Miracle-dz/UniFAR-FTUs huggingface dataset:
QuantiFERON-TB Gold Plus Assay in Patients With Latent vs. Active Tuberculosis in a Low Incidence Setting: Level of IFN-γ, CD4/CD8 Responses, and Release of IL-2, IP-10, and MIG

Objectives We analyzed the results of the QuantiFERON Glod Plus assay (QFT) and cytokine patterns associated with active tuberculosis (ATB) among patients with positive QFT. Methods A total of 195 patients are QFT-positive, among which 24 had an ATB and 171 had a latent tuberculosis infection (LTBI). Interferon-gamma (IFN-γ) secretion was analyzed relative to interleukin-2 (IL-2), IFN-γ inducible protein or CXCL-10 (IP-10), and monokine induced by IFN-γ or CXCL-9 (MIG) secretion, and then compared between two sets of peptide antigens [tube 1 - cluster of differentiation 4 (CD4+) T cell stimulation; tube 2 - CD4+/CD8+ T cell response]. Results Higher IFN-γ responses were measured in the ATB group (p = 0.0089). The results showed that there was a lower ratio of tube 1/tube 2 IFN-γ concentrations in the ATB group (p = 0.0009), and a median [interquartile ranges (IQR)] difference between the two sets at −0.82 IU/ml (−1.67 to 0.18) vs. −0.07 IU/ml (−0.035 to 0.11, p < 0.0001) in the ATB group compared to the LTBI group, respectively. In addition, patients with low ratios of IL-2/IFN-γ, IP-10/IFN-γ, and MIG/IFN-γ were much more likely to have ATB. Conclusion High levels of IFN-γ secretion, preferential IFN-γ response in tube 2, and lower secretion of IL-2, IP-10, and MIG release relative to IFN-γ secretion were more likely observed in subjects with ATB. These features of T cell response may be helpful in low prevalence settings to suspect ATB in patients tested positive for IFN-γ release assays (IGRA).
Neurological Adverse Events Associated With Esketamine: A Disproportionality Analysis for Signal Detection Leveraging the FDA Adverse Event Reporting System

Esketamine was approved for the treatment of treatment-resistant depression in 2019. After the approval of esketamine, numerous concerns have been raised regarding its long-term safety and tolerability. A previous systematic pharmacovigilance study on esketamine-related adverse events (AEs) was published in 2020; however, it has not been updated 2 years later. The primary aim of this study was to detect and characterize neurological safety signals of esketamine to partially update the knowledge in this field using the FDA pharmacovigilance database. Reporting odds ratio (ROR) was calculated for esketamine-related neurological AEs from 2019 to 2021 with a signal considered when the lower limit of the 95% confidence interval (CI) of ROR (ROR025) exceeded one. Severe and non-severe cases were compared using an independent samples t-test or chi-squared (χ2) test, and a rating scale was used to prioritize the signals. The database contained 720 cases of esketamine-associated neurological AEs, with 21 signals detected, ranging from a ROR025 of 1.05 (disturbance in attention) to 204.00 (sedation). 16 latest neurological AEs emerged in the second year of marketing approval of esketamine, with eight signals detected. The associations between esketamine and nervous system disorders persisted when stratifying by sex, age, and reporter type, whereas the spectrum of neurological AEs differed in stratification regimens. Esketamine dosage, antidepressant polypharmacy, or co-prescription with benzodiazepines affected AEs severity (t = 2.41, p = 0.017; χ2 = 6.75, p = 0.009; and χ2 = 4.10, p = 0.043; respectively), while age and sex did not (p = 0.053 and p = 0.397, respectively). Three signals were categorized as moderate clinical priority [i.e., sedation, dizziness, and dysgeusia (priority points 7, 5, and 5, respectively)], showing the same early failure type profiles. Notably, seven detected disproportionality signals were not previously detected in clinical trials. Although the majority of results were in line with those obtained in the previous study, there were discrepancies in the spectrum of neurological AEs and the effects of several risk factors on AEs severity among the two studies that should be recognized and managed early in clinical treatments.
DNA Barcoding Reveals High Hidden Species Diversity of Chinese Waters in the Cephalopoda

