Miracle-dz/UniFAR-FTUs huggingface dataset:
Making inference with messy (citizen science) data: when are data accurate enough and how can they be improved?

Measurement or observation error is common in ecological data: as citizen scientists and automated algorithms play larger roles processing growing volumes of data to address problems at large scales, concerns about data quality and strategies for improving it have received greater focus. However, practical guidance pertaining to fundamental data quality questions for data users or managers-how accurate do data need to be and what is the best or most efficient way to improve it? -remains limited. We present a generalizable framework for evaluating data quality and identifying remediation practices, and demonstrate the framework using trail camera images classified using crowdsourcing to determine acceptable rates of misclassification and identify optimal remediation strategies for analysis using occupancy models. We used expert validation to estimate baseline classification accuracy and simulation to determine the sensitivity of two occupancy estimators (standard and false-positive extensions) to different empirical misclassification rates. We used regression techniques to identify important predictors of misclassification and prioritize remediation strategies. More than 93% of images were accurately classified, but simulation results suggested that most species were not identified accurately enough to permit distribution estimation at our predefined threshold for accuracy (<5% absolute bias). A model developed to screen incorrect classifications predicted misclassified images with >97% accuracy: enough to meet our accuracy threshold. Occupancy models that accounted for false-positive error provided even more accurate inference even at high rates of misclassification (30%). As simulation suggested occupancy models were less sensitive to additional false-negative error, screening models or fitting occupancy models accounting for false-positive error emerged as efficient data remediation solutions. Combining simulation-based sensitivity analysis with empirical estimation of baseline error and its variability allows users and managers of potentially error-prone data to identify and fix problematic data more efficiently. It may be particularly helpful for "big data" efforts dependent upon citizen scientists or automated classification algorithms with many downstream users, but given the ubiquity of observation or measurement error, even conventional studies may benefit from focusing more attention upon data quality.
Socioeconomic position during pregnancy and DNA methylation signatures at three stages across early life: epigenome-wide association studies in the ALSPAC birth cohort

BACKGROUND Socioeconomic experiences are recognized determinants of health, and recent work has shown that social disadvantages in early life may induce sustained biological changes at molecular level that are detectable later in life. However, the dynamics and persistence of biological embedding of socioeconomic position (SEP) remains vastly unexplored. METHODS Using the data from the ALSPAC birth cohort, we performed epigenome-wide association studies of DNA methylation changes at three life stages (birth, n = 914; childhood at mean age 7.5 years, n = 973; and adolescence at mean age 15.5 years, n = 974), measured using the Illumina HumanMethylation450 Beadchip, in relation to pregnancy SEP indicators (maternal and paternal education and occupation). RESULTS Across the four early life SEP metrics investigated, only maternal education was associated with methylation levels at birth, and four CpGs mapped to SULF1, GLB1L2 and RPUSD1 genes were identified [false discovery rate (FDR)-corrected P-value <0.05]. No epigenetic signature was found associated with maternal education in child samples, but methylation levels at 20 CpG loci were found significantly associated with maternal education in adolescence. Although no overlap was found between the differentially methylated CpG sites at different ages, we identified two CpG sites at birth and during adolescence which are 219 bp apart in the SULF1 gene that encodes an heparan sulphatase involved in modulation of signalling pathways. Using data from an independent birth cohort, the ENVIRONAGE cohort, we were not able to replicate these findings. CONCLUSIONS Taken together, our results suggest that parental SEP, and particularly maternal education, may influence the offspring's methylome at birth and adolescence.
Regulation of acetate metabolism and coordination with the TCA cycle via a processed small RNA

