Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards Strain-Level Complexity: Sequencing Depth Required for Comprehensive Single-Nucleotide Polymorphism Analysis of the Human Gut Microbiome

Intestinal bacteria strains play crucial roles in maintaining host health. Researchers have increasingly recognized the importance of strain-level analysis in metagenomic studies. Many analysis tools and several cutting-edge sequencing techniques like single cell sequencing have been proposed to decipher strains in metagenomes. However, strain-level complexity is far from being well characterized up to date. As the indicator of strain-level complexity, metagenomic single-nucleotide polymorphisms (SNPs) have been utilized to disentangle conspecific strains. Lots of SNP-based tools have been developed to identify strains in metagenomes. However, the sufficient sequencing depth for SNP and strain-level analysis remains unclear. We conducted ultra-deep sequencing of the human gut microbiome and constructed an unbiased framework to perform reliable SNP analysis. SNP profiles of the human gut metagenome by ultra-deep sequencing were obtained. SNPs identified from conventional and ultra-deep sequencing data were thoroughly compared and the relationship between SNP identification and sequencing depth were investigated. The results show that the commonly used shallow-depth sequencing is incapable to support a systematic metagenomic SNP discovery. In contrast, ultra-deep sequencing could detect more functionally important SNPs, which leads to reliable downstream analyses and novel discoveries. We also constructed a machine learning model to provide guidance for researchers to determine the optimal sequencing depth for their projects (SNPsnp, https://github.com/labomics/SNPsnp). To conclude, the SNP profiles based on ultra-deep sequencing data extend current knowledge on metagenomics and highlights the importance of evaluating sequencing depth before starting SNP analysis. This study provides new ideas and references for future strain-level investigations.
Unemployed + Sick = More Deserving? A Survey Experiment on How the Medicalization of Unemployment Affects Public Opinion

The literature on the social legitimacy of welfare benefits has shown that sick persons are perceived more deserving than unemployed individuals. However, these studies examine sick and unemployed persons as distinct groups, while unemployment and sickness are in fact strongly related. Policymakers across Europe have been increasingly concerned with discouraging a medicalization of unemployment and activating sick unemployed persons. Therefore, it is crucial to understand welfare attitudes toward this group. Using a factorial survey fielded with a representative sample of German-speaking adults (N=2,621), we investigate how sickness affects attitudes toward a hypothetical unemployed person on three dimensions: benefit levels, conditions, and sanctions. Respondents allocated similar benefit levels to unemployed persons regardless of whether they have an illness. Yet, they were more hesitant to apply existing conditions (e.g., active job search, job training) or sanction benefits when the unemployed person was also sick. This is except for conditions that tie benefits to obligatory health services (back training or psychological counseling) which was supported by the majority of respondents. Our research shows that the German public is not more generous and only partially more lenient toward sick unemployed persons as there is strong support for conditions targeted at overcoming ill health for this group. The findings underscore that sickness matters for how unemployed persons are perceived, but the impact varies across different dimensions of welfare attitudes.
Pallidal Structural Changes Related to Levodopa-induced Dyskinesia in Parkinson's Disease

Background Despite the clinical impact of levodopa-induced dyskinesia (LID) in Parkinson's disease (PD), the mechanism, especially the role of basal ganglia (BG), is not fully elucidated yet. We investigated the BG structural changes related to LID in PD using a surface-based shape analysis technique. Methods We recruited patients with PD who developed LID within 3 years (LID group, 28 patients) and who did not develop it after 7 years (non-LID group, 35 patients) from levodopa treatment for the extreme case-control study. BG structure volumes were measured using volumetry analysis and the surface-based morphometry feature (i.e., Jacobian) from the subcortical surface vertices. We compared the volume and Jacobian of meshes in the regions between the two groups. We also performed a correlation analysis between local atrophy and the severity of LID. Additionally, we evaluated structural connectivity profiles from globus pallidus interna and externa (GPi and GPe) to other brain structures based on the group comparison. Results The demographic and clinical data showed no significant difference except for disease duration, treatment duration, parkinsonism severity, and levodopa equivalent dose. The LID group had more local atrophies of vertices in the right GPi than the non-LID group, despite no difference in volumes. Furthermore, the LID group demonstrated significantly reduced structural connectivity between left GPi and thalamus. Conclusion This is the first demonstration of distinct shape alterations of basal ganglia structures, especially GPi, related to LID in PD. Considering both direct and indirect BG pathways share the connection between GPi and thalamus, the BG pathway plays a crucial role in the development of LID.
Understanding the Phytoremediation Mechanisms of Potentially Toxic Elements: A Proteomic Overview of Recent Advances

