Miracle-dz/UniFAR-FTUs huggingface dataset:
In situ study of metabolic response of Arabidopsis thaliana leaves to salt stress by neutral desorption-extractive electrospray ionization mass spectrometry.

Abstract：Salt stress is one of the most common factors limiting plant cultivation. In this study, metabolic responses to salt stress in Arabidopsis thaliana (A. thaliana) leaves were analyzed in situ by neutral desorption-extractive electrospray ionization mass spectrometry (ND-EESI-MS) without any sample pretreatment. Metabolic changes of A. thaliana leaves were observed in response to salt stress conditions, including the levels of serine, glutamic acid, arginine, cinnamic acid, ferulic acid, caffeic acid, protocatechuic acid, epicatechin, morin, myricetin, apigravin and β-cotonefuran. The content of serine increased under 50, 100 and 200 mM NaCl salt stress, reaching to the highest level at 200 mM NaCl, but decreased under the maximum concentration of 300 mM NaCl. Similar phenomenon was observed for arginine, glutamic acid, cinnamic acid, caffeic acid, ferulic acid and epicatechin respectively involved in the metabolic pathway of shikimate-phenylpropanoid. Both principal component analysis (PCA) and partial least squares discrimination analysis (PLS-DA) showed that the salt stress treatment groups of the higher concentrations (200 mM and 300 mM) could be well distinguished from those of the lower concentrations (50 mM and 100 mM) and the control. Marker metabolites, like m/z 261 (apigravin) and m/z 305 (β-cotonefuran) were assistantly selected from the fingerprints by variable importance for the projection (VIP). Our results indicated the potential of ND-EESI-MS method for the rapid recognition of metabolic conditions in plant leaves under salt stress.
Enhancing 2D Representation via Adjacent Views for 3D Shape Retrieval

Multi-view shape descriptors obtained from various 2D images are commonly adopted in 3D shape retrieval. One major challenge is that significant shape information are discarded during 2D view rendering through projection. In this paper, we propose a convolutional neural network based method, CenterNet, to enhance each individual 2D view using its neighboring ones. By exploiting cross-view correlations, CenterNet learns how adjacent views can be maximally incorporated for an enhanced 2D representation to effectively describe shapes. We observe that a very small amount of, e.g., six, enhanced 2D views, are already sufficient for a panoramic shape description. Thus, by simply aggregating features from six enhanced 2D views, we arrive at a highly compact yet discriminative shape descriptor. The proposed shape descriptor significantly outperforms state-of-the-art 3D shape retrieval methods on the ModelNet and ShapeNetCore55 benchmarks, and also exhibits robustness against object occlusion.
Transitions to adulthood: self‐governance and disciplining in the making of patient citizens

Abstract Young people develop new behaviours and redefine their identities during health transitions when they move from paediatric to adult healthcare environments. Their identities help to guide their health‐related actions in response to life changes. Young people's health is increasingly recognised as important, yet we lack understanding of how health transitions shape identities and how they relate to other transitions to adulthood. We conducted a longitudinal interview study with young people with sickle cell disease to explore how young people define new identities as they transition to adulthood. We show how ‘disciplining at a distance’ via healthcare self‐management discourses and neoliberal norms governing adolescence play out in the tensions participants encounter when they are crafting new identities. Health transitions involve struggles to negotiate competing demands for self‐discipline. It is crucial to create enabling spaces for young people to protect their health while still developing identities that help them achieve life goals.
Dextran-Benzoporphyrin Derivative (BPD) Coated Superparamagnetic Iron Oxide Nanoparticle (SPION) Micelles for T2-weighted Magnetic Resonance Imaging and Photodynamic Therapy.

Photodynamic therapy (PDT) has attracted extensive attention in recent years as a non-invasive and locally targeted cancer treatment approach. Nanoparticles have been used to improve the solubility and pharmacokinetics of the photosensitizers required for PDT; however, nanoparticles also suffer from many shortcomings including uncontrolled drug release and low tumor accumulation. Herein, we describe a novel biodegradable nanoplatform for the delivery of the clinically used PDT photosensitizer benzoporphyrin derivative monoacid ring A (BPD-MA) to tumors. Specifically, the hydrophobic photosensitizer BPD was covalently conjugated to the amine groups of a dextran-b-oligo (amidoamine) (dOA) dendron copolymer, forming amphiphilic Dextran-BPD conjugates that can self-assemble into nanometer-sized micelles in water. To impart additional imaging capabilities to these micelles, superparamagnetic iron oxide nanoparticles (SPIONs) were encapsulated within the hydrophobic core to serve as a magnetic resonance imaging (MRI) contrast agent. The use of a photosensitizer as a hydrophobic building block enabled facile and reproducible synthesis and high drug loading capacity (~30%, w/w). Furthermore, covalent conjugation of BPD to Dextran prevents the premature release of drug during systemic circulation. In vivo studies show that the intravenous administration of Dextran-BPD coated SPION nanoparticles results in significant MR contrast enhancement within tumors 24 h post-injection and PDT led to a significant reduction in the tumor growth rate.
SEA version 3.0: a comprehensive extension and update of the Super-Enhancer archive

