Miracle-dz/UniFAR-FTUs huggingface dataset:
An Improved Tat/Rev Induced Limiting Dilution Assay With Enhanced Sensitivity and Breadth of Detection

Tat/Rev Induced Limiting Dilution Assay (TILDA) is instrumental in estimating the size of latent reservoirs of HIV-1. Here, we report an optimized TILDA containing a broader detection range compared to the reported methods and high sensitivity. Giving priority to sequence conservation, we positioned the two forward primers and the probe in exon-1 of HIV-1. The reverse primers are positioned in highly conserved regions of exon-7. The optimized TILDA detected eight molecular clones belonging to five major genetic subtypes of HIV-1 with a comparable detection sensitivity. Using the optimized assay, we show that only a minor proportion of CD4+ T cells of primary clinical samples can spontaneously generate multiply spliced viral transcripts. A significantly larger proportion of the cells produced viral transcripts following activation. The optimized TILDA is suitable to characterize HIV-1 latent reservoirs and the therapeutic strategies intended to target the reservoir size.
Identifying Imaging Genetics Biomarkers of Alzheimer’s Disease by Multi-Task Sparse Canonical Correlation Analysis and Regression

Imaging genetics combines neuroimaging and genetics to assess the relationships between genetic variants and changes in brain structure and metabolism. Sparse canonical correlation analysis (SCCA) models are well-known tools for identifying meaningful biomarkers in imaging genetics. However, most SCCA models incorporate only diagnostic status information, which poses challenges for finding disease-specific biomarkers. In this study, we proposed a multi-task sparse canonical correlation analysis and regression (MT-SCCAR) model to reveal disease-specific associations between single nucleotide polymorphisms and quantitative traits derived from multi-modal neuroimaging data in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort. MT-SCCAR uses complementary information carried by multiple-perspective cognitive scores and encourages group sparsity on genetic variants. In contrast with two other multi-modal SCCA models, MT-SCCAR embedded more accurate neuropsychological assessment information through linear regression and enhanced the correlation coefficients, leading to increased identification of high-risk brain regions. Furthermore, MT-SCCAR identified primary genetic risk factors for Alzheimer’s disease (AD), including rs429358, and found some association patterns between genetic variants and brain regions. Thus, MT-SCCAR contributes to deciphering genetic risk factors of brain structural and metabolic changes by identifying potential risk biomarkers.
The Impact of Vascular Risk Factors on Post-stroke Cognitive Impairment: The Nor-COAST Study

Introduction: Post-stroke cognitive impairment (PSCI) is common, but evidence on the impact of vascular risk factors is lacking. We explored the association between pre-stroke vascular risk factors and PSCI and studied the course of PSCI. Materials and Methods: Vascular risk factors were collected at baseline in stroke survivors (n = 635). Cognitive assessments of attention, executive function, memory, language, and the Montreal Cognitive Assessment (MoCA) were performed at 3 and/or 18 months post-stroke. Stroke severity was assessed with the National Institutes of Health Stroke Scale (NIHSS). PSCI was measured with global z; MoCA z-score; and z-score of the four assessed cognitive domains. Mixed-effect linear regression was applied with global z, MoCA z-score, and z-scores of the cognitive domains as dependent variables. Independent variables were the vascular risk factors (hypertension, hypercholesterolemia, smoking, diabetes mellitus, atrial fibrillation, coronary heart disease, previous stroke), time, and the interaction between these. The analyses were adjusted for age, education, and sex. There were between 5 and 25% missing data for the variables for PSCI. Results: Mean age was 71.6 years (SD 11.7); 42% were females; and the mean NIHSS score at admittance was 3.8 (SD 4.8). Regardless of vascular risk factors, global z, MoCA, and all the assessed cognitive domains were impaired at 3 and 18 months, with MoCA being the most severely impaired. Atrial fibrillation (AF) was associated with poorer language at 18 months and coronary heart disease (CHD) with poorer MoCA at 18 months (LR = 12.80, p = 0.002, and LR = 8.32, p = 0.004, respectively). Previous stroke was associated with poorer global z and attention at 3 and 18 months (LR = 15.46, p < 0.001, and LR = 16.20, p < 0.001). In patients without AF, attention improved from 3 to 18 months, and in patients without CHD, executive function improved from 3 to 18 months (LR = 10.42, p < 0.001, and LR = 9.33, p = 0.009, respectively). Discussion: Our findings indicate that a focal stroke lesion might be related to pathophysiological processes leading to global cognitive impairment. The poorer prognosis of PSCI in patients with vascular risk factors emphasizes the need for further research on complex vascular risk factor interventions to prevent PSCI.
Evaluation of the Radiomics Method for the Prediction of Atypical Adenomatous Hyperplasia in Patients With Subcentimeter Pulmonary Ground-Glass Nodules

