, respectively. The alloys sintered at 550 °C and 600 °C exhibited a reduced yield strength and hardness due to the loss of Zn element.
Estimation of China Fusion Engineering Test Reactor performance and burning fraction in different pellet fueling scenarios by a multi-species radial transport model
Authors: LIN Weisheng , WANG Xiaogang , XU Xueqiao , KONG Defeng , WANG Yumin , CHEN Jiale , WANG Zhanhui , XIAO Chijie
Published: January 2022

Tritium self-sufficiency in future deuterium–tritium fusion reactors is a crucial challenge. As an engineering test reactor, the China Fusion Engineering Test Reactor requires a burning fraction of 3% for the goal to test the accessibility to the future fusion plant. To self-consistently simulate burning plasmas with profile changes in pellet injection scenarios and to estimate the corresponding burning fraction, a one-dimensional multi-species radial transport model is developed in the BOUT++ framework. Several pellet-fueling scenarios are then tested in the model. The results show that the increased fueling depth improves the burning fraction by particle confinement improvement and fusion power increase. Nevertheless, by increasing the depth, the pellet cooling-down may significantly lower the temperature in the core region. Taking the density perturbation into consideration, the reasonable parameters of the fueling scenario in these simulations are estimated as pellet radius

r

p

=
3

mm
,

injection rate

=

4

Hz
,

and pellet injection velocity

=

1000
–
2000

m

s

−
1

without drift or

450

m

s

−
1

with high-field-side drift.
Activation of two dopants, Bi and Er in δ-doped layer in Si crystal
Authors: Murata Koichi , Yagi Shuhei , Kanazawa Takashi , Tsubomatsu Satoshi , Kirkham Christopher , Nittoh Koh-ichi , Bowler David R , Miki Kazushi
Published: January 2022

Conventional doping processes are no longer viable for realizing extreme structures, such as a δ-doped layer with multiple elements, such as the heavy Bi, within the silicon crystal. Here, we demonstrate the formation of (Bi + Er)-δ-doped layer based on surface nanostructures, i.e. Bi nanolines, as the dopant source by molecular beam epitaxy. The concentration of both Er and Bi dopants is controlled by adjusting the amount of deposited Er atoms, the growth temperature during Si capping and surfactant techniques. Subsequent post-annealing processing is essential in this doping technique to obtain activated dopants in the δ-doped layer. Electric transport measurement and photoluminescence study revealed that both Bi and Er dopants were activated after post-annealing at moderate temperature.
hDirect-MAP: projection-free single-cell modeling of response to checkpoint immunotherapy
Authors: Lu Yong , Xue Gang , Zheng Ningbo , Han Kun , Yang Wenzhong , Wang Rui-Sheng , Wu Lingyun , Miller Lance D , Pardee Timothy , Triozzi Pierre L , Lo Hui-Wen , Watabe Kounosuke , Wong Stephen T C , Pasche Boris C , Zhang Wei , Jin Guangxu
Published: January 2022

There is a lack of robust generalizable predictive biomarkers of response to immune checkpoint blockade in multiple types of cancer. We develop hDirect-MAP, an algorithm that maps T cells into a shared high-dimensional (HD) expression space of diverse T cell functional signatures in which cells group by the common T cell phenotypes rather than dimensional reduced features or a distorted view of these features. Using projection-free single-cell modeling, hDirect-MAP first removed a large group of cells that did not contribute to response and then clearly distinguished T cells into response-specific subpopulations that were defined by critical T cell functional markers of strong differential expression patterns. We found that these grouped cells cannot be distinguished by dimensional-reduction algorithms but are blended by diluted expression patterns. Moreover, these identified response-specific T cell subpopulations enabled a generalizable prediction by their HD metrics. Tested using five single-cell RNA-seq or mass cytometry datasets from basal cell carcinoma, squamous cell carcinoma and melanoma, hDirect-MAP demonstrated common response-specific T cell phenotypes that defined a generalizable and accurate predictive biomarker.
From pairwise to multiple spliced alignment
Authors: Jammali Safa , Djossou Abigaïl , Ouédraogo Wend-Yam D D , Nevers Yannis , Chegrane Ibrahim , Ouangraoua Aïda
Published: January 2022

Motivation

Alternative splicing is a ubiquitous process in eukaryotes that allows distinct transcripts to be produced from the same gene. Yet, the study of transcript evolution within a gene family is still in its infancy. One prerequisite for this study is the availability of methods to compare sets of transcripts while accounting for their splicing structure. In this context, we generalize the concept of pairwise spliced alignments (PSpAs) to multiple spliced alignments (MSpAs). MSpAs have several important purposes in addition to empowering the study of the evolution of transcripts. For instance, it is a key to improving the prediction of gene models, which is important to solve the growing problem of genome annotation. Despite its essentialness, a formal definition of the concept and methods to compute MSpAs are still lacking.