Abstract Super-enhancers (SEs) are critical for the transcriptional regulation of gene expression. We developed the super-enhancer archive version 3.0 (SEA v. 3.0, http://sea.edbc.org) to extend SE research. SEA v. 3.0 provides the most comprehensive archive to date, consisting of 164 545 super-enhancers. Of these, 80 549 are newly identified from 266 cell types/tissues/diseases using an optimized computational strategy, and 52 have been experimentally confirmed with manually curated references. We now support super-enhancers in 11 species including 7 new species (zebrafish, chicken, chimp, rhesus, sheep, Xenopus tropicalis and stickleback). To facilitate super-enhancer functional analysis, we added several new regulatory datasets including 3 361 785 typical enhancers, chromatin interactions, SNPs, transcription factor binding sites and SpCas9 target sites. We also updated or developed new criteria query, genome visualization and analysis tools for the archive. This includes a tool based on Shannon Entropy to evaluate SE cell type specificity, a new genome browser that enables the visualization of SE spatial interactions based on Hi-C data, and an enhanced enrichment analysis interface that provides online enrichment analyses of SE related genes. SEA v. 3.0 provides a comprehensive database of all available SE information across multiple species, and will facilitate super-enhancer research, especially as related to development and disease.
Intraoperative Recording of Auditory Brainstem Responses for Monitoring of Floating Mass Transducer Coupling Efficacy During Revision Surgery-Proof of Concept.

OBJECTIVE The objective of the study was to measure auditory brainstem responses elicited by stimulation via a semi-implantable active middle ear implant with an electromagnetically driven floating mass transducer to quantify the coupling efficacy (=vibroplasty in situ thresholds - bone conduction thresholds) in a patient during a revision surgery. PATIENTS One patient, reimplanted with an active middle ear implant in a revision surgery. INTERVENTION(S) Diagnostic. MAIN OUTCOME MEASURE(S) Intraoperative auditory brainstem responses evoked by stimulation via an active middle ear implant in a calibrated set-up directly indicating the coupling efficacy magnitude (auditory brainstem response threshold = coupling efficacy), as well as pre- and postoperative bone conduction and vibroplasty in situ thresholds. RESULTS The intraoperative auditory brainstem response threshold was detected at 0 dB nHL, i.e., the magnitude of coupling efficacy was determined intraoperatively to be 0 dB. The actual postoperative coupling efficacy (=postoperative vibroplasty in situ - postoperative bone conduction thresholds) was -2.5 dB. CONCLUSIONS The coupling efficacy determined intraoperatively was consistent with the postoperative coupling efficacy. The described method seems to be a promising tool to objectively quantify the magnitude of coupling efficacy in active middle ear implant surgeries.
A proline-rich motif on VGLUT1 reduces synaptic vesicle super-pool and spontaneous release frequency

Glutamate secretion at excitatory synapses is tightly regulated to allow for the precise tuning of synaptic strength. Vesicular Glutamate Transporters (VGLUT) accumulate glutamate into synaptic vesicles (SV) and thereby regulate quantal size. Further, the number of release sites and the release probability of SVs maybe regulated by the organization of active-zone proteins and SV clusters. In the present work, we uncover a mechanism mediating an increased SV clustering through the interaction of VGLUT1 second proline-rich domain, endophilinA1 and intersectin1. This strengthening of SV clusters results in a combined reduction of axonal SV super-pool size and miniature excitatory events frequency. Our findings support a model in which clustered vesicles are held together through multiple weak interactions between Src homology three and proline-rich domains of synaptic proteins. In mammals, VGLUT1 gained a proline-rich sequence that recruits endophilinA1 and turns the transporter into a regulator of SV organization and spontaneous release.
Improved safety checklist analysis approach using intelligent video surveillance in the construction industry: a case study

The construction industry is extremely high risk, and safety checklist analysis is a widely used approach for safety assessment. To overcome its limitations, this article proposes an improved safety checklist analysis approach using intelligent video surveillance to replace on-site inspection. Then, a case study on metro tunnel construction is adopted to illustrate the process. First, the checklist is prepared. Second, the inspection items are correlated with construction areas, and intelligent cameras are positioned to cover the major areas of the construction site to guarantee that all the items can be checked. Thus, problems with inspection items are automatically identified and recorded. Third, the inspection items are marked by a remote scoring mechanism for safety assessment. Finally, the efficiency of the improved approach is tested by a comparative analysis among three groups. The application results indicate the feasibility of the improved approach for evaluating the safety management performance at construction sites.
Bioremediation of Artificial Diesel-Contaminated Soil Using Bacterial Consortium Immobilized to Plasma-Pretreated Wood Waste

