Miracle-dz/UniFAR-FTUs huggingface dataset:
A Cocurricular Program That Encourages Specific Study Skills and Habits Improves Academic Performance and Retention of First-Year Undergraduates in Introductory Biology

Students must master content for success in science, technology, engineering, and mathematics (STEM), but “how to” is rarely taught in college. Faculty are reluctant to sacrifice class time, believe such instruction is remedial, or assume students possess or will attain these skills independently. To determine whether explicit instruction would improve skills and performance by first-year undergraduates likely to major in STEM, we invited all students in an introductory biology course to participate in an 8-week Co-Curricular (CoC) program. Students who participated improved time management, used more methods to plan and organize their study, and used a variety of active-learning strategies. A validated model was used to predict students’ probability of achieving a “C+” or better in the course. The model, based on 5 years of data, used students’ demographic characteristics and previous academic performance to provide a measure of their preparedness. Students with low and medium preparedness who participated in CoC performed better than those who did not participate. All students who participated were retained in the course compared with 88.7% of students who did not participate. Specific behavioral changes at the start of STEM gateway courses can dramatically improve student metacognition, retention, and academic performance, particularly for students underrepresented in the discipline.
DNA-Damage-Induced Alternative Splicing of p53

Simple Summary The tumor suppressor p53 is frequently mutated across numerous cancer types and has an essential role in the response to DNA-damaging agents, such as irradiation. DNA damage can induce different forms of the p53 protein, and the different forms of the p53 protein can elicit distinct types of cell death. Specifically, the activation of full-length p53 typically results in cellular apoptosis, while the induction of the alternatively spliced isoform, the beta isoform of p53 (p53β), results in cellular senescence. In this report, we review the known roles of p53β and introduce novel insights into p53β function. Abstract Cellular responses to DNA damage and other stresses are important determinants of mutagenesis and impact the development of a wide range of human diseases. TP53 is highly mutated in human cancers and plays an essential role in stress responses and cell fate determination. A central dogma of p53 induction after DNA damage has been that the induction results from a transient increase in the half-life of the p53 protein. Our laboratory recently demonstrated that this long-standing paradigm is an incomplete picture of p53 regulation by uncovering a critical role for protein translational regulation in p53 induction after DNA damage. These investigations led to the discovery of a DNA-damage-induced alternative splicing (AS) pathway that affects p53 and other gene products. The damage-induced AS of p53 pre-mRNA generates the beta isoform of p53 (p53β) RNA and protein, which is specifically required for the induction of cellular senescence markers after ionizing irradiation (IR). In an attempt to elucidate the mechanisms behind the differential regulation and apparent functional divergence between full-length (FL) p53 and the p53β isoform (apoptosis versus senescence, respectively), we identified the differential transcriptome and protein interactome between these two proteins that may result from the unique 10-amino-acid tail in p53β protein.
Autophagy mediates grain yield and nitrogen stress resistance by modulating nitrogen remobilization in rice

Autophagy, a conserved cellular process in eukaryotes, has evolved to a sophisticated process to dispose of intracellular constituents and plays important roles in plant development, metabolism, and efficient nutrients remobilization under suboptimal nutrients conditions. Here, we show that OsATG8b, an AUTOPHAGY-RELATED8 (ATG8) gene in rice, was highly induced by nitrogen (N) starvation. Elevated expression of OsATG8b significantly increased ATG8 lipidation, autophagic flux, and grain yield in rice under both sufficient and deficient N conditions. Overexpressing of OsATG8b could greatly increase the activities of enzymes related to N metabolism. Intriguingly, the 15N-labeling assay further revealed that more N was remobilized to seeds in OsATG8b-overexpressing rice, which significantly increased the N remobilization efficiency (NRE), N harvest index, N utilization efficiency (NUE), and N uptake efficiency (NUpE). Conversely, the osatg8b knock-out mutants had the opposite results on these characters. The substantial transcriptional changes of the overexpressed transgenic lines indicated the presence of complex signaling to developmental, metabolic process, and hormone, etc. Excitingly, the transgenic rice under different backgrounds all similarly be boosted in yield and NUE with OsATG8b overexpression. This work provides an excellent candidate gene for improving N remobilization, utilization, and yield in crops simultaneously.
Vegetative Responses of Apple Trees Following Benzyladenine and Growth Regulator Sprays

