bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stripenn detects architectural stripes from chromatin conformation data using computer vision
Authors: Yoon Sora , Chandra Aditi , Vahedi Golnaz 
Published: March 2022

AbstractArchitectural stripes tend to form at genomic regions harboring genes with salient roles in cell identity and function. Therefore, the accurate identification and quantification of these features are essential for understanding lineage-specific gene regulation. Here, we present Stripenn, an algorithm rooted in computer vision to systematically detect and quantitate architectural stripes from chromatin conformation measurements using various technologies. We demonstrate that Stripenn outperforms existing methods and highlight its biological applications in the context of B and T lymphocytes. By comparing stripes across distinct cell types and different species, we find that these chromatin features are highly conserved and form at genes with prominent roles in cell-type-specific processes. In summary, Stripenn is a computational method that borrows concepts from widely used image processing techniques to demarcate and quantify architectural stripes.
PUMILIO proteins promote colorectal cancer growth via suppressing p21
Authors: Gong Yuanyuan , Liu Zukai , Yuan Yihang , Yang Zhenzhen , Zhang Jiawei , Lu Qin , Wang Wei , Fang Chao , Lin Haifan , Liu Sanhong 
Published: March 2022

AbstractPUMILIO (PUM) proteins belong to the highly conserved PUF family post-transcriptional regulators involved in diverse biological processes. However, their function in carcinogenesis remains under-explored. Here, we report that Pum1 and Pum2 display increased expression in human colorectal cancer (CRC). Intestine-specific knockout of Pum1 and Pum2 in mice significantly inhibits the progression of colitis-associated cancer in the AOM/DSS model. Knockout or knockdown of Pum1 and/or Pum2 in human CRC cells result in a significant decrease in the tumorigenicity and delayed G1/S transition. We identify p21/Cdkn1a as a direct target of PUM1. Abrogation of the PUM1 binding site in the p21 mRNA also results in decreased cancer cell growth and delayed G1/S transition. Furthermore, intravenous injection of nanoparticle-encapsulated anti-Pum1 and Pum2 siRNAs reduces colorectal tumor growth in murine orthotopic colon cancer models. These findings reveal the requirement of PUM proteins for CRC progression and their potential as therapeutic targets.
Quantum transport and localization in 1d and 2d tight-binding lattices
Authors: Karamlou Amir H. , Braumüller Jochen , Yanay Yariv , Di Paolo Agustin , Harrington Patrick M. , Kannan Bharath , Kim David , Kjaergaard Morten , Melville Alexander , Muschinske Sarah , Niedzielski Bethany M. , Vepsäläinen Antti , Winik Roni , Yoder Jonilyn L. , Schwartz Mollie , Tahan Charles , Orlando Terry P. , Gustavsson Simon , Oliver William D. 
Published: March 2022

AbstractParticle transport and localization phenomena in condensed-matter systems can be modeled using a tight-binding lattice Hamiltonian. The ideal experimental emulation of such a model utilizes simultaneous, high-fidelity control and readout of each lattice site in a highly coherent quantum system. Here, we experimentally study quantum transport in one-dimensional and two-dimensional tight-binding lattices, emulated by a fully controllable 3 × 3 array of superconducting qubits. We probe the propagation of entanglement throughout the lattice and extract the degree of localization in the Anderson and Wannier-Stark regimes in the presence of site-tunable disorder strengths and gradients. Our results are in quantitative agreement with numerical simulations and match theoretical predictions based on the tight-binding model. The demonstrated level of experimental control and accuracy in extracting the system observables of interest will enable the exploration of larger, interacting lattices where numerical simulations become intractable.
Patients seeking stem cell therapies—a prospective qualitative analysis from a Regenerative Medicine Consult Service
Authors: Arthurs Jennifer R. , Nordan Lisa M. , Hultgren Brian H. , Heckman Michael G. , Martinez Dayana , Master Zubin , Shapiro Shane A. 
Published: March 2022

