Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational methods and points for attention in absolute configuration determination

With the rapid development of high performance computers and computational methods, including software, an increasing number of experimental chemists have tried to use computational methods such as optical rotation (OR, including the matrix model), optical rotatory dispersion (ORD), electronic circular dichroism (ECD or CD), vibrational circular dichroism (VCD), and magnetic shielding constants—nuclear magnetic resonance (NMR)—to explain and/or assign absolute configuration (AC) for various compounds. Such reports in the field of natural products have increased dramatically. However, every method has its range of application. This leads, in some cases, to incorrect conclusions by researchers who are not familiar with these methods. In this review, we provide experimental chemists and researchers with more computational details and suitable suggestions, and especially hope that this experience may help readers avoid computational pitfalls. Finally, we discuss the use of simplified models to replace original complex structures with a long side chain. The fundamental basis for using models to represent complex chiral compounds, such as in OR calculations, is the existence of conformation pairs with near canceling conformer contributions that justify the use of models rather than the original compounds. Using examples, we here introduce the transition state (TS) calculation, which may benefit readers in this area for use and mastery for their AC study. This review will summarize the general concepts involved in the study of AC determinations.
Abundance, diversity, and composition of root-associated microbial communities varied with tall fescue cultivars under water deficit

The plant breeding program has developed many cultivars of tall fescue (Festuca arundinacea) with low maintenance and stress tolerance. While the root-associated microbial community helps confer stress tolerance in the host plant, it is still largely unknown how the microbiota varies with plant cultivars under water stress. The study aimed to characterize drought-responsive bacteria and fungi in the roots and rhizosphere of different tall fescue cultivars. Intact grass-soil cores were collected from six cultivars grown in a field trial under no-irrigation for 3 years. Tall fescue under irrigation was also sampled from an adjacent area as the contrast. Bacterial and fungal communities in roots, rhizosphere, and bulk soil were examined for abundance, diversity, and composition using quantitative-PCR and high-throughput amplicon sequencing of 16S rRNA gene and ITS regions, respectively. Differences in microbial community composition and structure between non-irrigated and irrigated samples were statistically significant in all three microhabitats. No-irrigation enriched Actinobacteria in all three microhabitats, but mainly enriched Basidiomycota in the root endosphere and only Glomeromycota in bulk soil. Tall fescue cultivars slightly yet significantly modified endophytic microbial communities. Cultivars showing better adaptability to drought encompassed more relatively abundant Actinobacteria, Basidiomycota, or Glomeromycota in roots and the rhizosphere. PICRUSt2-based predictions revealed that the relative abundance of functional genes in roots related to phytohormones, antioxidant enzymes, and nutrient acquisition was enhanced under no-irrigation. Significant associations between Streptomyces and putative drought-ameliorating genes underscore possible mechanics for microbes to confer tall fescue with water stress tolerance. This work sheds important insight into the potential use of endophytic microbes for screening drought-adaptive genotypes and cultivars.
GM-CSF, Flt3-L and IL-4 affect viability and function of conventional dendritic cell types 1 and 2

