Miracle-dz/UniFAR-FTUs huggingface dataset:
Metagenomics and metabolomics analysis to investigate the effect of Shugan decoction on intestinal microbiota in irritable bowel syndrome rats

Background The effect of Shugan Decoction (SGD) on intestinal motility and visceral hypersensitivity in Water avoid stress (WAS)-induced diarrhea predominant irritable bowel syndrome (IBS-D) model rats has been confirmed. However, the mechanisms of its action involved in the treatment of IBS-D need to be further studied. Intestinal microbiota plays an important role in maintaining intestinal homeostasis and normal physiological function. Changes in the intestinal microbiota and its metabolites are thought to participate in the pathophysiological process of IBS. Aim This study aimed to analyze the influence of SGD on intestinal microbiota and fecal metabolites in IBS-D rats by multiple omics techniques, including metagenomic sequencing and metabolomics. Methods We measured the intestinal motility and visceral sensitivity of three groups of rats by fecal pellets output and colorectal distension (CRD) experiment. In addition, metagenome sequencing analysis was performed to explore the changes in the number and types of intestinal microbiota in IBS-D model rats after SGD treatment. Finally, we also used untargeted metabolomic sequencing to screen the metabolites and metabolic pathways closely related to the therapeutic effect of SGD. Results We found that compared with the rats in the control group, the fecal pellets output of the rats in the WAS group increased and the visceral sensitivity threshold was decreased (P < 0.05). Compared with the rats in the WAS group, the fecal pellets output of the SGD group was significantly decreased, and the visceral sensitivity threshold increased (P < 0.05). Besides, compared with the rats in the WAS group, the relative abundance of Bacteroidetes increased in SGD group, while that of Firmicutes decreased at the phylum level, and at the species level, the relative abundance of Bacteroides sp. CAG:714, Lactobacillus reuteri and Bacteroides Barnesiae in SGD group increased, but that of bacterium D42-87 decreased. In addition, compared with the WAS group, several metabolic pathways were significantly changed in SGD group, including Taurine and hypotaurine metabolism, Purine metabolism, Sulfur metabolism, ABC transporters, Arginine and proline metabolism and Bile secretion. Conclusion SGD can regulate specific intestinal microbiota and some metabolic pathways, which may explain its effect of alleviating visceral hypersensitivity and abnormal intestinal motility in WAS-induced IBS-D rats.
Short-term oral pre-exposure prophylaxis against HIV-1 modulates the transcriptome of foreskin tissue in young men in Africa

Whilst short-term oral pre-exposure prophylaxis (PrEP) with antiretroviral drugs in men who have sex with men has shown protection against HIV-1 infection, the impact of this regimen on the in vivo foreskin transcriptome is unknown. We collected foreskin tissue after voluntary medical male circumcision from 144 young men (72 from Uganda and 72 from South Africa) randomized to one to two doses of either oral tenofovir (TFV) disoproxil fumarate (FTC-TDF) or tenofovir alafenamide (FTC-TAF) or no drug (untreated controls). This novel approach allowed us to examine the impact of short-term oral PrEP on transcriptome of the male genital tract. A single dose of FTC-TDF did not affect the foreskin transcriptome in relation to control arm, however one dose of FTC-TAF induced upregulation of four genes AKAP8, KIAA0141, HSCB and METTL17. Following two doses of either FTC-TDF or FTC-TAF, there was an increase in 34 differentially expressed genes for FTC-TDF and 15 for FTC-TAF, with nine DEGs in common: KIAA0141, SAFB2, CACTIN, FXR2, AKAP8, HSCB, CLNS1A, DDX27 and DCAF15. Functional analysis of differentially expressed genes revealed modulation of biological processes related to mitochondrial stress (KIAA0141, HSCB and METTL17), anti-viral and anti-inflammatory pathways (CACTIN and AKAP8). Our results show that short-course on-demand oral PrEP in men modulates genes in foreskin tissue which are likely unfavorable to HIV acquisition and replication. We also describe an upregulated expression of genes involved in diverse mitochondria biology which may potentially result in worsened mitochondria-related. These results warrant further studies to assess the role of short-course and prolonged oral PrEP on biological processes of the foreskin mucosa.
stepRNA: Identification of Dicer cleavage signatures and passenger strand lengths in small RNA sequences

