bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating the COVID-19 prevalence and mortality using a novel data-driven hybrid model based on ensemble empirical mode decomposition
Authors: Wang Yongbin , Xu Chunjie , Yao Sanqiao , Wang Lei , Zhao Yingzheng , Ren Jingchao , Li Yuchun 
Published: November 2021

AbstractIn this study, we proposed a new data-driven hybrid technique by integrating an ensemble empirical mode decomposition (EEMD), an autoregressive integrated moving average (ARIMA), with a nonlinear autoregressive artificial neural network (NARANN), called the EEMD-ARIMA-NARANN model, to perform time series modeling and forecasting based on the COVID-19 prevalence and mortality data from 28 February 2020 to 27 June 2020 in South Africa and Nigeria. By comparing the accuracy level of forecasting measurements with the basic ARIMA and NARANN models, it was shown that this novel data-driven hybrid model did a better job of capturing the dynamic changing trends of the target data than the others used in this work. Our proposed mixture technique can be deemed as a helpful policy-supportive tool to plan and provide medical supplies effectively. The overall confirmed cases and deaths were estimated to reach around 176,570 [95% uncertainty level (UL) 173,607 to 178,476] and 3454 (95% UL 3384 to 3487), respectively, in South Africa, along with 32,136 (95% UL 31,568 to 32,641) and 788 (95% UL 775 to 804) in Nigeria on 12 July 2020 using this data-driven EEMD-ARIMA-NARANN hybrid technique. The contributions of this study include three aspects. First, the proposed hybrid model can better capture the dynamic dependency characteristics compared with the individual models. Second, this new data-driven hybrid model is constructed in a more reasonable way relative to the traditional mixture model. Third, this proposed model may be generalized to estimate the epidemic patterns of COVID-19 in other regions.
Persistent Plasmodium falciparum infections enhance transmission-reducing immunity development
Authors: Ayanful-Torgby Ruth , Sarpong Esther , Abagna Hamza B. , Donu Dickson , Obboh Evans , Mensah Benedicta A. , Adjah Joshua , Williamson Kim C. , Amoah Linda E. 
Published: November 2021

AbstractSubclinical infections that serve as reservoir populations to drive transmission remain a hurdle to malaria control. Data on infection dynamics in a geographical area is required to strategically design and implement malaria interventions. In a longitudinal cohort, we monitored Plasmodium falciparum infection prevalence and persistence, and anti-parasite immunity to gametocyte and asexual antigens for 10 weeks. Of the 100 participants, only 11 were never infected, whilst 16 had persistent infections detected by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), and one participant had microscopic parasites at all visits. Over 70% of the participants were infected three or more times, and submicroscopic gametocyte prevalence was high, ≥ 48% of the parasite carriers. Naturally induced responses against recombinant Pfs48/45.6C, Pfs230proC, and EBA175RIII–V antigens were not associated with either infection status or gametocyte carriage, but the antigen-specific IgG titers inversely correlated with parasite and gametocyte densities consistent with partial immunity. Longitudinal analysis of gametocyte diversity indicated at least four distinct clones circulated throughout the study period. The high prevalence of children infected with distinct gametocyte clones coupled with marked variation in infection status at the individual level suggests ongoing transmission and should be targeted in malaria control programs.
Prognostic value of galectin-3 and right ventricular function for long-term mortality in heart failure patients treated with cardiac resynchronization therapy
Authors: Zaborska Beata , Pilichowska-Paszkiet Ewa , Makowska Ewa , Sygitowicz Grażyna , Słomski Tomasz , Zaborski Michał , Budaj Andrzej 
Published: November 2021