Objectives We aimed to develop a prediction model to distinguish atypical adenomatous hyperplasia (AAH) from early lung adenocarcinomas in patients with subcentimeter pulmonary ground-glass nodules (GGNs), which may help avoid aggressive surgical resection for patients with AAH. Methods Surgically confirmed cases of AAH and lung adenocarcinomas manifesting as GGNs of less than 1 cm were retrospectively collected. A prediction model based on radiomics and clinical features identified from a training set of cases was built to differentiate AAH from lung adenocarcinomas and tested on a validation set. Results Four hundred and eighty-five eligible cases were included and randomly assigned to the training (n = 339) or the validation sets (n = 146). The developed radiomics prediction model showed good discrimination performance to distinguish AAH from adenocarcinomas in both the training and the validation sets, with, respectively, 84.1% and 82.2% of accuracy, and AUCs of 0.899 (95% CI: 0.867–0.931) and 0.881 (95% CI: 0.827–0.936). Conclusion The prediction model based on radiomics and clinical features can help differentiate AAH from adenocarcinomas manifesting as subcentimeter GGNs and may prevent aggressive resection for AAH patients, while reserving this treatment for adenocarcinomas.
Predictive Value of Serum Cytokeratin 19 Level for the Feasibility of Conserving Ovaries in Endometrial Cancer

Objective: To determine the predictive value of cytokeratin 19 (CK19) for evaluating the safety of ovarian preservation in patients with endometrial cancer (EC). Methods: Five hundred and seventeen EC patients hospitalized from November 2010 to June 2016 were reviewed retrospectively. Pre-operative tumor biomarkers including CA125, HE4, CK19, and CA19-9 were obtained. Predictive biomarkers associated with ovarian metastasis were selected using univariate and multivariate Logistic regression. The cut-off values were determined by receiver operating characteristic (ROC) curves. Kaplan-Meier method and Cox multivariate regression model was used to perform survival analysis. Results: Among clinical parameters and biomarkers included, age > 65, type II EC, CA125 ≥ 35 u/ml, CK19 > 3.3 ng/ml, and myometrial invasion ≥ 50% depth appeared as significant predictors of the risk of ovarian involvement in univariable logistic analysis. In multivariable analysis, CK19 > 3.3 ng/ml (OR = 11.541, 95%CI: 1.968–67.668, P = 0.007) and Type II EC (OR = 8.336, 95%CI: 1.456–47.722, P = 0.017) were independent risk predictors of ovarian metastasis in pre-menopausal women. In pre-menopausal women with Type I EC (n = 142), CK19 level could satisfactorily predict the risk of ovarian metastasis (AUC = 0.860, 95%CI: 0.792–0.912, P < 0.001), and when the cut-off point was set as 2.45 ng/ml, the negative predictive value and negative likelihood ratio were 99% and 0.19, with the maximum Youden index of 0.598. Conclusions: The present study advocates the necessity of incorporating serum CK19 measurement into the pre-operative evaluation of EC, especially as extension of current standard approach with ovarian preservation counseling.
Phosphorylation of Dynamin-Related Protein 1 (DRP1) Regulates Mitochondrial Dynamics and Skeletal Muscle Wasting in Cancer Cachexia