Significance In bacteria, small RNAs pair with target mRNAs to rapidly adjust gene expression in response to environmental and physiological changes. In this study, we identified a small RNA, SdhX, in Escherichia coli, whose expression is dependent on expression of tricarboxylic acid cycle genes. SdhX adjusts carbon flux by negatively regulating acetate kinase levels, improving growth on acetate. SdhX also leads to increased resistance to hydroxyurea, as do deletions of acetate kinase. Balancing metabolic flux is important for all bacterial cells, and SdhX plays a major role in this process by linking expression of tricarboxylic acid cycle genes to regulation of acetate metabolism, thus playing a role in gating overflow metabolism. Bacterial regulatory small RNAs act as crucial regulators in central carbon metabolism by modulating translation initiation and degradation of target mRNAs in metabolic pathways. Here, we demonstrate that a noncoding small RNA, SdhX, is produced by RNase E-dependent processing from the 3′UTR of the sdhCDAB-sucABCD operon, encoding enzymes of the tricarboxylic acid (TCA) cycle. In Escherichia coli, SdhX negatively regulates ackA, which encodes an enzyme critical for degradation of the signaling molecule acetyl phosphate, while the downstream pta gene, encoding the enzyme critical for acetyl phosphate synthesis, is not significantly affected. This discoordinate regulation of pta and ackA increases the accumulation of acetyl phosphate when SdhX is expressed. Mutations in sdhX that abolish regulation of ackA lead to more acetate in the medium (more overflow metabolism), as well as a strong growth defect in the presence of acetate as sole carbon source, when the AckA-Pta pathway runs in reverse. SdhX overproduction confers resistance to hydroxyurea, via regulation of ackA. SdhX abundance is tightly coupled to the transcription signals of TCA cycle genes but escapes all known posttranscriptional regulation. Therefore, SdhX expression directly correlates with transcriptional input to the TCA cycle, providing an effective mechanism for the cell to link the TCA cycle with acetate metabolism pathways.
Multi-Shape Task Placement Algorithm Based on Low Fragmentation Resource Management on 2D Heterogeneous Dynamic Partial Reconfigurable Devices

The Dynamic Partial Reconfiguration function of reconfigurable devices permits tasks to be performed simultaneously on a single device. Nevertheless, task placement and resource management problems emerge with the parallelism of reconfigurable devices. Traditional task placement algorithms are based on the assumption of a homogeneous architecture and simplify the task as a rectangular shape, which inevitably results in internal unused areas, thereby wasting a significant amount of programmable resources. To address the resource waste that comes with the assumption of a rectangular task shape and improve the placement quality, we adopted an interval list set to manage available programmable resources for a heterogeneous reconfigurable device and proposed an interval-based placement algorithm combined with a low-fragmentation selection strategy targeting the placement problem of multi-shape tasks. The efficiency of the proposed approach is proved theoretically, and simulation results demonstrate that the rejection ratio is decreased by at least 8.9% with an average fragmentation reduction of 18.1%.
Imaging for Small UAV-Borne FMCW SAR

Unmanned aerial vehicle borne frequency modulated continuous wave synthetic aperture radars are attracting more and more attention due to their low cost and flexible operation capacity, including the ability to capture images at different elevation angles for precise target identification. However, small unmanned aerial vehicles suffer from large trajectory deviation and severe range-azimuth coupling due to their simple navigational control and susceptibility to air turbulence. In this paper, we utilize the squint minimization technique to reduce this coupling while simultaneously eliminating intra-pulse motion-induced effects with an additional spectrum scaling. After which, the modified range doppler algorithm is derived for second order range compression and block-wise range cell migration correction. Raw data-based motion compensation is carried out with a doppler tracker. Squinted azimuth dependent phase gradient algorithm is employed to deal with azimuth dependent parameters and inexact deramping, with minimum entropy-based autofocusing algorithms. Finally, azimuth nonlinear chirp scaling is used for azimuth compression. Simulation and real data experiment results presented verify the effectiveness of the above signal processing approach.
The neurosteroid pregnenolone promotes degradation of key proteins in the innate immune signaling to suppress inflammation