The enzyme Dicer is a component of many small RNA (sRNA) pathways involved in RNA processing for post-transcriptional regulation, anti-viral response and control of transposable elements. Cleavage of double-stranded RNA by Dicer produces a signature overhanging sequence at the 3’ end of the sRNA sequence relative to a complementary passenger strand in a RNA duplex. There is a need for reliable tools to computationally search for Dicer cleavage signatures to help characterise families of sRNAs. This is increasingly important due to the rising popularity of sRNA sequencing, especially in non-model organisms. Here, we present stepRNA, a fast, local tool that identifies (i) overhang signatures strongly indicative of Dicer cleavage in RNA sequences, and (ii) the length of the passenger strand in sRNAs duplexes. We demonstrate the use of stepRNA with simulated and biological datasets to detect Dicer cleavage signatures in experimentally validated examples. Compared to currently available tools, stepRNA is more accurate, requires only sRNA sequence data rather than a reference genome, and provides information about other important features such as passenger strand length. stepRNA is freely available at https://github.com/Vicky-Hunt-Lab/stepRNA and is easily installable.
Extracorporeal cardiopulmonary resuscitation in adults and children: A review of literature, published guidelines and pediatric single-center program building experience

Extracorporeal cardiopulmonary resuscitation (ECPR) is an adjunct supportive therapy to conventional cardiopulmonary resuscitation (CCPR) employing veno-arterial extracorporeal membrane oxygenation (VA-ECMO) in the setting of refractory cardiac arrest. Its use has seen a significant increase in the past decade, providing hope for good functional recovery to patients with cardiac arrest refractory to conventional resuscitation maneuvers. This review paper aims to summarize key findings from the ECPR literature available to date as well as the recommendations for ECPR set forth by leading national and international resuscitation societies. Additionally, we describe the successful pediatric ECPR program at Texas Children's Hospital, highlighting the logistical, technical and educational features of the program.
Mapping the big data analytics in sharing economy: A bibliometric literature review

This paper offers a holistic review of the role of big data analytics in sharing economy (SE). Academic literature in this field is analyzed to show the theoretical foundation, important papers, and key themes underlying the field by using various bibliometric analysis tools. We conduct a citation and co-citation analysis on literature concerning big data analytics in sharing economy, which published in the 12-year period from 2010–2021. A total of 205 papers were screened from Web of Science (WoS) database for our analysis. In the citation analysis, we depend on the degree centrality and betweenness centrality to identify 48 important papers. In the co-citation analysis, four major research themes are identified: sustainable business model, efficient match-making, trust building and innovation and value cocreation. The research also highlights future research directions and critical areas for the application of big data analytics in the SE context, which may help to produce in-depth studies.
Revisiting the internet of things: New trends, opportunities and grand challenges

The Internet of Things (IoT) has brought the dream of ubiquitous data access from physical environments into reality. IoT embeds sensors and actuators in physical objects so that they can communicate and exchange data between themselves to improve efficiency along with enabling real-time intelligent services and offering better quality of life to people. The number of deployed IoT devices has rapidly grown in the past five years in a way that makes IoT the most disruptive technology in recent history. In this paper, we reevaluate the position of IoT in our life and provide deep insights on its enabling technologies, applications, rising trends and grand challenges. The paper also highlights the role of artificial intelligence to make IoT the top transformative technology that has been ever developed in human history.
Mitochondrial dysfunction of induced pluripotent stem cells-based neurodegenerative disease modeling and therapeutic strategy

Neurodegenerative diseases (NDDs) are disorders in which neurons are lost owing to various factors, resulting in a series of dysfunctions. Their rising prevalence and irreversibility have brought physical pain to patients and economic pressure to both individuals and society. However, the pathogenesis of NDDs has not yet been fully elucidated, hampering the use of precise medication. Induced pluripotent stem cell (IPSC) modeling provides a new method for drug discovery, and exploring the early pathological mechanisms including mitochondrial dysfunction, which is not only an early but a prominent pathological feature of NDDs. In this review, we summarize the iPSC modeling approach of Alzheimer’s disease, Parkinson’s disease, and Amyotrophic lateral sclerosis, as well as outline typical mitochondrial dysfunction and recapitulate corresponding therapeutic strategies.
Apnoeic oxygenation during paediatric intubation: A systematic review

