Miracle-dz/UniFAR-FTUs huggingface dataset:
Parsing Sage and Rosemary in Time: The Machine Learning Race to Crack Olfactory Perception.

Color and pitch perception are largely understandable from characteristics of a physical stimuli: the wavelengths of light and sound waves, respectively. By contrast, understanding olfactory percepts from odorous stimuli (volatile molecules) is much more challenging. No intuitive set of molecular features is up to the task. Here in Chemical Senses, the Ray lab reports using a predictive modeling framework--first breaking molecular structure into thousands of features and then using this to train a predictive statistical model on a wide range of perceptual descriptors--to create a tool for predicting the odor character of hundreds of thousands of available but previously uncharacterized molecules (Kowalewski, Huynh and Ray, 2021). This will allow future investigators to representatively sample the space of odorous molecules as well as identify previously unknown odorants with a target odor character. Here I put this work into the context of other modeling efforts and highlight the urgent need for large new datasets and transparent benchmarks for the field to make and evaluate modeling breakthroughs, respectively.
A novel calibration for L-shell x-ray fluorescence measurements of bone lead concentration using the strontium Kβ/Kα ratio

Objective. Lead (Pb) is a well-known toxic element. In vivo bone Pb concentration measurement is a long-term exposure metric complementary to blood Pb concentration measurement which is a metric of recent exposure. In vivo human tibia bone Pb measurements using Pb K-shell or L-shell x-ray fluorescence (KXRF or LXRF) emissions were developed in the 1980s. KXRF bone Pb measurements using Cd-109 gamma rays and coherent-to-fluorescence ratio to account for differences between phantom and in vivo measurements, was employed in human studies. Bone Pb LXRF method employed x-ray tubes. However, calibration procedures using ultrasound measurements of the soft tissue thickness (STT) proved inaccurate. Approach. In this study, bone and soft tissue (ST) phantoms simulated in vivo bone Pb measurements. Seven plaster-of-Paris cylindrical bone phantoms containing 1.01 mg g−1 of strontium (Sr) were doped with Pb in 0, 8, 16, 29, 44, 59, and 74 μg g−1 concentrations. Polyoxymethylene (POM), resin, and wax were each used to fabricate four ST phantoms in the approximate 1–4 mm thickness range. Pb LXRF measurements were performed using a previously developed optimal grazing incidence position method. Main results. Linear attenuation coefficients measurements of ST materials indicated that POM and resin mimicked well attenuation of Pb x-rays in skin and adipose tissue, respectively. POM and resin data indicated a bone Pb detection limit of 20 μg g−1 for a 2 mm STT. Derived relationships between the Pb concentration, Pb LXRF and Sr K β /K α ratio data did not require STT knowledge. Applied to POM and resin data, the new calibration method yielded unbiased results. Significance. In vivo bone Pb measurements in children were suggested following considerations of radiation dose, STT, detectability and distribution of Pb and Sr in bone. This research meets with the concerns regarding the negative effects of low levels of Pb exposure on neurodevelopment of children.
Nutrigenomic analyses reveal miRNAs and mRNAs affected by feed restriction in the mammary gland of midlactation dairy cows

The objective of this study was to investigate the effects of feed restriction on mammary miRNAs and coding gene expression in midlactation cows. Five Holstein cows and 6 Montbéliarde cows underwent 6 days of feed restriction, during which feed allowance was reduced to meet 50% of their net energy for lactation requirements. Mammary biopsies were performed before and at the end of the restriction period. Mammary miRNA and mRNA analyses were performed using high-throughput sequencing and microarray analyses, respectively. Feed restriction induced a negative energy balance and decreased milk production and fat and protein yields in both breeds. Feed restriction modified the expression of 27 miRNAs and 374 mRNAs in mammary glands from Holstein cows, whereas no significant miRNA change was observed in Montbéliarde cows. Among the 27 differentially expressed miRNAs, 8 miRNAs were associated with dairy QTL. Analysis of target genes indicate that the 8 most abundantly expressed miRNAs control transcripts related to lipid metabolism, mammary remodeling and stress response. A comparison between the mRNAs targeted by the 8 most strongly expressed miRNAs and 374 differentially expressed mRNAs identified 59 mRNAs in common. The bioinformatic analyses of these 59 mRNAs revealed their implication in lipid metabolism and endothelial cell proliferation. These effects of feed restriction on mammary miRNAs and mRNAs observed in Holstein cows suggest a potential role of miRNAs in mammary structure and lipid biosynthesis that could explain changes in milk production and composition.
Intervention Effect of the Integration Model on Negative Emotions of Adolescents during the Outbreak of Corona Virus Disease 2019.

