Miracle-dz/UniFAR-FTUs huggingface dataset:
Universal and differential transcriptional regulatory pathways involved in the preparation of summer and winter diapauses in Pieris melete

Abstract Much progress has been made in understanding the environmental and hormonal systems regulating winter diapause. However, transcriptional regulation of summer diapause is still largely unknown, making it difficult to understand an all-around regulation profile of seasonal adaptation. To bridge this gap, comparison RNA-seq to profile the transcriptome and to examine differential gene expression profiles between non-diapause, summer diapause, and winter diapause groups were performed. A total number of 113 million reads were generated and assembled into 79,117 unigenes, with 37,492 unigenes categorized into 58 functional gene ontology groups, 25 clusters of orthologous group categories, and 256 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. KEGG analysis mapped 2108 differentially expressed genes to 48 and 67 pathways for summer and winter diapauses, respectively. Enrichment statistics showed that 11 identical pathways similarly overlapped in the top 20 enriched functional groups both related to summer and winter diapauses. We also identified 35 key candidate genes for universal and differential functions related to summer and winter diapause preparation. Furthermore, we identified some genes involved in the signaling and metabolic pathways that may be the key drivers to integrate environmental signals into the summer and winter diapause preparation. The current study provided valuable insights into global molecular mechanisms underpinning diapause preparation.
Dose–Response Study of Microcystin Congeners MCLA, MCLR, MCLY, MCRR, and MCYR Administered Orally to Mice

Microcystins are common freshwater cyanobacterial toxins that affect liver function. The toxicities of five microcystin congeners (microcystin-LA (MCLA), MCLR, MCLY, MCRR, and MCYR) commonly observed in harmful algal blooms (HABs) were evaluated in BALB/c mice after a single oral administration of doses ranging from those that were no observed adverse effect levels (NOAELs) to lowest observed adverse effect levels (LOAELs). Animals were monitored for changes in behavior and appearance, and euthanized 24 h after dosing. Test endpoints included clinical changes, necropsy observations, and serum indicators of hepatic toxicity and general homeostasis. Doses were 0.5–7 mg/kg MCLA, 0.5–11 mg/kg MCLR, 1–7 mg/kg MCLY, 7–22 mg/kg MCRR, and 3–11 mg/kg MCYR. MCLA at 3 mg/kg elevated liver/body weight ratio and liver score, ALT, AST, and GLDH, indicating hepatic toxicity, reduced serum glucose and highly elevated total serum bilirubin. MCLR and MCLY induced similar effects with LOAELs of 5 mg/kg, although a greater extent and severity of effects were observed in MCLR animals. MCRR exposure at 22 mg/kg was associated with reduced serum glucose. MCYR induced scattered liver effects at 7 mg/kg and reduced serum glucose levels at 5 mg/kg. The results indicate significant differences in congener-induced toxicity after microcystin exposure.
A high-resolution record of early Paleozoic climate

Significance The Cambrian–Ordovician (541 million to 443 million y ago) climate record is poorly constrained due to the sparsity of carbonate fossils typically used for temperature reconstructions. We demonstrate that the abundant carbonate sediments from this time can preserve isotopic compositions and trends similar to those of fossil material and combine sediment records into a high-resolution proxy record of Late Cambrian and Ordovician climate. Examination of this record in the context of evolutionary and tectonic changes demonstrates that Earth’s climate was tightly coupled to tectonic and volcanic activity and played a strong role in biodiversity trends during the time of early animal evolution. The spatial coverage and temporal resolution of the Early Paleozoic paleoclimate record are limited, primarily due to the paucity of well-preserved skeletal material commonly used for oxygen-isotope paleothermometry. Bulk-rock δ18O datasets can provide broader coverage and higher resolution, but are prone to burial alteration. We assess the diagenetic character of two thick Cambro–Ordovician carbonate platforms with minimal to moderate burial by pairing clumped and bulk isotope analyses of micritic carbonates. Despite resetting of the clumped-isotope thermometer at both sites, our samples indicate relatively little change to their bulk δ18O due to low fluid exchange. Consequently, both sequences preserve temporal trends in δ18O. Motivated by this result, we compile a global suite of bulk rock δ18O data, stacking overlapping regional records to minimize diagenetic influences on overall trends. We find good agreement of bulk rock δ18O with brachiopod and conodont δ18O trends through time. Given evidence that the δ18O value of seawater has not evolved substantially through the Phanerozoic, we interpret this record as primarily reflecting changes in tropical, nearshore seawater temperatures and only moderately modified by diagenesis. Focusing on the samples with the most enriched, and thus likely least-altered, δ18O values, we reconstruct Late Cambrian warming, Early Ordovician extreme warmth, and cooling around the Early–Middle Ordovician boundary. Our record is consistent with models linking the Great Ordovician Biodiversification Event to cooling of previously very warm tropical oceans. In addition, our high-temporal-resolution record suggests previously unresolved transient warming and climate instability potentially associated with Late Ordovician tectonic events.
Gamifying quantitative face-to-face interviews in rural India: An empirical evaluation based on the basic psychological needs theory