AbstractRecently, associations between the biomarker galectin-3 and numerous pathological processes involved in heart failure (HF) and right ventricular (RV) function have been observed. We aimed to assess the long-term prognostic ability of galectin-3 and RV function parameters for all-cause mortality in HF patients treated with cardiac resynchronization therapy (CRT). We prospectively studied 63 symptomatic HF patients with a left ventricular (LV) ejection fraction (EF) ≤ 35%. The median serum galectin-3 concentration was 13.4 ng/mL (IQR 11.05, 17.15). A detailed assessment of LV and RV geometry and function was performed with echocardiography. CRT defibrillator implantation was achieved in all patients without major complications. The follow-up lasted 5 years. In the multivariable Cox regression model, independent predictors for all-cause mortality were log baseline galectin-3 and baseline RV function expressed as tricuspid annular plane systolic excursion with HR 2.96 (p = 0.037) and HR 0.88 (p = 0.023), respectively. Analysis of subgroups defined by galectin-3 concentration and CRT response showed that patients with high baseline galectin-3 concentrations and a lack of response to CRT had a significantly lower probability of survival. In our patient cohort, the baseline galectin-3 concentration and RV function were independent predictors of long-term all-cause mortality in HFrEF patients following CRT implantation.
Identifying spatio-temporal seizure propagation patterns in epilepsy using Bayesian inference
Authors: Vattikonda Anirudh N. , Hashemi Meysam , Sip Viktor , Woodman Marmaduke M. , Bartolomei Fabrice , Jirsa Viktor K. 
Published: November 2021

AbstractFocal drug resistant epilepsy is a neurological disorder characterized by seizures caused by abnormal activity originating in one or more regions together called as epileptogenic zone. Treatment for such patients involves surgical resection of affected regions. Epileptogenic zone is typically identified using stereotactic EEG recordings from the electrodes implanted into the patient’s brain. Identifying the epileptogenic zone is a challenging problem due to the spatial sparsity of electrode implantation. We propose a probabilistic hierarchical model of seizure propagation patterns, based on a phenomenological model of seizure dynamics called Epileptor. Using Bayesian inference, the Epileptor model is optimized to build patient specific virtual models that best fit to the log power of intracranial recordings. First, accuracy of the model predictions and identifiability of the model are investigated using synthetic data. Then, model predictions are evaluated against a retrospective patient cohort of 25 patients with varying surgical outcomes. In the patients who are seizure free after surgery, model predictions showed good match with the clinical hypothesis. In patients where surgery failed to achieve seizure freedom model predictions showed a strong mismatch. Our results demonstrate that proposed probabilistic model could be a valuable tool to aid the clinicians in identifying the seizure focus.
Comprehensive functional core microbiome comparison in genetically obese and lean hosts under the same environment
Authors: Martínez-Álvaro Marina , Zubiri-Gaitán Agostina , Hernández Pilar , Greenacre Michael , Ferrer Alberto , Blasco Agustín 
Published: November 2021

AbstractOur study provides an exhaustive comparison of the microbiome core functionalities (captured by 3,936 microbial gene abundances) between hosts with divergent genotypes for intramuscular lipid deposition. After 10 generations of divergent selection for intramuscular fat in rabbits and 4.14 phenotypic standard deviations (SD) of selection response, we applied a combination of compositional and multivariate statistical techniques to identify 122 cecum microbial genes with differential abundances between the lines (ranging from −0.75 to +0.73 SD). This work elucidates that microbial biosynthesis lipopolysaccharides, peptidoglycans, lipoproteins, mucin components, and NADH reductases, amongst others, are influenced by the host genetic determination for lipid accretion in muscle. We also differentiated between host-genetically influenced microbial mechanisms regulating lipid deposition in body or intramuscular reservoirs, with only 28 out of 122 MGs commonly contributing to both. Importantly, the results of this study are of relevant interest for the efficient development of strategies fighting obesity.
KMT2D deficiency disturbs the proliferation and cell cycle activity of dental epithelial cell line (LS8) partially via Wnt signaling
Authors: Pang Liping , Tian Hua , Gao Xuejun , Wang Weiping , Wang Xiaoyan , Zhang Zhichun 
Published: November 2021