BACKGROUND The World Health Organization has declared the Corona Virus Disease 2019 (COVID-19) epidemic as a public health emergency of international concern. Given the sudden infection from and extensive dispersion of COVID-19 and the absence of specific drugs, those infected are in danger if they are not treated in time. Consequently, COVID-19 has become an important factor influencing adolescents' mental health. The purpose of this study is to explore the intervention effect of the integration model on the negative emotions of adolescents during the COVID-19 epidemic. SUBJECTS AND METHODS Adolescents were randomly selected from five middle schools in Zhejiang Province of China from May 2020 to July 2020. First, the Self-rating Anxiety Scale, Positive and Negative Affect Scale, and Psychological Well-Being Scale were used for measurement. Then, 72 patients with moderate and severe anxiety symptoms were chosen as the research objects, and the intervention and comparison time was determined to be eight weeks. The subjects were randomly divided into the experiment group (35 members) and the control group (34 members). The integration model was employed on the experiment group. RESULTS Grade, physical condition, and sleep time are important factors influencing the anxiety level of adolescents during the COVID-19 period, and the anxiety risk of adolescents is higher during their third year of junior high school. After the intervention, the SAS score of the experiment group is lower than that of the control group, and the decrease in the SAS score is higher in the experiment group than in the control group (P<0.01). Moreover, the positive emotion score of the experiment group is higher than that of the control group, and the negative emotion score of the former is lower than that of the latter. The variances in the positive and negative emotion scores are higher in the experiment group than in the control group (P<0.01). The variance in the overall well-being index is also greater in the experiment group than in the control group (P<0.01). CONCLUSION The intervention using the integrated model can significantly reduce negative emotions such as anxiety, increase positive emotions, and improve the overall well-being of adolescents during the epidemic period.
Maternal Pregnancy Intention and Developmental Outcomes in Brazilian Preschool-Aged Children

This article has supplementary material on the web site: www.jdbp. org. ABSTRACT: Objective: This study aims to characterize the association between maternal pregnancy intention and socioemotional developmental outcomes in a Brazilian sample of preschool-aged children. Methods: Data from children aged 4 to 5 years and their primary caregivers in Embu das Artes, a Brazilian municipality in the state of São Paulo, were collected in 2016. Maternal pregnancy intention was defined as intended or unintended, which was then further stratified as mistimed or unwanted. Outcomes included socioemotional developmental delay, internalizing and externalizing behaviors, and school readiness. We estimated risk ratios (RRs) for unadjusted and inverse-probability–weighted regression adjustment (IPWRA) analyses using 2-level (intended vs unintended) and 3-level (intended vs mistimed vs unwanted) exposure definitions. Results: Of 1,034 total mothers, 40.7% reported their pregnancy as intended, 46.0% as mistimed, and 13.4% as unwanted. In both unadjusted and IPWRA analyses comparing intended and unintended pregnancies, all associations failed to reach statistical significance. In the IPWRA analysis using the 3-level exposure definition, unwanted pregnancies were associated with higher risk of socioemotional developmental delay (RR = 1.14; 95% confidence interval [CI], 1.01–1.28) and co-occurring internalizing and externalizing behaviors (RR = 1.11, 95% CI, 1.00–1.22), compared with intended pregnancies. Conclusion: There was higher risk of poor child outcomes among unwanted compared with intended pregnancies, whereas mistimed pregnancies were not associated with poor outcomes. Further research using standardized definitions of pregnancy intention along with targeted interventions that increase access to family planning services and counseling for parents of children born after unintended pregnancies is needed.
Proteomic identification of biomarkers in maternal plasma that predict the outcome of rescue cerclage for cervical insufficiency