Species delimitation by traditional morphological methods is challenging in cephalopods due to their flexible bodies, changeable pigment traits, and sometimes high morphological homoplasy. Molecular information provides important assistance for taxonomic decision. In this study, we applied three species delimitation methods on 132 cephalopods from 7 families along Chinese waters, and we found anunderestimated species diversity in these taxa. A maximum of 56 molecular operational taxonomic units was detected, and possible cryptic diversities were revealed in Loliolus beka, Uroteuthis edulis, Octopus minor, Amphioctopus fangsiao, and Hapalochlaena lunulate. This study provides molecular evidence for the hidden species diversity along Chinese waters, and it provides insight into further taxonomic research on these morphologically variable taxa.
Reanalyzing the Maia and McClelland (2004) Empirical Data: How Do Participants Really Behave in the Iowa Gambling Task?

Background Since 2007, the Iowa Gambling Task (IGT) has been a standardized clinical assessment tool for assessing decision behavior in 13 psychiatric/neurological conditions. After the publication of Maia and McClelland's (1) article, there were two responses in 2005 from Bechara et al. and Maia and McClelland, respectively, discussing whether implicit emotion or explicit knowledge influences the development of foresighted decision strategies under uncertain circumstances (e.g., as simulated in the IGT). Methods and Results We reanalyze and verify the data obtained by Maia and McClelland (1) in their study “What participants really know in the Iowa Gambling Task” and find that decision-makers were lured into shortsighted decisions by the prospect of immediate gains and losses. Conclusion Although the findings of this reanalysis cannot support any arguments concerning the effect of either implicit emotion or explicit knowledge, we find evidence that, based on the gain–loss frequency in the IGT, participants behave myopically. This is consistent with most IGT-related articles (58 out of 86) in Lee et al.'s (2) cross-cultural review. Alternatively, under uncertain circumstances, there is probably no such thing as foresighted decision strategy irrespective of the proposed mechanisms of implicit emotion or explicit knowledge.
Predicting the Intention and Adoption of Near Field Communication Mobile Payment

With the increasing use of mobile devices and new technologies, electronic payments, such as near field communication (NFC) mobile payments, are gaining traction and gradually replacing the currency-based cash payment methods. Despite multiple initiatives by various parties to encourage mobile payments, adoption rates in developing countries have remained low. The purpose of this research is to explore the prime determinants of NFC mobile-payment adoption intention and to develop a model of mobile payment adoption that includes perceived risk (PR) as one of the major elements by extending the UTAUT2 theory components. An online survey was used to acquire data from 370 NFC mobile payments users for the current study. To validate the components and their correlations, structural equation modelling (SEM) was implemented. According to the findings, performance expectancy (PE), hedonic motivation (HM), social influence (SI), and facilitating conditions (FC) have substantial impacts on the consumers’ intentions to adopt NFC mobile payments (INFC). Effort expectancy (EE) and PR were reported to have no considerable effects on the adoption intention. In addition, INFC is revealed to be a major mediator between the associations of the actual adoption of NFC mobile payment (ANFC) with PE, HM, and SI. The findings of the study would assist providers and marketers in better understanding of the consumers’ behavior, designing effective marketing strategies to enhance the consumers’ positive intentions, and achieving the mass adoption of NFC mobile payments in different environmental contexts.
A Chromosome-Level Reference Genome of Chinese Balloon Flower (Platycodon grandiflorus)

