Miracle-dz/UniFAR-FTUs huggingface dataset:
High-Level Acquisition of Maternal Oral Bacteria in Formula-Fed Infant Oral Microbiota

Acquisition of oral bacteria during infancy can affect the subsequent formation of stable oral microbiota. This study focused on the mother-to-infant transmission of oral bacteria, a major acquisition route of infant oral microbiota, and demonstrated that most infants acquired oral bacteria from their biological mother even at the single-nucleotide level. ABSTRACT The influx of maternal oral microbes is considered to play an important role in the acquisition and development of infant oral microbiota. In this study, we examined tongue swab samples from 448 mother-infant pairs at 4-month checkups. The bacterial composition of each sample was determined using PacBio single-molecule long-read sequencing of the full-length 16S rRNA gene and the amplicon sequence variant (ASV) approach. Although the infant oral microbiota was distinctly different from the mother oral microbiota, ASVs shared with their biological mother accounted for a median relative abundance of 9.7% (range of 0.0 to 99.3%), which was significantly higher than that of ASVs shared with unrelated mothers. This shared abundance was strongly associated with the feeding method of infants rather than their delivery mode or antibiotic exposure, and formula-fed infants had higher shared abundance than exclusively breastfed infants. Our study presents strain-level evidence for mother-to-infant transmission of oral bacteria and suggests that colonization of maternal oral bacteria is higher in formula-fed infants. IMPORTANCE Acquisition of oral bacteria during infancy can affect the subsequent formation of stable oral microbiota. This study focused on the mother-to-infant transmission of oral bacteria, a major acquisition route of infant oral microbiota, and demonstrated that most infants acquired oral bacteria from their biological mother even at the single-nucleotide level. Our results also indicated that the occupancies of maternal oral bacteria in infant oral microbiota were associated with the feeding methods of infants. These data could increase understanding of the early development of oral microbiota in infants and its potential associations with oral microbiota-related diseases.
Enabling QTY Server for Designing Water-Soluble α-Helical Transmembrane Proteins

Water-soluble expression and purification are of considerable importance for protein identification and characterization. However, there has been a lack of an effective method for water-soluble expression of membrane proteins, which has severely hampered their studies. ABSTRACT Membrane proteins, particularly those that are α-helical, such as transporters and G-protein-coupled receptors (GPCRs), have significant biological relevance. However, their expression and purification pose difficulties because of their poor water solubilities, which impedes progress in this field. The QTY method, a code-based protein-engineering approach, was recently developed to produce soluble transmembrane proteins. Here, we describe a comprehensive Web server built for QTY design and its relevance for in silico analyses. Typically, the simple design model is expected to require only 2 to 4 min of computer time, and the library design model requires 2 to 5 h, depending on the target protein size and the number of transmembrane helices. Detailed protocols for using the server with both the simple design and library design modules are provided. Methods for experiments following the QTY design are also included to facilitate the implementation of this approach. The design pipeline was further evaluated using microbial transmembrane proteins and structural alignment between the designed proteins and their origins by employing AlphaFold2. The results reveal that mutants generated by the developed pipeline were highly identical to their origins in terms of three-dimensional (3D) structures. In summary, the utilization of our Web server and associated protocols will enable QTY-based protein engineering to be implemented in a convenient, fast, accurate, and rational manner. The Protein Solubilizing Server (PSS) is publicly available at http://pss.sjtu. edu.cn. IMPORTANCE Water-soluble expression and purification are of considerable importance for protein identification and characterization. However, there has been a lack of an effective method for water-soluble expression of membrane proteins, which has severely hampered their studies. Here, an enabling comprehensive Web server, PSS, was developed for designing water-soluble mutants of α-helical membrane proteins, based on QTY design, a code-based protein-engineering approach. With microbial transmembrane proteins and GPCRs as examples, we systematically evaluated the server and demonstrated its successful performance. PSS is readily available for worldwide users as a Web-based tool, rendering QTY-based protein engineering convenient, efficient, accurate, and rational.
MiR-29a Increase in Aging May Function as a Compensatory Mechanism Against Cardiac Fibrosis Through SERPINH1 Downregulation