AbstractDespite patient demand for stem cell therapies (SCTs) for musculoskeletal conditions, there remains limited research on why patients seek SCTs or their sources of information. We employ three questions into a consult intake form: (1) Why are you interested in stem cell treatment for your condition? (2) How did you find out about stem cell treatment for your condition? (3) Have you contacted a stem cell clinic? Responses analyzed, using a qualitative content analysis approach to identify themes reveal many patients seek SCTs to treat pain or delay surgery which may align with some current clinical evidence while other patients express motivations as expected outcomes (e.g., SCTs are better than standard of care or can regenerate tissue) which are not supported by current medical evidence. These differences suggests that patient-centered counseling may help patients by addressing misconceptions and increasing health literacy about expected outcomes of SCTs for treating musculoskeletal conditions.
A robust method for designing multistable systems by embedding bistable subsystems
Authors: Wu Siyuan , Zhou Tianshou , Tian Tianhai 
Published: March 2022

AbstractAlthough multistability is an important dynamic property of a wide range of complex systems, it is still a challenge to develop mathematical models for realising high order multistability using realistic regulatory mechanisms. To address this issue, we propose a robust method to develop multistable mathematical models by embedding bistable models together. Using the GATA1-GATA2-PU.1 module in hematopoiesis as the test system, we first develop a tristable model based on two bistable models without any high cooperative coefficients, and then modify the tristable model based on experimentally determined mechanisms. The modified model successfully realises four stable steady states and accurately reflects a recent experimental observation showing four transcriptional states. In addition, we develop a stochastic model, and stochastic simulations successfully realise the experimental observations in single cells. These results suggest that the proposed method is a general approach to develop mathematical models for realising multistability and heterogeneity in complex systems.
Open access dataset of task-free hemodynamic activity in 4-month-old infants during sleep using fNIRS
Authors: Blanco Borja , Molnar Monika , Carreiras Manuel , Caballero-Gaudes César 
Published: March 2022

AbstractSpontaneous, task-free, hemodynamic activity of the brain provides useful information about its functional organization, as it can describe how different brain regions communicate to each other. Neuroimaging studies measuring the spontaneous activity of the brain are conducted while the participants are not engaged in a particular task or receiving any external stimulation. This approach is particularly useful in developmental populations as brain activity can be measured without the need for infant compliance and the risks of data contamination due to motion artifacts. In this project we sought to i) characterize the intrinsic functional organization of the brain in 4-month-old infants and ii) investigate whether bilingualism, as a specific environmental factor, could lead to adaptations on functional brain network development at this early age. Measures of spontaneous hemodynamic activity were acquired in 4-month-old infants (n = 104) during natural sleep using functional near-infrared spectroscopy (fNIRS). Emphasis was placed on acquiring high-quality data that could lead to reproducible results and serve as a valuable resource for researchers investigating the developing functional connectome.
City- and county-level spatio-temporal energy consumption and efficiency datasets for China from 1997 to 2017
Authors: Chen Jiandong , Liu Jialu , Qi Jie , Gao Ming , Cheng Shulei , Li Ke , Xu Chong 
Published: March 2022

AbstractUnderstanding the evolution of energy consumption and efficiency in China would contribute to assessing the effectiveness of the government’s energy policies and the feasibility of meeting its international commitments. However, sub-national energy consumption and efficiency data have not been published for China, hindering the identification of drivers of differences in energy consumption and efficiency, and implementation of differentiated energy policies between cities and counties. This study estimated the energy consumption of 336 cities and 2,735 counties in China by combining Defense Meteorological Satellite Program/Operational Line-scan System (DMSP/OLS) and Suomi National Polar-Orbiting Partnership/Visible Infrared Imaging Radiometer Suite (NPP/VIIRS) satellite nighttime light data using particle swarm optimization-back propagation (PSO-BP). The energy efficiency of these cities and counties was measured using energy consumption per unit GDP and data envelopment analysis (DEA). These data can facilitate further research on energy consumption and efficiency issues at the city and county levels in China. The developed estimation methods can also be used in other developing countries and regions where official energy statistics are limited.
Pronounced mito-nuclear discordance and various Wolbachia infections in the water ringlet Erebia pronoe have resulted in a complex phylogeographic structure
Authors: Wendt Martin , Kulanek Dustin , Varga Zoltan , Rákosy Laszlo , Schmitt Thomas 
Published: March 2022

