Miracle-dz/UniFAR-FTUs huggingface dataset:
Screening for Lung Cancer With Low-Dose Computed Tomography: Updated Evidence Report and Systematic Review for the US Preventive Services Task Force.

Importance Lung cancer is the leading cause of cancer-related death in the US. Objective To review the evidence on screening for lung cancer with low-dose computed tomography (LDCT) to inform the US Preventive Services Task Force (USPSTF). Data Sources MEDLINE, Cochrane Library, and trial registries through May 2019; references; experts; and literature surveillance through November 20, 2020. Study Selection English-language studies of screening with LDCT, accuracy of LDCT, risk prediction models, or treatment for early-stage lung cancer. Data Extraction and Synthesis Dual review of abstracts, full-text articles, and study quality; qualitative synthesis of findings. Data were not pooled because of heterogeneity of populations and screening protocols. Main Outcomes and Measures Lung cancer incidence, lung cancer mortality, all-cause mortality, test accuracy, and harms. Results This review included 223 publications. Seven randomized clinical trials (RCTs) (N = 86 486) evaluated lung cancer screening with LDCT; the National Lung Screening Trial (NLST, N = 53 454) and Nederlands-Leuvens Longkanker Screenings Onderzoek (NELSON, N = 15 792) were the largest RCTs. Participants were more likely to benefit than the US screening-eligible population (eg, based on life expectancy). The NLST found a reduction in lung cancer mortality (incidence rate ratio [IRR], 0.85 [95% CI, 0.75-0.96]; number needed to screen [NNS] to prevent 1 lung cancer death, 323 over 6.5 years of follow-up) with 3 rounds of annual LDCT screening compared with chest radiograph for high-risk current and former smokers aged 55 to 74 years. NELSON found a reduction in lung cancer mortality (IRR, 0.75 [95% CI, 0.61-0.90]; NNS to prevent 1 lung cancer death of 130 over 10 years of follow-up) with 4 rounds of LDCT screening with increasing intervals compared with no screening for high-risk current and former smokers aged 50 to 74 years. Harms of screening included radiation-induced cancer, false-positive results leading to unnecessary tests and invasive procedures, overdiagnosis, incidental findings, and increases in distress. For every 1000 persons screened in the NLST, false-positive results led to 17 invasive procedures (number needed to harm, 59) and fewer than 1 person having a major complication. Overdiagnosis estimates varied greatly (0%-67% chance that a lung cancer was overdiagnosed). Incidental findings were common, and estimates varied widely (4.4%-40.7% of persons screened). Conclusions and Relevance Screening high-risk persons with LDCT can reduce lung cancer mortality but also causes false-positive results leading to unnecessary tests and invasive procedures, overdiagnosis, incidental findings, increases in distress, and, rarely, radiation-induced cancers. Most studies reviewed did not use current nodule evaluation protocols, which might reduce false-positive results and invasive procedures for false-positive results.
Effect of Spermidine on Biofilm Formation in Escherichia coli K-12

Previous reports have speculated on the effect of polyamines on bacterial biofilm formation. However, the regulation of biofilm formation by polyamines in Escherichia coli has not yet been assessed. ABSTRACT Polyamines are essential for biofilm formation in Escherichia coli, but it is still unclear which polyamines are primarily responsible for this phenomenon. To address this issue, we constructed a series of E. coli K-12 strains with mutations in genes required for the synthesis and metabolism of polyamines. Disruption of the spermidine synthase gene (speE) caused a severe defect in biofilm formation. This defect was rescued by the addition of spermidine to the medium but not by putrescine or cadaverine. A multidrug/spermidine efflux pump membrane subunit (MdtJ)-deficient strain was anticipated to accumulate more spermidine and result in enhanced biofilm formation compared to the MdtJ+ strain. However, the mdtJ mutation did not affect intracellular spermidine or biofilm concentrations. E. coli has the spermidine acetyltransferase (SpeG) and glutathionylspermidine synthetase/amidase (Gss) to metabolize intracellular spermidine. Under biofilm-forming conditions, not Gss but SpeG plays a major role in decreasing the too-high intracellular spermidine concentrations. Additionally, PotFGHI can function as a compensatory importer of spermidine when PotABCD is absent under biofilm-forming conditions. Last, we report here that, in addition to intracellular spermidine, the periplasmic binding protein (PotD) of the spermidine preferential ABC transporter is essential for stimulating biofilm formation. IMPORTANCE Previous reports have speculated on the effect of polyamines on bacterial biofilm formation. However, the regulation of biofilm formation by polyamines in Escherichia coli has not yet been assessed. The identification of polyamines that stimulate biofilm formation is important for developing novel therapies for biofilm-forming pathogens. This study sheds light on biofilm regulation in E. coli. Our findings provide conclusive evidence that only spermidine can stimulate biofilm formation in E. coli cells, not putrescine or cadaverine. Last, ΔpotD inhibits biofilm formation even though the spermidine is synthesized inside the cells from putrescine. Since PotD is significant for biofilm formation and there is no ortholog of the PotABCD transporter in humans, PotD could be a target for the development of biofilm inhibitors.
Down-Regulation of TMPO-AS1 Induces Apoptosis in Lung Carcinoma Cells by Regulating miR-143-3p/CDK1 Axis