Deregulation of microRNA (miRNA) profile has been reportedly linked to the aging process, which is a dominant risk factor for many pathologies. Among the miRNAs with documented roles in aging-related cardiac diseases, miR-18a, -21a, -22, and -29a were mainly associated with hypertrophy and/or fibrosis; however, their relationship to aging was not fully addressed before. The purpose of this paper was to evaluate the variations in the expression levels of these miRNAs in the aging process. To this aim, multiple organs were harvested from young (2–3-months-old), old (16–18-months-old), and very old (24–25-months-old) mice, and the abundance of the miRNAs was evaluated by quantitative real-time (RT)-PCR. Our studies demonstrated that miR-21a, miR-22, and miR-29a were upregulated in the aged heart. Among them, miR-29a was highly expressed in many other organs, i.e., the brain, the skeletal muscle, the pancreas, and the kidney, and its expression was further upregulated during the natural aging process. Western blot, immunofluorescence, and xCELLigence analyses concurrently indicated that overexpression of miR-29a in the muscle cells decreased the collagen levels as well as cell migration and proliferation. Computational prediction analysis and overexpression studies identified SERPINH1, a specific chaperone of procollagens, as a potential miR-29a target. Corroborating to this, significantly downregulated SERPINH1 levels were found in the skeletal muscle, the heart, the brain, the kidney, and the pancreas harvested from very old animals, thereby indicating the role of the miR-29a-SERPINH1 axis in the aging process. In vitro analysis of miR-29a effects on fibroblast and cardiac muscle cells pointed toward a protective role of miR-29a on aging-related fibrosis, by reducing cell migration and proliferation. In conclusion, our study indicates an adaptive increase of miR-29 in the natural aging process and suggests its role as a transcriptional repressor of SERPINH1, with a potential therapeutic value against adverse matrix remodeling and aging-associated tissue fibrosis.
Dynamic Semantic World Models and Increased Situational Awareness for Highly Automated Inland Waterway Transport

Automated surface vessels must integrate many tasks and motions at the same time. Moreover, vessels as well as monitoring and control services need to react to physical disturbances, to dynamically allocate software resources available within a particular environment, and to communicate with various other actors in particular navigation and traffic situations. In this work, the responsibility for the situational awareness is given to a mediator that decides how: 1) to assess the impact of the actual physical environment on the quality and performance of the ongoing task executions; 2) to make sure these tasks satisfy the system requirements; and 3) to be robust against disturbances. This paper proposes a set of semantic world models within the context of inland waterway transport, and discusses policies and methodologies to compose, use, and connect these models. Model-conform entities and relations are composed dynamically, that is, corresponding to the opportunities and challenges offered by the actual situation. The semantic world models discussed in this work are divided into two main categories: 1) the semantic description of a vessel’s own properties and relationships, called the internal world model, or body model, and 2) the semantic description of its local environment, called the external world model, or map. A range of experiments illustrate the potential of using such models to decide the reactions of the application at runtime. Furthermore, three dynamic, context-dependent, ship domains are integrated in the map as two-dimensional geometric entities around a moving vessel to increase the situational awareness of automated vessels. Their geometric representations depend on the associated relations; for example, with: 1) the motion of the vessel, 2) the actual, desired, or hypothesised tasks, 3) perception sensor information, and 4) other geometries, e.g., features from the Inland Electronic Navigational Charts. The ability to unambiguously understand the environmental context, as well as the motion or position of surrounding entities, allows for resource-efficient and straightforward control decisions. The semantic world models facilitate knowledge sharing between actors, and significantly enhance explainability of the actors’ behaviour and control decisions.
Temporary Adjustment or Normative Change? Fertility and Marriage Preferences of Syrian Refugees in Turkey in the Context of Forced Migration