Pregnenolone is a steroid hormone precursor that is synthesized in various steroidogenic tissues, in the brain, and in lymphocytes. In addition to serving as the precursor for other steroid hormones, pregnenolone exerts its own effect as an anti-inflammatory molecule to maintain immune homeostasis in various inflammatory conditions. Pregnenolone and its metabolic derivatives have been shown to have beneficial effects in the brain, including enhancing memory and learning, reversing depressive disorders, and modulating cognitive functions. A decreased level of pregnenolone has been observed in neuroinflammatory diseases, which emphasizes its role in neuroprotection and neuroregeneration. Although the anti-inflammatory property of pregnenolone was recognized several decades ago, its mechanism of action remains unknown. Here we report that pregnenolone promotes ubiquitination and degradation of the TLR2/4 adaptor protein TIRAP and TLR2 in macrophages and microglial cells. Pregnenolone and its metabolites suppressed the secretion of tumor necrosis factor α and interleukin-6 mediated through TLR2 and TLR4 signaling. Pregnenolone has been reported to induce activation of cytoplasmic linker protein 170, and this protein has recently been shown to promote targeted degradation of TIRAP. We observed enhanced degradation of TIRAP and TLR4 suppression by cytoplasmic linker protein 170 in the presence of pregnenolone. Our experimental data reveal novel nongenomic targets of pregnenolone and provide important leads to understand its role in restoring immune homeostasis in various inflammatory conditions.
New Alkoxy Flavone Derivatives Targeting Caspases: Synthesis and Antitumor Activity Evaluation

The antitumor activity of natural flavonoids has been exhaustively reported. Previously it has been demonstrated that prenylation of flavonoids allows the discovery of new compounds with improved antitumor activity through the activation of caspase-7 activity. The synthesis of twenty-five flavonoids (4–28) with one or more alkyl side chains was carried out. The synthetic approach was based on the reaction with alkyl halide in alkaline medium by microwave (MW) irradiation. The in vitro cell growth inhibitory activity of synthesized compounds was investigated in three human tumor cell lines. Among the tested compounds, derivatives 6, 7, 9, 11, 13, 15, 17, and 18 revealed potent growth inhibitory activity (GI50 < 10 μM), being the growth inhibitory effect of compound 13 related with a pronounced caspase-7 activation on MCF-7 breast cancer cells and yeasts expressing human caspase-7. A quantitative structure-activity relationship (QSAR) model predicted that hydrophilicity, pattern of ring substitution/shape, and presence of partial negative charged atoms were the descriptors implied in the growth inhibitory effect of synthesized compounds. Docking studies on procaspase-7 allowed predicting the binding of compound 13 to the allosteric site of procaspase-7.
Investigation of the Underlying Genes and Mechanism of Macrophage-Enriched Ruptured Atherosclerotic Plaques Using Bioinformatics Method

Aim: The study aimed to identify the underlying differentially expressed genes (DEGs) and mechanism of macrophage-enriched rupture atherosclerotic plaque using bioinformatics methods. Methods: GSE41571, which includes six stable samples and five ruptured atherosclerotic samples, was downloaded from the GEO database. After preprocessing, DEGs between ruptured and stable atherosclerotic samples were identified using LIMMA. Gene Ontology biological process (GO_BP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of DEGs were performed using the Database for Annotation, Visualization, and Integration Discovery (DAVID) online tool. Based on the STRING database, protein-protein interactions (PPIs) network among DEGs were constructed. Regulatory relationships between miRNAs/transcriptional factors (TFs) and target genes were predicted using Enrichr, and regulatory networks were visualized using Cytoscape. Results: A total of 268 DEGs (64 up-regulated and 204 down-regulated DEGs) were identified between ruptured and stable samples. In the PPI network, collagen type III alpha 1 chain (COL3A1), collagen type I alpha 2 chain (COL1A2), and asporin (ASPN) were more than 15 interaction degrees. In the miRNA-target network, miR21 was highlighted with highest degrees and ASPN could be targeted by miR21. Functional enrichment analysis showed that COL3A1 and COL1A2 were significantly enriched in extracellular matrix organization and cell adhesion GO_BP terms. Pre-platelet basic protein (PPBP) was the most significantly up-regulated gene in ruptured atherosclerotic samples and enriched in immune response and inflammatory response GO_BP terms. Conclusions: Down-regulated COL3A1, COL1A2 and ASPN, and up-regulated PPBP might perform critical promotional roles in atherosclerotic plaque rupture. Furthermore, miR21 might be potential target to prevent atherosclerotic rupture.
NAP Family CG5017 Chaperone Pleiotropically Regulates Human AHR Target Genes Expression in Drosophila Testis