Objective Standardized face-to-face interviews are widely used in low and middle-income countries to collect data for social science and health research. Such interviews can be long and tedious. In an attempt to improve the respondents’ experience of interviews, we developed a concept of gamified interview format by including a game element. Gamification is reported to increase engagement in tasks, but results from rigorously developed research are equivocal, and a theory of gamification is still needed. Materials & methods We evaluated the proposed gamification with a randomized controlled trial based on self-determination theory, specifically on the basic psychological needs theory. In total, 1266 respondents were interviewed. Single and multiple mediation analyses were used to understand the effects of the gamified interview format. Results Our evaluation showed that the gamification we had developed did not improve the outcome, the experience of the interview reported by respondent. The effect of the gamified interview format depended on the ability of respondents: gamification can be counterproductive if it overburdens the respondents. However, the basic psychological needs theory explained the mechanisms of action of gamification well: feeling competent and related to others improved the reported experience of the interview. Conclusion We emphasize the need to develop context-specific gamification and invite researchers to conduct equivalently rigorous evaluations of gamification in future studies.
Validation of the Stress in Children (SiC) Questionnaire in a Sample of Greek Pupils.

Aim The purpose of this study was to validate a Greek version of the Stress in Children (SiC) Questionnaire and assess its psychometric qualities in a Greek pediatric sample. Materials and Methods Healthy children aged 8-12 years, attending schools of various areas of Attica, the largest region in Greece, were eligible to participate in the study. Data were collected from May 2016 until June 2017, anonymously, though three self-reported questionnaires, a simple demographic questionnaire, the SiC Questionnaire and the State and Trait Anxiety in Children Questionnaire. Results Questionnaires were completed by 100 pupils (54 boys, 46 girls) aged (mean ± SD) 10.6 ± 1.26 years. A three-factor structure ("Distress", "Presence of well-being", and "Presence of social support") accounted for 41.33% of variance. Reliability Cronbach's alpha of "Distress", "Presence of well-being" and "Presence of social support" factors was equal to 0.75, 0.75 and 0.61, respectively. Regarding concurrent validity, positive correlations were found between "Distress" and both trait anxiety (rho=0.59, p<0.0001) and state anxiety (rho=0.61, p<0.0001). Correlations were also found between "Presence of Wellbeing" and age (rho=-0.24, p=0.019), state (rho=-0.36, p=0.006) and trait anxiety (rho=-0.45, p<0.0001). Conclusions The Greek version of SiC Questionnaire demonstrated satisfactory psychometric properties (content validity, internal reliability) that support its use in Greek children.
Comparison of Spectroscopic Techniques for Determining the Peroxide Value of 19 Classes of Naturally Aged, Plant-Based Edible Oils