Results

We introduce the MSpA problem and the SplicedFamAlignMulti (SFAM) method, to compute the MSpA of a gene family. Like most multiple sequence alignment (MSA) methods that are generally greedy heuristic methods assembling pairwise alignments, SFAM combines all PSpAs of coding DNA sequences and gene sequences of a gene family into an MSpA. It produces a single structure that represents the superstructure and models of the gene family. Using real vertebrate and simulated gene family data, we illustrate the utility of SFAM for computing accurate gene family superstructures, MSAs, inferring splicing orthologous groups and improving gene-model annotations.

Availability and implementation

The supporting data and implementation of SFAM are freely available at https://github.com/UdeS-CoBIUS/SpliceFamAlignMulti.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Cross-species prediction of essential genes in insects
Authors: Marques de Castro Giovanni , Hastenreiter Zandora , Silva Monteiro Thiago Augusto , Martins da Silva Thieres Tayroni , Pereira Lobo Francisco
Published: January 2022

Motivation

Insects possess a vast phenotypic diversity and key ecological roles. Several insect species also have medical, agricultural and veterinary importance as parasites and disease vectors. Therefore, strategies to identify potential essential genes in insects may reduce the resources needed to find molecular players in central processes of insect biology. However, most predictors of essential genes in multicellular eukaryotes using machine learning rely on expensive and laborious experimental data to be used as gene features, such as gene expression profiles or protein–protein interactions, even though some of this information may not be available for the majority of insect species with genomic sequences available.

Results

Here, we present and validate a machine learning strategy to predict essential genes in insects using sequence-based intrinsic attributes (statistical and physicochemical data) together with the predictions of subcellular location and transcriptomic data, if available. We gathered information available in public databases describing essential and non-essential genes for Drosophila melanogaster (fruit fly, Diptera) and Tribolium castaneum (red flour beetle, Coleoptera). We proceeded by computing intrinsic and extrinsic attributes that were used to train statistical models in one species and tested by their capability of predicting essential genes in the other. Even models trained using only intrinsic attributes are capable of predicting genes in the other insect species, including the prediction of lineage-specific essential genes. Furthermore, the inclusion of RNA-Seq data is a major factor to increase classifier performance.

Availability and implementation

The code, data and final models produced in this study are freely available at https://github.com/g1o/GeneEssentiality/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Context Matters: How an Ecological-Belonging Intervention Can Reduce Inequities in STEM
Authors: Hammarlund Sarah P , Scott Cheryl , Binning Kevin R , Cotner Sehoya
Published: January 2022

Doubts about belonging in the classroom are often shouldered disproportionately by students from historically marginalized groups, which can lead to underperformance. Ecological-belonging interventions use a classroom-based activity to instill norms that adversity is normal, temporary, and surmountable. Building on prior studies, we sought to identify the conditions under which such interventions are effective. In a chemistry course (study 1), students from underrepresented ethnic backgrounds underperformed relative to their peers in the absence of the intervention. This performance gap was eliminated by the intervention. In an introductory biology course (study 2), there were no large performance gaps in the absence of the intervention, and the intervention had no effect. Study 2 also explored the role of the instructor that delivers the intervention. The intervention boosted scores in the classrooms of instructors with a fixed (versus growth-oriented) intelligence mindset. Our results suggest that ecological-belonging interventions are more effective in more threatening classroom contexts.
Rel/NF-κB Transcription Factors Emerged at the Onset of Opisthokonts
Authors: Leger Michelle M , Ros-Rocher Núria , Najle Sebastián R , Ruiz-Trillo Iñaki
Published: January 2022

The Rel/NF-κB transcription factor family has myriad roles in immunity, development, and differentiation in animals, and was considered a key innovation for animal multicellularity. Rel homology domain-containing proteins were previously hypothesized to have originated in a last common ancestor of animals and some of their closest unicellular relatives. However, key taxa were missing from previous analyses, necessitating a systematic investigation into the distribution and evolution of these proteins. Here, we address this knowledge gap by surveying taxonomically broad data from eukaryotes, with a special emphasis on lineages closely related to animals. We report an earlier origin for Rel/NF-κB proteins than previously described, in the last common ancestor of animals and fungi, and show that even in the sister group to fungi, these proteins contain elements that in animals are necessary for the subcellular regulation of Rel/NF-κB.
Remarks about the unification types of some locally tabular normal modal logics
Authors: Balbiani Philippe , Gencer ÇiĞdem , Rostamigiv Maryam , Tinchev Tinko
Published: January 2022