Potentially toxic elements (PTEs) such as cadmium (Cd), lead (Pb), chromium (Cr), and arsenic (As), polluting the environment, pose a significant risk and cause a wide array of adverse changes in plant physiology. Above threshold accumulation of PTEs is alarming which makes them prone to ascend along the food chain, making their environmental prevention a critical intervention. On a global scale, current initiatives to remove the PTEs are costly and might lead to more pollution. An emerging technology that may help in the removal of PTEs is phytoremediation. Compared to traditional methods, phytoremediation is eco-friendly and less expensive. While many studies have reported several plants with high PTEs tolerance, uptake, and then storage capacity in their roots, stem, and leaves. However, the wide application of such a promising strategy still needs to be achieved, partly due to a poor understanding of the molecular mechanism at the proteome level controlling the phytoremediation process to optimize the plant’s performance. The present study aims to discuss the detailed mechanism and proteomic response, which play pivotal roles in the uptake of PTEs from the environment into the plant’s body, then scavenge/detoxify, and finally bioaccumulate the PTEs in different plant organs. In this review, the following aspects are highlighted as: (i) PTE’s stress and phytoremediation strategies adopted by plants and (ii) PTEs induced expressional changes in the plant proteome more specifically with arsenic, cadmium, copper, chromium, mercury, and lead with models describing the metal uptake and plant proteome response. Recently, interest in the comparative proteomics study of plants exposed to PTEs toxicity results in appreciable progress in this area. This article overviews the proteomics approach to elucidate the mechanisms underlying plant’s PTEs tolerance and bioaccumulation for optimized phytoremediation of polluted environments.
Neoadjuvant Therapy With Cabozantinib as a Bridge to Liver Transplantation in Patients With Hepatocellular Carcinoma (HCC): A Case Report

Liver transplant (LT) is the treatment of choice for unresectable, localized hepatocellular carcinoma (HCC). However, transplant is not recommended for patients who have extensive tumor growth and do not meet specific criteria. For these cases, “bridging” therapies are often used to either downstage or prevent tumor progression while patients are on the transplant list. Various pre-transplant therapies have been used, including transarterial chemoembolization, radiofrequency ablation, and systemic therapies. Sorafenib is a well-known systemic agent used for HCC, but research is limited on its use as well as the use of newer agents as bridging therapy. Prospective studies are also lacking. We discuss cases of two patients diagnosed with HCC and treated systemically with cabozantinib prior to transplant without treatment-related complications. This suggests that cabozantinib could be safely used after sorafenib therapy to control disease related to HCC while awaiting liver transplantation.
Genetic Analysis and Functional Study of a Pedigree With Bruck Syndrome Caused by PLOD2 Variant