Evidence has shown that long non-coding RNAs (lncRNA) play pivotal roles in cancer promotion as well as suppression. But the molecular mechanism of lncRNA TMPO antisense transcript 1 (TMPO-AS1) in lung cancer (LC) remains unclear. This study mainly investigated the effect of TMPO-AS1 in LC treatment. TMPO-AS1 was tested by Kaplan-Meier method. Quantitative real time polymerase chain reaction (qRT-PCR) was employed to assess the expressions of TMPO-AS1, miR-143-3p, and CDK1 respectively in LC tissues and cell lines. TMPO-AS1, miR-143-3p and CDK1 expressions in LC cells were regulated through cell transfection, followed by MTT for cell viability detection. Besides, dual-luciferase reporter assays were performed to verify the interrelated microRNA of TMPO-AS1 and the target of miR-143-3p. Western blot experiments were used to examine the expressions of apoptosis-related proteins, and flow cytometry tested the cell apoptosis in treated cells. TMPO-AS1 and CDK1 were overexpressed in LC tissues and cells, while miR-143-3p level was suppressed. The decrease of TMPO-AS1 led to the increase of miR-143-3p, which further resulted in the reduction of CDK1. Down-regulating TMPO-AS1 reduced LC cell viability, motivated cell apoptosis, as well as promoted the expressions of Bcl and CCND1 and restrained Caspase-3 level, but all these consequences were abrogated by miR-143-3p inhibitor. Simultaneously, siCDK1 could reverse the anti-apoptosis and pro-activity functions of miR-143-3p inhibitor in LC cells. Down-regulation of TMPO-AS1 has the effects of pro-apoptosis in LC by manipulating miR-143-3p/CDK1, which is hopeful to be a novel therapy for LC patients.
Temperature‐associated decreases in demographic rates of Afrotropical bird species over 30 years

Tropical mountains harbor globally significant levels of biodiversity and endemism. Climate change threatens many tropical montane species, yet little research has assessed the effects of climate change on the demographic rates of tropical species, particularly in the Afrotropics. Here, we report on the demographic rates of 21 Afrotropical bird species over 30 years in montane forests in Tanzania. We used mark–recapture analyses to model rates of population growth, recruitment, and apparent survival as functions of annual mean temperature and annual precipitation. For over one‐half of focal species, decreasing population growth rates were associated with increasing temperature. Due to the trend in temperature over time, we substituted a time covariate for the temperature covariate in top‐ranked population growth rate models. Temperature was a better explanatory covariate than time for 6 of the 12 species, or 29% of all focal species. Population growth rates were also lower for species found further below their elevational midpoint and for smaller‐bodied species. Changes in population growth rates were more closely tied to changes in recruitment than to changes in apparent survival. There were no consistent associations between demographic rates and precipitation. This study demonstrates temperature‐associated demographic impacts for 6 (29%) of 21 focal species in an Afrotropical understory bird community and highlights the need to incorporate the impacts of climate change on demographic rates into conservation planning across the tropics.
Circular RNA circ_0000467 regulates colorectal cancer development via miR-382-5p/EN2 axis