Chinese balloon flower (Platycodon grandiflorus) is the sole species in genus Platycoldon within the Campanulaceae family. The typical blue purple or white flowers of P. grandiflorus are frequently used for ornamental purposes (Lv et al., 2021). As a traditional oriental medicine used to treat chronic inflammatory diseases, P. grandiflorus roots have rich pharmacological activities such as expectorant antitussive, anti-inflammatory, immune regulatory and antitumor effects (Choi et al., 2010; Nyakudya et al., 2014; Buchwald et al., 2020; Ke et al., 2020; Lee et al., 2020). The dried form of the Platycodi radix is officially listed as a traditional herbal medicine in the Chinese, Korean and Japanese Pharmacopoeia (Su et al., 2021). Platycodi radix is also being pickled in northeast China, and made into kimchi in the Korean Peninsula. The market demand of P. grandiflorus follows the development and application of medicine, food, health products, cosmetics, ornamental and other fields (Ji et al., 2020), and its market prospects are bright. Over 100 secondary metabolites have been isolated from P. grandiflorus including triterpenoid saponins, flavonoids, polyphenols, polysaccharide and so on (Zhang et al., 2015; Qiu et al., 2019; Huang et al., 2021). So far, the pharmacological and metabolic pathways of the main active ingredient triterpenoid saponins have been studied (Kim et al., 2020; Kim et al., 2021; Yu et al., 2021). However, the molecular basis of biochemical pathways for P. grandiflorus secondary metabolites is overall poorly understood, hindering the progress of molecular breeding and metabolic engineering of P. grandiflorus towards increased production and utilization of its natural products. A high-quality genome assembly of the P. grandiflorus will significantly accelerate the genetic characterization of secondary metabolic pathways, their regulatory mechanisms and genome-assisted breeding. Previously, a draft genome sequence of P. grandiflorus (2n = 2x = 18) was assembled using Illumina short reads by Kim et al. yielding a quite fragmented assembly with scaffold N50 of 277 kb (Kim et al. 2020). In this study, we assembled and annotated a chromosome-scale reference genome for P. grandiflorus cultivar XJD. This genome assembly has a total length of 622.86 Mb anchored to nine chromosomes with a high contiguity (contig N50 = 29.34Mb, scaffold N50 = 65.83 Mb), representing a significant improvement over the previously published draft genome of P. grandiflorus (Kim et al., 2020). The chromosome-scale genome assembly will advance our understanding of genome function and evolution of P. grandiflorus, and facilitate its molecular breeding and metabolic engineering. Edited by: Sunil Kumar Sahu, Beijing Genomics Institute (BGI), China
Diagnostic Value of Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing in Pneumocystis jirovecii Pneumonia in Non-HIV Immunosuppressed Patients

Introduction This study aims to assess the value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in the diagnosis of Pneumocystis jirovecii pneumonia (PJP) and its mixed infection in non-human immunodeficiency virus (HIV) immunosuppressed patients. Methods A total of 198 non-HIV immunosuppressed patients with severe pneumonia were enrolled, including 77 PJP patients and 121 patients infected by other pathogens. BALF-mNGS and traditional detection methods were used. Results The positive detection rate of various pathogens of BALF-mNGS was higher than that of the conventional methods, especially for mixed pathogens. The sensitivity and specificity of BALF-mNGS for the diagnosis of PJP were 97.40% and 85.12%, respectively. Compared with traditional methods, the sensitivity of BALF-mNGS was significantly higher than that of blood fungal G (BG)/lactate dehydrogenase (LDH) and BALF-microscopy (p<0.05), and its specificity was significantly higher than that of BG/LDH (p<0.05). In addition, the average detection time of BALF-mNGS (32.76 ± 10.32 h) was also significantly shorter than conventional methods (p<0.01), especially for mixed infections that were common in non-HIV immunosuppressed patients. In patients only detected as positive by BALF-mNGS, the underlying diseases mainly manifested as hematological malignancies with agranulocytosis and within 8 months after hematopoietic stem cell or solid organ transplantation. Conclusions BALF-mNGS technology is faster, more sensitive, and more comprehensive in detecting P. jirovecii and its mixed infection in immunosuppressed patients.
Color Constancy via Multi-Scale Region-Weighed Network Guided by Semantics

In obtaining color constancy, estimating the illumination of a scene is the most important task. However, due to unknown light sources and the influence of the external imaging environment, the estimated illumination is prone to color ambiguity. In this article, a learning-based multi-scale region-weighed network guided by semantic features is proposed to estimate the illuminated color of the light source in a scene. Cued by the human brain's processing of color constancy, we use image semantics and scale information to guide the process of illumination estimation. First, we put the image and its semantics into the network, and then obtain the region weights of the image at different scales. After that, through a special weight-pooling layer (WPL), the illumination on each scale is estimated. The final illumination is calculated by weighting each scale. The results of extensive experiments on Color Checker and NUS 8-Camera datasets show that the proposed approach is superior to the current state-of-the-art methods in both efficiency and effectiveness.
Sarcopenia and Systemic Inflammation Response Index Predict Response to Systemic Therapy for Hepatocellular Carcinoma and Are Associated With Immune Cells