Objective This review assesses the effect of apnoeic oxygenation during paediatric intubation on rates of hypoxaemia, successful intubation on the first attempt and other adverse events. Data sources The databases searched included PubMed, Medline, CINAHL, EMBASE and The Cochrane Library. An electronic search for unpublished studies was also performed. Study selection We screened studies that include children undergoing intubation, studies that evaluate the use of apnoeic oxygenation by any method or device with outcomes of hypoxaemia, intubation outcome and adverse events were eligible for inclusion. Data extraction Screening, risk of bias, quality of evidence and data extraction was performed by two independent reviewers, with conflicts resolved by a third reviewer where consensus could not be reached. Data synthesis From 362 screened studies, fourteen studies (N = 2442) met the eligibility criteria. Randomised controlled trials (N = 482) and studies performed in the operating theatre (N = 835) favoured the use of apnoeic oxygenation with a reduced incidence of hypoxaemia (RR: 0.34, 95% CI: 0.24 to 0.47, p < 0.001, I2 = 0% and RR: 0.27, 95% CI: 0.11 to 0.68, p = 0.005, I2 = 68% respectively). Studies in the ED and PICU were of lower methodological quality, displaying heterogeneity in their results and were unsuitable for meta-analysis. Among the studies reporting first attempt intubation success, there were inconsistent effects reported and data were not suitable for meta-analysis. Conclusion There is a growing body of evidence to support the use of apnoeic oxygenation during the intubation of children. Further research is required to determine optimal flow rates and delivery technique. The use of humidified high-flow oxygen shows promise as an effective technique based on data in the operating theatre, however its efficacy has not been shown to be superior to low flow oxygen in either the elective anesthetic or emergency intubation situations Systematic Review Registration: This review was prospectively registered in the PROSPERO international register of systematic reviews (Reference: CRD42020170884, registered April 28, 2020).
The Ultraviolet–Infrared Color–Magnitude Relation of Star-forming Galaxies

In this note we identify and characterize the ultraviolet-infrared color-magnitude relation of star-forming galaxies. The ultraviolet to mid-infrared flux ratios of star-forming galaxies span over two orders of magnitude and show a clear dependence on absolute magnitude from M_W3 ~ -13 to M_W3 ~ -25, which may present problems for models of galaxy spectral energy distributions that have been largely verified on ~L* galaxies. The color-magnitude relation of star-forming galaxies illustrates the broadband spectral diversity of star-forming galaxies that results from established correlations between the physical properties and mass, including the mass-metallicity relation.
Evaluation of the peritumoral features using radiomics and deep learning technology in non-spiculated and noncalcified masses of the breast on mammography

Objective To assess the significance of peritumoral features based on deep learning in classifying non-spiculated and noncalcified masses (NSNCM) on mammography. Methods We retrospectively screened the digital mammography data of 2254 patients who underwent surgery for breast lesions in Harbin Medical University Cancer Hospital from January to December 2018. Deep learning and radiomics models were constructed. The classification efficacy in ROI and patient levels of AUC, accuracy, sensitivity, and specificity were compared. Stratified analysis was conducted to analyze the influence of primary factors on the AUC of the deep learning model. The image filter and CAM were used to visualize the radiomics and depth features. Results For 1298 included patients, 771 (59.4%) were benign, and 527 (40.6%) were malignant. The best model was the deep learning combined model (2 mm), in which the AUC was 0.884 (P < 0.05); especially the AUC of breast composition B reached 0.941. All the deep learning models were superior to the radiomics models (P < 0.05), and the class activation map (CAM) showed a high expression of signals around the tumor of the deep learning model. The deep learning model achieved higher AUC for large size, age >60 years, and breast composition type B (P < 0.05). Conclusion Combining the tumoral and peritumoral features resulted in better identification of malignant NSNCM on mammography, and the performance of the deep learning model exceeded the radiomics model. Age, tumor size, and the breast composition type are essential for diagnosis.
Genomic profiling and network-level understanding uncover the potential genes and the pathways in hepatocellular carcinoma