AbstractSeveral morphological and mitochondrial lineages of the alpine ringlet butterfly species Erebia pronoe have been described, indicating a complex phylogenetic structure. However, the existing data were insufficient and allow neither a reconstruction of the biogeographic history, nor an assessment of the genetic lineages. Therefore, we analysed mitochondrial (COI, NDI) and nuclear (EF1α, RPS5) gene sequences and compared them with sequences from the sister species Erebia melas. Additionally, we combined this information with morphometric data of the male genitalia and the infection patterns with Wolbachia strains, based on a WSP analysis. We obtained a distinct phylogeographic structure within the E. pronoe-melas complex with eight well-distinguishable geographic groups, but also a remarkable mito-nuclear discordance. The mito-nuclear discordance in E. melas and E. pronoe glottis can be explained by different ages of Wolbachia infections with different Wolbachia strains, associated selective sweeps, and hybridisation inhibition. Additionally, we found indications for incipient speciation of E. pronoe glottis in the Pyrenees and a pronounced range dynamic within and among the other high mountain systems of Europe. Our results emphasize the importance of combined approaches in reconstructing biogeographic patterns and evaluating phylogeographic splits.
Nigratine as dual inhibitor of necroptosis and ferroptosis regulated cell death
Authors: Delehouzé Claire , Comte Arnaud , Leon-Icaza Stephen Adonai , Cougoule Céline , Hauteville Marcelle , Goekjian Peter , Bulinski Jeannette Chloë , Dimanche-Boitrel Marie-Thérèse , Meunier Etienne , Rousselot Morgane , Bach Stéphane 
Published: March 2022

AbstractNigratine (also known as 6E11), a flavanone derivative of a plant natural product, was characterized as highly specific non-ATP competitive inhibitor of RIPK1 kinase, one of the key components of necroptotic cell death signaling. We show here that nigratine inhibited both necroptosis (induced by Tumor Necrosis Factor-α) and ferroptosis (induced by the small molecules glutamate, erastin, RSL3 or cumene hydroperoxide) with EC50 in the µM range. Taken together, our data showed that nigratine is a dual inhibitor of necroptosis and ferroptosis cell death pathways. These findings open potential new therapeutic avenues for treating complex necrosis-related diseases.
Effects of COVID-19 lockdowns on shorebird assemblages in an urban South African sandy beach ecosystem
Authors: Lewis Jemma , Collison Jayden , Pillay Deena 
Published: March 2022

AbstractHuman pressures are pervasive in coastal ecosystems, but their effect magnitudes are masked by methodological limitations. Government lockdowns associated with the global COVID-19 pandemic can address this gap since lockdowns are effectively manipulations of human presence in ecosystems at scales unachievable otherwise. We illustrate this using a study on shorebirds in an urban South African sandy beach ecosystem. Data collected prior to (2019) and during the COVID-19 (2020) pandemic indicated an inverse relationship between shorebird and human numbers, but this was stronger in 2020. In 2020, human exclusion resulted in a six-fold increase in shorebird abundance relative to 2019. Following easing of lockdowns, shorebird abundance declined by 79.6% with a 34.1% increase in human density. Our findings highlight the sensitivity of shorebirds to recreational disturbance, the potential for current methodological approaches to underestimate repercussions of disturbance and the capacity for COVID-19 lockdowns to refine understanding of human-induced stress in ecosystems.
Investigation of the hydrodynamic characteristics of an axial flow pump system under special utilization conditions
Authors: Zhang Xiaowen , Tang Fangping 
Published: March 2022