Background Systemic therapies, including immune checkpoint inhibitors (ICIs) and tyrosine kinase inhibitors (TKIs), have challenged the use of conventional therapies for hepatocellular carcinoma (HCC). It is crucial to determine which patients could benefit most from combination therapy. This study aims to examine the associations of sarcopenia and systemic inflammation response index (SIRI) with the treatment responses and efficacies in patients with HCC treated with ICIs and tyrosine kinase inhibitors TKIs, as well as investigate the correlation between sarcopenia and inflammatory or immune states. Methods We reviewed 160 patients with HCC treated with TKIs and ICIs. The patients’ psoas muscle size was measured on axial computed tomography scans and normalized for the patients’ height squared. This value was referred to as the psoas muscle index (PMI). Sarcopenia was determined from PMI and their relationships with patients’ clinicopathological characteristics, inflammation indexes, peripheral blood T-cell subsets and survival were evaluated. Results Sarcopenia and systemic inflammation response index (SIRI) were independent predictors for overall survival and progression-free survival. Patients with high PMI and low SIRI demonstrated significantly better median overall survival and progression-free survival (36.0 months and 9.6 months, respectively) than those with either low PMI or high SIRI (20.8 months and 6.0 months, respectively) and those with both high SIRI and low PMI (18.6 months and 3.0 months, respectively). Portal vein tumor thrombus (P=0.003), eastern cooperative oncology group performance status score of 1 (P=0.048), high alkaline phosphatase (P=0.037), high neutrophil-to-lymphocyte ratio (NLR) (P=0.012), low lymphocyte-to-monocyte ratio (LMR) (P=0.031), high platelet-to-lymphocyte ratio (PLR) (P=0.022) and high SIRI (P=0.012) were closely associated with an increased incidence of sarcopenia. PMI was negatively correlated with SIRI (r = -0.175, P=0.003), NLR (r = -0.169, P=0.036), and PLR (r = -0.328, P=0.000) and was significantly positively correlated with LMR (r = 0.232, P=0.004). The CD3+ and CD4+ T-cell counts of the high PMI group were significantly higher than those of the low PMI group. Conclusion Sarcopenia and high SIRI were associated with reduced survival in patients with HCC treated with ICIs and TKIs. Sarcopenia could affect inflammatory states and the immune microenvironment.
Factors Influencing Adolescents' Dietary Behaviors in the School and Home Environment in Addis Ababa, Ethiopia

Background Malnutrition affects many adolescents in Ethiopia. Over one-third of adolescent girls and two-thirds of boys are thin. Overweight and obesity in Ethiopia is mostly a concern in urban populations of higher wealth quintiles. Urbanization and globalization of diets is shifting food environments. The objective of this study was to assess whether food environments in and around schools in urban Ethiopia influence dietary diversity, quality, BMI status or perceptions of adolescents. Methods Twelve high schools were selected in Addis Ababa (private/government). From each school, 20 pupils aged 15–19 years were randomly selected (n = 217) and interviewed about assets in their households, their diets (categorized into 10 food groups of the Minimum Dietary Diversity, the Global Dietary Recommendations scores and four categories of the NOVA classification based on level of processing) and their use of pocket money. In addition, food environment audits were conducted within the school compound and a 0.5 km radius around each school and types of food outlets. Results On average there were 436 food outlets and 246 food or drink advertisements around each school. The majority of the advertisements (89.9%) were of ultra-processed foods, mostly sugar-sweetened beverages (SSBs). Most were positioned on food outlets (89.1%). SSBs or sweets were visibly on display in 26.3% of the outlets and fresh fruits and vegetables in 17.9% of outlets. Dietary diversity of adolescents was poor with an average of 3.6 food groups out of 10 consumed in the last 24 h. Ultra-processed foods and beverages were consumed by 23.5% of adolescents. The majority of adolescents spent their pocket money on SSBs, sweets or fried foods. Our analysis found that higher assets in adolescents' households were associated with higher dietary diversity and consumption of healthy food groups. We found no association between the food environment and dietary indicators or the BMI-z-score. Conclusion While the school food environments investigated were not conducive with promoting healthy dietary behaviors, we cannot conclude that these environmental factors directly influence adolescents' diets. The pervasive advertising and availability of unhealthy foods and beverages requires policy action for healthy school food environments.
Modeling Soil Carbon Under Diverse Cropping Systems and Farming Management in Contrasting Climatic Regions in Europe