Objective We sought to identify plasma protein biomarkers that are predictive of the outcome of rescue cerclage in patients with cervical insufficiency. Methods This retrospective cohort study included 39 singleton pregnant women undergoing rescue cerclage for cervical insufficiency (17–25 weeks) who gave plasma samples. Three sets of pooled plasma samples from controls (cerclage success, n = 10) and cases (cerclage failure, n = 10, defined as spontaneous preterm delivery at <33 weeks) were labeled with 6-plex tandem mass tag (TMT) reagents and analyzed by liquid chromatography-tandem mass spectrometry. Differentially expressed proteins between the two groups were selected from the TMT-based quantitative analysis. Multiple reaction monitoring-mass spectrometry (MRM-MS) analysis was further used to verify the candidate proteins of interest in patients with cervical insufficiency in the final cohort (n = 39). Results From MRM-MS analysis of the 40 proteins showing statistically significant changes (P < 0.05) from the TMT-based quantitative analysis, plasma IGFBP-2, PSG4, and PGLYRP2 levels were found to be significantly increased, whereas plasma MET and LXN levels were significantly decreased in women with cerclage failure. Of these, IGFBP-2, PSG4, and LXN levels in plasma were independent of cervical dilatation. A multiple-biomarker panel was developed for the prediction of cerclage failure, using a stepwise regression procedure, which included the plasma IGFBP-2, PSG4, and LXN (area under the curve [AUC] = 0.916). The AUC for this multiple-biomarker panel was significantly greater than the AUC for any single biomarker included in the multi-biomarker model. Conclusions Proteomic analysis identified useful and independent plasma biomarkers (IGFBP-2, PSG4, and LXN; verified by MRM) that predict poor pregnancy outcome following rescue cerclage. Their combined analysis in a multi-biomarker panel significantly improved predictability.
Multilayer Graphynes for Lithium Ion Battery Anode

Graphynes, two-dimensional layers of sp- and sp2-bonded carbon atoms, have recently received considerable attention because of their potential as new Dirac materials. Here, focusing on their large surface area, we explore the applicability of graphynes as lithium ion battery anodes through the first-principles density functional calculations. We have found that Li potential energies are in the range suitable to be used as anodes. Furthermore, the maximum composite of Li-intercalated multilayer α- and γ-graphynes is found to be C6Li3, which corresponds to a specific capacity of 1117 mAh g–1, twice as large as the previous theoretical prediction for graphynes. The volumetric capacity of Li-intercalated multilayer α- and γ-graphynes is 1364 and 1589 mAh cm–3, respectively. Both specific and volumetric capacities of Li-intercalated graphynes are significantly larger than the corresponding value of graphite, from which we conclude that multilayer graphynes can serve as high-capacity lithium ion battery anodes.
All genera of Flaviviridae host a conserved Xrn1-resistant RNA motif

ABSTRACT After infection by flaviviruses like Zika and West Nile virus, eukaryotic hosts employ the well-conserved endoribonuclease Xrn1 to degrade the viral genomic RNA. Within the 3ʹ untranslated regions, this enzyme encounters intricate Xrn1-resistant structures. This results in the accumulation of subgenomic flaviviral RNAs, an event that improves viral growth and aggravates viral pathogenicity. Xrn1-resistant RNAs have been established throughout the flaviviral genus, but not yet throughout the entire Flaviviridae family. In this work, we use previously determined characteristics of these structures to identify homologous sequences in many members of the genera pegivirus, hepacivirus and pestivirus. We used structural alignment and mutational analyses to establish that these sequences indeed represent Xrn1-resistant RNA and that they employ the general features of the flaviviral xrRNAs, consisting of a double pseudoknot formed by five base-paired regions stitched together by a crucial triple base interaction. Furthermore, we demonstrate that the pestivirus Bungowannah virus produces subgenomic RNA in vivo. Altogether, these results indicate that viruses make use of a universal Xrn1-resistant RNA throughout the Flaviviridae family.
Use of amplicon-based sequencing for testing fetal identity and monogenic traits with Single Circulating Trophoblast (SCT) as one form of cell-based NIPT