Conventional type 1 dendritic cells (cDC1) and conventional type 2 dendritic cells (cDC2) have attracted increasing attention as alternatives to monocyte-derived dendritic cells (moDCs) in cancer immunotherapy. Use of cDCs for therapy has been hindered by their low numbers in peripheral blood. In the present study, we found that extensive spontaneous apoptosis and cDC death in culture within 24hrs represent an additional challenge. Different media conditions that maintain cDC viability and function were investigated. CD141+ cDC1 and CD1c+ cDC2 were isolated from healthy blood donor buffy coats. Low viabilities were found with CellGenix DC, RPMI-1640, and X-VIVO 15 standard culture media and with several supplements at 24hrs and 48hrs. Among multiple factors it was found that GM-CSF improved both cDC1 and cDC2 viability, whereas Flt3-L and IL-4 only increased viability of cDC1 and cDC2, respectively. Combinations of these three cytokines improved viability of both cDCs further, both at 24hrs and 48hrs time points. Although these cytokines have been extensively investigated for their role in myeloid cell differentiation, and are also used clinically, their effects on mature cDCs remain incompletely known, in particular effects on pro-inflammatory or tolerogenic cDC features. HLA-DR, CD80, CD83, CD86, PD-L1 and PD-L2 cDC membrane expressions were relatively little affected by GM-CSF, IL-4 and Flt3-L cytokine supplements compared to the strong induction following Toll-like receptor (TLR) stimulation for 24hrs. With minor exceptions the three cytokines appeared to be permissive to the TLR-induced marker expression. Allogeneic mixed leukocyte reaction showed that the cytokines promoted T-cell proliferation and revealed a potential to boost both Th1 and Th2 polarizing cytokines. GM-CSF and Flt3-L and their combination improved the capability of cDC1 for dextran uptake, while in cDC2, dextran capture was improved by GM-CSF. The data suggest that GM-CSF, IL-4 and Flt3-L and combinations might be beneficial for DC viability and function in vitro. Limited viability of cDCs could be a confounding variable experimentally and in immunotherapy.
Open questions in human lung organoid research

Organoids have become a prominent model system in pulmonary research. The ability to establish organoid cultures directly from patient tissue has expanded the repertoire of physiologically relevant preclinical model systems. In addition to their derivation from adult lung stem/progenitor cells, lung organoids can be derived from fetal tissue or induced pluripotent stem cells to fill a critical gap in modelling pulmonary development in vitro. Recent years have seen important progress in the characterisation and refinement of organoid culture systems. Here, we address several open questions in the field, including how closely organoids recapitulate the tissue of origin, how well organoids recapitulate patient cohorts, and how well organoids capture diversity within a patient. We advocate deeper characterisation of models using single cell technologies, generation of more diverse organoid biobanks and further standardisation of culture media.
A nonlinear associations of metabolic score for insulin resistance index with incident diabetes: A retrospective Chinese cohort study

Background The Metabolic score of insulin resistance (METS-IR) has recently been accepted as a reliable alternative to insulin resistance (IR), which was demonstrated to be consistent with the hyperinsulinemic-euglycemic clamp. Few pieces of research have focused on the relationship between METS-IR and diabetes in Chinese. The purpose of this research was to explore the effect of METS-IR on new-onset diabetes in a large multicenter Chinese study. Methods At the baseline of this retrospective longitudinal research, 116855 participators were included in the Chinese cohort study administered from 2010 to 2016. The subjects were stratified by quartiles of METS-IR. To assess the effect of METS-IR on incident diabetes, the Cox regression model was constructed in this study. Stratification analysis and interaction tests were applied to detect the potential effect of METS-IR and incident diabetes among multiple subgroups. To verify whether there was a dose-response relationship between METS-IR and diabetes, a smooth curve fitting was performed. In addition, to further determine the performance of METS -IR in predicting incident diabetes, the receiver operating characteristic curve (ROC) was conducted. Results The average age of the research participators was 44.08 ± 12.93 years, and 62868 (53.8%) were men. METS-IR were significant relationship with new-onset diabetes after adjusting for possible variables (Hazard ratio [HR]: 1.077; 95% confidence interval [CI]: 1.073-1.082, P < 0.0001), the onset risk for diabetes in Quartile 4 group was 6.261-fold higher than those in Quartile 1 group. Moreover, stratified analyses and interaction tests showed that interaction was detected in the subgroup of age, body mass index, systolic blood pressure, diastolic blood pressure, and fasting plasma glucose, there was no significant interaction between males and females. Furthermore, a dose-response correlation was detected between METS-IR and incident diabetes, the nonlinear relationship was revealed and the inflection point of METS-IR was calculated to be 44.43. When METS-IR≥44.43, compared with METS-IR < 44.43, the trend was gradually saturated, with log-likelihood ratio test P < 0.001. Additionally, the area under receiver operating characteristic of the METS-IR in predicting incident diabetes was 0.729, 0.718, and 0.720 at 3, 4, and 5 years, respectively. Conclusions METS-IR was correlated with incident diabetes significantly, and showed a nonlinear relationship. This study also found that METS-IR had good discrimination of diabetes.
Effect of yeast culture supplementation in sows during late gestation and lactation on growth performance, antioxidant properties, and intestinal microorganisms of offspring weaned piglets