ABSTRACT Circular RNAs (CircRNAs), belonging to non-coding RNAs, exert a crucial modulatory role in cancer progression. In this study, circRNA microarray analysis was utilized to screen differentially expressed circRNA in colorectal cancer (CRC) and circ_0000467 was identified as one circRNA whose expression was significantly upregulated in CRC. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) indicated that circ_0000467 and engrailed-2 (EN2) expression levels were up-modulated, while the expression level of miR-382-5p was down-modulated in CRC tissues. The depletion of circ_0000467 expression was found to impede the multiplication, migration, invasion, and epithelial-mesenchymal transition (EMT) processes in CRC cells, which were examined by 3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) and Transwell experiments. Dual-luciferase reporter assay was used to verify the targeting relationship between circ_0000467 and miR-382-5p. It was also revealed that circ_0000467 could up-regulate EN2 expression via repressing miR-382-5p in CRC cells. Furthermore, EN2 overexpression counteracted the suppressing effects of circ_0000467 knockdown on the malignant behaviors of CRC cells. To sum up, circ_0000467 facilitates CRC development by modulating the miR-382-5p/EN2 axis, and circ_0000467 is a promising target for CRC therapy.
Combined Inhibition of p38MAPK and PIKfyve Synergistically Disrupts Autophagy to Selectively Target Cancer Cells

This study demonstrates that PIKfyve and p38MAPK cooperate to regulate lysosome homeostasis and their combined inhibition synergistically blocks autophagy to reduce cancer cell viability in vitro and in vivo. In nutrient-poor conditions, autophagy buffers metabolic stress and counteracts the effects of chemotherapy and radiation on cancer cells, which depend on autophagy for survival. However, clinical trials targeting autophagy have failed to produce successful anticancer treatments using currently available inhibitors. Recent studies have shown that PIKfyve kinase inhibitors disrupt lysosome function in autophagy and can selectively kill certain cancer cells. Analysis of biochemical changes caused by PIKfyve inhibition revealed that resistant cells contain significantly higher levels of cellular p38MAPK protein and phosphorylation. Expression of the lysosomal protein, lysosomal-associated membrane protein 2, carrying phosphomimetic mutations of the p38MAPK phosphorylation sites prevented all effects caused by PIKfyve inhibition–induced lysosome dysfunction. Thus, the activation of p38MAPK in response to PIKfyve inhibition revealed a novel compensatory role in maintaining lysosome function in autophagy. The functional cooperation between the cellular PIKfyve and p38MAPK pathways in regulating lysosome homeostasis was especially important in cancer cells. Combined inhibition of PIKfyve and p38MAPK activities synergistically blocked autophagy-mediated protein degradation, prevented cathepsin maturation, and markedly reduced the viability of multiple cancer cell types without affecting the viability of normal cells. Furthermore, combined PIKfyve and p38MAPK inhibitors synergistically reduced tumor growth in mice bearing xenografts of human colorectal adenocarcinoma, suggesting a novel way to target cancer cells by prolonged inhibition of autophagy using lower drug concentrations. Significance: This study demonstrates that PIKfyve and p38MAPK cooperate to regulate lysosome homeostasis and their combined inhibition synergistically blocks autophagy to reduce cancer cell viability in vitro and in vivo.
Shuffle GAN With Autoencoder: A Deep Learning Approach to Separate Moving and Stationary Targets in SAR Imagery

Synthetic aperture radar (SAR) has been widely applied in both civilian and military fields because it provides high-resolution images of the ground target regardless of weather conditions, day or night. In SAR imaging, the separation of moving and stationary targets is of great significance as it is capable of removing the ambiguity stemming from inevitable moving targets in stationary scene imaging and suppressing clutter in moving target imaging. The newly emerged generative adversarial networks (GANs) have great performance in many other signal processing areas; however, they have not been introduced to radar imaging tasks. In this work, we propose a novel shuffle GAN with autoencoder separation method to separate the moving and stationary targets in SAR imagery. The proposed algorithm is based on the independence of well-focused stationary targets and blurred moving targets for creating adversarial constraints. Note that the algorithm operates in a totally unsupervised fashion without requiring a sample set that contains mixed and separated SAR images. Experiments are carried out on synthetic and real SAR data to validate the effectiveness of the proposed method.
High incidence of stroke in young adults in Tartu, Estonia, 2013 to 2017: A prospective population‐based study