Turkey has the highest number of refugees in the world and is currently home to 3.7 million Syrians who had to flee from their country due to the conflict that started in 2011. This paper aims to focus on the fertility and marriage preferences of Syrian refugees by using a widely used qualitative research method Focus Group Discussions. The main findings revealed that socio-demographic indicators, the departure and arrival conditions in home and host country and the current place of residence had affected how families and individuals adjusted themselves and how they changed their fertility and marriage plans since their arrival in Turkey. Yet, the main findings also showed that while forced migration caused normative changes on some, some others reacted and saw these changes just as a temporary adjustment.
Identification of Five Ferroptosis-Related LncRNAs as Novel Prognosis and Diagnosis Signatures for Renal Cancer

Background: Ferroptosis is a novel regulated cell death that is characterized by iron-dependent oxidative damage. Renal cancer is the second most common cancer of the urinary system, which is highly correlated with iron metabolism. The aim of our present study was to identify suitable ferroptosis-related prognosis signatures for renal cancer. Methods: We downloaded the RNA-seq count data of renal cancer from The Cancer Genome Atlas database and used the DESeq2, Survival, and Cox regression analyses to screen the prognosis signatures. Results: We identified 5 ferroptosis-related differentially expressed lncRNAs (FR-DELs) (DOCK8-AS1, SNHG17, RUSC1-AS1, LINC02609, and LUCAT1) to be independently correlated with the overall survival (OS) of patients with renal cancer. The risk assessment model and diagnosis model constructed by those 5 FR-DELs could well predict the outcome and the diagnosis of renal cancer. Conclusion: Our present study not only suggested those 5 FR-DELs could be used as prognosis and diagnosis signatures for renal cancer but also provided strategies for other cancers in the screening of ferroptosis-related biomarkers.
Self-Regulation in Preschool: Examining Its Factor Structure and Associations With Pre-academic Skills and Social-Emotional Competence

Self-regulation in early childhood is an important predictor of success across a variety of indicators in life, including health, well-being, and earnings. Although conceptually self-regulation has been defined as multifaceted, previous research has not investigated whether there is conceptual and empirical overlap between the factors that comprise self-regulation or if they are distinct. In this study, using a bifactor model, we tested the shared and unique variance among self-regulation constructs and prediction to pre-academic and social-emotional skills. The sample included 932 preschool children (Mage = 48 months, SD = 6.55; 49% female), their parents, and their teachers in the United States. Children’s self-regulation was assessed using measures of executive function, behavioral self-regulation, and emotion regulation. The bifactor model demonstrated a common overarching self-regulation factor, as well as distinct executive function and emotion regulation factors. The common overarching self-regulation factor and executive function predicted children’s pre-academic (i.e., mathematics and literacy) and social-emotional skills. The emotion regulation factor predicted children’s social-emotional skills. Identifying the shared and unique aspects of self-regulation may have important implications for supporting children’s regulatory skills as well as their success in school.
Phosphoproteomic Analysis of Haemaphysalis longicornis Saliva Reveals the Influential Contributions of Phosphoproteins to Blood-Feeding Success