Background Cancer-associated cachexia (CAC) is a syndrome characterized by skeletal muscle atrophy, and the underlying mechanisms are still unclear. Recent research studies have shed light on a noteworthy link between mitochondrial dynamics and muscle physiology. In the present study, we investigate the role of dynamin-related protein 1 (DRP1), a pivotal factor of mitochondrial dynamics, in myotube atrophy during cancer-associated cachexia. Methods Seventy-six surgical patients, including gastrointestinal tumor and benign disease, were enrolled in the study and divided to three groups: control, non-cachexia, and cancer-associated cachexia. Demographic data were collected. Their rectus abdominis samples were acquired intraoperatively. Muscle fiber size, markers of ubiquitin proteasome system (UPS), mitochondrial ultrastructure, and markers of mitochondrial function and dynamics were assayed. A cachexia model in vitro was established via coculturing a C2C12 myotube with media from C26 colon cancer cells. A specific DRP1 inhibitor, Mdivi-1, and a lentivirus of DRP1 knockdown/overexpression were used to regulate the expression of DRP1. Muscle diameter, mitochondrial morphology, mass, reactive oxygen species (ROS), membrane potential, and markers of UPS, mitochondrial function, and dynamics were determined. Results Patients of cachexia suffered from a conspicuous worsened nutrition status and muscle loss compared to patients of other groups. Severe mitochondrial swelling and enlarged area were observed, and partial alterations in mitochondrial function were found in muscle. Analysis of mitochondrial dynamics indicated an upregulation of phosphorylated DRP1 at the ser616 site. In vitro, cancer media resulted in the atrophy of myotube. This was accompanied with a prominent unbalance of mitochondrial dynamics, as well as enhanced mitochondrial ROS and decreased mitochondrial function and membrane potential. However, certain concentrations of Mdivi-1 and DRP1 knockdown rebalanced the mitochondrial dynamics, mitigating this negative phenotype caused by cachexia. Moreover, overexpression of DRP1 aggravated these phenomena. Conclusion In clinical patients, cachexia induces abnormal mitochondrial changes and possible fission activation for the atrophied muscle. Our cachexia model in vitro further demonstrates that unbalanced mitochondrial dynamics contributes to this atrophy and mitochondrial impairment, and rebuilding the balance by regulating of DRP1 could ameliorate these alterations.
Characterization of Tigecycline Resistance Among Tigecycline Non-susceptible Klebsiella pneumoniae Isolates From Humans, Food-Producing Animals, and in vitro Selection Assay

Emergence of extensively drug-resistant isolates of Klebsiella pneumoniae has prompted increased reliance on the last-resort antibiotics such as tigecycline (TGC) for treating infections caused by these pathogens. Consumption of human antibiotics in the food production industry has been found to contribute to the current antibiotic resistance crisis. In the current study, we aimed to investigate the mechanisms of TGC resistance among 18 TGC-non-susceptible (resistant or intermediate) K. pneumoniae (TGC-NSKP) isolates obtained from human (n = 5), food animals (n = 7), and in vitro selection experiment (n = 6). Isolates were genotyped by multilocus sequence typing (MLST). ramR, acrR, rpsJ, tetA, and mgrB (for colistin resistance) genes were sequenced. The presence of tetX, tetX1, and carbapenemase genes was examined by PCR. Susceptibility to different classes of antibiotics was evaluated by disc diffusion and broth macrodilution methods. The expression level of acrB was quantified by RT-qPCR assay. The 12 TGC-NSKP isolates [minimum inhibitory concentrations (MICs) = 4–32 mg/l] belonged to 10 distinct sequence types including ST37 (n = 2), ST11, ST15, ST45, ST1326 (animal isolates); ST147 (n = 2, human and animal isolates); and ST16, ST377, ST893, and ST2935 (human isolates). Co-resistance to TGC and colistin was identified among 57 and 40% of animal and human isolates, respectively. All human TGC-NSKP isolates carried carbapenemase genes (blaOXA–48, blaNDM–1, and blaNDM–5). tetX/X1 genes were not detected in any isolates. About 83% of TGC-NSKP isolates (n = 15) carried ramR and/or acrR alterations including missense/nonsense mutations (A19V, L44Q, I141T, G180D, A28T, R114L, T119S, Y59stop, and Q122stop), insertions (positions +205 and +343), or deletions (position +205) for ramR, and R90G substitution or frameshift mutations for acrR. In one isolate ramR amplicon was not detected using all primers used in this study. Among seven colistin-resistant isolates, five harbored inactivated/mutated MgrB due to premature termination by nonsense mutations, insertion of IS elements, and frameshift mutations. All isolates revealed wild-type RpsJ and TetA (if present). Increased expression of acrB gene was detected among all resistant isolates, with the in vitro selected mutants showing the highest values. A combination of RamR and AcrR alterations was involved in TGC non-susceptibility in the majority of studied isolates.
Light-Controlled Friction by Carboxylic Azobenzene Molecular Self-Assembly Layers