Previous studies conducted elsewhere in the world have demonstrated an increase in the incidence of ischemic stroke (IS) in younger ages. We sought to determine stroke incidence and 28‐day case‐fatality rates in 15‐ to 54‐year‐old residents of Tartu, Estonia from 2013 to 2017.
Multi-Dimensional Visual Data Completion via Low-Rank Tensor Representation Under Coupled Transform

This paper addresses the tensor completion problem, which aims to recover missing information of multi-dimensional images. How to represent a low-rank structure embedded in the underlying data is the key issue in tensor completion. In this work, we suggest a novel low-rank tensor representation based on coupled transform, which fully exploits the spatial multi-scale nature and redundancy in spatial and spectral/temporal dimensions, leading to a better low tensor multi-rank approximation. More precisely, this representation is achieved by using two-dimensional framelet transform for the two spatial dimensions, one/two-dimensional Fourier transform for the temporal/spectral dimension, and then Karhunen–Loéve transform (via singular value decomposition) for the transformed tensor. Based on this low-rank tensor representation, we formulate a novel low-rank tensor completion model for recovering missing information in multi-dimensional visual data, which leads to a convex optimization problem. To tackle the proposed model, we develop the alternating directional method of multipliers (ADMM) algorithm tailored for the structured optimization problem. Numerical examples on color images, multispectral images, and videos illustrate that the proposed method outperforms many state-of-the-art methods in qualitative and quantitative aspects.
Identification of permissive amber suppression sites for efficient non-canonical amino acid incorporation in mammalian cells

Abstract The genetic code of mammalian cells can be expanded to allow the incorporation of non-canonical amino acids (ncAAs) by suppressing in-frame amber stop codons (UAG) with an orthogonal pyrrolysyl-tRNA synthetase (PylRS)/tRNAPylCUA (PylT) pair. However, the feasibility of this approach is substantially hampered by unpredictable variations in incorporation efficiencies at different stop codon positions within target proteins. Here, we apply a proteomics-based approach to quantify ncAA incorporation rates at hundreds of endogenous amber stop codons in mammalian cells. With these data, we compute iPASS (Identification of Permissive Amber Sites for Suppression; available at www.bultmannlab.eu/tools/iPASS), a linear regression model to predict relative ncAA incorporation efficiencies depending on the surrounding sequence context. To verify iPASS, we develop a dual-fluorescence reporter for high-throughput flow-cytometry analysis that reproducibly yields context-specific ncAA incorporation efficiencies. We show that nucleotides up- and downstream of UAG synergistically influence ncAA incorporation efficiency independent of cell line and ncAA identity. Additionally, we demonstrate iPASS-guided optimization of ncAA incorporation rates by synonymous exchange of codons flanking the amber stop codon. This combination of in silico analysis followed by validation in living mammalian cells substantially simplifies identification as well as adaptation of sites within a target protein to confer high ncAA incorporation rates.
NIH Toolbox executive function measures with developmental extensions: Reliability and validity with preschoolers in emergency housing

ABSTRACT Research has shown that executive function (EF) skills are associated with resilience in preschoolers experiencing risk and adversity, but these studies have typically relied on large batteries of tasks to measure children’s EF skills. There is a need for brief, reliable EF assessments that can be used in the field with diverse young children. The current study assessed the validity and test-retest reliability of two tablet-based EF tasks from the NIH Toolbox: The Dimensional Change Card Sort (DCCS) and the Flanker Inhibitory Control and Attention Test, each with a developmental extension (Dext) that is triggered when a child struggles with the standardized versions. Dext versions include easier levels intended to improve task accessibility for younger and disadvantaged children. Eighty-six preschoolers residing in emergency housing participated in two study sessions about one week apart, completing tablet-based DCCS-Dext and Flanker-Dext tasks, along with a table-top EF task (Peg-Tapping) and measures of vocabulary and numeracy. The majority of participants triggered the Dext portion of the DCCS and almost half triggered the Dext portion of the Flanker, underscoring the need for extensions of the Toolbox EF tasks to lower the floor of these measures. The Dext EF measures were positively associated with Peg-Tapping, after controlling for age and vocabulary, indicating construct validity. They were also correlated with math achievement, suggesting criterion validity. DCCS-Dext and Flanker-Dext showed moderate test-retest reliability after one week. Together, these findings demonstrate the value of developmental extensions for assessing EF skills among children experiencing risk and adversity.
Caregiver overload and factors associated with care provided to patients under palliative care.