Introduction The effects of maternal addition of yeast cultures on offspring gut development and intestinal microorganisms are not yet known, so the aim of this study was to investigate the effects of maternal addition of yeast cultures to the diet of sows during late gestation and lactation on growth performance, antioxidant properties and intestinal microorganisms of offspring weaned piglets. Methods 40 Landrace × Yorkshire sows (3–7 of parity) with similar backfat were randomly divided into two treatment groups: control diet (CON) and control diet +2.0 g/kg yeast culture (XPC), and the trial started on day 90 of gestation and ended on day 21 of lactation. Results The results showed that maternal addition of yeast culture significantly increased weaned piglet weight and mean daily gain (p < 0.05), with a tendency to increase litter weight gain (p = 0.083) and liver weight (p = 0.076) compared to the control group. The content of thymus malondialdehyde (MDA) was significantly higher (p < 0.05) and the content of colon total antioxidant capacity (T-AOC) was significantly lower (p < 0.05) in the offspring weaned piglets of the XPC group compared to the control group. The expression of thymus SOD1 and SOD2, spleen SOD1, jejunum SOD2, and colon GPX1, SOD1, and SOD2 were significantly downregulated in the XPC group of offspring weaned piglets compared with the control group (p < 0.05). The intestinal morphology and the content of short-chain fatty acids in colonic chyme did not differ between the two groups (p > 0.05). Compared with the control group, the XPC group significantly increased the relative abundance of colonic chyme Bacteroidetes (p < 0.05), tended to decrease the relative abundance of Lactobacillus (p = 0.078), and tended to increase the relative abundance of Alloprevotella (p = 0.055). The XPC group significantly upregulated Blautia and Fournierella (p < 0.05) and significantly downregulated Candidatus_Competibacter, Nitrospira, Dechloromonas, Haliangium, and Oscillospira (p < 0.05). Discussion In conclusion, maternal addition of yeast cultures improved the growth performance of offspring weaned piglets and changed the intestinal microbial community, but did not improve their antioxidant performance.
Low-intensity continuous ultrasound to inhibit cancer cell migration

In recent years, it has been verified that collective cell migration is a fundamental step in tumor spreading and metastatic processes. In this paper, we demonstrate for the first time how low-intensity ultrasound produces long-term inhibition of collective migration of epithelial cancer cells in wound healing processes. In particular, we show how pancreatic tumor cells, PANC-1, grown as monolayers in vitro respond to these waves at frequencies close to 1 MHz and low intensities (<100 mW cm−2) for 48–72 h of culture after some minutes of a single ultrasound irradiation. This new strategy opens a new line of action to block the spread of malignant cells in cancer processes. Despite relevant spatial variations of the acoustic pressure amplitude induced in the assay, the cells behave as a whole, showing a collective dynamic response to acoustic performance. Experiments carried out with samples without previous starving showed remarkable effects of the LICUs from the first hours of culture, more prominent than those with experiments with monolayers subjected to fasting prior to the experiments. This new strategy to control cell migration demonstrating the effectiveness of LICUS on not starved cells opens a new line of action to study effects of in vivo ultrasonic actuation on tumor tissues with malignant cells. This is a proof-of-concept study to demonstrate the physical effects of ultrasound stimulation on tumor cell migration. An in-depth biological study of the effects of ultrasounds and underlying biological mechanisms is on-going but out of the scope of this article.
Design and immunological evaluation of two-component protein nanoparticle vaccines for East Coast fever

