Miracle-dz/UniFAR-FTUs huggingface dataset:
The evolution of the micro-morphology and micro-structure of particles from diesel engine in combination with exhaust gas recirculation

ABSTRACT In this study, small angle X-ray scattering (SAXS), scanning electron microscopy (SEM), and atomic force microscopy (AFM) were used to investigate the microstructure, spatial structure, and structural rigidity of the particles in the particulate matter (PM) produced at different exhaust gas recirculation (EGR) rates, exhaust compositions and temperatures as well as the size and number of gaps in the aggregates. The results showed that with increasing EGR rate and exhaust temperature, the aggregate size of the PM and the number of primary carbon particles increased significantly, the electronic density difference in the PM decreased gradually, the statistical mean distance between the PM decreased, the size and number of gaps in the aggregates decreased significantly, the spatial structure gradually became tighter, the Young’s moduli of the powders increased gradually, the structural rigidity increased, the liquid bridge force and the van der Waals force increased gradually, the type of cohesive force changed from the liquid bridge force to a combination of the liquid bridge force and the van der Waals force, and the van der Waals force played a more prominent role. In contrast to the particles that formed due to the introduction of exhaust gas, the particles that formed due to the introduction of CO2 exhibited a chain structure, and the cohesive force decreased significantly, which resulted in loose particle packing. The particles that formed due to the introduction of only N2 mainly exhibited a clustered structure, the cohesive force did not change significantly, and the primary carbon particles were tightly packed. The particle gap sizes ranged from 4 to 6 nm, 3 to 4 nm and 11 to 13 nm when exhaust gas, N2 and CO2 were introduced, respectively. The N2 in the exhaust gas was the main factor responsible for the aggregation of particles and the improvement of the structural rigidity, whereas CO2 in the exhaust gas increased the statistical mean distance between the particles and decreased the packing density of the structure and the structural rigidity.
Subjective Well-Being, Critical Race Theory, and the Assessment of Measurement Invariance Across Racial Groups

The present study explores how Black and White youth respond to measures of subjective well-being within the context of critical race theory (CRT). Three levels of measurement invariance (i.e., configural, metric and scalar) were examined for indicators of subjective well-being. We hypothesized that there would be limited measurement invariance across groups based on the premise established by CRT that youth of color experience and perceive life differently than their White peers, which was supported. The findings of this study demonstrate that the measures work as expected within groups, but there is a considerable lack of invariance across groups. This study also provides some evidence that racial/ethnic differences cannot be taken for granted when assessing SWB in youth.
Living with grandparents: Multi-generational families and the academic performance of grandchildren in China

Previous studies on social stratification and intergenerational mobility have mostly focused on the effects of parents on their children’s socioeconomic status (SES) attainment, but less attention has been paid to the important role played by grandparents in the life chances of their grandchildren, and its underlying mechanism. By analyzing a national survey sample data of junior high school students in China, this study examines the influence factors of living with grandparents and their effect on the academic performance of adolescents, and the intermediate mechanism. The study finds that (a) three-generation cohabitation occurs when there is a functional need for the nuclear family, and children with lower SES, working mothers, or single-parent families are more likely to experience cohabitation between grandparents and grandchildren; (b) living with grandparents has significant positive effects on adolescents’ academic performance after controlling for other factors; (c) the effect of living with grandparents is moderated by the family’s SES and family structure, and students from lower-SES or single-parent families benefit more from living with grandparents; and (d) living with grandparents to a certain extent benefits grandchildren’s academic performance by enhancing family social capital investment. Households in which grandparents cohabit invest significantly more in the social capital of children than those who do not have grandparents cohabiting. The results of this study show that in modern society, family kinship networks still play a very important role in the status attainment and social mobility of individuals. Therefore, scholars should pay more attention to the important role of extended families in social stratification and mobility and its micro-mechanisms.
When the Future “Spills Under”: General Self-Efficacy Moderates the Influence of Expected Exercise on Present Intellectual Performance

