Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel UHPLC-MS/MS Method for Measuring 8-iso-Prostaglandin F2α in Bronchoalveolar Lavage Fluid

In August 2019, the Centers for Disease Control and Prevention (CDC) received the first reports of lung injuries that were eventually termed e-cigarette, or vaping, product use–associated lung injury (EVALI). As part of the investigation, CDC laboratories rapidly developed assays for analyzing substances in bronchoalveolar lavage (BAL) fluid collected from EVALI case patients. This report describes the development and validation of a high-throughput isotope dilution UHPLC-MS/MS method for measuring a major oxidative stress biomarker, 8-iso-prostaglandin F2α (8-isoprostane), in BAL fluid samples. The method showed good sensitivity, 17.6 pg/ml LOD, and requires only 50 μl of sample volume. The method had high throughput with an analytical run time of 11 min. The within-day and between-day coefficient of variation (CV) were below 2%. Accuracy, calculated from spiked recovery, at three spiking levels, ranged from 95.5–101.8%. This novel UHPLC-MS/MS method characterizes oxidative stress in lung epithelial tissue and thus helps to elucidate potential pathologic processes.
A FACS-Free Purification Method to Study Estrogen Signaling, Organoid Formation, and Metabolic Reprogramming in Mammary Epithelial Cells

Few in vitro models are used to study mammary epithelial cells (MECs), and most of these do not express the estrogen receptor α (ERα). Primary MECs can be used to overcome this issue, but methods to purify these cells generally require flow cytometry and fluorescence-activated cell sorting (FACS), which require specialized instruments and expertise. Herein, we present in detail a FACS-free protocol for purification and primary culture of mouse MECs. These MECs remain differentiated for up to six days with >85% luminal epithelial cells in two-dimensional culture. When seeded in Matrigel, they form organoids that recapitulate the mammary gland’s morphology in vivo by developing lumens, contractile cells, and lobular structures. MECs express a functional ERα signaling pathway in both two- and three-dimensional cell culture, as shown at the mRNA and protein levels and by the phenotypic characterization. Extracellular metabolic flux analysis showed that estrogens induce a metabolic switch favoring aerobic glycolysis over mitochondrial respiration in MECs grown in two-dimensions, a phenomenon known as the Warburg effect. We also performed mass spectrometry (MS)-based metabolomics in organoids. Estrogens altered the levels of metabolites from various pathways, including aerobic glycolysis, citric acid cycle, urea cycle, and amino acid metabolism, demonstrating that ERα reprograms cell metabolism in mammary organoids. Overall, we have optimized mouse MEC isolation and purification for two- and three-dimensional cultures. This model represents a valuable tool to study how estrogens modulate mammary gland biology, and particularly how these hormones reprogram metabolism during lactation and breast carcinogenesis.
Effects of Defects on the Temperature‐Dependent Thermal Conductivity of Suspended Monolayer Molybdenum Disulfide Grown by Chemical Vapor Deposition

It is understood that defects of the atomic arrangement of the lattice in 2D molybdenum disulfide (MoS2) grown by chemical vapor deposition (CVD) can have a profound effect on the electronic and optical properties. Beyond these it is a major prerequisite to also understand the fundamental effect of such defects on phonon transport, to guarantee the successful integration of MoS2 into the solid‐state devices. A comprehensive joint experiment‐theory investigation to explore the effect of lattice defects on the thermal transport of the suspended MoS2 monolayer grown by CVD is presented. The measured room temperature thermal conductivity values are 30 ± 3.3 and 35.5 ± 3 W m−1 K−1 for two samples, which are more than two times smaller than that of their exfoliated counterpart. High‐resolution transmission electron microscopy shows that these CVD‐grown samples are polycrystalline in nature with low angle grain boundaries, which is primarily responsible for their reduced thermal conductivity. Higher degree of polycrystallinity and aging effects also result in smoother temperature dependency of thermal conductivity (κ) at temperatures below 100 K. First‐principles lattice dynamics simulations are carried out to understand the role of defects such as isotopes, vacancies, and grain boundaries on the phonon scattering rates of our CVD‐grown samples.
Inhibition of Aspirin-Induced Gastrointestinal Injury: Systematic Review and Network Meta-Analysis