Nowadays, reversible friction regulation has become the focus of scientists in terms of the flexible regulatory structure of photosensitive materials and theories since this facilitates rapid development in this field. Meanwhile, as an external stimulus, light possesses great potential and advantages in spatiotemporal control and remote triggering. In this work, we demonstrated two photo-isomerized organic molecular layers, tetra-carboxylic azobenzene (NN4A) and dicarboxylic azobenzene (NN2A), which were selected to construct template networks on the surface of the highly oriented pyrolytic graphite (HOPG) to study the friction properties, corresponding to the arrangement structure of self-assembled layers under light regulation. First of all, the morphology of the self-assembled layers were characterized by a scanning tunneling microscope (STM), then the nanotribological properties of the template networks were measured by atomic force microscope (AFM). Their friction coefficients are respectively changed by about 0.6 and 2.3 times under light control. The density functional theory (DFT) method was used to calculate the relationship between the force intensity and the friction characteristics of the self-assembled systems under light regulation. Herein, the use of external light stimulus plays a significant role in regulating the friction properties of the interface of the nanometer, hopefully serving as a fundamental basis for further light-controlling research for the future fabrication of advanced on-surface devices.
Anti-Predator Vigilance as an Indicator of the Costs and Benefits of Supplemental Feeding in Newly Released ‘Alalā (Corvus hawaiiensis)

Although supplemental feeding is commonly used as a conservation strategy during animal translocations, it comes with a number of pros and cons which can be hard to quantify. Providing additional food resources may lead to improved physical health, survivorship, and reproduction. However, offering predictable food sources could make individuals more conspicuous to predators and less aware of their surroundings, disrupting their natural predator-prey dynamic. Decisions such as release cohort size and supplemental feeder design could influence the balance of these costs and benefits, depending on how animals behave in the face of predation risk and static food sources. Additionally, animals released to the wild from long term human care must balance foraging and predation risk while adjusting to a novel environment. To help conservation managers make informed decisions in light of these potential costs, we studied the behavior of a cohort of 11 conservation-bred ‘alalā (Corvus hawaiiensis) at supplemental feeding stations after release into the wild. Vigilance, foraging behavior and social group size was quantified via 1,320 trail camera videos of ‘alalā over the span of 12 months. We found that vigilance increased over time since release, suggesting that ‘alalā learn and adjust to their novel surroundings. Both vigilance and eating decreased with group size, indicating that although conspecifics may share the burden of scanning for threats, they also increase competition for food. We also found that the design of the feeder may have limited birds' abilities to express anti-predator behavior since less vigilance was observed in individuals that manipulated the feeder. Yet, birds may have been able to offset these costs since they increasingly scrounged for food scraps next to the feeder as time progressed. We discuss how changes to behavior over time, social interactions, and feeder design should all be considered when planning supplemental feeding as part of wildlife translocations.
Effect of Dietary Supplementation With Mixed Organic Acids on Immune Function, Antioxidative Characteristics, Digestive Enzymes Activity, and Intestinal Health in Broiler Chickens