We examined whether an expected future activity (exercise vs. relaxation) impacts a present behavior (performance on an intellectual task) that occurs prior to this activity. Across two experiments (n = 320 and n = 466), the influence of expected exercise compared to relaxation on present intellectual performance was moderated by general self-efficacy (GSE)—a core personality trait that determines people’s confidence that they can surmount physically or intellectually challenging activities. Participants high in GSE had better intellectual performance when they were expecting to exercise versus relax, whereas the effect reversed under low GSE. Moderated mediation analyses suggested that task-focused attention (i.e., participants’ level of focus while solving the intellectual task) accounted for a significant proportion of variance between the future activity (exercise vs. relaxation) and present intellectual performance across different GSE levels. These findings document a previously unexplored channel through which future expectations shape present outcomes.
Long-term effects of NPK fertilizers and organic manures on soil organic carbon and carbon management index under a double-cropping rice system in Southern China

ABSTRACT The effects of manure and chemical fertilizer on soil bulk density, soil organic carbon (SOC), and the role of carbon management index (CMI) in soil quality evaluation were studied under a double-cropping rice system in a long-term experiment. The experiment included five fertilizer treatments: without fertilizer input (CK), chemical fertilizer alone (MF), rice straw residue plus chemical fertilizer (RF), 30% organic matter plus 70% chemical fertilizer (LOM), and 60% organic matter plus 40% chemical fertilizer (HOM). RF, LOM, HOM treatments increased SOC content relative to MF treatment in the paddy fields at 0–20 cm. RF, LOM, HOM treatments were more effective for increasing CMI, lability index, lability of C, and SOC stocks, as compared with MF treatment. Based on rice grain yield and carbon storage, integrated fertilization of chemical fertilizer and organic manure proved to be the most effective practices for improving crop productivity and SOC sequestration.
Acetylation regulates the oligomerization state and activity of RNase J, the major ribonuclease of Helicobacter pylori

In the pathogenic bacterium Helicobacter pylori, post-transcriptional regulation is dominated by the activity of a protein complex, known as the RNA degradosome, composed of the essential ribonuclease RNase J and the DEAD-box RNA helicase RhpA. Here, we describe post-translational modifications of this protein complex that affect its activity. Cell-extracted RNase J is acetylated on multiple residues, one of which, K649, impacts strongly on RNase J oligomerization, which in turn influences recruitment into the degradosome and ribonuclease activity. Corroborating the link between oligomerization and activity, mutations targeting K649 and other residues affect the dimerization and in vitro activity of RNase J. Our crystal structure of RNase J reveals loops that gate access to the active site and rationalizes how oligomerization state influences activity. We show that the acetylated residues of RNase J are important for H. pylori morphology, highlighting that the modifications affect the cellular function of RNase J. We propose acetylation as a regulatory level controlling the activity of RNase J and the H. pylori RNA degradosome.
A flexible summary-based colocalization method with application to the mucin Cystic Fibrosis lung disease modifier locus

Mucus obstruction is a central feature in the Cystic Fibrosis (CF) airways. A genome-wide association study (GWAS) of lung disease by the CF Gene Modifier Consortium (CFGMC) identified a significant locus containing two mucin genes, MUC20 and MUC4. Expression quantitative trait locus (eQTL) analysis using human nasal epithelial (HNE) from 94 CF Canadians in the CFGMC demonstrated MUC4 eQTLs that mirrored the lung association pattern in the region, suggesting that MUC4 expression may mediate CF lung disease. Complications arose, however, with colocalization testing using existing methods: the locus is complex and the associated SNPs span a 0.2Mb region with high linkage disequilibrium and evidence of eQTLs for multiple genes and tissues (heterogeneity). We previously developed the Simple Sum (SS), a powerful colocalization test in regions with heterogeneity, but SS assumed eQTLs to be present to achieve type I error control. Here we propose a two-stage SS (SS2) colocalization test that avoids a prior eQTL assumptions, accounts for multiple hypothesis testing and the composite null hypothesis and enables meta-analysis. We compare SS2 to published approaches through simulation and demonstrate type I error control for all settings with the greatest power in the presence of high LD and heterogeneity. Applying SS2 to the MUC20/MUC4 CF lung disease locus with eQTLs from CF HNE revealed significant colocalization with MUC4 (p = 1.71×10−5) rather than MUC20. The SS2 is a powerful method to inform the responsible gene(s) at a locus and guide future functional studies. SS2 has been implemented in the application LocusFocus (locusfocus.research.sickkids.ca).
The miR-430 locus with extreme promoter density is a transcription body organizer, which facilitates long range regulation in zygotic genome activation