AbstractIn actual operation, axial flow pump stations are often used for various special purposes to meet changing needs. However, because the hydrodynamic characteristics of axial flow pump systems are still unclear when used for special purposes, there are many risks when pump systems are used for special purposes. To explore the hydrodynamic characteristics of an axial flow pump system under special utilization conditions, a high-precision full-feature test bench for an axial flow pump system is established in this paper. For the first time, an energy characteristics experiment and a pressure fluctuation measurement for a pump are carried out for a large axial flow pump system model under zero head, reverse pump and reverse power generation conditions. Then, ANSYS CFX software is used to solve the continuous equation and Reynolds average Navier–Stokes equation, combined with the SST k–ω turbulence model, and the characteristic curve and internal flow field of the pump system under special conditions are obtained. Finally, the numerical simulation results are compared with the experimental results. The results show that the velocity gradient distribution in the pump is uniform under the near zero head condition (NZHC), and there is no obvious flow collision and reflux phenomenon in the pump. Compared with the designed condition (DC), the peak-to-peak value (PPV) of pressure pulsation at the inlet of the impeller decreased by 67.16%, and the PPV at the outlet of the impeller decreased by 8.14% at H = 0 m. The maximum value of the main frequency amplitude (MFA) in the impeller area appears at the impeller inlet. Under reverse pump conditions (RPC), the phenomenon of unstable flow in the pump system is obvious, and a large range of recirculation zones appears in the nonworking face of the blade. Compared with the DC, the PPV of the impeller inlet at the optimal point of RPC increased by 122.61%, and the impeller outlet PPV increased by 11.37%. The maximum value of MFA in the impeller area appears at the impeller inlet. Under the reverse power generation condition (RPGC), no obvious flow separation was found in the nonworking face of the impeller. Compared to the DC, the PPV of the impeller inlet at the optimal point of the RPGC increased by 65.34%, and the PPV of the impeller outlet increased by 206.40%.
How atoms of polycrystalline Nb20.6Mo21.7Ta15.6W21.1V21.0 refractory high-entropy alloys rearrange during the melting process
Authors: Ju Shin-Pon , Li Chen-Chun , Shih Huai-Ting 
Published: March 2022

AbstractThe melting mechanism of single crystal and polycrystalline Nb20.6Mo21.7Ta15.6W21.1V21.0 refractory high entropy alloys (RHEAs) were investigated by the molecular dynamics (MD) simulation using the second-nearest neighbor modified embedded-atom method (2NN MEAM) potential. For the single crystal RHEA, the density profile displays an abrupt drop from 11.25 to 11.00 g/cm3 at temperatures from 2910 to 2940 K, indicating all atoms begin significant local structural rearrangement. For polycrystalline RHEAs, a two-stage melting process is found. In the first melting stage, the melting of the grain boundary (GB) regions firstly occurs at the pre-melting temperature, which is relatively lower than the corresponding system-melting point. At the pre-melting temperature, most GB atoms have enough kinetic energies to leave their equilibrium positions, and then gradually induce the rearrangement of grain atoms close to GB. In the second melting stage at the melting point, most grain atoms have enough kinetic energies to rearrange, resulting in the chemical short-ranged order changes of all pairs.
The association between prehospital vital signs of children and their critical clinical outcomes at hospitals
Authors: Kurosawa Hiroshi , Shiima Yuko , Miyakoshi Chisato , Nezu Mari , Someya Maki , Yoshida Minae , Nagase Hiroaki , Nozu Kandai , Kosaka Yoshiyuki , Iijima Kazumoto 
Published: March 2022

AbstractVital signs are important for patient assessment, but little is known about interpreting those of children in prehospital settings. We conducted an observational study to investigate the association between prehospital vital signs of children and their clinical outcomes in hospitals. We plotted the data of patients with critical outcomes on published reference ranges, such as those of healthy children to evaluate the clinical relevance. Of the 18,493 children screened, 4477 transported to tertiary hospitals were included in the analysis. The outcomes 12 h after being transported to a tertiary hospital were as follows: deceased, 41; hospitalization with critical deterioration events, 65; hospitalization without critical deterioration events, 1086; returned home, 3090; and unknown, 195. The reference ranges of the heart rates (sensitivity: 57.7%, specificity: 67.5%) and respiratory rates (sensitivity: 54.5%, specificity: 67.7%) of healthy children worked best to detect the critical outcomes. Therefore, the reference ranges of healthy children were concluded to be suitable in prehospital settings; however, excessive reliance on vital signs carried potential risks due to their limited sensitivities and specificities. Future studies are warranted to investigate indicators with higher sensitivities and specificities.
An approach to prepare high-purity TiSi2 for clean utilization of Ti-bearing blast furnace slag
Authors: Li Zhanchao , Lei Yun , Ma Wenhui , Zhang Yakun , Wang Shiding , Ren Yongsheng , Lv Guoqiang 
Published: March 2022