It is already known that unifiable formulas in normal modal logic $\textbf {K}+\square ^{2}\bot $ are either finitary or unitary and unifiable formulas in normal modal logic $\textbf {Alt}_{1}+\square ^{2}\bot $ are unitary. In this paper, we prove that for all $d{\geq }3$, unifiable formulas in normal modal logic $\textbf {K}+\square ^{d}\bot $ are either finitary or unitary and unifiable formulas in normal modal logic $\textbf {Alt}_{1}+\square ^{d}\bot $ are unitary.
Do NGO Restrictions Limit Terrorism? Smear Campaigns or Counterterrorism Tools
Authors: Koo Jeong-Woo , Murdie Amanda
Published: January 2022

Do initiatives to limit nongovernmental organization (NGO) activities work to limit terrorist attacks? Despite regime rhetoric, we argue that NGO restrictions and repression can heighten grievances and limit nonviolent options for citizens to express dissent, broadening support for terrorists and increasing terrorist incidents. Using novel data on NGO restrictions, we fail to find evidence that legal restrictions on NGOs reduce the number of terrorist attacks. Once we account for the unobservable factors that influence both the adoption of these initiatives and the terrorist violence via treatment effects regression models, we find much evidence that NGO restrictions instead exacerbate terrorism. Our findings call into question the counterterrorism and security benefits often used by regime leaders to justify restrictions and all-out repression to NGOs.
Caregivers’ Experience of Medication Adherence Barriers during Pediatric Hematopoietic Stem Cell Transplant: A Qualitative Study
Authors: Chardon Marie L , Klages Kimberly L , Joffe Naomi E , Pai Ahna L H
Published: January 2022

Objective

Medications are critical for reducing morbidity and mortality risk in pediatric hematopoietic stem cell transplant (HCT). Nonetheless, medication adherence is suboptimal in this population. Identifying and managing barriers to medication management (i.e., medication barriers) is a key component of supporting medication adherence. However, understanding how medication barriers uniquely impact the pediatric HCT population and which barriers characterize each treatment stage remain unclear. Therefore, this study examined caregiver-perceived medication barriers over the course of pediatric HCT.

Methods

Semi-structured qualitative interviews and demographic questionnaires were completed by 29 caregivers of children (≤12 years) who had received an HCT in the past 24 months and were either still admitted to, or had been discharged from, the hospital.

Results

Grounded methodology revealed 21 qualitative themes grouped into 6 hierarchical categories. Findings reflected barriers to be present across HCT treatment but to differ based on treatment stage with only child medication refusal being a consistent barrier across all stages. Barriers were particularly prevalent after hospital discharge post-HCT when caregivers assumed full responsibility for medication management. In addition, families approaching hospital discharge often lacked insight about these post-discharge barriers such that they did not report anticipating the range of barriers described by caregivers who had already been discharged from the hospital and taken on full responsibility for medication management.

Conclusions

Findings support the benefit of medication barrier assessment across HCT treatment. These results suggest that families may benefit from intervention to address the specific barriers they experience around medication adherence especially during the post-HCT outpatient period.
Dwarfism associated with wandering splenomegaly
Authors: Petroianu Andy , Sabino Kelly Renata
Published: January 2022

Dwarfism associated with splenomegaly during teenage years is known. The purpose of this report was to present the first case of dwarfism associated with wandering splenomegaly. A 14-year-old boy presented a wandering splenomegaly and torsion of the splenic pedicle associated with a retarded growth and sexual underdevelopment characterized by lack of sexual maturity and absence of secondary sexual physical appearance. The patient was submitted to detorsion of the spleen, and splenopexy. After the surgery, the patient grew up, and his sexual characteristics developed to normal. The size of the spleen reduced from the 22 × 16 × 13 cm to 14 × 12 × 10 cm after the surgical procedure. This is the first report of dwarfism associated with wandering splenomegaly, which was successfully treated without partial or total splenectomy. After releasing the venous blood flow, the spleen reduced its dimension and the patient grew up to the expected family size.
Haro 11 – Untying the knots of the nuclear starburst
Authors: Sirressi M , Adamo A , Hayes M , Bik A , Strandänger M , Runnholm A , Oey M S , Östlin G , Menacho V , Smith L J
Published: January 2022