In anamniote embryos the major wave of zygotic genome activation (ZGA) starts during the mid-blastula transition. This major wave of ZGA is facilitated by several mechanisms, including dilution of repressive maternal factors and accumulation of activating transcription factors during the fast cell division cycles preceding the mid-blastula transition. However, a set of genes escape global genome repression and are activated substantially earlier, during what is called, the minor wave of genome activation. While the mechanisms underlying the major wave of genome activation have been studied extensively, the minor wave of genome activation is little understood. In zebrafish the earliest expressed RNA polymerase II (Pol II) transcribed genes are activated in a pair of large transcription bodies depleted of chromatin, abundant in elongating Pol II and nascent RNAs (Hadzhiev et al., 2019; Hilbert et al., 2021). This transcription body includes the miR-430 gene cluster required for maternal mRNA clearance. Here we explored the genomic, chromatin organisation and cis-regulatory mechanisms of the minor wave of genome activation occurring in the transcription body. By long read genome sequencing we identified a remarkable cluster of miR-430 genes with over 300 promoters and spanning 0.6 Mb, which represent the highest promoter density of the genome. We demonstrate that the miR-430 gene cluster is required for the formation of the transcription body and acts as a transcription organiser for minor wave activation of a set of zinc finger genes scattered on the same chromosome arm, which share promoter features with the miR-430 cluster. These promoter features are shared among minor wave genes overall and include the TATA-box and sharp transcription start site profile. Single copy miR-430 promoter transgene reporter experiments indicate the importance of promoter-autonomous mechanisms regulating escape from global repression of the early embryo. These results together suggest that formation of the transcription body in the early embryo is the result of high promoter density coupled to a minor wave-specific core promoter code for transcribing key minor wave ZGA genes, which are required for the overhaul of the transcriptome during early embryonic development.
Ability of nucleoside-modified mRNA to encode HIV-1 envelope trimer nanoparticles

The success of nucleoside-modified mRNAs in lipid nanoparticles (mRNA-LNP) as COVID-19 vaccines heralded a new era of vaccine development. For HIV-1, multivalent envelope (Env) trimer protein nanoparticles are superior immunogens compared to trimers alone for priming of broadly neutralizing antibody (bnAb) B cell lineages. The successful expression of complex multivalent nanoparticle immunogens with mRNAs has not been demonstrated. Here we show that mRNAs can encode antigenic Env trimers on ferritin nanoparticles that initiate bnAb precursor B cell expansion and induce serum autologous tier 2 neutralizing activity in bnAb precursor VH + VL knock-in mice. Next generation sequencing demonstrated acquisition of critical mutations, and monoclonal antibodies that neutralized heterologous HIV-1 isolates were isolated. Thus, mRNA- LNP can encode complex immunogens and are of use in design of germline-targeting and sequential boosting immunogens for HIV-1 vaccine development.
Investigating the active substance and mechanism of Jing-Fu-Kang granules via mass spectrometry technology and network pharmacology method