Background: Administration of aspirin has the potential for significant side effects of gastrointestinal (GI) injury mainly caused by gastric acid stimulation, especially in long-term users or users with original gastrointestinal diseases. The debate on the optimal treatment of aspirin-induced gastrointestinal injury is ongoing. We aimed to compare and rank the different treatments for aspirin-induced gastrointestinal injury based on current evidence. Methods: We searched PubMed, EMBASE, Cochrane Library (Cochrane Central Register of Controlled Trials), and Chinese databases for published randomized controlled trials (RCTs) of different treatments for aspirin-induced gastrointestinal injury from inception to 1 May 2021. All of the direct and indirect evidence included was rated by network meta-analysis under a Bayesian framework. Results: A total of 10 RCTs, which comprised 503 participants, were included in the analysis. The overall quality of evidence was rated as moderate to high. Eleven different treatments, including omeprazole, lansoprazole, rabeprazole, famotidine, geranylgeranylacetone, misoprostol, ranitidine bismuth citrate, chili, phosphatidylcholine complex, omeprazole plus rebamipide, and placebo, were evaluated in terms of preventing gastrointestinal injury. It was suggested that omeprazole plus rebamipide outperformed other treatments, whereas geranylgeranylacetone and placebo were among the least treatments. Conclusion: This is the first systematic review and network meta-analysis of different treatments for aspirin-induced gastrointestinal injury. Our study suggested that omeprazole plus rebamipide might be considered the best option to treat aspirin-induced gastrointestinal injury. More multicenter, high quality, large sample size randomized controlled trials will confirm the advantages of these medicines in the treatment of aspirin-induced gastrointestinal injury in the future.
The Induction of Alpha-1 Antitrypsin by Vitamin D in Human T Cells Is TGF-β Dependent: A Proposed Anti-inflammatory Role in Airway Disease

Background: Vitamin D upregulates anti-inflammatory and antimicrobial pathways that promote respiratory health. Vitamin D synthesis is initiated following skin exposure to sunlight, however nutritional supplementation can be required to address deficiency, for example during the winter months or due to cultural constraints. We recently reported that 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) treatment induced alpha-1 antitrypsin (AAT) expression in CD4+, but not CD8+ T cells, with evidence supporting an immunoregulatory role. Research Question: To understand the relationship between vitamin D, lung AAT levels and T lymphocytes further we investigated whether TGF-β is required as a co-factor for 1,25(OH)2D3-induced upregulation of AAT by vitamin D in CD8+ T cells in vitro and correlated circulating vitamin D levels with lung AAT levels in vivo. Results: 1,25(OH)2D3 in combination with TGF-β1 increased AAT expression by CD8+ T cells, as well as VDR and RXRα gene expression, which may partly explain the requirement for TGF-β. CD4+ T cells may also require autocrine stimulation with TGF-β as a co-factor since 1,25(OH)2D3 was associated with increased TGF-β bioactivity and neutralisation of TGF-β partially abrogated 1,25(OH)2D3-induced SERPINA1 gene expression. Neither CD4+ nor CD8+ T cells responded to the circulating vitamin D precursor, 25-hydroxyvitamin D3 for induction of SERPINA1, suggesting that local generation of 1,25(OH)2D3 is required. Transcriptional gene profiling studies previously demonstrated that human bronchial epithelial cells rapidly increased TGF-β2 gene expression in response to 1,25(OH)2D3. Here, human epithelial cells responded to precursor 25(OH)D3 to increase bioactive TGF-β synthesis. CD8+ T cells responded comparably to TGF-β1 and TGF-β2 to increase 1,25(OH)2D3-induced AAT. However, CD8+ T cells from adults with AAT-deficiency, homozygous for the Z allele of SERPINA1, were unable to mount this response. AAT levels in the airways of children with asthma and controls correlated with circulating 25(OH)D3. Conclusions: Vitamin D increases AAT expression in human T cells and this response is impaired in T cells from individuals homozygous for the Z allele of SERPINA1 in a clinic population. Furthermore, a correlation between circulating vitamin D and airway AAT is reported. We propose that vitamin D-induced AAT contributes to local immunomodulation and airway health effects previously attributed to vitamin D.
The Role of Neutrophil Extracellular Traps in Cancer