Star formation is a clustered process that regulates the structure and evolution of galaxies. We investigate this process in the dwarf galaxy Haro 11, forming stars in three knots (A, B, and C). The exquisite resolution of HST imaging allows us to resolve the starburst into tens of bright star clusters. We derive masses between 105 and $10^7\, \rm M_{\odot }$ and ages younger than 20 Myr, using photometric modelling. We observe that the clustered star formation has propagated from knot C (the oldest) through knot A (in between) towards knot B (the youngest). We use aperture-matched ultraviolet and optical spectroscopy (HST + MUSE) to independently study the stellar populations of Haro 11 and determine the physical properties of the stellar populations and their feedback in 1-kpc diameter regions. We discuss these results in light of the properties of the ionized gas within the knots. We interpret the broad blue-shifted components of the optical emission lines as outflowing gas (vmax ∼ 400 km/s). The strongest outflow is detected in knot A with a mass rate of $\dot{M}_{\mathrm{ out}}\sim 10\, \rm M_{\odot }/yr$, 10 times higher than the star formation in the same region. Knot B hosts a young and not fully developed outflow, whereas knot C has likely been already evacuated. Because Haro 11 has properties similar to high-redshift unresolved galaxies, our work can additionally aid the understanding of star formation at high redshift, a window that will be opened by upcoming facilities.
A Phase Ib Study of Lucitanib (AL3810) in a Cohort of Patients with Recurrent and Metastatic Nasopharyngeal Carcinoma
Authors: Zhang Yang , Luo Fan , Ma Yu-Xiang , Liu Qian-Wen , Yang Yun-Peng , Fang Wen-Feng , Huang Yan , Zhou Ting , Li Jin , Pan Hong-Ming , Yang Lei , Qin Shu-Kui , Zhao Hong-Yun , Zhang Li
Published: January 2022

Background

Lucitanib is a novel multi-target inhibitor of FGFR1-3, VEGFR 1-3, and PDGFR α/β. Here, we evaluated the safety, tolerability, and preliminary efficacy of lucitanib in recurrent and metastatic nasopharyngeal carcinoma (RM-NPC).

Methods

Patients with pretreated RM-NPC were randomly divided into two treatment arms: continuous or intermittent treatment. The primary endpoint was safety and tolerability. Secondary endpoints were objective response rate (ORR), disease control rate (DCR), and progression-free survival (PFS).

Results

One hundred percent of patients in the continuous arm and 90% of patients in the intermittent arm had at least one treatment-related AE (TRAE). Grade ≥3 related TRAEs occurred in 5 patients in the continuous arm (5/10, 50%). No TRAEs grade >3 occurred in the intermittent arm. The ORR and DCR of the continuous arm was 20% and 90%, and the intermittent arm was 10% and 60%, respectively. All responses were observed by the first evaluation. The duration of response was more than 1 year, with two patients still on treatment with sustained response at more than 3 years.

Conclusion

Lucitanib has promising clinical activity and tolerable safety profile in heavily pretreated patients with NPC. Patients who responded to lucitanib treatment generally achieved a long DoR. Lucitanib is now being evaluated in phase II/III studies.

ClinicalTrials.gov identifier

NCT03260179
SCATTER RADIATION INTENSITIES IN HORIZONTAL AND VERTICAL PLANES ABOUT DIGITAL BREAST TOMOSYNTHESIS SYSTEM
Authors: Varcoe Joshua G , Barnes Peter
Published: January 2022

Digital breast tomosynthesis (DBT) is a main imaging modality for breast imaging. However, shielding calculations for DBT are commonly based on previous technology with softer beam spectra. In addition, shielding calculations often assume some patient attenuation is provided in locations to the posterior of the patient but without quantification of this attenuation. In this work, recent research in DBT shielding is validated by measuring scatter radiation in the vertical plane. It is also extended upon by measuring the scatter radiation in the horizontal plane and the effect of patient attenuation. These measurements are weighted by our local patient compressed breast thickness distribution to provide a simple scattering factor. Air kerma distributions are provided demonstrating the distribution of scatter radiation around the DBT system in the presence of patient body attenuation. The highest air kerma measured in any direction from a 4-view per patient screening tomosynthesis exam based on the local patient workload is 55 μGy at 1 m. This value can be used to conservatively treat the scatter radiation as an isotropic distribution for shielding assessments. This work is consistent with many recent publications, with the notable exception of the forward scattered peak which is smaller than previous studies. Under our locally encountered breast thickness distribution, the increased scatter radiation and consequent increased minimum shielding requirements is small in most cases. With 400 patients per week, the air kerma at 1 m is 22 mGy and, for a fully occupied public area 2 m away, this requires a gypsum plasterboard thickness of 45.6 mm which is 5.3 mm more than previous data suggests. Although the increase is minimal, standard manufacturing thicknesses of shielding material may not be automatically assumed to be sufficient and careful consideration of the scatter radiation is warranted.