Benzyladenine (BA) stimulated lateral branching on young apple (Malus domestica Borkh.) trees at con- centrations as low as 100 mg·liter -1 . BA reduced lateral shoot length indirectly through increased intersboot com- petition, whereas daminozide reduced lateral shoot growth as a direct effect of the chemical inhibition. Daminozide reduced the number of spurs that were induced by BA to grow into lateral shoots. BA reduced the size of terminal buds on spurs that were stimulated to grow into lateral shoots. When daminozide was included with BA, spur quality was increased, as determined by Increased bud size. The positive effect of daminozide on BA-treated spurs was indirect, and other growth retardants used in combination with BA may be equally effective at improving spur quality. It may not be possible to stimulate lateral branching with BA on young trees just coming into production without causing an unacceptable amount of thinning. However, on bearing 'Empire' trees, lateral shoot growth was increased with BA while still achieving an appropriate level of thinning. In general, there was no advantage to applying BA in a split application. Chemical names used: N-(phenylmethyl)-1H-purine-6-amine (benzyladenin e (BA)); bu- tanedioic acid mono(2,2-dimethylhydrazide) (daminozide). Benzyladenine (BA) alone or in combination with GA. ,+, increased lateral branching on young apple trees (Elfving, 1984; Forshey, 1982; Greene and Miller, 1988; Miller and Eldridge, 1986). These studies were performed on young, sparsely branched trees with the specified purpose of increasing potential bearing surface by stimulating lateral branch development. As trees come into production, emphasis generally shifts from enhanced can- opy development to stimulation of flowering and spur devel- opment. BA induced lateral branching in 4-year-old 'Macspur McIntosh' at concentration s up to 500 mg·liter
The value of virtual bronchoscopic navigation and radial endobronchial ultrasound-guided transbronchial lung cryobiopsies for pulmonary lymphangitic carcinomatosis

Background Pulmonary lymphangitic carcinomatosis (PLC) is characterized by malignant infiltration into lung lymphatic channels from a primary site and is often observed in advanced malignant tumors. This study aimed to evaluate the diagnostic yield of transbronchial lung cryobiopsy in PLC guided by radial endobronchial ultrasound and virtual bronchoscopic navigation (VBN). Methods This prospective study enrolled 40 patients with clinical and radiologic features indicating PLC. The radial endobronchial ultrasound probe was initially advanced to the region of interest of the desired lobe near the pleura with guidance by VBN. Transbronchial lung biopsy and transbronchial lung cryobiopsy were both performed in the same ROI of all patients with the obtained samples being sent to the pathology laboratory for diagnostic analysis. Procedural complications were recorded. Results The average number of transbronchial lung biopsy and transbronchial lung cryobiopsy specimens were 4 (3 to 6) and 2 (1 to 3), respectively (t=10.43, P<0.01), with the corresponding mean diameters per biopsy being 3.7 and 8.7 mm (t=12.37, P<0.01). The diagnostic yields of transbronchial lung biopsy and transbronchial lung cryobiopsy were 70% (28/40) and 92.5% (37/40), respectively. The final positive predictive values of transbronchial lung cryobiopsy and transbronchial lung biopsy for PLC were 94.4% (34/36) and 77.8% (28/36), respectively (χ2=23.94, P<0.01). Further, 52.2% (12/23) and 81.5% (22/27) of the patients in the transbronchial lung biopsy and transbronchial lung cryobiopsy groups, respectively, were diagnosed with non-small lung cancer after further molecular analysis (χ2=19.56, P<0.01). Only 2 (5%) cases presented postoperative pneumothorax. Moreover, 0 (0%), 3 (7.5%), and 17 (42.5%) patients presented severe, moderate, and mild bleeding, respectively. There were no other adverse events or deaths. Conclusions Transbronchial lung cryobiopsy with the guidance of radial endobronchial ultrasound and VBN without fluoroscopy has a good diagnostic yield for PLC; moreover, it allows one to obtain adequate and intact tissue samples for further molecular analysis.
Dissemination kinetics and pathology of canine Leptospira icterohaemorrhagiae isolate in a guinea pig infection model