Neutrophils are vital components of innate and adaptive immunity. It is widely acknowledged that in various pathological conditions, neutrophils are activated and release condensed DNA strands, triggering the formation of neutrophil extracellular traps (NETs). NETs have been shown to be effective in fighting against microbial infections and modulating the pathogenesis and progression of diseases, including malignant tumors. This review describes the current knowledge on the biological characteristics of NETs. Additionally, the mechanisms of NETs in cancer are discussed, including the involvement of signaling pathways and the crosstalk between other cancer-related mechanisms, including inflammasomes and autophagy. Finally, based on previous and current studies, the roles of NET formation and the potential therapeutic targets and strategies related to NETs in several well-studied types of cancers, including breast, lung, colorectal, pancreatic, blood, neurological, and cutaneous cancers, are separately reviewed and discussed.
Exploring Evidence of Non-coding RNA Translation With Trips-Viz and GWIPS-Viz Browsers

Detection of translation in so-called non-coding RNA provides an opportunity for identification of novel bioactive peptides and microproteins. The main methods used for these purposes are ribosome profiling and mass spectrometry. A number of publicly available datasets already exist for a substantial number of different cell types grown under various conditions, and public data mining is an attractive strategy for identification of translation in non-coding RNAs. Since the analysis of publicly available data requires intensive data processing, several data resources have been created recently for exploring processed publicly available data, such as OpenProt, GWIPS-viz, and Trips-Viz. In this work we provide a detailed demonstration of how to use the latter two tools for exploring experimental evidence for translation of RNAs hitherto classified as non-coding. For this purpose, we use a set of transcripts with substantially different patterns of ribosome footprint distributions. We discuss how certain features of these patterns can be used as evidence for or against genuine translation. During our analysis we concluded that the MTLN mRNA, previously misannotated as lncRNA LINC000116, likely encodes only a short proteoform expressed from shorter RNA transcript variants.
A Novel Risk Scoring Tool to Predict Saphenous Vein Graft Occlusion After Cardiac Artery Bypass Graft Surgery

Objectives: Coronary artery bypass grafting (CABG) success is reduced by graft occlusion. Understanding factors associated with graft occlusion may improve patient outcomes. The aim of this study was to develop a predictive risk score for saphenous vein graft (SVG) occlusion after CABG. Methods: This retrospective cohort study enrolled 3,716 CABG patients from January 2012 to March 2013. The development cohort included 2,477 patients and the validation cohort included 1,239 patients. The baseline clinical data at index CABG was analyzed for their independent impact on graft occlusion in our study using Cox proportional hazards regression. The predictive risk scoring tool was weighted by beta coefficients from the final model. Concordance (c)-statistics and comparison of the predicted and observed probabilities of predicted risk were used for discrimination and calibration. Results: A total of 959 (25.8%) out of 3,716 patients developed at least one late SVG occlusion. Significant risk factors for occlusion were female sex [beta coefficients (β) = 0.52], diabetes (β = 0.21), smoking (currently) (β = 0.32), hyperuricemia (β = 0.22), dyslipidemia (β = 0.52), prior percutaneous coronary intervention (PCI) (β = 0.21), a rising number of SVG (β = 0.12) and lesion vessels (β = 0.45). On-pump surgery (β = −0.46) and the use of angiotensin-converting enzyme inhibitors (ACEI)/angiotensin receptor blockers (ARB) (β = −0.59) and calcium channel blockers (CCB) (β = −0.23) were protective factors. The risk scoring tool with 11 variables was developed from the derivation cohort, which delineated each patient into risk quartiles. The c-statistic for this model was 0.71 in the validation cohort. Conclusions: An easy-to-use risk scoring tool which included female sex, diabetes, smoking, hyperuricemia, dyslipidemia, prior PCI, a rising number of SVG and lesion vessels, on-pump surgery, the use of ACEI/ ARB and CCB was developed and validated. The scoring tool accurately estimated the risk of late SVG occlusion after CABG (c-statistic = 0.71).
Thinking About Behavior: Perspective on Meta-Behavior in Education