Abstract
Lysine methyltransferase 2D (KMT2D), as one of the key histone methyltransferases responsible for histone 3 lysine 4 methylation (H3K4me), has been proved to be the main pathogenic gene of Kabuki syndrome disease. Kabuki patients with KMT2D mutation frequently present various dental abnormalities, including abnormal tooth number and crown morphology. However, the exact function of KMT2D in tooth development remains unclear. In this report, we systematically elucidate the expression pattern of KMT2D in early tooth development and outline the molecular mechanism of KMT2D in dental epithelial cell line. KMT2D and H3K4me mainly expressed in enamel organ and Kmt2d knockdown led to the reduction in cell proliferation activity and cell cycling activity in dental epithelial cell line (LS8). RNA-sequencing (RNA-seq) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis screened out several important pathways affected by Kmt2d knockdown including Wnt signaling. Consistently, Top/Fop assay confirmed the reduction in Wnt signaling activity in Kmt2d knockdown cells. Nuclear translocation of β-catenin was significantly reduced by Kmt2d knockdown, while lithium chloride (LiCl) partially reversed this phenomenon. Moreover, LiCl partially reversed the decrease in cell proliferation activity and G1 arrest, and the down-regulation of Wnt-related genes in Kmt2d knockdown cells. In summary, the present study uncovered a pivotal role of histone methyltransferase KMT2D in dental epithelium proliferation and cell cycle homeostasis partially through regulating Wnt/β-catenin signaling. The findings are important for understanding the role of KMT2D and histone methylation in tooth development.
Stable feature selection based on brain storm optimisation for high‐dimensional data
Authors: Li Mengmeng , Liu Yi , Zheng Qibin , Qin Wei , Ren Xiaoguang 
Published: November 2021

AbstractFeature selection is a widely used data pre‐processing method. However, the research on feature selection stability is very rare. Although there are some related studies that mainly focus on filters rather than wrappers, especially wrappers based on evolutionary algorithms. In this paper, a stable feature selection method called stable brain storm optimisation (SBSO) is proposed. It puts forward a new population initialisation strategy, which treats stable feature selection results as guide information for initialisation and utilises such chaos to initialise population. SBSO also sets up an information archive to store the historical optimal individuals dynamically. A large number of experiments show that SBSO gives excellent classification performance when compared with other methods, and superior feature selection stability when compared with other wrappers.
Unitary coupled-cluster based self-consistent polarization propagator theory: A quadratic unitary coupled-cluster singles and doubles scheme
Authors: Liu Junzi , Cheng Lan 
Published: November 2021

The development of a quadratic unitary coupled-cluster singles and doubles (qUCCSD) based self-consistent polarization propagator method is reported. We present a simple strategy for truncating the commutator expansion of the unitary version of coupled-cluster transformed Hamiltonian H̄. The qUCCSD method for the electronic ground state includes up to double commutators for the amplitude equations and up to cubic commutators for the energy expression. The qUCCSD excited-state eigenvalue equations include up to double commutators for the singles–singles block of H̄, single commutators for the singles–doubles and doubles–singles blocks, and the bare Hamiltonian for the doubles–doubles block. Benchmark qUCCSD calculations of the ground-state properties and excitation energies for representative molecules demonstrate significant improvement of the accuracy and robustness over the previous UCC3 scheme derived using Møller–Plesset perturbation theory.
A digital bandwidth interleaved structure correction method based on itemized correction
Authors: Zhou Yi , Ye Peng , Zhang Qinchuan , Yang Kuojun , Jiang Jun , Huang Wuhuang , Zhao Yu , Zhang Yijiao 
Published: November 2021

To satisfy the input bandwidth and sampling rate requirements of data acquisition systems, digital bandwidth-interleaved analog-to-digital converters (DBI-ADCs) offer a practical parallel structure. However, the existing DBI-ADC correction methods are broadly inadequate in terms of design, testing, and implementation. Moreover, the evaluation and correction of the most significant feature of the DBI-ADC structure—wideband acquisition performance—is also imperfect. This paper proposes an itemized correction method for DBI-ADC structures. The proposed method simplifies the complex correction filter bank design algorithm into multiple simple correction filters and then separates and corrects the various errors of the DBI-ADC system. This dramatically simplifies the design, testing, and implementation process of the system, resulting in a highly convenient method for practical engineering. In addition, this method achieves a good correction effect, with an appropriate balance between the correction effect and the project implementation. Simulation results and experimental results verify the effectiveness of the proposed method.
Probing the theoretical and computational limits of dissipative design
Authors: Chennakesavalu Shriram , Rotskoff Grant M. 
Published: November 2021