ABSTRACT Despite significant progress made in elucidating the mechanism of acute human leptospirosis in different organs, there is a paucity of information in organs such as the heart, pancreas, brain, and adrenal gland. This study was designed to establish leptospire dissemination kinetics and patho-morphological changes associated with these orangs in the guinea pig infection model using cultural isolation (CI), polymerase chain reaction (PCR), Warthin Starry silver stain (WSss), immunohistochemistry (IH), and transmission electron microscopy (TEM). Twenty guinea pigs were inoculated intra-peritoneally with a low dosage of 1 × 107 Leptospira interrogans serovar Icterohaemorrhagiae and 10 as control using distilled water. The guinea pigs were sacrificed at post-infection day (p.i.d.) ½, 1, 3, 5, and 7 followed by the harvest of the brain, pancreas, adrenal gland, heart, lungs, liver, kidneys, and spleen for CI, PCR, HE, WSss, IH, and TEM evaluations. The study revealed early dissemination of Leptospira organism in the brain, heart, pancreas, and adrenal gland and exerted various histopathological changes that were not explicitly elucidated in previous studies. This study revealed that the virulent pathogenic isolate of Leptospira organism obtained from clinically infected dog mimicked the same clinical manifestations, gross and histopathological changes especially in organs that were not previously evaluated.
Theoretical exploration of the ROS-photogenerating mechanisms of α-tocopherolquinone

Vitamin E (VE) is one of the most popular bio-antioxidants, while meta-analysis indicates that high levels of supplementation with VE may increase all-cause mortality. In this study, the photosensitisation mechanisms of α-tocopherolquinone (α-TQ), one of the important oxidation products of VE, were explored by means of quantum chemical calculations. The results indicate that excited state α-TQ can photogenerate thermodynamically various reactive oxygen species (ROS), e.g. 1O2 and , and the corresponding ROS-photogenerating mechanisms in different solvents were illustrated. The present results are helpful to understand the paradoxical activities of VE.
Inhibition of aerobic glycolysis alleviates sepsis-induced acute kidney injury by promoting lactate/Sirtuin 3/AMPK-regulated autophagy

Metabolism reprogramming influences the severity of organ dysfunction, progression to fibrosis, and development of disease in acute kidney injury (AKI). Previously we showed that inhibition of aerobic glycolysis improved survival rates and protected septic mice from kidney injury. However, the underlying mechanisms remain unclear. In the present study, it was revealed that sepsis or lipopolysaccharide (LPS) enhanced aerobic glycolysis as evidenced by increased lactate production and upregulated mRNA expression of glycolysis-related genes in kidney tissues and human renal tubular epithelial (HK-2) cells. The aerobic glycolysis inhibitor 2-deoxy-D-glucose (2-DG) downregulated glycolysis, and improved kidney injury induced by sepsis. 2-DG treatments increased the expression of sirtuin 3 (SIRT3) and phosphorylation-AMP-activated protein kinase (p-AMPK), following promoted autophagy and attenuated apoptosis of tubular epithelial cells in septic mice and in LPS-treated HK-2 cells. However, the glycolysis metabolite lactate downregulated SIRT3 and p-AMPK expression, inhibited autophagy and enhanced apoptosis in LPS-treated HK-2 cells. Furthermore, pharmacological blockade of autophagy with 3-methyladenine (3-MA) partially abolished the protective effect of 2-DG in sepsis-induced AKI. These findings indicated that inhibition of aerobic glycolysis protected against sepsis-induced AKI by promoting autophagy via the lactate/SIRT3/AMPK pathway.
Insulin Resistance Is Associated With Enhanced Brain Glucose Uptake During Euglycemic Hyperinsulinemia: A Large-Scale PET Cohort