Jing-Fu-Kang granules (JFKG) is a famous Chinese patent medicine for the treatment of cervical spondylosis around the China, whereas the active substance and mechanism are not completely investigated clearly. In the current study, a rapid separation and identification method using UPLC-QE-Orbitrap-MS was established, 97 chemical constituents from JFKG were identified, and 16 prototype components from plasma samples after administration of JFKG were observed within 16 min. The structures of typical compounds were preliminarily speculated by comparing the retention time and fragmentation pattern. Furthermore, multiple databases were used to integrate the compound targets of JFKG, and the disease targets related to cervical spondylosis. After the intersection of the two sets of targets, a protein-protein interaction (PPI) network and a TCM-component-target-pathway-disease network were established, then using the DAVID database to perform gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis on the common targets to find related pathways. Finally, a total of 531 common targets and 136 pathways were found to participate in the mechanism. Our findings will help to further confirm the mechanism of JFKG for relieving cervical spondylosis, which will improve the scientific rationality of JFKG in clinical use, and can also assist in guiding doctors.
Titin switches from an extensible spring to a mechanical rectifier upon muscle activation

In contracting striated muscle titin acts as a spring in parallel with the array of myosin motors in each half-sarcomere and could prevent the intrinsic instability of thousands of serially linked half-sarcomeres, if its stiffness, at physiological sarcomere lengths (SL), were ten times larger than reported. Here we define titin mechanical properties during tetanic stimulation of single fibres of frog muscle by suppressing myosin motor responses with Para-Nitro-Blebbistatin, which is able to freeze thick filament in the resting state. We discover that thin filament activation switches I-band titin spring from the large SL-dependent extensibility of the OFF-state to an ON-state in which titin acts as a SL-independent mechanical rectifier, allowing free shortening while opposing stretch with an effective stiffness 4 pN nm−1 per half-thick filament. In this way during contraction titin limits weak half-sarcomere elongation to a few % and, also, provides an efficient link for mechanosensing-based thick filament activation.
Arabidopsis Spliceosome Factor SmD3 Modulates Immunity to Pseudomonas syringae Infection

SmD3 is a core component of the small nuclear ribonucleoprotein (snRNP) that is essential for pre-mRNA splicing. The role of Arabidopsis SmD3 in plant immunity was assessed by testing sensitivity of smd3a and smd3b mutants to Pseudomonas syringae pv. tomato (Pst) DC3000 infection and its pathogenesis effectors flagellin (flg22), EF-Tu (elf18) and coronatine (COR). Both smd3 mutants exhibited enhanced susceptibility to Pst accompanied by marked changes in the expression of key pathogenesis markers. mRNA levels of these factors were also altered upon treatment with Pseudomonas effectors. We showed that SmD3-b dysfunction impairs mainly stomatal immunity as a result of defects in stomatal development. Our genome-wide transcriptome analysis of the smd3b-1 mutant infected with Pst revealed that lack of SmD3-b deregulates defense against Pst infection at the transcriptional and posttranscriptional levels including defects in splicing and an altered pattern of alternative splicing. Other changes in the smd3b-1 mutant involved enhanced elf18- and flg22-induced callose deposition, reduction of flg22-triggered production of early ROS and boost of secondary ROS caused by Pst infection. Together, our data indicate that SmD3 contributes to the plant immune response possibly via regulation of mRNA splicing of key pathogenesis factors.
A gene-by-gene mosaic of dosage compensation strategies on the human X chromosome

Dosage compensation in humans - ensuring the viability and fitness of females, with two X chromosomes, and males, with one - is thought to be achieved chromosome-wide by heterochromatinization of one X chromosome during female development. We reassessed this through quantitative gene-by-gene analyses of expression in individuals with one to four X chromosomes, tolerance for loss-of-function mutations, regulation by miRNAs, allele-specific expression, and the presence of homologous genes on the Y chromosome. We found a mosaic of dosage compensation strategies on the human X chromosome reflecting gene-by-gene differences in multiple dimensions, including sensitivity to under- or over-expression. These insights enrich our understanding of Turner, Klinefelter, and other sex chromosome aneuploidy syndromes, and of sex-chromosome-mediated effects on health and disease in euploid males and females.
Classifying Urban Fabrics into Mobile Call Activity with Supervised Machine Learning