A major challenge for cell-based non-invasive prenatal testing (NIPT) is to distinguish individual presumptive fetal cells from maternal cells in female pregnancies. We have sought a rapid, robust, versatile, and low-cost next-generation sequencing method to facilitate this process. Toward this goal, single isolated cells underwent whole genome amplification prior to genotyping. Multiple highly polymorphic genomic regions (including HLA-A and HLA-B) with 10–20 very informative single nucleotide polymorphisms (SNPs) within a 200 bp interval were amplified with a modified method based on other publications. To enhance the power of cell identification, approximately 40 Human Identification SNP (Applied Biosystems) test amplicons were also utilized. Using SNP results to compare to sex chromosome data from NGS as a reliable standard, the true positive rate for genotyping was 83.4%, true negative 6.6%, false positive 3.3%, and false negative 6.6%. These results would not be sufficient for clinical diagnosis, but they demonstrate the general validity of the approach and suggest that deeper genotyping of single cells could be completely reliable. A paternal DNA sample is not required using this method. The assay also successfully detected pathogenic variants causing Tay Sachs disease, cystic fibrosis, and hemoglobinopathies in single lymphoblastoid cells, and disease-causing variants in three cell-based NIPT cases. This method could be applicable for any monogenic diagnosis.
CpG content-dependent associations between transcription factors and histone modifications

Understanding the factors that underlie the epigenetic regulation of genes is crucial to understand the gene regulatory machinery as a whole. Several experimental and computational studies examined the relationship between different factors involved. Here we investigate the relationship between transcription factors (TFs) and histone modifications (HMs), based on ChIP-seq data in cell lines. As it was shown that gene regulation by TFs differs depending on the CpG class of a promoter, we study the impact of the CpG content in promoters on the associations between TFs and HMs. We suggest an approach based on sparse linear regression models to infer associations between TFs and HMs with respect to CpG content. A study of the partial correlation of HMs for the two classes of high and low CpG content reveals possible CpG dependence and potential candidates for confounding factors in our models. We show that the models are accurate, inferred associations reflect known biological relationships, and we give new insight into associations with respect to CpG content. Moreover, analysis of a ChIP-seq dataset in HepG2 cells of the HM H3K122ac, an HM about little is known, reveals novel TF associations and supports a previously established link to active transcription.
The impact of inflammatory bowel disease on women's lives

Purpose of review Inflammatory bowel disease (IBD) affects women differently than men. This review outlines the current thinking on the impact of IBD, Crohn's disease and ulcerative colitis, on women's health. Recent findings IBD symptoms worsen during the menstrual cycle without corelating to disease activity. Endometriosis is more frequent in women with than those without IBD. Low fertility rate is rather because of voluntary childlessness than severe disease, perianal involvement, and ileal pouch anal anastomosis (IPAA) surgery. For women with ulcerative colitis, in-vitro fertilization successfully overcomes the post-IPAA infertility. The use of biologics and thiopurines throughout pregnancy is well tolerated for both the mother and the child but the use of small molecule therapy still needs more data. These medications increase the risk of cervical cancer, anal cancer, and aggressive vulvar cancer. More screening efforts are required to keep patients healthy. Women with Crohn's disease report worse psychological well being less resilience than men but they develop more escape and avoidance strategies to cope with the disease. Depression impairs the quality of sexual life but sexual dysfunction is rarely discussed with the provider. Summary Understanding the effects of sex on IBD allows personalized care and improves women's quality of life.
A Review of Dung Beetle Introductions in the Antipodes and North America: Status, Opportunities, and Challenges