Bioaugmentation is a bioremediation option based on increasing the natural in-situ microbial population that possesses the ability to degrade the contaminating pollutant. In this study, a diesel-degrading consortium was obtained from an oil-contaminated soil. The diesel-degrading consortium was grown on wood waste that was plasma-pretreated. This plasma treatment led to an increase of bacterial attachment and diesel degradation rates. On the 7th day the biofilm viability on the plasma-treated wood waste reached 0.53 ± 0.02 OD 540 nm, compared to the non-treated wood waste which was only 0.34 ± 0.02. Biofilm attached to plasma-treated and untreated wood waste which was inoculated into artificially diesel-contaminated soil (0.15% g/g) achieved a degradation rate of 9.3 mg day−1 and 7.8 mg day−1, respectively. While, in the soil that was inoculated with planktonic bacteria, degradation was only 5.7 mg day−1. Exposing the soil sample to high temperature (50 °C) or to different soil acidity did not influence the degradation rate of the biofilm attached to the plasma-treated wood waste. The two most abundant bacterial distributions at the family level were Xanthomonadaceae and Sphingomonadaceae. To our knowledge, this is the first study that showed the advantages of biofilm attached to plasma-pretreated wood waste for diesel biodegradation in soil.
Prediction and Understanding of Resilience in Albertan Families: Longitudinal Study of Disaster Responses (PURLS) – Protocol

Exposure to a natural disaster in childhood can have serious, long-lasting consequences, impacting physical and mental health, development, and learning. Although many children experience negative effects after a disaster, the majority do not, and what differentiates these groups is not well understood. Some of the factors that influence disaster-related outcomes in the midst of adversity include parents’ mental health, the home environment, and socioeconomic status. Furthermore, genetics has also a role to play in how children respond to stressors. We had the opportunity to conduct a natural experiment of disaster recovery following the Alberta 2013 Flood. This paper presents the detailed protocol on prediction of resilience in Albertan families, and validation with cortisol data. In addition, data collection procedures, developing resiliency screening tools, candidate gene identification, genotyping, DNA methylation, and genomic analyses are described to achieve the research objectives. This study produced new knowledge by using pre- and post-disaster information on children’s health and development, including children’s genetics and responses to stress. This information has been identified as important to governments and other organizations invested in early child development. Our comprehensive research plan generates evidence that can be mobilized population-based approaches to improve child and family resiliency.
Evolutionary coupling saturation mutagenesis: Coevolution‐guided identification of distant sites influencing Bacillus naganoensis pullulanase activity

Pullulanases are well‐known debranching enzymes hydrolyzing α‐1,6‐glycosidic linkages. To date, engineering of pullulanase is mainly focused on catalytic pocket or domain tailoring based on structure/sequence information. Saturation mutagenesis‐involved directed evolution is, however, limited by the low number of mutational sites compatible with combinatorial libraries of feasible size. Using Bacillus naganoensis pullulanase as a target protein, here we introduce the ‘evolutionary coupling saturation mutagenesis’ (ECSM) approach: residue pair covariances are calculated to identify residues for saturation mutagenesis, focusing directed evolution on residue pairs playing important roles in natural evolution. Evolutionary coupling (EC) analysis identified seven residue pairs as evolutionary mutational hotspots. Subsequent saturation mutagenesis yielded variants with enhanced catalytic activity. The functional pairs apparently represent distant sites affecting enzyme activity.
Periodontal status and dental behaviour of heart transplant recipients and healthy controls

Abstract Objective: The aim of this study was to compare the periodontal status and dental behaviour of heart transplant recipients with systemically healthy controls. Material and Methods: Forty heart transplant recipients and 40 systemically healthy patients were included. A questionnaire was used to record demographic, systemic health and dental behaviour data, and the following clinical parameters were recorded: plaque index, bleeding on probing, probing depth, gingival recession, and clinical attachment level. Results: Mean probing depth (p = .045), mean gingival recession (p = .016), mean clinical attachment level (p = .021) and mean plaque index scores (p = .001) were higher in heart transplant recipients than the systemically healthy group. However, bleeding on probing was similar in both groups (p > .05). Tooth brushing frequency and number of participants who used dental floss/interdental brush was lower in the heart transplant group. Conclusion: Considering the poor oral hygiene and high clinical periodontal parameters of heart transplant recipients, periodontal evaluation should be done regularly before and after transplantation. The patient’s daily oral hygiene regimens should be evaluated carefully in this evaluation session and modified based on their gingival health, manual skill and motivational levels. The importance of oral health and its effects on systemic health should also be explained to the transplant recipients in detail.
Uncontrolled Diabetes as an Associated Factor with Dynapenia in Adults Aged 50 Years or Older: Sex Differences