Strong spatial relationships exist between call volume and human activities. In this paper, we show machine learning models can classify base station coverage areas into classes of mobile call profile based on areas geographic and demographic properties. We propose the novel approach of taking clustered Call Detail Records (CDR) based time series as ground truth, and passing heterogeneous features as inputs. These features were land use and points of interest retrieved from OpenStreetMap database, and demographic data provided Facebook Research. Together, they allowed the creation of a representation of urban fabric. CDR clusters were then characterized by these features through SHAP model interpretation. Three models were tested in the region of Dakar with CDR coming from D4D-Senegal Challenge. Results exceeded the accuracy of systematic most common class classification and the accuracy of models trained only on population dataset. Additionally, models generalization capacity were evaluated in Thies, with results equalling those of the baseline.
EMoCy: Towards Physiological Signals-Based Stress Detection

The prompt detection of stress can prevent long-term consequences on people’s health, economy and society. In this work, we present EMoCy, a reproducible methodology and analysis pipeline for automatic and continuous stress detection based on physiological signals. By providing reproducible experiments and exploring more constrained settings with state-of-the-art accuracy, we set new benchmarks for future works on stress detection. Our study includes signal selection and preprocessing, feature engineering, and classification using machine learning algorithms. We have tested our approach on WESAD dataset using blood volume pulse, electrodermal activity, and respiration signals. We identify a set of features that allow us to reach effective detection using low sampling frequency and short time windows. This reduces the computational power and the detection delay, going towards real-time applications on wearable devices. Using 60s windows, we reach an accuracy of 0.972 and an F1 score of 0.979 on the stress/baseline discrimination task. Moreover, our machine learning models achieve an accuracy greater than 0.93 on windows of 25s sampled at 64Hz. We have also observed that it is possible to obtain a good estimate of the models’ performance by training them with a small window overlap.
Toward Building an Academic Search Engine Understanding the Purposes of the Matched Sentences in an Abstract

This paper introduces an automatic approach to understand the purposes of each sentence in the abstract of an academic document. Specifically, computers can label each sentence in the abstract as being related to one or several of six aspects – “BACKGROUND”, “OBJECTIVES”, “METHODS”, “RESULTS”, “CONCLUSIONS”, and “OTHERS”. Experimental results obtained on a real dataset show that the labeling methodology outperforms baseline methods. We also build a prototype academic search engine to demonstrate the use of this new design. Users may search for articles containing keywords related to any of these six aspects to better meet their search goals.
Energy-Efficient MU-Massive-MIMO Hybrid Precoder Design: Low-Resolution Phase Shifters and Digital-to-Analog Converters for 2D Antenna Array Structures

This paper investigates a multi-user massive multiple-input multiple-output (MU-mMIMO) hybrid precoding (HP) scheme using low-resolution phase shifters (PSs) and digital-to-analog converters (DACs). The proposed HP approach involves two stages: RF beamforming based on the slowly time-varying channel second-order correlation matrix, and baseband MU precoding based on the instantaneous effective baseband channel to mitigate MU-interference by a regularized zero-forcing (RZF) technique. We consider three HP design architectures: (i) HP using full-resolution PSs and DACs, with a baseband transfer block for constant-modulus RF beamformer, (ii) HP using <inline-formula> <tex-math notation="LaTeX">$b$ </tex-math></inline-formula>-bit PSs and full-resolution DACs, with an orthogonal matching pursuit (OMP) based algorithm that can approach the optimal unconstrained RF beamformer, and (iii) HP using <inline-formula> <tex-math notation="LaTeX">$b$ </tex-math></inline-formula>-bit PSs and <inline-formula> <tex-math notation="LaTeX">$q$ </tex-math></inline-formula>-bit DACs, taking into account also DAC quantization noise. Illustrative results show that the proposed HP schemes with low-resolution PSs can approach the sum-rate of full-resolution PSs by using only 2-bit PSs, while offering higher energy efficiency. Furthermore, a study of sum-rate results for various PS and DAC quantization levels reveals that HP can achieve near-optimal performance with only 2-bit PSs and 5-bit DACs. Moreover, a comparison of the different array configurations, namely, uniform linear array (ULA), uniform circular array (UCA), uniform rectangular array (URA), and concentric circular array (CCA), indicates that URA and CCA outperform UCA and ULA in terms of spectral and energy efficiencies.