Studies on metacognitive skills have started in the past 30 years and cover various fields, including education. In general, metacognitive skills refer to awareness and monitoring cognitive processes and their ability to sharpen the mind enhancement process. However, much attention has been given to metacognition alone and less focusing on its manifestation in behaviors. Thus, this study aims to conceptualize how metacognitive concepts can be adapted in the context of behaviors. In achieving this, an in-depth analysis of relevant behavioral theories and metacognitive models was conducted. The proposed conceptual framework, named the meta-behavior framework, underscores the importance of the thinking process before an individual engages in action. Undoubtfully, this skill is vital in influencing an individual to plan, monitor and evaluate his/her actions in daily life. In short, the proposed framework is essential in expanding the current knowledge terrain on psychology, which specifically provides a new perspective in understanding how the thinking process determines behavior.
A Short, Multimodal Activity Break Incorporated Into the Learning Context During the Covid-19 Pandemic: Effects of Physical Activity and Positive Expressive Writing on University Students' Mental Health—Results and Recommendations From a Pilot Study

Physical inactivity, sedentary behavior and mental ill health, due to high levels of perceived stress or self-reported depressive symptoms, are highly prevalent among university students. There are concerns that these behaviors and mental symptoms have significantly increased during the current Covid-19 pandemic, partly because academic life has changed considerably from face-to-face communication to e-learning and studying at home. Self-regulation and physical activity are hard to maintain during pandemic lockdowns. Short activity breaks could be helpful to avoid physical inactivity and sustain mental health. The breaks should comprise short and easy-implementable physical activity exercises that can be integrated into the learning context. Moreover, cognitive interventions, such as writing about positive events and feelings might help as coping strategy for self-regulation during study breaks. This study investigated and compared the effects of a physical activity intervention and a cognitive intervention (positive expressive writing) on mental health among university students. Both interventions are particularly suitable for use at home. N = 20 university students, studying in Germany, were assigned to a physical activity group or a cognitive intervention group. The physical activity intervention consisted of a mix of physical exercises including endurance exercises, muscular strength, relaxation, and ballroom dance movements. The interventions were carried out guided, once a week, for 5–10 mins at the beginning of classes. The effects of group × time showed no significant interaction on self-reported perceived stress, mood, quality of life (QoL) assessed online and compared at the beginning of the term before the intervention (T0) and at the end of the term after the intervention (T3). However, the physical activity group reported a similar physical activity level per day over time, while the cognitive intervention group showed a decrease in physical activity from T0 to T3. Low-dose, short physical activity interventions as well as cognitive interventions consisting of positive expressive writing could buffer university students' perceived stress, mood, and QoL across the term. Moreover, both interventions seem to be promising in buffering the negative side effects of stress during the Covid-19 pandemic.
Time Restricted Eating: A Dietary Strategy to Prevent and Treat Metabolic Disturbances

Time-restricted eating (TRE), a dietary approach limiting the daily eating window, has attracted increasing attention in media and research. The eating behavior in our modern society is often characterized by prolonged and erratic daily eating patterns, which might be associated with increased risk of obesity, diabetes, and cardiovascular diseases. In contrast, recent evidence suggests that TRE might support weight loss, improve cardiometabolic health, and overall wellbeing, but the data are controversial. The present work reviews how TRE affects glucose and lipid metabolism based on clinical trials published until June 2021. A range of trials demonstrated that TRE intervention lowered fasting and postprandial glucose levels in response to a standard meal or oral glucose tolerance test, as well as mean 24-h glucose and glycemic excursions assessed using continuous glucose monitoring. In addition, fasting insulin decreases and improvement of insulin sensitivity were demonstrated. These changes were often accompanied by the decrease of blood triglyceride and cholesterol levels. However, a number of studies found that TRE had either adverse or no effects on glycemic and lipid traits, which might be explained by the different study designs (i.e., fasting/eating duration, daytime of eating, changes of calorie intake, duration of intervention) and study subject cohorts (metabolic status, age, gender, chronotype, etc.). To summarize, TRE represents an attractive and easy-to-adapt dietary strategy for the prevention and therapy of glucose and lipid metabolic disturbances. However, carefully controlled future TRE studies are needed to confirm these effects to understand the underlying mechanisms and assess the applicability of personalized interventions.
The Evolutionary Dynamics of Repetitive DNA and Its Impact on the Genome Diversification in the Genus Sorghum