OBJECTIVE Whereas insulin resistance is expressed as reduced glucose uptake in peripheral tissues, the relationship between insulin resistance and brain glucose metabolism remains controversial. Our aim was to examine the association of insulin resistance and brain glucose uptake (BGU) during a euglycemic hyperinsulinemic clamp in a large sample of study participants across a wide range of age and insulin sensitivity. RESEARCH DESIGN AND METHODS [18F]-fluorodeoxyglucose positron emission tomography (PET) data from 194 participants scanned under clamp conditions were compiled from a single-center cohort. BGU was quantified by the fractional uptake rate. We examined the association of age, sex, M value from the clamp, steady-state insulin and free fatty acid levels, C-reactive protein levels, HbA1c, and presence of type 2 diabetes with BGU using Bayesian hierarchical modeling. RESULTS Insulin sensitivity, indexed by the M value, was associated negatively with BGU in all brain regions, confirming that in insulin-resistant participants BGU was enhanced during euglycemic hyperinsulinemia. In addition, the presence of type 2 diabetes was associated with additional increase in BGU. On the contrary, age was negatively related to BGU. Steady-state insulin levels, C-reactive protein and free fatty acid levels, sex, and HbA1c were not associated with BGU. CONCLUSIONS In this large cohort of participants of either sex across a wide range of age and insulin sensitivity, insulin sensitivity was the best predictor of BGU.
Micro-pursuit: A class of fixational eye movements correlating with smooth, predictable, small-scale target trajectories

Humans generate ocular pursuit movements when a moving target is tracked throughout the visual field. In this article, we show that pursuit can be generated and measured at small amplitudes, at the scale of fixational eye movements, and tag these eye movements as micro-pursuits. During micro-pursuits, gaze direction correlates with a target's smooth, predictable target trajectory. We measure similarity between gaze and target trajectories using a so-called maximally projected correlation and provide results in three experimental data sets. A first observation of micro-pursuit is provided in an implicit pursuit task, where observers were tasked to maintain their gaze fixed on a static cross at the center of screen, while reporting changes in perception of an ambiguous, moving (Necker) cube. We then provide two experimental paradigms and their corresponding data sets: a first replicating micro-pursuits in an explicit pursuit task, where observers had to follow a moving fixation cross (Cross), and a second with an unambiguous square (Square). Individual and group analyses provide evidence that micro-pursuits exist in both the Necker and Cross experiments but not in the Square experiment. The interexperiment analysis results suggest that the manipulation of stimulus target motion, task, and/or the nature of the stimulus may play a role in the generation of micro-pursuits.
The Effect of Plantago major on Wound Healing in Preclinical Studies: A Systematic Review.

BACKGROUND Plantago major is a medicinal plant that has been used for centuries to treat various health conditions including wounds. PURPOSE To investigate the effectiveness of the topical use of P major in healing skin wounds in animal models. METHODS Using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, a systematic review was conducted. Seven (7) electronic databases (Virtual Health Library, Public/Publisher MEDLINE, Scopus, Web of Science, Embase, Cumulative Index of Nursing and Allied Health Literature, and CAB Direct) were searched for controlled studies published in English from January 2006 to March 2020. The Collaborative Approach to Meta Analysis and Review of Animal Data from Experimental Studies tools guided the evaluation of the studies and determined their quality. The Systematic Review Center for Laboratory Animal Experimentation was used to assess the risk of bias. RESULTS Of the 176 publications identified, 4 met the inclusion criteria. Studies included 20 to 100 animals and varying concentrations of P major. There were no reports of losses during research. Wound healing was assessed between 17 and 21 days following wounding. The best response in terms of wound contraction rate occurred with 10%, 20%, and 50% concentrations when compared with control groups. One (1) study did not have an animal ethics committee review. All studies had a high risk of bias and a lack of methodological rigor. CONCLUSION The results of this review did not find evidence about the in vivo effectiveness of P major for wound healing. More rigorous preclinical studies with adequate sample sizes are required to identify the best concentrations and formulations as well as increase understanding about the mechanisms of action of P major in wound healing.
Tracking Internal Frames of Reference for Consistent Molecular Distribution Functions

