bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract

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

Abstract
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

Abstract

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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

AbstractThere 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

Abstract

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

Abstract

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

Abstract
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.