Background Bruck syndrome (BS) is a rare autosomal recessive inherited osteogenesis imperfecta disease characterized by increased bone fragility and joint contracture. The pathogenic gene of type I BS is FKBPl0, whereas that of type II BS is PLOD2. No significant difference has been found in the clinical phenotype between the two types of BS. In this study, we performed genetic analysis of a BS pedigree caused by PLOD2 variant and studied the corresponding cellular function. Methods Serum biochemistry, parathyroid hormone (PTH), 25-hydroxyvitamin D [25-(OH) D], osteocalcin, and 24-h urinary calcium levels of a family member with BS was assessed. The genes of the proband were analyzed by second-generation sequencing and exon capture techniques. Sanger sequencing was also performed for the suspected responsible variant of the family member. Wild- and variant-type lentivirus plasmids were constructed by gene cloning and transfected into HEK293T cells. Cell function was verified by real-time quantitative polymerase chain reaction, western blotting, and immunofluorescence detection. Results In this pedigree, the proband was found to have a homozygous variant c.1856G > A (p.Arg619His) in exon 17 of PLOD2 (NM_182943.3). His consanguineous parents and sisters were p.Arg619His heterozygous carriers. The mRNA expression of PLOD2 in the constructed p.Arg619His variant cells was significantly upregulated, while the expression of PLOD2 and collagen I protein in the cell lysate was significantly downregulated. Immunofluorescence revealed that the wild-type PLOD2 was mainly located in the cytoplasm, and the expression of the PLOD2 protein after c.1856G > A variant was significantly downregulated, with almost no expression, aligning with the western blot results. The serum sodium, potassium, calcium, phosphorus, magnesium, alkaline phosphatase, PTH, 25-(OH) D, osteocalcin, and 24 h urinary calcium levels of the proband, his parents, and sisters were normal. Conclusion Through gene and cell function analyses, PLOD2 Arg619His missense variant was preliminarily confirmed to cause BS by reducing protein expression.
Identification of Angiogenesis-Related Prognostic Biomarkers Associated With Immune Cell Infiltration in Breast Cancer

Background: This study aimed to explore the prognostic value of angiogenesis-related genes (ARGs) and their association with immune cell infiltration (ICI) in breast cancer (BC). Methods: Transcriptome data of BC were obtained from the TCGA and GEO databases. Differentially expressed ARGs were identified by the limma package. The identification of key genes and construction of the risk score model were performed by univariate and multivariate Cox regression algorithms. The prognostic value of the risk score was assessed by ROC curves and nomogram. GO, KEGG pathway, and GSEA were used to investigate the biological functions of differentially expressed genes (DEGs), and CIBERSORT, ssGSEA, and xCell algorithms were performed to estimate the ICI in high-risk and low-risk groups. The correlations between prognostic biomarkers and differentially distributed immune cells were assessed. Moreover, a ceRNA regulatory network based on prognostic biomarkers was constructed and visualized by Cytoscape software. Results: A total of 18 differentially expressed ARGs were identified between tumor and adjacent normal tissue samples. TNFSF12, SCG2, COL4A3, and TNNI3 were identified as key prognostic genes by univariate and multivariate Cox regression analyses. The risk score model was further constructed based on the four-gene signature and validated in GSE7390 and GSE88770 datasets. ROC curves and nomogram indicated that the risk score had good accuracy for determining BC patient survival. Biological function analysis showed that DEGs in high- and low-risk groups had a high enrichment in immune-related biological processes and signaling pathways. Moreover, significantly different ICIs were found between high- and low-risk groups, such as memory B cells, CD8+ T cells, resting memory CD4+ T cells, follicular helper T cells, regulatory T cells, monocytes, M2 macrophages, and neutrophils, and each prognostic biomarker was significantly correlated with one or more immune cell types. Conclusion: The current study identified novel prognostic ARGs and developed a prognostic model for predicting survival in patients with BC. Furthermore, this study indicated that ICI may act as a bond between angiogenesis and BC. These findings enhance our understanding of angiogenesis in BC and provide novel guidance on developing therapeutic targets for BC patients.
Emergence of Neonatal Sepsis Caused by MCR-9- and NDM-1-Co-Producing Enterobacter hormaechei in China

Mobile colistin resistance (mcr) genes represent an emerging threat to public health. Reports on the prevalence, antimicrobial profiles, and clonality of MCR-9-producing Enterobacter cloacae complex (ECC) isolates on a national scale in China are limited. We screened 3,373 samples from humans, animals, and the environment and identified eleven MCR-9-positive ECC isolates. We further investigated their susceptibility, epidemiology, plasmid profiles, genetic features, and virulence potential. Ten strains were isolated from severe bloodstream infection cases, especially three of them were recovered from neonatal sepsis. Enterobacter hormaechei was the most predominant species among the MCR-9-producing ECC population. Moreover, the co-existence of MCR-9, CTX-M, and SHV-12 encoding genes in MCR-9-positive isolates was globally observed. Notably, mcr-9 was mainly carried by IncHI2 plasmids, and we found a novel ~187 kb IncFII plasmid harboring mcr-9, with low similarity with known plasmids. In summary, our study presented genomic insights into genetic characteristics of MCR-9-producing ECC isolates retrieved from human, animal, and environment samples with one health perspective. This study is the first to reveal NDM-1- and MCR-9-co-producing ECC from neonatal sepsis in China. Our data highlights the risk for the hidden spread of the mcr-9 colistin resistance gene.
Deep Personality Trait Recognition: A Survey