The peroxide value of edible oils is a measure of the degree of oxidation, which directly relates to the freshness of the oil sample. Several studies previously reported in the literature have paired various spectroscopic techniques with multivariate analyses to rapidly determine peroxide values using field portable and process instrumentation; those efforts presented “best-case scenarios” with oils from narrowly defined training and test sets. The purpose of this paper is to evaluate the use of near- and mid-infrared absorption and Raman scattering spectroscopies on oil samples from different oil classes, including seasonal and vendor variations, to determine which measurement technique or combination thereof is best for predicting peroxide values. Following peroxide value assays of each oil class using an established titration-based method, global and global-subset calibration models were constructed from spectroscopic data collected on the 19 oil classes used in this study. Spectra from each optical technique were used to create partial least squares regression calibration models to predict the peroxide value of unknown oil samples. A global peroxide value model based on near-infrared (8 mm optical path length) oil measurements produced the lowest RMSEP (4.9), followed by 24 mm optical path length near infrared (5.1), Raman (6.9) and 50 µm optical path length mid-infrared (7.3). However, it was determined that the Raman RMSEP resulted from chance correlations. Global peroxide value models based on low-level fusion of the NIR (8 and 24 mm optical path length) data and all infrared data produced the same RMSEP of 5.1. Global subset models, based on any of the spectroscopies and olive oil training sets from any class (pure, extra light, extra virgin), all failed to extrapolate to the non-olive oils. However, the near-infrared global subset model built on extra virgin olive oil could extrapolate to test samples from other olive oil classes. This work demonstrates the difficulty of developing a truly global method for determining peroxide value of oils. Graphical Abstract
Nonlinear Effects in the Piezoresistivity of p‐Type Silicon

Piezoresistivity measurements are carried out on heavily doped ion-implanted p-type resistors on the surfaces of cantilever beams cut from a (100) silicon wafer. Tensile and compressive stresses, up to 85 MPa along the [110] direction, are applied by bending the beams with a micrometer. Nonlinear effects are clearly seen in the measurements where the resistor contains sections both parallel and perpendicular to the stress. The results are analyzed in terms of the first- and second-order piezoresistance coefficients. Values of the piezoresistance coefficients are calculated using analytical expressions for the strain dependent energy-wave vector relations of the valence bands and the known deformation potentials. The results of the calculations are compared with the experimental data including some earlier measurements reported in literature. The calculated values of the first-order coefficients are found to agree fairly well with the experimental data. The calculated second-order coefficients are able to describe the observed anisotropy in the nonlinear piezoresistivity of the second order in stress. Piezowiderstandsmessungen an stark dotierten, ionenimplantierten p-Typ-Widerstanden auf aus einer (100)-Siliziumscheibe geschnittenen Balken werden durchgefuhrt. Sowohl Zug als auch Kompression bis 85 MPa in [110]-Bichtung werden durch Biegung des Balkens mit einem Mikrometer ausgefuhrt. Nichtlineare Phanomene bei den Messungen sind klar zu sehen, bei denen der Widerstand Anteile sowohl parallel als auch senkrecht zur Spannung enthalt. Die Resultate werden mit den Piezowiderstandskoeffizienten erster und zweiter Ordnung analysiert. Bei den Berechnungen der Piezowiderstandskoeffizienten werden analytische Ausdrucke fur die deformationsabhangigen Energie-Wellenvektor-Relationen der Valenzbander und die bekannten Deformationspotentiale benutzt. Die Ergebnisse der Berechnungen werden mit den experimentellen Daten einschlieslich fruherer Daten aus der Literatur verglichen. Die berechneten Werte der Koeffizienten erster Ordnung stimmen ziemlich gut mit den Experimenten uberein. Die berechneten Koeffizienten zweiter Ordnung konnen die beobachtete Anisotropie im nichtlinearen Piezowiderstandseffekt beschreiben.
Genome-wide association study of cyanogenic glycosides, proline, sugars and pigments in Eucalyptus cladocalyx after eighteen consecutive dry summers.