Self-assembly, the process by which interacting components form well-defined and often intricate structures, is typically thought of as a spontaneous process arising from equilibrium dynamics. When a system is driven by external nonequilibrium forces, states statistically inaccessible to the equilibrium dynamics can arise, a process sometimes termed direct self-assembly. However, if we fix a given target state and a set of external control variables, it is not well-understood (i) how to design a protocol to drive the system toward the desired state nor (ii) the cost of persistently perturbing the stationary distribution. In this work, we derive a bound that relates the proximity to the chosen target with the dissipation associated with the external drive, showing that high-dimensional external control can guide systems toward target distribution but with an inevitable cost. Remarkably, the bound holds arbitrarily far from equilibrium. Second, we investigate the performance of deep reinforcement learning algorithms and provide evidence for the realizability of complex protocols that stabilize otherwise inaccessible states of matter.
A pathway toward high-throughput quantum Monte Carlo simulations for alloys: A case study of two-dimensional (2D) GaSxSe1−x
Authors: Wines Daniel , Saritas Kayahan , Ataca Can 
Published: November 2021

The study of alloys using computational methods has been a difficult task due to the usually unknown stoichiometry and local atomic ordering of the different structures experimentally. In order to combat this, first-principles methods have been coupled with statistical methods such as the cluster expansion formalism in order to construct the energy hull diagram, which helps to determine if an alloyed structure can exist in nature. Traditionally, density functional theory (DFT) has been used in such workflows. In this paper, we propose to use chemically accurate many-body variational Monte Carlo (VMC) and diffusion Monte Carlo (DMC) methods to construct the energy hull diagram of an alloy system due to the fact that such methods have a weaker dependence on the starting wavefunction and density functional, scale similarly to DFT with the number of electrons, and have had demonstrated success for a variety of materials. To carry out these simulations in a high-throughput manner, we propose a method called Jastrow sharing, which involves recycling the optimized Jastrow parameters between alloys with different stoichiometries. We show that this eliminates the need for extra VMC Jastrow optimization calculations and results in significant computational cost savings (on average 1/4 savings of total computational time). Since it is a novel post-transition metal chalcogenide alloy series that has been synthesized in its few-layer form, we used monolayer GaSxSe1−x as a case study for our workflow. By extensively testing our Jastrow sharing procedure for monolayer GaSxSe1−x and quantifying the cost savings, we demonstrate how a pathway toward chemically accurate high-throughput simulations of alloys can be achieved using many-body VMC and DMC methods.
Plant ecological genomics at the limits of life in the Atacama Desert
Authors: Eshel Gil , Araus Viviana , Undurraga Soledad , Soto Daniela C. , Moraga Carol , Montecinos Alejandro , Moyano Tomás , Maldonado Jonathan , Díaz Francisca P. , Varala Kranthi , Nelson Chase W. , Contreras-López Orlando , Pal-Gabor Henrietta , Kraiser Tatiana , Carrasco-Puga Gabriela , Nilo-Poyanco Ricardo , Zegar Charles M. , Orellana Ariel , Montecino Martín , Maass Alejandro , Allende Miguel L. , DeSalle Robert , Stevenson Dennis W. , González Mauricio , Latorre Claudio , Coruzzi Gloria M. , Gutiérrez Rodrigo A. 
Published: November 2021

SignificanceIn the current changing climate, it is essential to improve crop production and resilience under dry and nutrient-poor conditions. Desert plants have naturally evolved to flourish under such conditions. Therefore, understanding the underlying mechanisms for their adaptation can potentially help to ensure food security. The Atacama Desert, the driest nonpolar place on Earth, offers a unique opportunity to explore plant adaptations to extreme environmental conditions. Here, we reveal how the adaptive strategies common or specific to the major plant lineages in the Atacama include enrichment of plant growth-promoting bacteria near their roots and positive selection of genes that are associated with key beneficial processes for plant survival. These strategies can potentially direct the molecular breeding or engineering of resilient crops.
Growth and thermal maturation of the Toba magma reservoir
Authors: Liu Ping-Ping , Caricchi Luca , Chung Sun-Lin , Li Xian-Hua , Li Qiu-Li , Zhou Mei-Fu , Lai Yu-Ming , Ghani Azman A. , Sihotang Theodora , Sheldrake Tom E. , Simpson Guy 
Published: November 2021