In molecular analysis, spatial distribution functions (SDF) are fundamental instruments in answering questions related to spatial occurrences and relations of atomic structures over time. Given a molecular trajectory, SDFs can, for example, reveal the occurrence of water in relation to particular structures and hence provide clues of hydrophobic and hydrophilic regions. For the computation of meaningful distribution functions, the definition of molecular reference structures is essential. Therefore we introduce the concept of an internal frame of reference (IFR) for labeled point sets that represent selected molecular structures, and we propose an algorithm for tracking the IFR over time and space using a variant of Kabsch’s algorithm. This approach lets us generate a consistent space for the aggregation of the SDF for molecular trajectories and molecular ensembles. We demonstrate the usefulness of the technique by applying it to temporal molecular trajectories as well as ensemble datasets. The examples include different docking scenarios with DNA, insulin, and aspirin.
Modeling transfer of vaginal microbiota from mother to infant in early life

Early-life microbiota has been linked to the development of chronic inflammatory diseases. It has been hypothesized that maternal vaginal microbiota is an important initial seeding source and therefore might have lifelong effects on disease risk. To understand maternal vaginal microbiota’s role in seeding the child’s microbiota and the extent of delivery mode-dependent transmission, we studied 665 mother–child dyads from the COPSAC2010 cohort. The maternal vaginal microbiota was evaluated twice in the third trimester and compared with the children’s fecal (at 1 week, 1 month, and 1 year of age) and airway microbiota (at 1 week, 1 month, and 3 months). Based on the concept of weighted transfer ratios (WTRs), we have identified bacterial orders for which the WTR displays patterns indicate persistent or transient transfer from the maternal vaginal microbiome, as well as orders that are shared at later time points independent of delivery mode, indicating a common reservoir.
Prognostic Impact of Percutaneous Coronary Intervention of Chronic Total Occlusion in Acute and Periprocedural Myocardial Infarction

Coronary chronic total occlusion (CTO) has gained increasing clinical attention as the most advanced form of coronary artery disease. Prior studies already indicated a clear association of CTO with adverse clinical outcomes, especially in patients with acute myocardial infarction (AMI) and concomitant CTO of the non-infarct-related coronary artery (non-IRA). Nevertheless, the prognostic impact of percutaneous coronary intervention (PCI) of CTO in the acute setting during AMI is still controversial. Due to the complexity of the CTO lesion, CTO-PCI leads to an increased risk of complications compared to non-occlusive coronary lesions. Therefore, this review outlines the prognostic impact of CTO-PCI in patients with AMI. In addition, the prognostic impact of periprocedural myocardial infarction caused by CTO-PCI will be discussed.
Control of the Morphology and Porosity of Hematite Particles through the Use of Tannic Acids

The shape and porosity of hematite particles formed from the forced hydrolysis of acidic FeCl3 solutions could be controlled by the use of two types of tannic acid (hydrolysable and non-hydrolysable) within the concentration range 0–2 × 10−2 wt%. The system with hydrolysable tannic acid (AL) initially provided quite small spherical particles at concentrations up to 10−2 wt% and finally irregular small hematite particles at 2 × 10−2 wt%. In the system with condensed non-hydrolysable tannic acid (KT), on the other hand, the hematite particles became ellipsoidal in shape at concentrations above10−2 wt%. The formation of ellipsoidal particles was explained by the adsorption of KT molecules onto the growing polynuclear primary particles. TEM and XRD measurements revealed that all the hematite particles produced from FeCl3/HCl solutions with tannic acids are polycrystalline. The rate of phase transformation from β-FeOOH to hematite was accelerated as the concentration of AL increased, whereas no significant change was observed for the KT system. Analysis by t-plots revealed that the porosity of the hematite particles changed from mesoporous to microporous when the concentration of AL increased. In contrast, the presence of very low amounts of KT molecules (10−5 and 10−4 wt%) produced non-porous hematite particles via strong aggregation of polynuclear (PN) particles by hydrogen bonding between hydroxy and carboxy groups. Not only the morphology but also the pore size of hematite particles was controlled from non-porous to mesoporous by using different kinds of tannic acids.