Automatic personality trait recognition has attracted increasing interest in psychology, neuropsychology, and computer science, etc. Motivated by the great success of deep learning methods in various tasks, a variety of deep neural networks have increasingly been employed to learn high-level feature representations for automatic personality trait recognition. This paper systematically presents a comprehensive survey on existing personality trait recognition methods from a computational perspective. Initially, we provide available personality trait data sets in the literature. Then, we review the principles and recent advances of typical deep learning techniques, including deep belief networks (DBNs), convolutional neural networks (CNNs), and recurrent neural networks (RNNs). Next, we describe the details of state-of-the-art personality trait recognition methods with specific focus on hand-crafted and deep learning-based feature extraction. These methods are analyzed and summarized in both single modality and multiple modalities, such as audio, visual, text, and physiological signals. Finally, we analyze the challenges and opportunities in this field and point out its future directions.
Pediatric Moyamoya Disease and Syndrome in Italy: A Multicenter Cohort

Background Moyamoya is a rare progressive cerebral arteriopathy, occurring as an isolated phenomenon (moyamoya disease, MMD) or associated with other conditions (moyamoya syndrome, MMS), responsible for 6–10% of all childhood strokes and transient ischemic attacks (TIAs). Methods We conducted a retrospective multicenter study on pediatric-onset MMD/MMS in Italy in order to characterize disease presentation, course, management, neuroradiology, and outcome in a European country. Results A total of 65 patients (34/65 women) with MMD (27/65) or MMS (38/65) were included. About 18% (12/65) of patients were asymptomatic and diagnosed incidentally during investigations performed for an underlying condition (incMMS), whereas 82% (53/65) of patients with MMD or MMS were diagnosed due to the presence of neurological symptoms (symptMMD/MMS). Of these latter, before diagnosis, 66% (43/65) of patients suffered from cerebrovascular events with or without other manifestations (ischemic stroke 42%, 27/65; TIA 32%, 21/65; and no hemorrhagic strokes), 18% (12/65) of them reported headache (in 4/12 headache was not associated with any other manifestation), and 26% (17/65) of them experienced multiple phenotypes (≥2 among: stroke/TIA/seizures/headache/others). Neuroradiology disclosed ≥1 ischemic lesion in 67% (39/58) of patients and posterior circulation involvement in 51% (30/58) of them. About 73% (47/64) of patients underwent surgery, and 69% (45/65) of them received aspirin, but after diagnosis, further stroke events occurred in 20% (12/61) of them, including operated patients (11%, 5/47). Between symptom onset and last follow-up, the overall patient/year incidence of stroke was 10.26% (IC 95% 7.58–13.88%). At last follow-up (median 4 years after diagnosis, range 0.5–15), 43% (26/61) of patients had motor deficits, 31% (19/61) of them had intellectual disability, 13% (8/61) of them had epilepsy, 11% (7/61) of them had behavioral problems, and 25% (13/52) of them had mRS > 2. The proportion of final mRS > 2 was significantly higher in patients with symptMMD/MMS than in patients with incMMS (p = 0.021). Onset age <4 years and stroke before diagnosis were significantly associated with increased risk of intellectual disability (p = 0.0010 and p = 0.0071, respectively) and mRS > 2 at follow-up (p = 0.0106 and p = 0.0009, respectively). Conclusions Moyamoya is a severe condition that may affect young children and frequently cause cerebrovascular events throughout the disease course, but may also manifest with multiple and non-cerebrovascular clinical phenotypes including headache (isolated or associated with other manifestations), seizures, and movement disorder. Younger onset age and stroke before diagnosis may associate with increased risk of worse outcome (final mRS > 2).
Anticholinergic Drug Exposure Increases the Risk of Delirium in Older Patients Undergoing Elective Surgery