Significance
Understanding the thermal state of magma reservoirs before supereruptions is crucial for interpreting the processes leading to such catastrophic events. Here, we show that the two supereruptions of Toba were preceded and followed by protracted magma influx at relatively constant average volumetric rate over the past 2.2 My. This suggests that increased magma flux is not essential before supereruptions. Instead, long-term thermal maturation of the magma reservoir related to significant magma pulses primes the system for eruption. Importantly, our results indicate that significant variations of monitoring parameters, such as increased surface deformation or degassing, may not occur before supereruptions. Our method can be widely applied to other large silicic magmatic systems to evaluate their potential to feed a supereruption.
Cellular microRNA-127-3p suppresses oncogenic herpesvirus-induced transformation and tumorigenesis via down-regulation of SKP2
Authors: Lee Soo Mi , Kaye Kenneth M. , Slack Frank J. 
Published: November 2021

Significance

Kaposi’s sarcoma (KS) is one of the most common cancers in sub-Saharan Africa. KS–associated herpesvirus (KSHV)-encoded miRNAs are expressed in KS and promote tumorigenesis, but the role of cellular miRNAs in KS tumorigenesis remains largely unexplored. We find that miR-127-3p is one of the most significantly down-regulated host miRNAs in KSHV-infected endothelial cells and KS patient tumors. We demonstrate that restoring miR-127-3p inhibits KSHV-induced transformation and tumorigenesis by directly targeting the oncogene SKP2 in vitro and in vivo. miR-127-3p–directed SKP2 repression increases p21
Cip1
and down-regulates cyclin E/A-CDK2, resulting in RB activation and suppression of E2F- and Myc-mediated transcriptional programs. This study reveals a critical tumor-suppressive function for miR-127-3p in KS, illuminating the miR-127-3p/SKP2 axis as a promising therapeutic avenue.
Differential phase register of Hes1 oscillations with mitoses underlies cell-cycle heterogeneity in ER
+
breast cancer cells
Authors: Sabherwal Nitin , Rowntree Andrew , Marinopoulou Elli , Pettini Tom , Hourihane Sean , Thomas Riba , Soto Ximena , Kursawe Jochen , Papalopulu Nancy 
Published: November 2021

Significance
Tumors exhibit heterogeneities that are not due to mutations, including cancer stem cells with different potencies. We show that the cancer stem-cell state predisposed to dormancy in vivo has a highly variable and long cell cycle. Using single-cell live imaging for the transcriptional repressor Hes1 (a key molecule in cancer), we show a type of circadian-like oscillatory expression of Hes1 in all cells in the population. The most potent cancer stem cells tend to divide around the trough of the Hes1 oscillatory wave, a feature predictive of a long cell cycle. A concept proposed here is that the position of cell division with respect to the Hes1 wave is predictive of its prospective cell-cycle length and cancer cellular substate.
Transcription as embodied entextualization
Authors: Cavanaugh Jillian R. 
Published: November 2021

Abstract
This article analyzes transcription as a form of knowledge production, distinguishing between the role of transcription as a tool and the contingent nature of transcription as a process. It uses the lens of embodied entextualization, or the culturally specific ways bodies are incorporated into as well as produce texts (Cavanaugh 2017), to illuminate the interdiscursive process of transcription and how it is shaped by social factors such as race, gender, politics, and class. I do so by presenting and analyzing text-objects from my own research on language ideologies and language shift in northern Italy at various stages of entextualization, highlighting the multiple choices that shape transcription and how such choices are in turn shaped by a number of factors often invisible in the final, or at least public, versions of these texts that circulate the most widely. Transcripts such as the ones I discuss endure as evidence, in published and other forms, even as intertextual gaps punctuate their interdiscursive reproduction across instantiations. This work raises questions about the role of transcripts as evidence, their authority, and their varying ontological statuses as text objects in order to further conversations about how scholarship about language in use may be reflexively undertaken.