Natural variation of cyanogenic glycosides, soluble sugars, proline and nondestructive optical sensing of pigments (chlorophyll, flavonols and anthocyanins) were examined in ex situ natural populations of Eucalyptus cladocalyx F. Muell. grown under dry environmental conditions in the southern Atacama Desert, in Chile. After 18 consecutive dry seasons, considerable plant-to-plant phenotypic variation for all the traits was observed in the field. For example, leaf hydrogen cyanide (HCN) concentrations varied from 0 (two acyanogenic individuals) to 1.54 mg cyanide g-1 dry weight. Subsequent genome-wide association study (GWAS) revealed associations with several genes with a known function in plants. HCN content was associated robustly with genes encoding Cytochrome P450 proteins, and with genes involved in the detoxification mechanism of HCN in cells (β-cyanoalanine synthase and cyanoalanine nitrilase). Another important finding was that sugars, proline and pigment content were linked to genes involved in transport, biosynthesis and/or catabolism. Estimates of genomic heritability (based on haplotypes) ranged between 0.46 and 0.84 (HCN and proline content, respectively). Proline and soluble sugars had the highest predictive ability of genomic prediction models (PA = 0.65 and PA = 0.71, respectively). PA values for HCN content and flavonols were relatively moderate, with estimates ranging from 0.44 to 0.50. These findings provide new understanding on the genetic architecture of cyanogenic capacity, and other key complex traits in cyanogenic E. cladocalyx. This article is protected by copyright. All rights reserved.
Anxiety in adolescents with severe asthma and response to treatment

Asthma is a complex and multifactorial disorder. Actually, anxiety may affect asthma, mainly concerning frequent exacerbations, pharmacoeconomic costs, and uncontrolled asthma. On the basis of this background, we tested the hypothesis that anxiety could affect severe asthma outcomes in asthmatic adolescents. Therefore, a longitudinal real-world study included 40 consecutive adolescents (22 males, 18 females, mean age 14.18 ± 1.97 years) with severe asthma and visited for the first time at a third-level pediatric clinic. The current study showed that anxiety is common in adolescents with severe asthma as about 60% of them was anxious. In addition, anxiety was associated with frequent use of bronchodilators on demand. This outcome may conceivably depend on the anxiety trait. Interestingly, depression was present only in anxious adolescents: this outcome underlines the close link between emotional disorders. Therefore, emotional aspect should be considered in the adolescent asthma management in clinical practice. (www.actabiomedica.it)
Alignment Targets, Curve Proportion and Mechanical Loading: Preliminary Analysis of an Ideal Shape Toward Reducing Proximal Junctional Kyphosis

Study Design: Retrospective cohort study. Objective: Investigate risk factors for PJK including theoretical kyphosis, mechanical loading at the UIV and age adjusted offset alignment. Methods: 373 ASD patients (62.7 yrs ± 9.9; 81%F) with 2-year follow up and UIV of at least L1 and LIV of sacrum were included. Images of patients without PJK, with PJK and with PJF were compared using standard spinopelvic parameters before and after the application of the validated virtual alignment method which corrects for the compensatory mechanisms of PJK. Age-adjusted offset, theoretical thoracic kyphosis and mechanical loading at the UIV were then calculated and compared between groups. A subanalysis was performed based on the location of the UIV (upper thoracic (UT) vs. Lower thoracic (LT)). Results: At 2-years 172 (46.1%) had PJK, and 21 (5.6%) developed PJF. As PJK severity increased, the post-operative global alignment became more posterior secondary to increased over-correction of PT, PI-LL, and SVA (all P < 0.005). Also, a larger under correction of the theoretical TK (flattening) and a smaller bending moment at the UIV (underloading of UIV) was found. Multivariate analysis demonstrated that PI-LL and bending moment offsets from normative values were independent predictors of PJK/PJF in UT group; PT and bending moment difference were independent predictors for LT group. Conclusions: Spinopelvic over correction, under correction of TK (flattening), and under loading of the UIV (decreased bending moment) were associated with PJK and PJF. These differences are often missed when compensation for PJK is not accounted for in post-operative radiographs.
Blood-Brain Barrier Disruption Increases Amyloid-Related Pathology in TgSwDI Mice