Abstract Background Epidemiological studies demonstrate an association between diabetes and low neuromuscular strength (NMS). However, none have grouped participants into nondiabetics (ND), undiagnosed diabetics (UDD), controlled diabetics (CD), and uncontrolled diabetics (UCD) or investigated what glycated hemoglobin levels (HbA1c) are associated with low NMS (dynapenia) by sex. Methods We analyzed the association between UDD, CD, and UCD and dynapenia, the extent to which the different groupings of these individuals modifies this association and the association between HbA1c levels and NMS, by sex, in a cross-sectional study involving 5,290 participants ≥50 years from the ELSA study. In the first two analyses, logistic regression models were used with dynapenia (grip strength <26 kg in men and <16 kg in women) as outcome and diabetes (ND, UDD, CD, and UCD) as exposure. Next, linear regression was performed with grip strength as the outcome, and the participants were classified based on HbA1c level as exposure. The models were adjusted by sociodemographic, behavioral, and clinical characteristics. Results Compared to ND, only UCD was associated with dynapenia (men OR = 2.37 95% CI 1.36–4.14; women OR = 1.67 95% CI 1.01–2.79). This association was less clear, particularly in women, when CD and UCD groups were merged. HbA1c ≥6.5% in men and ≥8.0% in women were associated with lower NMS. Conclusions UCD increases the chance of dynapenia in both sexes. The different groupings based on diabetes status modify the association between UCD and dynapenia. The threshold of HbA1c associated with reduced NMS is lower in men compared to women.
The mental health and depression of rural-to-urban migrant workers compared to non-migrant workers in Shanghai: a cross-sectional study.

BACKGROUND Migrant workers worldwide commonly are susceptible to mental disorders. Since the 1980s, there has been a large-scale increase in the number of migrant workers in China; this development parallels the acceleration of socio-economic transformation. Studies addressing this population rarely focus on workers' mental health or psychological well-being, yet it is imperative to understand the mental health status of rural-to-urban migrant workers and study the relationship between migration and mental health. METHODS A cross-sectional survey of 3286 participants (response rate 85.4%) was conducted among different work units in Shanghai. All of the variables of this survey were assessed by a self-administered questionnaire, with depression measured by the Patient Health Questionnaire-9 (PHQ-9) scale and poor mental health (PMH) measured by the World Health Organization 5-Item Well-Being Index (WHO-5) scale. Pearson's χ2 test and logistic regression were used to compare migrants with urbanites, and to identify factors related to mental health outcomes. RESULTS Migrant workers (15.3%) had a slightly higher prevalence of depression than non-migrant (12.0%) workers, with notable PMH (26.9%) among participants >45 y of age. In the logistic regression models, those who reported low job satisfaction, unhealthy organizations, poor physical health (self-rated) and long working hours were 2.86 (95% CI 2.14 to 3.84), 1.42 (95% CI 1.06 to 1.91), 1.89 (95% CI 1.41 to 2.55) and 1.48 (95% CI 1.08 to 2.03) times more likely to have depression, respectively. Similarly, workers >45 y of age were 2.92 (95% CI 1.65 to 5.16) and 1.80 (95% CI 1.01 to 3.21) times more likely to have PMH for low job satisfaction and unhealthy organizations, respectively. CONCLUSIONS There are numerous potential causes affecting the mental health of Chinese internal migrant workers. Strengthening the construction of healthy organizations and enhancing workers' job satisfaction may improve the mental health status or psychological well-being of this group.
Beyond episodic remembering: elaborative retrieval of lifetime periods in young and older adults

ABSTRACT Relative to young adults, cognitively normal older adults commonly generate more semantic details and fewer episodic details in their descriptions of unique life events. It remains unclear whether this reflects a specific change to episodic memory or a broader alteration to autobiographical narration. To explore age differences across different types of autobiographical narration, we created a lifetime period narrative task that involves describing extended events. For comparison, participants also described unique life events. All autobiographical narratives were scored for episodic, semantic, and other detail generation. Relative to young adults, older adults generated more detailed narratives for remote and recent lifetime periods, which was driven by their increased retrieval of personal and general semantic details. Older adults also generated more semantic details for unique life event narratives, along with reduced episodic detail. More broadly, in both groups lifetime period narratives were largely based on semantic details, whereas episodic details were more prominent in the descriptions of unique life events. These findings indicate that the elevated generation of semantic details associated with normal cognitive aging is reflected in multiple types of autobiographical narration. We suggest that lifetime period narration is a spared aspect of autobiographical memory among older adults.