Tick saliva, an essential chemical secretion of the tick salivary gland, is indispensable for tick survival owing to the physiological influence it exerts on the host defence mechanisms via the instrumentality of its cocktail of pharmacologically active molecules (proteins and peptides). Much research about tick salivary proteome has been performed, but how most of the individual salivary proteins are utilized by ticks to facilitate blood acquisition and pathogen transmission is not yet fully understood. In addition, the phosphorylation of some proteins plays a decisive role in their function. However, due to the low phosphorylation level of protein, especially for a small amount of protein, it is more difficult to study phosphorylation. Maybe, for this reason, the scarcity of works on the phosphorylated tick salivary proteomes still abound. Here, we performed a phosphoproteomic analysis of Haemaphysalis longicornis tick saliva via TiO2 enrichment and the most advanced Thermo Fisher Orbitrap Exploris 480 mass spectrometer for identification. A total of 262 phosphorylated tick saliva proteins were identified and were subjected to functional annotation/enrichment analysis. Cellular and metabolic process terms accounted for the largest proportion of the saliva proteins, with the participation of these proteins in vital intracellular and extracellular transport-oriented processes such as vesicle-mediated transport, exocytic process, cell adhesion, and movement of cell/subcellular component. “Endocytosis”, “Protein processing in endoplasmic reticulum”, and “Purine metabolism” were the most significantly enriched pathways. The knockdown (RNAi) of Tudor domain-containing protein (TCP), actin-depolymerizing factors (ADF), programmed cell death protein (PD), and serine/threonine-protein kinase (SPK) resulted in the dissociation of collagen fibers and the pilosebaceous unit, increased inflammatory infiltrates/granulocytes (possibly heterophiles), and the depletion of the epithelium. Ticks injected with SPK dsRNA engorged normally but with a change in skin colour (possibly an autoimmune reaction) and the failure to produce eggs pointing to a possible role of SPK in reproduction and host immune modulation. Ticks injected with ADF dsRNA failed to acquire blood, underscoring the role of ADF in facilitating tick feeding. The results of this study showed the presence of phosphorylation in tick saliva and highlight the roles of salivary phosphoproteins in facilitating tick feeding.
Features of Psychotic Symptoms in Methamphetamine Use Disorder Patients and Ketamine Use Disorder Patients: A Cross-Sectional Study

Background Methamphetamine and ketamine are commonly used club drugs. Both of them have been reported to mimic psychotic symptoms of schizophrenia. However, the prevalence and detailed features of psychotic symptoms among methamphetamine use disorder (MUD) and ketamine use disorder (KUD) patients are largely unknown. This study aimed to measure psychotic symptoms among patients with MUD and KUD. Methods A total sample of 842 patients from voluntary drug rehabilitation centers, including 462 MUD patients and 380 KUD patients, were invited to this study. The Positive and Negative Syndrome Scale (PANSS) was applied to assess psychotic symptoms in these two groups of patients. Results The prevalence of psychotic symptoms was significantly higher among MUD patients than KUD patients (75.1 vs. 50.5%, 95% CI: 3.532 – 11.858, p < 0.001). Compared with KUD patients, MUD patients were more likely to experience positive symptoms (PANSS positive scores: 11.5 ± 6.07 vs. 15.1 ± 8.22, P < 0.001) and negative symptoms (PANSS negative scores: 12.4 ± 6.60 vs. 14.5 ± 8.63, P < 0.001), but not general symptoms (PANSS general scores: 31.2 ± 13.90 vs. 32.2 ± 15.13, P < 0.001). Conclusions The current study found that more than half of MUD and KUD patients experienced psychotic symptoms, and that patients with MUD are more likely to experience positive and negative symptoms than patients with KUD. The findings provide a new perspective for exploring the neuropathological mechanism of psychotic symptoms of schizophrenia.
Biofortified Wheat Increases Dietary Zinc Intake: A Randomised Controlled Efficacy Study of Zincol-2016 in Rural Pakistan