In Alzheimer’s disease (AD), several studies have reported blood-brain barrier (BBB) breakdown with compromised function. P-glycoprotein (P-gp) and breast cancer resistance protein (BCRP) are transport proteins localized at the BBB luminal membrane and play an important role in the clearance of amyloid-β (Aβ). The purpose of this study was to investigate the effect of pharmacological inhibition of Aβ efflux transporters on BBB function and Aβ accumulation and related pathology. Recently, we have developed an in vitro high-throughput screening assay to screen for compounds that modulate the integrity of a cell-based BBB model, which identified elacridar as a disruptor of the monolayer integrity. Elacridar, an investigational compound known for its P-gp and BCRP inhibitory effect and widely used in cancer research. Therefore, it was used as a model compound for further evaluation in a mouse model of AD, namely TgSwDI. TgSwDI mouse is also used as a model for cerebral amyloid angiopathy (CAA). Results showed that P-gp and BCRP inhibition by elacridar disrupted the BBB integrity as measured by increased IgG extravasation and reduced expression of tight junction proteins, increased amyloid deposition due to P-gp, and BCRP downregulation and receptor for advanced glycation end products (RAGE) upregulation, increased CAA and astrogliosis. Further studies revealed the effect was mediated by activation of NF-κB pathway. In conclusion, results suggest that BBB disruption by inhibiting P-gp and BCRP exacerbates AD pathology in a mouse model of AD, and indicate that therapeutic drugs that inhibit P-gp and BCRP could increase the risk for AD.
Lipoamino acid coated superparamagnetic iron oxide nanoparticles concentration and time dependently enhanced growth of human hepatocarcinoma cell line (Hep-G2)

Superparamagnetic iron oxide nanoparticles (SPION) have been widely used in medicine for magnetic resonance imaging, hyperthermia, and drug delivery applications. The effect of SPION on animal cells has been a controversial issue on which there are many contradictions. This study focused on preparation of SPION with novel biocompatible coatings, their characterization, and cytotoxicity evaluation. An amino acid (glycine) and two novel lipo-amino acids (2 amino-hexanoic acid and 2 amino-hexadecanoic acid) coated magnetic nanoparticles were characterized by various physicochemical means such as X-ray diffraction (XRD), transmission electron microscopy (TEM), vibrating sample magnetometry (VSM), differential scanning calorimetry (DSC), and infrared spectroscopy (FT-IR). The cytotoxicity profile of the synthesized nanoparticles on Hep-G2 cells as measured by MTT assay showed the nanoparticles are nontoxic and the cell growth is promoted by SPION. Moreover, lipoamino acid coating SPION appear more beneficial than the other ones. By increasing concentration of SPION, growth enhancing impact will attenuate and toxicity will appear. Although the aggregation of SPION can affect the results, the gradual delivery of ferric/ferrous ions into cells is the main cause of this growth promotion effect. Conclusively, this study shows that lipoamino acid coating SPION can be used for various biomedical purposes.
The statistical mechanics of free and protein -bound DNA by Monte Carlo simulation

OF THE DISSERTATION The Statistical Mechanics of Free and Protein-bound DNA by Monte Carlo Simulation by Luke Czapla Dissertation Director: Wilma K. Olson There are many challenges involved in the simulation of DNA. In this work, novel Monte Carlo techniques are developed and applied to understanding the biophysical properties of DNA. A coarse-grained model is applied to feasibly simulate long DNA chains of hundreds to thousands of base pairs, using a reduced base-pair step representation of the DNA. Using this model, a canonical Monte Carlo simulation of DNA is developed to characterize the structure and flexibility of double-helical DNA. By applying a unique algorithm for generating uncorrelated DNA conformations a priori, limitations of the original Metropolis Monte Carlo algorithm are avoided. Furthermore, there is developing experimental evidence that non-specifically associating proteins that induce DNA bending modulate the in-vivo flexibility of DNA. To investigate the effect of these proteins, a grand canonical Monte Carlo simulation technique is developed, extending the model of free DNA to incorporate non-specific protein-DNA interactions. In this technique, DNA chains are simulated with varying numbers of bound proteins. Ubiquitous DNA architectural proteins such as the prokaroytic nucleoid protein HU and the eukaryotic HMG-box proteins are investigated with this technique. By incorporating structural information from the protein-DNA complexes currently available in the Nucleic Acid Database, models of these DNA-binding proteins