Introduction Postoperative delirium (POD) is a common and serious adverse event of surgery in older people. Because of its great impact on patients' safety and quality of life, identification of modifiable risk factors could be useful. Although preoperative medication intake is assumed to be an important modifiable risk factor, the impact of anticholinergic drugs on the occurrence of POD seems underestimated in elective surgery. The aim of this study was to investigate the association between preoperative anticholinergic burden and POD. We hypothesized that a high preoperative anticholinergic burden is an independent, potentially modifiable predisposing and precipitating factor of POD in older people. Methods Between November 2017 and April 2019, 1,470 patients of 70 years and older undergoing elective orthopedic, general, cardiac, or vascular surgery were recruited in the randomized, prospective, multicenter PAWEL trial. Anticholinergic burden of a sub-cohort of 899 patients, who did not receive a multimodal intervention for preventing POD, was assessed by two different tools at hospital admission: The established Anticholinergic Risk Scale (ARS) and the recently developed Anticholinergic Burden Score (ABS). POD was detected by confusion assessment method (CAM) and a validated post discharge medical record review. Logistic regression analyses were performed to evaluate the association between anticholinergic burden and POD. Results POD was observed in 210 of 899 patients (23.4%). Both ARS and ABS were independently associated with POD. The association persisted after adjustment for relevant confounding factors such as age, sex, comorbidities, preoperative cognitive and physical status, number of prescribed drugs, surgery time, type of surgery and anesthesia, usage of heart-lung-machine, and treatment in intensive care unit. If a patient was taking one of the 56 drugs listed in the ABS, risk for POD was 2.7-fold higher (OR = 2.74, 95% CI = 1.55–4.94) and 1.5-fold higher per additional point on the ARS (OR = 1.54, 95% CI = 1.15–2.02). Conclusion Preoperative anticholinergic drug exposure measured by ARS or ABS was independently associated with POD in older patients undergoing elective surgery. Therefore, identification, discontinuation or substitution of anticholinergic medication prior to surgery may be a promising approach to reduce the risk of POD in older patients.
Mechanism of Electroacupuncture Against Cerebral Ischemia–Reperfusion Injury: Reducing Inflammatory Response and Cell Pyroptosis by Inhibiting NLRP3 and Caspase-1

Cell pyroptosis is one of the main forms of neuronal injury after cerebral ischemia–reperfusion. It is accompanied by an inflammatory reaction and regulated by the caspase gene family. Electroacupuncture (EA) can reduce neuronal injury caused by cerebral ischemia–reperfusion, and we speculated that EA can prevent neuronal pyroptosis after cerebral ischemia–reperfusion by regulating the nucleotide-binding oligomerization domain-like receptor protein 3 (NLRP3)/caspase-1 pathway. The cerebral ischemia–reperfusion injury model of C57 and caspase-1 gene knockout (Cas-1 ko) mice was established by Longa's method. EA was conducted at acupoints Chize (LU5), Hegu (LI4), Sanyinjiao (SP6), and Zusanli (ST36) for 1.5 h after cerebral ischemia–reperfusion injury for 20 min, and observation was carried out after 24 h. Neurological deficit scores evaluated the neurological function, cerebral infarction volume was observed by triphenyl tetrazolium chloride (TTC) staining, hematoxylin and eosin (H&E) staining, TUNEL and caspase-1 double-labeled fluorescence staining, and NLRP3 and caspase-1 double-labeled immunofluorescence staining that were used to observe the morphology of neurons in hippocampus, and the protein expression of NLRP3, pro-caspase-1, cleaved caspase-1 p20, pro-interleukin-1β (IL-1β), cleaved IL-1β, and GSDMD was detected by Western blot assay. Results showed that EA could reduce the score of neurological deficit, reduce the volume of cerebral infarction and improve the degree of nerve cell injury, and inhibit NLRP3, pro-caspase-1, cleaved caspase-1 p20, pro-IL-1β, cleaved IL-1β, and GSDMD protein expression. In summary, EA plays a neuroprotective role by reducing the pyroptotic neurons that were caspase 1-mediated and inflammatory response after cerebral ischemia–reperfusion.