To study the regulatory mechanism of the Aryl hydrocarbon receptor (AHR), target genes of transcription are necessary for understanding the normal developmental and pathological processes. Here, we examined the effects of human AHR ligands on male fecundity. To induce ectopic human AhR gene expression, we used Drosophila melanogaster transformed with human AhR under the control of a yeast UAS promoter element capable of activation in the two-component UAS-GAL4 system. We found that exogenous AHR ligands decrease the number of Drosophila gonadal Tj-positive cells. We also found both an increase and decrease of AHR target gene expression, including in genes that control homeostasis and testis development. This suggests that gonadal AHR activation may affect the expression of gene networks that control sperm production and could be critical for fertility not just in Drosophila but also in humans. Finally, we found that the activation of the expression for some AHR target genes depends on the expression of testis-specific chaperone CG5017 in gonadal cells. Since CG5017 belongs to the nucleosome assembly protein (NAP) family and may participate in epigenetic regulation, we propose that this nucleotropic chaperone is essential to provide the human AHR with access to only the defined set of its target genes during spermatogenesis.
Principles of Data Conversion System Design

This advanced text and reference covers the design and implementation of integrated circuits for analog-to-digital and digital-toanalog conversion. It begins with basic concepts and systematically leads the reader to advanced topics, describing design issues and techniques at both circuit and system level. Gain a system-level perspective of data conversion units and their trade-offs with this state-of-the art book. Topics covered include: sampling circuits and architectures, D/A and A/D architectures; comparator and op amp design; calibration techniques; testing and characterization; and more!
Information literacy and its application in nursing education

Information literacy has been embedded by the university into the first year nursing curriculum. Embedding this literacy will not necessarily ensure the nursing graduates will apply this skill to the provision of high quality evidence-based health care. For this to happen information literacy skills gained in the classroom must contribute to sound decision making based on best practice evidence. This paper discusses the findings of a three phases research project designed to (i) determine the information literacy skills, confidence and problem solving abilities of students entering the university's Bachelor of Nursing Program; (ii) determine if information literacy skills, confidence and problem solving abilities improve as a result of embedding information literacy instruction into a nursing course; and iii) ascertain whether there are any differences in information literacy skills, confidence and problem solving abilities based on the students demographic information. Data were collected in two sequential semesters using a questionnaire administered to the students. The response rates in semester one and two were 45 and 56 per cent respectively. Student confidence and awareness regarding information literacy is positively affected by learning experiences from semester one to semester two. Students indicated that they need both specific and regular instruction to adequately retain learning. Overall the study suggests that embedding information literacy instruction into the first year, first semester nursing program is beneficial. By the second semester the information literacy confidence and awareness of students increased as a result of intra-curricular instruction, however, problem solving skills need to be improved.
The impact of water consumption on hydration and cognition among schoolchildren: Methods and results from a crossover trial in rural Mali

Adequate provision of safe water, basic sanitation, and hygiene (WASH) facilities and behavior change can reduce pupil absence and infectious disease. Increased drinking water quantity may also improve educational outcomes through the effect of hydration on attention, concentration, and short-term memory. A pilot study was conducted to adapt field measures of short-term cognitive performance and hydration, to evaluate levels of hydration, and to investigate the impact of providing supplementary drinking water on the cognitive performance of pupils attending water-scarce schools in rural Mali. Using a cross-over trial design, data were collected under normal school conditions (control condition) on one visit day; on the other, participants were given a bottle of water that was refilled throughout the day (water condition). Morning and afternoon hydration was assessed using specific gravity and urine color. Cognitive performance was evaluated using six paper-based tests. Three percent of pupils were dehydrated on the morning of each visit. The prevalence of dehydration increased in the afternoon, but was lower under the water condition. Although there was a trend indicating drinking water may improve cognitive test performance, as has been shown in studies in other settings, results were not statistically significant and were masked by a “practice effect. ”
Long noncoding RNA AK089579 inhibits epithelial‐to‐mesenchymal transition of peritoneal mesothelial cells by competitively binding to microRNA‐296‐3p via DOK2 in peritoneal fibrosis