An approach to achieve the dual purposes of the simultaneous preparation of high-purity TiSi2 and the clean utilization of Ti-bearing blast furnace slag.
Images2Poem in different contexts with Dual‐CharRNN
Authors: Yan Jie , Xie Yuxiang , Luan Xidao 
Published: March 2022

AbstractImage to caption has attracted extensive research attention recently. However, image to poetry, especially Chinese classical poetry, is much more challenging. Previous works mainly focus on generating coherent poetry without taking the contexts of poetry into account. In this paper, we propose an Images2Poem with the Dual‐CharRNN model which exploits images to generate Chinese classical poems in different contexts. Specifically, we first extract a few keywords representing elements from the given image based on multi‐label image classification. Then, these keywords are expanded to related ones with the planning‐based model. Finally, we employ Dual‐CharRNN to generate Chinese classical poetry in different contexts. A comprehensive evaluation of human judgements demonstrates that our model achieves promising performance and is effective in enhancing poetry's semantic consistency, readability, and aesthetics. We present an Images2Poem with the Dual‐CharRNN model exploiting images to generate Chinese classical poems in different contexts, which effectively improves the semantic consistency, readability and aesthetics of the generated poetry.
A novel digital‐signal‐processor‐based maximum‐power‐point tracking control design for a vertical‐axis wind‐turbine generation system using neural network compensator
Authors: Tsai Ming‐Fa , Tseng Chung‐Shi , Hung Yu‐Hsiang , Tsai Kuo‐Lung 
Published: March 2022

AbstractThis paper presents a novel maximum‐power‐point tracking algorithm of a vertical‐axis wind‐turbine (VAWT) generation system using neural network compensator on the basis of a digital signal processing chip. First, the mechanical power versus rotation‐speed curve of a 3‐kW VAWT generator was constructed by means of the measurement data in various wind speeds. Because the slope of the wind‐turbine output power is a non‐linear function of the generator output current, air density, wind speed, and the characteristics of the wind‐turbine generator, the analytic solution for the maximum power is difficult to obtain due to its complexity, nonlinearity, and uncertainties of parameters. The innovation of this study is to obtain the maximum power of the wind‐turbine system using a recurrent neural network (RNN) by transferring the maximum‐power‐point tracking problem into a unit‐step‐command regulation problem despite the variation of the wind speed, ambient air density, and the load electrical characteristics. The uncertainties in the system are compensated by the RNN, which is composed of three‐layer networks with three neurons and feedback loops in the hidden layer for capturing the characteristics of the wind‐turbine generator system. Without the necessity of wind speed sensor, it only needs the generator output current and rotation speed as the inputs of the input layer. This structure containing only six neurons totally is simpler than the existing work. The duty cycle of the boost converter is determined by a proportional‐integral controller, the parameters of which are determined via a genetic algorithm by the minimisation of a performance index function with the help of MATLAB simulation tool. From the simulation and experimental results, the validity of the proposed control scheme was verified under various wind speed conditions. The performance efficiency and the tip speed ratio in each case of the experiment is near the optimal values of 0.28 and 4.3, respectively. The output power achieves 2048.4 W at the wind speed of 11 m/s in the steady state.
The influences of substrates' physical properties on enzymatic PET hydrolysis: Implications for PET hydrolase engineering
Authors: Pasula Rupali Reddy , Lim Sierin , Ghadessy Farid J. , Sana Barindra 
Published: March 2022

AbstractPlastic pollution in diverse terrestrial and marine environments is a widely recognised and growing problem. Bio‐recycling and upcycling of plastic waste is a potential solution to plastic pollution, as these processes convert plastic waste into useful materials. Polyethylene terephthalate (PET) is the most abundant plastic waste, and this material can be degraded by a class of recently discovered bacterial esterase enzymes known as PET hydrolases (PETase). Investigations of the enzymatic hydrolysis of diverse PET molecules have clearly revealed that the biodegradability of various PET substrates depends on both their chemical structure and physical properties, including polymer length, crystallinity, glass transition temperature, surface area, and surface charge. This review summarises the known impacts of crystallinity and other physical properties on enzymatic PET hydrolysis.