OBJECTIVES To identify overload and associated factors among caregivers of adult patients receiving palliative care. METHODS Descriptive, quantitative, and cross-sectional study addressing 40 adults under palliative care and their respective caregivers enrolled in the Home Care System in Ribeirão Preto, Brazil. Data concerning the patients included demographic profile and Mini-Mental State Examination. A form was used to collect the caregivers' demographic data along with the Zarit Burden Interview Scale, Self-Reporting Questionnaire, Beck Depression Inventory, and Coping Strategies Inventory. RESULTS Regarding the patients, 84.2% were women, 52.6% were over 80, 65.8% had no partner, and 76.3% presented cognitive impairment. The caregivers were mostly women (84.5%), aged 56.67 years old on average, were the patients' children (42.5%); had no partner (55%), and lived with the patient (77.5%). The mean score obtained in the burden scale was 28.78 points, 32.5% had stress, and 42.5% depression. Regarding coping strategies, the ones most frequently used were positive reappraisal (12.8), withdrawal (10.2), and problem solution (9.7). A positive and statistically significant correlation was found between time spent with care (days and hours) and escape/avoidance with overload. Linear regression analysis revealed an association between being a woman (p=0.002), number of days spent with care (p=0.004), and depression (p<0.001) with overload. CONCLUSIONS Being a woman, spending more days providing care, and depressive symptoms were associated with caregiver overload.
Exploring male condom use among women in South Africa: a review of the literature

The male condom is the most cost-effective method for prevention of HIV and other sexually transmitted infections (STIs), yet in high-burden countries, promotion of its use remains difficult to achieve, especially among high-risk individuals. This review reports on women’s perspectives of male condom use and identifies outcome measures that will assist in understanding barriers to male condom use in a South African setting. The Boolean search method was used to retrieve literature, from which 18 studies met the inclusion criteria. The use of the male condom was generally low and inconsistent. Use was higher among women who engaged in transactional sex. Most women had difficulty in negotiating condom use with their partners, particularly if they were in male-dominated relationships or were financially dependent on their partner. Women with higher education levels were able to negotiate use more easily. Interventions for assertive negotiation skills were useful. However, the stigma of infidelity and HIV infection are barriers to condom use. Incorrect use further reduces protection. This review emphasises that women are a vulnerable group who are not always able to control their own protection. Further implementation of the health policies promoting interventions for condom use are required to assist women in taking control of their own protection. Intervention measures should be adapted to include the male population so that they understand and accept condom use. Education to address unequal gender dynamics within relationships is also essential. Much work is required to make women feel less vulnerable in their relationships.
Molecular Monolayers and Interfacial Electron Transfer of Pseudomonas aeruginosa Azurin on Au(111)

We provide a comprehensive approach to the formation and characterization of molecular monolayers of the blue copper protein Pseudomonas aeruginosa azurin on Au(111) in aqueous ammonium acetate solution. Main issues are adsorption patterns, reductive desorption, properties of the double layer, and long-range electrochemical electron transfer between the electrode and the copper center. Voltammetry, electrochemical impedance spectroscopy (EIS), in situ scanning tunneling microscopy (STM), and X-ray photoelectron spectroscopy (XPS) have been employed to disclose features of these issues. Zn-substituted azurin, cystine, and 1-butanethiol are investigated for comparison. Cyclic voltammetric and capacitance measurements show qualitatively that azurin is adsorbed at submicromolar concentrations over a broad potential range. The characteristics of reductive desorption suggest that azurin is adsorbed via its disulfide group to form a monolayer. The adsorption of this protein on Au(111) via a gold−sulfur binding m.