Nanoparticle vaccines usually prime stronger immune responses than soluble antigens. Within this class of subunit vaccines, the recent development of computationally designed self-assembling two-component protein nanoparticle scaffolds provides a powerful and versatile platform for displaying multiple copies of one or more antigens. Here we report the generation of three different nanoparticle immunogens displaying 60 copies of p67C, an 80 amino acid polypeptide from a candidate vaccine antigen of Theileria parva, and their immunogenicity in cattle. p67C is a truncation of p67, the major surface protein of the sporozoite stage of T. parva, an apicomplexan parasite that causes an often-fatal bovine disease called East Coast fever (ECF) in sub-Saharan Africa. Compared to I32-19 and I32-28, we found that I53-50 nanoparticle scaffolds displaying p67C had the best biophysical characteristics. p67C-I53-50 also outperformed the other two nanoparticles in stimulating p67C-specific IgG1 and IgG2 antibodies and CD4+ T-cell responses, as well as sporozoite neutralizing capacity. In experimental cattle vaccine trials, p67C-I53-50 induced significant immunity to ECF, suggesting that the I53-50 scaffold is a promising candidate for developing novel nanoparticle vaccines. To our knowledge this is the first application of computationally designed nanoparticles to the development of livestock vaccines.
Tuning curves vs. population responses, and perceptual consequences of receptive-field remapping

Sensory processing is often studied by examining how a given neuron responds to a parameterized set of stimuli (tuning curve) or how a given stimulus evokes responses from a parameterized set of neurons (population response). Although tuning curves and the corresponding population responses contain the same information, they can have different properties. These differences are known to be important because the perception of a stimulus should be decoded from its population response, not from any single tuning curve. The differences are less studied in the spatial domain where a cell's spatial tuning curve is simply its receptive field (RF) profile. Here, we focus on evaluating the common belief that perrisaccadic forward and convergent RF shifts lead to forward (translational) and convergent (compressive) perceptual mislocalization, respectively, and investigate the effects of three related factors: decoders' awareness of RF shifts, changes of cells' covering density near attentional locus (the saccade target), and attentional response modulation. We find that RF shifts alone produce either no shift or an opposite shift of the population responses depending on whether or not decoders are aware of the RF shifts. Thus, forward RF shifts do not predict forward mislocalization. However, convergent RF shifts change cells' covering density for aware decoders (but not for unaware decoders) which may predict convergent mislocalization. Finally, attentional modulation adds a convergent component to population responses for stimuli near the target. We simulate the combined effects of these factors and discuss the results with extant mislocalization data. We speculate that perisaccadic mislocalization might be the flash-lag effect unrelated to perisaccadic RF remapping but to resolve the issue, one has to address the question of whether or not perceptual decoders are aware of RF shifts.
Clinical characteristics and long-term outcome of patients with gastrointestinal involvement in eosinophilic granulomatosis with polyangiitis

Objective This study aims to investigate clinical characteristics, potential risk factors, as well as long-term outcome in EGPA patients with GI involvement. Methods A total of 94 EGPA patients were included in this cohort study. We retrospectively reviewed the clinical data, treatment, and outcome of 21 EGPA patients with GI involvement and compared them with other 73 EGPA patients without GI involvement. Multivariate logistic regression was used to find potential risk factors associated with GI involvement in EGPA patients. Results Compared with EGPA patients without GI involvement, EGPA patients with GI involvement had higher level of hs-CRP (65.1 (24.5-138.9) vs. 21.3 (5.7-39.1) mg/L, p=0.005), higher grades of Birmingham vasculitis activity score (BVAS) (20 (13-29.5) vs. 12 (16-19), p=0.022), higher Five Factor Score (FFS) (1 (1-2) vs. 0 (0-1), p<0.001), and were more likely to have weight loss (66.7% vs. 38.4%, p=0.021) at baseline. In EGPA patients with GI involvement, the most common gastrointestinal symptoms were abdominal pain (90.5%) and diarrhea (42.9%). Weight loss was identified as a potential risk factor for GI involvement in EGPA patients (OR = 4.304, 95% CI 1.339–13.841). During follow-up, EGPA patients with GI involvement showed lower 1-year cumulative survival rate (75.2% vs. 100.0%, P <0.0001) and 3-year cumulative survival rate (67.7% vs. 100.0%, P<0.0001), lower long-term remission rate (33.3% vs. 86.3%, P<0.001), but higher 1-year cumulative relapse rate (19.2% vs. 3.8%, P=0.03) and 3-year cumulative relapse rate (54.6% vs. 13.1%, P<0.001) compared with patients without GI involvement. Conclusion EGPA patients with GI involvement had distinct features from those without GI involvement, including higher hs-CRP level, higher BVAS and FFS scores. EGPA patients with GI involvement showed lower cumulative survival rate, lower long-term remission rate and higher cumulative relapse rate compared with those without GI involvement.
Primary mapping of quantitative trait loci regulating multivariate horticultural phenotypes of watermelon (Citrullus lanatus L.)