Sustainable agriculture has been identified as key to achieving the 2030 Agenda for the Sustainable Development Goals, which aims to end poverty and hunger and address climate change while maintaining natural resources. Soil organic carbon (SOC) sequestration is a key soil function for ecosystem services, and storing carbon (C) in soil by changing traditional management practices can represent an important step toward the development of more sustainable agricultural systems in Europe. Within the European project Diverfarming, the process-based ecosystem model ECOSSE was modified and evaluated in four long-term experiments (>8 years) to assess the impact of crop diversification and agricultural management in SOC dynamics. ECOSSE was able to simulate SOC under dry conditions in Mediterranean regions in Spain and Italy. In the site of Murcia, Spain, the addition of manure and cover crop in the diversified systems produced an increase of SOC in 9 years, when compared with the conventional management (16% measured increase, 32% simulated increase). The effect of tillage management on SOC stock in dry soil, in Foggia, Italy and Huesca, Spain, was also modeled, and a positive impact on SOC was predicted when no tillage was practiced. Finally, ECOSSE was used to understand the impact of diversifications in Boreal regions, Finland, where different proportions of legumes and grass were considered in a 4-year crop rotation compared with conventional cereal rotations. Experiments and modeling showed that the loss of SOC in conventional cereal was compensated when grass was introduced in the rotations. A good agreement (NRMSE <10%) and a nonsignificant bias were observed between model and experimental data for all sites. Mitigation scenarios considered in the modeling analysis for the test site Huesca showed that an integrated management of no tillage and manure is the best strategy to increase SOC, ∼51% over 20 years, compared with the baseline scenario (current farmers practice). This study demonstrated the ability of the modified version of ECOSSE to simulate SOC dynamics in diversified cropping systems, with various soil management practices and different climatic conditions.
Pathological Osteoclasts and Precursor Macrophages in Inflammatory Arthritis

Macrophages comprise a variety of subsets with diverse biological functions, including inflammation, tissue repair, regeneration, and fibrosis. In the bone marrow, macrophages differentiate into multinucleated osteoclasts, which have a unique bone-destroying capacity and play key roles in physiological bone remodelling. In contrast, osteoclasts are also involved in inflammatory bone erosion in arthritis and it has been unclear whether the osteoclasts in different tissue settings arise from similar monocytoid precursors and share similar phenotypes. Rapid progresses in the sequencing technologies have provided many important insights regarding the heterogeneity of different types of osteoclasts. The application of single-cell RNA sequencing (scRNA-seq) to the osteoclast precursor-containing macrophages enabled to identify the specific subpopulation differentiating into pathological mature osteoclasts in joints. Furthermore, an intravital imaging technology using two-photon microscopy has succeeded in visualizing the real-time dynamics of immune cells in the synovial microenvironment. These technologies together contributed to characterize the unique macrophages in the inflamed synovium, termed “arthritis-associated osteoclastogenic macrophages (AtoMs)”, causing the pathological bone destruction in inflammatory arthritis. Here, we review and discuss how novel technologies help to better understand the role of macrophages in inflammatory arthritis, especially focusing of osteoclastogenesis at the pannus-bone interface.
Research on Reservoir Characteristics and Main Controlling Factors of Longwangmiao Formation of Cambrian in Sichuan Basin

Based on the 4 measured profiles, 17 observation profiles, and 13 drilling core macroscopic and microscopic characteristics of the Cambrian Longwangmiao Formation in the Sichuan Basin, combined with analysis and testing, and reservoir logging interpretation, the reservoir characteristics and main controlling factors of the Longwangmiao Formation are analyzed. The marginal bank of the underwater paleo-uplift of the restricted platform and the point bank facies within the platform belong to the sedimentary facies belts that are most conducive to the formation and evolution of the reservoir. However, the later transformation of dolomitization and dissolution played decisive roles in the formation of the reservoir. The Caledonian epigenetic karstification is the main reason for the lack of the overlying stratum of the Cambrian in the Sichuan Basin, and it is also the most important factor for the formation of large-scale dissolved cavities in the Longwangmiao Formation in the Sichuan Basin.