Data integration with phenotypes such as gene expression, pathways or function, and protein-protein interactions data has proven to be a highly promising technique for improving human complex diseases, particularly cancer patient outcome prediction. Hepatocellular carcinoma is one of the most prevalent cancers, and the most common cause is chronic HBV and HCV infection, which is linked to the majority of cases, and HBV and HCV play a role in multistep carcinogenesis progression. We examined the list of known hepatocellular carcinoma biomarkers with the publicly available expression profile dataset of hepatocellular carcinoma infected with HCV from day 1 to day 10 in this study. The study covers an overexpression pattern for the selected biomarkers in clinical hepatocellular carcinoma patients, a combined investigation of these biomarkers with the gathered temporal dataset, temporal expression profiling changes, and temporal pathway enrichment following HCV infection. Following a temporal analysis, it was discovered that the early stages of HCV infection tend to be more harmful in terms of expression shifting patterns, and that there is no significant change after that, followed by a set of genes that are consistently altered. PI3K, cAMP, TGF, TNF, Rap1, NF-kB, Apoptosis, Longevity regulating pathway, signaling pathways regulating pluripotency of stem cells, Cytokine-cytokine receptor interaction, p53 signaling, Wnt signaling, Toll-like receptor signaling, and Hippo signaling pathways are just a few of the most commonly enriched pathways. The majority of these pathways are well-known for their roles in the immune system, infection and inflammation, and human illnesses like cancer. We also find that ADCY8, MYC, PTK2, CTNNB1, TP53, RB1, PRKCA, TCF7L2, PAK1, ITPR2, CYP3A4, UGT1A6, GCK, and FGFR2/3 appear to be among the prominent genes based on the networks of genes and pathways based on the copy number alterations, mutations, and structural variants study.
Plant growth forms dictate adaptations to the local climate

Adaptive radiation is a significant driver of biodiversity. Primarily studied in animal systems, mechanisms that trigger adaptive radiations remain poorly understood in plants. A frequently claimed indicator of adaptive radiation in plants is growth form diversity when tied to the occupation of different habitats. However, it remains obscure whether morphological adaptations manifest as growth form diversity per se or as its constituent traits. We use the classic Aeonium radiation from the Canary Islands to ask whether adaptation across climatic space is structured by growth form evolution. Using morphological sampling with site-associated climate in a phylogenetic context, we find that growth forms dictate adaptations to the local environment. Furthermore, we demonstrate that the response of specific traits to analogous environments is antagonistic when growth forms are different. This finding suggests for the first time that growth forms represent particular ecological functions, allowing the co-occurrence of closely related species, being a product of divergent selection during evolution in sympatry.
TSG 101 associates with PARP 1 and is essential for PARylation and DNA damage-induced NF- j B activation

In a genome-wide screening for components of the dsDNA-break-induced IKK-NF- j B pathway, we identified scores of regulators, including tumor susceptibility gene TSG 101 . TSG 101 is essential for DNA damage-induced formation of cellular poly(ADP-ribose) (PAR). TSG 101 binds to PARP 1 and is required for PARP 1 activation. This function of TSG 101 is independent of its role in the ESCRT-I endosomal sorting complex. In the absence of TSG 101 , the PAR-dependent formation of a nuclear PARP 1 -IKK c signalosome, which triggers IKK activation, is impaired. According to its requirement for PARP 1 and NF- j B activation, TSG 101 -deficient cells are defective in DNA repair and apoptosis protection. Loss of TSG 101 results in PARP 1 trapping at damage sites and mimics the effect of pharmacological PARP inhibition. We also show that the loss of TSG 101 in connection with inactivated tumor suppressors BRCA 1 / 2 in breast cancer cells is lethal. Our results imply TSG 101 as a thera-peutic target to achieve synthetic lethality in cancer treatment.
High-sensitivity optical measurement of mechanical Brownian motion