Polyploidization is an evolutionary event leading to structural changes of the genome(s), particularly allopolyploidization, which combines different genomes of distinct species. The tetraploid species, Sorghum halepense, is assumed an allopolyploid species formed by hybridization between diploid S. bicolor and S. propinquum. The repeat profiles of S. bicolor, S. halepense, and their relatives were compared to elucidate the repeats’ role in shaping their genomes. The repeat frequencies and profiles of the three diploid accessions (S. bicolor, S. bicolor ssp. verticilliflorum, and S. bicolor var. technicum) and two tetraploid accessions (S. halepense) are similar. However, the polymorphic distribution of the subtelomeric satellites preferentially enriched in the tetraploid S. halepense indicates drastic genome rearrangements after the allopolyploidization event. Verified by CENH3 chromatin immunoprecipitation (ChIP)-sequencing and fluorescence in situ hybridization (FISH) analysis the centromeres of S. bicolor are mainly composed of the abundant satellite SorSat137 (CEN38) and diverse CRMs, Athila of Ty3_gypsy and Ty1_copia-SIRE long terminal repeat (LTR) retroelements. A similar centromere composition was found in S. halepense. The potential contribution of S. bicolor in the formation of tetraploid S. halepense is discussed.
The Impact of Attachment on Depression in Married Seniors: Chain Mediating Effects of Self-Esteem and Rumination

In this study, we discuss the effects of attachment on depression and the mediating roles of self-esteem and rumination in Chinese seniors. We assessed 431 using the Experiences in Close Relationships Inventory, the Rosenberg Self-Esteem Scale, the Ruminative Responses Scale, and the Short Form of Center for Epidemiologic Studies Depression Scale. Both attachment anxiety and attachment avoidance significantly predicted depression in seniors. Attachment anxiety and attachment avoidance positively predicted rumination but negatively predicted self-esteem. Structural equation models showed that rumination and self-esteem fully mediated the effects of attachment anxiety and attachment avoidance on depression. The attachment of seniors is related to depression, and self-esteem and rumination have chain mediating effects between attachment and depression.
Beyond Average: Providers' Assessments of Indices for Measuring Pain Intensity in Patients With Chronic Pain

Introduction: Effective clinical care for chronic pain requires accurate, comprehensive, meaningful pain assessment. This study investigated healthcare providers' perspectives on seven pain measurement indices for capturing pain intensity. Methods: Semi-structured telephone interviews were conducted with a purposeful sample from four US regions of 20 healthcare providers who treat patients with chronic pain. The qualitative interview guide included open-ended questions to address perspectives on pain measurement, and included quantitative ratings of the importance of seven indices [average pain, worst pain, least pain, time in no/low pain, time in high pain, fluctuating pain, unpredictable pain]. Qualitative interview data were read, coded and analyzed for themes and final interpretation. Standard quantitative methods were used to analyze index importance ratings. Results: Despite concerns regarding 10-point visual analog and numeric rating scales, almost all providers used them. Providers most commonly asked about average pain, although they expressed misgivings about patient reporting and the index's informational value. Some supplemented average with worst and least pain, and most believed pain intensity is best understood within the context of patient functioning. Worst pain received the highest mean importance rating (7.60), average pain the second lowest rating (5.65), and unpredictable pain the lowest rating (5.20). Discussion: Assessing average pain intensity obviates obtaining clinical insight into daily contextual factors relating to pain and functioning. Pain index use, together with timing, functionality and disability, may be most effective for understanding the meaning to patients of high pain, how pain affects their life, how life affects their pain, and how pain changes and responds to treatment.