A new variety of zinc biofortified wheat (Zincol-2016) was released in Pakistan in 2016. The primary aim of this study was to examine the effects of consuming Zincol-2016 wheat flour on biochemical and functional markers of zinc status in a population with widespread zinc deficiency. An individually-randomised, double-blind, placebo-controlled cross over design was used. Fifty households were recruited to participate in the study, with each household included at least one woman of reproductive age (16–49 years) who was neither pregnant nor breast feeding or currently taking nutritional supplements. All households were provided with control flour for an initial 2-week baseline period, followed by the intervention period where households were randomly allocated in a 1:1 ratio to receive biofortified flour (group A; n = 25) and control flour (group B; n = 25) for 8-weeks, then switched to the alternate flour for 8-weeks. The trial has been registered with the ISRCTN (https://www.isrctn.com), ID ISRCTN83678069. The primary outcome measure was plasma zinc concentration, and the secondary outcome measures were plasma selenium and copper concentrations, plasma copper:zinc ratio and fatty acid desaturase and elongase activity indices. Nutrient intake was assessed using 24-h dietary recall interviews. Mineral concentrations in plasma were measured using inductively coupled plasma mass spectrometry and free fatty acids and sphingolipids by mass spectrometry. Linear Mixed Model regression and General Linear Model with repeated measures were used to analyse the outcomes. Based on an average flour consumption of 224 g/day, Zincol-2016 flour provided an additional daily zinc intake of between 3.0 and 6.0 mg for white and whole grain flour, respectively. No serious adverse events were reported. This resulted in significant, increase in plasma zinc concentration after 4 weeks [mean difference 41.5 μg/L, 95% CI (6.9–76.1), p = 0.02]. This was not present after 8 weeks (p = 0.6). There were no consistent significant effects of the intervention on fatty acid desaturase and elongase activity indices. Regular consumption of Zincol-2016 flour increased the daily zinc intake of women of reproductive age by 30–60%, however this was not associated with a sustained improvement in indices of zinc status.
Auditory Brain Stem Responses in the C57BL/6J Fragile X Syndrome-Knockout Mouse Model

Sensory hypersensitivity, especially in the auditory system, is a common symptom in Fragile X syndrome (FXS), the most common monogenic form of intellectual disability. However, linking phenotypes across genetic background strains of mouse models has been a challenge and could underly some of the issues with translatability of drug studies to the human condition. This study is the first to characterize the auditory brain stem response (ABR), a minimally invasive physiological readout of early auditory processing that is also used in humans, in a commonly used mouse background strain model of FXS, C57BL/6J. We measured morphological features of pinna and head and used ABR to measure the hearing range, and monaural and binaural auditory responses in hemizygous males, homozygous females, and heterozygous females compared with those in wild-type mice. Consistent with previous study, we showed no difference in morphological parameters across genotypes or sexes. There was no significant difference in hearing range between the sexes or genotypes, however there was a trend towards high frequency hearing loss in male FXS mice. In contrast, female mice with homozygous FXS had a decreased amplitude of wave IV of the monaural ABR, while there was no difference in males for amplitudes and no change in latency of ABR waveforms across sexes and genotypes. Finally, males with FXS had an increased latency of the binaural interaction component (BIC) at 0 interaural timing difference compared with that in wild-type males. These findings further clarify auditory brain stem processing in FXS by adding more information across genetic background strains allowing for a better understanding of shared phenotypes.
Single-Cell Monitoring of Activated Innate Immune Signaling by a d2eGFP-Based Reporter Mimicking Time-Restricted Activation of IFNB1 Expression

The innate immune system represents a balanced first line of defense against infection. Type I interferons (IFNs) are key regulators of the response to viral infections with an essential early wave of IFN-β expression, which is conditional, time-restricted, and stochastic in its nature. The possibility to precisely monitor individual cells with active IFNB1 transcription during innate signaling requires a robust reporter system that mimics the endogenous IFN-β signal. Here, we present a reporter system based on expression of a destabilized version of eGFP (d2eGFP) from a stably integrated reporter cassette containing the IFNB1 promoter and 3’-untranslated region, enabling both spatial and temporal detection of regulated IFNB1 expression. Specifically, this reporter permits detection, quantification, and isolation of cells actively producing d2eGFP in a manner that fully mimics IFN-β production allowing tracking of IFNB1 gene activation and repression in monocytic cells and keratinocytes. Using induced d2eGFP expression as a readout for activated immune signaling at the single-cell level, we demonstrate the application of the reporter for FACS-based selection of cells with genotypes supporting cGAS-STING signaling. Our studies provide a novel approach for monitoring on/off-switching of innate immune signaling and form the basis for investigating genotypes affecting immune regulation at the single-cell level.