The purpose of this study was to explore the effect of dietary supplementation with mixed organic acids on intestinal health, enzyme activity, and antioxidative characteristics in broilers. A total of 192 1-day-old chicks were evenly allocated to three experimental groups with eight replicates, a basal diet with 0 (Control), 3,000 mg/kg (LMOA), 6,000 mg/kg (HMOA) mixed organic acid. The tissue and serum samples were gathered on 21 and 42 d of the experiment. An increased (P < 0.05) concentration of IgA, D-lactate (D-LA), and interleukin-10 (IL-10) in the serum of broilers diets with HMOA was observed. The levels of total antioxidant capacity (T-AOC) and catalase activity (CAT) in serum were enhanced (P < 0.05) with dietary and mixed organic acid, respectively, and increased (P < 0.05) content of superoxide dismutase (SOD) and CAT in the duodenum of broilers diets with LMOA was noticed. Also, LMOA decreased (P < 0.05) the pH value of the duodenum and enhanced (P < 0.05) the amylase activity of the pancreas, the tight junction protein (mainly Claudin-1, Claudin-2, and ZO-1) in the duodenum of broilers fed with mixed organic acid were promoted (P < 0.05), and the LMOA group performed better in the small intestine. In cecum microbiota, LMOA and HMOA modulated the structure of microbiota and mainly reduced the relative abundance of Escherichia coli. In brief, dietary supplemented mixed organic acid improved the health status of broilers by promoting the immune function, enhancing the antioxidative characteristics and tight junction proteins expression as well as cecum microbiota. However, LMOA groups may be a better fit considering the comprehensive effects of experiments and economic costs.
Identification of Gray Leaf Spot Disease Candidate Gene in Narrow-Leafed Lupin (Lupinus angustifolius L.)

Selection for resistance against gray leaf spot (GLS) is a major objective in the lupin breeding programs. A segregation ratio of 1:1 (resistant:susceptible) in F8 recombinant inbred lines (RIL8) derived from a cross between a breeding line 83A:476 (resistant to GLS) and a wild accession P27255 (susceptible to GLS) indicated that GLS was controlled by a single major gene. To develop molecular markers linked to GLS, in the beginning, only 11 resistant lines and six susceptible lines from the 83A:476 and P27255 population were genotyped with MFLP markers, and three MFLP markers were identified to be co-segregated with GLS. This method was very efficient, but the markers were located outside of the gene, and could not be used in other germplasms. Then QTL analysis and fine mapping were conducted to identify the gene. Finally, the gene was narrowed down to a 241-kb region containing two disease resistance genes. To further identify the candidate gene, DNA variants between accessions Tanjil (resistant to GLS) and Unicrop (susceptible to GLS) were analyzed. The results indicated that only one SNP was detected in the 241 kb region. This SNP was located in the TMV resistance protein N-like gene region and also identified between 83A:476 and P27255. Genotyping the Tanjil/Unicrop RIL8 population showed that this SNP co-segregated with GLS resistance. The phylogenetic tree analysis of this gene among 18 lupin accessions indicates that Australian resistant breeding line/varieties were clustered into one group and carry two resistant alleles, while susceptible accessions were clustered into different groups.
Nondestructive Testing for Corrosion Evaluation of Metal under Coating

The use of steel has grown rapidly over the past decades. However, corrosion under coating detection still presents challenges for nondestructive testing (NDT) techniques. One of such challenges is the lift-off introduced by complex structures. Inaccessibility due to structure leads corrosion to be undetected, which can lead to catastrophic failure. Furthermore, lift-off effects reduce the sensitivities. The limitations of existing NDT techniques heighten the need for novel approaches to the characterization of corrosion. This paper begins with a discussion of the challenges associated with corrosion detection of metal under coating. Secondly, reviews are given of the most NDT methods used for the detection of corrosion under coating. The different techniques based on nondestructive testing methods such as ultrasonic, acoustic, electromagnetic, radiographic, and thermographic have been detailed out. This review presents the significance and advantages provided by the emerging NDT techniques. In the end, the trends and identified problems are summarized.
Networked Unmanned Aerial Vehicles for Surveillance and Monitoring: A Survey

As a typical cyber-physical system, networked unmanned aerial vehicles (UAVs) have received much attention in recent years. Emerging communication technologies and high-performance control methods enable networked UAVs to operate as aerial sensor networks to collect more complete and consistent information with significantly improved mobility and flexibility than traditional sensing platforms. One of the main applications of networked UAVs is surveillance and monitoring, which constitute essential components of a well-functioning public safety system and many industrial applications. Although the existing literature on surveillance and monitoring UAVs is extensive, a comprehensive survey on this topic is lacking. This article classifies publications on networked UAVs for surveillance and monitoring using the targets of interest and analyzes several typical problems on this topic, including the control, navigation, and deployment optimization of UAVs. The related research gaps and future directions are also presented.