Peritoneal fibrosis (PF) represents a well‐recognized complication associated with continuous ambulatory peritoneal dialysis therapy, characterized by a reversible epithelial‐to‐mesenchymal transition (EMT) at the early stage. The aim of the current study was to investigate the effects linked with the long noncoding RNA (IncRNA) AK089579 on the EMT of peritoneal mesothelial cells (PMCs) as well as the associated regulatory mechanisms of AK089579 downstream of tyrosine kinase 2 (DOK2) and microRNA‐296‐3p (miR‐296‐3p). Enrichment analysis, gene intersection association analysis, and a gene‐gene intersection network were initially constructed to ascertain whether AK089579 regulated the expression of DOK2 through the mediation of miR‐296‐3p via the Janus kinase 2 (JAK2)/signal transducer and activator of transcription 3 (STAT3) signaling pathway in PF. After the PF mouse model had been constructed, the expression of the proteins associated with the JAK2/STAT3 signaling pathway and EMT and PMC migration and invasion were all determined accordingly. Based on the obtained results, AK089579 was determined to function as a competing endogenous RNA for miR‐296‐3p while acting to up‐regulate the expression of DOK2, which is a target gene of miR‐296‐3p. AK089579 was detected to confer an inhibitory effect on the activation of the JAK2/STAT3 signaling pathway, whereby the migration and invasion of PMCs among the mice models were suppressed. Meanwhile, up‐regulated miR‐296‐3p and down‐regulated DOK2 produced contrasting effects when compared with the aforementioned findings. Treatment with wpl0066, a JAK2/STAS3 signaling pathway inhibitor, was shown to reverse the effects exerted by up‐regulated miR‐296‐3p. Taken together, the central findings of the current study present evidence highlighting the capability of the IncRNA AK089579 to bind competitively to miR‐296‐3p and indirectly enhance the expression of DOK2, which in turn suppresses the activation of the JAK2/STAT3 signaling pathway, whereby the EMT, migration, and invasion of PMCs was inhibited in PF. —Zhang, X. W. , Wang, L. , Ding, H. Long noncoding RNA AK089579 inhibits epithelial‐to‐mesenchymal transition of peritoneal mesothelial cells by competitively binding to microRNA‐296‐3p via DOK2 in peritoneal fibrosis. FASEB J. 33, 5112–5125 (2019). www.fasebj. org
Child and Adolescent Predictors of Smoking Involvement in Emerging Adulthood

Objective: This study examined the differential relationship of externalizing behavior, internalizing behavior, social context, and their interactions to three developmental indicators of smoking involvement: onset (age), amount of smoking, and dependence symptomatology. Method: Participants (n = 504, 73% male) from a high-risk community-based longitudinal study were followed from age 12–14 to young adulthood (18–20). Smoking involvement was conceptualized as a process involving differences in (a) age of onset of smoking, (b) amount of smoking at age 18–20, and (c) level of nicotine dependence symptomatology at age 18–20. Survival analysis was used to predict onset of smoking, regression for smoking level, and zero-inflated Poisson regression for nicotine dependence. Results: Externalizing (teacher report) and internalizing behavior (youth self-report), prior to the onset of smoking, predicted different components of smoking and nicotine dependence in young adulthood. Parental smoking predicted all levels of smoking involvement. Peer smoking was related to early onset of smoking, but not higher levels of smoking involvement. Externalizing and internalizing behavior interacted to predict nicotine dependence level, with higher levels of internalizing behavior predicting higher levels of dependence symptoms, even at low levels of externalizing behavior. Conclusions: Externalizing and internalizing behavior and social context are independent and interacting risk factors that come into play at different points in the developmental process occurring between smoking onset and dependence. This study provides important information for theoretical models of smoking progression and shows that different types of risk should be targeted for prevention at different points in smoking progression.