Watermelon fruits exhibit a remarkable diversity of important horticultural phenotypes. In this study, we initiated a primary quantitative trait loci (QTL) mapping to identify the candidate regions controlling the ovary, fruit, and seed phenotypes. Whole genome sequencing (WGS) was carried out for two differentiated watermelon lines, and 350 Mb (96%) and 354 Mb (97%) of re-sequenced reads covered the reference de novo genome assembly, individually. A total of 45.53% non-synonymous single nucleotide polymorphism (nsSNPs) and 54.47% synonymous SNPs (sSNPs) were spotted, which produced 210 sets of novel SNP-based cleaved amplified polymorphism sequence (CAPS) markers by depicting 46.25% co-dominant polymorphism among parent lines and offspring. A biparental F2:3 mapping population comprised of 100 families was used for trait phenotyping and CAPS genotyping, respectively. The constructed genetic map spanned a total of 2,398.40 centimorgans (cM) in length and averaged 11.42 cM, with 95.99% genome collinearity. A total of 33 QTLs were identified at different genetic positions across the eight chromosomes of watermelon (Chr-01, Chr-02, Chr-04, Chr-05, Chr-06, Chr-07, Chr-10, and Chr-11); among them, eight QTLs of the ovary, sixteen QTLs of the fruit, and nine QTLs of the seed related phenotypes were classified with 5.32–25.99% phenotypic variance explained (PVE). However, twenty-four QTLs were identified as major-effect and nine QTLs were mapped as minor-effect QTLs across the flanking regions of CAPS markers. Some QTLs were exhibited as tightly localized across the nearby genetic regions and explained the pleiotropic effects of multigenic nature. The flanking QTL markers also depicted significant allele specific contributions and accountable genes were predicted for respective traits. Gene Ontology (GO) functional enrichment was categorized in molecular function (MF), cellular components (CC), and biological process (BP); however, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were classified into three main classes of metabolism, genetic information processing, and brite hierarchies. The principal component analysis (PCA) of multivariate phenotypes widely demonstrated the major variability, consistent with the identified QTL regions. In short, we assumed that our identified QTL regions provide valuable genetic insights regarding the watermelon phenotypes and fine genetic mapping could be used to confirm them.
Life after lockdown: The experiences of older adults in a contactless digital world

Introduction The digital response to the Coronavirus (COVID-19) pandemic and its effects on the lives of older adults has been well-documented, but less is known about how they experienced the post-lockdown re-emergence into a relatively contactless digital society. Methods We report the findings from a qualitative survey (n = 93) and subsequent interviews (n = 9) with older adults aged 50+, where they describe their struggles with some of the newly implemented digital interactions. These struggles cover a range of settings but include using contactless payments, QR codes and apps to facilitate transactions in cafes, bars, and restaurants. Results A thematic analysis of our data revealed the intrinsic (e.g. digital literacy) and extrinsic (e.g. malfunctioning technology) factors that limited social inclusion for these participants, and that sometimes even led to moments of public humiliation. Discussion Our findings shed light on some of the motivational factors that underpin the age-related digital divide, whilst also highlighting the role of self-directed agism in limiting motivations to learn new digital routines.