We describe an experiment in which a laser beam is sent into a high-finesse optical cavity with a mirror coated on a mechanical resonator. We show that the reflected light is very sensitive to small mirror displacements. We have observed the Brownian motion of the resonator with a very high sensitivity corresponding to a minimum observable displacement of 2 × 10−19 m/√Hz.
A Supervised Approach for Sentiment Lexicon Generation using Word Skipgrams

This Ph.D. thesis work proposes the design, development and evaluation of a supervised approach for sentiment lexicon generation. It is based on the hypothesis that an efficient use of the skipgram modelling can improve sentiment analysis tasks and reduce the resources needed maintaining an acceptable level of quality. In summary, the novelty of this approach lies in the use of skipgrams as information units and the way they are efficiently generated, weighed and filtered, taking advantage of the useful information they provide about the sequentiality of the language.
Locomotion of a passively flapping flat plate

Locomotion of a passively flapping flat plate has been studied numerically by means of a multiblock lattice Boltzmann method. A flexible plate is modelled by a rigid plate with a torsion spring acting about the pivot at the leading edge of the plate. A dynamic model of this kind is called a lumped-torsional-flexibility model. When the leading edge is forced to heave sinusoidally, the plate pitches passively and propels itself in the horizontal direction as a result of the fluid–plate interaction. We have investigated various aspects of the mechanics behind the behaviour of the flapping plate, including the periodic- and non-periodic-flow states, the spontaneous motion of the plate, vortical structure and how they compare to similar propulsion systems in animals. In the periodic-flow regime, two dynamical responses of the passively pitching plate (forward and backward movements) are observed. Which movement will occur depends only on the frequency ratio F of the natural frequency of the system and the heaving frequency associated with the lumped torsional flexibility. It is found that the plate will select the forward movement when F > 1 and the backward movement when F ≤ 1. In the forward-movement regime, analysis of the dynamical behaviours and propulsive properties of the passively pitching plate indicates that the torsional flexibility can remarkably improve the propulsive performance. In addition, four kinds of vortex structures in the near wake are identified, which mainly depend on the forward speed of the plate. Finally the forward movement is compared to the flapping-based locomotion of swimming and flying animals. The results obtained in this study are consistent with the observations and measurements of swimming and flying animals; thus, they may provide physical insights into understanding of the propulsive mechanisms of the flapping wings and fins of animals.
Quantum physics and human language

Human languages employ constructions that tacitly assume specific properties of the limited range of phenomena they evolved to describe. These assumed properties are true features of that limited context, but may not be general or precise properties of all the physical situations allowed by fundamental physics. In brief, human languages contain ‘excess baggage’ that must be qualified, discarded, or otherwise reformed to give a clear account in the context of fundamental physics of even the everyday phenomena that the languages evolved to describe. The surest route to clarity is to express the constructions of human languages in the language of fundamental physical theory, not the other way around. These ideas are illustrated by an analysis of the verb ‘to happen’ and the word ‘reality’ in special relativity and the modern quantum mechanics of closed systems.
Quasar outflow energetics from broad absorption line variability

Quasar outflows have long been recognized as potential contributors to the co-evolution between supermassive black holes (SMBHs) and their host galaxies. The role of outflows in AGN feedback processes can be better understood by placing observational constraints on wind locations and kinetic energies. We utilize broad absorption line (BAL) variability to investigate the properties of a sample of 71 BAL quasars with P$\thinspace$V broad absorption. The presence of P$\thinspace$V BALs indicates that other BALs like C$\thinspace$IV are saturated, such that variability in those lines favours clouds crossing the line of sight. We use these constraints with measurements of BAL variability to estimate outflow locations and energetics. Our data set consists of multiple-epoch spectra from the Sloan Digital Sky Survey and MDM Observatory. We detect significant (4$\sigma$) BAL variations from 10 quasars in our sample over rest frame time-scales between 10$^{22}$ cm$^{-2}$), yield outflow kinetic luminosities between ~ 0.001-1 times the bolometric luminosity of the quasar, indicating that many absorber energies within our sample are viable for AGN feedback.