Abstract Following the introduction of cattle, exotic dung beetles (Coleoptera: Aphodiidae, Geotrupidae, Scarabaeidae) were imported into the Antipodes (Australia and New Zealand) and North America (primarily the United States) to accelerate the degradation of cattle dung on pastures. The history of dung beetle introductions between the two regions is similar but has not previously been assessed: this is important as new introductions are continuing in the regions. Here, we review these introduction programs, report on their current status, and discuss methodological advances. In doing so, we examine the accidental introduction of exotic (i.e., adventive) species and the contribution of both deliberately introduced and adventive species to endemic dung beetle faunas. Further, we provide a list of pest and parasite species whose populations can be reduced by dung beetle activity. We also identify a combined total of 37 introduced and 47 adventive dung beetle species that have become established in the Antipodes and North America, with exotic species dominating dung beetle assemblages from pasture habitats. Climatic and edaphic matches, the size of founding populations, abiotic and biotic stressors, and the time of year when releases are made are all critical determinants that affect the success of dung beetle introduction programs. Finally, we discuss opportunities, plus the risks and challenges associated with dung beetle introductions. We hope that this review will aid in the success of future introduction programs, either to enhance ecosystem services in areas that they are needed, or potentially to reestablish native species in regions where they have been extirpated.
Hydrogen sulfide restores cardioprotective effects of remote ischemic preconditioning in aged rats via HIF-1α/Nrf2 signaling pathway

The present study explored the therapeutic potential of hydrogen sulfide (H2S) in restoring aging-induced loss of cardioprotective effect of remote ischemic preconditioning (RIPC) along with the involvement of signaling pathways. The left hind limb was subjected to four short cycles of ischemia and reperfusion (IR) in young and aged male rats to induce RIPC. The hearts were subjected to IR injury on the Langendorff apparatus after 24 h of RIPC. The measurement of lactate dehydrogenase, creatine kinase and cardiac troponin served to assess the myocardial injury. The levels of H2S, cystathionine β-synthase (CBS), cystathionine γ-lyase (CSE), nuclear factor erythroid 2-related factor 2 (Nrf2), and hypoxia-inducible factor (HIF-1α) were also measured. There was a decrease in cardioprotection in RIPC-subjected old rats in comparison to young rats along with a reduction in the myocardial levels of H2S, CBS, CSE, HIF-1α, and nuclear: cytoplasmic Nrf2 ratio. Supplementation with sodium hydrogen sulfide (NaHS, an H2S donor) and l-cysteine (H2S precursor) restored the cardioprotective actions of RIPC in old hearts. It increased the levels of H2S, HIF-1α, and Nrf2 ratio without affecting CBS and CSE. YC-1 (HIF-1α antagonist) abolished the effects of NaHS and l-cysteine in RIPC-subjected old rats by decreasing the Nrf2 ratio and HIF-1α levels, without altering H2S.The late phase of cardioprotection of RIPC involves an increase in the activity of H2S biosynthetic enzymes, which increases the levels of H2S to upregulate HIF-1α and Nrf2. H2S has the potential to restore aging-induced loss of cardioprotective effects of RIPC by upregulating HIF-1α/Nrf2 signaling.
Overview On Extraction and Separation of Rare Earth Elements from Red Mud: Focus on Scandium

ABSTRACT The article provides an overview of the methods used for processing of red mud to extract rare earth elements (REEs). Red mud is a toxic and highly alkaline waste. Several methods have been adopted and been practiced all over the world for the processing of red mud. Complex processing of red mud is cost-effective since red mud contains elements such as iron, aluminum, titanium, calcium, and rare earth metals. It has been observed that the acid leaching of red mud can almost completely recover the rare earth elements in the solution with various individual techniques and also a combination of them. Therefore, the choice of extraction method depends on the form in which the element occurs in the solution. However, relatively low concentrations of rare earth in the solution and significant amounts of impurities increase the cost of getting the final commercial products. To ensure the cost-effectiveness of the process involving rare earth’s extraction from red mud, it is necessary to increase their content by several times. This article presents the various studies that have been carried out in these aspects and the possibility of making this resource a sustainable one for REE extraction with a special focus on scandium replenishment.